feat: broker related entities

app/api/v1/endpoints/broker.py

@@ -181,6 +181,20 @@ def _lookup_scientific_name(db: Session, *, taxon_id: str | int) -> Optional[str
     return db.query(Organism.scientific_name).filter(Organism.taxon_id == tax_id_int).scalar()
 
 
+def _lookup_project_id(db: Session, *, entity_id: UUID) -> Optional[UUID]:
+    project_id = db.query(Experiment.project_id).filter(Experiment.id == entity_id).scalar()
+    if not project_id:
+        return None
+    return project_id
+
+
+def _lookup_sample_id(db: Session, *, entity_id: UUID) -> Optional[UUID]:
+    sample_id = db.query(Experiment.sample_id).filter(Experiment.id == entity_id).scalar()
+    if not sample_id:
+        return None
+    return sample_id
+
+
 def _create_new_draft_submission_after_rejection(
     db: Session,
     *,
@@ -303,15 +317,26 @@ def _get_accession_for_entity(
     """Lookup accession from accession_registry for a given entity."""
     if not entity_id:
         return None
-    return (
-        db.query(AccessionRegistry.accession)
-        .filter(
-            AccessionRegistry.entity_type == entity_type,
-            AccessionRegistry.entity_id == entity_id,
-            AccessionRegistry.authority == authority,
+    if entity_type == "sample":
+        return (
+            db.query(AccessionRegistry.secondary_accession)
+            .filter(
+                AccessionRegistry.entity_type == entity_type,
+                AccessionRegistry.entity_id == entity_id,
+                AccessionRegistry.authority == authority,
+            )
+            .scalar()
+        )
+    else:
+        return (
+            db.query(AccessionRegistry.accession)
+            .filter(
+                AccessionRegistry.entity_type == entity_type,
+                AccessionRegistry.entity_id == entity_id,
+                AccessionRegistry.authority == authority,
+            )
+            .scalar()
         )
-        .scalar()
-    )
 
 
 def _extract_broker_prerequisites(
@@ -384,6 +409,13 @@ def _build_contract_entity(
     files = _extract_run_files(prepared_payload) if entity_type == BrokerEntityType.RUN else None
     scientific_name = _lookup_scientific_name(db, taxon_id=taxon_id)
 
+    if entity_type == BrokerEntityType.EXPERIMENT:
+        project_id = _lookup_project_id(db, entity_id=entity_id)
+        sample_id = _lookup_sample_id(db, entity_id=entity_id)
+    else:
+        project_id = None
+        sample_id = None
+
     if entity_type in (BrokerEntityType.EXPERIMENT, BrokerEntityType.SAMPLE):
         title = _derive_claim_title(
             db, entity_type=entity_type, entity_id=entity_id, taxon_id=taxon_id
@@ -396,6 +428,8 @@ def _build_contract_entity(
         id=entity_id,
         taxon_id=str(taxon_id),
         scientific_name=scientific_name,
+        project_id=project_id,
+        sample_id=sample_id,
         payload=prepared_payload or None,
         prerequisites=prerequisites if _prerequisites_to_dict(prerequisites) else None,
         files=files,

app/schemas/broker_contract.py

@@ -36,6 +36,8 @@ class BrokerClaimEntity(BaseModel):
     id: UUID
     taxon_id: str
     scientific_name: Optional[str] = None
+    project_id: Optional[UUID] = None
+    sample_id: Optional[UUID] = None
     payload: Optional[Dict[str, Any]] = None
     prerequisites: Optional[BrokerPrerequisites] = None
     files: Optional[List[BrokerFileMetadata]] = None