Rlabkey: labkey.domain.createAndLoad – R documentation

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labkey.domain.createAndLoad

Create a new LabKey domain and load data

Description

Create a domain of the type specified by the domainKind. A LabKey domain represents a table in a specific schema. Once the domain is created the data from the data frame will be imported.

Usage

labkey.domain.createAndLoad(baseUrl=NULL, folderPath,
    name, description="", df, domainKind, options=NULL, schemaName=NULL)

Arguments

`baseUrl`	a string specifying the `baseUrl` for the labkey server
`folderPath`	a string specifying the `folderPath`
`name`	a string specifying the name of the domain to create
`description`	(optional) a string specifying the domain description
`df`	a data frame specifying fields to infer. The data frame must have column names as well as row data to infer the type of the field from.
`domainKind`	a string specifying the type of domain to create
`options`	(optional) a list containing options specific to the domain kind
`schemaName`	(optional) a string specifying the schema name to import the data into

Details

Will create a domain of the specified domain type, valid types are

"IntList": A list with an integer key field
"VarList": A list with a string key field
"StudyDatasetVisit": A dataset in a visit based study
"StudyDatasetDate": A dataset in a date based study
"IssueDefinition": An issue list domain
"SampleSet": Sample set
"DataClass": Data class

The options parameter should contain a list of attributes that are specific to the domain kind specified. The list of valid options for each domain kind are:

IntList and VarList
- keyName (required) : The name of the field in the domain design which identifies the key field
StudyDatasetVisit and StudyDatasetDate
- datasetId : Specifies a dataset ID to use, the default is to auto generate an ID
- categoryId : Specifies an existing category ID
- categoryName : Specifies an existing category name
- demographics : (TRUE | FALSE) Determines whether the dataset is created as demographic
- keyPropertyName : The name of an additional key field to be used in conjunction with participantId and (visitId or date) to create unique records
- useTimeKeyField : (TRUE | FALSE) Specifies to use the time portion of the date field as an additional key
IssueDefinition
- providerName : The type of issue list to create (IssueDefinition (default) or AssayRequestDefinition)
- singularNoun : The singular name to use for items in the issue definition (defaults to issue)
- pluralNoun : The plural name (defaults to issues)
SampleSet
- idCols : The columns to use when constructing the concatenated unique ID. Can be up to 3 numeric IDs which represent the zero-based position of the fields in the domain.
- parentCol : The column to represent the parent identifier in the sample set. This is a numeric value representing the zero-based position of the field in the domain.
- nameExpression : The name expression to use for creating unique IDs
DataClass
- sampleSet : The ID of the sample set if this data class is associated with a sample set.
- nameExpression : The name expression to use for creating unique IDs

Value

A list containing the newly uploaded data frame rows.

Author(s)

Karl Lum

Examples

library(Rlabkey)

## Prepare a data.frame
participants = c("0001","0001","0002","0002","0007","0008")
Visit = c("V1", "V2", "V2", "V1", "V2", "V1")
IntValue = c(256:261)
dataset = data.frame("ParticipantID" = participants, Visit,
    "IntegerValue" = IntValue, check.names = FALSE)

## Create the dataset and import
labkey.domain.createAndLoad(baseUrl="http://labkey", folderPath="home",
    name="demo dataset", df=dataset, domainKind="StudyDatasetVisit")

Rlabkey

Data Exchange Between R and 'LabKey' Server

v2.6.0

Apache License 2.0

Authors

Peter Hussey

Initial release

2021-02-02