#21 line separator

NAMESPACE

@@ -3,6 +3,7 @@
 export(closeWorkflow)
 export(executeWorkflow)
 export(executeWorkflowJob)
+export(extract_cell_components)
 export(extract_kvp)
 export(filter_sf_by_cqlfilter)
 export(geoflow_action)
@@ -19,6 +20,7 @@ export(geoflow_relation)
 export(geoflow_right)
 export(geoflow_software)
 export(geoflow_subject)
+export(get_line_separator)
 export(handle_contacts_csv)
 export(handle_contacts_df)
 export(handle_contacts_excel)
@@ -41,6 +43,7 @@ export(register_entity_handlers)
 export(register_software)
 export(sanitize_date)
 export(sanitize_str)
+export(set_line_separator)
 export(str_to_posix)
 import(DBI)
 import(R6)

R/closeWorkflow.R

@@ -43,4 +43,5 @@ closeWorkflow <- function(config){
     config$software$csw_config <- NULL
   }
   setwd(config$wd)
+  set_line_separator() #default line separator
 }

R/executeWorkflowJob.R

@@ -115,7 +115,7 @@ executeWorkflowJob <- function(config, jobdir){
               src_entities <- config$src_entities
               src_entities$Identifier <- sapply(1:nrow(src_entities), function(i){
                 identifier <- src_entities[i, "Identifier"]
-                if(!endsWith(identifier,";")) identifier <- paste0(identifier, ";\n")
+                if(!endsWith(identifier, .geoflow$LINE_SEPARATOR)) identifier <- paste0(identifier, .geoflow$LINE_SEPARATOR)
                 if(regexpr("doi", identifier)>0) return(identifier)
                 if(out_zenodo_dois[i,"Status"] == "published") return(identifier)
                 identifier <- paste0(identifier, "doi:", out_zenodo_dois[i,"DOI_for_allversions"])

R/geoflow_data.R

@@ -21,7 +21,7 @@ geoflow_data <- R6Class("geoflow_data",
     features = NULL,
     initialize = function(str = NULL){
       if(!is.null(str)){
-        data_props <-  unlist(strsplit(sanitize_str(str), ";"))
+        data_props <-  extract_cell_components(sanitize_str(str))
         data_props <- lapply(data_props, function(data_prop){
           return(extract_kvp(data_prop))
         })

R/geoflow_handler_contact.R

@@ -31,7 +31,7 @@ handle_contacts_df <- function(config, source){
 
     srcId <- sanitize_str(source_contact[,"Identifier"])
     if(!is.na(srcId)){
-      identifiers <- unlist(strsplit(srcId, ";"))
+      identifiers <- extract_cell_components(srcId)
       if(length(identifiers)>0){
         invisible(lapply(identifiers, function(identifier){
           id_obj <- geoflow_kvp$new(str = identifier)

R/geoflow_handler_entity.R

@@ -21,7 +21,7 @@ handle_entities_df <- function(config, source){
 
     #types
     src_type <- sanitize_str(source_entity[,"Type"])
-    types <- if(!is.na(src_type)) unlist(strsplit(src_type, ";")) else list()
+    types <- if(!is.na(src_type)) extract_cell_components(src_type) else list()
     if(length(types)>0){
       if(length(types)==1){
         entity$setType("generic", types)
@@ -38,7 +38,7 @@ handle_entities_df <- function(config, source){
     }
 
     #identifier
-    identifiers <- unlist(strsplit(sanitize_str(source_entity[,"Identifier"]), ";"))
+    identifiers <-extract_cell_components(sanitize_str(source_entity[,"Identifier"]))
     for(identifier in identifiers){
       if(regexpr(":",identifier) == -1){
         entity$setIdentifier("id", identifier)
@@ -53,7 +53,7 @@ handle_entities_df <- function(config, source){
 
     #description
     src_description <- sanitize_str(source_entity[,"Description"])
-    descriptions <- if(!is.na(src_description)) unlist(strsplit(src_description, ";")) else list()
+    descriptions <- if(!is.na(src_description)) extract_cell_components(src_description) else list()
     if(length(descriptions)>0){
       if(length(descriptions)==1){
         if(regexpr(":",descriptions) == -1){
@@ -76,7 +76,7 @@ handle_entities_df <- function(config, source){
 
     #subjects
     src_subject <- sanitize_str(source_entity[,"Subject"])
-    subjects <- if(!is.na(src_subject)) unlist(strsplit(src_subject, ";")) else list()
+    subjects <- if(!is.na(src_subject)) extract_cell_components(src_subject) else list()
     if(length(subjects)>0){
       invisible(lapply(subjects, function(subject){
         subject_obj <- geoflow_subject$new(str = subject)
@@ -86,7 +86,7 @@ handle_entities_df <- function(config, source){
 
