Browse code

fix some check warning

Simone authored on 17/10/2017 12:25:52
Showing 9 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: 0.99.4
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+Version: 0.99.5
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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 GMQL functionalities into R environemnt.
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@@ -22,7 +22,7 @@ Encoding: UTF-8
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 LazyData: true
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 RoxygenNote: 6.0.1
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 Imports: httr, rJava,GenomicRanges, rtracklayer, data.table, utils, plyr, xml2, methods, S4Vectors, dplyr, stats
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-Depends: R(>= 3.3.3)
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+Depends: R(>= 3.4.0)
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 VignetteBuilder: knitr
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 Suggests: BiocStyle, knitr, rmarkdown
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 biocViews: Software,Infrastructure,DataImport
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@@ -26,8 +26,10 @@
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 #'
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 importGMQL.gtf <- function(datasetName)
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 {
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-  datasetName <- paste0(datasetName,"/files")
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-
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+  datasetName <- sub("/*[/]$","",datasetName)
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+  if(basename(datasetName) !="files")
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+    datasetName <- paste0(datasetName,"/files")
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+  
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   if(!dir.exists(datasetName))
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     stop("Directory does not exists")
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@@ -86,7 +88,9 @@ importGMQL.gtf <- function(datasetName)
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 #'
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 importGMQL.gdm <- function(datasetName)
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 {
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-  datasetName <- paste0(datasetName,"/files")
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+  datasetName <- sub("/*[/]$","",datasetName)
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+  if(basename(datasetName) !="files")
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+    datasetName <- paste0(datasetName,"/files")
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   if(!dir.exists(datasetName))
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     stop("Directory does not exists")
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@@ -154,6 +154,9 @@ readDataset <- function(dataset, parser = "CustomParser", is_local=TRUE,
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 #'
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 #'
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 #' @importFrom S4Vectors metadata
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+#' @importFrom rJava J
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+#' @importFrom rJava .jarray
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+#' 
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 #' @param samples GrangesList
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 #' 
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 #'
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@@ -171,9 +174,14 @@ read <- function(samples)
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     stop("only GrangesList")
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   meta <- S4Vectors::metadata(samples)
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-  if(is.null(meta)) {
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+  if(is.null(meta) || length(meta)==0) {
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+    #repeat meta for each sample in samples list
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+    len <- length(samples)
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     warning("GrangesList has no metadata. we provide two metadata for you")
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-    meta_matrix <- matrix(c("Provider","Polimi", "Application", "R-GMQL"),ncol = 2,byrow = TRUE)
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+    index_meta <- rep(1:len,each = len)
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+    rep_meta <- rep(c("Provider","Polimi", "Application", "R-GMQL"),times=len)
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+    meta_matrix <- matrix(rep_meta,ncol = 2,byrow = TRUE)
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+    meta_matrix <- cbind(index_meta,meta_matrix)
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   }
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   else {
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     unlist_meta <- unlist(meta)
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@@ -185,7 +193,8 @@ read <- function(samples)
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   df <- data.frame(samples)
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   df <- df[-2] #delete group_name
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   region_matrix <- as.matrix(sapply(df, as.character))
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-  region_matrix<- region_matrix[,setdiff(colnames(region_matrix),"width")]
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+  region_matrix[is.na(region_matrix)] <- "NA"
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+  region_matrix <- region_matrix[,setdiff(colnames(region_matrix),"width")]
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   col_types <- sapply(df,class)
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   col_names <- names(col_types)
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   #re order the schema?
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@@ -203,6 +212,12 @@ read <- function(samples)
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   }
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   rownames(schema_matrix) <- NULL
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   colnames(schema_matrix) <- NULL
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+  
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+  schema_matrix <- .jarray(schema_matrix,dispatch = TRUE)
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+  meta_matrix <- .jarray(meta_matrix,dispatch = TRUE)
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+  region_matrix <- .jarray(region_matrix,dispatch = TRUE)
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+  
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+
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   WrappeR <- J("it/polimi/genomics/r/Wrapper")
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   response <- WrappeR$read(meta_matrix,region_matrix,schema_matrix)
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   DAGgraph(response)
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@@ -233,7 +248,9 @@ read <- function(samples)
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 #' 
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 #' @param is_remote single logical value used in order to set the processing mode.
