diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 76f895df..d95f3521 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -17,55 +17,8 @@ on: default: "develop" jobs: - test: - name: "🧪 Test with coverage" - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.11", "3.10"] - env: - OS: linux - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - steps: - - name: "🛍️ Checkout repository" - uses: actions/checkout@v4 - with: - ref: ${{ github.event.inputs.branch || github.ref }} - - name: "🐍 Setup Python" - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - - name: "🧪 Run test and generate coverage report" - working-directory: . - run: | - echo "codecov.dev" > VERSION - make test - - name: "📦 Upload coverage artifact" - uses: actions/upload-artifact@v4 - with: - name: coverage-report-${{ matrix.python-version }} - path: ./coverage.xml - - upload: - name: "☁️ Upload coverage to Codecov" - runs-on: ubuntu-latest - needs: test - steps: - - name: "🛍️ Checkout repository" - uses: actions/checkout@v4 - with: - ref: ${{ github.event.inputs.branch || github.ref }} - - name: "📥 Download coverage artifact" - uses: actions/download-artifact@v4 - with: - name: coverage-report-3.10 - - name: "☁️ Upload coverage to Codecov" - uses: codecov/codecov-action@v3 - with: - token: ${{ secrets.CODECOV_UPLOAD_TOKEN_MMIF_PYTHON }} - files: ./coverage.xml - flags: unittests - env_vars: OS,PYTHON - name: coverage - fail_ci_if_error: true - + test-and-codecov: + name: "🤙 Call SDK test workflow" + uses: clamsproject/.github/.github/workflows/sdk-codecov.yml@main + secrets: + CC_REPO_UPLOAD_TOKEN: ${{ secrets.CODECOV_UPLOAD_TOKEN_MMIF_PYTHON }} diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index cfa70826..6be5812e 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -6,8 +6,7 @@ on: - '[0-9]+.[0-9]+.[0-9]+' jobs: - packge-and-upload: + package-and-upload: name: "🤙 Call SDK publish workflow" uses: clamsproject/.github/.github/workflows/sdk-publish.yml@main secrets: inherit - diff --git a/CHANGELOG.md b/CHANGELOG.md index 489fad7d..00679065 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,33 @@ +## releasing 1.0.19 (2024-07-29) +### Overview +Patch to fix a critical bug. + +### Changes +- bugfix when `Annotation` instance and "warnings" view both are involved, MMIF is not properly returned (#299) + +## releasing 1.0.18 (2024-07-15) +### Overview +Patch release with a bugfix. + +### Additions +- document location (docloc) plugins now have a common function to provide formatting guidelines (https://github.com/clamsproject/mmif-python/issues/297) +### Changes +- fixed bug when adding custom properties to a newly generated `TextDocument` object (https://github.com/clamsproject/mmif-python/issues/290) + +## releasing 1.0.17 (2024-06-26) +### Overview +This release adds caching mechanism for annotation alignments (via `Alignment` annotation, the alignment via `targets` property is not yet supported). + +### Additions +- `Annotation` class now has [`.aligned_to_by(alignment: Annotation)`](https://clams.ai/mmif-python/latest/autodoc/mmif.serialize.html#mmif.serialize.annotation.Annotation.aligned_to_by) and [`.get_all_aligned()`](https://clams.ai/mmif-python/latest/autodoc/mmif.serialize.html#mmif.serialize.annotation.Annotation.get_all_aligned) method to quickly retrieve cached alignment counterparts (https://github.com/clamsproject/mmif-python/issues/285). The caching occurs + 1. when MMIF JSON is deserialized + 2. when `view.add_annotation` or `view.new_annotation` is called + +### Changes +- `mmif.utils.text_document_helper.slice_text` received a major speed boost from the alignment caching. + + ## releasing 1.0.16 (2024-06-14) ### Overview This release includes an _experimental_ implementation for helpers to slice `text_value` from text documents. diff --git a/docs/0.3.0/.buildinfo b/docs/0.3.0/.buildinfo index 8442cd8a..aea9190f 100644 --- a/docs/0.3.0/.buildinfo +++ b/docs/0.3.0/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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Python Module Index

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Python Module Index

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mmif.serialize module1.0.14
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diff --git a/docs/0.5.0/autodoc/mmif.vocabulary.html b/docs/0.5.0/autodoc/mmif.vocabulary.html index f44f11c9..0b868be5 100644 --- a/docs/0.5.0/autodoc/mmif.vocabulary.html +++ b/docs/0.5.0/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

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diff --git a/docs/0.5.0/genindex.html b/docs/0.5.0/genindex.html index f117ed9f..de131b2b 100644 --- a/docs/0.5.0/genindex.html +++ b/docs/0.5.0/genindex.html @@ -607,6 +607,9 @@

V

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diff --git a/docs/0.5.0/index.html b/docs/0.5.0/index.html index 70d74670..b437b30f 100644 --- a/docs/0.5.0/index.html +++ b/docs/0.5.0/index.html @@ -184,6 +184,9 @@

Indices and tables1.0.14

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diff --git a/docs/0.5.0/introduction.html b/docs/0.5.0/introduction.html index fbfab5d7..871c77c2 100644 --- a/docs/0.5.0/introduction.html +++ b/docs/0.5.0/introduction.html @@ -217,6 +217,9 @@

MMIF Serialization1.0.14
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diff --git a/docs/0.5.0/py-modindex.html b/docs/0.5.0/py-modindex.html index f7584f57..43edab85 100644 --- a/docs/0.5.0/py-modindex.html +++ b/docs/0.5.0/py-modindex.html @@ -188,6 +188,9 @@

Python Module Index

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mmif.serialize module1.0.14
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diff --git a/docs/0.5.1/autodoc/mmif.vocabulary.html b/docs/0.5.1/autodoc/mmif.vocabulary.html index df430b9c..50bfca9e 100644 --- a/docs/0.5.1/autodoc/mmif.vocabulary.html +++ b/docs/0.5.1/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

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MMIF Serialization1.0.14
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Python Module Index

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mmif.serialize module1.0.14
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mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -184,7 +184,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -285,6 +285,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

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MMIF Serialization1.0.14
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Python Module Index

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0.5.2

-

1.0.4

+

1.0.5

0.5.1

0.5.0

@@ -219,6 +219,9 @@
1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.0/.buildinfo b/docs/1.0.0/.buildinfo index 74b23336..33c66672 100644 --- a/docs/1.0.0/.buildinfo +++ b/docs/1.0.0/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 8170e5fd3b7cdd8e88ea3c8e035273df +config: c8bb5f006508ec55e82e294452c95a43 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.0/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.0/.doctrees/autodoc/mmif.serialize.doctree index 7dd15e3b..f3382714 100644 Binary files a/docs/1.0.0/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.0/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.0/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.0/.doctrees/autodoc/mmif.vocabulary.doctree index d409e6df..b078dffc 100644 Binary files a/docs/1.0.0/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.0/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.0/.doctrees/consumer-tutorial.doctree b/docs/1.0.0/.doctrees/consumer-tutorial.doctree index 9335fe20..018d867f 100644 Binary files a/docs/1.0.0/.doctrees/consumer-tutorial.doctree and b/docs/1.0.0/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.0/.doctrees/environment.pickle b/docs/1.0.0/.doctrees/environment.pickle index 97a83490..f117db7a 100644 Binary files a/docs/1.0.0/.doctrees/environment.pickle and b/docs/1.0.0/.doctrees/environment.pickle differ diff --git a/docs/1.0.0/.doctrees/index.doctree b/docs/1.0.0/.doctrees/index.doctree index 695bf70f..172e1a62 100644 Binary files a/docs/1.0.0/.doctrees/index.doctree and b/docs/1.0.0/.doctrees/index.doctree differ diff --git a/docs/1.0.0/.doctrees/introduction.doctree b/docs/1.0.0/.doctrees/introduction.doctree index a7b61a4e..00d7822c 100644 Binary files a/docs/1.0.0/.doctrees/introduction.doctree and b/docs/1.0.0/.doctrees/introduction.doctree differ diff --git a/docs/1.0.0/.doctrees/modules.doctree b/docs/1.0.0/.doctrees/modules.doctree index e3504d31..99e248be 100644 Binary files a/docs/1.0.0/.doctrees/modules.doctree and b/docs/1.0.0/.doctrees/modules.doctree differ diff --git a/docs/1.0.0/.doctrees/target-versions.doctree b/docs/1.0.0/.doctrees/target-versions.doctree index c487abf3..682bf151 100644 Binary files a/docs/1.0.0/.doctrees/target-versions.doctree and b/docs/1.0.0/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.0/autodoc/mmif.serialize.html b/docs/1.0.0/autodoc/mmif.serialize.html index 24e062bb..c389416c 100644 --- a/docs/1.0.0/autodoc/mmif.serialize.html +++ b/docs/1.0.0/autodoc/mmif.serialize.html @@ -1156,6 +1156,9 @@

mmif.serialize module1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.0/autodoc/mmif.vocabulary.html b/docs/1.0.0/autodoc/mmif.vocabulary.html index 97aa5a66..a87563fa 100644 --- a/docs/1.0.0/autodoc/mmif.vocabulary.html +++ b/docs/1.0.0/autodoc/mmif.vocabulary.html @@ -103,7 +103,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -184,7 +184,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -285,6 +285,9 @@

mmif.vocabulary module1.0.14

1.0.15
1.0.16
+
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V

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Indices and tables1.0.14

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MMIF Serialization1.0.14
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Python Module Index

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mmif.serialize module1.0.14
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mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -184,7 +184,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -285,6 +285,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

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MMIF Serialization1.0.14
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Python Module Index

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mmif.serialize module1.0.14
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mmif.utils module1.0.14
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mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -193,7 +193,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -295,6 +295,9 @@

mmif.vocabulary module1.0.14

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mmif_docloc_http package1.0.14

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V

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Indices and tables1.0.14
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diff --git a/docs/1.0.10/introduction.html b/docs/1.0.10/introduction.html index f8513bb1..19d41f63 100644 --- a/docs/1.0.10/introduction.html +++ b/docs/1.0.10/introduction.html @@ -226,6 +226,9 @@

MMIF Serialization1.0.14
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mmif_docloc_http package1.0.14
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Bulit-in Document Location Scheme Plugins1.0.14
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Python Module Index

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(mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.typevers"]], "version (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.version"]], "version (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.version"]], "mmif_docloc_http": [[3, "module-mmif_docloc_http"]], "resolve() (in module mmif_docloc_http)": [[3, "mmif_docloc_http.resolve"]]}}) \ No newline at end of file diff --git a/docs/1.0.10/target-versions.html b/docs/1.0.10/target-versions.html index ebd1627c..9871b036 100644 --- a/docs/1.0.10/target-versions.html +++ b/docs/1.0.10/target-versions.html @@ -94,7 +94,7 @@

1.0.10

-

1.0.4

+

1.0.5

1.0.9

1.1.0

@@ -254,6 +254,9 @@
1.0.14
1.0.15
1.0.16
+
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+
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+
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1.0.3
1.0.4
diff --git a/docs/1.0.11/.buildinfo b/docs/1.0.11/.buildinfo index ce6cea69..5a8625e6 100644 --- a/docs/1.0.11/.buildinfo +++ b/docs/1.0.11/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 3566ef9191f7aeb71d4922d1bd27ac75 +config: 46452f9a817b6281b274e0147d90a685 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.11/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.11/.doctrees/autodoc/mmif.serialize.doctree index dcdacabc..1886ec9e 100644 Binary files a/docs/1.0.11/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.11/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.11/.doctrees/autodoc/mmif.utils.doctree b/docs/1.0.11/.doctrees/autodoc/mmif.utils.doctree index bc322962..c87cfa4a 100644 Binary files a/docs/1.0.11/.doctrees/autodoc/mmif.utils.doctree and b/docs/1.0.11/.doctrees/autodoc/mmif.utils.doctree differ diff --git a/docs/1.0.11/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.11/.doctrees/autodoc/mmif.vocabulary.doctree index 4ded859c..98687a7f 100644 Binary files a/docs/1.0.11/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.11/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.11/.doctrees/autodoc/mmif_docloc_http.doctree b/docs/1.0.11/.doctrees/autodoc/mmif_docloc_http.doctree index 8452b77b..80a6225a 100644 Binary files a/docs/1.0.11/.doctrees/autodoc/mmif_docloc_http.doctree and b/docs/1.0.11/.doctrees/autodoc/mmif_docloc_http.doctree differ diff --git a/docs/1.0.11/.doctrees/consumer-tutorial.doctree b/docs/1.0.11/.doctrees/consumer-tutorial.doctree index 572c224d..a67a26e3 100644 Binary files a/docs/1.0.11/.doctrees/consumer-tutorial.doctree and b/docs/1.0.11/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.11/.doctrees/environment.pickle b/docs/1.0.11/.doctrees/environment.pickle index c59c5e65..925fd4fc 100644 Binary files a/docs/1.0.11/.doctrees/environment.pickle and b/docs/1.0.11/.doctrees/environment.pickle differ diff --git a/docs/1.0.11/.doctrees/index.doctree b/docs/1.0.11/.doctrees/index.doctree index f739a62f..020c2f05 100644 Binary files a/docs/1.0.11/.doctrees/index.doctree and b/docs/1.0.11/.doctrees/index.doctree differ diff --git a/docs/1.0.11/.doctrees/introduction.doctree b/docs/1.0.11/.doctrees/introduction.doctree index e44f9f28..f7532bdf 100644 Binary files a/docs/1.0.11/.doctrees/introduction.doctree and b/docs/1.0.11/.doctrees/introduction.doctree differ diff --git a/docs/1.0.11/.doctrees/modules.doctree b/docs/1.0.11/.doctrees/modules.doctree index b6f5004f..b300c999 100644 Binary files a/docs/1.0.11/.doctrees/modules.doctree and b/docs/1.0.11/.doctrees/modules.doctree differ diff --git a/docs/1.0.11/.doctrees/plugins.doctree b/docs/1.0.11/.doctrees/plugins.doctree index 4c51b358..86abec8a 100644 Binary files a/docs/1.0.11/.doctrees/plugins.doctree and b/docs/1.0.11/.doctrees/plugins.doctree differ diff --git a/docs/1.0.11/.doctrees/target-versions.doctree b/docs/1.0.11/.doctrees/target-versions.doctree index c37857be..9ef81d37 100644 Binary files a/docs/1.0.11/.doctrees/target-versions.doctree and b/docs/1.0.11/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.11/autodoc/mmif.serialize.html b/docs/1.0.11/autodoc/mmif.serialize.html index 67dbeb1d..0c15cc78 100644 --- a/docs/1.0.11/autodoc/mmif.serialize.html +++ b/docs/1.0.11/autodoc/mmif.serialize.html @@ -1298,6 +1298,9 @@

mmif.serialize module1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
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diff --git a/docs/1.0.11/autodoc/mmif.utils.html b/docs/1.0.11/autodoc/mmif.utils.html index b324919e..ac4100cf 100644 --- a/docs/1.0.11/autodoc/mmif.utils.html +++ b/docs/1.0.11/autodoc/mmif.utils.html @@ -559,6 +559,9 @@

mmif.utils module1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
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diff --git a/docs/1.0.11/autodoc/mmif.vocabulary.html b/docs/1.0.11/autodoc/mmif.vocabulary.html index 1fb0b93b..bd73e529 100644 --- a/docs/1.0.11/autodoc/mmif.vocabulary.html +++ b/docs/1.0.11/autodoc/mmif.vocabulary.html @@ -107,7 +107,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -183,7 +183,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -280,6 +280,9 @@

mmif.vocabulary module1.0.14

1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
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V

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Python Module Index

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\u2026": [[5, "for-more"]], "Contents": [[5, null]], "API documentation:": [[5, null]], "Indices and tables": [[5, "indices-and-tables"]], "Getting Started": [[6, "getting-started"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "mmif package": [[7, "mmif-package"]], "Developing plugins for MMIF Python SDK": [[8, "developing-plugins-for-mmif-python-sdk"]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Target MMIF Versions": [[9, "target-mmif-versions"]], "Target Specification Versions": [[9, "id1"]]}, "indexentries": {"annotation (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Annotation"]], "annotationproperties (class in mmif.serialize.annotation)": [[0, 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mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -183,7 +183,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -280,6 +280,9 @@

mmif.vocabulary module1.0.14

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mmif_docloc_http package1.0.14

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diff --git a/docs/1.0.12/genindex.html b/docs/1.0.12/genindex.html index fbd35fb5..38f82c18 100644 --- a/docs/1.0.12/genindex.html +++ b/docs/1.0.12/genindex.html @@ -710,6 +710,9 @@

V

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diff --git a/docs/1.0.12/index.html b/docs/1.0.12/index.html index 71548b95..5cd61352 100644 --- a/docs/1.0.12/index.html +++ b/docs/1.0.12/index.html @@ -209,6 +209,9 @@

Indices and tables1.0.14
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diff --git a/docs/1.0.12/introduction.html b/docs/1.0.12/introduction.html index d8ae8071..9ba95c4b 100644 --- a/docs/1.0.12/introduction.html +++ b/docs/1.0.12/introduction.html @@ -226,6 +226,9 @@

MMIF Serialization1.0.14
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diff --git a/docs/1.0.12/modules.html b/docs/1.0.12/modules.html index 37121b9a..30a969d7 100644 --- a/docs/1.0.12/modules.html +++ b/docs/1.0.12/modules.html @@ -370,6 +370,9 @@

mmif_docloc_http package1.0.14
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diff --git a/docs/1.0.12/plugins.html b/docs/1.0.12/plugins.html index ff014635..0fe64d21 100644 --- a/docs/1.0.12/plugins.html +++ b/docs/1.0.12/plugins.html @@ -215,6 +215,9 @@

Bulit-in Document Location Scheme Plugins1.0.14
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diff --git a/docs/1.0.12/py-modindex.html b/docs/1.0.12/py-modindex.html index 11c41d22..6d582a15 100644 --- a/docs/1.0.12/py-modindex.html +++ b/docs/1.0.12/py-modindex.html @@ -204,6 +204,9 @@

Python Module Index

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mmif.serialize module1.0.14
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mmif.utils module1.0.14
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mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -183,7 +183,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -280,6 +280,9 @@

mmif.vocabulary module1.0.14

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mmif_docloc_http package1.0.14

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V

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Indices and tables1.0.14
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diff --git a/docs/1.0.13/introduction.html b/docs/1.0.13/introduction.html index 52bd1d87..76975247 100644 --- a/docs/1.0.13/introduction.html +++ b/docs/1.0.13/introduction.html @@ -226,6 +226,9 @@

MMIF Serialization1.0.14
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Bulit-in Document Location Scheme Plugins1.0.14
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Python Module Index

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"consum": 4, "welcom": 5, "python": [5, 8], "": 5, "document": [5, 8], "multimedia": 5, "interchang": 5, "format": 5, "For": 5, "more": 5, "content": 5, "api": 5, "indic": 5, "tabl": 5, "get": 6, "start": 6, "overview": [6, 8], "prerequisit": 6, "instal": 6, "develop": 8, "plugin": 8, "sdk": 8, "locat": 8, "scheme": 8, "bulit": 8, "target": 9, "version": 9, "specif": 9}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 58}, "alltitles": {"mmif.serialize module": [[0, "mmif-serialize-module"]], "mmif.serialize.model module": [[0, "module-mmif.serialize.model"]], "mmif.serialize.mmif module": [[0, "module-mmif.serialize.mmif"]], "mmif.serialize.view module": [[0, "module-mmif.serialize.view"]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], "mmif.utils module": [[1, "mmif-utils-module"]], "mmif.utils.video_document_helper module": [[1, "module-mmif.utils.video_document_helper"]], "mmif.utils.sequence_helper module": [[1, "module-mmif.utils.sequence_helper"]], "mmif.vocabulary module": [[2, "mmif-vocabulary-module"]], "mmif.vocabulary.annotation_types module": [[2, "module-mmif.vocabulary.annotation_types"]], "mmif.vocabulary.document_types module": [[2, "module-mmif.vocabulary.document_types"]], "mmif_docloc_http package": [[3, "mmif-docloc-http-package"], [7, "mmif-docloc-http-package"]], "MMIF consumer": [[4, "mmif-consumer"]], "Welcome to mmif-python\u2019s documentation!": [[5, "welcome-to-mmif-python-s-documentation"]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "mmif-python": [[5, "mmif-python"]], "For more \u2026": [[5, "for-more"]], "Contents": [[5, null]], "API documentation:": [[5, null]], "Indices and tables": [[5, "indices-and-tables"]], "Getting Started": [[6, "getting-started"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "mmif package": [[7, "mmif-package"]], "Developing plugins for MMIF Python SDK": [[8, "developing-plugins-for-mmif-python-sdk"]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Target MMIF Versions": [[9, "target-mmif-versions"]], "Target Specification Versions": [[9, "id1"]]}, "indexentries": {"annotation (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Annotation"]], "annotationproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.AnnotationProperties"]], "contain (class in mmif.serialize.view)": [[0, "mmif.serialize.view.Contain"]], "datadict (class in mmif.serialize.model)": [[0, 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mmif.utils module1.0.14
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mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -183,7 +183,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -280,6 +280,9 @@

mmif.vocabulary module1.0.14

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mmif_docloc_http package1.0.14

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V

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Indices and tables1.0.14
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MMIF Serialization1.0.14
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Bulit-in Document Location Scheme Plugins1.0.14
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Python Module Index

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"Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "mmif package": [[7, "mmif-package"]], "Developing plugins for MMIF Python SDK": [[8, "developing-plugins-for-mmif-python-sdk"]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Target MMIF Versions": [[9, "target-mmif-versions"]], "Target Specification Versions": [[9, "id1"]]}, "indexentries": {"annotation (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Annotation"]], "annotationproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.AnnotationProperties"]], "contain (class in mmif.serialize.view)": [[0, "mmif.serialize.view.Contain"]], "datadict (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataDict"]], "datalist (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataList"]], "document (class in 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1.0.14

-

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+

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1.0.13

1.0.4

@@ -269,6 +269,9 @@
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diff --git a/docs/1.0.15/.buildinfo b/docs/1.0.15/.buildinfo index 5923fed1..8f76a982 100644 --- a/docs/1.0.15/.buildinfo +++ b/docs/1.0.15/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: bc17a0a0613c15821fee4c97959fdb83 +config: 351631c98f3b1423841c5c902e4999bf tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.15/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.15/.doctrees/autodoc/mmif.serialize.doctree index a9bf23d7..72126083 100644 Binary files a/docs/1.0.15/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.15/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.15/.doctrees/autodoc/mmif.utils.doctree b/docs/1.0.15/.doctrees/autodoc/mmif.utils.doctree index 12d2faa5..ba73bd34 100644 Binary files a/docs/1.0.15/.doctrees/autodoc/mmif.utils.doctree and b/docs/1.0.15/.doctrees/autodoc/mmif.utils.doctree differ diff --git a/docs/1.0.15/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.15/.doctrees/autodoc/mmif.vocabulary.doctree index 3dc44f1b..74f46477 100644 Binary files a/docs/1.0.15/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.15/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.15/.doctrees/autodoc/mmif_docloc_http.doctree b/docs/1.0.15/.doctrees/autodoc/mmif_docloc_http.doctree index c7ceb036..e4fa4394 100644 Binary files a/docs/1.0.15/.doctrees/autodoc/mmif_docloc_http.doctree and b/docs/1.0.15/.doctrees/autodoc/mmif_docloc_http.doctree differ diff --git a/docs/1.0.15/.doctrees/consumer-tutorial.doctree b/docs/1.0.15/.doctrees/consumer-tutorial.doctree index 9f145497..01e1521f 100644 Binary files a/docs/1.0.15/.doctrees/consumer-tutorial.doctree and b/docs/1.0.15/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.15/.doctrees/environment.pickle b/docs/1.0.15/.doctrees/environment.pickle index bcf67b06..87bd03fa 100644 Binary files a/docs/1.0.15/.doctrees/environment.pickle and b/docs/1.0.15/.doctrees/environment.pickle differ diff --git a/docs/1.0.15/.doctrees/index.doctree b/docs/1.0.15/.doctrees/index.doctree index 6f1c7103..c51bee1c 100644 Binary files a/docs/1.0.15/.doctrees/index.doctree and b/docs/1.0.15/.doctrees/index.doctree differ diff --git a/docs/1.0.15/.doctrees/introduction.doctree b/docs/1.0.15/.doctrees/introduction.doctree index efcb85a4..800908e4 100644 Binary files a/docs/1.0.15/.doctrees/introduction.doctree and b/docs/1.0.15/.doctrees/introduction.doctree differ diff --git a/docs/1.0.15/.doctrees/modules.doctree b/docs/1.0.15/.doctrees/modules.doctree index 779077f5..d216c1f4 100644 Binary files a/docs/1.0.15/.doctrees/modules.doctree and b/docs/1.0.15/.doctrees/modules.doctree differ diff --git a/docs/1.0.15/.doctrees/plugins.doctree b/docs/1.0.15/.doctrees/plugins.doctree index 76e1aed5..e85e540d 100644 Binary files a/docs/1.0.15/.doctrees/plugins.doctree and b/docs/1.0.15/.doctrees/plugins.doctree differ diff --git a/docs/1.0.15/.doctrees/target-versions.doctree b/docs/1.0.15/.doctrees/target-versions.doctree index acfaa421..0dd5fdef 100644 Binary files a/docs/1.0.15/.doctrees/target-versions.doctree and b/docs/1.0.15/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.15/autodoc/mmif.serialize.html b/docs/1.0.15/autodoc/mmif.serialize.html index 2972bfcc..0cd65366 100644 --- a/docs/1.0.15/autodoc/mmif.serialize.html +++ b/docs/1.0.15/autodoc/mmif.serialize.html @@ -1393,6 +1393,9 @@

mmif.serialize module1.0.14
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diff --git a/docs/1.0.15/autodoc/mmif.utils.html b/docs/1.0.15/autodoc/mmif.utils.html index a6124f60..6520cc37 100644 --- a/docs/1.0.15/autodoc/mmif.utils.html +++ b/docs/1.0.15/autodoc/mmif.utils.html @@ -596,6 +596,9 @@

mmif.utils module1.0.14
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diff --git a/docs/1.0.15/autodoc/mmif.vocabulary.html b/docs/1.0.15/autodoc/mmif.vocabulary.html index b02e2190..c5ad7ef1 100644 --- a/docs/1.0.15/autodoc/mmif.vocabulary.html +++ b/docs/1.0.15/autodoc/mmif.vocabulary.html @@ -107,7 +107,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -183,7 +183,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -280,6 +280,9 @@

mmif.vocabulary module1.0.14

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mmif_docloc_http package1.0.14

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diff --git a/docs/1.0.15/consumer-tutorial.html b/docs/1.0.15/consumer-tutorial.html index 3ab3ef75..107e08ca 100644 --- a/docs/1.0.15/consumer-tutorial.html +++ b/docs/1.0.15/consumer-tutorial.html @@ -153,6 +153,9 @@
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diff --git a/docs/1.0.15/genindex.html b/docs/1.0.15/genindex.html index 5bf5a5fb..1d4c3086 100644 --- a/docs/1.0.15/genindex.html +++ b/docs/1.0.15/genindex.html @@ -749,6 +749,9 @@

V

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diff --git a/docs/1.0.15/index.html b/docs/1.0.15/index.html index 83f5adf3..2e29e809 100644 --- a/docs/1.0.15/index.html +++ b/docs/1.0.15/index.html @@ -209,6 +209,9 @@

Indices and tables1.0.14
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MMIF Serialization1.0.14
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mmif_docloc_http package1.0.14
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Python Module Index

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mmif.serialize module1.0.14
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mmif.utils module1.0.14
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diff --git a/docs/1.0.16/autodoc/mmif.vocabulary.html b/docs/1.0.16/autodoc/mmif.vocabulary.html index 522de61f..e564b48a 100644 --- a/docs/1.0.16/autodoc/mmif.vocabulary.html +++ b/docs/1.0.16/autodoc/mmif.vocabulary.html @@ -107,7 +107,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -183,7 +183,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -280,6 +280,9 @@

mmif.vocabulary module1.0.14

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mmif_docloc_http package1.0.14

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V

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Indices and tables1.0.14
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diff --git a/docs/1.0.16/introduction.html b/docs/1.0.16/introduction.html index 6bb7310b..812504a5 100644 --- a/docs/1.0.16/introduction.html +++ b/docs/1.0.16/introduction.html @@ -226,6 +226,9 @@

MMIF Serialization1.0.14
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diff --git a/docs/1.0.16/modules.html b/docs/1.0.16/modules.html index d2400812..37f8c525 100644 --- a/docs/1.0.16/modules.html +++ b/docs/1.0.16/modules.html @@ -384,6 +384,9 @@

mmif_docloc_http package1.0.14
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Bulit-in Document Location Scheme Plugins1.0.14
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diff --git a/docs/1.0.16/py-modindex.html b/docs/1.0.16/py-modindex.html index f93854ca..bf8175f0 100644 --- a/docs/1.0.16/py-modindex.html +++ b/docs/1.0.16/py-modindex.html @@ -204,6 +204,9 @@

