Merge pull request #274 from CanDIG/daisieh/cohort

DIG-1522: change cohort to program
CanDIG · Nov 25, 2024 · ac1b6de · ac1b6de
2 parents a7cec23 + d4cac22
commit ac1b6de
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Showing 11 changed files with 101 additions and 101 deletions.
diff --git a/chord_metadata_service/mohpackets/apis/clinical_data.py b/chord_metadata_service/mohpackets/apis/clinical_data.py
@@ -211,8 +211,8 @@ def query_donors(request, filters: DonorExplorerFilterSchema = Query(...)):
             systemictherapy__drug_name__in=filter_dict["systemic_therapy_drug_name"]
         )
 
-    if filter_dict["exclude_cohorts"]:
-        queryset = queryset.exclude(program_id__in=filter_dict["exclude_cohorts"])
+    if filter_dict["exclude_programs"]:
+        queryset = queryset.exclude(program_id__in=filter_dict["exclude_programs"])
 
     class Unnest(Func):
         contains_subquery = True

diff --git a/chord_metadata_service/mohpackets/apis/discovery.py b/chord_metadata_service/mohpackets/apis/discovery.py
@@ -32,7 +32,7 @@
     DiagnosisAgeCountSchema,
     DiscoveryDonorSchema,
     GenderCountSchema,
-    PatientPerCohortSchema,
+    PatientPerProgramSchema,
     PrimarySiteCountSchema,
     ProgramDiscoverySchema,
     TreatmentTypeCountSchema,
@@ -74,8 +74,8 @@ def discover_programs(request):
 @discovery_router.get("/donors/", response=List[DiscoveryDonorSchema])
 def discover_donors(request):
     """
-    Return the number of donors per cohort in the database.
-    Note: This function is identical to `discover_patients_per_cohort`
+    Return the number of donors per program in the database.
+    Note: This function is identical to `discover_patients_per_program`
     and is here because the frontend ingest uses it. It's probably best
     to clean up later.
     """
@@ -126,20 +126,20 @@ def discover_sidebar_list(request):
 ###############################################
 
 
-@overview_router.get("/cohort_count/", response=Dict[str, int])
+@overview_router.get("/program_count/", response=Dict[str, int])
 @decorate_view(cache_page(CACHE_DURATION))
-def discover_cohort_count(request):
+def discover_program_count(request):
     """
-    Return the number of cohorts in the database.
+    Return the number of programs in the database.
     """
-    return {"cohort_count": Program.objects.count()}
+    return {"program_count": Program.objects.count()}
 
 
-@overview_router.get("/patients_per_cohort/", response=List[PatientPerCohortSchema])
+@overview_router.get("/patients_per_program/", response=List[PatientPerProgramSchema])
 @decorate_view(cache_page(CACHE_DURATION))
-def discover_patients_per_cohort(request):
+def discover_patients_per_program(request):
     """
-    Return the number of patients per cohort in the database.
+    Return the number of patients per program in the database.
     """
     result = (
         Donor.objects.values("program_id")

diff --git a/chord_metadata_service/mohpackets/apis/explorer.py b/chord_metadata_service/mohpackets/apis/explorer.py
@@ -70,8 +70,8 @@ def explorer_donor(request, filters: DonorExplorerFilterSchema = Query(...)):
             systemictherapy__drug_name__in=filter_dict["systemic_therapy_drug_name"]
         )
 
-    if filter_dict["exclude_cohorts"]:
-        queryset = queryset.exclude(program_id__in=filter_dict["exclude_cohorts"])
+    if filter_dict["exclude_programs"]:
+        queryset = queryset.exclude(program_id__in=filter_dict["exclude_programs"])
 
