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

 Package: RGMQL

 Type: Package

 Title: GenoMetric Query Language for R/Bioconductor

-Version: 0.99.22

+Version: 0.99.23

 Author: Simone Pallotta, Marco Masseroli

 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>

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

@@ -55,7 +55,7 @@ LazyData: true

 RoxygenNote: 6.0.1

 Imports: httr, rJava,GenomicRanges, rtracklayer, data.table, utils, plyr, xml2, 

     methods, S4Vectors, dplyr, stats

-Depends: R(<= 3.4.2)

+Depends: R(>= 3.4.2)

 VignetteBuilder: knitr

 Suggests: BiocStyle, knitr, rmarkdown

 biocViews: Software,Infrastructure,DataImport,Network

@@ -53,7 +53,6 @@ export(order)

 export(project)

 export(read)

 export(read_dataset)

-export(register_gmql)

 export(remote_processing)

 export(run_query)

 export(run_query_fromfile)

@@ -114,8 +114,8 @@ init_gmql <- function(output_format = "gtf", remote_processing = FALSE,

 #' r = read_dataset(test_path,"ANNParser")

 #' 

 #' ## read remote public dataset stored into GMQL system repository 

-#' init_gmql()

-#' r = read_dataset("public.HG19_TCGA_dnaseq",is_local = FALSE)

+#' 

+#' r2 = read_dataset("public.HG19_TCGA_dnaseq",is_local = FALSE)

 #' 

 #' }

 #' 

@@ -18,7 +18,7 @@ if(getRversion() >= "3.1.0")

 #' @param username string name used during signup

 #' @param password string password used during signup

 #'

-#' @seealso  \code{\link{register_gmql}} \code{\link{logout_gmql}}

+#' @seealso \code{\link{logout_gmql}}

 #'

 #' @details

 #' if both username and password are NULL you will be logged as guest

@@ -84,7 +84,7 @@ login_gmql <- function(url, username = NULL, password = NULL)

 #' @param url string url of server: It must contain the server address 

 #' and base url; service name is added automatically

 #'

-#' @seealso \code{\link{register_gmql}} \code{\link{login_gmql}}

+#' @seealso \code{\link{login_gmql}}

 #'

 #' @details

 #' After logout the authentication token will be invalidated.

@@ -120,65 +120,5 @@ logout_gmql <- function(url)

     }

 }

-#' Sign up to GMQL

-#'

-#' Sign up to GMQL REST services suite

-#' using the proper GMQL web service available on a remote server

-#'

-#' @import httr

-#'

-#' @param url string url of server: It must contain the server address 

-#' and base url; service name will be added automatically

-#' @param name string name of the user (can contain space)

-#' @param lastname string last name of the user (can contain space)

-#' @param mail string email (as spacified in RFC format)

-#' @param username string name you want to authenticate with

-#' @param password string password you want to authenticate with

-#'

-#' @seealso \code{\link{login_gmql}} \code{\link{logout_gmql}}

-#'

-#' @details

-#' After registration you receive an authentication token, 

-#' (i.e you are logged in after sing up, no need to subsequent 

-#' calling of login function)

-#' As token remains vaild on server (until the next login / registration) 

-#' a user can safely use a token for a previous session as a convenience, 

-#' this token is saved in Global environment to perform subsequent REST call 

-#' even on complete R restart (if is environemnt has been saved, of course ...)

-#' If error occures a specific error is printed

-#'

-#' @return None

-#'

-#' @examples

-#' 

-#' ### this user already exist, it's a test account, don't use it!!!

