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Merge pull request #884 from microbiomedata/877-implement-mongodb-transaction-for-api-endpoint
Configure MongoDB Replica Set and implement example MongoDB transaction
2 parents 25a6cbd + d6563c2 commit 4273f49

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‎.docker/mongo_init/initialize_replica_set.sh

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#! /bin/sh
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###############################################################################
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# Overview
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# --------
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# This shell script uses `mongosh` to: (a) check whether the specified MongoDB
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# instance is a member of a replica set and, if is isn't, (b) creates a replica
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# set of which that MongoDB instance is the sole member.
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#
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# This shell script was designed to be run within a Docker container based upon
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# the `mongo:8.0.4` container image (i.e., https://hub.docker.com/_/mongo).
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#
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# Positional parameters
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# ---------------------
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# 1. MongoDB hostname (e.g., "mongo")
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# 2. MongoDB port (e.g., "27017")
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# 3. MongoDB username (e.g., "admin")
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# 4. MongoDB password (e.g., "root")
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#
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# References
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# ----------
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# 1. https://www.mongodb.com/docs/manual/reference/method/rs.status/
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# 2. https://www.mongodb.com/docs/mongodb-shell/reference/options/
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# 3. https://www.warp.dev/terminus/docker-compose-health-check
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###############################################################################
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echo 'Setting up replica set.'
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echo '
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try {
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rs.status();
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} catch (e) {
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rs.initiate({ _id: "rs0", members: [{ _id: 0, host: "localhost" }] });
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}
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' | mongosh \
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--host "${1}" \
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--port "${2}" \
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--username "${3}" \
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--password "${4}"
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echo 'Finished setting up replica set.'
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# Exit with a status code of 0.
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exit 0

‎.github/workflows/python-app.yml

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
3-
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# This GitHub Actions workflow spins up the "test" Docker Compose stack and runs automated tests within it.
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# Reference: https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions
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name: Python application
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# Note: The following events will trigger this workflow:
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# Reference: https://docs.github.com/en/actions/managing-workflow-runs-and-deployments/managing-workflow-runs/manually-running-a-workflow
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workflow_dispatch: { }
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4 # update version to maintain consistency across workflows
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# Prepare the MongoDB keyfile to be mounted by the `mongo` container.
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#
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# Note: This is to prevent MongoDB from reporting the error:
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# > "permissions on /path/to/keyfile are too open"
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#
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# Note: This involves making the file be readable _only_ by the OS user that MongoDB runs as.
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#
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# In containers using the `mongo` image, that user is named `mongodb` and has a
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# UID of `999`. That user belongs to a group named `mongodb`, whose GID is `999`.
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# You can verify this by looking at the Dockerfile layers on Docker Hub.
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# Reference: https://hub.docker.com/layers/library/mongo/8.0.5/images/sha256-90bf5066fed8a3cd59345d963922bc5cb557d4b4b2a0e38dfd9ee299c405741b
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#
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# The GHA Runner will allow me to `chmod 600` the file, but not `chown 999:999` it.
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# Since the GHA Runner will not allow me to `chown` the file, I use a Docker container
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# to (effectively) accomplish that. Since—after I use the Docker container to change
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# the file's owner—the GHA Runner will not allow me to then `chmod` the file, I opt to
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# accomplish that within the Docker container as well.
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#
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# The reason—within the Docker container—I do not `chmod` or `chown` the original file
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# directly, is that I am under the impression that ownership/permission changes made
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# within a container to mounted files that already exist on the host will not be seen
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# by the host. I have not found official documentation supporting this yet.
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# TODO: Include a reference about changing mounted file's permission within container.
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#
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- name: Restrict access to MongoDB keyfile
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run: |
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mkdir _tmp
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docker run --rm \
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-v ./mongoKeyFile:/mongoKeyFile \
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-v ./_tmp:/out \
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alpine \
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sh -c 'cp /mongoKeyFile /out/mongoKeyFile && chmod 600 /out/mongoKeyFile && chown 999:999 /out/mongoKeyFile'
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mv _tmp/mongoKeyFile ./mongoKeyFile
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rmdir _tmp
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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# make lint
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- name: Build and run containers upon which test runner depends
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run: make up-test
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- name: Build test runner container image
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- name: Build container image for test runner
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run: make test-build
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- name: Run tests
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run: make test-run

