@@ -1294,6 +1294,9 @@ sample_region <- function(url, datasetName,sampleName) {

             samples <- GenomicRanges::makeGRangesFromDataFrame(

                 df,

                 keep.extra.columns = TRUE,

+                seqnames.field = c("seqnames", "seqname",

+                                   "chromosome", "chrom",

+                                   "chr", "chromosome_name"),

                 start.field = "left",

                 end.field = "right",

                 strand.field="strand"

@@ -1272,22 +1272,20 @@ sample_region <- function(url, datasetName,sampleName) {

             col.names = FALSE,

             row.names = FALSE

         )

+        vector_field <- vapply(

+            list$fields, function(x) x$name, character(1)

+        )

         if (identical(schema_type, "gtf")) {

-            samples <- tryCatch(

-                expr = {

-                    rtracklayer::import(temp, format = "gtf")

-                },

-                error = function(e){ 

-                    rtracklayer::import(temp, format = "gff", version = "3")

-                },

-                warning = function(w){

-                    rtracklayer::import(temp, format = "gff", version = "3")

-                }

+            attr_col_names <- vector_field[

+              !vector_field %in% c(

+                "seqname", "seqid", "start", "end", "strand"

+              )]

+            samples <- rtracklayer::import(

+                temp, 

+                format = "gtf",

+                colnames = attr_col_names

             )

         } else {

-            vector_field <- vapply(

-                list$fields, function(x) x$name, character(1)

-            )

             df <- data.table::fread(temp, header = FALSE, sep = "\t")

             a <- df[1, 2]

             if(is.na(as.numeric(a)))

@@ -1273,7 +1273,17 @@ sample_region <- function(url, datasetName,sampleName) {

             row.names = FALSE

         )

         if (identical(schema_type, "gtf")) {

-            samples <- rtracklayer::import(temp, format = "gtf")

+            samples <- tryCatch(

+                expr = {

+                    rtracklayer::import(temp, format = "gtf")

+                },

+                error = function(e){ 

+                    rtracklayer::import(temp, format = "gff", version = "3")

+                },

+                warning = function(w){

+                    rtracklayer::import(temp, format = "gff", version = "3")

+                }

+            )

         } else {

             vector_field <- vapply(

                 list$fields, function(x) x$name, character(1)

@@ -1352,3 +1352,25 @@ serialize_query <- function(url,output_gtf,base64) {

     schema

 }

+.metadata_matrix <- function(url, datasetName) {

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

+  URL <- paste0(url, "/metadata/", datasetName, "/", "dataset/matrix")

+  authToken = GMQL_credentials$authToken

+  h <- c(

+      'X-Auth-Token' = authToken, 

+      'Accpet' = 'application/json',

+      'Content-Type' = 'application/json')

+  req <- httr::POST(

+      URL, 

+      body = '{"attributes": []}' ,

+      httr::add_headers(h), 

+      encode = "json"

+  )

+  content <- httr::content(req,"parsed")

+

+  if (req$status_code != 200) {

+    stop(content)

+  } else {

+    return(content)

+  }

+}

@@ -893,8 +893,6 @@ show_schema <- function(url, datasetName) {

 #' }

 #' if schemaName is NULL, it looks for a XML schema file to read in the 

 #' folderPath

-#' @param isGMQL logical value indicating whether it is uploaded a GMQL 

-#' dataset or not

 #'

 #' @return None

 #'

@@ -1,11 +1,11 @@

 if(getRversion() >= "2.15.1") {

-  utils::globalVariables("GMQL_credentials")

-  utils::globalVariables("remote_url")

+    utils::globalVariables("GMQL_credentials")

+    utils::globalVariables("remote_url")

 }

 if(getRversion() >= "3.1.0") {

-  utils::suppressForeignCheck("GMQL_credentials")

-  utils::suppressForeignCheck("remote_url")

+    utils::suppressForeignCheck("GMQL_credentials")

+    utils::suppressForeignCheck("remote_url")

 }

@@ -50,47 +50,51 @@ if(getRversion() >= "3.1.0") {

 #' @export

 #' 

 login_gmql <- function(url, username = NULL, password = NULL) {

-  if(!.is_login_expired(url)) {

-    print("Login still valid")

-    return(invisible(NULL))

-  }

-  

-  as_guest <- TRUE

-  

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

-    as_guest <- FALSE

-  

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

-  

-  if(as_guest) {

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

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

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

-  } else {

-    req <- httr::GET(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")

-  }

-  

-  content <- httr::content(req)

-  

-  if(req$status_code != 200)

-    stop(content$errorString)

-  else {

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

-    GMQL_remote <- list(

-      "remote_url" = url, 

-      "authToken" = content$authToken,

-      "username" = username,

-      "password" = password

-    )

