nmdc-runtime 2.4.0__tar.gz → 2.5.0__tar.gz

nmdc_runtime-2.5.0/.docker/mongo_init/initialize_replica_set.sh

@@ -0,0 +1,44 @@
+#! /bin/sh
+
+###############################################################################
+# Overview
+# --------
+# This shell script uses `mongosh` to: (a) check whether the specified MongoDB
+# instance is a member of a replica set and, if is isn't, (b) creates a replica
+# set of which that MongoDB instance is the sole member.
+#
+# This shell script was designed to be run within a Docker container based upon
+# the `mongo:8.0.4` container image (i.e., https://hub.docker.com/_/mongo).
+#
+# Positional parameters
+# ---------------------
+# 1. MongoDB hostname (e.g., "mongo")
+# 2. MongoDB port     (e.g., "27017")
+# 3. MongoDB username (e.g., "admin")
+# 4. MongoDB password (e.g., "root")
+#
+# References
+# ----------
+# 1. https://www.mongodb.com/docs/manual/reference/method/rs.status/
+# 2. https://www.mongodb.com/docs/mongodb-shell/reference/options/
+# 3. https://www.warp.dev/terminus/docker-compose-health-check
+###############################################################################
+
+echo 'Setting up replica set.'
+
+echo '
+  try {
+    rs.status();
+  } catch (e) {
+    rs.initiate({ _id: "rs0", members: [{ _id: 0, host: "localhost" }] });
+  }
+' | mongosh \
+  --host "${1}" \
+  --port "${2}" \
+  --username "${3}" \
+  --password "${4}"
+
+echo 'Finished setting up replica set.'
+
+# Exit with a status code of 0.
+exit 0

nmdc_runtime-2.5.0/.dockerignore

@@ -0,0 +1,29 @@
+.env*
+!.env.example
+!.env.test
+.idea
+deployment
+.eggs
+.pytest_cache
+build
+dist
+
+# Omit the Docker configuration/specification files from the image build context,
+# so we can edit them without invalidating existing image layers.
+# Reference: https://docs.docker.com/build/concepts/context/#dockerignore-files
+/.dockerignore
+/.docker
+/.gitpod.Dockerfile
+/docker-compose.yml
+/docker-compose.test.yml
+/nmdc_runtime/Dockerfile
+
+# Omit any local Python virtual environment from the image build context. The
+# image build process includes its own package download/installation step.
+/venv
+/.venv
+
+# Omit residual files left behind by some tests.
+/neon.db
+/neon_api_cache.sqlite
+/neon_cache.sqlite

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/.env.example

@@ -51,4 +51,4 @@ INFO_BANNER_INNERHTML='Announcement: Something important is about to happen. If
 
 # To get the latest mongo dump directory, run e.g.
 # ssh -i ~/.ssh/nersc -q ${NERSC_USERNAME}@dtn01.nersc.gov 'bash -s ' < util/get_latest_nmdc_prod_dump_dir.sh 2>/dev/null
-MONGO_REMOTE_DUMP_DIR=/global/cfs/projectdirs/m3408/nmdc-mongodumps/dump_nmdc-prod_2024-11-26_20-12-40
+MONGO_REMOTE_DUMP_DIR=/global/cfs/projectdirs/m3408/nmdc-mongodumps/dump_nmdc-prod_2025-02-12_20-12-02

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/.env.test

@@ -20,4 +20,4 @@ API_SITE_ID=nmdc-runtime
 API_SITE_CLIENT_ID=chws-tk74-51
 API_SITE_CLIENT_SECRET=070d56033559e3096d4f82d30aabdd51c3b8a57ac20d24f743a27444d5edc3db
 
-MINTING_SERVICE_ID=nmdc:minter_service_11
+MINTING_SERVICE_ID=nmdc:minter_service_11

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/.github/workflows/build-and-release-to-spin.yml

@@ -9,7 +9,7 @@ on:
     paths:
       - '.github/workflows/build-and-release-to-spin.yml'
       - 'Makefile'
-      - '**.Dockerfile'
+      - '**/Dockerfile'
       - '**.py'
       - 'requirements/main.txt'
 
