Merge pull request #493 from inbo/492-github-action-voor-automatische…

…-deployment-op-nieuwe-omgeving

👷 Add deployment uat workflow

.github/workflows/deployment_uat.yml

@@ -0,0 +1,35 @@
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - uat
+jobs:
+  build:
+    name: Build and upload Docker image
+    runs-on: [self-hosted]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: ${{ secrets.AWS_DEFAULT_REGION }}
+          role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }}
+
+      - name: Login to Amazon ECR
+        id: login-ecr
+        uses: aws-actions/amazon-ecr-login@v2
+
+      - name: Build, tag, and push docker image to Amazon ECR
+        env:
+          REGISTRY: ${{ steps.login-ecr.outputs.registry }}
+          REPOSITORY: ${{ secrets.AWS_ECR_REPOSITORY }}
+          IMAGE_TAG: ${{ github.sha }}
+          UAT_TAG: uat
+        run: |
+          docker build --build-arg GIT_SHA=${{ github.sha }} -t $REGISTRY/$REPOSITORY:$IMAGE_TAG -t $REGISTRY/$REPOSITORY:$UAT_TAG .
+          docker push $REGISTRY/$REPOSITORY:$IMAGE_TAG
+          docker push $REGISTRY/$REPOSITORY:$UAT_TAG

.gitignore

@@ -54,3 +54,6 @@ reporting-grofwild/inst/extdata/spatialData*.RData
 # Local copy of data files
 /dataS3
 /data
+
+# AWS connection
+/scripts/putSecret.sh

Dockerfile

@@ -1,63 +1,63 @@
-FROM openanalytics/r-ver:4.0.5
+FROM rocker/r-ver:4.3.2
 
 LABEL maintainer="Machteld Varewyck [email protected]"
 
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    gdal-bin \
-    libproj15 \
-    libgeos-3.8.0 libgeos-c1v5  \
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    libgdal-dev \
+    libproj22 \
+    libgeos3.10.2 libgeos-c1v5  \
     libcurl4-openssl-dev \
     curl \
     ca-certificates \
     pandoc \
-    libudunits2-0 \
+    libudunits2-dev \
     libmagick++-dev \
     libssl-dev \
     lmodern \
     fonts-cantarell \
+    texlive-latex-extra \
+    texlive-xetex \
+    texlive-fonts-recommended \
     texlive-plain-generic \
-    texlive-fonts-extra \
-    && rm -rf /var/lib/apt/lists/*
+    lmodern \
+    wget && \
+    wget https://downloads.vivaldi.com/stable/vivaldi-stable_6.8.3381.55-1_$(dpkg --print-architecture).deb && \
+    apt-get install --no-install-recommends -y ./vivaldi-stable*.deb && \
+    rm -rf /var/lib/apt/lists/*
 
 # Use the remotes package instead of devtools as it is much lighter
 RUN R -q -e "install.packages('remotes')"
 
-RUN R -q -e "remotes::install_cran(c('shiny', 'sf', 'dplyr', 'plyr', 'reshape2', 'mgcv', 'stringr', 'leaflet', 'flexdashboard', 'testthat', 'shinyjs', 'data.table', 'tinytex', 'tidyr', 'arrow', 'kableExtra'))"
-RUN R -q -e "remotes::install_version('DT', version = '0.23', repos = 'https://cloud.r-project.org', upgrade = 'never')"
-RUN R -q -e "remotes::install_version('plotly', version = '4.10.1', repos = 'https://cloud.r-project.org', upgrade = 'never')" 
-RUN R -q -e "remotes::install_version('rmarkdown', version = '2.18', repos = 'https://cloud.r-project.org', upgrade = 'never')"
-RUN R -q -e "remotes::install_version('magick', version = '2.7.3', repos = 'https://cloud.r-project.org', upgrade = 'never')"
+RUN R -q -e "options(warn = 2); remotes::install_cran(c('shiny', 'sf', 'dplyr', 'plyr', 'reshape2', 'mgcv', 'stringr', 'leaflet', 'flexdashboard', 'testthat', 'shinyjs', 'data.table', 'tinytex', 'tidyr', 'arrow', 'kableExtra', 'webshot2'))"
+RUN R -q -e "options(warn = 2); remotes::install_version('DT', version = '0.23', repos = 'https://cloud.r-project.org', upgrade = 'never')"
+RUN R -q -e "options(warn = 2); remotes::install_version('plotly', version = '4.10.1', repos = 'https://cloud.r-project.org', upgrade = 'never')" 
+RUN R -q -e "options(warn = 2); remotes::install_version('rmarkdown', version = '2.18', repos = 'https://cloud.r-project.org', upgrade = 'never')"
+RUN R -q -e "options(warn = 2); remotes::install_version('magick', version = '2.7.3', repos = 'https://cloud.r-project.org', upgrade = 'never')"
 # NOTE: Need at least these versions of plotly, rmarkdown and magick for dashboard rmarkdown to work
 
