Changelog • QBMS

QBMS 1.5.0 2024-09-19

CRAN release: 2024-09-18

Updated the core QBMS script to replace the non-CRAN async R package with the CRAN-standard future and future.apply packages.
Updated the core QBMS script to substitute the deprecated httr R package with the recommended httr2 package.
Add new gigwa_get_allelematrix() function that boosting the marker data retrieval speed by more than 10 times.
Add new gigwa_get_markers() function to retrieve the marker map that describe the physical positions of the markers on the chromosomes.
Add new gigwa_get_sequences() function to retrieve the list of sequences in the selected GIGWA project.
Improve get_trial_obs_ontology() function performance for systems supports BrAPI v2 /search/variables endpoint.
Improve package documentation with enhanced details.
Implement an internal central mechanism to handle all BrAPI POST /search endpoints, including the 202 status code or searchResultsDbId response.

CRAN release: 2024-03-07

Add EBS support using BrAPI v2 calls.
Implement a new generic internal mechanism that supports both BrAPI versions 1 and 2 calls for all core functions.
Support the OAuth 2.0 authentication (Authorization Code Grant flow) using the new login_oauth2() function.
Support external authorization option and set access token value manually using the new set_token() function.
Support downloading TerraClimate netCDF data files to extract their data offline using the new ini_terraclimate() function.
Add the new scan_brapi_endpoints() utility function to scan available BrAPI endpoints in the configured data source server.
Enhance the gigwa_get_variants() function by adding 3 extra filtering parameters: start position, end position, and reference sequence name.
Fix the BreedBase login problem due to the form encoding issue by adding the new function login_breedbase() to pass the correct/expected encoding.
Add HWSD v2.0 support to query and retrieve the FAO harmonized soil data.
Resolved several minor bugs reported by EBS, BreedBase, and DeltaBreed users for improved stability.

CRAN release: 2023-03-28

CRAN release: 2023-03-28

Implement caching techniques wherever applicable for faster response times to improve user experience. Thanks to Johan Steven Aparicio for initiating this.
Improve the performance of multi-page API calls by optionally enabling asynchronous calls to prevent blocking behavior by fetching all requested pages simultaneously.
Add TerraClimate support to query and retrieve climate data (including the 19 BIOCLIM variables).
Add a new get_germplasm_attributes() function to retrieve germplasm attributes. Thanks to Johan Steven Aparicio for his contribution.
Add a new gigwa_get_metadata() function to retrieve metadata from GIGWA database.
Add new get_qbms_connection() and set_qbms_connection() functions to support connecting to multiple providers. Thanks to Francisco Agosto-Perez for the suggestions.
The get_pedigree_table() function can properly detect and handle backcross cases.
Fix the error message when calling the get_pedigree_table() function if there is no case of similar genotype names. Thanks to Johan Steven Aparicio for reporting this.

CRAN release: 2022-05-19

Add GIGWA support (required version 2.4.1 or higher) to query and retrieve SNPs data for GWAS and GS analysis pipelines.
Tiny usability enhancements (e.g., automate path parameter setting, show the server name in the login window, add progress bar to the get_program_studies function).
Fix mistakenly redundant location names/info returned by the get_program_studies function.

CRAN release: 2022-03-02

Add BreedBase support using BrAPI v1 calls.
Add functionality to get the pedigree table starting from germplasm dataset.
Improve set_qbms_config to generalize the way of getting the server domain from the URL.
Default timeout become 120 sec instead of 10.
Set default encoding for HTTP content to UTF-8.

Fix filter by year functionality in the list_trials function.
Fix get_germplasm_data by replaced the deprecated germplasm-search call.
Minimize package dependencies (rbindx replaced plyr::rbind.fill, rbindlistx replaced data.table::rbindlist, and use merge to replace dplyr::left_join).
Resolve compatibility issues with BrAPI changes in BMS version 19.
Enable to set the connection time_out in the set_qbms_config function.
Get entry type (test or check) in the get_germplasm_list returned data frame.

Fix the issue of empty list in get_germplasm_data returned results.
Fix retrieving error when the study has no data!
Enhance returned info by the get_program_studies function to include study settings and number of test/check entries.

Simplify configuration by required only the URL of the BMS login page.
Improve the performance of the internal get_program_trials function by passing the programDbId in the /trials GET call.
Add debug_qbms function to get the internal config/state object.

Fix the “get_trial_data” function bug when you have more than one study in the same location.
Function “list_studies” returns studyName also, and function “set_study” input is studyName now.
Simplify the “get_germplasm_list” function output by getting rid of nested lists.
Deprecate the “list_all_studies” function in favor of “get_program_studies” function.

Call BrAPI directly (i.e. not required “CIP-RIU/brapi” from GitHub anymore).
Add a function to get all data of the current active trial (combined all studies).
Add a function to get a list of studies where given germplasm has been used.
Add a function to get a specific germplasm data from all program trials.
Handle BrAPI pagination in a proper way.