1. The 'provider' field (IEC or External) removed from the response f…

…or the assayclasses endpoint. 2. The 'isepc' field in the response for the dataset-types endpoints renamed to 'is_externally_processed'. 3. The 'isepic' parameter for the dataset-types endpoints is renamed to 'is_externally_processed'. 4. The 'is_externally_processed' field in the response for the dataset-types endpoints is now boolean. 5. The SmartAPI YAML updated to reflect the changes in the assayclasses and dataset-types endpoints.
x-atlas-consortia · Sep 23, 2024 · 9865f9c · 9865f9c
1 parent c85baba
commit 9865f9c
Show file tree

Hide file tree

Showing 6 changed files with 26 additions and 29 deletions.
diff --git a/hs-ontology-api-spec.yaml b/hs-ontology-api-spec.yaml
@@ -129,7 +129,7 @@ paths:
               - sennet
               - HuBMAP
               - SenNet
-        - name: isepic
+        - name: is_externally_processed
           in: query
           required: false
           description: filter on whether dataset types are for EPIC datasets
@@ -179,7 +179,7 @@ paths:
               - sennet
               - HuBMAP
               - SenNet
-        - name: isepic
+        - name: is_externally_processed
           in: query
           required: false
           description: filter on whether dataset types are for EPIC datasets
@@ -1969,10 +1969,6 @@ components:
                   type: string
                   description: whether datasets generated by the processing workflow associated with the assay class are "primary" (from the original experiment); "derived"/"processed" (from post-experimental data processing); or "epic" (Externally Processed Integrated Collections)
                   example: primary
-                provider:
-                  type: string
-                  description: the provider of datasets generated by the processing workflow associate with the assay class. Possible values are "IEC" (corresponding to datasets generated by the HuBMAP/SenNet Infrastructure and Engagement Component) or "External" (complete datasets coming directly from a HuBMAP/SenNet lab--e.g., a Tissue Mapping Center).
-                  example: IEC
                 vitessce_hints:
                   type: array
                   description: set of keys used to identify the type of visualization that the Vitessce application should use to represent datasets associated with the assay class.
@@ -2017,7 +2013,7 @@ components:
                   items:
                     type: string
                     example: IMC2D
-                isepic:
+                is_externally_processed:
                   type: string
                   description: whether the dataset type is for an EPIC dataset
                   example: false
diff --git a/src/hs_ontology_api/cypher/assayclass.cypher b/src/hs_ontology_api/cypher/assayclass.cypher
@@ -164,14 +164,7 @@ CALL
         AND ppii.CUI = context+':C004009 CUI'
         RETURN DISTINCT CASE WHEN NOT ppii.CUI IS null THEN true ELSE false END AS contains_full_genetic_sequences
 }
-// provider
-CALL
-{
-        WITH CUIRBD,context
-        OPTIONAL MATCH (pRBD:Concept)-[:has_provider]->(pProvider:Concept)-[:CODE]-(cProvider:Code)-[r:PT]->(tProvider:Term)
-        WHERE pRBD.CUI=CUIRBD AND r.CUI=pProvider.CUI AND cProvider.SAB=context
-        RETURN DISTINCT tProvider.name AS provider
-}
+
 // active status
 CALL
 {
@@ -182,7 +175,12 @@ CALL
 }
 CALL
 {
-WITH context, CodeRBD, NameRBD, assaytype, dir_schema, tbl_schema, vitessce_hints,process_state,pipeline_shorthand,description,dataset_type,pdr_category,fig2_aggregated_assaytype,fig2_modality,fig2_category,is_multiassay,must_contain,MeasCodes,contains_full_genetic_sequences,provider,active_status
+WITH
+context, CodeRBD, NameRBD, assaytype, dir_schema, tbl_schema,
+vitessce_hints,process_state,pipeline_shorthand,
+description,dataset_type,pdr_category,
+fig2_aggregated_assaytype,fig2_modality,fig2_category,
+is_multiassay,must_contain,MeasCodes,contains_full_genetic_sequences,active_status
 RETURN
 {
         rule_description:
@@ -194,7 +192,6 @@ RETURN
                 process_state:process_state,
                 pipeline_shorthand:pipeline_shorthand, description:description,
                 is_multiassay:is_multiassay, must_contain:must_contain,
-                provider:provider,
                 active_status:active_status,
                 dataset_type:
                 {

