v1.3.0

What's Changed

• BI-2185 - Germplasm name validation "/" by @nickpalladino in #459
• [BI-2009] - Dynamic Concatenation of Entity + ObsUnitID (Exp UI) by @HMS17 in #458
• Update species migration to work with new uuids by @nickpalladino in #462
• BI-2212 - Update Postgres Version by @mlm483 in #454
• BI-2654 - Tests Failing with Opaque SQL Syntax Error by @mlm483 in #468
• BI-2650 - Re-enable disabled tests for brapi server uuid update by @nickpalladino in #464
• [BI-2632] Germplasm download from single list no longer working by @davedrp in #463
• BI-2664 - Add missing Honey Bee entry to species migration by @nickpalladino in #470
• [BI-2628] Replace Static ObsUnitID column to Dynamic Sub-entity ObsUnitID column in APpend Workflow by @dmeidlin in #469
• BI-2680 - BrAPI Prod PR bi-api test ci minimal starting point by @nickpalladino in #477
• BI-2623 - BI-API processing of observation dependencies taking too long by @nickpalladino in #476
• BI-2694 - Field Book pulling sub-entity observation units by @nickpalladino in #480
• BI-2540 - Update bi_user Table for Alternate OAuth Provider(s) by @mlm483 in #473
• merge release/1.1.1 into develop by @mlm483 in #488
• BI-2269 - Two experiments with the same title loaded to rel-test: Concurency by @nickpalladino in #478
• [BI-2110] New Append Exp Validations by @dmeidlin in #483
• [BI-2193] Improve/Correct Sub-Entity Tabular View by @HMS17 in #487
• [BI-2234] - Improve exp dataset export file by @HMS17 in #490
• [BI-2755] - improve default sub-unit sort by @HMS17 in #491
• [BI-2641] WIP by @davedrp in #493
• BI-2743 - Create Sub Entity Dataset, create obs level by @nickpalladino in #489
• [BI-2786] Remove code to add treatments to additional info by @jloux-brapi in #495
• [BI-2751] - Germplasm entry number weirdness by @HMS17 in #494
• BI-2796 - Autocompletions for dataset names in the program including other experiments displayed but unable to select by @nickpalladino in #497
• [BI-2791] Exp File Name Improvement by @HMS17 in #499
• [BI-2744] DeltaBreed:Create exp, create obs level CI by @HMS17 in #498
• [BI-2757] Fix observations not saving on sub entity dataset append by @jloux-brapi in #501
• [BI-2778] Deprecate additionalinfo usage for level and use obs unit lvl by @HMS17 in #500
• [BI-2803] Create new obsVarCount stat for both Experiment creation and appends use case by @jloux-brapi in #502
• [BI-2816] Unknown error when creating new exp with more than one exp title by @HMS17 in #503
• [BI-2814] Create Sub Entity Dataset: Update OUs to supply levelNameDbIds by @jloux-brapi in #506
• [BI-2813] Set levelNameDbIds in OUs in experiment creation use case by @jloux-brapi in #507
• BI-2783 - Logic In Germplasm Import Dependent on Name Lookup by @davedrp in #508
• [BI-2823] Remove sub entity level name from level relationships in sub entity dataset creation by @davedrp in #509
• BI-2805 - Fix autocomplete to work with new BrAPI levelNames by @nickpalladino in #505
• BI-2836 - Unable to retrieve program dataset names error message by @nickpalladino in #511
• BI-2825 - Add Sunflower to list of species by @davedrp in #512
• BI-2801 - Connection Pool Error while trying to download sub-entity file by @nickpalladino in #510
• BI-2860: Made changes to the end point to limit the access. by @humsika in #518
• Release/1.3 by @nickpalladino in #519

Full Changelog: v1.2.0...v1.3.0

v1.2.0

What's Changed

• [BI-2578][BI-2489] - Optimize BrAPI Germplasm Search by @jloux-brapi in #447
• [BI-2579] Refresh cache after import completes by @jloux-brapi in #448
• merge release/1.1 into develop by @mlm483 in #461
• BI-2654 - Tests Failing with Opaque SQL Syntax Error by @mlm483 in #465
• BI-2616 - Increased signup token expiration from 1hr to 24hr by @nickpalladino in #467
• Bug/bi 2632 by @davedrp in #471
• BI-2639 - List referencing existing germplasm - very slow and impacting jobs timer by @nickpalladino in #472
• BI-2656 - Append Workflow Requires Timestamps by @mlm483 in #475
• BI-2656 - Additional Logging by @mlm483 in #484
• BI-2656 - Append with Prior Observations Blank Edge Case by @mlm483 in #485
• Merge release/1.1.1 into main by @mlm483 in #486

