diff options
91 files changed, 778 insertions, 708 deletions
@@ -11,15 +11,15 @@ lazy val core = (project in file(".")) "com.fasterxml.jackson.module" %% "jackson-module-scala" % "2.8.3", "com.github.pureconfig" %% "pureconfig" % "0.7.2", "com.lihaoyi" %% "fastparse" % "0.3.7", - "com.typesafe.akka" %% "akka-http" % "10.0.9", + "com.typesafe.akka" %% "akka-http" % "10.0.10", "com.typesafe.play" %% "play" % "2.5.15", "com.typesafe.scala-logging" %% "scala-logging" % "3.5.0", "io.getquill" %% "quill-jdbc" % "1.2.1", "io.github.cloudify" %% "spdf" % "1.4.0", "org.davidbild" %% "tristate-core" % "0.2.0", "org.davidbild" %% "tristate-play" % "0.2.0" exclude ("com.typesafe.play", "play-json"), - "xyz.driver" %% "core" % "1.2.1", - "xyz.driver" %% "domain-model" % "0.17.1", + "xyz.driver" %% "core" % "1.2.2", + "xyz.driver" %% "domain-model" % "0.17.8", "ch.qos.logback" % "logback-classic" % "1.1.7", "com.fasterxml.jackson.datatype" % "jackson-datatype-jsr310" % "2.8.4", "com.github.spullara.mustache.java" % "scala-extensions-2.11" % "0.9.4", diff --git a/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala index 0daa84d..dc03a52 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala @@ -1,6 +1,6 @@ package xyz.driver.pdsuicommon.db -import java.sql.PreparedStatement +import java.sql.{JDBCType, PreparedStatement} import java.time.LocalDateTime import slick.jdbc.{JdbcProfile, PositionedParameters, SQLActionBuilder, SetParameter} @@ -38,6 +38,12 @@ object SlickQueryBuilder { }) } } + + implicit object SetQueryParameter extends SetParameter[AnyRef] { + def apply(v: AnyRef, pp: PositionedParameters) = { + pp.setObject(v, JDBCType.BINARY.getVendorTypeNumber) + } + } } final case class SlickTableLink(keyColumnName: String, foreignTableName: String, foreignKeyColumnName: String) @@ -175,6 +181,16 @@ sealed trait SlickQueryBuilderParameters { } else sql } + def concatenateParameters(sql: SQLActionBuilder, first: Boolean, tail: Seq[AnyRef]): SQLActionBuilder = { + if (tail.nonEmpty) { + if (!first) { + concatenateParameters(sql concat sql""",${tail.head}""", false, tail.tail) + } else { + concatenateParameters(sql"""(${tail.head}""", false, tail.tail) + } + } else sql concat sql")" + } + filter match { case x if isEmpty(x) => sql"" @@ -196,7 +212,7 @@ sealed trait SlickQueryBuilderParameters { // So, to handle NotEq for nullable fields we need to use more complex SQL expression. // http://dev.mysql.com/doc/refman/5.7/en/working-with-null.html val escapedColumn = escapeDimension(dimension) - sql"(#${escapedColumn} is null or #${escapedColumn} != ${value.toString})" + sql"(#${escapedColumn} is null or #${escapedColumn} != $value)" case Atom.Binary(dimension, op, value) => val operator = op match { @@ -208,7 +224,7 @@ sealed trait SlickQueryBuilderParameters { case Lt => sql"<" case LtEq => sql"<=" } - sql"#${escapeDimension(dimension)}" concat operator concat sql"""${value.toString}""" + sql"#${escapeDimension(dimension)}" concat operator concat sql"""$value""" case Atom.NAry(dimension, op, values) => val sqlOp = op match { @@ -217,8 +233,7 @@ sealed trait SlickQueryBuilderParameters { } val formattedValues = if (values.nonEmpty) { - val condition = s"(${values.map(v => "'" + v.toString + "'").mkString(",")})" - sql"#${condition}" + concatenateParameters(sql"", true, values) } else sql"NULL" sql"#${escapeDimension(dimension)}" concat sqlOp concat formattedValues diff --git a/src/main/scala/xyz/driver/pdsuicommon/domain/FuzzyValue.scala b/src/main/scala/xyz/driver/pdsuicommon/domain/FuzzyValue.scala deleted file mode 100644 index 36c3de7..0000000 --- a/src/main/scala/xyz/driver/pdsuicommon/domain/FuzzyValue.scala +++ /dev/null @@ -1,40 +0,0 @@ -package xyz.driver.pdsuicommon.domain - -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils - -sealed trait FuzzyValue - -object FuzzyValue { - case object Yes extends FuzzyValue - case object No extends FuzzyValue - case object Maybe extends FuzzyValue - - private val yes = "Yes" - private val no = "No" - private val maybe = "Maybe" - - val All: Set[FuzzyValue] = - Set(Yes, No, Maybe) - - def fromBoolean(x: Boolean): FuzzyValue = - if (x) Yes else No - - implicit def toPhiString(x: FuzzyValue): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - - val fromString: PartialFunction[String, FuzzyValue] = { - case fuzzy => - fuzzy.toLowerCase.capitalize match { - case `yes` => Yes - case `no` => No - case `maybe` => Maybe - } - } - - def valueToString(x: FuzzyValue): String = x match { - case Yes => `yes` - case No => `no` - case Maybe => `maybe` - } -} diff --git a/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala b/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala index a53f1dd..9383a1c 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala @@ -3,7 +3,7 @@ package xyz.driver.pdsuicommon.json import java.text.SimpleDateFormat import com.fasterxml.jackson.annotation.JsonInclude -import com.fasterxml.jackson.databind.ObjectMapper +import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper} import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule import com.fasterxml.jackson.module.scala.DefaultScalaModule import com.fasterxml.jackson.module.scala.experimental.ScalaObjectMapper @@ -15,6 +15,7 @@ object JsonSerializer { mapper.registerModule(new JavaTimeModule) mapper.setDateFormat(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'")) mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL) + mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false) def serialize(value: Any): String = { mapper.writeValueAsString(value) diff --git a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala index 83c4e6f..6d2a068 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala @@ -15,6 +15,7 @@ import xyz.driver.pdsuidomain.formats.json.sprayformats.trial._ import xyz.driver.pdsuidomain.formats.json.sprayformats.trialhistory._ import xyz.driver.pdsuidomain.formats.json.sprayformats.trialissue._ import xyz.driver.core.swagger.CustomSwaggerJsonConverter._ +import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData @@ -32,7 +33,7 @@ object CustomSwaggerJsonFormats { ) val customTrialCurationProperties = immutable.Map[Class[_], Property]( classOf[Trial.Status] -> stringProperty(), - classOf[Trial.Condition] -> stringProperty(), + classOf[CancerType] -> stringProperty(), classOf[TrialHistory.Action] -> stringProperty(), classOf[TrialHistory.State] -> stringProperty() ) ++ customCommonProperties diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala index 42ac55b..f35c3fd 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala @@ -2,31 +2,14 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDate +import xyz.driver.entities.assays.AssayType import xyz.driver.pdsuicommon.logging._ import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuicommon.utils.Utils -import xyz.driver.pdsuidomain.entities.DirectReport.ReportType object DirectReport { - - sealed trait ReportType extends Product with Serializable { - def oneOf(xs: ReportType*): Boolean = xs.contains(this) - - def oneOf(xs: Set[ReportType]): Boolean = xs.contains(this) - } - - object ReportType { - case object IHC extends ReportType - case object DNA extends ReportType - case object CFDNA extends ReportType - - val All = Set(IHC, DNA, CFDNA) - implicit def toPhiString(x: ReportType): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - implicit def toPhiString(x: DirectReport): PhiString = { import x._ - phi"DirectReport(id=$id, patientId=$patientId, reportType=$reportType, date=${Unsafe(date)}, " + + phi"DirectReport(id=$id, patientId=$patientId, reportType=${Unsafe(reportType)}, date=${Unsafe(date)}, " + phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, " + phi"providerName=${Unsafe(providerName)})" } @@ -34,8 +17,8 @@ object DirectReport { final case class DirectReport(id: UuidId[DirectReport], patientId: UuidId[Patient], - reportType: ReportType, + reportType: AssayType, date: LocalDate, - documentType: String, - providerType: String, + documentType: DocumentType, + providerType: ProviderType, providerName: String) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala index eccb254..258aa03 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala @@ -308,13 +308,7 @@ object DocumentType { object Document { - final case class Meta(predicted: Option[Boolean], startPage: Double, endPage: Double) { - - /** - * Return a regular meta: this meta is considered as not predicted - */ - def confirmed: Meta = copy(predicted = predicted.map(_ => false)) - } + final case class Meta(startPage: Double, endPage: Double) class DocumentStatusSerializer extends JsonSerializer[Status] { def serialize(value: Status, gen: JsonGenerator, serializers: SerializerProvider): Unit = { @@ -419,6 +413,8 @@ object Document { providerTypeId <- Validators.nonEmpty("providerTypeId")(input.providerTypeId) + institutionName <- Validators.nonEmpty("institutionName")(input.institutionName) + meta <- Validators.nonEmpty("meta")(input.meta) startDate <- Validators.nonEmpty("startDate")(input.startDate) @@ -456,6 +452,7 @@ final case class Document(id: LongId[Document] = LongId(0L), providerName: Option[String], // not null providerTypeId: Option[LongId[ProviderType]], // not null requiredType: Option[Document.RequiredType], + institutionName: Option[String], meta: Option[TextJson[Meta]], // not null startDate: Option[LocalDate], // not null endDate: Option[LocalDate], diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala index 2f5924c..50b49ad 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDateTime +import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.domain.{LongId, StringId} import xyz.driver.pdsuicommon.logging._ @@ -18,3 +19,24 @@ object EligibilityArm { phi"Arm(id=$id, name=${Unsafe(x.name)}, trialId=${Unsafe(x.trialId)})" } } + +final case class EligibilityArmDisease(eligibilityArmId: LongId[EligibilityArm], disease: CancerType) + +object EligibilityArmDisease { + + implicit def toPhiString(x: EligibilityArmDisease): PhiString = { + phi"EligibilityArmDisease(eligibilityArmId=${Unsafe(x.eligibilityArmId)}, disease=${Unsafe(x.disease)})" + } + +} + +final case class EligibilityArmWithDiseases(eligibilityArm: EligibilityArm, + eligibilityArmDiseases: Seq[EligibilityArmDisease]) + +object EligibilityArmWithDiseases { + + implicit def toPhiString(x: EligibilityArmWithDiseases): PhiString = { + import x._ + phi"EligibilityArmWithDiseases(eligibilityArm=$eligibilityArm, eligibilityArmDiseases=$eligibilityArmDiseases)" + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala index fbd468f..352cf55 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala @@ -1,7 +1,7 @@ package xyz.driver.pdsuidomain.entities -import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} +import xyz.driver.pdsuicommon.domain.{LongId, TextJson} import xyz.driver.pdsuicommon.logging._ import xyz.driver.pdsuidomain.entities.ExtractedData.Meta @@ -37,7 +37,7 @@ object ExtractedDataLabel { implicit def toPhiString(x: ExtractedDataLabel): PhiString = { import x._ - phi"ExtractedDataLabel(id=$id, dataId=$dataId, labelId=$labelId, categoryId=$categoryId, value=$value)" + phi"ExtractedDataLabel(id=$id, dataId=$dataId, labelId=$labelId, categoryId=$categoryId, value=${Unsafe(value)})" } } @@ -45,4 +45,4 @@ final case class ExtractedDataLabel(id: LongId[ExtractedDataLabel], dataId: LongId[ExtractedData], labelId: Option[LongId[Label]], categoryId: Option[LongId[LabelCategory]], - value: Option[FuzzyValue]) + value: Option[LabelValue]) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecord.scala index 9b33af4..ed35db4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecord.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecord.scala @@ -22,55 +22,45 @@ object MedicalRecord { )) trait Meta { @JsonProperty("type") def metaType: String - def predicted: Option[Boolean] - - /** - * Return a regular meta: this meta is considered as not predicted - */ - def confirmed: Meta } object Meta { - final case class Duplicate(predicted: Option[Boolean], - startPage: Double, + final case class Duplicate(startPage: Double, endPage: Double, startOriginalPage: Double, endOriginalPage: Option[Double]) extends Meta { - override val metaType = "duplicate" - override def confirmed: Duplicate = copy(predicted = predicted.map(_ => false)) + override val metaType = "duplicate" } object Duplicate { implicit def toPhiString(x: Duplicate): PhiString = { import x._ - phi"Duplicate(predicted=${x.predicted}, startPage=${Unsafe(startPage)}, endPage=${Unsafe(endPage)}, " + + phi"Duplicate(startPage=${Unsafe(startPage)}, endPage=${Unsafe(endPage)}, " + phi"startOriginalPage=${Unsafe(startOriginalPage)}, endOriginalPage=${Unsafe(endOriginalPage)}" } } - final case class Reorder(predicted: Option[Boolean], items: Seq[Int]) extends Meta { - override val metaType = "reorder" - override def confirmed: Reorder = copy(predicted = predicted.map(_ => false)) + final case class Reorder(items: Seq[Int]) extends Meta { + override val metaType = "reorder" } object Reorder { implicit def toPhiString(x: Reorder): PhiString = { import x._ - phi"Reorder(predicted=${x.predicted}, items=${Unsafe(items.toString)})" + phi"Reorder(items=${Unsafe(items.toString)})" } } - final case class Rotation(predicted: Option[Boolean], items: Map[String, Int]) extends Meta { - override val metaType = "rotation" - override def confirmed: Rotation = copy(predicted = predicted.map(_ => false)) + final case class Rotation(items: Map[String, Int]) extends Meta { + override val metaType = "rotation" } object Rotation { implicit def toPhiString(x: Rotation): PhiString = { import x._ - phi"Rotation(predicted=${x.predicted}, items=${Unsafe(items.toString)})" + phi"Rotation(items=${Unsafe(items.toString)})" } } @@ -166,8 +156,6 @@ final case class MedicalRecord(id: LongId[MedicalRecord], caseId: Option[CaseId], physician: Option[String], meta: Option[TextJson[List[Meta]]], - predictedMeta: Option[TextJson[List[Meta]]], - predictedDocuments: Option[TextJson[List[Document]]], lastUpdate: LocalDateTime) { import MedicalRecord.Status._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala index 6be0b88..598b11e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala @@ -2,6 +2,8 @@ package xyz.driver.pdsuidomain.entities import java.time.{LocalDate, LocalDateTime} +import xyz.driver.entities.common.FullName +import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ import xyz.driver.pdsuicommon.utils.Utils @@ -52,14 +54,14 @@ object Patient { final case class Patient(id: UuidId[Patient], status: Patient.Status, - name: String, + name: FullName[Patient], dob: LocalDate, assignee: Option[StringId[User]], previousStatus: Option[Patient.Status], previousAssignee: Option[StringId[User]], lastActiveUserId: Option[StringId[User]], isUpdateRequired: Boolean, - condition: String, + disease: CancerType, orderId: PatientOrderId, lastUpdate: LocalDateTime) { diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala index 469b21c..79a19ed 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala @@ -2,7 +2,8 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDateTime -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId} +import xyz.driver.entities.labels.LabelValue +import xyz.driver.pdsuicommon.domain.