-RUN R -q -e "remotes::install_github('inbo/[email protected]')"
-RUN R -q -e "install.packages('oaStyle', repos = c(rdepot = 'https://repos.openanalytics.eu/repo/public', getOption('repos')))"
-
-# to prevent bobbing with shinycssloaders
-RUN R -q -e "remotes::install_github('daattali/shinycssloaders')"
+RUN R -q -e "options(warn = 2); remotes::install_github(c('inbo/[email protected]', 'daattali/shinycssloaders'))"
 
 # For the rmarkdown pdf report
-RUN R -e "tinytex::install_tinytex()" 
-ENV PATH="/root/bin:${PATH}" 
-# many packages needed for kableExtra background feature
-RUN R -e "tinytex::tlmgr_install(pkgs = c('fancyhdr', 'sectsty', 'titling', 'grffile', 'texlive-scripts', 'mathspec', 'multirow', 'wrapfig', 'colortbl', 'pdflscape', 'tabu', 'varwidth', 'threeparttable', 'threeparttablex', 'environ', 'trimspaces', 'ulem', 'makecell'))" 
+RUN R -q -e "options(warn = 2); install.packages('oaStyle', repos = c(rdepot = 'https://repos.openanalytics.eu/repo/public', getOption('repos')))"
+#RUN R -e "tinytex::install_tinytex()" 
+#ENV PATH="/root/bin:${PATH}" 
+## many packages needed for kableExtra background feature
+#RUN R -e "tinytex::tlmgr_install(pkgs = c('fancyhdr', 'sectsty', 'titling', 'grffile', 'texlive-scripts', 'mathspec', 'multirow', 'wrapfig', 'colortbl', 'pdflscape', 'tabu', 'varwidth', 'threeparttable', 'threeparttablex', 'environ', 'trimspaces', 'ulem', 'makecell'))" 
 
-# For downloading the maps
-# Attention: do not install phantomjs directly, will not work then!
-RUN R -q -e "remotes::install_cran('webshot')"
-RUN R -e "webshot::install_phantomjs()"
+# Configure browser for using webshot2
+ENV CHROMOTE_CHROME=/usr/bin/vivaldi
 
 # Git sha
 ARG GIT_SHA
 ENV GIT_SHA=$GIT_SHA
 
 # For access to S3 on UAT
-# For calculating areas - fix #435
-RUN R -q -e "remotes::install_cran(c('config', 'aws.s3', 'aws.ec2metadata', 'lwgeom'))"
+RUN R -q -e "options(warn = 2); remotes::install_cran(c('config', 'aws.s3', 'aws.ec2metadata', 'aws.signature'))"
 
 
 # Install the package without the source files ending up in the Docker image
 COPY reporting-grofwild /tmp/package
-RUN R -q -e "remotes::install_local('/tmp/package', dependencies=FALSE)"
+RUN R -q -e "options(warn = 2); remotes::install_local('/tmp/package', dependencies=FALSE)"
 
 # set host
 COPY Rprofile.site /usr/local/lib/R/etc/

README.md

@@ -32,21 +32,21 @@ Configure connection to [S3 data buckets](https://docs.aws.amazon.com/cli/latest
 Run docker image, public app. 
 
 ```
-sudo docker run -p 3001:3838 inbo/wildapp R -e "Sys.setenv('AWS_DEFAULT_REGION'='eu-west-1','AWS_ACCESS_KEY_ID'='xxx','AWS_SECRET_ACCESS_KEY'='xxx'); reportingGrofwild::runWildApp(public=TRUE)" 
+sudo docker run -it -v ~/.aws:/root/.aws -p 3001:3838 inbo/wildapp R -e "reportingGrofwild::setupS3(); reportingGrofwild::runWildApp(public=TRUE)" 
 ```
 
 Browse to `localhost:3001`.
 
