Merge from BI Server#2

Merged

jloux-brapi merged 66 commits intobrapi-server-v2from

Jan 8, 2025

Commits on Dec 17, 2024

[BI-1771] - performance experiments

mlm483
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[BI-1771] - added germplasm-related indexes
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[BI-1771] - reverted index annotation

mlm483
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[BI-1771] - reverted whitespace changes

mlm483
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[BI-1771] - made create_indexes.sql idempotent

mlm483
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[BI-1909] Exploring converting *ToOne relationships to lazy loading and how performance can be improved for fetching OUs, Observations, and ObsVars

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

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

timparsons
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[BI-1909] suggested changes

timparsons
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Create pull.yml

timparsons
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[BI-1945] - saving work in progress

mlm483
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[BI-1945] - store additionalInfo on primary entities as JSONB

mlm483
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[BI-1945] - optimized imports

mlm483
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[BI-1945] - updated template, readme
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[BI-1945] - cleaned up SQL dummy data migrations

mlm483
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[BI-1945] - updated template

mlm483
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[BI-1945] - removed unused class

mlm483
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[BI-1945] - renamed method

mlm483
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[BI-1945] - handled null case

mlm483
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[BI-1945] - added stringtype=unspecified to template

mlm483
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[BI-1945] - removed debug log

mlm483
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[BI-1945] - optimized imports

mlm483
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[BI-1945] - removed additionalInfo joins

mlm483
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[BI-1945] - updated README.md

mlm483
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[BI-1945] - added ON DELETE CASCADE to xref linking tables

mlm483
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[BI-2051] - batched inserts for efficiency

mlm483
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[BI-2051] - removed comment

mlm483
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[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 …

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

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

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

mlm483
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Filter out pedigree nodes with null germplasm

nickpalladino
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Updated comment

nickpalladino
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[BI-2109] - added migration for datasets

mlm483
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[BI-2109] - made migration safer

mlm483
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[BI-2304] - added migrations for list position

mlm483
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[BI-2304] - fixed migration

mlm483
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[BI-2304] - preserve list order without changing API

mlm483
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[BI-2304] - used zero-indexing in migration

mlm483
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[BI-2304] - changes based on review

mlm483
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create batch entity and controller endpoints

dmeidlin
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json deserialize searchrequest sub-types

dmeidlin
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return batchDbID in POST batches response results

dmeidlin
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refactor

dmeidlin
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add constraint to cascade on delete for list_item

dmeidlin
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add soft_deleted column to list tables

dmeidlin
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modify list repository to include clause softDelete=falsee

dmeidlin
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use where clause and transactional annotations

dmeidlin
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soft-delete batch lists

dmeidlin
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add hard delete of single trial

dmeidlin
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create hard-delete endpoint for single sample

dmeidlin
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cascade delete for trial and sample

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add soft_delete columns to trial and sample related tables

dmeidlin
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create sample service soft-delete method

dmeidlin
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add soft-delete method to trial service

dmeidlin
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create Trial and Sample components

dmeidlin
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optimize imports

dmeidlin
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respond with 204 for successful delete

dmeidlin
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return entity dbids in response for POST deleteBatch

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

dmeidlin
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create new exception class for wrong batch delete type

dmeidlin
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delete batch entity when deleting batch contents

dmeidlin
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add cascade delete constraints for study foreign keys

dmeidlin
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rename batch to batch delete

dmeidlin
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Solve dummy data migration issues
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Commits on Dec 19, 2024

Merge pull request #75 from plantbreeding/keycloak-dev-docker
jloux-brapi
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