@@ -78,7 +78,10 @@ jobs:
         with:
           context: .
           push: ${{ env.IS_ORIGINAL_REPO }}
-          file: nmdc_runtime/${{ matrix.image }}.Dockerfile
+          file: nmdc_runtime/Dockerfile
+          # Note: Since our `Dockerfile` describes multiple stages, we use the `target` option to specify a stage.
+          #       Reference: https://github.com/marketplace/actions/build-and-push-docker-images#inputs
+          target: ${{ matrix.image }}
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
 

nmdc_runtime-2.5.0/.github/workflows/python-app.yml

@@ -0,0 +1,91 @@
+# This GitHub Actions workflow spins up the "test" Docker Compose stack and runs automated tests within it.
+# Reference: https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions
+name: Python application
+
+# Note: The following events will trigger this workflow:
+#       1. Someone pushes a commit to `main` that includes changes to any of the listed files.
+#       2. Someone opens a pull request that includes changes to any of the listed files.
+#       3. Someone clicks the "Run workflow" button on the "Actions" tab on GitHub.
+#
+#  References:
+#  - https://docs.github.com/en/actions/writing-workflows/choosing-when-your-workflow-runs/triggering-a-workflow#example-including-paths
+#  - https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet
+#
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - '.github/workflows/python-app.yml'
+      - 'Makefile'
+      - '**/Dockerfile'
+      - '**.py'
+      - 'requirements/main.txt'
+      # Every file in the `data` directory or in any of its subdirectories:
+      - 'metadata-translation/notebooks/data/**'
+  pull_request:
+    paths:
+      - '.github/workflows/python-app.yml'
+      - 'Makefile'
+      - '**/Dockerfile'
+      - '**.py'
+      - 'requirements/main.txt'
+      - 'metadata-translation/notebooks/data/**'
+  # Allow developers to trigger this workflow manually via the "Actions" page on GitHub.
+  # Reference: https://docs.github.com/en/actions/managing-workflow-runs-and-deployments/managing-workflow-runs/manually-running-a-workflow
+  workflow_dispatch: { }
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4 # update version to maintain consistency across workflows
+    # Prepare the MongoDB keyfile to be mounted by the `mongo` container.
+    #
+    # Note: This is to prevent MongoDB from reporting the error:
+    #       > "permissions on /path/to/keyfile are too open"
+    #
+    # Note: This involves making the file be readable _only_ by the OS user that MongoDB runs as.
+    #
+    #       In containers using the `mongo` image, that user is named `mongodb` and has a
+    #       UID of `999`. That user belongs to a group named `mongodb`, whose GID is `999`.
+    #       You can verify this by looking at the Dockerfile layers on Docker Hub.
+    #       Reference: https://hub.docker.com/layers/library/mongo/8.0.5/images/sha256-90bf5066fed8a3cd59345d963922bc5cb557d4b4b2a0e38dfd9ee299c405741b
+    #
+    #       The GHA Runner will allow me to `chmod 600` the file, but not `chown 999:999` it.
+    #       Since the GHA Runner will not allow me to `chown` the file, I use a Docker container
+    #       to (effectively) accomplish that. Since—after I use the Docker container to change
+    #       the file's owner—the GHA Runner will not allow me to then `chmod` the file, I opt to
+    #       accomplish that within the Docker container as well.
+    #
+    #       The reason—within the Docker container—I do not `chmod` or `chown` the original file
+    #       directly, is that I am under the impression that ownership/permission changes made
+    #       within a container to mounted files that already exist on the host will not be seen
+    #       by the host. I have not found official documentation supporting this yet.
+    #       TODO: Include a reference about changing mounted file's permission within container.
+    #
+    - name: Restrict access to MongoDB keyfile
+      run: |
+        mkdir _tmp
+        docker run --rm \
+          -v ./mongoKeyFile:/mongoKeyFile \
+          -v ./_tmp:/out \
+          alpine \
+          sh -c 'cp /mongoKeyFile /out/mongoKeyFile && chmod 600 /out/mongoKeyFile && chown 999:999 /out/mongoKeyFile'
+        mv _tmp/mongoKeyFile ./mongoKeyFile
+        rmdir _tmp
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+# deprecated: Consider merging python.app.yml and lint.yml
+#    - name: Lint with flake8
+#      run: |
+#        pip install flake8
+#        make lint
+    - name: Build and run containers upon which test runner depends
+      run: make up-test
+    - name: Build container image for test runner
+      run: make test-build
+    - name: Run tests
+      run: make test-run

