diff options
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats')
9 files changed, 216 insertions, 72 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala index 732bcad..8da719c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala @@ -1,6 +1,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats 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 @@ -29,7 +30,7 @@ object criterion { val categoryId = fields .get("categoryId") - .map(_.convertTo[LongId[Category]]) + .map(_.convertTo[LongId[LabelCategory]]) val value = fields .get("value") @@ -72,6 +73,11 @@ object criterion { .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[Arm]]]].getOrElse(List.empty[LongId[Arm]])) @@ -87,7 +93,8 @@ object criterion { criterion = orig.criterion.copy( meta = meta, text = text, - isCompound = isCompound + isCompound = isCompound, + inclusion = inclusion ), armIds = arms, labels = labels @@ -105,7 +112,8 @@ object criterion { "text" -> obj.criterion.text.toJson, "isCompound" -> obj.criterion.isCompound.toJson, "labels" -> obj.labels.map(_.toJson).toJson, - "trialId" -> obj.criterion.trialId.toJson + "trialId" -> obj.criterion.trialId.toJson, + "inclusion" -> obj.criterion.inclusion.toJson ) override def read(json: JsValue): RichCriterion = json match { @@ -128,6 +136,11 @@ object criterion { .map(_.convertTo[String]) .getOrElse("") + val inclusion = fields + .get("inclusion") + .map(_.convertTo[Option[Boolean]]) + .getOrElse(None) + val arms = fields .get("arms") .map(_.convertTo[List[LongId[Arm]]]) @@ -145,7 +158,8 @@ object criterion { trialId = trialId, text = text, isCompound = isCompound, - meta = meta + meta = meta, + inclusion = inclusion ), armIds = arms, labels = labels diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala index baf1b4e..e3f6a9c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala @@ -28,6 +28,25 @@ object document { implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat3(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"Intervention 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 Intervention 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)) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala deleted file mode 100644 index 8119d35..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala +++ /dev/null @@ -1,13 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.sprayformats - -import spray.json._ -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.entities.DocumentType - -object documenttype { - import DefaultJsonProtocol._ - import common._ - - implicit val format: RootJsonFormat[DocumentType] = jsonFormat2(DocumentType.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala new file mode 100644 index 0000000..b836e1c --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala @@ -0,0 +1,101 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +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 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.sprayformats.document._ + import xyz.driver.pdsuidomain.formats.json.sprayformats.record._ + import xyz.driver.pdsuidomain.formats.json.sprayformats.export._ + + implicit val molecularDocumentFormat: RootJsonFormat[MolecularEvidenceDocument] = jsonFormat7( + MolecularEvidenceDocument) + implicit val clinicalDocumentFormat: RootJsonFormat[ClinicalEvidenceDocument] = jsonFormat7(ClinicalEvidenceDocument) + + implicit val evidenceDocumentFormat: RootJsonFormat[EvidenceDocument] = + GadtJsonFormat.create[EvidenceDocument]("documentType") { + 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) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala index 20b6ed0..39d5c59 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala @@ -1,6 +1,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ +import xyz.driver.entities.labels.Label +import xyz.driver.pdsuidomain.entities.{Arm, Criterion} import xyz.driver.pdsuidomain.entities.export.patient._ import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} @@ -8,42 +10,24 @@ object export { import DefaultJsonProtocol._ import common._ import record._ + import document._ - implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] = jsonFormat5( - ExportPatientLabelEvidenceDocument.apply) + implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] = + jsonFormat5(ExportPatientLabelEvidenceDocument.apply) - implicit val patientLabelEvidenceWriter: JsonWriter[ExportPatientLabelEvidence] = - new JsonWriter[ExportPatientLabelEvidence] { - override def write(obj: ExportPatientLabelEvidence): JsValue = - JsObject( - "evidenceId" -> obj.id.toJson, - "labelValue" -> obj.value.toJson, - "evidenceText" -> obj.evidenceText.toJson, - "document" -> obj.document.toJson - ) - } + implicit val patientLabelEvidenceFormat: RootJsonFormat[ExportPatientLabelEvidence] = + jsonFormat(ExportPatientLabelEvidence.apply, "evidenceId", "labelValue", "evidenceText", "document") - implicit