.gitignore

@@ -378,3 +378,5 @@ tags
 .renku.lock
 .renku/tmp
 .renku/cache
+
+.vscode

.gitlab-ci.yml

-# renku: v1.dev20180723
-
 variables:
   GIT_STRATEGY: fetch
   GIT_SSL_NO_VERIFY: "true"
   GIT_SUBMODULE_STRATEGY: recursive
   GIT_LFS_SKIP_SMUDGE: 1
+  DOCKER_BUILDKIT: 1
+
+.docker-before-script: &docker_before_script  # This is an anchor
+  before_script:
+    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN http://$CI_REGISTRY
+
+.git-before-script: &git_before_script
+  before_script:
+    - git config --global user.name "CR (covid cron)"
+    - git config --global user.email "beepbop@example.com"
+    - url_host=`git remote get-url origin | sed -e "s/https:\/\/gitlab-ci-token:.*@//g"`
+    - cd /tmp/
+    - git clone "https://oauth2:${CI_PUSH_TOKEN}@${url_host}"
+    - cd covid-19-public-data
+    - git lfs install --local
+    - git checkout $CI_COMMIT_BRANCH
+    - PATH=$PATH:~/.local/bin
 
 stages:
   - build
+  - datasets-update
+  - notebooks-update
+  - finalize-update
 
 image_build:
   stage: build
   image: docker:stable
-  before_script:
-    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN http://$CI_REGISTRY
+  except:
+    - /^auto-update.*$/
+  <<: *docker_before_script
+
+  script: |
+    CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7)
+
+    # export the short SHA for other stages
+    echo "CI_COMMIT_SHA_7=$CI_COMMIT_SHA_7" >> build.env
+
+    # build image
+    docker build --build-arg BUILDKIT_INLINE_CACHE=1 \
+      --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 \
+      --cache-from $CI_REGISTRY_IMAGE .
+
+    # push with commit-sha tag and latest
+    docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7
+    docker tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 $CI_REGISTRY_IMAGE:latest
+    docker push $CI_REGISTRY_IMAGE:latest
+  artifacts:
+    reports:
+      dotenv: build.env
+
+datasets:
+  stage: datasets-update
+  image:
+    name: ${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHA_7}
+    entrypoint: [""]
+
+  only:
+    - schedules
+  <<: *git_before_script
+  script:
+    - export BRANCH_NAME=auto-update-datasets-${CI_COMMIT_SHA_7}
+    - git checkout -b $BRANCH_NAME
+    # Johns Hopkins
+    - renku dataset update covid-19_jhu-csse
+    - renku dataset add covid-19_jhu-csse --force --source csse_covid_19_data/csse_covid_19_daily_reports https://github.com/CSSEGISandData/COVID-19.git
+
+    # Open Data Zürich
+    - renku dataset update openzh-covid-19
+
+    # Italy
+    - renku dataset update covid-19-italy
+
+    # Spain
+    - renku dataset update covid-19-spain
+
+    # NYT US data
+    - renku dataset update covid-19-us-nyt
+
+    # ECDC
+    - wget -O /tmp/covid-19-ecdc.csv https://opendata.ecdc.europa.eu/covid19/casedistribution/csv
+    - renku dataset add covid-19-ecdc /tmp/covid-19-ecdc.csv --overwrite || true
+
+    # chile data has not been updated for a long time
+    # - renku dataset add covid-19-chile -s data/*.csv  -s data/covid19_chile.rds https://github.com/itoledor/coronavirus.git --force || true
+
+    # Covidtracker no longer collecting data
+    # TODO: transition to federal data sources: https://covidtracking.com/analysis-updates/federal-covid-data-single-stream
+    # - renku dataset add covidtracker https://ocgptweb.azurewebsites.net/CSVDownload -d covidtracker.csv --force || true
+    # - renku rerun data/covidtracking/states-metadata.json data/covidtracking/states-daily.json
+    - git push --set-upstream origin $BRANCH_NAME
+
+notebooks:
+  stage: notebooks-update
+  image:
+    name: ${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHA_7}
+    entrypoint: [""]
+  only:
+    refs:
+      - schedules
+  <<: *git_before_script
   script:
-    - CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7)
-    - docker build --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 .
-    - docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7
-  tags:
-    - image-build
+    - export BRANCH_NAME=auto-update-notebooks-${CI_COMMIT_SHA_7}
+    - git checkout auto-update-datasets-${CI_COMMIT_SHA_7}
+    - git checkout -b $BRANCH_NAME
+    - renku update --all
+    - git push --set-upstream origin $BRANCH_NAME
+
+finalize:
+  stage: finalize-update
+  image:
+    name: ${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHA_7}
+    entrypoint: [""]
+  only:
+    - schedules
+  <<: *git_before_script
+  script: |
+    set -x
+
+    # install jq
+    wget -O ~/.local/bin/jq https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64
+    chmod u+x ~/.local/bin/jq
+
+    # push the updated branch to a common name
+    export BRANCH_NAME="auto-update"_$(date -u +"%Y-%m-%d_%H-%M")
+    git checkout auto-update-notebooks-${CI_COMMIT_SHA_7} || git checkout auto-update-datasets-${CI_COMMIT_SHA_7}
+    git rev-parse --abbrev-ref HEAD
+    git checkout -b $BRANCH_NAME
+    git push origin $BRANCH_NAME
+
+    # create MR
+    BODY="{
+      \"id\": ${CI_PROJECT_ID},
+      \"source_branch\": \"${BRANCH_NAME}\",
+      \"target_branch\": \"master\",
+      \"remove_source_branch\": true,
+      \"title\": \"Automatic update - ${BRANCH_NAME}\"
+      }";
+
+    MR_ID=$(curl -s -X POST "https://renkulab.io/gitlab/api/v4/projects/${CI_PROJECT_ID}/merge_requests" \
+      --header "PRIVATE-TOKEN: ${CI_PUSH_TOKEN}" \
+      --header "Content-Type: application/json" \
+      --data "${BODY}" | jq .iid)
+
+    # merge MR
+    RES=$(curl -s -X PUT "https://renkulab.io/gitlab/api/v4/projects/${CI_PROJECT_ID}/merge_requests/${MR_ID}/merge" \
+      --header "PRIVATE-TOKEN: ${CI_PUSH_TOKEN}" \
+      --header "Content-Type: application/json")
+    echo $RES
+
+    # clean up branches
+    git push origin --delete auto-update-notebooks-${CI_COMMIT_SHA_7} || true
+    git push origin --delete auto-update-datasets-${CI_COMMIT_SHA_7} || true

.renku/metadata.yml

-'@context':
-  created: schema:dateCreated
-  schema: http://schema.org/
-  name: schema:name
-  updated: schema:dateUpdated
-  version: schema:schemaVersion
-'@type': schema:Project
-created: 2020-03-11T21:43:12.736Z
-name: covid-19-dashboard
-updated: 2020-03-11T21:43:12.736Z
-version: '1'
+# Dummy file kept for backwards compatibility, does not contain actual version
+'http://schema.org/schemaVersion': '9'
\ No newline at end of file