@@ -1,7 +1,7 @@

 Package: RGMQL

 Type: Package

 Title: GenoMetric Query Language for R/Bioconductor

-Version: 0.99.12

+Version: 1.0.1

 Author: Simone Pallotta, Marco Masseroli

 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>

 Description: This package brings the GenoMetric Query Language (GMQL)

@@ -23,7 +23,7 @@ License: Artistic-2.0

 URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/

 Encoding: UTF-8

 LazyData: true

-RoxygenNote: 6.0.1

+RoxygenNote: 6.1.0

 Imports:

     httr,

     rJava,

@@ -98,27 +98,21 @@ export_gmql <- function(samples, dir_out, is_gtf)

     files_sub_dir <- file.path(dir_out,"files")

     dir.create(files_sub_dir)

     cnt = .counter()

+    file_ext = ""

     #col_names <- .get_schema_names(samples)

     if(to_GTF)

     {

         #write region

         lapply(samples,function(x,dir){

-            anonymusFile <- file()

+            #anonymusFile <- file()

             sample_name <- file.path(dir,paste0("S_",cnt(),".gtf"))

-            g <- rtracklayer::export(x,sample_name,format = "gtf")

-            lines <- readLines(anonymusFile)

-            lines <- lines[-(1:3)] #delete first 3 lines

+            g <- rtracklayer::export(x,format = "gtf",is.na)

+            #lines <- readLines(sample_name)

+            lines <- g[-(1:3)] #delete first 3 lines

             writeLines(lines,sample_name)

-            close(anonymusFile)

-        },files_sub_dir)

-        cnt = .counter(0)

-        meta <- metadata(samples)

-

-        #write metadata

-        lapply(meta,function(x,dir){

-            sample_name <- file.path(dir,paste0("S_",cnt(),".gtf"))

-            .write_metadata(x,sample_name)

+            #close(anonymusFile)

         },files_sub_dir)

+        file_ext = ".gtf"

     }

     else

     {

@@ -126,20 +120,23 @@ export_gmql <- function(samples, dir_out, is_gtf)

         lapply(samples,function(x,dir){

             sample_name <- file.path(dir,paste0("S_",cnt(),".gdm"))

             region_frame <- data.frame(x)

+            region_frame <- region_frame[-4] # delete width column

             region_frame$start = region_frame$start - 1

             write.table(region_frame,sample_name,col.names = FALSE,

                             row.names = FALSE, sep = '\t',quote = FALSE)

         },files_sub_dir)

-

-        cnt = .counter(0)

-        meta <- metadata(samples)

-

-        #write metadata

-        lapply(meta,function(x,dir){

-            sample_name <- file.path(dir,paste0("S_",cnt(),".gdm"))

-            .write_metadata(x,sample_name)

-        },files_sub_dir)

+        file_ext = ".gdm"

     }

+    

+    cnt = .counter(0)

+    meta <- metadata(samples)

+    

+    #write metadata

+    lapply(meta,function(x,dir){

+        sample_name <- file.path(dir,paste0("S_",cnt(),file_ext))

+        .write_metadata(x,sample_name)

+    },files_sub_dir)

+    

     # first regions to get column names

     col_names <- vapply(elementMetadata(samples[[1]]),class,character(1)) 

     # write schema XML

@@ -148,7 +145,6 @@ export_gmql <- function(samples, dir_out, is_gtf)

 }

-

 .write_metadata <- function(meta_list,sample_name)

 {

     #create my own list if metadata empty

@@ -189,19 +185,18 @@ export_gmql <- function(samples, dir_out, is_gtf)

     xml2::xml_attr(root,"name") <- "DatasetName_SCHEMAS"

     xml2::xml_attr(root,"xmlns") <- "http://genomic.elet.polimi.it/entities"

     xml2::xml_add_child(root,"gmqlSchema")

+    gmqlSchema <- xml2::xml_child(root,1) #gmqlSchema

     if(to_GTF)

     {

-        xml2::xml_attr(root,"type") <- "gtf"

-        xml2::xml_attr(root,"coordinate_system") <- "1-based"

+        xml2::xml_attr(gmqlSchema,"type") <- "gtf"

+        xml2::xml_attr(gmqlSchema,"coordinate_system") <- "1-based"

     }

     else

     {

-        xml2::xml_attr(root,"type") <- "tab"

-        xml2::xml_attr(root,"coordinate_system") <- "0-based"

