diff options
Diffstat (limited to 'src/main/scala')
12 files changed, 280 insertions, 34 deletions
diff --git a/src/main/scala/xyz/driver/pdsuicommon/db/QueryBuilder.scala b/src/main/scala/xyz/driver/pdsuicommon/db/QueryBuilder.scala index aa32166..0bf1ed6 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/db/QueryBuilder.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/db/QueryBuilder.scala @@ -57,10 +57,10 @@ sealed trait QueryBuilderParameters { def toSql(countQuery: Boolean, fields: Set[String], namingStrategy: NamingStrategy): (String, QueryBuilder.Binder) = { val escapedTableName = namingStrategy.table(tableData.tableName) val fieldsSql: String = if (countQuery) { - val suffix: String = (tableData.lastUpdateFieldName match { + val suffix: String = tableData.lastUpdateFieldName match { case Some(lastUpdateField) => s", max($escapedTableName.${namingStrategy.column(lastUpdateField)})" case None => "" - }) + } "count(*)" + suffix } else { if (fields == QueryBuilderParameters.AllFields) { diff --git a/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala b/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala index 8aff397..e0adeb8 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala @@ -13,10 +13,15 @@ import scala.util.Try object SearchFilterParser { private object BinaryAtomFromTuple { - def unapply(input: (SearchFilterExpr.Dimension, (String, String))): Option[SearchFilterExpr.Atom.Binary] = { + def unapply(input: (SearchFilterExpr.Dimension, (String, Any))): Option[SearchFilterExpr.Atom.Binary] = { val (dimensionName, (strOperation, value)) = input + val updatedValue = value match { + case s: String => s.safeTrim + case a => a + } + parseOperation(strOperation.toLowerCase).map { op => - SearchFilterExpr.Atom.Binary(dimensionName, op, value.safeTrim) + SearchFilterExpr.Atom.Binary(dimensionName, op, updatedValue.asInstanceOf[AnyRef]) } } } @@ -68,7 +73,7 @@ object SearchFilterParser { } private val numericOperatorParser: Parser[String] = { - P((IgnoreCase("gt") | IgnoreCase("lt")) ~ IgnoreCase("eq").?).! + P(IgnoreCase("eq") | ((IgnoreCase("gt") | IgnoreCase("lt")) ~ IgnoreCase("eq").?)).! } private val naryOperatorParser: Parser[String] = P(IgnoreCase("in")).! @@ -91,10 +96,12 @@ object SearchFilterParser { private val nAryValueParser: Parser[String] = P(CharPred(_ != ',').rep(min = 1).!) + private val longParser: Parser[Long] = P(CharIn('0' to '9').rep(1).!.map(_.toLong)) + private val binaryAtomParser: Parser[SearchFilterExpr.Atom.Binary] = P( dimensionParser ~ whitespaceParser ~ ( - (commonOperatorParser.! ~/ whitespaceParser ~/ AnyChar.rep(min = 1).!) - | (numericOperatorParser.! ~/ whitespaceParser ~/ numberParser.!) + (numericOperatorParser.! ~ whitespaceParser ~ (longParser | numberParser.!)) | + (commonOperatorParser.! ~ whitespaceParser ~ AnyChar.rep(min = 1).!) ) ~ End ).map { case BinaryAtomFromTuple(atom) => atom diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala index 1f73184..839fead 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala @@ -14,6 +14,8 @@ import xyz.driver.pdsuicommon.validation.Validators import xyz.driver.pdsuicommon.validation.Validators.Validator import xyz.driver.pdsuidomain.entities.Document.Meta +import scalaz.Equal + final case class ProviderType(id: LongId[ProviderType], name: String) object ProviderType { @@ -124,6 +126,8 @@ object DocumentType { } } + implicit def equal: Equal[DocumentType] = Equal.equal[DocumentType](_ == _) + implicit def toPhiString(x: DocumentType): PhiString = { import x._ phi"DocumentType(id=$id, name=${Unsafe(name)})" diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala index a8c22a2..a838d64 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala @@ -2,10 +2,186 @@ package xyz.driver.pdsuidomain.entities import xyz.driver.pdsuicommon.domain.