-  

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

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

-  }

+    if(!.is_login_expired(url)) {

+        print("Login still valid")

+        return(invisible(NULL))

+    }

+    

+    as_guest <- TRUE

+    

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

+        as_guest <- FALSE

+    

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

+    

+    if(as_guest) {

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

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

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

+    } else {

+        req <- httr::GET(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")

+    }

+    

+    content <- httr::content(req)

+    

+    if(req$status_code != 200)

+        stop(content$errorString)

+    else {

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

+        GMQL_remote <- list(

+            "remote_url" = url, 

+            "authToken" = content$authToken,

+            "username" = username,

+            "password" = password

+        )

+        

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

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

+    }

 }

 #' Logout from GMQL

@@ -124,24 +128,24 @@ login_gmql <- function(url, username = NULL, password = NULL) {

 #' @export

 #'

 logout_gmql <- function(url) {

-  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)

-  

-  if(req$status_code !=200)

-    stop(content$error)

-  else {

-    #delete token from environment

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

-      rm(GMQL_credentials, envir = .GlobalEnv)

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

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

+    

+    authToken = GMQL_credentials$authToken

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

-    print(content)

-  }

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

+    content <- httr::content(req)

+    

+    if(req$status_code !=200)

+        stop(content$error)

+    else {

+        #delete token from environment

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

+            rm(GMQL_credentials, envir = .GlobalEnv)

+        

+        print(content)

+    }

 }

 #' Register into remote GMQL

 #' 

@@ -185,46 +189,46 @@ logout_gmql <- function(url) {

 #' @export

 #'

 register_gmql <- function(

-  url, 

-  username, 

-  psw, 

-  email, 

-  first_name, 

-  last_name

+    url, 

+    username, 

+    psw, 

+    email, 

+    first_name, 

+    last_name

 ) {

-  req <- httr::GET(url)

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

-  

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

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

-  reg_body <- list(

-    "firstName" = first_name, 

-    "lastName" = last_name,

-    "username" = username, 

-    "email" = email, 

-    "password" = psw

-  )

-  

-  req <- httr::POST(

-    URL, 

-    body = reg_body, 

-    httr::add_headers(h), 

-    encode = "json"

-  )

-  

-  content <- httr::content(req,"parsed")

-  if(req$status_code != 200) {

-    stop(content)

-  } else {

-    GMQL_remote <- list(

-      "remote_url" = url, 

-      "authToken" = content$authToken,

-      "username" = username,

-      "password" = psw

+    req <- httr::GET(url)

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

+    

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

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

+    reg_body <- list(

+        "firstName" = first_name, 

+        "lastName" = last_name,

+        "username" = username, 

+        "email" = email, 

+        "password" = psw

+    )

+    

+    req <- httr::POST(

+        URL, 

+        body = reg_body, 

+        httr::add_headers(h), 

+        encode = "json"

     )

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

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

-  }

+    

+    content <- httr::content(req,"parsed")

+    if(req$status_code != 200) {

+        stop(content)

+    } else {

+        GMQL_remote <- list(

+            "remote_url" = url, 

+            "authToken" = content$authToken,

+            "username" = username,

+            "password" = psw

+        )

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

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

+    }

 }

@@ -265,17 +269,17 @@ register_gmql <- function(

 #' @export

 #'

 show_queries_list <- function(url) {

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

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

-  authToken = GMQL_credentials$authToken

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

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

-  content <- httr::content(req,"parsed")

-  if(req$status_code == 200) {

-    return(content)

-  } else {

-    stop(content$error)

-  }

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

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

+    authToken = GMQL_credentials$authToken

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

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

+    content <- httr::content(req,"parsed")

+    if(req$status_code == 200) {

+        return(content)

+    } else {

+        stop(content$error)

+    }

 }

 #' Save GMQL query

@@ -323,24 +327,24 @@ show_queries_list <- function(url) {

 #' @export

 #'

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

-  req <- httr::GET(url)

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

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

-  authToken = GMQL_credentials$authToken

-  h <- c(

-    'Accept' = 'text/plain',

-    'X-Auth-Token' = authToken,

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

-  )

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

-  content <- httr::content(req)

-  

-  if(req$status_code == 200) {

-    # print Saved

-    print(content) 

-  } else {

-    stop(content$error)

-  }

+    req <- httr::GET(url)

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

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

+    authToken = GMQL_credentials$authToken

+    h <- c(

+        'Accept' = 'text/plain',

+        'X-Auth-Token' = authToken,

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

+    )

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

+    content <- httr::content(req)

+    

+    if(req$status_code == 200) {

+        # print Saved

+        print(content) 

+    } else {

+        stop(content$error)

+    }

 }

 #' @param filePath string local file path of a txt file containing a GMQL query

@@ -350,12 +354,12 @@ save_query <- function(url, queryName, queryTxt) {

 #' @export

 #' 

 save_query_fromfile <- function(url, queryName, filePath) {

-  if(!file.exists(filePath)) {

-    stop("file does not exist")

