diff options
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/entities/export')
8 files changed, 0 insertions, 245 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala deleted file mode 100644 index 3b7a6ad..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala +++ /dev/null @@ -1,28 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Label, RawPatientLabel} - -case class ExportPatientLabel(id: LongId[Label], name: String, evidences: List[ExportPatientLabelEvidence]) - -object ExportPatientLabel extends PhiLogging { - - implicit def toPhiString(x: ExportPatientLabel): PhiString = { - import x._ - phi"ExportPatientLabel(id=$id, evidences=$evidences)" - } - - def fromRaw(labelId: LongId[Label], rawPatientLabels: List[RawPatientLabel]): ExportPatientLabel = { - val firstLabel = rawPatientLabels.headOption - if (firstLabel.isEmpty) { - logger.warn(phi"rawPatientLabels is empty, labelId: $labelId") - } - - ExportPatientLabel( - id = labelId, - name = firstLabel.map(_.label).getOrElse(""), - evidences = rawPatientLabels.map(ExportPatientLabelEvidence.fromRaw) - ) - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala deleted file mode 100644 index ff0fb6c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{ExtractedData, RawPatientLabel} - -case class ExportPatientLabelEvidence(id: LongId[ExtractedData], - value: FuzzyValue, - evidenceText: String, - document: ExportPatientLabelEvidenceDocument) - -object ExportPatientLabelEvidence { - - implicit def toPhiString(x: ExportPatientLabelEvidence): PhiString = { - import x._ - phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=$value, " + - phi"evidenceText=${Unsafe(evidenceText)}, document=$document)" - } - - def fromRaw(x: RawPatientLabel) = ExportPatientLabelEvidence( - id = x.evidenceId, - value = x.value, - evidenceText = x.evidenceText, - document = ExportPatientLabelEvidenceDocument( - x.documentId, - x.requestId, - x.documentType, - x.providerType, - x.startDate - ) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala deleted file mode 100644 index 978c4b8..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala +++ /dev/null @@ -1,30 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import java.time.LocalDate - -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Document, RawPatientLabel, RecordRequestId} - -case class ExportPatientLabelEvidenceDocument(documentId: LongId[Document], - requestId: RecordRequestId, - documentType: String, - providerType: String, - date: LocalDate) - -object ExportPatientLabelEvidenceDocument extends PhiLogging { - - implicit def toPhiString(x: ExportPatientLabelEvidenceDocument): PhiString = { - import x._ - phi"ExportPatientLabelEvidenceDocument(documentId=$documentId, requestId=$requestId, " + - phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, date=$date)" - } - - def fromRaw(x: RawPatientLabel) = ExportPatientLabelEvidenceDocument( - documentId = x.documentId, - requestId = x.requestId, - documentType = x.documentType, - providerType = x.providerType, - date = x.startDate - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala deleted file mode 100644 index 718255b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala +++ /dev/null @@ -1,25 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Patient, RawPatientLabel} - -import scala.collection.breakOut - -case class ExportPatientWithLabels(patientId: UuidId[Patient], labelVersion: Long, labels: List[ExportPatientLabel]) - -object ExportPatientWithLabels { - - implicit def toPhiString(x: ExportPatientWithLabels): PhiString = { - import x._ - phi"ExportPatientWithLabels(patientId=$patientId, version=${Unsafe(labelVersion)}, labels=$labels)" - } - - def fromRaw(patientId: UuidId[Patient], rawPatientRefs: List[RawPatientLabel]) = ExportPatientWithLabels( - patientId = patientId, - labelVersion = 1L, // TODO It is needed to replace this mock label version. - labels = rawPatientRefs - .groupBy(_.labelId) - .map(Function.tupled(ExportPatientLabel.fromRaw))(breakOut) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala deleted file mode 100644 index a3a0e90..