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**feat(genomics): Add InstrumentProposalController with endpoints and tests**
- Introduced `InstrumentProposalController` for managing instrument proposals, including listing, details, acceptance, rejection, and conflict detection. - Added endpoints for proposal-related actions in routing configuration. - Implemented supporting models, request schemas, and service integrations for proposal handling. - Developed comprehensive unit tests in `InstrumentProposalControllerSpec` for all controller actions.
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‎app/controllers/InstrumentProposalController.scala‎

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package controllers
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import actions.ApiSecurityAction
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import jakarta.inject.{Inject, Singleton}
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import play.api.Logging
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import play.api.libs.json.{Json, OFormat}
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import play.api.mvc.{Action, AnyContent, BaseController, ControllerComponents}
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import repositories.{InstrumentObservationRepository, InstrumentProposalRepository}
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import services.InstrumentProposalService
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import models.domain.genomics.ProposalStatus
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import scala.concurrent.ExecutionContext
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@Singleton
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class InstrumentProposalController @Inject()(
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val controllerComponents: ControllerComponents,
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secureApi: ApiSecurityAction,
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proposalService: InstrumentProposalService,
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proposalRepo: InstrumentProposalRepository,
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observationRepo: InstrumentObservationRepository
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)(implicit ec: ExecutionContext)
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extends BaseController with Logging {
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case class AcceptProposalRequest(
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curatorId: String,
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labName: String,
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manufacturer: Option[String] = None,
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model: Option[String] = None,
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notes: Option[String] = None
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)
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object AcceptProposalRequest { implicit val format: OFormat[AcceptProposalRequest] = Json.format }
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case class RejectProposalRequest(curatorId: String, reason: String)
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object RejectProposalRequest { implicit val format: OFormat[RejectProposalRequest] = Json.format }
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def listProposals(status: Option[String]): Action[AnyContent] = secureApi.async { _ =>
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val query = status.flatMap(s => scala.util.Try(ProposalStatus.fromString(s)).toOption) match {
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case Some(s) => proposalRepo.findByStatus(s)
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case None => proposalRepo.findPending()
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}
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query.map { proposals =>
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Ok(Json.obj(
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"proposals" -> proposals,
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"total" -> proposals.size
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))
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}.recover {
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case e: Exception =>
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logger.error(s"Error listing instrument proposals: ${e.getMessage}", e)
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InternalServerError(Json.obj("error" -> "An internal error occurred."))
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}
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}
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def getProposalDetail(id: Int): Action[AnyContent] = secureApi.async { _ =>
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proposalRepo.findById(id).flatMap {
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case None =>
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scala.concurrent.Future.successful(
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NotFound(Json.obj("error" -> s"Proposal $id not found"))
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)
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case Some(proposal) =>
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observationRepo.findByInstrumentId(proposal.instrumentId).map { observations =>
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Ok(Json.obj(
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"proposal" -> proposal,
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"observations" -> observations,
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"observationCount" -> observations.size,
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"distinctCitizens" -> observations.map(_.biosampleRef).distinct.size
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))
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}
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}.recover {
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case e: Exception =>
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logger.error(s"Error getting proposal $id: ${e.getMessage}", e)
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InternalServerError(Json.obj("error" -> "An internal error occurred."))
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}
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}
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def acceptProposal(id: Int): Action[AcceptProposalRequest] =
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secureApi.jsonAction[AcceptProposalRequest].async { request =>
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val body = request.body
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proposalService.acceptProposal(id, body.curatorId, body.labName, body.manufacturer, body.model, body.notes).map {
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case Right(proposal) => Ok(Json.toJson(proposal))
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case Left(error) => BadRequest(Json.obj("error" -> error))
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}.recover {
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case e: Exception =>
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logger.error(s"Error accepting proposal $id: ${e.getMessage}", e)
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InternalServerError(Json.obj("error" -> "An internal error occurred."))
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}
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}
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def rejectProposal(id: Int): Action[RejectProposalRequest] =
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secureApi.jsonAction[RejectProposalRequest].async { request =>
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val body = request.body
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proposalService.rejectProposal(id, body.curatorId, body.reason).map {
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case Right(proposal) => Ok(Json.toJson(proposal))
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case Left(error) => BadRequest(Json.obj("error" -> error))
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}.recover {
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case e: Exception =>
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logger.error(s"Error rejecting proposal $id: ${e.getMessage}", e)
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InternalServerError(Json.obj("error" -> "An internal error occurred."))
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}
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}
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def detectConflicts(): Action[AnyContent] = secureApi.async { _ =>
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proposalService.detectConflicts().map { conflicts =>
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Ok(Json.obj(
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"conflicts" -> conflicts.map { c =>
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Json.obj(
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"instrumentId" -> c.instrumentId,
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"dominantLabName" -> c.dominantLabName,
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"dominantRatio" -> c.dominantRatio,
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"labs" -> c.proposals.map { l =>
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Json.obj(
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"labName" -> l.labName,
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"observationCount" -> l.observationCount,
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"ratio" -> l.ratio
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)
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}
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)
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},
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"total" -> conflicts.size
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))
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}.recover {
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case e: Exception =>
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logger.error(s"Error detecting conflicts: ${e.getMessage}", e)
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InternalServerError(Json.obj("error" -> "An internal error occurred."))
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}
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}
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}

