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.gitlab-ci.yml
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.gitlab-ci.yml
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stages:
- build
- deploy
- extract
- report
file-list-build:
stage: build
image:
name: gcr.io/kaniko-project/executor:debug
entrypoint: [""]
script:
- mkdir -p /kaniko/.docker
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
- /kaniko/executor --context $CI_PROJECT_DIR/k8s-job/file-list-image --destination $CI_REGISTRY_IMAGE/file-list:$CI_COMMIT_TAG
file-indexer-build:
stage: build
image:
name: gcr.io/kaniko-project/executor:debug
entrypoint: [""]
script:
- mkdir -p /kaniko/.docker
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
- /kaniko/executor --context $CI_PROJECT_DIR/k8s-job/file-indexing-image --destination $CI_REGISTRY_IMAGE/file-indexing:$CI_COMMIT_TAG
file-ingester-build:
stage: build
image:
name: gcr.io/kaniko-project/executor:debug
entrypoint: [""]
script:
- mkdir -p /kaniko/.docker
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
- /kaniko/executor --context $CI_PROJECT_DIR/k8s-job/file-ingestion --destination $CI_REGISTRY_IMAGE/file-ingestion:$CI_COMMIT_TAG
.deploy:
stage: deploy
image:
name: roffe/kubectl
script:
- kubectl -n ${KUBE_NAMESPACE} apply -f ${INDEXER_CONFIGMAP}
- kubectl -n ${KUBE_NAMESPACE} delete -f k8s-job/job/job.yaml | kubectl -n ${KUBE_NAMESPACE} apply -f k8s-job/job/job.yaml
- kubectl -n ${KUBE_NAMESPACE} describe job/job-wq-1
.extract-metabolights:
image: "python:3.5"
stage: extract
before_script:
- pip install --upgrade pip
- pip install -r requirements.txt
script:
- python scripts/extract-omicsdi-datasets.py metabolights
artifacts:
paths:
- data/metabolights.csv
expire_in: 1 week
.extract-pride:
image: "python:3.5"
stage: extract
before_script:
- pip install --upgrade pip
- pip install -r requirements.txt
script:
- python scripts/extract-omicsdi-datasets.py pride
artifacts:
paths:
- data/pride.csv
expire_in: 1 week
.extract-arrayexpress:
image: "python:3.5"
stage: extract
before_script:
- pip install --upgrade pip
- pip install -r requirements.txt
script:
- python scripts/extract-omicsdi-datasets.py arrayexpress
artifacts:
paths:
- data/arrayexpress.csv
expire_in: 1 week
.extract-eva:
image: "python:3.5"
stage: extract
before_script:
- pip install --upgrade pip
- pip install -r requirements.txt
script:
- python scripts/extract-omicsdi-datasets.py eva
artifacts:
paths:
- data/eva.csv
expire_in: 1 week
.extract-expression-atlas:
image: "python:3.5"
stage: extract
before_script:
- pip install --upgrade pip
- pip install -r requirements.txt
script:
- python scripts/extract-omicsdi-datasets.py expression-atlas
artifacts:
paths:
- data/expression-atlas.csv
expire_in: 1 week
.report:
image: "alpine"
stage: report
script:
- wc -l data/*.csv | tee data/report.txt
artifacts:
paths:
- data/