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/.gitignore

@@ -15,6 +15,7 @@ downloads/
 eggs/
 .eggs/
 lib/
+!/tests/lib/
 lib64/
 parts/
 sdist/

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/Makefile

@@ -38,25 +38,39 @@ update: update-deps init
 up-dev:
 	docker compose up --build --force-recreate --detach --remove-orphans
 
+# Restores the MongoDB dump residing in `./tests/nmdcdb` on the Docker host, into the MongoDB server in the dev stack.
 dev-reset-db:
 	docker compose \
-		exec mongo /bin/bash -c "./app_tests/mongorestore-nmdc-testdb.sh"
+		exec mongo /bin/bash -c "/mongorestore-nmdc-testdb.sh"
 
+# Uses Docker Compose to build and spin up the stack upon which the `test` container (i.e. the test runner) depends.
+#
+# Note: This does not build or spin up the `test` container, itself, since the `test` container's Docker Compose service
+#       has the "donotstart" profile specified for it in `docker-compose.test.yml`.
+#
 up-test:
 	docker compose --file docker-compose.test.yml \
 		up --build --force-recreate --detach --remove-orphans
 
+# Uses Docker Compose to build the container image for the `test` container (i.e. the test runner).
 test-build:
 	docker compose --file docker-compose.test.yml build test
 
-test-dbinit:
+# Restores the MongoDB dump residing in `./tests/nmdcdb` on the Docker host, into the MongoDB server in the test stack.
+test-reset-db:
 	docker compose --file docker-compose.test.yml \
 		exec mongo /bin/bash -c "/mongorestore-nmdc-testdb.sh"
 
-# Tip: If you append a file path to this "recipe", pytest will run only the tests defined in that file.
-#      For example, append `tests/test_api/test_endpoints.py` to have pytest only run the endpoint tests.
+# Uses Docker Compose to spin up the `test` container (i.e. the test runner), effectively running the tests.
+#
+# Tip: If you append `ARGS=` and a file path to the `make` command, pytest will run only the tests defined in that file.
+#      For example, to run only the tests defined in `tests/test_api/test_endpoints.py`:
+#      ```
+#      $ make test-run ARGS="tests/test_api/test_endpoints.py"
+#      ```
+#
 test-run:
-	docker compose --file docker-compose.test.yml run test
+	docker compose --file docker-compose.test.yml run test $(ARGS)
 
 test: test-build test-run
 

{nmdc_runtime-2.4.0/nmdc_runtime.egg-info → nmdc_runtime-2.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nmdc_runtime
-Version: 2.4.0
+Version: 2.5.0
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston
@@ -17,6 +17,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: requires-python
 Dynamic: summary
 
@@ -37,8 +38,7 @@ houses the LinkML schema specification, as well as generated artifacts (e.g. JSO
 * [nmdc-server](https://github.com/microbiomedata/nmdc-server)
 houses code specific to the data portal -- its database, back-end API, and front-end application.
 
-* [workflow_documentation](https://docs.microbiomedata.org/workflows/)
-references workflow code spread across several repositories, that take source data and produce computed data.
+* Workflows — documented in the [workflows](https://docs.microbiomedata.org/workflows/) section of the NMDC documentation website — take source data and produce computed data.
 
