Merge pull request #329 from seattleflu/sample-api-update

Sample API update

Author: davereinhart

lib/id3c/api/datastore.py

@@ -468,6 +468,8 @@ def store_sample(session: DatabaseSession, sample: dict) -> Any:
         collection_barcode = sample.pop("collection_id", None)
         collection_identifier = find_identifier(session, collection_barcode) if collection_barcode else None
 
+        access_role = sample.pop("access_role", None)
+
         result = {
             "sample_barcode": sample_barcode,
             "collection_barcode": collection_barcode
@@ -517,7 +519,8 @@ def store_sample(session: DatabaseSession, sample: dict) -> Any:
                     collection_identifier       = collection_identifier.uuid if collection_identifier else None,
                     collection_date             = collected_date,
                     encounter_id                = None,
-                    additional_details          = sample)
+                    additional_details          = sample,
+                    access_role                 = access_role)
 
             result["sample"] = sample
             result["status"] = status

lib/id3c/api/schemas.py

@@ -90,7 +90,10 @@
         },
         "notes": {
             "type": "string"
-        }
+        },
+        "access_role": {
+            "type": "string"
+        },
     },
     "anyOf": [
         { "required":

lib/id3c/api/static/index.html

@@ -143,7 +143,14 @@ <h3 class="code">POST /v1/warehouse/sample</h3>
             "collection_matrix": "dry"
         }
         </pre>
-
+        <p>An "access_role" value is required for samples from specific projects to enable row-level security:
+          <pre>
+          {
+            ...
+            "access_role": "some_db_role"
+            ...
+          }
+        </pre>
     <h3 class="code">GET /v1/warehouse/identifier-set-uses</h3>
     <p>Retrieve metadata about all identifier set uses.
 

lib/id3c/db/__init__.py

@@ -186,7 +186,8 @@ def upsert_sample(db: DatabaseSession,
                   collection_identifier: Optional[str],
                   collection_date: Optional[str],
                   encounter_id: Optional[int],
-                  additional_details: dict) -> Tuple[Any, str]:
+                  additional_details: dict,
+                  access_role: Optional[str] = None) -> Tuple[Any, str]:
     """
     Upsert sample by its *identifier* and/or *collection_identifier*.
     An existing sample has its *identifier*, *collection_identifier*,
@@ -200,13 +201,15 @@ def upsert_sample(db: DatabaseSession,
         "collection_date": collection_date,
         "encounter_id": encounter_id,
         "additional_details": Json(additional_details) if additional_details else None,
+        "additional_details_without_prov": Json({k: additional_details[k] for k in additional_details if k != '_provenance'}) if additional_details else None,
+        "access_role": access_role,
     }
 
     # Look for existing sample(s)
     with db.cursor() as cursor:
         cursor.execute("""
             select
-                sample_id as id, identifier, collection_identifier, encounter_id, details,
+                sample_id as id, identifier, collection_identifier, encounter_id, details, access_role,
                 row (
                     identifier,
                     collection_identifier
@@ -223,8 +226,9 @@ def upsert_sample(db: DatabaseSession,
                 row(
                     coalesce(%(collection_date)s, collected)::timestamp,
                     coalesce(%(encounter_id)s::integer, encounter_id),
-                    coalesce(details, '{}'::jsonb) || coalesce(%(additional_details)s, '{}')::jsonb
-                )::text as metadata_changed
+                    coalesce(details, '{}'::jsonb) || coalesce(%(additional_details_without_prov)s, '{}')::jsonb
+                )::text as metadata_changed,
+                row(access_role)::text != row(coalesce(%(access_role)s, access_role))::text as access_role_changed
             from warehouse.sample
             where identifier = %(identifier)s
                 or collection_identifier = %(collection_identifier)s
@@ -239,12 +243,13 @@ def upsert_sample(db: DatabaseSession,
         status = 'created'
 
         sample = db.fetch_row("""
-            insert into warehouse.sample (identifier, collection_identifier, collected, encounter_id, details)
+            insert into warehouse.sample (identifier, collection_identifier, collected, encounter_id, details, access_role)
                 values (%(identifier)s,
                         %(collection_identifier)s,
                         date_or_null(%(collection_date)s),
                         %(encounter_id)s,
-                        %(additional_details)s)
+                        %(additional_details)s,
+                        %(access_role)s)
             returning sample_id as id, identifier, collection_identifier, encounter_id
             """, data)
 
@@ -256,9 +261,10 @@ def upsert_sample(db: DatabaseSession,
         LOG.info(f"Updating existing sample {sample.id}")
         LOG.info(f"Sample.identifiers_changed is «{sample.identifiers_changed}» ")
         LOG.info(f"Sample.metadata_changed is «{sample.metadata_changed}» ")
+        LOG.info(f"Sample.access_role_changed is «{sample.access_role_changed}» ")
 
         # can safely skip upsert if metadata is unchanged and not updating identifiers or if all data is unchanged
-        if sample.metadata_changed == False and (not update_identifiers or sample.identifiers_changed == False):
+        if sample.metadata_changed == False and sample.access_role_changed == False and (not update_identifiers or sample.identifiers_changed == False):
             LOG.info(f"Skipping upsert for sample {sample.id} «{sample.identifier}» (no change).")
             return sample, status
 
@@ -286,16 +292,22 @@ def upsert_sample(db: DatabaseSession,
                  if overwrite_collection_date else SQL("""
                     collected = coalesce(collected, date_or_null(%(collection_date)s)), """)
 
+        # Update access_role if value changed
+        access_role_update_composable = SQL("""
+             access_role = %(access_role)s, """) if sample.access_role_changed else SQL("")
+
         sample = db.fetch_row(SQL("""
             update warehouse.sample
                 set {}
+                    {}
                     {}
                     encounter_id = coalesce(%(encounter_id)s, encounter_id),
                     details = coalesce(details, {}) || %(additional_details)s
              where sample_id = %(sample_id)s
             returning sample_id as id, identifier, collection_identifier, encounter_id
             """).format(identifiers_update_composable,
                 collected_update_composable,
+                access_role_update_composable,
                 Literal(Json({}))),
                 { **data, "sample_id": sample.id })