diff options
author | Marvin Bertin <marvin.bertin@gmail.com> | 2017-10-10 16:31:00 -0700 |
---|---|---|
committer | GitHub <noreply@github.com> | 2017-10-10 16:31:00 -0700 |
commit | 385a9a99e5a95c3d623cddd927c37564e32dbd2d (patch) | |
tree | 0671a39174899dce09ade3c571ef21bab6172e0e /src/main/scala/xyz/driver/pdsuidomain/formats/json | |
parent | 0653b90dddc294fddb0e81059aef00b202113d78 (diff) | |
parent | 9c95eb7247cb0818af9a9e4afe884698360f994c (diff) | |
download | rest-query-385a9a99e5a95c3d623cddd927c37564e32dbd2d.tar.gz rest-query-385a9a99e5a95c3d623cddd927c37564e32dbd2d.tar.bz2 rest-query-385a9a99e5a95c3d623cddd927c37564e32dbd2d.zip |
Merge pull request #35 from drivergroup/trial-46-disease-entity
Trial 46 disease entity
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/formats/json')
36 files changed, 317 insertions, 232 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala index 1869ff3..3f1ecfe 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala @@ -2,7 +2,6 @@ package xyz.driver.pdsuidomain.formats.json.document import java.time.{LocalDate, ZoneId, ZonedDateTime} import xyz.driver.pdsuicommon.domain.{LongId, StringId, TextJson} -import xyz.driver.pdsuicommon.json.JsonSerializer import xyz.driver.pdsuidomain.entities._ import play.api.data.validation.ValidationError @@ -20,6 +19,7 @@ final case class ApiDocument(id: Long, provider: Option[String], providerTypeId: Option[Long], requiredType: Option[String], + institutionName: Option[String], status: Option[String], previousStatus: Option[String], assignee: Option[String], @@ -46,6 +46,7 @@ final case class ApiDocument(id: Long, providerName = this.provider, providerTypeId = this.providerTypeId.map(LongId(_)), requiredType = this.requiredType.map(extractRequiredType), + institutionName = this.institutionName, meta = this.meta.map(x => TextJson(JsonSerializer.deserialize[Document.Meta](x))), startDate = this.startDate, endDate = this.endDate, @@ -74,6 +75,7 @@ object ApiDocument { (JsPath \ "provider").formatNullable[String] and (JsPath \ "providerTypeId").formatNullable[Long] and (JsPath \ "requiredType").formatNullable[String] and + (JsPath \ "institutionName").formatNullable[String] and (JsPath \ "status").formatNullable(statusFormat) and (JsPath \ "previousStatus").formatNullable(statusFormat) and (JsPath \ "assignee").formatNullable[String] and @@ -96,6 +98,7 @@ object ApiDocument { provider = document.providerName, providerTypeId = document.providerTypeId.map(_.id), requiredType = document.requiredType.map(Document.RequiredType.requiredTypeToString), + institutionName = document.institutionName, status = Option(Document.Status.statusToString(document.status)), previousStatus = document.previousStatus.map(Document.Status.statusToString), assignee = document.assignee.map(_.id), diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala index eae0c62..032ddf6 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala @@ -23,6 +23,7 @@ final case class ApiPartialDocument(recordId: Option[Long], endDate: Tristate[LocalDate], provider: Tristate[String], providerTypeId: Tristate[Long], + institutionName: Tristate[String], status: Option[String], assignee: Tristate[String], meta: Tristate[String]) { @@ -42,6 +43,7 @@ final case class ApiPartialDocument(recordId: Option[Long], providerName = provider.cata(Some(_), None, orig.providerName), providerTypeId = providerTypeId.map(LongId[ProviderType]).cata(Some(_), None, orig.providerTypeId), requiredType = orig.requiredType, + institutionName = institutionName.cata(Some(_), None, orig.institutionName), meta = meta.cata(x => Some(TextJson(JsonSerializer.deserialize[Meta](x))), None, orig.meta), startDate = startDate.cata(Some(_), None, orig.startDate), endDate = endDate.cata(Some(_), None, orig.endDate), @@ -67,6 +69,7 @@ final case class ApiPartialDocument(recordId: Option[Long], providerName = provider.toOption, providerTypeId = providerTypeId.map(LongId[ProviderType]).toOption, requiredType = None, + institutionName = institutionName.toOption, meta = meta.map(x => TextJson(JsonSerializer.deserialize[Meta](x))).toOption, previousStatus = None, assignee = None, @@ -90,6 +93,7 @@ object