Merge pull request #29 from monarch-initiative/mapping-flip

Changed assumption about direction of replacement in mapping files.
monarch-initiative · Sep 24, 2022 · 3c5962a · 3c5962a
2 parents a95f1c5 + 49c86dd
commit 3c5962a
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/cat_merge/mapping_utils.py b/cat_merge/mapping_utils.py
@@ -5,16 +5,16 @@
 def apply_mappings(edges: DataFrame, mapping: DataFrame):
 
     edges.rename(columns={'subject':'original_subject'}, inplace=True)
-    subject_mapping = mapping.rename(columns={'object_id':'subject'})
-    subject_mapping = subject_mapping[["subject","subject_id"]]
-    edges = edges.merge(subject_mapping, how='left', left_on='original_subject', right_on='subject_id').drop(['subject_id'],axis=1)
+    subject_mapping = mapping.rename(columns={'subject_id':'subject'})
+    subject_mapping = subject_mapping[["subject","object_id"]]
+    edges = edges.merge(subject_mapping, how='left', left_on='original_subject', right_on='object_id').drop(['object_id'],axis=1)
     edges['subject'] = np.where(edges.subject.isnull(), edges.original_subject, edges.subject)
     edges['original_subject'] = np.where(edges.subject == edges.original_subject, None, edges.original_subject)
 
     edges.rename(columns={'object':'original_object'}, inplace=True)
-    object_mapping = mapping.rename(columns={'object_id':'object'})
-    object_mapping = object_mapping[["object", "subject_id"]]
-    edges = edges.merge(object_mapping, how='left', left_on='original_object', right_on='subject_id').drop(['subject_id'],axis=1)
+    object_mapping = mapping.rename(columns={'subject_id':'object'})
+    object_mapping = object_mapping[["object", "object_id"]]
+    edges = edges.merge(object_mapping, how='left', left_on='original_object', right_on='object_id').drop(['object_id'],axis=1)
     edges['object'] = np.where(edges.object.isnull(), edges.original_object, edges.object)
     edges['original_object'] = np.where(edges.object == edges.original_object, None, edges.original_object)
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cat-merge"
-version = "0.1.15"
+version = "0.1.16"
 description = ""
 authors = [
     "Monarch Initiative <info@monarchinitiative.org>",

diff --git a/tests/unit/test_apply_mappings.py b/tests/unit/test_apply_mappings.py
@@ -18,13 +18,13 @@ def edges():
 def mapping():
     mapping = u"""\
     subject_id  predicate       object_id
-    XGene:1     skos:exactMatch Gene:1
-    XGene:2     skos:exactMatch Gene:2
-    XGene:3     skos:exactMatch Gene:3
-    XDisease:1  skos:exactMatch Disease:1
-    XDisease:2  skos:exactMatch Disease:2
-    XDisease:3  skos:exactMatch Disease:3
-    XDisease:4  skos:exactMatch Disease:4
+    Gene:1     skos:exactMatch XGene:1
+    Gene:2     skos:exactMatch XGene:2
+    Gene:3     skos:exactMatch XGene:3
+    Disease:1  skos:exactMatch XDisease:1
+    Disease:2  skos:exactMatch XDisease:2
+    Disease:3  skos:exactMatch XDisease:3
+    Disease:4  skos:exactMatch XDisease:4
     """
     return string_df(mapping)