Commit d7b6a88e authored by Nathanaël Perraudin's avatar Nathanaël Perraudin
Browse files

Merge branch 'master' into 'master'

Master

See merge request !1
parents cfddccd6 3ae42674
Pipeline #22065 passed with stage
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......@@ -347,3 +347,24 @@ data/covid-19-spain/ccaa_covid19_uci.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-spain/ccaa_covid19_uci_long.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-spain/nacional_covid19.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-spain/readme.md filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/03-26-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/03-28-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/03-29-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/03-27-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/03-25-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/03-30-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/03-31-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-01-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-02-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19_jhu-csse/csse_covid_19_daily_reports/04-03-2020.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-27.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-26_tests.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-28.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-04-03.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-30.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-25.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-29.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-04-02.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-26.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-03-31.csv filter=lfs diff=lfs merge=lfs -text
data/covid-19-chile/covid19_chile_2020-04-01.csv filter=lfs diff=lfs merge=lfs -text
......@@ -378,3 +378,5 @@ tags
.renku.lock
.renku/tmp
.renku/cache
.vscode
......@@ -59,11 +59,13 @@ update:
- export BRANCH_NAME="update"_$(date -u +"%Y-%m-%d_%H-%M")
- PATH=$PATH:~/.local/bin
- git checkout -b $BRANCH_NAME
- renku dataset update covid-19_jhu-csse
- 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
- renku dataset update covid-19-tweet-ids
- renku dataset update openzh-covid-19
- renku dataset update covid-19-italy
- renku dataset update covid-19-spain
- renku dataset add covid-19-chile -s data/*.csv -s data/covid19_chile.rds https://github.com/itoledor/coronavirus.git --force
- renku rerun data/covidtracking/states-metadata.json data/covidtracking/states-daily.json
- renku update --with-siblings
- git push --set-upstream origin $BRANCH_NAME
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added: '2020-03-19T10:45:32.448526+00:00'
based_on: null
......@@ -227,7 +227,7 @@ files:
- schema:DigitalDocument
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_label: data/covid-19-italy/dpc-covid19-ita-province.json@67c741bd2f0e24de0fb807f13268c3df9c02ce4b
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'@type':
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......@@ -254,7 +254,7 @@ files:
- schema:DigitalDocument
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_label: dati-json/dpc-covid19-ita-province.json@8defe421b88123392e3f2b913bb113733d40f8d0
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added: '2020-03-19T10:45:51.627833+00:00'
based_on: null
......@@ -282,7 +282,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
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_label: data/covid-19-italy/dpc-covid19-ita-regioni.json@67c741bd2f0e24de0fb807f13268c3df9c02ce4b
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......@@ -309,7 +309,7 @@ files:
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_label: dati-json/dpc-covid19-ita-regioni.json@fa65fedf2783b8223c41a9b3fc2577af636d58db
_label: dati-json/dpc-covid19-ita-regioni.json@8defe421b88123392e3f2b913bb113733d40f8d0
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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@67c741bd2f0e24de0fb807f13268c3df9c02ce4b
_label: data/covid-19-italy/dpc-covid19-ita-province.csv@fd7e3634f9d0963d2323a7a7b5de3ad8eb224c90
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'@type':
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......@@ -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@fa65fedf2783b8223c41a9b3fc2577af636d58db
_label: dati-province/dpc-covid19-ita-province.csv@8defe421b88123392e3f2b913bb113733d40f8d0
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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@67c741bd2f0e24de0fb807f13268c3df9c02ce4b
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......@@ -419,7 +419,7 @@ files:
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- wfprov:Artifact
_id: https://github.com/blob/c6c0d46c82068c1439857e63f871bae1fda5f92d/dati-regioni/dpc-covid19-ita-regioni.csv
_label: dati-regioni/dpc-covid19-ita-regioni.csv@fa65fedf2783b8223c41a9b3fc2577af636d58db
_label: dati-regioni/dpc-covid19-ita-regioni.csv@8defe421b88123392e3f2b913bb113733d40f8d0
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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@67c741bd2f0e24de0fb807f13268c3df9c02ce4b
_label: data/covid-19-italy/dpc-covid19-ita-andamento-nazionale.csv@fd7e3634f9d0963d2323a7a7b5de3ad8eb224c90
_project:
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......@@ -474,7 +474,7 @@ files:
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- 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@fa65fedf2783b8223c41a9b3fc2577af636d58db
_label: dati-andamento-nazionale/dpc-covid19-ita-andamento-nazionale.csv@8defe421b88123392e3f2b913bb113733d40f8d0
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added: '2020-03-19T10:47:15.130679+00:00'
based_on: null
......@@ -502,7 +502,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
_id: https://renkulab.io/blob/d0b8e0d440de1d96cf57e35c9a47a2699d6f5106/data/covid-19-italy/dati-andamento-nazionale-description.json
_label: data/covid-19-italy/dati-andamento-nazionale-description.json@ba96bbf0f7d54cd9ca144fa283b36c7aa83fd4d6
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......@@ -529,7 +529,7 @@ files:
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added: '2020-03-22T21:42:08.484068+00:00'
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......@@ -557,7 +557,7 @@ files:
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_id: https://renkulab.io/blob/f1d2951e579144735588f5810bdf7f433c41cc13/data/covid-19-italy/dati-regioni-description.json
_label: data/covid-19-italy/dati-regioni-description.json@ba96bbf0f7d54cd9ca144fa283b36c7aa83fd4d6
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......@@ -584,7 +584,7 @@ files:
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......