ApiPartialDocument { (JsPath \ "endDate").readTristate[LocalDate] and (JsPath \ "provider").readTristate[String] and (JsPath \ "providerTypeId").readTristate[Long] and + (JsPath \ "institutionName").readTristate[String] and (JsPath \ "status").readNullable[String]( Reads .of[String] @@ -115,6 +119,7 @@ object ApiPartialDocument { (JsPath \ "endDate").writeTristate[LocalDate] and (JsPath \ "provider").writeTristate[String] and (JsPath \ "providerTypeId").writeTristate[Long] and + (JsPath \ "institutionName").writeTristate[String] and (JsPath \ "status").writeNullable[String] and (JsPath \ "assignee").writeTristate[String] and (JsPath \ "meta").writeTristate(Writes[String](Json.parse)) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala index e7eb022..71423e8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala @@ -1,20 +1,36 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.EligibilityArm import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases} -final case class ApiEligibilityArm(id: Long, name: String, originalName: String, trialId: String) { +final case class ApiEligibilityArm(id: Long, + name: String, + originalName: String, + trialId: String, + diseases: Seq[String]) { - def toDomain: EligibilityArm = EligibilityArm( - id = LongId(this.id), - name = this.name, - originalName = this.originalName, - trialId = StringId(this.trialId), - deleted = None // if we have an ApiEligibilityArm object, the EligibilityArm itself has not been deleted - ) + def toDomain: EligibilityArmWithDiseases = { + val eligibilityArm = EligibilityArm( + id = LongId(this.id), + name = this.name, + originalName = this.originalName, + trialId = StringId(this.trialId), + deleted = None // if we have an ApiEligibilityArm object, the EligibilityArm itself has not been deleted + ) + EligibilityArmWithDiseases( + eligibilityArm, + this.diseases.map { disease => + val condition = CancerType + .fromString(disease) + .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) + EligibilityArmDisease(eligibilityArm.id, condition) + } + ) + } } object ApiEligibilityArm { @@ -23,13 +39,19 @@ object ApiEligibilityArm { (JsPath \ "id").format[Long] and (JsPath \ "name").format[String] and (JsPath \ "originalName").format[String] and - (JsPath \ "trialId").format[String] + (JsPath \ "trialId").format[String] and + (JsPath \ "diseases").format[Seq[String]] )(ApiEligibilityArm.apply, unlift(ApiEligibilityArm.unapply)) - def fromDomain(arm: EligibilityArm): ApiEligibilityArm = ApiEligibilityArm( - id = arm.id.id, - name = arm.name, - originalName = arm.originalName, - trialId = arm.trialId.id - ) + def fromDomain(eligibilityArmWithDiseases: EligibilityArmWithDiseases): ApiEligibilityArm = { + import eligibilityArmWithDiseases.{eligibilityArm, eligibilityArmDiseases} + + ApiEligibilityArm( + id = eligibilityArm.id.id, + name = eligibilityArm.name, + originalName = eligibilityArm.originalName, + trialId = eligibilityArm.trialId.id, + diseases = eligibilityArmDiseases.map(_.disease.toString) + ) + } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala index 6f55c10..087fed5 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala @@ -1,17 +1,30 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.EligibilityArm import play.api.libs.json.{Format, Json} +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases} + +final case class ApiCreateEligibilityArm(name: String, trialId: String, diseases: Seq[String]) { -final case class ApiCreateEligibilityArm(name: String, trialId: String) { + def toDomain: EligibilityArmWithDiseases = { + val eligibilityArm = EligibilityArm( + id = LongId(0), + name = name, + trialId = StringId(trialId), + originalName = name + ) - def toDomain = EligibilityArm( - id = LongId(0), - name = name, - trialId = StringId(trialId), - originalName = name - ) + EligibilityArmWithDiseases( + eligibilityArm, + diseases.map { disease => + val condition = CancerType + .fromString(disease) + .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) + EligibilityArmDisease(eligibilityArm.id, condition) + } + ) + } } object ApiCreateEligibilityArm { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala index cc3d460..aca22ef 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala @@ -1,11 +1,20 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm -import xyz.driver.pdsuidomain.entities.EligibilityArm import play.api.libs.json.