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Merge pull request #36 from metabolomics-us/QA
FIEHNLAB-1600/FixSimilarityService,FIEHNLAB-1130/Documentation,Simplifying Deployment
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| # README # | ||
| # MassBank of North America Application | ||
|
|
||
| ports for cluster service nodes: | ||
| ## Common: | ||
| - Highly Recommended to use Linux OS (Preferably Ubuntu LTS 18.04 or 20.04) | ||
| - Ensure you have the following installed | ||
| - Node Version Manager(NVM) | ||
| - Docker Engine (And Docker-Compose) | ||
| - NPM (Node Package Manager) | ||
| - Angular CLI 10.2.3 | ||
| - IntelliJ IDEA Ultimate | ||
| - Maven 3 (Should be baked into IntelliJ) | ||
| - Git | ||
| - AWS CLI (for ECR to pull docker images) | ||
| - Java 1.8_292 (open_jdk x64) | ||
| - Scala 2.13 | ||
| - Installs in IntelliJ | ||
| - Right-click the main 'mona' project and click 'Add Framework Support' | ||
| - Gain Access to the following | ||
| - Internal mona-config private repo | ||
| - You'll need admin access and will need to generate a Personal Access Token (https://github.com/settings/tokens) | ||
| - Then open your `~/.bash_rc` and set the following variables, 'GIT_USER' and 'GIT_PASS' to your github username and | ||
| new personal access token. This allows the discovery service to work as intended | ||
| - Note: You'll need to set these tokens on the IPA and GOSE servers as they expire every year (you can configure | ||
| how quickly these expire). | ||
| - Access to AWS account and ability to push to ECR | ||
| - Admin access to public mona repo | ||
| - You'll need a settings.xml file for your maven 'User Settings File' this will include the nexus profile | ||
| and all the necessary repo's for pulling down libraries. Please ask a developer on the team for this config | ||
| and store file at `~/.m2` | ||
|
|
||
|
|
||
| ## Starting Development: | ||
| - There are 3 scripts in the project to easily start development | ||
| - `./start_corsproxy.sh` | ||
| - Solves CORS issues when connecting the frontend to the microservices | ||
| - `./start_docker_dev.sh` | ||
| - Starts all necessary docker microservices | ||
| - `./start_frontend.sh` | ||
| - Starts the Angular 10 frontend with ng serve to develop on the fly | ||
|
|
||
| ## PROD Deployment: | ||
| - Production deployment is simple with docker | ||
| - Bring down the application with: `docker stack rm mona` | ||
| - Bring the application back up with `docker stack deploy -c docker-compose-prod.yml` | ||
| - Note: You may need to force the newest images to pull down with `docker-compose -f docker-compose-prod.yml pull` | ||
|
|
||
| ## Running Test Suite With IntelliJ and Maven: | ||
| - Using the built-in Maven tab, we can run the full scala test suite | ||
| - Make sure the following Maven profiles are selected (and only those): nexus, scala, scala-test | ||
| - Run the following docker-compose file: `docker-compose -f docker-compose-test.yml -d` | ||
| - Finally, run `mvn clean install` on the 'backend(root)' | ||
|
|
||
| ## Generate new Docker Images: | ||
| - Make sure the following Maven profiles are selected (and only those): nexus, scala, docker | ||
| - The following services can be built into docker images: discovery, bootstrap, webhooks-server,curation-scheduler, | ||
| repository, persistence-server, auth-server, similarity, proxy, download-scheduler, and curation-runner | ||
| - `mvn clean install` will build a local docker image for the corresponding service | ||
| - `mvn clean deploy` will build the docker image and deploy it to ECR (make sure you signed in to AWS CLI) | ||
| - default tag is 'test' you can easily configure that in the main mona pom.xml | ||
| - NOTE: For the proxy service pom.xml, you'll need to configure the 'ng.env' variable to 'staging' or 'prod' | ||
| depending on if the build is for IPA('staging') or GOSE('prod'); | ||
|
|
||
| ## Important Development Notes: | ||
| - Make sure project sdk/jdk is set to Java 1.8_292 | ||
| - Make sure to configure Maven in IntelliJ IDEA to use the same project jdk which should be Java 1.8_292 | ||
| - Make sure you added framework support for scala 2.13 in IntelliJ for the mona project | ||
| - When making a new branch for git, naming convention should typically have a ticket number (i.e. FIEHN-1234) following | ||
| a slash and a description of the ticket (i.e. FIEHN-1234/ThisIsATicket). | ||
| - If your having issues pulling packages with maven, you can troubleshoot with deleting your `~/.m2/repository` directory. | ||
| Additionally, ensure you have the correct 'settings.xml' file in `~/.m2`. If problems still persist, try the 'Invalidate | ||
| Caches' under File tab in IntelliJ IDEA. | ||
|
|
||
|
|
||
| ### ports for cluster service nodes: | ||
| - persistence svr: 2222 | ||
| - configuration svr: 1111 | ||
| - discovery service: 8761 | ||
| - auth server: 3333 | ||
| - proxy service: 8080 (entry point) | ||
|
|
||
|
|
||
| ports for in-memory node: | ||
| ### ports for in-memory node: | ||
| - embedded mongo db: 27017 | ||
| - mona rest client: 8080 | ||
| - elasticsearch client: 9200 | ||
| - elasticsearch web???: 9300 | ||
|
|
||
| Building the nodes: | ||
|
|
||
| Common: | ||
| - check/setup docker configuration | ||
| for Mac/Win: | ||
| eval "$(docker-machine env default)" | ||
| for linux: | ||
| N/A | ||
| - run 'mvn clean install' on the backend folder to compile and create the docker images | ||
|
|
||
| To run the in-memory node docker continer: | ||
| - To create the containers manually: | ||
| run 'docker run [--name <whateveryouwanttonameyourimage>] -p=80:8080 [-p=9200:9200 -p=9300:9300 -p=27017:27017] eros.fiehnlab.ucdavis.edu/mona-memory-node' | ||
| to start the docker container of choice | ||
|
|
||
| To run the cluster service nodes using docker compose: (WIP) | ||
| - To run the cluster node using docker-compose: | ||
| 'cd app/compose' | ||
| run 'docker-compose up -d' | ||
|
|
||
| - elasticsearch web: 9300 |
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