@@ -26,7 +26,11 @@

 #' @param region_attributes vector of strings that extracts only region

 #' attributes  specified; if NULL no regions attribute is taken and the output

 #' is only GRanges made up by the region coordinate attributes

-#' (seqnames, start, end, strand)

+#' (seqnames, start, end, strand);

+#' It is also possible to assign the \code{\link{FULL}} with or without 

+#' its input parameter; in case was without the `except` parameter, 

+#' all the region attributes are taken, otherwise all the region attributes 

+#' are taken except the input attribute defined by except.

 #' @param suffix name for each metadata column of GRanges. By default it is the

 #' value of the metadata attribute named "antibody_target". This string is

 #' taken from sample metadata file or from metadata() associated.

@@ -61,19 +65,14 @@

 #' sorted_grl <- sort(grl)

 #' filter_and_extract(sorted_grl, region_attributes = c("pvalue", "peak"))

 #' 

-#' ## It is also possible to define the region attributes, using the FULL() 

-#' ## function parameter, in order to includes every region 

-#' ## attributes present into the schema file

+#' ## This statement imports a GMQL dataset as GRangesList and filters it

+#' ## including all the region attributes

 #' 

 #' sorted_grl_full <- sort(grl)

-#' filter_and_extract(sorted_grl, region_attributes = FULL())

+#' filter_and_extract(sorted_grl_full, region_attributes = FULL())

 #' 

-#' grl <- import_gmql(test_path, TRUE)

-#' sorted_grl <- sort(grl)

-#' filter_and_extract(sorted_grl, region_attributes = FULL())

-#' 

-#' ## Also, we can inlcude a list of region attribute inside the FULL() 

-#' ## function to exlucde that regions

+#' ## This statement imports a GMQL dataset as GRangesList and filters it

+#' ## including all the region attributes except "jaccard" and "score"

 #' 

 #' sorted_grl_full_except <- sort(grl)

 #' filter_and_extract(

@@ -75,13 +75,21 @@ execute <- function() {

   remote <- WrappeR$is_remote_processing()

   if(remote) {

-    lapply(data_list,function(x){

+    lapply(data_list,function(x) {

       if(!is.null(x[[1]]) && !is.na(x[[1]]))

-        upload_dataset(url,x[[2]],x[[1]],x[[3]])})

+        upload_dataset(url,x[[2]],x[[1]],x[[3]]) 

+    })

   } else {

-    lapply(data_list,function(x){

-      if(!is.null(x[[2]]) && !is.na(x[[2]]))

-        download_dataset(url,x[[2]],x[[1]])})

+    lapply(data_list,function(x) {

+      if(!is.null(x[[2]]) && !is.na(x[[2]])) {

+        path <- x[[1]]

+        # create downloads folder where putting all the downloading dataset

+        if(!dir.exists(path))

+          dir.create(path)

+        

+        download_dataset(url,x[[2]], path) 

+      }

+    })

   }

 }

@@ -150,7 +158,7 @@ gmql_materialize <- function(input_data, name, dir_out) {

   if(!remote_proc) {

     dir_out <- sub("/*[/]$","",dir_out)

-    res_dir_out <- file.path(dir_out,name)

+    res_dir_out <- file.path(dir_out, name)

     if(!dir.exists(res_dir_out))

       dir.create(res_dir_out)

   }

@@ -68,11 +68,11 @@ login_gmql <- function(url, username = NULL, password = NULL) {

     req <- httr::GET(URL,httr::add_headers(h))

   } else {

     req <- httr::GET(url)

-    real_URL <- req$url

+    real_URL <- sub("/*[/]$","",req$url)

     h <- c('Accept'="Application/json",'Content-Type'='Application/json')

     URL <- paste0(real_URL,"/login")

     body <- list('username' = username,'password' = password)

-    req <- httr::POST(URL,httr::add_headers(h),body = body,encode = "json")

+    req <- httr::POST(URL, httr::add_headers(h), body = body, encode = "json")

   }

   content <- httr::content(req)

@@ -87,9 +87,9 @@ login_gmql <- function(url, username = NULL, password = NULL) {

       "username" = username,

       "password" = password

     )

-    

-    assign("GMQL_credentials",GMQL_remote,.GlobalEnv)

-    print(paste("your Token is",GMQL_remote$authToken))

+  

+    assign("GMQL_credentials", GMQL_remote, .GlobalEnv)

+    print(paste("your Token is", GMQL_remote$authToken))

   }

 }

@@ -124,11 +124,12 @@ login_gmql <- function(url, username = NULL, password = NULL) {

 #' @export

 #'

 logout_gmql <- function(url) {

-  authToken = GMQL_credentials$authToken

   url <- sub("/*[/]$","",url)

