openbis integration in sample registration

[KochTobi]

What happened?

This issue is regarding creating samples and experiments.
All those entities are created in the database and in openbis as data is attached to them. However in some cases, failures can cause inconsistencies between openbis and the database.

For more complex actions like the registering of samples failure can cause unexpected inconsistency.

---
title: "sample registration"
---
sequenceDiagram
SampleRegistrationServiceV2 ->> BatchRegistrationService : register batch
BatchRegistrationService ->> BatchDomainService : register
BatchDomainService ->> BatchRepository : add
BatchRepository ->> QbicBatchRepo : save
BatchDomainService ->> DomainEventDispatcher : dispatch batch registered
BatchDomainService ->> BatchRegistrationService : BatchId
BatchRegistrationService ->> SampleRegistrationServiceV2 : BatchId
SampleRegistrationServiceV2 ->> SampleRepository : addAll
SampleRepository ->> SampleJpaRepository : saveAll
SampleRepository ->> SampleDataRepository(OpenBIS) : addSamplesToProject
SampleDataRepository(OpenBIS) ->> OpenBis : createExperiment
SampleDataRepository(OpenBIS) ->> OpenBis : createOpenbisSample
SampleRepository -->> SampleRegistrationServiceV2 : Collection<Sample>
SampleRegistrationServiceV2 ->> ConfoundingVariableService : setVariableLevelsForSamples
ConfoundingVariableService ->> ConfoundingVariableRepository : existsAllById
ConfoundingVariableRepository -->> ConfoundingVariableService : yes
ConfoundingVariableService ->> ConfoundingVariableLevelRepository : save
ConfoundingVariableService -->> SampleRegistrationServiceV2 : List<ConfoundingVariableLevel>
SampleRegistrationServiceV2 ->> BatchRegistrationService : addSamplesToBatch
BatchRegistrationService ->> BatchRepository : find
BatchRegistrationService ->> BatchRepository : update

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Consider an exception after the experiment was created. The experiment stays the same in openbis but the samples and sample batch are rolled back in the database.

Additionally, the experiment and sample codes are derived from listed objects in openbis. When experiments are deleted in openbis, they are placed in the trashcan currently. Identifiers of objects in the trashcan are still considered present even though those objects are not listed with the API. So after a "rollback" of a failure after the experiment was created, the experiment still exists in the trash can. The next sample registration will fail as well as the experiment code is already taken.

What browsers are you seeing the problem on?

No response

Relevant log output

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