diff --git a/src/hs_ontology_api/cypher/datasettypes.cypher b/src/hs_ontology_api/cypher/datasettypes.cypher
@@ -72,9 +72,9 @@ CALL
    WHERE pDatasetType.CUI = CUIDatasetType
    AND cEpic.CODE = 'C004034'
    AND cEpic.SAB = context
-   RETURN DISTINCT CASE WHEN pEpic IS NULL THEN 'false' ELSE 'true' END AS isepic
+   RETURN DISTINCT CASE WHEN pEpic IS NULL THEN false ELSE true END AS is_externally_processed
 }
-WITH  dataset_type,pdr_category,fig2_aggregated_assaytype,fig2_modality,fig2_category,assaytypes,isepic
+WITH  dataset_type,pdr_category,fig2_aggregated_assaytype,fig2_modality,fig2_category,assaytypes,is_externally_processed
 $epictype_filter
 RETURN
 {
@@ -87,5 +87,5 @@ RETURN
             category:fig2_category
         },
         assaytypes:assaytypes,
-        isepic:isepic
+        is_externally_processed:is_externally_processed
 } AS dataset_types
diff --git a/src/hs_ontology_api/routes/datasettypes/datasettypes_controller.py b/src/hs_ontology_api/routes/datasettypes/datasettypes_controller.py
@@ -25,7 +25,7 @@ def datasettypes_get(name=None):
     # Validate parameters.
 
     # Check for invalid parameter names.
-    err = validate_query_parameter_names(parameter_name_list=['application_context','isepic'])
+    err = validate_query_parameter_names(parameter_name_list=['application_context','is_externally_processed'])
     if err != 'ok':
         return make_response(err, 400)
 
@@ -44,9 +44,9 @@ def datasettypes_get(name=None):
 
     # Check for valid isepic. The parameter is case-insensitive
     val_enum = ['TRUE','FALSE']
-    isepic = request.args.get('isepic')
+    isepic = request.args.get('is_externally_processed')
     if isepic is not None:
-        err = validate_parameter_value_in_enum(param_name='isepic', param_value=isepic.upper(),
+        err = validate_parameter_value_in_enum(param_name='is_externally_processed', param_value=isepic.upper(),
                                            enum_list=val_enum)
         if err != 'ok':
             return make_response(err, 400)

diff --git a/src/hs_ontology_api/utils/neo4j_logic.py b/src/hs_ontology_api/utils/neo4j_logic.py
@@ -1500,7 +1500,7 @@ def datasettypes_get_logic(neo4j_instance,datasettype=None, context=None, isepic
         :param neo4j_instance: neo4j connection
         :param datasettype: dataset_type
         :param context: application context--i.e., HUBMAP or SENNET
-        :param isepic: optional filter to Epic dataset types
+        :param isepic: optional filter to Epic (externally processed) dataset types
 
         """
     datasettypes: [dict] = []
@@ -1518,7 +1518,11 @@ def datasettypes_get_logic(neo4j_instance,datasettype=None, context=None, isepic
         querytxt = querytxt.replace('$datasettype_filter','')
 
     if isepic in ['true','false']:
-        querytxt = querytxt.replace('$epictype_filter', f"WHERE isepic='{isepic}'")
+        if isepic == 'true':
+            isepicbool = True
+        else:
+            isepicbool = False
+        querytxt = querytxt.replace('$epictype_filter', f"WHERE is_externally_processed={isepicbool}")
     else:
         querytxt = querytxt.replace('$epictype_filter','')
 

diff --git a/test/test_api.sh b/test/test_api.sh
@@ -186,19 +186,19 @@ echo
 echo | tee -a test.out
 echo | tee -a test.out
 
-echo "3. /dataset-types?application_context=HUBMAP&isepic=mango => invalid parameter; should return custom 400" | tee -a test.out
+echo "3. /dataset-types?application_context=HUBMAP&is_externally_processed=mango => invalid parameter; should return custom 400" | tee -a test.out
 curl --request GET \
- --url "${UBKG_URL}/dataset-types?application_context=HUBMAP&isepic=mango" \
+ --url "${UBKG_URL}/dataset-types?application_context=HUBMAP&is_externally_processed=mango" \
  --header "Accept: application/json" | cut -c1-60 | tee -a test.out
 echo
 echo "4. /dataset-types?application_context=HUBMAP => valid; should return 200" | tee -a test.out
 curl --request GET \
  --url "${UBKG_URL}/dataset-types?application_context=HUBMAP" \
  --header "Accept: application/json" | cut -c1-60 | tee -a test.out
 echo
-echo "5. /dataset-types?application_context=HUBMAP&isepic=false => valid; should return 200" | tee -a test.out
+echo "5. /dataset-types?application_context=HUBMAP&is_externally_processed=false => valid; should return 200" | tee -a test.out
 curl --request GET \
- --url "${UBKG_URL}/dataset-types?application_context=HUBMAP&isepic=true" \
+ --url "${UBKG_URL}/dataset-types?application_context=HUBMAP&is_externally_processed=true" \
  --header "Accept: application/json" | tee -a test.out