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JamesKaneJamesKane
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**feat(genomics): Add instrument observation domain and related services**
- Introduced `InstrumentObservation` model, repository, services, and table schema for genomic instrument observations. - Added migration to create `instrument_observation` table with necessary indices for optimized queries. - Implemented CRUD operations in `InstrumentObservationRepository`. - Updated `AtmosphereEventHandler` to handle `InstrumentObservation` events for create, update, and delete actions. - Wrote unit tests to ensure correctness of repository methods, event handling, and confidence field mapping.
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9 files changed

Lines changed: 479 additions & 19 deletions

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‎app/models/dal/DatabaseSchema.scala‎

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@@ -76,6 +76,7 @@ object DatabaseSchema {
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val sequenceLibraries = TableQuery[SequenceLibrariesTable]
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val sequencingLabs = TableQuery[SequencingLabsTable]
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val sequencerInstruments = TableQuery[SequencerInstrumentsTable]
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val instrumentObservations = TableQuery[InstrumentObservationTable]
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val specimenDonors = TableQuery[SpecimenDonorsTable]
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val validationServices = TableQuery[ValidationServicesTable]
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val testTypeDefinition = TableQuery[TestTypeTable]

‎app/models/dal/domain/genomics/InstrumentObservationTable.scala‎

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package models.dal.domain.genomics
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import models.dal.MyPostgresProfile.api.*
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import models.domain.genomics.{InstrumentObservation, ObservationConfidence}
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import slick.ast.BaseTypedType
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import java.time.LocalDateTime
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class InstrumentObservationTable(tag: Tag) extends Table[InstrumentObservation](tag, "instrument_observation") {
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implicit private val confidenceMapper: BaseTypedType[ObservationConfidence] =
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MappedColumnType.base[ObservationConfidence, String](_.dbValue, ObservationConfidence.fromString)
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def id = column[Int]("id", O.PrimaryKey, O.AutoInc)
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def atUri = column[String]("at_uri", O.Unique)
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def atCid = column[Option[String]]("at_cid")
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def instrumentId = column[String]("instrument_id")
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def labName = column[String]("lab_name")
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def biosampleRef = column[String]("biosample_ref")
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def sequenceRunRef = column[Option[String]]("sequence_run_ref")
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def platform = column[Option[String]]("platform")
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def instrumentModel = column[Option[String]]("instrument_model")
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def flowcellId = column[Option[String]]("flowcell_id")
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def runDate = column[Option[LocalDateTime]]("run_date")
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def confidence = column[ObservationConfidence]("confidence")
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def createdAt = column[LocalDateTime]("created_at")
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def updatedAt = column[Option[LocalDateTime]]("updated_at")
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def * = (
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id.?, atUri, atCid, instrumentId, labName, biosampleRef,
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sequenceRunRef, platform, instrumentModel, flowcellId,
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runDate, confidence, createdAt, updatedAt
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).mapTo[InstrumentObservation]
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}

‎app/models/domain/genomics/InstrumentObservation.scala‎

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package models.domain.genomics
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import play.api.libs.json.{Json, OFormat}
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import java.time.LocalDateTime
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case class InstrumentObservation(
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id: Option[Int] = None,
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atUri: String,
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atCid: Option[String] = None,
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instrumentId: String,
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labName: String,
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biosampleRef: String,
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sequenceRunRef: Option[String] = None,
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platform: Option[String] = None,
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instrumentModel: Option[String] = None,
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flowcellId: Option[String] = None,
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runDate: Option[LocalDateTime] = None,
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confidence: ObservationConfidence = ObservationConfidence.Inferred,
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createdAt: LocalDateTime = LocalDateTime.now(),
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updatedAt: Option[LocalDateTime] = None
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)
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object InstrumentObservation {
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implicit val format: OFormat[InstrumentObservation] = Json.format[InstrumentObservation]
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}
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sealed trait ObservationConfidence {
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def dbValue: String
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}
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object ObservationConfidence {
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case object Known extends ObservationConfidence { val dbValue = "KNOWN" }
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case object Inferred extends ObservationConfidence { val dbValue = "INFERRED" }
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case object Guessed extends ObservationConfidence { val dbValue = "GUESSED" }
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def fromString(s: String): ObservationConfidence = s.toUpperCase match {
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case "KNOWN" => Known
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case "INFERRED" => Inferred
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case "GUESSED" => Guessed
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case other => throw new IllegalArgumentException(s"Unknown ObservationConfidence: $other")
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}
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implicit val format: play.api.libs.json.Format[ObservationConfidence] = new play.api.libs.json.Format[ObservationConfidence] {
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def reads(json: play.api.libs.json.JsValue) = json match {
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case play.api.libs.json.JsString(s) => play.api.libs.json.JsSuccess(fromString(s))
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case _ => play.api.libs.json.JsError("String value expected")
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}
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def writes(c: ObservationConfidence) = play.api.libs.json.JsString(c.dbValue)
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}
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}

