Merge pull request #834 from hms-dbmi-cellenics/biomage-changes-4

Changes 4

.github/workflows/ci.yaml

@@ -34,14 +34,14 @@ jobs:
           EOF
           )
 
-          UNCHECKED_BODY="${UNCHECKED_BODY//'%'/'%25'}"
-          UNCHECKED_BODY="${UNCHECKED_BODY//$'\n'/'%0A'}"
-          UNCHECKED_BODY="${UNCHECKED_BODY//$'\r'/'%0D'}"
-
           echo "Unchecked PR body"
           echo $UNCHECKED_BODY
 
-          echo "::set-output name=body::$UNCHECKED_BODY"
+          # This sets multiline strings into the output variable
+          # See https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#example-of-a-multiline-string
+          echo "body<<EOF" >> "$GITHUB_OUTPUT"
+          echo "$UNCHECKED_BODY" >> "$GITHUB_OUTPUT"
+          echo "EOF" >> "$GITHUB_OUTPUT"
 
       - id: uncheck-integration-checkbox
         name: Uncheck the integration checkbox
@@ -148,7 +148,7 @@ jobs:
           # This will take a ref like `refs/heads/master`
           # and turn it into `refs-heads-master`
           REF_ID=$(echo $GITHUB_REF | sed 's/\//-/g')
-          echo "::set-output name=ref-id::$REF_ID"
+          echo "ref-id=$REF_ID" >> $GITHUB_OUTPUT
 
           # the final tag is something like:
           # refs-heads-master-a4f8bc313dae
@@ -175,13 +175,13 @@ jobs:
           # IMAGE_TAG is used in the Build Docker Image step.
           # We can easily build the image-tag from REF_ID and COMMIT_SHA for non-production releases.
           # But we can not easily create the image tag for production releases, so we're bulding it here
-          echo "::set-output name=image-tag::$IMAGE_TAG"
+          echo "image-tag=$IMAGE_TAG" >> $GITHUB_OUTPUT
 
           # This will take a GitHub repo name like `hms-dbmi-cellenics/releases`
           # and turns it into `releases`. This will be the name of the
           # ECR repository.
           IMAGE_REPO_NAME=$(echo $GITHUB_REPOSITORY | awk -F '/' '{print $2}')
-          echo "::set-output name=repo-name::$IMAGE_REPO_NAME"
+          echo "repo-name=$IMAGE_REPO_NAME" >> $GITHUB_OUTPUT
 
       - id: set-up-creds
         name: Configure AWS credentials
@@ -260,7 +260,7 @@ jobs:
         name: Fill out a new HelmRelease resource
         run: |-
           export DEPLOYMENT_NAME=$(echo $GITHUB_REPOSITORY | awk -F '/' '{print $2}')
-          echo "::set-output name=deployment-name::$DEPLOYMENT_NAME"
+          echo "deployment-name=$DEPLOYMENT_NAME" >> $GITHUB_OUTPUT
 
           if [ "${{ matrix.environment }}" = "production" ]; then
             export SANDBOX_ID="default"
@@ -304,7 +304,7 @@ jobs:
             export MANIFEST_PATH="./staging"
           fi
 
-          echo "::set-output name=kubernetes-env::$KUBERNETES_ENV"
+          echo "kubernetes-env=$KUBERNETES_ENV" >> $GITHUB_OUTPUT
 
           export NAMESPACE="$DEPLOYMENT_NAME-$SANDBOX_ID"
           export CHART_SOURCE_NAME="$DEPLOYMENT_NAME-chart"

.github/workflows/nextjs_bundle_analysis.yaml

@@ -94,10 +94,12 @@ jobs:
         if: success() && github.event.number
         run: |
           body=$(cat .next/analyze/__bundle_analysis_comment.txt)
-          body="${body//'%'/'%25'}"
-          body="${body//$'\n'/'%0A'}"
-          body="${body//$'\r'/'%0D'}"
-          echo ::set-output name=body::$body
+
+          # This sets multiline strings into the output variable
+          # See https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#example-of-a-multiline-string
+          echo "body<<EOF" >> "$GITHUB_OUTPUT"
+          echo "$body" >> "$GITHUB_OUTPUT"
+          echo "EOF" >> "$GITHUB_OUTPUT"
 
       - name: Find Comment
         uses: peter-evans/find-comment@v1

.github/workflows/pr_validate.yaml

@@ -68,19 +68,19 @@ jobs:
 
           echo "Is staging N/A?"
           echo $IS_STAGING_NA
-          echo "::set-output name=is-staging-na::$IS_STAGING_NA"
+          echo "is-staging-na=$IS_STAGING_NA" >> $GITHUB_OUTPUT
 
           echo "Full URL:"
           echo $URL
-          echo "::set-output name=url::$URL"
+          echo "url=$URL" >> $GITHUB_OUTPUT
 