-  }

-  

-  queryTxt <- readLines(filePath)

-  save_query(url,queryName,queryTxt)

+    if(!file.exists(filePath)) {

+        stop("file does not exist")

+    }

+    

+    queryTxt <- readLines(filePath)

+    save_query(url,queryName,queryTxt)

 }

 #############################

@@ -415,28 +419,28 @@ save_query_fromfile <- function(url, queryName, filePath) {

 #' @export

 #'

 run_query <- function(url, queryName, query, output_gtf = TRUE) {

-  if(output_gtf)

-    out <- "GTF"

-  else

-    out <- "TAB"

-  

-  req <- httr::GET(url)

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

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

-  authToken = GMQL_credentials$authToken

-  h <- c(

-    'Accept' = "Application/json",

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

-    'X-Auth-Token' = authToken

-  )

-  

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

-  content <- httr::content(req,"parsed")

-  if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    return(content)

-  }

+    if(output_gtf)

+        out <- "GTF"

+    else

+        out <- "TAB"

+    

+    req <- httr::GET(url)

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

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

+    authToken = GMQL_credentials$authToken

+    h <- c(

+        'Accept' = "Application/json",

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

+        'X-Auth-Token' = authToken

+    )

+    

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

+    content <- httr::content(req,"parsed")

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        return(content)

+    }

 }

 #' @import httr

@@ -447,13 +451,13 @@ run_query <- function(url, queryName, query, output_gtf = TRUE) {

 #' @export

 #' 

 run_query_fromfile <- function(url, filePath, output_gtf = TRUE) {

-  if (!file.exists(filePath)) {

-    stop("file does not exist")

-  }

-  

-  query <- readLines(filePath)

-  queryName <- sub('\\..*$', '', basename(filePath))

-  run_query(url, queryName, query, output_gtf)

+    if (!file.exists(filePath)) {

+        stop("file does not exist")

+    }

+    

+    query <- readLines(filePath)

+    queryName <- sub('\\..*$', '', basename(filePath))

+    run_query(url, queryName, query, output_gtf)

 }

 #' Compile GMQL query

@@ -501,27 +505,27 @@ run_query_fromfile <- function(url, filePath, output_gtf = TRUE) {

 #' @export

 #'

 compile_query <- function(url, query) {

-  authToken = GMQL_credentials$authToken

-  h <- c(

-    'Accept' = "Application/json",

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

-    'X-Auth-Token' = authToken

-  )

-  req <- httr::GET(url)

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

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

-  req <- httr::POST(

-    URL, 

-    body = query ,

-    httr::add_headers(h), 

-    encode = "json"

-  )

-  content <- httr::content(req, "parsed")

-  if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    return(content)

-  }

+    authToken = GMQL_credentials$authToken

+    h <- c(

+        'Accept' = "Application/json",

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

+        'X-Auth-Token' = authToken

+    )

+    req <- httr::GET(url)

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

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

+    req <- httr::POST(

+        URL, 

+        body = query ,

+        httr::add_headers(h), 

+        encode = "json"

+    )

+    content <- httr::content(req, "parsed")

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        return(content)

+    }

 }

 #' @name compile_query

@@ -529,12 +533,12 @@ compile_query <- function(url, query) {

 #' @export

 #'

 compile_query_fromfile <- function(url ,filePath) {

-  if (!file.exists(filePath)) {

-    stop("file does not exist")

-  }

-  

-  query <- readLines(filePath)

-  compile_query(url, query)

+    if (!file.exists(filePath)) {

+        stop("file does not exist")

+    }

+    

+    query <- readLines(filePath)

+    compile_query(url, query)

 }

 #' Stop a job

@@ -574,17 +578,17 @@ compile_query_fromfile <- function(url ,filePath) {

 #' @export

 #'

 stop_job <- function(url, job_id) {

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

-  URL <- paste0(url, "/jobs/", job_id, "/stop")

-  authToken = GMQL_credentials$authToken

-  h <- c('X-Auth-Token' = authToken, 'Accept' = 'text/plain')

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

-  content <- httr::content(req, "parsed")

-  if (req$status_code != 200) {

-    stop(content)

-  } else {

-    print(content)

-  }

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

+    URL <- paste0(url, "/jobs/", job_id, "/stop")

+    authToken = GMQL_credentials$authToken

+    h <- c('X-Auth-Token' = authToken, 'Accept' = 'text/plain')

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

+    content <- httr::content(req, "parsed")

+    if (req$status_code != 200) {

+        stop(content)

+    } else {

+        print(content)

