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Merge from BI server#1

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BrapiCoordinatorSelby wants to merge 93 commits intoplantbreeding:bi-server-implplantbreeding/brapi-Java-ProdServer:bi-server-implfrom Breeding-Insight:brapi-server-v2Breeding-Insight/brapi-Java-TestServer:brapi-server-v2Copy head branch name to clipboard

+6,456-12,492

Commits

Commits on Dec 14, 2022

• Merge pull request #7 from Breeding-Insight/release/0.7

  Show description for 7309c14
  nickpalladino

  authored
  7309c14

Commits on Dec 15, 2022

• Update pom.xml

  timparsons

  authored
  0f40c8b

Commits on Jun 27, 2023

• Merge pull request #10 from Breeding-Insight/bug/BI-1781

  Show description for 7383fac
  nickpalladino

  authored
  7383fac

Commits on Jul 6, 2023

• Merge branch 'plantbreeding/brapi-Java-TestServer:brapi-server-v2' into develop

  timparsons

  committed
  7f64183

Commits on Aug 1, 2023

• [BI-1771] - performance experiments

  Show description for c23c0a9
  mlm483

  committed
  c23c0a9

Commits on Aug 3, 2023

• [BI-1771] - added germplasm-related indexes

  mlm483

  committed
  9a35d3f

• [BI-1771] - reverted index annotation

  mlm483

  committed
  e1f6cf9

• [BI-1771] - reverted whitespace changes

  mlm483

  committed
  bf0cc00

Commits on Aug 14, 2023

• [BI-1771] - made create_indexes.sql idempotent

  Show description for fb08a50
  mlm483

  committed
  fb08a50

Commits on Aug 15, 2023

• [BI-1771] - set hibernate.ddl-auto to create-only

  mlm483

  committed
  deb9572

Commits on Aug 18, 2023

• Merge pull request #11 from Breeding-Insight/bug/BI-1771

  Show description for 43c67e6
  mlm483

  authored
  43c67e6

Commits on Aug 22, 2023

• Merging release v0.8

  timparsons

  authored
  5a29d77

Commits on Sep 13, 2023

• [BI-1909] Exploring converting *ToOne relationships to lazy loading and how performance can be improved for fetching OUs, Observations, and ObsVars