{LongId, StringId} import xyz.driver.pdsuicommon.logging._ object PatientCriterion { @@ -18,15 +19,15 @@ object PatientCriterion { /** * @see https://driverinc.atlassian.net/wiki/display/MTCH/EV+Business+Process */ - def getEligibilityStatus(criterionValue: Option[Boolean], primaryValue: Option[FuzzyValue]): Option[FuzzyValue] = { + def getEligibilityStatus(criterionValue: Option[Boolean], primaryValue: Option[LabelValue]): Option[LabelValue] = { primaryValue match { case None => None - case Some(FuzzyValue.Maybe) => Some(FuzzyValue.Maybe) - case Some(_) if criterionValue.isEmpty => Some(FuzzyValue.Maybe) + case Some(LabelValue.Maybe) => Some(LabelValue.Maybe) + case Some(_) if criterionValue.isEmpty => Some(LabelValue.Maybe) case Some(status) => Some( - FuzzyValue.fromBoolean( - FuzzyValue.fromBoolean( + LabelValue.fromBoolean( + LabelValue.fromBoolean( criterionValue.getOrElse(throw new IllegalArgumentException("Criterion should not be empty"))) == status )) } @@ -47,12 +48,12 @@ final case class PatientCriterion(id: LongId[PatientCriterion], criterionText: String, criterionValue: Option[Boolean], criterionIsDefining: Boolean, - eligibilityStatus: Option[FuzzyValue], - verifiedEligibilityStatus: Option[FuzzyValue], + eligibilityStatus: Option[LabelValue], + verifiedEligibilityStatus: Option[LabelValue], isVerified: Boolean, isVisible: Boolean, lastUpdate: LocalDateTime) { - def isIneligibleForEv: Boolean = eligibilityStatus.contains(FuzzyValue.No) && isVerified + def isIneligibleForEv: Boolean = eligibilityStatus.contains(LabelValue.No) && isVerified } object PatientCriterionArm { diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala index 8ee5b3c..ff272a8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala @@ -1,6 +1,7 @@ package xyz.driver.pdsuidomain.entities -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} +import xyz.driver.entities.labels.LabelValue +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuicommon.logging._ object PatientTrialArm { @@ -37,22 +38,22 @@ object PatientTrialArmGroup { /** * @see https://driverinc.atlassian.net/wiki/display/DMPD/EV+Business+Process */ - def getEligibilityStatusForRc(criterionList: TraversableOnce[PatientCriterion]): Option[FuzzyValue] = { - def isEligible: Boolean = criterionList.forall(_.verifiedEligibilityStatus.contains(FuzzyValue.Yes)) - def isIneligible: Boolean = criterionList.exists(_.verifiedEligibilityStatus.contains(FuzzyValue.No)) + def getEligibilityStatusForRc(criterionList: TraversableOnce[PatientCriterion]): Option[LabelValue] = { + def isEligible: Boolean = criterionList.forall(_.verifiedEligibilityStatus.contains(LabelValue.Yes)) + def isIneligible: Boolean = criterionList.exists(_.verifiedEligibilityStatus.contains(LabelValue.No)) def isUnknown: Boolean = criterionList.forall(_.verifiedEligibilityStatus.isEmpty) - if (isEligible) Some(FuzzyValue.Yes) - else if (isIneligible) Some(FuzzyValue.No) + if (isEligible) Some(LabelValue.Yes) + else if (isIneligible) Some(LabelValue.No) else if (isUnknown) None - else Some(FuzzyValue.Maybe) + else Some(LabelValue.Maybe) } } final case class PatientTrialArmGroup(id: LongId[PatientTrialArmGroup], eligibleTrialId: UuidId[PatientEligibleTrial], - eligibilityStatus: Option[FuzzyValue], - verifiedEligibilityStatus: Option[FuzzyValue], + eligibilityStatus: Option[LabelValue], + verifiedEligibilityStatus: Option[LabelValue], isVerified: Boolean) object PatientTrialArmGroupView { @@ -69,8 +70,8 @@ final case class PatientTrialArmGroupView(id: LongId[PatientTrialArmGroup], patientId: UuidId[Patient], trialId: StringId[Trial], hypothesisId: UuidId[Hypothesis], - eligibilityStatus: Option[FuzzyValue], - verifiedEligibilityStatus: Option[FuzzyValue], + eligibilityStatus: Option[LabelValue], + verifiedEligibilityStatus: Option[LabelValue], isVerified: Boolean) { def applyTo(trialArmGroup: PatientTrialArmGroup) = { diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala index d10c7d2..4c0f4ef 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala @@ -1,7 +1,7 @@ package xyz.driver.pdsuidomain.entities -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, UuidId} +import xyz.driver.entities.labels.{Label, LabelValue} +import xyz.driver.pdsuicommon.domain.{LongId, UuidId} import xyz.driver.pdsuicommon.logging._ object PatientLabel { @@ -17,8 +17,8 @@ final case class PatientLabel(id: LongId[PatientLabel], patientId: UuidId[Patient], labelId: LongId[Label], score: Int, - primaryValue: Option[FuzzyValue], - verifiedPrimaryValue: Option[FuzzyValue], + primaryValue: Option[LabelValue], + verifiedPrimaryValue: Option[LabelValue], isImplicitMatch: Boolean, isVisible: Boolean) @@ -32,7 +32,7 @@ object PatientLabelEvidence { final case class PatientLabelEvidence(id: LongId[PatientLabelEvidence], patientLabelId: LongId[PatientLabel], - value: FuzzyValue, + value: LabelValue, evidenceText: String, reportId: Option[UuidId[DirectReport]], documentId: Option[LongId[Document]], diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala index 3311d96..6055921 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala @@ -2,28 +2,28 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDate -import xyz.driver.entities.labels.Label +import xyz.driver.entities.labels.{Label, LabelValue} import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ object PatientLabelEvidenceView { implicit def toPhiString(x: PatientLabelEvidenceView): PhiString = { import x._ - phi"PatientLabelEvidenceView(id=$id, value=$value, documentId=$documentId, " + + phi"PatientLabelEvidenceView(id=$id, value=${Unsafe(value)}, documentId=$documentId, " + phi"evidenceId=$evidenceId, reportId=$reportId, patientId=$patientId, labelId=$labelId, " + phi"isImplicitMatch=$isImplicitMatch)" } } final case class PatientLabelEvidenceView(id: LongId[PatientLabelEvidence], - value: FuzzyValue, + value: LabelValue, evidenceText: String, documentId: Option[LongId[Document]], evidenceId: Option[LongId[ExtractedData]], reportId: Option[UuidId[DirectReport]], - documentType: String, + documentType: DocumentType, date: Option[LocalDate], // Document.startDate is optional - providerType: String, + providerType: ProviderType, patientId: UuidId[Patient], labelId: LongId[Label], isImplicitMatch: Boolean) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala deleted file mode 100644 index 689eaa4..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala +++ /dev/null @@ -1,31 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDate - -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, UuidId} -import xyz.driver.pdsuicommon.logging._ - -final case class RawPatientLabel(patientId: UuidId[Patient], - labelId: LongId[Label], - value: FuzzyValue, - evidenceId: LongId[ExtractedData], - evidenceText: String, - disease: String, - documentId: LongId[Document], - requestId: RecordRequestId, - documentType: DocumentType, - providerType: ProviderType, - startDate: LocalDate, - endDate: Option[LocalDate]) - -object RawPatientLabel { - - implicit def toPhiString(x: RawPatientLabel): PhiString = { - import x._ - phi"RawPatientLabel(patientId=$patientId, labelId=$labelId, value=$value, evidenceId=${Unsafe(evidenceId)}, " + - phi"evidenceText=${Unsafe(evidenceText)}, documentId=$documentId, requestId=${Unsafe(requestId)}, " + - phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, " + - phi"startDate=$startDate, endDate=$endDate)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala deleted file mode 100644 index bdbc4ea..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuicommon.logging._ - -final case class RawTrialLabel(nctId: StringId[Trial], - trialId: UuidId[Trial], - condition: String, - lastReviewed: LocalDateTime, - armName: String, - armId: LongId[Arm], - labelId: LongId[Label], - value: Option[Boolean], - criterionId: LongId[Criterion], - criteria: String, - criterionArmId: LongId[Arm], - isCompound: Boolean, - isDefining: Boolean) - -object RawTrialLabel { - - implicit def toPhiString(x: RawTrialLabel): PhiString = { - import x._ - phi"RawTrialLabel(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, lastReviewed=$lastReviewed, " + - phi"armId=$armId, armName=${Unsafe(armName)}, labelId=$labelId, value=$value, " + - phi"criterionId=$criterionId, criteria=${Unsafe(criteria)}, criterionArmId=$criterionArmId, " + - phi"isCompound=$isCompound, isDefining=$isDefining)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala index bd86057..ac5feef 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala @@ -58,24 +58,6 @@ object Trial { } final case class Locations(locations: List[String]) - - sealed trait Condition - - object Condition { - - case object Breast extends Condition - case object Lung extends Condition - case object Prostate extends Condition - - def fromString(condition: String): Option[Condition] = condition match { - case "Breast" => Some(Breast) - case "Lung" => Some(Lung) - case "Prostate" => Some(Prostate) - case _ => None - } - - val All: Set[Condition] = Set(Breast, Lung, Prostate) - } } final case class Trial(id: StringId[Trial], 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 2edd707..957e607 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 @@ -3,7 +3,6 @@ package xyz.driver.pdsuidomain.entities.export.patient import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.RawPatientLabel final case class ExportPatientLabel(id: LongId[Label], evidences: List[ExportPatientLabelEvidence]) @@ -13,8 +12,4 @@ object ExportPatientLabel extends PhiLogging { import x._ phi"ExportPatientLabel(id=$id, evidences=$evidences)" } - - def fromRaw(labelId: LongId[Label], rawPatientLabels: List[RawPatientLabel]): ExportPatientLabel = { - ExportPatientLabel(id = labelId, 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 index fb40339..6472a6b 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala @@ -1,11 +1,12 @@ package xyz.driver.pdsuidomain.entities.export.patient +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{ExtractedData, RawPatientLabel} +import xyz.driver.pdsuidomain.entities.ExtractedData final case class ExportPatientLabelEvidence(id: LongId[ExtractedData], - value: FuzzyValue, + value: LabelValue, evidenceText: String, document: ExportPatientLabelEvidenceDocument) @@ -13,20 +14,8 @@ object ExportPatientLabelEvidence { implicit def toPhiString(x: ExportPatientLabelEvidence): PhiString = { import x._ - phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=$value, " + + phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=${Unsafe(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 index 7003615..467170b 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala @@ -19,12 +19,4 @@ object ExportPatientLabelEvidenceDocument extends PhiLogging { phi"ExportPatientLabelEvidenceDocument(documentId=$documentId, requestId=$requestId, " + phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, date=$date)" } - - def fromRaw(x: RawPatientLabel) = ExportPatientLabelEvidenceDocument( - documentId = x.documentId, - requestId = x.requestId, - documentType = x.documentType, - providerType = x.providerType, - date = x.startDate - ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala index bd6173b..8fb2660 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala @@ -2,9 +2,7 @@ package xyz.driver.pdsuidomain.entities.export.patient import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Patient, RawPatientLabel} - -import scala.collection.breakOut +import xyz.driver.pdsuidomain.entities.Patient final case class ExportPatientWithLabels(patientId: UuidId[Patient], labelVersion: Long, @@ -16,12 +14,4 @@ object ExportPatientWithLabels { import x._ phi"ExportPatientWithLabels(patientId=$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/ExportTrialArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala index 5a9a406..24fe641 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala @@ -2,9 +2,9 @@ package xyz.driver.pdsuidomain.entities.export.trial import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.Arm +import xyz.driver.pdsuidomain.entities.EligibilityArm -final case class ExportTrialArm(armId: LongId[Arm], armName: String) +final case class ExportTrialArm(armId: LongId[EligibilityArm], armName: String) object ExportTrialArm { 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 index 1f06e0d..8376e34 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala @@ -3,12 +3,12 @@ package xyz.driver.pdsuidomain.entities.export.trial import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, RawTrialLabel} +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm} final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion], value: Option[Boolean], labelId: LongId[Label], - armIds: Set[LongId[Arm]], + armIds: Set[LongId[EligibilityArm]], criteria: String, isCompound: Boolean, isDefining: Boolean) @@ -20,14 +20,4 @@ object ExportTrialLabelCriterion { 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 index cf55694..3681945 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 @@ -4,13 +4,10 @@ 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 +import xyz.driver.pdsuidomain.entities.Trial final case class ExportTrialWithLabels(nctId: StringId[Trial], trialId: UuidId[Trial], - condition: String, lastReviewed: LocalDateTime, labelVersion: Long, arms: List[ExportTrialArm], @@ -20,35 +17,7 @@ object ExportTrialWithLabels { implicit def toPhiString(x: ExportTrialWithLabels): PhiString = { import x._ - phi"TrialWithLabels(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, " + + phi"TrialWithLabels(nctId=$nctId, trialId=$trialId}, " + phi"lastReviewed=$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 trial 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) - ) - } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala index 7318ff6..f77c2e0 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala @@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.fakes.entities import java.time.{LocalDate, LocalDateTime, LocalTime} import xyz.driver.core.generators.{nextDouble, nextOption} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.{Trial, TrialHistory} import scala.util.Random @@ -29,8 +29,6 @@ object common { 1 + Random.nextInt(28) // all months have at least 28 days ) - def nextCondition = generators.oneOf[Trial.Condition](Trial.Condition.All) - def nextTrialAction = generators.oneOf[TrialHistory.Action](TrialHistory.Action.All) def nextTrialState = generators.oneOf[TrialHistory.State](TrialHistory.State.All) @@ -52,9 +50,6 @@ object common { ranges.map(_._1) -> ranges.flatMap(_._2) } - def nextFuzzyValue(): FuzzyValue = - generators.oneOf[FuzzyValue](FuzzyValue.All) - def nextStartAndEndPages: (Option[Double], Option[Double]) = genBoundedRangeOption[Double](nextDouble(), nextDouble()) diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala index 7f3c410..5febd8f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala @@ -1,22 +1,22 @@ package xyz.driver.pdsuidomain.fakes.entities import xyz.driver.entities.labels.Label -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial} import xyz.driver.pdsuidomain.entities.export.trial._ +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm, Trial} object export { - import xyz.driver.core.generators._ import common._ + import xyz.driver.core.generators._ def nextExportTrialArm(): ExportTrialArm = - ExportTrialArm(armId = nextLongId[Arm], armName = nextString(100)) + ExportTrialArm(armId = nextLongId[EligibilityArm], armName = nextString(100)) def nextExportTrialLabelCriterion(): ExportTrialLabelCriterion = ExportTrialLabelCriterion( criterionId = nextLongId[Criterion], value = nextOption[Boolean](nextBoolean()), labelId = nextLongId[Label], - armIds = setOf(nextLongId[Arm]), + armIds = setOf(nextLongId[EligibilityArm]), criteria = nextString(100), isCompound = nextBoolean(), isDefining = nextBoolean() @@ -26,7 +26,6 @@ object export { ExportTrialWithLabels( nctId = nextStringId[Trial], trialId = nextUuidId[Trial], - condition = nextString(100), lastReviewed = nextLocalDateTime, labelVersion = nextInt(100).toLong, arms = listOf(nextExportTrialArm()), diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala index 1ac75ab..0dadc41 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala @@ -40,12 +40,7 @@ object DocumentGen { def nextDocumentMeta(): Document.Meta = { val (startPage, endPage) = nextStartAndEndPage() - - Document.Meta( - nextOption(nextBoolean()), - startPage, - endPage - ) + Document.Meta(startPage, endPage) } def nextDocumentMetaJson(): TextJson[Document.Meta] = { @@ -68,6 +63,7 @@ object DocumentGen { providerName = nextOption(nextString()), providerTypeId = nextOption(nextLongId[ProviderType]), requiredType = nextOption(nextDocumentRequiredType()), + institutionName = nextOption(nextString()), meta = nextOption(nextDocumentMetaJson()), startDate = dates._1, endDate = dates._2, diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala index 3fcc4cb..85bab8c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala @@ -1,9 +1,9 @@ package xyz.driver.pdsuidomain.fakes.entities.rep +import xyz.driver.core.generators import xyz.driver.core.generators._ -import xyz.driver.entities.labels.Label +import xyz.driver.entities.labels.