......@@ -171,7 +171,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
_id: https://renkulab.io/blob/deee6e09be393f17dfcb1843d330e20c707c0ef1/data/covid-19-spain/nacional_covid19.csv
_label: data/covid-19-spain/nacional_covid19.csv@3ebde896795fbb07559fc39a5003972b8b207a65
_label: data/covid-19-spain/nacional_covid19.csv@dba52495ccfc7268a68cbdc5589d7cb0901cd6d5
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......@@ -198,7 +198,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
_id: https://github.com/blob/58d96d8ce648eefd56c70bfd5349b308bf11420a/COVID 19/nacional_covid19.csv
_label: COVID 19/nacional_covid19.csv@9b073a6c0c46e119e364a5900bb3598eafafb974
_label: COVID 19/nacional_covid19.csv@5c378920de6b26ce009c4f6a9ca500499fd349a4
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added: '2020-03-26T16:21:45.569123+00:00'
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......@@ -289,7 +289,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
_id: https://renkulab.io/blob/deee6e09be393f17dfcb1843d330e20c707c0ef1/data/covid-19-spain/ccaa_covid19_altas.csv
_label: data/covid-19-spain/ccaa_covid19_altas.csv@3ebde896795fbb07559fc39a5003972b8b207a65
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......@@ -316,7 +316,7 @@ files:
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......@@ -371,7 +371,7 @@ files:
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_id: https://renkulab.io/blob/deee6e09be393f17dfcb1843d330e20c707c0ef1/data/covid-19-spain/ccaa_covid19_fallecidos.csv
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......@@ -453,7 +453,7 @@ files:
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......@@ -535,7 +535,7 @@ files:
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......@@ -599,7 +599,7 @@ files:
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_id: https://renkulab.io/blob/deee6e09be393f17dfcb1843d330e20c707c0ef1/data/covid-19-spain/nacional_covid19_rango_edad.csv
_label: data/covid-19-spain/nacional_covid19_rango_edad.csv@3ebde896795fbb07559fc39a5003972b8b207a65
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- prov:Location
......@@ -854,7 +854,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
_id: https://github.com/blob/21eb603844468cb5454f126aeeec4f18753c898a/COVID 19/nacional_covid19_rango_edad.csv
_label: COVID 19/nacional_covid19_rango_edad.csv@a917b6cf2a29f648878353b60b74464ec62e0788
_label: COVID 19/nacional_covid19_rango_edad.csv@162a2991031335523d1dcfcc82af12be6213887a
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added: '2020-03-26T16:21:45.950327+00:00'
based_on: null
......@@ -955,7 +955,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
_id: https://renkulab.io/blob/deee6e09be393f17dfcb1843d330e20c707c0ef1/data/covid-19-spain/ccaa_covid19_fallecidos_long.csv
_label: data/covid-19-spain/ccaa_covid19_fallecidos_long.csv@3ebde896795fbb07559fc39a5003972b8b207a65
_label: data/covid-19-spain/ccaa_covid19_fallecidos_long.csv@dba52495ccfc7268a68cbdc5589d7cb0901cd6d5
_project:
'@type':
- prov:Location
......@@ -982,7 +982,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
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_label: COVID 19/ccaa_covid19_fallecidos_long.csv@460abf5dc1f250af321286680eef7f6bd81e9744
_label: COVID 19/ccaa_covid19_fallecidos_long.csv@28385da4b887bfbfc84d7b5f9631bb578cc91fe9
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......@@ -1055,7 +1055,7 @@ files:
- schema:DigitalDocument
- wfprov:Artifact
_id: https://renkulab.io/blob/deee6e09be393f17dfcb1843d330e20c707c0ef1/data/covid-19-spain/ccaa_covid19_altas_long.csv
_label: data/covid-19-spain/ccaa_covid19_altas_long.csv@3ebde896795fbb07559fc39a5003972b8b207a65
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'@type':
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......@@ -1082,7 +1082,7 @@ files:
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based_on: null
......@@ -1155,7 +1155,7 @@ files:
- schema:DigitalDocument
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......@@ -1182,7 +1182,7 @@ files:
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......@@ -1255,7 +1255,7 @@ files:
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......@@ -1282,7 +1282,7 @@ files:
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......@@ -1337,7 +1337,7 @@ files:
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......@@ -1364,7 +1364,7 @@ files:
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......