{LongId, StringId} import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod +import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod._ -final case class InterventionType(id: LongId[InterventionType], name: String) +sealed trait InterventionType { + val id: LongId[InterventionType] + val name: String + val deliveryMethods: Set[DeliveryMethod] +} object InterventionType { + + final case object RadiationTherapy extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](1) + val name: String = "Radiation therapy" + val deliveryMethods: Set[DeliveryMethod] = commonMethods + } + + final case object Chemotherapy extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](2) + val name: String = "Chemotherapy" + val deliveryMethods: Set[DeliveryMethod] = commonMethods + } + + final case object TargetedTherapy extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](3) + val name: String = "Targeted therapy" + val deliveryMethods: Set[DeliveryMethod] = commonMethods + } + + final case object Immunotherapy extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](4) + val name: String = "Immunotherapy" + val deliveryMethods: Set[DeliveryMethod] = commonMethods + } + + final case object Surgery extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](5) + val name: String = "Surgery" + val deliveryMethods: Set[DeliveryMethod] = commonMethods + } + + final case object HormoneTherapy extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](6) + val name: String = "Hormone therapy" + val deliveryMethods: Set[DeliveryMethod] = commonMethods + } + + final case object Other extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](7) + val name: String = "Other" + val deliveryMethods: Set[DeliveryMethod] = commonMethods + } + + final case object Radiation extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](8) + val name: String = "Radiation" + val deliveryMethods: Set[DeliveryMethod] = Set( + ExternalRadiationTherapy, + Brachytherapy, + SystemicRadiationTherapyIV, + SystemicRadiationTherapyOral, + ProtonBeamTherapy + ) + } + + final case object SurgeryProcedure extends InterventionType { + val id: LongId[InterventionType] = LongId[InterventionType](9) + val name: String = "Surgery/Procedure" + val deliveryMethods: Set[DeliveryMethod] = Set( + RadioFrequencyAblationRFA, + Cryoablation, + TherapeuticConventionalSurgery, + RoboticAssistedLaparoscopicSurgery + ) + } + + def typeFromString: PartialFunction[String, InterventionType] = { + case "Radiation therapy" => RadiationTherapy + case "Chemotherapy" => Chemotherapy + case "Targeted therapy" => TargetedTherapy + case "Immunotherapy" => Immunotherapy + case "Surgery" => Surgery + case "Hormone therapy" => HormoneTherapy + case "Other" => Other + case "Radiation" => Radiation + case "Surgery/Procedure" => SurgeryProcedure + } + + sealed trait DeliveryMethod + object DeliveryMethod { + case object IntravenousInfusionIV extends DeliveryMethod + case object IntramuscularInjection extends DeliveryMethod + case object SubcutaneousInjection extends DeliveryMethod + case object IntradermalInjection extends DeliveryMethod + case object SpinalInjection extends DeliveryMethod + case object Oral extends DeliveryMethod + case object Topical extends DeliveryMethod + case object TransdermalPatch extends DeliveryMethod + case object Inhalation extends DeliveryMethod + case object Rectal extends DeliveryMethod + case object ExternalRadiationTherapy extends DeliveryMethod + case object Brachytherapy extends DeliveryMethod + case object SystemicRadiationTherapyIV extends DeliveryMethod + case object SystemicRadiationTherapyOral extends DeliveryMethod + case object ProtonBeamTherapy extends DeliveryMethod + case object RadioFrequencyAblationRFA extends DeliveryMethod + case object Cryoablation extends DeliveryMethod + case object TherapeuticConventionalSurgery extends DeliveryMethod + case object RoboticAssistedLaparoscopicSurgery