‎app/modules/BaseModule.scala‎

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@@ -54,6 +54,9 @@ class BaseModule extends AbstractModule {
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.to(classOf[BiosampleOriginalHaplogroupRepositoryImpl])
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.asEagerSingleton()
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bind(classOf[InstrumentObservationRepository])
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.to(classOf[InstrumentObservationRepositoryImpl])
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.asEagerSingleton()
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bind(classOf[SequenceFileRepository])
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.to(classOf[SequenceFileRepositoryImpl])

‎app/repositories/InstrumentObservationRepository.scala‎

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package repositories
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import jakarta.inject.{Inject, Singleton}
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import models.dal.DatabaseSchema
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import models.domain.genomics.{InstrumentObservation, ObservationConfidence}
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import play.api.db.slick.DatabaseConfigProvider
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import slick.ast.BaseTypedType
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import java.time.LocalDateTime
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import scala.concurrent.{ExecutionContext, Future}
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trait InstrumentObservationRepository {
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def create(observation: InstrumentObservation): Future[InstrumentObservation]
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def findByAtUri(atUri: String): Future[Option[InstrumentObservation]]
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def findByInstrumentId(instrumentId: String): Future[Seq[InstrumentObservation]]
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def findByLabName(labName: String): Future[Seq[InstrumentObservation]]
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def findByBiosampleRef(biosampleRef: String): Future[Seq[InstrumentObservation]]
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def update(observation: InstrumentObservation): Future[Boolean]
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def deleteByAtUri(atUri: String): Future[Boolean]
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}
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@Singleton
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class InstrumentObservationRepositoryImpl @Inject()(
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override protected val dbConfigProvider: DatabaseConfigProvider
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)(implicit override protected val ec: ExecutionContext)
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extends BaseRepository(dbConfigProvider)
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with InstrumentObservationRepository {
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import models.dal.MyPostgresProfile.api.*
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implicit private val confidenceMapper: BaseTypedType[ObservationConfidence] =
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MappedColumnType.base[ObservationConfidence, String](_.dbValue, ObservationConfidence.fromString)
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private val observations = DatabaseSchema.domain.genomics.instrumentObservations
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override def create(observation: InstrumentObservation): Future[InstrumentObservation] = {
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db.run(
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(observations returning observations.map(_.id)
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into ((o, id) => o.copy(id = Some(id)))) += observation
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)
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}
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override def findByAtUri(atUri: String): Future[Option[InstrumentObservation]] = {
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db.run(observations.filter(_.atUri === atUri).result.headOption)
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}
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override def findByInstrumentId(instrumentId: String): Future[Seq[InstrumentObservation]] = {
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db.run(observations.filter(_.instrumentId === instrumentId).result)
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}
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override def findByLabName(labName: String): Future[Seq[InstrumentObservation]] = {
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db.run(observations.filter(_.labName === labName).result)
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}
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override def findByBiosampleRef(biosampleRef: String): Future[Seq[InstrumentObservation]] = {
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db.run(observations.filter(_.biosampleRef === biosampleRef).result)
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}
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override def update(observation: InstrumentObservation): Future[Boolean] = {
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db.run(
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observations.filter(_.atUri === observation.atUri)
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.map(o => (o.atCid, o.instrumentId, o.labName, o.biosampleRef, o.sequenceRunRef,
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o.platform, o.instrumentModel, o.flowcellId, o.runDate, o.confidence, o.updatedAt))
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.update((observation.atCid, observation.instrumentId, observation.labName,
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observation.biosampleRef, observation.sequenceRunRef, observation.platform,
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observation.instrumentModel, observation.flowcellId, observation.runDate,
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observation.confidence, Some(LocalDateTime.now())))
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).map(_ > 0)
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}
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override def deleteByAtUri(atUri: String): Future[Boolean] = {
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db.run(observations.filter(_.atUri === atUri).delete.map(_ > 0))
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}
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}