val patientLabelWriter: JsonWriter[ExportPatientLabel] = new JsonWriter[ExportPatientLabel] { - override def write(obj: ExportPatientLabel): JsValue = - JsObject( - "labelId" -> obj.id.toJson, - "evidence" -> obj.evidences.map(_.toJson).toJson - ) - } + implicit val patientLabelFormat: RootJsonFormat[ExportPatientLabel] = + jsonFormat(ExportPatientLabel.apply, "labelId", "evidence") - implicit val patientWithLabelsWriter: JsonWriter[ExportPatientWithLabels] = new JsonWriter[ExportPatientWithLabels] { - override def write(obj: ExportPatientWithLabels): JsValue = - JsObject( - "patientId" -> obj.patientId.toJson, - "labelVersion" -> obj.labelVersion.toJson, - "labels" -> obj.labels.map(_.toJson).toJson - ) - } + implicit val patientWithLabelsFormat: RootJsonFormat[ExportPatientWithLabels] = + jsonFormat(ExportPatientWithLabels.apply, "patientId", "labelVersion", "labels") implicit val trialArmFormat: RootJsonFormat[ExportTrialArm] = jsonFormat2(ExportTrialArm.apply) - implicit val trialLabelCriterionWriter: JsonWriter[ExportTrialLabelCriterion] = - new JsonWriter[ExportTrialLabelCriterion] { + implicit val trialLabelCriterionFormat: RootJsonFormat[ExportTrialLabelCriterion] = + new RootJsonFormat[ExportTrialLabelCriterion] { override def write(obj: ExportTrialLabelCriterion): JsValue = JsObject( "value" -> obj.value @@ -60,19 +44,49 @@ object export { "isCompound" -> obj.isCompound.toJson, "isDefining" -> obj.isDefining.toJson ) - } - implicit val trialWithLabelsWriter: JsonWriter[ExportTrialWithLabels] = new JsonWriter[ExportTrialWithLabels] { - override def write(obj: ExportTrialWithLabels) = - JsObject( - "nctId" -> obj.nctId.toJson, - "trialId" -> obj.trialId.toJson, - "disease" -> obj.condition.toJson, - "lastReviewed" -> obj.lastReviewed.toJson, - "labelVersion" -> obj.labelVersion.toJson, - "arms" -> obj.arms.toJson, - "criteria" -> obj.criteria.map(_.toJson).toJson - ) - } + override def read(json: JsValue): ExportTrialLabelCriterion = { + + val fields = Seq("value", "labelId", "criterionId", "criterionText", "armIds", "isCompound", "isDefining") + + json.asJsObject.getFields(fields: _*) match { + case Seq(JsString(valueString), + labelId, + criterionId, + JsString(criterionText), + JsArray(armIdsVector), + JsBoolean(isCompound), + JsBoolean(isDefining)) => + val value = valueString match { + case "Yes" => Option(true) + case "No" => Option(false) + case "Unknown" => Option.empty[Boolean] + } + + ExportTrialLabelCriterion( + longIdFormat[Criterion].read(criterionId), + value, + longIdFormat[Label].read(labelId), + armIdsVector.map(longIdFormat[Arm].read).toSet, + criterionText, + isCompound, + isDefining + ) + + case _ => + deserializationError( + s"Cannot find required fields ${fields.mkString(", ")} in ExportTrialLabelCriterion object!") + } + } + } + implicit val trialWithLabelsFormat: RootJsonFormat[ExportTrialWithLabels] = + jsonFormat(ExportTrialWithLabels.apply, + "nctId", + "trialId", + "disease", + "lastReviewed", + "labelVersion", + "arms", + "criteria") } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala index 42473bc..d6eadbd 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala @@ -1,6 +1,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ +import xyz.driver.entities.labels.{Label, LabelCategory} import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData @@ -39,7 +40,7 @@ object extracteddata { val categoryId = fields .get("categoryId") - .map(_.convertTo[LongId[Category]]) + .map(_.convertTo[LongId[LabelCategory]]) val value = fields .get("value") diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala index 53e927d..b091746 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala @@ -1,6 +1,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providerttype.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providerttype.scala deleted file mode 100644 index 385feb2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providerttype.scala +++ /dev/null @@ -1,12 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.sprayformats - -import spray.json._ -import xyz.driver.pdsuidomain.entities.ProviderType - -object providertype { - import DefaultJsonProtocol._ - import common._ - - implicit val providerTypeFormat: RootJsonFormat[ProviderType] = jsonFormat2(ProviderType.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala index e378dbd..8eef44a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala @@ -36,6 +36,25 @@ object record { } } + 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"Intervention 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 Intervention type, but got $json") + } + + override def write(obj: ProviderType) = + JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) + } + implicit val caseIdFormat = new RootJsonFormat[CaseId] { override def write(caseId: CaseId): JsString = JsString(caseId.toString) override def read(json: JsValue): CaseId = json match { |