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data/covid-19_jhu-csse/csse_covid_19_daily_reports/06-02-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/10-05-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-14-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-15-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-16-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-18-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-17-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-19-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-20-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-23-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-24-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-26-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-25-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-27-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-28-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-22-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-21-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-31-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/01-02-2022.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-29-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/01-01-2022.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/12-30-2021.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/01-03-2022.csv filter=lfs diff=lfs merge=lfs -text
.gitignore
View file @ dce0c83e
......@@ -378,3 +378,5 @@ tags
.renku.lock
.renku/tmp
.renku/cache
.vscode
.gitlab-ci.yml
View file @ dce0c83e
# 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/activity_index.yaml 0 → 100644
View file @ dce0c83e
data/atlas/wikidata:
6d16a55d66783ed7db5182398c031944f089ec3c:
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data/covid-19_rates:
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- .renku/workflow/42de7a674b2741888a97c447b86cdb16_migrated.yaml
runs/wikidata-pop-data.run.ipynb:
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- .renku/workflow/0dfa4041dce645f9b16a227db04aeaa5_papermill.yaml
8877d3c1bcd753483d45564209732fc8c8eb83a8:
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.renku/datasets/720e46f5-0f38-48be-86ef-1fcbae258a6f/metadata.yml deleted 100644 → 0
View file @ 63958a21
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.renku/datasets/bcd7b8bf-840d-45fd-9912-bb26be595d7f/metadata.yml deleted 100644 → 0
View file @ 63958a21
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.renku/datasets/bf528a35-35b9-40ee-9036-c08ba2581d91/metadata.yml deleted 100644 → 0
View file @ 63958a21
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.renku/datasets/e9212b58-4994-482b-801c-ed90a960bd04/metadata.yml deleted 100644 → 0
View file @ 63958a21
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.renku/datasets/f6726a5b-f973-45d5-b873-30fa0dff772f/metadata.yml deleted 100644 → 0
View file @ 63958a21
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.renku/metadata.yml
View file @ dce0c83e
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\ No newline at end of file
.renku/metadata/00/15/00150e422ed54ddbbda22c453176eb3a4eed0eae5f1f4faaa198776d4b266e46 0 → 100644
View file @ dce0c83e
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{
"@renku_data_type": "BTrees.OOBTree.OOBucket",
"@renku_oid": "63db8520b11141c5b61f403cba32d01cdcc17c43313945a1b6f94bba208fb70e",
"@renku_reference": true
}
]
},
"@renku_oid": "0077083dda104a60b7ca1e7460496b4017f745aa24b240078ed894d5738d7339"
}
\ No newline at end of file

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