‎app/services/firehose/AtmosphereEventHandler.scala‎

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@@ -27,7 +27,8 @@ class AtmosphereEventHandler @Inject()(
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testTypeService: TestTypeService,
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genotypeDataRepository: GenotypeDataRepository,
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populationBreakdownRepository: PopulationBreakdownRepository,
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haplogroupReconciliationRepository: HaplogroupReconciliationRepository
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haplogroupReconciliationRepository: HaplogroupReconciliationRepository,
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instrumentObservationRepository: InstrumentObservationRepository
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)(implicit ec: ExecutionContext) extends Logging {
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def handle(event: FirehoseEvent): Future[FirehoseResult] = {
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case e: GenotypeEvent => handleGenotype(e)
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case e: PopulationBreakdownEvent => handlePopulationBreakdown(e)
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case e: HaplogroupReconciliationEvent => handleHaplogroupReconciliation(e)
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// Add other handlers as needed
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case e: InstrumentObservationEvent => handleInstrumentObservation(e)
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case _ =>
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logger.warn(s"Unhandled event type: ${event.getClass.getSimpleName} for ${event.atUri}")
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Future.successful(FirehoseResult.Success(event.atUri, "", None, "Ignored (Not Implemented)"))
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}
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}
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// --- Instrument Observation Handling ---
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private def handleInstrumentObservation(event: InstrumentObservationEvent): Future[FirehoseResult] = {
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event.action match {
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case FirehoseAction.Create => createInstrumentObservation(event)
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case FirehoseAction.Update => updateInstrumentObservation(event)
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case FirehoseAction.Delete => deleteInstrumentObservation(event)
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}
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}
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private def createInstrumentObservation(event: InstrumentObservationEvent): Future[FirehoseResult] = {
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event.payload match {
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case Some(record) =>
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instrumentObservationRepository.findByAtUri(record.atUri).flatMap {
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case Some(_) =>
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Future.successful(FirehoseResult.Conflict(event.atUri, "Instrument observation already exists"))
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case None =>
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val observation = InstrumentObservation(
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atUri = record.atUri,
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atCid = event.atCid,
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instrumentId = record.instrumentId,
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labName = record.labName,
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biosampleRef = record.biosampleRef,
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sequenceRunRef = record.sequenceRunRef,
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platform = record.platform,
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instrumentModel = record.instrumentModel,
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flowcellId = record.flowcellId,
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runDate = record.runDate.map(i => LocalDateTime.ofInstant(i, ZoneId.systemDefault())),
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confidence = record.confidence
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.map(ObservationConfidence.fromString)
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.getOrElse(ObservationConfidence.Inferred)
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)
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instrumentObservationRepository.create(observation).map { created =>
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logger.info(s"Created instrument observation for instrument ${record.instrumentId} at lab ${record.labName}")
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FirehoseResult.Success(event.atUri, UUID.randomUUID().toString, None, "Instrument observation created")
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}
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}
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case None =>
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Future.successful(FirehoseResult.ValidationError(event.atUri, "Missing payload for InstrumentObservationEvent"))
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}
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}
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private def updateInstrumentObservation(event: InstrumentObservationEvent): Future[FirehoseResult] = {
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event.payload match {
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case Some(record) =>
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instrumentObservationRepository.findByAtUri(event.atUri).flatMap {
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case Some(existing) =>
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val updated = existing.copy(
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atCid = event.atCid,
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instrumentId = record.instrumentId,
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labName = record.labName,
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biosampleRef = record.biosampleRef,
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sequenceRunRef = record.sequenceRunRef,
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platform = record.platform,
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instrumentModel = record.instrumentModel,
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flowcellId = record.flowcellId,
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runDate = record.runDate.map(i => LocalDateTime.ofInstant(i, ZoneId.systemDefault())),
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confidence = record.confidence
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.map(ObservationConfidence.fromString)
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.getOrElse(existing.confidence)
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)
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instrumentObservationRepository.update(updated).map { success =>
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if (success) FirehoseResult.Success(event.atUri, UUID.randomUUID().toString, None, "Instrument observation updated")
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else FirehoseResult.Error(event.atUri, "Failed to update instrument observation")
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}
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case None =>
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Future.successful(FirehoseResult.NotFound(event.atUri))
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}
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case None =>
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Future.successful(FirehoseResult.ValidationError(event.atUri, "Missing payload for InstrumentObservationEvent"))
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}
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}
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private def deleteInstrumentObservation(event: InstrumentObservationEvent): Future[FirehoseResult] = {
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instrumentObservationRepository.deleteByAtUri(event.atUri).map { deleted =>
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if (deleted) FirehoseResult.Success(event.atUri, "", None, "Instrument observation deleted")
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else FirehoseResult.NotFound(event.atUri)
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}
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}
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}

‎conf/evolutions/default/67.sql‎

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-- # --- !Ups
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CREATE TABLE public.instrument_observation (
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id SERIAL PRIMARY KEY,
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at_uri VARCHAR(512) UNIQUE NOT NULL,
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at_cid VARCHAR(128),
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instrument_id VARCHAR(255) NOT NULL,
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lab_name VARCHAR(255) NOT NULL,
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biosample_ref VARCHAR(512) NOT NULL,
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sequence_run_ref VARCHAR(512),
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platform VARCHAR(100),
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instrument_model VARCHAR(255),
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flowcell_id VARCHAR(255),
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run_date TIMESTAMP,
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confidence VARCHAR(20) DEFAULT 'INFERRED' CHECK (confidence IN ('KNOWN', 'INFERRED', 'GUESSED')),
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created_at TIMESTAMP NOT NULL DEFAULT NOW(),
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updated_at TIMESTAMP
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);
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CREATE INDEX idx_instrument_obs_instrument ON public.instrument_observation (instrument_id);
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CREATE INDEX idx_instrument_obs_lab ON public.instrument_observation (lab_name);
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CREATE INDEX idx_instrument_obs_biosample ON public.instrument_observation (biosample_ref);
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CREATE INDEX idx_instrument_obs_at_uri ON public.instrument_observation (at_uri);
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-- # --- !Downs
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DROP TABLE IF EXISTS public.instrument_observation;

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