@@ -58,7 +58,7 @@ init_gmql <- function(

   # mettere attesa da input keyboard, controllare se token già esiste 

   # da sessione precedente

   if(!is.null(url) && !exists("GMQL_credentials", envir = .GlobalEnv))

-    login_gmql(url,username,password)

+    login_gmql(url, username, password)

   WrappeR <- J("it/polimi/genomics/r/Wrapper")

   WrappeR$initGMQL(out_format,remote_processing)

@@ -51,7 +51,12 @@ execute <- function() {

       if(identical(outformat, "gtf"))

         isGTF <- TRUE

-      url <- WrappeR$get_url()

+      credential <- get("GMQL_credentials", envir = .GlobalEnv)

+      url <- credential$remote_url

+      

+      if(is.null(url))

+        stop("url from GMQL_credentials is missing")

+      

       .download_or_upload(datasets)

       res <- serialize_query(url,isGTF,val)

     }

@@ -61,7 +66,13 @@ execute <- function() {

 .download_or_upload <- function(datasets) {

   WrappeR <- J("it/polimi/genomics/r/Wrapper")

   data_list <- apply(datasets, 1, as.list)

-  url <- WrappeR$get_url()

+  

+  credential <- get("GMQL_credentials", envir = .GlobalEnv)

+  url <- credential$remote_url

+  

+  if(is.null(url))

+    stop("url from GMQL_credentials is missing")

+  

   remote <- WrappeR$is_remote_processing()

   if(remote) {

     lapply(data_list,function(x){

@@ -74,9 +85,9 @@ execute <- function() {

   }

 }

-collect.GMQLDataset <- function(x, dir_out = getwd(), name = "ds1") {

+collect.GMQLDataset <- function(x,  name = "ds1", dir_out = getwd()) {

   ptr_data <- value(x)

-  gmql_materialize(ptr_data, dir_out, name)

+  gmql_materialize(ptr_data, name, dir_out)

 }

@@ -37,6 +37,21 @@

 #' \item{"application" = "RGMQL"}

 #' }

 #'

+#' NOTE: 

+#' The folder layout must obey the following rules and adopt 

+#' the following layout:

+#' The dataset folder can have any name, but must contains the 

+#' sub-folders named: "files".

+#' The sub-folder "files" contains the dataset files and 

+#' the schema xml file.

+#' The schema files adopt the following the naming conventions:

+#' 

+#' - "schema.xml"

+#' - "test.schema"

+#' 

+#' The names must be in LOWERCASE. Any other schema file 

+#' will not be conisdered, if both are present, "test.schema" will be used. 

+#'

 #' @examples

 #' 

 #' ## This statement initializes and runs the GMQL server for local execution 

@@ -61,6 +76,7 @@

 #' login_gmql(remote_url)

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

 #' 

+#' 

 #' @name read_gmql

 #' @rdname read-function

 #' @export

@@ -82,22 +98,24 @@ read_gmql <- function(

     if(basename(dataset) !="files")

       dataset <- file.path(dataset,"files")

-    schema_XML <- .retrieve_schema(dataset)

+    schema_XML <- .retrieve_schema(dataset, T)

     schema_matrix <- .jnull("java/lang/String")

     url <- .jnull("java/lang/String")

     coords_sys <- .jnull("java/lang/String")

     type <- .jnull("java/lang/String")

   } else {

-    url <- WrappeR$get_url()

-    if(is.null(url))

-      stop("You have to log on using login function")

     if(!exists("GMQL_credentials", envir = .GlobalEnv))

       stop("You have to log on using login function")

+    credential <- get("GMQL_credentials", envir = .GlobalEnv)

+    url <- credential$remote_url

+    if(is.null(url))

+      stop("You have to log on using login function")

+    

     if(identical(parser_name,"CUSTOMPARSER")) {

-      list <- show_schema(url,dataset)

+      list <- show_schema(url, dataset)

       coords_sys <- list$coordinate_system

       type <- list$type

       schema_names <- vapply(

@@ -60,8 +60,9 @@ login_gmql <- function(url, username = NULL, password = NULL) {

   if(!is.null(username) || !is.null(password))

     as_guest <- FALSE

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

+  

   if(as_guest) {

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

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

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

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

@@ -69,7 +70,7 @@ login_gmql <- function(url, username = NULL, password = NULL) {

     req <- httr::GET(url)

     real_URL <- req$url

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

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

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

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

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

   }

@@ -79,7 +80,6 @@ login_gmql <- function(url, username = NULL, password = NULL) {

   if(req$status_code != 200)

     stop(content$errorString)

   else {

-    WrappeR <- J("it/polimi/genomics/r/Wrapper")

     url <- paste0(url,"/")

     GMQL_remote <- list(

       "remote_url" = url, 

@@ -88,7 +88,6 @@ login_gmql <- function(url, username = NULL, password = NULL) {

       "password" = password

     )

-    WrappeR$save_tokenAndUrl(GMQL_remote$authToken,url)

     assign("GMQL_credentials",GMQL_remote,.GlobalEnv)

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

   }

@@ -124,8 +123,7 @@ login_gmql <- function(url, username = NULL, password = NULL) {

 #' @rdname logout_gmql

 #' @export

 #'

-logout_gmql <- function(url)

