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Master to spanish-beacon #320

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Master to spanish-beacon #320

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1f8d674
Makefile ready
costero-e Apr 15, 2024
cfe7ffa
changing container name for mongo
costero-e Apr 15, 2024
778b8dd
beacon ri demo renamed
costero-e Apr 17, 2024
5a5f957
fixing cohorts analyses parameter query
costero-e Apr 24, 2024
64fab7d
deleting container name for db
costero-e Apr 24, 2024
fdcb62b
Merge pull request #319 from EGA-archive/develop
costero-e Apr 24, 2024
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4 changes: 2 additions & 2 deletions beacon/conf.py
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Expand Up @@ -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/'

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2 changes: 1 addition & 1 deletion beacon/db/cohorts.py
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Expand Up @@ -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:
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64 changes: 39 additions & 25 deletions deploy/Makefile
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@@ -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
4 changes: 2 additions & 2 deletions deploy/conf.py
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Expand Up @@ -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/'

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115 changes: 0 additions & 115 deletions deploy/data/cohorts_av.json
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79 changes: 0 additions & 79 deletions deploy/data/datasets_av.json
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