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)

v0.6.0

About the release

v0.6 is the latest release in preparation for the Breeding Insight v1.0 public release. This release continues the development of genealogy management and ontologies, and introduces the new jobs module. This release reflects a smaller work effort than the previous release. Moving forward Breeding Insight plans to continue smaller more frequent software releases.

New features

Germplasm Details

• Hyperlinks to germplasm details from across user interface
• Summary of germplasm details
• Pedigree view: explore pedigree relationships with an interactive interface.

Ontology

• Ability to share an ontology across programs

Jobs

• Monitor data upload status asynchronously via the new jobs module.

Detailed Release Information

Features

• [BI-1459] - Create job status page to view running and completed background jobs @timparsons (#185)
• [BI-1420] - Allow Germplasm to Have Synonyms @ctucker3 (#180)
• [BI-1375] - Make GIDs clickable links @HMS17 (#177)
• [BI-1366] - Subscribe a program to a shared ontology @ctucker3 (#175)
• [BI-1365] - Scope ontology terms to be within a program when saved over BrAPI @nickpalladino (#172)
• [BI-1364] - View a shared ontology that a program is subscribed to @dmeidlin (#179)
• [BI-1363] - Share a program's ontology with other programs @ctucker3 (#166)
• [BI-1339] - Germplasm Details Page @HMS17 (#176)

Bugfixes

• [BI-1487] - The method name is a concatenation of the method description and the method class on the Ontology Term page. @ctucker3 (#191)
• [BI-1446] - Missing error messages below the required fields on Term create page @ctucker3 (#190)
• [BI-1445] - Trait Column value not the same as entered in the the Term creation @HMS17 (#189)