{Format, Json} +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuidomain.entities.{EligibilityArmDisease, EligibilityArmWithDiseases} -final case class ApiPartialEligibilityArm(name: String) { +final case class ApiPartialEligibilityArm(name: String, diseases: Seq[String]) { - def applyTo(arm: EligibilityArm): EligibilityArm = arm.copy(name = name) + def applyTo(armWithDisease: EligibilityArmWithDiseases): EligibilityArmWithDiseases = { + val arm = armWithDisease.eligibilityArm.copy(name = name) + val armDiseases = diseases.map { disease => + EligibilityArmDisease( + armWithDisease.eligibilityArm.id, + CancerType.fromString(disease).getOrElse(throw new NoSuchElementException(s"unknown condition $disease"))) + } + EligibilityArmWithDiseases(arm, armDiseases) + } } object ApiPartialEligibilityArm { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala index e0f23e3..c7a6de9 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala @@ -3,7 +3,6 @@ package xyz.driver.pdsuidomain.formats.json.evidence import java.time.LocalDate import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue import xyz.driver.pdsuidomain.entities.PatientLabelEvidenceView final case class ApiPatientLabelEvidence(id: Long, @@ -22,13 +21,13 @@ object ApiPatientLabelEvidence { def fromDomain(x: PatientLabelEvidenceView) = ApiPatientLabelEvidence( id = x.id.id, - value = FuzzyValue.valueToString(x.value), + value = x.value.toString, evidenceText = x.evidenceText, documentId = x.documentId.map(_.id), evidenceId = x.evidenceId.map(_.id), reportId = x.reportId.map(_.toString), - documentType = x.documentType, + documentType = x.documentType.name, date = x.date.get, - providerType = x.providerType + providerType = x.providerType.name ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala index d486749..edb0603 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala @@ -1,11 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.{Criterion, CriterionLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} /** * @param value Yes|No @@ -34,7 +34,7 @@ object ApiCriterionLabel { labelId = x.labelId.map(_.id), categoryId = x.categoryId.map(_.id), value = x.value.map { x => - FuzzyValue.valueToString(FuzzyValue.fromBoolean(x)) + LabelValue.fromBoolean(x).toString }, isDefining = x.isDefining ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala index f8161af..1497679 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala @@ -1,11 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.{ExtractedData, ExtractedDataLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long], value: Option[String]) { @@ -14,7 +14,7 @@ final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long dataId = dataId, labelId = id.map(LongId[Label]), categoryId = categoryId.map(LongId[LabelCategory]), - value = value.map(FuzzyValue.fromString) + value = value.flatMap(LabelValue.fromString) ) } @@ -27,8 +27,8 @@ object ApiExtractedDataLabel { Format(Reads .of[String] .filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) )(ApiExtractedDataLabel.apply, unlift(ApiExtractedDataLabel.unapply)) @@ -36,6 +36,6 @@ object ApiExtractedDataLabel { def fromDomain(dataLabel: ExtractedDataLabel) = ApiExtractedDataLabel( id = dataLabel.labelId.map(_.id), categoryId = dataLabel.categoryId.map(_.id), - value = dataLabel.value.map(FuzzyValue.valueToString) + value = dataLabel.value.map(_.toString) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala index db430ae..585d4ed 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala @@ -7,6 +7,8 @@ import xyz.driver.pdsuicommon.domain.{StringId, UuidId} import xyz.driver.pdsuidomain.entities.