Add back NA counts when corresponding samples are filtered out of study view #3692

Workflow file for this run

.github/workflows/cbioportal-performance-test.yml at 9b70b7c

	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

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Add back NA counts when corresponding samples are filtered out of study view #3692

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Add back NA counts when corresponding samples are filtered out of study view #3692

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