Rlabkey (version 2.8.0)

labkey.pipeline.startAnalysis: 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.

See Also

labkey.pipeline.getPipelineContainer, labkey.pipeline.getProtocols, labkey.pipeline.getFileStatus

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
)

# }