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  • jovicic/covid-19-public-data
  • sofiane.sarni/covid-19-public-data
  • mojulian/covid-19-public-data
  • paul.ronga/covid-19-public-data
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......@@ -378,3 +378,5 @@ tags
.renku.lock
.renku/tmp
.renku/cache
.vscode
# 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
This diff is collapsed.
'@context':
'@version': 1.1
_id: '@id'
_project:
'@context':
'@version': 1.1
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created: schema:dateCreated
creator:
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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
based_on: schema:isBasedOn
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/286c58b1-dbbc-4caa-a23a-fcb001d5ac51
_label: 286c58b1-dbbc-4caa-a23a-fcb001d5ac51
_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
- schema:Person
_id: mailto:cramakri@ethz.ch
affiliation: null
alternate_name: null
email: cramakri@ethz.ch
label: Chandrasekhar Ramakrishnan
name: Chandrasekhar Ramakrishnan
name: covid-19-dashboard
updated: '2020-03-11T21:43:12.736000+00:00'
version: '1'
based_on: null
created: '2020-03-19T00:31:17.209963+00:00'
creator:
- '@type':
- prov:Person
- schema:Person
_id: mailto:rok.roskar@sdsc.ethz.ch
affiliation: null
alternate_name: null
email: rok.roskar@sdsc.ethz.ch
label: Rok Roskar
name: Rok Roskar
date_published: null
description: Covid-19 data for Italy obtained from https://github.com/pcm-dpc/COVID-19
files:
- '@type':
- prov:Entity
- 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@5d77bbb3d92723a71c34da3e93460c1d98e4a189
_project:
'@type':
- prov:Location
- schema:Project
_id: https://localhost/projects/cramakri/covid-19-dashboard
created: '2020-03-11T21:43:12.736000+00:00'
creator:
'@type':
- prov:Person
- schema:Person
_id: mailto:cramakri@ethz.ch
affiliation: null
alternate_name: null
email: cramakri@ethz.ch
label: Chandrasekhar Ramakrishnan
name: Chandrasekhar Ramakrishnan
name: covid-19-dashboard
updated: '2020-03-11T21:43:12.736000+00:00'
version: '1'
added: '2020-03-19T10:45:32.702343+00:00'
based_on:
'@type':
- prov:Entity
- 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@7470ab0daaaab0518ae7aa8cc71fd87d5c33ada5
_project: null
added: '2020-03-19T10:45:32.448526+00:00'
based_on: null
creator: []
name: dpc-covid19-ita-andamento-nazionale.json
path: dati-json/dpc-covid19-ita-andamento-nazionale.json
url: https://github.com/pcm-dpc/COVID-19.git
creator:
- '@type':
- prov:Person
- schema:Person
_id: mailto:rosini@agid.gov.it
affiliation: null
alternate_name: null
email: rosini@agid.gov.it
label: Umberto Rosini
name: Umberto Rosini
name: dpc-covid19-ita-andamento-nazionale.json
path: data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.json
url: https://github.com/pcm-dpc/COVID-19.git
- '@type':
- prov:Entity
- 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@b69963509326683ca9ee686792fd9735111dc5ef
_project:
'@type':
- prov:Location
- schema:Project
_id: https://localhost/projects/cramakri/covid-19-dashboard
created: '2020-03-11T21:43:12.736000+00:00'
creator:
'@type':
- prov:Person
- schema:Person
_id: mailto:cramakri@ethz.ch
affiliation: null
alternate_name: null
email: cramakri@ethz.ch
label: Chandrasekhar Ramakrishnan
name: Chandrasekhar Ramakrishnan
name: covid-19-dashboard
updated: '2020-03-11T21:43:12.736000+00:00'
version: '1'
added: '2020-03-19T10:45:51.900112+00:00'
based_on:
'@type':
- prov:Entity
- 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@71b44ac1987457c16a2af5466eeb96c02f45020f
_project: null
added: '2020-03-19T10:45:51.627833+00:00'
based_on: null
creator: []
name: dpc-covid19-ita-province.json
path: dati-json/dpc-covid19-ita-province.json
url: https://github.com/pcm-dpc/COVID-19.git
creator:
- '@type':
- prov:Person
- schema:Person
_id: mailto:rosini@agid.gov.it
affiliation: null
alternate_name: null
email: rosini@agid.gov.it
label: Umberto Rosini
name: Umberto Rosini
name: dpc-covid19-ita-province.json
path: data/covid-19-italy/dpc-covid19-ita-province.json
url: https://github.com/pcm-dpc/COVID-19.git
- '@type':
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- 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@f7fc43ab3c49beaa0c73b1f7f4e421b5163f0add
_project:
'@type':
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_id: https://localhost/projects/cramakri/covid-19-dashboard
created: '2020-03-11T21:43:12.736000+00:00'
creator:
'@type':
- prov:Person
- schema:Person
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affiliation: null
alternate_name: null
email: cramakri@ethz.ch
label: Chandrasekhar Ramakrishnan
name: Chandrasekhar Ramakrishnan
name: covid-19-dashboard
updated: '2020-03-11T21:43:12.736000+00:00'
version: '1'
added: '2020-03-19T10:46:24.413348+00:00'
based_on:
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- prov:Entity
- 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@71b44ac1987457c16a2af5466eeb96c02f45020f
_project: null
added: '2020-03-19T10:46:24.163477+00:00'
based_on: null
creator: []
name: dpc-covid19-ita-regioni.json
path: dati-json/dpc-covid19-ita-regioni.json
url: https://github.com/pcm-dpc/COVID-19.git
creator:
- '@type':
- prov:Person
- schema:Person
_id: mailto:rosini@agid.gov.it
affiliation: null
alternate_name: null
email: rosini@agid.gov.it
label: Umberto Rosini
name: Umberto Rosini
name: dpc-covid19-ita-regioni.json
path: data/covid-19-italy/dpc-covid19-ita-regioni.json
url: https://github.com/pcm-dpc/COVID-19.git
- '@type':
- prov:Entity
- schema:DigitalDocument
- wfprov:Artifact
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created: '2020-03-11T21:43:12.736000+00:00'
creator:
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affiliation: null
alternate_name: null
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label: Chandrasekhar Ramakrishnan
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name: covid-19-dashboard
updated: '2020-03-11T21:43:12.736000+00:00'
version: '1'
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based_on:
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creator: []
name: dpc-covid19-ita-province.csv
path: dati-province/dpc-covid19-ita-province.csv
url: https://github.com/pcm-dpc/COVID-19.git
creator:
- '@type':
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- schema:Person
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affiliation: null
alternate_name: null
email: rosini@agid.gov.it
label: Umberto Rosini
name: Umberto Rosini
name: dpc-covid19-ita-province.csv
path: data/covid-19-italy/dpc-covid19-ita-province.csv
url: https://github.com/pcm-dpc/COVID-19.git
- '@type':
- prov:Entity
- 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@8a04a14a3682521eff2bb0814755a2317f926dce
_project:
'@type':
- prov:Location
- schema:Project
_id: https://localhost/projects/cramakri/covid-19-dashboard
created: '2020-03-11T21:43:12.736000+00:00'
creator:
'@type':
- prov:Person
- schema:Person
_id: mailto:cramakri@ethz.ch
affiliation: null
alternate_name: null
email: cramakri@ethz.ch
label: Chandrasekhar Ramakrishnan
name: Chandrasekhar Ramakrishnan
name: covid-19-dashboard
updated: '2020-03-11T21:43:12.736000+00:00'
version: '1'
added: '2020-03-19T10:47:00.639038+00:00'
based_on:
'@type':
- prov:Entity
- 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@c6c0d46c82068c1439857e63f871bae1fda5f92d
_project: null
added: '2020-03-19T10:47:00.393956+00:00'
based_on: null
creator: []
name: dpc-covid19-ita-regioni.csv
path: dati-regioni/dpc-covid19-ita-regioni.csv
url: https://github.com/pcm-dpc/COVID-19.git
creator:
- '@type':
- prov:Person
- schema:Person
_id: mailto:rosini@agid.gov.it
affiliation: null
alternate_name: null
email: rosini@agid.gov.it
label: Umberto Rosini
name: Umberto Rosini
name: dpc-covid19-ita-regioni.csv
path: data/covid-19-italy/dpc-covid19-ita-regioni.csv
url: https://github.com/pcm-dpc/COVID-19.git
- '@type':
- prov:Entity
- schema:DigitalDocument
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_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@2f28b89c0b8580175181291e152ec03ad8d87a51
_project:
'@type':
- prov:Location
- schema:Project
_id: https://localhost/projects/cramakri/covid-19-dashboard
created: '2020-03-11T21:43:12.736000+00:00'
creator:
'@type':
- prov:Person
- schema:Person
_id: mailto:cramakri@ethz.ch
affiliation: null
alternate_name: null
email: cramakri@ethz.ch
label: Chandrasekhar Ramakrishnan
name: Chandrasekhar Ramakrishnan
name: covid-19-dashboard
updated: '2020-03-11T21:43:12.736000+00:00'
version: '1'
added: '2020-03-19T10:47:15.357288+00:00'
based_on:
'@type':
- prov:Entity
- 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@7470ab0daaaab0518ae7aa8cc71fd87d5c33ada5
_project: null
added: '2020-03-19T10:47:15.130679+00:00'
based_on: null
creator: []
name: dpc-covid19-ita-andamento-nazionale.csv
path: dati-andamento-nazionale/dpc-covid19-ita-andamento-nazionale.csv
url: https://github.com/pcm-dpc/COVID-19.git
creator:
- '@type':
- prov:Person
- schema:Person
_id: mailto:rosini@agid.gov.it
affiliation: null
alternate_name: null
email: rosini@agid.gov.it
label: Umberto Rosini
name: Umberto Rosini
name: dpc-covid19-ita-andamento-nazionale.csv
path: data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.csv
url: https://github.com/pcm-dpc/COVID-19.git
identifier: 286c58b1-dbbc-4caa-a23a-fcb001d5ac51
in_language: null
keywords: []
license: null
name: covid-19-italy
path: .renku/datasets/286c58b1-dbbc-4caa-a23a-fcb001d5ac51
same_as: null
short_name: covid-19-italy
tags: []
url: https://renkulab.io/datasets/286c58b1-dbbc-4caa-a23a-fcb001d5ac51
version: null
'@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