Bug fix: filter on context parameter

dd-api-spec.yaml

@@ -864,11 +864,14 @@ paths:
             example: UBERON
         - name: context
           in: query
-          required: true
-          description: A UBKG context to which to limit the response. Possible values are base_context, data_distillery_context, hubmap_sennet_context
+          required: false
+          description: A UBKG context to which to limit the response. Possible values are base_context, data_distillery_context, hubmap_sennet_context. Sources from base_context are included with other contexts.
           schema:
             type: string
-            example: base_context
+            enum:
+              - base_context
+              - hubmap_sennet_context
+              - data_distillery_context
       responses:
         '200':
           description: An array of Concepts with preferred terms that exactly match the specified string
@@ -1527,9 +1530,11 @@ components:
                   description: citation reference
                   properties:
                     PMID:
+                      type: string
                       description: PubMedID, if applicable
                       example: 37953324
                     url:
+                      type: string
                       description: full URL to the citation
                       example: "https://pubmed.ncbi.nlm.nih.gov/37953324"
               contexts:
@@ -1539,9 +1544,11 @@ components:
                   type: string
                   example: base_context
               description:
+                type: string
                 description: longform description of the source
                 example: "An ontology for describing the classification of human diseases organized by etiology."
               download_date:
+                type: string
                 description: Date when the source was obtained, in format YYYY_MM_DD
                 example: "2024_02_24"
               home_urls:
@@ -1558,26 +1565,34 @@ components:
                   description: license
                   properties:
                     type:
+                      type: string
                       description: the type of license
                       example: Creative Commons license (creativecommons.org)
                     subtype:
+                      type: string
                       description: the subtype of license
                       example: CCO
                     version:
-                      description: the versoin of the license
+                      type: string
+                      description: the version of the license
                       example: version 4
               name:
+                type: string
                 description: name of the source
                 example: Human Disease Ontology
               sab:
+                type: string
                 description: acronym for Source ABbreviation
                 example: DOID
               source_etl:
+                type: string
                 description: the parameter provided to the UBKG generation framework ETL script. For sources that are from OWL files, source_etl is the URL to the OWL; for other sources, source_etl is a command for one of the python scripts that the generation framework uses to import the source.
                 example: "http://purl.obolibrary.org/obo/doid.owl"
               source_type:
+                type: string
                 description: The type of source file. Possible values are owl, api, ftp, ubkg_edge_node, umls, and simpleknowledge.
                 example: owl
               source_version:
+                type: string
                 description: A reference to the version of the source. If the source is an OWL file, the usual version is the date extracted from the VersionIRI of the file; if from a website, the file date. Dates are in format YYYY_MM_DD.
                 example: "2024_04_22"

src/ubkg_api/common_routes/common_neo4j_logic.py

@@ -1062,10 +1062,11 @@ def sources_get_logic(neo4j_instance, sab=None, context=None) -> dict:
         querytxt = querytxt.replace('$sabfilter', f" AND t.name IN {sab}")
 
     # Filter by ubkg context.
+    # JAS 24 May 2024 bug fix - replace t.name with tContext.name
     if len(context) == 0:
         querytxt = querytxt.replace('$contextfilter', '')
     else:
-        querytxt = querytxt.replace('$contextfilter', f" AND t.name IN {context}")
+        querytxt = querytxt.replace('$contextfilter', f" AND tContext.name IN {context}")
 
     # Set timeout for query based on value in app.cfg.
     query = neo4j.Query(text=querytxt, timeout=neo4j_instance.timeout)

src/ubkg_api/common_routes/sources/sources_controller.py

@@ -23,6 +23,16 @@ def sources_get():
 
     sab = parameter_as_list(param_name='sab')
     context = parameter_as_list(param_name='context')
+    # JAS 24 May 2024
+    # Validate context parameter against enum.
+    val_enum = ['base_context', 'data_distillery_context', 'hubmap_sennet_context']
+    if context is not None:
+        for c in context:
+            c = c.lower()
+            err = validate_parameter_value_in_enum(param_name='context', param_value=c,
+                                               enum_list=val_enum)
+        if err != 'ok':
+            return make_response(err, 400)
 
     result = sources_get_logic(neo4j_instance, sab=sab, context=context)
     iserr = result is None or result == []

tests/test_dd_api.sh

@@ -1240,15 +1240,23 @@ curl --request GET \
 echo | tee -a test.out
 echo | tee -a test.out
 
