diff options
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/formats')
27 files changed, 251 insertions, 441 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/category/ApiCategory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/category/ApiCategory.scala deleted file mode 100644 index f1e15f3..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/category/ApiCategory.scala +++ /dev/null @@ -1,23 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.category - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuidomain.entities.CategoryWithLabels -import xyz.driver.pdsuidomain.formats.json.label.ApiLabel - -final case class ApiCategory(id: Long, name: String, labels: List[ApiLabel]) - -object ApiCategory { - - implicit val format: Format[ApiCategory] = ( - (JsPath \ "id").format[Long] and - (JsPath \ "name").format[String] and - (JsPath \ "labels").format[List[ApiLabel]] - )(ApiCategory.apply, unlift(ApiCategory.unapply)) - - def fromDomain(categoryWithLabels: CategoryWithLabels) = ApiCategory( - id = categoryWithLabels.category.id.id, - name = categoryWithLabels.category.name, - labels = categoryWithLabels.labels.map(x => ApiLabel(x.id.id, x.name, x.categoryId.id)) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala index 4986b17..43b5494 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala @@ -14,7 +14,8 @@ final case class ApiCriterion(id: Long, text: Option[String], isCompound: Boolean, labels: Seq[ApiCriterionLabel], - trialId: String) { + trialId: String, + inclusion: Option[Boolean]) { def toDomain = RichCriterion( criterion = Criterion( @@ -22,7 +23,8 @@ final case class ApiCriterion(id: Long, trialId = StringId[Trial](trialId), text, isCompound, - meta.getOrElse("") + meta.getOrElse(""), + inclusion ), armIds = arms.map(LongId[Arm]), labels = labels.map(_.toDomain(LongId[Criterion](id))) @@ -40,7 +42,8 @@ object ApiCriterion { (JsPath \ "text").formatNullable[String] and (JsPath \ "isCompound").format[Boolean] and (JsPath \ "labels").format(seqJsonFormat[ApiCriterionLabel]) and - (JsPath \ "trialId").format[String] + (JsPath \ "trialId").format[String] and + (JsPath \ "inclusion").formatNullable[Boolean] )(ApiCriterion.apply, unlift(ApiCriterion.unapply)) def fromDomain(richCriterion: RichCriterion) = ApiCriterion( @@ -50,6 +53,7 @@ object ApiCriterion { text = richCriterion.criterion.text, isCompound = richCriterion.criterion.isCompound, labels = richCriterion.labels.map(ApiCriterionLabel.fromDomain), - trialId = richCriterion.criterion.trialId.id + trialId = richCriterion.criterion.trialId.id, + inclusion = richCriterion.criterion.inclusion ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala index ab7641f..d72a9b4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala @@ -13,7 +13,8 @@ final case class ApiNewCriterion(meta: Option[String], text: Option[String], isCompound: Option[Boolean], labels: Seq[ApiCriterionLabel], - trialId: String) { + trialId: String, + inclusion: Option[Boolean]) { def toDomain = RichCriterion( criterion = Criterion( @@ -21,7 +22,8 @@ final case class ApiNewCriterion(meta: Option[String], meta = meta.getOrElse(""), trialId = StringId(trialId), isCompound = isCompound.getOrElse(false), - text = text + text = text, + inclusion = inclusion ), armIds = arms.getOrElse(Seq.empty).map(LongId[Arm]), labels = labels.map(_.toDomain(LongId(Long.MaxValue))) // A developer should specify right criterionId himself @@ -38,6 +40,7 @@ object ApiNewCriterion { (JsPath \ "text").formatNullable[String] and (JsPath \ "isCompound").formatNullable[Boolean] and (JsPath \ "labels").format(seqJsonFormat[ApiCriterionLabel]) and - (JsPath \ "trialId").format[String] + (JsPath \ "trialId").format[String] and + (JsPath \ "inclusion").formatNullable[Boolean] )(ApiNewCriterion.apply, unlift(ApiNewCriterion.unapply)) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala index 2bcda56..77989f0 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala @@ -14,6 +14,7 @@ final case class ApiUpdateCriterion(meta: Tristate[String], arms: Tristate[Seq[Long]], text: Option[String], isCompound: Option[Boolean], + inclusion: Tristate[Boolean], labels: