implement #374

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: geoflow
-Version: 0.20230906
-Date: 2023-09-06
+Version: 0.20231109
+Date: 2023-11-09
 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/>), 

NAMESPACE

@@ -5,6 +5,7 @@ export(check_packages)
 export(closeWorkflow)
 export(create_geoflow_data_from_dbi)
 export(debugWorkflow)
+export(describeOGCRelation)
 export(enrich_text_from_entity)
 export(executeWorkflow)
 export(executeWorkflowJob)

R/geoflow_action.R

@@ -339,10 +339,18 @@ register_actions <- function(){
         enrich_with_relations = list(def = "When enabled, enrichs entity with OGC relations", class = "logical", default = TRUE),
         enrich_with_relation_wms = list(def = "When enabled, enrichs entity with a base WMS link relation", class = "logical", default = TRUE),
         enrich_with_relation_wms_thumbnail = list(def = "When enabled, enrichs entity with a WMS-based thumbnail relation", class = "logical", default = TRUE),
+        describe_wms_relation_with_category = list(def = "When enabled, the WMS main relation description will be appended with the mention 'Map access'", class = "logical", default = TRUE),
+        describe_wms_relation_with_ogc_service_description = list(def = "When enabled, the WMS main relation description will be appended with the mention 'OGC Web Map Service (WMS)'", class = "logical", default = TRUE),
         enrich_with_relation_wfs = list(def = "When enabled, enrichs entity with a base WFS link relation (applies to 'vector' only)", class = "logical", default = TRUE),
         enrich_with_relation_wfs_download_links = list(def = "When enabled, enrichs entity with WFS format-specific (GML, GeoJSON, SHAPE-ZIP, CSV) links for download purpose (applies to 'vector' only).", class = "logical", default = TRUE),
+        describe_wfs_relation_with_category = list(def = "When enabled, the WFS relations description will be appended with the mention 'Data (features) access' for the base WFS link or 'Data download' in case of download links", class = "logical", default = TRUE),
+        describe_wfs_relation_with_ogc_service_description = list(def = "When enabled, the WFS relations description will be appended with the mention 'OGC Web Feature Service (WFS)'", class = "logical", default = TRUE),
+        describe_wfs_relation_with_format = list(def = "When enabled, the WFS download relations description will be appended with the mention of the download format", class = "logical", default = TRUE),
         enrich_with_relation_wcs = list(def = "When enabled, enrichs entity with a base WCS link relation (applies to 'grid' only)", class = "logical", default = TRUE),
         enrich_with_relation_wcs_download_links = list(def = "When enabled, enrichs entity with WCS format-specific links for download purpose (applies to 'grid' only). Only GeoTIFF at now.", class = "logical", default = TRUE),
+        describe_wcs_relation_with_category = list(def = "When enabled, the WCS relations description will be appended with the mention 'Data (coverage) access' for the base WCS link or 'Data download' in case of download links", class = "logical", default = TRUE),
+        describe_wcs_relation_with_ogc_service_description = list(def = "When enabled, the WCS relations description will be appended with the mention 'OGC Web Coverage Service (WCS)'", class = "logical", default = TRUE),
+        describe_wcs_relation_with_format = list(def = "When enabled, the WCS download relations description will be appended with the mention of the download format", class = "logical", default = TRUE),
         overwrite_upload = list(def = "When set to TRUE (default), in case a layer already exists, data upload will be re-done (if upload is set to true in entity Data).", class = "logical", default = TRUE),
         overwrite_layer = list(def = "When set to TRUE (default), in case a layer already exists, layer will be republished.", class = "logical", default = TRUE),
         overwrite = list(def = "When set to TRUE (default), in case a layer already exists, data upload will be re-done (if upload is set to true in entity Data), and layer will be re-published. This option preveals over options 'overwrite_upload' and 'overwrite_layer'", class = "logical", default = TRUE)

R/geoflow_data.R

@@ -63,6 +63,13 @@ geoflow_data <- R6Class("geoflow_data",
     store = NULL,
     #'@field layername layer name
     layername = NULL,
+    #'@field layertitle layer title
+    layertitle = NULL,
+    #'@field layerdesc layer description
+    layerdesc = NULL,
+    #'@field layeruri layer URI
+    #'layeruri layer URI
+    layeruri = NULL,
     #'@field styles styles
     styles = list(),
     #'@field styleUpload upload styles
@@ -222,10 +229,21 @@ geoflow_data <- R6Class("geoflow_data",
         }
 