{Label, LabelValue} import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuidomain.fakes.entities.common._ import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.entities.export.patient._ import xyz.driver.pdsuidomain.fakes.entities.common.{nextLocalDate, nextLongId} @@ -26,7 +26,7 @@ object ExportPatientGen { def nextExportPatientLabelEvidence(documentId: LongId[Document]): ExportPatientLabelEvidence = { ExportPatientLabelEvidence( id = nextLongId[ExtractedData], - value = nextFuzzyValue(), + value = generators.oneOf[LabelValue](LabelValue.Yes, LabelValue.No, LabelValue.Maybe), evidenceText = nextString(), document = nextExportPatientLabelEvidenceDocument(documentId) ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala index 8e77445..70ddd10 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala @@ -1,7 +1,8 @@ package xyz.driver.pdsuidomain.fakes.entities.rep +import xyz.driver.core.generators import xyz.driver.core.generators._ -import xyz.driver.entities.labels.{Label, LabelCategory} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} import xyz.driver.pdsuicommon.domain.{LongId, TextJson} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.entities.ExtractedData.Meta @@ -85,7 +86,7 @@ object ExtractedDataGen { dataId = nextLongId[ExtractedData], labelId = nextOption(nextLongId[Label]), categoryId = nextOption(nextLongId[LabelCategory]), - value = nextOption(nextFuzzyValue()) + value = nextOption(generators.oneOf[LabelValue](LabelValue.Yes, LabelValue.No, LabelValue.Maybe)) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala index 2777116..254968a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala @@ -49,15 +49,10 @@ object MedicalRecordGen { generators.oneOf[MedicalRecordHistory.Action](MedicalRecordHistory.Action.All) def nextMedicalRecordMetaReorder(): MedicalRecord.Meta.Reorder = { - val itemsNumber = - maxItemsInCollectionNumber - val items = scala.util.Random - .shuffle(Seq.tabulate(itemsNumber)(identity)) - - MedicalRecord.Meta.Reorder( - predicted = nextOption(nextBoolean), - items = items - ) + val itemsNumber = maxItemsInCollectionNumber + val items = scala.util.Random.shuffle(Seq.tabulate(itemsNumber)(identity)) + + MedicalRecord.Meta.Reorder(items) } def nextMedicalRecordMetaDuplicate(): MedicalRecord.Meta.Duplicate = { @@ -67,7 +62,6 @@ object MedicalRecordGen { nextInt(pageMaxNumber, startPageGen) MedicalRecord.Meta.Duplicate( - predicted = nextOption(nextBoolean), startPage = startPageGen.toDouble, endPage = endPageGen.toDouble, startOriginalPage = startPageGen.toDouble, @@ -76,17 +70,9 @@ object MedicalRecordGen { } def nextMedicalRecordMetaRotation(): MedicalRecord.Meta.Rotation = { - val items = - Array - .tabulate(maxItemsInCollectionNumber)( - index => nextString() -> index - ) - .toMap - - MedicalRecord.Meta.Rotation( - predicted = nextOption(nextBoolean()), - items = items - ) + val items = Array.tabulate(maxItemsInCollectionNumber)(index => nextString() -> index).toMap + + MedicalRecord.Meta.Rotation(items = items) } def nextMedicalRecordMeta(): MedicalRecord.Meta = { @@ -94,7 +80,6 @@ object MedicalRecordGen { } def nextMedicalRecord(): MedicalRecord = { - val id = nextLongId[MedicalRecord] MedicalRecord( id = nextLongId[MedicalRecord], status = nextMedicalRecordStatus(), @@ -108,8 +93,6 @@ object MedicalRecordGen { caseId = nextOption(CaseId(generators.nextString())), physician = nextOption(generators.nextString()), meta = nextOption(nextMedicalRecordMetasJson()), - predictedMeta = nextOption(nextMedicalRecordMetasJson()), - predictedDocuments = nextOption(nextDocuments(id)), lastUpdate = nextLocalDateTime ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala index 86ea765..ade0115 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala @@ -6,8 +6,8 @@ import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion object trialcuration { - import xyz.driver.core.generators import common._ + import xyz.driver.core.generators import xyz.driver.pdsuidomain.entities.InterventionType._ def nextTrial(): Trial = Trial( diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala index 1869ff3..3f1ecfe 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala @@ -2,7 +2,6 @@ package xyz.driver.pdsuidomain.formats.json.document import java.time.{LocalDate, ZoneId, ZonedDateTime} import xyz.driver.pdsuicommon.domain.{LongId, StringId, TextJson} -import xyz.driver.pdsuicommon.json.JsonSerializer import xyz.driver.pdsuidomain.entities._ import play.api.data.validation.ValidationError @@ -20,6 +19,7 @@ final case class ApiDocument(id: Long, provider: Option[String], providerTypeId: Option[Long], requiredType: Option[String], + institutionName: Option[String], status: Option[String], previousStatus: Option[String], assignee: Option[String], @@ -46,6 +46,7 @@ final case class ApiDocument(id: Long, providerName = this.provider, providerTypeId = this.providerTypeId.map(LongId(_)), requiredType = this.requiredType.map(extractRequiredType), + institutionName = this.institutionName, meta = this.meta.map(x => TextJson(JsonSerializer.deserialize[Document.Meta](x))), startDate = this.startDate, endDate = this.endDate, @@ -74,6 +75,7 @@ object ApiDocument { (JsPath \ "provider").formatNullable[String] and (JsPath \ "providerTypeId").formatNullable[Long] and (JsPath \ "requiredType").formatNullable[String] and + (JsPath \ "institutionName").formatNullable[String] and (JsPath \ "status").formatNullable(statusFormat) and (JsPath \ "previousStatus").formatNullable(statusFormat) and (JsPath \ "assignee").formatNullable[String] and @@ -96,6 +98,7 @@ object ApiDocument { provider = document.providerName, providerTypeId = document.providerTypeId.map(_.id), requiredType = document.requiredType.map(Document.RequiredType.requiredTypeToString), + institutionName = document.institutionName, status = Option(Document.Status.statusToString(document.status)), previousStatus = document.previousStatus.map(Document.Status.statusToString), assignee = document.assignee.map(_.id), diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala index eae0c62..032ddf6 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala @@ -23,6 +23,7 @@ final case class ApiPartialDocument(recordId: Option[Long], endDate: Tristate[LocalDate], provider: Tristate[String], providerTypeId: Tristate[Long], + institutionName: Tristate[String], status: Option[String], assignee: Tristate[String], meta: Tristate[String]) { @@ -42,6 +43,7 @@ final case class ApiPartialDocument(recordId: Option[Long], providerName = provider.cata(Some(_), None, orig.providerName), providerTypeId = providerTypeId.map(LongId[ProviderType]).cata(Some(_), None, orig.providerTypeId), requiredType = orig.requiredType, + institutionName = institutionName.cata(Some(_), None, orig.institutionName), meta = meta.cata(x => Some(TextJson(JsonSerializer.deserialize[Meta](x))), None, orig.meta), startDate = startDate.cata(Some(_), None, orig.startDate), endDate = endDate.cata(Some(_), None, orig.endDate), @@ -67,6 +69,7 @@ final case class ApiPartialDocument(recordId: Option[Long], providerName = provider.toOption, providerTypeId = providerTypeId.map(LongId[ProviderType]).toOption, requiredType = None, + institutionName = institutionName.toOption, meta = meta.map(x => TextJson(JsonSerializer.deserialize[Meta](x))).toOption, previousStatus = None, assignee = None, @@ -90,6 +93,7 @@ object ApiPartialDocument { (JsPath \ "endDate").readTristate[LocalDate] and (JsPath \ "provider").readTristate[String] and (JsPath \ "providerTypeId").readTristate[Long] and + (JsPath \ "institutionName").readTristate[String] and (JsPath \ "status").readNullable[String]( Reads .of[String] @@ -115,6 +119,7 @@ object ApiPartialDocument { (JsPath \ "endDate").writeTristate[LocalDate] and (JsPath \ "provider").writeTristate[String] and (JsPath \ "providerTypeId").writeTristate[Long] and + (JsPath \ "institutionName").writeTristate[String] and (JsPath \ "status").writeNullable[String] and (JsPath \ "assignee").writeTristate[String] and (JsPath \ "meta").writeTristate(Writes[String](Json.parse)) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala index e7eb022..71423e8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala @@ -1,20 +1,36 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.EligibilityArm import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases} -final case class ApiEligibilityArm(id: Long, name: String, originalName: String, trialId: String) { +final case class ApiEligibilityArm(id: Long, + name: String, + originalName: String, + trialId: String, + diseases: Seq[String]) { - def toDomain: EligibilityArm = EligibilityArm( - id = LongId(this.id), - name = this.name, - originalName = this.originalName, - trialId = StringId(this.trialId), - deleted = None // if we have an ApiEligibilityArm object, the EligibilityArm itself has not been deleted - ) + def toDomain: EligibilityArmWithDiseases = { + val eligibilityArm = EligibilityArm( + id = LongId(this.id), + name = this.name, + originalName = this.originalName, + trialId = StringId(this.trialId), + deleted = None // if we have an ApiEligibilityArm object, the EligibilityArm itself has not been deleted + ) + EligibilityArmWithDiseases( + eligibilityArm, + this.diseases.map { disease => + val condition = CancerType + .fromString(disease) + .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) + EligibilityArmDisease(eligibilityArm.id, condition) + } + ) + } } object ApiEligibilityArm { @@ -23,13 +39,19 @@ object ApiEligibilityArm { (JsPath \ "id").format[Long] and (JsPath \ "name").format[String] and (JsPath \ "originalName").format[String] and - (JsPath \ "trialId").format[String] + (JsPath \ "trialId").format[String] and + (JsPath \ "diseases").format[Seq[String]] )(ApiEligibilityArm.apply, unlift(ApiEligibilityArm.unapply)) - def fromDomain(arm: EligibilityArm): ApiEligibilityArm = ApiEligibilityArm( - id = arm.id.id, - name = arm.name, - originalName = arm.originalName, - trialId = arm.trialId.id - ) + def fromDomain(eligibilityArmWithDiseases: EligibilityArmWithDiseases): ApiEligibilityArm = { + import eligibilityArmWithDiseases.{eligibilityArm, eligibilityArmDiseases} + + ApiEligibilityArm( + id = eligibilityArm.id.id, + name = eligibilityArm.name, + originalName = eligibilityArm.originalName, + trialId = eligibilityArm.trialId.id, + diseases = eligibilityArmDiseases.map(_.disease.toString) + ) + } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala index 6f55c10..087fed5 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala @@ -1,17 +1,30 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.EligibilityArm import play.api.libs.json.{Format, Json} +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases} + +final case class ApiCreateEligibilityArm(name: String, trialId: String, diseases: Seq[String]) { -final case class ApiCreateEligibilityArm(name: String, trialId: String) { + def toDomain: EligibilityArmWithDiseases = { + val eligibilityArm = EligibilityArm( + id = LongId(0), + name = name, + trialId = StringId(trialId), + originalName = name + ) - def toDomain = EligibilityArm( - id = LongId(0), - name = name, - trialId = StringId(trialId), - originalName = name - ) + EligibilityArmWithDiseases( + eligibilityArm, + diseases.map { disease => + val condition = CancerType + .fromString(disease) + .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) + EligibilityArmDisease(eligibilityArm.id, condition) + } + ) + } } object ApiCreateEligibilityArm { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala index cc3d460..aca22ef 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala @@ -1,11 +1,20 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm -import xyz.driver.pdsuidomain.entities.EligibilityArm import play.api.libs.json.{Format, Json} +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuidomain.entities.{EligibilityArmDisease, EligibilityArmWithDiseases} -final case class ApiPartialEligibilityArm(name: String) { +final case class ApiPartialEligibilityArm(name: String, diseases: Seq[String]) { - def applyTo(arm: EligibilityArm): EligibilityArm = arm.copy(name = name) + def applyTo(armWithDisease: EligibilityArmWithDiseases): EligibilityArmWithDiseases = { + val arm = armWithDisease.eligibilityArm.copy(name = name) + val armDiseases = diseases.map { disease => + EligibilityArmDisease( + armWithDisease.eligibilityArm.id, + CancerType.fromString(disease).getOrElse(throw new NoSuchElementException(s"unknown condition $disease"))) + } + EligibilityArmWithDiseases(arm, armDiseases) + } } object ApiPartialEligibilityArm { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala index e0f23e3..c7a6de9 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala @@ -3,7 +3,6 @@ package xyz.driver.pdsuidomain.formats.json.evidence import java.time.LocalDate import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue import xyz.driver.pdsuidomain.entities.PatientLabelEvidenceView final case class ApiPatientLabelEvidence(id: Long, @@ -22,13 +21,13 @@ object ApiPatientLabelEvidence { def fromDomain(x: PatientLabelEvidenceView) = ApiPatientLabelEvidence( id = x.id.id, - value = FuzzyValue.valueToString(x.value), + value = x.value.toString, evidenceText = x.evidenceText, documentId = x.documentId.map(_.id), evidenceId = x.evidenceId.map(_.id), reportId = x.reportId.map(_.toString), - documentType = x.documentType, + documentType = x.documentType.name, date = x.date.get, - providerType = x.providerType + providerType = x.providerType.name ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala index d486749..edb0603 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala @@ -1,11 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.{Criterion, CriterionLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} /** * @param value Yes|No @@ -34,7 +34,7 @@ object ApiCriterionLabel { labelId = x.labelId.map(_.id), categoryId = x.categoryId.map(_.id), value = x.value.map { x => - FuzzyValue.valueToString(FuzzyValue.fromBoolean(x)) + LabelValue.fromBoolean(x).toString }, isDefining = x.isDefining ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala index f8161af..1497679 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala @@ -1,11 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.{ExtractedData, ExtractedDataLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long], value: Option[String]) { @@ -14,7 +14,7 @@ final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long dataId = dataId, labelId = id.map(LongId[Label]), categoryId = categoryId.map(LongId[LabelCategory]), - value = value.map(FuzzyValue.fromString) + value = value.flatMap(LabelValue.fromString) ) } @@ -27,8 +27,8 @@ object ApiExtractedDataLabel { Format(Reads .of[String] .filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) )(ApiExtractedDataLabel.apply, unlift(ApiExtractedDataLabel.unapply)) @@ -36,6 +36,6 @@ object ApiExtractedDataLabel { def fromDomain(dataLabel: ExtractedDataLabel) = ApiExtractedDataLabel( id = dataLabel.labelId.map(_.id), categoryId = dataLabel.categoryId.map(_.id), - value = dataLabel.value.map(FuzzyValue.valueToString) + value = dataLabel.value.map(_.toString) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala index db430ae..585d4ed 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala @@ -7,6 +7,8 @@ import xyz.driver.pdsuicommon.domain.{StringId, UuidId} import xyz.driver.pdsuidomain.entities.