-  

   URL <- paste0(url,"/logout")

+  

+  authToken = GMQL_credentials$authToken

   h <- c('X-Auth-Token' = authToken)

+  

   req <- httr::GET(URL, httr::add_headers(h))

   content <- httr::content(req)

@@ -192,9 +193,9 @@ register_gmql <- function(

   last_name

 ) {

   req <- httr::GET(url)

-  real_URL <- req$url

+  url <- sub("/*[/]$","",req$url)

-  URL <- paste0(real_URL,"register")

+  URL <- paste0(url,"/register")

   h <- c('Accept' = "Application/json")

   reg_body <- list(

     "firstName" = first_name, 

@@ -221,7 +222,7 @@ register_gmql <- function(

       "username" = username,

       "password" = psw

     )

-    assign("GMQL_credentials", GMQL_remote,.GlobalEnv)

+    assign("GMQL_credentials", GMQL_remote, .GlobalEnv)

     print(paste("your Token is", GMQL_remote$authToken))

   }

 }

@@ -323,8 +324,8 @@ show_queries_list <- function(url) {

 #'

 save_query <- function(url, queryName, queryTxt) {

   req <- httr::GET(url)

-  real_URL <- req$url

-  URL <- paste0(real_URL,"query/",queryName,"/save")

+  url <- sub("/*[/]$","",req$url)

+  URL <- paste0(url,"/query/",queryName,"/save")

   authToken = GMQL_credentials$authToken

   h <- c(

     'Accept' = 'text/plain',

@@ -420,8 +421,8 @@ run_query <- function(url, queryName, query, output_gtf = TRUE) {

     out <- "TAB"

   req <- httr::GET(url)

-  real_URL <- req$url

-  URL <- paste0(real_URL,"queries/run/",queryName,"/",out)

+  url <- sub("/*[/]$","",req$url)

+  URL <- paste0(url,"/queries/run/",queryName,"/",out)

   authToken = GMQL_credentials$authToken

   h <- c(

     'Accept' = "Application/json",

@@ -507,8 +508,8 @@ compile_query <- function(url, query) {

     'X-Auth-Token' = authToken

   )

   req <- httr::GET(url)

-  real_URL <- req$url

-  URL <- paste0(real_URL, "queries/compile")

+  url <- sub("/*[/]$","",req$url)

+  URL <- paste0(url, "/queries/compile")

   req <- httr::POST(

     URL, 

     body = query ,

@@ -964,8 +965,8 @@ upload_dataset <- function(

   names(list_files) <- list_files_names

   req <- httr::GET(url)

-  real_URL <- req$url

-  URL <- paste0(real_URL, "datasets/", datasetName, "/uploadSample")

+  real_URL <- sub("/*[/]$","",req$url)

+  URL <- paste0(real_URL, "/datasets/", datasetName, "/uploadSample")

   authToken = GMQL_credentials$authToken

   h <- c('X-Auth-Token' = authToken, 'Accept:' = 'Application/json')

@@ -979,7 +980,7 @@ upload_dataset <- function(

       list_files

     )

     list_files <- unlist(list_files, recursive = FALSE)

-    URL <- paste0(real_URL, "datasets/", datasetName, "/uploadSample")

+    URL <- paste0(real_URL, "/datasets/", datasetName, "/uploadSample")

   } else {

     schemaList <- c(

       "narrowpeak",

@@ -994,7 +995,7 @@ upload_dataset <- function(

     URL <- paste0(

       real_URL,

-      "datasets/",

+      "/datasets/",

       datasetName,

       "/uploadSample?schemaName=",

       schema_name

@@ -1044,8 +1045,8 @@ upload_dataset <- function(

 #'

 delete_dataset <- function(url, datasetName) {

   req <- httr::GET(url)

-  real_URL <- req$url

-  URL <- paste0(real_URL, "datasets/", datasetName)

+  real_URL <- sub("/*[/]$","",req$url)

+  URL <- paste0(real_URL, "/datasets/", datasetName)

   authToken = GMQL_credentials$authToken

   h <- c('X-Auth-Token' = authToken, 'Accept:' = 'application/json')

   req <- httr::DELETE(URL, httr::add_headers(h))

@@ -1305,9 +1306,9 @@ serialize_query <- function(url,output_gtf,base64) {

   }

   url <- sub("/*[/]$","",url)

   req <- httr::GET(url)

-  real_URL <- req$url

+  real_URL <- sub("/*[/]$","",req$url)

   authToken = GMQL_credentials$authToken

-  URL <- paste0(real_URL,"queries/dag/",out)

+  URL <- paste0(real_URL,"/queries/dag/",out)

   h <- c(

     'Accept' = "Application/json",

     'Content-Type' = 'text/plain',