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

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

 Encoding: UTF-8

 LazyData: true

-RoxygenNote: 6.1.1

+RoxygenNote: 7.1.1

 Imports:

     httr,

     rJava,

@@ -1,6 +1,5 @@

-.counter <- function(zero = 0)

-{

+.counter <- function(zero = 0) {

     i <- zero

     function() {

         i <<- i + 1

@@ -8,16 +7,14 @@

     }

 }

-.add_metadata <- function(files)

-{

+.add_metadata <- function(files) {

     x <- scan(files, what="", sep="\n")

     y <- strsplit(x, "\t")

     names(y) <- vapply(y, `[[`,character(1), 1)

     listMeta <- lapply(y, `[`, -1)

 }

-.schema_header <- function(datasetName)

-{

+.schema_header <- function(datasetName) {

     schema_name <- list.files(datasetName, pattern = "*.schema$",

                                 full.names = TRUE)

@@ -36,8 +33,7 @@

     vector_field <- unlist(list_field)

 }

-.schema_type_coordinate <- function(datasetName)

-{

+.schema_type_coordinate <- function(datasetName) {

     schema_name <- list.files(datasetName, pattern = "*.schema$",

                               full.names = TRUE)

@@ -58,8 +54,7 @@

 }

 # aggregates factory

-.aggregates <- function(meta_data,class)

-{

+.aggregates <- function(meta_data,class) {

     if(!is.list(meta_data))

         stop("meta_data: invalid input")

@@ -88,8 +83,7 @@

 # meta join condition

-.join_condition <- function(cond)

-{

+.join_condition <- function(cond) {

     cond_matrix <- NULL

     def <- cond$condition$def

     if(!is.null(def))

@@ -105,8 +99,7 @@

     cond_matrix

 }

-.check_input <- function(value)

-{

+.check_input <- function(value) {

     if(!is.character(value))

         stop("no valid data")

@@ -114,8 +107,7 @@

         stop("no multiple string")

 }

-.check_logical <- function(value)

-{

+.check_logical <- function(value) {

     if(!is.logical(value))

         stop("no valid data")

@@ -123,18 +115,15 @@

         stop("no multiple string")

 }

-.is_login_expired <- function(url)

-{

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

-    {

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

-        {

+.is_login_expired <- function(url) {

+    if(exists("GMQL_credentials", envir = .GlobalEnv)) {

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

             authToken <- GMQL_credentials$authToken

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

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

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

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

-            if(req$status_code !=200)

+            if(req$status_code != 200)

                 return(TRUE)

             else

                 return(FALSE)

@@ -142,5 +131,3 @@

     }

     return(TRUE)

 }

-

-

@@ -31,23 +31,20 @@

 #' @aliases condition_evaluation

 #' @rdname condition_eval_func

 #' @export

-conds <- function(default = c(""), full = c(""), exact = c(""))

-{

+conds <- function(default = c(""), full = c(""), exact = c("")) {

     df <- .condition("DEF",default)

     fn <- .condition("FULL",full)

     ex <- .condition("EXACT",exact)

     list("condition" = list("def" = df, "full" = fn, "exact" = ex))

 }

-.condition <- function(cond, array)

-{

+.condition <- function(cond, array) {

     array = array[!array %in% ""]

     array = array[!duplicated(array)]

     if(!length(array))

         join_condition_matrix <- NULL

-    else

-    {

+    else {

         join_condition_matrix <- t(vapply(array, function(x) {

             new_value = c(cond, x)

             matrix <- matrix(new_value)

@@ -55,5 +52,3 @@ conds <- function(default = c(""), full = c(""), exact = c(""))

     }

     join_condition_matrix

 }

-

-

@@ -43,10 +43,8 @@ execute <- function()

     val <- response[2]

     if(error)

         stop(val)

-    else

-    {

-        if(remote_proc)

-        {

+    else {

+        if(remote_proc) {

             isGTF <- FALSE

             outformat <- WrappeR$outputMaterialize()

             if(identical(outformat, "gtf"))

@@ -59,29 +57,24 @@ execute <- function()

     }

 }

-.download_or_upload <- function()

-{

+.download_or_upload <- function() {

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

     datasets <- .jevalArray(WrappeR$get_dataset_list(),simplify = TRUE)

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

     url <- WrappeR$get_url()

     remote <- WrappeR$is_remote_processing()

-    if(remote)

-    {

+    if(remote) {

         lapply(data_list,function(x){

             if(!is.null(x[[1]]) && !is.na(x[[1]]))

                 upload_dataset(url,x[[2]],x[[1]],x[[3]],FALSE)})

-    }

-    else

-    {

+    } else {

         lapply(data_list,function(x){

             if(!is.null(x[[2]]) && !is.na(x[[2]]))

                 download_dataset(url,x[[2]],x[[1]])})

     }

 }

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

-{

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

     ptr_data <- value(x)

     gmql_materialize(ptr_data, dir_out, name)

 }

@@ -137,12 +130,10 @@ collect.GMQLDataset <- function(x, dir_out = getwd(), name = "ds1")

