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, <>, 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.


Changes in version 2.2.5 o Issue 36894: labkey.domain.get fix to translate NULL values for string props to NA o Issue 36837: correctly parse GROUP CONCAT response with array of string values

Changes in version 2.2.4 o New function to set and get module properties o allow getting baseUrl using labkey.getBaseUrl o allow NA translation behavior to be overridden in insertRows and importRows

Changes in version 2.2.3 o New helper functions for RStudio integration o New helper functions for use with R transform scripts to process run properties from server o New function to save experiment runs for an assay or a non-assay backed protocol

Changes in version 2.2.2 o New APIs for getting, creating, inferring and dropping LabKey domains (requires LabKey server version 18.2 or later) o Fix for Issue #18: labkey.executeSql breaks when using the containerFilter option o Add labkey.setDebugMode(TRUE) option to output GET/POST raw response info o Fix for labkey.selectRows() API support for colSelect=c(*) regression o Support for RStudio integration

Changes in version 2.2.1 o Support for LabKey CSRF tokens (cross site request forgery)

Changes in version 2.2.0 o Refactor HTTP client library to use httr instead of rcurl

Changes in version 2.1.136 o Account for colNameOpt = "rname" in the makeDF.R colSelect check o Remove call to open empty window on package load o Default to POST for labkey.selectRows, with param for method

Changes in version 2.1.135 o Change the cast of integers from numeric to integer (Issue #30464) o labkey.selectRows updates for colSelect and showHidden properties (Issue #30465) o Fix for encoding extended characters in folderPath param (Issue #22034)

Changes in version 2.1.134 o fix for getQueryDetails to get all column details instead of just default view column list o revert previous versions usage of fasttime library for date parsing

Changes in version 2.1.133 o performance improvements for makeDF, using listToMatrix function o update date parser to use fasttime library for POSIXct function

Changes in version 2.1.132 o fix for Issue 24231: support for date + time o add new table search filter param option: Q o fix issue with baseUrl parameter being overridden in labkey.saveBatch

Changes in version 2.1.131 o fix for Issue 26956 o added labkey.setDefaults support for baseUrl

Changes in version 2.1.130 o makeFilter() operators may now be either upper or lower case (formerly upper case only) o added labkey.setDefaults and support for authentication via an API key

Changes in version 2.1.129 o add parameter to selectRows for including display values for lookup fields in response

Changes in version 2.1.128 o allow NA values in insertRows and importRows

Changes in version 2.1.127 o change sslversion default values in curlOptions to TLSv1 o fix to handle maxRows and rowOffset for labkey.executeSql o fix for labkey.getFolders includeSubfolders for non-Guest access o add additional parameters to existing functions (labkey.executeSql: colSort, parameters; labkey.selectRows: parameters; labkey.getFolders: includeEffectivePermissions) o updated user guide

Changes in version 2.1.126 o change ssl.verifyhost default values in curlOptions from boolean to numeric o add "containerFilter" parameter to labkey.executeSql function

Changes in version 2.1.125 o set cainfo for RCurl requests to point to a certificate bundle throught the environment variable RLABKEY_CAINFO_FILE o new functions to get and set curl options : labkey.curlOptions, labkey.setCurlOptions

Changes in version 2.1.124 o replace usage of fromJSON2 with fromJSON o add between and not between filter types o fix to handle results from multi-valued columns

Changes in version 2.1.123 o added labkey.importRows o performance improvement for labkey.importRows, labkey.insertRows, labkey.deleteRows, labkey.updateRows o The following filter types were added to the makeFilter function: MEMBER_OF

Changes in version 2.1.122 o fix URL-encoding for spaces in parameter names

Changes in version 2.1.121 o fix to error message on failed API call (deleteRows, insertRows, updateRows, etc.) o fix URL encoding of schemaName in executeSql call

Changes in version 2.1.120 o minor documentation updates o fix to error message on failed insertRows call

Changes in version 2.1.119 o add new labkey.makeRemotePath function o minor documentation fixes

Changes in version 2.1.118 o convert factors to strings for toJSON usages in labkey.insertRows, labkey.updateRows, and labkey.deleteRows

Changes in version 2.1.117 o Changes to use curlEscape instead of URLencode for schemaName, queryName, lookupKey, assayName, viewName, and colSelect o Add parsing of new JSON date format o The following filter types were added to the makeFilter function: DATE_GREATER_THAN_OR_EQUAL, DATE_LESS_THAN_OR_EQUAL, IN, NOT_IN, EQUALS_NONE_OF, CONTAINS_ONE_OF, and CONTAINS_NONE_OF

Changes in version 2.1.116 Minor change to makeFiler.R to use curlEscape instead of URLencode for encoding the colFilter parameters.

Changes in version 2.1.110 Major expansion of Rlabkey. Added metadata functions, session-based access function, much faster rjson parsing on returned data sets, many bug fixes related to null handling.
See the Rlabkey Users Guide for an overview of the package.

Changes in Version 0.0.9 o Misc bug fixes

Changes in Version 0.0.8 o The following filter names have been added in the makeFilter function: QC_VALUE NOT_QC_VALUE

Changes in Version 0.0.7 o In previous versions this package would only bring labkey data into R that had hidden columns (ie, keys or other identifiers not usually shown to the user). Now any labkey data, with or without hidden columns, can be brought into R.

Changes in Version 0.0.6 o Replaced the stripAllHidden argument with showHidden. This affects the labkey.selectRows and labkey.executeSql functions and was done for clarity. The old default stripAllHidden=TRUE is replaced by the new default showHidden=FALSE which has the same functionality. See documentation for details. o The old stripAllHidden flag was removed from labkey.insertRows, labkey.updateRows and labkey.deleteRows. It served no use in these functions. The stripAllHidden (now replaced by showHidden) is only meaningfull when data are being returned to the user. o The following filter names have been modified in the makeFilter function: EQUALS -> EQUAL NOT_EQUALS -> NOT_EQUAL NOT_EQUAL_OR_NULL -> NOT_EQUAL_OR_MISSING IS_MISSING -> MISSING IS_NOT_MISSING -> NOT_MISSING GREATER_THAN_OR_EQUAL_TO -> GREATER_THAN_OR_EQUAL LESS_THAN_OR_EQUAL_TO -> LESS_THAN_OR_EQUAL

The filter name changes were made for clarity and consistency with the other software packages that retrieve data from a Labkey database.

Changes in Version 0.0.5 o modified the makeDF function to speed up data frame creation from the meta data o labkey.deleteRows function now accepts an entire row of data as input instead of just the Key column

Changes in Version 0.0.4 o first CRAN release of the Rlabkey package

Reference manual

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2.8.2 by Cory Nathe, 2 months ago

Browse source code at

Authors: Peter Hussey

Documentation:   PDF Manual  

Apache License 2.0 license

Imports Rcpp

Depends on httr, jsonlite

Linking to Rcpp

Imported by DataSpaceR, nprcgenekeepr.

See at CRAN