NEWS

DataSpaceR 0.7.7 (2025-02-20)

Fixed issues querying mab and donor information.
Added workarounds for errors and warnings when trying to verify certs and querying the database with GROUP_CONCAT operations.

Fixed bug concerning missing cookie session name for app reports which will update this package to work when run on CDS as in a report.
Show NI data in available datasets active binding which will allow users to look for NI (non-integrated) data in DSR.
Set active binding names to snake case which is in effort to standardize fields names used in the API.
Add all authors to publication table which will allow users to find publication by authors who were not listed as the primary author.

Added virusMetadata field to DataSpaceConnection which shows virus metadata for viruses used in NAb assays (thanks @helenmiller16 #26)
Added availablePublications field to DataSpaceConnection which summarizes all available publications (thanks @helenmiller16 #27)
Added downloadPublicationData method to DataSpaceConnection which will download available publication data for a specified publication (thanks @helenmiller16 #27)
Added a vignette: Accessing Publication Data (thanks @helenmiller16 #27)
Made PKMAb dataset available to retrieve in DataSpaceStudy (thanks @helenmiller16 and @jmtaylor-fhcrc #27)
Relaxed some assumptions when pulling non-integrated data, which allows users to pull non-integrated mab data, like in cvd812. (thanks @helenmiller16 #28)
Fixed a test for mabGridSummary$geometric_mean_curve_ic50 calculation to reflect updated data. (thanks @helenmiller16 #28)
Updated documentation using the R6 documentation syntax in roxygen

Remove tolower in functions that check study names. (thanks @jmtaylor-fhcrc #23)
Update DataSpaceStudy methods for non-integrated datasets. (thanks @helenmiller16 #24)

Added DataSpaceMab class and several methods and fields in DataSpaceConnection to allow access to monoclonal antibody data (thanks @jmtaylor-fhcrc #14, #19, #21)

Write the netrc in temporary directory as default in writeNetrc. (CRAN requirement)

Modified getDataset method in DataSpaceStudy to take mergeExtra as an argument in order to merge extra information (demographics and treatment arm). #5

Adjusted the package to use the latest version of Rlabkey (v2.2) and httr packages.

Modified DataSpaceConnection and DataSpaceStudy classes to convert data.frame objects to data.table.
Added a package startup message on the terms of use.
Created getGroup method in DataSpaceConnection class and deprecated groupId in getStudy method.

Included additional columns (short_name, type, status, stage, species, start_date, strategy) in availableStudies.
Updated the introductory vignette.

Added availableGroups field to DataSpaceConnection class.
Modified getStudy method in DataSpaceConnection to take groupId as an argument in order to create a DataSpaceStudy object for a particular group.

Updated DataSpaceConnection class and connectDS constructor to be not study-specific.

Added getVariableInfo method to DataSpaceConnection class.
Changed variable names in getAvailableDatasets to lowercase.
Added treatmentArm field to DataSpaceConnection class.
Removed getAvailableDatasets method (now a private method).
Changed the default connection from staging (dataspace-staging.cavd.org) to production (dataspace.cavd.org).
Added an option to connect to the staging server.
Renamed write_netrc and check_netrc to writeNetrc and checkNetrc.

Initialized the package with connectDS() and other basic functions.
Added a test framework on tests to test the package.
Added .travis.yml to build and check the package automatically. (not used yet)
Added codecov.yml to track code coverage. (not used yet)
Added README.Rmd to introduce the package.
Added NEWS.md to track changes to the package.
Added _pkgdown.yml and /docs to build a package website.
Added a introductory vignette called Intro_to_DataSpaceR.Rmd.