Python Module Index

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+1,35 @@ +mmif.serialize module +===================== + +mmif.serialize.model module +--------------------------- + +.. automodule:: mmif.serialize.model + :members: + :undoc-members: + :show-inheritance: + +mmif.serialize.mmif module +-------------------------- + +.. automodule:: mmif.serialize.mmif + :members: + :undoc-members: + :show-inheritance: + +mmif.serialize.view module +-------------------------- + +.. automodule:: mmif.serialize.view + :members: + :undoc-members: + :show-inheritance: + +mmif.serialize.annotation module +-------------------------------- + +.. automodule:: mmif.serialize.annotation + :members: + :undoc-members: + :show-inheritance: + diff --git a/docs/1.0.17/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.17/_sources/autodoc/mmif.utils.rst.txt new file mode 100644 index 00000000..9a6ecc44 --- /dev/null +++ b/docs/1.0.17/_sources/autodoc/mmif.utils.rst.txt @@ -0,0 +1,18 @@ +mmif.utils module +================= + +mmif.utils.video_document_helper module +---------------------------------------- + +.. automodule:: mmif.utils.video_document_helper + :members: + :undoc-members: + :show-inheritance: + +mmif.utils.sequence_helper module +--------------------------------- + +.. automodule:: mmif.utils.sequence_helper + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.17/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.17/_sources/autodoc/mmif.vocabulary.rst.txt new file mode 100644 index 00000000..d250c6a3 --- /dev/null +++ b/docs/1.0.17/_sources/autodoc/mmif.vocabulary.rst.txt @@ -0,0 +1,18 @@ +mmif.vocabulary module +====================== + +mmif.vocabulary.annotation\_types module +---------------------------------------- + +.. automodule:: mmif.vocabulary.annotation_types + :members: + :undoc-members: + :show-inheritance: + +mmif.vocabulary.document\_types module +-------------------------------------- + +.. automodule:: mmif.vocabulary.document_types + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.17/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.17/_sources/autodoc/mmif_docloc_http.rst.txt new file mode 100644 index 00000000..b76c8df5 --- /dev/null +++ b/docs/1.0.17/_sources/autodoc/mmif_docloc_http.rst.txt @@ -0,0 +1,11 @@ +mmif_docloc_http package +======================== + +MMIF document location helper module for `http` and `https` schemes. +If you want to write your own docloc scheme handler, please use the source code of this module as a reference. +See this :ref:`plug-in section ` for more information. + +.. automodule:: mmif_docloc_http + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.17/_sources/consumer-tutorial.rst.txt b/docs/1.0.17/_sources/consumer-tutorial.rst.txt new file mode 100644 index 00000000..c54634e2 --- /dev/null +++ b/docs/1.0.17/_sources/consumer-tutorial.rst.txt @@ -0,0 +1,17 @@ +.. _consumer-tutorial: + +MMIF consumer +================================= + +A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. + +MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. + +#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) +#. Must listen to ``5000`` port. +#. Must expose ``/display`` route . +#. ``/display`` router should response to ``GET`` requests. +#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. +#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. + +We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.17/_sources/index.rst.txt b/docs/1.0.17/_sources/index.rst.txt new file mode 100644 index 00000000..beb56aae --- /dev/null +++ b/docs/1.0.17/_sources/index.rst.txt @@ -0,0 +1,26 @@ +Welcome to mmif-python's documentation! +======================================= + +.. mdinclude:: ../README.md + +.. toctree:: + :maxdepth: 2 + :caption: Contents + + introduction + plugins + target-versions + +.. toctree:: + :maxdepth: 2 + :caption: API documentation: + + modules + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/1.0.17/_sources/introduction.rst.txt b/docs/1.0.17/_sources/introduction.rst.txt new file mode 100644 index 00000000..cfd9eaf7 --- /dev/null +++ b/docs/1.0.17/_sources/introduction.rst.txt @@ -0,0 +1,89 @@ +.. _introduction: + +Getting Started +=============== + + +Overview +--------- + +MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. +``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. + +Prerequisites +------------- + +* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. + +Installation +--------------- + +Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. + +.. code-block:: bash + + pip install mmif-python + +This will install a package `mmif` to local python. + +The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. + +.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. + +MMIF Serialization +--------------------------- + +:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. + +.. code-block:: python + + import mmif + from mmif import Mmif + + mmif_str = """{ + "metadata": { + "mmif": "http://mmif.clams.ai/1.0.0" + }, + "documents": [ + { + "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", + "properties": { + "id": "m1", + "mime": "video/mp4", + "location": "file:///var/archive/video-0012.mp4" + } + }, + { + "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", + "properties": { + "id": "m2", + "mime": "text/plain", + "location": "file:///var/archive/video-0012-transcript.txt" + } + } + ], + "views": []}""" + mmif_obj = Mmif(mmif_str) + + +Few notes; + +#. MMIF does not carry the primary source files in it. +#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. + +When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. + +To get subcomponents, you can use various getters implemented in subclasses. For example; + +.. code-block:: python + + from mmif.vocabulary.document_types import DocumentTypes + + for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): + with open(video.location_path(), 'b') as in_video: + # do something with the video file + + +For a full list of available helper methods, please refer to :ref:`the API documentation `. + diff --git a/docs/1.0.17/_sources/modules.rst.txt b/docs/1.0.17/_sources/modules.rst.txt new file mode 100644 index 00000000..4bb9307d --- /dev/null +++ b/docs/1.0.17/_sources/modules.rst.txt @@ -0,0 +1,20 @@ +.. _apidoc: + +mmif package +============ + +.. toctree:: + :maxdepth: 4 + + autodoc/mmif.serialize + autodoc/mmif.vocabulary + autodoc/mmif.utils + +mmif_docloc_http package +======================== + +.. toctree:: + :maxdepth: 2 + + autodoc/mmif_docloc_http + diff --git a/docs/1.0.17/_sources/plugins.rst.txt b/docs/1.0.17/_sources/plugins.rst.txt new file mode 100644 index 00000000..9907c495 --- /dev/null +++ b/docs/1.0.17/_sources/plugins.rst.txt @@ -0,0 +1,83 @@ +.. _plugins: + +Developing plugins for MMIF Python SDK +====================================== + + +Overview +-------- + +As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. + + +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. +``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. + +Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). + +This document contains information about how to write plugins for ``mmif-python``. + +.. _docloc_plugin: + +Document Location Scheme Plugins +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. + +To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; + +#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. +#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; + +.. code-block:: python + + import mmif_docloc_s3 + resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') + # then resolved must be a local file path that can be used to open the file + + +Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. + +(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) + +.. code-block:: sh + + $ tree . + . + ├── mmif_docloc_dummy + │ └── __init__.py + ├── pyproject.toml + └── setup.cfg + + $ cat pyproject.toml + [build-system] + requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + $ cat setup.cfg + [metadata] + name = mmif_docloc_dummy # this name is IMPORTANT + version = 0.0.1 + description = a plugin to mmif-pyhon to handle `dummy` location scheme + + +And the plugin code. + +.. code-block:: python + + # mmif_docloc_dummy/__init__.py + doc_types = {'video': 'mp4'} + + def resolve(docloc): + scheme = 'dummy' + if docloc.startswith(f'{scheme}://'): + doc_id, doc_type = docloc.split('.') + return f'/path/to/{doc_id}.{doc_types[doc_type]}' + else: + raise ValueError(f'cannot handle document location scheme: {docloc}') + +Bulit-in Document Location Scheme Plugins +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. +Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.17/_sources/target-versions.rst.txt b/docs/1.0.17/_sources/target-versions.rst.txt new file mode 100644 index 00000000..34216d3e --- /dev/null +++ b/docs/1.0.17/_sources/target-versions.rst.txt @@ -0,0 +1,10 @@ +.. _target-versions: + +Target MMIF Versions +==================== + +This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. + +.. csv-table:: Target Specification Versions + :file: target-versions.csv + :header-rows: 1 diff --git a/docs/1.0.17/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.17/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/docs/1.0.17/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/docs/1.0.17/_static/basic.css b/docs/1.0.17/_static/basic.css new file mode 100644 index 00000000..cfc60b86 --- /dev/null +++ b/docs/1.0.17/_static/basic.css @@ -0,0 +1,921 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + 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-- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + 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---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = docUrlRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = docUrlRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/docs/1.0.17/_static/sphinx_highlight.js b/docs/1.0.17/_static/sphinx_highlight.js new file mode 100644 index 00000000..aae669d7 --- /dev/null +++ b/docs/1.0.17/_static/sphinx_highlight.js @@ -0,0 +1,144 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + parent.insertBefore( + span, + parent.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/docs/1.0.17/autodoc/mmif.serialize.html b/docs/1.0.17/autodoc/mmif.serialize.html new file mode 100644 index 00000000..798fea03 --- /dev/null +++ b/docs/1.0.17/autodoc/mmif.serialize.html @@ -0,0 +1,1473 @@ + + + + + + + mmif.serialize module — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.serialize module

+
+

mmif.serialize.model module

+

The model module contains the classes used to represent an +abstract MMIF object as a live Python object.

+

The MmifObject class or one of its derivatives is subclassed by +all other classes defined in this SDK, except for MmifObjectEncoder.

+

These objects are generally instantiated from JSON, either as a string +or as an already-loaded Python dictionary. This base class provides the +core functionality for deserializing MMIF JSON data into live objects +and serializing live objects into MMIF JSON data. Specialized behavior +for the different components of MMIF is added in the subclasses.

+
+
+class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject, Generic[T, S]

+
+
+empty()[source]
+
+ +
+
+get(key: T, default=None) → S | None[source]
+
+ +
+
+items()[source]
+
+ +
+
+keys()[source]
+
+ +
+
+update(other, overwrite)[source]
+
+ +
+
+values()[source]
+
+ +
+ +
+
+class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None, *_)[source]
+

Bases: MmifObject, Generic[T]

+

The DataList class is an abstraction that represents the +various lists found in a MMIF file, such as documents, subdocuments, +views, and annotations.

+
+
Parameters:
+

mmif_obj (Union[str, list]) – the data that the list contains

+
+
+
+
+append(value, overwrite)[source]
+
+ +
+
+deserialize(mmif_json: str | list) → None[source]
+

Passes the input data into the internal deserializer.

+
+ +
+
+empty()[source]
+
+ +
+
+get(key: str) → T | None[source]
+

Standard dictionary-style get() method, albeit with no default +parameter. Relies on the implementation of __getitem__.

+

Will return None if the key is not found.

+
+
Parameters:
+

key – the key to search for

+
+
Returns:
+

the value matching that key

+
+
+
+ +
+ +
+
+class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: object

+

Abstract superclass for MMIF related key-value pair objects.

+

Any MMIF object can be initialized as an empty placeholder or +an actual representation with a JSON formatted string or equivalent +dict object argument.

+

This superclass has four specially designed instance variables, and these +variable names cannot be used as attribute names for MMIF objects.

+
    +

  1. _unnamed_attributes: +Only can be either None or an empty dictionary. If it’s set to None, +it means the class won’t take any Additional Attributes in the +JSON schema sense. If it’s an empty dict, users can throw any k-v +pairs to the class, as long as the key is not a “reserved” name, +and those additional attributes will be stored in this dict while +in memory.

    2. +

  2. _attribute_classes: +This is a dict from a key name to a specific python class to use for +deserialize the value. Note that a key name in this dict does NOT +have to be a named attribute, but is recommended to be one.

    3. +

  3. _required_attributes: +This is a simple list of names of attributes that are required in +the object. When serialize, an object will skip its empty (e.g. +zero-length, or None) attributes unless they are in this list. +Otherwise, the serialized JSON string would have empty +representations (e.g. "", []).

    4. +

  4. _exclude_from_diff: +This is a simple list of names of attributes that should be excluded +from the diff calculation in __eq__.

    5. +
+

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. +Maybe there is a better way to utilize type hints (e.g. getting them +as a programmatically), but for now developers should be careful to +add types to hints as well as to this dict.

+

Also note that those special attributes MUST be set in the __init__() +before calling super method, otherwise deserialization will not work.

+

And also, a subclass that has one or more named attributes, it must +set those attributes in the __init__() before calling super method. +When serializing a MmifObject, all empty attributes will be ignored, +so for optional named attributes, you must leave the values empty +(len == 0), but NOT None. Any None-valued named attributes will cause +issues with current implementation.

+
+
Parameters:
+

mmif_obj – JSON string or dict to initialize an object. +If not given, an empty object will be initialized, sometimes with +an ID value automatically generated, based on its parent object.

+
+
+
+
+deserialize(mmif_json: str | dict) → None[source]
+

Takes a JSON-formatted string or a simple dict that’s json-loaded from +such a string as an input and populates object’s fields with the values +specified in the input.

+
+
Parameters:
+

mmif_json – JSON-formatted string or dict from such a string +that represents a MMIF object

+
+
+
+ +
+
+disallow_additional_properties() → None[source]
+

Call this method in __init__() to prevent the insertion +of unnamed attributes after initialization.

+
+ +
+
+id_delimiter: ClassVar[str] = ':'[source]
+
+ +
+
+static is_empty(obj) → bool[source]
+

return True if the obj is None or “emtpy”. The emptiness first defined as +having zero length. But for objects that lack __len__ method, we need +additional check.

+
+ +
+
+reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
+
+ +
+
+serialize(pretty: bool = False) → str[source]
+

Generates JSON representation of an object.

+
+
Parameters:
+

pretty – If True, returns string representation with indentation.

+
+
Returns:
+

JSON string of the object.

+
+
+
+ +
+
+set_additional_property(key: str, value: Any) → None[source]
+

Method to set values in _unnamed_attributes.

+
+
Parameters:
+
    +

  • key – the attribute name

    • +

  • value – the desired value

    • +
+
+
Returns:
+

None

+
+
Raise:
+

AttributeError if additional properties are disallowed by disallow_additional_properties()

+
+
+
+ +
+
+view_prefix: ClassVar[str] = 'v_'[source]
+
+ +
+ +
+
+class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
+

Bases: JSONEncoder

+

Encoder class to define behaviors of de-/serialization

+
+
+default(obj: MmifObject)[source]
+

Overrides default encoding behavior to prioritize MmifObject.serialize().

+
+ +
+ +
+
+

mmif.serialize.mmif module

+

The mmif module contains the classes used to represent a full MMIF +file as a live Python object.

+

See the specification docs and the JSON Schema file for more information.

+
+
+class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
+

Bases: MmifObject

+

MmifObject that represents a full MMIF file.

+
+
Parameters:
+
    +

  • mmif_obj – the JSON data

    • +

  • validate – whether to validate the data against the MMIF JSON schema.

    • +
+
+
+
+
+add_document(document: Document, overwrite=False) → None[source]
+

Appends a Document object to the documents list.

+

Fails if there is already a document with the same ID in the MMIF object.

+
+
Parameters:
+
    +

  • document – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+add_view(view: View, overwrite=False) → None[source]
+

Appends a View object to the views list.

+

Fails if there is already a view with the same ID in the MMIF object.

+
+
Parameters:
+
    +

  • view – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+generate_capital_annotations()[source]
+

Automatically convert any “pending” temporary properties from +Document objects to Annotation objects . The generated Annotation +objects are then added to the last View in the views lists.

+

See https://github.com/clamsproject/mmif-python/issues/226 for rationale +behind this behavior and discussion.

+
+ +
+
+get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
+

Finds views where alignments between two given annotation types occurred.

+
+
Returns:
+

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

+
+
+
+ +
+
+get_all_views_contain(*at_types: TypesBase | str) → List[View][source]
+

Returns the list of all views in the MMIF if given types +are present in that view’s ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the list of views that contain the type

+
+
+
+ +
+
+get_all_views_with_error() → List[View][source]
+

Returns the list of all views in the MMIF that have errors.

+
+
Returns:
+

the list of views that contain errors but no annotations

+
+
+
+ +
+
+get_annotations_between_time(start: int | float, end: int | float, time_unit: str = 'ms', at_types: List[str | TypesBase] = []) → Iterator[Annotation][source]
+

Finds annotations that are anchored between the given time points.

+
+
Parameters:
+
    +

  • start – the start time point in the unit of input_unit

    • +

  • end – the end time point in the unit of input_unit

    • +

  • time_unit – the unit of the input time points. Default is ms.

    • +

  • at_types – a list of annotation types to filter with. Any type in this list will be included in the return.

    • +
+
+
Returns:
+

an iterator of Annotation objects that are anchored between the given time points

+
+
+
+ +
+
+get_document_by_id(doc_id: str) → Document[source]
+

Finds a Document object with the given ID.

+
+
Parameters:
+

doc_id – the ID to search for

+
+
Returns:
+

a reference to the corresponding document, if it exists

+
+
Raises:
+

KeyError – if there is no corresponding document

+
+
+
+ +
+
+get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
+

Method to get the location of first document of given type.

+
+
Parameters:
+

m_type – the type to search for

+
+
Returns:
+

the value of the location field in the corresponding document

+
+
+
+ +
+
+get_documents_by_app(app_id: str) → List[Document][source]
+

Method to get all documents object queries by its originated app name.

+
+
Parameters:
+

app_id – the app name to search for

+
+
Returns:
+

a list of documents matching the requested app name, or an empty list if the app not found

+
+
+
+ +
+
+get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
+

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

+
+
Parameters:
+
    +

  • prop_key – the metadata key to search for

    • +

  • prop_value – the metadata value to match

    • +
+
+
Returns:
+

a list of documents matching the requested metadata key-value pair

+
+
+
+ +
+
+get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
+

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

+
+
Parameters:
+

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

+
+
Returns:
+

a list of documents matching the requested type, or an empty list if none found.

+
+
+
+ +
+
+get_documents_in_view(vid: str | None = None) → List[Document][source]
+

Method to get all documents object queries by a view id.

+
+
Parameters:
+

vid – the source view ID to search for

+
+
Returns:
+

a list of documents matching the requested source view ID, or an empty list if the view not found

+
+
+
+ +
+
+get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
+

This method returns the file paths of documents of given type. +Only top-level documents have locations, so we only check them.

+
+
Parameters:
+

m_type – the type to search for

+
+
Returns:
+

a list of the values of the location fields in the corresponding documents

+
+
+
+ +
+
+get_end(annotation: Annotation) → int | float[source]
+

An alias to get_anchor_point method with start=False.

+
+ +
+
+get_last_error() → str | None[source]
+

Returns the last error message found in the views.

+
+
Returns:
+

the error message in human-readable format, or None if no error is found

+
+
+
+ +
+
+get_start(annotation: Annotation) → int | float[source]
+

An alias to get_anchor_point method with start=True.

+
+ +
+
+get_view_by_id(req_view_id: str) → View[source]
+

Finds a View object with the given ID.

+
+
Parameters:
+

req_view_id – the ID to search for

+
+
Returns:
+

a reference to the corresponding view, if it exists

+
+
Raises:
+

Exception – if there is no corresponding view

+
+
+
+ +
+
+get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
+

Returns the last view appended that contains the given +types in its ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the view, or None if the type is not found

+
+
+
+ +
+
+get_view_with_error() → View | None[source]
+

Returns the last view appended that contains an error.

+
+
Returns:
+

the view, or None if no error is found

+
+
+
+ +
+
+get_views_contain(*at_types: TypesBase | str) → List[View][source]
+

Returns the list of all views in the MMIF if given types +are present in that view’s ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the list of views that contain the type

+
+
+
+ +
+
+get_views_for_document(doc_id: str) → List[View][source]
+

Returns the list of all views that have annotations anchored on a particular document. +Note that when the document is inside a view (generated during the pipeline’s running), +doc_id must be prefixed with the view_id.

+
+ +
+
+get_views_with_error() → List[View][source]
+

Returns the list of all views in the MMIF that have errors.

+
+
Returns:
+

the list of views that contain errors but no annotations

+
+
+
+ +
+
+new_view() → View[source]
+

Creates an empty view with a new ID and appends it to the views list.

+
+
Returns:
+

a reference to the new View object

+
+
+
+ +
+
+new_view_id() → str[source]
+

Fetches an ID for a new view.

+
+
Returns:
+

the ID

+
+
+
+ +
+
+sanitize()[source]
+

Sanitizes a Mmif object by running some safeguards. +Concretely, it performs the following before returning the JSON string.

+
    +

  1. validating output using built-in MMIF jsonschema

    2. +

  2. remove non-existing annotation types from contains metadata

    3. +
+
+ +
+
+serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
+

Serializes the MMIF object to a JSON string.

+
+
Parameters:
+
    +

  • sanitize – If True, performs some sanitization of before returning +the JSON string. See sanitize() for details.

    • +

  • autogenerate_capital_annotations – If True, automatically convert +any “pending” temporary properties from Document objects to +Annotation objects. See generate_capital_annotations() for +details.

    • +

  • pretty – If True, returns string representation with indentation.

    • +
+
+
Returns:
+

JSON string of the MMIF object.

+
+
+
+ +
+
+static validate(json_str: bytes | str | dict) → None[source]
+

Validates a MMIF JSON object against the MMIF Schema. +Note that this method operates before processing by MmifObject._load_str, +so it expects @ and not _ for the JSON-LD @-keys.

+
+
Raises:
+

jsonschema.exceptions.ValidationError – if the input fails validation

+
+
Parameters:
+

json_str – a MMIF JSON dict or string

+
+
Returns:
+

None

+
+
+
+ +
+ +
+
+

mmif.serialize.view module

+

The view module contains the classes used to represent a MMIF view +as a live Python object.

+

In MMIF, views are created by apps in a pipeline that are annotating +data that was previously present in the MMIF file.

+
+
+class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: DataDict[str, str]

+

Contain object that represents the metadata of a single +annotation type in the contains metadata of a MMIF view.

+
+ +
+
+class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None, parent_mmif=None, *_)[source]
+

Bases: MmifObject

+

View object that represents a single view in a MMIF file.

+

A view is identified by an ID, and contains certain metadata, +a list of annotations, and potentially a JSON-LD @context +IRI.

+

If view_obj is not provided, an empty View will be generated.

+
+
Parameters:
+

view_obj – the JSON data that defines the view

+
+
+
+
+add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
+

Adds an annotation to the current view.

+

Fails if there is already an annotation with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
+
+
Raises:
+

KeyError – if overwrite is set to False and +an annotation with the same ID exists +in the view

+
+
Returns:
+

the same Annotation object passed in as annotation

+
+
+
+ +
+
+add_document(document: Document, overwrite=False) → Annotation[source]
+

Appends a Document object to the annotations list.

+

Fails if there is already a document with the same ID in the annotations list.

+
+
Parameters:
+
    +

  • document – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+get_annotation_by_id(ann_id) → Annotation[source]
+
+ +
+
+get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
+

Look for certain annotations in this view, specified by parameters

+
+
Parameters:
+
    +

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • +

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • +
+
+
+
+ +
+
+get_document_by_id(doc_id) → Document[source]
+
+ +
+
+get_documents() → List[Document][source]
+
+ +
+
+get_error() → str | None[source]
+

Get the “text” representation of the error occurred during +processing. Text representation is supposed to be human-readable. +When ths view does not have any error, returns None.

+
+ +
+
+has_error() → bool[source]
+
+ +
+
+has_warnings()[source]
+
+ +
+
+new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
+

Generates a new mmif.serialize.annotation.Annotation +object and adds it to the current view.

+

Fails if there is already an annotation with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
    +

  • at_type – the desired @type of the annotation.

    • +

  • aid – the desired ID of the annotation, when not given, +the mmif SDK tries to automatically generate an ID based on +Annotation type and existing annotations in the view.

    • +

  • overwrite – if set to True, will overwrite an +existing annotation with the same ID.

    • +
+
+
Raises:
+

KeyError – if overwrite is set to False and +an annotation with the same ID exists +in the view.

+
+
Returns:
+

the generated mmif.serialize.annotation.Annotation

+
+
+
+ +
+
+new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
+

Adds a new element to the contains metadata.

+
+
Parameters:
+
    +

  • at_type – the @type of the annotation type being added

    • +

  • contains_metadata – any metadata associated with the annotation type

    • +
+
+
Returns:
+

the generated Contain object

+
+
+
+ +
+
+new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
+

Generates a new mmif.serialize.annotation.Document +object, particularly typed as TextDocument and adds it to the current view.

+

Fails if there is already a text document with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
    +

  • text – text content of the new document

    • +

  • lang – ISO 639-1 code of the language used in the new document

    • +

  • did – the desired ID of the document, when not given, +the mmif SDK tries to automatically generate an ID based on +Annotation type and existing documents in the view.

    • +

  • overwrite – if set to True, will overwrite an +existing document with the same ID

    • +
+
+
Raises:
+

KeyError – if overwrite is set to False and +an document with the same ID exists +in the view

+
+
Returns:
+

the generated mmif.serialize.annotation.Document

+
+
+
+ +
+
+set_error(err_message: str, err_trace: str) → None[source]
+
+ +
+ +
+
+class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+

ViewMetadata object that represents the metadata object within a MMIF view.

+
+
Parameters:
+

viewmetadata_obj – the JSON data that defines the metadata

+
+
+
+
+add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
+

Add a configuration key-value pair to the app_configuration dictionary.

+
+ +
+
+add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
+
+ +
+
+add_parameter(param_key: str, param_value: str)[source]
+

Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

+
+ +
+
+add_parameters(**runtime_params: str)[source]
+

Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

+
+ +
+
+add_warnings(*warnings: Warning)[source]
+
+ +
+
+emtpy_warnings()[source]
+
+ +
+
+get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
+

Get a configuration value from the app_configuration dictionary.

+
+ +
+
+get_error_as_text() → str[source]
+
+ +
+
+get_parameter(param_key: str) → str[source]
+

Get a runtime parameter from the view metadata.

+
+ +
+
+has_error() → bool[source]
+
+ +
+
+has_warnings()[source]
+
+ +
+
+new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
+

Adds a new element to the contains dictionary.

+
+
Parameters:
+
    +

  • at_type – the @type of the annotation type being added

    • +

  • contains_metadata – any metadata associated with the annotation type

    • +
+
+
Returns:
+

the generated Contain object

+
+
+
+ +
+
+set_error(message: str, stack_trace: str)[source]
+
+ +
+ +
+
+

mmif.serialize.annotation module

+

The annotation module contains the classes used to represent a +MMIF annotation as a live Python object.

+

In MMIF, annotations are created by apps in a pipeline as a part +of a view. For documentation on how views are represented, see +mmif.serialize.view.

+
+
+class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+

MmifObject that represents an annotation in a MMIF view.

+
+
+add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
+

Adds a property to the annotation’s properties.

+
+
Parameters:
+
    +

  • name – the name of the property

    • +

  • value – the property’s desired value

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+aligned_to_by(alignment: Annotation) → Annotation | None[source]
+

Retrieves the other side of Alignment annotation that has this annotation on one side.

+
+
Parameters:
+

alignment – Alignment annotation that has this annotation on one side

+
+
Returns:
+

the annotation that this annotation is aligned to (other side of Alignment), +or None if this annotation is not used in the Alignment.

+
+
+
+ +
+
+property at_type: TypesBase[source]
+
+ +
+
+static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
+
+ +
+
+get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
+

A special getter for Annotation properties. This is to allow for +directly accessing properties without having to go through the +properties object, or view-level annotation properties encoded in the +view.metadata.contains dict. Note that the regular props will take +the priority over the ephemeral props when there are conflicts.

+
+ +
+
+get_all_aligned() → Iterator[Annotation][source]
+

Generator to iterate through all alignments and aligned annotations. Note that this generator will yield +the Alignment annotations as well. Every odd-numbered yield will be an Alignment annotation, and every +even-numbered yield will be the aligned annotation. If there’s a specific annotation type that you’re looking +for, you need to filter the generated results outside.

+
+
Returns:
+

yields the alignment annotation and the aligned annotation. +The order is decided by the order of appearance of Alignment annotations in the MMIF

+
+
+
+ +
+
+get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
+

A special getter for Annotation properties. This is to allow for +directly accessing properties without having to go through the +properties object, or view-level annotation properties encoded in the +view.metadata.contains dict. Note that the regular props will take +the priority over the ephemeral props when there are conflicts.

+
+ +
+
+property id: str[source]
+
+ +
+
+is_document()[source]
+
+ +
+
+is_type(at_type: str | TypesBase) → bool[source]
+

Check if the @type of this object matches.

+
+ +
+
+property long_id: str[source]
+
+ +
+
+property parent: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject, MutableMapping[str, T]

+

AnnotationProperties object that represents the +properties object within a MMIF annotation.

+
+
Parameters:
+

mmif_obj – the JSON data that defines the properties

+
+
+
+ +
+
+class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: Annotation

+

Document object that represents a single document in a MMIF file.

+

A document is identified by an ID, and contains certain attributes +and potentially contains the contents of the document itself, +metadata about how the document was created, and/or a list of +subdocuments grouped together logically.

+

If document_obj is not provided, an empty Document will be generated.

+
+
Parameters:
+

document_obj – the JSON data that defines the document

+
+
+
+
+add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
+

Adds a property to the document’s properties.

+

Unlike the parent Annotation class, added properties of a +Document object can be lost during serialization unless it belongs +to somewhere in a Mmif object. This is because we want to keep +Document object as “read-only” as possible. Thus, if you want to add +a property to a Document object,

+
    +

  • add the document to a Mmif object (either in the documents list or +in a view from the views list), or

    • +

  • directly write to Document.properties instead of using this method +(which is not recommended).

    • +
+

With the former method, the SDK will record the added property as a +Annotation annotation object, separate from the original Document +object. See Mmif.generate_capital_annotations() for more.

+

A few notes to keep in mind:

+
    +

  1. You can’t overwrite an existing property of a Document object.

    2. +

  2. A MMIF can have multiple Annotation objects with the same +property name but different values. When this happens, the SDK will +only keep the latest value (in order of appearances in views list) of +the property, effectively overwriting the previous values.

    3. +
+
+ +
+
+get(prop_name)[source]
+

A special getter for Document properties. The major difference from +the super class’s Annotation.get() method is that Document +class has one more set of “pending” properties, that are added after +the Document object is created and will be serialized as a separate +Annotation object of which @type = Annotation. The +pending properties will take the priority over the regular properties +when there are conflicts.

+
+ +
+
+get_property(prop_name)[source]
+

A special getter for Document properties. The major difference from +the super class’s Annotation.get() method is that Document +class has one more set of “pending” properties, that are added after +the Document object is created and will be serialized as a separate +Annotation object of which @type = Annotation. The +pending properties will take the priority over the regular properties +when there are conflicts.

+
+ +
+
+property location: str | None[source]
+

location property must be a legitimate URI. That is, should the document be a local file +then the file:// scheme must be used. +Returns None when no location is set.

+
+ +
+
+location_address() → str | None[source]
+

Retrieves the full address from the document location URI. +Returns None when no location is set.

+
+ +
+
+location_path(nonexist_ok=True) → str | None[source]
+

Retrieves a path that’s resolved to a pathname in the local file system. +To obtain the original value of the “path” part in the location string +(before resolving), use properties.location_path_literal method. +Returns None when no location is set.

