Rlabkey: labkey.provenance.createProvenanceParams – R documentation

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labkey.provenance.createProvenanceParams

Create provenance parameter object

Description

Helper function to create the data structure that can be used in provenance related APIs. Note: this function is in beta and not yet final, changes should be expected so exercise caution when using it.

Usage

labkey.provenance.createProvenanceParams(recordingId=NULL, name=NULL, description=NULL,
        materialInputs=NULL, materialOutputs=NULL, dataInputs=NULL, dataOutputs=NULL,
        inputObjectUriProperty=NULL, outputObjectUriProperty=NULL, objectInputs=NULL,
        objectOutputs=NULL, provenanceMap=NULL)

Arguments

`recordingId`	(optional) the recording ID to associate with other steps using the same ID
`name`	(optional) the name of this provenance step
`description`	(optional) the description of this provenance step
`materialInputs`	(optional) the list of materials (samples) to be used as the provenance run input. The data structure should be a dataframe with the column name describing the data type (lsid, id)
`materialOutputs`	(optional) the list of materials (samples) to be used as the provenance run output. The data structure should be a dataframe with the column name describing the data type (lsid, id)
`dataInputs`	(optional) the list of data inputs to be used for the run provenance map
`dataOutputs`	(optional) the list of data outputs to be used for the run provenance map
`inputObjectUriProperty`	(optional) for incoming data rows, the column name to interpret as the input to the provenance map. Defaults to : 'prov:objectInputs'
`outputObjectUriProperty`	(optional) for provenance mapping, the column name to interpret as the output to the provenance map. Defaults to : 'lsid'
`objectInputs`	(optional) the list of object inputs to be used for the run provenance map
`objectOutputs`	(optional) the list of object outputs to be used for the run provenance map
`provenanceMap`	(optional) the provenance map to be used directly for the run step. The data structure should be a dataframe with the column names of 'from' and 'to' to indicate which sides of the mapping the identifiers refer to

Details

This function can be used to generate a provenance parameter object which can then be used as an argument in the other provenance related functions to assemble provenance runs. This is a premium feature and requires the Provenance LabKey module to function correctly.

Value

A list containing elements describing the passed in provenance parameters.

Author(s)

Karl Lum

Examples

## create provenance params with material inputs and data outputs
library(Rlabkey)

mi <- data.frame(lsid=c("urn:lsid:labkey.com:Sample.251.MySamples:sample1",
        "urn:lsid:labkey.com:Sample.251.MySamples:sample2"))
do <- data.frame(
        lsid="urn:lsid:labkey.com:AssayRunTSVData.Folder-251:12c70994-7ce5-1038-82f0-9c1487dbd334")

p <- labkey.provenance.createProvenanceParams(name="step1", description="initial step",
        materialInputs=mi, dataOutputs=do)

## create provenance params with object inputs (from an assay run)
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)

Rlabkey

Data Exchange Between R and 'LabKey' Server

v2.6.0

Apache License 2.0

Authors

Peter Hussey

Initial release

2021-02-02