Addressing invalid merge from dev-integrate. Importing into new branc…

…h of main source files changed in branch jas/assayclasses_optional_hierarchy.

hs-ontology-api-spec.yaml

@@ -46,6 +46,12 @@ paths:
           schema:
             type: string
             example: AF
+        - name: provide-hierarchy-info
+          in: query
+          required: false
+          description: optional response filter - if true, then the response will contain hierarchy information for the dataset type. The default is blank, or false.
+          schema:
+            type: string
       responses:
         '200':
           description: A JSON array of assay classification objects
@@ -97,6 +103,12 @@ paths:
               - primary
               - derived
               - epic
+        - name: provide-hierarchy-info
+          in: query
+          required: false
+          description: optional response filter - if true, then the response will contain hierarchy information for the dataset type. The default is blank, or false.
+          schema:
+            type: string
       responses:
         '200':
           description: An assay classification objects
@@ -1781,28 +1793,10 @@ components:
                   type: string
                   description: identifier for the table schema for files in datasets generated by the processing workflow associated with the assay classification
                   example: imc-v
-                measurement_assay:
-                  type: object
-                  description: corresponds to the generic experiment or assay modality used to generate a "raw" dataset from a tissue sample.
-                  properties:
-                    codes:
-                      type: array
-                      description: set of codes from biomedical vocabularies for the measurement assay
-                      items:
-                        type: object
-                        properties:
-                          code:
-                            type: string
-                            description: code from a biomedical vocabulary or ontology
-                            example: OBI:0003096
-                          term:
-                            type: string
-                            description: preferred term for the code in the biomedical vocabulary or ontology
-                            example: imaging mass cytometry assay
-                    contains_full_genetic_sequences:
-                      type: boolean
-                      description: whether the measurement assay generates full genetic sequences from the sample. Full genetic sequencing information from human sources is considered Patient Identifying Information (PII), which is protected.
-                      example: false
+                contains_full_genetic_sequences:
+                    type: boolean
+                    description: whether the measurement assay generates full genetic sequences from the sample. Full genetic sequencing information from human sources is considered Patient Identifying Information (PII), which is protected.
+                    example: false
                 is_multiassay:
                   type: boolean
                   description: indicates whether the assay class is for a "multi-assay". Multi-assays use more than one experimental modality on samples to generate datasets--e.g., both RNAseq and ATACseq.