{Patient, PatientOrderId} import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath} +import xyz.driver.entities.common.FullName +import xyz.driver.entities.patient final case class ApiPatient(id: String, status: String, @@ -17,24 +19,35 @@ final case class ApiPatient(id: String, previousAssignee: Option[String], lastActiveUser: Option[String], lastUpdate: ZonedDateTime, - condition: String, + disease: String, orderId: UUID) { private def extractStatus(status: String): Patient.Status = PatientStatus.statusFromString .applyOrElse(status, (s: String) => throw new NoSuchElementException(s"Unknown status $s")) + private def parseName(name: String): FullName[Patient] = + name.split(" ") match { + case Array() => throw new NoSuchElementException(s"Patient's name cannot be empty") + case Array(first) => FullName.fromStrings[Patient](first, "", "") + case Array(first, last) => FullName.fromStrings[Patient](first, "", last) + case Array(first, middle, last) => FullName.fromStrings[Patient](first, middle, last) + case _ => throw new NoSuchElementException(s"Patient's name is ambiguous") + } + def toDomain = Patient( id = UuidId(this.id), status = extractStatus(this.status), - name = this.name, + name = parseName(this.name), dob = this.dob, assignee = this.assignee.map(StringId(_)), previousStatus = this.previousStatus.map(extractStatus), previousAssignee = this.previousAssignee.map(StringId(_)), lastActiveUserId = this.lastActiveUser.map(StringId(_)), isUpdateRequired = false, - condition = this.condition, + disease = patient.CancerType + .fromString(this.disease) + .getOrElse(throw new IllegalArgumentException(s"Unknown cancer type ${this.disease}")), orderId = PatientOrderId(this.orderId), lastUpdate = this.lastUpdate.toLocalDateTime ) @@ -53,21 +66,21 @@ object ApiPatient { (JsPath \ "previousAssignee").formatNullable[String] and (JsPath \ "lastActiveUser").formatNullable[String] and (JsPath \ "lastUpdate").format[ZonedDateTime] and - (JsPath \ "condition").format[String] and + (JsPath \ "disease").format[String] and (JsPath \ "orderId").format[UUID] )(ApiPatient.apply, unlift(ApiPatient.unapply)) def fromDomain(patient: Patient) = ApiPatient( id = patient.id.toString, status = PatientStatus.statusToString(patient.status), - name = patient.name, + name = patient.name.toString(), dob = patient.dob, assignee = patient.assignee.map(_.id), previousStatus = patient.previousStatus.map(PatientStatus.statusToString), previousAssignee = patient.previousAssignee.map(_.id), lastActiveUser = patient.lastActiveUserId.map(_.id), lastUpdate = ZonedDateTime.of(patient.lastUpdate, ZoneId.of("Z")), - condition = patient.condition, + disease = patient.disease.toString, orderId = patient.orderId.id ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala index 4136715..55c8149 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala @@ -5,7 +5,7 @@ import java.util.UUID import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial final case class ApiPatientEligibleTrial(id: Long, @@ -30,8 +30,8 @@ object ApiPatientEligibleTrial { Reads .of[String] .filter(ValidationError("unknown eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) and @@ -45,7 +45,7 @@ object ApiPatientEligibleTrial { trialTitle = eligibleTrialWithTrial.trial.title, arms = eligibleTrialWithTrial.arms.map(_.armName), hypothesisId = eligibleTrialWithTrial.group.hypothesisId.id, - eligibleTrialWithTrial.group.verifiedEligibilityStatus.map(FuzzyValue.valueToString), + eligibleTrialWithTrial.group.verifiedEligibilityStatus.map(_.toString), eligibleTrialWithTrial.group.isVerified ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala index 91d0a0e..d92872c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala @@ -6,15 +6,14 @@ import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue final case class ApiPartialPatientLabel(primaryValue: Option[String], verifiedPrimaryValue: Tristate[String]) { def applyTo(orig: PatientLabel): PatientLabel = { orig.copy( - primaryValue = primaryValue.map(FuzzyValue.fromString).orElse(orig.primaryValue), - verifiedPrimaryValue = - verifiedPrimaryValue.cata(x => Some(FuzzyValue.fromString(x)), None, orig.verifiedPrimaryValue) + primaryValue = primaryValue.flatMap(LabelValue.fromString).orElse(orig.primaryValue), + verifiedPrimaryValue = verifiedPrimaryValue.cata(x => LabelValue.fromString(x), None, orig.verifiedPrimaryValue) ) } } @@ -26,8 +25,8 @@ object ApiPartialPatientLabel { Format(Reads .of[String] .filter(ValidationError("unknown primary value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) and (JsPath \ "verifiedPrimaryValue").formatTristate[String]( @@ -35,8 +34,8 @@ object ApiPartialPatientLabel { Reads .of[String] .filter(ValidationError("unknown verified primary value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala index fc8687b..cc8532d 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala @@ -4,7 +4,7 @@ import xyz.driver.pdsuidomain.entities.PatientLabel import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue final case class ApiPatientLabel(id: Long, labelId: Long, @@ -20,25 +20,33 @@ object ApiPatientLabel { implicit val apiPatientLabelJsonFormat: Format[ApiPatientLabel] = ( (JsPath \ "id").format[Long] and (JsPath \ "labelId").format[Long] and - (JsPath \ "primaryValue").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false - }), Writes.of[String])) and - (JsPath \ "verifiedPrimaryValue").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false - }), Writes.of[String])) and + (JsPath \ "primaryValue").formatNullable[String]( + Format(Reads + .of[String] + .filter(ValidationError("unknown value"))({ + case x if LabelValue.fromString(x).isDefined => true + case _ => false + }), + Writes.of[String])) and + (JsPath \ "verifiedPrimaryValue").formatNullable[String]( + Format(Reads + .of[String] + .filter(ValidationError("unknown value"))({ + case x if LabelValue.fromString(x).isDefined => true + case _ => false + }), + Writes.of[String])) and (JsPath \ "score").format[Int] and (JsPath \ "isImplicitMatch").format[Boolean] and (JsPath \ "isVisible").format[Boolean] and (JsPath \ "isVerified").format[Boolean] - ) (ApiPatientLabel.apply, unlift(ApiPatientLabel.unapply)) + )(ApiPatientLabel.apply, unlift(ApiPatientLabel.unapply)) def fromDomain(patientLabel: PatientLabel, isVerified: Boolean): ApiPatientLabel = ApiPatientLabel( id = patientLabel.id.id, labelId = patientLabel.labelId.id, - primaryValue = patientLabel.primaryValue.map(FuzzyValue.valueToString), - verifiedPrimaryValue = patientLabel.verifiedPrimaryValue.map(FuzzyValue.valueToString), + primaryValue = patientLabel.primaryValue.map(_.toString), + verifiedPrimaryValue = patientLabel.verifiedPrimaryValue.map(_.toString), score = patientLabel.score, isImplicitMatch = patientLabel.isImplicitMatch, isVisible = patientLabel.isVisible, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala index ae64c33..16b9cc9 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala @@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.patient.label import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.entities.PatientLabel final case class ApiPatientLabelDefiningCriteria(labelId: Long, value: Option[String]) @@ -16,14 +16,14 @@ object ApiPatientLabelDefiningCriteria { Format(Reads .of[String] .filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) )(ApiPatientLabelDefiningCriteria.apply, unlift(ApiPatientLabelDefiningCriteria.unapply)) def fromDomain(x: PatientLabel) = ApiPatientLabelDefiningCriteria( labelId = x.labelId.id, - value = x.verifiedPrimaryValue.map(FuzzyValue.valueToString) + value = x.verifiedPrimaryValue.map(_.toString) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala index 399bc7d..09538b8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala @@ -6,16 +6,16 @@ import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue final case class ApiPartialPatientCriterion(eligibilityStatus: Option[String], verifiedEligibilityStatus: Tristate[String]) { def applyTo(orig: PatientCriterion): PatientCriterion = { orig.copy( - eligibilityStatus = eligibilityStatus.map(FuzzyValue.fromString).orElse(orig.eligibilityStatus), + eligibilityStatus = eligibilityStatus.flatMap(LabelValue.fromString).orElse(orig.eligibilityStatus), verifiedEligibilityStatus = - verifiedEligibilityStatus.cata(x => Some(FuzzyValue.fromString(x)), None, orig.verifiedEligibilityStatus) + verifiedEligibilityStatus.cata(x => LabelValue.fromString(x), None, orig.verifiedEligibilityStatus) ) } } @@ -28,8 +28,8 @@ object ApiPartialPatientCriterion { Reads .of[String] .filter(ValidationError("unknown eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) and @@ -38,8 +38,8 @@ object ApiPartialPatientCriterion { Reads .of[String] .filter(ValidationError("unknown verified eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala index 4b08970..b7616a1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.patient.trial -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.PatientCriterion import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion final case class ApiPartialPatientCriterionList(id: Long, @@ -13,7 +14,7 @@ final case class ApiPartialPatientCriterionList(id: Long, def toDomain: DraftPatientCriterion = DraftPatientCriterion( id = LongId[PatientCriterion](id), - eligibilityStatus = eligibilityStatus.map(FuzzyValue.fromString), + eligibilityStatus = eligibilityStatus.flatMap(LabelValue.fromString), isVerified = isVerified ) } @@ -26,8 +27,8 @@ object ApiPartialPatientCriterionList { Reads .of[String] .filter(ValidationError("unknown eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) and diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala index 6eeb40b..b9bf772 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala @@ -2,12 +2,12 @@ package xyz.driver.pdsuidomain.formats.json.patient.trial import java.time.{ZoneId, ZonedDateTime} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.{PatientCriterion, PatientCriterionArm} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} -import xyz.driver.entities.labels.Label +import xyz.driver.entities.labels.{Label, LabelValue} final case class ApiPatientCriterion(id: Long, labelId: Long, @@ -39,13 +39,13 @@ object ApiPatientCriterion { (JsPath \ "criterionIsCompound").format[Boolean] and (JsPath \ "arms").format[List[String]] and (JsPath \ "eligibilityStatus").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) and (JsPath \ "verifiedEligibilityStatus").formatNullable[String](Format( Reads.of[String].filter(ValidationError("unknown status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) and (JsPath \ "isVerified").format[Boolean] and (JsPath \ "isVisible").format[Boolean] and @@ -61,13 +61,13 @@ object ApiPatientCriterion { criterionId = patientCriterion.criterionId.id, criterionText = patientCriterion.criterionText, criterionValue = patientCriterion.criterionValue.map { x => - FuzzyValue.valueToString(FuzzyValue.fromBoolean(x)) + LabelValue.fromBoolean(x).toString }, criterionIsDefining = patientCriterion.criterionIsDefining, criterionIsCompound = patientCriterion.criterionValue.isEmpty, arms = arms.map(_.armName), - eligibilityStatus = patientCriterion.eligibilityStatus.map(FuzzyValue.valueToString), - verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(FuzzyValue.valueToString), + eligibilityStatus = patientCriterion.eligibilityStatus.map(_.toString), + verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(_.toString), isVerified = patientCriterion.isVerified, isVisible = patientCriterion.isVisible, lastUpdate = ZonedDateTime.of(patientCriterion.lastUpdate, ZoneId.of("Z")) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala index 2e5943e..1f8c683 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala @@ -22,8 +22,6 @@ final case class ApiCreateRecord(disease: String, patientId: String, requestId: caseId = None, physician = None, meta = None, - predictedMeta = None, - predictedDocuments = None, lastUpdate = LocalDateTime.now() ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala index e7b58cd..fc0a2e7 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala @@ -101,8 +101,6 @@ final case class ApiRecord(id: Long, Some(TextJson(JsonSerializer.deserialize[List[MedicalRecord.Meta]](this.meta))) } }, - predictedMeta = None, - predictedDocuments = None, lastUpdate = this.lastUpdate.toLocalDateTime() ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala new file mode 100644 index 0000000..2a670c4 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala @@ -0,0 +1,39 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import java.time.LocalDateTime + +import spray.json.{RootJsonFormat, _} +import xyz.driver.pdsuicommon.db.Pagination +import xyz.driver.pdsuidomain.formats.json.sprayformats.common._ + +final case class ListResponse[+T](items: Seq[T], meta: ListResponse.Meta) + +object ListResponse extends DefaultJsonProtocol { + private val itemsField = "items" + private val metaField = "meta" + + final case class Meta(itemsCount: Int, pageNumber: Int, pageSize: Int, lastUpdate: Option[LocalDateTime]) + + object Meta { + def apply(itemsCount: Int, pagination: Pagination, lastUpdate: Option[LocalDateTime]): Meta = { + Meta( + itemsCount, + pagination.pageNumber, + pagination.pageSize, + lastUpdate + ) + } + } + + implicit val listResponseMetaFormat: RootJsonFormat[Meta] = jsonFormat4(Meta.apply) + + implicit def listResponseMetaWriter[T: JsonWriter]: RootJsonWriter[ListResponse[T]] = + new RootJsonWriter[ListResponse[T]] { + override def write(listResponse: ListResponse[T]): JsValue = { + JsObject( + itemsField -> listResponse.items.map(_.toJson).toJson, + metaField -> listResponse.meta.toJson + ) + } + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala index dbd0a43..61e0e7f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala @@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.{LocalDate, LocalDateTime, ZoneId, ZonedDateTime} import spray.json._ -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} object common { @@ -55,14 +55,6 @@ object common { } } - implicit def fuzzyValueFormat: RootJsonFormat[FuzzyValue] = new RootJsonFormat[FuzzyValue] { - override def write(value: FuzzyValue): JsString = JsString(FuzzyValue.valueToString(value)) - override def read(json: JsValue): FuzzyValue = json match { - case JsString(value) => FuzzyValue.fromString(value) - case _ => deserializationError(s"Expected value as FuzzyValue, but got $json") - } - } - implicit val integerFormat: RootJsonFormat[Integer] = new RootJsonFormat[Integer] { override def write(obj: Integer): JsNumber = JsNumber(obj.intValue()) override def read(json: JsValue): Integer = json match { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala index 7526d9c..a43e92a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala @@ -10,7 +10,7 @@ object criterion { import DefaultJsonProtocol._ import common._ - implicit val criterionLabelWriter = new JsonWriter[CriterionLabel] { + implicit val criterionLabelWriter = new RootJsonWriter[CriterionLabel] { override def write(obj: CriterionLabel) = JsObject( "labelId" -> obj.labelId.toJson, "categoryId" -> obj.categoryId.