diff --git a/.github/actions/create-bee/action.yml b/.github/actions/create-bee/action.yml index 72405750..9a9b7193 100644 --- a/.github/actions/create-bee/action.yml +++ b/.github/actions/create-bee/action.yml @@ -14,7 +14,7 @@ inputs: required: false type: string custom_version_json: - description: 'json containing custom versions to push. e.g. {"tsps":{"appVersion":"0.0.81-66ceced"}}' + description: 'json containing custom versions to push. e.g. {"teaspoons":{"appVersion":"0.0.81-66ceced"}}' required: false type: string @@ -32,7 +32,7 @@ runs: { "run-name": "${{ inputs.run_name }}", "bee-name": "${{ inputs.bee_name }}", - "bee-template-name": "tsps-e2e-azure-tests", + "bee-template-name": "teaspoons-e2e-azure-tests", "version-template": "dev", "custom-version-json": "${{ inputs.custom_version_json }}" } diff --git a/.github/actions/landing-zone-attach/action.yml b/.github/actions/landing-zone-attach/action.yml index 3e3cda5d..e1be51cf 100644 --- a/.github/actions/landing-zone-attach/action.yml +++ b/.github/actions/landing-zone-attach/action.yml @@ -29,7 +29,7 @@ runs: ref: refs/heads/main token: '${{ inputs.token }}' # this is using a protected landing zone we created for our tests - # https://broadworkbench.atlassian.net/wiki/spaces/TSPS/pages/3116793878/End+to+End+Test+Infrastructure + # https://broadworkbench.atlassian.net/wiki/spaces/Teaspoons/pages/3116793878/End+to+End+Test+Infrastructure inputs: >- { "run-name": "${{ inputs.run_name }}", diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index 84231b6f..e1cdab27 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -138,7 +138,7 @@ jobs: SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} with: status: failure - channel: "#terra-tsps-alerts" + channel: "#terra-teaspoons-alerts" username: "Teaspoons push to main branch" author_name: "build-and-test" icon_emoji: ":triangular_ruler:" diff --git a/.github/workflows/run-e2e-tests.yaml b/.github/workflows/run-e2e-tests.yaml index 930a3a1c..0bfcb36a 100644 --- a/.github/workflows/run-e2e-tests.yaml +++ b/.github/workflows/run-e2e-tests.yaml @@ -32,7 +32,7 @@ jobs: if [ -z ${{ inputs.custom-app-version }} ]; then echo "e2e-test-version-ref={}" >> "$GITHUB_OUTPUT" else - echo "e2e-test-version-ref={\\\"tsps\\\": {\\\"appVersion\\\":\\\"${{ inputs.custom-app-version }}\\\"} }" >> "$GITHUB_OUTPUT" + echo "e2e-test-version-ref={\\\"teaspoons\\\": {\\\"appVersion\\\":\\\"${{ inputs.custom-app-version }}\\\"} }" >> "$GITHUB_OUTPUT" fi params-gen: runs-on: ubuntu-latest @@ -108,7 +108,7 @@ jobs: permissions: contents: read id-token: write - uses: broadinstitute/dsp-reusable-workflows/.github/workflows/run_tsps_e2e_tests.yaml@main + uses: broadinstitute/dsp-reusable-workflows/.github/workflows/run_teaspoons_e2e_tests.yaml@main with: billing-project-name: '${{ needs.params-gen.outputs.project-name }}' bee-name: '${{ needs.params-gen.outputs.bee-name }}' @@ -136,6 +136,6 @@ jobs: uses: broadinstitute/sherlock/.github/workflows/client-report-workflow.yaml@main if: github.ref == 'refs/heads/main' with: - notify-slack-channels-upon-workflow-completion: "#terra-tsps-alerts" + notify-slack-channels-upon-workflow-completion: "#terra-teaspoons-alerts" permissions: id-token: write diff --git a/.github/workflows/tag-publish.yml b/.github/workflows/tag-publish.yml index 9cf2753c..164beb4f 100644 --- a/.github/workflows/tag-publish.yml +++ b/.github/workflows/tag-publish.yml @@ -177,7 +177,7 @@ jobs: env: SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} with: - channel: '#terra-tsps-alerts' + channel: '#terra-teaspoons-alerts' status: failure author_name: Publish image fields: job @@ -191,7 +191,7 @@ jobs: if: ${{ needs.bump-check.outputs.is-bump == 'no' }} with: new-version: ${{ needs.tag-publish-docker-deploy.outputs.tag }} - chart-name: 'tsps' + chart-name: 'teaspoons' permissions: contents: 'read' id-token: 'write' @@ -203,7 +203,7 @@ jobs: if: ${{ needs.bump-check.outputs.is-bump == 'no' && github.event_name != 'pull_request' }} with: new-version: ${{ needs.tag-publish-docker-deploy.outputs.tag }} - chart-name: 'tsps' + chart-name: 'teaspoons' environment-name: 'dev' secrets: sync-git-token: ${{ secrets.BROADBOT_TOKEN }} diff --git a/.github/workflows/workflow-tester.yml b/.github/workflows/workflow-tester.yml index 6b85f461..ac0dc361 100644 --- a/.github/workflows/workflow-tester.yml +++ b/.github/workflows/workflow-tester.yml @@ -100,7 +100,7 @@ jobs: SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} with: status: ${{ job.status }} - channel: "#terra-tsps-alerts" + channel: "#terra-teaspoons-alerts" username: "Teaspoons push to main branch" author_name: "build-and-test" icon_emoji: ":triangular_ruler:" diff --git a/README.md b/README.md index 967a1426..8391e13a 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ## Overview -Terra Scientific Pipelines Service, or teaspoons, facilitates running a number of defined scientific pipelines +Terra Scientific Pipelines Service, or Teaspoons, facilitates running a number of defined scientific pipelines on behalf of users that users can't run themselves in Terra. The most common reason for this is that the pipeline accesses proprietary data that users are not allowed to access directly, but that may be used as e.g. a reference panel for imputation. @@ -62,7 +62,7 @@ To run locally: If using Intellij (only IDE we use on the team), you can run the server with a debugger. Follow the steps above but instead of running `./gradlew bootRun` to spin up the server, you can run (debug) the App.java class through intellij and set breakpoints in the code. Be sure to set the -GOOGLE_APPLICATION_CREDENTIALS=config/tsps-sa.json in the Run/Debug configuration Environment Variables. +GOOGLE_APPLICATION_CREDENTIALS=config/teaspoons-sa.json in the Run/Debug configuration Environment Variables. ### Running Tests/Linter Locally - Testing @@ -82,7 +82,7 @@ SonarQube and want to debug the problem locally, you need to get the sonar token before running the gradle task. ```shell -export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/tsps) +export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/teaspoons) ./gradlew sonarqube ``` @@ -100,7 +100,7 @@ does all the setup for you. Clone that repo and make sure you're either on Broad to the VPN. Then run the following command: ```shell -./firecloud/psql-connect.sh dev tsps +./firecloud/psql-connect.sh dev teaspoons ``` ### Deploying to dev @@ -109,8 +109,8 @@ Upon merging to main, the dev environment will be automatically deployed via the (that workflow is defined [here](https://github.com/DataBiosphere/terra-scientific-pipelines-service/blob/main/.github/workflows/tag-publish.yml)). The two tasks `report-to-sherlock` and `set-version-in-dev` will prompt Sherlock to deploy the new version to dev. -You can check the status of the deployment in [Beehive](https://beehive.dsp-devops.broadinstitute.org/apps/tsps) and in -[ArgoCD](https://ap-argocd.dsp-devops.broadinstitute.org/applications/ap-argocd/tsps-dev). +You can check the status of the deployment in [Beehive](https://beehive.dsp-devops.broadinstitute.org/apps/teaspoons) and in +[ArgoCD](https://ap-argocd.dsp-devops.broadinstitute.org/applications/ap-argocd/teaspoons-dev). For more information about deployment to dev, check out DevOps' [excellent documentation](https://docs.google.com/document/d/1lkUkN2KOpHKWufaqw_RIE7EN3vN4G2xMnYBU83gi8VA/). @@ -123,7 +123,7 @@ See [this DSP blog post](https://broadworkbench.atlassian.net/wiki/x/AoGlrg) for ### Running the end-to-end tests The end-to-end test is