 #' @export

 setMethod("collect", "GMQLDataset",collect.GMQLDataset)

-gmql_materialize <- function(input_data, dir_out, name)

-{

+gmql_materialize <- function(input_data, dir_out, name) {

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

     remote_proc <- WrappeR$is_remote_processing()

-    if(!remote_proc)

-    {

+    if(!remote_proc) {

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

         res_dir_out <- file.path(dir_out,name)

         if(!dir.exists(res_dir_out))

@@ -226,8 +217,7 @@ setMethod("take", "GMQLDataset",

                 gmql_take(ptr_data, rows)

             })

-gmql_take <- function(input_data, rows)

-{

+gmql_take <- function(input_data, rows) {

     rows <- as.integer(rows[1])

     if(rows<0)

         stop("rows cannot be negative")

@@ -259,9 +249,11 @@ gmql_take <- function(input_data, rows)

     sampleList <- lapply(list, function(x){

         x <- x[-1]

         names(x) <- seq_name

-        start_numeric = as.numeric(levels(x$start))[x$start]

+    #    start_numeric = as.numeric(levels(x$start))[x$start]

+        start_numeric = as.numeric(x$start)

         start_numeric = start_numeric + 1

-        levels(x$start)[x$start] = start_numeric

+        x$start =  start_numeric

+        #levels(x$start)[x$start] = start_numeric

         g <- GenomicRanges::makeGRangesFromDataFrame(x,

                                     keep.extra.columns = TRUE,

                                     start.field = "start",

@@ -277,8 +269,7 @@ gmql_take <- function(input_data, rows)

     return(gRange_list)

 }

-.metadata_from_frame_to_list <- function(metadata_frame)

-{

+.metadata_from_frame_to_list <- function(metadata_frame) {

     meta_frame <- as.data.frame(metadata_frame)

     list <- split(meta_frame, meta_frame[1])

     name_value_list <- lapply(list, function(x){x <- x[-1]})

@@ -96,7 +96,7 @@ read_gmql <- function(dataset, parser = "CustomParser", is_local = TRUE,

         if(!length(schema_SCHEMA))

             schema_XML <- xml_schema

         else

-            schema_XML <- schema_SCHEMA

+            schema_XML <- dataset

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

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

similarity index 100%

rename from inst/example/DATASET/files/dataset.schema

rename to inst/example/DATASET/files/test.schema

@@ -1,9 +1,9 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_merge.R

-\docType{methods}

 \name{aggregate}

 \alias{aggregate}

 \alias{aggregate,GMQLDataset-method}

+\alias{aggregate-method}

 \title{Method aggregate}

 \usage{

 \S4method{aggregate}{GMQLDataset}(x, groupBy = conds())

@@ -1,14 +1,20 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_order.R

-\docType{methods}

 \name{arrange}

 \alias{arrange}

 \alias{arrange,GMQLDataset-method}

+\alias{arrange-method}

 \title{Method arrange}

 \usage{

-\S4method{arrange}{GMQLDataset}(.data, metadata_ordering = NULL,

-  regions_ordering = NULL, fetch_opt = "", num_fetch = 0L,

-  reg_fetch_opt = "", reg_num_fetch = 0L)

+\S4method{arrange}{GMQLDataset}(

+  .data,

+  metadata_ordering = NULL,

+  regions_ordering = NULL,

+  fetch_opt = "",

+  num_fetch = 0L,

+  reg_fetch_opt = "",

+  reg_num_fetch = 0L

+)

 }

 \arguments{

 \item{.data}{GMQLDataset class object}

@@ -1,9 +1,9 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_materialize.R

-\docType{methods}

 \name{collect}

 \alias{collect}

 \alias{collect,GMQLDataset-method}

+\alias{collect-method}

 \title{Method collect}

 \usage{

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

@@ -1,15 +1,14 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/AllGenerics.R, R/gmql_cover.R

-\docType{methods}

 \name{cover}

 \alias{cover}

 \alias{cover,GMQLDataset-method}

+\alias{cover-method}

 \title{Method cover}

 \usage{

 cover(.data, ...)

-\S4method{cover}{GMQLDataset}(.data, min_acc, max_acc, groupBy = conds(),

-  variation = "cover", ...)

+\S4method{cover}{GMQLDataset}(.data, min_acc, max_acc, groupBy = conds(), variation = "cover", ...)