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala index e3f6a9c..69e8b75 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala @@ -26,7 +26,7 @@ object document { "PN" -> RequiredType.PN ) - implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat3(Meta.apply) + implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat2(Meta.apply) implicit val documentTypeFormat: RootJsonFormat[DocumentType] = new RootJsonFormat[DocumentType] { override def read(json: JsValue): DocumentType = json match { @@ -40,7 +40,7 @@ object document { .fromString(name) .getOrElse(deserializationError(s"Unknown document type: $name")) - case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json") + case _ => deserializationError(s"Expected Json Object as Document type, but got $json") } override def write(obj: DocumentType) = @@ -73,6 +73,11 @@ object document { .map(_.convertTo[Option[LongId[ProviderType]]]) .getOrElse(orig.providerTypeId) + val institutionName = fields + .get("institutionName") + .map(_.convertTo[Option[String]]) + .getOrElse(orig.institutionName) + val meta = fields .get("meta") .map(_.convertTo[Option[TextJson[Meta]]]) @@ -93,6 +98,7 @@ object document { typeId = typeId, providerName = provider, providerTypeId = providerTypeId, + institutionName = institutionName, meta = meta, startDate = startDate, endDate = endDate @@ -111,6 +117,7 @@ object document { "provider" -> document.providerName.toJson, "providerTypeId" -> document.providerTypeId.toJson, "requiredType" -> document.requiredType.toJson, + "institutionName" -> document.institutionName.toJson, "startDate" -> document.startDate.toJson, "endDate" -> document.endDate.toJson, "status" -> document.status.toJson, @@ -145,6 +152,10 @@ object document { .get("providerTypeId") .map(_.convertTo[LongId[ProviderType]]) + val institutionName = fields + .get("institutionName") + .map(_.convertTo[String]) + val meta = fields .get("meta") .map(_.convertTo[TextJson[Meta]]) @@ -168,6 +179,7 @@ object document { providerName = provider, providerTypeId = providerTypeId, requiredType = None, + institutionName = institutionName, meta = meta, previousStatus = None, assignee = None, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala index b836e1c..3c2465f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala @@ -21,7 +21,7 @@ object eligibility { implicit val clinicalDocumentFormat: RootJsonFormat[ClinicalEvidenceDocument] = jsonFormat7(ClinicalEvidenceDocument) implicit val evidenceDocumentFormat: RootJsonFormat[EvidenceDocument] = - GadtJsonFormat.create[EvidenceDocument]("documentType") { + GadtJsonFormat.create[EvidenceDocument]("evidenceDocumentType") { case _: MolecularEvidenceDocument => "Molecular" case _: ClinicalEvidenceDocument => "Clinical" } { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala index 39d5c59..1c4b6b4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala @@ -2,15 +2,16 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.entities.labels.Label -import xyz.driver.pdsuidomain.entities.{Arm, Criterion} +import xyz.driver.formats.json.labels._ import xyz.driver.pdsuidomain.entities.export.patient._ import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm} object export { import DefaultJsonProtocol._ import common._ - import record._ import document._ + import record._ implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] = jsonFormat5(ExportPatientLabelEvidenceDocument.apply) @@ -67,7 +68,7 @@ object export { longIdFormat[Criterion].read(criterionId), value, longIdFormat[Label].read(labelId), - armIdsVector.map(longIdFormat[Arm].read).toSet, + armIdsVector.map(longIdFormat[EligibilityArm].read).toSet, criterionText, isCompound, isDefining @@ -81,12 +82,5 @@ object export { } implicit val trialWithLabelsFormat: RootJsonFormat[ExportTrialWithLabels] = - jsonFormat(ExportTrialWithLabels.apply, - "nctId", - "trialId", - "disease", - "lastReviewed", - "labelVersion", - "arms", - "criteria") + jsonFormat(ExportTrialWithLabels.apply, "nctId", "trialId", "lastReviewed", "labelVersion", "arms", "criteria") } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala index d6eadbd..5d5585a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} +import xyz.driver.pdsuicommon.domain.{LongId, TextJson} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData +import xyz.driver.formats.json.labels._ object extracteddata { import DefaultJsonProtocol._ @@ -44,7 +45,7 @@ object extracteddata { val value = fields .get("value") - .map(_.convertTo[FuzzyValue]) + .map(_.convertTo[LabelValue]) ExtractedDataLabel( id = LongId(0), diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala index 724c391..2b0dfe5 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala @@ -3,6 +3,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.core.json.EnumJsonFormat import xyz.driver.pdsuidomain.entities._ +import xyz.driver.formats.json.common._ +import xyz.driver.formats.json.patient._ object patient { import DefaultJsonProtocol._ @@ -26,7 +28,7 @@ object patient { } } - implicit val patientWriter: JsonWriter[Patient] = new JsonWriter[Patient] { + implicit val patientWriter: RootJsonWriter[Patient] = new RootJsonWriter[Patient] { override def write(patient: Patient): JsValue = JsObject( "id" -> patient.id.toJson, @@ -38,7 +40,7 @@ object patient { "previousAssignee" -> patient.previousAssignee.toJson, "lastActiveUser" -> patient.lastActiveUserId.toJson, "lastUpdate" -> patient.lastUpdate.toJson, - "condition" -> patient.condition.toJson, + "disease" -> patient.disease.toJson, "orderId" -> patient.orderId.toJson ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala index b091746..7e8c220 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala @@ -1,10 +1,10 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion +import xyz.driver.pdsuidomain.services.PatientCriterionService.{DraftPatientCriterion, RichPatientCriterion} +import xyz.driver.formats.json.labels._ object patientcriterion { import DefaultJsonProtocol._ @@ -15,13 +15,13 @@ object patientcriterion { val eligibilityStatus = if (fields.contains("eligibilityStatus")) { fields .get("eligibilityStatus") - .map(_.convertTo[FuzzyValue]) + .map(_.convertTo[LabelValue]) } else orig.eligibilityStatus val verifiedEligibilityStatus = if (fields.contains("verifiedEligibilityStatus")) { fields .get("verifiedEligibilityStatus") - .map(_.convertTo[FuzzyValue]) + .map(_.convertTo[LabelValue]) } else orig.verifiedEligibilityStatus orig.copy( @@ -38,30 +38,27 @@ object patientcriterion { override def read(json: JsValue) = json.convertTo[List[JsValue]].map(_.convertTo[DraftPatientCriterion]) } - implicit val patientCriterionWriter: JsonWriter[(PatientCriterion, LongId[Label], List[PatientCriterionArm])] = - new JsonWriter[(PatientCriterion, LongId[Label], List[PatientCriterionArm])] { - override def write(obj: (PatientCriterion, LongId[Label], List[PatientCriterionArm])): JsValue = { - val criterion = obj._1 - val labelId = obj._2 - val arms = obj._3 + implicit val patientCriterionWriter: RootJsonWriter[RichPatientCriterion] = + new RootJsonWriter[RichPatientCriterion] { + override def write(obj: RichPatientCriterion): JsValue = { JsObject( - "id" -> criterion.id.toJson, - "labelId" -> labelId.toJson, - "nctId" -> criterion.nctId.toJson, - "criterionId" -> criterion.criterionId.toJson, - "criterionText" -> criterion.criterionText.toJson, - "criterionValue" -> criterion.criterionValue.map { + "id" -> obj.patientCriterion.id.toJson, + "labelId" -> obj.labelId.toJson, + "nctId" -> obj.patientCriterion.nctId.toJson, + "criterionId" -> obj.patientCriterion.criterionId.toJson, + "criterionText" -> obj.patientCriterion.criterionText.toJson, + "criterionValue" -> obj.patientCriterion.criterionValue.map { case true => "Yes" case false => "No" }.toJson, - "criterionIsDefining" -> criterion.criterionIsDefining.toJson, - "criterionIsCompound" -> criterion.criterionValue.isEmpty.toJson, - "arms" -> arms.map(_.armName).toJson, - "eligibilityStatus" -> criterion.eligibilityStatus.toJson, - "verifiedEligibilityStatus" -> criterion.verifiedEligibilityStatus.toJson, - "isVerified" -> criterion.isVerified.toJson, - "isVisible" -> criterion.isVisible.toJson, - "lastUpdate" -> criterion.lastUpdate.toJson + "criterionIsDefining" -> obj.patientCriterion.criterionIsDefining.toJson, + "criterionIsCompound" -> obj.patientCriterion.criterionValue.isEmpty.toJson, + "arms" -> obj.armList.map(_.armName).toJson, + "eligibilityStatus" -> obj.patientCriterion.eligibilityStatus.toJson, + "verifiedEligibilityStatus" -> obj.patientCriterion.verifiedEligibilityStatus.toJson, + "isVerified" -> obj.patientCriterion.isVerified.toJson, + "isVisible" -> obj.patientCriterion.isVisible.toJson, + "lastUpdate" -> obj.patientCriterion.lastUpdate.toJson ) } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala index b97570a..746c7b4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala @@ -2,12 +2,13 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuidomain.entities.PatientLabel +import xyz.driver.formats.json.labels._ object patientdefiningcriteria { import DefaultJsonProtocol._ import common._ - implicit val patientLabelDefiningCriteriaWriter: JsonWriter[PatientLabel] = new JsonWriter[PatientLabel] { + implicit val patientLabelDefiningCriteriaWriter: RootJsonWriter[PatientLabel] = new RootJsonWriter[PatientLabel] { override def write(obj: PatientLabel) = JsObject( "id" -> obj.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala index 894e453..342d3a8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala @@ -3,6 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial +import xyz.driver.formats.json.labels._ object patienteligibletrial { import DefaultJsonProtocol._ @@ -21,8 +22,8 @@ object patienteligibletrial { case _ => deserializationError(s"Expected Json Object as partial PatientTrialArmGroupView, but got $json") } - implicit val patientEligibleTrialWriter: JsonWriter[RichPatientEligibleTrial] = - new JsonWriter[RichPatientEligibleTrial] { + implicit val patientEligibleTrialWriter: RootJsonWriter[RichPatientEligibleTrial] = + new RootJsonWriter[RichPatientEligibleTrial] { override def write(obj: RichPatientEligibleTrial) = JsObject( "id" -> obj.group.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala index 4f2783c..b8c0058 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientHypothesisService.RichPatientHypothesis object patienthypothesis { import DefaultJsonProtocol._ @@ -18,18 +19,29 @@ object patienthypothesis { case _ => deserializationError(s"Expected Json Object as partial PatientHypothesis, but got $json") } - implicit val patientHypothesisWriter: JsonWriter[(PatientHypothesis, Boolean)] = - new JsonWriter[(PatientHypothesis, Boolean)] { - override def write(obj: (PatientHypothesis, Boolean)): JsValue = { - val patientHypothesis = obj._1 - val isRationaleRequired = obj._2 + implicit val richPatientHypothesisWriter: RootJsonWriter[RichPatientHypothesis] = + new RootJsonWriter[RichPatientHypothesis] { + override def write(obj: RichPatientHypothesis): JsValue = { JsObject( - "id" -> patientHypothesis.id.toJson, - "patientId" -> patientHypothesis.patientId.toJson, - "hypothesisId" -> patientHypothesis.hypothesisId.toJson, - "matchedTrials" -> patientHypothesis.matchedTrials.toJson, - "rationale" -> patientHypothesis.rationale.toJson, - "isRationaleRequired" -> isRationaleRequired.toJson + "id" -> obj.patientHypothesis.id.toJson, + "patientId" -> obj.patientHypothesis.patientId.toJson, + "hypothesisId" -> obj.patientHypothesis.hypothesisId.toJson, + "matchedTrials" -> obj.patientHypothesis.matchedTrials.toJson, + "rationale" -> obj.patientHypothesis.rationale.toJson, + "isRationaleRequired" -> obj.isRequired.toJson + ) + } + } + + implicit val patientHypothesisWriter: RootJsonWriter[PatientHypothesis] = + new RootJsonWriter[PatientHypothesis] { + override def write(obj: PatientHypothesis): JsValue = { + JsObject( + "id" -> obj.id.toJson, + "patientId" -> obj.patientId.toJson, + "hypothesisId" -> obj.hypothesisId.toJson, + "matchedTrials" -> obj.matchedTrials.toJson, + "rationale" -> obj.rationale.toJson ) } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala index 7d35bd1..d325a53 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala @@ -40,7 +40,7 @@ object patientissue { } - implicit val patientIssueWriter = new JsonWriter[PatientIssue] { + implicit val patientIssueWriter = new RootJsonWriter[PatientIssue] { override def write(obj: PatientIssue) = JsObject( "id" -> obj.id.toJson, "text" -> obj.text.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala index 3b52833..57dca1e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala @@ -1,8 +1,12 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientLabelService.RichPatientLabel +import xyz.driver.formats.json.labels._ +import xyz.driver.pdsuidomain.formats.json.sprayformats.record._ +import xyz.driver.pdsuidomain.formats.json.sprayformats.document._ object patientlabel { import DefaultJsonProtocol._ @@ -12,12 +16,12 @@ object patientlabel { case JsObject(fields) => val primaryValue = fields .get("primaryValue") - .map(_.convertTo[Option[FuzzyValue]]) + .map(_.convertTo[Option[LabelValue]]) .getOrElse(orig.primaryValue) val verifiedPrimaryValue = fields .get("verifiedPrimaryValue") - .map(_.convertTo[Option[FuzzyValue]]) + .map(_.convertTo[Option[LabelValue]]) .getOrElse(orig.verifiedPrimaryValue) orig.copy( @@ -28,25 +32,23 @@ object patientlabel { case _ => deserializationError(s"Expected Json Object as PatientLabel, but got $json") } - implicit val patientLabelWriter: JsonWriter[(PatientLabel, Boolean)] = new JsonWriter[(PatientLabel, Boolean)] { - override def write(obj: (PatientLabel, Boolean)): JsValue = { - val patientLabel = obj._1 - val isVerified = obj._2 + implicit val richPatientLabelWriter: RootJsonWriter[RichPatientLabel] = new RootJsonWriter[RichPatientLabel] { + override def write(obj: RichPatientLabel): JsValue = { JsObject( - "id" -> patientLabel.id.toJson, - "labelId" -> patientLabel.labelId.toJson, - "primaryValue" -> patientLabel.primaryValue.toJson, - "verifiedPrimaryValue" -> patientLabel.verifiedPrimaryValue.toJson, - "score" -> patientLabel.score.toJson, - "isImplicitMatch" -> patientLabel.isImplicitMatch.toJson, - "isVisible" -> patientLabel.isVisible.toJson, - "isVerified" -> isVerified.toJson + "id" -> obj.patientLabel.id.toJson, + "labelId" -> obj.patientLabel.labelId.toJson, + "primaryValue" -> obj.patientLabel.primaryValue.toJson, + "verifiedPrimaryValue" -> obj.patientLabel.verifiedPrimaryValue.toJson, + "score" -> obj.patientLabel.score.toJson, + "isImplicitMatch" -> obj.patientLabel.isImplicitMatch.toJson, + "isVisible" -> obj.patientLabel.isVisible.toJson, + "isVerified" -> obj.isVerified.toJson ) } } - implicit val patientLabelEvidenceWriter: JsonWriter[PatientLabelEvidenceView] = - new JsonWriter[PatientLabelEvidenceView] { + implicit val patientLabelEvidenceWriter: RootJsonWriter[PatientLabelEvidenceView] = + new RootJsonWriter[PatientLabelEvidenceView] { override def write(evidence: PatientLabelEvidenceView): JsValue = JsObject( "id" -> evidence.