Browse code

fixed url

Simone authored on 25/08/2018 15:36:54
Showing25 changed files

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@@ -1,7 +1,7 @@
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 Package: RGMQL
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 Type: Package
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 Title: GenoMetric Query Language for R/Bioconductor
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-Version: 1.0.1
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+Version: 1.0.2
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 Author: Simone Pallotta, Marco Masseroli
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 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
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 Description: This package brings the GenoMetric Query Language (GMQL)
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@@ -37,7 +37,7 @@
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 #' 
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 #' ## This statement initializes GMQL with remote processing
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/
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 #' init_gmql(remote_processing = TRUE, url = remote_url)
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 #' 
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 #' @export
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@@ -58,7 +58,7 @@
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 #' ## repository. For a public dataset in a (remote) GMQL repository the 
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 #' ## prefix "public." is needed before dataset name
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)
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 #' 
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@@ -45,7 +45,7 @@ if(getRversion() >= "3.1.0")
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 #' @examples
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' @name login_gmql
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@@ -120,7 +120,7 @@ login_gmql <- function(url, username = NULL, password = NULL)
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 #' 
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 #' ## Login to GMQL REST services suite as guest, then logout
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' logout_gmql(remote_url)
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 #' 
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@@ -183,7 +183,7 @@ logout_gmql <- function(url)
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 #' 
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 #' ## Register to GMQL REST services suite 
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' \dontrun{
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 #' register_gmql(remote_url,"foo","foo","foo@foo.com","foo","foo")
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 #' }
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@@ -251,7 +251,7 @@ register_gmql <- function(url, username, psw, email,
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 #' @examples
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 #' 
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 #' ## Login to GMQL REST services suite
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## List all queries executed on remote GMQL system 
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@@ -300,7 +300,7 @@ show_queries_list <- function(url)
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 #' 
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## This statement saves query written directly as input string parameter 
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@@ -388,7 +388,7 @@ save_query_fromfile <- function(url, queryName, filePath)
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 #' 
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## Run query as string input parameter
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@@ -468,7 +468,7 @@ run_query_fromfile <- function(url, filePath, output_gtf = TRUE)
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 #' 
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## This statement gets the query as text string and runs the compile 
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@@ -544,7 +544,7 @@ compile_query_fromfile <- function(url ,filePath)
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 #' 
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 #' ## Login to GMQL REST services suite at remote url
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## This statement shows all jobs at GMQL remote system and selects one 
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@@ -591,7 +591,7 @@ stop_job <- function(url, job_id)
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 #' @examples
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## List all jobs
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@@ -670,7 +670,7 @@ trace_job <- function(url, job_id)
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 #' @examples
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## List all jobs
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@@ -721,7 +721,7 @@ show_jobs_list <- function(url)
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 #' 
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## List all datasets
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@@ -775,7 +775,7 @@ show_datasets_list <- function(url)
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 #' 
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## This statement shows all samples present into public dataset 
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@@ -825,7 +825,7 @@ show_samples_list <- function(url,datasetName)
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 #' @examples
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## Show schema of public dataset 'Example_Dataset_1'
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@@ -894,7 +894,7 @@ show_schema <- function(url,datasetName)
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 #' 
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 #' ## Login to GMQL REST services suite at remote url
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 #' 
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-#' remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url <- "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## Upload of GMQL dataset with "dataset1" as name, without specifying any 
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@@ -1005,7 +1005,7 @@ upload_dataset <- function(url, datasetName, folderPath, schemaName = NULL,
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 #' 
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 #' ## This dataset does not exist
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 #' 
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-#' remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url <- "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' delete_dataset(remote_url, "test1_20170604_180908_RESULT_DS")
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 #' 
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@@ -1058,7 +1058,7 @@ delete_dataset <- function(url,datasetName)
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 #' 
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 #' \dontrun{
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' download_dataset(remote_url, "Example_Dataset_1", path = getwd())
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 #' 
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@@ -1149,7 +1149,7 @@ download_as_GRangesList <- function(url,datasetName)
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 #' @examples
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## This statement retrieves metadata of sample 'S_00000' from public 
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@@ -1213,7 +1213,7 @@ sample_metadata <- function(url, datasetName,sampleName)
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 #' 
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 #' ## Login to GMQL REST services suite as guest
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 #' 
