QBMS 1.0.0 2024-03-07
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.
QBMS 0.9.1 2023-03-28
CRAN release: 2023-03-28
- Hot fix the reported validation issue in the
gigwa_set_db()function.
QBMS 0.9.0 2023-03-20
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()andset_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.
QBMS 0.8.0 2022-05-18
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.
QBMS 0.7.0 2022-03-03
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.
QBMS 0.6.0 2021-10-08
- 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.
QBMS 0.5.0 2021-07-08
- 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.
QBMS 0.4.1 2020-10-16
- 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.
QBMS 0.4.0 2020-07-03
- Convert it into an R package.
- Add set_qbms_config function to setup connection configuration variables.
- Use the double colon approach for functions from external packages.
- Fix the deprecated API call in the get_trial_obs_ontology function.
QBMS 0.3.1 2020-06-09
- 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.
QBMS 0.3.0 2020-06-02
- 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.
QBMS 0.2.0 2019-08-20
- Adopt tidyverse style guide https://style.tidyverse.org/
- Add functions documentation using roxygen2 format.
- Add basic error handling to the functions.
- Add a function to retrieve the traits ontology of a trial.