fix #384

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: geoflow
-Version: 0.20240419
-Date: 2024-04-19
+Version: 0.20240502
+Date: 2024-05-02
 Title: Tools to Orchestrate Geospatial (Meta)Data Management Workflows and Manage FAIR Services
 Description: An engine to facilitate the orchestration and execution of metadata-driven data management workflows, in compliance with FAIR 
   (Findable, Accessible, Interoperable and Reusable) data management principles. By means of a pivot metadata model, relying on the DublinCore standard (<https://dublincore.org/>), 

R/executeWorkflowJob.R

@@ -135,6 +135,8 @@ executeWorkflowJob <- function(config, jobdir = NULL, queue = NULL, monitor = NU
               config$logger.info("SkipDataDownload is false: copying and fetching data...")
               #we copy data to job data dir (for data files)
               entity$copyDataToJobDir(config, jobdir)
+              #enrich with data types
+              entity$enrichWithDatatypes(config, jobdir)
               #vector data: we enrich entity with features
               #control is added in case of entity already enriched with features/coverages (when loaded from custom R entity handlers)
               if(!skipEnrichWithData) if(is.null(entity$data$features) && is.null(entity$data$coverages)){

R/geoflow_entity.R

@@ -574,37 +574,28 @@ geoflow_entity <- R6Class("geoflow_entity",
 
     },
 
-    #'@description This function will enrich the entity data objects with data features (vector data) or coverages (grid data). This method will overwrite 
-    #' spatial metadata such as the bounding box (unless global option \code{skipDynamicBbox} is enabled). Note that the user spatial extent is not overwriten 
-    #' since it may contain finer geometries than a bounding box.
+    #'@description Function that will scan zip data files and resolve data objects sourceType and uploadType
     #'@param config geoflow config object
     #'@param jobdir relative path of the job directory
-    enrichWithData = function(config, jobdir = NULL){
+    enrichWithDatatypes = function(config, jobdir = NULL){
 
       if(is.null(jobdir)) jobdir <- config$job
       wd <- getwd()
       setwd("./data")
 
-      skipDynamicBbox <- if(!is.null(config$profile$options$skipDynamicBbox)) config$profile$options$skipDynamicBbox else FALSE
-      enrichDataStrategy <- if(!is.null(config$profile$options$enrichDataStrategy)) config$profile$options$enrichDataStrategy else "first"
-      #TODO enrichDataSourceStrategy <- if(!is.null(config$profile$options$enrichDataSourceStrategy)) config$profile$options$enrichDataSourceStrategy else "first"
-
       data_objects <- list()
       if(is.null(self$data$dir)){
         data_objects <- list(self$data)
       }else{
         data_objects <- self$data$getData()
       }
 
-      srid <- if(!is.null(self$srid)) self$srid else ""
-      data_srids <- c()
-
       if(length(data_objects)>0){
 
         data_objects <- lapply(1:length(data_objects), function(k){
-
+          
           data_object = data_objects[[k]]
-
+          
           datasource <- data_object$source[[1]] #TODO we still look at first source
           datasource_name = NULL
           datasource_ext = NULL
@@ -623,7 +614,7 @@ geoflow_entity <- R6Class("geoflow_entity",
             #setwd(wd)
             #return(NULL)
           }
-
+          
           #in case of a datasource type requiring a file we check its presence
           #if absent we abort the function enrich With features
           types_without_file <- c("dbtable","dbview","dbquery")
@@ -637,7 +628,7 @@ geoflow_entity <- R6Class("geoflow_entity",
 