New Contributors

• @jloux-brapi made their first contribution in #447

Full Changelog: v1.1.0...v1.2.0

v1.1.0

Features

• [BI-2573] - Germplasm file import assigns pedigree incorrectly @nickpalladino (#451)
• [BI-2431] - Sample submission delete BrAPI server changes @nickpalladino (#440)
• [BI-2380] - Add Delete Option to Samples View @nickpalladino (#440)
• [BI-2379] - Create Delete Endpoint for Deltabreed Sample Controller @nickpalladino (#440)
• [BI-2376] - Create Delete Endpoint for Deltabreed Experiment Controller @mlm483 (#437)
• [BI-2374] - Create Endpoints on BJTS for Processing Batch Delete Operations @dmeidlin (#434)
• [BI-2373] - Add Delete Option to Germplasm Lists View @dmeidlin (#434)
• [BI-2372] - Create Deltabreed List Controller @dmeidlin (#434)
• [BI-2047] - Pull Existing Observation Values For An Experiment Into Field-Book @mlm483 (#443)

Bugfixes

• [BI-2595] - Regression: Transactional Email IOException @mlm483 (#457, #455)
• [BI-2594] - Germplasm list table wrong when duplicate names are included @nickpalladino (#453)
• [BI-2593] - Circular Dependency False Positive Pecan Data @nickpalladino (#452)
• [BI-2585] - BJTS migration fail due to DB field name change @davedrp (#449)
• [BI-2543] - Germplasm circular dependency @nickpalladino (#451)
• [BI-2424] - Refactor getObservationUnitsByDbId for clarity @mlm483 (#439)
• [BI-2343] - GID and List Entry Number filtering not informative @HMS17 (#435)
• [BI-2187] - Non-sequential GIDs After Circular Dependency Error @davedrp (#445)
• [BI-2156] - Upgrade Apache Tika to 2.3.0+ @mlm483 (#457, #442, #432)

v1.0.0

Features

• [BI-2304] - Support Duplicate Germplasm in Lists Referencing Existing Germplasm @mlm483 (#401) (#409)
• [BI-2295] - Allow Experimental Collaborators To View Collaborators @HMS17 (#396)
• [BI-2258] - Experimental Collaborator DAO and Services for Experiments and Observations @mlm483 (#385)
• [BI-2257] - Experimental Collaborator DAO and Services for experimental_program_user_role @mlm483 (#383) (#387)
• [BI-2256] - Experimental Collaborator BI-API Changes @nickpalladino (#390)
• [BI-2255] - Experimental Collaborator Micronaut Changes @davedrp (#388)
• [BI-2254] - Experimental Collaborator DB Changes @mlm483 (#382)
• [BI-2227] - Modify Upload Experiment and Observations File to accept without sub units @nickpalladino (#394)
• [BI-2226] - Experiment and Observations Template: Remove 2 sub-obs columns @nickpalladino (#394)
• [BI-2163] - Add multiple species to the species list when creating a program @nickpalladino (#373) (#381)
• [BI-2134] - Append experimental dataset workflow @dmeidlin (#359) (#372) (#384) (#389) (#391) @davedrp (#376)
• [BI-2132] - Create new experiment workflow @nickpalladino (#366) (#375)
• [BI-2122] - Workflows Backend Selector @nickpalladino (#355) @dmeidlin (#360) (#379)
• [BI-2115] - Experiment Import Workflows Refactor @nickpalladino (#352)
• [BI-2067] - Merge Tim's FieldBook BrAPI program endpoint with Mr.Bean work @HMS17 (#407) (#410)
• [BI-2038] - Make BrAPI v2 /commoncropnames and /programs only return information relevant to Delta Breed program @nickpalladino (#328)
• [BI-2005] - Expand Exp Template @nickpalladino (#323)
• [BI-1692] - Change role names @HMS17 (#377) (#386)

