Package: Rlabkey 3.4.1

Rlabkey: Data Exchange Between R and 'LabKey' Server

The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, <https://www.labkey.com/>, 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.

Authors:Peter Hussey [aut], Cory Nathe [cre]

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Rlabkey.pdf |Rlabkey.html✨
Rlabkey/json (API)
NEWS

# Install 'Rlabkey' in R:
install.packages('Rlabkey', repos = c('https://cnathe.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.16 score 1 packages 388 scripts 1.5k downloads 1 mentions 90 exports 9 dependencies

Last updated 12 days agofrom:56abf21ae8. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64OKNov 19 2024
R-4.5-linux-x86_64OKNov 19 2024
R-4.4-win-x86_64OKNov 19 2024
R-4.4-mac-x86_64OKNov 19 2024
R-4.4-mac-aarch64OKNov 19 2024
R-4.3-win-x86_64OKNov 19 2024
R-4.3-mac-x86_64OKNov 19 2024
R-4.3-mac-aarch64OKNov 19 2024

Exports:getFolderPathgetLookupsgetRowsgetSchemagetSessionlabkey.acceptSelfSignedCertslabkey.curlOptionslabkey.deleteRowslabkey.domain.createlabkey.domain.createAndLoadlabkey.domain.createConditionalFormatlabkey.domain.createConditionalFormatQueryFilterlabkey.domain.createDesignlabkey.domain.createIndiceslabkey.domain.droplabkey.domain.FILTER_TYPESlabkey.domain.getlabkey.domain.inferFieldslabkey.domain.savelabkey.executeSqllabkey.experiment.createDatalabkey.experiment.createMateriallabkey.experiment.createRunlabkey.experiment.lineagelabkey.experiment.SAMPLE_DERIVATION_PROTOCOLlabkey.experiment.saveBatchlabkey.experiment.saveRunslabkey.getBaseUrllabkey.getDefaultViewDetailslabkey.getFolderslabkey.getLookupDetailslabkey.getModulePropertylabkey.getQuerieslabkey.getQueryDetailslabkey.getQueryViewslabkey.getRequestOptionslabkey.getSchemaslabkey.importRowslabkey.insertRowslabkey.makeRemotePathlabkey.moveRowslabkey.pipeline.getFileStatuslabkey.pipeline.getPipelineContainerlabkey.pipeline.getProtocolslabkey.pipeline.startAnalysislabkey.provenance.addRecordingSteplabkey.provenance.createProvenanceParamslabkey.provenance.startRecordinglabkey.provenance.stopRecordinglabkey.query.importlabkey.rstudio.initReportlabkey.rstudio.initRStudiolabkey.rstudio.initSessionlabkey.rstudio.isInitializedlabkey.rstudio.saveReportlabkey.saveBatchlabkey.security.createContainerlabkey.security.deleteContainerlabkey.security.getContainerslabkey.security.impersonateUserlabkey.security.moveContainerlabkey.security.renameContainerlabkey.security.stopImpersonatinglabkey.selectRowslabkey.setCurlOptionslabkey.setDebugModelabkey.setDefaultslabkey.setModulePropertylabkey.setWafEncodinglabkey.storage.createlabkey.storage.deletelabkey.storage.updatelabkey.transform.getRunPropertyValuelabkey.transform.readRunPropertiesFilelabkey.truncateTablelabkey.updateRowslabkey.webdav.deletelabkey.webdav.downloadFolderlabkey.webdav.getlabkey.webdav.listDirlabkey.webdav.mkDirlabkey.webdav.mkDirslabkey.webdav.pathExistslabkey.webdav.putlabkey.whoAmIlsFolderslsProjectslsSchemasmakeFiltersaveResults

