diff options
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/formats')
30 files changed, 0 insertions, 2564 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/arm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/arm.scala deleted file mode 100644 index 69029b6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/arm.scala +++ /dev/null @@ -1,44 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ - -object arm { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToArm(json: JsValue, orig: Arm): Arm = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Arm json object does not contain `name` field: $json")) - orig.copy(name = name) - - case _ => deserializationError(s"Expected Json Object as partial Arm, but got $json") - } - - implicit val armFormat: RootJsonFormat[Arm] = new RootJsonFormat[Arm] { - override def write(obj: Arm): JsValue = - JsObject( - "id" -> obj.id.toJson, - "name" -> obj.name.toJson, - "originalName" -> obj.originalName.toJson, - "trialId" -> obj.trialId.toJson - ) - - override def read(json: JsValue): Arm = json.asJsObject.getFields("trialId", "name") match { - case Seq(trialId, name) => - Arm( - id = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[Arm]]]).getOrElse(LongId(0)), - name = name.convertTo[String], - trialId = trialId.convertTo[StringId[Trial]], - originalName = name.convertTo[String] - ) - - case _ => deserializationError(s"Expected Json Object as Arm, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/bridgeuploadqueue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/bridgeuploadqueue.scala deleted file mode 100644 index 6725a15..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/bridgeuploadqueue.scala +++ /dev/null @@ -1,68 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue -import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue.Item - -object bridgeuploadqueue { - import DefaultJsonProtocol._ - import common._ - - implicit val queueUploadItemFormat: RootJsonFormat[BridgeUploadQueue.Item] = new RootJsonFormat[Item] { - override def write(obj: Item) = - JsObject( - "kind" -> obj.kind.toJson, - "tag" -> obj.tag.toJson, - "created" -> obj.created.toJson, - "attempts" -> obj.attempts.toJson, - "nextAttempt" -> obj.nextAttempt.toJson, - "completed" -> obj.completed.toJson - ) - - override def read(json: JsValue): Item = json match { - case JsObject(fields) => - val kind = fields - .get("kind") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"BridgeUploadQueue.Item json object does not contain `kind` field: $json")) - - val tag = fields - .get("tag") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"BridgeUploadQueue.Item json object does not contain `tag` field: $json")) - - val created = fields - .get("created") - .map(_.convertTo[LocalDateTime]) - .getOrElse( - deserializationError(s"BridgeUploadQueue.Item json object does not contain `created` field: $json")) - - val attempts = fields - .get("attempts") - .map(_.convertTo[Int]) - .getOrElse( - deserializationError(s"BridgeUploadQueue.Item json object does not contain `attempts` field: $json")) - - val nextAttempt = fields - .get("nextAttempt") - .map(_.convertTo[LocalDateTime]) - .getOrElse( - deserializationError(s"BridgeUploadQueue.Item json object does not contain `nextAttempt` field: $json")) - - BridgeUploadQueue.Item( - kind = kind, - tag = tag, - created = created, - attempts = attempts, - nextAttempt = nextAttempt, - completed = true, - dependencyKind = None, - dependencyTag = None - ) - - case _ => deserializationError(s"Expected Json Object as BridgeUploadQueue.Item, but got $json") - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/common.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/common.scala deleted file mode 100644 index 26adb9c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/common.scala +++ /dev/null @@ -1,66 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDate, LocalDateTime, ZoneId, ZonedDateTime} - -import spray.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} - -object common { - - implicit def longIdFormat[T] = new RootJsonFormat[LongId[T]] { - override def write(id: LongId[T]): JsNumber = JsNumber(id.id) - override def read(json: JsValue): LongId[T] = json match { - case JsNumber(value) => LongId(value.toLong) - case _ => deserializationError(s"Expected number as LongId, but got $json") - } - } - - implicit def stringIdFormat[T] = new RootJsonFormat[StringId[T]] { - override def write(id: StringId[T]): JsString = JsString(id.toString) - override def read(json: JsValue): StringId[T] = json match { - case JsString(value) => StringId(value) - case _ => deserializationError(s"Expected string as StringId, but got $json") - } - } - - implicit def uuidIdFormat[T] = new RootJsonFormat[UuidId[T]] { - override def write(id: UuidId[T]): JsString = JsString(id.toString) - override def read(json: JsValue): UuidId[T] = json match { - case JsString(value) => UuidId(value) - case _ => deserializationError(s"Expected string as UuidId, but got $json") - } - } - - implicit def dateTimeFormat = new RootJsonFormat[LocalDateTime] { - override def write(date: LocalDateTime): JsString = JsString(ZonedDateTime.of(date, ZoneId.of("Z")).toString) - override def read(json: JsValue): LocalDateTime = json match { - case JsString(value) => ZonedDateTime.parse(value).toLocalDateTime - case _ => deserializationError(s"Expected date as LocalDateTime, but got $json") - } - } - - implicit def zonedDateTimeFormat = new RootJsonFormat[ZonedDateTime] { - override def write(date: ZonedDateTime): JsString = JsString(date.toString) - override def read(json: JsValue): ZonedDateTime = json match { - case JsString(value) => ZonedDateTime.parse(value) - case _ => deserializationError(s"Expected date as ZonedDateTime, but got $json") - } - } - - implicit def dateFormat = new RootJsonFormat[LocalDate] { - override def write(date: LocalDate): JsString = JsString(date.toString) - override def read(json: JsValue): LocalDate = json match { - case JsString(value) => LocalDate.parse(value) - case _ => deserializationError(s"Expected date as LocalDate, 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 { - case JsNumber(value) => value.toInt - case _ => deserializationError(s"Expected number as Integer, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion.scala deleted file mode 100644 index c4e89f0..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion.scala +++ /dev/null @@ -1,175 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion - -object criterion { - import DefaultJsonProtocol._ - import common._ - - implicit val criterionLabelWriter: RootJsonWriter[CriterionLabel] = new RootJsonWriter[CriterionLabel] { - override def write(obj: CriterionLabel) = JsObject( - "labelId" -> obj.labelId.toJson, - "categoryId" -> obj.categoryId.toJson, - "value" -> obj.value.map { - case true => "Yes" - case false => "No" - }.toJson, - "isDefining" -> obj.isDefining.toJson - ) - } - - def jsValueToCriterionLabel(json: JsValue, criterionId: LongId[Criterion]): CriterionLabel = json match { - case JsObject(fields) => - val labelId = fields - .get("labelId") - .flatMap(_.convertTo[Option[LongId[Label]]]) - - val categoryId = fields - .get("categoryId") - .flatMap(_.convertTo[Option[LongId[LabelCategory]]]) - - val value = fields - .get("value") - .flatMap(_.convertTo[Option[String]]) - .map { - case "Yes" => true - case "No" => false - case other => - deserializationError(s"Unknown `value` of CriterionLabel object: expected `yes` or `no`, but got $other") - } - - val isDefining = fields - .get("isDefining") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"CriterionLabel json object does not contain `isDefining` field: $json")) - - CriterionLabel( - id = LongId(0L), - labelId = labelId, - criterionId = criterionId, - categoryId = categoryId, - value = value, - isDefining = isDefining - ) - - case _ => deserializationError(s"Expected Json Object as CriterionLabel, but got $json") - } - - def applyUpdateToCriterion(json: JsValue, orig: RichCriterion): RichCriterion = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - - val isCompound = fields - .get("isCompound") - .exists(_.convertTo[Boolean]) - - val meta = fields - .get("meta") - .map(_.convertTo[Option[String]].getOrElse("{}")) - .getOrElse(orig.criterion.meta) - - val inclusion = fields - .get("inclusion") - .map(_.convertTo[Option[Boolean]]) - .getOrElse(orig.criterion.inclusion) - - val arms = fields - .get("arms") - .map(_.convertTo[Option[List[LongId[EligibilityArm]]]].getOrElse(List.empty[LongId[EligibilityArm]])) - .getOrElse(orig.armIds) - - val labels = fields - .get("labels") - .map(_.convertTo[Option[List[JsValue]]].getOrElse(List.empty[JsValue])) - .map(_.map(l => jsValueToCriterionLabel(l, orig.criterion.id))) - .getOrElse(orig.labels) - - orig.copy( - criterion = orig.criterion.copy( - meta = meta, - text = text, - isCompound = isCompound, - inclusion = inclusion - ), - armIds = arms, - labels = labels - ) - - case _ => deserializationError(s"Expected Json Object as partial Criterion, but got $json") - } - - implicit val richCriterionFormat: RootJsonFormat[RichCriterion] = new RootJsonFormat[RichCriterion] { - override def write(obj: RichCriterion): JsValue = - JsObject( - "id" -> obj.criterion.id.toJson, - "meta" -> Option(obj.criterion.meta).toJson, - "arms" -> obj.armIds.toJson, - "text" -> obj.criterion.text.toJson, - "isCompound" -> obj.criterion.isCompound.toJson, - "labels" -> obj.labels.map(_.toJson).toJson, - "trialId" -> obj.criterion.trialId.toJson, - "inclusion" -> obj.criterion.inclusion.toJson - ) - - override def read(json: JsValue): RichCriterion = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[Criterion]]]) - - val trialId = fields - .get("trialId") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationError(s"Criterion json object does not contain `trialId` field: $json")) - - val text = fields - .get("text") - .flatMap(_.convertTo[Option[String]]) - - val isCompound = fields - .get("isCompound") - .exists(_.convertTo[Boolean]) - - val meta = fields - .get("meta") - .flatMap(_.convertTo[Option[String]]) - - val inclusion = fields - .get("inclusion") - .flatMap(_.convertTo[Option[Boolean]]) - - val arms = fields - .get("arms") - .map(_.convertTo[Seq[LongId[EligibilityArm]]]) - .getOrElse(Seq.empty[LongId[EligibilityArm]]) - - val labels = fields - .get("labels") - .map(_.convertTo[Seq[JsValue]]) - .map(_.map(l => jsValueToCriterionLabel(l, LongId(0)))) - .getOrElse(Seq.empty[CriterionLabel]) - - RichCriterion( - criterion = Criterion( - id = id.getOrElse(LongId(0)), - trialId = trialId, - text = text, - isCompound = isCompound, - meta = meta.getOrElse(""), - inclusion = inclusion - ), - armIds = arms, - labels = labels - ) - - case _ => deserializationError(s"Expected Json Object as Criterion, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document.scala deleted file mode 100644 index 66e95f3..