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala index 8eef44a..65687c1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala @@ -67,7 +67,6 @@ object record { override def write(obj: Duplicate) = JsObject( "type" -> "duplicate".toJson, - "predicted" -> obj.predicted.toJson, "startPage" -> obj.startPage.toJson, "endPage" -> obj.endPage.toJson, "startOriginalPage" -> obj.startOriginalPage.toJson, @@ -76,10 +75,6 @@ object record { override def read(json: JsValue): Duplicate = json match { case JsObject(fields) => - val predicted = fields - .get("predicted") - .map(_.convertTo[Boolean]) - val startPage = fields .get("startPage") .map(_.convertTo[Double]) @@ -101,7 +96,6 @@ object record { .map(_.convertTo[Double]) Duplicate( - predicted = predicted, startPage = startPage, endPage = endPage, startOriginalPage = startOriginalPage, @@ -114,27 +108,16 @@ object record { implicit val reorderMetaFormat: RootJsonFormat[Reorder] = new RootJsonFormat[Reorder] { override def write(obj: Reorder) = - JsObject( - "type" -> "reorder".toJson, - "predicted" -> obj.predicted.toJson, - "items" -> obj.items.toJson - ) + JsObject("type" -> "reorder".toJson, "items" -> obj.items.toJson) override def read(json: JsValue): Reorder = json match { case JsObject(fields) => - val predicted = fields - .get("predicted") - .map(_.convertTo[Boolean]) - val items = fields .get("items") .map(_.convertTo[Seq[Int]]) .getOrElse(deserializationError(s"Reorder meta json object does not contain `items` field: $json")) - Reorder( - predicted = predicted, - items = items - ) + Reorder(items) case _ => deserializationError(s"Expected JsObject as Reorder meta of medical record, but got $json") } @@ -142,27 +125,16 @@ object record { implicit val rotateMetaFormat: RootJsonFormat[Rotation] = new RootJsonFormat[Rotation] { override def write(obj: Rotation) = - JsObject( - "type" -> "rotation".toJson, - "predicted" -> obj.predicted.toJson, - "items" -> obj.items.toJson - ) + JsObject("type" -> "rotation".toJson, "items" -> obj.items.toJson) override def read(json: JsValue): Rotation = json match { case JsObject(fields) => - val predicted = fields - .get("predicted") - .map(_.convertTo[Boolean]) - val items = fields .get("items") .map(_.convertTo[Map[String, Int]]) .getOrElse(deserializationError(s"Rotation meta json object does not contain `items` field: $json")) - Rotation( - predicted = predicted, - items = items - ) + Rotation(items = items) case _ => deserializationError(s"Expected JsObject as Rotation meta of medical record, but got $json") } @@ -233,8 +205,6 @@ object record { caseId = None, physician = None, meta = None, - predictedMeta = None, - predictedDocuments = None, lastUpdate = LocalDateTime.now() ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala index a778000..b25ed1d 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala @@ -9,8 +9,8 @@ import xyz.driver.pdsuidomain.entities._ object trial { import DefaultJsonProtocol._ - import common._ import Trial._ + import common._ implicit val trialStatusFormat = new EnumJsonFormat[Status]( "New" -> Status.New, @@ -24,13 +24,7 @@ object trial { "Archived" -> Status.Archived ) - implicit val conditionFormat = new EnumJsonFormat[Condition]( - "Breast" -> Condition.Breast, - "Lung" -> Condition.Lung, - "Prostate" -> Condition.Prostate - ) - - implicit val trialWriter: JsonWriter[Trial] = new JsonWriter[Trial] { + implicit val trialWriter: RootJsonWriter[Trial] = new RootJsonWriter[Trial] { override def write(obj: Trial) = JsObject( "id" -> obj.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala index 572f44d..d1ca191 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala @@ -44,7 +44,7 @@ object trialissue { } - implicit val trialIssueWriter = new JsonWriter[TrialIssue] { + implicit val trialIssueWriter = new RootJsonWriter[TrialIssue] { override def write(obj: TrialIssue) = JsObject( "id" -> obj.id.toJson, "text" -> obj.text.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala index fbf506b..133a2c8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala @@ -2,11 +2,11 @@ package xyz.driver.pdsuidomain.formats.json.trial import java.time.{ZoneId, ZonedDateTime} import java.util.UUID -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities.Trial import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} +import xyz.driver.pdsuidomain.entities.Trial final case class ApiTrial(id: String, externalId: UUID, diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala index b34b34e..1e0f65e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala @@ -5,7 +5,7 @@ import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuicommon.error.DomainError import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.EligibilityArm +import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmWithDiseases, SlotArm} import scala.concurrent.Future @@ -19,10 +19,14 @@ object EligibilityArmService { def userMessage: String = "EligibilityArm not found" } + trait SlotArmNotFoundError { + def userMessage: String = "SlotArm not found" + } + sealed trait GetByIdReply object GetByIdReply { - final case class Entity(x: EligibilityArm) extends GetByIdReply + final case class Entity(x: EligibilityArmWithDiseases) extends GetByIdReply type Error = GetByIdReply with DomainError @@ -39,7 +43,7 @@ object EligibilityArmService { object GetListReply { type Error = GetListReply with DomainError - final case class EntityList(xs: Seq[EligibilityArm], totalFound: Int) extends GetListReply + final case class EntityList(xs: Seq[EligibilityArmWithDiseases], totalFound: Int) extends GetListReply case object AuthorizationError extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError @@ -48,7 +52,7 @@ object EligibilityArmService { sealed trait UpdateReply object UpdateReply { - final case class Updated(updated: EligibilityArm) extends UpdateReply + final case class Updated(updated: EligibilityArmWithDiseases) extends UpdateReply type Error = UpdateReply with DomainError @@ -59,7 +63,7 @@ object EligibilityArmService { final case class CommonError(userMessage: String) extends UpdateReply with DomainError - final case class AlreadyExistsError(x: EligibilityArm) extends UpdateReply with DomainError { + final case class AlreadyExistsError(x: EligibilityArmWithDiseases) extends UpdateReply with DomainError { val userMessage = s"The arm with such name of trial already exists." } @@ -71,16 +75,18 @@ object EligibilityArmService { sealed trait CreateReply object CreateReply { - final case class Created(x: EligibilityArm) extends CreateReply + final case class Created(x: EligibilityArmWithDiseases) extends CreateReply type Error = CreateReply with DomainError case object AuthorizationError extends CreateReply with DefaultAccessDeniedError with DomainError.AuthorizationError + case object NotFoundError extends CreateReply with SlotArmNotFoundError with DomainError.NotFoundError + final case class CommonError(userMessage: String) extends CreateReply with DomainError - final case class AlreadyExistsError(x: EligibilityArm) extends CreateReply with DomainError { + final case class AlreadyExistsError(x: EligibilityArmWithDiseases) extends CreateReply with DomainError { val userMessage = s"The arm with this name of trial already exists." } @@ -114,13 +120,19 @@ trait EligibilityArmService { pagination: Option[Pagination] = None)( implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] - def getById(armId: LongId[EligibilityArm])( + def getByEligibilityId(armId: LongId[EligibilityArm])( implicit requestContext: AuthenticatedRequestContext): Future[GetByIdReply] - def create(draftEligibilityArm: EligibilityArm)( + def getBySlotId(armId: LongId[SlotArm], + filter: SearchFilterExpr = SearchFilterExpr.Empty, + sorting: Option[Sorting] = None, + pagination: Option[Pagination] = None)( + implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] + + def create(slotArmId: LongId[SlotArm], draftEligibilityArm: EligibilityArmWithDiseases)( implicit requestContext: AuthenticatedRequestContext): Future[CreateReply] - def update(origEligibilityArm: EligibilityArm, draftEligibilityArm: EligibilityArm)( + def update(origEligibilityArm: EligibilityArmWithDiseases, draftEligibilityArm: EligibilityArmWithDiseases)( implicit requestContext: AuthenticatedRequestContext): Future[UpdateReply] def delete(id: LongId[EligibilityArm])(implicit requestContext: AuthenticatedRequestContext): Future[DeleteReply] diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala index 7395400..c09dd9a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala @@ -4,6 +4,7 @@ import xyz.driver.core.Id import xyz.driver.core.rest.AuthorizedServiceRequestContext import xyz.driver.entities.patient.{CancerType, Patient} import xyz.driver.entities.users.AuthUserInfo +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.eligibility.{MatchedPatient, MismatchRankedLabels} import xyz.driver.pdsuidomain.entities.Arm @@ -14,6 +15,6 @@ trait EligibilityVerificationService { def getMatchedPatients()(implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): ListT[Future, MatchedPatient] - def getMismatchRankedLabels(patientId: Id[Patient], cancerType: CancerType, excludedArms: Seq[Id[Arm]])( + def getMismatchRankedLabels(patientId: Id[Patient], cancerType: CancerType, excludedArms: Seq[LongId[Arm]])( implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): Future[MismatchRankedLabels] } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala index 6d85f85..4d0e188 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala @@ -2,7 +2,7 @@ package xyz.driver.pdsuidomain.services import java.time.LocalDateTime -import xyz.driver.entities.labels.Label +import xyz.driver.entities.labels.{Label, LabelValue} import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain._ @@ -15,7 +15,7 @@ import scala.concurrent.Future object PatientCriterionService { final case class DraftPatientCriterion(id: LongId[PatientCriterion], - eligibilityStatus: Option[FuzzyValue], + eligibilityStatus: Option[LabelValue], isVerified: Option[Boolean]) { def applyTo(orig: PatientCriterion) = { orig.copy( @@ -37,13 +37,21 @@ object PatientCriterionService { def userMessage: String = "Access denied" } + final case class RichPatientCriterion(patientCriterion: PatientCriterion, + labelId: LongId[Label], + armList: List[PatientCriterionArm]) + + object RichPatientCriterion { + implicit def toPhiString(x: RichPatientCriterion): PhiString = { + phi"RichPatientCriterion(patientCriterion=${x.patientCriterion}, labelId=${x.labelId}, arms=${x.armList})" + } + } + sealed trait GetListReply object GetListReply { type Error = GetListReply with DomainError - final case class EntityList(xs: Seq[(PatientCriterion, LongId[Label], List[PatientCriterionArm])], - totalFound: Int, - lastUpdate: Option[LocalDateTime]) + final case class EntityList(xs: Seq[RichPatientCriterion], totalFound: Int, lastUpdate: Option[LocalDateTime]) extends GetListReply case object AuthorizationError @@ -60,8 +68,7 @@ object PatientCriterionService { object GetByIdReply { type Error = GetByIdReply with DomainError - final case class Entity(x: PatientCriterion, labelId: LongId[Label], armList: List[PatientCriterionArm]) - extends GetByIdReply + final case class Entity(x: RichPatientCriterion) extends GetByIdReply case object AuthorizationError extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError @@ -74,8 +81,8 @@ object PatientCriterionService { final case class CommonError(userMessage: String) extends GetByIdReply with DomainError implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x, labelId, armList) => phi"GetByIdReply.Entity(entity=$x, labelId=$labelId, armList=$armList)" + case x: DomainError => phi"GetByIdReply.Error($x)" + case Entity(x) => phi"GetByIdReply.Entity($x)" } } @@ -83,8 +90,7 @@ object PatientCriterionService { object UpdateReply { type Error = UpdateReply with DomainError - final case class Updated(x: PatientCriterion, labelId: LongId[Label], armList: List[PatientCriterionArm]) - extends UpdateReply + final case class Updated(x: RichPatientCriterion) extends UpdateReply case object UpdatedList extends UpdateReply diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala index abb3f8a..d9013c6 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala @@ -1,12 +1,12 @@ package xyz.driver.pdsuidomain.services -import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} import xyz.driver.pdsuicommon.domain.{LongId, UuidId} import xyz.driver.pdsuicommon.error.DomainError import xyz.driver.pdsuicommon.logging._ import xyz.driver.pdsuidomain.entities.{Trial, _} +import xyz.driver.pdsuidomain.services.PatientCriterionService.RichPatientCriterion import scala.concurrent.Future @@ -71,8 +71,7 @@ object PatientEligibleTrialService { sealed trait GetCriterionListOfGroupReply object GetCriterionListOfGroupReply { - final case class EntityList(xs: Seq[(PatientCriterion, LongId[Label], List[PatientCriterionArm])], totalFound: Int) - extends GetCriterionListOfGroupReply + final case class EntityList(xs: Seq[RichPatientCriterion], totalFound: Int) extends GetCriterionListOfGroupReply type Error = GetCriterionListOfGroupReply with DomainError diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala index f782cab..07734ed 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala @@ -23,9 +23,17 @@ object PatientHypothesisService { def userMessage: String = "Access denied" } + final case class RichPatientHypothesis(patientHypothesis: PatientHypothesis, isRequired: Boolean) + + object RichPatientHypothesis { + implicit def toPhiString(x: RichPatientHypothesis): PhiString = { + phi"RichPatientHypothesis(patientHypothesis=${x.patientHypothesis}, isRequired=${x.isRequired})" + } + } + sealed trait GetListReply object GetListReply { - final case class EntityList(xs: Seq[(PatientHypothesis, Boolean)], totalFound: Int) extends GetListReply + final case class EntityList(xs: Seq[RichPatientHypothesis], totalFound: Int) extends GetListReply case object AuthorizationError extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError @@ -38,7 +46,7 @@ object PatientHypothesisService { sealed trait GetByIdReply object GetByIdReply { - final case class Entity(x: PatientHypothesis, isRequired: Boolean) extends GetByIdReply + final case class Entity(x: RichPatientHypothesis) extends GetByIdReply type Error = GetByIdReply with DomainError @@ -53,8 +61,8 @@ object PatientHypothesisService { final case class CommonError(userMessage: String) extends GetByIdReply with DomainError implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x, isRequired) => phi"GetByIdReply.Entity($x, $isRequired)" + case x: DomainError => phi"GetByIdReply.Error($x)" + case Entity(x) => phi"GetByIdReply.Entity($x)" } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala index 2a4d7fc..cede890 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala @@ -24,9 +24,17 @@ object PatientLabelService { def userMessage: String = "Access denied" } + final case class RichPatientLabel(patientLabel: PatientLabel, isVerified: Boolean) + + object RichPatientLabel { + implicit def toPhiString(x: RichPatientLabel): PhiString = { + phi"RichPatientLabel(patientLabel=${x.patientLabel}, isVerified=${x.isVerified})" + } + } + sealed trait GetListReply object GetListReply { - final case class EntityList(xs: Seq[(PatientLabel, Boolean)], totalFound: Int) extends GetListReply + final case class EntityList(xs: Seq[RichPatientLabel], totalFound: Int) extends GetListReply case object AuthorizationError extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError @@ -52,7 +60,7 @@ object PatientLabelService { sealed trait GetByLabelIdReply object GetByLabelIdReply { - final case class Entity(x: PatientLabel, isVerified: Boolean) extends GetByLabelIdReply + final case class Entity(x: RichPatientLabel) extends GetByLabelIdReply type Error = GetByLabelIdReply with DomainError @@ -68,7 +76,7 @@ object PatientLabelService { implicit def toPhiString(reply: GetByLabelIdReply): PhiString = reply match { case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x, y) => phi"GetByIdReply.Entity($x, $y)" + case Entity(x) => phi"GetByIdReply.Entity($x)" } } @@ -76,7 +84,7 @@ object PatientLabelService { object UpdateReply { type Error = UpdateReply with DomainError - final case class Updated(updated: PatientLabel, isVerified: Boolean) extends UpdateReply + final case class Updated(updated: RichPatientLabel) extends UpdateReply case object NotFoundError extends UpdateReply with DefaultNotFoundError with DomainError.NotFoundError @@ -89,8 +97,8 @@ object PatientLabelService { final case class CommonError(userMessage: String) extends UpdateReply with DomainError implicit def toPhiString(reply: UpdateReply): PhiString = reply match { - case Updated(x, y) => phi"Updated($x, $y)" - case x: Error => DomainError.toPhiString(x) + case Updated(x) => phi"Updated($x)" + case x: Error => DomainError.toPhiString(x) } } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala index 5bd99a8..92233e4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala @@ -5,6 +5,7 @@ import java.time.LocalDateTime import akka.NotUsed import akka.stream.scaladsl.Source import akka.util.ByteString +import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain.StringId @@ -68,6 +69,20 @@ object TrialService { extends GetTrialWithLabelsReply with DomainError.AuthorizationError with DefaultAccessDeniedError } + sealed trait GetTrialsWithLabelsReply + object GetTrialsWithLabelsReply { + type Error = GetTrialsWithLabelsReply with DomainError + + final case class EntityList(xs: Seq[ExportTrialWithLabels]) extends GetTrialsWithLabelsReply + + case object NotFoundError extends GetTrialsWithLabelsReply with DomainError.NotFoundError { + def userMessage: String = "Trials for disease are not found" + } + + case object AuthorizationError + extends GetTrialsWithLabelsReply with DomainError.AuthorizationError with DefaultAccessDeniedError + } + sealed trait UpdateReply object UpdateReply { type Error = UpdateReply with DomainError @@ -94,9 +109,12 @@ trait TrialService { def getById(id: StringId[Trial])(implicit requestContext: AuthenticatedRequestContext): Future[GetByIdReply] - def getTrialWithLabels(trialId: StringId[Trial], condition: String)( + def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)( implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] + def getTrialsWithLabels(cancerType: CancerType)( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] + def getPdfSource(trialId: StringId[Trial])( implicit requestContext: AuthenticatedRequestContext): Future[Source[ByteString, NotUsed]] diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala index 1e1a3ea..c9b5443 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala @@ -5,6 +5,7 @@ import xyz.driver.core.