fixed bug, source-type was not passed down

README.md

@@ -44,6 +44,21 @@ Commands:
   map-data       Map data in a source schema using a transformation.
 ```
 
+### map-data
+
+```
+cd tests/input/examples/personinfo_basic
+linkml-tr map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml  data/Container-001.yaml
+```
+
+### derive-schema
+
+```
+cd tests/input/examples/personinfo_basic
+linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
+```
+
+
 ## Examples
 
 See the tests folder for most up to date examples

src/linkml_transformer/cli/cli.py

@@ -57,27 +57,6 @@ def main(verbose: int, quiet: bool):
     logger.info(f"Logger {logger.name} set to level {logger.level}")
 
 
-@main.command()
-@output_option
-@transformer_specification_option
-@output_format_options
-@click.argument("schema")
-def derive_schema(schema, transformer_specification, output, output_format, **kwargs):
-    """Derive a schema from a source schema and a mapping."""
-    logging.info(f"Transforming {schema} using {transformer_specification}")
-    tr = SchemaMapper()
-    tr.source_schemaview = SchemaView(schema)
-    specification = yaml_loader.load(
-        transformer_specification, target_class=TransformationSpecification
-    )
-    target_schema = tr.derive_schema(specification)
-    if output:
-        file = open(output, "w", encoding="utf-8")
-    else:
-        file = sys.stdout
-    file.write(yaml_dumper.dumps(target_schema))
-
-
 @main.command()
 @output_option
 @transformer_specification_option
@@ -106,13 +85,47 @@ def map_data(
     with open(input) as file:
         input_obj = yaml.safe_load(file)
     tr.index(input_obj, source_type)
-    tr_obj = tr.transform(input_obj)
+    tr_obj = tr.transform(input_obj, source_type)
     if output:
         file = open(output, "w", encoding="utf-8")
     else:
         file = sys.stdout
     file.write(yaml_dumper.dumps(tr_obj))
 
 
+@main.command()
+@output_option
+@transformer_specification_option
+@output_format_options
+@click.argument("schema")
+def derive_schema(schema, transformer_specification, output, output_format, **kwargs):
+    """Derive a schema from a source schema and a transformation specification.
+
+    This can be thought of as "copying" the source to a target, using the transformation
+    specification as a "patch"
+
+    Notes:
+
+        the implementation is currently incomplete; the derived schema may not be valid
+        linkml, e.g. there may be "dangling" references.
+
+    Example:
+
+        linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
+    """
+    logging.info(f"Transforming {schema} using {transformer_specification}")
+    tr = SchemaMapper()
+    tr.source_schemaview = SchemaView(schema)
+    specification = yaml_loader.load(
+        transformer_specification, target_class=TransformationSpecification
+    )
+    target_schema = tr.derive_schema(specification)
+    if output:
+        file = open(output, "w", encoding="utf-8")
+    else:
+        file = sys.stdout
+    file.write(yaml_dumper.dumps(target_schema))
+
+
 if __name__ == "__main__":
     main()

src/linkml_transformer/utils/inverter.py

@@ -0,0 +1,5 @@
+from linkml_transformer.datamodel.transformer_model import TransformationSpecification
+
+
+def invert_transformation_specification(specification: TransformationSpecification) -> TransformationSpecification:
+    raise NotImplementedError

tests/test_transformer/test_object_transformer.py

@@ -1,8 +1,10 @@
+import itertools
 import unittest
 
 import yaml
 from linkml_runtime import SchemaView
 from linkml_runtime.dumpers import yaml_dumper
+from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition, SchemaDefinition
 from linkml_runtime.loaders import yaml_loader
 
 import tests.input.examples.flattening.model.denormalized_model as sssom_tgt_dm
@@ -224,6 +226,35 @@ def test_denormalized_object_transform(self):
         self.assertEqual(mapping.object_id, "Y:1")
         self.assertEqual(mapping.object_name, "y1")
 
+    @unittest.skip("TODO")
+    def test_cardinalities(self):
+        tf = [True, False]
+        class_name = "MyClass"
+        att_name = "my_att"
+        val = "v1"
+        for source_multivalued, target_multivalued in itertools.product(tf, tf):
+            def mk(mv: bool):
+                cls = ClassDefinition(class_name)
+                att = SlotDefinition(att_name, multivalued=mv)
+                cls.attributes[att.name] = att
+                schema = SchemaDefinition(name="test", id="test", classes=[cls])
+                return schema
+            source_schema = mk(source_multivalued)
+            target_schema = mk(target_multivalued)
+            specification = TransformationSpecification("test")
+            cd = ClassDerivation(class_name, populated_from=class_name)
+            specification.class_derivations[class_name] = cd
+            cd.slot_derivations[att_name] = SlotDerivation(att_name, populated_from=class_name)
+            source_instance = {att_name: [val] if source_multivalued else val}
+            tr = ObjectTransformer(specification=specification,
+                                   source_schemaview=SchemaView(source_schema))
+            target_instance = tr.transform(source_instance, class_name)
+            print(target_instance)
+
+
+
+
+
 
 if __name__ == "__main__":
     unittest.main()