 * This repo (nmdc-runtime)
    * houses code that takes source data and computed data, and transforms it
@@ -156,6 +156,9 @@ Tests can be found in `tests` and are run with the following commands:
 ```bash
 make up-test
 make test
+
+# Run a Specific test file eg. tests/test_api/test_endpoints.py
+make test ARGS="tests/test_api/test_endpoints.py"
 ```
 
 As you create Dagster solids and pipelines, add tests in `tests/` to check that your code behaves as
@@ -164,6 +167,16 @@ desired and does not break over time.
 [For hints on how to write tests for solids and pipelines in Dagster, see their documentation
 tutorial on Testing](https://docs.dagster.io/tutorial/testable).
 
+### RAM usage
+
+The `dagster-daemon` and `dagster-dagit` containers can consume a lot of RAM. If tests are failing and the console of
+the `test` container shows "Error 137," here is something you can try as a workaround: In Docker Desktop, go to 
+"Settings > Resources > Advanced," and increase the memory limit. One of our team members has
+found **12 GB** to be sufficient for running the tests.
+
+> Dedicating 12 GB of RAM to Docker may be prohibitive for some prospective developers.
+> There is an open [issue](https://github.com/microbiomedata/nmdc-runtime/issues/928) about the memory requirement.
+
 ## Publish to PyPI
 
 This repository contains a GitHub Actions workflow that publishes a Python package to [PyPI](https://pypi.org/project/nmdc-runtime/).

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/README.md

@@ -15,8 +15,7 @@ houses the LinkML schema specification, as well as generated artifacts (e.g. JSO
 * [nmdc-server](https://github.com/microbiomedata/nmdc-server)
 houses code specific to the data portal -- its database, back-end API, and front-end application.
 
-* [workflow_documentation](https://docs.microbiomedata.org/workflows/)
-references workflow code spread across several repositories, that take source data and produce computed data.
+* Workflows — documented in the [workflows](https://docs.microbiomedata.org/workflows/) section of the NMDC documentation website — take source data and produce computed data.
 
 * This repo (nmdc-runtime)
    * houses code that takes source data and computed data, and transforms it
@@ -134,6 +133,9 @@ Tests can be found in `tests` and are run with the following commands:
 ```bash
 make up-test
 make test
+
+# Run a Specific test file eg. tests/test_api/test_endpoints.py
+make test ARGS="tests/test_api/test_endpoints.py"
 ```
 
 As you create Dagster solids and pipelines, add tests in `tests/` to check that your code behaves as
@@ -142,6 +144,16 @@ desired and does not break over time.
 [For hints on how to write tests for solids and pipelines in Dagster, see their documentation
 tutorial on Testing](https://docs.dagster.io/tutorial/testable).
 
+### RAM usage
+
+The `dagster-daemon` and `dagster-dagit` containers can consume a lot of RAM. If tests are failing and the console of
+the `test` container shows "Error 137," here is something you can try as a workaround: In Docker Desktop, go to 
+"Settings > Resources > Advanced," and increase the memory limit. One of our team members has
+found **12 GB** to be sufficient for running the tests.
+
+> Dedicating 12 GB of RAM to Docker may be prohibitive for some prospective developers.
+> There is an open [issue](https://github.com/microbiomedata/nmdc-runtime/issues/928) about the memory requirement.
+
 ## Publish to PyPI
 
 This repository contains a GitHub Actions workflow that publishes a Python package to [PyPI](https://pypi.org/project/nmdc-runtime/).