 }

 \arguments{

 \item{.data}{GMQLDataset class object}

@@ -1,6 +1,5 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/AllGenerics.R, R/gmql_extend.R

-\docType{methods}

 \name{extend}

 \alias{extend}

 \alias{extend,GMQLDataset-method}

@@ -1,13 +1,12 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_select.R

-\docType{methods}

 \name{filter}

 \alias{filter}

 \alias{filter,GMQLDataset-method}

+\alias{filter-method}

 \title{Method filter}

 \usage{

-\S4method{filter}{GMQLDataset}(.data, m_predicate = NULL,

-  r_predicate = NULL, semijoin = NULL)

+\S4method{filter}{GMQLDataset}(.data, m_predicate = NULL, r_predicate = NULL, semijoin = NULL)

 }

 \arguments{

 \item{.data}{GMQLDataset class object}

@@ -4,8 +4,13 @@

 \alias{filter_and_extract}

 \title{Filter and extract function}

 \usage{

-filter_and_extract(data, metadata = NULL, metadata_prefix = NULL,

-  region_attributes = NULL, suffix = "antibody_target")

+filter_and_extract(

+  data,

+  metadata = NULL,

+  metadata_prefix = NULL,

+  region_attributes = NULL,

+  suffix = "antibody_target"

+)

 }

 \arguments{

 \item{data}{string GMQL dataset folder path or GRangesList

@@ -1,14 +1,18 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_group.R

-\docType{methods}

 \name{group_by}

 \alias{group_by}

 \alias{group_by,GMQLDataset-method}

+\alias{group_by-method}

 \title{Method group_by}

 \usage{

-\S4method{group_by}{GMQLDataset}(.data, groupBy_meta = conds(),

-  groupBy_regions = c(""), region_aggregates = NULL,

-  meta_aggregates = NULL)

+\S4method{group_by}{GMQLDataset}(

+  .data,

+  groupBy_meta = conds(),

+  groupBy_regions = c(""),

+  region_aggregates = NULL,

+  meta_aggregates = NULL

+)

 }

 \arguments{

 \item{.data}{GMQLDataset object}

@@ -4,8 +4,13 @@

 \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 

@@ -1,6 +1,5 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/AllGenerics.R, R/gmql_map.R

-\docType{methods}

 \name{map}

 \alias{map}

 \alias{map,GMQLDataset-method}

@@ -9,8 +8,7 @@

 \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}

@@ -1,14 +1,19 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_join.R

-\docType{methods}

 \name{merge}

 \alias{merge}

 \alias{merge,GMQLDataset,GMQLDataset-method}

+\alias{merge-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}

@@ -5,8 +5,7 @@

 \alias{read_GRangesList}

 \title{Function read}

 \usage{

-read_gmql(dataset, parser = "CustomParser", is_local = TRUE,

-  is_GMQL = TRUE)

+read_gmql(dataset, parser = "CustomParser", is_local = TRUE, is_GMQL = TRUE)

 read_GRangesList(samples)

 }

@@ -41,7 +40,7 @@ remote processing.

 }

 \details{

 Normally, a GMQL dataset contains an XML schema file that contains

-name of region attributes. (e.g chr, start, stop, strand)

+name of region attributes. (e.g chr, start, stop, strand)"

 The CustomParser reads this XML schema; 

 if you already know what kind of schema your files have, use one of the 

 parsers defined, without reading any XML schema.

@@ -1,14 +1,20 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_project.R

-\docType{methods}

 \name{select}

 \alias{select}

 \alias{select,GMQLDataset-method}

+\alias{select-method}

 \title{Method select}

 \usage{

-\S4method{select}{GMQLDataset}(.data, metadata = NULL,

-  metadata_update = NULL, all_but_meta = FALSE, regions = NULL,

-  regions_update = NULL, all_but_reg = FALSE)

+\S4method{select}{GMQLDataset}(

+  .data,

+  metadata = NULL,

+  metadata_update = NULL,

+  all_but_meta = FALSE,

+  regions = NULL,

+  regions_update = NULL,

+  all_but_reg = FALSE

+)

 }

 \arguments{

 \item{.data}{GMQLDataset class object}

@@ -1,13 +1,12 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_difference.R

-\docType{methods}

 \name{setdiff}

 \alias{setdiff}

 \alias{setdiff,GMQLDataset,GMQLDataset-method}

+\alias{setdiff-method}

 \title{Method setdiff}

 \usage{

-\S4method{setdiff}{GMQLDataset,GMQLDataset}(x, y, joinBy = conds(),

-  is_exact = FALSE)

+\S4method{setdiff}{GMQLDataset,GMQLDataset}(x, y, joinBy = conds(), is_exact = FALSE)

 }

 \arguments{

 \item{x}{GMQLDataset class object}

@@ -1,6 +1,5 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/AllGenerics.R, R/gmql_materialize.R

-\docType{methods}

 \name{take}

 \alias{take}

 \alias{take,GMQLDataset-method}

@@ -1,9 +1,9 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_union.R

-\docType{methods}

 \name{union}

 \alias{union}

 \alias{union,GMQLDataset,GMQLDataset-method}

+\alias{union-method}

 \title{Method union}

 \usage{

 \S4method{union}{GMQLDataset,GMQLDataset}(x, y)

@@ -4,8 +4,7 @@

 \alias{upload_dataset}

 \title{Upload dataset}

 \usage{

-upload_dataset(url, datasetName, folderPath, schemaName = NULL,

-  isGMQL = TRUE)

+upload_dataset(url, datasetName, folderPath, schemaName = NULL, isGMQL = TRUE)

 }

 \arguments{

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