         #layername (if any)
-        #not mandatory, can be used for subset layers
         if(!is.null(data_props$layername)){
           self$setLayername(data_props$layername$values[[1]])
         }
+        #layertitle (if any)
+        if(!is.null(data_props$layertitle)){
+          self$setLayertitle(data_props$layertitle$values[[1]])
+        }
+        #layerdesc (if any)
+        if(!is.null(data_props$layerdesc)){
+          self$setLayerdesc(data_props$layerdesc$values[[1]])
+        }
+        #layeruri (if any)
+        if(!is.null(data_props$layeruri)){
+          self$setLayeruri(data_props$layeruri$values[[1]])
+        }
 
         #sql
         if(!is.null(data_props$sql)){
@@ -411,6 +429,8 @@ geoflow_data <- R6Class("geoflow_data",
 
         #datadir
         if(any(sapply(data_props, function(x){x$key=="dir"}))){
+          accessor <- NULL
+          accessor_software <- NULL
           data_dir <- data_props$dir$values[[1]]
           self$dir <- data_dir
           ext_data_files <- list()
@@ -470,7 +490,31 @@ geoflow_data <- R6Class("geoflow_data",
             ext_data_files <-ext_data_files[!endsWith(ext_data_files,".sld")]
           }
 
+          #detect presence of data files register
+          data_files_register <- NULL
+          data_files_register_file = ext_data_files[basename(ext_data_files) == "register.csv"]
+          if(length(data_files_register_file)>0){
+            data_files_register_file = data_files_register_file[1]
+            target_register_file = data_files_register_file
+            if(!is.null(accessor)){
+              target_register_file <- file.path(tempdir(), "register.csv")
+              accessor$download(
+                resource = data_files_register_file,
+                file = "register.csv", 
+                path = target_register_file,
+                software = accessor_software,
+                unzip = FALSE
+              )
+            }
+            data_files_register = as.data.frame(readr::read_csv(target_register_file))
+            register_colnames = c("code","uri","label","definition")
+            if(!all(register_colnames %in% colnames(data_files_register))){
+             stop("A data files register has been found but doesn't follow the standard structure (code,uri,label,definition)") 
+            }
+          }
+
           #geoflow build children
+          ext_data_files = ext_data_files[basename(ext_data_files) != "register.csv"]
           if(length(ext_data_files)>0){
             self$data <- lapply(ext_data_files, function(data_file){
               ext_data <- self$clone(deep = TRUE) #clone parent geoflow_data to inherit all needed properties
@@ -497,6 +541,7 @@ geoflow_data <- R6Class("geoflow_data",
                 ext_data$setSourceType(sourceType)
               }
               if((is.null(self$uploadType) || self$uploadType == "other") && !is.null(sourceType)){
+                print(sourceType)
                 if(sourceType != "zip") ext_data$setUploadType(sourceType)
                 if(!is.null(ext_data$uploadType)) if(ext_data$uploadType == "geotiff") ext_data$setSpatialRepresentationType("grid")
               }
@@ -507,6 +552,17 @@ geoflow_data <- R6Class("geoflow_data",
               if(!hasStoreDeclared) ext_data$setStore(ext_data_name)
               ext_data$setLayername(ext_data_name)
 
+              #inherit layer metadata from data file register (if any)
+              if(!is.null(data_files_register)){
+                register_entry = data_files_register[data_files_register$code == ext_data_name,]
+                if(nrow(register_entry)>0){
+                  register_entry = register_entry[1L,]
+                  if(!is.na(register_entry$uri)) ext_data$setLayeruri(register_entry$uri)
+                  if(!is.na(register_entry$label)) ext_data$setLayertitle(register_entry$label)
+                  if(!is.na(register_entry$definition)) ext_data$setLayerdesc(register_entry$definition)
+                }
+              }
+
               if(self$styleUpload){
                 #we add all sld files to each child so they can be downloaded if needed
                 if(length(ext_sld_files)>0) for(ext_sld_file in ext_sld_files) {
@@ -718,6 +774,24 @@ geoflow_data <- R6Class("geoflow_data",
       self$layername <- layername
     },
 
+    #'@description Sets a layer title, object of class \code{character}. If available, used as target layer title in SDI-related action.
+    #'@param layertitle layertitle
+    setLayertitle = function(layertitle){
+      self$layertitle = layertitle
+    },
+
+    #'@description Sets a layer description, object of class \code{character}. If available, used as target layer description/abstract in SDI-related actions.
+    #'@param layerdesc layerdesc
+    setLayerdesc = function(layerdesc){
+      self$layerdesc = layerdesc
+    },
+
+    #'@description Sets a layer URI, object of class \code{character}. If available, used as annotating URI for layer metadata (eg. in ISO 19115 action).
+    #'@param layeruri layeruri
+    setLayeruri = function(layeruri){
+      self$layeruri = layeruri
+    },
+
     #'@description Adds a style name, object of class \code{character}. Used as layer style name(s) for GeoServer action.
     #'@param style style
     addStyle = function(style){