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-#' remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+#' remote_url = "http://www.gmql.eu/gmql-rest/"
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 #' login_gmql(remote_url)
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 #' 
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 #' ## This statement retrieves regions data of sample "S_00000" from public 
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@@ -29,7 +29,7 @@ using the proper GMQL web service available on a remote server
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## This statement gets the query as text string and runs the compile 
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 ## This dataset does not exist
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-remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url <- "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 delete_dataset(remote_url, "test1_20170604_180908_RESULT_DS")
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@@ -39,7 +39,7 @@ If error occurs, a specific error is printed
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 \dontrun{
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 download_dataset(remote_url, "Example_Dataset_1", path = getwd())
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 It initializes and runs GMQL server for executing GMQL query.
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 It also performs a login to GMQL REST services suite, if needed
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 }
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-\examples{
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-
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-## This statement initializes GMQL with local processing with sample files 
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-## output format as tab-delimited
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-
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-init_gmql("tab", FALSE)
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-
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-## This statement initializes GMQL with remote processing
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-
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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-init_gmql(remote_processing = TRUE, url = remote_url)
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-
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-}
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@@ -28,7 +28,7 @@ If error occurs, a specific error is printed
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 \examples{
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## List all jobs
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@@ -34,7 +34,7 @@ been saved). If error occurs, a specific error is printed
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 \examples{
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 }
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@@ -26,7 +26,7 @@ If error occurs, a specific error is printed
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 ## Login to GMQL REST services suite as guest, then logout
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 logout_gmql(remote_url)
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@@ -74,7 +74,7 @@ dataPeak = read_gmql(test_path,"NarrowPeakParser")
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 ## repository. For a public dataset in a (remote) GMQL repository the 
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 ## prefix "public." is needed before dataset name
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)
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@@ -40,7 +40,7 @@ is printed.
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 ## Register to GMQL REST services suite 
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 \dontrun{
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 register_gmql(remote_url,"foo","foo","foo@foo.com","foo","foo")
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 }
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@@ -44,7 +44,7 @@ If error occurs, a specific error is printed
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## Run query as string input parameter
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@@ -27,7 +27,7 @@ If error occurs, a specific error is printed
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 \examples{
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## This statement retrieves metadata of sample 'S_00000' from public 
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@@ -32,7 +32,7 @@ If error occurs, a specific error is printed
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## This statement retrieves regions data of sample "S_00000" from public 
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@@ -35,7 +35,7 @@ in repository, you will overwrite it; if no error occurs, it prints:
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## This statement saves query written directly as input string parameter 
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@@ -28,7 +28,7 @@ If error occurs, a specific error is printed
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## List all datasets
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@@ -26,7 +26,7 @@ If error occurs, a specific error is printed
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 \examples{
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## List all jobs
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@@ -27,7 +27,7 @@ If error occurs, a specific error is printed
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 \examples{
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 ## Login to GMQL REST services suite
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## List all queries executed on remote GMQL system 
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@@ -34,7 +34,7 @@ If error occurs, a specific error is printed
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## This statement shows all samples present into public dataset 
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@@ -32,7 +32,7 @@ If error occurs, a specific error is printed
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 \examples{
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 ## Login to GMQL REST services suite as guest
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## Show schema of public dataset 'Example_Dataset_1'
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@@ -27,7 +27,7 @@ If error occurs, a specific error is printed
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 ## Login to GMQL REST services suite at remote url
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-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## This statement shows all jobs at GMQL remote system and selects one 
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@@ -54,7 +54,7 @@ test_path <- system.file("example", "DATASET_GDM", package = "RGMQL")
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 ## Login to GMQL REST services suite at remote url
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-remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/"
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+remote_url <- "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 ## Upload of GMQL dataset with "dataset1" as name, without specifying any 
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@@ -428,7 +428,7 @@ Upon successful logon, you get a request token that you must use
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 in every subsequent REST call.
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 Login can be performed using the *login_gmql()* function:
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 ```{r, init with login}
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-test_url = "http://genomic.deib.polimi.it/gmql-rest-r/"
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+test_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(test_url)
433 433
 ```
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 It saves the token in the Global R environment within the variable