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@@ -9,14 +9,14 @@ build: | |
| 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 cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/analyses.json deploy-db-1:tmp/analyses.json | ||
| docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/biosamples.json deploy-db-1:tmp/biosamples.json | ||
| docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/cohorts.json deploy-db-1:tmp/cohorts.json | ||
| docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/datasets.json deploy-db-1:tmp/datasets.json | ||
| docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/genomicVariations.json deploy-db-1:tmp/genomicVariations.json | ||
| docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/individuals.json deploy-db-1:tmp/individuals.json | ||
| docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/runs.json deploy-db-1:tmp/runs.json | ||
| docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/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 | ||
|
|
@@ -25,5 +25,19 @@ build: | |
| 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 cp data/analyses.json deploy-db-1:tmp/analyses.json | ||
| docker cp data/biosamples.json deploy-db-1:tmp/biosamples.json | ||
| docker cp data/cohorts.json deploy-db-1:tmp/cohorts.json | ||
| docker cp data/datasets.json deploy-db-1:tmp/datasets.json | ||
| docker cp data/genomicVariations.json deploy-db-1:tmp/genomicVariations.json | ||
| docker cp data/individuals.json deploy-db-1:tmp/individuals.json | ||
| docker cp data/runs.json deploy-db-1:tmp/runs.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 beacon python beacon/reindex.py | ||
| docker exec beacon python beacon/db/extract_filtering_terms.py | ||