Commit aa4f218b authored by Andreas Bleuler's avatar Andreas Bleuler
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Merge branch 'master' into 'master'

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......@@ -411,3 +411,167 @@ data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-19-2020.csv filter=lfs dif
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-20-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-21-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-22-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-23-2020.csv filter=lfs diff=lfs merge=lfs -text
data/distancing-metrics/measures-us/bu-edu.csv filter=lfs diff=lfs merge=lfs -text
data/distancing-metrics/mobility/apple/applemobilitytrends.csv filter=lfs diff=lfs merge=lfs -text
data/distancing-metrics/mobility/google/Global_Mobility_Report.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-25-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-26-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-24-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-04-19.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-27-2020.csv filter=lfs diff=lfs merge=lfs -text
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data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-02-2020.csv filter=lfs diff=lfs merge=lfs -text
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data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-05-2020.csv filter=lfs diff=lfs merge=lfs -text
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data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-06-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-08-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-09-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-10-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-11-2020.csv filter=lfs diff=lfs merge=lfs -text
data/distancing-metrics/** filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-12-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-13-2020.csv filter=lfs diff=lfs merge=lfs -text
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data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-15-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-16-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-17-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-21-2020.csv filter=lfs diff=lfs merge=lfs -text
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data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-27-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/05-28-2020.csv filter=lfs diff=lfs merge=lfs -text
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# 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
......@@ -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
......
'@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