editing Makefile and max granularity

beacon/conf/conf.py

@@ -23,7 +23,7 @@
 alternative_url = 'https://beacon.ega-archive.org/api'
 create_datetime = '2021-11-29T12:00:00.000000'
 update_datetime = ''
-default_beacon_granularity = "record" # boolean, count or record
+max_beacon_granularity = "record" # boolean, count or record
 security_levels = ['PUBLIC', 'REGISTERED', 'CONTROLLED']
 documentation_url = 'https://b2ri-documentation-demo.ega-archive.org/'
 alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges','phenotypicFeatures.onset.iso8601duration']

beacon/connections/mongo/Makefile

@@ -1,19 +1,10 @@
 build:
-	docker cp data/analyses.json mongoprod:tmp/analyses.json
-	docker cp data/biosamples.json mongoprod:tmp/biosamples.json
-	docker cp data/cohorts.json mongoprod:tmp/cohorts.json
-	docker cp data/datasets.json mongoprod:tmp/datasets.json
-	docker cp data/genomicVariations.json mongoprod:tmp/genomicVariations.json
-	docker cp data/individuals.json mongoprod:tmp/individuals.json
-	docker cp data/runs.json mongoprod:tmp/runs.json
-	docker cp data/targets.json mongoprod:tmp/targets.json
-	docker cp data/caseLevelData.json mongoprod:tmp/caseLevelData.json
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/targets.json --collection targets
-	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/caseLevelData.json --collection caseLevelData
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/datasets.json --collection datasets
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/individuals.json --collection individuals
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/cohorts.json --collection cohorts
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/analyses.json --collection analyses
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/biosamples.json --collection biosamples
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/genomicVariations.json --collection genomicVariations
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/runs.json --collection runs
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/targets.json --collection targets
+	docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/caseLevelData.json --collection caseLevelData

beacon/request/parameters.py

@@ -9,7 +9,7 @@
 )
 from strenum import StrEnum
 from typing import List, Optional, Union
-from beacon.conf.conf import api_version, default_beacon_granularity
+from beacon.conf.conf import api_version, max_beacon_granularity
 from humps.main import camelize
 from aiohttp.web_request import Request
 from aiohttp import web
@@ -83,7 +83,7 @@ class RequestQuery(CamelModel):
     pagination: Pagination = Pagination()
     request_parameters: Union[list,dict] = {}
     test_mode: bool = False
-    requested_granularity: Granularity = Granularity(default_beacon_granularity)
+    requested_granularity: Granularity = Granularity(max_beacon_granularity)
     scope: str = None
 
 class SequenceQuery(BaseModel):

beacon/response/builder.py

@@ -1,7 +1,7 @@
 from aiohttp.web_request import Request
 from beacon.response.catalog import build_beacon_record_response_by_dataset, build_beacon_count_response, build_beacon_collection_response, build_beacon_info_response, build_map, build_configuration, build_entry_types, build_beacon_service_info_response, build_filtering_terms_response, build_beacon_boolean_response, build_beacon_none_response
 from beacon.logs.logs import log_with_args, LOG
-from beacon.conf.conf import level, default_beacon_granularity
+from beacon.conf.conf import level, max_beacon_granularity
 from beacon.request.classes import Granularity
 from beacon.source.manage import analyses, biosamples, cohorts, datasets, g_variants, individuals, runs, filtering_terms
 
@@ -39,11 +39,11 @@ async def builder(self, request: Request, datasets, qparams, entry_type, entry_i
         if testMode == True:
             datasets = ['test']
         datasets_docs, datasets_count, count, entity_schema, include, datasets = await module.execute_function(self, entry_type, datasets, qparams, entry_id)
-        if include != 'NONE' and granularity == Granularity.RECORD and default_beacon_granularity == 'record':
+        if include != 'NONE' and granularity == Granularity.RECORD and max_beacon_granularity == 'record':
             response = build_beacon_record_response_by_dataset(self, datasets, datasets_docs, datasets_count, count, qparams, entity_schema)
-        elif include == 'NONE' and granularity == Granularity.RECORD and default_beacon_granularity == 'record':
+        elif include == 'NONE' and granularity == Granularity.RECORD and max_beacon_granularity == 'record':
             response = build_beacon_none_response(self, datasets_docs["NONE"], count, qparams, entity_schema)
-        elif granularity == Granularity.COUNT or granularity == Granularity.RECORD and default_beacon_granularity in ['count', 'record']:
+        elif granularity == Granularity.COUNT and max_beacon_granularity in ['count', 'record'] or granularity == Granularity.RECORD and max_beacon_granularity in ['count']:
             response = build_beacon_count_response(self, count, qparams, entity_schema)
         else:
             response = build_beacon_boolean_response(self, count, qparams, entity_schema)

beacon/response/catalog.py

@@ -314,7 +314,7 @@ def build_configuration(self):
                 'productionStatus': conf.environment.upper()
             },
             'securityAttributes': {
-                'defaultGranularity': conf.default_beacon_granularity,
+                'defaultGranularity': conf.max_beacon_granularity,
                 'securityLevels': conf.security_levels
             },
             'entryTypes': entry_types['entryTypes']

docker-compose.yml

@@ -67,11 +67,11 @@ services:
 
   db:
     image: mongo:5
-    command: --wiredTigerCacheSizeGB 4
+    command: --wiredTigerCacheSizeGB 4 -port 27018
     hostname: mongo
     container_name: mongoprod
     ports:
-      - 27017:27017
+      - 27018:27017
     environment:
       MONGO_INITDB_ROOT_USERNAME: root
       MONGO_INITDB_ROOT_PASSWORD: example