R/geoflow_data_accessor.R

@@ -384,7 +384,7 @@ register_data_accessors <- function(){
           stop(errMsg)
         }
         cat(sprintf("[geoflow] OCS data accessor: Download data '%s' from '%s' to '%s'\n", file, resource, path))
-        software$downloadFile(relPath = dirname(resource), filename = basename(resource), outdir = getwd())
+        software$downloadFile(relPath = dirname(resource), filename = basename(resource), outdir = dirname(path))
         if(unzip & endsWith(path, "zip")){
           utils::unzip(zipfile = path, exdir = getwd(), unzip = getOption("unzip"))
         }

R/geoflow_entity.R

@@ -1485,7 +1485,14 @@ geoflow_entity <- R6Class("geoflow_entity",
             new_wms <- geoflow_relation$new()
             new_wms$setKey("wms")
             new_wms$setName(layername)
-            new_wms$setDescription(sprintf("%s - Map access - OGC Web Map Service (WMS)",layername))
+            new_wms$setDescription(
+              describeOGCRelation(
+                self, data_object, service = "WMS", download = FALSE, format = NULL,
+                handle_category = geosapi_action$getOption("describe_wms_relation_with_category"), 
+                handle_ogc_service_description = geosapi_action$getOption("describe_wms_relation_with_ogc_service_description"), 
+                handle_format = FALSE
+              )
+            )
             new_wms$setLink(sprintf("%s/%s/ows?service=WMS", 
                                     geoserver_base_url, 
                                     config$software$output$geoserver_config$properties$workspace))
@@ -1502,7 +1509,14 @@ geoflow_entity <- R6Class("geoflow_entity",
               new_wfs <- geoflow_relation$new()
               new_wfs$setKey("wfs")
               new_wfs$setName(layername)
-              new_wfs$setDescription(sprintf("%s - Data (features) access - OGC Web Feature Service (WFS)", layername))
+              new_wfs$setDescription(
+                describeOGCRelation(
+                  self, data_object, service = "WFS", download = FALSE, format = NULL,
+                  handle_category = geosapi_action$getOption("describe_wfs_relation_with_category"), 
+                  handle_ogc_service_description = geosapi_action$getOption("describe_wfs_relation_with_ogc_service_description"), 
+                  handle_format = FALSE
+                )
+              )
               new_wfs$setLink(sprintf("%s/%s/ows?service=WFS", 
                                       geoserver_base_url, 
                                       config$software$output$geoserver_config$properties$workspace))
@@ -1517,7 +1531,14 @@ geoflow_entity <- R6Class("geoflow_entity",
               new_wfs_gml <- geoflow_relation$new()
               new_wfs_gml$setKey("download")
               new_wfs_gml$setName(layername)
-              new_wfs_gml$setDescription(sprintf("%s - Data download - OGC Web Feature Service (WFS) - GML format", layername))
+              new_wfs_gml$setDescription(
+                describeOGCRelation(
+                  self, data_object, service = "WFS", download = TRUE, format = "GML",
+                  handle_category = geosapi_action$getOption("describe_wfs_relation_with_category"), 
+                  handle_ogc_service_description = geosapi_action$getOption("describe_wfs_relation_with_ogc_service_description"), 
+                  handle_format = geosapi_action$getOption("describe_wfs_relation_with_format")
+                )
+              )
               new_wfs_gml$setLink(sprintf("%s/%s/ows?service=WFS&request=GetFeature&version=1.0.0&typeName=%s", 
                                           geoserver_base_url, 
                                           config$software$output$geoserver_config$properties$workspace,
@@ -1528,7 +1549,14 @@ geoflow_entity <- R6Class("geoflow_entity",
               new_wfs_geojson <- geoflow_relation$new()
               new_wfs_geojson$setKey("download")
               new_wfs_geojson$setName(layername)
-              new_wfs_geojson$setDescription(sprintf("%s - Data download - OGC Web Feature Service (WFS) - GeoJSON format", layername))
+              new_wfs_geojson$setDescription(
+                describeOGCRelation(
+                  self, data_object, service = "WFS", download = TRUE, format = "GeoJSON",
+                  handle_category = geosapi_action$getOption("describe_wfs_relation_with_category"), 
+                  handle_ogc_service_description = geosapi_action$getOption("describe_wfs_relation_with_ogc_service_description"), 
+                  handle_format = geosapi_action$getOption("describe_wfs_relation_with_format")
+                )
+              )
               new_wfs_geojson$setLink(sprintf("%s/%s/ows?service=WFS&request=GetFeature&version=1.0.0&typeName=%s&outputFormat=json", 
