diff --git a/beacon/request/handlers.py b/beacon/request/handlers.py index ba6e9718..16b244cc 100644 --- a/beacon/request/handlers.py +++ b/beacon/request/handlers.py @@ -160,6 +160,7 @@ async def wrapper(request: Request): datasets_docs={} datasets_count={} #LOG.debug(response_datasets) + new_count=0 loop = asyncio.get_running_loop() for dataset in response_datasets: with ThreadPoolExecutor() as pool: diff --git a/deploy/Makefile b/deploy/Makefile index 6120a59b..88eb2bf9 100644 --- a/deploy/Makefile +++ b/deploy/Makefile @@ -23,5 +23,21 @@ build: docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/analyses.json mongoega:tmp/analyses.json + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/biosamples.json mongoega:tmp/biosamples.json + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/cohorts.json mongoega:tmp/cohorts.json + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/datasets.json mongoega:tmp/datasets.json + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/genomicVariations.json mongoega:tmp/genomicVariations.json + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/individuals.json mongoega:tmp/individuals.json + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/runs.json mongoega:tmp/runs.json + docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/tcga-coad/filtering_terms.json mongoega:tmp/filtering_terms.json + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/runs.json --collection runs + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations + docker exec mongoega mongoimport --jsonArray --uri "mongodb://root:example@127.0.0.1:27020/beacon?authSource=admin" --file /tmp/filtering_terms.json --collection filtering_terms docker exec beacon python beacon/reindex.py docker exec beacon python beacon/db/extract_filtering_terms.py \ No newline at end of file