Merge pull request #251 from Knowledge-Graph-Hub/fix-bug-in-chembl-in…

…gest Fix folder naming in ChemblTransform
Knowledge-Graph-Hub · Jun 26, 2020 · 3c352ac · 3c352ac
2 parents 85bf8fc + 1adcac6
commit 3c352ac
Showing 1 changed file with 6 additions and 5 deletions.
diff --git a/kg_covid_19/transform_utils/chembl/chembl_transform.py b/kg_covid_19/transform_utils/chembl/chembl_transform.py
@@ -16,8 +16,9 @@ class ChemblTransform(Transform):
     """
 
     def __init__(self, input_dir: str = None, output_dir: str = None):
-        source_name = 'ChEMBL SARS-CoV-2 subset'
+        source_name = 'ChEMBL'
         super().__init__(source_name, input_dir, output_dir)
+        self.subset = 'SARS-CoV-2 subset'
         self._end = None
         self._node_header: Set = set()
         self._edge_header: Set = set()
@@ -139,7 +140,7 @@ def parse_chembl_activity(self, data: List):
             edge_properties['assay'] = f"CHEMBL.ASSAY:{edge_properties['assay']}"
             if edge_properties['uo_units']:
                 edge_properties['uo_units'] = edge_properties['uo_units'].replace('_', ':')
-            edge_properties['provided_by'] = self.source_name
+            edge_properties['provided_by'] = f"{self.source_name} {self.subset}"
             edges.append(edge_properties)
         return edges
 
@@ -170,7 +171,7 @@ def parse_chembl_molecules(self, data: List):
             node_properties = self.parse_doc_fields(record['_source'], allowed_properties, remap)
             node_properties['category'] = '|'.join(node_category)
             node_properties['id'] = f"CHEMBL.COMPOUND:{molecule_id}"
-            node_properties['provided_by'] = self.source_name
+            node_properties['provided_by'] = f"{self.source_name} {self.subset}"
             nodes.append(node_properties)
         return nodes
 
@@ -208,7 +209,7 @@ def parse_chembl_assay(self, data: List):
             node_properties['node_type'] = node_type
             if node_properties['bao_format']:
                 node_properties['bao_format'] = node_properties['bao_format'].replace('_', ':')
-            node_properties['provided_by'] = self.source_name
+            node_properties['provided_by'] = f"{self.source_name} {self.subset}"
             nodes.append(node_properties)
         return nodes
 
@@ -239,7 +240,7 @@ def parse_chembl_document(self, data: List):
             else:
                 node_properties['id'] = f"CHEMBL.DOCUMENT:{document_id}"
             node_properties['category'] = '|'.join(node_category)
-            node_properties['provided_by'] = self.source_name
+            node_properties['provided_by'] = f"{self.source_name} {self.subset}"
             nodes.append(node_properties)
         return nodes