NEWS.md

In icarda-git/QBMS: Query the Breeding Management System(s)

QBMS 1.5.0 2024-09-19

• 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.

QBMS 1.0.0 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

• Hot fix the reported validation issue in the gigwa_set_db() function.

QBMS 0.9.0 2023-03-20

• 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.

QBMS 0.8.0 2022-05-18

• 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

• 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.

QBMS 0.1.0 2019-07-24

• Initial version.

icarda-git/QBMS documentation built on Sept. 25, 2024, 10:45 p.m.