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

trustgraph-flow/trustgraph/extract/kg/agent/extract.py

@@ -104,7 +104,6 @@ class Processor(FlowProcessor):
         tpls = Triples(
             metadata = Metadata(
                 id = metadata.id,
-                metadata = [],
                 user = metadata.user,
                 collection = metadata.collection,
             ),
@@ -117,7 +116,6 @@ class Processor(FlowProcessor):
         ecs = EntityContexts(
             metadata = Metadata(
                 id = metadata.id,
-                metadata = [],
                 user = metadata.user,
                 collection = metadata.collection,
             ),
@@ -216,10 +214,6 @@ class Processor(FlowProcessor):
                 extraction_data, v.metadata
             )
 
-            # Put document metadata into triples
-            for t in v.metadata.metadata:
-                triples.append(t)
-        
             # Emit outputs
             if triples:
                 await self.emit_triples(flow("triples"), v.metadata, triples)

trustgraph-flow/trustgraph/extract/kg/definitions/extract.py

@@ -218,7 +218,6 @@ class Processor(FlowProcessor):
                     flow("triples"),
                     Metadata(
                         id=v.metadata.id,
-                        metadata=[],
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),
@@ -232,7 +231,6 @@ class Processor(FlowProcessor):
                     flow("entity-contexts"),
                     Metadata(
                         id=v.metadata.id,
-                        metadata=[],
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),

trustgraph-flow/trustgraph/extract/kg/ontology/extract.py

@@ -306,10 +306,6 @@ class Processor(FlowProcessor):
                 flow, chunk, ontology_subset, prompt_variables
             )
 
-            # Add metadata triples
-            for t in v.metadata.metadata:
-                triples.append(t)
-
             # Generate ontology definition triples
             ontology_triples = self.build_ontology_triples(ontology_subset)
 
@@ -558,7 +554,6 @@ class Processor(FlowProcessor):
         t = Triples(
             metadata=Metadata(
                 id=metadata.id,
-                metadata=[],
                 user=metadata.user,
                 collection=metadata.collection,
             ),
@@ -571,7 +566,6 @@ class Processor(FlowProcessor):
         ec = EntityContexts(
             metadata=Metadata(
                 id=metadata.id,
-                metadata=[],
                 user=metadata.user,
                 collection=metadata.collection,
             ),

trustgraph-flow/trustgraph/extract/kg/relationships/extract.py

@@ -219,7 +219,6 @@ class Processor(FlowProcessor):
                     flow("triples"),
                     Metadata(
                         id=v.metadata.id,
-                        metadata=[],
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),

trustgraph-flow/trustgraph/extract/kg/rows/processor.py

@@ -272,7 +272,6 @@ class Processor(FlowProcessor):
                     extracted = ExtractedObject(
                         metadata=Metadata(
                             id=f"{v.metadata.id}:{schema_name}",
-                            metadata=[],
                             user=v.metadata.user,
                             collection=v.metadata.collection,
                         ),