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Rlabkey (version 3.3.0)

Data Exchange Between R and 'LabKey' Server

Description

The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, , into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a 'LabKey' Server, provided they have appropriate permissions to do so.

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Version

Install

install.packages('Rlabkey')

Monthly Downloads

1,298

Version

3.3.0

License

Apache License 2.0

Maintainer

Last Published

August 19th, 2024

Functions in Rlabkey (3.3.0)

Rlabkey-package

Exchange data between LabKey Server and R

labkey.domain.FILTER_TYPES

Provide comparator access

Get related data fields that are available to include in a query on a given query object

labkey.acceptSelfSignedCerts

Convenience method to configure Rlabkey connections to accept self-signed certificates

labkey.experiment.saveBatch

Saves a modified experiment batch

Creates and returns a LabKey Server session

labkey.domain.create

Create a new LabKey domain

labkey.experiment.saveRuns

labkey.curlOptions

Returns the current set of Curl options that are being used in the existing session

labkey.domain.createConditionalFormat

Create a conditional format data frame

labkey.domain.createConditionalFormatQueryFilter

Create a conditional format query filter

labkey.domain.drop

Delete a LabKey domain

Returns the folder path associated with a session

labkey.importRows

Import rows of data into a LabKey Server

labkey.domain.save

Updates an existing LabKey domain

labkey.domain.inferFields

Infer field metadata from a data frame

labkey.domain.createDesign

Helper function to create a domain design data structure

labkey.executeSql

Retrieve data from a LabKey Server using SQL commands

labkey.getRequestOptions

Helper function to get the HTTP request options for a specific method type.

labkey.domain.createAndLoad

Create a new LabKey domain and load data

labkey.getSchemas

Retrieve a list of available schemas from a labkey database

labkey.experiment.createRun

Create an experiment run object

labkey.experiment.createData

Create an experiment data object

labkey.experiment.lineage

Get lineage parent/child relationships for experiment objects

labkey.getFolders

Retrieve a list of folders accessible to the current user

Retrieve data from LabKey Server

labkey.pipeline.getFileStatus

Gets the protocol file status for a pipeline

labkey.security.impersonateUser

Start impersonating a user

labkey.experiment.createMaterial

Create an experiment material object

labkey.insertRows

Insert new rows of data into a LabKey Server

labkey.getQueryViews

Retrieve a list of available named views defined on a query in a schema

labkey.getLookupDetails

Retrieve detailed information on a LabKey query

labkey.makeRemotePath

Build a file path to data on a remote machine

labkey.setDefaults

Set the default parameters used for all http or https requests

labkey.domain.get

Returns the metadata for an existing LabKey domain

labkey.provenance.addRecordingStep

Add a step to a provenance recording

labkey.domain.createIndices

Helper function to create a domain design indices list

labkey.provenance.createProvenanceParams

Create provenance parameter object

labkey.getQueryDetails

Retrieve detailed information on a LabKey query

labkey.setModuleProperty

Set module property value

Call the whoami API

labkey.selectRows

Retrieve data from a labkey database

labkey.experiment.SAMPLE_DERIVATION_PROTOCOL

Constant for the Simple Derivation Protocol

labkey.pipeline.getProtocols

Gets the protocols that have been saved for a particular pipeline

labkey.moveRows

Move rows of data from a LabKey database

labkey.provenance.startRecording

Start a provenance recording

labkey.query.import

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

labkey.security.moveContainer

Moves an existing container, which may be a folder or workbook

labkey.getBaseUrl

Get the default baseUrl parameter used for all http or https requests

labkey.storage.delete

Delete a LabKey Freezer Manager storage item

labkey.webdav.listDir

List the contents of a LabKey Server folder via WebDAV

labkey.security.createContainer

Creates a new container, which may be a project, folder, or workbook, on the server

labkey.webdav.mkDir

Create a folder via WebDAV

labkey.saveBatch

Save an assay batch object to a labkey database

labkey.setCurlOptions

Modify the current set of Curl options that are being used in the existing session

labkey.transform.getRunPropertyValue

Assay transform script helper function to get a run property value from a data.frame

labkey.storage.create

Create a new LabKey Freezer Manager storage item

labkey.storage.update

Update a LabKey Freezer Manager storage item

labkey.pipeline.startAnalysis

Start an analysis of a set of files using a pipeline

labkey.pipeline.getPipelineContainer

Gets the container in which the pipeline is defined

labkey.webdav.put

Upload a file via WebDAV

labkey.rstudio.initRStudio

Initialize a RStudio session for LabKey integration

List the available schemas

labkey.truncateTable

Delete all rows from a table

labkey.rstudio.isInitialized

Check valid rlabkey session

labkey.security.renameContainer

Rename an existing container at the given container path

labkey.transform.readRunPropertiesFile

Assay transform script helper function to read a run properties file

labkey.webdav.mkDirs

Create a folder via WebDAV

labkey.webdav.pathExists

Tests if a path exists on a LabKey Server via WebDAV

labkey.security.stopImpersonating

Stop impersonating a user

labkey.rstudio.initReport

Initialize a RStudio session for LabKey R report source editing

labkey.webdav.delete

Deletes the provided file/folder on a LabKey Server via WebDAV

labkey.rstudio.initSession

Initialize a RStudio session for LabKey integration using a time one request id

labkey.rstudio.saveReport

Update RStudio report source back to LabKey

labkey.updateRows

Update existing rows of data in a labkey database

Builds filters to be used in labkey.selectRows and getRows

labkey.setWafEncoding

Helper function to enable/disable wafEncoding mode.

labkey.getDefaultViewDetails

Retrieve the fields of a LabKey query view

labkey.security.deleteContainer

Deletes an existing container, which may be a project, folder, or workbook

labkey.getModuleProperty

Get effective module property value

labkey.getQueries

Retrieve a list of available queries for a specified LabKey schema

List the available folder paths

labkey.webdav.downloadFolder

Recursively download a folder via WebDAV

labkey.webdav.get

Download a file via WebDAV

Returns an object representing a LabKey schema

List the projects available at a given LabKey Server address

labkey.security.getContainers

Returns information about the specified container

labkey.provenance.stopRecording

Stop a provenance recording

labkey.setDebugMode

Helper function to enable/disable debug mode.

Returns an object representing a LabKey schema

labkey.deleteRows

Delete rows of data from a LabKey database