closurizer 0.7.0__tar.gz → 0.7.2__tar.gz

{closurizer-0.7.0 → closurizer-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: closurizer
-Version: 0.7.0
+Version: 0.7.2
 Summary: Add closure expansion fields to kgx files following the Golr pattern
 Author: Kevin Schaper
 Author-email: kevin@tislab.org

{closurizer-0.7.0 → closurizer-0.7.2}/closurizer/closurizer.py

@@ -8,10 +8,14 @@ def edge_columns(field: str, include_closure_fields: bool =True):
     column_text = f"""
        {field}.name as {field}_label, 
        {field}.category as {field}_category,
-       {field}.namespace as {field}_namespace,
-       list_aggregate({field}_closure.closure, 'string_agg', '|') as {field}_closure,
-       list_aggregate({field}_closure_label.closure_label,'string_agg', '|') as {field}_closure_label,    
+       {field}.namespace as {field}_namespace,       
     """
+    if include_closure_fields:
+        column_text += f"""
+        {field}_closure.closure as {field}_closure,
+        {field}_closure_label.closure_label as {field}_closure_label,
+        """
+
     if field in ['subject', 'object']:
         column_text += f"""
         {field}.in_taxon as {field}_taxon,
@@ -152,17 +156,32 @@ def add_closure(kg_archive: str,
     """
     print(nodes_query)
 
+
     if not dry_run:
-        db.query(edges_query)
-        db.query(f"""
+
+
+        edge_closure_replacements = [
+            f"""
+            list_aggregate({field}_closure, 'string_agg', '|') as {field}_closure,
+            list_aggregate({field}_closure_label, 'string_agg', '|') as {field}_closure_label
+            """
+            for field in edge_fields
+        ]
+
+        edge_closure_replacements = "REPLACE (\n" + ",\n".join(edge_closure_replacements) + ")\n"
+
+        edges_export_query = f"""
         -- write denormalized_edges as tsv
-        copy (select * from denormalized_edges) to '{edges_output_file}' (header, delimiter '\t')
-        """)
-        db.query(nodes_query)
-        db.query(f"""
+        copy (select * {edge_closure_replacements} from denormalized_edges) to '{edges_output_file}' (header, delimiter '\t')
+        """
+        print(edges_export_query)
+        db.query(edges_export_query)
+
+        nodes_export_query = f"""
         -- write denormalized_nodes as tsv
         copy (select * from denormalized_nodes) to '{nodes_output_file}' (header, delimiter '\t')
-        """)
+        """
+        print(nodes_export_query)
 
 
         # Clean up extracted node & edge files

{closurizer-0.7.0 → closurizer-0.7.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "closurizer"
-version = "0.7.0"
+version = "0.7.2"
 description = "Add closure expansion fields to kgx files following the Golr pattern"
 authors = ["Kevin Schaper <kevin@tislab.org>"]