{Patient, PatientOrderId} import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath} +import xyz.driver.entities.common.FullName +import xyz.driver.entities.patient final case class ApiPatient(id: String, status: String, @@ -17,24 +19,35 @@ final case class ApiPatient(id: String, previousAssignee: Option[String], lastActiveUser: Option[String], lastUpdate: ZonedDateTime, - condition: String, + disease: String, orderId: UUID) { private def extractStatus(status: String): Patient.Status = PatientStatus.statusFromString .applyOrElse(status, (s: String) => throw new NoSuchElementException(s"Unknown status $s")) + private def parseName(name: String): FullName[Patient] = + name.split(" ") match { + case Array() => throw new NoSuchElementException(s"Patient's name cannot be empty") + case Array(first) => FullName.fromStrings[Patient](first, "", "") + case Array(first, last) => FullName.fromStrings[Patient](first, "", last) + case Array(first, middle, last) => FullName.fromStrings[Patient](first, middle, last) + case _ => throw new NoSuchElementException(s"Patient's name is ambiguous") + } + def toDomain = Patient( id = UuidId(this.id), status = extractStatus(this.status), - name = this.name, + name = parseName(this.name), dob = this.dob, assignee = this.assignee.map(StringId(_)), previousStatus = this.previousStatus.map(extractStatus), previousAssignee = this.previousAssignee.map(StringId(_)), lastActiveUserId = this.lastActiveUser.map(StringId(_)), isUpdateRequired = false, - condition = this.condition, + disease = patient.CancerType + .fromString(this.disease) + .getOrElse(throw new IllegalArgumentException(s"Unknown cancer type ${this.disease}")), orderId = PatientOrderId(this.orderId), lastUpdate = this.lastUpdate.toLocalDateTime ) @@ -53,21 +66,21 @@ object ApiPatient { (JsPath \ "previousAssignee").formatNullable[String] and (JsPath \ "lastActiveUser").formatNullable[String] and (JsPath \ "lastUpdate").format[ZonedDateTime] and - (JsPath \ "condition").format[String] and + (JsPath \ "disease").format[String] and (JsPath \ "orderId").format[UUID] )(ApiPatient.apply, unlift(ApiPatient.unapply)) def fromDomain(patient: Patient) = ApiPatient( id = patient.id.toString, status = PatientStatus.statusToString(patient.status), - name = patient.name, + name = patient.name.toString(), dob = patient.dob, assignee = patient.assignee.map(_.id), previousStatus = patient.previousStatus.map(PatientStatus.statusToString), previousAssignee = patient.previousAssignee.map(_.id), lastActiveUser = patient.lastActiveUserId.map(_.id), lastUpdate = ZonedDateTime.of(patient.lastUpdate, ZoneId.of("Z")), - condition = patient.condition, + disease = patient.disease.toString, orderId = patient.orderId.id ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala index 4136715..55c8149 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala @@ -5,7 +5,7 @@ import java.util.UUID import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial final case class ApiPatientEligibleTrial(id: Long, @@ -30,8 +30,8 @@ object ApiPatientEligibleTrial { Reads .of[String] .filter(ValidationError("unknown eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) and @@ -45,7 +45,7 @@ object ApiPatientEligibleTrial { trialTitle = eligibleTrialWithTrial.trial.title, arms = eligibleTrialWithTrial.arms.map(_.armName), hypothesisId = eligibleTrialWithTrial.group.hypothesisId.id, - eligibleTrialWithTrial.group.verifiedEligibilityStatus.map(FuzzyValue.valueToString), + eligibleTrialWithTrial.group.verifiedEligibilityStatus.map(_.toString), eligibleTrialWithTrial.group.isVerified ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala index 91d0a0e..d92872c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala @@ -6,15 +6,14 @@ import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue final case class ApiPartialPatientLabel(primaryValue: Option[String], verifiedPrimaryValue: Tristate[String]) { def applyTo(orig: PatientLabel): PatientLabel = { orig.copy( - primaryValue = primaryValue.map(FuzzyValue.fromString).orElse(orig.primaryValue), - verifiedPrimaryValue = - verifiedPrimaryValue.cata(x => Some(FuzzyValue.fromString(x)), None, orig.verifiedPrimaryValue) + primaryValue = primaryValue.flatMap(LabelValue.fromString).orElse(orig.primaryValue), + verifiedPrimaryValue = verifiedPrimaryValue.cata(x => LabelValue.fromString(x), None, orig.verifiedPrimaryValue) ) } } @@ -26,8 +25,8 @@ object ApiPartialPatientLabel { Format(Reads .of[String] .filter(ValidationError("unknown primary