           SANDBOX=$(pcregrep -o2 -M "$REGEX" <<\EOF
           ${{ github.event.pull_request.body }}
           EOF
           )
           echo "Extracted sandbox:"
           echo $SANDBOX
-          echo "::set-output name=sandbox::$SANDBOX"
+          echo "sandbox=$SANDBOX" >> $GITHUB_OUTPUT
 
       - id: reach-staging
         if: steps.extract-staging.outputs.url != 'N/A'
@@ -129,8 +129,8 @@ jobs:
           fi
           echo $SHOULD_RUN_E2E
 
-          echo "::set-output name=should-e2e-cancel::$SHOULD_CANCEL_E2E"
-          echo "::set-output name=should-e2e-run::$SHOULD_RUN_E2E"
+          echo "should-e2e-cancel=$SHOULD_CANCEL_E2E" >> $GITHUB_OUTPUT
+          echo "should-e2e-run=$SHOULD_RUN_E2E" >> $GITHUB_OUTPUT
 
       - id: cancel
         name: Cancel if staging is not N/A and box is not checked
@@ -150,12 +150,12 @@ jobs:
         run: |-
           echo "SHA of latest GitHub branch commit:"
           echo ${{ github.event.pull_request.head.sha }}
-          echo "::set-output name=github_sha::${{ github.event.pull_request.head.sha }}"
+          echo "github_sha=${{ github.event.pull_request.head.sha }}" >> $GITHUB_OUTPUT
 
           REPO_NAME=$(echo $GITHUB_REPOSITORY | awk -F '/' '{print $2}')
           echo "Repo name:"
           echo $REPO_NAME
-          echo "::set-output name=repo_name::$REPO_NAME"
+          echo "repo_name=$REPO_NAME" >> $GITHUB_OUTPUT
 
       - id: extract-integration-test-ref
         if: steps.check-e2e-run.outputs.should-e2e-run == 'true'
@@ -173,7 +173,7 @@ jobs:
           )
 
           echo "Ref given is $INTEGRATION_TEST_REF, setting it as is."
-          echo "::set-output name=ref::$INTEGRATION_TEST_REF"
+          echo "ref=$INTEGRATION_TEST_REF" >> $GITHUB_OUTPUT
 
       - id: run-integration-test
         if: steps.check-e2e-run.outputs.should-e2e-run == 'true'
@@ -202,14 +202,14 @@ jobs:
           EOF
           )
 
-          UNCHECKED_BODY="${UNCHECKED_BODY//'%'/'%25'}"
-          UNCHECKED_BODY="${UNCHECKED_BODY//$'\n'/'%0A'}"
-          UNCHECKED_BODY="${UNCHECKED_BODY//$'\r'/'%0D'}"
-
           echo "Unchecked PR body"
           echo $UNCHECKED_BODY
 
-          echo "::set-output name=body::$UNCHECKED_BODY"
+          # This sets multiline strings into the output variable
+          # See https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#example-of-a-multiline-string
+          echo "body<<EOF" >> "$GITHUB_OUTPUT"
+          echo "$UNCHECKED_BODY" >> "$GITHUB_OUTPUT"
+          echo "EOF" >> "$GITHUB_OUTPUT"
 
       - id: uncheck-integration-checkbox
         if: failure()

src/__test__/components/data-exploration/generic-gene-table/LaunchPathwayAnalysisModal.test.jsx

@@ -15,15 +15,15 @@ import downloadFromUrl from 'utils/downloadFromUrl';
 import writeToFile from 'utils/writeToFileURL';
 
 import launchPathwayService from 'utils/pathwayAnalysis/launchPathwayService';
-import getDiffExprGenes from 'utils/differentialExpression/getDiffExprGenes';
-import getBackgroundExpressedGenes from 'utils/differentialExpression/getBackgroundExpressedGenes';
+import getDiffExprGenes from 'utils/extraActionCreators/differentialExpression/getDiffExprGenes';
+import getBackgroundExpressedGenes from 'utils/extraActionCreators/differentialExpression/getBackgroundExpressedGenes';
 import { pathwayServices } from 'utils/pathwayAnalysis/pathwayConstants';
 import enrichrSpecies from 'utils/pathwayAnalysis/enrichrConstants';
 import endUserMessages from 'utils/endUserMessages';
 
 jest.mock('utils/pathwayAnalysis/launchPathwayService');
-jest.mock('utils/differentialExpression/getDiffExprGenes');
-jest.mock('utils/differentialExpression/getBackgroundExpressedGenes');
+jest.mock('utils/extraActionCreators/differentialExpression/getDiffExprGenes');
+jest.mock('utils/extraActionCreators/differentialExpression/getBackgroundExpressedGenes');
 
 jest.mock('utils/http/handleError');
 jest.mock('utils/downloadFromUrl');