{ "_id": "6aca91e7fe5cc25786e8b9f0", "Type": "Package", "Package": "QBMS", "Title": "Query the Breeding Management System(s)", "Version": "3.0.0", "Date": "2026-09-14", "Authors@R": "c(\nperson(\"Khaled\", \"Al-Shamaa\", , \"k.el-shamaa@cgiar.org\", role = c(\"aut\", \"cre\")),\nperson(\"Mariano Omar\", \"Crimi\", , \"m.crimi@cgiar.org\", role = \"ctb\"),\nperson(\"Zakaria\", \"Kehel\", , \"z.kehel@cgiar.org\", role = \"ctb\"),\nperson(\"Johan\", \"Aparicio\", , \"j.aparicio@cgiar.org\", role = \"ctb\"),\nperson(\"ICARDA\", role = \"cph\")\n)", "Author": "Khaled Al-Shamaa [aut, cre], Mariano Omar Crimi [ctb], Zakaria\nKehel [ctb], Johan Aparicio [ctb], ICARDA [cph]", "Maintainer": "Khaled Al-Shamaa ", "Description": "This R package assists breeders in linking data systems\nwith their analytic pipelines, a crucial step in digitizing\nbreeding processes. It supports querying and retrieving\nphenotypic and genotypic data from systems like 'EBS'\n, 'BMS'\n, 'BreedBase' ,\n'Germinate'\n,\n'DeltaBreed' , and 'GIGWA'\n (using 'BrAPI'\n calls). Extra helper functions support\nenvironmental data sources, including 'TerraClimate'\n and 'FAO'\n'HWSDv2' soil database.", "License": "GPL (>= 3)", "URL": "https://icarda.github.io/QBMS/", "BugReports": "https://github.com/icarda/QBMS/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "NeedsCompilation": "no", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libgdal-dev gdal-bin libgeos-dev make\nlibuv1-dev libnetcdf-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev zlib1g-dev", "Repository": "https://icarda.r-universe.dev", "Date/Publication": "2026-10-10 18:23:02 UTC", "RemoteUrl": "https://github.com/icarda/qbms", "RemoteRef": "HEAD", "RemoteSha": "f38ebb0a756fc3034e736e184ae3df3fc45c53d3", "Packaged": { "Date": "2026-10-10 18:58:42 UTC", "User": "root" }, "_user": "icarda", "_type": "src", "_file": "QBMS_3.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/1b83a888f7e34a870b8146c87fc285503a9e6bebcbce6f4e66cf9d0b8983854c", "_filesize": 371483, "_sha256": 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"get_germplasm_data", "get_germplasm_list", "get_hwsd2", "get_marker_map", "get_pedigree_table", "get_program_studies", "get_qbms_connection", "get_study_data", "get_study_info", "get_terraclimate", "get_trial_data", "get_trial_obs_ontology", "get_trial_pedigree", "get_variants", "get_variantset", "gigwa_get_allelematrix", "gigwa_get_markers", "gigwa_get_metadata", "gigwa_get_samples", "gigwa_get_sequences", "gigwa_get_variants", "gigwa_list_dbs", "gigwa_list_projects", "gigwa_list_runs", "gigwa_set_db", "gigwa_set_project", "gigwa_set_run", "ini_hwsd2", "ini_terraclimate", "list_crops", "list_programs", "list_studies", "list_trials", "list_variantsets", "login", "login_bms", "login_breedbase", "login_germinate", "login_gigwa", "login_oauth2", "qbms_wizard", "qbms_wizard_server", "qbms_wizard_ui", "scan_brapi_endpoints", "set_crop", "set_program", "set_qbms_config", "set_qbms_connection", "set_study", "set_token", "set_trial", "set_variantset" ], "_help": [ { "page": "brapi_get_call", "title": "Internal Function for Core BrAPI GET Calls", "topics": [ "brapi_get_call" ] }, { "page": "brapi_map", "title": "BrAPI Mapping Table", "topics": [ "brapi_map" ] }, { "page": "brapi_post_search_allelematrix", "title": "Internal Function Used for Core BrAPI POST Calls (Allele Matrix Search)", "topics": [ "brapi_post_search_allelematrix" ] }, { "page": "brapi_post_search_call", "title": "Internal Function Used for Core BrAPI POST Calls", "topics": [ "brapi_post_search_call" ] }, { "page": "build_pedigree_table", "title": "Building Pedigree Table Recursively", "topics": [ "build_pedigree_table" ] }, { "page": "calc_biovars", "title": "Calculate the Bioclimatic Variables", "topics": [ "calc_biovars" ] }, { "page": "debug_qbms", "title": "Debug Internal QBMS Status Object", "topics": [ "debug_qbms" ] }, { "page": "engine_workflows", "title": "Engine Workflow Step Definitions", "topics": [ "engine_workflows" ] }, { "page": "get_async_page", "title": "Asynchronously Fetch a Single API Page", "topics": [ "get_async_page" ] }, { "page": "get_async_pages", "title": "Asynchronously Fetch Multiple API Pages", "topics": [ "get_async_pages" ] }, { "page": "get_auth_step_type", "title": "Get Authentication Step Type", "topics": [ "get_auth_step_type" ] }, { "page": "get_brapi_url", "title": "Get the BrAPI Endpoint URL for a given QBMS function", "topics": [ "get_brapi_url" ] }, { "page": "get_engine_config_params", "title": "Get Engine-Specific Configuration Parameters", "topics": [ "get_engine_config_params" ] }, { "page": "get_germplasm_attributes", "title": "Retrieve Attributes for a Specified Germplasm", "topics": [ "get_germplasm_attributes" ] }, { "page": "get_germplasm_data", "title": "Retrieve Observations Data for a Specified Germplasm.", "topics": [ "get_germplasm_data" ] }, { "page": "get_germplasm_id", "title": "Get Germplasm ID for a Specified Germplasm Name", "topics": [ "get_germplasm_id" ] }, { "page": "get_germplasm_list", "title": "Get the Germplasm List of the Current Active Study", "topics": [ "get_germplasm_list" ] }, { "page": "get_hwsd2", "title": "Get HWSD v2 Soil Data for a Given Location(s)", "topics": [ "get_hwsd2" ] }, { "page": "get_login_details", "title": "Login Pop-Up Window", "topics": [ "get_login_details" ] }, { "page": "get_marker_map", "title": "Get marker position information", "topics": [ "get_marker_map" ] }, { "page": "get_next_step", "title": "Get Next Step", "topics": [ "get_next_step" ] }, { "page": "get_parents", "title": "Get Direct Parents", "topics": [ "get_parents" ] }, { "page": "get_pedigree_table", "title": "Get the Pedigree Table", "topics": [ "get_pedigree_table" ] }, { "page": "get_prev_step", "title": "Get Previous Step", "topics": [ "get_prev_step" ] }, { "page": "get_program_studies", "title": "Get the List of Trials, Studies, and Locations Information for the Current Selected Program", "topics": [ "get_program_studies" ] }, { "page": "get_program_trials", "title": "Retrieve the List of Trials for the Active Breeding Program", "topics": [ "get_program_trials" ] }, { "page": "get_qbms_connection", "title": "Get the QBMS Connection", "topics": [ "get_qbms_connection" ] }, { "page": "get_step_sequence", "title": "Get Full Step Sequence", "topics": [ "get_step_sequence" ] }, { "page": "get_study_data", "title": "Get the Observations Data of the Current Active Study", "topics": [ "get_study_data" ] }, { "page": "get_study_info", "title": "Get the Details/Metadata of the Current Active Study", "topics": [ "get_study_info" ] }, { "page": "get_terraclimate", "title": "Get TerraClimate Data for a Given Coordinate(s)", "topics": [ "get_terraclimate" ] }, { "page": "get_trial_data", "title": "Get the Observations Data of the Current Active Trial", "topics": [ "get_trial_data" ] }, { "page": "get_trial_obs_ontology", "title": "Get the Traits Ontology/Metadata of the Current Active Trial", "topics": [ "get_trial_obs_ontology" ] }, { "page": "get_trial_pedigree", "title": "Get the Pedigree table for the Selected Trial", "topics": [ "get_trial_pedigree" ] }, { "page": "get_variants", "title": "Get Marker Matrix from the Selected Variant Set", "topics": [ "get_variants" ] }, { "page": "get_variantset", "title": "Get Marker Matrix from the Selected Variant Set", "topics": [ "get_variantset" ] }, { "page": "gigwa_get_allelematrix", "title": "Get Markers Matrix in the Selected GIGWA Run", "topics": [ "gigwa_get_allelematrix" ] }, { "page": "gigwa_get_markers", "title": "Get Markers Map in the Selected GIGWA Run", "topics": [ "gigwa_get_markers" ] }, { "page": "gigwa_get_metadata", "title": "Get the Metadata of the Current Active GIGWA Run", "topics": [ "gigwa_get_metadata" ] }, { "page": "gigwa_get_samples", "title": "Get the Samples List of the Current Active GIGWA Project", "topics": [ "gigwa_get_samples" ] }, { "page": "gigwa_get_sequences", "title": "Get the Sequences of the Current Active GIGWA Project", "topics": [ "gigwa_get_sequences" ] }, { "page": "gigwa_get_variants", "title": "Get Available Variants in the Selected GIGWA Run", "topics": [ "gigwa_get_variants" ] }, { "page": "gigwa_list_dbs", "title": "List GIGWA Databases", "topics": [ "gigwa_list_dbs" ] }, { "page": "gigwa_list_projects", "title": "Get the List of All Projects in the Selected GIGWA Database", "topics": [ "gigwa_list_projects" ] }, { "page": "gigwa_list_runs", "title": "Get the List of the Run Names Available in the Selected GIGWA Project", "topics": [ "gigwa_list_runs" ] }, { "page": "gigwa_set_db", "title": "Set the Current Active GIGWA Database by Name", "topics": [ "gigwa_set_db" ] }, { "page": "gigwa_set_project", "title": "Set the Current Active GIGWA Project", "topics": [ "gigwa_set_project" ] }, { "page": "gigwa_set_run", "title": "Set the Current Active GIGWA Run", "topics": [ "gigwa_set_run" ] }, { "page": "ini_hwsd2", "title": "Download and Setup HWSD v2.0 Data Files to Extract their Data Offline", "topics": [ "ini_hwsd2" ] }, { "page": "ini_terraclimate", "title": "Download TerraClimate netCDF Data Files to Extract their Data Offline", "topics": [ "ini_terraclimate" ] }, { "page": "list_crops", "title": "Retrieve Supported Crops from the Server", "topics": [ "list_crops" ] }, { "page": "list_locations", "title": "Get the List of Locations Information of the Current Selected Crop", "topics": [ "list_locations" ] }, { "page": "list_programs", "title": "Retrieve Breeding Programs for the Active Crop", "topics": [ "list_programs" ] }, { "page": "list_studies", "title": "Get the List of Studies in the Current Active Trial", "topics": [ "list_studies" ] }, { "page": "list_trials", "title": "List Trials in the Current Active Breeding Program", "topics": [ "list_trials" ] }, { "page": "list_variantsets", "title": "List Variant Sets in the Selected Study", "topics": [ "list_variantsets" ] }, { "page": "login", "title": "Login to a BrAPI Server", "topics": [ "login" ] }, { "page": "login_bms", "title": "Login to the Server", "topics": [ "login_bms" ] }, { "page": "login_breedbase", "title": "Login to the BreedBase Server", "topics": [ "login_breedbase" ] }, { "page": "login_germinate", "title": "Login to the Germinate Server", "topics": [ "login_germinate" ] }, { "page": "login_gigwa", "title": "Login to the GIGWA Server", "topics": [ "login_gigwa" ] }, { "page": "login_oauth2", "title": "Login using OAuth 2.0 Authentication", "topics": [ "login_oauth2" ] }, { "page": "navigation_step_ui", "title": "Navigation Step UI Factory", "topics": [ "navigation_step_ui" ] }, { "page": "normalize_options", "title": "Normalize QBMS List Function Results", "topics": [ "normalize_options" ] }, { "page": "qbms_wizard", "title": "QBMS Connection Wizard (Console / Gadget mode)", "topics": [ "qbms_wizard" ] }, { "page": "qbms_wizard_server", "title": "QBMS Wizard Module Server", "topics": [ "qbms_wizard_server" ] }, { "page": "qbms_wizard_ui", "title": "QBMS Wizard Module UI", "topics": [ "qbms_wizard_ui" ] }, { "page": 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