Predicate modifier fix (#389)

* Add `predicate_modifier` as blank column if absent while `remove_mappings`

* formatted

* fixed flake8 error

* Add predicate_modifier check wherever KEY_FEATURES are used.

* replaced previous logic

* fixed error

* mkdir sssom before copying into via workflow

* moved from makefile to workflow

* install dependencies

* removed poetry just installed black

* removed extra optional column

.github/workflows/update_context.yml

@@ -13,11 +13,18 @@ jobs:
       - name: Work around permission issue
         run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
 
+      - name: Install Black
+        run: |
+          pip install --upgrade pip
+          pip install black
+
       - name: Update schema files
         run: make all_schema
 
       - name: Update sssom context
-        run: make deploy-dm
+        run: |
+          mkdir -p sssom
+          make deploy-dm
 
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v3

src/sssom/util.py

@@ -189,16 +189,20 @@ def clean_prefix_map(self, strict: bool = True) -> None:
             # self.df = filter_out_prefixes(self.df, missing_prefixes)
         self.prefix_map = new_prefixes
 
-    def remove_mappings(self, msdf: "MappingSetDataFrame"):
+    def remove_mappings(self, msdf: "MappingSetDataFrame") -> None:
         """Remove mappings in right msdf from left msdf.
 
         :param msdf: MappingSetDataframe object to be removed from primary msdf object.
         """
+        merge_on = KEY_FEATURES.copy()
+        if self.df is not None and PREDICATE_MODIFIER not in self.df.columns:
+            merge_on.remove(PREDICATE_MODIFIER)
+
         self.df = (
             pd.merge(
                 self.df,
                 msdf.df,
-                on=KEY_FEATURES,
+                on=merge_on,
                 how="outer",
                 suffixes=("", "_2"),
                 indicator=True,