nmdc_runtime-2.5.0/docker-compose.test.yml

@@ -0,0 +1,144 @@
+services:
+
+  # Postgres server used by Dagster.
+  #
+  # > This service runs the postgres DB used by dagster for run storage, schedule storage,
+  # > and event log storage.
+  # > Tests use `postgres:11` image.
+  # > https://github.com/dagster-io/dagster/blob/0.11.9/python_modules/libraries/dagster-postgres/dagster_postgres_tests/docker-compose.yml
+  #
+  dagster-postgresql:
+    image: postgres:11
+    environment:
+      POSTGRES_USER: "postgres_user"
+      POSTGRES_PASSWORD: "postgres_password"
+      POSTGRES_DB: "postgres_db"
+    volumes:
+      - postgres_data:/var/lib/postgresql/data
+
+  # Web server that hosts the Dagster web UI.
+  #
+  # > This service runs dagit.
+  # > Since our instance uses the QueuedRunCoordinator, any runs submitted from dagit will be put on
+  # > a queue and later dequeued and launched by dagster-daemon.
+  #
+  dagster-dagit:
+    build:
+      context: .
+      dockerfile: nmdc_runtime/Dockerfile
+      target: dagster
+    entrypoint: ["tini", "--", "../lib/nmdc_runtime/site/entrypoint-dagit.sh"]
+    expose:
+      - "3000"
+    ports:
+      - "3000:3000"
+    environment:
+      DAGSTER_POSTGRES_USER: "postgres_user"
+      DAGSTER_POSTGRES_PASSWORD: "postgres_password"
+      DAGSTER_POSTGRES_DB: "postgres_db"
+    depends_on:
+      - dagster-postgresql
+    restart: on-failure
+    volumes:
+      - ./:/opt/dagster/lib
+    env_file: .env.test
+
+  # Dagster daemon.
+  #
+  # > This service runs the dagster-daemon process, which is responsible for taking runs
+  # > off of the queue and launching them, as well as creating runs from schedules or sensors.
+  #
+  dagster-daemon:
+    build:
+      context: .
+      dockerfile: nmdc_runtime/Dockerfile
+      target: dagster
+    entrypoint: ["tini", "--", "../lib/nmdc_runtime/site/entrypoint-daemon.sh"]
+    restart: on-failure
+    environment:
+      DAGSTER_POSTGRES_USER: "postgres_user"
+      DAGSTER_POSTGRES_PASSWORD: "postgres_password"
+      DAGSTER_POSTGRES_DB: "postgres_db"
+    depends_on:
+      dagster-postgresql: { condition: service_started }
+      # Wait until the MongoDB replica set has been set up by the "init container"
+      # before starting this Dagster daemon container.
+      mongo-init: { condition: service_completed_successfully }
+    volumes:
+      - ./:/opt/dagster/lib
+    env_file: .env.test
+
+  # Uvicorn server hosting the FastAPI application.
+  fastapi:
+    build:
+      context: .
+      dockerfile: nmdc_runtime/Dockerfile
+      target: fastapi
+    ports:
+      - "8000:8000"
+    volumes:
+      - .:/code
+    # Wait until the MongoDB replica set has been set up by the "init container"
+    # before starting this FastAPI container.
+    depends_on:
+      mongo-init: { condition: service_completed_successfully }
+    env_file: .env.test
+
+  # Short-lived MongoDB server used to initialize the one used by the FastAPI application.
+  mongo-init:
+    image: mongo:8.0.4
+    volumes:
+      - ./wait-for-it.sh:/wait-for-it.sh:ro
+      - .docker/mongo_init/initialize_replica_set.sh:/initialize_replica_set.sh:ro
+    depends_on:
+      mongo: { condition: service_started }
+    entrypoint: /bin/bash /wait-for-it.sh --host=mongo --port=27017 --timeout=20 -- /bin/sh /initialize_replica_set.sh mongo 27017 admin root
+
+  # MongoDB server used by the FastAPI application.
+  mongo:
+    image: mongo:8.0.4
+    ports:
+      - "27018:27017"
+    restart: unless-stopped
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: admin
+      MONGO_INITDB_ROOT_PASSWORD: root
+    # Configure MongoDB to run in replica set mode, so we can use MongoDB transactions.
+    #
+    # Note: Including a KeyFile is necessary when doing the combination of (a) running MongoDB in
+    #       replica set mode and (b) running MongoDB with authentication enabled.
+    #
+    command: ["--replSet", "rs0", "--bind_ip_all", "--keyFile", "/keyFile"]
+    volumes:
+      - mongo_data:/data/db
+      - ./mongoKeyFile:/keyFile:ro
+      - ./tests/nmdcdb:/nmdcdb_dump:ro
+      - ./tests/mongorestore-nmdc-testdb.sh:/mongorestore-nmdc-testdb.sh:ro
+
+  # Test runner.
+  test:
+    # Prevent Docker Compose from starting this service automatically.
+    # Reference: https://stackoverflow.com/a/65957695
+    profiles:
+      - donotstart
+    build:
+      context: .
+      dockerfile: nmdc_runtime/Dockerfile
+      target: test
+    env_file: .env.test
+    depends_on:
+      mongo-init: { condition: service_completed_successfully }
+      mongo: { condition: service_started }
+      fastapi: { condition: service_started }
+      dagster-daemon: { condition: service_started }
+      dagster-dagit: { condition: service_started }
+    volumes:
+      - .:/code
+
+volumes:
+  postgres_data:
+    driver: local
+  mongo_data:
+    driver: local
+
+name: nmdc-runtime-test

