Merge branch 'master' into 'master'

Master See merge request !1

Merge branch 'master' into 'master'
Master See merge request !1
aa4f218b · Andreas Bleuler · 4bf2dde4 · 2188da4b · aa4f218b · aa4f218b
Commit aa4f218b authored Sep 29, 2020 by Andreas Bleuler
--- a/.gitattributes
+++ b/.gitattributes
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+data/covid-19_jhu-csse/csse_covid_19_daily_reports/09-25-2020.csv filter=lfs diff=lfs merge=lfs -text
+data/covid-19_jhu-csse/csse_covid_19_daily_reports/09-26-2020.csv filter=lfs diff=lfs merge=lfs -text
+data/covid-19_jhu-csse/csse_covid_19_daily_reports/09-27-2020.csv filter=lfs diff=lfs merge=lfs -text
+data/covid-19_jhu-csse/csse_covid_19_daily_reports/09-28-2020.csv filter=lfs diff=lfs merge=lfs -text
--- a/.gitlab-ci.yml
+++ b/.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
+    - PATH=$PATH:~/.local/bin

 stages:
  - build
-  - periodic
+  - datasets-update
+  - notebooks-update
+  - finalize-update

 image_build:
  stage: build
  image: docker:stable
  except:
-    refs:
-      - schedules
-  before_script:
-    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN http://$CI_REGISTRY
-  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
+    - /^auto-update.*$/
+    - schedules
+  <<: *docker_before_script

-update_build:
+  script: |
+    CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7)
+    docker build --build-arg BUILDKIT_INLINE_CACHE=1 \
+      --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 \
+      --cache-from $CI_REGISTRY_IMAGE .
+    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
+
+update-build:
  stage: build
  image: docker:stable
  only:
-    refs:
-      - schedules
-  before_script:
-    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN http://$CI_REGISTRY
-  script:
-    - docker build --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA-update .
-    - docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA-update
-  tags:
-    - image-build
+    - schedules
+  <<: *docker_before_script

-update:
-  stage: periodic
+  script: |
+    docker build --build-arg BUILDKIT_INLINE_CACHE=1 \
+      --tag $CI_REGISTRY_IMAGE:${CI_COMMIT_SHORT_SHA}-update \
+      --cache-from $CI_REGISTRY_IMAGE .
+    docker push $CI_REGISTRY_IMAGE:${CI_COMMIT_SHORT_SHA}-update
+    docker tag $CI_REGISTRY_IMAGE:${CI_COMMIT_SHORT_SHA}-update ${CI_REGISTRY_IMAGE}:latest
+    docker push $CI_REGISTRY_IMAGE:latest
+
+datasets:
+  stage: datasets-update
  image:
-    name: $CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA-update
+    name: ${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}-update
    entrypoint: [""]

