labkey.query.import: Bulk import an R data frame into a LabKey Server table using...

In Rlabkey: Data Exchange Between R and 'LabKey' Server

Bulk import an R data frame into a LabKey Server table using file import.

Description

Bulk import an R data frame into a LabKey Server table using file import.

Usage

labkey.query.import(baseUrl, folderPath,
    schemaName, queryName, toImport, options = NULL)

Arguments

baseUrl	a string specifying the baseUrlfor the labkey server
folderPath	a string specifying the folderPath
schemaName	a string specifying the schemaName for the query
queryName	a string specifying the queryName
toImport	a data frame containing rows of data to be imported
options	(optional) a list containing options specific to the import action of the query

Details

This command mimics the "Import bulk data" option that you see in the LabKey server UI for a table/query. It takes the passed in toImport data frame and writes it to a temp file to be posted to the import action for the given LabKey query. It is very similar to the labkey.importRows command but will be much more performant.

Multiple rows of data can be imported in bulk using the toImport data frame. The names of the data in the data frame must be the column names from the LabKey Server.

LabKey data types support different import options. The list of valid options for each query will vary, but some common examples include:

• insertOption (string) : Whether the import action should be done as an insert, creating new rows for each provided row of the data frame, or a merge. When merging during import, any data you provide for the rows representing records that already exist will replace the previous values. Note that when updating an existing record, you only need to provide the columns you wish to update, existing data for other columns will be left as is. Available options are "INSERT" and "MERGE". Defaults to "INSERT".

• auditBehavior (string) : Set the level of auditing details for this import action. Available options are "SUMMARY" and "DETAILED". SUMMARY - Audit log reflects that a change was made, but does not mention the nature of the change. DETAILED - Provides full details on what change was made, including values before and after the change. Defaults to the setting as specified by the LabKey query.

• importLookupByAlternateKey (boolean) : Allows lookup target rows to be resolved by values rather than the target's primary key. This option will only be available for lookups that are configured with unique column information. Defaults to FALSE.

Value

A list is returned with the row count for the number of affected rows. If options are provided, additional details may be included in the response object related to those options.

Author(s)

Cory Nathe

See Also

labkey.insertRows, labkey.updateRows, labkey.importRows

Examples

## Not run: 

## Note that users must have the necessary permissions in the database
## to be able to modify data through the use of these functions
# library(Rlabkey)

df <- data.frame(
    name=c("test1","test2","test3"),
    customInt=c(1:3),
    customString=c("aaa", "bbb", "ccc")
)

importedInfo <- labkey.query.import(
    "http://localhost:8080/labkey",
    folderPath="/apisamples", schemaName="samples", queryName="SampleType1",
    toImport=df, options=list(insertOption = "MERGE", auditBehavior = "DETAILED")
)

importedInfo$rowCount


## End(Not run)

Rlabkey documentation built on Nov. 8, 2023, 1:06 a.m.