  timparsons

  committed
  7fce804

Commits on Sep 15, 2023

• [BI-1909] NPE fix, converting sysouts to use Logger

  timparsons

  committed
  441814a

Commits on Sep 19, 2023

• [BI-1909] Updating GermplasmService to eagerly fetch related date for searches

  Show description for 0f9ec46
  timparsons

  committed
  0f9ec46

Commits on Sep 22, 2023

• [BI-1909] suggested changes

  timparsons

  committed
  57da450

Commits on Sep 25, 2023

• Merge pull request #14 from Breeding-Insight/bug/BI-1909

  Show description for 504e1de
  timparsons

  authored
  504e1de

• Merge branch 'release/0.8.1' into develop

  timparsons

  committed
  8f4d7b1

Commits on Oct 23, 2023

• Merge pull request #15 from plantbreeding/brapi-server-v2

  Show description for 0e343c6
  mlm483

  authored
  0e343c6

Commits on Oct 26, 2023

• [BI-1945] - saving work in progress

  mlm483

  committed
  fc92574

• [BI-1945] - store additionalInfo on primary entities as JSONB

  mlm483

  committed
  9bc8ade

• [BI-1945] - optimized imports

  mlm483

  committed
  65f061d

• [BI-1945] - updated template, readme

  mlm483

  committed
  4789ff9

• [BI-1945] - cleaned up SQL dummy data migrations

  mlm483

  committed
  fdcca4d

• [BI-1945] - updated template

  mlm483

  committed
  3e2e3a0

• [BI-1945] - removed unused class

  mlm483

  committed
  0690839

• [BI-1945] - renamed method

  mlm483

  committed
  ed01390

Commits on Oct 27, 2023

• [BI-1945] - handled null case

  mlm483

  committed
  aa0f1a5

• [BI-1945] - added stringtype=unspecified to template

  mlm483

  committed
  8bd3c32

Commits on Nov 6, 2023

• [BI-1945] - removed debug log

  mlm483

  committed
  03eedc4

• [BI-1945] - optimized imports

  mlm483

  committed
  a1f546b

• [BI-1945] - removed additionalInfo joins

  Show description for b4ac393
  mlm483

  committed
  b4ac393

• [BI-1945] - updated README.md

  mlm483

  committed
  0f0c6d2

Commits on Nov 8, 2023

• Merge pull request #18 from Breeding-Insight/release/0.8.1

  Show description for 7efbb52
  mlm483

  authored
  7efbb52

Commits on Nov 9, 2023

• Create pull.yml

  timparsons

  authored
  404343a

Commits on Nov 13, 2023

• Merge pull request #17 from Breeding-Insight/feature/BI-1945

  Show description for 73923fa
  mlm483

  authored
  73923fa

Commits on Nov 14, 2023

• [BI-1945] - added ON DELETE CASCADE to xref linking tables

  mlm483

  committed
  c537709

Commits on Nov 21, 2023

• Merge pull request #20 from Breeding-Insight/feature/BI-1945-fix

  Show description for 57848e3
  mlm483

  authored
  57848e3

Commits on Feb 5, 2024

• [BI-2040] The fetchScaleValidValueCategories() method was causing the problem. It was not needed. The ScaleVlalidValueCategories were present (even though it is set to fetch LAZY) because of the SQ…

  Show description for 65bd99a
  davedrp

  committed
  65bd99a

• [BI-2040] removed all calls to fetchXXXXX(page) and the methods themsleves

  davedrp

  committed
  4447807

• [BI-2040] removed unused import-statements from ObservationVariableService.java

  davedrp

  committed
  22b5fdd

Commits on Feb 6, 2024

• [BI-2051] - batched inserts for efficiency

  mlm483

  committed
  1b6b9fb

Commits on Feb 8, 2024

• [BI-2051] - removed comment

  mlm483

  committed
  f38b21e

Commits on Feb 12, 2024

• Merge pull request #22 from Breeding-Insight/bug/BI-2051

  Show description for 28c33bc
  mlm483

  authored
  28c33bc

• Merge pull request #21 from Breeding-Insight/bug/BI-2040

  Show description for ed22fdd
  davedrp

  authored
  ed22fdd

Commits on Feb 22, 2024

• Merge pull request #23 from plantbreeding/brapi-server-v2

  Show description for 0c5b914
  mlm483

  authored
  0c5b914

Commits on Mar 11, 2024

• [BI-2078] - made performance improvements (thanks BrapiCoordinatorSelby)