  only:
-    refs:
-      - schedules
+    - schedules
+  <<: *git_before_script
  script:
-    - git config --global user.name "CR (covid cron)"
-    - git config --global user.email "cramakri+covid-cron@ethz.ch"
-    - url_host=`git remote get-url origin | sed -e "s/https:\/\/gitlab-ci-token:.*@//g"`
-    - cd /tmp/
-    - git clone "https://gitlab-ci-token:${CI_TAG_UPLOAD_TOKEN}@${url_host}"
-    - cd covid-19-public-data
-    - git lfs install --local
-    - export BRANCH_NAME="update"_$(date -u +"%Y-%m-%d_%H-%M")
-    - PATH=$PATH:~/.local/bin
+    - export BRANCH_NAME=auto-update-datasets-${CI_COMMIT_SHORT_SHA}
    - git checkout -b $BRANCH_NAME
    - 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
@@ -66,9 +77,72 @@ update:
    - renku dataset update covid-19-italy
    - renku dataset update covid-19-spain
    - renku dataset update covid-19-us-nyt
-    - renku dataset add covid-19-ecdc -d covid-19-ecdc.csv https://opendata.ecdc.europa.eu/covid19/casedistribution/csv --force || true
-    - renku dataset add covid-19-chile -s data/*.csv  -s data/covid19_chile.rds https://github.com/itoledor/coronavirus.git --force
-    - renku dataset add covidtracker https://ocgptweb.azurewebsites.net/CSVDownload -d covidtracker.csv --force
+    - 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
+    - renku dataset add covid-19-chile -s data/*.csv  -s data/covid19_chile.rds https://github.com/itoledor/coronavirus.git --force || true
+    - 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_SHORT_SHA}-update
+    entrypoint: [""]
+  only:
+    refs:
+      - schedules
+  <<: *git_before_script
+  script:
+    - export BRANCH_NAME=auto-update-notebooks-${CI_COMMIT_SHORT_SHA}
+    - git checkout auto-update-datasets-${CI_COMMIT_SHORT_SHA}
+    - git checkout -b $BRANCH_NAME
    - renku update --with-siblings
    - git push --set-upstream origin $BRANCH_NAME
+
+finalize:
+  stage: finalize-update
+  image:
+    name: ${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}-update
+    entrypoint: [""]
+  only:
+    - schedules
+  <<: *git_before_script
+  when: always
+  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_SHORT_SHA} || git checkout auto-update-datasets-${CI_COMMIT_SHORT_SHA}
+    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_SHORT_SHA} || true
+    git push origin --delete auto-update-datasets-${CI_COMMIT_SHORT_SHA} || true
--- a/.renku/datasets/286c58b1-dbbc-4caa-a23a-fcb001d5ac51/metadata.yml
+++ b/.renku/datasets/286c58b1-dbbc-4caa-a23a-fcb001d5ac51/metadata.yml
@@ -151,7 +151,7 @@ _project:
    name: Chandrasekhar Ramakrishnan
  name: covid-19-dashboard
  updated: '2020-03-11T21:43:12.736000+00:00'
-  version: '3'
+  version: '4'
 based_on: null
 created: '2020-03-19T00:31:17.209963+00:00'
 creator:
@@ -172,7 +172,7 @@ files:
  - schema:DigitalDocument
  - wfprov:Artifact
  _id: https://renkulab.io/blob/5d77bbb3d92723a71c34da3e93460c1d98e4a189/data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.json
-  _label: data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.json@77a13c632ec707e781a9989edc53c518f5fffb14
+  _label: data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.json@721a0eb95e2b7a7fe0aa7a3530715b83a754498b
  _project:
    '@type':
    - prov:Location
@@ -199,7 +199,7 @@ files:
    - schema:DigitalDocument
    - wfprov:Artifact
    _id: https://github.com/blob/7470ab0daaaab0518ae7aa8cc71fd87d5c33ada5/dati-json/dpc-covid19-ita-andamento-nazionale.json
-    _label: dati-json/dpc-covid19-ita-andamento-nazionale.json@613258ed78dfe0d0ea18f56e82537d3369267a38
+    _label: dati-json/dpc-covid19-ita-andamento-nazionale.json@e38c0c6fda87230d9bea5819ea9833fd4d41cfa9
    _project: null
    added: '2020-03-19T10:45:32.448526+00:00'
    based_on: null
@@ -227,7 +227,7 @@ files:
  - schema:DigitalDocument
  - wfprov:Artifact
  _id: https://renkulab.io/blob/b69963509326683ca9ee686792fd9735111dc5ef/data/covid-19-italy/dpc-covid19-ita-province.json
-  _label: data/covid-19-italy/dpc-covid19-ita-province.json@77a13c632ec707e781a9989edc53c518f5fffb14
+  _label: data/covid-19-italy/dpc-covid19-ita-province.json@721a0eb95e2b7a7fe0aa7a3530715b83a754498b
  _project:
    '@type':
    - prov:Location
