diff options
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/entities')
6 files changed, 65 insertions, 63 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/LinkedPatient.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/LinkedPatient.scala index e82bcc3..1b30c64 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/LinkedPatient.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/LinkedPatient.scala @@ -11,6 +11,4 @@ object LinkedPatient { } } -case class LinkedPatient(userId: LongId[User], - patientId: UuidId[Patient], - trialId: StringId[Trial]) +case class LinkedPatient(userId: LongId[User], patientId: UuidId[Patient], trialId: StringId[Trial]) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala index 60298b9..34e3741 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala @@ -8,7 +8,7 @@ import xyz.driver.pdsuicommon.logging._ object PatientLabelEvidenceView { implicit def toPhiString(x: PatientLabelEvidenceView): PhiString = { import x._ - phi"PatientLabelEvidenceViewRepository.Row(id=$id, value=$value, documentId=$documentId, " + + phi"PatientLabelEvidenceView(id=$id, value=$value, documentId=$documentId, " + phi"evidenceId=$evidenceId, reportId=$reportId, patientId=$patientId, labelId=$labelId, " + phi"isImplicitMatch=$isImplicitMatch)" } diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/UserHistory.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/UserHistory.scala index b55369e..4abb205 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/UserHistory.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/UserHistory.scala @@ -21,7 +21,7 @@ object UserHistory { def forDocument(executor: LongId[User], documentId: LongId[Document], state: UserHistory.State, - action: UserHistory.Action): UserHistory = UserHistory ( + action: UserHistory.Action): UserHistory = UserHistory( id = LongId(0L), executor = executor, documentId = Some(documentId), @@ -32,7 +32,7 @@ object UserHistory { def forRecord(executor: LongId[User], recordId: LongId[MedicalRecord], state: UserHistory.State, - action: UserHistory.Action): UserHistory = UserHistory ( + action: UserHistory.Action): UserHistory = UserHistory( id = LongId(0L), executor = executor, recordId = Some(recordId), @@ -43,7 +43,7 @@ object UserHistory { def forTrial(executor: LongId[User], trialId: StringId[Trial], state: UserHistory.State, - action: UserHistory.Action): UserHistory = UserHistory ( + action: UserHistory.Action): UserHistory = UserHistory( id = LongId(0L), executor = executor, trialId = Some(trialId), @@ -54,7 +54,7 @@ object UserHistory { def forPatient(executor: LongId[User], patientId: UuidId[Patient], state: UserHistory.State, - action: UserHistory.Action): UserHistory = UserHistory ( + action: UserHistory.Action): UserHistory = UserHistory( id = LongId(0L), executor = executor, patientId = Some(patientId), @@ -70,40 +70,40 @@ object UserHistory { } object State { - case object Clean extends State - case object Organize extends State - case object Extract extends State - case object Summarize extends State + case object Clean extends State + case object Organize extends State + case object Extract extends State + case object Summarize extends State case object Criteriarize extends State - case object Verify extends State - case object Curate extends State - case object Review extends State - case object Flag extends State + case object Verify extends State + case object Curate extends State + case object Review extends State + case object Flag extends State val All: Set[State] = Set[State](Clean, Organize, Extract, Summarize, Criteriarize, Verify, Curate, Review, Flag) val fromString: PartialFunction[String, State] = { - case "Clean" => State.Clean - case "Organize" => State.Organize - case "Extract" => State.Extract - case "Summarize" => State.Summarize + case "Clean" => State.Clean + case "Organize" => State.Organize + case "Extract" => State.Extract + case "Summarize" => State.Summarize case "Criteriarize" => State.Criteriarize - case "Verify" => State.Verify - case "Curate" => State.Curate - case "Review" => State.Review - case "Flag" => State.Flag + case "Verify" => State.Verify + case "Curate" => State.Curate + case "Review" => State.Review + case "Flag" => State.Flag } def stateToString(x: State): String = x match { - case State.Clean => "Clean" - case State.Organize => "Organize" - case State.Extract => "Extract" - case State.Summarize => "Summarize" + case State.Clean => "Clean" + case State.Organize => "Organize" + case State.Extract => "Extract" + case State.Summarize => "Summarize" case State.Criteriarize => "Criteriarize" - case State.Verify => "Verify" - case State.Curate => "Curate" - case State.Review => "Review" - case State.Flag => "Flag" + case State.Verify => "Verify" + case State.Curate => "Curate" + case State.Review => "Review" + case State.Flag => "Flag" } implicit def toPhiString(x: State): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) @@ -117,31 +117,31 @@ object UserHistory { } object Action { - case object Start extends Action - case object Submit extends Action + case object Start extends Action + case object Submit extends Action case object Unassign extends Action - case object Resolve extends Action - case object Flag extends Action - case object Archive extends Action + case object Resolve extends Action + case object Flag extends Action + case object Archive extends Action val All: Set[Action] = Set[Action](Start, Submit, Unassign, Resolve, Flag, Archive) val fromString: PartialFunction[String, Action] = { - case "Start" => Action.Start - case "Submit" => Action.Submit + case "Start" => Action.Start + case "Submit" => Action.Submit case "Unassign" => Action.Unassign - case "Resolve" => Action.Resolve - case "Flag" => Action.Flag - case "Archive" => Action.Archive + case "Resolve" => Action.Resolve + case "Flag" => Action.Flag + case "Archive" => Action.Archive } def actionToString(x: Action): String = x match { - case Action.Start => "Start" - case Action.Submit => "Submit" + case Action.Start => "Start" + case Action.Submit => "Submit" case Action.Unassign => "Unassign" - case Action.Resolve => "Resolve" - case Action.Flag => "Flag" - case Action.Archive => "Archive" + case Action.Resolve => "Resolve" + case Action.Flag => "Flag" + case Action.Archive => "Archive" } implicit def toPhiString(x: Action): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) 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 index 5474413..5135c21 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala @@ -4,9 +4,7 @@ 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]) +final case class ExportPatientLabel(id: LongId[Label], name: String, evidences: List[ExportPatientLabelEvidence]) object ExportPatientLabel extends PhiLogging { 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 index e6262ed..bd6173b 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala @@ -6,7 +6,9 @@ import xyz.driver.pdsuidomain.entities.{Patient, RawPatientLabel} import scala.collection.breakOut -final case class ExportPatientWithLabels(patientId: UuidId[Patient], labelVersion: Long, labels: List[ExportPatientLabel]) +final case class ExportPatientWithLabels(patientId: UuidId[Patient], + labelVersion: Long, + labels: List[ExportPatientLabel]) object ExportPatientWithLabels { @@ -15,8 +17,7 @@ object ExportPatientWithLabels { phi"ExportPatientWithLabels(patientId=$patientId, version=${Unsafe(labelVersion)}, labels=$labels)" } - def fromRaw(patientId: UuidId[Patient], - rawPatientRefs: List[RawPatientLabel]) = ExportPatientWithLabels( + 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 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 index 1655a88..60b74ff 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala @@ -36,16 +36,21 @@ object ExportTrialWithLabels { 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) + 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) ) } |