🚀 Add GitHub Pipelines

.github/workflows/deployment_uat.yml

@@ -0,0 +1,29 @@
+on: [push, pull_request]
+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: inbo-exotenportaal-portal
+          IMAGE_TAG: ${{ github.sha }}
+        run: |
+          docker build -t $REGISTRY/$REPOSITORY:$IMAGE_TAG .
+          docker push $REGISTRY/$REPOSITORY:$IMAGE_TAG

.gitignore

@@ -58,3 +58,6 @@ alienSpecies/alienSpecies-tests/
 
 # aws secret 
 /script/
+
+# temporary translations file
+/alienSpecies/inst/extdata/translations.csv

README.md

@@ -18,22 +18,11 @@ Enkele relevante URLS:
 # Build/Run docker image
 
 The dockerfile needs to be updated only when some of the **dependencies** for `alienSpecies` changed.
-This file is generated automatically by packamon: please do not edit by hand. 
-The following commands are run to update this dockerfile.
-
-```
-if (!require(packamon))
-  install.packages("packamon", repos = c(rdepot = "https://repos.openanalytics.eu/repo/public", getOption("repos")))
-library(packamon)
-writeDockerfile(sourceDir = ".", installSource = TRUE,
-overwrite = TRUE, shinyFunction = "alienSpecies::runShiny()")
-```
-
-Then, to build the docker image with the latest dockerfile, run in bash
+To build the docker image with the latest dockerfile, run in bash
 
 ```
 cd git/alien-species-portal
-docker build -t inbo/alienspecies .
+docker build --build-arg GIT_SHA=$(git rev-parse HEAD) -t inbo/alienspecies .
 ```
 
 Run the new docker image from bash. You need to point docker to the .aws folder on your local system to retrieve the credentials.

alienSpecies/DESCRIPTION

@@ -1,14 +1,15 @@
 Package: alienSpecies
 Type: Package
 Title: Portal for alien and invasive species indicators
-Version: 0.0.5
+Version: 1.0.0
 Date: 2023-11-30
 Author: Machteld Varewyck, Yingjie Zhang, Eva Adriaensen
 Maintainer: Machteld Varewyck <[email protected]>
 Description: INBO shiny application based on the TRIAS package.
 Encoding: UTF-8
 License: MIT + file LICENSE
 Imports: 
+    arrow,
     aws.ec2metadata,
     aws.s3,
     aws.signature,
@@ -17,28 +18,31 @@ Imports:
     dplyr,
     DT,
     ggplot2,
+    ggspatial,
     htmltools,
     htmlwidgets,
+    httr,
     INBOtheme (<= 0.5.9),
     jsonlite,
-    leaflet,
+    leaflet (>= 2.2.0),
     leaflet.extras,
     methods,
     plotly,
     reshape2,
     rgbif,
-	shiny,
-	shinycssloaders,
-	sf,
-	testthat (>= 3.0.0),
+	  shiny,
+	  shinycssloaders,
+	  sf,
+    terra,
+	  testthat (>= 3.0.0),
     tidyr,
-	tidyverse,
-	trias (>= 2.0.3),
-	webshot,
-	xtable
+	  tidyverse,
+	  trias (>= 2.0.8),
+	  webshot,
+	  xtable
 Suggests:
     shinyjs
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Remotes: 
     inbo/[email protected],
     trias-project/[email protected]

