Timeline instances by pendingintent · Pull Request #43 · pendingintent/soa-workbench

pendingintent · 2025-12-19T18:37:32Z

Added ScheduledActivityInstance
Changed database column from raw_header to label
Fixed all tests to remvoe references to visit.raw_header

…d not use the first gap

Copilot

Pull request overview

This PR renames the database column from raw_header to label across the codebase and introduces a new "Scheduled Activity Instances" feature for managing timeline instances within the Schedule of Activities (SoA) builder.

Key Changes

Renamed raw_header to label throughout all database schemas, API endpoints, and test fixtures
Added comprehensive instance management with CRUD operations, audit trails, and UI templates
Enhanced visit records with description and encounter_uid fields

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
validate_soa.py	Updated derive_nominal_day to use 'label' instead of 'raw_header'
tests/test_web_api.py	Changed test fixture to use 'label' field
tests/test_ui_visit_create.py	Updated UI test to use 'label' parameter
tests/test_ui_set_visit_epoch.py	Updated visit creation test with 'label'
tests/test_instances_audit.py	New comprehensive test for instance CRUD and audit trail
tests/test_deletion.py	Renamed parameter from raw_header to label
tests/test_bulk_import.py	Updated bulk import payload to use 'label'
tests/conftest.py	Enhanced test isolation with database cleanup utilities
src/usdm/generate_scheduled_activity_instances.py	New module to generate USDM-compliant instance exports
src/soa_builder/web/utils.py	Added helper functions for encounter and epoch UID lookups
src/soa_builder/web/templates/instances.html	New UI template for instance management
src/soa_builder/web/templates/freeze_modal.html	Removed raw_header from visit display
src/soa_builder/web/templates/edit.html	Updated visit display to use 'label' field
src/soa_builder/web/templates/base.html	Added navigation link to instances page
src/soa_builder/web/schemas.py	Added InstanceCreate/Update schemas; updated Visit schemas
src/soa_builder/web/routers/visits.py	Extensive refactoring: renamed fields, added encounter_uid generation, added delete endpoint
src/soa_builder/web/routers/timings.py	Updated UID generation logic and error messages
src/soa_builder/web/routers/instances.py	New router with complete instance CRUD operations
src/soa_builder/web/migrate_database.py	Added migration for visit label/description columns
src/soa_builder/web/initialize_database.py	Updated schema with label, encounter_uid; added instances and related tables
src/soa_builder/web/db.py	Enhanced database connection logic with pytest detection
src/soa_builder/web/audit.py	Added instance audit recording function
src/soa_builder/web/app.py	Integrated instances router; updated all raw_header references to label
src/soa_builder/schedule.py	Updated VisitStub dataclass to use 'label'
src/soa_builder/normalization.py	Changed Visit dataclass and SQL schema to use 'label'
src/soa_builder/cli.py	Updated visit loading to use 'label' key
normalize_soa.py	Updated Visit dataclass and build logic for 'label'
README_endpoints.md	Updated API documentation to reflect 'label' parameter
README.md	Updated documentation describing 'label' column and test database setup

Comments suppressed due to low confidence (3)

src/soa_builder/web/app.py:1

Remove large block of commented-out code. This function has been moved to the visits router and is no longer needed here.

from __future__ import annotations

src/soa_builder/web/app.py:1

Remove large block of commented-out code. This function logic has been replaced with a call to the visits router.

from __future__ import annotations

src/soa_builder/web/app.py:1

Remove commented-out code. This function has been replaced with an active implementation above.

from __future__ import annotations

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

src/soa_builder/web/templates/instances.html

src/soa_builder/web/initialize_database.py

src/soa_builder/web/routers/visits.py

src/soa_builder/web/routers/timings.py

src/soa_builder/web/routers/instances.py

Updated variable reference Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

spelling Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

removed commented-out code Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 29 out of 29 changed files in this pull request and generated 6 comments.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

src/soa_builder/web/routers/instances.py

Copilot · 2025-12-19T18:42:51Z

src/soa_builder/web/routers/visits.py

-    )
-    new_raw_header = new_raw_header.strip()
+
+    new_label = payload.label if payload.label is not None else before["label"]


Remove commented-out code. The variable new_name is assigned on line 178 but this commented line suggests there was refactoring. If the strip operation is no longer needed, remove this comment.

Suggested change

new_label = payload.label if payload.label is not None else before["label"]

Copilot · 2025-12-19T18:42:51Z

src/soa_builder/web/routers/instances.py

+    """
+    next_n = 1
+    while next_n in used_nums:
+        next_n += 1
+    """


Remove commented-out code. This appears to be old logic for filling gaps in ID sequences, which has been replaced by the max+1 approach on lines 123-124.

Suggested change

"""

next_n = 1

while next_n in used_nums:

next_n += 1

"""

Copilot · 2025-12-19T18:42:51Z

src/soa_builder/web/app.py

+'''@app.delete("/soa/{soa_id}/visits/{visit_id}")
 def delete_visit(soa_id: int, visit_id: int):


Remove large blocks of commented-out code (lines 3029-3065). This delete_visit function has been moved to the visits router, so the old implementation should be removed rather than commented out.

Copilot · 2025-12-19T18:42:52Z

src/soa_builder/web/app.py

+    '''
    """Create a visit (UI form).


Remove large blocks of commented-out code (lines 4014-4072). This old ui_add_visit implementation has been replaced by calls to the visits router, so the commented code should be deleted.