Tristate[Seq[ApiCriterionLabel]]) { def applyTo(orig: RichCriterion): RichCriterion = RichCriterion( @@ -27,7 +28,8 @@ final case class ApiUpdateCriterion(meta: Tristate[String], meta = meta.cata(identity, "{}", orig.meta), text = text.orElse(orig.text), isCompound = isCompound.getOrElse(orig.isCompound), - trialId = orig.trialId + trialId = orig.trialId, + inclusion = inclusion.cata(x => Some(x), None, orig.inclusion) ) } @@ -45,6 +47,7 @@ object ApiUpdateCriterion { (JsPath \ "arms").readTristate(seqJsonFormat[Long]) and (JsPath \ "text").readNullable[String] and (JsPath \ "isCompound").readNullable[Boolean] and + (JsPath \ "inclusion").readTristate[Boolean] and (JsPath \ "labels").readTristate(seqJsonFormat[ApiCriterionLabel]) )(ApiUpdateCriterion.apply _) @@ -53,6 +56,7 @@ object ApiUpdateCriterion { (JsPath \ "arms").writeTristate(seqJsonFormat[Long]) and (JsPath \ "text").writeNullable[String] and (JsPath \ "isCompound").writeNullable[Boolean] and + (JsPath \ "inclusion").writeTristate[Boolean] and (JsPath \ "labels").writeTristate(seqJsonFormat[ApiCriterionLabel]) )(unlift(ApiUpdateCriterion.unapply)) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala index 8b4974f..22bea6b 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala @@ -2,15 +2,14 @@ package xyz.driver.pdsuidomain.formats.json.document import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.DocumentType final case class ApiDocumentType(id: Long, name: String) { - def toDomain = DocumentType( - id = LongId(this.id), - name = this.name - ) + def toDomain: DocumentType = + DocumentType + .fromString(name) + .getOrElse(throw new IllegalArgumentException(s"Unknown document type name $name")) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala index c0eddad..9c0c216 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala @@ -2,15 +2,14 @@ package xyz.driver.pdsuidomain.formats.json.document import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.ProviderType final case class ApiProviderType(id: Long, name: String) { - def toDomain = ProviderType( - id = LongId(this.id), - name = this.name - ) + def toDomain: ProviderType = + ProviderType + .fromString(name) + .getOrElse(throw new IllegalArgumentException(s"Unknown provider type name $name")) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabel.scala deleted file mode 100644 index 0ef1c68..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabel.scala +++ /dev/null @@ -1,28 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.export - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.export.patient.ExportPatientLabel - -final case class ApiExportPatientLabel(id: String, evidences: List[ApiExportPatientLabelEvidence]) { - - def toDomain = ExportPatientLabel( - id = LongId(this.id.toLong), - evidences = this.evidences.map(_.toDomain) - ) - -} - -object ApiExportPatientLabel { - - implicit val format: Format[ApiExportPatientLabel] = ( - (JsPath \ "labelId").format[String] and - (JsPath \ "evidence").format[List[ApiExportPatientLabelEvidence]] - )(ApiExportPatientLabel.apply, unlift(ApiExportPatientLabel.unapply)) - - def fromDomain(label: ExportPatientLabel) = ApiExportPatientLabel( - id = label.id.toString, - evidences = label.evidences.map(ApiExportPatientLabelEvidence.fromDomain) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabelEvidence.scala deleted file mode 100644 index d141762..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabelEvidence.scala +++ /dev/null @@ -1,38 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.export - -import play.api.libs.functional.syntax._ -import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.export.patient.ExportPatientLabelEvidence - -final case class ApiExportPatientLabelEvidence(evidenceId: String, - labelValue: String, - evidenceText: String, - document: ApiExportPatientLabelEvidenceDocument) { - - def toDomain = ExportPatientLabelEvidence( - id = LongId(this.evidenceId.toLong), - value = FuzzyValue.fromString - .applyOrElse(this.labelValue, (s: String) => throw new NoSuchElementException(s"Unknown fuzzy value $s")), - evidenceText = this.evidenceText, - document = this.document.toDomain - ) - -} - -object