value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) and (JsPath \ "verifiedPrimaryValue").formatTristate[String]( @@ -35,8 +34,8 @@ object ApiPartialPatientLabel { Reads .of[String] .filter(ValidationError("unknown verified primary value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala index fc8687b..cc8532d 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala @@ -4,7 +4,7 @@ import xyz.driver.pdsuidomain.entities.PatientLabel import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue final case class ApiPatientLabel(id: Long, labelId: Long, @@ -20,25 +20,33 @@ object ApiPatientLabel { implicit val apiPatientLabelJsonFormat: Format[ApiPatientLabel] = ( (JsPath \ "id").format[Long] and (JsPath \ "labelId").format[Long] and - (JsPath \ "primaryValue").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false - }), Writes.of[String])) and - (JsPath \ "verifiedPrimaryValue").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false - }), Writes.of[String])) and + (JsPath \ "primaryValue").formatNullable[String]( + Format(Reads + .of[String] + .filter(ValidationError("unknown value"))({ + case x if LabelValue.fromString(x).isDefined => true + case _ => false + }), + Writes.of[String])) and + (JsPath \ "verifiedPrimaryValue").formatNullable[String]( + Format(Reads + .of[String] + .filter(ValidationError("unknown value"))({ + case x if LabelValue.fromString(x).isDefined => true + case _ => false + }), + Writes.of[String])) and (JsPath \ "score").format[Int] and (JsPath \ "isImplicitMatch").format[Boolean] and (JsPath \ "isVisible").format[Boolean] and (JsPath \ "isVerified").format[Boolean] - ) (ApiPatientLabel.apply, unlift(ApiPatientLabel.unapply)) + )(ApiPatientLabel.apply, unlift(ApiPatientLabel.unapply)) def fromDomain(patientLabel: PatientLabel, isVerified: Boolean): ApiPatientLabel = ApiPatientLabel( id = patientLabel.id.id, labelId = patientLabel.labelId.id, - primaryValue = patientLabel.primaryValue.map(FuzzyValue.valueToString), - verifiedPrimaryValue = patientLabel.verifiedPrimaryValue.map(FuzzyValue.valueToString), + primaryValue = patientLabel.primaryValue.map(_.toString), + verifiedPrimaryValue = patientLabel.verifiedPrimaryValue.map(_.toString), score = patientLabel.score, isImplicitMatch = patientLabel.isImplicitMatch, isVisible = patientLabel.isVisible, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala index ae64c33..16b9cc9 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala @@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.patient.label import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.entities.PatientLabel final case class ApiPatientLabelDefiningCriteria(labelId: Long, value: Option[String]) @@ -16,14 +16,14 @@ object ApiPatientLabelDefiningCriteria { Format(Reads .of[String] .filter(ValidationError("unknown value"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) )(ApiPatientLabelDefiningCriteria.apply, unlift(ApiPatientLabelDefiningCriteria.unapply)) def fromDomain(x: PatientLabel) = ApiPatientLabelDefiningCriteria( labelId = x.labelId.id, - value = x.verifiedPrimaryValue.map(FuzzyValue.valueToString) + value = x.verifiedPrimaryValue.map(_.toString) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala index 399bc7d..09538b8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala @@ -6,16 +6,16 @@ import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue final case class ApiPartialPatientCriterion(eligibilityStatus: Option[String], verifiedEligibilityStatus: Tristate[String]) { def applyTo(orig: PatientCriterion): PatientCriterion = { orig.copy( - eligibilityStatus = eligibilityStatus.map(FuzzyValue.fromString).orElse(orig.eligibilityStatus), + eligibilityStatus = eligibilityStatus.flatMap(LabelValue.fromString).orElse(orig.eligibilityStatus), verifiedEligibilityStatus = - verifiedEligibilityStatus.cata(x => Some(FuzzyValue.fromString(x)), None, orig.verifiedEligibilityStatus) + verifiedEligibilityStatus.cata(x => LabelValue.fromString(x), None, orig.verifiedEligibilityStatus) ) } } @@ -28,8 +28,8 @@ object ApiPartialPatientCriterion { Reads .of[String] .filter(ValidationError("unknown eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) and @@ -38,8 +38,8 @@ object ApiPartialPatientCriterion { Reads .of[String] .filter(ValidationError("unknown verified eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala index 4b08970..b7616a1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.patient.trial -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.PatientCriterion import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion final case class ApiPartialPatientCriterionList(id: Long, @@ -13,7 +14,7 @@ final case class ApiPartialPatientCriterionList(id: Long, def toDomain: DraftPatientCriterion = DraftPatientCriterion( id = LongId[PatientCriterion](id), - eligibilityStatus = eligibilityStatus.map(FuzzyValue.fromString), + eligibilityStatus = eligibilityStatus.flatMap(LabelValue.fromString), isVerified = isVerified ) } @@ -26,8 +27,8 @@ object ApiPartialPatientCriterionList { Reads .of[String] .filter(ValidationError("unknown eligibility status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String] )) and diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala index 6eeb40b..b9bf772 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala @@ -2,12 +2,12 @@ package xyz.driver.pdsuidomain.formats.json.patient.trial import java.time.{ZoneId, ZonedDateTime} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.{PatientCriterion, PatientCriterionArm} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} -import xyz.driver.entities.labels.Label +import xyz.driver.entities.labels.{Label, LabelValue} final case class ApiPatientCriterion(id: Long, labelId: Long, @@ -39,13 +39,13 @@ object ApiPatientCriterion { (JsPath \ "criterionIsCompound").format[Boolean] and (JsPath \ "arms").format[List[String]] and (JsPath \ "eligibilityStatus").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) and (JsPath \ "verifiedEligibilityStatus").formatNullable[String](Format( Reads.of[String].filter(ValidationError("unknown status"))({ - case x if FuzzyValue.fromString.isDefinedAt(x) => true - case _ => false + case x if LabelValue.fromString(x).isDefined => true + case _ => false }), Writes.of[String])) and (JsPath \ "isVerified").format[Boolean] and (JsPath \ "isVisible").format[Boolean] and @@ -61,13 +61,13 @@ object ApiPatientCriterion { criterionId = patientCriterion.criterionId.id, criterionText = patientCriterion.criterionText, criterionValue = patientCriterion.criterionValue.map { x => - FuzzyValue.valueToString(FuzzyValue.fromBoolean(x)) + LabelValue.fromBoolean(x).toString }, criterionIsDefining = patientCriterion.criterionIsDefining, criterionIsCompound = patientCriterion.criterionValue.isEmpty, arms = arms.map(_.armName), - eligibilityStatus = patientCriterion.eligibilityStatus.map(FuzzyValue.valueToString), - verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(FuzzyValue.valueToString), + eligibilityStatus = patientCriterion.eligibilityStatus.map(_.toString), + verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(_.toString), isVerified = patientCriterion.isVerified, isVisible = patientCriterion.isVisible, lastUpdate = ZonedDateTime.of(patientCriterion.lastUpdate, ZoneId.of("Z")) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala index 2e5943e..1f8c683 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala @@ -22,8 +22,6 @@ final case class ApiCreateRecord(disease: String, patientId: String, requestId: caseId = None, physician = None, meta = None, - predictedMeta = None, - predictedDocuments = None, lastUpdate = LocalDateTime.now() ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala index e7b58cd..fc0a2e7 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala @@ -101,8 +101,6 @@ final case class ApiRecord(id: Long, Some(TextJson(JsonSerializer.deserialize[List[MedicalRecord.Meta]](this.meta))) } }, - predictedMeta = None, - predictedDocuments = None, lastUpdate = this.lastUpdate.toLocalDateTime() ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala new file mode 100644 index 0000000..2a670c4 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala @@ -0,0 +1,39 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import java.time.LocalDateTime + +import spray.json.