-echo "4. /sources?sab=HPOMP GET => valid SAB; should return 200" | tee -a test.out
+echo "4. /sources?context=x GET => invalid context; should return custom 404" | tee -a test.out
+curl --request GET \
+ --url "${UBKG_URL}/sources?context=x" \
+ --header "Accept: application/json" \
+ --header "X-API-KEY:$apikey" | cut -c1-60 | tee -a test.out
+echo | tee -a test.out
+echo | tee -a test.out
+
+echo "5. /sources?sab=HPOMP GET => valid SAB; should return 200" | tee -a test.out
 curl --request GET \
  --url "${UBKG_URL}/sources?sab=HPOMP" \
  --header "Accept: application/json" \
  --header "X-API-KEY:$apikey" | cut -c1-60 | tee -a test.out
 echo | tee -a test.out
 echo | tee -a test.out
 
-echo "5. /sources?context=base_context GET => valid context; should return 200" | tee -a test.out
+echo "6. /sources?context=base_context GET => valid context; should return 200" | tee -a test.out
 curl --request GET \
  --url "${UBKG_URL}/sources?context=base_context" \
  --header "Accept: application/json" \

tests/test_ubkg_api.sh

@@ -1103,17 +1103,24 @@ curl --request GET \
 echo | tee -a test.out
 echo | tee -a test.out
 
-echo "4. /sources?sab=HPOMP GET => valid SAB; should return 200" | tee -a test.out
+echo "4. /sources?context=x GET => invalid context; should return custom 400" | tee -a test.out
 curl --request GET \
- --url "${UBKG_URL}/sources?sab=HPOMP" \
+ --url "${UBKG_URL}/sources?context=x" \
  --header "Accept: application/json" | tee -a test.out
 echo | tee -a test.out
 echo | tee -a test.out
 
-echo "5. /sources?context=base_context GET => valid context; should return 200" | tee -a test.out
+echo "5. /sources?sab=HPOMP GET => valid SAB; should return 200" | tee -a test.out
+curl --request GET \
+ --url "${UBKG_URL}/sources?sab=HPOMP" \
+ --header "Accept: application/json" | cut -c1-60 | tee -a test.out
+echo | tee -a test.out
+echo | tee -a test.out
+
+echo "6. /sources?context=base_context GET => valid context; should return 200" | tee -a test.out
 curl --request GET \
  --url "${UBKG_URL}/sources?context=base_context" \
- --header "Accept: application/json" | tee -a test.out
+ --header "Accept: application/json" | cut -c1-60 | tee -a test.out
 echo | tee -a test.out
 echo | tee -a test.out
 

ubkg-api-spec.yaml

@@ -845,7 +845,7 @@ paths:
           description: No Concepts with terms matching the specified string.
         '5XX':
           description: Unknown error
-/sources:
+  /sources:
     get:
       operationId: sources_get
       summary: Returns a list of Concept nodes with preferred terms that exactly match the specified string.
@@ -859,11 +859,14 @@ paths:
             example: UBERON
         - name: context
           in: query
-          required: true
-          description: A UBKG context to which to limit the response. Possible values are base_context, data_distillery_context, hubmap_sennet_context
+          required: false
+          description: A UBKG context to which to limit the response. Possible values are base_context, data_distillery_context, hubmap_sennet_context. The sources from base_context are included with any other context.
           schema:
             type: string
-            example: base_context
+            enum:
+              - base_context
+              - hubmap_sennet_context
+              - data_distillery_context
       responses:
         '200':
           description: An array of Concepts with preferred terms that exactly match the specified string
@@ -1534,9 +1537,11 @@ components:
                   type: string
                   example: base_context
               description:
+                type: string
                 description: longform description of the source
                 example: "An ontology for describing the classification of human diseases organized by etiology."
               download_date:
+                type: string
                 description: Date when the source was obtained, in format YYYY_MM_DD
                 example: "2024_02_24"
               home_urls:
@@ -1559,20 +1564,25 @@ components:
                       description: the subtype of license
                       example: CCO
                     version:
-                      description: the versoin of the license
+                      description: the version of the license
                       example: version 4
               name:
+                type: string
                 description: name of the source
                 example: Human Disease Ontology
               sab:
+                type: string
                 description: acronym for Source ABbreviation
                 example: DOID
               source_etl:
+                type: string
                 description: the parameter provided to the UBKG generation framework ETL script. For sources that are from OWL files, source_etl is the URL to the OWL; for other sources, source_etl is a command for one of the python scripts that the generation framework uses to import the source.
                 example: "http://purl.obolibrary.org/obo/doid.owl"
               source_type:
+                type: string
                 description: The type of source file. Possible values are owl, api, ftp, ubkg_edge_node, umls, and simpleknowledge.
                 example: owl
               source_version:
+                type: string
                 description: A reference to the version of the source. If the source is an OWL file, the usual version is the date extracted from the VersionIRI of the file; if from a website, the file date. Dates are in format YYYY_MM_DD.
                 example: "2024_04_22"