+        xml2::xml_attr(gmqlSchema,"type") <- "tab"

+        xml2::xml_attr(gmqlSchema,"coordinate_system") <- "0-based"

     }

-    gmqlSchema <- xml2::xml_child(root,1)

-

     names_node <- names(node_list)

     mapply(function(type,text){

@@ -37,7 +37,7 @@

 #' 

 #' ## This statement initializes GMQL with remote processing

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' init_gmql(remote_processing = TRUE, url = remote_url)

 #' 

 #' @export

@@ -58,7 +58,7 @@

 #' ## repository. For a public dataset in a (remote) GMQL repository the 

 #' ## prefix "public." is needed before dataset name

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)

 #' 

@@ -45,7 +45,7 @@ if(getRversion() >= "3.1.0")

 #' @examples

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' @name login_gmql

@@ -120,7 +120,7 @@ login_gmql <- function(url, username = NULL, password = NULL)

 #' 

 #' ## Login to GMQL REST services suite as guest, then logout

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/

 #' login_gmql(remote_url)

 #' logout_gmql(remote_url)

 #' 

@@ -183,7 +183,7 @@ logout_gmql <- function(url)

 #' 

 #' ## Register to GMQL REST services suite 

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' \dontrun{

 #' register_gmql(remote_url,"foo","foo","foo@foo.com","foo","foo")

 #' }

@@ -251,7 +251,7 @@ register_gmql <- function(url, username, psw, email,

 #' @examples

 #' 

 #' ## Login to GMQL REST services suite

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## List all queries executed on remote GMQL system 

@@ -300,7 +300,7 @@ show_queries_list <- function(url)

 #' 

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## This statement saves query written directly as input string parameter 

@@ -388,7 +388,7 @@ save_query_fromfile <- function(url, queryName, filePath)

 #' 

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## Run query as string input parameter

@@ -468,7 +468,7 @@ run_query_fromfile <- function(url, filePath, output_gtf = TRUE)

 #' 

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## This statement gets the query as text string and runs the compile 

@@ -544,7 +544,7 @@ compile_query_fromfile <- function(url ,filePath)

 #' 

 #' ## Login to GMQL REST services suite at remote url

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## This statement shows all jobs at GMQL remote system and selects one 

@@ -591,7 +591,7 @@ stop_job <- function(url, job_id)

 #' @examples

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## List all jobs

@@ -670,7 +670,7 @@ trace_job <- function(url, job_id)

 #' @examples

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## List all jobs

@@ -721,7 +721,7 @@ show_jobs_list <- function(url)

 #' 

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## List all datasets

@@ -775,7 +775,7 @@ show_datasets_list <- function(url)

 #' 

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## This statement shows all samples present into public dataset 

@@ -825,7 +825,7 @@ show_samples_list <- function(url,datasetName)

 #' @examples

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## Show schema of public dataset 'Example_Dataset_1'

@@ -894,7 +894,7 @@ show_schema <- function(url,datasetName)

 #' 

 #' ## Login to GMQL REST services suite at remote url

 #' 

-#' remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url <- "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## Upload of GMQL dataset with "dataset1" as name, without specifying any 

@@ -1005,7 +1005,7 @@ upload_dataset <- function(url, datasetName, folderPath, schemaName = NULL,

 #' 

 #' ## This dataset does not exist

 #' 

-#' remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url <- "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' delete_dataset(remote_url, "test1_20170604_180908_RESULT_DS")

 #' 

@@ -1058,7 +1058,7 @@ delete_dataset <- function(url,datasetName)

 #' 

 #' \dontrun{

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' download_dataset(remote_url, "Example_Dataset_1", path = getwd())

 #' 

@@ -1149,7 +1149,7 @@ download_as_GRangesList <- function(url,datasetName)

 #' @examples

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## This statement retrieves metadata of sample 'S_00000' from public 

@@ -1213,7 +1213,7 @@ sample_metadata <- function(url, datasetName,sampleName)

 #' 

 #' ## Login to GMQL REST services suite as guest

 #' 

-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+#' remote_url = "http://www.gmql.eu/gmql-rest/"

 #' login_gmql(remote_url)

 #' 