Dependencies:askpasscurlhttrjsonlitemimeopensslR6Rcppsys

Readme and manuals

Help Manual

Help pageTopics
Exchange data between LabKey Server and RRlabkey-package Rlabkey
Returns the folder path associated with a sessiongetFolderPath
Get related data fields that are available to include in a query on a given query objectgetLookups
Retrieve data from LabKey ServergetRows
Returns an object representing a LabKey schemagetSchema
Creates and returns a LabKey Server sessiongetSession
Convenience method to configure Rlabkey connections to accept self-signed certificateslabkey.acceptSelfSignedCerts
Returns the current set of Curl options that are being used in the existing sessionlabkey.curlOptions
Delete rows of data from a LabKey databaselabkey.deleteRows
Create a new LabKey domainlabkey.domain.create
Create a new LabKey domain and load datalabkey.domain.createAndLoad
Create a conditional format data framelabkey.domain.createConditionalFormat
Create a conditional format query filterlabkey.domain.createConditionalFormatQueryFilter
Helper function to create a domain design data structurelabkey.domain.createDesign
Helper function to create a domain design indices listlabkey.domain.createIndices
Delete a LabKey domainlabkey.domain.drop
Provide comparator accesslabkey.domain.FILTER_TYPES
Returns the metadata for an existing LabKey domainlabkey.domain.get
Infer field metadata from a data framelabkey.domain.inferFields
Updates an existing LabKey domainlabkey.domain.save
Retrieve data from a LabKey Server using SQL commandslabkey.executeSql
Create an experiment data objectlabkey.experiment.createData
Create an experiment material objectlabkey.experiment.createMaterial
Create an experiment run objectlabkey.experiment.createRun
Get lineage parent/child relationships for experiment objectslabkey.experiment.lineage
Constant for the Simple Derivation Protocollabkey.experiment.SAMPLE_DERIVATION_PROTOCOL
Saves a modified experiment batchlabkey.experiment.saveBatch
Saves Runs.labkey.experiment.saveRuns
Get the default baseUrl parameter used for all http or https requestslabkey.getBaseUrl
Retrieve the fields of a LabKey query viewlabkey.getDefaultViewDetails
Retrieve a list of folders accessible to the current userlabkey.getFolders
Retrieve detailed information on a LabKey querylabkey.getLookupDetails
Get effective module property valuelabkey.getModuleProperty
Retrieve a list of available queries for a specified LabKey schemalabkey.getQueries
Retrieve detailed information on a LabKey querylabkey.getQueryDetails
Retrieve a list of available named views defined on a query in a schemalabkey.getQueryViews
Helper function to get the HTTP request options for a specific method type.labkey.getRequestOptions
Retrieve a list of available schemas from a labkey databaselabkey.getSchemas
Import rows of data into a LabKey Serverlabkey.importRows
Insert new rows of data into a LabKey Serverlabkey.insertRows
Build a file path to data on a remote machinelabkey.makeRemotePath
Move rows of data from a LabKey databaselabkey.moveRows
Gets the protocol file status for a pipelinelabkey.pipeline.getFileStatus
Gets the container in which the pipeline is definedlabkey.pipeline.getPipelineContainer
Gets the protocols that have been saved for a particular pipelinelabkey.pipeline.getProtocols
Start an analysis of a set of files using a pipelinelabkey.pipeline.startAnalysis
Add a step to a provenance recordinglabkey.provenance.addRecordingStep
Create provenance parameter objectlabkey.provenance.createProvenanceParams
Start a provenance recordinglabkey.provenance.startRecording
Stop a provenance recordinglabkey.provenance.stopRecording
Bulk import an R data frame into a LabKey Server table using file import.labkey.query.import
Initialize a RStudio session for LabKey R report source editinglabkey.rstudio.initReport
Initialize a RStudio session for LabKey integrationlabkey.rstudio.initRStudio
Initialize a RStudio session for LabKey integration using a time one request idlabkey.rstudio.initSession
Check valid rlabkey sessionlabkey.rstudio.isInitialized
Update RStudio report source back to LabKeylabkey.rstudio.saveReport
Save an assay batch object to a labkey databaselabkey.saveBatch
Creates a new container, which may be a project, folder, or workbook, on the serverlabkey.security.createContainer
Deletes an existing container, which may be a project, folder, or workbooklabkey.security.deleteContainer
Returns information about the specified containerlabkey.security.getContainers
Start impersonating a userlabkey.security.impersonateUser
Moves an existing container, which may be a folder or workbooklabkey.security.moveContainer
Rename an existing container at the given container pathlabkey.security.renameContainer
Stop impersonating a userlabkey.security.stopImpersonating
Retrieve data from a labkey databaselabkey.selectRows
Modify the current set of Curl options that are being used in the existing sessionlabkey.setCurlOptions
Helper function to enable/disable debug mode.labkey.setDebugMode
Set the default parameters used for all http or https requestslabkey.setDefaults
Set module property valuelabkey.setModuleProperty
Helper function to enable/disable wafEncoding mode.labkey.setWafEncoding
Create a new LabKey Freezer Manager storage itemlabkey.storage.create
Delete a LabKey Freezer Manager storage itemlabkey.storage.delete
Update a LabKey Freezer Manager storage itemlabkey.storage.update
Assay transform script helper function to get a run property value from a data.framelabkey.transform.getRunPropertyValue
Assay transform script helper function to read a run properties filelabkey.transform.readRunPropertiesFile
Delete all rows from a tablelabkey.truncateTable
Update existing rows of data in a labkey databaselabkey.updateRows
Deletes the provided file/folder on a LabKey Server via WebDAVlabkey.webdav.delete
Recursively download a folder via WebDAVlabkey.webdav.downloadFolder
Download a file via WebDAVlabkey.webdav.get
List the contents of a LabKey Server folder via WebDAVlabkey.webdav.listDir
Create a folder via WebDAVlabkey.webdav.mkDir
Create a folder via WebDAVlabkey.webdav.mkDirs
Tests if a path exists on a LabKey Server via WebDAVlabkey.webdav.pathExists
Upload a file via WebDAVlabkey.webdav.put
Call the whoami APIlabkey.whoAmI
List the available folder pathslsFolders
List the projects available at a given LabKey Server addresslsProjects
List the available schemaslsSchemas
Builds filters to be used in labkey.selectRows and getRowsmakeFilter
Returns an object representing a LabKey schemasaveResults