  mlm483

  committed
  60d2cd2

Commits on Mar 12, 2024

• Merge pull request #26 from Breeding-Insight/release/0.9

  Show description for a3e3835
  mlm483

  authored
  a3e3835

Commits on Mar 19, 2024

• Merge pull request #25 from Breeding-Insight/bug/BI-2078

  Show description for dd070f7
  mlm483

  authored
  dd070f7

• Merge pull request #27 from Breeding-Insight/bug/BI-2078

  Show description for d295cfa
  mlm483

  authored
  d295cfa

Commits on Apr 10, 2024

• Merge pull request #28 from Breeding-Insight/release/0.9

  Show description for e6a3d48
  mlm483

  authored
  e6a3d48

Commits on Apr 12, 2024

• Merge pull request #24 from plantbreeding/brapi-server-v2

  Show description for 08a3b9d
  mlm483

  authored
  08a3b9d

Commits on Apr 15, 2024

• Merge pull request #29 from Breeding-Insight/release/0.9

  Show description for 24dbf87
  mlm483

  authored
  24dbf87

Commits on Apr 17, 2024

• Filter out pedigree nodes with null germplasm

  nickpalladino

  committed
  4452e8a

Commits on Apr 19, 2024

• Updated comment

  nickpalladino

  committed
  aaf7fbd

Commits on May 2, 2024

• Merge pull request #30 from Breeding-Insight/helium-integration

  Show description for f9c8ca8
  nickpalladino

  authored
  f9c8ca8

Commits on Jun 5, 2024

• Merge pull request #32 from Breeding-Insight/release/0.9.1

  Show description for b412589
  mlm483

  authored
  b412589

Commits on Jun 28, 2024

• [BI-2109] - added migration for datasets

  mlm483

  committed
  6e53be5

Commits on Jul 2, 2024

• [BI-2109] - made migration safer

  mlm483

  committed
  8e06edf

Commits on Jul 10, 2024

• Merge pull request #33 from Breeding-Insight/feature/BI-2109

  Show description for 31d1129
  mlm483

  authored
  31d1129

Commits on Aug 28, 2024

• Merge pull request #31 from plantbreeding/brapi-server-v2

  Show description for 4da5d94
  pull[bot]

  authored
  4da5d94

Commits on Sep 18, 2024

• [BI-2304] - added migrations for list position

  mlm483

  committed
  3377138

Commits on Sep 19, 2024

• [BI-2304] - fixed migration

  mlm483

  committed
  ea85b8c

Commits on Sep 20, 2024

• [BI-2304] - preserve list order without changing API

  mlm483

  committed
  0c6952b

• [BI-2304] - used zero-indexing in migration

  mlm483

  committed
  06b8cac

Commits on Oct 2, 2024

• [BI-2304] - changes based on review

  mlm483

  committed
  76665ab

Commits on Oct 7, 2024

• Merge pull request #37 from Breeding-Insight/feature/BI-2304

  Show description for 86153e9
  mlm483

  authored
  86153e9

Commits on Nov 8, 2024

• Merge pull request #39 from Breeding-Insight/release/1.0

  Show description for 8ec5466
  mlm483

  authored
  8ec5466

Commits on Dec 13, 2024

• create batch entity and controller endpoints

  dmeidlin

  committed
  e9e8acd

• json deserialize searchrequest sub-types

  dmeidlin

  committed
  492aabd

• return batchDbID in POST batches response results

  dmeidlin

  committed
  46134a2

• refactor

  dmeidlin

  committed
  f2927aa

• add constraint to cascade on delete for list_item

  dmeidlin

  committed
  c33a8b6

• add soft_deleted column to list tables

  dmeidlin

  committed
  b5f09ec

• modify list repository to include clause softDelete=falsee

  dmeidlin

  committed
  a226dee

• use where clause and transactional annotations

  dmeidlin

  committed
  5f26eec

• soft-delete batch lists

  dmeidlin

  committed
  0aa634a

• add hard delete of single trial

  dmeidlin

  committed
  04dfa6c

• create hard-delete endpoint for single sample

  dmeidlin

  committed
  fe1ae79

• cascade delete for trial and sample

  dmeidlin

  committed
  f3283f4

• add soft_delete columns to trial and sample related tables

  dmeidlin

  committed
  aa7386e

• create sample service soft-delete method

  dmeidlin

  committed
  008e033

• add soft-delete method to trial service

  dmeidlin

  committed
  80838e1

• create Trial and Sample components

  dmeidlin

  committed
  6aab414

• optimize imports

  dmeidlin

  committed
  e94040c

• respond with 204 for successful delete

  dmeidlin

  committed
  5d915ba

• return entity dbids in response for POST deleteBatch

  dmeidlin

  committed
  1d4a768

• add batchDeleteDbId query param to GET endpoints for lists, trials, samples

  dmeidlin

  committed
  a07aa4e

• create new exception class for wrong batch delete type

  dmeidlin

  committed
  8f33016

• delete batch entity when deleting batch contents

  dmeidlin

  committed
  f251236

• add cascade delete constraints for study foreign keys

  dmeidlin

  committed
  e1761f8

• rename batch to batch delete

  dmeidlin

  committed
  b2a6ee3

• Merge pull request #38 from Breeding-Insight/hackathon/delete-germplasm

  Show description for dbe8cac
  dmeidlin

  authored
  dbe8cac