{Id, generators} import xyz.driver.entities.patient import xyz.driver.entities.patient.Patient import xyz.driver.entities.users.AuthUserInfo +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.eligibility.MismatchRankedLabels import xyz.driver.pdsuidomain.entities.{Arm, eligibility} import xyz.driver.pdsuidomain.services.EligibilityVerificationService @@ -21,7 +22,7 @@ class FakeEligibilityVerificationService extends EligibilityVerificationService override def getMismatchRankedLabels(patientId: Id[Patient], cancerType: patient.CancerType, - excludedArms: Seq[Id[Arm]])( + excludedArms: Seq[LongId[Arm]])( implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): Future[eligibility.MismatchRankedLabels] = Future.successful( MismatchRankedLabels( diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala index 9253f88..0431d95 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala @@ -7,11 +7,12 @@ import akka.stream.scaladsl.Source import akka.util.ByteString import xyz.driver.core.generators import xyz.driver.entities.labels.Label +import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial} import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm, Trial} import xyz.driver.pdsuidomain.services.TrialService import scala.concurrent.Future @@ -56,30 +57,36 @@ class FakeTrialService extends TrialService { implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] = Future.successful(GetListReply.EntityList(Seq(trial), 1, None)) - override def getTrialWithLabels(trialId: StringId[Trial], condition: String)( - implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] = { - Future.successful( - GetTrialWithLabelsReply.Entity(ExportTrialWithLabels( - StringId[Trial]("NCT" + generators.nextInt(999999).toString), - UuidId[Trial](generators.nextUuid()), - generators.oneOf("adenocarcinoma", "breast", "prostate"), - LocalDateTime.now(), - labelVersion = 1L, - generators.listOf(new ExportTrialArm( - LongId[Arm](generators.nextInt(999999).toLong), + override def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] = + Future.successful(GetTrialWithLabelsReply.Entity(nextExportTrialWithLabels())) + + override def getTrialsWithLabels(cancerType: CancerType)( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] = + Future.successful(GetTrialsWithLabelsReply.EntityList(generators.seqOf(nextExportTrialWithLabels()))) + + private def nextExportTrialWithLabels() = + ExportTrialWithLabels( + StringId[Trial]("NCT" + generators.nextInt(999999).toString), + UuidId[Trial](generators.nextUuid()), + LocalDateTime.now(), + labelVersion = 1L, + generators.listOf( + new ExportTrialArm( + LongId[EligibilityArm](generators.nextInt(999999).toLong), generators.nextName().value )), - generators.listOf(new ExportTrialLabelCriterion( + generators.listOf( + new ExportTrialLabelCriterion( LongId[Criterion](generators.nextInt(999999).toLong), generators.nextOption(generators.nextBoolean()), LongId[Label](generators.nextInt(999999).toLong), - generators.setOf(LongId[Arm](generators.nextInt(999999).toLong)), + generators.setOf(LongId[EligibilityArm](generators.nextInt(999999).toLong)), generators.nextName().value, generators.nextBoolean(), generators.nextBoolean() )) - ))) - } + ) def update(origTrial: Trial, draftTrial: Trial)( implicit requestContext: AuthenticatedRequestContext): Future[UpdateReply] = diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala index f6879d0..8869106 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala @@ -8,6 +8,7 @@ import xyz.driver.core.rest.{AuthorizedServiceRequestContext, RestService, Servi import xyz.driver.entities.patient import xyz.driver.entities.patient.Patient import xyz.driver.entities.users.AuthUserInfo +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.eligibility.{MatchedPatient, MismatchRankedLabels} import xyz.driver.pdsuidomain.entities.{Arm, eligibility} import xyz.driver.pdsuidomain.services.EligibilityVerificationService @@ -33,11 +34,11 @@ class RestEligibilityVerificationService(transport: ServiceTransport, baseUri: U override def getMismatchRankedLabels(patientId: Id[Patient], cancerType: patient.CancerType, - excludedArms: Seq[Id[Arm]])( + excludedArms: Seq[LongId[Arm]])( implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): Future[eligibility.MismatchRankedLabels] = { val query = - Seq("disease" -> cancerType.toString.toUpperCase, "ineligible_arms" -> excludedArms.map(_.value).mkString(",")) + Seq("disease" -> cancerType.toString.toUpperCase, "ineligible_arms" -> excludedArms.map(_.id).mkString(",")) val request = get(baseUri, s"/v1/patients/$patientId/labels", query) optionalResponse[MismatchRankedLabels](transport.sendRequest(ctx)(request)) diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala index 7e33919..ea719e1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala @@ -16,7 +16,9 @@ import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels import xyz.driver.pdsuidomain.formats.json.ListResponse import xyz.driver.pdsuidomain.formats.json.trial.ApiTrial import xyz.driver.pdsuidomain.services.TrialService +import spray.json.DefaultJsonProtocol._ import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ +import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuidomain.formats.json.sprayformats.export._ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit protected val materializer: Materializer, @@ -36,9 +38,9 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote } } - def getTrialWithLabels(trialId: StringId[Trial], disease: String)( + def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)( implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$disease/$trialId")) + val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$cancerType/$trialId")) for { response <- transport.sendRequestGetResponse(requestContext)(request) reply <- apiResponse[ExportTrialWithLabels](response) @@ -47,6 +49,17 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote } } + def getTrialsWithLabels(cancerType: CancerType)( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] = { + val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$cancerType")) + for { + response <- transport.sendRequestGetResponse(requestContext)(request) + reply <- apiResponse[Seq[ExportTrialWithLabels]](response) + } yield { + GetTrialsWithLabelsReply.EntityList(reply) + } + } + def getPdfSource(trialId: StringId[Trial])( implicit requestContext: AuthenticatedRequestContext): Future[Source[ByteString, NotUsed]] = { val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/source")) diff --git a/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala index f851680..7d8a418 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala @@ -78,10 +78,11 @@ class DocumentSuite extends BaseSuite { providerName = Some("etst"), providerTypeId = Some(LongId(123)), requiredType = None, + institutionName = Some("institution name"), startDate = Some(lastUpdate.toLocalDate.minusDays(2)), endDate = None, lastUpdate = lastUpdate, - meta = Some(TextJson(Document.Meta(None, 1.1, 2.2))) + meta = Some(TextJson(Document.Meta(1.1, 2.2))) ) } } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala index 481e92f..e6dd4a1 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala @@ -24,6 +24,7 @@ class DocumentFormatSuite extends FlatSpec with Matchers { typeId = Some(LongId(10)), providerName = Some("provider 21"), providerTypeId = Some(LongId(21)), + institutionName = Some("institution name"), requiredType = Some(Document.RequiredType.OPN), meta = None, startDate = None, @@ -33,7 +34,7 @@ class DocumentFormatSuite extends FlatSpec with Matchers { writtenJson should be( """{"id":1,"recordId":101,"physician":"physician","typeId":10,"provider":"provider 21","providerTypeId":21, - "requiredType":"OPN","startDate":null,"endDate":null,"status":"New","assignee":null,"previousStatus":null, + "requiredType":"OPN","institutionName":"institution name","startDate":null,"endDate":null,"status":"New","assignee":null,"previousStatus":null, "previousAssignee":null,"lastActiveUser":null,"lastUpdate":"2017-08-10T18:00Z","meta":null}""".parseJson) val createDocumentJson = @@ -41,34 +42,31 @@ class DocumentFormatSuite extends FlatSpec with Matchers { val expectedCreatedDocument = orig.copy( id = LongId(0), lastUpdate = LocalDateTime.MIN, - requiredType = None + requiredType = None, + institutionName = None ) val parsedCreatedDocument = documentFormat.read(createDocumentJson) parsedCreatedDocument should be(expectedCreatedDocument) val updateDocumentJson = - """{"startDate":"2017-08-10","endDate":"2018-08-10","meta":{"predicted":true,"startPage":1.0,"endPage":2.0}}""".parseJson + """{"startDate":"2017-08-10","endDate":"2018-08-10","meta":{"startPage":1.0,"endPage":2.0}}""".parseJson val expectedUpdatedDocument = orig.copy( startDate = Some(LocalDate.parse("2017-08-10")), endDate = Some(LocalDate.parse("2018-08-10")), - meta = Some(TextJson(Document.Meta(predicted = Some(true), startPage = 1.0, endPage = 2.0))) + meta = Some(TextJson(Document.Meta(startPage = 1.0, endPage = 2.0))) ) val parsedUpdatedDocument = applyUpdateToDocument(updateDocumentJson, orig) parsedUpdatedDocument should be(expectedUpdatedDocument) } "Json format for Document.Meta" should "read and write correct JSON" in { - val meta = Document.Meta(predicted = None, startPage = 1.0, endPage = 2.0) + val meta = Document.Meta(startPage = 1.0, endPage = 2.0) val writtenJson = documentMetaFormat.write(meta) writtenJson should be("""{"startPage":1.0,"endPage":2.0}""".parseJson) - val metaJsonWithoutPredicted = """{"startPage":1.0,"endPage":2.0}""".parseJson - val parsedMetaWithoutPredicted = documentMetaFormat.read(metaJsonWithoutPredicted) - parsedMetaWithoutPredicted should be(meta) - - val metaJsonWithPredicted = """{"predicted":true,"startPage":1.0,"endPage":2.0}""".parseJson - val parsedMetaWithPredicted = documentMetaFormat.read(metaJsonWithPredicted) - parsedMetaWithPredicted should be(meta.copy(predicted = Some(true))) + val metaJson = """{"startPage":1.0,"endPage":2.0}""".parseJson + val parsedMeta = documentMetaFormat.read(metaJson) + parsedMeta should be(meta) } } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala index a451905..3eaf93f 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala @@ -3,9 +3,10 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.{LocalDate, LocalDateTime} import java.util.UUID -import spray.json._ import org.scalatest.{FlatSpec, Matchers} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} +import spray.json._ +import xyz.driver.entities.labels.LabelValue +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.{DocumentType, ProviderType, RecordRequestId} class ExportFormatSuite extends FlatSpec with Matchers { @@ -27,13 +28,13 @@ class ExportFormatSuite extends FlatSpec with Matchers { evidences = List( ExportPatientLabelEvidence( id = LongId(11), - value = FuzzyValue.Yes, + value = LabelValue.Yes, evidenceText = "evidence text 11", document = document ), ExportPatientLabelEvidence( id = LongId(12), - value = FuzzyValue.No, + value = LabelValue.No, evidenceText = "evidence text 12", document = document ) @@ -44,13 +45,13 @@ class ExportFormatSuite extends FlatSpec with Matchers { evidences = List( ExportPatientLabelEvidence( id = LongId(12), - value = FuzzyValue.Yes, + value = LabelValue.Yes, evidenceText = "evidence text 12", document = document ), ExportPatientLabelEvidence( id = LongId(13), - value = FuzzyValue.Yes, + value = LabelValue.Yes, evidenceText = "evidence text 13", document = document ) @@ -106,7 +107,6 @@ class ExportFormatSuite extends FlatSpec with Matchers { val trialWithLabels = ExportTrialWithLabels( nctId = StringId("NCT000001"), trialId = UuidId("40892a07-c638-49d2-9795-1edfefbbcc7c"), - condition = "Breast", lastReviewed = LocalDateTime.parse("2017-08-10T18:00:00"), labelVersion = 1L, arms = arms, @@ -115,7 +115,7 @@ class ExportFormatSuite extends FlatSpec with Matchers { val writtenJson = trialWithLabelsFormat.write(trialWithLabels) writtenJson should be( - """{"nctId":"NCT000001","trialId":"40892a07-c638-49d2-9795-1edfefbbcc7c","disease":"Breast","lastReviewed":"2017-08-10T18:00Z", + """{"nctId":"NCT000001","trialId":"40892a07-c638-49d2-9795-1edfefbbcc7c","lastReviewed":"2017-08-10T18:00Z", "labelVersion":1,"arms":[{"armId":1,"armName":"arm 1"},{"armId":2,"armName":"arm 2"}],"criteria":[ {"value":"Yes","labelId":21,"criterionId":10,"criterionText":"criteria 10 text","armIds":[1,2],"isCompound":false,"isDefining":false}, {"value":"Unknown","labelId":21,"criterionId":11,"criterionText":"criteria 11 text","armIds":[2],"isCompound":true,"isDefining":false}]}""".parseJson) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala index c3df80a..1feca6a 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala @@ -2,7 +2,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import org.scalatest.{FlatSpec, Matchers} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson} +import xyz.driver.entities.labels.LabelValue +import xyz.driver.pdsuicommon.domain.{LongId, TextJson} import xyz.driver.pdsuidomain.entities.ExtractedData.Meta import xyz.driver.pdsuidomain.entities.{ExtractedData, ExtractedDataLabel} import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData @@ -24,14 +25,14 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers { dataId = extractedData.id, labelId = None, categoryId = None, - value = Some(FuzzyValue.Yes) + value = Some(LabelValue.Yes) ), ExtractedDataLabel( id = LongId(2), dataId = extractedData.id, labelId = Some(LongId(12)), categoryId = Some(LongId(1)), - value = Some(FuzzyValue.No) + value = Some(LabelValue.No) ) ) val origRichExtractedData = RichExtractedData( @@ -64,14 +65,14 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers { dataId = extractedData.id, labelId = Some(LongId(20)), categoryId = Some(LongId(1)), - value = Some(FuzzyValue.Yes) + value = Some(LabelValue.Yes) ), ExtractedDataLabel( id = LongId(0), dataId = extractedData.id, labelId = Some(LongId(12)), categoryId = Some(LongId(1)), - value = Some(FuzzyValue.No) + value = Some(LabelValue.No) ) ) val expectedUpdatedExtractedData = origRichExtractedData.copy( diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponseSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponseSuite.scala new file mode 100644 index 0000000..17d4cfb --- /dev/null +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponseSuite.scala @@ -0,0 +1,104 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import java.time.LocalDateTime +import java.util.UUID + +import spray.json._ +import org.scalatest.{FlatSpec, Matchers} +import xyz.driver.pdsuicommon.domain.