upload_dataset: Upload dataset

In DEIB-GECO/RGMQL: GenoMetric Query Language for R/Bioconductor

Upload dataset

Description

It uploads a folder (GMQL or not) containing sample files using the proper GMQL web service available on a remote server: a new dataset is created on remote repository

Usage

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

Arguments

url	string url of server: It must contain the server address and base url; service name is added automatically
datasetName	name of dataset to create in repository
folderPath	string local path to the folder containing the samples files
schemaName	string name of schema used to parse the samples; schemaName available are: NARROWPEAK BROADPEAK VCF BED BEDGRAPH if schemaName is NULL, it looks for a XML schema file to read in the folderPath

Details

If no error occurs, it prints "Upload Complete", otherwise a specific error is printed

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.

Value

None

Examples

## Not run: 

## This statement defines the path to the folder "DATASET_GDM" in the 
## subdirectory "example" of the package "RGMQL"

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

## Login to GMQL REST services suite at remote url

remote_url <- "http://www.gmql.eu/gmql-rest/"
login_gmql(remote_url)

## Upload of GMQL dataset with "dataset1" as name, without specifying any 
## schema 

upload_dataset(remote_url, "dataset1", folderPath = test_path)


## End(Not run)

DEIB-GECO/RGMQL documentation built on Feb. 17, 2024, 10:39 p.m.