 Run docker image, private app for specific KBO.
 
 ```
-sudo docker run -p 3001:3838 inbo/wildapp R -e "Sys.setenv('AWS_DEFAULT_REGION'='eu-west-1','AWS_ACCESS_KEY_ID'='xxx','AWS_SECRET_ACCESS_KEY'='xxx'); reportingGrofwild::runWildApp(public=FALSE, kbo = xxx)" 
+sudo docker run -it -v ~/.aws:/root/.aws -p 3001:3838 inbo/wildapp R -e "reportingGrofwild::setupS3(); reportingGrofwild::runWildApp(public=FALSE, kbo = xxx)" 
 ```
 
 In a similar way, an R session can be started to run specific functions of the reportingGrofwild R package.
 
 ```
-sudo docker run -p 3001:3838 inbo/wildapp R
+sudo docker run -it -p 3001:3838 inbo/wildapp R
 ```
 
 

reporting-grofwild/DESCRIPTION

@@ -5,12 +5,13 @@ Title: Grof Wild analysis for INBO
 Type: Package
 Author: Machteld Varewyck, Laure Cougnaud, Eva Adriaensen
 Description: Data visualization of grof wild in Vlaanderen.
-Version: 0.3.5
+Version: 0.3.6
 Date: 2024-06-03
 Imports:
     arrow,
     aws.ec2metadata,
     aws.s3,
+    aws.signature,
     config,
     data.table,
     DT, 
@@ -19,7 +20,7 @@ Imports:
     htmlwidgets,
     INBOtheme, 
     leaflet, 
-    methods, 
+    methods,
     mgcv, 
     plotly,
     plyr, 
@@ -33,10 +34,9 @@ Imports:
     stringr,
     testthat,
     units,
-    webshot
+    webshot2
 Suggests:
     kableExtra,
-    lwgeom,
     magick,
     oaStyle,
     rmarkdown

reporting-grofwild/NAMESPACE

@@ -173,6 +173,7 @@ importFrom(aws.s3,s3read_using)
 importFrom(aws.s3,s3save)
 importFrom(aws.s3,s3write_using)
 importFrom(aws.s3,save_object)
+importFrom(aws.signature,read_credentials)
 importFrom(config,get)
 importFrom(data.table,rbindlist)
 importFrom(flexdashboard,gauge)
@@ -238,4 +239,4 @@ importFrom(utils,read.csv)
 importFrom(utils,tail)
 importFrom(utils,write.csv)
 importFrom(utils,write.table)
-importFrom(webshot,webshot)
+importFrom(webshot2,webshot)

reporting-grofwild/R/data_s3.R

@@ -3,23 +3,38 @@
 #' 
 #' INFO: https://www.gormanalysis.com/blog/connecting-to-aws-s3-with-r/
 #' @param awsFile path to AWS file
+#' @param inboUserName set NULL if not a inbo user, for inbo user, provide your user name firstName_lastName
 #' @return no return value, ENV variables are set correctly
 #' 
 #' @author mvarewyck
+#' @importFrom aws.signature read_credentials
 #' @export
-setupS3 <- function(awsFile = "~/.aws/credentials") {
+setupS3 <- function(awsFile = "~/.aws/credentials", inboUserName = NULL) {
+
+  #"sander_devisscher"
+  profile <- if (is.null(inboUserName)) 
+      "inbo-fauna" else 
+      sprintf("inbo-uat-%s", gsub("_", "-", inboUserName))
+
+  # for inbo user on their PC
+  userProfile <- Sys.getenv("USERPROFILE", unset = NA)
+
+
+  if (!is.na(userProfile))
+    awsFile <- normalizePath(file.path(userProfile, ".aws", "credentials"))
+
 