     class Unnest(Func):
         contains_subquery = True

diff --git a/chord_metadata_service/mohpackets/docs/schema_version.txt b/chord_metadata_service/mohpackets/docs/schema_version.txt
@@ -1 +1 @@
-827f8485764cf524dee24e3835778864ea25dd27
+982eaf7e95bf11e8d11bad15bda8d8935c30b905
diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.json b/chord_metadata_service/mohpackets/docs/schemas/schema.json
@@ -66,7 +66,7 @@
                         }
                     }
                 },
-                "description": "Return the number of donors per cohort in the database.\nNote: This function is identical to `discover_patients_per_cohort`\nand is here because the frontend ingest uses it. It's probably best\nto clean up later.",
+                "description": "Return the number of donors per program in the database.\nNote: This function is identical to `discover_patients_per_program`\nand is here because the frontend ingest uses it. It's probably best\nto clean up later.",
                 "tags": [
                     "discovery"
                 ]
@@ -96,10 +96,10 @@
                 ]
             }
         },
-        "/v3/discovery/overview/cohort_count/": {
+        "/v3/discovery/overview/program_count/": {
             "get": {
-                "operationId": "chord_metadata_service_mohpackets_apis_discovery_discover_cohort_count",
-                "summary": "Discover Cohort Count",
+                "operationId": "chord_metadata_service_mohpackets_apis_discovery_discover_program_count",
+                "summary": "Discover Program Count",
                 "parameters": [],
                 "responses": {
                     "200": {
@@ -117,16 +117,16 @@
                         }
                     }
                 },
-                "description": "Return the number of cohorts in the database.",
+                "description": "Return the number of programs in the database.",
                 "tags": [
                     "overview"
                 ]
             }
         },
-        "/v3/discovery/overview/patients_per_cohort/": {
+        "/v3/discovery/overview/patients_per_program/": {
             "get": {
-                "operationId": "chord_metadata_service_mohpackets_apis_discovery_discover_patients_per_cohort",
-                "summary": "Discover Patients Per Cohort",
+                "operationId": "chord_metadata_service_mohpackets_apis_discovery_discover_patients_per_program",
+                "summary": "Discover Patients Per Program",
                 "parameters": [],
                 "responses": {
                     "200": {
@@ -135,7 +135,7 @@
                             "application/json": {
                                 "schema": {
                                     "items": {
-                                        "$ref": "#/components/schemas/PatientPerCohortSchema"
+                                        "$ref": "#/components/schemas/PatientPerProgramSchema"
                                     },
                                     "title": "Response",
                                     "type": "array"
@@ -144,7 +144,7 @@
                         }
                     }
                 },
-                "description": "Return the number of patients per cohort in the database.",
+                "description": "Return the number of patients per program in the database.",
                 "tags": [
                     "overview"
                 ]
@@ -1156,12 +1156,12 @@
                     },
                     {
                         "in": "query",
-                        "name": "exclude_cohorts",
+                        "name": "exclude_programs",
                         "schema": {
                             "items": {
                                 "type": "string"
                             },
-                            "title": "Exclude Cohorts",
+                            "title": "Exclude Programs",
                             "type": "array"
                         },
                         "required": false
@@ -3854,12 +3854,12 @@
                     },
                     {
                         "in": "query",
-                        "name": "exclude_cohorts",
+                        "name": "exclude_programs",
                         "schema": {
                             "items": {
                                 "type": "string"
                             },
-                            "title": "Exclude Cohorts",
+                            "title": "Exclude Programs",
                             "type": "array"
                         },
                         "required": false
@@ -3930,7 +3930,7 @@
                 "title": "DiscoveryDonorSchema",
                 "type": "object"
             },
-            "PatientPerCohortSchema": {
+            "PatientPerProgramSchema": {
                 "properties": {
                     "program_id": {
                         "title": "Program Id",
@@ -3945,7 +3945,7 @@
                     "program_id",
                     "patients_count"
                 ],
-                "title": "PatientPerCohortSchema",
+                "title": "PatientPerProgramSchema",
                 "type": "object"
             },
             "GenderCountSchema": {
@@ -9023,11 +9023,11 @@
                         "title": "Systemic Therapy Drug Name",
                         "type": "array"
                     },
-                    "exclude_cohorts": {
+                    "exclude_programs": {
                         "items": {
                             "type": "string"
                         },
-                        "title": "Exclude Cohorts",
+                        "title": "Exclude Programs",
                         "type": "array"
                     }
                 },

diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.md b/chord_metadata_service/mohpackets/docs/schemas/schema.md
@@ -62,8 +62,8 @@ Return all the programs in the database.
 
 *Discover Donors*
 
-Return the number of donors per cohort in the database.
-Note: This function is identical to `discover_patients_per_cohort`
+Return the number of donors per program in the database.
+Note: This function is identical to `discover_patients_per_program`
 and is here because the frontend ingest uses it. It's probably best
 to clean up later.
 
