Rlabkey (version 2.8.0)

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)

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

Value

Returns the object representation of the experiment batch.

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.

See Also

labkey.experiment.createData, labkey.experiment.createMaterial, labkey.experiment.createRun

Examples

# NOT RUN {
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)

## import an assay run which includes plate metadata

df <- data.frame(participantId=c(1:3), visitId = c(10,20,30), welllocation = c("A1", "D11", "F12"))

runConfig <- fromJSON(txt='{"assayId": 310,
    "name" : "api imported run with plate metadata",
    "properties" : {
        "PlateTemplate" : "urn:lsid:labkey.com:PlateTemplate.Folder-6:d8bbec7d-34cd-1038-bd67-b3bd"
    }}
}')

plateMetadata <- fromJSON(txt='{
      "control" : {
        "positive" : {"dilution":  0.005},
        "negative" : {"dilution":  1.0}
      },
      "sample" : {
        "SA01" : {"dilution": 1.0, "ID" : 111, "Barcode" : "BC_111", "Concentration" : 0.0125},
        "SA02" : {"dilution": 2.0, "ID" : 222, "Barcode" : "BC_222"},
        "SA03" : {"dilution": 3.0, "ID" : 333, "Barcode" : "BC_333"},
        "SA04" : {"dilution": 4.0, "ID" : 444, "Barcode" : "BC_444"}
      }
    }')

run <- labkey.experiment.createRun(runConfig, dataRows = df, plateMetadata = plateMetadata)
labkey.experiment.saveBatch(
    baseUrl="http://labkey/", folderPath="home",
    assayConfig=list(assayId = 310), runList=run
)

# }