add base_path

improve dockerfile

Dockerfile

@@ -3,6 +3,18 @@ FROM rocker/r-ver:4.3.3
 RUN apt-get update -y && apt-get install -y  make pandoc zlib1g-dev libcurl4-openssl-dev libssl-dev libicu-dev libpng-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev git libudunits2-dev libxt6 && rm -rf /var/lib/apt/lists/*
 RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
 
+# Add Docker's official GPG key:
+RUN apt-get update -y
+RUN apt-get install ca-certificates curl -y
+RUN install -m 0755 -d /etc/apt/keyrings
+RUN curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
+RUN chmod a+r /etc/apt/keyrings/docker.asc
+
+# Add the repository to Apt sources:
+RUN echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
+RUN apt-get update -y
+RUN apt-get install -y docker-ce docker-ce-cli
+
 RUN mkdir /.cache
 RUN chmod 777 /.cache .
 WORKDIR /code

app/main.R

@@ -121,9 +121,11 @@ ui <- function(id) {
 server <- function(id) {
   shiny$moduleServer(id, function(input, output, session) {
     ns <- session$ns
-
+
+    base_path <- Sys.getenv("BASE_PATH")
+
     session_dir <- file.path(
-      "shared",
+      paste0(base_path, "shared"),
       paste0(
         Sys.time() |> format(format = "%Y-%m-%d_%H-%M-%S"),
         "_",

app/view/honeybee/beekeeper_control.R

@@ -138,8 +138,8 @@ beekeeper_control_server <- function(
 
         # BEWARE !!!!!!!!!!!!
         # HARDCODED paths follows
-
-        file_copy(file.path("shared", "uc-pollinators", "beehave", "Beehave_BeeMapp2015_Netlogo6version_PolygonAggregation.nlogo"),
+        
+        file_copy(file.path("app", "data", "honeybee", "Beehave_BeeMapp2015_Netlogo6version_PolygonAggregation.nlogo"),
           file.path(run_dir, "Beehave_BeeMapp2015_Netlogo6version_PolygonAggregation.nlogo"),
           overwrite = TRUE
         )
@@ -172,9 +172,11 @@ beekeeper_control_server <- function(
           file = locations_file,
           row.names = FALSE
         )
-
         # Run workflow ----
-        docker_call <- paste0("shared/uc-pollinators/scripts/cloud/cloud_execution.sh shared/uc-pollinators/R ", run_dir, " shared/uc-pollinators/scripts/cloud")
+        # docker_call <- paste0("shared/uc-pollinators/scripts/cloud/cloud_execution.sh shared/uc-pollinators/R ", run_dir, " shared/uc-pollinators/scripts/cloud")
+        # Execute docker run, no socket should be needed for this
+        docker_call <- paste0('docker run -v "', Sys.getenv("SCRIPT_PATH"), '":"/scripts" -v "', Sys.getenv("R_PATH"), '":"/R" -v "', paste0(Sys.getenv("DATA_PATH"), stringr::str_remove(run_dir, paste0(Sys.getenv("HOME_PATH"), "shared"))), '":"/data" -e INPUT_DIR="/data" -e OUTPUT_DIR="/data/output" -e MAP="map.tif" -e LOOKUP_TABLE="lookup_table.csv" -e LOCATIONS="locations.csv" -e PARAMETERS="parameters.csv" -e MODEL_PATH="/data/Beehave_BeeMapp2015_Netlogo6version_PolygonAggregation.nlogo" -e CPUS="1" --cpus 1 --platform linux/amd64 --entrypoint /scripts/run_docker_flow.sh ghcr.io/biodt/beehave:0.3.7')
+
         system(docker_call)
 
         # Update output data ----