+    }

 }

 #' Show a job log or trace

@@ -626,18 +630,18 @@ stop_job <- function(url, job_id) {

 #' @export

 #'

 show_job_log <- function(url, job_id) {

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

-  URL <- paste0(url, "/jobs/", job_id, "/log")

-  authToken = GMQL_credentials$authToken

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

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

-  content <- httr::content(req, "parsed")

-  

-  if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    print(unlist(content, use.names = FALSE))

-  }

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

+    URL <- paste0(url, "/jobs/", job_id, "/log")

+    authToken = GMQL_credentials$authToken

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

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

+    content <- httr::content(req, "parsed")

+    

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        print(unlist(content, use.names = FALSE))

+    }

 }

@@ -649,18 +653,18 @@ show_job_log <- function(url, job_id) {

 #' @export

 #'

 trace_job <- function(url, job_id) {

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

-  URL <- paste0(url, "/jobs/", job_id, "/trace")

-  authToken = GMQL_credentials$authToken

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

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

-  content <- httr::content(req, "parsed")

- 

-   if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    return(content)

-  }

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

+    URL <- paste0(url, "/jobs/", job_id, "/trace")

+    authToken = GMQL_credentials$authToken

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

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

+    content <- httr::content(req, "parsed")

+    

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        return(content)

+    }

 }

 #' Show all jobs

@@ -694,18 +698,18 @@ trace_job <- function(url, job_id) {

 #' @export

 #' 

 show_jobs_list <- function(url) {

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

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

-  authToken = GMQL_credentials$authToken

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

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

-  content <- httr::content(req, "parsed")

-  

-  if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    return(content)

-  }

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

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

+    authToken = GMQL_credentials$authToken

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

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

+    content <- httr::content(req, "parsed")

+    

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        return(content)

+    }

 }

 #############################

@@ -746,18 +750,18 @@ show_jobs_list <- function(url) {

 #' @export

 #'

 show_datasets_list <- function(url) {

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

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

-  authToken = GMQL_credentials$authToken

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

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

-  content <- httr::content(req, "parsed") #JSON

-  

-  if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    return(content)

-  }

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

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

+    authToken = GMQL_credentials$authToken

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

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

+    content <- httr::content(req, "parsed") #JSON

+    

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        return(content)

+    }

 }

@@ -801,18 +805,18 @@ show_datasets_list <- function(url) {

 #' @rdname show_samples_list

 #' @export

 show_samples_list <- function(url, datasetName) {

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

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

-  authToken = GMQL_credentials$authToken

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

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

-  content <- httr::content(req, "parsed")

-  

-  if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    return(content)

-  }

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

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

+    authToken = GMQL_credentials$authToken

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

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

+    content <- httr::content(req, "parsed")

+    

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        return(content)

+    }

 }

 #' Show dataset schema

@@ -852,18 +856,18 @@ show_samples_list <- function(url, datasetName) {

 #' @export

 #'

 show_schema <- function(url, datasetName) {

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

-  URL <- paste0(url, "/datasets/", datasetName, "/schema")

-  authToken = GMQL_credentials$authToken

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

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

-  content <- httr::content(req, "parsed")

-  

-  if (req$status_code != 200) {

-    stop(content$error)

-  } else {

-    return(content)

-  }

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

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

+    authToken = GMQL_credentials$authToken

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

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

+    content <- httr::content(req, "parsed")

+    

+    if (req$status_code != 200) {

+        stop(content$error)

+    } else {

+        return(content)

+    }

 }

 #' Upload dataset

@@ -938,76 +942,75 @@ show_schema <- function(url, datasetName) {

 #' @export

 #'

 upload_dataset <- function(

-  url,

-  datasetName,

-  folderPath,

-  schemaName = NULL

+    url,

+    datasetName,

+    folderPath,

+    schemaName = NULL

 ) {

-  

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

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

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

-  

-  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)

-  })

-  

-  list_files_names <- vapply(list_files, function(x) {

-    paste0("file", count())

-  }, character(1))

-  

-  names(list_files) <- list_files_names

-  req <- httr::GET(url)

-  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')

-  

-  schema_name <- tolower(schemaName)

-  

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

-    schema <- .retrieve_schema(folderPath)

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

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

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

-    list_files <- list(

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

-      list_files

-    )

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

+    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)

+    })

+    

+    list_files_names <- vapply(list_files, function(x) {

+        paste0("file", count())

+    }, character(1))

+    

+    names(list_files) <- list_files_names

+    req <- httr::GET(url)

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

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

-  } else {

-    schemaList <- c(

-      "narrowpeak",

-      "vcf",

-      "broadpeak",

-      "bed",

-      "bedgraph"

-    )

-    if (!schema_name %in% schemaList) {

-      stop("schema not admissable")

+    authToken = GMQL_credentials$authToken

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

+    

+    schema_name <- tolower(schemaName)

+    

+    if (is.null(schemaName) || 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",