@@ -254,7 +254,7 @@ files:
    - schema:DigitalDocument
    - wfprov:Artifact
    _id: https://github.com/blob/71b44ac1987457c16a2af5466eeb96c02f45020f/dati-json/dpc-covid19-ita-province.json
-    _label: dati-json/dpc-covid19-ita-province.json@613258ed78dfe0d0ea18f56e82537d3369267a38
+    _label: dati-json/dpc-covid19-ita-province.json@e38c0c6fda87230d9bea5819ea9833fd4d41cfa9
    _project: null
    added: '2020-03-19T10:45:51.627833+00:00'
    based_on: null
@@ -282,7 +282,7 @@ files:
  - schema:DigitalDocument
  - wfprov:Artifact
  _id: https://renkulab.io/blob/f7fc43ab3c49beaa0c73b1f7f4e421b5163f0add/data/covid-19-italy/dpc-covid19-ita-regioni.json
-  _label: data/covid-19-italy/dpc-covid19-ita-regioni.json@77a13c632ec707e781a9989edc53c518f5fffb14
+  _label: data/covid-19-italy/dpc-covid19-ita-regioni.json@721a0eb95e2b7a7fe0aa7a3530715b83a754498b
  _project:
    '@type':
    - prov:Location
@@ -309,7 +309,7 @@ files:
    - schema:DigitalDocument
    - wfprov:Artifact
    _id: https://github.com/blob/71b44ac1987457c16a2af5466eeb96c02f45020f/dati-json/dpc-covid19-ita-regioni.json
-    _label: dati-json/dpc-covid19-ita-regioni.json@613258ed78dfe0d0ea18f56e82537d3369267a38
+    _label: dati-json/dpc-covid19-ita-regioni.json@e38c0c6fda87230d9bea5819ea9833fd4d41cfa9
    _project: null
    added: '2020-03-19T10:46:24.163477+00:00'
    based_on: null
@@ -337,7 +337,7 @@ files:
  - schema:DigitalDocument
  - wfprov:Artifact
  _id: https://renkulab.io/blob/214fa7d617f2957a734045fba3c01cf145af6649/data/covid-19-italy/dpc-covid19-ita-province.csv
-  _label: data/covid-19-italy/dpc-covid19-ita-province.csv@77a13c632ec707e781a9989edc53c518f5fffb14
+  _label: data/covid-19-italy/dpc-covid19-ita-province.csv@721a0eb95e2b7a7fe0aa7a3530715b83a754498b
  _project:
    '@type':
    - prov:Location
@@ -364,7 +364,7 @@ files:
    - schema:DigitalDocument
    - wfprov:Artifact
    _id: https://github.com/blob/8395f2eb33233e2d5785f0c248177263c105cf73/dati-province/dpc-covid19-ita-province.csv
-    _label: dati-province/dpc-covid19-ita-province.csv@613258ed78dfe0d0ea18f56e82537d3369267a38
+    _label: dati-province/dpc-covid19-ita-province.csv@e38c0c6fda87230d9bea5819ea9833fd4d41cfa9
    _project: null
    added: '2020-03-19T10:46:47.013799+00:00'
    based_on: null
@@ -392,7 +392,7 @@ files:
  - schema:DigitalDocument
  - wfprov:Artifact
  _id: https://renkulab.io/blob/8a04a14a3682521eff2bb0814755a2317f926dce/data/covid-19-italy/dpc-covid19-ita-regioni.csv
-  _label: data/covid-19-italy/dpc-covid19-ita-regioni.csv@77a13c632ec707e781a9989edc53c518f5fffb14
+  _label: data/covid-19-italy/dpc-covid19-ita-regioni.csv@721a0eb95e2b7a7fe0aa7a3530715b83a754498b
  _project:
    '@type':
    - prov:Location
@@ -419,7 +419,7 @@ files:
    - schema:DigitalDocument
    - wfprov:Artifact
    _id: https://github.com/blob/c6c0d46c82068c1439857e63f871bae1fda5f92d/dati-regioni/dpc-covid19-ita-regioni.csv
-    _label: dati-regioni/dpc-covid19-ita-regioni.csv@613258ed78dfe0d0ea18f56e82537d3369267a38
+    _label: dati-regioni/dpc-covid19-ita-regioni.csv@e38c0c6fda87230d9bea5819ea9833fd4d41cfa9
    _project: null
    added: '2020-03-19T10:47:00.393956+00:00'
    based_on: null
@@ -447,7 +447,7 @@ files:
  - schema:DigitalDocument
  - wfprov:Artifact
  _id: https://renkulab.io/blob/2f28b89c0b8580175181291e152ec03ad8d87a51/data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.csv
-  _label: data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.csv@77a13c632ec707e781a9989edc53c518f5fffb14
+  _label: data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.csv@721a0eb95e2b7a7fe0aa7a3530715b83a754498b
  _project:
    '@type':
    - prov:Location
@@ -474,7 +474,7 @@ files:
    - schema:DigitalDocument
    - wfprov:Artifact
    _id: https://github.com/blob/7470ab0daaaab0518ae7aa8cc71fd87d5c33ada5/dati-andamento-nazionale/dpc-covid19-ita-andamento-nazionale.csv
-    _label: dati-andamento-nazionale/dpc-covid19-ita-andamento-nazionale.csv@613258ed78dfe0d0ea18f56e82537d3369267a38
+    _label: dati-andamento-nazionale/dpc-covid19-ita-andamento-nazionale.csv@e38c0c6fda87230d9bea5819ea9833fd4d41cfa9
    _project: null
    added: '2020-03-19T10:47:15.130679+00:00'
    based_on: null

