From 1f8d6744c14da1b5dae86e2a48812de729990640 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oriol=20L=C3=B3pez-Doriga?= Date: Mon, 15 Apr 2024 21:27:34 +0200 Subject: [PATCH] Makefile ready --- deploy/Makefile | 30 ++++++++++++++++++++++-------- 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/deploy/Makefile b/deploy/Makefile index 40072f42..7f9afa82 100644 --- a/deploy/Makefile +++ b/deploy/Makefile @@ -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:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts @@ -25,5 +25,19 @@ build: docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/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:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets + docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals + docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts + docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses + docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples + docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs + docker exec deploy-db-1 mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/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 \ No newline at end of file