extends DeliveryMethod + + def fromString: PartialFunction[String, DeliveryMethod] = { + case "Intravenous Infusion (IV)" => IntravenousInfusionIV + case "Intramuscular Injection" => IntramuscularInjection + case "Subcutaneous Injection" => SubcutaneousInjection + case "Intradermal Injection" => IntradermalInjection + case "Spinal Injection" => SpinalInjection + case "Oral" => Oral + case "Topical" => Topical + case "Transdermal Patch" => TransdermalPatch + case "Inhalation" => Inhalation + case "Rectal" => Rectal + case "External Radiation Therapy" => ExternalRadiationTherapy + case "Brachytherapy" => Brachytherapy + case "Systemic Radiation Therapy (IV)" => SystemicRadiationTherapyIV + case "Systemic Radiation Therapy (Oral)" => SystemicRadiationTherapyOral + case "Proton Beam Therapy" => ProtonBeamTherapy + case "Radio-Frequency Ablation (RFA)" => RadioFrequencyAblationRFA + case "Cryoablation" => Cryoablation + case "Therapeutic Conventional Surgery" => TherapeuticConventionalSurgery + case "Robotic Assisted Laparoscopic Surgery" => RoboticAssistedLaparoscopicSurgery + } + + def methodToString(x: DeliveryMethod): String = x match { + case IntravenousInfusionIV => "Intravenous Infusion (IV)" + case IntramuscularInjection => "Intramuscular Injection" + case SubcutaneousInjection => "Subcutaneous Injection" + case IntradermalInjection => "Intradermal Injection" + case SpinalInjection => "Spinal Injection" + case Oral => "Oral" + case Topical => "Topical" + case TransdermalPatch => "Transdermal Patch" + case Inhalation => "Inhalation" + case Rectal => "Rectal" + case ExternalRadiationTherapy => "External Radiation Therapy" + case Brachytherapy => "Brachytherapy" + case SystemicRadiationTherapyIV => "Systemic Radiation Therapy (IV)" + case SystemicRadiationTherapyOral => "Systemic Radiation Therapy (Oral)" + case ProtonBeamTherapy => "Proton Beam Therapy" + case RadioFrequencyAblationRFA => "Radio-Frequency Ablation (RFA)" + case Cryoablation => "Cryoablation" + case TherapeuticConventionalSurgery => "Therapeutic Conventional Surgery" + case RoboticAssistedLaparoscopicSurgery => "Robotic Assisted Laparoscopic Surgery" + } + } + + val commonMethods = Set[DeliveryMethod]( + IntravenousInfusionIV, + IntramuscularInjection, + SubcutaneousInjection, + IntradermalInjection, + SpinalInjection, + Oral, + Topical, + TransdermalPatch, + Inhalation, + Rectal + ) + + val All: Map[LongId[InterventionType], InterventionType] = Map[LongId[InterventionType], InterventionType]( + LongId[InterventionType](1) -> RadiationTherapy, + LongId[InterventionType](2) -> Chemotherapy, + LongId[InterventionType](3) -> TargetedTherapy, + LongId[InterventionType](4) -> Immunotherapy, + LongId[InterventionType](5) -> Surgery, + LongId[InterventionType](6) -> HormoneTherapy, + LongId[InterventionType](7) -> Other, + LongId[InterventionType](8) -> Radiation, + LongId[InterventionType](9) -> SurgeryProcedure + ) + implicit def toPhiString(x: InterventionType): PhiString = { import x._ phi"InterventionType(id=$id, name=${Unsafe(name)})" @@ -29,12 +205,23 @@ final case class Intervention(id: LongId[Intervention], originalType: Option[String], dosage: String, originalDosage: String, - isActive: Boolean) + isActive: Boolean, + deliveryMethod: Option[String]) { + def deliveryMethodIsCorrect: Boolean = { + if (this.typeId.nonEmpty) { + this.deliveryMethod.nonEmpty && + InterventionType.All + .getOrElse(this.typeId.get, throw new IllegalArgumentException(s"Not found Intervention type ${this.typeId}")) + .deliveryMethods + .contains(DeliveryMethod.fromString(this.deliveryMethod.get)) + } else true + } +} object Intervention { implicit def toPhiString(x: Intervention): PhiString = { import x._ - phi"Intervention(id=$id, trialId=$trialId, name=${Unsafe(name)}, typeId=$typeId, isActive=$isActive)" + phi"Intervention(id=$id, trialId=$trialId, name=${Unsafe(name)}, typeId=$typeId, isActive=$isActive, deliveryMethod=${Unsafe(deliveryMethod)})" } } 