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document.scala +++ /dev/null @@ -1,221 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDate, LocalDateTime} - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, TextJson} -import xyz.driver.pdsuidomain.entities._ - -object document { - import DefaultJsonProtocol._ - import Document._ - import common._ - - implicit val documentStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "Organized" -> Status.Organized, - "Extracted" -> Status.Extracted, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged, - "Archived" -> Status.Archived - ) - - implicit val requiredTypeFormat: RootJsonFormat[RequiredType] = new EnumJsonFormat[RequiredType]( - "OPN" -> RequiredType.OPN, - "PN" -> RequiredType.PN - ) - - implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat2(Meta.apply) - - implicit val documentTypeFormat: RootJsonFormat[DocumentType] = new RootJsonFormat[DocumentType] { - override def read(json: JsValue): DocumentType = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Document type json object does not contain `name` field: $json")) - - DocumentType - .fromString(name) - .getOrElse(deserializationError(s"Unknown document type: $name")) - - case _ => deserializationError(s"Expected Json Object as Document type, but got $json") - } - - override def write(obj: DocumentType) = - JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) - } - - implicit val fullDocumentMetaFormat = new RootJsonFormat[TextJson[Meta]] { - override def write(obj: TextJson[Meta]): JsValue = obj.content.toJson - override def read(json: JsValue) = TextJson(documentMetaFormat.read(json)) - } - - def applyUpdateToDocument(json: JsValue, orig: Document): Document = json match { - case JsObject(fields) => - val physician = fields - .get("physician") - .map(_.convertTo[String]) - - val typeId = fields - .get("typeId") - .map(_.convertTo[Option[LongId[DocumentType]]]) - .getOrElse(orig.typeId) - - val provider = fields - .get("provider") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.providerName) - - val providerTypeId = fields - .get("providerTypeId") - .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]]]) - .getOrElse(orig.meta) - - val startDate = fields - .get("startDate") - .map(_.convertTo[Option[LocalDate]]) - .getOrElse(orig.startDate) - - val endDate = fields - .get("endDate") - .map(_.convertTo[Option[LocalDate]]) - .getOrElse(orig.endDate) - - orig.copy( - physician = physician.orElse(orig.physician), - typeId = typeId, - providerName = provider, - providerTypeId = providerTypeId, - institutionName = institutionName, - meta = meta, - startDate = startDate, - endDate = endDate - ) - - case _ => deserializationError(s"Expected Json Object as partial Document, but got $json") - } - - implicit val documentFormat: RootJsonFormat[Document] = new RootJsonFormat[Document] { - override def write(document: Document): JsValue = - JsObject( - "id" -> document.id.toJson, - "recordId" -> document.recordId.toJson, - "physician" -> document.physician.toJson, - "typeId" -> document.typeId.toJson, - "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, - "previousStatus" -> document.previousStatus.toJson, - "assignee" -> document.assignee.toJson, - "previousAssignee" -> document.previousAssignee.toJson, - "meta" -> document.meta.toJson, - "lastActiveUser" -> document.lastActiveUserId.toJson, - "lastUpdate" -> document.lastUpdate.toJson, - "labelVersion" -> document.labelVersion.toJson - ) - - override def read(json: JsValue): Document = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[Document]]]) - - val recordId = fields - .get("recordId") - .map(_.convertTo[LongId[MedicalRecord]]) - .getOrElse(deserializationError(s"Document create json object does not contain `recordId` field: $json")) - - val status = fields - .get("status") - .flatMap(_.convertTo[Option[Document.Status]]) - - val previousStatus = fields - .get("previousStatus") - .flatMap(_.convertTo[Option[Document.Status]]) - - val physician = fields - .get("physician") - .flatMap(_.convertTo[Option[String]]) - - val typeId = fields - .get("typeId") - .flatMap(_.convertTo[Option[LongId[DocumentType]]]) - - val requiredType = fields - .get("requiredType") - .flatMap(_.convertTo[Option[Document.RequiredType]]) - - val provider = fields - .get("provider") - .flatMap(_.convertTo[Option[String]]) - - val providerTypeId = fields - .get("providerTypeId") - .flatMap(_.convertTo[Option[LongId[ProviderType]]]) - - val institutionName = fields - .get("institutionName") - .flatMap(_.convertTo[Option[String]]) - - val meta = fields - .get("meta") - .flatMap(_.convertTo[Option[TextJson[Meta]]]) - - val startDate = fields - .get("startDate") - .flatMap(_.convertTo[Option[LocalDate]]) - - val endDate = fields - .get("endDate") - .flatMap(_.convertTo[Option[LocalDate]]) - - val lastUpdate = fields - .get("lastUpdate") - .flatMap(_.convertTo[Option[LocalDateTime]]) - - val labelVersion = fields - .get("labelVersion") - .flatMap(_.convertTo[Option[Int]]) - - Document( - id = id.getOrElse(LongId(0)), - recordId = recordId, - status = status.getOrElse(Document.Status.New), - physician = physician, - typeId = typeId, - startDate = startDate, - endDate = endDate, - providerName = provider, - providerTypeId = providerTypeId, - requiredType = requiredType, - institutionName = institutionName, - meta = meta, - previousStatus = previousStatus, - assignee = None, - previousAssignee = None, - lastActiveUserId = None, - lastUpdate = lastUpdate.getOrElse(LocalDateTime.MIN), - labelVersion = labelVersion.getOrElse(0) - ) - - case _ => deserializationError(s"Expected Json Object as Document, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documenthistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/documenthistory.scala deleted file mode 100644 index 1652f7b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documenthistory.scala +++ /dev/null @@ -1,35 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object documenthistory { - import DefaultJsonProtocol._ - import DocumentHistory._ - import common._ - - implicit val documentStateFormat = new EnumJsonFormat[State]( - "New" -> State.New, - "Extract" -> State.Extract, - "Done" -> State.Done, - "Review" -> State.Review, - "Flag" -> State.Flag, - "Archive" -> State.Archive - ) - - implicit val documentActionFormat = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive, - "PostEvidence" -> Action.PostEvidence, - "CreateDocument" -> Action.CreateDocument, - "ReadDocument" -> Action.ReadDocument - ) - - implicit val documentHistoryFormat: RootJsonFormat[DocumentHistory] = jsonFormat6(DocumentHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documentissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/documentissue.scala deleted file mode 100644 index 037a3ad..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documentissue.scala +++ /dev/null @@ -1,72 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities._ - -object documentissue { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToDocumentIssue(json: JsValue, orig: DocumentIssue): DocumentIssue = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"DocumentIssue json object does not contain `text` field: $json")) - - val archiveRequired = fields - .get("archiveRequired") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"DocumentIssue json object does not contain `archiveRequired` field: $json")) - - val startPage = fields.get("startPage").map(_.convertTo[Option[Double]]) - val endPage = fields.get("endPage").map(_.convertTo[Option[Double]]) - - orig.copy( - text = text, - archiveRequired = archiveRequired, - startPage = startPage.getOrElse(orig.startPage), - endPage = endPage.getOrElse(orig.endPage) - ) - - case _ => deserializationError(s"Expected Json Object as partial DocumentIssue, but got $json") - - } - - def jsValueToDocumentIssue(json: JsValue, - documentId: LongId[Document], - userId: xyz.driver.core.Id[User]): DocumentIssue = - json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"DocumentIssue json object does not contain `text` field: $json")) - - val id = fields.get("id").map(_.convertTo[LongId[DocumentIssue]]) - val startPage = fields.get("startPage").flatMap(_.convertTo[Option[Double]]) - val endPage = fields.get("endPage").flatMap(_.convertTo[Option[Double]]) - - DocumentIssue( - id = id.getOrElse(LongId(0)), - userId = userId, - documentId = documentId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text, - archiveRequired = false, - startPage = startPage, - endPage = endPage - ) - - case _ => deserializationError(s"Expected Json Object as DocumentIssue, but got $json") - } - - implicit val documentIssueFormat: RootJsonFormat[DocumentIssue] = jsonFormat9(DocumentIssue.