support #386

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: geoflow
-Version: 0.20240502
-Date: 2024-05-02
+Version: 0.20240513
+Date: 2024-05-13
 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/geoflow_handler.R

@@ -48,6 +48,10 @@ geoflow_handler <- R6Class("geoflow_handler",
     options = list(),
     #'@field available_options available options
     available_options = list(),
+    #'@field status status
+    status = "active",
+    #'@field notes notes
+    notes = "",
 
     #'@description Initializes a \link{geoflow_handler}
     #'@param id id
@@ -57,15 +61,20 @@ geoflow_handler <- R6Class("geoflow_handler",
     #'@param script a handler script
     #'@param options action options
     #'@param available_options available options for the action
+    #'@param status status (active/deprecated)
+    #'@param notes notes
     initialize = function(id, def = "", packages = list(), fun = NULL, script = NULL, 
-                          options = list(), available_options = list()){
+                          options = list(), available_options = list(),
+                          status = "active", notes = ""){
       self$id <- id
       self$def <- def
       self$packages <- packages
       self$fun <- fun
       self$script <- script
       self$options <- options
       self$available_options <- available_options
+      self$status = status
+      self$notes = notes
     },
 
     #'@description Check that all packages required for the handler are available, if yes,

R/geoflow_handler_contact.R

@@ -71,6 +71,8 @@ list_contact_handlers <- function(raw = FALSE){
         id = handler$id,
         definition = handler$def,
         packages = paste(handler$packages, collapse=","),
+        status = handler$status,
+        notes = handler$notes,
         stringsAsFactors = FALSE
       ))
     }))

R/geoflow_handler_dictionary.R

@@ -71,6 +71,8 @@ list_dictionary_handlers <- function(raw = FALSE){
         id = handler$id,
         definition = handler$def,
         packages = paste(handler$packages, collapse=","),
+        status = handler$status,
+        notes = handler$notes,
         stringsAsFactors = FALSE
       ))
     }))

R/geoflow_handler_entity.R

@@ -17,20 +17,27 @@ register_entity_handlers <- function(){
       def = "Handle metadata entities from a CSV file",
       fun = source(system.file("metadata/entity", "entity_handler_csv.R", package = "geoflow"))$value,
       available_options = list(
-        guess_max = list(def = "Guess max argument, see readr::read_csv", default = 0)
+        guess_max = list(def = "Guess max argument, see readr::read_csv", default = 0),
+        enrich_from_dbi = list(def = "Enrich entity data from DBI software", default = FALSE)
       )
     ),
     geoflow_handler$new(
       id = "excel",
       def = "Handle metadata entities from a Microsoft Excel (xls,xlsx) file",
       packages = list("readxl"),
-      fun = source(system.file("metadata/entity", "entity_handler_excel.R", package = "geoflow"))$value
+      fun = source(system.file("metadata/entity", "entity_handler_excel.R", package = "geoflow"))$value,
+      available_options = list(
+        enrich_from_dbi = list(def = "Enrich entity data from DBI software", default = FALSE)
+      )
     ),
     geoflow_handler$new(
       id = "gsheet",
       def = "Handle metadata entities from a Google spreadsheet",
       packages = list("gsheet"),
-      fun = source(system.file("metadata/entity", "entity_handler_gsheet.R", package = "geoflow"))$value
+      fun = source(system.file("metadata/entity", "entity_handler_gsheet.R", package = "geoflow"))$value,
+      available_options = list(
+        enrich_from_dbi = list(def = "Enrich entity data from DBI software", default = FALSE)
+      )
     ),
     geoflow_handler$new(
       id = "dbi",
@@ -42,19 +49,25 @@ register_entity_handlers <- function(){
       id = "dbi_csv",
       def = "Handle DBI metadata entities from a CSV file",
       packages = list("DBI", "RSQLite", "RPostgres"),
-      fun = source(system.file("metadata/entity", "entity_handler_dbi_csv.R", package = "geoflow"))$value
+      fun = source(system.file("metadata/entity", "entity_handler_dbi_csv.R", package = "geoflow"))$value,
+      status = "deprecated",
+      notes = "Use 'csv' handler enabling option 'enrich_from_dbi"
     ),
     geoflow_handler$new(
       id = "dbi_excel",
       def = "Handle DBI metadata entities from a Microsoft Excel (xls, xlsx) file",
       packages = list("readxl"),
-      fun = source(system.file("metadata/entity", "entity_handler_dbi_excel.R", package = "geoflow"))$value
+      fun = source(system.file("metadata/entity", "entity_handler_dbi_excel.R", package = "geoflow"))$value,
+      status = "deprecated",
+      notes = "Use 'excel' handler enabling option 'enrich_from_dbi"
     ),
     geoflow_handler$new(
       id = "dbi_gsheet",
       def = "Handle DBI metadata entities from a Google spreadsheet",
       packages = list("gsheet"),
-      fun = source(system.file("metadata/entity", "entity_handler_dbi_gsheet.R", package = "geoflow"))$value
+      fun = source(system.file("metadata/entity", "entity_handler_dbi_gsheet.R", package = "geoflow"))$value,
+      status = "deprecated",
+      notes = "Use 'gsheet' handler enabling option 'enrich_from_dbi"
     ),
     geoflow_handler$new(
       id = "dataverse",
@@ -66,7 +79,10 @@ register_entity_handlers <- function(){
       id = "ocs",
       def = "Handle metadata entities from a tabulat data source (csv or excel) hosted on an OCS cloud",
       packages = list("ocs4R"),
-      fun = source(system.file("metadata/entity", "entity_handler_ocs.R", package = "geoflow"))$value
+      fun = source(system.file("metadata/entity", "entity_handler_ocs.R", package = "geoflow"))$value,
+      available_options = list(
+        enrich_from_dbi = list(def = "Enrich entity data from DBI software", default = FALSE)
+      )
     ),
     geoflow_handler$new(
       id = "ncdf",
@@ -151,6 +167,8 @@ list_entity_handlers <- function(raw = FALSE){
         id = handler$id,
         definition = handler$def,
         packages = paste(handler$packages, collapse=","),
+        status = handler$status,
+        notes = handler$notes,
         stringsAsFactors = FALSE
       ))
     }))