+
+
Parameters:
+

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

+
+
+
+ +
+
+location_scheme() → str | None[source]
+

Retrieves URI scheme of the document location. +Returns None when no location is set.

+
+ +
+
+property text_language: str[source]
+
+ +
+
+property text_value: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: AnnotationProperties

+

DocumentProperties object that represents the +properties object within a MMIF document.

+
+
Parameters:
+

mmif_obj – the JSON data that defines the properties

+
+
+
+
+property location: str | None[source]
+

location property must be a legitimate URI. That is, should the document be a local file +then the file:// scheme must be used. +Returns None when no location is set.

+
+ +
+
+location_address() → str | None[source]
+

Retrieves the full address from the document location URI. +Returns None when no location is set.

+
+ +
+
+location_path() → str | None[source]
+
+ +
+
+location_path_literal() → str | None[source]
+

Retrieves only path name of the document location (hostname is ignored). +Returns None when no location is set.

+
+ +
+
+location_path_resolved(nonexist_ok=True) → str | None[source]
+

Retrieves only path name of the document location (hostname is ignored), +and then try to resolve the path name in the local file system. +This method should be used when the document scheme is file or empty. +For other schemes, users should install mmif-locdoc-<scheme> plugin.

+

Returns None when no location is set. +Raise ValueError when no code found to resolve the given location scheme.

+
+ +
+
+location_scheme() → str | None[source]
+

Retrieves URI scheme of the document location. +Returns None when no location is set.

+
+ +
+
+property text_language: str[source]
+
+ +
+
+property text_value: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+
+
+property lang: str[source]
+
+ +
+
+property value: str[source]
+
+ +
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
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+
0.4.7
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/autodoc/mmif.utils.html b/docs/1.0.17/autodoc/mmif.utils.html new file mode 100644 index 00000000..88e3e1fc --- /dev/null +++ b/docs/1.0.17/autodoc/mmif.utils.html @@ -0,0 +1,619 @@ + + + + + + + mmif.utils module — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.utils module

+
+

mmif.utils.video_document_helper module

+
+
+mmif.utils.video_document_helper.capture(video_document: Document)[source]
+

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

+
+
Parameters:
+

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

+
+
Returns:
+

OpenCV VideoCapture object

+
+
+
+ +
+
+mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
+

Converts start and end points in a TimeFrame annotation a different time unit.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • out_unit – time unit to which the point is converted

    • +
+
+
Returns:
+

tuple of frame numbers, seconds/milliseconds, or ISO notation of TimeFrame’s start and end

+
+
+
+ +
+
+mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
+

Converts a time point included in an annotation to a different time unit. +The input annotation must have timePoint property.

+
+
Parameters:
+
    +

  • mmif – input MMIF to obtain fps and input timeunit

    • +

  • timepoint – Annotation instance with timePoint property

    • +

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • +
+
+
Returns:
+

frame number (integer) or second/millisecond (float) of input timepoint

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
+

Extracts frames from a video document as a list of numpy.ndarray. +Use with sample_frames() function to get the list of frame numbers first.

+
+
Parameters:
+
    +

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • +

  • framenums – integers representing the frame numbers to extract

    • +

  • as_PIL – return PIL.Image.Image instead of ndarray

    • +
+
+
Returns:
+

frames as a list of ndarray or Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
+

Extracts the middle frame of a time interval annotation as a numpy ndarray.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • as_PIL – return Image instead of ndarray

    • +
+
+
Returns:
+

frame as a numpy.ndarray or PIL.Image.Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
+

Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • as_PIL – return Image instead of ndarray

    • +
+
+
Returns:
+

frame as a numpy.ndarray or PIL.Image.Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
+

Converts a frame number to a millisecond value.

+
+ +
+
+mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
+

Converts a frame number to a second value.

+
+ +
+
+mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
+
+

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

+
+

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. +xisting

+
+ +
+
+mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
+

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

+
+
Parameters:
+

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

+
+
Returns:
+

frames per second as a float, rounded to 2 decimal places

+
+
+
+ +
+
+mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
+

Calculates the middle frame number of a time interval annotation.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +
+
+
Returns:
+

middle frame number as an integer

+
+
+
+ +
+
+mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
+

Calculates the representative frame number from an annotation.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • +
+
+
Returns:
+

representative frame number as an integer

+
+
+
+ +
+
+mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
+

Converts a millisecond value to a frame number.

+
+ +
+
+mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
+

Helper function to sample frames from a time interval. +Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

+
+
Parameters:
+
    +

  • start_frame – start frame of the interval

    • +

  • end_frame – end frame of the interval

    • +

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • +
+
+
+
+ +
+
+mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
+

Converts a second value to a frame number.

+
+ +
+
+

mmif.utils.sequence_helper module

+

This module provides helpers for handling sequence labeling. Specifically, it provides

+
    +

  • a generalized label re-mapper for “post-binning” of labels

    • +

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • +

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • +
+

However, it DOES NOT provide

+
    +

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • +

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • +
+

Some functions can use optional external libraries (e.g., numpy) for better performance. +Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

+
+
+mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
+

Build a label remapper dictionary from source and destination labels.

+
+
Parameters:
+
    +

  • src_labels – a list of all labels on the source side

    • +

  • dst_labels – a dict from source labels to destination labels. +Source labels not in this dict will be remapped to a negative label (-).

    • +
+
+
Returns:
+

a dict that exhaustively maps source labels to destination labels

+
+
+
+ +
+
+mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
+

Build lists of scores indexed by the label names.

+
+
Parameters:
+
    +

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • +

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • +

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label +common choices are max, min, or sum

    • +
+
+
Returns:
+

    +

  1. a dictionary that maps label names to their index in the score list

    2. +

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. +
+

+
+
+
+ +
+
+mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
+

Given a list of scores, a score threshold, and smoothing parameters, +identify the intervals of “positive” scores by “trimming” the short +positive sequences (“spseq”) and short negative sequences (“snseq”). To +decide the positivity, first step is binarization of the scores by the +min_score threshold. Given Sr as “raw” input real-number scores +list, and min_score=0.5,

+
+
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
+
+
+
+

the binarization is done by simply comparing each score to the +threshold to get S list of binary scores

+
+
1.0 :                                     |                      
+0.9 :                |                    |                      
+0.8 :          |     |  |           |     |              |       
+0.7 :          |     |  |           |     |  |           |       
+0.6 :    |     |     |  |           |     |  |           |     | 
+0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
+0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
+0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
+0.0 +------------------------------------------------------------
+raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
+ S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
+
+
+
+

Note that the size of a positive or negative sequence can be as small +as 1.

+

Then, here are examples of smoothing a list of binary scores into +intervals, by trimming “very short” (under thresholds) sequences of +positive or negative:

+
+

Note

+

legends:

+
    +

  • t is unit index (e.g. time index)

    • +

  • S is the list of binary scores (zeros and ones)

    • +

  • I is the list of intervals after smoothing

    • +
+
+
    +

  1. with params min_spseq_size==1, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
+
    +
    +

    Explanation: min_snseq_size is used to smooth short sequences +of negative predictions. In this, zeros from t[7:10] are smoothed +into “one” I, while zeros from t[13:19] are kept as “zero” I. Note +that the “short” snseqs at the either ends (t[0:1]) are never +smoothed.

    +
    +
    2. +

  2. with params min_spseq_size==4, min_snseq_size==2

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: min_spseq_size is used to smooth short sequences +of positive predictions. In this example, the spseqs of ones from +both t[10:13] and t[19:20] are smoothed. Note that the “short” +spseqs at the either ends (t[19:20]) are always smoothed.

    +
    +
    3. +

  3. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: When two threshold parameters are working together, +the algorithm will prioritize the smoothing of the snseqs over the +smoothing of the spseqs. Thus, in this example, the snseq t[7:10] +gets first smoothed “up” before the spseq t[10:13] is smoothed +“down”, resulting in a long final I.

    +
    +
    4. +

  4. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
+
    +
    +

    Explanation: Since smoothing of snseqs is prioritized, short spseqs +at the beginning or the end can be kept.

    +
    +
    5. +

  5. with params min_spseq_size==1, min_snseq_size==1

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
+
    +
    +

    Explanation: When both width thresholds are set to 1, the algorithm +works essentially in the “stitching” only mode.

    +
    +
    6. +
+
+
Parameters:
+
    +

  • scores – SORTED list of scores to be smoothed. The score list +is assumed to be “exhaust” the entire time or space of +the underlying document segment. +(Sorted by the start, and then by the end of anchors)

    • +

  • min_score – minimum threshold to use to discard +low-scored units (strictly less than)

    • +

  • min_spseq_size – minimum size of a positive sequence not to be +smoothed (greater or equal to)

    • +

  • min_snseq_size – minimum size of a negative sequence not to be +smoothed (greater or equal to)

    • +
+
+
Returns:
+

list of tuples of start(inclusive)/end(exclusive) indices +of the “positive” sequences. Negative sequences (regardless of +their size) are not included in the output.

+
+
+
+ +
+
+mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
+

Simple check for a list of annotations to see if they have the same label set.

+
+
Raise:
+

AttributeError if an element in the input list doesn’t have the labelset property

+
+
Raise:
+

ValueError if different labelset values are found

+
+
Returns:
+

a list of the common labelset value (list of label names)

+
+
+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
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+
0.4.3
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/autodoc/mmif.vocabulary.html b/docs/1.0.17/autodoc/mmif.vocabulary.html new file mode 100644 index 00000000..3acea0ec --- /dev/null +++ b/docs/1.0.17/autodoc/mmif.vocabulary.html @@ -0,0 +1,303 @@ + + + + + + + mmif.vocabulary module — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.vocabulary module

+
+

mmif.vocabulary.annotation_types module

+
+
+class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
+

Bases: AnnotationTypesBase

+

This class contains the CLAMS annotation types +defined in the spec version 1.0.5 as class variables.

+
+
+Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
+
+ +
+
+Annotation = http://mmif.clams.ai/vocabulary/Annotation/v5[source]
+
+ +
+
+BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v4[source]
+
+ +
+
+Chapter = http://mmif.clams.ai/vocabulary/Chapter/v5[source]
+
+ +
+
+Interval = http://mmif.clams.ai/vocabulary/Interval/v4[source]
+
+ +
+
+Polygon = http://mmif.clams.ai/vocabulary/Polygon/v4[source]
+
+ +
+
+Region = http://mmif.clams.ai/vocabulary/Region/v4[source]
+
+ +
+
+Relation = http://mmif.clams.ai/vocabulary/Relation/v4[source]
+
+ +
+
+Span = http://mmif.clams.ai/vocabulary/Span/v4[source]
+
+ +
+
+TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v5[source]
+
+ +
+
+TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v4[source]
+
+ +
+
+VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v4[source]
+
+ +
+
+version: str[source]
+
+ +
+ +
+
+

mmif.vocabulary.document_types module

+
+
+class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
+

Bases: DocumentTypesBase

+

This class contains the CLAMS document types +defined in the spec version 1.0.5 as class variables.

+
+
+AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
+
+ +
+
+Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
+
+ +
+
+ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
+
+ +
+
+TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
+
+ +
+
+VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
+
+ +
+
+version: str[source]
+
+ +
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
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+
0.4.5
+
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+
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+
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+
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+
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+
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+
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+
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+
1.0.10
+
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+
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+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/autodoc/mmif_docloc_http.html b/docs/1.0.17/autodoc/mmif_docloc_http.html new file mode 100644 index 00000000..df0d172d --- /dev/null +++ b/docs/1.0.17/autodoc/mmif_docloc_http.html @@ -0,0 +1,183 @@ + + + + + + + mmif_docloc_http package — mmif-python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif_docloc_http package

+

MMIF document location helper module for http and https schemes. +If you want to write your own docloc scheme handler, please use the source code of this module as a reference. +See this plug-in section for more information.

+
+
+mmif_docloc_http.resolve(docloc)[source]
+
+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/consumer-tutorial.html b/docs/1.0.17/consumer-tutorial.html new file mode 100644 index 00000000..b26c4b04 --- /dev/null +++ b/docs/1.0.17/consumer-tutorial.html @@ -0,0 +1,176 @@ + + + + + + + MMIF consumer — mmif-python documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • MMIF consumer
    • +
  • +
    • +
+
+
+
+
+ +
+

MMIF consumer

+

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

+

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

+
    +

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. +

  2. Must listen to 5000 port.

    3. +

  3. Must expose /display route .

    4. +

  4. /display router should response to GET requests.

    5. +

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. +

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. +
+

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/genindex.html b/docs/1.0.17/genindex.html new file mode 100644 index 00000000..f39cd0c6 --- /dev/null +++ b/docs/1.0.17/genindex.html @@ -0,0 +1,778 @@ + + + + + + Index — mmif-python documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ A + | B + | C + | D + | E + | F + | G + | H + | I + | K + | L + | M + | N + | P + | R + | S + | T + | U + | V + +
+

A

+ + + +
+ +

B

+ + + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

E

+ + + +
+ +

F

+ + + +
+ +

G

+ + + +
+ +

H

+ + + +
+ +

I

+ + + +
+ +

K

+ + +
+ +

L

+ + + +
+ +

M

+ + + +
+ +

N

+ + + +
+ +

P

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + + +
+ +

U

+ + +
+ +

V

+ + + +
+ + + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/index.html b/docs/1.0.17/index.html new file mode 100644 index 00000000..00d78484 --- /dev/null +++ b/docs/1.0.17/index.html @@ -0,0 +1,232 @@ + + + + + + + Welcome to mmif-python’s documentation! — mmif-python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Welcome to mmif-python’s documentation!
    • +
  • +
    • +
+
+
+
+
+ +
+

Welcome to mmif-python’s documentation!

+
+

MultiMedia Interchange Format

+

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

+
+
+

mmif-python

+

mmif-python is a Python implementation of the MMIF data format. +mmif-python provides various helper classes and functions to handle MMIF JSON in Python, +including ;

+
    +

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. +

  2. validation of MMIF JSON

    3. +

  3. handling of CLAMS vocabulary types

    4. +

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. +
+
+
+

For more …

+ +
+

Contents

+ +
+
+

API documentation:

+ +
+
+
+
+

Indices and tables

+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/introduction.html b/docs/1.0.17/introduction.html new file mode 100644 index 00000000..921bf497 --- /dev/null +++ b/docs/1.0.17/introduction.html @@ -0,0 +1,249 @@ + + + + + + + Getting Started — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Getting Started
    • +
  • +
    • +
+
+
+
+
+ +
+

Getting Started

+
+

Overview

+

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. +mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

+
+
+

Prerequisites

+
    +

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • +
+
+
+

Installation

+

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

+
pip install mmif-python
+
+
+

This will install a package mmif to local python.

+

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

+
+

Note

+

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

+
+
+
+

MMIF Serialization

+

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

+
import mmif
+from mmif import Mmif
+
+mmif_str = """{
+"metadata": {
+  "mmif": "http://mmif.clams.ai/1.0.0"
+},
+"documents": [
+  {
+    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
+    "properties": {
+      "id": "m1",
+      "mime": "video/mp4",
+      "location": "file:///var/archive/video-0012.mp4"
+    }
+  },
+  {
+    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
+    "properties": {
+      "id": "m2",
+      "mime": "text/plain",
+      "location": "file:///var/archive/video-0012-transcript.txt"
+    }
+  }
+],
+"views": []}"""
+mmif_obj = Mmif(mmif_str)
+
+
+

Few notes;

+
    +

  1. MMIF does not carry the primary source files in it.

    2. +

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. +
+

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

+

To get subcomponents, you can use various getters implemented in subclasses. For example;

+
from mmif.vocabulary.document_types import DocumentTypes
+
+for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
+  with open(video.location_path(), 'b') as in_video:
+    # do something with the video file
+
+
+

For a full list of available helper methods, please refer to the API documentation.

+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/modules.html b/docs/1.0.17/modules.html new file mode 100644 index 00000000..4cac7320 --- /dev/null +++ b/docs/1.0.17/modules.html @@ -0,0 +1,409 @@ + + + + + + + mmif package — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • mmif package
    • +
  • +
    • +
+
+
+
+
+ +
+

mmif package

+
+ +
+
+
+

mmif_docloc_http package

+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/objects.inv b/docs/1.0.17/objects.inv new file mode 100644 index 00000000..801c14e8 Binary files /dev/null and b/docs/1.0.17/objects.inv differ diff --git a/docs/1.0.17/plugins.html b/docs/1.0.17/plugins.html new file mode 100644 index 00000000..6b1d7ad8 --- /dev/null +++ b/docs/1.0.17/plugins.html @@ -0,0 +1,238 @@ + + + + + + + Developing plugins for MMIF Python SDK — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Developing plugins for MMIF Python SDK
    • +
  • +
    • +
+
+
+
+
+ +
+

Developing plugins for MMIF Python SDK

+
+

Overview

+

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

+

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. +mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

+

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

+

This document contains information about how to write plugins for mmif-python.

+
+

Document Location Scheme Plugins

+

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

+

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

+
    +

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. +

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. +
+
import mmif_docloc_s3
+resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
+# then resolved must be a local file path that can be used to open the file
+
+
+

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

+

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

+
$ tree .
+.
+├── mmif_docloc_dummy
+│   └── __init__.py
+├── pyproject.toml
+└── setup.cfg
+
+ $ cat pyproject.toml
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+$ cat setup.cfg
+[metadata]
+name = mmif_docloc_dummy  # this name is IMPORTANT
+version = 0.0.1
+description = a plugin to mmif-pyhon to handle `dummy` location scheme
+
+
+

And the plugin code.

+
# mmif_docloc_dummy/__init__.py
+doc_types = {'video': 'mp4'}
+
+def resolve(docloc):
+    scheme = 'dummy'
+    if docloc.startswith(f'{scheme}://'):
+        doc_id, doc_type = docloc.split('.')
+        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
+    else:
+        raise ValueError(f'cannot handle document location scheme: {docloc}')
+
+
+
+
+

Bulit-in Document Location Scheme Plugins

+

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. +Take a look at mmif_docloc_http module for details.

+
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.17/py-modindex.html b/docs/1.0.17/py-modindex.html new file mode 100644 index 00000000..92b66a26 --- /dev/null +++ b/docs/1.0.17/py-modindex.html @@ -0,0 +1,227 @@ + + + + + + Python Module Index — mmif-python documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Python Module Index
    • +
  • +
    • +
+
+
+
+
+ + +

Python Module Index

+ +
+ m +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
+ m
+ mmif +
    + mmif.serialize.annotation +
    + mmif.serialize.mmif +
    + mmif.serialize.model +
    + mmif.serialize.view +
    + mmif.utils.sequence_helper +
    + mmif.utils.video_document_helper +
    + mmif.vocabulary.annotation_types +
    + mmif.vocabulary.document_types +
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(mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.new_view_id"]], "parent (mmif.serialize.annotation.annotation property)": [[0, "mmif.serialize.annotation.Annotation.parent"]], "reserved_names (mmif.serialize.model.mmifobject attribute)": [[0, "mmif.serialize.model.MmifObject.reserved_names"]], "sanitize() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.sanitize"]], "serialize() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.serialize"]], "serialize() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.serialize"]], "set_additional_property() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.set_additional_property"]], "set_error() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.set_error"]], "set_error() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.set_error"]], "text_language (mmif.serialize.annotation.document 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module mmif.utils.sequence_helper)": [[1, "mmif.utils.sequence_helper.build_label_remapper"]], "build_score_lists() (in module mmif.utils.sequence_helper)": [[1, "mmif.utils.sequence_helper.build_score_lists"]], "capture() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.capture"]], "convert_timeframe() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timeframe"]], "convert_timepoint() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timepoint"]], "extract_frames_as_images() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_frames_as_images"]], "extract_mid_frame() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_mid_frame"]], "extract_representative_frame() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_representative_frame"]], "framenum_to_millisecond() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.framenum_to_millisecond"]], "framenum_to_second() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.framenum_to_second"]], "get_annotation_property() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_annotation_property"]], "get_framerate() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_framerate"]], "get_mid_framenum() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_mid_framenum"]], "get_representative_framenum() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_representative_framenum"]], "millisecond_to_framenum() (in module mmif.utils.video_document_helper)": [[1, 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"mmif.vocabulary.annotation_types.AnnotationTypes.Annotation"]], "annotationtypes (class in mmif.vocabulary.annotation_types)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes"]], "audiodocument (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.AudioDocument"]], "boundingbox (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.BoundingBox"]], "chapter (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Chapter"]], "document (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.Document"]], "documenttypes (class in mmif.vocabulary.document_types)": [[2, "mmif.vocabulary.document_types.DocumentTypes"]], "imagedocument (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.ImageDocument"]], "interval (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Interval"]], "polygon (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Polygon"]], "region (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Region"]], "relation (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Relation"]], "span (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Span"]], "textdocument (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.TextDocument"]], "timeframe (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.TimeFrame"]], "timepoint (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.TimePoint"]], "videodocument (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.VideoDocument"]], "videoobject (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.VideoObject"]], "mmif.vocabulary.annotation_types": [[2, "module-mmif.vocabulary.annotation_types"]], "mmif.vocabulary.document_types": [[2, "module-mmif.vocabulary.document_types"]], "version (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.version"]], "version (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.version"]], "mmif_docloc_http": [[3, "module-mmif_docloc_http"]], "resolve() (in module mmif_docloc_http)": [[3, "mmif_docloc_http.resolve"]]}}) \ No newline at end of file diff --git a/docs/1.0.17/target-versions.html b/docs/1.0.17/target-versions.html new file mode 100644 index 00000000..90a084eb --- /dev/null +++ b/docs/1.0.17/target-versions.html @@ -0,0 +1,298 @@ + + + + + + + Target MMIF Versions — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Target MMIF Versions
    • +
  • +
    • +
+
+
+
+
+ +
+

Target MMIF Versions

+

This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.17

1.0.5

1.0.16

1.0.4

1.0.15

1.0.4

1.0.14

1.0.4

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.17 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/.buildinfo b/docs/1.0.18/.buildinfo new file mode 100644 index 00000000..dd6995d1 --- /dev/null +++ b/docs/1.0.18/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. 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+1,35 @@ +mmif.serialize module +===================== + +mmif.serialize.model module +--------------------------- + +.. automodule:: mmif.serialize.model + :members: + :undoc-members: + :show-inheritance: + +mmif.serialize.mmif module +-------------------------- + +.. automodule:: mmif.serialize.mmif + :members: + :undoc-members: + :show-inheritance: + +mmif.serialize.view module +-------------------------- + +.. automodule:: mmif.serialize.view + :members: + :undoc-members: + :show-inheritance: + +mmif.serialize.annotation module +-------------------------------- + +.. automodule:: mmif.serialize.annotation + :members: + :undoc-members: + :show-inheritance: + diff --git a/docs/1.0.18/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.18/_sources/autodoc/mmif.utils.rst.txt new file mode 100644 index 00000000..9a6ecc44 --- /dev/null +++ b/docs/1.0.18/_sources/autodoc/mmif.utils.rst.txt @@ -0,0 +1,18 @@ +mmif.utils module +================= + +mmif.utils.video_document_helper module +---------------------------------------- + +.. automodule:: mmif.utils.video_document_helper + :members: + :undoc-members: + :show-inheritance: + +mmif.utils.sequence_helper module +--------------------------------- + +.. automodule:: mmif.utils.sequence_helper + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.18/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.18/_sources/autodoc/mmif.vocabulary.rst.txt new file mode 100644 index 00000000..d250c6a3 --- /dev/null +++ b/docs/1.0.18/_sources/autodoc/mmif.vocabulary.rst.txt @@ -0,0 +1,18 @@ +mmif.vocabulary module +====================== + +mmif.vocabulary.annotation\_types module +---------------------------------------- + +.. automodule:: mmif.vocabulary.annotation_types + :members: + :undoc-members: + :show-inheritance: + +mmif.vocabulary.document\_types module +-------------------------------------- + +.. automodule:: mmif.vocabulary.document_types + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.18/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.18/_sources/autodoc/mmif_docloc_http.rst.txt new file mode 100644 index 00000000..b76c8df5 --- /dev/null +++ b/docs/1.0.18/_sources/autodoc/mmif_docloc_http.rst.txt @@ -0,0 +1,11 @@ +mmif_docloc_http package +======================== + +MMIF document location helper module for `http` and `https` schemes. +If you want to write your own docloc scheme handler, please use the source code of this module as a reference. +See this :ref:`plug-in section ` for more information. + +.. automodule:: mmif_docloc_http + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.18/_sources/consumer-tutorial.rst.txt b/docs/1.0.18/_sources/consumer-tutorial.rst.txt new file mode 100644 index 00000000..c54634e2 --- /dev/null +++ b/docs/1.0.18/_sources/consumer-tutorial.rst.txt @@ -0,0 +1,17 @@ +.. _consumer-tutorial: + +MMIF consumer +================================= + +A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. + +MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. + +#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) +#. Must listen to ``5000`` port. +#. Must expose ``/display`` route . +#. ``/display`` router should response to ``GET`` requests. +#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. +#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. + +We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.18/_sources/index.rst.txt b/docs/1.0.18/_sources/index.rst.txt new file mode 100644 index 00000000..beb56aae --- /dev/null +++ b/docs/1.0.18/_sources/index.rst.txt @@ -0,0 +1,26 @@ +Welcome to mmif-python's documentation! +======================================= + +.. mdinclude:: ../README.md + +.. toctree:: + :maxdepth: 2 + :caption: Contents + + introduction + plugins + target-versions + +.. toctree:: + :maxdepth: 2 + :caption: API documentation: + + modules + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/1.0.18/_sources/introduction.rst.txt b/docs/1.0.18/_sources/introduction.rst.txt new file mode 100644 index 00000000..cfd9eaf7 --- /dev/null +++ b/docs/1.0.18/_sources/introduction.rst.txt @@ -0,0 +1,89 @@ +.. _introduction: + +Getting Started +=============== + + +Overview +--------- + +MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. +``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. + +Prerequisites +------------- + +* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. + +Installation +--------------- + +Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. + +.. code-block:: bash + + pip install mmif-python + +This will install a package `mmif` to local python. + +The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. + +.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. + +MMIF Serialization +--------------------------- + +:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. + +.. code-block:: python + + import mmif + from mmif import Mmif + + mmif_str = """{ + "metadata": { + "mmif": "http://mmif.clams.ai/1.0.0" + }, + "documents": [ + { + "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", + "properties": { + "id": "m1", + "mime": "video/mp4", + "location": "file:///var/archive/video-0012.mp4" + } + }, + { + "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", + "properties": { + "id": "m2", + "mime": "text/plain", + "location": "file:///var/archive/video-0012-transcript.txt" + } + } + ], + "views": []}""" + mmif_obj = Mmif(mmif_str) + + +Few notes; + +#. MMIF does not carry the primary source files in it. +#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. + +When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. + +To get subcomponents, you can use various getters implemented in subclasses. For example; + +.. code-block:: python + + from mmif.vocabulary.document_types import DocumentTypes + + for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): + with open(video.location_path(), 'b') as in_video: + # do something with the video file + + +For a full list of available helper methods, please refer to :ref:`the API documentation `. + diff --git a/docs/1.0.18/_sources/modules.rst.txt b/docs/1.0.18/_sources/modules.rst.txt new file mode 100644 index 00000000..4bb9307d --- /dev/null +++ b/docs/1.0.18/_sources/modules.rst.txt @@ -0,0 +1,20 @@ +.. _apidoc: + +mmif package +============ + +.. toctree:: + :maxdepth: 4 + + autodoc/mmif.serialize + autodoc/mmif.vocabulary + autodoc/mmif.utils + +mmif_docloc_http package +======================== + +.. toctree:: + :maxdepth: 2 + + autodoc/mmif_docloc_http + diff --git a/docs/1.0.18/_sources/plugins.rst.txt b/docs/1.0.18/_sources/plugins.rst.txt new file mode 100644 index 00000000..1af39426 --- /dev/null +++ b/docs/1.0.18/_sources/plugins.rst.txt @@ -0,0 +1,89 @@ +.. _plugins: + +Developing plugins for MMIF Python SDK +====================================== + + +Overview +-------- + +As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. + + +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. +``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. + +Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). + +This document contains information about how to write plugins for ``mmif-python``. + +.. _docloc_plugin: + +Document Location Scheme Plugins +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. + +To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; + +#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. +#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; +#. Optionally (but highly recommended), the top module also can provide another function named ``help``. The function must take no arguments and return a :class:`str` that explains how the input string to the ``resolve`` function should be formatted. + +.. code-block:: python + + import mmif_docloc_s3 + resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') + # then resolved must be a local file path that can be used to open the file + + +Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. + +(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) + +.. code-block:: sh + + $ tree . + . + ├── mmif_docloc_dummy + │ └── __init__.py + ├── pyproject.toml + └── setup.cfg + + $ cat pyproject.toml + [build-system] + requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + $ cat setup.cfg + [metadata] + name = mmif_docloc_dummy # this name is IMPORTANT + version = 0.0.1 + description = a plugin to mmif-pyhon to handle `dummy` location scheme + + +And the plugin code. + +.. code-block:: python + + # mmif_docloc_dummy/__init__.py + doc_types = {'video': 'mp4'} + + def resolve(docloc): + scheme = 'dummy' + if docloc.startswith(f'{scheme}://'): + doc_id, doc_type = docloc.split('.') + return f'/path/to/{doc_id}.{doc_types[doc_type]}' + else: + raise ValueError(f'cannot handle document location scheme: {docloc}') + + def help(): + return "location format: `.video`" + + + +Bulit-in Document Location Scheme Plugins +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. +Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.18/_sources/target-versions.rst.txt b/docs/1.0.18/_sources/target-versions.rst.txt new file mode 100644 index 00000000..34216d3e --- /dev/null +++ b/docs/1.0.18/_sources/target-versions.rst.txt @@ -0,0 +1,10 @@ +.. _target-versions: + +Target MMIF Versions +==================== + +This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. + +.. csv-table:: Target Specification Versions + :file: target-versions.csv + :header-rows: 1 diff --git a/docs/1.0.18/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.18/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/docs/1.0.18/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/docs/1.0.18/_static/searchtools.js b/docs/1.0.18/_static/searchtools.js new file mode 100644 index 00000000..97d56a74 --- /dev/null +++ b/docs/1.0.18/_static/searchtools.js @@ -0,0 +1,566 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = docUrlRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = docUrlRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/docs/1.0.18/_static/sphinx_highlight.js b/docs/1.0.18/_static/sphinx_highlight.js new file mode 100644 index 00000000..aae669d7 --- /dev/null +++ b/docs/1.0.18/_static/sphinx_highlight.js @@ -0,0 +1,144 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + parent.insertBefore( + span, + parent.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/docs/1.0.18/autodoc/mmif.serialize.html b/docs/1.0.18/autodoc/mmif.serialize.html new file mode 100644 index 00000000..3847db45 --- /dev/null +++ b/docs/1.0.18/autodoc/mmif.serialize.html @@ -0,0 +1,1473 @@ + + + + + + + mmif.serialize module — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.serialize module

+
+

mmif.serialize.model module

+

The model module contains the classes used to represent an +abstract MMIF object as a live Python object.