specified in `.github/workflows/run-e2e-tests.yaml`. It calls [the test script defined -in the dsp-reusable-workflows repo](https://github.com/broadinstitute/dsp-reusable-workflows/blob/main/e2e-test/tsps_e2e_test.py). +in the dsp-reusable-workflows repo](https://github.com/broadinstitute/dsp-reusable-workflows/blob/main/e2e-test/teaspoons_e2e_test.py). The end-to-end test is automatically run nightly on the dev environment. diff --git a/scripts/write-config.sh b/scripts/write-config.sh index 31b08b36..1e62ec24 100755 --- a/scripts/write-config.sh +++ b/scripts/write-config.sh @@ -181,7 +181,7 @@ function vaultgetdb { } # grab teaspoons service account json from vault -vaultget "secret/dsde/firecloud/${fcenv}/tsps/tsps-account.json" "${outputdir}/tsps-sa.json" +vaultget "secret/dsde/firecloud/${fcenv}/teaspoons/teaspoons-account.json" "${outputdir}/teaspoons-sa.json" # We made it to the end, so record the target and avoid redos echo "$target" > "${outputdir}/target.txt" diff --git a/service/build.gradle b/service/build.gradle index 74f6c10c..7d83b476 100644 --- a/service/build.gradle +++ b/service/build.gradle @@ -114,7 +114,7 @@ dependencies { // set GOOGLE_APPLICATION_CREDENTIALS if this file exists - should only exist when // write-config.sh is run. // GOOGLE_APPLICATION_CREDENTIALS is set for us when running in a deployed environment -def googleCredentialsFile = "${rootDir}/config/tsps-sa.json" +def googleCredentialsFile = "${rootDir}/config/teaspoons-sa.json" bootRun { if(project.file(googleCredentialsFile).exists()) { environment.put("GOOGLE_APPLICATION_CREDENTIALS", "${googleCredentialsFile}") diff --git a/service/src/main/java/bio/terra/pipelines/dependencies/stairway/JobService.java b/service/src/main/java/bio/terra/pipelines/dependencies/stairway/JobService.java index f7a8f416..5d68869f 100644 --- a/service/src/main/java/bio/terra/pipelines/dependencies/stairway/JobService.java +++ b/service/src/main/java/bio/terra/pipelines/dependencies/stairway/JobService.java @@ -155,8 +155,7 @@ public JobResultOrException retrieveJobResult( switch (flightState.getFlightStatus()) { case FATAL: - logAlert( - "Teaspoons Stairway flight {} encountered dismal failure", flightState.getFlightId()); + logAlert("Stairway flight {} encountered dismal failure", flightState.getFlightId()); return handleFailedFlight(flightState); case ERROR: return handleFailedFlight(flightState); @@ -263,8 +262,7 @@ private JobResultOrException handleFailedFlight(FlightState flightState) .exception(new InternalServerErrorException("wrap non-runtime exception", exception)); } } - logAlert( - "Teaspoons Stairway flight {} failed with no exception given", flightState.getFlightId()); + logAlert("Stairway flight {} failed with no exception given", flightState.getFlightId()); throw new InvalidResultStateException("Failed operation with no exception reported."); } diff --git a/service/src/main/resources/application.yml b/service/src/main/resources/application.yml index da165440..2adcdb03 100644 --- a/service/src/main/resources/application.yml +++ b/service/src/main/resources/application.yml @@ -20,7 +20,7 @@ env: leonardo: ${LEONARDO_ADDRESS:https://leonardo.dsde-dev.broadinstitute.org} workspacemanager: ${WORKSPACE_MANAGER_ADDRESS:https://workspace.dsde-dev.broadinstitute.org} ingress: - domainName: ${TSPS_INGRESS_DOMAIN_NAME:localhost:8080} + domainName: ${TEAPSOONS_INGRESS_DOMAIN_NAME:localhost:8080} kubernetes: in-kubernetes: ${TERRA_COMMON_KUBERNETES_IN_KUBERNETES:false} pod-name: ${TERRA_COMMON_KUBERNETES_POD_NAME:} @@ -138,7 +138,7 @@ terra.common: # these values are used by TCL stairway: - cluster-name-suffix: tsps-stairway + cluster-name-suffix: teaspoons-stairway force-clean-start: false # ${env.db.init} max-parallel-flights: 50 migrate-upgrade: true