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 60b74ff..cf55694 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 @@ -27,7 +27,7 @@ object ExportTrialWithLabels { def fromRaw(rawData: List[RawTrialLabel]): ExportTrialWithLabels = { val trials: Set[StringId[Trial]] = rawData.map(_.nctId)(breakOut) - assert(trials.size == 1, "There are more than one trials in the rawData") + assert(trials.size == 1, "There are more than one trial in the rawData") val trial = rawData.head ExportTrialWithLabels( @@ -43,9 +43,7 @@ object ExportTrialWithLabels { ExportTrialArm(armId, rawTrials.head.armName) }(breakOut), criteria = rawData - .groupBy { x => - (x.criterionId, x.labelId) - } + .groupBy(x => (x.criterionId, x.labelId)) .map { case (_, rawTrialLabels) => val armIds = rawTrialLabels.map(_.criterionArmId).toSet @@ -53,5 +51,4 @@ object ExportTrialWithLabels { }(breakOut) ) } - } 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 ac7412c..f9a267f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala @@ -7,6 +7,7 @@ import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion object trialcuration { import xyz.driver.core.generators import common._ + import xyz.driver.pdsuidomain.entities.InterventionType._ def nextTrial(): Trial = Trial( id = nextStringId[Trial], @@ -76,7 +77,8 @@ object trialcuration { originalType = Option(generators.nextString()), dosage = generators.nextString(), originalDosage = generators.nextString(), - isActive = generators.nextBoolean() + isActive = generators.nextBoolean(), + deliveryMethod = Option(generators.nextString()) ) def nextInterventionArm(interventionId: LongId[Intervention]): InterventionArm = InterventionArm( @@ -129,9 +131,16 @@ object trialcuration { name = generators.nextString() ) - def nextInterventionType(): InterventionType = InterventionType( - id = nextLongId[InterventionType], - name = generators.nextString() + def nextInterventionType(): InterventionType = generators.oneOf[InterventionType]( + RadiationTherapy, + Chemotherapy, + TargetedTherapy, + Immunotherapy, + Surgery, + HormoneTherapy, + Other, + Radiation, + SurgeryProcedure ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiIntervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiIntervention.scala index f306a71..072ed25 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiIntervention.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiIntervention.scala @@ -12,6 +12,7 @@ final case class ApiIntervention(id: Long, isActive: Boolean, arms: List[Long], trialId: String, + deliveryMethod: Option[String], originalName: String, originalDosage: String, originalType: Option[String]) { @@ -26,7 +27,8 @@ final case class ApiIntervention(id: Long, originalType = this.originalType.map(id => id.toString), dosage = this.dosage, originalDosage = this.originalDosage, - isActive = this.isActive + isActive = this.isActive, + deliveryMethod = this.deliveryMethod ) InterventionWithArms(intervention, this.arms.map { armId => @@ -47,6 +49,7 @@ object ApiIntervention { (JsPath \ "isActive").format[Boolean] and (JsPath \ "arms").format[List[Long]] and (JsPath \ "trialId").format[String] and + (JsPath \ "deliveryMethod").formatNullable[String] and (JsPath \ "originalName").format[String] and (JsPath \ "originalDosage").format[String] and (JsPath \ "originalType").formatNullable[String] @@ -64,6 +67,7 @@ object ApiIntervention { isActive = intervention.isActive, arms = arms.map(_.armId.id), trialId = intervention.trialId.id, + deliveryMethod = intervention.deliveryMethod, originalName = intervention.originalName, originalDosage = intervention.originalDosage, originalType = intervention.originalType diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiInterventionType.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiInterventionType.scala index ebef225..3db8bfa 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiInterventionType.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiInterventionType.scala @@ -2,23 +2,25 @@ package xyz.driver.pdsuidomain.formats.json.intervention import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.InterventionType +import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod -final case class ApiInterventionType(id: Long, name: String) { +final case class ApiInterventionType(id: Long, name: String, deliveryMethods: List[String]) { - def toDomain = InterventionType(id = LongId[InterventionType](id), name = name) + def toDomain = InterventionType.typeFromString(name) } object ApiInterventionType { implicit val format: Format[ApiInterventionType] = ( (JsPath \ "id").format[Long] and - (JsPath \ "name").format[String] + (JsPath \ "name").format[String] and + (JsPath \ "deliveryMethods").format[List[String]] )(ApiInterventionType.apply, unlift(ApiInterventionType.unapply)) def fromDomain(interventionType: InterventionType) = ApiInterventionType( id = interventionType.id.id, - name = interventionType.name + name = interventionType.name, + deliveryMethods = interventionType.deliveryMethods.map(DeliveryMethod.methodToString).toList ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiPartialIntervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiPartialIntervention.scala index 74f16e1..28a8555 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiPartialIntervention.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention/ApiPartialIntervention.scala @@ -16,6 +16,7 @@ final case class ApiPartialIntervention(name: Option[String], typeId: Option[Long], dosage: Option[String], isActive: Option[Boolean], + deliveryMethod: Option[String], arms: Option[List[Long]]) { def applyTo(orig: InterventionWithArms): InterventionWithArms = { @@ -26,7 +27,8 @@ final case class ApiPartialIntervention(name: Option[String], name = name.getOrElse(origIntervention.name), typeId = typeId.map(LongId(_)).orElse(origIntervention.typeId), dosage = dosage.getOrElse(origIntervention.dosage), - isActive = isActive.getOrElse(origIntervention.isActive) + isActive = isActive.getOrElse(origIntervention.isActive), + deliveryMethod = deliveryMethod.orElse(origIntervention.deliveryMethod) ), arms = draftArmList.getOrElse(orig.arms) ) @@ -50,7 +52,8 @@ final case class ApiPartialIntervention(name: Option[String], originalType = Option(""), dosage = dosage.getOrElse(""), originalDosage = dosage.getOrElse(""), - isActive = isActive.getOrElse(false) + isActive = isActive.getOrElse(false), + deliveryMethod = deliveryMethod ), arms = arms.map(_.map(x => InterventionArm(armId = LongId(x), interventionId = LongId(0)))).getOrElse(List.empty) @@ -69,6 +72,7 @@ object ApiPartialIntervention { (JsPath \ "typeId").readNullable[Long] and (JsPath \ "dosage").readNullable[String] and (JsPath \ "isActive").readNullable[Boolean] and + (JsPath \ "deliveryMethod").readNullable[String] and (JsPath \ "arms").readNullable[List[Long]] )(ApiPartialIntervention.apply _) @@ -78,6 +82,7 @@ object ApiPartialIntervention { (JsPath \ "typeId").writeNullable[Long] and (JsPath \ "dosage").writeNullable[String] and (JsPath \ "isActive").writeNullable[Boolean] and + (JsPath \ "deliveryMethod").writeNullable[String] and (JsPath \ "arms").writeNullable[List[Long]] )(unlift(ApiPartialIntervention.unapply)) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiUpdateRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiUpdateRecord.scala index 47bc493..05d5a60 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiUpdateRecord.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiUpdateRecord.scala @@ -37,7 +37,7 @@ object ApiUpdateRecord { JsSuccess(Json.stringify(x)) }) .map { - case Tristate.Present("{}") => Tristate.Absent + case Tristate.Present("[]") => Tristate.Absent case x => x } )(ApiUpdateRecord.apply _) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala index dcbe886..2ced434 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod import xyz.driver.pdsuidomain.entities._ object intervention { @@ -18,6 +19,7 @@ object intervention { "isActive" -> obj.intervention.isActive.toJson, "arms" -> obj.arms.map(_.armId).toJson, "trialId" -> obj.intervention.trialId.toJson, + "deliveryMethod" -> obj.intervention.deliveryMethod.toJson, "originalName" -> obj.intervention.originalName.toJson, "originalDosage" -> obj.intervention.originalDosage.toJson, "originalType" -> obj.intervention.originalType.toJson @@ -48,6 +50,10 @@ object intervention { .get("isActive") .exists(_.convertTo[Boolean]) + val deliveryMethod = fields + .get("deliveryMethod") + .map(_.convertTo[String]) + val arms = fields .get("arms") .map(_.convertTo[List[LongId[SlotArm]]].map(x => InterventionArm(armId = x, interventionId = LongId(0)))) @@ -63,7 +69,8 @@ object intervention { originalType = None, dosage = dosage, originalDosage = dosage, - isActive = isActive + isActive = isActive, + deliveryMethod = deliveryMethod ), arms = arms ) @@ -90,6 +97,10 @@ object intervention { .get("isActive") .map(_.convertTo[Boolean]) + val deliveryMethod = fields + .get("deliveryMethod") + .map(_.convertTo[String]) + val origIntervention = orig.intervention val arms = fields .get("arms") @@ -100,7 +111,8 @@ object intervention { name = name.getOrElse(origIntervention.name), typeId = typeId.orElse(origIntervention.typeId), dosage = dosage.getOrElse(origIntervention.dosage), - isActive = isActive.getOrElse(origIntervention.isActive) + isActive = isActive.getOrElse(origIntervention.isActive), + deliveryMethod = deliveryMethod.orElse(origIntervention.deliveryMethod) ), arms = arms.getOrElse(orig.arms) ) @@ -108,6 +120,25 @@ object intervention { case _ => deserializationError(s"Expected Json Object as partial Intervention, but got $json") } - implicit val interventionTypeFormat: RootJsonFormat[InterventionType] = jsonFormat2(InterventionType.apply) + implicit val interventionTypeFormat: JsonFormat[InterventionType] = new RootJsonFormat[InterventionType] { + override def read(json: JsValue) = json match { + case JsObject(fields) => + val name = fields + .get("name") + .map(_.convertTo[String]) + .getOrElse(deserializationError(s"Intervention type json object does not contain `name` field: $json")) + + InterventionType.typeFromString(name) + + case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json") + } + + override def write(obj: InterventionType) = + JsObject( + "id" -> obj.id.toJson, + "name" -> obj.name.toJson, + "deliveryMethods" -> obj.deliveryMethods.map(DeliveryMethod.methodToString).toJson + ) + } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala index f826b98..b77e6df 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala @@ -34,9 +34,9 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote } } - def getTrialWithLabels(trialId: StringId[Trial], condition: String)( + def getTrialWithLabels(trialId: StringId[Trial], disease: String)( implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$trialId")) + val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$disease/$trialId")) for { response <- transport.sendRequestGetResponse(requestContext)(request) reply <- apiResponse[ApiExportTrialWithLabels](response) @@ -47,7 +47,7 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote def getPdfSource(trialId: StringId[Trial])( implicit requestContext: AuthenticatedRequestContext): Future[Source[ByteString, NotUsed]] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/${trialId}/source")) + val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/source")) for { response <- transport.sendRequestGetResponse(requestContext)(request) reply <- apiResponse[HttpEntity](response) |