NickAkhmetov/Add spatial field

VERSION

@@ -1 +1 @@
-3.6.14
+3.6.15

search-api-spec.yaml

@@ -1141,11 +1141,11 @@ paths:
   '/reindex-status/{identifier}':
     get:
       summary: Retrieves a json containing information about a particularitem in the queue including its priority level, and its position in the queue.
-      description: To retrieve infomration about an individual entity in the queue, include either the id used when submitting the reindex request (uuid or hubmap_id) or the job_id (returned when submitting the request) as a path variable.
+      description: To retrieve infomration about an individual entity in the queue, include either the id used when submitting the reindex request (uuid or hubmap_id) or the reference_id (returned when submitting the request) as a path variable.
       parameters:
         - name: identifier
           in: path
-          description: The id of the chosen entity. Either the original id used during reindex submission (uuid or HuBMAP ID, whichever was used) or the job_id returned when the reindex was submitted.
+          description: The id of the chosen entity. Either the original id used during reindex submission (uuid or HuBMAP ID, whichever was used) or the reference_id returned when the reindex was submitted.
       responses:
         '200':
           description: Returns the status data as a json describing the current state of the chosen entity.

src/hubmap_translation/addl_index_transformations/portal/add_assay_details.py

@@ -211,6 +211,10 @@ def get_assay_type_for_viz(doc):
         # Check if the main entity can be visualized by portal-visualization.
         doc['visualization'] = has_visualization(doc, get_assay_type_for_viz)
 
+        # Set the 'spatial' field for search based off of the presence of the 'spatial' hint
+        if ('spatial' in assay_details.get('vitessce-hints', [])):
+            doc['spatial'] = True
+
         if not doc['visualization']:
             # If an entity doesn't have a visualization,
             # check its descendants for a supporting image pyramid.
@@ -225,9 +229,9 @@ def get_assay_type_for_descendants(descendant):
                     uuid = descendant
                 return _get_assay_details_by_uuid(uuid, transformation_resources)
 
-            # Filter any unpublished/non-QA descendants
+            # Filter any unpublished/non-QA descendants and multi-assay splits
             descendants = [descendant for descendant in descendants if [
-                'Published', 'QA'].count(descendant.get('status')) > 0]
+                'Published', 'QA'].count(descendant.get('status')) > 0 and descendant.get('creation_action') != CreationAction.MULTI_ASSAY_SPLIT]
             # Sort by the descendant's last modified timestamp, descending
             descendants.sort(
                 key=lambda x: x['last_modified_timestamp'],

src/hubmap_translation/addl_index_transformations/portal/tests/test_assay_details.py

@@ -125,6 +125,57 @@ def test_processed_dataset_type(mocker):
     assert input_processed_doc == output_processed_doc
 
 
+def mock_spatial_soft_assay(uuid=None, headers=None):
+    return mock_response({
+        "assaytype": "salmon_rnaseq_sciseq",
+        "contains-pii": True,
+        "pipeline-shorthand": "Salmon",
+        "description": "sciRNA-seq [Salmon]",
+        "primary": False,
+        "vitessce-hints": [
+            "is_sc",
+            "rna",
+            "spatial"
+        ]
+    })
+
+
+def test_spatial_dataset_type(mocker):
+    mocker.patch('requests.get', side_effect=[
+                 mock_spatial_soft_assay(),
+                 mock_empty_descendants()])
+    input_processed_doc = {
+        'uuid': '22684b9011fc5aea5cb3f89670a461e8',
+        'dataset_type': 'RNAseq [Salmon]',
+        'entity_type': 'Dataset',
+        'creation_action': 'Central Process'
+    }
+
+    output_processed_doc = {
+        'assay_display_name': ['sciRNA-seq [Salmon]'],
+        'dataset_type': 'RNAseq [Salmon]',
+        'entity_type': 'Dataset',
+        'mapped_data_types': ['sciRNA-seq [Salmon]'],
+        'pipeline': 'Salmon',
+        'raw_dataset_type': 'RNAseq',
+        'assay_modality': 'single',
+        'creation_action': 'Central Process',
+        'processing': 'processed',
+        'processing_type': 'hubmap',
+        'uuid': '22684b9011fc5aea5cb3f89670a461e8',
+        'soft_assaytype': 'salmon_rnaseq_sciseq',
+        'vitessce-hints': [
+            "is_sc",
+            "rna",
+            "spatial"
+        ],
+        'visualization': True,
+        'spatial': True,
+    }
+    add_assay_details(input_processed_doc, mock_transformation_resources)
+    assert input_processed_doc == output_processed_doc
+
+
 def mock_empty_soft_assay(uuid=None, headers=None):
     return mock_response({})
 

src/hubmap_translator.py

@@ -704,7 +704,7 @@ def enqueue_reindex(self, entity_id, reindex_queue, priority):
             logger.info(f"Enqueueing reindex for {entity['entity_type']} of uuid: {entity_id}")
             subsequent_priority = max(priority, 2)
 
-            job_id = reindex_queue.enqueue(
+            reference_id = reindex_queue.enqueue(
                 job_metadata = {"uuid": entity.get('uuid'), "hubmap_id": entity.get('hubmap_id')},
                 task_func=reindex_entity_queued_wrapper,
                 entity_id=entity_id,
@@ -816,7 +816,7 @@ def enqueue_reindex(self, entity_id, reindex_queue, priority):
                     priority=subsequent_priority
                 )
             logger.info(f"Finished executing translate() on {entity['entity_type']} of uuid: {entity_id}")
-            return job_id
+            return reference_id
         except ValueError as e:
             raise ValueError(e)
         except RedisError as e:

src/requirements.txt

@@ -1,4 +1,4 @@
-Flask==3.0.3
+Flask==3.1.3
 jsonschema==4.25.1
 # The commons package requires requests>=2.22.0 and PyYAML>=5.3.1
 requests==2.32.5
@@ -11,7 +11,7 @@ portal-visualization==0.5.1
 # Default is main branch specified in search-api's docker-compose.development.yml if not set
 # git+https://github.com/hubmapconsortium/commons.git@${COMMONS_BRANCH}#egg=hubmap-commons
 
-hubmap-commons==2.1.22
+hubmap-commons==2.1.23
 atlas-consortia-jobq>=0.1.0
 # The use of `-r` lets us specify the transitive requirements in one place
 -r search-adaptor/src/requirements.txt