Copilot · 2025-12-19T18:42:52Z

src/soa_builder/web/app.py

+'''
+def ui_delete_visit(request: Request, soa_id: int, visit_id: int):


Remove commented-out duplicate function definition (lines 5737-5756). The active implementation exists above on lines 5718-5734.

spelling Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 29 out of 29 changed files in this pull request and generated 5 comments.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2025-12-19T18:44:39Z

tests/conftest.py

+        value of ``SOA_BUILDER_DB`` if set) so local/prod data are never touched.
+- Removes any stale WAL/SHM files at the start of the test session to avoid
+        "disk I/O" errors from interrupted runs.


The indentation alignment is inconsistent. The continuation lines (3-6) should align with the opening quote, not be indented further with leading spaces.

Suggested change

value of ``SOA_BUILDER_DB`` if set) so local/prod data are never touched.

- Removes any stale WAL/SHM files at the start of the test session to avoid

"disk I/O" errors from interrupted runs.

value of ``SOA_BUILDER_DB`` if set) so local/prod data are never touched.

- Removes any stale WAL/SHM files at the start of the test session to avoid

"disk I/O" errors from interrupted runs.

src/soa_builder/web/routers/visits.py

src/soa_builder/web/app.py

Copilot · 2025-12-19T18:44:40Z

src/soa_builder/web/app.py



-@app.delete("/soa/{soa_id}/visits/{visit_id}")
+'''@app.delete("/soa/{soa_id}/visits/{visit_id}")


This endpoint is commented out with triple quotes, creating a multi-line string literal instead of a comment. This leaves dead code in the module that will never execute but might confuse readers about whether it's active. Use proper comment syntax (#) or remove the code entirely if it's been replaced by the router implementation.

Copilot · 2025-12-19T18:44:40Z

src/soa_builder/web/app.py

+    '''
    """Create a visit (UI form).


Similar to the previous issue, large blocks of code are commented out using triple quotes (lines 4014-4072). This creates inactive code that clutters the file. Remove this commented code since the functionality has been moved to the visits_router.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 29 out of 29 changed files in this pull request and generated 2 comments.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2025-12-19T18:46:37Z

tests/conftest.py

+- Forces tests to use a dedicated SQLite file: ``soa_builder_web_tests.db`` (or the
+        value of ``SOA_BUILDER_DB`` if set) so local/prod data are never touched.


Corrected spelling of 'remvoe' to 'remove' in the PR description.

Copilot · 2025-12-19T18:46:37Z

src/soa_builder/web/routers/visits.py

+    # cur.execute("SELECT COUNT(*) FROM visit WHERE soa_id=?", (soa_id,))
+    # order_index = cur.fetchone()[0] + 1


Remove commented-out code on lines 88-89. The old implementation should be removed rather than left as commented code, as the new implementation starting at line 92 is the active approach.

Suggested change

# cur.execute("SELECT COUNT(*) FROM visit WHERE soa_id=?", (soa_id,))

# order_index = cur.fetchone()[0] + 1

pendingintent added 8 commits December 18, 2025 11:43

Added endpoints for timeline instances

72da06d

Added encounter_uid to instances table; unit tests; update schemas

2b72de1

Added encounter select to the instances UI

77be202

Added epoch select to instances UI

cddd5c0

Generate the USDM JSON for ScheduledActivityInstances

dc1a177

Changed logic in create to always assign _uid as max(existing) + 1 an…

e6bd825

…d not use the first gap

Added db migration for label and description columns to visit table

3bac37c

Fixed test suite to use updated visit.label instead of visit.raw_header

d293978

Copilot AI review requested due to automatic review settings December 19, 2025 18:37

pendingintent self-assigned this Dec 19, 2025

pendingintent added bug Something isn't working documentation Improvements or additions to documentation enhancement New feature or request labels Dec 19, 2025

pendingintent added this to the v1.2-beta milestone Dec 19, 2025

Copilot AI reviewed Dec 19, 2025

View reviewed changes

Update src/soa_builder/web/templates/instances.html

5316e50

Updated variable reference Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI review requested due to automatic review settings December 19, 2025 18:41

pendingintent and others added 4 commits December 19, 2025 13:41

Update src/soa_builder/web/initialize_database.py

92db6f1

spelling Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update src/soa_builder/web/routers/visits.py

ee29011

removed commented-out code Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update src/soa_builder/web/routers/timings.py

5cb2301

removed commented-out code Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update src/soa_builder/web/routers/instances.py

2ec99d5

removed commented-out code Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI reviewed Dec 19, 2025

View reviewed changes

Update src/soa_builder/web/routers/instances.py

9bf6b07

spelling Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI review requested due to automatic review settings December 19, 2025 18:43

Copilot AI reviewed Dec 19, 2025

View reviewed changes

Update src/soa_builder/web/routers/visits.py

26e4e60

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI review requested due to automatic review settings December 19, 2025 18:45

Update src/soa_builder/web/app.py

afd052d

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot AI reviewed Dec 19, 2025

View reviewed changes

Removed commented out code

e3e45c3

pendingintent merged commit 6c05141 into master Dec 19, 2025
6 checks passed

		'''@app.delete("/soa/{soa_id}/visits/{visit_id}")
		def delete_visit(soa_id: int, visit_id: int):

		'''
		def ui_delete_visit(request: Request, soa_id: int, visit_id: int):



		@app.delete("/soa/{soa_id}/visits/{visit_id}")
		'''@app.delete("/soa/{soa_id}/visits/{visit_id}")

		- Forces tests to use a dedicated SQLite file: ``soa_builder_web_tests.db`` (or the
		value of ``SOA_BUILDER_DB`` if set) so local/prod data are never touched.

		# cur.execute("SELECT COUNT(*) FROM visit WHERE soa_id=?", (soa_id,))
		# order_index = cur.fetchone()[0] + 1

Conversation

pendingintent commented Dec 19, 2025

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Key Changes

Reviewed changes

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Dec 19, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants