Add samples field to custom filters to allow fetching samples without session #3515
Workflow file for this run
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| name: cbioportal-performance-test | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| jobs: | |
| deploy_portal_and_test_study_view_endpoints: | |
| if: github.repository == 'cbioportal/cbioportal' && contains(github.event.pull_request.labels.*.name, 'run-performance-tests') | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout git repo | |
| uses: actions/checkout@v1 | |
| - name: Extract PR number | |
| # create the docker image tag by extracting pr number from github | |
| run: echo "##[set-output name=image_tag;]$(export set GITHUB_REF_TMP=${GITHUB_REF#refs/pull/};echo cbioportal-performance-test-${GITHUB_REF_TMP%/merge})" | |
| id: extract_tags | |
| - name: Rename deployment | |
| run: | | |
| sed "s/cbioportal-performance-test\b/${{ steps.extract_tags.outputs.image_tag }}/g" .github/k8s/cbioportal_performance_test.yaml > /tmp/cbioportal_performance_test.yaml | |
| - name: Docker build with cache | |
| uses: whoan/docker-build-with-cache-action@v4 | |
| with: | |
| username: "${{ secrets.DOCKER_USERNAME_PIPELINES }}" | |
| password: "${{ secrets.DOCKER_PASSWORD_PIPELINES }}" | |
| image_name: cbioportalpipelines/cbioportal | |
| image_tag: ${{ steps.extract_tags.outputs.image_tag }} | |
| context: . | |
| dockerfile: docker/web/Dockerfile | |
| pull_image_and_stages: false | |
| - name: Set context for kubectl cluster | |
| uses: azure/k8s-set-context@v1 | |
| with: | |
| method: service-account | |
| k8s-url: ${{ secrets.K8S_URL }} | |
| k8s-secret: ${{ secrets.K8S_SECRET }} | |
| - name: Deploy to kubernetes | |
| uses: Azure/[email protected] | |
| with: | |
| namespace: performance-test | |
| manifests: | | |
| /tmp/cbioportal_performance_test.yaml | |
| images: 'cbioportalpipelines/cbioportal:${{ steps.extract_tags.outputs.image_tag }}' | |
| action: deploy | |
| kubectl-version: 'v1.15.12' | |
| - name: Extract pod name | |
| run: echo "##[set-output name=pod_name;]$(kubectl get pods --namespace=performance-test --selector=run=${{ steps.extract_tags.outputs.image_tag }} | tail -1| cut -f1 -d' ')" | |
| id: extract_pod_name | |
| - name: Install curl | |
| run: | | |
| kubectl exec -it --namespace performance-test ${{ steps.extract_pod_name.outputs.pod_name }} -- bash -c "sleep_f () { sleep 0.3; }; sleep_f; apt-get update; sleep_f; apt-get -y install curl; sleep_f; apt-get -y install jq" | |
| - name: POST Request for /filtered-samples endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/filtered-samples/fetch" | |
| run: | | |
| kubectl exec -it --namespace=performance-test ${{ steps.extract_pod_name.outputs.pod_name }} -- bash -c "curl --max-time $MAX_WAIT_TIME_IN_SECONDS -s -X POST '$URL' -H 'accept: application/json' -H 'Content-Type: application/json' -d '{\"studyIds\": [ \"genie_public\" ]}' | jq --join-output --compact-output '[.[]|{sampleId: .\"sampleId\", studyId: \"genie_public\"}]' > samples.json; jq --join-output --compact-output '{sampleIdentifiers: [.[]]}' samples.json > sampleIdentifiers.json" | |
| - name: POST Request for /mutated-genes endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/mutated-genes/fetch" | |
| SEARCH_STR: "entrezGeneId" | |
| POST_BODY: "{\"studyIds\": [ \"genie_public\" ]}" | |
| run: | | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 0 | |
| - name: POST Request for /cna-genes endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/cna-genes/fetch" | |
| SEARCH_STR: "entrezGeneId" | |
| POST_BODY: "@sampleIdentifiers.json" | |
| run: | | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 0 | |
| - name: POST Request for /treatments/patient endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/treatments/patient" | |
| POST_BODY: "@sampleIdentifiers.json" | |
| run: | | |
| # TODO: change if treatment data is ever added | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "NA" "$POST_BODY" 1 0 | |
| - name: POST Request for /treatments/sample endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/treatments/sample" | |
| POST_BODY: "@sampleIdentifiers.json" | |
| run: | | |
| # TODO: change if treatment data is ever added | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "NA" "$POST_BODY" 1 0 | |
| - name: POST Request for /structuralvariant-genes/fetch endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/structuralvariant-genes/fetch" | |
| SEARCH_STR: "entrezGeneId" | |
| POST_BODY: "@sampleIdentifiers.json" | |
| run: | | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 0 | |