README.md

@@ -2,7 +2,7 @@
 
 [![Build Status](https://github.com/r-geoflow/geoflow/actions/workflows/r-cmd-check.yml/badge.svg?branch=master)](https://github.com/r-geoflow/geoflow/actions/workflows/r-cmd-check.yml)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/geoflow)](https://cran.r-project.org/package=geoflow)
-[![Github_Status_Badge](https://img.shields.io/badge/Github-0.20240502-blue.svg)](https://github.com/r-geoflow/geoflow)
+[![Github_Status_Badge](https://img.shields.io/badge/Github-0.202405013-blue.svg)](https://github.com/r-geoflow/geoflow)
 [![DOI](https://zenodo.org/badge/DOI//10.5281/zenodo.3138920.svg)](https://doi.org//10.5281/zenodo.3138920)
 
 **R engine to orchestrate and run (meta)data workflows**

inst/metadata/entity/entity_handler_csv.R

@@ -7,7 +7,8 @@ handle_entities_csv <- function(handler, source, config, handle = TRUE){
   if(!handle) return(source)
 
   #apply generic handler
-  handle_entities_df <- source(system.file("metadata/entity", "entity_handler_df.R", package = "geoflow"))$value
+  handler_script = if(handler$getOption("enrich_from_dbi")) "entity_handler_dbi_df.R" else "entity_handler_df.R"
+  handle_entities_df <- source(system.file("metadata/entity", handler_script, package = "geoflow"))$value
   entities <- handle_entities_df(handler, source, config)
   return(entities)
 }

inst/metadata/entity/entity_handler_excel.R

@@ -15,7 +15,8 @@ handle_entities_excel <- function(handler, source, config, handle = TRUE){
   if(!handle) return(source)
 
   #apply generic handler
-  handle_entities_df <- source(system.file("metadata/entity", "entity_handler_df.R", package = "geoflow"))$value
+  handler_script = if(handler$getOption("enrich_from_dbi")) "entity_handler_dbi_df.R" else "entity_handler_df.R"
+  handle_entities_df <- source(system.file("metadata/entity", handler_script, package = "geoflow"))$value
   entities <- handle_entities_df(handler, source, config)
   return(entities)
 }

inst/metadata/entity/entity_handler_gsheet.R

@@ -6,7 +6,8 @@ handle_entities_gsheet <- function(handler, source, config, handle = TRUE){
   if(!handle) return(source)
 
   #apply generic handler
-  handle_entities_df <- source(system.file("metadata/entity", "entity_handler_df.R", package = "geoflow"))$value
+  handler_script = if(handler$getOption("enrich_from_dbi")) "entity_handler_dbi_df.R" else "entity_handler_df.R"
+  handle_entities_df <- source(system.file("metadata/entity", handler_script, package = "geoflow"))$value
   entities <- handle_entities_df(handler, source, config)
   return(entities)
 }