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibility.scala deleted file mode 100644 index 925ba65..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibility.scala +++ /dev/null @@ -1,108 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json.DefaultJsonProtocol._ -import spray.json._ -import DefaultJsonProtocol._ -import xyz.driver.core.Id -import xyz.driver.core.json._ -import xyz.driver.entities.labels.LabelValue -import xyz.driver.pdsuidomain.entities.eligibility._ - -object eligibility { - import export._ - import xyz.driver.formats.json.assay._ - import xyz.driver.formats.json.common._ - import xyz.driver.formats.json.labels._ - import xyz.driver.formats.json.process._ - import xyz.driver.pdsuidomain.formats.json.document._ - import xyz.driver.pdsuidomain.formats.json.record._ - import xyz.driver.pdsuidomain.formats.json.export._ - - implicit val molecularDocumentFormat: RootJsonFormat[MolecularEvidenceDocument] = jsonFormat7( - MolecularEvidenceDocument) - implicit val clinicalDocumentFormat: RootJsonFormat[ClinicalEvidenceDocument] = jsonFormat7(ClinicalEvidenceDocument) - - implicit val evidenceDocumentFormat: RootJsonFormat[EvidenceDocument] = - GadtJsonFormat.create[EvidenceDocument]("evidenceDocumentType") { - case _: MolecularEvidenceDocument => "Molecular" - case _: ClinicalEvidenceDocument => "Clinical" - } { - case "Molecular" => molecularDocumentFormat - case "Clinical" => clinicalDocumentFormat - } - - implicit object evidenceFormat extends RootJsonFormat[Evidence] { - - override def write(evidence: Evidence): JsValue = { - JsObject( - "evidenceId" -> evidence.evidenceId.toJson, - "evidenceText" -> evidence.evidenceText.toJson, - "labelValue" -> evidence.labelValue.toJson, - "document" -> evidence.document.toJson, - "isPrimaryValue" -> evidence.isPrimaryValue.toJson - ) - } - - override def read(json: JsValue): Evidence = { - json match { - case JsObject(fields) => - val evidenceId = fields - .get("evidenceId") - .map(_.convertTo[Id[Evidence]]) - - val evidenceText = fields - .get("evidenceText") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Evidence json object do not contain 'evidenceText' field: $json")) - - val labelValue = fields - .get("labelValue") - .map(_.convertTo[LabelValue]) - .getOrElse(deserializationError(s"Evidence json object do not contain 'labelValue' field: $json")) - - val isDriverDocument = fields - .get("document") - .flatMap { - case JsObject(fieldMap) => - fieldMap - .get("isDriverDocument") - .map(_.convertTo[Boolean]) - case _ => deserializationError(s"Expected Json Object as 'isDriverDocument', but got $json") - } - .getOrElse(deserializationError(s"Evidence json object do not contain 'document' field: $json")) - - val document = customDocumentParser(isDriverDocument, fields, json) - - val isPrimaryValue = fields - .get("isPrimaryValue") - .map(_.convertTo[Option[Boolean]]) - .getOrElse(deserializationError(s"Evidence json object do not contain 'isPrimaryValue' field: $json")) - - Evidence(evidenceId, evidenceText, labelValue, document, isPrimaryValue) - case _ => deserializationError(s"Expected Json Object as 'Evidence', but got $json") - } - } - - def customDocumentParser(isDriverDocument: Boolean, - fields: Map[String, JsValue], - json: JsValue): EvidenceDocument = { - fields.get("document").fold { deserializationError(s"Expected Json Object as 'Document', but got $json") } { - document => - if (isDriverDocument) document.convertTo[MolecularEvidenceDocument] - else document.convertTo[ClinicalEvidenceDocument] - } - } - } - - implicit def labelWithEvidenceJsonFormat: RootJsonFormat[LabelEvidence] = jsonFormat2(LabelEvidence) - - implicit def labelRankingFormat: RootJsonFormat[LabelMismatchRank] = jsonFormat4(LabelMismatchRank) - implicit def labelRankingsFormat: RootJsonFormat[MismatchRankedLabels] = jsonFormat2(MismatchRankedLabels) - - implicit def matchedPatientFormat: RootJsonFormat[MatchedPatient] = jsonFormat6(MatchedPatient) - - implicit lazy val eligibleTrialFormat: RootJsonFormat[EligibleTrial] = jsonFormat2(EligibleTrial.apply) - implicit lazy val eligibleArmFormat: RootJsonFormat[EligibleArm] = jsonFormat2(EligibleArm.apply) - implicit lazy val eligibleCriterionFormat: RootJsonFormat[EligibleCriterion] = jsonFormat2(EligibleCriterion.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm.scala deleted file mode 100644 index 5827f62..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm.scala +++ /dev/null @@ -1,107 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.patient.CancerType -import xyz.driver.formats.json.patient._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ - -object eligibilityarm { - - import DefaultJsonProtocol._ - import common._ - - private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = { - deserializationError(s"$className json object do not contain '$field' field: $json") - } - - private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = { - deserializationError(s"Expected Json Object as $className, but got $json") - } - - implicit def eligibilityArmWithDiseasesWriter: RootJsonWriter[EligibilityArmWithDiseases] = - new RootJsonWriter[EligibilityArmWithDiseases] { - override def write(obj: EligibilityArmWithDiseases): JsValue = { - JsObject( - "id" -> obj.eligibilityArm.id.toJson, - "name" -> obj.eligibilityArm.name.toJson, - "originalName" -> obj.eligibilityArm.originalName.toJson, - "trialId" -> obj.eligibilityArm.trialId.toJson, - "diseases" -> obj.eligibilityArmDiseases.map(_.disease.toJson).toJson - ) - } - } - - implicit def eligibilityArmWithDiseasesReader: RootJsonReader[EligibilityArmWithDiseases] = { - new RootJsonReader[EligibilityArmWithDiseases] { - implicit val className: String = "create EligibilityArmWithDiseases" - - override def read(json: JsValue): EligibilityArmWithDiseases = { - json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[EligibilityArm]]]) - - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("name", json)) - - val trialId = fields - .get("trialId") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationErrorFieldMessage("trialId", json)) - - val diseases = fields - .get("diseases") - .map(_.convertTo[Seq[String]]) - .getOrElse(deserializationErrorFieldMessage("diseases", json)) - - val eligibilityArm = EligibilityArm( - id = id.getOrElse(LongId(0)), - name = name, - trialId = trialId, - originalName = name - ) - - EligibilityArmWithDiseases( - eligibilityArm, - diseases.map { disease => - val condition = CancerType - .fromString(disease) - .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) - EligibilityArmDisease(eligibilityArm.id, condition) - } - ) - case _ => deserializationErrorEntityMessage(json) - } - } - } - } - - def applyUpdateToEligibilityArmWithDiseases(json: JsValue, - orig: EligibilityArmWithDiseases): EligibilityArmWithDiseases = { - implicit val className: String = "update EligibilityArmWithDiseases" - json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(orig.eligibilityArm.name) - - val diseases = fields - .get("diseases") - .map(_.convertTo[Seq[CancerType]].map(x => EligibilityArmDisease(orig.eligibilityArm.id, x))) - .getOrElse(orig.eligibilityArmDiseases) - - orig.copy( - eligibilityArm = orig.eligibilityArm - .copy(name = name), - eligibilityArmDiseases = diseases - ) - - case _ => deserializationErrorEntityMessage(json) - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala deleted file mode 100644 index 8fb7d03..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala +++ /dev/null @@ -1,127 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json.idFormat -import xyz.driver.entities.labels.Label -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.export.patient._ -import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} -import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm} - -object export { - import DefaultJsonProtocol._ - import common._ - import document._ - import record._ - - private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = { - deserializationError(s"$className json object do not contain '$field' field: $json") - } - - private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = { - deserializationError(s"Expected Json Object as $className, but got $json") - } - - implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] = - jsonFormat5(ExportPatientLabelEvidenceDocument.apply) - - implicit val patientLabelEvidenceFormat: RootJsonFormat[ExportPatientLabelEvidence] = - jsonFormat(ExportPatientLabelEvidence.apply, "evidenceId", "labelValue", "evidenceText", "document") - - implicit val patientLabelFormat: RootJsonFormat[ExportPatientLabel] = - jsonFormat(ExportPatientLabel.apply, "labelId", "evidence") - - implicit val patientWithLabelsFormat: RootJsonFormat[ExportPatientWithLabels] = - jsonFormat(ExportPatientWithLabels.apply, "patientId", "labelVersion", "labels") - - implicit val trialArmFormat: RootJsonFormat[ExportTrialArm] = jsonFormat3(ExportTrialArm.apply) - - implicit val trialLabelCriterionFormat: RootJsonFormat[ExportTrialLabelCriterion] = - new RootJsonFormat[ExportTrialLabelCriterion] { - implicit val className: String = "ExportTrialLabelCriterion" - - override def write(obj: ExportTrialLabelCriterion): JsValue = - JsObject( - "value" -> obj.value - .map { - case true => "Yes" - case false => "No" - } - .getOrElse("Unknown") - .toJson, - "labelId" -> obj.labelId.toJson, - "criterionId" -> obj.criterionId.toJson, - "criterionText" -> obj.criteria.toJson, - "armIds" -> obj.armIds.toJson, - "isCompound" -> obj.isCompound.toJson, - "isDefining" -> obj.isDefining.toJson, - "inclusion" -> obj.inclusion.toJson - ) - - override def read(json: JsValue): ExportTrialLabelCriterion = { - json match { - case JsObject(fields) => - val value = fields - .get("value") - .map(_.convertTo[String]) - .map { - case "Yes" => Option(true) - case "No" => Option(false) - case "Unknown" => Option.empty[Boolean] - } - .getOrElse(deserializationErrorFieldMessage("value", json)) - - val labelId = fields - .get("labelId") - .map(_.convertTo[LongId[Label]]) - .getOrElse(deserializationErrorFieldMessage("labelId", json)) - - val criterionId = fields - .get("criterionId") - .map(_.convertTo[LongId[Criterion]]) - .getOrElse(deserializationErrorFieldMessage("criterionId", json)) - - val criterionText = fields - .get("criterionText") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("criterionText", json)) - - val armIds = fields - .get("armIds") - .map(_.convertTo[Set[LongId[EligibilityArm]]]) - .getOrElse(deserializationErrorFieldMessage("armIds", json)) - - val isCompound = fields - .get("isCompound") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("isCompound", json)) - - val isDefining = fields - .get("isDefining") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("isDefining", json)) - - val inclusion = fields - .get("inclusion") - .flatMap(_.convertTo[Option[Boolean]]) - - ExportTrialLabelCriterion( - criterionId, - value, - labelId, - armIds, - criterionText, - isCompound, - isDefining, - inclusion - ) - - case _ => deserializationErrorEntityMessage(json) - } - } - } - - implicit val trialWithLabelsFormat: RootJsonFormat[ExportTrialWithLabels] = - jsonFormat(ExportTrialWithLabels.apply, "nctId", "trialId", "lastReviewed", "labelVersion", "arms", "criteria") -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/extracteddata.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/extracteddata.scala deleted file mode 100644 index 232bb39..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/extracteddata.scala +++ /dev/null @@ -1,155 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuicommon.domain.{LongId, TextJson} -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData - -object extracteddata { - import DefaultJsonProtocol._ - import ExtractedData._ - import common._ - - implicit val metaKeywordFormat: RootJsonFormat[Meta.Keyword] = jsonFormat4(Meta.Keyword) - implicit val metaTextLayerPositionFormat: RootJsonFormat[Meta.TextLayerPosition] = jsonFormat3( - Meta.TextLayerPosition) - implicit val metaEvidenceFormat: RootJsonFormat[Meta.Evidence] = jsonFormat3(Meta.Evidence) - - implicit val extractedDataMetaFormat: RootJsonFormat[Meta] = jsonFormat2(Meta.apply) - implicit val fullExtractedDataMetaFormat = new RootJsonFormat[TextJson[Meta]] { - override def write(obj: TextJson[Meta]): JsValue = obj.content.toJson - override def read(json: JsValue): TextJson[Meta] = TextJson(extractedDataMetaFormat.read(json)) - } - - implicit val extractedDataLabelWriter: JsonWriter[ExtractedDataLabel] = new JsonWriter[ExtractedDataLabel] { - override def write(label: ExtractedDataLabel): JsObject = { - JsObject( - "id" -> label.labelId.toJson, - "categoryId" -> label.categoryId.toJson, - "value" -> label.value.toJson - ) - } - } - - def applyLabelsForExtractedData(json: JsValue, dataId: LongId[ExtractedData]): ExtractedDataLabel = json match { - case JsObject(fields) => - val labelId = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[Label]]]) - - val categoryId = fields - .get("categoryId") - .flatMap(_.convertTo[Option[LongId[LabelCategory]]]) - - val value = fields - .get("value") - .flatMap(_.convertTo[Option[LabelValue]]) - - ExtractedDataLabel( - id = LongId(0), - dataId = dataId, - labelId = labelId, - categoryId = categoryId, - value = value - ) - - case _ => deserializationError(s"Expected Json Object as ExtractedDataLabel, but got $json") - } - - def applyUpdateToExtractedData(json: JsValue, orig: RichExtractedData): RichExtractedData = json match { - case JsObject(fields) => - val keywordId = fields - .get("keywordId") - .map(_.convertTo[Option[LongId[Keyword]]]) - .getOrElse(orig.extractedData.keywordId) - - val evidence = fields - .get("evidence") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.extractedData.evidenceText) - - val meta = fields - .get("meta") - .map(_.convertTo[Option[TextJson[Meta]]]) - .getOrElse(orig.extractedData.meta) - - val labels = fields - .get("labels") - .map( - _.convertTo[Option[List[JsValue]]] - .getOrElse(List.empty[JsValue]) - .map(l => applyLabelsForExtractedData(l, orig.extractedData.id))) - .getOrElse(orig.labels) - - val extractedData = orig.extractedData.copy( - keywordId = keywordId, - evidenceText = evidence, - meta = meta - ) - - orig.copy( - extractedData = extractedData, - labels = labels - ) - - case _ => deserializationError(s"Expected Json Object as partial ExtractedData, but got $json") - } - - implicit val extractedDataFormat: RootJsonFormat[RichExtractedData] = new RootJsonFormat[RichExtractedData] { - override def write(richData: RichExtractedData): JsValue = - JsObject( - "id" -> richData.extractedData.id.toJson, - "documentId" -> richData.extractedData.documentId.toJson, - "keywordId" -> richData.extractedData.keywordId.toJson, - "evidence" -> richData.extractedData.evidenceText.toJson, - "meta" -> richData.extractedData.meta.toJson, - "labels" -> richData.labels.map(_.toJson).toJson - ) - - override def read(json: JsValue): RichExtractedData = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[ExtractedData]]]) - - val documentId = fields - .get("documentId") - .map(_.convertTo[LongId[Document]]) - .getOrElse( - deserializationError(s"ExtractedData create json object does not contain `documentId` field: $json")) - - val keywordId = fields - .get("keywordId") - .flatMap(_.convertTo[Option[LongId[Keyword]]]) - - val evidence = fields - .get("evidence") - .flatMap(_.convertTo[Option[String]]) - - val meta = fields - .get("meta") - .flatMap(_.convertTo[Option[TextJson[Meta]]]) - - val labels = fields - .get("labels") - .map(_.convertTo[List[JsValue]]) - .getOrElse(List.empty[JsValue]) - .map(l => applyLabelsForExtractedData(l, LongId(0))) - - val extractedData = ExtractedData( - id = id.getOrElse(LongId(0L)), - documentId = documentId, - keywordId = keywordId, - evidenceText = evidence, - meta = meta - ) - - RichExtractedData(extractedData, labels) - - case _ => deserializationError(s"Expected Json Object as ExtractedData, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/hypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/hypothesis.scala deleted file mode 100644 index c5f6141..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/hypothesis.scala +++ /dev/null @@ -1,12 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuidomain.entities._ - -object hypothesis { - import DefaultJsonProtocol._ - import common._ - - implicit val hypothesisFormat: RootJsonFormat[Hypothesis] = jsonFormat4(Hypothesis.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala deleted file mode 100644 index bf528e6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala +++ /dev/null @@ -1,147 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod -import xyz.driver.pdsuidomain.entities._ - -object intervention { - import DefaultJsonProtocol._ - import common._ - - implicit def interventionFormat: RootJsonFormat[InterventionWithArms] = new RootJsonFormat[InterventionWithArms] { - override def write(obj: InterventionWithArms) = - JsObject( - "id" -> obj.intervention.id.toJson, - "name" -> obj.intervention.name.toJson, - "typeId" -> obj.intervention.typeId.toJson, - "dosage" -> obj.intervention.dosage.toJson, - "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 - ) - - override def read(json: JsValue): InterventionWithArms = json match { - case JsObject(fields) => - val trialId = fields - .get("trialId") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationError(s"Intervention json object does not contain `trialId` field: $json")) - - val typeId = fields - .get("typeId") - .flatMap(_.convertTo[Option[LongId[InterventionType]]]) - - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse("") - - val dosage = fields - .get("dosage") - .map(_.convertTo[String]) - - val isActive = fields - .get("isActive") - .exists(_.convertTo[Boolean]) - - val deliveryMethod = fields - .get("deliveryMethod") - .flatMap(_.convertTo[Option[String]]) - - val arms = fields - .get("arms") - .map(_.convertTo[List[LongId[SlotArm]]]) - .map(_ map (x => InterventionArm(armId = x, interventionId = LongId(0L)))) - .getOrElse(List.empty[InterventionArm]) - - InterventionWithArms( - intervention = Intervention( - id = LongId(0L), - trialId = trialId, - name = name, - originalName = name, - typeId = typeId, - originalType = None, - dosage = dosage.getOrElse(""), - originalDosage = dosage.getOrElse(""), - isActive = isActive, - deliveryMethod = deliveryMethod - ), - arms = arms - ) - - case _ => deserializationError(s"Expected Json Object as create Intervention json, but got $json") - } - } - - def applyUpdateToInterventionWithArms(json: JsValue, orig: InterventionWithArms): InterventionWithArms = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - - val typeId = fields - .get("typeId") - .map(_.convertTo[Option[LongId[InterventionType]]]) - - val dosage = fields - .get("dosage") - .map(_.convertTo[String]) - - val isActive = fields - .get("isActive") - .map(_.convertTo[Boolean]) - - val deliveryMethod = fields - .get("deliveryMethod") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.intervention.deliveryMethod) - - val origIntervention = orig.intervention - val arms = fields - .get("arms") - .map(_.convertTo[List[LongId[SlotArm]]].map(x => InterventionArm(x, orig.intervention.id))) - - orig.copy( - intervention = origIntervention.copy( - name = name.getOrElse(origIntervention.name), - typeId = typeId.getOrElse(origIntervention.typeId), - dosage = dosage.getOrElse(origIntervention.dosage), - isActive = isActive.getOrElse(origIntervention.isActive), - deliveryMethod = deliveryMethod - ), - arms = arms.getOrElse(orig.arms) - ) - - case _ => deserializationError(s"Expected Json Object as partial Intervention, but got $json") - } - - implicit def interventionTypeFormat: JsonFormat[InterventionType] = new RootJsonFormat[InterventionType] { - override def read(json: JsValue): InterventionType = 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) - .getOrElse(deserializationError(s"Unknown intervention type: $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/formats/json/listresponse.