diff --git a/.dockerignore b/.dockerignore index fdd9cdf..15fac95 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,2 +1,3 @@ *.vcf.gz -ri_tools/vcf/files_to_read/*vcf.gz \ No newline at end of file +ri_tools/vcf/files_to_read/*vcf.gz +beacon/connections/mongo/data/datasets/* \ No newline at end of file diff --git a/beacon/connections/mongo/reindex.py b/beacon/connections/mongo/reindex.py index a40c041..708e112 100644 --- a/beacon/connections/mongo/reindex.py +++ b/beacon/connections/mongo/reindex.py @@ -33,6 +33,14 @@ client.beacon.validate_collection("synonyms") except Exception: db=client.beacon.create_collection(name="synonyms") +try: + client.beacon.validate_collection("caseLevelData") +except Exception: + db=client.beacon.create_collection(name="caseLevelData") +try: + client.beacon.validate_collection("targets") +except Exception: + db=client.beacon.create_collection(name="targets") try: client.beacon.drop_collection("counts") except Exception: diff --git a/docker-compose.yml b/docker-compose.yml index e57b8e4..cb66798 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -67,6 +67,7 @@ services: db: image: mongo:5 + command: --wiredTigerCacheSizeGB 4 hostname: mongo container_name: mongoprod ports: diff --git a/ri-tools/conf/conf.py b/ri-tools/conf/conf.py index 9ea7631..9590156 100644 --- a/ri-tools/conf/conf.py +++ b/ri-tools/conf/conf.py @@ -7,6 +7,7 @@ reference_genome='GRCh37' # Choose one between NCBI36, GRCh37, GRCh38 datasetId='COVID_pop11_fin_2' case_level_data=False +num_rows=7000000 ### MongoDB parameters ### database_host = 'mongo'