Rlabkey: labkey.provenance.stopRecording – R documentation

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labkey.provenance.stopRecording

Stop a provenance recording

Description

Function to end a provenance recording and create and save the provenance run on the server. Note: this function is in beta and not yet final, changes should be expected so exercise caution when using it.

Usage

labkey.provenance.stopRecording(baseUrl=NULL, folderPath, provenanceParams = NULL)

Arguments

`baseUrl`	a string specifying the `baseUrl` for the labkey server
`folderPath`	a string specifying the `folderPath`
`provenanceParams`	the provenance parameter object which contains the options to include in this recording step

Details

Function to stop the provenance recording associated with the recording ID, this will create a provenance run using all the steps (with inputs and outputs) associated with the recording ID. The recording ID that was obtained from a previous startRecording function call must be passed into the provenanceParams config. This is a premium feature and requires the Provenance LabKey module to function correctly.

Value

The serialized provenance run that was created.

Author(s)

Karl Lum

Examples

library(Rlabkey)

## object inputs (from an assay run) and material inputs
##
oi <- labkey.selectRows(baseUrl="https://labkey.org/labkey/", folderPath = "Provenance",
        schemaName="assay.General.titer",
        queryName="Data",
        colSelect= c("LSID"),
        colFilter=makeFilter(c("Run/RowId","EQUAL","253")))
mi <- data.frame(lsid=c("urn:lsid:labkey.com:Sample.251.MySamples:sample1",
        "urn:lsid:labkey.com:Sample.251.MySamples:sample2"))

p <- labkey.provenance.createProvenanceParams(name="step1", description="initial step",
        objectInputs=oi[["LSID"]], materialInputs=mi)
r <- labkey.provenance.startRecording(baseUrl="https://labkey.org/labkey/",
        folderPath = "Provenance", provenanceParams=p)
run <- labkey.provenance.stopRecording(baseUrl="https://labkey.org/labkey/",
        folderPath = "Provenance",
        provenanceParams=labkey.provenance.createProvenanceParams(name="final step",
            recordingId=r$recordingId))

Rlabkey

Data Exchange Between R and 'LabKey' Server

v2.6.0

Apache License 2.0

Authors

Peter Hussey

Initial release

2021-02-02