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Pivotal ID # 172671360: Warn users about upcoming public release #324

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merged 3 commits into from
Jan 26, 2021

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jhoanmanuelms
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https://www.pivotaltracker.com/story/show/172671360

  • Log error instead of failing when getting extended submissions
  • Fix notification messages

- Log error instead of failing when getting extended submissions
- Fix notification messages
@jhoanmanuelms jhoanmanuelms self-assigned this Jan 22, 2021
Avoid propagating null instances of the extended submission
}
val submissions = page.content.filterNotNull()

return PageImpl(submissions, page.pageable, submissions.size.toLong())
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@Juan-EBI Juan-EBI Jan 25, 2021

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I think this logic should in the service.

    @Transactional(readOnly = true)
    override fun getExtendedSubmissions(filter: SubmissionFilter, offset: Long, limit: Int): Page<Result<ExtSubmission>> {
        val filterSpecs = SubmissionFilterSpecification(filter)
        val pageable = OffsetPageRequest(offset, limit, Sort.by(defaultOrder))

        return submissionRepository
            .findAll(filterSpecs.specification, pageable, EntityGraphs.named(SIMPLE_GRAPH))
            .map { runCatching { getExtByAccNoAndVersion(it.accNo, it.version) } }
    }

and in the service.

    fun getExtendedSubmissions(request: ExtPageRequest): Page<ExtSubmission> {
        val filter = SubmissionFilter(
            rTimeFrom = request.fromRTime,
            rTimeTo = request.toRTime,
            released = request.released
        )
        return submissionRepository
            .getExtendedSubmissions(filter, request.offset, request.limit)
            .onEach { it.onFailure { logger.error .... } }
            .map { it.getOrNull() }
            ....
    }

I would also add a unit test or many check that page is calculated correctly.

- Improve error processing
- Add unit test to validate the page is properly processed
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@Juan-EBI Juan-EBI left a comment

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LGTM

@jhoanmanuelms jhoanmanuelms merged commit 8e25209 into master Jan 26, 2021
@jhoanmanuelms jhoanmanuelms deleted the bugfix/pivotal-172671360-processing-errors branch January 26, 2021 15:20
jhoanmanuelms added a commit that referenced this pull request Mar 20, 2021
Feature
* Pivotal ID # 176052254: JSON Submission Attributes Validation (#310)
* Pivotal #ID:175163839: Submission Query Operations In Mongo (#319)
* Pivotal-176168841: Allow to check inactive user registration (#315)
* Pivotal ID # 176522202: Ext Submission serialization (#322)
* Pivotal ID # 172671360: Warn users about upcoming public release (#324)
* Pivotal #ID 176479707: Mongo implement draft funtionality (#327)
* Pivotal #ID 176479720: Mongo Metadata Query (#328)
* Pivotal ID # 175163839: Mongo Submission Stats (#331)
* Pivotal ID # 176886357: Async Submission Request (#334)
* Pivotal ID # 176977556: Delete Submissions In Mongo (#341)
* Pivotal ID #176679139: Ext Submission File List Refactor (#344)
* Pivotal ID # 177042374: Delete Draft After Submission (#349)
* Pivotal ID# 174948695: PTSubmit Delete Operation (#351)
* Pivotal #ID 177076728: Use PMC new streaming API (#346)
* Pivotal ID # 177267343: Validate EU-ToxRisk Submissions (#352)

Bugfix
* Pivotal ID # 176052264: Inner Folder Mapping (#311)
* Pivotal ID # 172671360: Ignore Empty Value Attributes (#314)
* Pivotal ID # 176377632: File list extension is missing in BIA studies (#321)
* Pivotal #ID 174642598: TSV Double Quotes (#350)
* Pivotal ID # 176501169: FTP Folders Missing (#335)

Chore
* Pivotal ID # 176377544: Add refresh users directory structure api endpoint (#320)
* Pivotal #ID 176479473:  Migrate biostudies test to TestContainers (#323)
* Pivotal ID # 176779952: Mongo iTests CI (#332)
* Pivotal #Id 176838189: Rename PMC mongo collections (#333)
* Pivotal #ID: 177040448: Store request as plain json (#336)
* Pivotal ID #175894089: Check if queues in RabbitMQ are persistent (#339)
* Pivotal ID #177074116 : model table section properly (#338)
* Pivotal ID # 176886824: Improve API Docs (#337)
* Pivotal #ID 177193125: Improve collection template validation (#345)

Co-authored-by: Juan <jcamilorada@ebi.ac.uk>
jhoanmanuelms added a commit that referenced this pull request Mar 21, 2021
Feature
* Pivotal ID # 176052254: JSON Submission Attributes Validation (#310)
* Pivotal #ID:175163839: Submission Query Operations In Mongo (#319)
* Pivotal-176168841: Allow to check inactive user registration (#315)
* Pivotal ID # 176522202: Ext Submission serialization (#322)
* Pivotal ID # 172671360: Warn users about upcoming public release (#324)
* Pivotal #ID 176479707: Mongo implement draft funtionality (#327)
* Pivotal #ID 176479720: Mongo Metadata Query (#328)
* Pivotal ID # 175163839: Mongo Submission Stats (#331)
* Pivotal ID # 176886357: Async Submission Request (#334)
* Pivotal ID # 176977556: Delete Submissions In Mongo (#341)
* Pivotal ID #176679139: Ext Submission File List Refactor (#344)
* Pivotal ID # 177042374: Delete Draft After Submission (#349)
* Pivotal ID# 174948695: PTSubmit Delete Operation (#351)
* Pivotal #ID 177076728: Use PMC new streaming API (#346)
* Pivotal ID # 177267343: Validate EU-ToxRisk Submissions (#352)

Bugfix
* Pivotal ID # 176052264: Inner Folder Mapping (#311)
* Pivotal ID # 172671360: Ignore Empty Value Attributes (#314)
* Pivotal ID # 176377632: File list extension is missing in BIA studies (#321)
* Pivotal #ID 174642598: TSV Double Quotes (#350)
* Pivotal ID # 176501169: FTP Folders Missing (#335)

Chore
* Pivotal ID # 176377544: Add refresh users directory structure api endpoint (#320)
* Pivotal #ID 176479473:  Migrate biostudies test to TestContainers (#323)
* Pivotal ID # 176779952: Mongo iTests CI (#332)
* Pivotal #Id 176838189: Rename PMC mongo collections (#333)
* Pivotal #ID: 177040448: Store request as plain json (#336)
* Pivotal ID #175894089: Check if queues in RabbitMQ are persistent (#339)
* Pivotal ID #177074116 : model table section properly (#338)
* Pivotal ID # 176886824: Improve API Docs (#337)
* Pivotal #ID 177193125: Improve collection template validation (#345)

Co-authored-by: Juan <jcamilorada@ebi.ac.uk>
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2 participants