Merge pull request #319 from EGA-archive/develop

Fixing analyses cohorts id parameter query

beacon/conf.py

@@ -9,8 +9,8 @@
 #
 # Beacon general info
 #
-beacon_id = 'org.ega-archive.ga4gh-approval-beacon-test'  # ID of the Beacon
-beacon_name = 'GA4GH Approval Beacon Test'  # Name of the Beacon service
+beacon_id = 'org.ega-archive.beacon-ri-demo'  # ID of the Beacon
+beacon_name = 'Beacon Reference Implementation demo'  # Name of the Beacon service
 api_version = 'v2.0.0'  # Version of the Beacon implementation
 uri = 'https://beacon-apis-demo.ega-archive.org/api/'
 

beacon/db/cohorts.py

@@ -82,7 +82,7 @@ def get_analyses_of_cohort(entry_id: Optional[str], qparams: RequestParams, data
     count = get_count(client.beacon.cohorts, query)
     with open("/beacon/beacon/request/cohorts.yml", 'r') as datasets_file:
         datasets_dict = yaml.safe_load(datasets_file)
-    cohort_ids=get_cross_query(datasets_dict[entry_id],'biosampleIds','id')
+    cohort_ids=get_cross_query(datasets_dict[entry_id],'biosampleIds','biosampleId')
     query = apply_filters(cohort_ids, qparams.query.filters, collection, {})
     schema = DefaultSchemas.ANALYSES
     with open("/beacon/beacon/request/datasets.yml", 'r') as datasets_file:

deploy/Makefile

@@ -1,29 +1,43 @@
 build:
-	docker-compose up -d --build
+	docker-compose up -d --build beacon permissions db
 	sleep 10
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.filtering_terms.deleteMany({})"'
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.analyses.deleteMany({})"'
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.biosamples.deleteMany({})"'
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.cohorts.deleteMany({})"'
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.datasets.deleteMany({})"'
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.genomicVariations.deleteMany({})"'
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.individuals.deleteMany({})"'
-	docker exec deploy-db-1 /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.runs.deleteMany({})"'
-	docker cp cancer_dataset/analyses.json deploy-db-1:tmp/analyses.json
-	docker cp cancer_dataset/biosamples.json deploy-db-1:tmp/biosamples.json
-	docker cp cancer_dataset/cohorts.json deploy-db-1:tmp/cohorts.json
-	docker cp cancer_dataset/datasets.json deploy-db-1:tmp/datasets.json
-	docker cp cancer_dataset/genomicVariations.json deploy-db-1:tmp/genomicVariations.json
-	docker cp cancer_dataset/individuals.json deploy-db-1:tmp/individuals.json
-	docker cp cancer_dataset/runs.json deploy-db-1:tmp/runs.json
-	docker cp cancer_dataset/filtering_terms.json deploy-db-1:tmp/filtering_terms.json
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations
-	docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/filtering_terms.json --collection filtering_terms
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.filtering_terms.deleteMany({})"'
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.analyses.deleteMany({})"'
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.biosamples.deleteMany({})"'
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.cohorts.deleteMany({})"'
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.datasets.deleteMany({})"'
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.genomicVariations.deleteMany({})"'
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.individuals.deleteMany({})"'
+	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.runs.deleteMany({})"'
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/analyses.json rimongo:tmp/analyses.json
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/biosamples.json rimongo:tmp/biosamples.json
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/cohorts.json rimongo:tmp/cohorts.json
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/datasets.json rimongo:tmp/datasets.json
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/genomicVariations.json rimongo:tmp/genomicVariations.json
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/individuals.json rimongo:tmp/individuals.json
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/runs.json rimongo:tmp/runs.json
+	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/filtering_terms.json rimongo:tmp/filtering_terms.json
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/filtering_terms.json --collection filtering_terms
+	docker cp data/analyses.json rimongo:tmp/analyses.json
+	docker cp data/biosamples.json rimongo:tmp/biosamples.json
+	docker cp data/cohorts.json rimongo:tmp/cohorts.json
+	docker cp data/datasets.json rimongo:tmp/datasets.json
+	docker cp data/genomicVariations.json rimongo:tmp/genomicVariations.json
+	docker cp data/individuals.json rimongo:tmp/individuals.json
+	docker cp data/runs.json rimongo:tmp/runs.json
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs
+	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations
 	docker exec beacon python beacon/reindex.py
 	docker exec beacon python beacon/db/extract_filtering_terms.py

deploy/conf.py

@@ -3,8 +3,8 @@
 #
 # Beacon general info
 #
-beacon_id = 'org.ega-archive.ga4gh-approval-beacon-test'  # ID of the Beacon
-beacon_name = 'GA4GH Approval Beacon Test'  # Name of the Beacon service
+beacon_id = 'org.ega-archive.beacon-ri-demo'  # ID of the Beacon
+beacon_name = 'Beacon Reference Implementation demo'  # Name of the Beacon service
 api_version = 'v2.0.0'  # Version of the Beacon implementation
 uri = 'https://beacon-apis-demo.ega-archive.org/api/'