Commit de522e80 authored by Jean-Francois Rey's avatar Jean-Francois Rey

mv list_figures.rds to data

parent 94f63563
Pipeline #2062 failed with stages
in 8 seconds
......@@ -28,7 +28,8 @@ GenData:
- "chmod -R +x $CLUSTER_WORKING_DIR"
- 'sed -i -e "s/TOKEN/$TRIGGERTOKEN/g" $CLUSTER_WORKING_DIR/clusterbash.sh'
- "export SSHPASS=$CLUSTER_PWD"
- 'sshpass -e ssh -o StrictHostKeyChecking=no $CLUSTER_USER@$CLUSTER_IP bash --login -i $CLUSTER_WORKING_DIR/launch_cluster.sh'
- 'sshpass -e ssh -o StrictHostKeyChecking=no $CLUSTER_USER@$CLUSTER_IP bash --login -i "sbatch -p pcbiom9x -D $CLUSTER_WORKING_DIR $CLUSTER_WORKING_DIR/clusterbash.sh"'
# - 'sshpass -e ssh -o StrictHostKeyChecking=no $CLUSTER_USER@$CLUSTER_IP bash --login -i $CLUSTER_WORKING_DIR/launch_cluster.sh'
GetData:
tags:
......@@ -41,12 +42,14 @@ GetData:
allow_failure: false
- when : manual
allow_failure: true
variables:
CLUSTER_WORKING_DIR: "/mnt/biomstock/Cluster/biometrie/parsi_covid/COVIDSHINYAPP/"
script:
- 'cp /mnt/biomstock/Cluster/biometrie/parsi_covid/COVIDSHINYAPP/list_figures.rds R/list_figures.rds'
- 'cp $CLUSTER_WORKING_DIR/list_figures.rds data/list_figures.rds'
- "Rscript R/immunity.R && mv immun_M3_k.rds data/"
artifacts:
paths:
- R/list_figures.rds
- data/list_figures.rds
- data/immun_M3_k.rds
expire_in: 2 weeks
......@@ -66,7 +69,6 @@ buildImageDocker:
dependencies:
- "GetData"
before_script:
- "mv R/list_figures.rds www/list_figures.rds"
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
stage: build_img
rules:
......
......@@ -26,7 +26,7 @@ The application is accessible at : [http://localhost:3838](http://localhost:3838
To update forecast data :
```
cd R && Rscript main_forecast_plotly.R
mv R/list_figures.rds www/list_figures.rds
mv R/list_figures.rds data/list_figures.rds
```
### Build Docker image
......
......@@ -181,7 +181,7 @@ dataDEATH = read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/
x = data.frame(dataDEATH)
### all possible forecasted countries
# possible_country_forecast = c('Sweden','Ireland','Portugal','Denmark','Germany','Austria','Romania','Poland')
list_figures <- readRDS(file = "www/list_figures.rds")
list_figures <- readRDS(file = "data/list_figures.rds")
possible_country_forecast = names(list_figures$list_figures_model0)
### select one country to forecast
# country_forecast = 'Ireland'
......@@ -190,7 +190,7 @@ possible_country_forecast = names(list_figures$list_figures_model0)
# envNew = new.env()
# list_figuresLINK = load(file = "www/list_figures.Rdata", envir = envNew)
# list_figures <- envNew[[list_figuresLINK]]
# list_figures <- readRDS(file = "www/list_figures.rds")
# list_figures <- readRDS(file = "data/list_figures.rds")
### select one country to forecast
x_func = function(date) {
......
......@@ -198,8 +198,10 @@ ui <- tagList(
tags$li("Forecast codes:",
a("Samuel Soubeyrand", href="https://informatique-mia.inra.fr/biosp/homepage-samuel-soubeyrand")),
tags$li("Server maintainer:",
a("Jean-François Rey", href="http://w3.avignon.inra.fr/jfrweb/"))
)
a("Jean-François Rey", href="http://w3.avignon.inra.fr/jfrweb/")),
tags$li("cluster compute:",
a("Loïc Houde", href="https://loic.biosp.org")),
a("Olivier Bonnefon", href="https://informatique-mia.inrae.fr/biosp/homepage-olivier-bonnefon"))
),
box(width = 12,
title = "Source of raw data",
......
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