                                               geoserver_base_url, 
                                               config$software$output$geoserver_config$properties$workspace,
@@ -1539,7 +1567,14 @@ geoflow_entity <- R6Class("geoflow_entity",
               new_wfs_shp <- geoflow_relation$new()
               new_wfs_shp$setKey("download")
               new_wfs_shp$setName(layername)
-              new_wfs_shp$setDescription(sprintf("%s - Data download - OGC Web Feature Service (WFS) - ESRI Shapefile format", layername))
+              new_wfs_shp$setDescription(
+                describeOGCRelation(
+                  self, data_object, service = "WFS", download = TRUE, format = "ESRI Shapefile",
+                  handle_category = geosapi_action$getOption("describe_wfs_relation_with_category"), 
+                  handle_ogc_service_description = geosapi_action$getOption("describe_wfs_relation_with_ogc_service_description"), 
+                  handle_format = geosapi_action$getOption("describe_wfs_relation_with_format")
+                )
+              )
               new_wfs_shp$setLink(sprintf("%s/%s/ows?service=WFS&request=GetFeature&version=1.0.0&typeName=%s&outputFormat=SHAPE-ZIP", 
                                           geoserver_base_url, 
                                           config$software$output$geoserver_config$properties$workspace,
@@ -1550,7 +1585,14 @@ geoflow_entity <- R6Class("geoflow_entity",
               new_wfs_csv <- geoflow_relation$new()
               new_wfs_csv$setKey("download")
               new_wfs_csv$setName(layername)
-              new_wfs_csv$setDescription(sprintf("%s - Data download - OGC Web Feature Service (WFS) - CSV format", layername))
+              new_wfs_csv$setDescription(
+                describeOGCRelation(
+                  self, data_object, service = "WFS", download = TRUE, format = "CSV",
+                  handle_category = geosapi_action$getOption("describe_wfs_relation_with_category"), 
+                  handle_ogc_service_description = geosapi_action$getOption("describe_wfs_relation_with_ogc_service_description"), 
+                  handle_format = geosapi_action$getOption("describe_wfs_relation_with_format")
+                )
+              )
               new_wfs_csv$setLink(sprintf("%s/%s/ows?service=WFS&request=GetFeature&version=1.0.0&typeName=%s&outputFormat=CSV", 
                                           geoserver_base_url, 
                                           config$software$output$geoserver_config$properties$workspace,
@@ -1569,7 +1611,14 @@ geoflow_entity <- R6Class("geoflow_entity",
               new_wcs <- geoflow_relation$new()
               new_wcs$setKey("wcs")
               new_wcs$setName(layername)
-              new_wcs$setDescription(sprintf("%s - Data (Coverage) access - OGC Web Coverage Service (WCS)", layername))
+              new_wcs$setDescription(
+                describeOGCRelation(
+                  self, data_object, service = "WCS", download = FALSE, format = NULL,
+                  handle_category = geosapi_action$getOption("describe_wcs_relation_with_category"), 
+                  handle_ogc_service_description = geosapi_action$getOption("describe_wcs_relation_with_ogc_service_description"), 
+                  handle_format = FALSE
+                )
+              )
               new_wcs$setLink(sprintf("%s/%s/ows?service=WCS", 
                                       geoserver_base_url, 
                                       config$software$output$geoserver_config$properties$workspace))
@@ -1585,7 +1634,14 @@ geoflow_entity <- R6Class("geoflow_entity",
               new_wcs_geotiff <- geoflow_relation$new()
               new_wcs_geotiff$setKey("download")
               new_wcs_geotiff$setName(layername)
-              new_wcs_geotiff$setDescription(sprintf("%s - Data download - OGC Web Coverage Service (WCS) - GeoTIFF format", layername))
+              new_wcs_geotiff$setDescription(
+                describeOGCRelation(
+                  self, data_object, service = "WCS", download = TRUE, format = "GeoTIFF",
+                  handle_category = geosapi_action$getOption("describe_wcs_relation_with_category"), 
+                  handle_ogc_service_description = geosapi_action$getOption("describe_wcs_relation_with_ogc_service_description"), 
+                  handle_format = geosapi_action$getOption("describe_wcs_relation_with_format")
+                )
+              )
               new_wcs_geotiff$setLink(sprintf("%s/%s/ows?service=WCS&request=GetCoverage&version=2.0.1&CoverageId=%s&format=image/geotiff", 
                                           geoserver_base_url, 
                                           config$software$output$geoserver_config$properties$workspace,