R: Create provenance parameter object

labkey.provenance.createProvenanceParams {Rlabkey} | R Documentation

## 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

### See Also

`labkey.provenance.startRecording`, `labkey.provenance.addRecordingStep`, `labkey.provenance.stopRecording`

### 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)

[Package Rlabkey version 2.8.1 Index]