 #' ## This statement retrieves regions data of sample "S_00000" from public 

@@ -3,29 +3,17 @@

 \name{AGGREGATES-Object}

 \alias{AGGREGATES-Object}

 \alias{SUM}

-\alias{AGGREGATES-Object}

 \alias{COUNT}

-\alias{AGGREGATES-Object}

 \alias{COUNTSAMP}

-\alias{AGGREGATES-Object}

 \alias{MIN}

-\alias{AGGREGATES-Object}

 \alias{MAX}

-\alias{AGGREGATES-Object}

 \alias{AVG}

-\alias{AGGREGATES-Object}

 \alias{MEDIAN}

-\alias{AGGREGATES-Object}

 \alias{STD}

-\alias{AGGREGATES-Object}

 \alias{BAG}

-\alias{AGGREGATES-Object}

 \alias{BAGD}

-\alias{AGGREGATES-Object}

 \alias{Q1}

-\alias{AGGREGATES-Object}

 \alias{Q2}

-\alias{AGGREGATES-Object}

 \alias{Q3}

 \title{AGGREGATES object class constructor}

 \usage{

@@ -2,7 +2,6 @@

 % Please edit documentation in R/web-services.R

 \name{compile_query}

 \alias{compile_query}

-\alias{compile_query}

 \alias{compile_query_fromfile}

 \title{Compile GMQL query}

 \usage{

@@ -29,7 +28,7 @@ using the proper GMQL web service available on a remote server

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## This statement gets the query as text string and runs the compile 

@@ -3,7 +3,6 @@

 \name{Cover-Param}

 \alias{Cover-Param}

 \alias{ALL}

-\alias{Cover-Param}

 \alias{ANY}

 \title{PARAM object class constructor}

 \usage{

@@ -3,7 +3,6 @@

 \docType{methods}

 \name{cover}

 \alias{cover}

-\alias{cover}

 \alias{cover,GMQLDataset-method}

 \title{Method cover}

 \usage{

@@ -29,7 +29,7 @@ is printed

 ## This dataset does not exist

-remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url <- "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 delete_dataset(remote_url, "test1_20170604_180908_RESULT_DS")

@@ -4,15 +4,10 @@

 \alias{DISTAL-Object}

 \alias{DL}

 \alias{DG}

-\alias{DISTAL-Object}

 \alias{DLE}

-\alias{DISTAL-Object}

 \alias{DGE}

-\alias{DISTAL-Object}

 \alias{MD}

-\alias{DISTAL-Object}

 \alias{UP}

-\alias{DISTAL-Object}

 \alias{DOWN}

 \title{DISTAL object class constructor}

 \usage{

@@ -39,7 +39,7 @@ If error occurs, a specific error is printed

 \dontrun{

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 download_dataset(remote_url, "Example_Dataset_1", path = getwd())

@@ -4,7 +4,6 @@

 \name{extend}

 \alias{extend}

 \alias{extend,GMQLDataset-method}

-\alias{extend}

 \alias{extend-method}

 \title{Method extend}

 \usage{

@@ -4,8 +4,8 @@

 \alias{init_gmql}

 \title{Init GMQL server}

 \usage{

-init_gmql(output_format = "GTF", remote_processing = FALSE, url = NULL,

-  username = NULL, password = NULL)

+init_gmql(output_format = "GTF", remote_processing = FALSE,

+  url = NULL, username = NULL, password = NULL)

 }

 \arguments{

 \item{output_format}{string that identifies the output format of all sample 

@@ -47,7 +47,7 @@ init_gmql("tab", FALSE)

 ## This statement initializes GMQL with remote processing

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 init_gmql(remote_processing = TRUE, url = remote_url)

 }

@@ -28,7 +28,7 @@ If error occurs, a specific error is printed

 \examples{

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## List all jobs

@@ -34,7 +34,7 @@ been saved). If error occurs, a specific error is printed

 \examples{

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 }

@@ -22,12 +22,3 @@ After logout the authentication token will be invalidated.

 The authentication token is removed from R Global environment.

 If error occurs, a specific error is printed

 }

-\examples{

-

-## Login to GMQL REST services suite as guest, then logout

-

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

-login_gmql(remote_url)

-logout_gmql(remote_url)

-

-}

@@ -4,13 +4,13 @@

 \name{map}

 \alias{map}

 \alias{map,GMQLDataset-method}

-\alias{map}

 \alias{map-method}

 \title{Method map}

 \usage{

 map(x, y, ...)

