add derived transformations spec example and file based transformatio…

…n spec

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "linkml-map"
-version = "0.0.0"
+version = "0.3.8.post1.dev0+aed82cf"
 description = "a framework for specifying and executing mappings between data models"
 authors = ["cmungall <[email protected]>"]
 readme = "README.md"
@@ -12,6 +12,7 @@ asteval = "^0.9.29"
 deepdiff = "^6.7.1"
 pydantic = ">=2.0.0"
 ucumvert = "^0.1.1"
+linkml-model = "^1.8.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.3.1"
@@ -24,7 +25,7 @@ mkdocs-windmill = "*"
 tox = "*"
 
 [tool.poetry-dynamic-versioning]
-enable = true
+enable = false
 vcs = "git"
 style = "pep440"
 

tests/test_transformer/test_biolink_subsetting.py

@@ -1,31 +1,62 @@
 from pathlib import Path
+from typing import List
+from pytest import fixture
+
 from linkml_runtime.dumpers import yaml_dumper
 import pytest
 from pprint import pprint
-from linkml_map.datamodel.transformer_model import TransformationSpecification
+from linkml_map.datamodel.transformer_model import TransformationSpecification, ClassDerivation, SlotDerivation
 from linkml_map.inference.schema_mapper import SchemaMapper
 from linkml_map.session import Session
 from linkml_runtime.utils.schemaview import SchemaView
 from src.linkml_map.utils.loaders import load_specification
 from linkml_map.transformer.transformer import Transformer
 from linkml_map.utils.multi_file_transformer import Transformation
+from linkml_model.meta import ClassDefinition
+from linkml.utils.schema_builder import SchemaBuilder
+from linkml_runtime.utils.formatutils import camelcase
 
+REPO_ROOT = Path(__file__).resolve().parent.parent
 
 
-
-def test_biolink_subsetting():
-    # Test that the subsetting of the Biolink Model is correct
-    # This test is a placeholder and should be replaced with a real test
-    repo_root = Path(__file__).resolve().parent.parent
+@fixture
+def biolink_schema():
     schema_url = "https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml"
     sv = SchemaView(schema_url)
+    return sv
+
+def test_biolink_subsetting_manual(biolink_schema):
+
+    transform_file = REPO_ROOT / "input/examples/biolink/transform/biolink-example-profile.transform.yaml"
+    # Initialize Session and SchemaBuilder
+    session = Session()
+
+    # Set the source schema in the session
+    session.set_source_schema(biolink_schema)
+
+    tr_spec = load_specification(transform_file)
+    mapper = SchemaMapper()
+    mapper.source_schemaview = biolink_schema
+
+    target_schema_obj = mapper.derive_schema(specification=tr_spec,
+                                             target_schema_id="biolink-profile",
+                                             target_schema_name="BiolinkProfile")
 
-    transform_file = repo_root / "input/examples/biolink/transform/biolink-example-profile.transform.yaml"
+
+    yaml_dumper.dump(target_schema_obj, str("biolink-profile.yaml"))
+
+    transformed_sv = SchemaView("biolink-profile.yaml")
+
+    for class_name in transformed_sv.all_classes():
+        print(class_name)
+
+
+def test_biolink_subset_auto(biolink_schema):
     # Initialize Session and SchemaBuilder
     session = Session()
 
     # Set the source schema in the session
-    session.set_source_schema(sv)
+    session.set_source_schema(biolink_schema)
 
     SUBSET_CLASSES = ["gene",
                       "disease",
@@ -36,13 +67,37 @@ def test_biolink_subsetting():
                       "phenotypic feature",
                       ]
 
+    class_derivations = get_biolink_class_derivations(biolink_schema, SUBSET_CLASSES)
+
+    ts = TransformationSpecification(class_derivations=class_derivations)
 
-    tr_spec = load_specification(transform_file)
     mapper = SchemaMapper()
-    mapper.source_schemaview = sv
+    mapper.source_schemaview = biolink_schema
 
-    target_schema_obj = mapper.derive_schema(specification=tr_spec,
+    target_schema_obj = mapper.derive_schema(specification=ts,
                                              target_schema_id="biolink-profile",
                                              target_schema_name="BiolinkProfile")
 
     yaml_dumper.dump(target_schema_obj, str("biolink-profile.yaml"))
+
+    transformed_sv = SchemaView("biolink-profile.yaml")
+
+    for class_name in transformed_sv.all_classes():
+        print(class_name)
+
+
+
+# Function to get Biolink class definitions
+def get_biolink_class_derivations(sv, subset_classes) -> dict:
+    # Example implementation to fetch class definitions
+    # This should be replaced with the actual implementation
+    class_derivations ={}
+    for class_name in subset_classes:
+        class_derivation = ClassDerivation(populated_from=class_name,
+                                           name=camelcase(class_name))
+        for slot in sv.get_class(class_name).slots:
+            slot_derivation = SlotDerivation(populated_from=slot, name=camelcase(slot))
+            class_derivation.slot_derivations[slot] = slot_derivation
+        class_derivations[camelcase(class_name)] = class_derivation
+    return class_derivations
+