closurizer 0.6.0__tar.gz → 0.7.1__tar.gz

{closurizer-0.6.0 → closurizer-0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: closurizer
-Version: 0.6.0
+Version: 0.7.1
 Summary: Add closure expansion fields to kgx files following the Golr pattern
 Author: Kevin Schaper
 Author-email: kevin@tislab.org
@@ -11,6 +11,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: SQLAlchemy (>=1.4.37,<2.0.0)
 Requires-Dist: click (>=8,<9)
-Requires-Dist: duckdb (>=0.10.2,<0.11.0)
+Requires-Dist: duckdb

{closurizer-0.6.0 → closurizer-0.7.1}/closurizer/cli.py

@@ -11,6 +11,7 @@ from closurizer.closurizer import add_closure
 @click.option('--additional-node-constraints', required=False,
               help='additional where clause constraints to apply to the generation of the denormalized nodes output')
 @click.option('--edge-fields', multiple=True, help='edge fields to expand with closure IDs, labels, etc')
+@click.option('--edge-fields-to-label', multiple=True, help='edge fields to with category, label, etc but not full closure exansion')
 @click.option('--node-fields', multiple=True, help='node fields to expand with closure IDs, labels, etc')
 @click.option('--grouping-fields', multiple=True, help='fields to populate a single value grouping_key field')
 @click.option('--dry-run', is_flag=True, help='A dry run will not write the output file, but will print the SQL query')
@@ -21,11 +22,13 @@ def main(kg: str,
          additional_node_constraints: str = None,
          dry_run: bool = False,
          edge_fields: List[str] = None,
+         edge_fields_to_label: List[str] = None,
          node_fields: List[str] = None,
          grouping_fields: List[str] = None):
     add_closure(kg_archive=kg,
                 closure_file=closure,
                 edge_fields=edge_fields,
+                edge_fields_to_label=edge_fields_to_label,
                 node_fields=node_fields,
                 edges_output_file=edges_output,
                 nodes_output_file=nodes_output,

{closurizer-0.6.0 → closurizer-0.7.1}/closurizer/closurizer.py

@@ -1,17 +1,21 @@
-from typing import List
+from typing import List, Optional
 
 import os
 import tarfile
 import duckdb
 
-def edge_columns(field):
+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,
@@ -19,14 +23,14 @@ def edge_columns(field):
         """
     return column_text
 
-def edge_joins(field):
+def edge_joins(field: str, include_closure_joins: bool =True):
     return f"""
     left outer join nodes as {field} on edges.{field} = {field}.id
     left outer join closure_id as {field}_closure on {field}.id = {field}_closure.id
     left outer join closure_label as {field}_closure_label on {field}.id = {field}_closure_label.id
     """
 
-def evidence_sum(evidence_fields):
+def evidence_sum(evidence_fields: List[str]):
     """ Sum together the length of each field after splitting on | """
     evidence_count_sum = "+".join([f"ifnull(len(split({field}, '|')),0)" for field in evidence_fields])
     return f"{evidence_count_sum} as evidence_count,"
@@ -73,12 +77,13 @@ def add_closure(kg_archive: str,
                 closure_file: str,
                 nodes_output_file: str,
                 edges_output_file: str,
-                node_fields: List[str] = None,
+                node_fields: List[str] = [],
                 edge_fields: List[str] = ['subject', 'object'],
-                additional_node_constraints: str = None,
+                edge_fields_to_label: List[str] = [],
+                additional_node_constraints: Optional[str] = None,
                 dry_run: bool  = False,
-                evidence_fields: List[str] = None,
-                grouping_fields: List[str] = None
+                evidence_fields: List[str] = ['has_evidence', 'publications'],
+                grouping_fields: List[str] = ['subject', 'negated', 'predicate', 'object']
                 ):
     print("Generating closure KG...")
     print(f"kg_archive: {kg_archive}")
@@ -86,16 +91,6 @@ def add_closure(kg_archive: str,
 
     db = duckdb.connect(database='monarch-kg.duckdb')
 
-    if edge_fields is None or len(edge_fields) == 0:
-        edge_fields = ['subject', 'object']
-
-    if evidence_fields is None or len(evidence_fields) == 0:
-        evidence_fields = ['has_evidence', 'publications']
-
-    if grouping_fields is None or len(grouping_fields) == 0:
-        grouping_fields = ['subject', 'negated', 'predicate', 'object']
-
-
     if not dry_run:
         print(f"fields: {','.join(edge_fields)}")
         print(f"output_file: {edges_output_file}")
@@ -139,10 +134,12 @@ def add_closure(kg_archive: str,
     create or replace table denormalized_edges as
     select edges.*, 
            {"".join([edge_columns(field) for field in edge_fields])}
+           {"".join([edge_columns(field, include_closure_fields=False) for field in edge_fields_to_label])} 
            {evidence_sum(evidence_fields)}
            {grouping_key(grouping_fields)}  
     from edges
         {"".join([edge_joins(field) for field in edge_fields])}
+        {"".join([edge_joins(field, include_closure_joins=False) for field in edge_fields_to_label])}
     """
 
     print(edges_query)

{closurizer-0.6.0 → closurizer-0.7.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "closurizer"
-version = "0.6.0"
+version = "0.7.1"
 description = "Add closure expansion fields to kgx files following the Golr pattern"
 authors = ["Kevin Schaper <kevin@tislab.org>"]
 
@@ -8,7 +8,7 @@ authors = ["Kevin Schaper <kevin@tislab.org>"]
 python = "^3.8"
 click = "^8"
 SQLAlchemy = "^1.4.37"
-duckdb = "^0.10.2"
+duckdb = "*"
 
 [tool.poetry.dev-dependencies]