Bugfixes

• [BI-2355] - Non-informative error message: regression @HMS17 (#423)
• [BI-2354] - Incorrect Case Sensitivity in Exp Import Error Message @mlm483 (#420) (#424)
• [BI-2344] - Incorrect Germplasm Export in Case of Duplicate Germplasm Names @mlm483 (#419) (#421)
• [BI-2338] - Germplasm file with problems is loading, but preventing download @nickpalladino (#416) (#425)
• [BI-2330] - MrBean DeltaBreed Integration /brapi/v2/observations/table endpoint (potential hackathon item) @mlm483 (#413) (#418)
• [BI-2328] - Experimental observation file import removes periods from column headers @davedrp (#411) (#417)
• [BI-2317] - System Admin Must Retain Full Read Access To All Programs @dmeidlin (#405)
• [BI-2310] - Exp import: extraneous error message @HMS17 (#403)
• [BI-2309] - BrAPI observationsunits response contains incorrect germplasmDbIds @nickpalladino (#402) (#406)
• [BI-2308] - Field Book BrAPI Integration - Importing Fields @nickpalladino (#402) (#406)
• [BI-2306] - Helium BrAPI integration filter by accessionNumber (potential hackathon item) @nickpalladino (#412)
• [BI-2283] - Modify the experiment_program_user_role.program_user_role_id FK to use ON DELETE CASCADE @mlm483 (#393)
• [BI-2274] - BrAPI germplasm search response incorrect @nickpalladino (#397) (#404)
• [BI-2267] - Trim trailing white space on breeding method file uploads @davedrp (#392) (#399)
• [BI-2266] - Correct entry numbers on all germplasm export list @mlm483 (#395)
• [BI-2203] - Insert sanbox email into bi_user table @davedrp (#408)
• [BI-2167] - Lat and long values are getting swapped in the exp download file @nickpalladino (#368)
• [BI-2126] - Env year missing from dataset view @davedrp (#380)
• [BI-2093] - (Performance) Observation Cache Refreshing After Every PUT During Overwrite @davedrp (#376)
• [BI-1975] - "Unknown" Breeding Method not recognized @nickpalladino (#369)

v0.9.1

Features

• [BI-2101] - Configure Transactional Email for Production DeltaBreed @mlm483 (#351)
• [BI-2100] - BrAPI Hackathon Integration of Helium with DeltaBreed @nickpalladino (#337)
• [BI-2058] - Add Observations and ObservationUnits to Redis Cache @mlm483 (#339)
• [BI-1993] - Accept NA observations @HMS17 (#330)
• [BI-1868] - Ontology: Display full name in table and details pane @HMS17 (#326)

Bugfixes

• [BI-2155] - Cannot create a new list referencing existing GIDs @dmeidlin (#363)
• [BI-2128] - Blank cells overwriting existing observations @mlm483 (#357)
• [BI-2127] - Position Information missing from exp download file @davedrp (#356)
• [BI-2104] - Can't create experiment with timestamped observations v0.9 @davedrp (#354)
• [BI-2065] - Experiment overwrite does not do all data validations on phenotype data @HMS17 (#340)

v0.9.0

Features

• [BI-2027] - Add More Detailed Logging Around Redis Cache @mlm483 (#322)
• [BI-1965] - Upgrade to Gigwa v2.6.2 @timparsons (#301)
• [BI-1965] - Upgrade to Gigwa v2.6.2 @mlm483 (#321)
• [BI-1956] - Add sorghum and hemp species migration @nickpalladino (#307)
• [BI-1945] - Store AdditionalInfo as JSONB in BrAPI Java TestServer @mlm483 (#312, #314)
• [BI-1922] - Add ability to download all germplasm in a program @davedrp (#311)
• [BI-1921] - Support Field Book Study Import from DeltaBreed @timparsons (#308)
• [BI-1915] - Export Ontology File @davedrp (#310)
• [BI-1914] - Improve exp dataset sort @davedrp (#303)
• [BI-1910] - Allow Breeder to Upload a Genotype Sample File @timparsons (#306)
• [BI-1890] - Experimental Test/Check Improvement @davedrp (#299)
• [BI-1867] - Ontology: Increase name length to 16 characters @HMS17 (#317)
• [BI-1847] - Experiment import template formatting improvements @mlm483 (#292)
• [BI-1265] - 4 Overwrite entity dataset @dmeidlin (#305, #327)
• [BI-2017] - Change Germplasm Upload to unify with sample submission @davedrp (#345)
• [BI-1680] - Somaclone Breeding Method @mlm483 (#346)

