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Developing BatchAnalysis

Contributing

For compliance reasons, all pull requests must be submitted with a Jira ID in the pull request title. You should include the Jira ID near the beginning of the title for better readability. For example: "[WM-1992] add statement to README.md and DEVELOPMENT.md about including Jira IDs in PR titles"

If there is more than one relevant ticket, include all of their Jira IDs. For example: "WM-1997, WM-2002, WM-2005: Fix for many bugs with the same root cause"

Setup

Please note: These setup steps were copied directly from ECM. Anything that seems "off" is probably a result of that. Feel free to submit a PR to fix this up!

Prerequisites:

  • Verify that your checked-out repo is protected by git-secrets

    • Run git-secrets --list from the repo root. A long list of configured rules should print out.
      • DSP-issued workstations should have everything pre-configured
    • If the command is not found, run brew install git-secrets
    • If there are no rules, use the script here to add them

  • Install Postgres 14: https://www.postgresql.org/download/

    • The app may be easier, just make sure to download the right version. It'll manage things for you and has a useful menulet where the server can be turned on and off. Don't forget to create a server if you go this route.

  • Install Adoptium Java 17 (Temurin). Here's an easy way on Mac, using jEnv to manage the active version:

    # if on Mac, you may need to install Terminal developer tools first
xcode-select --install

brew install jenv
# follow postinstall instructions to activate jEnv...

# to add previously installed versions of Java to jEnv, list them:
# /usr/libexec/java_home -V
# and then add them:
# jenv add /Library/Java/JavaVirtualMachines/<JAVA VERSION HERE>/Contents/Home

brew install --cask temurin@17

jenv add /Library/Java/JavaVirtualMachines/temurin-17.jdk/Contents/Home
# Note: if this command does not work, ensure that you activated jEnv
# as specified above

NOTE: You may encounter issues with the application when running an unexpected version of Java. So make sure you are running Temurin-17 as specified above.

Database Configuration

The Batch Analysis service relies on a Postgresql database server. There are two options for running the Postgres server:

  • Manual setup: Setup Postgres using whatever method you like.
  • Convenient app setup: Install the convenient app, and create a database called cbas_db.

To create the database using the terminal, first enter psql to enter Postgres interactive mode.

N.B. If you used the convenient app, you should run psql as /Applications/Postgres.app/Contents/Versions/14/bin/psql. To add Postgres commands to your path, run the following command:

sudo mkdir -p /etc/paths.d && echo /Applications/Postgres.app/Contents/Versions/14/bin | sudo tee /etc/paths.d/postgresapp

Once you are in interactive mode, run the following commands:

CREATE USER cbas_user;
CREATE DATABASE cbas_db;
GRANT ALL PRIVILEGES ON DATABASE cbas_db TO cbas_user;

Now run the following command in the terminal to initialize the database:

psql -h 127.0.0.1 -U postgres -f ./common/postgres-init.sql

Dependencies

this section is a work-in-progress

Workspace Data Service (WDS)

Create an empty WDS database in the PostgreSQL server you created above.

CREATE DATABASE wds;

Start a WDS container with the following command: Replace [YOUR_USERNAME] with something like mspector

docker run \
  --name "WDS_6786552" \
  -e WDS_DB_HOST='host.docker.internal' \
  -e WDS_DB_USER='[YOUR_USERNAME]' \
  -e SAM_URL=https://sam.dsde-dev.broadinstitute.org/ \
  -p 8001:8080 us.gcr.io/broad-dsp-gcr-public/terra-workspace-data-service:0.2.57

A few notes:

  • The --name flag is optional, but recommended for easier container management.
  • At the time of this writing, us.gcr.io/broad-dsp-gcr-public/terra-workspace-data-service does not have an image with the latest tag. Take care to specify the intended tag!

With the container running, initialize an instance with any UUID, e.g. UUID 00000000-0000-0000-0000-000000000000. Note that CBAS UI expects an instance with UUID 15f36863-30a5-4cab-91f7-52be439f1175.

curl -X 'POST' \
  'http://localhost:8001/instances/v0.2/15f36863-30a5-4cab-91f7-52be439f1175/' \
  -H 'accept: */*' \
  -d ''

Then add a record FOO1 of type FOO to the instance you just created. Make sure to use the same UUID:

curl -X 'PUT' \
  'http://localhost:8001/15f36863-30a5-4cab-91f7-52be439f1175/records/v0.2/FOO/FOO1' \
  -H 'accept: */*' \
  -H 'Content-Type: application/json' \
  -d '{
  "attributes": {
    "foo_rating": 1000
  }
}'

In the wds database, the record will be written to a schema with the same name as the instance ID. Select that schema with the following SQL command (for e.g. the instance ID 15f36863-30a5-4cab-91f7-52be439f1175):

SET search_path TO "15f36863-30a5-4cab-91f7-52be439f1175";

This command needs to be run each time you wish to directly query the database. To set it permanently, you can run the following command with your instance ID:

ALTER DATABASE wds SET search_path TO "15f36863-30a5-4cab-91f7-52be439f1175";

Then, run the Postgres command \dt to show the existing tables. You can then use psql commands to view items in the table FOO:

SELECT * FROM "FOO";

You should see a row with name FOO1 and foo_rating 1000.

Running

Running Tests

All unit tests can be run with a Gradle configuration that runs :service:unitTest. If you get a message Test events were not received, this means nothing has changed since the previous test run. Integration tests can be run by following the instructions in the integration README.

Running The Service Locally

Run in IntelliJ (recommended) or use the command line:

cd service
../gradlew bootRun

Then navigate to the Swagger: http://localhost:8080/swagger-ui.html

IntelliJ Setup

  1. Open the repo normally (File > New > Project From Existing Sources). Select the folder, and then select Gradle as the external model.
  2. In project structure (the folder icon with a little tetromino over it in the upper right corner), make sure the project SDK is set to Java 17 (>= 17.0.3). If not, IntelliJ should detect it on your system in the dropdown, otherwise click "Add JDK..." and navigate to the folder from the last step.
  3. Set up google-java-format. We use the spotless checker to force code to a standard format. Installing the IntelliJ plug-in and library makes it easier to get it in the right format from the start.
  4. See some optional tips below in the "Tips" section.

Tips

  • Check out gng, it'll save you typing ./gradlew over and over, and also takes care of knowing when you're not in the root directory so you don't have to figure out the appropriate number of ../s.
  • In IntelliJ, instead of running the local server with bootRun, use the Spring Boot configuration that IntelliJ auto-generates (-cp cbas.service.main, main class bio.terra.cbas.App). To edit it, click on it (in the upper right of the window), and click Edit Configurations.
    • For readable logs, put human-readable-logging in the Active Profiles field.

Pushing a new image

New images are built and pushed automatically each time a PR is merged. Developers may want to do this manually in order to test in-development CBAS versions in non-local environments.

First, log into GCP using gcloud auth login. You need this to authenticate to push the image. You may also need to run gcloud auth configure-docker prior to pushing the image.

TAG="my-custom-image-name"
cd service/
../gradlew :service:jibDockerBuild --image=us.gcr.io/broad-dsp-gcr-public/cbas:$TAG -Djib.console=plain
docker push us.gcr.io/broad-dsp-gcr-public/cbas:$TAG