alienSpecies/NAMESPACE

@@ -5,6 +5,7 @@ export(barplotLenteNesten)
 export(checkS3)
 export(combineActiveData)
 export(combineNestenData)
+export(combineVespaData)
 export(comboTreeInput)
 export(countNestenServer)
 export(countNestenUI)
@@ -24,8 +25,8 @@ export(createSummaryNesten)
 export(createSummaryRegions)
 export(createTabularData)
 export(createTaxaChoices)
-export(createTaxaChoices2)
 export(createTimeseries)
+export(decodeText)
 export(displayName)
 export(downloadS3)
 export(drawBullet)
@@ -34,6 +35,7 @@ export(filterSelectServer)
 export(filterSelectUI)
 export(getDutchNames)
 export(getGbifOccurrence)
+export(getPathLogo)
 export(loadGbif)
 export(loadMetaData)
 export(loadOccupancyData)
@@ -47,7 +49,11 @@ export(mapHeatServer)
 export(mapHeatUI)
 export(mapOccurrence)
 export(mapPopup)
+export(mapRaster)
+export(mapRasterServer)
+export(mapRasterUI)
 export(mapRegions)
+export(mapRegionsFacet)
 export(mapRegionsServer)
 export(mapRegionsUI)
 export(matchCombo)
@@ -59,12 +65,14 @@ export(plotModuleUI)
 export(plotTrias)
 export(plotTriasServer)
 export(plotTriasUI)
+export(plotlyReport)
 export(readS3)
 export(replicateColors)
 export(runShiny)
 export(setupS3)
 export(simpleCap)
 export(summarizeTimeSeries)
+export(summarizeYearGroupData)
 export(tableIndicators)
 export(tableIndicatorsServer)
 export(tableIndicatorsUI)
@@ -76,6 +84,8 @@ export(titleModuleUI)
 export(translate)
 export(trendYearRegion)
 export(vectorToTitleString)
+export(versionServer)
+export(versionUI)
 export(welcomeSectionServer)
 export(welcomeSectionUI)
 export(writeS3)
@@ -96,6 +106,9 @@ importFrom(INBOtheme,inbo_lichtgrijs)
 importFrom(INBOtheme,inbo_palette)
 importFrom(INBOtheme,inbo_steun_blauw)
 importFrom(INBOtheme,theme_inbo)
+importFrom(arrow,open_dataset)
+importFrom(arrow,read_parquet)
+importFrom(arrow,write_parquet)
 importFrom(aws.ec2metadata,is_ec2)
 importFrom(aws.ec2metadata,metadata)
 importFrom(aws.s3,get_bucket_df)
@@ -119,7 +132,10 @@ importFrom(data.table,setDT)
 importFrom(data.table,setkey)
 importFrom(data.table,setkeyv)
 importFrom(data.table,setnames)
+importFrom(data.table,year)
 importFrom(dplyr,all_of)
+importFrom(dplyr,case_when)
+importFrom(dplyr,collect)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
@@ -128,15 +144,21 @@ importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,ungroup)
+importFrom(ggplot2,ggsave)
+importFrom(ggspatial,annotation_map_tile)
 importFrom(htmltools,div)
 importFrom(htmlwidgets,saveWidget)
+importFrom(httr,GET)
+importFrom(httr,http_status)
 importFrom(jsonlite,toJSON)
 importFrom(leaflet,`%>%`)
 importFrom(leaflet,addCircleMarkers)
 importFrom(leaflet,addLegend)
 importFrom(leaflet,addMarkers)
+importFrom(leaflet,addRasterImage)
 importFrom(leaflet,addScaleBar)
 importFrom(leaflet,addTiles)
+importFrom(leaflet,colorNumeric)
 importFrom(leaflet,leaflet)
 importFrom(leaflet,leafletOutput)
 importFrom(leaflet,markerClusterOptions)
@@ -163,9 +185,14 @@ importFrom(shiny,singleton)
 importFrom(shinycssloaders,withSpinner)
 importFrom(stats,aggregate)
 importFrom(stats,as.formula)
+importFrom(stats,complete.cases)
+importFrom(terra,rast)
+importFrom(terra,values)
 importFrom(testthat,test_file)
 importFrom(tidyr,pivot_wider)
 importFrom(utils,capture.output)
+importFrom(utils,download.file)
+importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
 importFrom(utils,tail)

alienSpecies/R/app_modules.R

@@ -10,7 +10,6 @@
 
 #' User input for controlling specific plot (ui-side)
 #' @param id character, module id, unique name per plot
-#' @param showGroup boolean, whether to show a select input field for group variable
 #' @param showSummary boolean, whether to show a select input field for summary choice
 #' @param showPeriod boolean, whether to show a slider input field for period (first_observed)
 #' @param showGewest boolean, whether to show filter for gewest
@@ -20,7 +19,7 @@
 #' @return ui object (tagList)
 #' @import shiny
 #' @export
-optionsModuleUI <- function(id, showGroup = FALSE, showSummary = FALSE, 
+optionsModuleUI <- function(id, showSummary = FALSE, 
   showPeriod = FALSE, showGewest = FALSE,
   exportData = TRUE, doWellPanel = TRUE) {
 
