labkey.experiment.saveBatch: Saves a modified experiment batch

Description

Saves a modified experiment batch.

Usage

labkey.experiment.saveBatch(baseUrl=NULL, folderPath,
    assayConfig = NULL, protocolName = NULL,
    batchPropertyList = NULL, runList)

Value

Returns the object representation of the experiment batch.

Arguments

baseUrl: (optional) a string specifying the baseUrl for the labkey server
folderPath: a string specifying the folderPath
assayConfig: (optional) a list specifying assay configuration information
protocolName: (optional) a string specifying the protocol name of the protocol to use
batchPropertyList: (optional) a list of batch properties
runList: a list of experiment run objects

Author

Karl Lum

Details

Saves a modified batch. Runs within the batch may refer to existing data and material objects, either inputs or outputs, by ID or LSID. Runs may also define new data and materials objects by not specifying an ID or LSID in their properties.

Runs can be created for either assay or non-assay backed protocols. For an assay backed protocol, either the assayId or the assayName and providerName name must be specified in the assayConfig parameter. If a non-assay backed protocol is to be used, specify the protocolName string value, note that currently only the simple : labkey.experiment.SAMPLE_DERIVATION_PROTOCOL is supported.

Refer to the labkey.experiment.createData, labkey.experiment.createMaterial, and labkey.experiment.createRun helper functions to assemble the data structure that saveBatch expects.

Examples

Run this code

if (FALSE) {

library(Rlabkey)

## uploads data to an existing assay

df <- data.frame(participantId=c(1:3), visitId = c(10,20,30), sex = c("f", "m", "f"))
bprops <- list(LabNotes="this is a simple demo")
bpl <- list(name=paste("Batch ", as.character(date())),properties=bprops)
run <- labkey.experiment.createRun(list(name="new assay run"), dataRows = df)
labkey.experiment.saveBatch(baseUrl="http://labkey/", folderPath="home",
    assayConfig=list(assayName="GPAT", providerName="General"),
    batchPropertyList=bpl, runList=run)

## create a non-assay backed run with samples as material inputs and outputs

m1 <- labkey.experiment.createMaterial(
        list(name = "87444063.2604.626"), sampleSetName = "Study Specimens")
m2 <- labkey.experiment.createMaterial(
        list(name = "87444063.2604.625"), sampleSetName = "Study Specimens")
run <- labkey.experiment.createRun(
        list(name="new run"), materialInputs = m1, materialOutputs = m2)
labkey.experiment.saveBatch(baseUrl="http://labkey/", folderPath="home",
        protocolName=labkey.experiment.SAMPLE_DERIVATION_PROTOCOL, runList=run)

}

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