Remove redundant metadata (#685)

The metadata field (list of triples) in the pipeline Metadata class
was redundant. Document metadata triples already flow directly from
librarian to triple-store via emit_document_provenance() - they don't
need to pass through the extraction pipeline.

Additionally, chunker and PDF decoder were overwriting metadata to []
anyway, so any metadata passed through the pipeline was being
discarded.

Changes:
- Remove metadata field from Metadata dataclass
  (schema/core/metadata.py)
- Update all Metadata instantiations to remove metadata=[]
  parameter
- Remove metadata handling from translators (document_loading,
  knowledge)
- Remove metadata consumption from extractors (ontology, agent)
- Update gateway serializers and import handlers
- Update all unit, integration, and contract tests

tests/contract/conftest.py

@@ -95,8 +95,7 @@ def sample_message_data():
         "Metadata": {
             "id": "test-doc-123",
             "user": "test_user",
-            "collection": "test_collection",
-            "metadata": []
+            "collection": "test_collection"
         },
         "Term": {
             "type": IRI,

tests/contract/test_message_contracts.py

@@ -401,25 +401,6 @@ class TestMetadataMessageContracts:
         assert metadata.id == "test-doc-123"
         assert metadata.user == "test_user"
         assert metadata.collection == "test_collection"
-        assert isinstance(metadata.metadata, list)
-
-    def test_metadata_with_triples_contract(self, sample_message_data):
-        """Test Metadata with embedded triples contract"""
-        # Arrange
-        triple = Triple(**sample_message_data["Triple"])
-        metadata_data = {
-            "id": "doc-with-triples",
-            "user": "test_user",
-            "collection": "test_collection",
-            "metadata": [triple]
-        }
-
-        # Act & Assert
-        assert validate_schema_contract(Metadata, metadata_data)
-
-        metadata = Metadata(**metadata_data)
-        assert len(metadata.metadata) == 1
-        assert metadata.metadata[0].s.iri == "http://example.com/subject"
 
     def test_error_schema_contract(self):
         """Test Error schema contract"""

tests/contract/test_rows_cassandra_contracts.py

@@ -24,7 +24,6 @@ class TestRowsCassandraContracts:
             id="test-doc-001",
             user="test_user",
             collection="test_collection",
-            metadata=[]
         )
         
         test_object = ExtractedObject(
@@ -50,7 +49,6 @@ class TestRowsCassandraContracts:
         assert hasattr(test_object.metadata, 'id')
         assert hasattr(test_object.metadata, 'user')
         assert hasattr(test_object.metadata, 'collection')
-        assert hasattr(test_object.metadata, 'metadata')
         
         # Verify types
         assert isinstance(test_object.schema_name, str)
@@ -154,7 +152,6 @@ class TestRowsCassandraContracts:
                 id="serial-001",
                 user="test_user",
                 collection="test_coll",
-                metadata=[]
             ),
             schema_name="test_schema",
             values=[{"field1": "value1", "field2": "123"}],
@@ -234,7 +231,6 @@ class TestRowsCassandraContracts:
                 id="meta-001",
                 user="user123",  # -> keyspace
                 collection="coll456",  # -> partition key
-                metadata=[{"key": "value"}]
             ),
             schema_name="table789",  # -> table name
             values=[{"field": "value"}],
@@ -262,7 +258,6 @@ class TestRowsCassandraContractsBatch:
             id="batch-doc-001",
             user="test_user",
             collection="test_collection",
-            metadata=[]
         )
         