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/listresponse.scala deleted file mode 100644 index 1e359d6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/listresponse.scala +++ /dev/null @@ -1,45 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json.DefaultJsonProtocol._ -import spray.json._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.formats.json.common._ - -object listresponse { - private val itemsField = "items" - private val metaField = "meta" - - implicit val listResponseMetaFormat: RootJsonFormat[ListResponse.Meta] = jsonFormat4(ListResponse.Meta.apply) - - implicit def listResponseWriter[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 - ) - } - } - - implicit def listResponseReader[T: JsonReader]: RootJsonReader[ListResponse[T]] = - new RootJsonReader[ListResponse[T]] { - override def read(json: JsValue): ListResponse[T] = json match { - case JsObject(fields) => - val items = fields - .get(itemsField) - .map { - case JsArray(elements) => elements.map(_.convertTo[T])(collection.breakOut) - case x => deserializationError(s"Expected Array as JsArray, but got $x") - } - .getOrElse(deserializationError(s"ListResponse json object does not contain `$itemsField` field: $json")) - - val meta = fields - .get(metaField) - .map(_.convertTo[ListResponse.Meta]) - .getOrElse(deserializationError(s"ListResponse json object does not contain `$metaField` field: $json")) - - ListResponse(items, meta) - case _ => deserializationError(s"Expected ListResponse json object, but got $json") - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala deleted file mode 100644 index 774a1ff..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala +++ /dev/null @@ -1,118 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDate, LocalDateTime} - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.entities.clinic.TestOrder -import xyz.driver.entities.common.FullName -import xyz.driver.entities.patient.CancerType -import xyz.driver.formats.json.common._ -import xyz.driver.formats.json.patient._ -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.entities._ - -object patient { - import DefaultJsonProtocol._ - import Patient._ - import common._ - - implicit val patientStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "Verified" -> Status.Verified, - "Reviewed" -> Status.Reviewed, - "Curated" -> Status.Curated, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged - ) - - implicit val patientFormat: RootJsonFormat[Patient] = new RootJsonFormat[Patient] { - override def write(patient: Patient): JsValue = - JsObject( - "id" -> patient.id.toJson, - "status" -> patient.status.toJson, - "name" -> patient.name.toJson, - "dob" -> patient.dob.toJson, - "assignee" -> patient.assignee.toJson, - "previousStatus" -> patient.previousStatus.toJson, - "previousAssignee" -> patient.previousAssignee.toJson, - "lastActiveUser" -> patient.lastActiveUserId.toJson, - "lastUpdate" -> patient.lastUpdate.toJson, - "disease" -> patient.disease.toJson, - "orderId" -> patient.orderId.toJson - ) - - override def read(json: JsValue): Patient = { - json match { - case JsObject(fields) => - val id = fields - .get("id") - .map(_.convertTo[UuidId[Patient]]) - .getOrElse(deserializationError(s"Patient create json object does not contain `id` field: $json")) - - val status = fields - .get("status") - .map(_.convertTo[Patient.Status]) - .getOrElse(deserializationError(s"Patient create json object does not contain `status` field: $json")) - - val name = fields - .get("name") - .map(_.convertTo[FullName[Patient]]) - .getOrElse(deserializationError(s"Patient create json object does not contain `name` field: $json")) - - val dob = fields - .get("dob") - .map(_.convertTo[LocalDate]) - .getOrElse(deserializationError(s"Patient create json object does not contain `dob` field: $json")) - - val assignee = fields - .get("assignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - - val previousStatus = fields - .get("previousStatus") - .flatMap(_.convertTo[Option[Patient.Status]]) - - val previousAssignee = fields - .get("previousAssignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - - val lastActiveUser = fields - .get("lastActiveUser") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - - val disease = fields - .get("disease") - .map(_.convertTo[CancerType]) - .getOrElse(deserializationError(s"Patient create json object does not contain `disease` field: $json")) - - val orderId = fields - .get("orderId") - .map(_.convertTo[xyz.driver.core.Id[TestOrder]]) - .getOrElse(deserializationError(s"Patient create json object does not contain `orderId` field: $json")) - - val lastUpdate = fields - .get("lastUpdate") - .map(_.convertTo[LocalDateTime]) - .getOrElse(deserializationError(s"Patient create json object does not contain `lastUpdate` field: $json")) - - Patient(id, - status, - name, - dob, - assignee, - previousStatus, - previousAssignee, - lastActiveUser, - isUpdateRequired = false, - disease, - orderId, - lastUpdate) - - case _ => deserializationError(s"Expected Json Object as Trial, but got $json") - } - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala deleted file mode 100644 index 035310b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala +++ /dev/null @@ -1,65 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.{Label, LabelValue} -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities._ - -object patientcriterion { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToPatientCriterion(json: JsValue, orig: PatientCriterion): PatientCriterion = json match { - case JsObject(fields) => - val eligibilityStatus = fields - .get("eligibilityStatus") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.eligibilityStatus) - - val verifiedEligibilityStatus = fields - .get("verifiedEligibilityStatus") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.verifiedEligibilityStatus) - - orig.copy( - eligibilityStatus = eligibilityStatus, - verifiedEligibilityStatus = verifiedEligibilityStatus - ) - - case _ => deserializationError(s"Expected Json Object as partial PatientCriterion, but got $json") - } - - implicit val draftPatientCriterionFormat: RootJsonFormat[DraftPatientCriterion] = jsonFormat3( - DraftPatientCriterion.apply) - implicit val draftPatientCriterionListReader = new JsonReader[List[DraftPatientCriterion]] { - override def read(json: JsValue) = json.convertTo[List[JsValue]].map(_.convertTo[DraftPatientCriterion]) - } - - implicit val patientCriterionFormat: RootJsonFormat[PatientCriterion] = jsonFormat14(PatientCriterion.apply) - implicit val patientCriterionArmFormat: RootJsonFormat[PatientCriterionArm] = jsonFormat3(PatientCriterionArm.apply) - - implicit val richPatientCriterionFormat: RootJsonFormat[RichPatientCriterion] = - new RootJsonFormat[RichPatientCriterion] { - override def read(json: JsValue): RichPatientCriterion = { - val fields = json.asJsObject.fields - val labelId = fields.getOrElse("labelId", deserializationError("field 'labelId' is missing")) - val arms = fields.getOrElse("armList", deserializationError("field 'arms' is missing")) - RichPatientCriterion( - json.convertTo[PatientCriterion], - labelId.convertTo[LongId[Label]], - arms.convertTo[List[PatientCriterionArm]] - ) - } - override def write(obj: RichPatientCriterion): JsValue = { - JsObject( - obj.patientCriterion.toJson.asJsObject.fields ++ - Map( - "labelId" -> obj.labelId.toJson, - "armList" -> obj.armList.toJson - ) - ) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientdefiningcriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientdefiningcriteria.scala deleted file mode 100644 index a67115c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientdefiningcriteria.scala +++ /dev/null @@ -1,18 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.entities.PatientLabel - -object patientdefiningcriteria { - import common._ - - implicit val patientLabelDefiningCriteriaWriter: RootJsonWriter[PatientLabel] = new RootJsonWriter[PatientLabel] { - override def write(obj: PatientLabel) = - JsObject( - "id" -> obj.id.toJson, - "value" -> obj.verifiedPrimaryValue.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala deleted file mode 100644 index d719c5c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala +++ /dev/null @@ -1,39 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.entities._ - -object patienteligibletrial { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToTrialArmGroup(json: JsValue, orig: PatientTrialArmGroupView): PatientTrialArmGroupView = - json match { - case JsObject(fields) => - val isVerified = fields - .get("isVerified") - .map(_.convertTo[Boolean]) - .getOrElse(orig.isVerified) - - orig.copy(isVerified = isVerified) - - case _ => deserializationError(s"Expected Json Object as partial PatientTrialArmGroupView, but got $json") - } - - implicit val patientEligibleTrialWriter: RootJsonWriter[RichPatientEligibleTrial] = - new RootJsonWriter[RichPatientEligibleTrial] { - override def write(obj: RichPatientEligibleTrial) = - JsObject( - "id" -> obj.group.id.toJson, - "patientId" -> obj.group.patientId.toJson, - "trialId" -> obj.group.trialId.toJson, - "trialTitle" -> obj.trial.title.toJson, - "arms" -> obj.arms.map(_.armName).toJson, - "hypothesisId" -> obj.trial.hypothesisId.toJson, - "verifiedEligibilityStatus" -> obj.group.verifiedEligibilityStatus.toJson, - "isVerified" -> obj.group.isVerified.