| - name: POST Request for /copy-number-segments/fetch endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/copy-number-segments/fetch?projection=META" | |
| SEARCH_STR: "seg" | |
| POST_BODY: "@samples.json" | |
| run: | | |
| # TODO: study view is querying with projection=META which does not return anything | |
| # update if we ever use a query that reutrns data (e.g SUMMARY) | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 1 | |
| - name: POST Request for /clinical-data-bin-counts endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/clinical-data-bin-counts/fetch?dataBinMethod=STATIC" | |
| SEARCH_STR: "MUTATION_COUNT" | |
| POST_BODY: "{\"attributes\":[{\"attributeId\":\"MUTATION_COUNT\",\"disableLogScale\":false},{\"attributeId\":\"FRACTION_GENOME_ALTERED\",\"disableLogScale\":false},{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"disableLogScale\":false},{\"attributeId\":\"AGE_AT_SEQ_REPORT_DAYS\",\"disableLogScale\":false},{\"attributeId\":\"INT_CONTACT\",\"disableLogScale\":false},{\"attributeId\":\"INT_DOD\",\"disableLogScale\":false},{\"attributeId\":\"SEQ_YEAR\",\"disableLogScale\":false}],\"studyViewFilter\":{\"studyIds\":[\"genie_public\"],\"patientTreatmentFilters\":{\"filters\":[]},\"sampleTreatmentFilters\":{\"filters\":[]}}}" | |
| run: | | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 0 | |
| - name: POST Request for /clinical-data-counts endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/clinical-data-counts/fetch" | |
| SEARCH_STR: "SAMPLE_COUNT" | |
| POST_BODY: "{\"attributes\":[{\"attributeId\":\"CANCER_TYPE\"},{\"attributeId\":\"CANCER_TYPE_DETAILED\"},{\"attributeId\":\"SAMPLE_COUNT\"},{\"attributeId\":\"SEX\"},{\"attributeId\":\"ETHNICITY\"},{\"attributeId\":\"SAMPLE_TYPE\"},{\"attributeId\":\"CENTER\"},{\"attributeId\":\"ONCOTREE_CODE\"},{\"attributeId\":\"PRIMARY_RACE\"},{\"attributeId\":\"SAMPLE_TYPE_DETAILED\"},{\"attributeId\":\"SECONDARY_RACE\"},{\"attributeId\":\"SEQ_ASSAY_ID\"},{\"attributeId\":\"TERTIARY_RACE\"}],\"studyViewFilter\":{\"studyIds\":[\"genie_public\"],\"patientTreatmentFilters\":{\"filters\":[]},\"sampleTreatmentFilters\":{\"filters\":[]}}}" | |
| run: | | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 0 | |
| - name: POST Request for /clinical-data-density-plot endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=50&xAxisEnd=1&xAxisStart=0&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=52&yAxisStart=0" | |
| SEARCH_STR: "count" | |
| POST_BODY: "@sampleIdentifiers.json" | |
| run: | | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 0 | |
| - name: POST Request for /sample-list-counts endpoint | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "http://localhost:8888/api/sample-lists-counts/fetch" | |
| SEARCH_STR: "count" | |
| POST_BODY: "{\"sampleTreatmentFilters\":{\"filters\":[]},\"patientTreatmentFilters\":{\"filters\":[]},\"studyIds\":[\"genie_public\"]}" | |
| run: | | |
| . ./.github/k8s/run_endpoint_test.sh ${{ steps.extract_pod_name.outputs.pod_name }} "$MAX_WAIT_TIME_IN_SECONDS" "$URL" "$SEARCH_STR" "$POST_BODY" 0 0 | |
| - name: Delete pod | |
| if: ${{ always() }} | |
| run: | | |
| kubectl delete -f /tmp/cbioportal_performance_test.yaml | |
| - name: DELETE request to dockerhub | |
| if: ${{ always() }} | |
| env: | |
| MAX_WAIT_TIME_IN_SECONDS: 180 | |
| URL: "https://hub.docker.com/v2/repositories/cbioportalpipelines/cbioportal/tags/${{ steps.extract_tags.outputs.image_tag }}/" | |
| OK_RESPONSE_CODE: 204 | |
| # DELETE request to URL with a MAX_WAIT_TIME_IN_SECONDS second limit | |
| # if curl fails, automatically exit with curl's non-zero exit code | |
| # else if we did not get a OK_RESPONSE_CODE exit with a non-zero exit code | |
| # else we are OK! | |
| run: | | |
| JWT_TOKEN_SECRET="`curl -s -H "Content-Type: application/json" -X POST -d '{"username": "'${{ secrets.DOCKER_USERNAME_PIPELINES }}'", "password": "${{ secrets.DOCKER_PASSWORD_PIPELINES }}"}' https://hub.docker.com/v2/users/login/ | sed 's/.*token": "//' | sed 's/"}//'`" | |
| echo ${JWT_TOKEN_SECRET} | |
| echo "curl --max-time $MAX_WAIT_TIME_IN_SECONDS -s -o /dev/null -w '%{http_code}' -X DELETE -H 'Authorization: JWT ${JWT_TOKEN_SECRET}' '$URL'" | |
| curl --max-time $MAX_WAIT_TIME_IN_SECONDS -s -o /dev/null -w "%{http_code}" -X DELETE -H "Authorization: JWT ${JWT_TOKEN_SECRET}" "$URL" > curl.out | |
| RESPONSE_CODE=`cat curl.out` | |
| if [ "$RESPONSE_CODE" != "$OK_RESPONSE_CODE" ]; then | |
| echo "Request failed with response code '$RESPONSE_CODE', expected '$OK_RESPONSE_CODE'" | |
| exit 1 | |
| else | |
| echo "Request succeeded with expected response code '$OK_RESPONSE_CODE'" | |
| exit 0 | |
| fi | |
| # Reference: https://github.com/marketplace/actions/build-docker-images-using-cache |