#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()