     #contacts
     src_contact <- sanitize_str(source_entity[,"Creator"])
-    contacts <- if(!is.na(src_contact)) unlist(strsplit(src_contact, ";")) else list()
+    contacts <- if(!is.na(src_contact)) extract_cell_components(src_contact) else list()
     if(length(contacts)>0){
       invisible(lapply(contacts, function(contact){
         contact_splits <- unlist(strsplit(contact, ":"))
@@ -108,7 +108,7 @@ handle_entities_df <- function(config, source){
 
     #relations
     src_relation <- sanitize_str(source_entity[,"Relation"])
-    relations <- if(!is.na(src_relation)) unlist(strsplit(src_relation, ";")) else list()
+    relations <- if(!is.na(src_relation)) extract_cell_components(src_relation) else list()
     if(length(relations)>0){
       invisible(lapply(relations, function(relation){
         relation_obj <- geoflow_relation$new(str = relation)
@@ -121,7 +121,7 @@ handle_entities_df <- function(config, source){
     if(!is.na(spatial_cov)){
       if(!startsWith(spatial_cov,"SRID=")) 
         stop("The spatial coverage should be a valid EWKT string, starting with the SRID definition (e.g. SRID=4326), followed by a semicolon and the WKT geometry")
-      spatial_cov <- unlist(strsplit(spatial_cov,";"))
+      spatial_cov <- unlist(strsplit(spatial_cov, ";"))
       if(length(spatial_cov)!=2) 
         stop("The spatial coverage should be a valid EWKT string, starting with the SRID definition (e.g. SRID=4326), followed by a semicolon and the WKT geometry")
       spatial_srid <- as.integer(unlist(strsplit(spatial_cov[1],"SRID="))[2])
@@ -138,7 +138,7 @@ handle_entities_df <- function(config, source){
 
     #Rights
     src_rights <- sanitize_str(source_entity[,"Rights"])
-    rights <- if(!is.na(src_rights)) unlist(strsplit(src_rights, ";")) else list()
+    rights <- if(!is.na(src_rights)) extract_cell_components(src_rights) else list()
     if(length(rights)>0){
       invisible(lapply(rights, function(right){
         right_obj <- geoflow_right$new(str = right)

R/geoflow_provenance.R

@@ -6,7 +6,7 @@ geoflow_provenance <- R6Class("geoflow_provenance",
      processes = list(),
      initialize = function(str = NULL){
        if(!is.null(str)){
-         data_props <-  unlist(strsplit(sanitize_str(str), ";"))
+         data_props <- extract_cell_components(sanitize_str(str))
          state_prop <- data_props[[1]]
          if(!startsWith(state_prop, "statement")){
            stop("The data 'statement' is mandatory")

R/geoflow_utils.R

@@ -2,8 +2,13 @@
 #'@export
 sanitize_str <- function(str){
   if(!is(str, "character")) return(str)
+  if(is.na(str)) return(NA)
   if(!is.na(str) & str=="") return(NA)
-  #str <- gsub("\n", ";", str)
+  startwith_n <- startsWith(str, "\n")
+  while(startwith_n){
+    str <- substr(str, 2, nchar(str))
+    startwith_n <- startsWith(str, "\n")
+  }
   str <- gsub(";;", ";", str)
   str <- gsub(",;", ",", str)
   str <- gsub(":;", ":", str)
@@ -94,4 +99,24 @@ filter_sf_by_cqlfilter <- function(sfdata, cqlfilter){
   sfdata.filtered <- try(eval(parse(text= sprintf("sfdata[%s,]",rfilter))))
   if(class(sfdata.filtered)[1]!="try-error") out <- sfdata.filtered
   return(out)
+}
+
+#'extract_cell_components
+#'@export
+extract_cell_components <- function(x){
+  lines <- unlist(strsplit(x, get_line_separator()))
+  return(lines)
+}
+
+#'set_line_separator
+#'@export
+set_line_separator <- function(x = ";\n"){
+  if(!is(x,"character")) stop("The line separator should be an object of class 'character'")
+  .geoflow$LINE_SEPARATOR <- x
+}
+
+#'get_line_separator
+#'@export
+get_line_separator <- function(){
+  return(.geoflow$LINE_SEPARATOR)
 }

R/initWorkflow.R

@@ -37,6 +37,15 @@ initWorkflow <- function(file){
     config$profile <- profile
   }
 
+  #options
+  if(!is.null(config$options)){
+    config$logger.info("Setting geoflow global options...")
+    if(!is.null(config$options$line_separator)){
+      config$logger.info(sprintf("Setting option 'line_separator' to '%s'", config$options$line_separator))
+      set_line_separator(config$options$line_separator)
+    }
+  }
+
   #working dir
   if(is.null(config$wd)) config$wd <- getwd()
 

R/profile.R

@@ -2,6 +2,9 @@
 
   assign(".geoflow", new.env(), envir= asNamespace(pkgname))
 
+  #default line separator
+  set_line_separator()
+
   #embedded handlers
   register_contact_handlers()
   register_entity_handlers()