nmdc_runtime-2.5.0/docker-compose.yml

@@ -0,0 +1,130 @@
+services:
+
+  # Postgres server used by Dagster.
+  #
+  # > This service runs the postgres DB used by dagster for run storage, schedule storage,
+  # > and event log storage.
+  # > Tests use `postgres:11` image.
+  # > https://github.com/dagster-io/dagster/blob/0.11.9/python_modules/libraries/dagster-postgres/dagster_postgres_tests/docker-compose.yml
+  #
+  dagster-postgresql:
+    image: postgres:11
+    environment:
+      POSTGRES_USER: "postgres_user"
+      POSTGRES_PASSWORD: "postgres_password"
+      POSTGRES_DB: "postgres_db"
+    volumes:
+      - postgres_data:/var/lib/postgresql/data
+
+  # Web server that hosts the Dagster web UI.
+  #
+  # > This service runs dagit.
+  # > Since our instance uses the QueuedRunCoordinator, any runs submitted from dagit will be put on
+  # > a queue and later dequeued and launched by dagster-daemon.
+  #
+  dagster-dagit:
+    build:
+      context: .
+      dockerfile: nmdc_runtime/Dockerfile
+      target: dagster
+    entrypoint: ["tini", "--", "../lib/nmdc_runtime/site/entrypoint-dagit.sh"]
+    expose:
+      - "3000"
+    ports:
+      - "3000:3000"
+    environment:
+      DAGSTER_POSTGRES_USER: "postgres_user"
+      DAGSTER_POSTGRES_PASSWORD: "postgres_password"
+      DAGSTER_POSTGRES_DB: "postgres_db"
+    depends_on:
+      - dagster-postgresql
+    restart: on-failure
+    volumes:
+      - ./:/opt/dagster/lib
+    env_file: .env
+
+  # Dagster daemon.
+  #
+  # > This service runs the dagster-daemon process, which is responsible for taking runs
+  # > off of the queue and launching them, as well as creating runs from schedules or sensors.
+  #
+  dagster-daemon:
+    build:
+      context: .
+      dockerfile: nmdc_runtime/Dockerfile
+      target: dagster
+    entrypoint: ["tini", "--", "../lib/nmdc_runtime/site/entrypoint-daemon.sh"]
+    restart: on-failure
+    environment:
+      DAGSTER_POSTGRES_USER: "postgres_user"
+      DAGSTER_POSTGRES_PASSWORD: "postgres_password"
+      DAGSTER_POSTGRES_DB: "postgres_db"
+    depends_on:
+      dagster-postgresql: { condition: service_started }
+      # Wait until the MongoDB replica set has been set up by the "init container"
+      # before starting this Dagster daemon container.
+      mongo-init: { condition: service_completed_successfully }
+    volumes:
+      - ./:/opt/dagster/lib
+    env_file: .env
+
+  # Uvicorn server hosting the FastAPI application.
+  fastapi:
+    build:
+      context: .
+      dockerfile: nmdc_runtime/Dockerfile
+      target: fastapi
+    ports:
+      - "8000:8000"
+    volumes:
+      - .:/code
+    # Wait until the MongoDB replica set has been set up by the "init container"
+    # before starting this FastAPI container.
+    depends_on:
+      mongo-init: { condition: service_completed_successfully }
+    command: ["uvicorn", "nmdc_runtime.api.main:app", "--reload", "--host", "0.0.0.0", "--port", "8000"]
+    env_file: .env
+
+  # Short-lived MongoDB server used to initialize the one used by the FastAPI application.
+  mongo-init:
+    image: mongo:8.0.4
+    volumes:
+      - ./wait-for-it.sh:/wait-for-it.sh:ro
+      - .docker/mongo_init/initialize_replica_set.sh:/initialize_replica_set.sh:ro
+    depends_on:
+      mongo: { condition: service_started }
+    entrypoint: /bin/bash /wait-for-it.sh --host=mongo --port=27017 --timeout=20 -- /bin/sh /initialize_replica_set.sh mongo 27017 admin root
+
+  # MongoDB server used by the FastAPI application.
+  # TODO: Why does this service (which is in the dev—not test—stack), mount descendants of `./tests` — is that intentional?
+  mongo:
+    image: mongo:8.0.4
+    ports:
+      - "27018:27017"
+    restart: unless-stopped
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: admin
+      MONGO_INITDB_ROOT_PASSWORD: root
+    # Configure MongoDB to run in replica set mode, so we can use MongoDB transactions.
+    #
+    # Note: Including a KeyFile is necessary when doing the combination of (a) running MongoDB in
+    #       replica set mode and (b) running MongoDB with authentication enabled.
+    #
+    command: ["--replSet", "rs0", "--bind_ip_all", "--keyFile", "/keyFile"]
+    volumes:
+      - mongo_data:/data/db
+      - ./mongoKeyFile:/keyFile:ro
+      - ./tests/nmdcdb:/nmdcdb_dump:ro
+      - ./tests/mongorestore-nmdc-testdb.sh:/mongorestore-nmdc-testdb.sh:ro
+
+volumes:
+  postgres_data:
+    driver: local
+  mongo_data:
+    driver: local
+
+secrets:
+  mongoKeyFile:
+    file: ./mongoKeyFile
+
+name: nmdc-runtime-dev