class: Workflow
cwlVersion: v1.0
hints: []
inputs:
input_1:
default: states-daily.json
streamable: false
type: string
input_2:
default: states-metadata.json
streamable: false
type: string
input_3:
default: out_folder
streamable: false
type: string
input_4:
default: data/covidtracking
streamable: false
type: string
input_5:
default:
class: File
path: ../../notebooks/process/download-covidtracking-data.ipynb
streamable: false
type: File
input_6:
default: runs/download-covidtracking-data.runs.ipynb
streamable: false
type: string
outputs:
output_0:
outputSource: step_3/output_0
streamable: false
type: File
output_2:
outputSource: step_3/output_1
streamable: false
type: Directory
requirements: []
steps:
step_1:
in:
filename: input_1
input_directory: step_3/output_1
out:
- output_file
run:
arguments: []
baseCommand:
- 'true'
class: CommandLineTool
cwlVersion: v1.0
hints: []
inputs:
filename:
default: states-daily.json
streamable: false
type: string
input_directory:
streamable: false
type: Directory
outputs:
output_file:
outputBinding:
glob: $(inputs.filename)
streamable: false
type: File
permanentFailCodes: []
requirements:
- &id001
class: InlineJavascriptRequirement
- &id002
class: InitialWorkDirRequirement
listing: $(inputs.input_directory.listing)
successCodes: []
temporaryFailCodes: []
step_2:
in:
filename: input_2
input_directory: step_3/output_1
out:
- output_file
run:
arguments: []
baseCommand:
- 'true'
class: CommandLineTool
cwlVersion: v1.0
hints: []
inputs:
filename:
default: states-metadata.json
streamable: false
type: string
input_directory:
streamable: false
type: Directory
outputs:
output_file:
outputBinding:
glob: $(inputs.filename)
streamable: false
type: File
permanentFailCodes: []
requirements:
- *id001
- *id002
successCodes: []
temporaryFailCodes: []
step_3:
in:
input_1: input_3
input_2: input_4
input_3: input_5
input_4: input_6
out:
- output_1
- output_0
run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
class: Workflow
cwlVersion: v1.0
hints: []
inputs:
input_1:
default:
class: File
path: ../../notebooks/covidtracking-dashboard.ipynb
streamable: false
type: File
input_10:
default:
class: File
path: ../../notebooks/openzh-covid-19-dashboard.ipynb
streamable: false
type: File
input_11:
default: runs/openzh-covid-19-dashboard.run.ipynb
streamable: false
type: string
input_12:
default: data_path
streamable: false
type: string
input_13:
default:
class: Directory
listing: []
path: ../../data/openzh-covid-19
streamable: false
type: Directory
input_14:
default:
class: File
path: ../../data/ch-population-statistics/ch-population-by-age-canton.xls
streamable: false
type: File
input_15:
default: ts_folder
streamable: false
type: string
input_16:
default:
class: Directory
listing: []
path: ../../data/covid-19_jhu-csse
streamable: false
type: Directory
input_17:
default: rates_folder
streamable: false
type: string
input_18:
default:
class: Directory
listing: []
path: ../../data/covid-19_rates
streamable: false
type: Directory
input_19:
default: geodata_path
streamable: false
type: string
input_2:
default: runs/covidtracking-dashboard.ipynb
streamable: false
type: string
input_20:
default:
class: File
path: ../../data/geodata/geo_data.csv