‎docker-compose.test.yml

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services:
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# This service runs the postgres DB used by dagster for run storage, schedule storage,
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# and event log storage.
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# Tests use `postgres:11` image.
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# https://github.com/dagster-io/dagster/blob/0.11.9/python_modules/libraries/dagster-postgres/dagster_postgres_tests/docker-compose.yml
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# Postgres server used by Dagster.
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#
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# > This service runs the postgres DB used by dagster for run storage, schedule storage,
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# > and event log storage.
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# > Tests use `postgres:11` image.
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# > https://github.com/dagster-io/dagster/blob/0.11.9/python_modules/libraries/dagster-postgres/dagster_postgres_tests/docker-compose.yml
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#
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dagster-postgresql:
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image: postgres:11
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container_name: dagster-postgresql
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volumes:
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- nmdc_runtime_test_postgres_data:/var/lib/postgresql/data
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environment:
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POSTGRES_USER: "postgres_user"
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POSTGRES_PASSWORD: "postgres_password"
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POSTGRES_DB: "postgres_db"
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volumes:
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- nmdc_runtime_test_postgres_data:/var/lib/postgresql/data
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# This service runs dagit.
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# Since our instance uses the QueuedRunCoordinator, any runs submitted from dagit will be put on
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# a queue and later dequeued and launched by dagster-daemon.
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# Web server that hosts the Dagster web UI.
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#
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# > This service runs dagit.
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# > Since our instance uses the QueuedRunCoordinator, any runs submitted from dagit will be put on
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# > a queue and later dequeued and launched by dagster-daemon.
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#
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dagster-dagit:
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build:
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context: .
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- "3000"
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ports:
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- "3000:3000"
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env_file:
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- .env.test
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environment:
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DAGSTER_POSTGRES_USER: "postgres_user"
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DAGSTER_POSTGRES_PASSWORD: "postgres_password"
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restart: on-failure
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volumes:
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- ./:/opt/dagster/lib
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env_file: .env.test
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# This service runs the dagster-daemon process, which is responsible for taking runs
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# off of the queue and launching them, as well as creating runs from schedules or sensors.
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# Dagster daemon.
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#
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# > This service runs the dagster-daemon process, which is responsible for taking runs
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# > off of the queue and launching them, as well as creating runs from schedules or sensors.
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#
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dagster-daemon:
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build:
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context: .
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container_name: dagster-daemon
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entrypoint: ["tini", "--", "../lib/nmdc_runtime/site/entrypoint-daemon.sh"]
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restart: on-failure
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env_file:
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- .env.test
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environment:
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DAGSTER_POSTGRES_USER: "postgres_user"
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DAGSTER_POSTGRES_PASSWORD: "postgres_password"
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DAGSTER_POSTGRES_DB: "postgres_db"
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depends_on:
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- dagster-postgresql
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dagster-postgresql: { condition: service_started }
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# Wait until the MongoDB replica set has been set up by the "init container"
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# before starting this Dagster daemon container.
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mongo-init: { condition: service_completed_successfully }
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volumes:
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- ./:/opt/dagster/lib
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env_file: .env.test
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# Uvicorn server hosting the FastAPI application.
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fastapi:
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build:
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context: .
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container_name: fastapi
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ports:
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- "8000:8000"
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env_file:
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- .env.test
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depends_on:
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- mongo
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volumes:
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- .:/code
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# Wait until the MongoDB replica set has been set up by the "init container"
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# before starting this FastAPI container.
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depends_on:
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mongo-init: { condition: service_completed_successfully }
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env_file: .env.test
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# Short-lived MongoDB server used to initialize the one used by the FastAPI application.
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mongo-init:
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image: mongo:8.0.4
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container_name: mongo-init
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volumes:
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- ./wait-for-it.sh:/wait-for-it.sh:ro
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- .docker/mongo_init/initialize_replica_set.sh:/initialize_replica_set.sh:ro
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depends_on:
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mongo: { condition: service_started }
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entrypoint: /bin/bash /wait-for-it.sh --host=mongo --port=27017 --timeout=20 -- /bin/sh /initialize_replica_set.sh mongo 27017 admin root
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# MongoDB server used by the FastAPI application.
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mongo:
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image: mongo:8.0.4
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container_name: mongo
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ports:
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- "27018:27017"
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volumes:
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- nmdc_runtime_test_mongo_data:/data/db
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- ~/nmdcdb-mongodump:/nmdc_dump:ro
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- ./tests/mongorestore-nmdc-testdb.sh:/mongorestore-nmdc-testdb.sh:ro
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restart: unless-stopped
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environment:
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MONGO_INITDB_ROOT_USERNAME: admin
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MONGO_INITDB_ROOT_PASSWORD: root
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# Configure MongoDB to run in replica set mode, so we can use MongoDB transactions.
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#
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# Note: Including a KeyFile is necessary when doing the combination of (a) running MongoDB in
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# replica set mode and (b) running MongoDB with authentication enabled.
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#
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command: ["--replSet", "rs0", "--bind_ip_all", "--keyFile", "/keyFile"]
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volumes:
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- nmdc_runtime_test_mongo_data:/data/db
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- ./mongoKeyFile:/keyFile:ro
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- ~/nmdcdb-mongodump:/nmdc_dump:ro
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- ./tests/mongorestore-nmdc-testdb.sh:/mongorestore-nmdc-testdb.sh:ro
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# Test runner.
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test:
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# Prevent Docker Compose from starting this service automatically.
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# Reference: https://stackoverflow.com/a/65957695
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dockerfile: nmdc_runtime/Dockerfile
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target: test
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container_name: test
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env_file:
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- .env.test
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env_file: .env.test
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depends_on:
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- mongo
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- fastapi
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- dagster-daemon
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- dagster-dagit
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mongo-init: { condition: service_completed_successfully }
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mongo: { condition: service_started }
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fastapi: { condition: service_started }
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dagster-daemon: { condition: service_started }
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dagster-dagit: { condition: service_started }
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volumes:
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- .:/code
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