Adding domain entitiesv0.1.0

8 files changed, 243 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..7d5de79
--- /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}
+
+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: $labelId")
+    }
+
+    ExportPatientLabel(
+      id = labelId,
+      name = firstLabel.map(_.label).getOrElse(""),
+      evidences = rawPatientLabels.map(ExportPatientLabelEvidence.fromRaw)
+    )
+  }
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala
new file mode 100644
index 0000000..ff0fb6c
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala
@@ -0,0 +1,32 @@
+package xyz.driver.pdsuidomain.entities.export.patient
+
+import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId}
+import xyz.driver.pdsuicommon.logging._
+import xyz.driver.pdsuidomain.entities.{ExtractedData, RawPatientLabel}
+
+case class ExportPatientLabelEvidence(id: LongId[ExtractedData],
+                                      value: FuzzyValue,
+                                      evidenceText: String,
+                                      document: ExportPatientLabelEvidenceDocument)
+
+object ExportPatientLabelEvidence {
+
+  implicit def toPhiString(x: ExportPatientLabelEvidence): PhiString = {
+    import x._
+    phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=$value, " +
+      phi"evidenceText=${Unsafe(evidenceText)}, document=$document)"
+  }
+
+  def fromRaw(x: RawPatientLabel) = ExportPatientLabelEvidence(
+    id = x.evidenceId,
+    value = x.value,
+    evidenceText = x.evidenceText,
+    document = ExportPatientLabelEvidenceDocument(
+      x.documentId,
+      x.requestId,
+      x.documentType,
+      x.providerType,
+      x.startDate
+    )
+  )
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala
new file mode 100644
index 0000000..d696569
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala
@@ -0,0 +1,30 @@
+package xyz.driver.pdsuidomain.entities.export.patient
+
+import java.time.LocalDateTime
+
+import xyz.driver.pdsuicommon.domain.LongId
+import xyz.driver.pdsuicommon.logging._
+import xyz.driver.pdsuidomain.entities.{Document, RawPatientLabel, RecordRequestId}
+
+case class ExportPatientLabelEvidenceDocument(documentId: LongId[Document],
+                                              requestId: RecordRequestId,
+                                              documentType: String,
+                                              providerType: String,
+                                              date: LocalDateTime)
+
+object ExportPatientLabelEvidenceDocument extends PhiLogging {
+
+  implicit def toPhiString(x: ExportPatientLabelEvidenceDocument): PhiString = {
+    import x._
+    phi"ExportPatientLabelEvidenceDocument(documentId=$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..418f20b
--- /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.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=$labels)"
+  }
+
+  def fromRaw(patientId: UuidId[Patient],
+              rawPatientRefs: List[RawPatientLabel]) = ExportPatientWithLabels(
+    patientId = patientId,
+    labelVersion = 1L, // TODO It is needed to replace this mock label version.
+    labels = rawPatientRefs
+      .groupBy(_.labelId)
+      .map(Function.tupled(ExportPatientLabel.fromRaw))(breakOut)
+  )
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala
new file mode 100644
index 0000000..a3a0e90
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrial.scala
@@ -0,0 +1,27 @@
+package xyz.driver.pdsuidomain.entities.export.trial
+
+import java.time.LocalDateTime
+
+import xyz.driver.pdsuicommon.domain.{StringId, UuidId}
+import xyz.driver.pdsuicommon.logging._
+import xyz.driver.pdsuidomain.entities.Trial
+
+case class ExportTrial(nctId: StringId[Trial],
+                       trialId: UuidId[Trial],
+                       condition: Trial.Condition,
+                       lastReviewed: LocalDateTime)
+
+object ExportTrial {
+
+  implicit def toPhiString(x: ExportTrial): PhiString = {
+    import x._
+    phi"ExportTrial(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, lastReviewed=$lastReviewed)"
+  }
+
+  def fromDomain(x: Trial) = ExportTrial(
+    nctId = x.id,
+    trialId = x.externalId,
+    condition = x.condition,
+    lastReviewed = x.lastUpdate
+  )
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala
new file mode 100644
index 0000000..abdade4
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala
@@ -0,0 +1,15 @@
+package xyz.driver.pdsuidomain.entities.export.trial
+
+import xyz.driver.pdsuicommon.domain.LongId
+import xyz.driver.pdsuicommon.logging._
+import xyz.driver.pdsuidomain.entities.Arm
+
+case class ExportTrialArm(armId: LongId[Arm], armName: String)
+
+object ExportTrialArm {
+
+  implicit def toPhiString(x: ExportTrialArm): PhiString = {
+    import x._
+    phi"ExportTrialArm(armId=$armId, armName=${Unsafe(armName)})"
+  }
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala
new file mode 100644
index 0000000..1dccaa5
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala
@@ -0,0 +1,32 @@
+package xyz.driver.pdsuidomain.entities.export.trial
+
+import xyz.driver.pdsuicommon.domain.LongId
+import xyz.driver.pdsuicommon.logging._
+import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Label, RawTrialLabel}
+
+case class ExportTrialLabelCriterion(criterionId: LongId[Criterion],
+                                     value: Option[Boolean],
+                                     labelId: LongId[Label],
+                                     armIds: Set[LongId[Arm]],
+                                     criteria: String,
+                                     isCompound: Boolean,
+                                     isDefining: Boolean)
+
+object ExportTrialLabelCriterion {
+
+  implicit def toPhiString(x: ExportTrialLabelCriterion): PhiString = {
+    import x._
+    phi"TrialLabelCriterion(criterionId=$criterionId, value=$value, labelId=$labelId, " +
+      phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining)"
+  }
+
+  def fromRaw(x: RawTrialLabel, armIds: Set[LongId[Arm]]) = ExportTrialLabelCriterion(
+    criterionId = x.criterionId,
+    value = x.value,
+    labelId = x.labelId,
+    armIds = armIds,
+    criteria = x.criteria,
+    isCompound = x.isCompound,
+    isDefining = x.isDefining
+  )
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala
new file mode 100644
index 0000000..251f6fb
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala
@@ -0,0 +1,51 @@
+package xyz.driver.pdsuidomain.entities.export.trial
+
+import java.time.LocalDateTime
+
+import xyz.driver.pdsuicommon.domain.{StringId, UuidId}
+import xyz.driver.pdsuicommon.logging._
+import xyz.driver.pdsuidomain.entities.{RawTrialLabel, Trial}
+
+import scala.collection.breakOut
+
+case class ExportTrialWithLabels(nctId: StringId[Trial],
+                                 trialId: UuidId[Trial],
+                                 condition: String,
+                                 lastReviewed: LocalDateTime,
+                                 labelVersion: Long,
+                                 arms: List[ExportTrialArm],
+                                 criteria: List[ExportTrialLabelCriterion])
+
+object ExportTrialWithLabels {
+
+  implicit def toPhiString(x: ExportTrialWithLabels): PhiString = {
+    import x._
+    phi"TrialWithLabels(nctId=$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)
+    )
+  }
+}