-{

+logout_gmql <- function(url) {

   authToken = GMQL_credentials$authToken

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

@@ -136,11 +134,8 @@ logout_gmql <- function(url)

   if(req$status_code !=200)

     stop(content$error)

-  else

-  {

+  else {

     #delete token from environment

-    WrappeR <- J("it/polimi/genomics/r/Wrapper")

-    WrappeR$delete_token()

     if(exists("authToken", where = GMQL_credentials))

       rm(GMQL_credentials, envir = .GlobalEnv)

@@ -220,16 +215,14 @@ register_gmql <- function(

   if(req$status_code != 200) {

     stop(content)

   } else {

-    WrappeR <- J("it/polimi/genomics/r/Wrapper")

     GMQL_remote <- list(

       "remote_url" = url, 

       "authToken" = content$authToken,

       "username" = username,

       "password" = psw

     )

-    WrappeR$save_tokenAndUrl(GMQL_remote$authToken,url)

-    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))

   }

 }

@@ -903,7 +896,22 @@ show_schema <- function(url, datasetName) {

 #' @details

 #' If no error occurs, it prints "Upload Complete", otherwise a specific error 

 #' is printed

-#'

+#' 

+#' NOTE: 

+#' The folder layout must obey the following rules and adopt 

+#' the following layout:

+#' The dataset folder can have any name, but must contains the 

+#' sub-folders named: "files".

+#' The sub-folder "files" contains the dataset files and 

+#' the schema xml file.

+#' The schema files adopt the following the naming conventions:

+#' 

+#' - "schema.xml"

+#' - "test.schema"

+#' 

+#' The names must be in LOWERCASE. Any other schema file 

+#' will not be conisdered, if both are present, "test.schema" will be used. 

+#' 

 #' @examples

 #'

 #' \dontrun{

@@ -935,16 +943,17 @@ upload_dataset <- function(

   schemaName = NULL

 ) {

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

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

   if(basename(folderPath) !="files")

     folderPath <- file.path(folderPath,"files")

-  files <- list.files(folderPath, full.names = TRUE)

+  files <- list.files(folderPath, pattern = "*(.gtf|.gdm)", full.names = TRUE)

   if (!length(files)) {

     stop("no files present")

   }

   count = .counter(0)

+  

   list_files <- lapply(files, function(x) {

     file <- httr::upload_file(x)

   })

@@ -962,7 +971,7 @@ upload_dataset <- function(

   schema_name <- tolower(schemaName)

-  if (is.null(schemaName)) {

+  if (is.null(schemaName) || identical(schema_name, "customparser")) {

     schema <- .retrieve_schema(folderPath)

     list_files <- list(

@@ -972,37 +981,24 @@ upload_dataset <- function(

     list_files <- unlist(list_files, recursive = FALSE)

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

   } else {

-    schema_name <- tolower(schemaName)

-    if (identical(schema_name, "customparser")) {

-      schema <- .retrieve_schema(folderPath)

-      

-      list_files <- list(

-        list("schema" = httr::upload_file(schema)),

-        list_files

-      )

-      list_files <- unlist(list_files, recursive = FALSE)

-      

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

-    }else {

-      schemaList <- c(

-        "narrowpeak",

-        "vcf",

-        "broadpeak",

-        "bed",

-        "bedgraph"

-      )

-      if (!schema_name %in% schemaList) {

-        stop("schema not admissable")

-      }

-      

-      URL <- paste0(

-        real_URL,

-        "datasets/",

-        datasetName,

-        "/uploadSample?schemaName=",

-        schema_name

-      )

+    schemaList <- c(

+      "narrowpeak",

+      "vcf",

+      "broadpeak",

+      "bed",

+      "bedgraph"

+    )

+    if (!schema_name %in% schemaList) {

+      stop("schema not admissable")

     }

+    

+    URL <- paste0(

+      real_URL,

+      "datasets/",

+      datasetName,

+      "/uploadSample?schemaName=",

+      schema_name

+    )

   }

   req <- httr::POST(URL, body = list_files , httr::add_headers(h))

@@ -1328,8 +1324,7 @@ serialize_query <- function(url,output_gtf,base64) {

 }

-

-.retrieve_schema <- function(folderPath) {

+.retrieve_schema <- function(folderPath, duringReading = F) {

   schema_SCHEMA <- list.files(

     folderPath, pattern = "test.schema$", full.names = TRUE

   )

@@ -1344,7 +1339,11 @@ serialize_query <- function(url,output_gtf,base64) {

   schema <- if(!length(schema_SCHEMA)) 

     xml_schema 

   else

-    schema_SCHEMA

+    if(!duringReading) {

+      schema_SCHEMA

+    } else {

+      folderPath

+    }

   schema

 }

@@ -6,15 +6,15 @@

 \alias{collect-method}

 \title{Method collect}

 \usage{

-\S4method{collect}{GMQLDataset}(x, dir_out = getwd(), name = "ds1")

+\S4method{collect}{GMQLDataset}(x, name = "ds1", dir_out = getwd())

 }

 \arguments{

 \item{x}{GMQLDataset class object}

+\item{name}{name of the result dataset. By default it is the string "ds1"}

+

 \item{dir_out}{destination folder path. By default it is the current 

 working directory of the R process}

-

-\item{name}{name of the result dataset. By default it is the string "ds1"}

 }

 \value{

 None