@@ -100,15 +100,15 @@ Retrieve the list of drug names and treatment for frontend usage
 
 <h1 id="moh-service-api-overview">overview</h1>
 
-## chord_metadata_service_mohpackets_apis_discovery_discover_cohort_count
+## chord_metadata_service_mohpackets_apis_discovery_discover_program_count
 
-<a id="opIdchord_metadata_service_mohpackets_apis_discovery_discover_cohort_count"></a>
+<a id="opIdchord_metadata_service_mohpackets_apis_discovery_discover_program_count"></a>
 
-`GET /v3/discovery/overview/cohort_count/`
+`GET /v3/discovery/overview/program_count/`
 
-*Discover Cohort Count*
+*Discover Program Count*
 
-Return the number of cohorts in the database.
+Return the number of programs in the database.
 
 > Example responses
 
@@ -121,15 +121,15 @@ Return the number of cohorts in the database.
 }
 ```
 
-## chord_metadata_service_mohpackets_apis_discovery_discover_patients_per_cohort
+## chord_metadata_service_mohpackets_apis_discovery_discover_patients_per_program
 
-<a id="opIdchord_metadata_service_mohpackets_apis_discovery_discover_patients_per_cohort"></a>
+<a id="opIdchord_metadata_service_mohpackets_apis_discovery_discover_patients_per_program"></a>
 
-`GET /v3/discovery/overview/patients_per_cohort/`
+`GET /v3/discovery/overview/patients_per_program/`
 
-*Discover Patients Per Cohort*
+*Discover Patients Per Program*
 
-Return the number of patients per cohort in the database.
+Return the number of patients per program in the database.
 
 > Example responses
 
@@ -876,7 +876,7 @@ Used by the query service to return donors along with their sample IDs, treatmen
 |treatment_type|query|array[string]|false|none|
 |primary_site|query|array[string]|false|none|
 |systemic_therapy_drug_name|query|array[string]|false|none|
-|exclude_cohorts|query|array[string]|false|none|
+|exclude_programs|query|array[string]|false|none|
 |page|query|integer|false|none|
 |page_size|query|integer|false|none|
 
@@ -1608,7 +1608,7 @@ This endpoint is called by the query service and bypasses user authorization.
 |treatment_type|query|array[string]|false|none|
 |primary_site|query|array[string]|false|none|
 |systemic_therapy_drug_name|query|array[string]|false|none|
-|exclude_cohorts|query|array[string]|false|none|
+|exclude_programs|query|array[string]|false|none|
 
 > Example responses
 
@@ -1683,12 +1683,12 @@ DiscoveryDonorSchema
 |program_id|string|true|none|none|
 |donors_count|string|true|none|none|
 
-<h2 id="tocS_PatientPerCohortSchema">PatientPerCohortSchema</h2>
+<h2 id="tocS_PatientPerProgramSchema">PatientPerProgramSchema</h2>
 
-<a id="schemapatientpercohortschema"></a>
-<a id="schema_PatientPerCohortSchema"></a>
-<a id="tocSpatientpercohortschema"></a>
-<a id="tocspatientpercohortschema"></a>
+<a id="schemapatientperprogramschema"></a>
+<a id="schema_PatientPerProgramSchema"></a>
+<a id="tocSpatientperprogramschema"></a>
+<a id="tocspatientperprogramschema"></a>
 
 ```json
 {
@@ -1698,7 +1698,7 @@ DiscoveryDonorSchema
 
 ```
 
-PatientPerCohortSchema
+PatientPerProgramSchema
 
 ### Properties
 
@@ -10547,7 +10547,7 @@ or
   "systemic_therapy_drug_name": [
     "string"
   ],
-  "exclude_cohorts": [
+  "exclude_programs": [
     "string"
   ]
 }
@@ -10563,7 +10563,7 @@ DonorExplorerFilterSchema
 |treatment_type|[string]|false|none|none|
 |primary_site|[string]|false|none|none|
 |systemic_therapy_drug_name|[string]|false|none|none|
-|exclude_cohorts|[string]|false|none|none|
+|exclude_programs|[string]|false|none|none|
 
 <h2 id="tocS_PagedQueryDonorSchema">PagedQueryDonorSchema</h2>
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		827f8485764cf524dee24e3835778864ea25dd27
		982eaf7e95bf11e8d11bad15bda8d8935c30b905