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthistory.scala deleted file mode 100644 index c9cdc63..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthistory.scala +++ /dev/null @@ -1,30 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object patienthistory { - import DefaultJsonProtocol._ - import PatientHistory._ - import common._ - - implicit val patientStateFormat: RootJsonFormat[State] = new EnumJsonFormat[State]( - "Verify" -> State.Verify, - "Curate" -> State.Curate, - "Review" -> State.Review, - "Flag" -> State.Flag - ) - - implicit val patientActionFormat: RootJsonFormat[Action] = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive - ) - - implicit val patientHistoryFormat: RootJsonFormat[PatientHistory] = jsonFormat6(PatientHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala deleted file mode 100644 index da991a4..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala +++ /dev/null @@ -1,35 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuidomain.entities._ - -object patienthypothesis { - import DefaultJsonProtocol._ - import common._ - import xyz.driver.core.json._ - - def applyUpdateToPatientHypothesis(json: JsValue, orig: PatientHypothesis): PatientHypothesis = json match { - case JsObject(fields) => - val rationale = if (fields.contains("rationale")) { - fields.get("rationale").map(_.convertTo[String]) - } else orig.rationale - - orig.copy(rationale = rationale) - - case _ => deserializationError(s"Expected Json Object as partial PatientHypothesis, but got $json") - } - - 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/patientissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala deleted file mode 100644 index ed05325..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala +++ /dev/null @@ -1,58 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuidomain.entities._ - -object patientissue { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToPatientIssue(json: JsValue, orig: PatientIssue): PatientIssue = { - json.asJsObject.getFields("text", "archiveRequired") match { - case Seq(text, archiveRequired) => - orig.copy( - text = text.convertTo[String], - archiveRequired = archiveRequired.convertTo[Boolean] - ) - - case _ => deserializationError(s"Expected Json Object as partial PatientIssue, but got $json") - } - } - - def jsValueToPatientIssue(json: JsValue, - patientId: UuidId[Patient], - userId: xyz.driver.core.Id[User]): PatientIssue = { - json.asJsObject.getFields("text") match { - case Seq(text) => - PatientIssue( - id = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[PatientIssue]]]).getOrElse(LongId(0)), - userId = userId, - patientId = patientId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text.convertTo[String], - archiveRequired = false - ) - - case _ => deserializationError(s"Expected Json Object as PatientIssue, but got $json") - } - - } - - implicit val patientIssueWriter: RootJsonWriter[PatientIssue] = new RootJsonWriter[PatientIssue] { - override def write(obj: PatientIssue) = JsObject( - "id" -> obj.id.toJson, - "text" -> obj.text.toJson, - "lastUpdate" -> obj.lastUpdate.toJson, - "userId" -> obj.userId.toJson, - "isDraft" -> obj.isDraft.toJson, - "archiveRequired" -> obj.archiveRequired.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientlabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientlabel.scala deleted file mode 100644 index 615b3a2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientlabel.scala +++ /dev/null @@ -1,65 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.LabelValue -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.formats.json.record._ -import xyz.driver.pdsuidomain.formats.json.document._ - -object patientlabel { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToPatientLabel(json: JsValue, orig: PatientLabel): PatientLabel = json match { - case JsObject(fields) => - val primaryValue = fields - .get("primaryValue") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.primaryValue) - - val verifiedPrimaryValue = fields - .get("verifiedPrimaryValue") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.verifiedPrimaryValue) - - orig.copy( - primaryValue = primaryValue, - verifiedPrimaryValue = verifiedPrimaryValue - ) - - case _ => deserializationError(s"Expected Json Object as PatientLabel, but got $json") - } - - implicit val patientLabelFormat: RootJsonFormat[PatientLabel] = jsonFormat8(PatientLabel.apply) - - implicit val richPatientLabelFormat: RootJsonFormat[RichPatientLabel] = new RootJsonFormat[RichPatientLabel] { - override def read(json: JsValue): RichPatientLabel = { - val isVerified = - json.asJsObject.fields.getOrElse("isVerified", deserializationError("isVerified field is missing")) - RichPatientLabel(json.convertTo[PatientLabel], isVerified.convertTo[Boolean]) - } - override def write(obj: RichPatientLabel): JsValue = { - val labelFields = obj.patientLabel.toJson.asJsObject.fields - JsObject(labelFields ++ Map("isVerified" -> obj.isVerified.toJson)) - } - } - - implicit val patientLabelEvidenceWriter: RootJsonWriter[PatientLabelEvidenceView] = - new RootJsonWriter[PatientLabelEvidenceView] { - override def write(evidence: PatientLabelEvidenceView): JsValue = - JsObject( - "id" -> evidence.id.toJson, - "value" -> evidence.value.toJson, - "evidenceText" -> evidence.evidenceText.toJson, - "documentId" -> evidence.documentId.toJson, - "evidenceId" -> evidence.evidenceId.toJson, - "reportId" -> evidence.reportId.toJson, - "documentType" -> evidence.documentType.toJson, - "date" -> evidence.date.toJson, - "providerType" -> evidence.providerType.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala deleted file mode 100644 index d3fe2c9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala +++ /dev/null @@ -1,213 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.Id -import xyz.driver.core.json._ -import xyz.driver.entities.clinic.ClinicalRecord -import xyz.driver.pdsuicommon.domain.{LongId, TextJson, UuidId} -import xyz.driver.pdsuidomain.entities.MedicalRecord.Meta._ -import xyz.driver.pdsuidomain.entities._ - -object record { - import DefaultJsonProtocol._ - import MedicalRecord._ - import common._ - - implicit val recordStatusFormat: EnumJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "Cleaned" -> Status.Cleaned, - "Reviewed" -> Status.Reviewed, - "Organized" -> Status.Organized, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged, - "Archived" -> Status.Archived - ) - - implicit val providerTypeFormat: RootJsonFormat[ProviderType] = new RootJsonFormat[ProviderType] { - override def read(json: JsValue): ProviderType = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Provider type json object does not contain `name` field: $json")) - - ProviderType - .fromString(name) - .getOrElse(deserializationError(s"Unknown provider type: $name")) - - case _ => deserializationError(s"Expected Json Object as Provider type, but got $json") - } - - override def write(obj: ProviderType) = - JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) - } - - implicit val duplicateMetaFormat: RootJsonFormat[Duplicate] = new RootJsonFormat[Duplicate] { - override def write(obj: Duplicate) = - JsObject( - "type" -> "duplicate".toJson, - "startPage" -> obj.startPage.toJson, - "endPage" -> obj.endPage.toJson, - "startOriginalPage" -> obj.startOriginalPage.toJson, - "endOriginalPage" -> obj.endOriginalPage.toJson - ) - - override def read(json: JsValue): Duplicate = json match { - case JsObject(fields) => - val startPage = fields - .get("startPage") - .map(_.convertTo[Double]) - .getOrElse(deserializationError(s"Duplicate meta json object does not contain `startPage` field: $json")) - - val endPage = fields - .get("endPage") - .map(_.convertTo[Double]) - .getOrElse(deserializationError(s"Duplicate meta json object does not contain `endPage` field: $json")) - - val startOriginalPage = fields - .get("startOriginalPage") - .map(_.convertTo[Double]) - .getOrElse( - deserializationError(s"Duplicate meta json object does not contain `startOriginalPage` field: $json")) - - val endOriginalPage = fields - .get("endOriginalPage") - .flatMap(_.convertTo[Option[Double]]) - - Duplicate( - startPage = startPage, - endPage = endPage, - startOriginalPage = startOriginalPage, - endOriginalPage = endOriginalPage - ) - - case _ => deserializationError(s"Expected JsObject as Duplicate meta of medical record, but got $json") - } - } - - implicit val reorderMetaFormat: RootJsonFormat[Reorder] = new RootJsonFormat[Reorder] { - override def write(obj: Reorder) = - JsObject("type" -> "reorder".toJson, "items" -> obj.items.toJson) - - override def read(json: JsValue): Reorder = json match { - case JsObject(fields) => - val items = fields - .get("items") - .map(_.convertTo[Seq[Int]]) - .getOrElse(deserializationError(s"Reorder meta json object does not contain `items` field: $json")) - - Reorder(items) - - case _ => deserializationError(s"Expected JsObject as Reorder meta of medical record, but got $json") - } - } - - implicit val rotateMetaFormat: RootJsonFormat[Rotation] = new RootJsonFormat[Rotation] { - override def write(obj: Rotation) = - JsObject("type" -> "rotation".toJson, "items" -> obj.items.toJson) - - override def read(json: JsValue): Rotation = json match { - case JsObject(fields) => - val items = fields - .get("items") - .map(_.convertTo[Map[String, Int]]) - .getOrElse(deserializationError(s"Rotation meta json object does not contain `items` field: $json")) - - Rotation(items = items) - - case _ => deserializationError(s"Expected JsObject as Rotation meta of medical record, but got $json") - } - } - - implicit val recordMetaTypeFormat: GadtJsonFormat[MedicalRecord.Meta] = { - GadtJsonFormat.create[Meta]("type")({ case m => m.metaType }) { - case "duplicate" => duplicateMetaFormat - case "reorder" => reorderMetaFormat - case "rotation" => rotateMetaFormat - } - } - - implicit val recordMetaFormat: RootJsonFormat[TextJson[List[Meta]]] = new RootJsonFormat[TextJson[List[Meta]]] { - override def write(obj: TextJson[List[Meta]]): JsArray = JsArray(obj.content.map(_.toJson).toVector) - override def read(json: JsValue): TextJson[List[Meta]] = json match { - case JsArray(values) => TextJson[List[Meta]](values.map(_.convertTo[Meta]).toList) - case _ => deserializationError(s"Expected array as Meta, but got $json") - } - } - - implicit val recordFormat: RootJsonFormat[MedicalRecord] = - new RootJsonFormat[MedicalRecord] { - override def write(record: MedicalRecord): JsValue = - JsObject( - "id" -> record.id.toJson, - "patientId" -> record.patientId.toJson, - "caseId" -> record.caseId.toJson, - "disease" -> record.disease.toJson, - "physician" -> record.physician.toJson, - "status" -> record.status.toJson, - "previousStatus" -> record.previousStatus.toJson, - "assignee" -> record.assignee.toJson, - "previousAssignee" -> record.previousAssignee.toJson, - "requestId" -> record.requestId.toJson, - "meta" -> record.meta.getOrElse(TextJson[List[Meta]](List.empty)).toJson, - "lastActiveUser" -> record.lastActiveUserId.toJson, - "lastUpdate" -> record.lastUpdate.toJson, - "totalPages" -> record.totalPages.toJson - ) - - override def read(json: JsValue): MedicalRecord = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[MedicalRecord]]]) - - val disease = fields - .get("disease") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"MedicalRecord json object does not contain `disease` field: $json")) - - val patientId = fields - .get("patientId") - .map(_.convertTo[UuidId[Patient]]) - .getOrElse(deserializationError(s"MedicalRecord json object does not contain `patientId` field: $json")) - - val requestId = fields - .get("requestId") - .map(_.convertTo[Id[ClinicalRecord]]) - .getOrElse(deserializationError(s"MedicalRecord json object does not contain `requestId` field: $json")) - - MedicalRecord( - id = id.getOrElse(LongId(0)), - status = MedicalRecord.Status.New, - previousStatus = None, - assignee = None, - previousAssignee = None, - lastActiveUserId = None, - patientId = patientId, - requestId = requestId, - disease = disease, - caseId = None, - physician = None, - meta = None, - lastUpdate = LocalDateTime.now(), - totalPages = 0 - ) - - case _ => deserializationError(s"Expected Json Object as MedicalRecord, but got $json") - } - } - - def applyUpdateToMedicalRecord(json: JsValue, orig: MedicalRecord): MedicalRecord = json match { - case JsObject(fields) => - val meta = fields - .get("meta") - .map(_.convertTo[Option[TextJson[List[Meta]]]]) - .getOrElse(orig.meta) - orig.copy(meta = meta) - - case _ => deserializationError(s"Expected Json Object as partial MedicalRecord, but got $json") - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordhistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordhistory.scala deleted file mode 100644 index be9dae9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordhistory.scala +++ /dev/null @@ -1,43 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object recordhistory { - import DefaultJsonProtocol._ - import MedicalRecordHistory._ - import common._ - - implicit val recordStateFormat = new EnumJsonFormat[State]( - "New" -> State.New, - "Clean" -> State.Clean, - "Organize" -> State.Organize, - "Review" -> State.Review, - "Done" -> State.Done, - "Flag" -> State.Flag, - "Archive" -> State.Archive - ) - - implicit val recordActionFormat = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive, - "SaveDuplicate" -> Action.SaveDuplicate, - "SaveReorder" -> Action.SaveReorder, - "SaveRotation" -> Action.SaveRotation, - "DeleteDuplicate" -> Action.DeleteDuplicate, - "DeleteReorder" -> Action.DeleteReorder, - "DeleteRotation" -> Action.DeleteRotation, - "CreateDocument" -> Action.CreateDocument, - "DeleteDocument" -> Action.DeleteDocument, - "CreateRecord" -> Action.CreateRecord, - "ReadRecord" -> Action.ReadRecord - ) - - implicit val recordHistoryFormat: RootJsonFormat[MedicalRecordHistory] = jsonFormat6(MedicalRecordHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordissue.scala deleted file mode 100644 index e7f2f65..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordissue.scala +++ /dev/null @@ -1,72 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities._ - -object recordissue { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToRecordIssue(json: JsValue, orig: MedicalRecordIssue): MedicalRecordIssue = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"MedicalRecordIssue json object does not contain `text` field: $json")) - - val archiveRequired = fields - .get("archiveRequired") - .map(_.convertTo[Boolean]) - .getOrElse( - deserializationError(s"MedicalRecordIssue json object does not contain `archiveRequired` field: $json")) - - val startPage = fields.get("startPage").map(_.convertTo[Double]) - val endPage = fields.get("endPage").map(_.convertTo[Double]) - - orig.copy( - text = text, - archiveRequired = archiveRequired, - startPage = startPage, - endPage = endPage - ) - - case _ => deserializationError(s"Expected Json Object as partial MedicalRecordIssue, but got $json") - - } - - def jsValueToRecordIssue(json: JsValue, - recordId: LongId[MedicalRecord], - userId: xyz.driver.core.Id[User]): MedicalRecordIssue = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"MedicalRecordIssue json object does not contain `text` field: $json")) - - val id = fields.get("id").flatMap(_.convertTo[Option[LongId[MedicalRecordIssue]]]).getOrElse(LongId(0)) - val startPage = fields.get("startPage").map(_.convertTo[Double]) - val endPage = fields.get("endPage").map(_.convertTo[Double]) - - MedicalRecordIssue( - id = id, - userId = userId, - recordId = recordId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text, - archiveRequired = false, - startPage = startPage, - endPage = endPage - ) - - case _ => deserializationError(s"Expected Json Object as MedicalRecordIssue, but got $json") - } - - implicit val recordIssueFormat: RootJsonFormat[MedicalRecordIssue] = jsonFormat9(MedicalRecordIssue.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm.scala deleted file mode 100644 index 60d6521..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm.scala +++ /dev/null @@ -1,44 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.{SlotArm, Trial} - -object slotarm { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToArm(json: JsValue, orig: SlotArm): SlotArm = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Arm json object does not contain `name` field: $json")) - orig.copy(name = name) - - case _ => deserializationError(s"Expected Json Object as partial Arm, but got $json") - } - - implicit def slotArmFormat: RootJsonFormat[SlotArm] = new RootJsonFormat[SlotArm] { - override def write(obj: SlotArm): JsValue = - JsObject( - "id" -> obj.id.toJson, - "name" -> obj.name.toJson, - "originalName" -> obj.originalName.toJson, - "trialId" -> obj.trialId.toJson - ) - - override def read(json: JsValue): SlotArm = json.asJsObject.getFields("trialId", "name") match { - case Seq(trialId, name) => - SlotArm( - id = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[SlotArm]]]).getOrElse(LongId(0)), - name = name.convertTo[String], - trialId = trialId.convertTo[StringId[Trial]], - originalName = name.convertTo[String] - ) - - case _ => deserializationError(s"Expected Json Object as Arm, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign.scala deleted file mode 100644 index 60c7e70..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign.scala +++ /dev/null @@ -1,29 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuidomain.entities._ - -object studydesign { - import DefaultJsonProtocol._ - import common._ - - implicit val studyDesignFormat: RootJsonFormat[StudyDesign] = new RootJsonFormat[StudyDesign] { - override def read(json: JsValue): StudyDesign = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Study design json object does not contain `name` field: $json")) - - StudyDesign - .fromString(name) - .getOrElse(deserializationError(s"Unknown study design: $name")) - - case _ => deserializationError(s"Expected Json Object as Study design, but got $json") - } - - override def write(obj: StudyDesign) = - JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala deleted file mode 100644 index cdc52d9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala +++ /dev/null @@ -1,187 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDateTime, ZoneId, ZonedDateTime} - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities._ - -object trial { - import DefaultJsonProtocol._ - import Trial._ - import common._ - - implicit val trialStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "ReviewSummary" -> Status.ReviewSummary, - "Summarized" -> Status.Summarized, - "PendingUpdate" -> Status.PendingUpdate, - "Update" -> Status.Update, - "ReviewCriteria" -> Status.ReviewCriteria, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged, - "Archived" -> Status.Archived - ) - - implicit val trialFormat: RootJsonFormat[Trial] = new RootJsonFormat[Trial] { - override def write(obj: Trial) = - JsObject( - "id" -> obj.id.toJson, - "externalid" -> obj.externalId.toJson, - "lastUpdate" -> ZonedDateTime.of(obj.lastUpdate, ZoneId.of("Z")).toJson, - "status" -> obj.status.toJson, - "assignee" -> obj.assignee.toJson, - "previousStatus" -> obj.previousStatus.toJson, - "previousAssignee" -> obj.previousAssignee.toJson, - "lastActiveUser" -> obj.lastActiveUserId.toJson, - "phase" -> obj.phase.toJson, - "hypothesisId" -> obj.hypothesisId.toJson, - "studyDesignId" -> obj.studyDesignId.toJson, - "originalStudyDesignId" -> obj.originalStudyDesign.toJson, - "isPartner" -> obj.isPartner.toJson, - "overview" -> obj.overview.toJson, - "overviewTemplate" -> obj.overviewTemplate.toJson, - "isUpdated" -> obj.isUpdated.toJson, - "title" -> obj.title.toJson, - "originalTitle" -> obj.originalTitle.toJson - ) - - override def read(json: JsValue): Trial = { - json match { - case JsObject(fields) => - val id = fields - .get("id") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationError(s"Trial create json object does not contain `id` field: $json")) - val externalid = fields - .get("externalid") - .map(_.convertTo[UuidId[Trial]]) - .getOrElse(deserializationError(s"Trial create json object does not contain `externalid` field: $json")) - val status = fields - .get("status") - .map(_.convertTo[Trial.Status]) - .getOrElse(deserializationError(s"Trial create json object does not contain `status` field: $json")) - val assignee = fields - .get("assignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - val previousStatus = fields - .get("previousStatus") - .flatMap(_.convertTo[Option[Trial.Status]]) - val previousAssignee = fields - .get("previousAssignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - val lastActiveUser = fields - .get("lastActiveUser") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - val lastUpdate = fields - .get("lastUpdate") - .map(_.convertTo[LocalDateTime]) - .getOrElse(deserializationError(s"Trial create json object does not contain `lastUpdate` field: $json")) - val phase = fields - .get("phase") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Trial create json object does not contain `phase` field: $json")) - val hypothesisId = fields - .get("hypothesisId") - .flatMap(_.convertTo[Option[UuidId[Hypothesis]]]) - val studyDesignId = fields - .get("studyDesignId") - .flatMap(_.convertTo[Option[LongId[StudyDesign]]]) - val originalStudyDesignId = fields - .get("originalStudyDesignId") - .flatMap(_.convertTo[Option[String]]) - val isPartner = fields - .get("isPartner") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"Trial create json object does not contain `isPartner` field: $json")) - val overview = fields - .get("overview") - .flatMap(_.convertTo[Option[String]]) - val overviewTemplate = fields - .get("overviewTemplate") - .map(_.convertTo[String]) - .getOrElse( - deserializationError(s"Trial create json object does not contain `overviewTemplate` field: $json")) - val isUpdated = fields - .get("isUpdated") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"Trial create json object does not contain `isUpdated` field: $json")) - val title = fields - .get("title") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Trial create json object does not contain `title` field: $json")) - val originalTitle = fields - .get("originalTitle") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Trial create json object does not contain `originalTitle` field: $json")) - - Trial( - id, - externalid, - status, - assignee, - previousStatus, - previousAssignee, - lastActiveUser, - lastUpdate, - phase, - hypothesisId, - studyDesignId, - originalStudyDesignId, - isPartner, - overview, - overviewTemplate, - isUpdated, - title, - originalTitle - ) - - case _ => deserializationError(s"Expected Json Object as Trial, but got $json") - } - } - } - - def applyUpdateToTrial(json: JsValue, orig: Trial): Trial = json match { - case JsObject(fields) => - val hypothesisId = fields - .get("hypothesisId") - .map(_.convertTo[Option[UuidId[Hypothesis]]]) - .getOrElse(orig.hypothesisId) - - val studyDesignId = fields - .get("studyDesignId") - .map(_.convertTo[Option[LongId[StudyDesign]]]) - .getOrElse(orig.studyDesignId) - - val overview = fields - .get("overview") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.overview) - - val title = fields - .get("title") - .map(_.convertTo[Option[String]].getOrElse("")) - .getOrElse(orig.title) - - val originalTitle = fields - .get("originalTitle") - .flatMap(_.convertTo[Option[String]]) - .getOrElse(orig.originalTitle) - - orig.copy( - hypothesisId = hypothesisId, - studyDesignId = studyDesignId, - overview = overview, - title = title, - originalTitle = originalTitle - ) - - case _ => deserializationError(s"Expected Json Object as Trial, but got $json") - } - - implicit val trialCreationRequestFormat: RootJsonFormat[TrialCreationRequest] = - jsonFormat3(TrialCreationRequest.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialhistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialhistory.scala deleted file mode 100644 index f71ec12..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialhistory.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object trialhistory { - import DefaultJsonProtocol._ - import TrialHistory._ - import common._ - - implicit val trialStateFormat = new EnumJsonFormat[State]( - "Summarize" -> State.Summarize, - "Criteriarize" -> State.Criteriarize, - "Review" -> State.Review, - "ReviewSummary" -> State.ReviewSummary, - "ReviewCriteria" -> State.ReviewCriteria, - "Flag" -> State.Flag - ) - - implicit val trialActionFormat = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive - ) - - implicit val trialHistoryFormat: RootJsonFormat[TrialHistory] = jsonFormat7(TrialHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialissue.scala deleted file mode 100644 index 79882c2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialissue.scala +++ /dev/null @@ -1,134 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json.{RootJsonReader, _} -import xyz.driver.core.{Id, auth} -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ - -object trialissue { - - import DefaultJsonProtocol._ - import common._ - - private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = { - deserializationError(s"$className json object do not contain '$field' field: $json") - } - - private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = { - deserializationError(s"Expected Json Object as $className, but got $json") - } - - def applyUpdateToTrialIssue(json: JsValue, orig: TrialIssue): TrialIssue = { - json.asJsObject.getFields("text", "evidence", "archiveRequired", "meta") match { - case Seq(text, evidence, archiveRequired, meta) => - orig.copy( - text = text.convertTo[String], - evidence = evidence.convertTo[String], - archiveRequired = archiveRequired.convertTo[Boolean], - meta = meta.convertTo[String] - ) - - case _ => deserializationError(s"Expected Json Object as partial TrialIssue, but got $json") - } - } - - def jsValueToTrialIssue(json: JsValue, trialId: StringId[Trial], userId: xyz.driver.core.Id[User]): TrialIssue = { - json.asJsObject.getFields("text", "evidence", "meta") match { - case Seq(text, evidence, meta) => - TrialIssue( - id = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[TrialIssue]]]).getOrElse(LongId(0)), - userId = userId, - trialId = trialId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text.convertTo[String], - evidence = evidence.convertTo[String], - archiveRequired = false, - meta = meta.convertTo[String] - ) - - case _ => deserializationError(s"Expected Json Object as TrialIssue, but got $json") - } - - } - - implicit val trialIssueWriter = new RootJsonWriter[TrialIssue] { - override def write(obj: TrialIssue) = JsObject( - "id" -> obj.id.toJson, - "text" -> obj.text.toJson, - "lastUpdate" -> obj.lastUpdate.toJson, - "userId" -> obj.userId.toJson, - "isDraft" -> obj.isDraft.toJson, - "evidence" -> obj.evidence.toJson, - "archiveRequired" -> obj.archiveRequired.toJson, - "meta" -> obj.meta.toJson - ) - } - - def trialIssueReader(trialId: StringId[Trial]): RootJsonReader[TrialIssue] = - new RootJsonReader[TrialIssue] { - implicit val className: String = "TrialIssue" - - override def read(json: JsValue): TrialIssue = json match { - case JsObject(fields) => - val id = fields - .get("id") - .map(_.convertTo[LongId[TrialIssue]]) - .getOrElse(deserializationErrorFieldMessage("id", json)) - - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("text", json)) - - val lastUpdate = fields - .get("lastUpdate") - .map(_.convertTo[LocalDateTime]) - .getOrElse(deserializationErrorFieldMessage("lastUpdate", json)) - - val userId = fields - .get("userId") - .map(_.convertTo[Id[auth.User]]) - .getOrElse(deserializationErrorFieldMessage("userId", json)) - - val isDraft = fields - .get("isDraft") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("isDraft", json)) - - val evidence = fields - .get("evidence") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("evidence", json)) - - val archiveRequired = fields - .get("archiveRequired") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("archiveRequired", json)) - - val meta = fields - .get("meta") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("meta", json)) - - TrialIssue( - id = id, - userId = userId, - trialId = trialId, - lastUpdate = lastUpdate, - isDraft = isDraft, - text = text, - evidence = evidence, - archiveRequired = archiveRequired, - meta = meta - ) - - case _ => deserializationErrorEntityMessage(json) - } - } - -} |