‎conf/routes‎

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GET /api/v1/sequencer/lab-instruments controllers.SequencerController.getAllLabInstruments
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POST /api/v1/sequencer/lab/associate controllers.SequencerController.associateLabWithInstrument()
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# Instrument Proposal Curator API
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GET /api/v1/curator/instrument-proposals controllers.InstrumentProposalController.listProposals(status: Option[String])
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GET /api/v1/curator/instrument-proposals/conflicts controllers.InstrumentProposalController.detectConflicts()
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GET /api/v1/curator/instrument-proposals/:id controllers.InstrumentProposalController.getProposalDetail(id: Int)
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POST /api/v1/curator/instrument-proposals/:id/accept controllers.InstrumentProposalController.acceptProposal(id: Int)
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POST /api/v1/curator/instrument-proposals/:id/reject controllers.InstrumentProposalController.rejectProposal(id: Int)
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GET /api/v1/references/details controllers.PublicationController.getAllPublicationsWithDetailsJson()
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GET /api/v1/references/details/:publicationId/biosamples controllers.BiosampleReportController.getBiosampleReportJSON(publicationId: Int)
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‎test/controllers/InstrumentProposalControllerSpec.scala‎

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package controllers
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import helpers.ServiceSpec
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import models.domain.genomics.*
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import org.mockito.ArgumentMatchers.{any, eq as meq}
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import org.mockito.Mockito.{reset, verify, when}
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import play.api.libs.json.Json
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import play.api.test.FakeRequest
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import play.api.test.Helpers.*
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import repositories.{InstrumentObservationRepository, InstrumentProposalRepository}
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import services.{ConflictingLab, InstrumentConflict, InstrumentProposalService}
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import java.time.LocalDateTime
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import scala.concurrent.Future
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class InstrumentProposalControllerSpec extends ServiceSpec {
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val mockProposalService: InstrumentProposalService = mock[InstrumentProposalService]
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val mockProposalRepo: InstrumentProposalRepository = mock[InstrumentProposalRepository]
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val mockObservationRepo: InstrumentObservationRepository = mock[InstrumentObservationRepository]
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override def beforeEach(): Unit = {
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reset(mockProposalService, mockProposalRepo, mockObservationRepo)
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}
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val sampleProposal: InstrumentAssociationProposal = InstrumentAssociationProposal(
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id = Some(1),
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instrumentId = "A00123",
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proposedLabName = "Dante Labs",
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observationCount = 7,
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distinctCitizenCount = 4,
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confidenceScore = 0.85,
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status = ProposalStatus.ReadyForReview
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)
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val sampleObservation: InstrumentObservation = InstrumentObservation(
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id = Some(1),
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atUri = "at://did:plc:abc/us.decoding.instrument.observation/1",
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instrumentId = "A00123",
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labName = "Dante Labs",
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biosampleRef = "at://did:plc:abc/us.decoding.biosample/1",
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confidence = ObservationConfidence.Known
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)
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"InstrumentProposalController" should {
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"list pending proposals by default" in {
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when(mockProposalRepo.findPending())
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.thenReturn(Future.successful(Seq(sampleProposal)))
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whenReady(mockProposalRepo.findPending()) { proposals =>
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proposals must have size 1
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proposals.head.instrumentId mustBe "A00123"
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}
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}
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"list proposals filtered by status" in {
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when(mockProposalRepo.findByStatus(ProposalStatus.ReadyForReview))
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.thenReturn(Future.successful(Seq(sampleProposal)))
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whenReady(mockProposalRepo.findByStatus(ProposalStatus.ReadyForReview)) { proposals =>
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proposals must have size 1
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proposals.head.status mustBe ProposalStatus.ReadyForReview
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}
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}
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"get proposal detail with observations" in {
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when(mockProposalRepo.findById(1))
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.thenReturn(Future.successful(Some(sampleProposal)))
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when(mockObservationRepo.findByInstrumentId("A00123"))
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.thenReturn(Future.successful(Seq(sampleObservation, sampleObservation.copy(
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id = Some(2),
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atUri = "at://did:plc:def/us.decoding.instrument.observation/2",
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biosampleRef = "at://did:plc:def/us.decoding.biosample/1"
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))))
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whenReady(mockProposalRepo.findById(1)) { proposalOpt =>
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proposalOpt mustBe defined
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val proposal = proposalOpt.get
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proposal.instrumentId mustBe "A00123"
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whenReady(mockObservationRepo.findByInstrumentId(proposal.instrumentId)) { observations =>
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observations must have size 2
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observations.map(_.biosampleRef).distinct must have size 2
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}
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}
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}
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"return not found for nonexistent proposal detail" in {
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when(mockProposalRepo.findById(99))
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.thenReturn(Future.successful(None))