Bugfixes

• [BI-2064] - Invalid message if required data is missing @davedrp (#334)
• [BI-2053] - Remove 'Scale class' notation showing under 'Units' @mlm483 (#331)
• [BI-2046] - Overwrite observations happening without reference to ObsUnitID @dmeidlin (#332)
• [BI-2045] - Failure to report error when uploading duplicated experiment name @davedrp (#333)
• [BI-2043] - Overwrite performance is very slow @mlm483 (#329)
• [BI-2028] - Duplicated accession names getting assigned duplicated GIDs after Exp&Obs upload @dmeidlin (#320)
• [BI-2019] - Pedigree Viewer Not Rendering @mlm483 (#324)
• [BI-2014] - Phenotypes and Observations not rendering, unable to download experiment @davedrp (#325)
• [BI-1960] - Exp import proceeds with multiple exp names & error message improvement @dmeidlin (#316)
• [BI-1930] - trait names are case sensitive @davedrp (#300)
• [BI-1852] - Duplicate breeding method can be created @davedrp (#294)
• [BI-1761] - Error message with the backend code. @dmeidlin (#319)
• [BI-1340] - Unable to edit a trait - Error getting editable status @mlm483 (#293)

Hotfixes

• [BI-1945-hotfix] - updated bind mount paths @mlm483 (#314)
• [BI-2053-fix] - Handled Trait Form Submission Code Path @mlm483 (#343)

v0.8.1

Detailed Release Information

Features

• [BI-1900] - Exp error message improvement: unrecognized column header @mlm483 (#296, #302)
• [BI-1872] - Generate Access Token for using BrAPI with DeltaBreed @timparsons (#289)
• [BI-1845] - Update any calls to fetch gemplasm lists via GET /lists to explicitly pass the list type as germplasm @mlm483 (#284)
• [BI-1831] - Add DatasetID to ObservationUnits @dmeidlin (#286)
• [BI-1818] - [bi-api] - BI-1645 - View exp: Obs dataset tab, details, and summary stats @dmeidlin (#268)
• [BI-1720] - Export Multiple Environment Datasets as Zip @mlm483 (#263, #274, #275)
• [BI-1647] - View Experiments: Observation Dataset Table @davedrp (#280)
• [BI-1618] - Import File Selection Behavior @davedrp (#262)
• [BI-1456] - Ontology Share - Improvement @dmeidlin (#261)
• [BI-1294] - Implement Caching Layer for Experiments @dmeidlin (#264)

Bugfixes

• [BI-1932] - GIDs missing from Observation dataset table @timparsons (#295)
• [BI-1911] - Environment Year Missing from Exp table @davedrp (#304)
• [BI-1909] - Unable to open observation dataset. @timparsons (#291)
• [BI-1881] - Remove Need to Provide Parents to processGermplasmForDisplay @mlm483 (#290)
• [BI-1880] - Error saving experiment import / partial upload in Breedbase @mlm483 (#287)
• [BI-1844] - Experiments & Observations file import didn't recognize the word TEST or CHECK @davedrp (#282)
• [BI-1819] - Experimental download file: phenotypes are out of order @dmeidlin (#266)
• [BI-1781] - Pedigree viewer not functional in programs connected to BrAPI test server @nickpalladino (#253)
• [BI-1771] - All germplasm and list tables not loading when DeltaBreed is connected to the BrAPI test server @mlm483 (#260, #283)

v0.8.0

Detailed Release Information

Features

• [BI-1716] - [bi-api] - BI-1644 - View experiment: Details, Summary Stats, Actions @davedrp (#254)
• [BI-1665] - Store observations when importing new environments @davedrp (#234)
• [BI-1651] - Allow programs to choose/create breeding methods @timparsons (#236)
• [BI-1650] - Store and fetch genotype data @timparsons (#228)
• [BI-1629] - Add filtering to OntologyTable @dmeidlin (#243)
• [BI-1616] - Add Filtering to Germplasm Lists Table @nickpalladino (#237)
• [BI-1615] - Add termType to Trait DB Table @HMS17 (#231)
• [BI-1613] - Add Term Type to Ontology Term Import @HMS17 (#233)
• [BI-1612] - Experiment Import Phenotype Data Persistence @nickpalladino (#220)
• [BI-1606] - Allow germplasm records to be in multiple lists @dmeidlin (#224)
• [BI-1583] - Error Message 1: Missing Data Worksheet @davedrp (#246)
• [BI-1555] - Cache program ontology terms @timparsons (#206)
• [BI-1548] - Experiments: User and Creation Date Refinement @nickpalladino (#238)
• [BI-1477] - Improve All Experiments Table @HMS17 (#230)
• [BI-1473] - Allow user to append existing germplasm with optional details @HMS17 (#211)
• [BI-1465] - 6.1 Observation Dataset Export File @dmeidlin (#259)
• [BI-1198] - 5.0 All Experiments Table @HMS17 (#201)
• [BI-1195] - 4.3 Exp Preview: Append Experiment with Observations @timparsons (#241)
• [BI-1194] - 4.2 Upload with timestamps @HMS17 (#225)
• [BI-1193] - 4.1 Associate phenotypes with experiment observation dataset @dmeidlin (#247, #256, #258)
• [BI-1183] - 3.1 Import Validations: Ontology-specific observation criteria @nickpalladino (#210)
• [BI-1147] - 2.0 Experimental Data Preview Universal Elements @dmeidlin (#219, #221)
• [BI-1129] - View Germplasm List @dmeidlin (#222, #240)