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala +++ /dev/null @@ -1,27 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.trial - -import java.time.LocalDateTime - -import xyz.driver.pdsuicommon.domain.{StringId, UuidId} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.Trial - -case class ExportTrial(nctId: StringId[Trial], - trialId: UuidId[Trial], - condition: Trial.Condition, - lastReviewed: LocalDateTime) - -object ExportTrial { - - implicit def toPhiString(x: ExportTrial): PhiString = { - import x._ - phi"ExportTrial(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, lastReviewed=$lastReviewed)" - } - - def fromDomain(x: Trial) = ExportTrial( - nctId = x.id, - trialId = x.externalId, - condition = x.condition, - lastReviewed = x.lastUpdate - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala deleted file mode 100644 index abdade4..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala +++ /dev/null @@ -1,15 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.trial - -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.Arm - -case class ExportTrialArm(armId: LongId[Arm], armName: String) - -object ExportTrialArm { - - implicit def toPhiString(x: ExportTrialArm): PhiString = { - import x._ - phi"ExportTrialArm(armId=$armId, armName=${Unsafe(armName)})" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala deleted file mode 100644 index 1dccaa5..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.trial - -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Label, RawTrialLabel} - -case class ExportTrialLabelCriterion(criterionId: LongId[Criterion], - value: Option[Boolean], - labelId: LongId[Label], - armIds: Set[LongId[Arm]], - criteria: String, - isCompound: Boolean, - isDefining: Boolean) - -object ExportTrialLabelCriterion { - - implicit def toPhiString(x: ExportTrialLabelCriterion): PhiString = { - import x._ - phi"TrialLabelCriterion(criterionId=$criterionId, value=$value, labelId=$labelId, " + - phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining)" - } - - def fromRaw(x: RawTrialLabel, armIds: Set[LongId[Arm]]) = ExportTrialLabelCriterion( - criterionId = x.criterionId, - value = x.value, - labelId = x.labelId, - armIds = armIds, - criteria = x.criteria, - isCompound = x.isCompound, - isDefining = x.isDefining - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala deleted file mode 100644 index 2580e54..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala +++ /dev/null @@ -1,56 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.trial - -import java.time.LocalDateTime - -import xyz.driver.pdsuicommon.domain.{StringId, UuidId} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{RawTrialLabel, Trial} - -import scala.collection.breakOut - -case class ExportTrialWithLabels(nctId: StringId[Trial], - trialId: UuidId[Trial], - condition: String, - lastReviewed: LocalDateTime, - labelVersion: Long, - arms: List[ExportTrialArm], - criteria: List[ExportTrialLabelCriterion]) - -object ExportTrialWithLabels { - - implicit def toPhiString(x: ExportTrialWithLabels): PhiString = { - import x._ - phi"TrialWithLabels(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, " + - phi"lastReviewed=$lastReviewed, labelVersion=${Unsafe(labelVersion)}, arms=$arms, criteria=$criteria)" - } - - def fromRaw(rawData: List[RawTrialLabel]): ExportTrialWithLabels = { - val trials: Set[StringId[Trial]] = rawData.map(_.nctId)(breakOut) - - assert(trials.size == 1, "There are more than one trials in the rawData") - val trial = rawData.head - - ExportTrialWithLabels( - nctId = trial.nctId, - trialId = trial.trialId, - condition = trial.condition, - lastReviewed = trial.lastReviewed, - labelVersion = 1, // TODO It is needed to replace this mock label version. - arms = rawData - .groupBy(_.armId) - .map { - case (armId, rawTrials) => - ExportTrialArm(armId, rawTrials.head.armName) - }(breakOut), - criteria = rawData - .groupBy { x => - (x.criterionId, x.labelId) - } - .map { - case (_, rawTrialLabels) => - val armIds = rawTrialLabels.map(_.criterionArmId).toSet - ExportTrialLabelCriterion.fromRaw(rawTrialLabels.head, armIds) - }(breakOut) - ) - } -} |