+

The MmifObject class or one of its derivatives is subclassed by +all other classes defined in this SDK, except for MmifObjectEncoder.

+

These objects are generally instantiated from JSON, either as a string +or as an already-loaded Python dictionary. This base class provides the +core functionality for deserializing MMIF JSON data into live objects +and serializing live objects into MMIF JSON data. Specialized behavior +for the different components of MMIF is added in the subclasses.

+
+
+class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject, Generic[T, S]

+
+
+empty()[source]
+
+ +
+
+get(key: T, default=None) → S | None[source]
+
+ +
+
+items()[source]
+
+ +
+
+keys()[source]
+
+ +
+
+update(other, overwrite)[source]
+
+ +
+
+values()[source]
+
+ +
+ +
+
+class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None, *_)[source]
+

Bases: MmifObject, Generic[T]

+

The DataList class is an abstraction that represents the +various lists found in a MMIF file, such as documents, subdocuments, +views, and annotations.

+
+
Parameters:
+

mmif_obj (Union[str, list]) – the data that the list contains

+
+
+
+
+append(value, overwrite)[source]
+
+ +
+
+deserialize(mmif_json: str | list) → None[source]
+

Passes the input data into the internal deserializer.

+
+ +
+
+empty()[source]
+
+ +
+
+get(key: str) → T | None[source]
+

Standard dictionary-style get() method, albeit with no default +parameter. Relies on the implementation of __getitem__.

+

Will return None if the key is not found.

+
+
Parameters:
+

key – the key to search for

+
+
Returns:
+

the value matching that key

+
+
+
+ +
+ +
+
+class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: object

+

Abstract superclass for MMIF related key-value pair objects.

+

Any MMIF object can be initialized as an empty placeholder or +an actual representation with a JSON formatted string or equivalent +dict object argument.

+

This superclass has four specially designed instance variables, and these +variable names cannot be used as attribute names for MMIF objects.

+
    +

  1. _unnamed_attributes: +Only can be either None or an empty dictionary. If it’s set to None, +it means the class won’t take any Additional Attributes in the +JSON schema sense. If it’s an empty dict, users can throw any k-v +pairs to the class, as long as the key is not a “reserved” name, +and those additional attributes will be stored in this dict while +in memory.

    2. +

  2. _attribute_classes: +This is a dict from a key name to a specific python class to use for +deserialize the value. Note that a key name in this dict does NOT +have to be a named attribute, but is recommended to be one.

    3. +

  3. _required_attributes: +This is a simple list of names of attributes that are required in +the object. When serialize, an object will skip its empty (e.g. +zero-length, or None) attributes unless they are in this list. +Otherwise, the serialized JSON string would have empty +representations (e.g. "", []).

    4. +

  4. _exclude_from_diff: +This is a simple list of names of attributes that should be excluded +from the diff calculation in __eq__.

    5. +
+

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. +Maybe there is a better way to utilize type hints (e.g. getting them +as a programmatically), but for now developers should be careful to +add types to hints as well as to this dict.

+

Also note that those special attributes MUST be set in the __init__() +before calling super method, otherwise deserialization will not work.

+

And also, a subclass that has one or more named attributes, it must +set those attributes in the __init__() before calling super method. +When serializing a MmifObject, all empty attributes will be ignored, +so for optional named attributes, you must leave the values empty +(len == 0), but NOT None. Any None-valued named attributes will cause +issues with current implementation.

+
+
Parameters:
+

mmif_obj – JSON string or dict to initialize an object. +If not given, an empty object will be initialized, sometimes with +an ID value automatically generated, based on its parent object.

+
+
+
+
+deserialize(mmif_json: str | dict) → None[source]
+

Takes a JSON-formatted string or a simple dict that’s json-loaded from +such a string as an input and populates object’s fields with the values +specified in the input.

+
+
Parameters:
+

mmif_json – JSON-formatted string or dict from such a string +that represents a MMIF object

+
+
+
+ +
+
+disallow_additional_properties() → None[source]
+

Call this method in __init__() to prevent the insertion +of unnamed attributes after initialization.

+
+ +
+
+id_delimiter: ClassVar[str] = ':'[source]
+
+ +
+
+static is_empty(obj) → bool[source]
+

return True if the obj is None or “emtpy”. The emptiness first defined as +having zero length. But for objects that lack __len__ method, we need +additional check.

+
+ +
+
+reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
+
+ +
+
+serialize(pretty: bool = False) → str[source]
+

Generates JSON representation of an object.

+
+
Parameters:
+

pretty – If True, returns string representation with indentation.

+
+
Returns:
+

JSON string of the object.

+
+
+
+ +
+
+set_additional_property(key: str, value: Any) → None[source]
+

Method to set values in _unnamed_attributes.

+
+
Parameters:
+
    +

  • key – the attribute name

    • +

  • value – the desired value

    • +
+
+
Returns:
+

None

+
+
Raise:
+

AttributeError if additional properties are disallowed by disallow_additional_properties()

+
+
+
+ +
+
+view_prefix: ClassVar[str] = 'v_'[source]
+
+ +
+ +
+
+class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
+

Bases: JSONEncoder

+

Encoder class to define behaviors of de-/serialization

+
+
+default(obj: MmifObject)[source]
+

Overrides default encoding behavior to prioritize MmifObject.serialize().

+
+ +
+ +
+
+

mmif.serialize.mmif module

+

The mmif module contains the classes used to represent a full MMIF +file as a live Python object.

+

See the specification docs and the JSON Schema file for more information.

+
+
+class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
+

Bases: MmifObject

+

MmifObject that represents a full MMIF file.

+
+
Parameters:
+
    +

  • mmif_obj – the JSON data

    • +

  • validate – whether to validate the data against the MMIF JSON schema.

    • +
+
+
+
+
+add_document(document: Document, overwrite=False) → None[source]
+

Appends a Document object to the documents list.

+

Fails if there is already a document with the same ID in the MMIF object.

+
+
Parameters:
+
    +

  • document – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+add_view(view: View, overwrite=False) → None[source]
+

Appends a View object to the views list.

+

Fails if there is already a view with the same ID in the MMIF object.

+
+
Parameters:
+
    +

  • view – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+generate_capital_annotations()[source]
+

Automatically convert any “pending” temporary properties from +Document objects to Annotation objects . The generated Annotation +objects are then added to the last View in the views lists.

+

See https://github.com/clamsproject/mmif-python/issues/226 for rationale +behind this behavior and discussion.

+
+ +
+
+get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
+

Finds views where alignments between two given annotation types occurred.

+
+
Returns:
+

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

+
+
+
+ +
+
+get_all_views_contain(*at_types: TypesBase | str) → List[View][source]
+

Returns the list of all views in the MMIF if given types +are present in that view’s ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the list of views that contain the type

+
+
+
+ +
+
+get_all_views_with_error() → List[View][source]
+

Returns the list of all views in the MMIF that have errors.

+
+
Returns:
+

the list of views that contain errors but no annotations

+
+
+
+ +
+
+get_annotations_between_time(start: int | float, end: int | float, time_unit: str = 'ms', at_types: List[str | TypesBase] = []) → Iterator[Annotation][source]
+

Finds annotations that are anchored between the given time points.

+
+
Parameters:
+
    +

  • start – the start time point in the unit of input_unit

    • +

  • end – the end time point in the unit of input_unit

    • +

  • time_unit – the unit of the input time points. Default is ms.

    • +

  • at_types – a list of annotation types to filter with. Any type in this list will be included in the return.

    • +
+
+
Returns:
+

an iterator of Annotation objects that are anchored between the given time points

+
+
+
+ +
+
+get_document_by_id(doc_id: str) → Document[source]
+

Finds a Document object with the given ID.

+
+
Parameters:
+

doc_id – the ID to search for

+
+
Returns:
+

a reference to the corresponding document, if it exists

+
+
Raises:
+

KeyError – if there is no corresponding document

+
+
+
+ +
+
+get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
+

Method to get the location of first document of given type.

+
+
Parameters:
+

m_type – the type to search for

+
+
Returns:
+

the value of the location field in the corresponding document

+
+
+
+ +
+
+get_documents_by_app(app_id: str) → List[Document][source]
+

Method to get all documents object queries by its originated app name.

+
+
Parameters:
+

app_id – the app name to search for

+
+
Returns:
+

a list of documents matching the requested app name, or an empty list if the app not found

+
+
+
+ +
+
+get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
+

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

+
+
Parameters:
+
    +

  • prop_key – the metadata key to search for

    • +

  • prop_value – the metadata value to match

    • +
+
+
Returns:
+

a list of documents matching the requested metadata key-value pair

+
+
+
+ +
+
+get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
+

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

+
+
Parameters:
+

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

+
+
Returns:
+

a list of documents matching the requested type, or an empty list if none found.

+
+
+
+ +
+
+get_documents_in_view(vid: str | None = None) → List[Document][source]
+

Method to get all documents object queries by a view id.

+
+
Parameters:
+

vid – the source view ID to search for

+
+
Returns:
+

a list of documents matching the requested source view ID, or an empty list if the view not found

+
+
+
+ +
+
+get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
+

This method returns the file paths of documents of given type. +Only top-level documents have locations, so we only check them.

+
+
Parameters:
+

m_type – the type to search for

+
+
Returns:
+

a list of the values of the location fields in the corresponding documents

+
+
+
+ +
+
+get_end(annotation: Annotation) → int | float[source]
+

An alias to get_anchor_point method with start=False.

+
+ +
+
+get_last_error() → str | None[source]
+

Returns the last error message found in the views.

+
+
Returns:
+

the error message in human-readable format, or None if no error is found

+
+
+
+ +
+
+get_start(annotation: Annotation) → int | float[source]
+

An alias to get_anchor_point method with start=True.

+
+ +
+
+get_view_by_id(req_view_id: str) → View[source]
+

Finds a View object with the given ID.

+
+
Parameters:
+

req_view_id – the ID to search for

+
+
Returns:
+

a reference to the corresponding view, if it exists

+
+
Raises:
+

Exception – if there is no corresponding view

+
+
+
+ +
+
+get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
+

Returns the last view appended that contains the given +types in its ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the view, or None if the type is not found

+
+
+
+ +
+
+get_view_with_error() → View | None[source]
+

Returns the last view appended that contains an error.

+
+
Returns:
+

the view, or None if no error is found

+
+
+
+ +
+
+get_views_contain(*at_types: TypesBase | str) → List[View][source]
+

Returns the list of all views in the MMIF if given types +are present in that view’s ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the list of views that contain the type

+
+
+
+ +
+
+get_views_for_document(doc_id: str) → List[View][source]
+

Returns the list of all views that have annotations anchored on a particular document. +Note that when the document is inside a view (generated during the pipeline’s running), +doc_id must be prefixed with the view_id.

+
+ +
+
+get_views_with_error() → List[View][source]
+

Returns the list of all views in the MMIF that have errors.

+
+
Returns:
+

the list of views that contain errors but no annotations

+
+
+
+ +
+
+new_view() → View[source]
+

Creates an empty view with a new ID and appends it to the views list.

+
+
Returns:
+

a reference to the new View object

+
+
+
+ +
+
+new_view_id() → str[source]
+

Fetches an ID for a new view.

+
+
Returns:
+

the ID

+
+
+
+ +
+
+sanitize()[source]
+

Sanitizes a Mmif object by running some safeguards. +Concretely, it performs the following before returning the JSON string.

+
    +

  1. validating output using built-in MMIF jsonschema

    2. +

  2. remove non-existing annotation types from contains metadata

    3. +
+
+ +
+
+serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
+

Serializes the MMIF object to a JSON string.

+
+
Parameters:
+
    +

  • sanitize – If True, performs some sanitization of before returning +the JSON string. See sanitize() for details.

    • +

  • autogenerate_capital_annotations – If True, automatically convert +any “pending” temporary properties from Document objects to +Annotation objects. See generate_capital_annotations() for +details.

    • +

  • pretty – If True, returns string representation with indentation.

    • +
+
+
Returns:
+

JSON string of the MMIF object.

+
+
+
+ +
+
+static validate(json_str: bytes | str | dict) → None[source]
+

Validates a MMIF JSON object against the MMIF Schema. +Note that this method operates before processing by MmifObject._load_str, +so it expects @ and not _ for the JSON-LD @-keys.

+
+
Raises:
+

jsonschema.exceptions.ValidationError – if the input fails validation

+
+
Parameters:
+

json_str – a MMIF JSON dict or string

+
+
Returns:
+

None

+
+
+
+ +
+ +
+
+

mmif.serialize.view module

+

The view module contains the classes used to represent a MMIF view +as a live Python object.

+

In MMIF, views are created by apps in a pipeline that are annotating +data that was previously present in the MMIF file.

+
+
+class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: DataDict[str, str]

+

Contain object that represents the metadata of a single +annotation type in the contains metadata of a MMIF view.

+
+ +
+
+class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None, parent_mmif=None, *_)[source]
+

Bases: MmifObject

+

View object that represents a single view in a MMIF file.

+

A view is identified by an ID, and contains certain metadata, +a list of annotations, and potentially a JSON-LD @context +IRI.

+

If view_obj is not provided, an empty View will be generated.

+
+
Parameters:
+

view_obj – the JSON data that defines the view

+
+
+
+
+add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
+

Adds an annotation to the current view.

+

Fails if there is already an annotation with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
+
+
Raises:
+

KeyError – if overwrite is set to False and +an annotation with the same ID exists +in the view

+
+
Returns:
+

the same Annotation object passed in as annotation

+
+
+
+ +
+
+add_document(document: Document, overwrite=False) → Annotation[source]
+

Appends a Document object to the annotations list.

+

Fails if there is already a document with the same ID in the annotations list.

+
+
Parameters:
+
    +

  • document – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+get_annotation_by_id(ann_id) → Annotation[source]
+
+ +
+
+get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
+

Look for certain annotations in this view, specified by parameters

+
+
Parameters:
+
    +

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • +

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • +
+
+
+
+ +
+
+get_document_by_id(doc_id) → Document[source]
+
+ +
+
+get_documents() → List[Document][source]
+
+ +
+
+get_error() → str | None[source]
+

Get the “text” representation of the error occurred during +processing. Text representation is supposed to be human-readable. +When ths view does not have any error, returns None.

+
+ +
+
+has_error() → bool[source]
+
+ +
+
+has_warnings()[source]
+
+ +
+
+new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
+

Generates a new mmif.serialize.annotation.Annotation +object and adds it to the current view.

+

Fails if there is already an annotation with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
    +

  • at_type – the desired @type of the annotation.

    • +

  • aid – the desired ID of the annotation, when not given, +the mmif SDK tries to automatically generate an ID based on +Annotation type and existing annotations in the view.

    • +

  • overwrite – if set to True, will overwrite an +existing annotation with the same ID.

    • +
+
+
Raises:
+

KeyError – if overwrite is set to False and +an annotation with the same ID exists +in the view.

+
+
Returns:
+

the generated mmif.serialize.annotation.Annotation

+
+
+
+ +
+
+new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
+

Adds a new element to the contains metadata.

+
+
Parameters:
+
    +

  • at_type – the @type of the annotation type being added

    • +

  • contains_metadata – any metadata associated with the annotation type

    • +
+
+
Returns:
+

the generated Contain object

+
+
+
+ +
+
+new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
+

Generates a new mmif.serialize.annotation.Document +object, particularly typed as TextDocument and adds it to the current view.

+

Fails if there is already a text document with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
    +

  • text – text content of the new document

    • +

  • lang – ISO 639-1 code of the language used in the new document

    • +

  • did – the desired ID of the document, when not given, +the mmif SDK tries to automatically generate an ID based on +Annotation type and existing documents in the view.

    • +

  • overwrite – if set to True, will overwrite an +existing document with the same ID

    • +
+
+
Raises:
+

KeyError – if overwrite is set to False and +an document with the same ID exists +in the view

+
+
Returns:
+

the generated mmif.serialize.annotation.Document

+
+
+
+ +
+
+set_error(err_message: str, err_trace: str) → None[source]
+
+ +
+ +
+
+class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+

ViewMetadata object that represents the metadata object within a MMIF view.

+
+
Parameters:
+

viewmetadata_obj – the JSON data that defines the metadata

+
+
+
+
+add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
+

Add a configuration key-value pair to the app_configuration dictionary.

+
+ +
+
+add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
+
+ +
+
+add_parameter(param_key: str, param_value: str)[source]
+

Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

+
+ +
+
+add_parameters(**runtime_params: str)[source]
+

Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

+
+ +
+
+add_warnings(*warnings: Warning)[source]
+
+ +
+
+emtpy_warnings()[source]
+
+ +
+
+get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
+

Get a configuration value from the app_configuration dictionary.

+
+ +
+
+get_error_as_text() → str[source]
+
+ +
+
+get_parameter(param_key: str) → str[source]
+

Get a runtime parameter from the view metadata.

+
+ +
+
+has_error() → bool[source]
+
+ +
+
+has_warnings()[source]
+
+ +
+
+new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
+

Adds a new element to the contains dictionary.

+
+
Parameters:
+
    +

  • at_type – the @type of the annotation type being added

    • +

  • contains_metadata – any metadata associated with the annotation type

    • +
+
+
Returns:
+

the generated Contain object

+
+
+
+ +
+
+set_error(message: str, stack_trace: str)[source]
+
+ +
+ +
+
+

mmif.serialize.annotation module

+

The annotation module contains the classes used to represent a +MMIF annotation as a live Python object.

+

In MMIF, annotations are created by apps in a pipeline as a part +of a view. For documentation on how views are represented, see +mmif.serialize.view.

+
+
+class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+

MmifObject that represents an annotation in a MMIF view.

+
+
+add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
+

Adds a property to the annotation’s properties.

+
+
Parameters:
+
    +

  • name – the name of the property

    • +

  • value – the property’s desired value

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+aligned_to_by(alignment: Annotation) → Annotation | None[source]
+

Retrieves the other side of Alignment annotation that has this annotation on one side.

+
+
Parameters:
+

alignment – Alignment annotation that has this annotation on one side

+
+
Returns:
+

the annotation that this annotation is aligned to (other side of Alignment), +or None if this annotation is not used in the Alignment.

+
+
+
+ +
+
+property at_type: TypesBase[source]
+
+ +
+
+static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
+
+ +
+
+get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
+

A special getter for Annotation properties. This is to allow for +directly accessing properties without having to go through the +properties object, or view-level annotation properties encoded in the +view.metadata.contains dict. Note that the regular props will take +the priority over the ephemeral props when there are conflicts.

+
+ +
+
+get_all_aligned() → Iterator[Annotation][source]
+

Generator to iterate through all alignments and aligned annotations. Note that this generator will yield +the Alignment annotations as well. Every odd-numbered yield will be an Alignment annotation, and every +even-numbered yield will be the aligned annotation. If there’s a specific annotation type that you’re looking +for, you need to filter the generated results outside.

+
+
Returns:
+

yields the alignment annotation and the aligned annotation. +The order is decided by the order of appearance of Alignment annotations in the MMIF

+
+
+
+ +
+
+get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
+

A special getter for Annotation properties. This is to allow for +directly accessing properties without having to go through the +properties object, or view-level annotation properties encoded in the +view.metadata.contains dict. Note that the regular props will take +the priority over the ephemeral props when there are conflicts.

+
+ +
+
+property id: str[source]
+
+ +
+
+is_document()[source]
+
+ +
+
+is_type(at_type: str | TypesBase) → bool[source]
+

Check if the @type of this object matches.

+
+ +
+
+property long_id: str[source]
+
+ +
+
+property parent: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject, MutableMapping[str, T]

+

AnnotationProperties object that represents the +properties object within a MMIF annotation.

+
+
Parameters:
+

mmif_obj – the JSON data that defines the properties

+
+
+
+ +
+
+class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: Annotation

+

Document object that represents a single document in a MMIF file.

+

A document is identified by an ID, and contains certain attributes +and potentially contains the contents of the document itself, +metadata about how the document was created, and/or a list of +subdocuments grouped together logically.

+

If document_obj is not provided, an empty Document will be generated.

+
+
Parameters:
+

document_obj – the JSON data that defines the document

+
+
+
+
+add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
+

Adds a property to the document’s properties.

+

Unlike the parent Annotation class, added properties of a +Document object can be lost during serialization unless it belongs +to somewhere in a Mmif object. This is because we want to keep +Document object as “read-only” as possible. Thus, if you want to add +a property to a Document object,

+
    +

  • add the document to a Mmif object (either in the documents list or +in a view from the views list), or

    • +

  • directly write to Document.properties instead of using this method +(which is not recommended).

    • +
+

With the former method, the SDK will record the added property as a +Annotation annotation object, separate from the original Document +object. See Mmif.generate_capital_annotations() for more.

+

A few notes to keep in mind:

+
    +

  1. You can’t overwrite an existing property of a Document object.

    2. +

  2. A MMIF can have multiple Annotation objects with the same +property name but different values. When this happens, the SDK will +only keep the latest value (in order of appearances in views list) of +the property, effectively overwriting the previous values.

    3. +
+
+ +
+
+get(prop_name)[source]
+

A special getter for Document properties. The major difference from +the super class’s Annotation.get() method is that Document +class has one more set of “pending” properties, that are added after +the Document object is created and will be serialized as a separate +Annotation object of which @type = Annotation. The +pending properties will take the priority over the regular properties +when there are conflicts.

+
+ +
+
+get_property(prop_name)[source]
+

A special getter for Document properties. The major difference from +the super class’s Annotation.get() method is that Document +class has one more set of “pending” properties, that are added after +the Document object is created and will be serialized as a separate +Annotation object of which @type = Annotation. The +pending properties will take the priority over the regular properties +when there are conflicts.

+
+ +
+
+property location: str | None[source]
+

location property must be a legitimate URI. That is, should the document be a local file +then the file:// scheme must be used. +Returns None when no location is set.

+
+ +
+
+location_address() → str | None[source]
+

Retrieves the full address from the document location URI. +Returns None when no location is set.

+
+ +
+
+location_path(nonexist_ok=True) → str | None[source]
+

Retrieves a path that’s resolved to a pathname in the local file system. +To obtain the original value of the “path” part in the location string +(before resolving), use properties.location_path_literal method. +Returns None when no location is set.

+
+
Parameters:
+

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

+
+
+
+ +
+
+location_scheme() → str | None[source]
+

Retrieves URI scheme of the document location. +Returns None when no location is set.

+
+ +
+
+property text_language: str[source]
+
+ +
+
+property text_value: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: AnnotationProperties

+

DocumentProperties object that represents the +properties object within a MMIF document.

+
+
Parameters:
+

mmif_obj – the JSON data that defines the properties

+
+
+
+
+property location: str | None[source]
+

location property must be a legitimate URI. That is, should the document be a local file +then the file:// scheme must be used. +Returns None when no location is set.

+
+ +
+
+location_address() → str | None[source]
+

Retrieves the full address from the document location URI. +Returns None when no location is set.

+
+ +
+
+location_path() → str | None[source]
+
+ +
+
+location_path_literal() → str | None[source]
+

Retrieves only path name of the document location (hostname is ignored). +Returns None when no location is set.

+
+ +
+
+location_path_resolved(nonexist_ok=True) → str | None[source]
+

Retrieves only path name of the document location (hostname is ignored), +and then try to resolve the path name in the local file system. +This method should be used when the document scheme is file or empty. +For other schemes, users should install mmif-locdoc-<scheme> plugin.

+

Returns None when no location is set. +Raise ValueError when no code found to resolve the given location scheme.

+
+ +
+
+location_scheme() → str | None[source]
+

Retrieves URI scheme of the document location. +Returns None when no location is set.

+
+ +
+
+property text_language: str[source]
+
+ +
+
+property text_value: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+
+
+property lang: str[source]
+
+ +
+
+property value: str[source]
+
+ +
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
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+
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+
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+
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+
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+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/autodoc/mmif.utils.html b/docs/1.0.18/autodoc/mmif.utils.html new file mode 100644 index 00000000..dc5c2eaf --- /dev/null +++ b/docs/1.0.18/autodoc/mmif.utils.html @@ -0,0 +1,619 @@ + + + + + + + mmif.utils module — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.utils module

+
+

mmif.utils.video_document_helper module

+
+
+mmif.utils.video_document_helper.capture(video_document: Document)[source]
+

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

+
+
Parameters:
+

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

+
+
Returns:
+

OpenCV VideoCapture object

+
+
+
+ +
+
+mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
+

Converts start and end points in a TimeFrame annotation a different time unit.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • out_unit – time unit to which the point is converted

    • +
+
+
Returns:
+

tuple of frame numbers, seconds/milliseconds, or ISO notation of TimeFrame’s start and end

+
+
+
+ +
+
+mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
+

Converts a time point included in an annotation to a different time unit. +The input annotation must have timePoint property.

+
+
Parameters:
+
    +

  • mmif – input MMIF to obtain fps and input timeunit

    • +

  • timepoint – Annotation instance with timePoint property

    • +

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • +
+
+
Returns:
+

frame number (integer) or second/millisecond (float) of input timepoint

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
+

Extracts frames from a video document as a list of numpy.ndarray. +Use with sample_frames() function to get the list of frame numbers first.

+
+
Parameters:
+
    +

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • +

  • framenums – integers representing the frame numbers to extract

    • +

  • as_PIL – return PIL.Image.Image instead of ndarray

    • +
+
+
Returns:
+

frames as a list of ndarray or Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
+

Extracts the middle frame of a time interval annotation as a numpy ndarray.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • as_PIL – return Image instead of ndarray

    • +
+
+
Returns:
+

frame as a numpy.ndarray or PIL.Image.Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
+

Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • as_PIL – return Image instead of ndarray

    • +
+
+
Returns:
+

frame as a numpy.ndarray or PIL.Image.Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
+

Converts a frame number to a millisecond value.

+
+ +
+
+mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
+

Converts a frame number to a second value.

+
+ +
+
+mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
+
+

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

+
+

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. +xisting

+
+ +
+
+mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
+

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

+
+
Parameters:
+

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

+
+
Returns:
+

frames per second as a float, rounded to 2 decimal places

+
+
+
+ +
+
+mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
+

Calculates the middle frame number of a time interval annotation.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +
+
+
Returns:
+

middle frame number as an integer

+
+
+
+ +
+
+mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
+

Calculates the representative frame number from an annotation.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • +
+
+
Returns:
+

representative frame number as an integer

+
+
+
+ +
+
+mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
+

Converts a millisecond value to a frame number.

+
+ +
+
+mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
+

Helper function to sample frames from a time interval. +Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

+
+
Parameters:
+
    +

  • start_frame – start frame of the interval

    • +

  • end_frame – end frame of the interval

    • +

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • +
+
+
+
+ +
+
+mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
+

Converts a second value to a frame number.

+
+ +
+
+

mmif.utils.sequence_helper module

+

This module provides helpers for handling sequence labeling. Specifically, it provides

+
    +

  • a generalized label re-mapper for “post-binning” of labels

    • +

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • +

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • +
+

However, it DOES NOT provide

+
    +

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • +

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • +
+

Some functions can use optional external libraries (e.g., numpy) for better performance. +Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

+
+
+mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
+

Build a label remapper dictionary from source and destination labels.

+
+
Parameters:
+
    +

  • src_labels – a list of all labels on the source side

    • +

  • dst_labels – a dict from source labels to destination labels. +Source labels not in this dict will be remapped to a negative label (-).

    • +
+
+
Returns:
+

a dict that exhaustively maps source labels to destination labels

+
+
+
+ +
+
+mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
+

Build lists of scores indexed by the label names.

+
+
Parameters:
+
    +

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • +

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • +

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label +common choices are max, min, or sum

    • +
+
+
Returns:
+

    +

  1. a dictionary that maps label names to their index in the score list

    2. +

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. +
+

+
+
+
+ +
+
+mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
+

Given a list of scores, a score threshold, and smoothing parameters, +identify the intervals of “positive” scores by “trimming” the short +positive sequences (“spseq”) and short negative sequences (“snseq”). To +decide the positivity, first step is binarization of the scores by the +min_score threshold. Given Sr as “raw” input real-number scores +list, and min_score=0.5,

+
+
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
+
+
+
+

the binarization is done by simply comparing each score to the +threshold to get S list of binary scores

+
+
1.0 :                                     |                      
+0.9 :                |                    |                      
+0.8 :          |     |  |           |     |              |       
+0.7 :          |     |  |           |     |  |           |       
+0.6 :    |     |     |  |           |     |  |           |     | 
+0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
+0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
+0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
+0.0 +------------------------------------------------------------
+raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
+ S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
+
+
+
+

Note that the size of a positive or negative sequence can be as small +as 1.

+

Then, here are examples of smoothing a list of binary scores into +intervals, by trimming “very short” (under thresholds) sequences of +positive or negative:

+
+

Note

+

legends:

+
    +

  • t is unit index (e.g. time index)

    • +

  • S is the list of binary scores (zeros and ones)

    • +

  • I is the list of intervals after smoothing

    • +
+
+
    +

  1. with params min_spseq_size==1, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
+
    +
    +

    Explanation: min_snseq_size is used to smooth short sequences +of negative predictions. In this, zeros from t[7:10] are smoothed +into “one” I, while zeros from t[13:19] are kept as “zero” I. Note +that the “short” snseqs at the either ends (t[0:1]) are never +smoothed.