ApiExportPatientLabelEvidence { - - implicit val format: Format[ApiExportPatientLabelEvidence] = ( - (JsPath \ "evidenceId").format[String] and - (JsPath \ "labelValue").format[String](Writes[String](x => JsString(x.toUpperCase))) and - (JsPath \ "evidenceText").format[String] and - (JsPath \ "document").format[ApiExportPatientLabelEvidenceDocument] - )(ApiExportPatientLabelEvidence.apply, unlift(ApiExportPatientLabelEvidence.unapply)) - - def fromDomain(evidence: ExportPatientLabelEvidence) = ApiExportPatientLabelEvidence( - evidenceId = evidence.id.toString, - labelValue = FuzzyValue.valueToString(evidence.value), - evidenceText = evidence.evidenceText, - document = ApiExportPatientLabelEvidenceDocument.fromDomain(evidence.document) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabelEvidenceDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabelEvidenceDocument.scala deleted file mode 100644 index 6999301..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientLabelEvidenceDocument.scala +++ /dev/null @@ -1,46 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.export - -import java.time.LocalDate -import java.util.UUID - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.RecordRequestId -import xyz.driver.pdsuidomain.entities.export.patient.ExportPatientLabelEvidenceDocument - -final case class ApiExportPatientLabelEvidenceDocument(documentId: String, - requestId: String, - documentType: String, - providerType: String, - date: LocalDate) { - - def toDomain = ExportPatientLabelEvidenceDocument( - documentId = LongId(this.documentId.toLong), - requestId = RecordRequestId(UUID.fromString(this.requestId)), - documentType = this.documentType, - providerType = this.providerType, - date = this.date - ) - -} - -object ApiExportPatientLabelEvidenceDocument { - - implicit val format: Format[ApiExportPatientLabelEvidenceDocument] = ( - (JsPath \ "documentId").format[String] and - (JsPath \ "requestId").format[String] and - (JsPath \ "documentType").format[String] and - (JsPath \ "providerType").format[String] and - (JsPath \ "date").format[LocalDate] - )(ApiExportPatientLabelEvidenceDocument.apply, unlift(ApiExportPatientLabelEvidenceDocument.unapply)) - - def fromDomain(document: ExportPatientLabelEvidenceDocument) = - ApiExportPatientLabelEvidenceDocument( - documentId = document.documentId.toString, - requestId = document.requestId.toString, - documentType = document.documentType, - providerType = document.providerType, - date = document.date - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientWithLabels.scala deleted file mode 100644 index fc9bab7..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportPatientWithLabels.scala +++ /dev/null @@ -1,31 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.export - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.entities.export.patient.ExportPatientWithLabels - -final case class ApiExportPatientWithLabels(patientId: String, labelVersion: Long, labels: List[ApiExportPatientLabel]) { - - def toDomain = ExportPatientWithLabels( - patientId = UuidId(this.patientId), - labelVersion = this.labelVersion, - labels = this.labels.map(_.toDomain) - ) - -} - -object ApiExportPatientWithLabels { - - implicit val format: Format[ApiExportPatientWithLabels] = ( - (JsPath \ "patientId").format[String] and - (JsPath \ "labelVersion").format[Long] and - (JsPath \ "labels").format[List[ApiExportPatientLabel]] - )(ApiExportPatientWithLabels.apply, unlift(ApiExportPatientWithLabels.unapply)) - - def fromDomain(patient: ExportPatientWithLabels) = ApiExportPatientWithLabels( - patientId = patient.patientId.toString, - labelVersion = patient.labelVersion, - labels = patient.labels.map(ApiExportPatientLabel.fromDomain) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialArm.scala deleted file mode 100644 index ea96f58..