enable validation in BioSamples

[amnonkhen]

ENA needs to send BioSamples a request to accession the sample as well as validate it. If it is implemented, communicate to ENA team how to do it, if not, implement it and communicate to ENA.

DOD:

• [x] Is ENA calling the same apis when it submits a single documents or a bulk submission?
• [x] change BioSamples to send the document to biovalidator, cancel accessioning if invalid
• [ ] return validation result to caller, e.g. ENA. Agree on format with Submissions team.
• [x] add some detail to the diagram below, to specify endpoints, main classes etc. (no need to delve into details)

[amnonkhen]

sequenceDiagram
    participant Client
    participant ENA
    participant BioSamples
    participant schema_store
    participant mongoDB

    Client->>ENA: submit XML doc
    ENA->>ENA: fix document
    ENA->>ENA: convert to json in BioSamples format
    note over ENA: by FAIRification team
    par new flow: validation in BioSamples 
        note over ENA: ENA calls biosamples the <br> same way as currently <br> through bulk submission endpoint
        note over BioSamples: [task] BioSamples send<br> doc to validation
        ENA->>BioSamples: send for validation & accessioning
        note over BioSamples: endpoint in BulkActionControllerV2 `/bulk-submit` <br> (now validates superuser submissions)
        loop for all samples in the submission
            BioSamples ->> schema_store: get schema by id
            schema_store ->> mongoDB: fetch from DB
            BioSamples ->> biovalidator: validate doc using schema
        end
        alt if no validation errors 
            BioSamples ->> mongoDB: persist samples
        end
        note over BioSamples: [task] build output
        BioSamples ->> BioSamples: build output with <br>validation results 
        BioSamples -->> ENA: validation results    
    end
    ENA->>ENA: build receipt
    ENA->>ENA: save in db
    ENA-->>Client: acknowledgement

[theisuru]

Some changes are in a draft pull request. Need to speak with @dipayan1985 about APIs ENA is using. I assume they are only using Bulk submission endpoint. If ENA also using POST, PUT v2 endpoints, these changes should also be done there. EBIBioSamples/biosamples-v4#714

[theisuru]

• ENA is only using bulk submission endpoint
• Currently we bypass validation if the user==superuser. With changes, we will introduce validation for all users including superuser.
• Change validation logic
  • Currently each samples is validated and persisted. If there is a validation error, samples upto the error is persisted.
  • New logic will do all validation first and then persist. If there is a validation error, no sample is persisted.