Add in infons.type for passages

autocorpus/bioc_passages.py

@@ -1,70 +1,87 @@
-"""BioC Passage builder script."""
-
-
-class BioCPassage:
-    """BioC Passage builder class."""
-
-    @classmethod
-    def from_title(cls, title, offset):
-        """Creates a BioCPassage object from a title.
-
-        Args:
-            title (str): Passage title
-            offset (int): Passage offset
-
-        Returns:
-            (dict): BioCPassage object
-        """
-        title_passage = {
-            "section_heading": "",
-            "subsection_heading": "",
-            "body": title,
-            "section_type": [{"iao_name": "document title", "iao_id": "IAO:0000305"}],
-        }
-        return cls(title_passage, offset)
-
-    def __build_passage(self, passage, offset):
-        defaultkeys = ["section_heading", "subsection_heading", "body", "section_type"]
-        passage_dict = {
-            "offset": offset,
-            "infons": {},
-            "text": passage["body"],
-            "sentences": [],
-            "annotations": [],
-            "relations": [],
-        }
-        for key in passage.keys():
-            if key not in defaultkeys:
-                passage_dict["infons"][key] = passage[key]
-        # TODO: currently assumes section_heading and subsection_heading will always exist, should ideally check for existence.
-        #  Also doesn't account for subsubsection headings which might exist
-        if passage["section_heading"] != "":
-            passage_dict["infons"]["section_title_1"] = passage["section_heading"]
-        if passage["subsection_heading"] != "":
-            passage_dict["infons"]["section_title_2"] = passage["subsection_heading"]
-        counter = 1
-        for section_type in passage["section_type"]:
-            passage_dict["infons"][f"iao_name_{counter}"] = section_type["iao_name"]
-            passage_dict["infons"][f"iao_id_{counter}"] = section_type["iao_id"]
-            counter += 1
-
-        return passage_dict
-
-    def __init__(self, passage, offset):
-        """Construct a passage object from the provided passage dict and offset.
-
-        Args:
-            passage (dict): Article passage dictionary
-            offset (int): Passage offset to use
-        """
-        self.offset = 0
-        self.passage = self.__build_passage(passage, offset)
-        pass
-
-    def as_dict(self):
-        """Returns a dictionary representation of the passage.
-
-        Returns:
-            (dict): Dictionary representation of the passage
-        """
-        return self.passage
+"""BioC Passage builder script."""
+
+
+class BioCPassage:
+    """BioC Passage builder class."""
+
+    @classmethod
+    def from_title(cls, title, offset):
+        """Creates a BioCPassage object from a title.
+
+        Args:
+            title (str): Passage title
+            offset (int): Passage offset
+
+        Returns:
+            (dict): BioCPassage object
+        """
+        title_passage = {
+            "section_heading": "",
+            "subsection_heading": "",
+            "body": title,
+            "section_type": [{"iao_name": "document title", "iao_id": "IAO:0000305"}],
+        }
+        return cls(title_passage, offset)
+
+    def __build_passage(self, passage, offset):
+        defaultkeys = ["section_heading", "subsection_heading", "body", "section_type"]
+        passage_dict = {
+            "offset": offset,
+            "infons": {},
+            "text": passage["body"],
+            "sentences": [],
+            "annotations": [],
+            "relations": [],
+        }
+        for key in passage.keys():
+            if key not in defaultkeys:
+                passage_dict["infons"][key] = passage[key]
+        # TODO: currently assumes section_heading and subsection_heading will always exist, should ideally check for existence.
+        #  Also doesn't account for subsubsection headings which might exist
+        if passage["section_heading"] != "":
+            passage_dict["infons"]["section_title_1"] = passage["section_heading"]
+        if passage["subsection_heading"] != "":
+            passage_dict["infons"]["section_title_2"] = passage["subsection_heading"]
+        counter = 1
+        for section_type in passage["section_type"]:
+            passage_dict["infons"][f"iao_name_{counter}"] = section_type["iao_name"]
+            passage_dict["infons"][f"iao_id_{counter}"] = section_type["iao_id"]
+            counter += 1
+        if passage_dict["infons"]["iao_id_1"] == "IAO:0000305":
+            passage_dict["infons"]["type"] = (
+                "title_1"  # Suggest to make this (title) title_1 instead of front
+            )
+        elif passage_dict["infons"]["iao_id_1"] == "IAO:0000320":
+            passage_dict["infons"]["type"] = (
+                "ref"  # does not look as nice, consider keeping as paragraph
+            )
+        else:
+            passage_dict["infons"]["type"] = "paragraph"
+            # TODO: make optional input to AutoCORPus to have section (sub)headers a separate passage in the document.
+            # section headers: # Suggest to make this (section) title_2
+            # passage_dict["infons"]["type"] = "title_1"
+            # subsection headers: # Suggest to make this (subsection) title_3
+            # passage_dict["infons"]["type"] = "title_2"
+            # subsubsection headers: # suggest not to use this as we only look at 2 levels currently, see above.
+            # passage_dict["infons"]["type"] = "title_3"
+
+        return passage_dict
+
+    def __init__(self, passage, offset):
+        """Construct a passage object from the provided passage dict and offset.
+
+        Args:
+            passage (dict): Article passage dictionary
+            offset (int): Passage offset to use
+        """
+        self.offset = 0
+        self.passage = self.__build_passage(passage, offset)
+        pass
+
+    def as_dict(self):
+        """Returns a dictionary representation of the passage.
+
+        Returns:
+            (dict): Dictionary representation of the passage
+        """
+        return self.passage