         batch_object = ExtractedObject(
@@ -308,10 +303,9 @@ class TestRowsCassandraContractsBatch:
         test_metadata = Metadata(
             id="empty-batch-001",
             user="test_user",
-            collection="test_collection", 
-            metadata=[]
+            collection="test_collection",
         )
-        
+
         empty_batch_object = ExtractedObject(
             metadata=test_metadata,
             schema_name="empty_schema",
@@ -332,9 +326,8 @@ class TestRowsCassandraContractsBatch:
             id="single-batch-001",
             user="test_user",
             collection="test_collection",
-            metadata=[]
         )
-        
+
         single_batch_object = ExtractedObject(
             metadata=test_metadata,
             schema_name="customer_records",
@@ -362,12 +355,11 @@ class TestRowsCassandraContractsBatch:
                 id="batch-serial-001",
                 user="test_user",
                 collection="test_coll",
-                metadata=[]
             ),
             schema_name="test_schema",
             values=[
                 {"field1": "value1", "field2": "123"},
-                {"field1": "value2", "field2": "456"},  
+                {"field1": "value2", "field2": "456"},
                 {"field1": "value3", "field2": "789"}
             ],
             confidence=0.92,
@@ -436,9 +428,8 @@ class TestRowsCassandraContractsBatch:
             id="partition-test-001",
             user="consistent_user",  # Same keyspace
             collection="consistent_collection",  # Same partition
-            metadata=[]
         )
-        
+
         batch_object = ExtractedObject(
             metadata=test_metadata,
             schema_name="partition_test",

tests/contract/test_structured_data_contracts.py

@@ -95,9 +95,8 @@ class TestStructuredDataSchemaContracts:
             id="structured-data-001",
             user="test_user",
             collection="test_collection",
-            metadata=[]
         )
-        
+
         # Act
         submission = StructuredDataSubmission(
             metadata=metadata,
@@ -121,9 +120,8 @@ class TestStructuredDataSchemaContracts:
             id="extracted-obj-001",
             user="test_user",
             collection="test_collection",
-            metadata=[]
         )
-        
+
         # Act
         obj = ExtractedObject(
             metadata=metadata,
@@ -147,9 +145,8 @@ class TestStructuredDataSchemaContracts:
             id="extracted-batch-001",
             user="test_user",
             collection="test_collection",
-            metadata=[]
         )
-        
+
         # Act - create object with multiple values
         obj = ExtractedObject(
             metadata=metadata,
@@ -180,11 +177,10 @@ class TestStructuredDataSchemaContracts:
         # Arrange
         metadata = Metadata(
             id="extracted-empty-001",
-            user="test_user", 
+            user="test_user",
             collection="test_collection",
-            metadata=[]
         )
-        
+
         # Act - create object with empty values array
         obj = ExtractedObject(
             metadata=metadata,
@@ -283,7 +279,6 @@ class TestStructuredEmbeddingsContracts:
             id="struct-embed-001",
             user="test_user",
             collection="test_collection",
-            metadata=[]
         )
 
         # Act
@@ -313,7 +308,7 @@ class TestStructuredDataSerializationContracts:
     def test_structured_data_submission_serialization(self):
         """Test StructuredDataSubmission serialization contract"""
         # Arrange
-        metadata = Metadata(id="test", user="user", collection="col", metadata=[])
+        metadata = Metadata(id="test", user="user", collection="col")
         submission_data = {
             "metadata": metadata,
             "format": "json",
@@ -328,7 +323,7 @@ class TestStructuredDataSerializationContracts:
     def test_extracted_object_serialization(self):
         """Test ExtractedObject serialization contract"""
         # Arrange
-        metadata = Metadata(id="test", user="user", collection="col", metadata=[])
+        metadata = Metadata(id="test", user="user", collection="col")
         object_data = {
             "metadata": metadata,
             "schema_name": "test_schema",
@@ -378,7 +373,7 @@ class TestStructuredDataSerializationContracts:
     def test_extracted_object_batch_serialization(self):
         """Test ExtractedObject batch serialization contract"""
         # Arrange
-        metadata = Metadata(id="test", user="user", collection="col", metadata=[])
+        metadata = Metadata(id="test", user="user", collection="col")
         batch_object_data = {
             "metadata": metadata,
             "schema_name": "test_schema",
@@ -397,7 +392,7 @@ class TestStructuredDataSerializationContracts:
     def test_extracted_object_empty_batch_serialization(self):
         """Test ExtractedObject empty batch serialization contract"""
         # Arrange
-        metadata = Metadata(id="test", user="user", collection="col", metadata=[])
+        metadata = Metadata(id="test", user="user", collection="col")
         empty_batch_data = {
             "metadata": metadata,
             "schema_name": "test_schema",