-#' 

-#' remote_url = "http://130.186.13.219/gmql-rest"

-#' register_gmql(remote_url, "jonh", "Doe", "jonh@doe.com", "JD", "JD46")

-#'

-#' @export

-#'

-register_gmql <- function(url, name, lastname, mail, username, password)

-{

-    info <- list('firstName'=name,

-                    'lastName'=lastname,

-                    'username'=username,

-                    'email'=mail,

-                    'password'=password)

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

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

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

-

-    content <- httr::content(req)

-

-    if(req$status_code !=200)

-        stop(content)

-    else

-    {

-        assign("authToken",content$authToken,.GlobalEnv)

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

-    }

-}

-

@@ -72,7 +72,7 @@ show_datasets_list <- function(url)

 #'

 #' remote_url <- "http://130.186.13.219/gmql-rest"

 #' login_gmql(remote_url)

-#' list <- show_samples_list(remote_url, "public.GRCh38_ENCODE_BROAD_MAY_2017")

+#' list <- show_samples_list(remote_url, "public.HG19_BED_ANNOTATION")

 #'

 #' @export

 #'

@@ -118,7 +118,7 @@ show_samples_list <- function(url,datasetName)

 #' ### show schema of public dataset

 #' remote_url <- "http://130.186.13.219/gmql-rest"

 #' login_gmql(remote_url)

-#' list <- show_schema(remote_url, "public.GRCh38_ENCODE_BROAD_MAY_2017")

+#' list <- show_schema(remote_url, "public.HG19_BED_ANNOTATION")

 #'

 #' @export

 #'

@@ -39,5 +39,5 @@ login_gmql(remote_url)

 }

 \seealso{

-\code{\link{register_gmql}} \code{\link{logout_gmql}}

+\code{\link{logout_gmql}}

 }

@@ -31,5 +31,5 @@ logout_gmql(remote_url)

 }

 \seealso{

-\code{\link{register_gmql}} \code{\link{login_gmql}}

+\code{\link{login_gmql}}

 }

@@ -58,8 +58,8 @@ test_path <- system.file("example", "DATASET", package = "RGMQL")

 r = read_dataset(test_path,"ANNParser")

 ## read remote public dataset stored into GMQL system repository 

-init_gmql()

-r = read_dataset("public.HG19_TCGA_dnaseq",is_local = FALSE)

+

+r2 = read_dataset("public.HG19_TCGA_dnaseq",is_local = FALSE)

 }

deleted file mode 100644

@@ -1,50 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/authOp.R

-\name{register_gmql}

-\alias{register_gmql}

-\title{Sign up to GMQL}

-\usage{

-register_gmql(url, name, lastname, mail, username, password)

-}

-\arguments{

-\item{url}{string url of server: It must contain the server address 

-and base url; service name will be added automatically}

-

-\item{name}{string name of the user (can contain space)}

-

-\item{lastname}{string last name of the user (can contain space)}

-

-\item{mail}{string email (as spacified in RFC format)}

-

-\item{username}{string name you want to authenticate with}

-

-\item{password}{string password you want to authenticate with}

-}

-\value{

-None

-}

-\description{

-Sign up to GMQL REST services suite

-using the proper GMQL web service available on a remote server

-}

-\details{

-After registration you receive an authentication token, 

-(i.e you are logged in after sing up, no need to subsequent 

-calling of login function)

-As token remains vaild on server (until the next login / registration) 

-a user can safely use a token for a previous session as a convenience, 

-this token is saved in Global environment to perform subsequent REST call 

-even on complete R restart (if is environemnt has been saved, of course ...)

-If error occures a specific error is printed

-}

-\examples{

-

-### this user already exist, it's a test account, don't use it!!!

-

-remote_url = "http://130.186.13.219/gmql-rest"

-register_gmql(remote_url, "jonh", "Doe", "jonh@doe.com", "JD", "JD46")

-

-}

-\seealso{

-\code{\link{login_gmql}} \code{\link{logout_gmql}}

-}

@@ -35,6 +35,6 @@ If error occures a specific error is printed

 remote_url <- "http://130.186.13.219/gmql-rest"

 login_gmql(remote_url)

-list <- show_samples_list(remote_url, "public.GRCh38_ENCODE_BROAD_MAY_2017")

+list <- show_samples_list(remote_url, "public.HG19_BED_ANNOTATION")

 }

@@ -35,6 +35,6 @@ If error occures a specific error is printed

 ### show schema of public dataset

 remote_url <- "http://130.186.13.219/gmql-rest"

 login_gmql(remote_url)

-list <- show_schema(remote_url, "public.GRCh38_ENCODE_BROAD_MAY_2017")

+list <- show_schema(remote_url, "public.HG19_BED_ANNOTATION")

 }