    +
    +
    2. +

  2. with params min_spseq_size==4, min_snseq_size==2

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: min_spseq_size is used to smooth short sequences +of positive predictions. In this example, the spseqs of ones from +both t[10:13] and t[19:20] are smoothed. Note that the “short” +spseqs at the either ends (t[19:20]) are always smoothed.

    +
    +
    3. +

  3. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: When two threshold parameters are working together, +the algorithm will prioritize the smoothing of the snseqs over the +smoothing of the spseqs. Thus, in this example, the snseq t[7:10] +gets first smoothed “up” before the spseq t[10:13] is smoothed +“down”, resulting in a long final I.

    +
    +
    4. +

  4. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
+
    +
    +

    Explanation: Since smoothing of snseqs is prioritized, short spseqs +at the beginning or the end can be kept.

    +
    +
    5. +

  5. with params min_spseq_size==1, min_snseq_size==1

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
+
    +
    +

    Explanation: When both width thresholds are set to 1, the algorithm +works essentially in the “stitching” only mode.

    +
    +
    6. +
+
+
Parameters:
+
    +

  • scores – SORTED list of scores to be smoothed. The score list +is assumed to be “exhaust” the entire time or space of +the underlying document segment. +(Sorted by the start, and then by the end of anchors)

    • +

  • min_score – minimum threshold to use to discard +low-scored units (strictly less than)

    • +

  • min_spseq_size – minimum size of a positive sequence not to be +smoothed (greater or equal to)

    • +

  • min_snseq_size – minimum size of a negative sequence not to be +smoothed (greater or equal to)

    • +
+
+
Returns:
+

list of tuples of start(inclusive)/end(exclusive) indices +of the “positive” sequences. Negative sequences (regardless of +their size) are not included in the output.

+
+
+
+ +
+
+mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
+

Simple check for a list of annotations to see if they have the same label set.

+
+
Raise:
+

AttributeError if an element in the input list doesn’t have the labelset property

+
+
Raise:
+

ValueError if different labelset values are found

+
+
Returns:
+

a list of the common labelset value (list of label names)

+
+
+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/autodoc/mmif.vocabulary.html b/docs/1.0.18/autodoc/mmif.vocabulary.html new file mode 100644 index 00000000..4450b2e5 --- /dev/null +++ b/docs/1.0.18/autodoc/mmif.vocabulary.html @@ -0,0 +1,303 @@ + + + + + + + mmif.vocabulary module — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.vocabulary module

+
+

mmif.vocabulary.annotation_types module

+
+
+class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
+

Bases: AnnotationTypesBase

+

This class contains the CLAMS annotation types +defined in the spec version 1.0.5 as class variables.

+
+
+Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
+
+ +
+
+Annotation = http://mmif.clams.ai/vocabulary/Annotation/v5[source]
+
+ +
+
+BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v4[source]
+
+ +
+
+Chapter = http://mmif.clams.ai/vocabulary/Chapter/v5[source]
+
+ +
+
+Interval = http://mmif.clams.ai/vocabulary/Interval/v4[source]
+
+ +
+
+Polygon = http://mmif.clams.ai/vocabulary/Polygon/v4[source]
+
+ +
+
+Region = http://mmif.clams.ai/vocabulary/Region/v4[source]
+
+ +
+
+Relation = http://mmif.clams.ai/vocabulary/Relation/v4[source]
+
+ +
+
+Span = http://mmif.clams.ai/vocabulary/Span/v4[source]
+
+ +
+
+TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v5[source]
+
+ +
+
+TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v4[source]
+
+ +
+
+VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v4[source]
+
+ +
+
+version: str[source]
+
+ +
+ +
+
+

mmif.vocabulary.document_types module

+
+
+class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
+

Bases: DocumentTypesBase

+

This class contains the CLAMS document types +defined in the spec version 1.0.5 as class variables.

+
+
+AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
+
+ +
+
+Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
+
+ +
+
+ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
+
+ +
+
+TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
+
+ +
+
+VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
+
+ +
+
+version: str[source]
+
+ +
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/autodoc/mmif_docloc_http.html b/docs/1.0.18/autodoc/mmif_docloc_http.html new file mode 100644 index 00000000..fe75a3d6 --- /dev/null +++ b/docs/1.0.18/autodoc/mmif_docloc_http.html @@ -0,0 +1,189 @@ + + + + + + + mmif_docloc_http package — mmif-python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif_docloc_http package

+

MMIF document location helper module for http and https schemes. +If you want to write your own docloc scheme handler, please use the source code of this module as a reference. +See this plug-in section for more information.

+
+
+mmif_docloc_http.help()[source]
+
+ +
+
+mmif_docloc_http.resolve(docloc)[source]
+
+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/consumer-tutorial.html b/docs/1.0.18/consumer-tutorial.html new file mode 100644 index 00000000..8dcfd65c --- /dev/null +++ b/docs/1.0.18/consumer-tutorial.html @@ -0,0 +1,176 @@ + + + + + + + MMIF consumer — mmif-python documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • MMIF consumer
    • +
  • +
    • +
+
+
+
+
+ +
+

MMIF consumer

+

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

+

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

+
    +

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. +

  2. Must listen to 5000 port.

    3. +

  3. Must expose /display route .

    4. +

  4. /display router should response to GET requests.

    5. +

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. +

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. +
+

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/genindex.html b/docs/1.0.18/genindex.html new file mode 100644 index 00000000..a60a822e --- /dev/null +++ b/docs/1.0.18/genindex.html @@ -0,0 +1,780 @@ + + + + + + Index — mmif-python documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ A + | B + | C + | D + | E + | F + | G + | H + | I + | K + | L + | M + | N + | P + | R + | S + | T + | U + | V + +
+

A

+ + + +
+ +

B

+ + + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

E

+ + + +
+ +

F

+ + + +
+ +

G

+ + + +
+ +

H

+ + + +
+ +

I

+ + + +
+ +

K

+ + +
+ +

L

+ + + +
+ +

M

+ + + +
+ +

N

+ + + +
+ +

P

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + + +
+ +

U

+ + +
+ +

V

+ + + +
+ + + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/index.html b/docs/1.0.18/index.html new file mode 100644 index 00000000..bc15f932 --- /dev/null +++ b/docs/1.0.18/index.html @@ -0,0 +1,232 @@ + + + + + + + Welcome to mmif-python’s documentation! — mmif-python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Welcome to mmif-python’s documentation!
    • +
  • +
    • +
+
+
+
+
+ +
+

Welcome to mmif-python’s documentation!

+
+

MultiMedia Interchange Format

+

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

+
+
+

mmif-python

+

mmif-python is a Python implementation of the MMIF data format. +mmif-python provides various helper classes and functions to handle MMIF JSON in Python, +including ;

+
    +

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. +

  2. validation of MMIF JSON

    3. +

  3. handling of CLAMS vocabulary types

    4. +

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. +
+
+
+

For more …

+ +
+

Contents

+ +
+
+

API documentation:

+ +
+
+
+
+

Indices and tables

+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/introduction.html b/docs/1.0.18/introduction.html new file mode 100644 index 00000000..77060241 --- /dev/null +++ b/docs/1.0.18/introduction.html @@ -0,0 +1,249 @@ + + + + + + + Getting Started — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Getting Started
    • +
  • +
    • +
+
+
+
+
+ +
+

Getting Started

+
+

Overview

+

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. +mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

+
+
+

Prerequisites

+
    +

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • +
+
+
+

Installation

+

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

+
pip install mmif-python
+
+
+

This will install a package mmif to local python.

+

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

+
+

Note

+

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

+
+
+
+

MMIF Serialization

+

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

+
import mmif
+from mmif import Mmif
+
+mmif_str = """{
+"metadata": {
+  "mmif": "http://mmif.clams.ai/1.0.0"
+},
+"documents": [
+  {
+    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
+    "properties": {
+      "id": "m1",
+      "mime": "video/mp4",
+      "location": "file:///var/archive/video-0012.mp4"
+    }
+  },
+  {
+    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
+    "properties": {
+      "id": "m2",
+      "mime": "text/plain",
+      "location": "file:///var/archive/video-0012-transcript.txt"
+    }
+  }
+],
+"views": []}"""
+mmif_obj = Mmif(mmif_str)
+
+
+

Few notes;

+
    +

  1. MMIF does not carry the primary source files in it.

    2. +

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. +
+

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

+

To get subcomponents, you can use various getters implemented in subclasses. For example;

+
from mmif.vocabulary.document_types import DocumentTypes
+
+for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
+  with open(video.location_path(), 'b') as in_video:
+    # do something with the video file
+
+
+

For a full list of available helper methods, please refer to the API documentation.

+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.18/modules.html b/docs/1.0.18/modules.html new file mode 100644 index 00000000..23dd65a2 --- /dev/null +++ b/docs/1.0.18/modules.html @@ -0,0 +1,410 @@ + + + + + + + mmif package — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • mmif package
    • +
  • +
    • +
+
+
+
+
+ +
+

mmif package

+
+ +
+
+
+

mmif_docloc_http package

+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.18 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
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+ + + \ No newline at end of file diff --git a/docs/1.0.18/objects.inv b/docs/1.0.18/objects.inv new file mode 100644 index 00000000..842472f8 Binary files /dev/null and b/docs/1.0.18/objects.inv differ diff --git a/docs/1.0.18/plugins.html b/docs/1.0.18/plugins.html new file mode 100644 index 00000000..90b3cbad --- /dev/null +++ b/docs/1.0.18/plugins.html @@ -0,0 +1,242 @@ + + + + + + + Developing plugins for MMIF Python SDK — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Developing plugins for MMIF Python SDK
    • +
  • +
    • +
+
+
+
+
+ +
+

Developing plugins for MMIF Python SDK

+
+

Overview

+

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

+

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. +mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

+

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

+

This document contains information about how to write plugins for mmif-python.

+
+

Document Location Scheme Plugins

+

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

+

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

+
    +

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. +

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. +

  3. Optionally (but highly recommended), the top module also can provide another function named help. The function must take no arguments and return a str that explains how the input string to the resolve function should be formatted.

    4. +
+
import mmif_docloc_s3
+resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
+# then resolved must be a local file path that can be used to open the file
+
+
+

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

+

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

+
$ tree .
+.
+├── mmif_docloc_dummy
+│   └── __init__.py
+├── pyproject.toml
+└── setup.cfg
+
+ $ cat pyproject.toml
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+$ cat setup.cfg
+[metadata]
+name = mmif_docloc_dummy  # this name is IMPORTANT
+version = 0.0.1
+description = a plugin to mmif-pyhon to handle `dummy` location scheme
+
+
+

And the plugin code.

+
# mmif_docloc_dummy/__init__.py
+doc_types = {'video': 'mp4'}
+
+def resolve(docloc):
+    scheme = 'dummy'
+    if docloc.startswith(f'{scheme}://'):
+        doc_id, doc_type = docloc.split('.')
+        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
+    else:
+        raise ValueError(f'cannot handle document location scheme: {docloc}')
+
+def help():
+    return "location format: `<DOCUMENT_ID>.video`"
+
+
+
+
+

Bulit-in Document Location Scheme Plugins

+

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. +Take a look at mmif_docloc_http module for details.

+
+
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+ + + \ No newline at end of file diff --git a/docs/1.0.18/py-modindex.html b/docs/1.0.18/py-modindex.html new file mode 100644 index 00000000..966205a2 --- /dev/null +++ b/docs/1.0.18/py-modindex.html @@ -0,0 +1,227 @@ + + + + + + Python Module Index — mmif-python documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
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Python Module Index

+ +
+ m +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
+ m
+ mmif +
    + mmif.serialize.annotation +
    + mmif.serialize.mmif +
    + mmif.serialize.model +
    + mmif.serialize.view +
    + mmif.utils.sequence_helper +
    + mmif.utils.video_document_helper +
    + mmif.vocabulary.annotation_types +
    + mmif.vocabulary.document_types +
+ mmif_docloc_http +
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+ + + + + + + + \ No newline at end of file diff --git a/docs/1.0.18/searchindex.js b/docs/1.0.18/searchindex.js new file mode 100644 index 00000000..9e7cb2bc --- /dev/null +++ b/docs/1.0.18/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["autodoc/mmif.serialize", "autodoc/mmif.utils", "autodoc/mmif.vocabulary", "autodoc/mmif_docloc_http", "consumer-tutorial", "index", "introduction", "modules", "plugins", "target-versions"], "filenames": ["autodoc/mmif.serialize.rst", "autodoc/mmif.utils.rst", "autodoc/mmif.vocabulary.rst", "autodoc/mmif_docloc_http.rst", "consumer-tutorial.rst", "index.rst", "introduction.rst", "modules.rst", "plugins.rst", "target-versions.rst"], "titles": ["mmif.serialize module", "mmif.utils module", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "terms": {"The": [0, 1, 4, 6, 8], 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attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.version"]], "help() (in module mmif_docloc_http)": [[3, "mmif_docloc_http.help"]], "mmif_docloc_http": [[3, "module-mmif_docloc_http"]], "resolve() (in module mmif_docloc_http)": [[3, "mmif_docloc_http.resolve"]]}}) \ No newline at end of file diff --git a/docs/1.0.18/target-versions.html b/docs/1.0.18/target-versions.html new file mode 100644 index 00000000..6a051728 --- /dev/null +++ b/docs/1.0.18/target-versions.html @@ -0,0 +1,301 @@ + + + + + + + Target MMIF Versions — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.18

1.0.5

1.0.17

1.0.5

1.0.16

1.0.4

1.0.15

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+1,37 @@ +mmif.serialize package +====================== + +Core package to provide serialization and deserialization of MMIF format. + +``model`` module +--------------------------- + +.. automodule:: mmif.serialize.model + :members: + :undoc-members: + :show-inheritance: + +``mmif`` module +-------------------------- + +.. automodule:: mmif.serialize.mmif + :members: + :undoc-members: + :show-inheritance: + +``view`` module +-------------------------- + +.. automodule:: mmif.serialize.view + :members: + :undoc-members: + :show-inheritance: + +``annotation`` module +-------------------------------- + +.. automodule:: mmif.serialize.annotation + :members: + :undoc-members: + :show-inheritance: + diff --git a/docs/1.0.19/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.19/_sources/autodoc/mmif.utils.rst.txt new file mode 100644 index 00000000..a9275023 --- /dev/null +++ b/docs/1.0.19/_sources/autodoc/mmif.utils.rst.txt @@ -0,0 +1,39 @@ +mmif.utils package +================== + +Package containing utility modules for handling different types of source +documents, and general implementation of common data structures and +algorithms. + +``video_document_helper`` module +---------------------------------------- + +.. automodule:: mmif.utils.video_document_helper + :members: + :undoc-members: + :show-inheritance: + +``text_document_helper`` module +--------------------------------- + +.. automodule:: mmif.utils.sequence_helper + :members: + :undoc-members: + :show-inheritance: + +``sequence_helper`` module +--------------------------------- + +.. automodule:: mmif.utils.sequence_helper + :members: + :undoc-members: + :show-inheritance: + +``sequence_helper`` module +--------------------------------- + +.. automodule:: mmif.utils.sequence_helper + :members: + :undoc-members: + :show-inheritance: + diff --git a/docs/1.0.19/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.19/_sources/autodoc/mmif.vocabulary.rst.txt new file mode 100644 index 00000000..17da0283 --- /dev/null +++ b/docs/1.0.19/_sources/autodoc/mmif.vocabulary.rst.txt @@ -0,0 +1,28 @@ +mmif.vocabulary module +====================== + +Module contains Enum-like classes for CLAMS vocabulary. + +.. autoclass:: mmif.vocabulary.ThingTypesBase + :show-inheritance: +.. autoclass:: mmif.vocabulary.ThingType + :members: + :undoc-members: + :show-inheritance: + +.. autoclass:: mmif.vocabulary.ClamsTypesBase + :show-inheritance: +.. autoclass:: mmif.vocabulary.AnnotationTypesBase + :show-inheritance: +.. autoclass:: mmif.vocabulary.DocumentTypesBase + :show-inheritance: + +.. autoclass:: mmif.vocabulary.AnnotationTypes + :members: + :undoc-members: + :show-inheritance: + +.. autoclass:: mmif.vocabulary.DocumentTypes + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.19/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.19/_sources/autodoc/mmif_docloc_http.rst.txt new file mode 100644 index 00000000..b76c8df5 --- /dev/null +++ b/docs/1.0.19/_sources/autodoc/mmif_docloc_http.rst.txt @@ -0,0 +1,11 @@ +mmif_docloc_http package +======================== + +MMIF document location helper module for `http` and `https` schemes. +If you want to write your own docloc scheme handler, please use the source code of this module as a reference. +See this :ref:`plug-in section ` for more information. + +.. automodule:: mmif_docloc_http + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/1.0.19/_sources/consumer-tutorial.rst.txt b/docs/1.0.19/_sources/consumer-tutorial.rst.txt new file mode 100644 index 00000000..c54634e2 --- /dev/null +++ b/docs/1.0.19/_sources/consumer-tutorial.rst.txt @@ -0,0 +1,17 @@ +.. _consumer-tutorial: + +MMIF consumer +================================= + +A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. + +MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. + +#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) +#. Must listen to ``5000`` port. +#. Must expose ``/display`` route . +#. ``/display`` router should response to ``GET`` requests. +#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. +#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. + +We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.19/_sources/index.rst.txt b/docs/1.0.19/_sources/index.rst.txt new file mode 100644 index 00000000..beb56aae --- /dev/null +++ b/docs/1.0.19/_sources/index.rst.txt @@ -0,0 +1,26 @@ +Welcome to mmif-python's documentation! +======================================= + +.. mdinclude:: ../README.md + +.. toctree:: + :maxdepth: 2 + :caption: Contents + + introduction + plugins + target-versions + +.. toctree:: + :maxdepth: 2 + :caption: API documentation: + + modules + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/1.0.19/_sources/introduction.rst.txt b/docs/1.0.19/_sources/introduction.rst.txt new file mode 100644 index 00000000..cfd9eaf7 --- /dev/null +++ b/docs/1.0.19/_sources/introduction.rst.txt @@ -0,0 +1,89 @@ +.. _introduction: + +Getting Started +=============== + + +Overview +--------- + +MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. +``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. + +Prerequisites +------------- + +* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. + +Installation +--------------- + +Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. + +.. code-block:: bash + + pip install mmif-python + +This will install a package `mmif` to local python. + +The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. + +.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. + +MMIF Serialization +--------------------------- + +:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. + +.. code-block:: python + + import mmif + from mmif import Mmif + + mmif_str = """{ + "metadata": { + "mmif": "http://mmif.clams.ai/1.0.0" + }, + "documents": [ + { + "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", + "properties": { + "id": "m1", + "mime": "video/mp4", + "location": "file:///var/archive/video-0012.mp4" + } + }, + { + "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", + "properties": { + "id": "m2", + "mime": "text/plain", + "location": "file:///var/archive/video-0012-transcript.txt" + } + } + ], + "views": []}""" + mmif_obj = Mmif(mmif_str) + + +Few notes; + +#. MMIF does not carry the primary source files in it. +#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. + +When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. + +To get subcomponents, you can use various getters implemented in subclasses. For example; + +.. code-block:: python + + from mmif.vocabulary.document_types import DocumentTypes + + for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): + with open(video.location_path(), 'b') as in_video: + # do something with the video file + + +For a full list of available helper methods, please refer to :ref:`the API documentation `. + diff --git a/docs/1.0.19/_sources/modules.rst.txt b/docs/1.0.19/_sources/modules.rst.txt new file mode 100644 index 00000000..4bb9307d --- /dev/null +++ b/docs/1.0.19/_sources/modules.rst.txt @@ -0,0 +1,20 @@ +.. _apidoc: + +mmif package +============ + +.. toctree:: + :maxdepth: 4 + + autodoc/mmif.serialize + autodoc/mmif.vocabulary + autodoc/mmif.utils + +mmif_docloc_http package +======================== + +.. toctree:: + :maxdepth: 2 + + autodoc/mmif_docloc_http + diff --git a/docs/1.0.19/_sources/plugins.rst.txt b/docs/1.0.19/_sources/plugins.rst.txt new file mode 100644 index 00000000..1af39426 --- /dev/null +++ b/docs/1.0.19/_sources/plugins.rst.txt @@ -0,0 +1,89 @@ +.. _plugins: + +Developing plugins for MMIF Python SDK +====================================== + + +Overview +-------- + +As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. + + +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. +``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. + +Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). + +This document contains information about how to write plugins for ``mmif-python``. + +.. _docloc_plugin: + +Document Location Scheme Plugins +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. + +To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; + +#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. +#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; +#. Optionally (but highly recommended), the top module also can provide another function named ``help``. The function must take no arguments and return a :class:`str` that explains how the input string to the ``resolve`` function should be formatted. + +.. code-block:: python + + import mmif_docloc_s3 + resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') + # then resolved must be a local file path that can be used to open the file + + +Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. + +(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) + +.. code-block:: sh + + $ tree . + . + ├── mmif_docloc_dummy + │ └── __init__.py + ├── pyproject.toml + └── setup.cfg + + $ cat pyproject.toml + [build-system] + requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + $ cat setup.cfg + [metadata] + name = mmif_docloc_dummy # this name is IMPORTANT + version = 0.0.1 + description = a plugin to mmif-pyhon to handle `dummy` location scheme + + +And the plugin code. + +.. code-block:: python + + # mmif_docloc_dummy/__init__.py + doc_types = {'video': 'mp4'} + + def resolve(docloc): + scheme = 'dummy' + if docloc.startswith(f'{scheme}://'): + doc_id, doc_type = docloc.split('.') + return f'/path/to/{doc_id}.{doc_types[doc_type]}' + else: + raise ValueError(f'cannot handle document location scheme: {docloc}') + + def help(): + return "location format: `.video`" + + + +Bulit-in Document Location Scheme Plugins +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. +Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.19/_sources/target-versions.rst.txt b/docs/1.0.19/_sources/target-versions.rst.txt new file mode 100644 index 00000000..34216d3e --- /dev/null +++ b/docs/1.0.19/_sources/target-versions.rst.txt @@ -0,0 +1,10 @@ +.. _target-versions: + +Target MMIF Versions +==================== + +This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. + +.. csv-table:: Target Specification Versions + :file: target-versions.csv + :header-rows: 1 diff --git a/docs/1.0.19/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.19/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/docs/1.0.19/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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// [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = docUrlRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = docUrlRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/docs/1.0.19/_static/sphinx_highlight.js b/docs/1.0.19/_static/sphinx_highlight.js new file mode 100644 index 00000000..aae669d7 --- /dev/null +++ b/docs/1.0.19/_static/sphinx_highlight.js @@ -0,0 +1,144 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + parent.insertBefore( + span, + parent.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/docs/1.0.19/autodoc/mmif.serialize.html b/docs/1.0.19/autodoc/mmif.serialize.html new file mode 100644 index 00000000..dd9bfbf0 --- /dev/null +++ b/docs/1.0.19/autodoc/mmif.serialize.html @@ -0,0 +1,1474 @@ + + + + + + + mmif.serialize package — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.serialize package

+

Core package to provide serialization and deserialization of MMIF format.

+
+

model module

+

The model module contains the classes used to represent an +abstract MMIF object as a live Python object.

+

The MmifObject class or one of its derivatives is subclassed by +all other classes defined in this SDK, except for MmifObjectEncoder.

+

These objects are generally instantiated from JSON, either as a string +or as an already-loaded Python dictionary. This base class provides the +core functionality for deserializing MMIF JSON data into live objects +and serializing live objects into MMIF JSON data. Specialized behavior +for the different components of MMIF is added in the subclasses.

+
+
+class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject, Generic[T, S]

+
+
+empty()[source]
+
+ +
+
+get(key: T, default=None) → S | None[source]
+
+ +
+
+items()[source]
+
+ +
+
+keys()[source]
+
+ +
+
+update(other, overwrite)[source]
+
+ +
+
+values()[source]
+
+ +
+ +
+
+class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None, *_)[source]
+

Bases: MmifObject, Generic[T]

+

The DataList class is an abstraction that represents the +various lists found in a MMIF file, such as documents, subdocuments, +views, and annotations.

+
+
Parameters:
+

mmif_obj (Union[str, list]) – the data that the list contains

+
+
+
+
+append(value, overwrite)[source]
+
+ +
+
+deserialize(mmif_json: str | list) → None[source]
+

Passes the input data into the internal deserializer.

+
+ +
+
+empty()[source]
+
+ +
+
+get(key: str) → T | None[source]
+

Standard dictionary-style get() method, albeit with no default +parameter. Relies on the implementation of __getitem__.

+

Will return None if the key is not found.

+
+
Parameters:
+

key – the key to search for

+
+
Returns:
+

the value matching that key

+
+
+
+ +
+ +
+
+class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: object

+

Abstract superclass for MMIF related key-value pair objects.

+

Any MMIF object can be initialized as an empty placeholder or +an actual representation with a JSON formatted string or equivalent +dict object argument.

+

This superclass has four specially designed instance variables, and these +variable names cannot be used as attribute names for MMIF objects.

+
    +

  1. _unnamed_attributes: +Only can be either None or an empty dictionary. If it’s set to None, +it means the class won’t take any Additional Attributes in the +JSON schema sense. If it’s an empty dict, users can throw any k-v +pairs to the class, as long as the key is not a “reserved” name, +and those additional attributes will be stored in this dict while +in memory.

    2. +

  2. _attribute_classes: +This is a dict from a key name to a specific python class to use for +deserialize the value. Note that a key name in this dict does NOT +have to be a named attribute, but is recommended to be one.

    3. +

  3. _required_attributes: +This is a simple list of names of attributes that are required in +the object. When serialize, an object will skip its empty (e.g. +zero-length, or None) attributes unless they are in this list. +Otherwise, the serialized JSON string would have empty +representations (e.g. "", []).

    4. +

  4. _exclude_from_diff: +This is a simple list of names of attributes that should be excluded +from the diff calculation in __eq__.

    5. +
+

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. +Maybe there is a better way to utilize type hints (e.g. getting them +as a programmatically), but for now developers should be careful to +add types to hints as well as to this dict.

+

Also note that those special attributes MUST be set in the __init__() +before calling super method, otherwise deserialization will not work.

+

And also, a subclass that has one or more named attributes, it must +set those attributes in the __init__() before calling super method. +When serializing a MmifObject, all empty attributes will be ignored, +so for optional named attributes, you must leave the values empty +(len == 0), but NOT None. Any None-valued named attributes will cause +issues with current implementation.

+
+
Parameters:
+

mmif_obj – JSON string or dict to initialize an object. +If not given, an empty object will be initialized, sometimes with +an ID value automatically generated, based on its parent object.

+
+
+
+
+deserialize(mmif_json: str | dict) → None[source]
+

Takes a JSON-formatted string or a simple dict that’s json-loaded from +such a string as an input and populates object’s fields with the values +specified in the input.

+
+
Parameters:
+

mmif_json – JSON-formatted string or dict from such a string +that represents a MMIF object

+
+
+
+ +
+
+disallow_additional_properties() → None[source]
+

Call this method in __init__() to prevent the insertion +of unnamed attributes after initialization.

+
+ +
+
+id_delimiter: ClassVar[str] = ':'[source]
+
+ +
+
+static is_empty(obj) → bool[source]
+

return True if the obj is None or “emtpy”. The emptiness first defined as +having zero length. But for objects that lack __len__ method, we need +additional check.

+
+ +
+
+reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
+
+ +
+
+serialize(pretty: bool = False) → str[source]
+

Generates JSON representation of an object.

+
+
Parameters:
+

pretty – If True, returns string representation with indentation.

+
+
Returns:
+

JSON string of the object.

+
+
+
+ +
+
+set_additional_property(key: str, value: Any) → None[source]
+

Method to set values in _unnamed_attributes.

+
+
Parameters:
+
    +

  • key – the attribute name

    • +

  • value – the desired value

    • +
+
+
Returns:
+

None

+
+
Raise:
+

AttributeError if additional properties are disallowed by disallow_additional_properties()

+
+
+
+ +
+
+view_prefix: ClassVar[str] = 'v_'[source]
+
+ +
+ +
+
+class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
+

Bases: JSONEncoder

+

Encoder class to define behaviors of de-/serialization

+
+
+default(obj: MmifObject)[source]
+

Overrides default encoding behavior to prioritize MmifObject.serialize().

+
+ +
+ +
+
+

mmif module

+

The mmif module contains the classes used to represent a full MMIF +file as a live Python object.

+

See the specification docs and the JSON Schema file for more information.

+
+
+class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
+

Bases: MmifObject

+

MmifObject that represents a full MMIF file.

+
+
Parameters:
+
    +

  • mmif_obj – the JSON data

    • +

  • validate – whether to validate the data against the MMIF JSON schema.

    • +
+
+
+
+
+add_document(document: Document, overwrite=False) → None[source]
+

Appends a Document object to the documents list.

+

Fails if there is already a document with the same ID in the MMIF object.

+
+
Parameters:
+
    +

  • document – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+add_view(view: View, overwrite=False) → None[source]
+

Appends a View object to the views list.

+

Fails if there is already a view with the same ID in the MMIF object.

+
+
Parameters:
+
    +

  • view – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+generate_capital_annotations()[source]
+

Automatically convert any “pending” temporary properties from +Document objects to Annotation objects . The generated Annotation +objects are then added to the last View in the views lists.

+

See https://github.com/clamsproject/mmif-python/issues/226 for rationale +behind this behavior and discussion.

+
+ +
+
+get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
+

Finds views where alignments between two given annotation types occurred.

+
+
Returns:
+

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

+
+
+
+ +
+
+get_all_views_contain(*at_types: TypesBase | str) → List[View][source]
+

Returns the list of all views in the MMIF if given types +are present in that view’s ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the list of views that contain the type

+
+
+
+ +
+
+get_all_views_with_error() → List[View][source]
+

Returns the list of all views in the MMIF that have errors.