--- a/.renku/datasets/46c02f05-393a-4a78-bd5d-d3bf2c23d577/metadata.yml
+++ b/.renku/datasets/46c02f05-393a-4a78-bd5d-d3bf2c23d577/metadata.yml
+'@context':
+  '@version': 1.1
+  _id: '@id'
+  _project:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      created: schema:dateCreated
+      creator:
+        '@context':
+          '@version': 1.1
+          _id: '@id'
+          affiliation: schema:affiliation
+          alternate_name: schema:alternateName
+          email: schema:email
+          label: rdfs:label
+          name: schema:name
+          prov: http://www.w3.org/ns/prov#
+          rdfs: http://www.w3.org/2000/01/rdf-schema#
+          schema: http://schema.org/
+        '@id': schema:creator
+      name: schema:name
+      prov: http://www.w3.org/ns/prov#
+      schema: http://schema.org/
+      updated: schema:dateUpdated
+      version: schema:schemaVersion
+    '@id': schema:isPartOf
+  created: schema:dateCreated
+  creator:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      affiliation: schema:affiliation
+      alternate_name: schema:alternateName
+      email: schema:email
+      label: rdfs:label
+      name: schema:name
+      prov: http://www.w3.org/ns/prov#
+      rdfs: http://www.w3.org/2000/01/rdf-schema#
+      schema: http://schema.org/
+    '@id': schema:creator
+  date_published: schema:datePublished
+  description: schema:description
+  files:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      _project:
+        '@context':
+          '@version': 1.1
+          _id: '@id'
+          created: schema:dateCreated
+          creator:
+            '@context':
+              '@version': 1.1
+              _id: '@id'
+              affiliation: schema:affiliation
+              alternate_name: schema:alternateName
+              email: schema:email
+              label: rdfs:label
+              name: schema:name
+              prov: http://www.w3.org/ns/prov#
+              rdfs: http://www.w3.org/2000/01/rdf-schema#
+              schema: http://schema.org/
+            '@id': schema:creator
+          name: schema:name
+          prov: http://www.w3.org/ns/prov#
+          schema: http://schema.org/
+          updated: schema:dateUpdated
+          version: schema:schemaVersion
+        '@id': schema:isPartOf
+      added: schema:dateCreated
+      based_on: schema:isBasedOn
+      creator:
+        '@context':
+          '@version': 1.1
+          _id: '@id'
+          affiliation: schema:affiliation
+          alternate_name: schema:alternateName
+          email: schema:email
+          label: rdfs:label
+          name: schema:name
+          prov: http://www.w3.org/ns/prov#
+          rdfs: http://www.w3.org/2000/01/rdf-schema#
+          schema: http://schema.org/
+        '@id': schema:creator
+      name: schema:name
+      path: prov:atLocation
+      prov: http://www.w3.org/ns/prov#
+      schema: http://schema.org/
+      url: schema:url
+      wfprov: http://purl.org/wf4ever/wfprov#
+    '@id': schema:hasPart
+  identifier: schema:identifier
+  in_language:
+    '@context':
+      '@version': 1.1
+      alternate_name: schema:alternateName
+      name: schema:name
+      schema: http://schema.org/
+    '@id': schema:inLanguage
+  keywords: schema:keywords
+  license: schema:license
+  name: schema:name
+  path: prov:atLocation
+  prov: http://www.w3.org/ns/prov#
+  same_as:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      schema: http://schema.org/
+      url: schema:url
+    '@id': schema:sameAs
+  schema: http://schema.org/
+  short_name: schema:alternateName
+  tags:
+    '@context':
+      '@version': 1.1
+      _id: '@id'
+      commit: schema:location
+      created: schema:startDate
+      dataset: schema:about
+      description: schema:description
+      name: schema:name
+      schema: http://schema.org/
+    '@id': schema:subjectOf
+  url: schema:url
+  version: schema:version
+  wfprov: http://purl.org/wf4ever/wfprov#
+'@type':
+- prov:Entity
+- schema:Dataset
+- wfprov:Artifact
+_id: https://renkulab.io/datasets/46c02f05-393a-4a78-bd5d-d3bf2c23d577
+_label: 46c02f05-393a-4a78-bd5d-d3bf2c23d577
+_project:
+  '@type':
+  - prov:Location
+  - schema:Project
+  _id: https://renkulab.io/projects/covid-19/covid-19-public-data
+  created: '2020-03-11T21:43:12.736000+00:00'
+  creator:
+    '@type':
+    - prov:Person