   # credentials are in ~/.aws/credentials OR manually copy/paste OR using aws.signature::
-  x <- rawToChar(readBin(awsFile, "raw", n = 1e5L))
-  profile <- Sys.getenv("AWS_PROFILE")
-  credentials <- strsplit(x, profile)[[1]][2]
+  x <- aws.signature::read_credentials(file = awsFile)[[profile]]
+
 
   Sys.setenv(
     AWS_DEFAULT_REGION = eval(parse(text = config::get("credentials", file = system.file("config.yml", package = "reportingGrofwild"))$region)),
-    AWS_ACCESS_KEY_ID = strsplit(strsplit(credentials, "aws_access_key_id = ")[[1]][2], "\n")[[1]][1], 
-    AWS_SECRET_ACCESS_KEY = strsplit(strsplit(credentials, "aws_secret_access_key = ")[[1]][2], "\n")[[1]][1]
+    AWS_ACCESS_KEY_ID = x$AWS_ACCESS_KEY_ID, 
+    AWS_SECRET_ACCESS_KEY = x$AWS_SECRET_ACCESS_KEY,
+    AWS_SESSION_TOKEN = x$AWS_SESSION_TOKEN 
   )
-
+    
 }
 
 
@@ -59,7 +74,7 @@ checkS3 <- function() {
     # Try to retrieve metadata from the instance
     metadata$instance_id()
   } else {
-    credentials <- Sys.getenv(c("AWS_DEFAULT_REGION", "AWS_ACCESS_KEY_ID", "AWS_SECRET_ACCESS_KEY"))
+    credentials <- Sys.getenv(c("AWS_DEFAULT_REGION", "AWS_ACCESS_KEY_ID", "AWS_SECRET_ACCESS_KEY", 'AWS_SESSION_TOKEN'))
     if (any(credentials == ""))
       stop("Please specify 'Sys.setenv()' for ", 
         paste(names(credentials)[which(credentials == "")], collapse = ", "))

reporting-grofwild/R/mapFlanders.R

@@ -456,7 +456,7 @@ mapFlanders <- function(
 #' @import shiny
 #' @import leaflet
 #' @importFrom sf st_coordinates
-#' @importFrom webshot webshot
+#' @importFrom webshot2 webshot
 #' @importFrom htmlwidgets saveWidget
 #' @export
 mapFlandersServer <- function(id, defaultYear, species, currentWbe = reactive(NULL),
@@ -1093,7 +1093,7 @@ mapFlandersServer <- function(id, defaultYear, species, currentWbe = reactive(NU
           htmlwidgets::saveWidget(finalMap(), file = tmpFile, selfcontained = FALSE)
 
           # convert temp .html file into .png for download
-          webshot::webshot(url = tmpFile, file = file,
+          webshot2::webshot(url = tmpFile, file = file,
             vwidth = 1000, vheight = 500, cliprect = "viewport")
 
         }

reporting-grofwild/R/mapSchade.R

@@ -274,7 +274,7 @@ mapSchade <- function(
 #' 
 #' @author mvarewyck
 #' @import shiny
-#' @importFrom webshot webshot
+#' @importFrom webshot2 webshot
 #' @importFrom leaflet renderLeaflet setView leafletProxy clearTiles
 #' @export
 mapSchadeServer <- function(id, schadeData, allSpatialData, timeRange, 
@@ -554,7 +554,7 @@ mapSchadeServer <- function(id, schadeData, allSpatialData, timeRange,
           htmlwidgets::saveWidget(results$perceelMap(), file = htmlFile, selfcontained = FALSE)
 
           # convert temp .html file into .png for download
-          webshot::webshot(url = htmlFile, file = pngFile,
+          webshot2::webshot(url = htmlFile, file = pngFile,
             vwidth = 1000, vheight = 500, cliprect = "viewport")
 