           #basefilename
           basefilename <- datasource_name
-
+          
           #inherit sourceType for source
           if(datasource_file_needed){
             data_object$sourceType = switch(datasource_ext,
@@ -646,7 +637,7 @@ geoflow_entity <- R6Class("geoflow_entity",
                 basefilepath = file.path(getwd(), paste0(basefilename,".zip"))
                 if(file.exists(basefilepath)){ 
                   #for srcType != "other"
-                  #(re-zipped files on 'basefinename' with 'other' sourceType do not exist, 
+                  #(re-zipped files on 'basefilename' with 'other' sourceType do not exist, 
                   #but are just copied, not unzipped/rezipped with different name)
                   zip_files = zip::zip_list(basefilepath)
                   if(any(endsWith(zip_files$filename, ".gpkg"))){
@@ -670,7 +661,8 @@ geoflow_entity <- R6Class("geoflow_entity",
             )
             #additional rule for uploadType
             if(datasource_ext == "zip") if(!is.null(data_object$uploadType)) if(data_object$uploadType == "other"){
-              data_object$uploadType = data_object$sourceType
+              config$logger.info(sprintf("Zip data archived scanned, setting uploadType based on sourceType '%s'", data_object$sourceType))
+              data_object$setUploadType(data_object$sourceType)
               if(data_object$uploadType == "geotiff") data_object$setSpatialRepresentationType("grid")
             }
             #overwrite top sourceType
@@ -684,6 +676,81 @@ geoflow_entity <- R6Class("geoflow_entity",
               self$data$data[[k]]$setSpatialRepresentationType(data_object$spatialRepresentationType)
             }
           }
+          return(data_object)
+        })
+
+        if(is.null(self$data$dir)){
+          self$data <- data_objects[[1]]
+        }else{
+          self$data$data <- data_objects
+        }
+      }
+      setwd(self$getEntityJobDirPath(config, jobdir))
+    },
+
+    #'@description This function will enrich the entity data objects with data features (vector data) or coverages (grid data). This method will overwrite 
+    #' spatial metadata such as the bounding box (unless global option \code{skipDynamicBbox} is enabled). Note that the user spatial extent is not overwriten 
+    #' since it may contain finer geometries than a bounding box.
+    #'@param config geoflow config object
+    #'@param jobdir relative path of the job directory
+    enrichWithData = function(config, jobdir = NULL){
+
+      if(is.null(jobdir)) jobdir <- config$job
+      wd <- getwd()
+      setwd("./data")
+
+      skipDynamicBbox <- if(!is.null(config$profile$options$skipDynamicBbox)) config$profile$options$skipDynamicBbox else FALSE
+      enrichDataStrategy <- if(!is.null(config$profile$options$enrichDataStrategy)) config$profile$options$enrichDataStrategy else "first"
+      #TODO enrichDataSourceStrategy <- if(!is.null(config$profile$options$enrichDataSourceStrategy)) config$profile$options$enrichDataSourceStrategy else "first"
+
+      data_objects <- list()
+      if(is.null(self$data$dir)){
+        data_objects <- list(self$data)
+      }else{
+        data_objects <- self$data$getData()
+      }
+
+      srid <- if(!is.null(self$srid)) self$srid else ""
+      data_srids <- c()
+
+      if(length(data_objects)>0){
+
+        data_objects <- lapply(1:length(data_objects), function(k){
+
+          data_object = data_objects[[k]]
+
+          datasource <- data_object$source[[1]] #TODO we still look at first source
+          datasource_name = NULL
+          datasource_ext = NULL
+          datasource_file = NULL
+          if(!is.null(datasource)){
+            datasource_parts <- unlist(strsplit(datasource, "\\.(?=[^\\.]+$)", perl=TRUE))
+            datasource_name <- datasource_parts[1]
+            datasource_ext <- datasource_parts[2]
+            datasource_file <- attr(datasource, "uri")
+            attributes(datasource) <- NULL
+            if(is.null(datasource_file)) datasource_file <- datasource
+          }
+
+          if(data_object$sourceType == "other"){
+            config$logger.warn("Metadata dynamic handling based on 'data' not implemented for source type 'other'")
+            #setwd(wd)
+            #return(NULL)
+          }
+
+          #in case of a datasource type requiring a file we check its presence
+          #if absent we abort the function enrich With features
+          types_without_file <- c("dbtable","dbview","dbquery")
+          datasource_file_needed <- !(data_object$sourceType %in% types_without_file)
+          if(datasource_file_needed && is.null(datasource_file)){
+            warnMsg <- sprintf("No source file/URL for datasource '%s'. Data source copying aborted!", datasource_name)
+            config$logger.warn(warnMsg)
+            #setwd(wd)
+            #return(NULL)
+          }
+
+          #basefilename
+          basefilename <- datasource_name
 
           #encoding mappings
           st_encoding <- switch(options("encoding")[[1]],