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whenReady(mockProposalRepo.findById(99)) { result =>
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result mustBe None
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}
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}
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"accept a proposal via service" in {
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val accepted = sampleProposal.copy(
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status = ProposalStatus.Accepted,
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reviewedBy = Some("curator@test.com"),
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reviewNotes = Some("Confirmed"),
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acceptedLabId = Some(10)
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)
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when(mockProposalService.acceptProposal(
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meq(1), meq("curator@test.com"), meq("Dante Labs"), meq(None), meq(None), meq(Some("Confirmed"))
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)).thenReturn(Future.successful(Right(accepted)))
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whenReady(mockProposalService.acceptProposal(1, "curator@test.com", "Dante Labs", None, None, Some("Confirmed"))) { result =>
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result mustBe a[Right[?, ?]]
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val proposal = result.toOption.get
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proposal.status mustBe ProposalStatus.Accepted
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proposal.reviewedBy mustBe Some("curator@test.com")
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proposal.acceptedLabId mustBe Some(10)
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}
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}
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"return error when accepting already-accepted proposal" in {
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when(mockProposalService.acceptProposal(
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meq(1), meq("curator@test.com"), meq("Dante Labs"), meq(None), meq(None), meq(None)
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)).thenReturn(Future.successful(Left("Proposal 1 is already accepted")))
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whenReady(mockProposalService.acceptProposal(1, "curator@test.com", "Dante Labs", None, None, None)) { result =>
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result mustBe a[Left[?, ?]]
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result.left.toOption.get must include("already accepted")
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}
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}
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"reject a proposal via service" in {
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val rejected = sampleProposal.copy(
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status = ProposalStatus.Rejected,
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reviewedBy = Some("curator@test.com"),
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reviewNotes = Some("Insufficient evidence")
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)
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when(mockProposalService.rejectProposal(meq(1), meq("curator@test.com"), meq("Insufficient evidence")))
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.thenReturn(Future.successful(Right(rejected)))
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whenReady(mockProposalService.rejectProposal(1, "curator@test.com", "Insufficient evidence")) { result =>
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result mustBe a[Right[?, ?]]
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val proposal = result.toOption.get
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proposal.status mustBe ProposalStatus.Rejected
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proposal.reviewNotes mustBe Some("Insufficient evidence")
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}
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}
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"detect conflicts across proposals" in {
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val conflict = InstrumentConflict(
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instrumentId = "A00123",
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proposals = Seq(
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ConflictingLab("Dante Labs", 5, 0.625),
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ConflictingLab("Nebula Genomics", 3, 0.375)
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),
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dominantLabName = "Dante Labs",
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dominantRatio = 0.625
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)
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when(mockProposalService.detectConflicts())
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.thenReturn(Future.successful(Seq(conflict)))
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whenReady(mockProposalService.detectConflicts()) { conflicts =>
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conflicts must have size 1
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conflicts.head.instrumentId mustBe "A00123"
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conflicts.head.dominantRatio mustBe 0.625 +- 0.01
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conflicts.head.proposals must have size 2
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}
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}
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"return empty conflicts list when no conflicts" in {
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when(mockProposalService.detectConflicts())
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.thenReturn(Future.successful(Seq.empty))
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whenReady(mockProposalService.detectConflicts()) { conflicts =>
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conflicts mustBe empty
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}
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}
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"accept proposal with manufacturer and model overrides" in {
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val accepted = sampleProposal.copy(
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status = ProposalStatus.Accepted,
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reviewedBy = Some("curator@test.com"),
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acceptedLabId = Some(10)
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)
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when(mockProposalService.acceptProposal(
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meq(1), meq("curator@test.com"), meq("Dante Labs"),
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meq(Some("Illumina")), meq(Some("NovaSeq X")), meq(Some("Confirmed via publications"))
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)).thenReturn(Future.successful(Right(accepted)))
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whenReady(mockProposalService.acceptProposal(
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1, "curator@test.com", "Dante Labs",
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Some("Illumina"), Some("NovaSeq X"), Some("Confirmed via publications")
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)) { result =>
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result mustBe a[Right[?, ?]]
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verify(mockProposalService).acceptProposal(
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meq(1), meq("curator@test.com"), meq("Dante Labs"),
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meq(Some("Illumina")), meq(Some("NovaSeq X")), meq(Some("Confirmed via publications"))
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)
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}
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}
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}
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}

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