Bugfixes

• [BI-1864] - Experiment Export doesn't consistently work @timparsons (#276)
• [BI-1855] - Create germplasm list not working @nickpalladino (#281)
• [BI-1842] - Append existing exp with observations isn't working @timparsons (#273)
• [BI-1832] - Treatment factors not being stored in BreedBase @nickpalladino (#272)
• [BI-1825] - Need to support legacy Trait names in BreedBase (without Program namespacing) @timparsons (#270)
• [BI-1803] - Excel formatting preventing ontology file import @mlm483 (#257)
• [BI-1798] - Unknowns missing from germplasm downloads @nickpalladino (#255)
• [BI-1779] - Import germplasm with unspecified breeding method @timparsons (#251)
• [BI-1778] - Environments locations and years @timparsons (#250)
• [BI-1760] - Error saving experiment import @mlm483 (#249)
• [BI-1741] - Genotype Import @timparsons (#244)
• [BI-1721] - Show All - Breeding Methods table @timparsons (#242)
• [BI-1689] - Jobs Count: Import germplasm incorrect count @mlm483 (#252)
• [BI-1632] - Unknown Pedigree not displaying for BrAPI-server programs @HMS17 (#217)
• [BI-1630] - De-activated programs still visible on Shared Ontology @HMS17 (#223)
• [BI-1440] - ISSUE: ERROR message in banner calls out "scale data type" when field is "scale class" @nickpalladino (#239)

v0.7.1

Hotfixes

• BI-1683 - Missing female parent in biparental cross results in dropped male parent v0.7 @timparsons (#235)

v0.7.0

Detailed Release Information

Features

• [BI-1638] - Cache germplasm data immediately after saving to BrAPI @timparsons (#218)
• [BI-1590] - Disallow Adding New Observation Unit to Existing Environment @HMS17 (#212)
• [BI-1528] - New Breeding Method - Creation of tetraploids by applied pressure shock @HMS17 (#198)
• [BI-1527] - New Breeding Method - Creation of triploids by applied pressure or temperature shock @HMS17 (#198)
• [BI-1494] - Improve pedigree view display @HMS17 (#198)
• [BI-1491] - New Breeding Method - Polyembryonic seed selection @HMS17 (#198)
• [BI-1478] - Add Pedigree to All Germplasm Table @HMS17 (#213)
• [BI-1443] - Refactor BRAPIDAOUtil @dmeidlin (#204)
• [BI-1230] - Truly unknown germplasm @HMS17 (#205)
• [BI-1224] - 4.1.1 Show list creator in Germplasm lists table @HMS17 (#194)
• [BI-1202] - 5.2 Sort Germplasm in All Germplasm table @ctucker3 (#157)
• [BI-1199] - 4.2 Choose file format for germplasm export @HMS17 (#193)
• [BI-1191] - 5.3 Filter Germplasm on All Germplasm Table @ctucker3 (#192)
• [BI-1189] - 4.0 Exp Preview & Commit: Create Exp Independent Variables @davedrp (#203)
• [BI-1189] - 4.0 Exp Preview & Commit: Create Exp Independent Variables @davedrp (#187)
• [BI-1146] - 3.0 Upload & Validate Independent Variables for New Experiment @davedrp (#187)
• [BI-1146] - 3.0 Upload & Validate Independent Variables for New Experiment @davedrp (#197)
• [BI-1146] - 3.0 Upload & Validate Independent Variables for New Experiment @davedrp (#182)
• [BI-693] - Upgrade Micronaut to 2.x @ctucker3 (#146)
  ​

Bugfixes

• [BI-1594] - Store Unique ‘Exp Unit IDs’ @davedrp (#216)
• [BI-1580] - BrAPIDAOUtils pagination only fetching first page of results @dmeidlin (#215)
• [BI-1579] - Breedbase progeny endpoint not BrAPI-compliant @HMS17 (#205)
• [BI-1574] - Exp Block # not displayed @dmeidlin (#207)