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 #' TRUE you will set a remote query processing mode otherwise will be local
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-#'
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+#' 
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+#' @return None
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+#' 
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 #' @examples
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 #' 
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 #' # initialize with remote processing off
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@@ -2,8 +2,8 @@
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 #  source("https://bioconductor.org/biocLite.R")
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 #  biocLite("RGMQL")
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-## ---- initialization, eval=FALSE-----------------------------------------
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-#  library('RGMQL')
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+## ---- initialization, eval=TRUE------------------------------------------
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+library('RGMQL')
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 ## ---- init, eval=FALSE---------------------------------------------------
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 #  initGMQL()
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@@ -21,6 +21,7 @@
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 #  data_out = readDataset("dataset_name_on_repo")
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 ## ---- read GRangesList, eval=FALSE---------------------------------------
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+#  library("GenomicRanges")
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 #  gr1 <- GRanges(seqnames = "chr2",
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 #  ranges = IRanges(103, 106),
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 #  strand = "+",
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@@ -62,9 +63,9 @@ library("RGMQL")
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 test_url = "http://130.186.13.219/gmql-rest"
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 login.GMQL(test_url)
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-## ---- eval=FALSE---------------------------------------------------------
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-#  test_url = "http://130.186.13.219/gmql-rest"
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-#  login.GMQL(test_url)
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-#  runQuery(test_url, "query_1", "DATA_SET_VAR = SELECT() HG19_TCGA_dnaseq;
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-#           MATERIALIZE DATA_SET_VAR INTO RESULT_DS;", output_gtf = FALSE)
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+## ---- eval=TRUE----------------------------------------------------------
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+test_url = "http://130.186.13.219/gmql-rest"
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+login.GMQL(test_url)
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+runQuery(test_url, "query_1", "DATA_SET_VAR = SELECT() HG19_TCGA_dnaseq; 
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+         MATERIALIZE DATA_SET_VAR INTO RESULT_DS;", output_gtf = FALSE)
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@@ -84,7 +84,7 @@ managing datasets (both GMQL or generic text plain dataset).
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 ### Initialization
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 Load and attach the GMQL package in an R session using library function:
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-```{r, initialization, eval=FALSE}
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+```{r, initialization, eval=TRUE}
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 library('RGMQL')
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 ```
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 Before starting using any GMQL operation we need to initialise the GMQL context 
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@@ -128,6 +128,7 @@ There is no need to explicitally download data since execution will trigger down
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 Also, for better integration in R environment and with other packages, we provide a function
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 to read from GrangesList, for example:
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 ```{r, read GRangesList, eval=FALSE}
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+library("GenomicRanges")
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 gr1 <- GRanges(seqnames = "chr2",
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 ranges = IRanges(103, 106),
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 strand = "+",
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@@ -223,7 +224,7 @@ wit this token you can call all the funciton in web services suite.
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 #### Execution
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 User can write the query as in the following example, as the second parameter of *runQuery*.
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-```{r, eval=FALSE}
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+```{r, eval=TRUE}
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 test_url = "http://130.186.13.219/gmql-rest"
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 login.GMQL(test_url)
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 runQuery(test_url, "query_1", "DATA_SET_VAR = SELECT() HG19_TCGA_dnaseq; 
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Binary files a/inst/doc/my-vignette.pdf and b/inst/doc/my-vignette.pdf differ
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Binary files a/inst/java/GMQL.jar and b/inst/java/GMQL.jar differ
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@@ -10,6 +10,9 @@ remote_processing(is_remote)
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 \item{is_remote}{single logical value used in order to set the processing mode.
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 TRUE you will set a remote query processing mode otherwise will be local}
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 }
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+\value{
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+None
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+}
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 \description{
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 It allows to enable or disable remote processing
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 }
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@@ -84,7 +84,7 @@ managing datasets (both GMQL or generic text plain dataset).
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 ### Initialization
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 Load and attach the GMQL package in an R session using library function:
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-```{r, initialization, eval=FALSE}
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+```{r, initialization, eval=TRUE}
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 library('RGMQL')
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 ```
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 Before starting using any GMQL operation we need to initialise the GMQL context 
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@@ -127,7 +127,8 @@ There is no need to explicitally download data since execution will trigger down
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 4. GrangesList:\newline
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 Also, for better integration in R environment and with other packages, we provide a function
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 to read from GrangesList, for example:
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-```{r, read GRangesList, eval=FALSE}
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+```{r, read GRangesList, eval=TRUE}
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+library("GenomicRanges")
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 gr1 <- GRanges(seqnames = "chr2",
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 ranges = IRanges(103, 106),
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 strand = "+",
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@@ -223,7 +224,7 @@ wit this token you can call all the funciton in web services suite.
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 #### Execution
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 User can write the query as in the following example, as the second parameter of *runQuery*.
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-```{r, eval=FALSE}
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+```{r, eval=TRUE}
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 test_url = "http://130.186.13.219/gmql-rest"
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 login.GMQL(test_url)
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 runQuery(test_url, "query_1", "DATA_SET_VAR = SELECT() HG19_TCGA_dnaseq;