-\S4method{map}{GMQLDataset}(x, y, ..., joinBy = conds(), count_name = "")

+\S4method{map}{GMQLDataset}(x, y, ..., joinBy = conds(),

+  count_name = "")

 }

 \arguments{

 \item{x}{GMQLDataset class object}

@@ -6,8 +6,9 @@

 \alias{merge,GMQLDataset,GMQLDataset-method}

 \title{Method merge}

 \usage{

-\S4method{merge}{GMQLDataset,GMQLDataset}(x, y, genometric_predicate = NULL,

-  region_output = "CAT", joinBy = conds(), reg_attr = c(""))

+\S4method{merge}{GMQLDataset,GMQLDataset}(x, y,

+  genometric_predicate = NULL, region_output = "CAT",

+  joinBy = conds(), reg_attr = c(""))

 }

 \arguments{

 \item{x}{GMQLDataset class object}

@@ -3,9 +3,7 @@

 \name{OPERATOR-Object}

 \alias{OPERATOR-Object}

 \alias{META}

-\alias{OPERATOR-Object}

 \alias{NIL}

-\alias{OPERATOR-Object}

 \alias{SQRT}

 \title{OPERATOR object class constructor}

 \usage{

@@ -3,7 +3,6 @@

 \name{Ordering-Functions}

 \alias{Ordering-Functions}

 \alias{DESC}

-\alias{Ordering-Functions}

 \alias{ASC}

 \title{Ordering functions}

 \usage{

@@ -2,7 +2,6 @@

 % Please edit documentation in R/gmql_read.R

 \name{read_gmql}

 \alias{read_gmql}

-\alias{read_gmql}

 \alias{read_GRangesList}

 \title{Function read}

 \usage{

@@ -74,7 +73,7 @@ dataPeak = read_gmql(test_path,"NarrowPeakParser")

 ## repository. For a public dataset in a (remote) GMQL repository the 

 ## prefix "public." is needed before dataset name

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)

@@ -40,7 +40,7 @@ is printed.

 ## Register to GMQL REST services suite 

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 \dontrun{

 register_gmql(remote_url,"foo","foo","foo@foo.com","foo","foo")

 }

@@ -2,7 +2,6 @@

 % Please edit documentation in R/web-services.R

 \name{run_query}

 \alias{run_query}

-\alias{run_query}

 \alias{run_query_fromfile}

 \title{Run a GMQL query}

 \usage{

@@ -44,7 +43,7 @@ If error occurs, a specific error is printed

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## Run query as string input parameter

@@ -27,7 +27,7 @@ If error occurs, a specific error is printed

 \examples{

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## This statement retrieves metadata of sample 'S_00000' from public 

@@ -32,7 +32,7 @@ If error occurs, a specific error is printed

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## This statement retrieves regions data of sample "S_00000" from public 

@@ -35,7 +35,7 @@ in repository, you will overwrite it; if no error occurs, it prints:

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## This statement saves query written directly as input string parameter 

@@ -28,7 +28,7 @@ If error occurs, a specific error is printed

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## List all datasets

@@ -26,7 +26,7 @@ If error occurs, a specific error is printed

 \examples{

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## List all jobs

@@ -27,7 +27,7 @@ If error occurs, a specific error is printed

 \examples{

 ## Login to GMQL REST services suite

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## List all queries executed on remote GMQL system 

@@ -34,7 +34,7 @@ If error occurs, a specific error is printed

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## This statement shows all samples present into public dataset 

@@ -32,7 +32,7 @@ If error occurs, a specific error is printed

 \examples{

 ## Login to GMQL REST services suite as guest

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## Show schema of public dataset 'Example_Dataset_1'

@@ -27,7 +27,7 @@ If error occurs, a specific error is printed

 ## Login to GMQL REST services suite at remote url

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## This statement shows all jobs at GMQL remote system and selects one 

@@ -4,7 +4,6 @@

 \name{take}

 \alias{take}

 \alias{take,GMQLDataset-method}

-\alias{take}

 \alias{take-method}

 \title{Method take}

 \usage{

@@ -54,7 +54,7 @@ test_path <- system.file("example", "DATASET_GDM", package = "RGMQL")

 ## Login to GMQL REST services suite at remote url

-remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url <- "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

 ## Upload of GMQL dataset with "dataset1" as name, without specifying any 

@@ -428,7 +428,7 @@ Upon successful logon, you get a request token that you must use

 in every subsequent REST call.

 Login can be performed using the *login_gmql()* function:

 ```{r, init with login}

-test_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+test_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(test_url)

 ```

 It saves the token in the Global R environment within the variable