@@ -49,6 +49,21 @@ generated:

 \item{"provider" = "PoliMi"}

 \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{

@@ -74,4 +89,5 @@ remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

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

+

 }

old mode 100644

new mode 100755

@@ -5,7 +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)

 read_GRangesList(samples)

 }

@@ -24,8 +24,6 @@ Default is CustomParser.}

 \item{is_local}{logical value indicating local or remote dataset}

-\item{is_GMQL}{logical value indicating GMQL dataset or not}

-

 \item{samples}{GRangesList}

 }

 \value{

@@ -40,7 +38,7 @@ 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.

@@ -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.

@@ -2,7 +2,6 @@

 % Please edit documentation in R/gmql_read.R

 \name{read_gmql}

 \alias{read_gmql}

-\alias{read_gmql}

 \alias{read_GRangesList}

 \title{Function read}

 \usage{

@@ -2,6 +2,7 @@

 % Please edit documentation in R/gmql_read.R

 \name{read_gmql}

 \alias{read_gmql}

+\alias{read_gmql}

 \alias{read_GRangesList}

 \title{Function read}

 \usage{

@@ -2,7 +2,6 @@

 % Please edit documentation in R/gmql_read.R

 \name{read_gmql}

 \alias{read_gmql}

-\alias{read_gmql}

 \alias{read_GRangesList}

 \title{Function read}

 \usage{

@@ -74,7 +73,7 @@ dataPeak = read_gmql(test_path,"NarrowPeakParser")

 ## repository. For a public dataset in a (remote) GMQL repository the 

 ## prefix "public." is needed before dataset name

-remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+remote_url = "http://www.gmql.eu/gmql-rest/"

 login_gmql(remote_url)

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

@@ -60,7 +60,7 @@ generated:

 ## and creation of results on disk. Then, with system.file() it defines 

 ## the path to the folder "DATASET" in the subdirectory "example" 

 ## of the package "RGMQL" and opens such folder as a GMQL dataset 

-## named "data" using customParser

+## named "data" using CustomParser

 init_gmql()

 test_path <- system.file("example", "DATASET", package = "RGMQL")

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

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_read.R

-\name{read_GMQL}

-\alias{read_GMQL}

-\alias{read_GMQL}

+\name{read_gmql}

+\alias{read_gmql}

+\alias{read_gmql}

 \alias{read_GRangesList}

 \title{Function read}

 \usage{

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

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

   is_GMQL = TRUE)

 read_GRangesList(samples)

@@ -14,14 +14,13 @@ read_GRangesList(samples)

 \arguments{

 \item{dataset}{folder path for GMQL dataset or dataset name on repository}

-\item{parser}{string used to parsing dataset files

-The Parser's available are:

+\item{parser}{string used to parsing dataset files.

+The Parsers available are:

 \itemize{

-\item{ANNParser}

-\item{BroadProjParser}

+\item{BedParser}

+\item{BroadPeakParser}

 \item{NarrowPeakParser}

-\item{RnaSeqParser}

-\item{CustomParser.}

+\item{CustomParser}

 }

 Default is CustomParser.}

@@ -36,20 +35,20 @@ GMQLDataset object. It contains the value to use as input

 for the subsequent GMQLDataset method

 }

 \description{

-It reads a GMQL dataset, as a folder containig some homogenus samples on 

-disk or as a GrangesList; it saving in Scala memory in a way that can be 

+It reads a GMQL dataset, as a folder containing some homogenus samples on 

+disk or as a GRangesList, saving it in Scala memory in a way that can be 

 referenced in R. It is also used to read a repository dataset in case of

 remote processing.

 }

 \details{

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

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

 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.

 If GRangesList has no metadata: i.e. metadata() is empty, two metadata are

-generated.

+generated:

 \itemize{

 \item{"provider" = "PoliMi"}

 \item{"application" = "RGMQL"}

@@ -57,19 +56,19 @@ generated.

 }

 \examples{

-## Thi statement initializes and runs the GMQL server for local execution 

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

 ## and creation of results on disk. Then, with system.file() it defines 

-## the path to the folders "DATASET" in the subdirectory "example" 

+## the path to the folder "DATASET" in the subdirectory "example" 

 ## of the package "RGMQL" and opens such folder as a GMQL dataset 

-## named "data"

+## named "data" using customParser

 init_gmql()

 test_path <- system.file("example", "DATASET", package = "RGMQL")

-data = read_GMQL(test_path)

+data = read_gmql(test_path)

 ## This statement opens such folder as a GMQL dataset named "data" using 

 ## "NarrowPeakParser" 

-dataPeak = read_GMQL(test_path,"NarrowPeakParser")

+dataPeak = read_gmql(test_path,"NarrowPeakParser")

 ## This statement reads a remote public dataset stored into GMQL system 

 ## repository. For a public dataset in a (remote) GMQL repository the 

@@ -77,6 +76,6 @@ dataPeak = read_GMQL(test_path,"NarrowPeakParser")

 remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

 login_gmql(remote_url)

-data1 = read_GMQL("public.Example_Dataset_1",is_local = FALSE)

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

 }

@@ -77,6 +77,6 @@ dataPeak = read_GMQL(test_path,"NarrowPeakParser")

 remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

 login_gmql(remote_url)

-data1 = read_GMQL("public.Example_Dataset1",is_local = FALSE)

+data1 = read_GMQL("public.Example_Dataset_1",is_local = FALSE)

 }

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

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_read.R

-\name{read_dataset}

-\alias{read_dataset}

-\alias{read_dataset}

-\alias{read}

+\name{read_GMQL}

+\alias{read_GMQL}

+\alias{read_GMQL}

+\alias{read_GRangesList}

 \title{Function read}

 \usage{

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

+read_GMQL(dataset, parser = "CustomParser", is_local = TRUE,

   is_GMQL = TRUE)

-read(samples)

+read_GRangesList(samples)

 }

 \arguments{

 \item{dataset}{folder path for GMQL dataset or dataset name on repository}

@@ -65,16 +65,18 @@ generated.

 init_gmql()

 test_path <- system.file("example", "DATASET", package = "RGMQL")

-data = read_dataset(test_path)

+data = read_GMQL(test_path)

 ## This statement opens such folder as a GMQL dataset named "data" using 

 ## "NarrowPeakParser" 

-dataPeak = read_dataset(test_path,"NarrowPeakParser")

+dataPeak = read_GMQL(test_path,"NarrowPeakParser")

 ## This statement reads a remote public dataset stored into GMQL system 

 ## repository. For a public dataset in a (remote) GMQL repository the 

 ## prefix "public." is needed before dataset name

-data1 = read_dataset("public.Example_Dataset1",is_local = FALSE)

+remote_url = "http://genomic.deib.polimi.it/gmql-rest-r/"

+login_gmql(remote_url)

+data1 = read_GMQL("public.Example_Dataset1",is_local = FALSE)

 }

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

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_read.R

-\name{read}

-\alias{read}

+\name{read_dataset}

+\alias{read_dataset}

 \alias{read_dataset}

 \alias{read}

 \title{Function read}

@@ -12,15 +12,13 @@ read_dataset(dataset, parser = "CustomParser", is_local = TRUE,

 read(samples)

 }

 \arguments{

-\item{dataset}{folder path for GMQL dataset or datasetname on repository}

+\item{dataset}{folder path for GMQL dataset or dataset name on repository}

 \item{parser}{string used to parsing dataset files

 The Parser's available are:

 \itemize{

-\item{BedParser}

 \item{ANNParser}

 \item{BroadProjParser}

-\item{BedParser}

 \item{NarrowPeakParser}

 \item{RnaSeqParser}

 \item{CustomParser.}

@@ -29,50 +27,54 @@ Default is CustomParser.}

 \item{is_local}{logical value indicating local or remote dataset}

-\item{is_GMQL}{logical value indicating if is a GMQL dataset or not}

+\item{is_GMQL}{logical value indicating GMQL dataset or not}

-\item{samples}{GrangesList}

+\item{samples}{GRangesList}

 }

 \value{

 GMQLDataset object. It contains the value to use as input 

 for the subsequent GMQLDataset method

 }

 \description{

-Read a GMQL dataset, folder containig some homogenus sample from disk 

-or GrangesList saving in Scala memory that can be referenced in R.

-Also used to read a repository dataset in case of remote processing.

+It reads a GMQL dataset, as a folder containig some homogenus samples on 

+disk or as a GrangesList; it saving in Scala memory in a way that can be 

+referenced in R. It is also used to read a repository dataset in case of

+remote processing.

 }

 \details{

 Normally a GMQL dataset contains an XML schema file that contains

-name of column header. (e.g chr, start, stop, strand)

-The CustomParser read this XML schema; 

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

-parser defined without reading any XML schema

+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.

-If GrangesList has no metadata: i.e. metadata() is empty, two metadata are

+If GRangesList has no metadata: i.e. metadata() is empty, two metadata are

 generated.