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialArm.scala +++ /dev/null @@ -1,27 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.export - -import play.api.libs.functional.syntax._ -import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.Arm -import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialArm - -final case class ApiExportTrialArm(armId: String, armName: String) { - - def toDomain: ExportTrialArm = { - ExportTrialArm(LongId[Arm](armId.toLong), armName) - } -} - -object ApiExportTrialArm { - - implicit val format: Format[ApiExportTrialArm] = ( - (JsPath \ "armId").format[String] and - (JsPath \ "armName").format[String] - )(ApiExportTrialArm.apply, unlift(ApiExportTrialArm.unapply)) - - def fromDomain(arm: ExportTrialArm) = ApiExportTrialArm( - armId = arm.armId.toString, - armName = arm.armName - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialLabelCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialLabelCriterion.scala deleted file mode 100644 index df1ebb4..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialLabelCriterion.scala +++ /dev/null @@ -1,55 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.export - -import play.api.libs.functional.syntax._ -import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialLabelCriterion -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Label} - -final case class ApiExportTrialLabelCriterion(value: String, - labelId: String, - criterionId: String, - criterionText: String, - armIds: List[String], - isCompound: Boolean, - isDefining: Boolean) { - - def toDomain: ExportTrialLabelCriterion = { - ExportTrialLabelCriterion( - LongId[Criterion](criterionId.toLong), - FuzzyValue.fromString.lift(value).map(_ == FuzzyValue.Yes), - LongId[Label](labelId.toLong), - armIds.map(armId => LongId[Arm](armId.toLong)).toSet, - criterionText, - isCompound, - isDefining - ) - } -} - -object ApiExportTrialLabelCriterion { - - implicit val format: Format[ApiExportTrialLabelCriterion] = ( - (JsPath \ "value").format[String](Writes[String](x => JsString(x.toUpperCase))) and - (JsPath \ "labelId").format[String] and - (JsPath \ "criterionId").format[String] and - (JsPath \ "criterionText").format[String] and - (JsPath \ "armIds").format[List[String]] and - (JsPath \ "isCompound").format[Boolean] and - (JsPath \ "isDefining").format[Boolean] - )(ApiExportTrialLabelCriterion.apply, unlift(ApiExportTrialLabelCriterion.unapply)) - - def fromDomain(x: ExportTrialLabelCriterion) = ApiExportTrialLabelCriterion( - value = x.value - .map { x => - FuzzyValue.valueToString(FuzzyValue.fromBoolean(x)) - } - .getOrElse("Unknown"), - labelId = x.labelId.toString, - criterionId = x.criterionId.toString, - criterionText = x.criteria, - armIds = x.armIds.map(_.toString).toList, - isCompound = x.isCompound, - isDefining = x.isDefining - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialWithLabels.scala deleted file mode 100644 index e383a1f..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export/ApiExportTrialWithLabels.scala +++ /dev/null @@ -1,53 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.export - -import java.time.{Instant, ZoneId} - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.{StringId, UuidId} -import xyz.driver.pdsuidomain.entities.Trial -import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels - -final case class ApiExportTrialWithLabels(nctId: String, - trialId: String, - condition: String, - lastReviewed: Long, - labelVersion: Long, - arms: List[ApiExportTrialArm], - criteria: List[ApiExportTrialLabelCriterion]) { - - def toDomain: ExportTrialWithLabels = { - ExportTrialWithLabels( - StringId[Trial](nctId), - UuidId[Trial](trialId), - condition, - lastReviewed = Instant.ofEpochMilli(lastReviewed).atZone(ZoneId.of("Z")).toLocalDateTime, - labelVersion, - arms.map(_.toDomain), - criteria.map(_.toDomain) - ) - } -} - -object ApiExportTrialWithLabels { - - implicit val format: Format[ApiExportTrialWithLabels] = ( - (JsPath \ "nctId").format[String] and - (JsPath \ "trialId").format[String] and - (JsPath \ "disease").format[String] and - (JsPath \ "lastReviewed").format[Long] and - (JsPath \ "labelVersion").format[Long] and - (JsPath \ "arms").format[List[ApiExportTrialArm]] and - (JsPath \ "criteria").format[List[ApiExportTrialLabelCriterion]] - )(ApiExportTrialWithLabels.apply, unlift(ApiExportTrialWithLabels.unapply)) - - def fromDomain(x: ExportTrialWithLabels) = ApiExportTrialWithLabels( - nctId = x.nctId.id, - trialId = x.trialId.toString, - condition = x.condition, - lastReviewed = x.lastReviewed.atZone(ZoneId.of("Z")).toEpochSecond, - labelVersion = x.labelVersion, - arms = x.arms.map(ApiExportTrialArm.fromDomain), - criteria = x.criteria.map(ApiExportTrialLabelCriterion.fromDomain) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/keyword/ApiKeyword.