Definitions should be enclosed in double quotes while updating via KG…

…CL (#520) * Definitions should be enclosed in double quotes * not needed * fixed definition to have double quotes * moved adding of quotes * reverted back to earlier solution * reverted everything * formatted and commented * removed comment * rolled back * removed unnecessary strip() * def double quotes while writing * undo line break * no need for double quote hardcoding * removing `def` specific code * remove single quotes from definition * Adding double quotes to new defs * strip single quotes * bumped setup-python version
INCATools · Apr 12, 2023 · 600fcf6 · 600fcf6
1 parent c1d4f55
commit 600fcf6
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Showing 4 changed files with 17 additions and 2 deletions.
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -49,7 +49,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

diff --git a/src/oaklib/implementations/pronto/pronto_implementation.py b/src/oaklib/implementations/pronto/pronto_implementation.py
@@ -837,6 +837,10 @@ def apply_patch(
             for syn in t.synonyms:
                 if syn.description == patch.old_value:
                     syn.description = patch.new_value
+        elif isinstance(patch, kgcl.NewTextDefinition):
+            t = self._entity(patch.about_node, strict=True)
+            xrefs = t.definition.xrefs if t.definition else []
+            t.definition = pronto.Definition(patch.new_value, xrefs=xrefs)
         elif isinstance(patch, kgcl.NodeTextDefinitionChange):
             t = self._entity(patch.about_node, strict=True)
             xrefs = t.definition.xrefs if t.definition else []

diff --git a/src/oaklib/implementations/simpleobo/simple_obo_implementation.py b/src/oaklib/implementations/simpleobo/simple_obo_implementation.py
@@ -802,12 +802,13 @@ def apply_patch(
             modified_entities.append(patch.about_node)
         elif isinstance(patch, kgcl.NewTextDefinition):
             t = self._stanza(patch.about_node, strict=True)
-            t.add_tag_value(TAG_DEFINITION, patch.new_value)
+            t.add_quoted_tag_value(TAG_DEFINITION, patch.new_value.strip("'"), xrefs=[])
             modified_entities.append(patch.about_node)
         elif isinstance(patch, kgcl.NodeTextDefinitionChange):
             t = self._stanza(patch.about_node, strict=True)
             for tv in t.tag_values:
                 if tv.tag == TAG_DEFINITION:
+                    # The strip() portion is to handle a KGCL bug
                     tv.replace_quoted_part(patch.new_value.strip("'"))
         elif isinstance(patch, kgcl.NewSynonym):
             t = self._stanza(patch.about_node, strict=True)

diff --git a/src/oaklib/implementations/simpleobo/simple_obo_parser.py b/src/oaklib/implementations/simpleobo/simple_obo_parser.py
@@ -520,6 +520,16 @@ def add_tag_value(self, tag: TAG, val: str) -> None:
         """
         self.tag_values.append(TagValue(tag, val))
 
+    def add_quoted_tag_value(self, tag: TAG, val: str, xrefs: List[str]) -> None:
+        """
+        Adds a tag-value pair
+
+        :param tag:
+        :param val:
+        :return:
+        """
+        self.tag_values.append(TagValue(tag, f"\"{val}\" [{','.join(xrefs)}]"))
+
     def add_tag_value_pair(self, tag: TAG, val1: str, val2: str) -> None:
         """
         Adds a tag-value pair where the value is a pair