diff options
author | vlad <vlad@driver.xyz> | 2017-06-30 19:38:37 -0700 |
---|---|---|
committer | vlad <vlad@driver.xyz> | 2017-06-30 19:38:37 -0700 |
commit | 96d81a36286e41035ff4068859a3b0f9da924fbc (patch) | |
tree | 8d9f0014140d1f07ca449b56adaba8ccb3d2fc59 /src/main/scala/xyz/driver/pdsuidomain/entities/export | |
parent | a997aa6539d1f0af4ab4fc395ff2033335da312a (diff) | |
download | rest-query-96d81a36286e41035ff4068859a3b0f9da924fbc.tar.gz rest-query-96d81a36286e41035ff4068859a3b0f9da924fbc.tar.bz2 rest-query-96d81a36286e41035ff4068859a3b0f9da924fbc.zip |
Latest PDS UI utils including all the domain stuffv0.1.12
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/entities/export')
8 files changed, 244 insertions, 0 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 new file mode 100644 index 0000000..5474413 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala @@ -0,0 +1,30 @@ +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} + +final 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: $labelId") + } + + ExportPatientLabel( + id = labelId, + name = firstLabel.map(_.label).getOrElse(""), + evidences = rawPatientLabels.map(ExportPatientLabelEvidence.fromRaw) + ) + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala new file mode 100644 index 0000000..fb40339 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala @@ -0,0 +1,32 @@ +package xyz.driver.pdsuidomain.entities.export.patient + +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.{ExtractedData, RawPatientLabel} + +final case class ExportPatientLabelEvidence(id: LongId[ExtractedData], + value: FuzzyValue, + evidenceText: String, + document: ExportPatientLabelEvidenceDocument) + +object ExportPatientLabelEvidence { + + implicit def toPhiString(x: ExportPatientLabelEvidence): PhiString = { + import x._ + phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=$value, " + + phi"evidenceText=${Unsafe(evidenceText)}, document=$document)" + } + + def fromRaw(x: RawPatientLabel) = ExportPatientLabelEvidence( + id = x.evidenceId, + value = x.value, + evidenceText = x.evidenceText, + document = ExportPatientLabelEvidenceDocument( + x.documentId, + x.requestId, + x.documentType, + x.providerType, + x.startDate + ) + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala new file mode 100644 index 0000000..99912bc --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala @@ -0,0 +1,30 @@ +package xyz.driver.pdsuidomain.entities.export.patient + +import java.time.LocalDate + +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.{Document, RawPatientLabel, RecordRequestId} + +final case class ExportPatientLabelEvidenceDocument(documentId: LongId[Document], + requestId: RecordRequestId, + documentType: String, + providerType: String, + date: LocalDate) + +object ExportPatientLabelEvidenceDocument extends PhiLogging { + + implicit def toPhiString(x: ExportPatientLabelEvidenceDocument): PhiString = { + import x._ + phi"ExportPatientLabelEvidenceDocument(documentId=$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 new file mode 100644 index 0000000..e6262ed --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala @@ -0,0 +1,26 @@ +package xyz.driver.pdsuidomain.entities.export.patient + +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.{Patient, RawPatientLabel} + +import scala.collection.breakOut + +final 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=$labels)" + } + + def fromRaw(patientId: UuidId[Patient], + rawPatientRefs: List[RawPatientLabel]) = ExportPatientWithLabels( + patientId = patientId, + labelVersion = 1L, // TODO It is needed to replace this mock label version. + labels = rawPatientRefs + .groupBy(_.labelId) + .map(Function.tupled(ExportPatientLabel.fromRaw))(breakOut) + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala new file mode 100644 index 0000000..1aed121 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala @@ -0,0 +1,27 @@ +package xyz.driver.pdsuidomain.entities.export.trial + +import java.time.LocalDateTime + +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.Trial + +final case class ExportTrial(nctId: StringId[Trial], + trialId: UuidId[Trial], + condition: Trial.Condition, + lastReviewed: LocalDateTime) + +object ExportTrial { + + implicit def toPhiString(x: ExportTrial): PhiString = { + import x._ + phi"ExportTrial(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, lastReviewed=$lastReviewed)" + } + + def fromDomain(x: Trial) = ExportTrial( + nctId = x.id, + trialId = x.externalId, + condition = x.condition, + lastReviewed = x.lastUpdate + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala new file mode 100644 index 0000000..5a9a406 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala @@ -0,0 +1,15 @@ +package xyz.driver.pdsuidomain.entities.export.trial + +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.Arm + +final case class ExportTrialArm(armId: LongId[Arm], armName: String) + +object ExportTrialArm { + + implicit def toPhiString(x: ExportTrialArm): PhiString = { + import x._ + phi"ExportTrialArm(armId=$armId, armName=${Unsafe(armName)})" + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala new file mode 100644 index 0000000..7bff22c --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala @@ -0,0 +1,32 @@ +package xyz.driver.pdsuidomain.entities.export.trial + +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Label, RawTrialLabel} + +final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion], + value: Option[Boolean], + labelId: LongId[Label], + armIds: Set[LongId[Arm]], + criteria: String, + isCompound: Boolean, + isDefining: Boolean) + +object ExportTrialLabelCriterion { + + implicit def toPhiString(x: ExportTrialLabelCriterion): PhiString = { + import x._ + phi"TrialLabelCriterion(criterionId=$criterionId, value=$value, labelId=$labelId, " + + phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining)" + } + + def fromRaw(x: RawTrialLabel, armIds: Set[LongId[Arm]]) = ExportTrialLabelCriterion( + criterionId = x.criterionId, + value = x.value, + labelId = x.labelId, + armIds = armIds, + criteria = x.criteria, + isCompound = x.isCompound, + isDefining = x.isDefining + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala new file mode 100644 index 0000000..1655a88 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala @@ -0,0 +1,52 @@ +package xyz.driver.pdsuidomain.entities.export.trial + +import java.time.LocalDateTime + +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.{RawTrialLabel, Trial} + +import scala.collection.breakOut + +final case class ExportTrialWithLabels(nctId: StringId[Trial], + trialId: UuidId[Trial], + condition: String, + lastReviewed: LocalDateTime, + labelVersion: Long, + arms: List[ExportTrialArm], + criteria: List[ExportTrialLabelCriterion]) + +object ExportTrialWithLabels { + + implicit def toPhiString(x: ExportTrialWithLabels): PhiString = { + import x._ + phi"TrialWithLabels(nctId=$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) + ) + } + +} |