           # save in reactive value

reporting-grofwild/R/mapSpread.R

@@ -181,7 +181,7 @@ mapVerkeer <- function(trafficData, layers = c("oversteek", "ecorasters"),
 #' @author mvarewyck
 #' @import shiny
 #' @import leaflet
-#' @importFrom webshot webshot
+#' @importFrom webshot2 webshot
 #' @importFrom htmlwidgets saveWidget
 #' @export
 mapSpreadServer <- function(id, regionLevel, locaties, allSpatialData, 
@@ -471,7 +471,7 @@ mapSpreadServer <- function(id, regionLevel, locaties, allSpatialData,
           htmlwidgets::saveWidget(finalMap(), file = tmpFile, selfcontained = FALSE)
 
           # convert temp .html file into .png for download
-          webshot::webshot(url = tmpFile, file = file,
+          webshot2::webshot(url = tmpFile, file = file,
             vwidth = 1000, vheight = 500, cliprect = "viewport")
 
         }

reporting-grofwild/inst/NEWS

@@ -1,3 +1,7 @@
+0.3.6
+    o replace webshot by webshot2
+    o convert dockerfile for ARM64    
+    o mimick aws configuration alien species portal
 0.3.5
     o add onderkaaklengte gauge bioindicator #332
     o add faunabeheerzones as choice for multiple graphs #473

reporting-grofwild/inst/config.yml

@@ -1,15 +1,16 @@
 default:
-  bucket: inbo-wbe-uat-data
+  bucket: inbo-faunabeheer-uat-eu-west-1-default
   credentials:
     region: Sys.getenv('AWS_DEFAULT_REGION', unset = 'eu-west-1')
     id: Sys.getenv('AWS_ACCESS_KEY_ID')
     secret: Sys.getenv('AWS_SECRET_ACCESS_KEY')
+    token: Sys.getenv('AWS_SESSION_TOKEN')
   datacheck: false
   defaultYear: 2023
 
 uat:
   datacheck: false
 
 production:
-  bucket: inbo-wbe-prd-data
+  bucket: inbo-faunabeheer-prd-eu-west-1-default
   datacheck: false

reporting-grofwild/inst/ui/app_private/global.R

@@ -22,6 +22,9 @@ addResourcePath("www", system.file("ui/www", package = "reportingGrofwild"))
 defaultYear <- as.numeric(format(Sys.Date(), "%Y")) - 1
 
 
+chromote::set_chrome_args(c('--headless','--no-sandbox'))
+
+
 ### Debugging
 ### -----------
 

reporting-grofwild/inst/ui/app_public/global.R

@@ -18,6 +18,9 @@ dataDir <- system.file("extdata", package = "reportingGrofwild")
 addResourcePath("www", system.file("ui/www", package = "reportingGrofwild"))
 
 
+chromote::set_chrome_args(c('--headless','--no-sandbox'))
+
+
 ### Debugging
 ### -----------
 

reporting-grofwild/inst/ui/www/plotDashboard.Rmd

@@ -75,7 +75,7 @@ tryCatch({
       # leaflet
       tmpFile <- tempfile(fileext = ".html")
       htmlwidgets::saveWidget(params$plot, file = tmpFile, selfcontained = FALSE)
-      webshot::webshot(url = tmpFile, vwidth = 1000, vheight = 500, cliprect = "viewport")
+      webshot2::webshot(url = tmpFile, vwidth = 1000, vheight = 500, cliprect = "viewport")
       
     } else if (!is.null(params$pdfTable)){
       

reporting-grofwild/inst/ui/www/reportDashboard.Rmd

@@ -26,7 +26,6 @@ knitr::opts_chunk$set(
   fig.width = 10, 
   fig.height = 8
 )
-options(tinytex.tlmgr_update = FALSE)
 ```
 
 ```{r locaties}
@@ -47,7 +46,7 @@ incProgress(amount = 0.1, detail = "Achtergrondinformatie")
 
 tmpFile <- tempfile(fileext = ".html")
 htmlwidgets::saveWidget(dash_results$dash_finalMap()$plot, file = tmpFile, selfcontained = FALSE)
-webshot::webshot(url = tmpFile, vwidth = 1000, vheight = 500, cliprect = "viewport")
+webshot2::webshot(url = tmpFile, vwidth = 1000, vheight = 500, cliprect = "viewport")
 ```
 
 ## Biotoop beschrijving