src/hs_ontology_api/cypher/assayclass.cypher

@@ -5,7 +5,11 @@
 // Obtain identifiers for rule-based datasets (assay classes) for the application context.
 // The assayclass_filter allows filtering by either the UBKG code or term (rule_description)
 // for the assay class.
-WITH '$context' AS context
+// OCT 2024 - filter response content based on
+// 1. whether to provide dataset type hierarchical information
+// 2. whether to provide measurement assay codes
+
+WITH '$context' AS context, '$provide_hierarchy_info' AS provide_hierarchy_info
 CALL
 {
         WITH context
@@ -65,6 +69,7 @@ CALL
         RETURN tdsProcess.name as process_state
 }
 // dataset_type
+
 // The dataset_type concepts in HUBMAP are cross-referenced to HRAVS concepts; however, the terms for the HRAVS concepts
 // are enclosed in a list, so use the HUBMAP terms.
 CALL
@@ -106,6 +111,29 @@ CALL
         WHERE pDatasetType.CUI=CUIDatasetType AND r.CUI=pFig2category.CUI AND cFig2category.SAB=context
         RETURN DISTINCT tFig2category.name AS fig2_category
 }
+// dataset_type summary
+// Oct 2024 - content driven by provide_hierarchy_info parameter.
+CALL
+{
+    WITH dataset_type, pdr_category, fig2_aggregated_assaytype, fig2_modality, fig2_category, provide_hierarchy_info
+    RETURN
+    CASE
+        WHEN provide_hierarchy_info='True'
+        THEN
+                {
+                        dataset_type:dataset_type,
+                        PDR_category:pdr_category,
+                        fig2:
+                        {
+                                aggregated_assaytype:fig2_aggregated_assaytype,
+                                modality:fig2_modality,
+                                category:fig2_category
+                        }
+                }
+        ELSE
+            dataset_type
+        END AS dataset_type_summary
+}
 // description
 CALL
 {
@@ -139,28 +167,13 @@ CALL
         WHERE pRBD.CUI=CUIRBD AND r.CUI=pDT.CUI AND cDT.SAB=context
         RETURN COLLECT(DISTINCT tDT.name) AS must_contain
 }
-// measurement assay CUI
-CALL
-{
-        WITH CUIRBD
-        OPTIONAL MATCH (pRBD:Concept)-[:has_measurement_assay]->(pMeas:Concept)
-        WHERE pRBD.CUI=CUIRBD
-        RETURN DISTINCT pMeas.CUI as CUIMeas
-}
-// Optional measurement codes
-CALL
-{
-        WITH CUIMeas
-        MATCH (pMeas:Concept)-[:CODE]->(cMeas:Code)-[:PT]->(tMeas:Term)
-        WHERE pMeas.CUI = CUIMeas
-        RETURN COLLECT(DISTINCT {code:cMeas.CodeID,term:tMeas.name}) AS MeasCodes
-}
-// whether the measurement assay contains full_genetic_sequencesi
+
+// whether the assay classification contains full_genetic_sequences
 CALL
 {
-        WITH CUIMeas,context
+        WITH CUIRBD,context
         OPTIONAL MATCH (pRBD:Concept)-[:contains]->(ppii:Concept)
-        WHERE pRBD.CUI=CUIMeas
+        WHERE pRBD.CUI=CUIRBD
         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
 }
@@ -173,14 +186,14 @@ CALL
         WHERE pRBD.CUI=CUIRBD AND r.CUI=pStatus.CUI and cStatus.SAB=context
         RETURN DISTINCT tStatus.name AS active_status
 }
+// Response
 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,active_status
+description,dataset_type_summary,
+is_multiassay,must_contain,active_status, contains_full_genetic_sequences
 RETURN
 {
         rule_description:
@@ -193,20 +206,11 @@ RETURN
                 pipeline_shorthand:pipeline_shorthand, description:description,
                 is_multiassay:is_multiassay, must_contain:must_contain,
                 active_status:active_status,
-                dataset_type:
-                {
-                        dataset_type:dataset_type, PDR_category:pdr_category,
-                        fig2:
-                        {
-                                aggregated_assaytype:fig2_aggregated_assaytype, modality:fig2_modality, category:fig2_category
-                        }
-                },
-                measurement_assay:{
-                        codes:MeasCodes,
-                        contains_full_genetic_sequences:contains_full_genetic_sequences
-                }
+                dataset_type:dataset_type_summary,
+                contains_full_genetic_sequences:contains_full_genetic_sequences
         }
-} AS rule_based_dataset
+}
+AS rule_based_dataset
 }
 WITH rule_based_dataset
 RETURN rule_based_dataset AS rule_based_datasets

src/hs_ontology_api/routes/assayclasses/assayclasses_controller.py

@@ -1,11 +1,43 @@
-from flask import Blueprint, jsonify, current_app, make_response,request
+from flask import Blueprint, jsonify, current_app, make_response,request, abort
 
 from ubkg_api.utils.http_error_string import (get_404_error_string, validate_query_parameter_names,
                                               validate_parameter_value_in_enum, validate_required_parameters)
 from hs_ontology_api.utils.neo4j_logic import assayclasses_get_logic
 
+from urllib.parse import urlencode
+
 assayclasses_blueprint = Blueprint('assayclasses_hs', __name__, url_prefix='/assayclasses')
 