@@ -31,8 +30,7 @@ optionsModuleUI <- function(id, showGroup = FALSE, showSummary = FALSE,
     fixedRow(
       if (showGewest)
         column(6, uiOutput(ns("gewest"))),
-      if (showGroup)
-        column(6, uiOutput(ns("group"))),
+      column(6, uiOutput(ns("group"))),
       if (showSummary)
         column(6, uiOutput(ns("summarizeBy"))),
       if (showPeriod)
@@ -65,8 +63,11 @@ plotModuleUI <- function(id, height = "600px") {
 
   ns <- NS(id)
 
-  withSpinner(plotlyOutput(ns("plot"), height = height))
-
+  if (id == "management2_lente-plotTrias")
+    # dirty fix: this plot stays hidden when behind spinner
+    plotlyOutput(ns("plot"), height = height) else
+    withSpinner(plotlyOutput(ns("plot"), height = height))
+
 }
 
 
@@ -103,6 +104,8 @@ tableModuleUI <- function(id, includeTotal = FALSE) {
 #' @param data reactive data.frame, data for chosen species
 #' @param period reactive numeric vector of length 2, selected period
 #' @param combine reactive boolean, see \code{\link{trendYearRegion}}
+#' @param groupChoices reactive character, defines the choices for group variable;
+#' if NULL no groupChoices available
 #' @return no return value; plot output object is created
 #' @author mvarewyck
 #' @import shiny
@@ -111,7 +114,7 @@ tableModuleUI <- function(id, includeTotal = FALSE) {
 #' @importFrom plotly ggplotly layout
 #' @export
 plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
-  outputType = NULL, triasFunction = NULL, triasArgs = NULL, 
+  outputType = NULL, triasFunction = NULL, triasArgs = NULL, groupChoices = NULL,
   period = NULL, combine = NULL) {
 
   moduleServer(id,
@@ -131,11 +134,9 @@ plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
 
       output$group <- renderUI({
 
-          choices <- c("", "lifeStage")
-          names(choices) <- c("", translate(uiText(), choices[-1])$title)
-
-          selectInput(inputId = ns("group"), label = translate(uiText(), "group")$title, 
-            choices = choices)
+          if (!is.null(groupChoices))
+            selectInput(inputId = ns("group"), label = translate(uiText(), "group")$title, 
+              choices = groupChoices())
 
         })
 
@@ -145,7 +146,7 @@ plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
           names(choices) <- translate(uiText(), choices)$title
 
           selectInput(inputId = ns("summarizeBy"), 
-            label = translate(uiText(), "summary")$title, choices = choices)
+            label = translate(uiText(), "summarizeBy")$title, choices = choices)
 
         })
 
@@ -181,7 +182,7 @@ plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
 
       argList <- reactive({
 
-          req(nrow(subData()) > 0)
+          validate(need(nrow(subData()) > 0, translate(uiText(), "noData")$title))
 
           argList <- c(
             list(
@@ -214,8 +215,11 @@ plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
 
       resultFct <- reactive({
 
-          toReturn <- tryCatch(
-            do.call(plotFunction, args = argList()),
+          req(argList())
+
+          toReturn <- tryCatch({
+              do.call(plotFunction, args = argList())
+            },
             error = function(err)
               validate(need(FALSE, err$message))
           )		
@@ -226,8 +230,9 @@ plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
 
         })
 
-
-      output$plot <- renderPlotly({  
+      finalPlot <- reactive({
+
+          req(resultFct())
 
           if (!is.null(triasFunction) && triasFunction == "apply_gam") {
             # remove title
@@ -239,9 +244,12 @@ plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
           } else resultFct()$plot
 
         })
-
-      if (!(plotFunction == "countOccupancy" |
-          (!is.null(triasFunction) && triasFunction %in% c("barplotLenteNesten", "countNesten"))))
+
+
+      output$plot <- renderPlotly(finalPlot())
+
+
+      if (plotFunction != "countOccupancy" & plotFunction != "countOccurrence")
         outputOptions(output, "plot", suspendWhenHidden = FALSE)
 
 
@@ -286,6 +294,15 @@ plotModuleServer <- function(id, plotFunction, data, uiText = NULL,
 
         })
 
+
+      reactive(c(
+        list(plot = if (!is.null(outputType) && outputType == "table")
+                req(resultFct()) else 
+                req(finalPlot())
+            ),
+        reactiveValuesToList(input)
+      ))
+
     })
 
 }