Merge pull request #2 from Knowledge-Graph-Hub/schema_and_test_tweaks

minor changes to schema and test merge.yaml to get a passing test

kg_microbe_merge/schema/merge_datamodel.py

@@ -1,5 +1,5 @@
 # Auto generated from merge_schema.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-08-05T20:11:15
+# Generation date: 2024-08-06T07:55:55
 # Schema: KGMergeSchema
 #
 # id: http://example.org/kg-merge-schema

kg_microbe_merge/schema/merge_schema.yaml

@@ -45,6 +45,7 @@ classes:
         description: Source graphs to be merged
         multivalued: true
         range: SourceGraph
+        inlined_as_list: true
       operations:
         description: Operations to perform on the merged graph
         range: Operations
@@ -64,7 +65,7 @@ classes:
       input:
         description: Input files for the source graph
         range: InputFiles
-  
+
   InputFiles:
     description: Input files for the source graph
     attributes:
@@ -73,7 +74,6 @@ classes:
       filename:
         description: List of filenames for the input files
         multivalued: true
-        inlined_as_list: true
 
   Operations:
     description: Details of an operation to perform on the merged graph
@@ -94,11 +94,9 @@ classes:
       node_facet_properties:
         description: List of node facet properties
         multivalued: true
-        inlined_as_list: true
       edge_facet_properties:
         description: List of edge facet properties
         multivalued: true
-        inlined_as_list: true
 
   Destination:
     description: Details of a destination for the merged graph

tests/data/test_merge_schema.yaml

@@ -0,0 +1,53 @@
+configuration:
+  output_directory: data/merged
+  checkpoint: false
+  curie_map:
+    # define non-canonical CURIE to IRI mappings (for RDF)
+  node_properties:
+    # define predicates that are to be treated as direct node properties (for RDF)
+  predicate_mappings:
+    # map non-canonical predicates to a property name (for RDF)
+  property_types:
+    # define the type for non-canonical properties for RDF export
+
+merged_graph:
+  name: kg-microbe graph
+  source:
+    - name: "NCBITaxon"
+      input:
+        format: tsv
+        filename:
+          - data/transformed/ontologies/ncbitaxon_nodes.tsv
+          - data/transformed/ontologies/ncbitaxon_edges.tsv
+    - name: "CHEBI"
+      input:
+        format: tsv
+        filename:
+          - data/transformed/ontologies/chebi_nodes.tsv
+          - data/transformed/ontologies/chebi_edges.tsv
+    - name: "ENVO"
+      input:
+        format: tsv
+        filename:
+          - data/transformed/ontologies/envo_nodes.tsv
+          - data/transformed/ontologies/envo_edges.tsv
+    - name: "GO"
+      input:
+        format: tsv
+        filename:
+          - data/transformed/ontologies/go_nodes.tsv
+          - data/transformed/ontologies/go_edges.tsv
+  operations:
+    - name: kgx.graph_operations.summarize_graph.generate_graph_stats
+      args:
+        graph_name: kg-microbe graph
+        filename: merged_graph_stats.yaml
+        node_facet_properties:
+          - provided_by
+        edge_facet_properties:
+          - provided_by
+          - source
+  destination:
+    - format: tsv
+      compression: tar.gz
+      filename: merged-kg

tests/test_merge_schema.py

@@ -0,0 +1,22 @@
+"""Data test."""
+import os
+import glob
+import unittest
+
+from linkml_runtime.loaders import yaml_loader
+from kg_microbe_merge.schema.merge_datamodel import MergeKG
+
+ROOT = os.path.join(os.path.dirname(__file__), '..')
+DATA_DIR = os.path.join(ROOT, "tests", "data")
+
+EXAMPLE_FILES = glob.glob(os.path.join(DATA_DIR, 'test_merge_schema.yaml'))
+
+
+class TestData(unittest.TestCase):
+    """Test data and datamodel."""
+
+    def test_data(self):
+        """Data test."""
+        for path in EXAMPLE_FILES:
+            obj = yaml_loader.load(path, target_class=MergeKG)
+            assert obj