 \itemize{

-\item{"Provider" = "Polimi"}

-\item{"Application" = "RGMQL"}

+\item{"provider" = "PoliMi"}

+\item{"application" = "RGMQL"}

 }

 }

 \examples{

-## read local dataset with CustomParser

+## Thi statement initializes and runs the GMQL server for local execution 

+## and creation of results on disk. Then, with system.file() it defines 

+## the path to the folders "DATASET" in the subdirectory "example" 

+## of the package "RGMQL" and opens such folder as a GMQL dataset 

+## named "data"

+

 init_gmql()

 test_path <- system.file("example", "DATASET", package = "RGMQL")

-r = read_dataset(test_path)

+data = read_dataset(test_path)

-\dontrun{

+## This statement opens such folder as a GMQL dataset named "data" using 

+## "NarrowPeakParser" 

+dataPeak = read_dataset(test_path,"NarrowPeakParser")

-## read local dataset with other Parser

-init_gmql()

-test_path <- system.file("example", "DATASET", package = "RGMQL")

-r = read_dataset(test_path,"ANNParser")

+## This statement reads a remote public dataset stored into GMQL system 

+## repository. For a public dataset in a (remote) GMQL repository the 

+## prefix "public." is needed before dataset name

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

-## If public dataset a prefix "public." is needed before dataset name

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

+data1 = read_dataset("public.Example_Dataset1",is_local = FALSE)

 }

-}

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

 \alias{read}

 \alias{read_dataset}

 \alias{read}

-\title{GMQL Function: READ}

+\title{Function read}

 \usage{

 read_dataset(dataset, parser = "CustomParser", is_local = TRUE,

   is_GMQL = TRUE)

@@ -34,15 +34,13 @@ Default is CustomParser.}

 \item{samples}{GrangesList}

 }

 \value{

-DataSet class object. It contains the value to use as input 

-for the subsequent GMQL function

+GMQLDataset object. It contains the value to use as input 

+for the subsequent GMQLDataset method

 }

 \description{

-Read a GMQL dataset or any other folder containig some homogenus sample

-from disk, saving in Scala memory that can be referenced in R

+Read a GMQL dataset, folder containig some homogenus sample from disk 

+or GrangesList saving in Scala memory that can be referenced in R.

 Also used to read a repository dataset in case of remote processing.

-

-Read a GrangesList saving in scala memory that can be referenced in R

 }

 \details{

 Normally a GMQL dataset contains an XML schema file that contains

@@ -50,6 +48,13 @@ name of column header. (e.g chr, start, stop, strand)

 The CustomParser read this XML schema; 

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

 parser defined without reading any XML schema

+

+If GrangesList has no metadata: i.e. metadata() is empty, two metadata are

+generated.

+\itemize{

+\item{"Provider" = "Polimi"}

+\item{"Application" = "RGMQL"}

+}

 }

 \examples{

@@ -66,7 +71,7 @@ test_path <- system.file("example", "DATASET", package = "RGMQL")

 r = read_dataset(test_path,"ANNParser")

 ## read remote public dataset stored into GMQL system repository 

-

+## If public dataset a prefix "public." is needed before dataset name

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

 }

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/Read.R

+% Please edit documentation in R/gmql_read.R

 \name{read}

 \alias{read}

 \alias{read_dataset}

new file mode 100644

@@ -0,0 +1,73 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/Read.R

+\name{read}

+\alias{read}

+\alias{read_dataset}

+\alias{read}

+\title{GMQL Function: READ}

+\usage{

+read_dataset(dataset, parser = "CustomParser", is_local = TRUE,

+  is_GMQL = TRUE)

+

+read(samples)

+}

+\arguments{

+\item{dataset}{folder path for GMQL dataset or datasetname on repository}

+

+\item{parser}{string used to parsing dataset files

+The Parser's available are:

+\itemize{

+\item{BedParser}

+\item{ANNParser}

+\item{BroadProjParser}

+\item{BedParser}

+\item{NarrowPeakParser}

+\item{RnaSeqParser}

+\item{CustomParser.}

+}

+Default is CustomParser.}

+

+\item{is_local}{logical value indicating local or remote dataset}

+

+\item{is_GMQL}{logical value indicating if is a GMQL dataset or not}

+

+\item{samples}{GrangesList}

+}

+\value{

+DataSet class object. It contains the value to use as input 

+for the subsequent GMQL function

+}

+\description{

+Read a GMQL dataset or any other folder containig some homogenus sample

+from disk, saving in Scala memory that can be referenced in R

+Also used to read a repository dataset in case of remote processing.

+

+Read a GrangesList saving in scala memory that can be referenced in R

+}

+\details{

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

+name of column header. (e.g chr, start, stop, strand)

+The CustomParser read this XML schema; 

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

+parser defined without reading any XML schema

+}

+\examples{

+

+## read local dataset with CustomParser

+init_gmql()

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

+r = read_dataset(test_path)

+

+\dontrun{

+

+## read local dataset with other Parser

+init_gmql()

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

+r = read_dataset(test_path,"ANNParser")

+

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

+

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

+

+}

+}