+def validate_param_as_boolean(param_name: str) ->str:
+    """
+    Evaluates a request parameter string as a boolean.
+
+    :param param_name: name of the request parameter
+    """
+
+    val_enum = ['TRUE', 'FALSE']
+    param_value = request.args.get(param_name)
+    if param_value is not None:
+        param_value = param_value.upper()
+
+    return validate_parameter_value_in_enum(param_name=param_name, param_value=param_value, enum_list=val_enum)
+
+def convert_param_to_boolean_string(param_name: str) -> str:
+    """
+    Converts a parameter string to a "boolean string"--i.e., "True" or "False"
+    :param param_name: name of parameter
+    """
+
+    param_value = request.args.get(param_name)
+    if param_value is None:
+        return 'False'
+
+    param_value = param_value.upper()
+    if param_value == 'TRUE':
+        return 'True'
+    else:
+        return 'False'
+
 @assayclasses_blueprint.route('', methods=['GET'])
 def assayclasses_expand_get():
     return assayclasses_get()
@@ -19,11 +51,16 @@ def assayclasses_get(name=None):
     in the testing rules json, with options to filter the list to those with specific property values.
     Filters are additive (i.e., boolean AND)
 
+    October 2024 - Request parameters added for:
+    provide_hierarchy_info: whether to display hierarchical information on the dataset type
+    provide_measurement_assay_codes: whether to display the measurement assay codes
+
     """
     # Validate parameters.
 
     # Check for invalid parameter names.
-    err = validate_query_parameter_names(parameter_name_list=['application_context','process_state','assaytype'])
+    err = validate_query_parameter_names(parameter_name_list=['application_context', 'process_state', 'assaytype',
+                                                              'provide-hierarchy-info'])
     if err != 'ok':
         return make_response(err, 400)
 
@@ -33,9 +70,11 @@ def assayclasses_get(name=None):
         return make_response(err, 400)
     application_context = request.args.get('application_context')
 
-    # Check for valid application context. The parameter is case-insensitive.
+    # Check for valid application context. The parameter is case-insensitive, but any error should return the
+    # value provided in the request.
     val_enum = ['HUBMAP','SENNET']
-    err = validate_parameter_value_in_enum(param_name='application_context', param_value=application_context.upper(), enum_list=val_enum)
+    err = validate_parameter_value_in_enum(param_name='application_context', param_value=application_context.upper(),
+                                           enum_list=val_enum)
     if err != 'ok':
         return make_response(err, 400)
     application_context = application_context.upper()
@@ -57,9 +96,17 @@ def assayclasses_get(name=None):
     if assaytype is not None and name is not None:
        assaytype = None
 
+    # Oct 2024 - filter response for dataset type hierarchy.
+    err = validate_param_as_boolean('provide-hierarchy-info')
+    if err != 'ok':
+        return make_response(err, 400)
+    provide_hierarchy_info = convert_param_to_boolean_string('provide-hierarchy-info')
+
+
     neo4j_instance = current_app.neo4jConnectionHelper.instance()
     result = assayclasses_get_logic(
-            neo4j_instance, assayclass=name, process_state=process_state, assaytype=assaytype, context=application_context)
+        neo4j_instance, assayclass=name, process_state=process_state, assaytype=assaytype,
+        context=application_context, provide_hierarchy_info=provide_hierarchy_info)
 
     if result is None or result == []:
         # Empty result

src/hs_ontology_api/utils/neo4j_logic.py

@@ -1282,8 +1282,11 @@ def field_entities_get_logic(neo4j_instance, field_name=None, source=None, entit
 
         return fieldentities
 
-def assayclasses_get_logic(neo4j_instance,assayclass=None, assaytype=None, process_state=None, context=None) -> dict:
+def assayclasses_get_logic(neo4j_instance,assayclass=None, assaytype=None, process_state=None,
+                           context=None, provide_hierarchy_info=None) -> dict:
     """
+    October 2024 - filter response for hierarchical information.
+
     July 2024
         Obtains information on the assay classes (rule-based dataset "kinds") that are specified in
         the testing rules json file.
@@ -1295,6 +1298,8 @@ def assayclasses_get_logic(neo4j_instance,assayclass=None, assaytype=None, proce
         :param assaytype: the assaytype
         :param context: application context--i.e., HUBMAP or SENNET
         :param process_state: in the enum ['primary','derived','epic']
+        :param provide_hierarchy_info: "string boolean" (i.e. the word "True" or "False") indicating
+                                        whether to include dataset hierarchical information in response
 
         example: if a assay class's rule has rule_description="non-DCWG primary AF" and rule code "HUBMAP:C200001", either
         "non-DCWG primary AF" or "C200001" will result in selection of the assay class. The application context is used
@@ -1309,6 +1314,9 @@ def assayclasses_get_logic(neo4j_instance,assayclass=None, assaytype=None, proce
     # Filter by application context.
     querytxt = querytxt.replace('$context', context)
 