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/keyword/ApiKeyword.scala deleted file mode 100644 index a9d02fc..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/keyword/ApiKeyword.scala +++ /dev/null @@ -1,23 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.keyword - -import xyz.driver.pdsuidomain.entities.KeywordWithLabels -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuidomain.formats.json.label.ApiLabel - -final case class ApiKeyword(id: Long, keyword: String, labels: List[ApiLabel]) - -object ApiKeyword { - - implicit val format: Format[ApiKeyword] = ( - (JsPath \ "id").format[Long] and - (JsPath \ "keyword").format[String] and - (JsPath \ "labels").format[List[ApiLabel]] - )(ApiKeyword.apply, unlift(ApiKeyword.unapply)) - - def fromDomain(keywordWithLabels: KeywordWithLabels) = ApiKeyword( - id = keywordWithLabels.keyword.id.id, - keyword = keywordWithLabels.keyword.keyword, - labels = keywordWithLabels.labels.map(x => ApiLabel(x.id.id, x.name, x.categoryId.id)) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala index 7a65af8..d486749 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.{Category, Criterion, CriterionLabel, Label} +import xyz.driver.pdsuidomain.entities.{Criterion, CriterionLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.entities.labels.{Label, LabelCategory} /** * @param value Yes|No @@ -18,7 +19,7 @@ final case class ApiCriterionLabel(labelId: Option[Long], id = LongId(0L), labelId = labelId.map(LongId[Label]), criterionId = criterionId, - categoryId = categoryId.map(LongId[Category]), + categoryId = categoryId.map(LongId[LabelCategory]), value = value.map { case "Yes" => true case "No" => false diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala index cb45025..f8161af 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.{Category, ExtractedData, ExtractedDataLabel, Label} +import xyz.driver.pdsuidomain.entities.{ExtractedData, ExtractedDataLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.entities.labels.{Label, LabelCategory} final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long], value: Option[String]) { @@ -12,7 +13,7 @@ final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long id = LongId(0), dataId = dataId, labelId = id.map(LongId[Label]), - categoryId = categoryId.map(LongId[Category]), + categoryId = categoryId.map(LongId[LabelCategory]), value = value.map(FuzzyValue.fromString) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiLabel.scala deleted file mode 100644 index 042b380..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiLabel.scala +++ /dev/null @@ -1,22 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.label - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuidomain.entities.Label - -final case class ApiLabel(id: Long, name: String, categoryId: Long) - -object ApiLabel { - - implicit val format: Format[ApiLabel] = ( - (JsPath \ "id").format[Long] and - (JsPath \ "name").format[String] and - (JsPath \ "categoryId").format[Long] - )(ApiLabel.apply, unlift(ApiLabel.unapply)) - - def fromDomain(x: Label) = ApiLabel( - id = x.id.id, - name = x.name, - categoryId = x.categoryId.id - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala index 75347f4..6eeb40b 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala @@ -3,10 +3,11 @@ package xyz.driver.pdsuidomain.formats.json.patient.trial import java.time.{ZoneId, ZonedDateTime} import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.{Label, PatientCriterion, PatientCriterionArm} +import xyz.driver.pdsuidomain.entities.{PatientCriterion, PatientCriterionArm} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} +import xyz.driver.entities.labels.Label final case class ApiPatientCriterion(id: Long, labelId: Long, 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 { |