labkey.pipeline.startAnalysis: Start an analysis of a set of files using a pipeline
In Rlabkey: Data Exchange Between R and 'LabKey' Server

labkey.pipeline.startAnalysis

R Documentation

Start an analysis of a set of files using a pipeline

Description

Starts analysis of a set of files using a particular protocol definition with a particular pipeline.

Usage

labkey.pipeline.startAnalysis(baseUrl=NULL, folderPath,
    taskId, protocolName, path, files, fileIds = list(),
    pipelineDescription = NULL, protocolDescription = NULL,
    jsonParameters = NULL, xmlParameters = NULL,
    allowNonExistentFiles = FALSE, saveProtocol = TRUE)

Arguments

`baseUrl`	a string specifying the `baseUrl` for the LabKey server
`folderPath`	a string specifying the `folderPath`
`taskId`	a string identifier for the pipeline
`protocolName`	a string name of the analysis protocol
`path`	a string for the relative path from the folder's pipeline root
`files`	a list of names of the files within the subdirectory described by the path property
`fileIds`	(optional) list of data IDs of files to be used as inputs for this pipeline. These correspond to the rowIds from the table ext.data. They do not need to be located within the file path provided. The user does need read access to the container associated with each file.
`pipelineDescription`	(optional) a string description displayed in the pipeline
`protocolDescription`	(optional) a string description of the analysis protocol
`jsonParameters`	(optional) a list of key / value pairs, or a JSON string representation, for the protocol description. Not allowed if a protocol with the same name has already been saved. If no protocol with the same name exists, either this property or xmlParameters must be specified.
`xmlParameters`	(optional) a string XML representation of the protocol description. Not allowed if a protocol with the same name has already been saved. If no protocol with the same name exists, either this property or jsonParameters must be specified.
`allowNonExistentFiles`	(optional) a boolean indicating if the pipeline should allow non existent files. Defaults to false.
`saveProtocol`	(optional) a boolean indicating if no protocol with this name already exists, whether or not to save this protocol definition for future use. Defaults to true.

Value

On success, the response will contain the jobGUID string value for the newly created pipeline job.

Author(s)

Cory Nathe

Examples

## Not run: 

labkey.pipeline.startAnalysis(
    baseUrl="http://labkey/",
    folderPath="home",
    taskId = "pipelinetest:pipeline:r-copy",
    protocolName = "Test protocol name",
    path="r-copy",
    files = list("sample.txt", "result.txt"),
    protocolDescription = "Test protocol description",
    pipelineDescription = "test pipeline description",
    jsonParameters = list(assay = "Test assay name", comment = "Test assay comment"),
    saveProtocol = TRUE
)


## End(Not run)

Rlabkey documentation built on Oct. 23, 2024, 5:06 p.m.