{LongId, UuidId} +import xyz.driver.pdsuidomain.entities.MedicalRecord.Status +import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.formats.json.sprayformats.record.recordFormat + +class ListResponseSuite extends FlatSpec with Matchers { + + private val lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00") + private val lastUpdateToLocal = "2017-08-10T18:00Z" + + private def metaJsonObjectAsString(meta: ListResponse.Meta) = { + import meta._ + val lastUpdate = meta.lastUpdate + .map(_ => s""","lastUpdate":"$lastUpdateToLocal"""") + .getOrElse("") + + s"""{"itemsCount":$itemsCount,"pageNumber":$pageNumber,"pageSize":$pageSize$lastUpdate}""" + } + + "Json format for ListResponse.Meta" should "read and write correct JSON" in { + val meta1 = + ListResponse.Meta( + itemsCount = 5, + pageNumber = 6, + pageSize = 7, + lastUpdate = None + ) + + val writtenJson1 = + ListResponse.listResponseMetaFormat.write(meta1) + + writtenJson1 should be(metaJsonObjectAsString(meta1).parseJson) + + val parsedItem1: ListResponse.Meta = + ListResponse.listResponseMetaFormat.read(writtenJson1) + + meta1 shouldBe parsedItem1 + + val meta2 = + ListResponse.Meta( + itemsCount = 1, + pageNumber = 4, + pageSize = 3, + lastUpdate = Some(lastUpdate) + ) + + val writtenJson2 = + ListResponse.listResponseMetaFormat.write(meta2) + + writtenJson2 should be(metaJsonObjectAsString(meta2).parseJson) + + val parsedItem2: ListResponse.Meta = + ListResponse.listResponseMetaFormat.read(writtenJson2) + + meta2 shouldBe parsedItem2 + } + + "Json format for ListResponse" should "write correct JSON" in { + + val orig = MedicalRecord( + id = LongId(1), + status = Status.New, + assignee = None, + previousStatus = None, + previousAssignee = None, + lastActiveUserId = None, + lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00"), + physician = Some("physician"), + meta = None, + disease = "Breast", + requestId = RecordRequestId(UUID.fromString("7b54a75d-4197-4b27-9045-b9b6cb131be9")), + caseId = None, + patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343") + ) + + val recordJsonAsString = + """{"id":1,"status":"New","assignee":null,"previousStatus":null,"previousAssignee":null,"lastActiveUser":null, + "lastUpdate":"2017-08-10T18:00Z","meta":[],"patientId":"748b5884-3528-4cb9-904b-7a8151d6e343","caseId":null, + "requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","disease":"Breast","physician":"physician"}""" + + val meta = + ListResponse.Meta( + itemsCount = 5, + pageNumber = 6, + pageSize = 7, + lastUpdate = None + ) + + val listResponse = ListResponse(Seq(orig), meta) + + val writtenJson = ListResponse.listResponseMetaWriter.write(listResponse) + val expectedJson = s"""{"items":[$recordJsonAsString],"meta":${metaJsonObjectAsString(meta)}}""" + + writtenJson should be(expectedJson.parseJson) + } + +} diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala index feedf2f..d9fb232 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala @@ -23,8 +23,6 @@ class MedicalRecordFormatSuite extends FlatSpec with Matchers { lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00"), physician = Some("physician"), meta = None, - predictedMeta = None, - predictedDocuments = None, disease = "Breast", requestId = RecordRequestId(UUID.fromString("7b54a75d-4197-4b27-9045-b9b6cb131be9")), caseId = None, @@ -52,28 +50,23 @@ class MedicalRecordFormatSuite extends FlatSpec with Matchers { caseId = None, physician = None, meta = None, - predictedMeta = None, - predictedDocuments = None, lastUpdate = LocalDateTime.now() ) val parsedCreatedRecord = recordFormat.read(createRecordJson).copy(lastUpdate = expectedCreatedRecord.lastUpdate) parsedCreatedRecord should be(expectedCreatedRecord) val updateRecordJson = - """{"meta":[{"type":"duplicate","predicted":true,"startPage":1.0,"endPage":2.0,"startOriginalPage":1.0}, + """{"meta":[{"type":"duplicate","startPage":1.0,"endPage":2.0,"startOriginalPage":1.0}, {"type":"reorder","items":[1,2]}, {"type":"rotation","items":{"item1":1,"item2":2}}]}""".parseJson val expectedUpdatedRecord = orig.copy( meta = Some( - TextJson(List( - Meta.Duplicate(predicted = Some(true), - startPage = 1.0, - endPage = 2.0, - startOriginalPage = 1.0, - endOriginalPage = None), - Meta.Reorder(predicted = None, items = Seq(1, 2)), - Meta.Rotation(predicted = None, items = Map("item1" -> 1, "item2" -> 2)) - ))) + TextJson( + List( + Meta.Duplicate(startPage = 1.0, endPage = 2.0, startOriginalPage = 1.0, endOriginalPage = None), + Meta.Reorder(Seq(1, 2)), + Meta.Rotation(Map("item1" -> 1, "item2" -> 2)) + ))) ) val parsedUpdatedRecord = applyUpdateToMedicalRecord(updateRecordJson, orig) parsedUpdatedRecord should be(expectedUpdatedRecord) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala index 43f9b48..b254013 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala @@ -4,9 +4,10 @@ import java.time.LocalDateTime import spray.json._ import org.scalatest.{FlatSpec, Matchers} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId} +import xyz.driver.entities.labels.LabelValue +import xyz.driver.pdsuicommon.domain.{LongId, StringId} import xyz.driver.pdsuidomain.entities.{PatientCriterion, PatientCriterionArm} -import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion +import xyz.driver.pdsuidomain.services.PatientCriterionService.{DraftPatientCriterion, RichPatientCriterion} class PatientCriterionFormatSuite extends FlatSpec with Matchers { import patientcriterion._ @@ -21,7 +22,7 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers { criterionText = "criterion text", criterionValue = Some(true), criterionIsDefining = false, - eligibilityStatus = Some(FuzzyValue.Yes), + eligibilityStatus = Some(LabelValue.Yes), verifiedEligibilityStatus = None, isVisible = true, isVerified = true, @@ -31,7 +32,8 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers { PatientCriterionArm(patientCriterionId = LongId(1), armId = LongId(31), armName = "arm 31"), PatientCriterionArm(patientCriterionId = LongId(1), armId = LongId(32), armName = "arm 32") ) - val writtenJson = patientCriterionWriter.write((orig, LongId(21), arms)) + val richPatientCriterion = RichPatientCriterion(orig, LongId(21), arms) + val writtenJson = patientCriterionWriter.write(richPatientCriterion) writtenJson should be( """{"id":1,"labelId":21,"nctId":"NCT00001","criterionId":101,"criterionText":"criterion text","criterionValue":"Yes", @@ -39,14 +41,14 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers { "isVisible":true,"isVerified":true,"lastUpdate":"2017-08-10T18:00Z","arms":["arm 31","arm 32"]}""".parseJson) val updatePatientCriterionJson = """{"verifiedEligibilityStatus":"No"}""".parseJson - val expectedUpdatedPatientCriterion = orig.copy(verifiedEligibilityStatus = Some(FuzzyValue.No)) + val expectedUpdatedPatientCriterion = orig.copy(verifiedEligibilityStatus = Some(LabelValue.No)) val parsedUpdatePatientCriterion = applyUpdateToPatientCriterion(updatePatientCriterionJson, orig) parsedUpdatePatientCriterion should be(expectedUpdatedPatientCriterion) val updateBulkPatientCriterionJson = """[{"id":1,"eligibilityStatus":"No"},{"id":2,"isVerified":false}]""".parseJson val expectedDraftPatientCriterionList = List( - DraftPatientCriterion(id = LongId(1), eligibilityStatus = Some(FuzzyValue.No), isVerified = None), + DraftPatientCriterion(id = LongId(1), eligibilityStatus = Some(LabelValue.No), isVerified = None), DraftPatientCriterion(id = LongId(2), eligibilityStatus = None, isVerified = Some(false)) ) val parsedDraftPatientCriterionList = draftPatientCriterionListReader.read(updateBulkPatientCriterionJson) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala index 1d28b2e..b8f6f8e 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala @@ -2,9 +2,10 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.LocalDateTime -import spray.json._ import org.scalatest.{FlatSpec, Matchers} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} +import spray.json._ +import xyz.driver.entities.labels.LabelValue +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.{PatientCriterionArm, PatientTrialArmGroupView, Trial} import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial @@ -37,8 +38,8 @@ class PatientEligibleTrialFormatSuite extends FlatSpec with Matchers { patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"), trialId = StringId("NCT000001"), hypothesisId = UuidId("e76e2fc4-a29c-44fb-a81b-8856d06bb1d4"), - eligibilityStatus = Some(FuzzyValue.Yes), - verifiedEligibilityStatus = Some(FuzzyValue.Yes), + eligibilityStatus = Some(LabelValue.Yes), + verifiedEligibilityStatus = Some(LabelValue.Yes), isVerified = false ) val arms = List( diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala index b1b6b2a..128cad1 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala @@ -4,6 +4,8 @@ import java.time.{LocalDate, LocalDateTime} import spray.json._ import org.scalatest.{FlatSpec, Matchers} +import xyz.driver.entities.common.FullName +import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.domain.UuidId import xyz.driver.pdsuidomain.entities.{Patient, PatientOrderId} @@ -14,23 +16,24 @@ class PatientFormatSuite extends FlatSpec with Matchers { val orig = Patient( id = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"), status = Patient.Status.New, - name = "John Doe", + name = FullName.fromStrings("John", "", "Doe"), dob = LocalDate.parse("1980-06-30"), assignee = None, previousStatus = None, previousAssignee = None, lastActiveUserId = None, isUpdateRequired = false, - condition = "breast", + disease = CancerType.Breast, orderId = PatientOrderId("7b54a75d-4197-4b27-9045-b9b6cb131be9"), lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00") ) val writtenJson = patientWriter.write(orig) writtenJson should be( - """{"id":"748b5884-3528-4cb9-904b-7a8151d6e343","dob":"1980-06-30","name":"John Doe","status":"New","assignee":null, + """{"id":"748b5884-3528-4cb9-904b-7a8151d6e343","dob":"1980-06-30", + "name":{"firstName":"John","middleName":"","lastName":"Doe"},"status":"New","assignee":null, "previousStatus":null,"previousAssignee":null,"lastActiveUser":null,"lastUpdate":"2017-08-10T18:00Z", - "orderId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","condition":"breast"}""".parseJson) + "orderId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","disease":"Breast"}""".parseJson) } } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala index 0e628a8..71cbbad 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala @@ -4,11 +4,12 @@ import spray.json._ import org.scalatest.{FlatSpec, Matchers} import xyz.driver.pdsuicommon.domain.UuidId import xyz.driver.pdsuidomain.entities.PatientHypothesis +import xyz.driver.pdsuidomain.services.PatientHypothesisService.RichPatientHypothesis class PatientHypothesisFormatSuite extends FlatSpec with Matchers { import patienthypothesis._ - "Json format for PatientHypothesis" should "read and write correct JSON" in { + "Json format for RichPatientHypothesis" should "read and write correct JSON" in { val orig = PatientHypothesis( id = UuidId("815d9715-1089-4775-b120-3afb983b9a97"), patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"), @@ -16,7 +17,7 @@ class PatientHypothesisFormatSuite extends FlatSpec with Matchers { rationale = None, matchedTrials = 1 ) - val writtenJson = patientHypothesisWriter.write((orig, true)) + val writtenJson = richPatientHypothesisWriter.write(RichPatientHypothesis(orig, isRequired = true)) writtenJson should be( """{"id":"815d9715-1089-4775-b120-3afb983b9a97","patientId":"748b5884-3528-4cb9-904b-7a8151d6e343", @@ -28,4 +29,19 @@ class PatientHypothesisFormatSuite extends FlatSpec with Matchers { parsedUpdatePatientHypothesis should be(expectedUpdatedPatientHypothesis) } + "Json format for patientHypothesis" should "read and write correct JSON" in { + val orig = PatientHypothesis( + id = UuidId("815d9715-1089-4775-b120-3afb983b9a97"), + patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"), + hypothesisId = UuidId("e76e2fc4-a29c-44fb-a81b-8856d06bb1d4"), + rationale = None, + matchedTrials = 1 + ) + val writtenJson = patientHypothesisWriter.write(orig) + + writtenJson should be( + """{"id":"815d9715-1089-4775-b120-3afb983b9a97","patientId":"748b5884-3528-4cb9-904b-7a8151d6e343", + "hypothesisId":"e76e2fc4-a29c-44fb-a81b-8856d06bb1d4","rationale":null,"matchedTrials":1}""".parseJson) + } + } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala index 67d678c..2122777 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala @@ -4,31 +4,33 @@ import java.time.LocalDate import spray.json._ import org.scalatest.{FlatSpec, Matchers} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, UuidId} -import xyz.driver.pdsuidomain.entities.{PatientLabel, PatientLabelEvidenceView} +import xyz.driver.entities.labels.LabelValue +import xyz.driver.pdsuicommon.domain.{LongId, UuidId} +import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientLabelService.RichPatientLabel class PatientLabelFormatSuite extends FlatSpec with Matchers { - "Json format for PatientLabel" should "read and write correct JSON" in { + "Json format for RichPatientLabel" should "read and write correct JSON" in { import patientlabel._ val orig = PatientLabel( id = LongId(1), patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"), labelId = LongId(20), - primaryValue = Some(FuzzyValue.Yes), + primaryValue = Some(LabelValue.Yes), verifiedPrimaryValue = None, isVisible = true, score = 1, isImplicitMatch = false ) - val writtenJson = patientLabelWriter.write((orig, true)) + val writtenJson = richPatientLabelWriter.write(RichPatientLabel(orig, isVerified = true)) writtenJson should be( """{"id":1,"labelId":20,"primaryValue":"Yes","verifiedPrimaryValue":null,"isVisible":true,"isVerified":true, "score":1,"isImplicitMatch":false}""".parseJson) val updatePatientLabelJson = """{"verifiedPrimaryValue":"No"}""".parseJson - val expectedUpdatedPatientLabel = orig.copy(verifiedPrimaryValue = Some(FuzzyValue.No)) + val expectedUpdatedPatientLabel = orig.copy(verifiedPrimaryValue = Some(LabelValue.No)) val parsedUpdatePatientLabel = applyUpdateToPatientLabel(updatePatientLabelJson, orig) parsedUpdatePatientLabel should be(expectedUpdatedPatientLabel) } @@ -37,14 +39,14 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers { import patientlabel._ val orig = PatientLabelEvidenceView( id = LongId(1), - value = FuzzyValue.Maybe, + value = LabelValue.Maybe, evidenceText = "evidence text", documentId = Some(LongId(21)), evidenceId = Some(LongId(10)), reportId = None, - documentType = "document type", + documentType = DocumentType.LaboratoryReport, date = Some(LocalDate.parse("2017-08-10")), - providerType = "provider type", + providerType = ProviderType.EmergencyMedicine, patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"), labelId = LongId(20), isImplicitMatch = false @@ -53,7 +55,8 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers { writtenJson should be( """{"id":1,"value":"Maybe","evidenceText":"evidence text","documentId":21,"evidenceId":10,"reportId":null, - "documentType":"document type","date":"2017-08-10","providerType":"provider type"}""".parseJson) + "documentType":{"id":3,"name":"Laboratory Report"},"date":"2017-08-10", + "providerType":{"id":26,"name":"Emergency Medicine"}}""".parseJson) } "Json format for PatientLabelDefiningCriteria" should "read and write correct JSON" in { @@ -62,8 +65,8 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers { id = LongId(1), patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"), labelId = LongId(20), - primaryValue = Some(FuzzyValue.Yes), - verifiedPrimaryValue = Some(FuzzyValue.Yes), + primaryValue = Some(LabelValue.Yes), + verifiedPrimaryValue = Some(LabelValue.Yes), isVisible = true, score = 1, isImplicitMatch = false diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala index a3da52f..c9dc85f 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala @@ -2,8 +2,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.LocalDateTime -import spray.json._ import org.scalatest.{FlatSpec, Matchers} +import spray.json._ import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.Trial |