+    # Oct 2024 - Filter by dataset hierarchy.
+    querytxt = querytxt.replace('$provide_hierarchy_info', provide_hierarchy_info)
+
     # Filter by assay class
     if assayclass is not None:
         querytxt = querytxt.replace('$assayclass_filter', f"AND (cRBD.CodeID = context+':{assayclass}' OR tRBD.name='{assayclass}')")
@@ -1328,7 +1336,9 @@ def assayclasses_get_logic(neo4j_instance,assayclass=None, assaytype=None, proce
     elif assayclass is None:
         querytxt = querytxt.replace('$assaytype_filter', f"AND REPLACE(tassaytype.name,'_assaytype','') = '{assaytype}'")
     else:
+
         querytxt = querytxt.replace('$assaytype_filter','')
+
     # Set timeout for query based on value in app.cfg.
     query = neo4j.Query(text=querytxt, timeout=neo4j_instance.timeout)
 

test/test_api.sh

@@ -71,7 +71,7 @@ echo | tee -a test.out
 
 
 echo "TESTS FOR: assayclasses GET" | tee -a test.out
-echo "SIGNATURE: /assayclasses?application_context=<context>&process_state=<process_state>" | tee -a test.out
+echo "SIGNATURE: /assayclasses?application_context=<context>&process_state=<process_state>&provide_hiearchy_info=<true,false>&provide_measurement_assay_codes=<true,false>" | tee -a test.out
 echo | tee -a test.out
 echo | tee -a test.out
 echo "1. /assayclasses?application_context=x => invalid application context; should return 400" | tee -a test.out
@@ -137,6 +137,40 @@ echo
 echo | tee -a test.out
 echo | tee -a test.out
 
+echo "9. /assayclasses/C200001 => invalid provide-hierarchy-info; should return 400" | tee -a test.out
+curl --request GET \
+ --url "${UBKG_URL}/assayclasses/C200001?application_context=HUBMAP&provide-hierarchy-info=x" \
+--header "Accept: application/json" | cut -c1-60 | tee -a test.out
+echo
+echo | tee -a test.out
+echo | tee -a test.out
+
+echo "10. /assayclasses/C200001 => valid provide-hierarchy-info; should return 200" | tee -a test.out
+curl --request GET \
+ --url "${UBKG_URL}/assayclasses/C200001?application_context=HUBMAP&provide-hierarchy-info=true" \
+--header "Accept: application/json" | cut -c1-60 | tee -a test.out
+echo
+echo | tee -a test.out
+echo | tee -a test.out
+
+echo "11. /assayclasses/C200001 => invalid provide-measurement-assay-codes should return 400" | tee -a test.out
+curl --request GET \
+ --url "${UBKG_URL}/assayclasses/C200001?application_context=HUBMAP&provide-measurement-assay-codes=x" \
+--header "Accept: application/json" | cut -c1-60 | tee -a test.out
+echo
+echo | tee -a test.out
+echo | tee -a test.out
+
+echo "12. /assayclasses/C200001 => valid provide-measurement-assay-codes; should return 200" | tee -a test.out
+curl --request GET \
+ --url "${UBKG_URL}/assayclasses/C200001?application_context=HUBMAP&provide-measurement-assay-codes=true" \
+--header "Accept: application/json" | cut -c1-60 | tee -a test.out
+echo
+echo | tee -a test.out
+echo | tee -a test.out
+
+exit;
+
 echo "TESTS FOR: dataset-types GET" | tee -a test.out
 echo "SIGNATURE: /dataset-types?application_context" | tee -a test.out
 echo | tee -a test.out