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/docs/admin.md

@@ -52,7 +52,7 @@ do so at the code level. A suitable template for this is the [implementation of
 /users](https://github.com/microbiomedata/nmdc-runtime/blob/1d0feb68fb5ed82ed82c06f9724ecc86f73d83ae/nmdc_runtime/api/endpoints/users.py#L78)
 endpoint. The endpoint code receives the requesting user model via the `get_current_active_user`
 dependency, and it uses the `check_can_create_user` function to verify that the requester can
-administer the "nmdc-runtime-useradmin" site. If not, a `403 Forbidden` expection is raised.
+administer the "nmdc-runtime-useradmin" site. If not, a `403 Forbidden` exception is raised.
 Otherwise, the endpoint logic continues for the authorized user.
 
 To add a site ID to an existing user's `site_admin` list, this must currently be done manually at

{nmdc_runtime-2.4.0 → nmdc_runtime-2.5.0}/docs/howto-guides/release-process.md

@@ -36,7 +36,7 @@ In order to make sure the schema, database, and NMDC Runtime API are in sync we
 
 Here is a summary of the process:
 
-1. [NMDC Schema](https://github.com/microbiomedata/nmdc-schema) repo releases new version. All releases must include a migration script (even if it is null / empty) to run against MongoDB. See [ADR 007](https://github.com/microbiomedata/NMDC_documentation/blob/main/decisions/0007-mongo-migration-scripts.md)
+1. [NMDC Schema](https://github.com/microbiomedata/nmdc-schema) repo releases new version. All releases must include a migration script (even if it is null / empty) to run against MongoDB. See [ADR 007](https://github.com/microbiomedata/issues/blob/main/decisions/0007-mongo-migration-scripts.md)
 2. Submit/Merge a PR with updated schema version and any related code changes.
 3. Build a new NMDC-runtime image so that it is ready to be deployed (See above). 
 4. Database (Mongo) is switched to read-only mode to prevent inconsistencies.