+
+
Returns:
+

the list of views that contain errors but no annotations

+
+
+
+ +
+
+get_annotations_between_time(start: int | float, end: int | float, time_unit: str = 'ms', at_types: List[str | TypesBase] = []) → Iterator[Annotation][source]
+

Finds annotations that are anchored between the given time points.

+
+
Parameters:
+
    +

  • start – the start time point in the unit of input_unit

    • +

  • end – the end time point in the unit of input_unit

    • +

  • time_unit – the unit of the input time points. Default is ms.

    • +

  • at_types – a list of annotation types to filter with. Any type in this list will be included in the return.

    • +
+
+
Returns:
+

an iterator of Annotation objects that are anchored between the given time points

+
+
+
+ +
+
+get_document_by_id(doc_id: str) → Document[source]
+

Finds a Document object with the given ID.

+
+
Parameters:
+

doc_id – the ID to search for

+
+
Returns:
+

a reference to the corresponding document, if it exists

+
+
Raises:
+

KeyError – if there is no corresponding document

+
+
+
+ +
+
+get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
+

Method to get the location of first document of given type.

+
+
Parameters:
+

m_type – the type to search for

+
+
Returns:
+

the value of the location field in the corresponding document

+
+
+
+ +
+
+get_documents_by_app(app_id: str) → List[Document][source]
+

Method to get all documents object queries by its originated app name.

+
+
Parameters:
+

app_id – the app name to search for

+
+
Returns:
+

a list of documents matching the requested app name, or an empty list if the app not found

+
+
+
+ +
+
+get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
+

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

+
+
Parameters:
+
    +

  • prop_key – the metadata key to search for

    • +

  • prop_value – the metadata value to match

    • +
+
+
Returns:
+

a list of documents matching the requested metadata key-value pair

+
+
+
+ +
+
+get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
+

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

+
+
Parameters:
+

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

+
+
Returns:
+

a list of documents matching the requested type, or an empty list if none found.

+
+
+
+ +
+
+get_documents_in_view(vid: str | None = None) → List[Document][source]
+

Method to get all documents object queries by a view id.

+
+
Parameters:
+

vid – the source view ID to search for

+
+
Returns:
+

a list of documents matching the requested source view ID, or an empty list if the view not found

+
+
+
+ +
+
+get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
+

This method returns the file paths of documents of given type. +Only top-level documents have locations, so we only check them.

+
+
Parameters:
+

m_type – the type to search for

+
+
Returns:
+

a list of the values of the location fields in the corresponding documents

+
+
+
+ +
+
+get_end(annotation: Annotation) → int | float[source]
+

An alias to get_anchor_point method with start=False.

+
+ +
+
+get_last_error() → str | None[source]
+

Returns the last error message found in the views.

+
+
Returns:
+

the error message in human-readable format, or None if no error is found

+
+
+
+ +
+
+get_start(annotation: Annotation) → int | float[source]
+

An alias to get_anchor_point method with start=True.

+
+ +
+
+get_view_by_id(req_view_id: str) → View[source]
+

Finds a View object with the given ID.

+
+
Parameters:
+

req_view_id – the ID to search for

+
+
Returns:
+

a reference to the corresponding view, if it exists

+
+
Raises:
+

Exception – if there is no corresponding view

+
+
+
+ +
+
+get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
+

Returns the last view appended that contains the given +types in its ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the view, or None if the type is not found

+
+
+
+ +
+
+get_view_with_error() → View | None[source]
+

Returns the last view appended that contains an error.

+
+
Returns:
+

the view, or None if no error is found

+
+
+
+ +
+
+get_views_contain(*at_types: TypesBase | str) → List[View][source]
+

Returns the list of all views in the MMIF if given types +are present in that view’s ‘contains’ metadata.

+
+
Parameters:
+

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

+
+
Returns:
+

the list of views that contain the type

+
+
+
+ +
+
+get_views_for_document(doc_id: str) → List[View][source]
+

Returns the list of all views that have annotations anchored on a particular document. +Note that when the document is inside a view (generated during the pipeline’s running), +doc_id must be prefixed with the view_id.

+
+ +
+
+get_views_with_error() → List[View][source]
+

Returns the list of all views in the MMIF that have errors.

+
+
Returns:
+

the list of views that contain errors but no annotations

+
+
+
+ +
+
+new_view() → View[source]
+

Creates an empty view with a new ID and appends it to the views list.

+
+
Returns:
+

a reference to the new View object

+
+
+
+ +
+
+new_view_id() → str[source]
+

Fetches an ID for a new view.

+
+
Returns:
+

the ID

+
+
+
+ +
+
+sanitize()[source]
+

Sanitizes a Mmif object by running some safeguards. +Concretely, it performs the following before returning the JSON string.

+
    +

  1. validating output using built-in MMIF jsonschema

    2. +

  2. remove non-existing annotation types from contains metadata

    3. +
+
+ +
+
+serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
+

Serializes the MMIF object to a JSON string.

+
+
Parameters:
+
    +

  • sanitize – If True, performs some sanitization of before returning +the JSON string. See sanitize() for details.

    • +

  • autogenerate_capital_annotations – If True, automatically convert +any “pending” temporary properties from Document objects to +Annotation objects. See generate_capital_annotations() for +details.

    • +

  • pretty – If True, returns string representation with indentation.

    • +
+
+
Returns:
+

JSON string of the MMIF object.

+
+
+
+ +
+
+static validate(json_str: bytes | str | dict) → None[source]
+

Validates a MMIF JSON object against the MMIF Schema. +Note that this method operates before processing by MmifObject._load_str, +so it expects @ and not _ for the JSON-LD @-keys.

+
+
Raises:
+

jsonschema.exceptions.ValidationError – if the input fails validation

+
+
Parameters:
+

json_str – a MMIF JSON dict or string

+
+
Returns:
+

None

+
+
+
+ +
+ +
+
+

view module

+

The view module contains the classes used to represent a MMIF view +as a live Python object.

+

In MMIF, views are created by apps in a pipeline that are annotating +data that was previously present in the MMIF file.

+
+
+class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: DataDict[str, str]

+

Contain object that represents the metadata of a single +annotation type in the contains metadata of a MMIF view.

+
+ +
+
+class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None, parent_mmif=None, *_)[source]
+

Bases: MmifObject

+

View object that represents a single view in a MMIF file.

+

A view is identified by an ID, and contains certain metadata, +a list of annotations, and potentially a JSON-LD @context +IRI.

+

If view_obj is not provided, an empty View will be generated.

+
+
Parameters:
+

view_obj – the JSON data that defines the view

+
+
+
+
+add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
+

Adds an annotation to the current view.

+

Fails if there is already an annotation with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
+
+
Raises:
+

KeyError – if overwrite is set to False and +an annotation with the same ID exists +in the view

+
+
Returns:
+

the same Annotation object passed in as annotation

+
+
+
+ +
+
+add_document(document: Document, overwrite=False) → Annotation[source]
+

Appends a Document object to the annotations list.

+

Fails if there is already a document with the same ID in the annotations list.

+
+
Parameters:
+
    +

  • document – the Document object to add

    • +

  • overwrite – if set to True, will overwrite +an existing view with the same ID

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+get_annotation_by_id(ann_id) → Annotation[source]
+
+ +
+
+get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
+

Look for certain annotations in this view, specified by parameters

+
+
Parameters:
+
    +

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • +

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • +
+
+
+
+ +
+
+get_document_by_id(doc_id) → Document[source]
+
+ +
+
+get_documents() → List[Document][source]
+
+ +
+
+get_error() → str | None[source]
+

Get the “text” representation of the error occurred during +processing. Text representation is supposed to be human-readable. +When ths view does not have any error, returns None.

+
+ +
+
+has_error() → bool[source]
+
+ +
+
+has_warnings()[source]
+
+ +
+
+new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
+

Generates a new mmif.serialize.annotation.Annotation +object and adds it to the current view.

+

Fails if there is already an annotation with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
    +

  • at_type – the desired @type of the annotation.

    • +

  • aid – the desired ID of the annotation, when not given, +the mmif SDK tries to automatically generate an ID based on +Annotation type and existing annotations in the view.

    • +

  • overwrite – if set to True, will overwrite an +existing annotation with the same ID.

    • +
+
+
Raises:
+

KeyError – if overwrite is set to False and +an annotation with the same ID exists +in the view.

+
+
Returns:
+

the generated mmif.serialize.annotation.Annotation

+
+
+
+ +
+
+new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
+

Adds a new element to the contains metadata.

+
+
Parameters:
+
    +

  • at_type – the @type of the annotation type being added

    • +

  • contains_metadata – any metadata associated with the annotation type

    • +
+
+
Returns:
+

the generated Contain object

+
+
+
+ +
+
+new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
+

Generates a new mmif.serialize.annotation.Document +object, particularly typed as TextDocument and adds it to the current view.

+

Fails if there is already a text document with the same ID +in the view, unless overwrite is set to True.

+
+
Parameters:
+
    +

  • text – text content of the new document

    • +

  • lang – ISO 639-1 code of the language used in the new document

    • +

  • did – the desired ID of the document, when not given, +the mmif SDK tries to automatically generate an ID based on +Annotation type and existing documents in the view.

    • +

  • overwrite – if set to True, will overwrite an +existing document with the same ID

    • +
+
+
Raises:
+

KeyError – if overwrite is set to False and +an document with the same ID exists +in the view

+
+
Returns:
+

the generated mmif.serialize.annotation.Document

+
+
+
+ +
+
+set_error(err_message: str, err_trace: str) → None[source]
+
+ +
+ +
+
+class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+

ViewMetadata object that represents the metadata object within a MMIF view.

+
+
Parameters:
+

viewmetadata_obj – the JSON data that defines the metadata

+
+
+
+
+add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
+

Add a configuration key-value pair to the app_configuration dictionary.

+
+ +
+
+add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
+
+ +
+
+add_parameter(param_key: str, param_value: str)[source]
+

Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

+
+ +
+
+add_parameters(**runtime_params: str)[source]
+

Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

+
+ +
+
+add_warnings(*warnings: Warning)[source]
+
+ +
+
+emtpy_warnings()[source]
+
+ +
+
+get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
+

Get a configuration value from the app_configuration dictionary.

+
+ +
+
+get_error_as_text() → str[source]
+
+ +
+
+get_parameter(param_key: str) → str[source]
+

Get a runtime parameter from the view metadata.

+
+ +
+
+has_error() → bool[source]
+
+ +
+
+has_warnings()[source]
+
+ +
+
+new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
+

Adds a new element to the contains dictionary.

+
+
Parameters:
+
    +

  • at_type – the @type of the annotation type being added

    • +

  • contains_metadata – any metadata associated with the annotation type

    • +
+
+
Returns:
+

the generated Contain object

+
+
+
+ +
+
+set_error(message: str, stack_trace: str)[source]
+
+ +
+ +
+
+

annotation module

+

The annotation module contains the classes used to represent a +MMIF annotation as a live Python object.

+

In MMIF, annotations are created by apps in a pipeline as a part +of a view. For documentation on how views are represented, see +mmif.serialize.view.

+
+
+class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+

MmifObject that represents an annotation in a MMIF view.

+
+
+add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
+

Adds a property to the annotation’s properties.

+
+
Parameters:
+
    +

  • name – the name of the property

    • +

  • value – the property’s desired value

    • +
+
+
Returns:
+

None

+
+
+
+ +
+
+aligned_to_by(alignment: Annotation) → Annotation | None[source]
+

Retrieves the other side of Alignment annotation that has this annotation on one side.

+
+
Parameters:
+

alignment – Alignment annotation that has this annotation on one side

+
+
Returns:
+

the annotation that this annotation is aligned to (other side of Alignment), +or None if this annotation is not used in the Alignment.

+
+
+
+ +
+
+property at_type: TypesBase[source]
+
+ +
+
+static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
+
+ +
+
+get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
+

A special getter for Annotation properties. This is to allow for +directly accessing properties without having to go through the +properties object, or view-level annotation properties encoded in the +view.metadata.contains dict. Note that the regular props will take +the priority over the ephemeral props when there are conflicts.

+
+ +
+
+get_all_aligned() → Iterator[Annotation][source]
+

Generator to iterate through all alignments and aligned annotations. Note that this generator will yield +the Alignment annotations as well. Every odd-numbered yield will be an Alignment annotation, and every +even-numbered yield will be the aligned annotation. If there’s a specific annotation type that you’re looking +for, you need to filter the generated results outside.

+
+
Returns:
+

yields the alignment annotation and the aligned annotation. +The order is decided by the order of appearance of Alignment annotations in the MMIF

+
+
+
+ +
+
+get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
+

A special getter for Annotation properties. This is to allow for +directly accessing properties without having to go through the +properties object, or view-level annotation properties encoded in the +view.metadata.contains dict. Note that the regular props will take +the priority over the ephemeral props when there are conflicts.

+
+ +
+
+property id: str[source]
+
+ +
+
+is_document()[source]
+
+ +
+
+is_type(at_type: str | TypesBase) → bool[source]
+

Check if the @type of this object matches.

+
+ +
+
+property long_id: str[source]
+
+ +
+
+property parent: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject, MutableMapping[str, T]

+

AnnotationProperties object that represents the +properties object within a MMIF annotation.

+
+
Parameters:
+

mmif_obj – the JSON data that defines the properties

+
+
+
+ +
+
+class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: Annotation

+

Document object that represents a single document in a MMIF file.

+

A document is identified by an ID, and contains certain attributes +and potentially contains the contents of the document itself, +metadata about how the document was created, and/or a list of +subdocuments grouped together logically.

+

If document_obj is not provided, an empty Document will be generated.

+
+
Parameters:
+

document_obj – the JSON data that defines the document

+
+
+
+
+add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
+

Adds a property to the document’s properties.

+

Unlike the parent Annotation class, added properties of a +Document object can be lost during serialization unless it belongs +to somewhere in a Mmif object. This is because we want to keep +Document object as “read-only” as possible. Thus, if you want to add +a property to a Document object,

+
    +

  • add the document to a Mmif object (either in the documents list or +in a view from the views list), or

    • +

  • directly write to Document.properties instead of using this method +(which is not recommended).

    • +
+

With the former method, the SDK will record the added property as a +Annotation annotation object, separate from the original Document +object. See Mmif.generate_capital_annotations() for more.

+

A few notes to keep in mind:

+
    +

  1. You can’t overwrite an existing property of a Document object.

    2. +

  2. A MMIF can have multiple Annotation objects with the same +property name but different values. When this happens, the SDK will +only keep the latest value (in order of appearances in views list) of +the property, effectively overwriting the previous values.

    3. +
+
+ +
+
+get(prop_name)[source]
+

A special getter for Document properties. The major difference from +the super class’s Annotation.get() method is that Document +class has one more set of “pending” properties, that are added after +the Document object is created and will be serialized as a separate +Annotation object of which @type = Annotation. The +pending properties will take the priority over the regular properties +when there are conflicts.

+
+ +
+
+get_property(prop_name)[source]
+

A special getter for Document properties. The major difference from +the super class’s Annotation.get() method is that Document +class has one more set of “pending” properties, that are added after +the Document object is created and will be serialized as a separate +Annotation object of which @type = Annotation. The +pending properties will take the priority over the regular properties +when there are conflicts.

+
+ +
+
+property location: str | None[source]
+

location property must be a legitimate URI. That is, should the document be a local file +then the file:// scheme must be used. +Returns None when no location is set.

+
+ +
+
+location_address() → str | None[source]
+

Retrieves the full address from the document location URI. +Returns None when no location is set.

+
+ +
+
+location_path(nonexist_ok=True) → str | None[source]
+

Retrieves a path that’s resolved to a pathname in the local file system. +To obtain the original value of the “path” part in the location string +(before resolving), use properties.location_path_literal method. +Returns None when no location is set.

+
+
Parameters:
+

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

+
+
+
+ +
+
+location_scheme() → str | None[source]
+

Retrieves URI scheme of the document location. +Returns None when no location is set.

+
+ +
+
+property text_language: str[source]
+
+ +
+
+property text_value: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: AnnotationProperties

+

DocumentProperties object that represents the +properties object within a MMIF document.

+
+
Parameters:
+

mmif_obj – the JSON data that defines the properties

+
+
+
+
+property location: str | None[source]
+

location property must be a legitimate URI. That is, should the document be a local file +then the file:// scheme must be used. +Returns None when no location is set.

+
+ +
+
+location_address() → str | None[source]
+

Retrieves the full address from the document location URI. +Returns None when no location is set.

+
+ +
+
+location_path() → str | None[source]
+
+ +
+
+location_path_literal() → str | None[source]
+

Retrieves only path name of the document location (hostname is ignored). +Returns None when no location is set.

+
+ +
+
+location_path_resolved(nonexist_ok=True) → str | None[source]
+

Retrieves only path name of the document location (hostname is ignored), +and then try to resolve the path name in the local file system. +This method should be used when the document scheme is file or empty. +For other schemes, users should install mmif-locdoc-<scheme> plugin.

+

Returns None when no location is set. +Raise ValueError when no code found to resolve the given location scheme.

+
+ +
+
+location_scheme() → str | None[source]
+

Retrieves URI scheme of the document location. +Returns None when no location is set.

+
+ +
+
+property text_language: str[source]
+
+ +
+
+property text_value: str[source]
+
+ +
+ +
+
+class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None, *_)[source]
+

Bases: MmifObject

+
+
+property lang: str[source]
+
+ +
+
+property value: str[source]
+
+ +
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
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+ + + \ No newline at end of file diff --git a/docs/1.0.19/autodoc/mmif.utils.html b/docs/1.0.19/autodoc/mmif.utils.html new file mode 100644 index 00000000..bbb89064 --- /dev/null +++ b/docs/1.0.19/autodoc/mmif.utils.html @@ -0,0 +1,1054 @@ + + + + + + + mmif.utils package — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.utils package

+

Package containing utility modules for handling different types of source +documents, and general implementation of common data structures and +algorithms.

+
+

video_document_helper module

+
+
+mmif.utils.video_document_helper.capture(video_document: Document)[source]
+

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

+
+
Parameters:
+

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

+
+
Returns:
+

OpenCV VideoCapture object

+
+
+
+ +
+
+mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
+

Converts start and end points in a TimeFrame annotation a different time unit.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • out_unit – time unit to which the point is converted

    • +
+
+
Returns:
+

tuple of frame numbers, seconds/milliseconds, or ISO notation of TimeFrame’s start and end

+
+
+
+ +
+
+mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
+

Converts a time point included in an annotation to a different time unit. +The input annotation must have timePoint property.

+
+
Parameters:
+
    +

  • mmif – input MMIF to obtain fps and input timeunit

    • +

  • timepoint – Annotation instance with timePoint property

    • +

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • +
+
+
Returns:
+

frame number (integer) or second/millisecond (float) of input timepoint

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
+

Extracts frames from a video document as a list of numpy.ndarray. +Use with sample_frames() function to get the list of frame numbers first.

+
+
Parameters:
+
    +

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • +

  • framenums – integers representing the frame numbers to extract

    • +

  • as_PIL – return PIL.Image.Image instead of ndarray

    • +
+
+
Returns:
+

frames as a list of ndarray or Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
+

Extracts the middle frame of a time interval annotation as a numpy ndarray.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • as_PIL – return Image instead of ndarray

    • +
+
+
Returns:
+

frame as a numpy.ndarray or PIL.Image.Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
+

Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +

  • as_PIL – return Image instead of ndarray

    • +
+
+
Returns:
+

frame as a numpy.ndarray or PIL.Image.Image

+
+
+
+ +
+
+mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
+

Converts a frame number to a millisecond value.

+
+ +
+
+mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
+

Converts a frame number to a second value.

+
+ +
+
+mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
+
+

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

+
+

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. +xisting

+
+ +
+
+mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
+

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

+
+
Parameters:
+

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

+
+
Returns:
+

frames per second as a float, rounded to 2 decimal places

+
+
+
+ +
+
+mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
+

Calculates the middle frame number of a time interval annotation.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • +
+
+
Returns:
+

middle frame number as an integer

+
+
+
+ +
+
+mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
+

Calculates the representative frame number from an annotation.

+
+
Parameters:
+
    +

  • mmif – Mmif instance

    • +

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • +
+
+
Returns:
+

representative frame number as an integer

+
+
+
+ +
+
+mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
+

Converts a millisecond value to a frame number.

+
+ +
+
+mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
+

Helper function to sample frames from a time interval. +Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

+
+
Parameters:
+
    +

  • start_frame – start frame of the interval

    • +

  • end_frame – end frame of the interval

    • +

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • +
+
+
+
+ +
+
+mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
+

Converts a second value to a frame number.

+
+ +
+
+

text_document_helper module

+

This module provides helpers for handling sequence labeling. Specifically, it provides

+
    +

  • a generalized label re-mapper for “post-binning” of labels

    • +

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • +

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • +
+

However, it DOES NOT provide

+
    +

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • +

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • +
+

Some functions can use optional external libraries (e.g., numpy) for better performance. +Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

+
+
+mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
+

Build a label remapper dictionary from source and destination labels.

+
+
Parameters:
+
    +

  • src_labels – a list of all labels on the source side

    • +

  • dst_labels – a dict from source labels to destination labels. +Source labels not in this dict will be remapped to a negative label (-).

    • +
+
+
Returns:
+

a dict that exhaustively maps source labels to destination labels

+
+
+
+ +
+
+mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
+

Build lists of scores indexed by the label names.

+
+
Parameters:
+
    +

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • +

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • +

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label +common choices are max, min, or sum

    • +
+
+
Returns:
+

    +

  1. a dictionary that maps label names to their index in the score list

    2. +

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. +
+

+
+
+
+ +
+
+mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
+

Given a list of scores, a score threshold, and smoothing parameters, +identify the intervals of “positive” scores by “trimming” the short +positive sequences (“spseq”) and short negative sequences (“snseq”). To +decide the positivity, first step is binarization of the scores by the +min_score threshold. Given Sr as “raw” input real-number scores +list, and min_score=0.5,

+
+
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
+
+
+
+

the binarization is done by simply comparing each score to the +threshold to get S list of binary scores

+
+
1.0 :                                     |                      
+0.9 :                |                    |                      
+0.8 :          |     |  |           |     |              |       
+0.7 :          |     |  |           |     |  |           |       
+0.6 :    |     |     |  |           |     |  |           |     | 
+0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
+0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
+0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
+0.0 +------------------------------------------------------------
+raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
+ S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
+
+
+
+

Note that the size of a positive or negative sequence can be as small +as 1.

+

Then, here are examples of smoothing a list of binary scores into +intervals, by trimming “very short” (under thresholds) sequences of +positive or negative:

+
+

Note

+

legends:

+
    +

  • t is unit index (e.g. time index)

    • +

  • S is the list of binary scores (zeros and ones)

    • +

  • I is the list of intervals after smoothing

    • +
+
+
    +

  1. with params min_spseq_size==1, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
+
    +
    +

    Explanation: min_snseq_size is used to smooth short sequences +of negative predictions. In this, zeros from t[7:10] are smoothed +into “one” I, while zeros from t[13:19] are kept as “zero” I. Note +that the “short” snseqs at the either ends (t[0:1]) are never +smoothed.

    +
    +
    2. +

  2. with params min_spseq_size==4, min_snseq_size==2

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: min_spseq_size is used to smooth short sequences +of positive predictions. In this example, the spseqs of ones from +both t[10:13] and t[19:20] are smoothed. Note that the “short” +spseqs at the either ends (t[19:20]) are always smoothed.

    +
    +
    3. +

  3. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: When two threshold parameters are working together, +the algorithm will prioritize the smoothing of the snseqs over the +smoothing of the spseqs. Thus, in this example, the snseq t[7:10] +gets first smoothed “up” before the spseq t[10:13] is smoothed +“down”, resulting in a long final I.

    +
    +
    4. +

  4. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
+
    +
    +

    Explanation: Since smoothing of snseqs is prioritized, short spseqs +at the beginning or the end can be kept.

    +
    +
    5. +

  5. with params min_spseq_size==1, min_snseq_size==1

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
+
    +
    +

    Explanation: When both width thresholds are set to 1, the algorithm +works essentially in the “stitching” only mode.

    +
    +
    6. +
+
+
Parameters:
+
    +

  • scores – SORTED list of scores to be smoothed. The score list +is assumed to be “exhaust” the entire time or space of +the underlying document segment. +(Sorted by the start, and then by the end of anchors)

    • +

  • min_score – minimum threshold to use to discard +low-scored units (strictly less than)

    • +

  • min_spseq_size – minimum size of a positive sequence not to be +smoothed (greater or equal to)

    • +

  • min_snseq_size – minimum size of a negative sequence not to be +smoothed (greater or equal to)

    • +
+
+
Returns:
+

list of tuples of start(inclusive)/end(exclusive) indices +of the “positive” sequences. Negative sequences (regardless of +their size) are not included in the output.

+
+
+
+ +
+
+mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
+

Simple check for a list of annotations to see if they have the same label set.

+
+
Raise:
+

AttributeError if an element in the input list doesn’t have the labelset property

+
+
Raise:
+

ValueError if different labelset values are found

+
+
Returns:
+

a list of the common labelset value (list of label names)

+
+
+
+ +
+
+

sequence_helper module

+

This module provides helpers for handling sequence labeling. Specifically, it provides

+
    +

  • a generalized label re-mapper for “post-binning” of labels

    • +

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • +

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • +
+

However, it DOES NOT provide

+
    +

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • +

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • +
+

Some functions can use optional external libraries (e.g., numpy) for better performance. +Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

+
+
+mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
+

Build a label remapper dictionary from source and destination labels.

+
+
Parameters:
+
    +

  • src_labels – a list of all labels on the source side

    • +

  • dst_labels – a dict from source labels to destination labels. +Source labels not in this dict will be remapped to a negative label (-).

    • +
+
+
Returns:
+

a dict that exhaustively maps source labels to destination labels

+
+
+
+ +
+
+mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
+

Build lists of scores indexed by the label names.

+
+
Parameters:
+
    +

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • +

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • +

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label +common choices are max, min, or sum

    • +
+
+
Returns:
+

    +

  1. a dictionary that maps label names to their index in the score list

    2. +

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. +
+

+
+
+
+ +
+
+mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
+

Given a list of scores, a score threshold, and smoothing parameters, +identify the intervals of “positive” scores by “trimming” the short +positive sequences (“spseq”) and short negative sequences (“snseq”). To +decide the positivity, first step is binarization of the scores by the +min_score threshold. Given Sr as “raw” input real-number scores +list, and min_score=0.5,

+
+
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
+
+
+
+

the binarization is done by simply comparing each score to the +threshold to get S list of binary scores

+
+
1.0 :                                     |                      
+0.9 :                |                    |                      
+0.8 :          |     |  |           |     |              |       
+0.7 :          |     |  |           |     |  |           |       
+0.6 :    |     |     |  |           |     |  |           |     | 
+0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
+0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
+0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
+0.0 +------------------------------------------------------------
+raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
+ S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
+
+
+
+

Note that the size of a positive or negative sequence can be as small +as 1.

+

Then, here are examples of smoothing a list of binary scores into +intervals, by trimming “very short” (under thresholds) sequences of +positive or negative:

+
+

Note

+

legends:

+
    +

  • t is unit index (e.g. time index)

    • +

  • S is the list of binary scores (zeros and ones)

    • +

  • I is the list of intervals after smoothing

    • +
+
+
    +

  1. with params min_spseq_size==1, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
+
    +
    +

    Explanation: min_snseq_size is used to smooth short sequences +of negative predictions. In this, zeros from t[7:10] are smoothed +into “one” I, while zeros from t[13:19] are kept as “zero” I. Note +that the “short” snseqs at the either ends (t[0:1]) are never +smoothed.

    +
    +
    2. +

  2. with params min_spseq_size==4, min_snseq_size==2

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: min_spseq_size is used to smooth short sequences +of positive predictions. In this example, the spseqs of ones from +both t[10:13] and t[19:20] are smoothed. Note that the “short” +spseqs at the either ends (t[19:20]) are always smoothed.

    +
    +
    3. +

  3. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: When two threshold parameters are working together, +the algorithm will prioritize the smoothing of the snseqs over the +smoothing of the spseqs. Thus, in this example, the snseq t[7:10] +gets first smoothed “up” before the spseq t[10:13] is smoothed +“down”, resulting in a long final I.

    +
    +
    4. +

  4. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
+
    +
    +

    Explanation: Since smoothing of snseqs is prioritized, short spseqs +at the beginning or the end can be kept.

    +
    +
    5. +

  5. with params min_spseq_size==1, min_snseq_size==1

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
+
    +
    +

    Explanation: When both width thresholds are set to 1, the algorithm +works essentially in the “stitching” only mode.

    +
    +
    6. +
+
+
Parameters:
+
    +

  • scores – SORTED list of scores to be smoothed. The score list +is assumed to be “exhaust” the entire time or space of +the underlying document segment. +(Sorted by the start, and then by the end of anchors)

    • +

  • min_score – minimum threshold to use to discard +low-scored units (strictly less than)

    • +

  • min_spseq_size – minimum size of a positive sequence not to be +smoothed (greater or equal to)

    • +

  • min_snseq_size – minimum size of a negative sequence not to be +smoothed (greater or equal to)

    • +
+
+
Returns:
+

list of tuples of start(inclusive)/end(exclusive) indices +of the “positive” sequences. Negative sequences (regardless of +their size) are not included in the output.

+
+
+
+ +
+
+mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
+

Simple check for a list of annotations to see if they have the same label set.

+
+
Raise:
+

AttributeError if an element in the input list doesn’t have the labelset property

+
+
Raise:
+

ValueError if different labelset values are found

+
+
Returns:
+

a list of the common labelset value (list of label names)

+
+
+
+ +
+
+

sequence_helper module

+

This module provides helpers for handling sequence labeling. Specifically, it provides

+
    +

  • a generalized label re-mapper for “post-binning” of labels

    • +

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • +

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • +
+

However, it DOES NOT provide

+
    +

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • +

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • +
+

Some functions can use optional external libraries (e.g., numpy) for better performance. +Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

+
+
+mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
+

Build a label remapper dictionary from source and destination labels.

