nmdc-runtime 1.8.0__tar.gz → 1.9.0__tar.gz

{nmdc_runtime-1.8.0 → nmdc_runtime-1.9.0}/Makefile

@@ -69,7 +69,7 @@ down-dev:
 	docker compose down
 
 down-test:
-	docker compose --file docker-compose.test.yml down
+	docker compose --file docker-compose.test.yml down --volumes
 
 follow-fastapi:
 	docker compose logs fastapi -f
@@ -97,14 +97,14 @@ nersc-mongo-tunnels:
 		-o ServerAliveInterval=60 \
 		${NERSC_USERNAME}@dtn02.nersc.gov
 
-mongorestore-nmdc-dev:
-	wget https://portal.nersc.gov/cfs/m3408/meta/mongodumps/mdb-nmdc-dev.tar.gz
-	tar zxvf mdb-nmdc-dev.tar.gz
-	rm -rf nmdc/._* # Not sure why ._* files are extracted.
-	mongorestore -h localhost:27018 -u admin -p root --authenticationDatabase=admin \
-		--drop --gzip -d nmdc nmdc
-	rm -rf nmdc/
-	rm mdb-nmdc-dev.tar.gz
+mongorestore-nmdc-db:
+	mkdir -p /tmp/remote-mongodump/nmdc
+	# SSH into the remote server, stream the dump directory as a gzipped tar archive, and extract it locally.
+	ssh -i ~/.ssh/nersc ${NERSC_USERNAME}@dtn01.nersc.gov \
+		'tar -czf - -C /global/cfs/projectdirs/m3408/nmdc-mongodumps/dump_nmdc-prod_2024-07-29_20-12-07/nmdc .' \
+		| tar -xzv -C /tmp/remote-mongodump/nmdc
+	mongorestore -v -h localhost:27018 -u admin -p root --authenticationDatabase=admin \
+		--drop --nsInclude='nmdc.*' --dir /tmp/remote-mongodump
 
 quick-blade:
 	python -c "from nmdc_runtime.api.core.idgen import generate_id; print(f'nmdc:nt-11-{generate_id(length=8, split_every=0)}')"

{nmdc_runtime-1.8.0/nmdc_runtime.egg-info → nmdc_runtime-1.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nmdc_runtime
-Version: 1.8.0
+Version: 1.9.0
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston

{nmdc_runtime-1.8.0 → nmdc_runtime-1.9.0}/docker-compose.test.yml

@@ -9,7 +9,7 @@ services:
     image: postgres:11
     container_name: dagster-postgresql
     volumes:
-      - nmdc_runtime_postgres_data:/var/lib/postgresql/data
+      - nmdc_runtime_test_postgres_data:/var/lib/postgresql/data
     environment:
       POSTGRES_USER: "postgres_user"
       POSTGRES_PASSWORD: "postgres_password"
@@ -80,7 +80,7 @@ services:
     ports:
       - "27018:27017"
     volumes:
-      - nmdc_runtime_mongo_data:/data/db
+      - nmdc_runtime_test_mongo_data:/data/db
       - ~/nmdcdb-mongodump:/nmdc_dump:ro
       - ./tests/mongorestore-nmdc-testdb.sh:/mongorestore-nmdc-testdb.sh:ro
     restart: unless-stopped
@@ -106,7 +106,7 @@ services:
       - .:/code
 
 volumes:
-  nmdc_runtime_postgres_data:
+  nmdc_runtime_test_postgres_data:
     driver: local
-  nmdc_runtime_mongo_data:
+  nmdc_runtime_test_mongo_data:
     driver: local