+
+
Parameters:
+
    +

  • src_labels – a list of all labels on the source side

    • +

  • dst_labels – a dict from source labels to destination labels. +Source labels not in this dict will be remapped to a negative label (-).

    • +
+
+
Returns:
+

a dict that exhaustively maps source labels to destination labels

+
+
+
+ +
+
+mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
+

Build lists of scores indexed by the label names.

+
+
Parameters:
+
    +

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • +

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • +

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label +common choices are max, min, or sum

    • +
+
+
Returns:
+

    +

  1. a dictionary that maps label names to their index in the score list

    2. +

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. +
+

+
+
+
+ +
+
+mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
+

Given a list of scores, a score threshold, and smoothing parameters, +identify the intervals of “positive” scores by “trimming” the short +positive sequences (“spseq”) and short negative sequences (“snseq”). To +decide the positivity, first step is binarization of the scores by the +min_score threshold. Given Sr as “raw” input real-number scores +list, and min_score=0.5,

+
+
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
+
+
+
+

the binarization is done by simply comparing each score to the +threshold to get S list of binary scores

+
+
1.0 :                                     |                      
+0.9 :                |                    |                      
+0.8 :          |     |  |           |     |              |       
+0.7 :          |     |  |           |     |  |           |       
+0.6 :    |     |     |  |           |     |  |           |     | 
+0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
+0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
+0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
+0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
+0.0 +------------------------------------------------------------
+raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
+ S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
+
+
+
+

Note that the size of a positive or negative sequence can be as small +as 1.

+

Then, here are examples of smoothing a list of binary scores into +intervals, by trimming “very short” (under thresholds) sequences of +positive or negative:

+
+

Note

+

legends:

+
    +

  • t is unit index (e.g. time index)

    • +

  • S is the list of binary scores (zeros and ones)

    • +

  • I is the list of intervals after smoothing

    • +
+
+
    +

  1. with params min_spseq_size==1, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
+
    +
    +

    Explanation: min_snseq_size is used to smooth short sequences +of negative predictions. In this, zeros from t[7:10] are smoothed +into “one” I, while zeros from t[13:19] are kept as “zero” I. Note +that the “short” snseqs at the either ends (t[0:1]) are never +smoothed.

    +
    +
    2. +

  2. with params min_spseq_size==4, min_snseq_size==2

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: min_spseq_size is used to smooth short sequences +of positive predictions. In this example, the spseqs of ones from +both t[10:13] and t[19:20] are smoothed. Note that the “short” +spseqs at the either ends (t[19:20]) are always smoothed.

    +
    +
    3. +

  3. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
+I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
+
    +
    +

    Explanation: When two threshold parameters are working together, +the algorithm will prioritize the smoothing of the snseqs over the +smoothing of the spseqs. Thus, in this example, the snseq t[7:10] +gets first smoothed “up” before the spseq t[10:13] is smoothed +“down”, resulting in a long final I.

    +
    +
    4. +

  4. with params min_spseq_size==4, min_snseq_size==4

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
+
    +
    +

    Explanation: Since smoothing of snseqs is prioritized, short spseqs +at the beginning or the end can be kept.

    +
    +
    5. +

  5. with params min_spseq_size==1, min_snseq_size==1

    +
    +
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
+I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
+
    +
    +

    Explanation: When both width thresholds are set to 1, the algorithm +works essentially in the “stitching” only mode.

    +
    +
    6. +
+
+
Parameters:
+
    +

  • scores – SORTED list of scores to be smoothed. The score list +is assumed to be “exhaust” the entire time or space of +the underlying document segment. +(Sorted by the start, and then by the end of anchors)

    • +

  • min_score – minimum threshold to use to discard +low-scored units (strictly less than)

    • +

  • min_spseq_size – minimum size of a positive sequence not to be +smoothed (greater or equal to)

    • +

  • min_snseq_size – minimum size of a negative sequence not to be +smoothed (greater or equal to)

    • +
+
+
Returns:
+

list of tuples of start(inclusive)/end(exclusive) indices +of the “positive” sequences. Negative sequences (regardless of +their size) are not included in the output.

+
+
+
+ +
+
+mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
+

Simple check for a list of annotations to see if they have the same label set.

+
+
Raise:
+

AttributeError if an element in the input list doesn’t have the labelset property

+
+
Raise:
+

ValueError if different labelset values are found

+
+
Returns:
+

a list of the common labelset value (list of label names)

+
+
+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/autodoc/mmif.vocabulary.html b/docs/1.0.19/autodoc/mmif.vocabulary.html new file mode 100644 index 00000000..230bd689 --- /dev/null +++ b/docs/1.0.19/autodoc/mmif.vocabulary.html @@ -0,0 +1,385 @@ + + + + + + + mmif.vocabulary module — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif.vocabulary module

+

Module contains Enum-like classes for CLAMS vocabulary.

+
+
+mmif.vocabulary.ThingTypesBase[source]
+

alias of TypesBase

+
+ +
+
+class mmif.vocabulary.ThingType(type_uri: str)[source]
+

Bases: TypesBase

+

This class contains the topmost CLAMS thing type +defined in the spec version 1.0.5 as a class variable.

+
+
+Thing = http://mmif.clams.ai/vocabulary/Thing/v1[source]
+
+ +
+
+base_uri: str[source]
+
+ +
+
+fuzzy_eq: bool[source]
+
+ +
+
+shortname: str[source]
+
+ +
+ +
+
+class mmif.vocabulary.ClamsTypesBase(type_uri, fuzzymode=True)[source]
+

Bases: TypesBase

+

Base class for CLAMS vocabulary types. Main +This class adds handling of MMIF specification versions +in initializer and comparators.

+
+ +
+
+class mmif.vocabulary.AnnotationTypesBase(type_uri, fuzzymode=True)[source]
+

Bases: ClamsTypesBase

+

Inherit from this class to build your own custom annotation +vocabularies.

+
+ +
+
+class mmif.vocabulary.DocumentTypesBase(type_uri, fuzzymode=True)[source]
+

Bases: ClamsTypesBase

+

Inherit from this class to build your own custom document +vocabularies.

+
+ +
+
+class mmif.vocabulary.AnnotationTypes(type_uri, fuzzymode=True)[source]
+

Bases: AnnotationTypesBase

+

This class contains the CLAMS annotation types +defined in the spec version 1.0.5 as class variables.

+
+
+Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
+
+ +
+
+Annotation = http://mmif.clams.ai/vocabulary/Annotation/v5[source]
+
+ +
+
+BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v4[source]
+
+ +
+
+Chapter = http://mmif.clams.ai/vocabulary/Chapter/v5[source]
+
+ +
+
+Interval = http://mmif.clams.ai/vocabulary/Interval/v4[source]
+
+ +
+
+Polygon = http://mmif.clams.ai/vocabulary/Polygon/v4[source]
+
+ +
+
+Region = http://mmif.clams.ai/vocabulary/Region/v4[source]
+
+ +
+
+Relation = http://mmif.clams.ai/vocabulary/Relation/v4[source]
+
+ +
+
+Span = http://mmif.clams.ai/vocabulary/Span/v4[source]
+
+ +
+
+TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v5[source]
+
+ +
+
+TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v4[source]
+
+ +
+
+VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v4[source]
+
+ +
+
+version: str[source]
+
+ +
+ +
+
+class mmif.vocabulary.DocumentTypes(type_uri, fuzzymode=True)[source]
+

Bases: DocumentTypesBase

+

This class contains the CLAMS document types +defined in the spec version 1.0.5 as class variables.

+
+
+AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
+
+ +
+
+Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
+
+ +
+
+ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
+
+ +
+
+TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
+
+ +
+
+VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
+
+ +
+
+version: str[source]
+
+ +
+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/autodoc/mmif_docloc_http.html b/docs/1.0.19/autodoc/mmif_docloc_http.html new file mode 100644 index 00000000..da77ac17 --- /dev/null +++ b/docs/1.0.19/autodoc/mmif_docloc_http.html @@ -0,0 +1,189 @@ + + + + + + + mmif_docloc_http package — mmif-python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mmif_docloc_http package

+

MMIF document location helper module for http and https schemes. +If you want to write your own docloc scheme handler, please use the source code of this module as a reference. +See this plug-in section for more information.

+
+
+mmif_docloc_http.help()[source]
+
+ +
+
+mmif_docloc_http.resolve(docloc)[source]
+
+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/consumer-tutorial.html b/docs/1.0.19/consumer-tutorial.html new file mode 100644 index 00000000..7faea640 --- /dev/null +++ b/docs/1.0.19/consumer-tutorial.html @@ -0,0 +1,176 @@ + + + + + + + MMIF consumer — mmif-python documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • MMIF consumer
    • +
  • +
    • +
+
+
+
+
+ +
+

MMIF consumer

+

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

+

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

+
    +

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. +

  2. Must listen to 5000 port.

    3. +

  3. Must expose /display route .

    4. +

  4. /display router should response to GET requests.

    5. +

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. +

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. +
+

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
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+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/genindex.html b/docs/1.0.19/genindex.html new file mode 100644 index 00000000..be09c76a --- /dev/null +++ b/docs/1.0.19/genindex.html @@ -0,0 +1,780 @@ + + + + + + Index — mmif-python documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ A + | B + | C + | D + | E + | F + | G + | H + | I + | K + | L + | M + | N + | P + | R + | S + | T + | U + | V + +
+

A

+ + + +
+ +

B

+ + + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

E

+ + + +
+ +

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+ + + +
+ +

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+ + + +
+ +

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+ + + +
+ +

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+ + + +
+ +

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+ + +
+ +

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+ + + +
+ +

M

+ + + +
+ +

N

+ + + +
+ +

P

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + + +
+ +

U

+ + +
+ +

V

+ + + +
+ + + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
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+
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+
0.3.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/index.html b/docs/1.0.19/index.html new file mode 100644 index 00000000..dffa2d42 --- /dev/null +++ b/docs/1.0.19/index.html @@ -0,0 +1,232 @@ + + + + + + + Welcome to mmif-python’s documentation! — mmif-python documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Welcome to mmif-python’s documentation!
    • +
  • +
    • +
+
+
+
+
+ +
+

Welcome to mmif-python’s documentation!

+
+

MultiMedia Interchange Format

+

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

+
+
+

mmif-python

+

mmif-python is a Python implementation of the MMIF data format. +mmif-python provides various helper classes and functions to handle MMIF JSON in Python, +including ;

+
    +

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. +

  2. validation of MMIF JSON

    3. +

  3. handling of CLAMS vocabulary types

    4. +

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. +
+
+
+

For more …

+ +
+

Contents

+ +
+
+

API documentation:

+ +
+
+
+
+

Indices and tables

+ +
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.4
+
1.0.5
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1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/introduction.html b/docs/1.0.19/introduction.html new file mode 100644 index 00000000..d2516e80 --- /dev/null +++ b/docs/1.0.19/introduction.html @@ -0,0 +1,249 @@ + + + + + + + Getting Started — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Getting Started
    • +
  • +
    • +
+
+
+
+
+ +
+

Getting Started

+
+

Overview

+

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. +This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. +mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

+
+
+

Prerequisites

+
    +

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • +
+
+
+

Installation

+

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

+
pip install mmif-python
+
+
+

This will install a package mmif to local python.

+

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

+
+

Note

+

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

+
+
+
+

MMIF Serialization

+

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

+
import mmif
+from mmif import Mmif
+
+mmif_str = """{
+"metadata": {
+  "mmif": "http://mmif.clams.ai/1.0.0"
+},
+"documents": [
+  {
+    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
+    "properties": {
+      "id": "m1",
+      "mime": "video/mp4",
+      "location": "file:///var/archive/video-0012.mp4"
+    }
+  },
+  {
+    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
+    "properties": {
+      "id": "m2",
+      "mime": "text/plain",
+      "location": "file:///var/archive/video-0012-transcript.txt"
+    }
+  }
+],
+"views": []}"""
+mmif_obj = Mmif(mmif_str)
+
+
+

Few notes;

+
    +

  1. MMIF does not carry the primary source files in it.

    2. +

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. +
+

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

+

To get subcomponents, you can use various getters implemented in subclasses. For example;

+
from mmif.vocabulary.document_types import DocumentTypes
+
+for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
+  with open(video.location_path(), 'b') as in_video:
+    # do something with the video file
+
+
+

For a full list of available helper methods, please refer to the API documentation.

+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
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+
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+
0.3.4
+
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+
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+
0.4.1
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
1.0.7
+
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+
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+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/modules.html b/docs/1.0.19/modules.html new file mode 100644 index 00000000..907a576f --- /dev/null +++ b/docs/1.0.19/modules.html @@ -0,0 +1,429 @@ + + + + + + + mmif package — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • mmif package
    • +
  • +
    • +
+
+
+
+
+ +
+

mmif package

+
+ +
+
+
+

mmif_docloc_http package

+
+ +
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
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+
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+
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+
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+
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+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
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+
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+
0.5.2
+
1.0.0
+
1.0.1
+
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+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.19/objects.inv b/docs/1.0.19/objects.inv new file mode 100644 index 00000000..7b9bedec Binary files /dev/null and b/docs/1.0.19/objects.inv differ diff --git a/docs/1.0.19/plugins.html b/docs/1.0.19/plugins.html new file mode 100644 index 00000000..fc6aa2ae --- /dev/null +++ b/docs/1.0.19/plugins.html @@ -0,0 +1,242 @@ + + + + + + + Developing plugins for MMIF Python SDK — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Developing plugins for MMIF Python SDK
    • +
  • +
    • +
+
+
+
+
+ +
+

Developing plugins for MMIF Python SDK

+
+

Overview

+

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

+

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. +mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

+

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

+

This document contains information about how to write plugins for mmif-python.

+
+

Document Location Scheme Plugins

+

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

+

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

+
    +

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. +

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. +

  3. Optionally (but highly recommended), the top module also can provide another function named help. The function must take no arguments and return a str that explains how the input string to the resolve function should be formatted.

    4. +
+
import mmif_docloc_s3
+resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
+# then resolved must be a local file path that can be used to open the file
+
+
+

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

+

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

+
$ tree .
+.
+├── mmif_docloc_dummy
+│   └── __init__.py
+├── pyproject.toml
+└── setup.cfg
+
+ $ cat pyproject.toml
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+$ cat setup.cfg
+[metadata]
+name = mmif_docloc_dummy  # this name is IMPORTANT
+version = 0.0.1
+description = a plugin to mmif-pyhon to handle `dummy` location scheme
+
+
+

And the plugin code.

+
# mmif_docloc_dummy/__init__.py
+doc_types = {'video': 'mp4'}
+
+def resolve(docloc):
+    scheme = 'dummy'
+    if docloc.startswith(f'{scheme}://'):
+        doc_id, doc_type = docloc.split('.')
+        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
+    else:
+        raise ValueError(f'cannot handle document location scheme: {docloc}')
+
+def help():
+    return "location format: `<DOCUMENT_ID>.video`"
+
+
+
+
+

Bulit-in Document Location Scheme Plugins

+

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. +Take a look at mmif_docloc_http module for details.

+
+
+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
0.4.5
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.8/py-modindex.html b/docs/1.0.19/py-modindex.html similarity index 92% rename from docs/1.0.8/py-modindex.html rename to docs/1.0.19/py-modindex.html index 58e91cac..95a87a8c 100644 --- a/docs/1.0.8/py-modindex.html +++ b/docs/1.0.19/py-modindex.html @@ -37,7 +37,7 @@ mmif-python
- 1.0.8 + 1.0.19
@@ -56,6 +56,7 @@

API documentation:

@@ -121,17 +122,17 @@

Python Module Index

    - mmif.utils.video_document_helper + mmif.utils.sequence_helper     - mmif.vocabulary.annotation_types + mmif.utils.video_document_helper - + -     - mmif.vocabulary.document_types + + mmif_docloc_http @@ -160,7 +161,7 @@

Python Module Index

Other Versions - v: 1.0.8 + v: 1.0.19
@@ -193,13 +194,16 @@

Python Module Index

1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
1.0.5
1.0.6
1.0.7
-
1.0.8
+
1.0.8
1.0.9
diff --git a/docs/1.0.19/search.html b/docs/1.0.19/search.html new file mode 100644 index 00000000..d296c67a --- /dev/null +++ b/docs/1.0.19/search.html @@ -0,0 +1,182 @@ + + + + + + Search — mmif-python documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
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+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
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+
0.4.1
+
0.4.2
+
0.4.3
+
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+
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+
0.4.6
+
0.4.7
+
0.4.8
+
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+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+
+
+ + + + + + + + \ No newline at end of file diff --git a/docs/1.0.19/searchindex.js b/docs/1.0.19/searchindex.js new file mode 100644 index 00000000..36b05b73 --- /dev/null +++ b/docs/1.0.19/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["autodoc/mmif.serialize", "autodoc/mmif.utils", "autodoc/mmif.vocabulary", "autodoc/mmif_docloc_http", "consumer-tutorial", "index", "introduction", "modules", "plugins", "target-versions"], "filenames": ["autodoc/mmif.serialize.rst", "autodoc/mmif.utils.rst", "autodoc/mmif.vocabulary.rst", "autodoc/mmif_docloc_http.rst", "consumer-tutorial.rst", "index.rst", "introduction.rst", "modules.rst", "plugins.rst", "target-versions.rst"], "titles": ["mmif.serialize package", "mmif.utils package", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "terms": {"core": [0, 8], 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(mmif.serialize.annotation.document method)": [[0, "mmif.serialize.annotation.Document.location_scheme"]], "location_scheme() (mmif.serialize.annotation.documentproperties method)": [[0, "mmif.serialize.annotation.DocumentProperties.location_scheme"]], "long_id (mmif.serialize.annotation.annotation property)": [[0, "mmif.serialize.annotation.Annotation.long_id"]], "mmif.serialize.annotation": [[0, "module-mmif.serialize.annotation"]], "mmif.serialize.mmif": [[0, "module-mmif.serialize.mmif"]], "mmif.serialize.model": [[0, "module-mmif.serialize.model"]], "mmif.serialize.view": [[0, "module-mmif.serialize.view"]], "module": [[0, "module-mmif.serialize.annotation"], [0, "module-mmif.serialize.mmif"], [0, "module-mmif.serialize.model"], [0, "module-mmif.serialize.view"], [1, "module-0"], [1, "module-1"], [1, "module-mmif.utils.sequence_helper"], [1, "module-mmif.utils.video_document_helper"], [3, "module-mmif_docloc_http"]], "new_annotation() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.new_annotation"]], "new_contain() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.new_contain"]], "new_contain() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.new_contain"]], "new_textdocument() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.new_textdocument"]], "new_view() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.new_view"]], "new_view_id() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.new_view_id"]], "parent (mmif.serialize.annotation.annotation property)": [[0, "mmif.serialize.annotation.Annotation.parent"]], "reserved_names (mmif.serialize.model.mmifobject attribute)": [[0, "mmif.serialize.model.MmifObject.reserved_names"]], "sanitize() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.sanitize"]], "serialize() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.serialize"]], "serialize() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.serialize"]], "set_additional_property() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.set_additional_property"]], "set_error() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.set_error"]], "set_error() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.set_error"]], "text_language (mmif.serialize.annotation.document property)": [[0, "mmif.serialize.annotation.Document.text_language"]], "text_language (mmif.serialize.annotation.documentproperties property)": [[0, "mmif.serialize.annotation.DocumentProperties.text_language"]], "text_value (mmif.serialize.annotation.document property)": [[0, "mmif.serialize.annotation.Document.text_value"]], "text_value (mmif.serialize.annotation.documentproperties property)": [[0, "mmif.serialize.annotation.DocumentProperties.text_value"]], "update() (mmif.serialize.model.datadict method)": [[0, "mmif.serialize.model.DataDict.update"]], "validate() (mmif.serialize.mmif.mmif static method)": [[0, "mmif.serialize.mmif.Mmif.validate"]], "value (mmif.serialize.annotation.text property)": [[0, "mmif.serialize.annotation.Text.value"]], "values() (mmif.serialize.model.datadict method)": [[0, "mmif.serialize.model.DataDict.values"]], "view_prefix (mmif.serialize.model.mmifobject attribute)": [[0, "mmif.serialize.model.MmifObject.view_prefix"]], "build_label_remapper() (in module mmif.utils.sequence_helper)": [[1, "id0"], [1, "id5"], [1, "mmif.utils.sequence_helper.build_label_remapper"]], "build_score_lists() (in module mmif.utils.sequence_helper)": [[1, "id1"], [1, "id6"], [1, "mmif.utils.sequence_helper.build_score_lists"]], "capture() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.capture"]], "convert_timeframe() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timeframe"]], "convert_timepoint() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timepoint"]], "extract_frames_as_images() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_frames_as_images"]], "extract_mid_frame() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_mid_frame"]], "extract_representative_frame() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_representative_frame"]], "framenum_to_millisecond() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.framenum_to_millisecond"]], "framenum_to_second() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.framenum_to_second"]], "get_annotation_property() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_annotation_property"]], "get_framerate() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_framerate"]], "get_mid_framenum() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_mid_framenum"]], "get_representative_framenum() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_representative_framenum"]], "millisecond_to_framenum() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.millisecond_to_framenum"]], "mmif.utils.sequence_helper": [[1, "module-0"], [1, "module-1"], [1, "module-mmif.utils.sequence_helper"]], "mmif.utils.video_document_helper": [[1, "module-mmif.utils.video_document_helper"]], "sample_frames() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.sample_frames"]], "second_to_framenum() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.second_to_framenum"]], "smooth_outlying_short_intervals() (in module mmif.utils.sequence_helper)": [[1, "id2"], [1, "id7"], [1, "mmif.utils.sequence_helper.smooth_outlying_short_intervals"]], "validate_labelset() (in module mmif.utils.sequence_helper)": [[1, "id3"], [1, "id8"], [1, "mmif.utils.sequence_helper.validate_labelset"]], "alignment (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Alignment"]], "annotation (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Annotation"]], "annotationtypes (class in mmif.vocabulary)": [[2, "mmif.vocabulary.AnnotationTypes"]], "annotationtypesbase (class in mmif.vocabulary)": [[2, "mmif.vocabulary.AnnotationTypesBase"]], "audiodocument (mmif.vocabulary.documenttypes attribute)": [[2, "mmif.vocabulary.DocumentTypes.AudioDocument"]], "boundingbox (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.BoundingBox"]], "chapter (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Chapter"]], "clamstypesbase (class in mmif.vocabulary)": [[2, "mmif.vocabulary.ClamsTypesBase"]], "document (mmif.vocabulary.documenttypes attribute)": [[2, "mmif.vocabulary.DocumentTypes.Document"]], "documenttypes (class in mmif.vocabulary)": [[2, "mmif.vocabulary.DocumentTypes"]], "documenttypesbase (class in mmif.vocabulary)": [[2, "mmif.vocabulary.DocumentTypesBase"]], "imagedocument (mmif.vocabulary.documenttypes attribute)": [[2, "mmif.vocabulary.DocumentTypes.ImageDocument"]], "interval (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Interval"]], "polygon (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Polygon"]], "region (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Region"]], "relation (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Relation"]], "span (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.Span"]], "textdocument (mmif.vocabulary.documenttypes attribute)": [[2, "mmif.vocabulary.DocumentTypes.TextDocument"]], "thing (mmif.vocabulary.thingtype attribute)": [[2, "mmif.vocabulary.ThingType.Thing"]], "thingtype (class in mmif.vocabulary)": [[2, "mmif.vocabulary.ThingType"]], "thingtypesbase (in module mmif.vocabulary)": [[2, "mmif.vocabulary.ThingTypesBase"]], "timeframe (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.TimeFrame"]], "timepoint (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.TimePoint"]], "videodocument (mmif.vocabulary.documenttypes attribute)": [[2, "mmif.vocabulary.DocumentTypes.VideoDocument"]], "videoobject (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.VideoObject"]], "base_uri (mmif.vocabulary.thingtype attribute)": [[2, "mmif.vocabulary.ThingType.base_uri"]], "fuzzy_eq (mmif.vocabulary.thingtype attribute)": [[2, "mmif.vocabulary.ThingType.fuzzy_eq"]], "shortname (mmif.vocabulary.thingtype attribute)": [[2, "mmif.vocabulary.ThingType.shortname"]], "version (mmif.vocabulary.annotationtypes attribute)": [[2, "mmif.vocabulary.AnnotationTypes.version"]], "version (mmif.vocabulary.documenttypes attribute)": [[2, "mmif.vocabulary.DocumentTypes.version"]], "help() (in module mmif_docloc_http)": [[3, "mmif_docloc_http.help"]], "mmif_docloc_http": [[3, "module-mmif_docloc_http"]], "resolve() (in module mmif_docloc_http)": [[3, "mmif_docloc_http.resolve"]]}}) \ No newline at end of file diff --git a/docs/1.0.19/target-versions.html b/docs/1.0.19/target-versions.html new file mode 100644 index 00000000..d2399800 --- /dev/null +++ b/docs/1.0.19/target-versions.html @@ -0,0 +1,304 @@ + + + + + + + Target MMIF Versions — mmif-python documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Target MMIF Versions
    • +
  • +
    • +
+
+
+
+
+ +
+

Target MMIF Versions

+

This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.19

1.0.5

1.0.18

1.0.5

1.0.17

1.0.5

1.0.16

1.0.4

1.0.15

1.0.4

1.0.14

1.0.4

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

+
+ + +
+
+ +
+
+
+
+ +
+ + Other Versions + v: 1.0.19 + + +
+
+ +
0.3.0
+
0.3.1
+
0.3.2
+
0.3.3
+
0.3.4
+
0.3.5
+
0.4.0
+
0.4.1
+
0.4.2
+
0.4.3
+
0.4.4
+
0.4.5
+
0.4.6
+
0.4.7
+
0.4.8
+
0.5.0
+
0.5.1
+
0.5.2
+
1.0.0
+
1.0.1
+
1.0.10
+
1.0.11
+
1.0.12
+
1.0.13
+
1.0.14
+
1.0.15
+
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
+
1.0.2
+
1.0.3
+
1.0.4
+
1.0.5
+
1.0.6
+
1.0.7
+
1.0.8
+
1.0.9
+
+
+
+ + + \ No newline at end of file diff --git a/docs/1.0.2/.buildinfo b/docs/1.0.2/.buildinfo index ecc95548..e6d96266 100644 --- a/docs/1.0.2/.buildinfo +++ b/docs/1.0.2/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 78be9b225c3803c46ee3681fa71e5d77 +config: 913b05527e7df355a440da1027d953ad tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.2/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.2/.doctrees/autodoc/mmif.serialize.doctree index 521f521e..467f6d45 100644 Binary files a/docs/1.0.2/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.2/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.2/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.2/.doctrees/autodoc/mmif.vocabulary.doctree index 8d98b826..69844abb 100644 Binary files a/docs/1.0.2/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.2/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.2/.doctrees/consumer-tutorial.doctree b/docs/1.0.2/.doctrees/consumer-tutorial.doctree index 68e30126..17251b97 100644 Binary files a/docs/1.0.2/.doctrees/consumer-tutorial.doctree and b/docs/1.0.2/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.2/.doctrees/environment.pickle b/docs/1.0.2/.doctrees/environment.pickle index 4302782f..32aa083a 100644 Binary files a/docs/1.0.2/.doctrees/environment.pickle and b/docs/1.0.2/.doctrees/environment.pickle differ diff --git a/docs/1.0.2/.doctrees/index.doctree b/docs/1.0.2/.doctrees/index.doctree index 854c892c..3bf6b2ad 100644 Binary files a/docs/1.0.2/.doctrees/index.doctree and b/docs/1.0.2/.doctrees/index.doctree differ diff --git a/docs/1.0.2/.doctrees/introduction.doctree b/docs/1.0.2/.doctrees/introduction.doctree index 8f13d592..d4ea6d21 100644 Binary files a/docs/1.0.2/.doctrees/introduction.doctree and b/docs/1.0.2/.doctrees/introduction.doctree differ diff --git a/docs/1.0.2/.doctrees/modules.doctree b/docs/1.0.2/.doctrees/modules.doctree index aa98c64c..946a8224 100644 Binary files a/docs/1.0.2/.doctrees/modules.doctree and b/docs/1.0.2/.doctrees/modules.doctree differ diff --git a/docs/1.0.2/.doctrees/plugins.doctree b/docs/1.0.2/.doctrees/plugins.doctree index c61b4002..fc5f8f33 100644 Binary files a/docs/1.0.2/.doctrees/plugins.doctree and b/docs/1.0.2/.doctrees/plugins.doctree differ diff --git a/docs/1.0.2/.doctrees/target-versions.doctree b/docs/1.0.2/.doctrees/target-versions.doctree index c6418d56..cefc6f99 100644 Binary files a/docs/1.0.2/.doctrees/target-versions.doctree and b/docs/1.0.2/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.2/autodoc/mmif.serialize.html b/docs/1.0.2/autodoc/mmif.serialize.html index 2b6dd513..7c2aea5c 100644 --- a/docs/1.0.2/autodoc/mmif.serialize.html +++ b/docs/1.0.2/autodoc/mmif.serialize.html @@ -1252,6 +1252,9 @@

mmif.serialize module1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/autodoc/mmif.vocabulary.html b/docs/1.0.2/autodoc/mmif.vocabulary.html index bf00efa8..ba874376 100644 --- a/docs/1.0.2/autodoc/mmif.vocabulary.html +++ b/docs/1.0.2/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/consumer-tutorial.html b/docs/1.0.2/consumer-tutorial.html index 110380d5..e90aba13 100644 --- a/docs/1.0.2/consumer-tutorial.html +++ b/docs/1.0.2/consumer-tutorial.html @@ -152,6 +152,9 @@
1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/genindex.html b/docs/1.0.2/genindex.html index fafbabeb..c155fbe9 100644 --- a/docs/1.0.2/genindex.html +++ b/docs/1.0.2/genindex.html @@ -633,6 +633,9 @@

V

1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/index.html b/docs/1.0.2/index.html index 37468ad1..c807b395 100644 --- a/docs/1.0.2/index.html +++ b/docs/1.0.2/index.html @@ -183,6 +183,9 @@

Indices and tables1.0.14

1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/introduction.html b/docs/1.0.2/introduction.html index c7cf65a8..4d9e411f 100644 --- a/docs/1.0.2/introduction.html +++ b/docs/1.0.2/introduction.html @@ -225,6 +225,9 @@

MMIF Serialization1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/modules.html b/docs/1.0.2/modules.html index 87696f06..c465697c 100644 --- a/docs/1.0.2/modules.html +++ b/docs/1.0.2/modules.html @@ -326,6 +326,9 @@
1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/plugins.html b/docs/1.0.2/plugins.html index f5e27976..93fe73dd 100644 --- a/docs/1.0.2/plugins.html +++ b/docs/1.0.2/plugins.html @@ -256,6 +256,9 @@

Utility Plugins1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/py-modindex.html b/docs/1.0.2/py-modindex.html index 72add056..8873797b 100644 --- a/docs/1.0.2/py-modindex.html +++ b/docs/1.0.2/py-modindex.html @@ -188,6 +188,9 @@

Python Module Index

1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
diff --git a/docs/1.0.2/search.html b/docs/1.0.2/search.html index a3266445..cd813e87 100644 --- a/docs/1.0.2/search.html +++ b/docs/1.0.2/search.html @@ -151,6 +151,9 @@
1.0.14
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b/docs/1.0.2/target-versions.html index 2a719f94..a94af52d 100644 --- a/docs/1.0.2/target-versions.html +++ b/docs/1.0.2/target-versions.html @@ -93,7 +93,7 @@

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@@ -229,6 +229,9 @@
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diff --git a/docs/1.0.3/.buildinfo b/docs/1.0.3/.buildinfo index b4ba9a2b..82163f19 100644 --- a/docs/1.0.3/.buildinfo +++ b/docs/1.0.3/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 443b8d9354ca40149d0de1e21d421f15 +config: 91e3767453acb794a27618e666ed5056 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.3/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.3/.doctrees/autodoc/mmif.serialize.doctree index 03a14711..8a2be92a 100644 Binary files a/docs/1.0.3/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.3/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.3/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.3/.doctrees/autodoc/mmif.vocabulary.doctree index 3ea1c347..d13f627d 100644 Binary files a/docs/1.0.3/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.3/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.3/.doctrees/consumer-tutorial.doctree b/docs/1.0.3/.doctrees/consumer-tutorial.doctree index 18ae2228..d4b05473 100644 Binary files a/docs/1.0.3/.doctrees/consumer-tutorial.doctree and b/docs/1.0.3/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.3/.doctrees/environment.pickle b/docs/1.0.3/.doctrees/environment.pickle index 31c8333f..5c881a69 100644 Binary files a/docs/1.0.3/.doctrees/environment.pickle and b/docs/1.0.3/.doctrees/environment.pickle differ diff --git a/docs/1.0.3/.doctrees/index.doctree b/docs/1.0.3/.doctrees/index.doctree index 90807980..3c4cf981 100644 Binary files a/docs/1.0.3/.doctrees/index.doctree and b/docs/1.0.3/.doctrees/index.doctree differ diff --git a/docs/1.0.3/.doctrees/introduction.doctree b/docs/1.0.3/.doctrees/introduction.doctree index f216b572..77ae2097 100644 Binary files a/docs/1.0.3/.doctrees/introduction.doctree and b/docs/1.0.3/.doctrees/introduction.doctree differ diff --git a/docs/1.0.3/.doctrees/modules.doctree b/docs/1.0.3/.doctrees/modules.doctree index 1ca65271..331a52ca 100644 Binary files a/docs/1.0.3/.doctrees/modules.doctree and b/docs/1.0.3/.doctrees/modules.doctree differ diff --git a/docs/1.0.3/.doctrees/plugins.doctree b/docs/1.0.3/.doctrees/plugins.doctree index 95451a65..c17fd5df 100644 Binary files a/docs/1.0.3/.doctrees/plugins.doctree and b/docs/1.0.3/.doctrees/plugins.doctree differ diff --git a/docs/1.0.3/.doctrees/target-versions.doctree b/docs/1.0.3/.doctrees/target-versions.doctree index 15544bec..867bde69 100644 Binary files a/docs/1.0.3/.doctrees/target-versions.doctree and b/docs/1.0.3/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.3/autodoc/mmif.serialize.html b/docs/1.0.3/autodoc/mmif.serialize.html index 6da3695f..f512c3b4 100644 --- a/docs/1.0.3/autodoc/mmif.serialize.html +++ b/docs/1.0.3/autodoc/mmif.serialize.html @@ -1252,6 +1252,9 @@

mmif.serialize module1.0.14
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diff --git a/docs/1.0.3/autodoc/mmif.vocabulary.html b/docs/1.0.3/autodoc/mmif.vocabulary.html index 09b4b3d6..3a8cf54c 100644 --- a/docs/1.0.3/autodoc/mmif.vocabulary.html +++ b/docs/1.0.3/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

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MMIF Serialization1.0.14
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Document Location Scheme Plugins1.0.14
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Python Module Index

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diff --git a/docs/1.0.4/.buildinfo b/docs/1.0.4/.buildinfo index 44d2c878..b8ce6eb9 100644 --- a/docs/1.0.4/.buildinfo +++ b/docs/1.0.4/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 69055628dce6492c1d9c1ddf7d8cfe8a +config: 8450493ec790ae438210399882530905 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.4/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.4/.doctrees/autodoc/mmif.serialize.doctree index 6f6daf71..0fc171c0 100644 Binary files a/docs/1.0.4/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.4/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.4/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.4/.doctrees/autodoc/mmif.vocabulary.doctree index 648ff926..7e7f4469 100644 Binary files a/docs/1.0.4/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.4/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.4/.doctrees/consumer-tutorial.doctree b/docs/1.0.4/.doctrees/consumer-tutorial.doctree index eebdc10a..35cf3485 100644 Binary files a/docs/1.0.4/.doctrees/consumer-tutorial.doctree and b/docs/1.0.4/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.4/.doctrees/environment.pickle b/docs/1.0.4/.doctrees/environment.pickle index 9ab91a4c..a228e0a8 100644 Binary files a/docs/1.0.4/.doctrees/environment.pickle and b/docs/1.0.4/.doctrees/environment.pickle differ diff --git a/docs/1.0.4/.doctrees/index.doctree b/docs/1.0.4/.doctrees/index.doctree index 55096101..4d4ce073 100644 Binary files a/docs/1.0.4/.doctrees/index.doctree and b/docs/1.0.4/.doctrees/index.doctree differ diff --git a/docs/1.0.4/.doctrees/introduction.doctree b/docs/1.0.4/.doctrees/introduction.doctree index 84b1c44f..3df1d042 100644 Binary files a/docs/1.0.4/.doctrees/introduction.doctree and b/docs/1.0.4/.doctrees/introduction.doctree differ diff --git a/docs/1.0.4/.doctrees/modules.doctree b/docs/1.0.4/.doctrees/modules.doctree index 7803d104..f059a36c 100644 Binary files a/docs/1.0.4/.doctrees/modules.doctree and b/docs/1.0.4/.doctrees/modules.doctree differ diff --git a/docs/1.0.4/.doctrees/plugins.doctree b/docs/1.0.4/.doctrees/plugins.doctree index f3893d94..5cb2fa00 100644 Binary files a/docs/1.0.4/.doctrees/plugins.doctree and b/docs/1.0.4/.doctrees/plugins.doctree differ diff --git a/docs/1.0.4/.doctrees/target-versions.doctree b/docs/1.0.4/.doctrees/target-versions.doctree index 4aa29e2d..582acfcc 100644 Binary files a/docs/1.0.4/.doctrees/target-versions.doctree and b/docs/1.0.4/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.4/autodoc/mmif.serialize.html b/docs/1.0.4/autodoc/mmif.serialize.html index 850184fe..f546081a 100644 --- a/docs/1.0.4/autodoc/mmif.serialize.html +++ b/docs/1.0.4/autodoc/mmif.serialize.html @@ -1252,6 +1252,9 @@

mmif.serialize module1.0.14
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diff --git a/docs/1.0.4/autodoc/mmif.vocabulary.html b/docs/1.0.4/autodoc/mmif.vocabulary.html index 5abb8490..08c04ba0 100644 --- a/docs/1.0.4/autodoc/mmif.vocabulary.html +++ b/docs/1.0.4/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

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MMIF Serialization1.0.14
1.0.15
1.0.16
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1.0.3
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Python Module Index

1.0.14
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diff --git a/docs/1.0.5/.buildinfo b/docs/1.0.5/.buildinfo index 67f41e6e..0d1feba1 100644 --- a/docs/1.0.5/.buildinfo +++ b/docs/1.0.5/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 86d99b88e293646e6ac8b09db6e9d699 +config: b8503b99d630f06c9ca93fa238949c47 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.5/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.5/.doctrees/autodoc/mmif.serialize.doctree index 52d4c531..d86c3f19 100644 Binary files a/docs/1.0.5/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.5/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.5/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.5/.doctrees/autodoc/mmif.vocabulary.doctree index 02aa61b2..58de7c5c 100644 Binary files a/docs/1.0.5/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.5/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.5/.doctrees/consumer-tutorial.doctree b/docs/1.0.5/.doctrees/consumer-tutorial.doctree index f949b95a..9c26eb8b 100644 Binary files a/docs/1.0.5/.doctrees/consumer-tutorial.doctree and b/docs/1.0.5/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.5/.doctrees/environment.pickle b/docs/1.0.5/.doctrees/environment.pickle index 369bc974..cefdfaae 100644 Binary files a/docs/1.0.5/.doctrees/environment.pickle and b/docs/1.0.5/.doctrees/environment.pickle differ diff --git a/docs/1.0.5/.doctrees/index.doctree b/docs/1.0.5/.doctrees/index.doctree index e739bb65..0576f06e 100644 Binary files a/docs/1.0.5/.doctrees/index.doctree and b/docs/1.0.5/.doctrees/index.doctree differ diff --git a/docs/1.0.5/.doctrees/introduction.doctree b/docs/1.0.5/.doctrees/introduction.doctree index 896c98e4..18415e7d 100644 Binary files a/docs/1.0.5/.doctrees/introduction.doctree and b/docs/1.0.5/.doctrees/introduction.doctree differ diff --git a/docs/1.0.5/.doctrees/modules.doctree b/docs/1.0.5/.doctrees/modules.doctree index 2973c697..bbdd02d3 100644 Binary files a/docs/1.0.5/.doctrees/modules.doctree and b/docs/1.0.5/.doctrees/modules.doctree differ diff --git a/docs/1.0.5/.doctrees/plugins.doctree b/docs/1.0.5/.doctrees/plugins.doctree index 71d41e83..beddb68b 100644 Binary files a/docs/1.0.5/.doctrees/plugins.doctree and b/docs/1.0.5/.doctrees/plugins.doctree differ diff --git a/docs/1.0.5/.doctrees/target-versions.doctree b/docs/1.0.5/.doctrees/target-versions.doctree index 8be051af..55564cfa 100644 Binary files a/docs/1.0.5/.doctrees/target-versions.doctree and b/docs/1.0.5/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.5/autodoc/mmif.serialize.html b/docs/1.0.5/autodoc/mmif.serialize.html index 4f05cf8c..936eb1ba 100644 --- a/docs/1.0.5/autodoc/mmif.serialize.html +++ b/docs/1.0.5/autodoc/mmif.serialize.html @@ -1252,6 +1252,9 @@

mmif.serialize module1.0.14
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diff --git a/docs/1.0.5/autodoc/mmif.vocabulary.html b/docs/1.0.5/autodoc/mmif.vocabulary.html index 50123019..aa387317 100644 --- a/docs/1.0.5/autodoc/mmif.vocabulary.html +++ b/docs/1.0.5/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

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1.0.2
1.0.3
1.0.4
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MMIF Serialization1.0.14
1.0.15
1.0.16
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1.0.18
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1.0.19
1.0.2
1.0.3
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Document Location Scheme Plugins1.0.14
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Python Module Index

1.0.14
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1.0.3
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diff --git a/docs/1.0.6/.buildinfo b/docs/1.0.6/.buildinfo index 910e6333..8b3a5c0b 100644 --- a/docs/1.0.6/.buildinfo +++ b/docs/1.0.6/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 4d13a831e153c73b2f48c10596fff98f +config: d4824303ed618e7f590e2cc49758c67d tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.6/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.6/.doctrees/autodoc/mmif.serialize.doctree index 065e5d23..0cf4899a 100644 Binary files a/docs/1.0.6/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.6/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.6/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.6/.doctrees/autodoc/mmif.vocabulary.doctree index 906e0416..162e0689 100644 Binary files a/docs/1.0.6/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.6/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.6/.doctrees/consumer-tutorial.doctree b/docs/1.0.6/.doctrees/consumer-tutorial.doctree index 0fed296b..1c2a02c3 100644 Binary files a/docs/1.0.6/.doctrees/consumer-tutorial.doctree and b/docs/1.0.6/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.6/.doctrees/environment.pickle b/docs/1.0.6/.doctrees/environment.pickle index 20b62134..949b6a00 100644 Binary files a/docs/1.0.6/.doctrees/environment.pickle and b/docs/1.0.6/.doctrees/environment.pickle differ diff --git a/docs/1.0.6/.doctrees/index.doctree b/docs/1.0.6/.doctrees/index.doctree index 24c2dc4e..f908e724 100644 Binary files a/docs/1.0.6/.doctrees/index.doctree and b/docs/1.0.6/.doctrees/index.doctree differ diff --git a/docs/1.0.6/.doctrees/introduction.doctree b/docs/1.0.6/.doctrees/introduction.doctree index e88010d0..1fa745f7 100644 Binary files a/docs/1.0.6/.doctrees/introduction.doctree and b/docs/1.0.6/.doctrees/introduction.doctree differ diff --git a/docs/1.0.6/.doctrees/modules.doctree b/docs/1.0.6/.doctrees/modules.doctree index cf204e2a..c238c103 100644 Binary files a/docs/1.0.6/.doctrees/modules.doctree and b/docs/1.0.6/.doctrees/modules.doctree differ diff --git a/docs/1.0.6/.doctrees/plugins.doctree b/docs/1.0.6/.doctrees/plugins.doctree index 138f1ed4..43b3c864 100644 Binary files a/docs/1.0.6/.doctrees/plugins.doctree and b/docs/1.0.6/.doctrees/plugins.doctree differ diff --git a/docs/1.0.6/.doctrees/target-versions.doctree b/docs/1.0.6/.doctrees/target-versions.doctree index 636c68e3..2c2741fc 100644 Binary files a/docs/1.0.6/.doctrees/target-versions.doctree and b/docs/1.0.6/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.6/autodoc/mmif.serialize.html b/docs/1.0.6/autodoc/mmif.serialize.html index 0bd79ee3..5f77782b 100644 --- a/docs/1.0.6/autodoc/mmif.serialize.html +++ b/docs/1.0.6/autodoc/mmif.serialize.html @@ -1252,6 +1252,9 @@

mmif.serialize module1.0.14
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diff --git a/docs/1.0.6/autodoc/mmif.vocabulary.html b/docs/1.0.6/autodoc/mmif.vocabulary.html index 0a2423c4..d1293721 100644 --- a/docs/1.0.6/autodoc/mmif.vocabulary.html +++ b/docs/1.0.6/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

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1.0.3
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MMIF Serialization1.0.14
1.0.15
1.0.16
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1.0.18
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1.0.19
1.0.2
1.0.3
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Document Location Scheme Plugins1.0.14
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Python Module Index

1.0.14
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1.0.3
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diff --git a/docs/1.0.7/.buildinfo b/docs/1.0.7/.buildinfo index f5c48268..f8e4e70c 100644 --- a/docs/1.0.7/.buildinfo +++ b/docs/1.0.7/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 8c1b03aa17fcbd2dec1a16ac60d0fa2d +config: 6a29e072540b27cb21a411bf7c270b42 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/1.0.7/.doctrees/autodoc/mmif.serialize.doctree b/docs/1.0.7/.doctrees/autodoc/mmif.serialize.doctree index f46722d5..3f0543f0 100644 Binary files a/docs/1.0.7/.doctrees/autodoc/mmif.serialize.doctree and b/docs/1.0.7/.doctrees/autodoc/mmif.serialize.doctree differ diff --git a/docs/1.0.7/.doctrees/autodoc/mmif.vocabulary.doctree b/docs/1.0.7/.doctrees/autodoc/mmif.vocabulary.doctree index 1ac6d6de..3db96b01 100644 Binary files a/docs/1.0.7/.doctrees/autodoc/mmif.vocabulary.doctree and b/docs/1.0.7/.doctrees/autodoc/mmif.vocabulary.doctree differ diff --git a/docs/1.0.7/.doctrees/consumer-tutorial.doctree b/docs/1.0.7/.doctrees/consumer-tutorial.doctree index 2e7b9b4e..41f5bc92 100644 Binary files a/docs/1.0.7/.doctrees/consumer-tutorial.doctree and b/docs/1.0.7/.doctrees/consumer-tutorial.doctree differ diff --git a/docs/1.0.7/.doctrees/environment.pickle b/docs/1.0.7/.doctrees/environment.pickle index 046f2a96..d6abcda9 100644 Binary files a/docs/1.0.7/.doctrees/environment.pickle and b/docs/1.0.7/.doctrees/environment.pickle differ diff --git a/docs/1.0.7/.doctrees/index.doctree b/docs/1.0.7/.doctrees/index.doctree index 5f7a934d..fc2f2f84 100644 Binary files a/docs/1.0.7/.doctrees/index.doctree and b/docs/1.0.7/.doctrees/index.doctree differ diff --git a/docs/1.0.7/.doctrees/introduction.doctree b/docs/1.0.7/.doctrees/introduction.doctree index f7e16d86..0186447c 100644 Binary files a/docs/1.0.7/.doctrees/introduction.doctree and b/docs/1.0.7/.doctrees/introduction.doctree differ diff --git a/docs/1.0.7/.doctrees/modules.doctree b/docs/1.0.7/.doctrees/modules.doctree index 59857827..799764b3 100644 Binary files a/docs/1.0.7/.doctrees/modules.doctree and b/docs/1.0.7/.doctrees/modules.doctree differ diff --git a/docs/1.0.7/.doctrees/plugins.doctree b/docs/1.0.7/.doctrees/plugins.doctree index 58819e71..f3d4486b 100644 Binary files a/docs/1.0.7/.doctrees/plugins.doctree and b/docs/1.0.7/.doctrees/plugins.doctree differ diff --git a/docs/1.0.7/.doctrees/target-versions.doctree b/docs/1.0.7/.doctrees/target-versions.doctree index 5f90ef9b..484a79c4 100644 Binary files a/docs/1.0.7/.doctrees/target-versions.doctree and b/docs/1.0.7/.doctrees/target-versions.doctree differ diff --git a/docs/1.0.7/autodoc/mmif.serialize.html b/docs/1.0.7/autodoc/mmif.serialize.html index 2559dd3c..b6ee576f 100644 --- a/docs/1.0.7/autodoc/mmif.serialize.html +++ b/docs/1.0.7/autodoc/mmif.serialize.html @@ -1252,6 +1252,9 @@

mmif.serialize module1.0.14
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diff --git a/docs/1.0.7/autodoc/mmif.vocabulary.html b/docs/1.0.7/autodoc/mmif.vocabulary.html index 64b55053..79fc2397 100644 --- a/docs/1.0.7/autodoc/mmif.vocabulary.html +++ b/docs/1.0.7/autodoc/mmif.vocabulary.html @@ -104,7 +104,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]

Bases: AnnotationTypesBase

This class contains the CLAMS annotation types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
@@ -185,7 +185,7 @@

mmif.vocabulary moduleclass mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]

Bases: DocumentTypesBase

This class contains the CLAMS document types -defined in the spec version 1.0.4 as class variables.

+defined in the spec version 1.0.5 as class variables.

AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
@@ -286,6 +286,9 @@

mmif.vocabulary module1.0.14

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V

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Indices and tables1.0.14

1.0.15
1.0.16
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1.0.18
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1.0.19
1.0.2
1.0.3
1.0.4
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MMIF Serialization1.0.14
1.0.15
1.0.16
+
1.0.17
+
1.0.18
+
1.0.19
1.0.2
1.0.3
1.0.4
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Document Location Scheme Plugins1.0.14
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Python Module Index

1.0.14
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1.0.3
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Indices and tables1.0.14
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diff --git a/docs/1.0.8/introduction.html b/docs/1.0.8/introduction.html index 9f251ce0..96d49e18 100644 --- a/docs/1.0.8/introduction.html +++ b/docs/1.0.8/introduction.html @@ -116,7 +116,7 @@

Installation

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

+

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

import mmif
 from mmif import Mmif
 
@@ -151,7 +151,7 @@ 
MMIF Serializationmmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

 
-
When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

+
When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

 
To get subcomponents, you can use various getters implemented in subclasses. For example;

 
from mmif.vocabulary.document_types import DocumentTypes
 
@@ -225,6 +225,9 @@ 
MMIF Serialization1.0.14
       
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diff --git a/docs/1.0.8/modules.html b/docs/1.0.8/modules.html
index d65a18ad..8fa8d099 100644
--- a/docs/1.0.8/modules.html
+++ b/docs/1.0.8/modules.html
@@ -91,195 +91,19 @@
 

 
@@ -347,6 +171,9 @@
       
1.0.14

       
1.0.15

       
1.0.16

+      
1.0.17

+      
1.0.18

+      
1.0.19

       
1.0.2

       
1.0.3

       
1.0.4

diff --git a/docs/1.0.8/objects.inv b/docs/1.0.8/objects.inv
index ccd885d3..51b6249d 100644
Binary files a/docs/1.0.8/objects.inv and b/docs/1.0.8/objects.inv differ
diff --git a/docs/1.0.8/plugins.html b/docs/1.0.8/plugins.html
index 08e323a9..bea84927 100644
--- a/docs/1.0.8/plugins.html
+++ b/docs/1.0.8/plugins.html
@@ -98,7 +98,7 @@ 
Overviewmmif-python.

 

 
Document Location Scheme Plugins

-
mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

+
mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

 
To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

 
    
 
  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.
    2. 
@@ -208,6 +208,9 @@ 
    Document Location Scheme Plugins1.0.14
       
    1.0.15
    
       
    1.0.16
    
+      
    1.0.17
    
+      
    1.0.18
    
+      
    1.0.19
    
       
    1.0.2
    
       
    1.0.3
    
       
    1.0.4
    
diff --git a/docs/1.0.8/search.html b/docs/1.0.8/search.html
index f49e0f25..f2f931e5 100644
--- a/docs/1.0.8/search.html
+++ b/docs/1.0.8/search.html
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    1.0.14
    
       
    1.0.15
    
       
    1.0.16
    
+      
    1.0.17
    
+      
    1.0.18
    
+      
    1.0.19
    
       
    1.0.2
    
       
    1.0.3
    
       
    1.0.4
    
diff --git a/docs/1.0.8/searchindex.js b/docs/1.0.8/searchindex.js
index 173ee996..459f4079 100644
--- a/docs/1.0.8/searchindex.js
+++ b/docs/1.0.8/searchindex.js
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Installation
 
MMIF Serialization

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mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

+
mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

 
import mmif
 from mmif import Mmif
 
@@ -152,7 +152,7 @@ 
MMIF Serializationmmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

 
-
When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

+
When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

 
To get subcomponents, you can use various getters implemented in subclasses. For example;

 
from mmif.vocabulary.document_types import DocumentTypes
 
@@ -226,6 +226,9 @@ 
MMIF Serialization1.0.14
       
1.0.15

       
1.0.16

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1.0.17

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1.0.18

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1.0.19

       
1.0.2

       
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1.0.4

diff --git a/docs/1.0.9/modules.html b/docs/1.0.9/modules.html
index 4a7fbac9..1cd02d33 100644
--- a/docs/1.0.9/modules.html
+++ b/docs/1.0.9/modules.html
@@ -95,196 +95,19 @@
 

 
@@ -363,6 +186,9 @@ 
mmif_docloc_http package1.0.14
       
1.0.15

       
1.0.16

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1.0.17

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1.0.18

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1.0.19

       
1.0.2

       
1.0.3

       
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diff --git a/docs/1.0.9/objects.inv b/docs/1.0.9/objects.inv
index 93670a75..e4d91247 100644
Binary files a/docs/1.0.9/objects.inv and b/docs/1.0.9/objects.inv differ
diff --git a/docs/1.0.9/plugins.html b/docs/1.0.9/plugins.html
index a386e874..008f942d 100644
--- a/docs/1.0.9/plugins.html
+++ b/docs/1.0.9/plugins.html
@@ -100,7 +100,7 @@ 
Overviewmmif-python.

 

 
Document Location Scheme Plugins

-
mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

+
mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

 
To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

 
    
 
  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.
    2. 
@@ -215,6 +215,9 @@ 
    Bulit-in Document Location Scheme Plugins1.0.14
       
    1.0.15
    
       
    1.0.16
    
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    1.0.17
    
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    1.0.18
    
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    1.0.19
    
       
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    1.0.4
    
diff --git a/docs/1.0.9/py-modindex.html b/docs/1.0.9/py-modindex.html
index 5de82ca0..9ebd162f 100644
--- a/docs/1.0.9/py-modindex.html
+++ b/docs/1.0.9/py-modindex.html
@@ -22,6 +22,10 @@
     
  
 
+    
+
 
 
 
@@ -93,47 +97,6 @@ 
    Python Module Index
    
       
      
        m
-     
-       
-       
-       mmif
-       
-     
-       
-          
-       mmif.serialize.annotation
-       
-     
-       
-          
-       mmif.serialize.mmif
-       
-     
-       
-          
-       mmif.serialize.model
-       
-     
-       
-          
-       mmif.serialize.view
-       
-     
-       
-          
-       mmif.utils.video_document_helper
-       
-     
-       
-          
-       mmif.vocabulary.annotation_types
-       
-     
-       
-          
-       mmif.vocabulary.document_types
-       
      
        
        
@@ -199,6 +162,9 @@ 
    Python Module Index
    
       
    1.0.14
    
       
    1.0.15
    
       
    1.0.16
    
+      
    1.0.17
    
+      
    1.0.18
    
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    1.0.19
    
       
    1.0.2
    
       
    1.0.3
    
       
    1.0.4
    
diff --git a/docs/1.0.9/search.html b/docs/1.0.9/search.html
index 680ee89d..667de562 100644
--- a/docs/1.0.9/search.html
+++ b/docs/1.0.9/search.html
@@ -152,6 +152,9 @@
       
    1.0.14
    
       
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    1.0.2
    
       
    1.0.3
    
       
    1.0.4
    
diff --git a/docs/1.0.9/searchindex.js b/docs/1.0.9/searchindex.js
index 7162b5aa..b7db25b3 100644
--- a/docs/1.0.9/searchindex.js
+++ b/docs/1.0.9/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/1.0.9/target-versions.html b/docs/1.0.9/target-versions.html
index d17949ca..7ddd2d9e 100644
--- a/docs/1.0.9/target-versions.html
+++ b/docs/1.0.9/target-versions.html
@@ -93,97 +93,94 @@
 
 
 
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@@ -251,6 +248,9 @@
       
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diff --git a/docs/latest b/docs/latest
index d941c12b..e7ad390e 120000
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+++ b/docs/latest
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\ No newline at end of file
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\ No newline at end of file
diff --git a/documentation/target-versions.csv b/documentation/target-versions.csv
index 361ce8df..79de2da9 100644
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+++ b/documentation/target-versions.csv
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 1.0.14,"1.0.4"
diff --git a/requirements.dev b/requirements.dev
index d12b58da..ec6113f7 100644
--- a/requirements.dev
+++ b/requirements.dev
@@ -13,3 +13,4 @@ sphinx-autobuild
 git+https://github.com/clamsproject/sphinx-multiversion.git@master
 twine
 m2r2
+setuptools>=70  # arbitrarily recent version
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 36f0c7cf..303c7cd1 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,8 @@
 from urllib import request
 
 import setuptools.command.build_py
-import setuptools.command.develop
+from setuptools.command.sdist import sdist
+from setuptools.command.develop import develop
 
 name = "mmif-python"
 version_fname = "VERSION"
@@ -254,15 +255,18 @@ def mod_run(self):
     return setuptools_cmd
 
 
+# Modernize cmdclass to ensure compatibility with setuptools >=80
 @prep_ext_files
-class SdistCommand(setuptools.command.sdist.sdist):
-    pass
-
+class SdistCommand(sdist):
+    def initialize_options(self):
+        super().initialize_options()
+        # Add any additional initialization logic here if needed
 
 @prep_ext_files
-class DevelopCommand(setuptools.command.develop.develop):
-    pass
-
+class DevelopCommand(develop):
+    def initialize_options(self):
+        super().initialize_options()
+        # Add any additional initialization logic here if needed
 
 cmdclass['sdist'] = SdistCommand
 cmdclass['develop'] = DevelopCommand
@@ -279,6 +283,17 @@ class DevelopCommand(setuptools.command.develop.develop):
 with open('requirements.seq') as requirements:
     seq_requires = requirements.readlines()
 
+extras_require = {
+    'seq': seq_requires,
+    'cv': cv_requires,
+    'dev': [
+        'pytest',
+        'pytest-pep8',
+        'pytest-cov',
+        'pytype',
+    ]
+}
+
 setuptools.setup(
     name=name,
     version=version,
@@ -301,21 +316,12 @@ class DevelopCommand(setuptools.command.develop.develop):
         'mmif': [f'{mmif_res_pkg}/*', f'{mmif_ver_pkg}/*', f'{mmif_vocabulary_pkg}/*'],
     },
     install_requires=requires,
-    extras_require={
-        'seq': seq_requires,
-        'cv': cv_requires,
-        'dev': [
-            'pytest',
-            'pytest-pep8',
-            'pytest-cov',
-            'pytype',
-        ]
-    },
+    extras_require=extras_require,
     python_requires='>=3.10',
     classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
-        'Intended Audience :: Developers ',
-        'License :: OSI Approved :: Apache Software License',
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'License :: Apache-2.0',
         'Programming Language :: Python :: 3 :: Only',
     ]
 )