{RootJsonFormat, _} +import xyz.driver.pdsuicommon.db.Pagination +import xyz.driver.pdsuidomain.formats.json.sprayformats.common._ + +final case class ListResponse[+T](items: Seq[T], meta: ListResponse.Meta) + +object ListResponse extends DefaultJsonProtocol { + private val itemsField = "items" + private val metaField = "meta" + + final case class Meta(itemsCount: Int, pageNumber: Int, pageSize: Int, lastUpdate: Option[LocalDateTime]) + + object Meta { + def apply(itemsCount: Int, pagination: Pagination, lastUpdate: Option[LocalDateTime]): Meta = { + Meta( + itemsCount, + pagination.pageNumber, + pagination.pageSize, + lastUpdate + ) + } + } + + implicit val listResponseMetaFormat: RootJsonFormat[Meta] = jsonFormat4(Meta.apply) + + implicit def listResponseMetaWriter[T: JsonWriter]: RootJsonWriter[ListResponse[T]] = + new RootJsonWriter[ListResponse[T]] { + override def write(listResponse: ListResponse[T]): JsValue = { + JsObject( + itemsField -> listResponse.items.map(_.toJson).toJson, + metaField -> listResponse.meta.toJson + ) + } + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala index dbd0a43..61e0e7f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala @@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.{LocalDate, LocalDateTime, ZoneId, ZonedDateTime} import spray.json._ -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} object common { @@ -55,14 +55,6 @@ object common { } } - implicit def fuzzyValueFormat: RootJsonFormat[FuzzyValue] = new RootJsonFormat[FuzzyValue] { - override def write(value: FuzzyValue): JsString = JsString(FuzzyValue.valueToString(value)) - override def read(json: JsValue): FuzzyValue = json match { - case JsString(value) => FuzzyValue.fromString(value) - case _ => deserializationError(s"Expected value as FuzzyValue, but got $json") - } - } - implicit val integerFormat: RootJsonFormat[Integer] = new RootJsonFormat[Integer] { override def write(obj: Integer): JsNumber = JsNumber(obj.intValue()) override def read(json: JsValue): Integer = json match { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala index 7526d9c..a43e92a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala @@ -10,7 +10,7 @@ object criterion { import DefaultJsonProtocol._ import common._ - implicit val criterionLabelWriter = new JsonWriter[CriterionLabel] { + implicit val criterionLabelWriter = new RootJsonWriter[CriterionLabel] { override def write(obj: CriterionLabel) = JsObject( "labelId" -> obj.labelId.toJson, "categoryId" -> obj.categoryId.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala index e3f6a9c..69e8b75 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala @@ -26,7 +26,7 @@ object document { "PN" -> RequiredType.PN ) - implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat3(Meta.apply) + implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat2(Meta.apply) implicit val documentTypeFormat: RootJsonFormat[DocumentType] = new RootJsonFormat[DocumentType] { override def read(json: JsValue): DocumentType = json match { @@ -40,7 +40,7 @@ object document { .fromString(name) .getOrElse(deserializationError(s"Unknown document type: $name")) - case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json") + case _ => deserializationError(s"Expected Json Object as Document type, but got $json") } override def write(obj: DocumentType) = @@ -73,6 +73,11 @@ object document { .map(_.convertTo[Option[LongId[ProviderType]]]) .getOrElse(orig.providerTypeId) + val institutionName = fields + .get("institutionName") + .map(_.convertTo[Option[String]]) + .getOrElse(orig.institutionName) + val meta = fields .get("meta") .map(_.convertTo[Option[TextJson[Meta]]]) @@ -93,6 +98,7 @@ object document { typeId = typeId, providerName = provider, providerTypeId = providerTypeId, + institutionName = institutionName, meta = meta, startDate = startDate, endDate = endDate @@ -111,6 +117,7 @@ object document { "provider" -> document.providerName.toJson, "providerTypeId" -> document.providerTypeId.toJson, "requiredType" -> document.requiredType.toJson, + "institutionName" -> document.institutionName.toJson, "startDate" -> document.startDate.toJson, "endDate" -> document.endDate.toJson, "status" -> document.status.toJson, @@ -145,6 +152,10 @@ object document { .get("providerTypeId") .map(_.convertTo[LongId[ProviderType]]) + val institutionName = fields + .get("institutionName") + .map(_.convertTo[String]) + val meta = fields .get("meta") .map(_.convertTo[TextJson[Meta]]) @@ -168,6 +179,7 @@ object document { providerName = provider, providerTypeId = providerTypeId, requiredType = None, + institutionName = institutionName, meta = meta, previousStatus = None, assignee = None, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala index b836e1c..3c2465f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala @@ -21,7 +21,7 @@ object eligibility { implicit val clinicalDocumentFormat: RootJsonFormat[ClinicalEvidenceDocument] = jsonFormat7(ClinicalEvidenceDocument) implicit val evidenceDocumentFormat: RootJsonFormat[EvidenceDocument] = - GadtJsonFormat.create[EvidenceDocument]("documentType") { + GadtJsonFormat.create[EvidenceDocument]("evidenceDocumentType") { case _: MolecularEvidenceDocument => "Molecular" case _: ClinicalEvidenceDocument => "Clinical" } { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala index 39d5c59..1c4b6b4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala @@ -2,15 +2,16 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.entities.labels.Label -import xyz.driver.pdsuidomain.entities.{Arm, Criterion} +import xyz.driver.formats.json.labels._ import xyz.driver.pdsuidomain.entities.export.patient._ import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm} object export { import DefaultJsonProtocol._ import common._ - import record._ import document._ + import record._ implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] = jsonFormat5(ExportPatientLabelEvidenceDocument.apply) @@ -67,7 +68,7 @@ object export { longIdFormat[Criterion].read(criterionId), value, longIdFormat[Label].read(labelId), - armIdsVector.map(longIdFormat[Arm].read).toSet, + armIdsVector.map(longIdFormat[EligibilityArm].read).toSet, criterionText, isCompound, isDefining @@ -81,12 +82,5 @@ object export { } implicit val trialWithLabelsFormat: RootJsonFormat[ExportTrialWithLabels] = - jsonFormat(ExportTrialWithLabels.apply, - "nctId", - "trialId", - "disease", - "lastReviewed", - "labelVersion", - "arms", - "criteria") + jsonFormat(ExportTrialWithLabels.apply, "nctId", "trialId", "lastReviewed", "labelVersion", "arms", "criteria") } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala index d6eadbd..5d5585a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson} +import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} +import xyz.driver.pdsuicommon.domain.{LongId, TextJson} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData +import xyz.driver.formats.json.labels._ object extracteddata { import DefaultJsonProtocol._ @@ -44,7 +45,7 @@ object extracteddata { val value = fields .get("value") - .map(_.convertTo[FuzzyValue]) + .map(_.convertTo[LabelValue]) ExtractedDataLabel( id = LongId(0), diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala index 724c391..2b0dfe5 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala @@ -3,6 +3,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.core.json.EnumJsonFormat import xyz.driver.pdsuidomain.entities._ +import xyz.driver.formats.json.common._ +import xyz.driver.formats.json.patient._ object patient { import DefaultJsonProtocol._ @@ -26,7 +28,7 @@ object patient { } } - implicit val patientWriter: JsonWriter[Patient] = new JsonWriter[Patient] { + implicit val patientWriter: RootJsonWriter[Patient] = new RootJsonWriter[Patient] { override def write(patient: Patient): JsValue = JsObject( "id" -> patient.id.toJson, @@ -38,7 +40,7 @@ object patient { "previousAssignee" -> patient.previousAssignee.toJson, "lastActiveUser" -> patient.lastActiveUserId.toJson, "lastUpdate" -> patient.lastUpdate.toJson, - "condition" -> patient.condition.toJson, + "disease" -> patient.disease.toJson, "orderId" -> patient.orderId.toJson ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala index b091746..7e8c220 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala @@ -1,10 +1,10 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion +import xyz.driver.pdsuidomain.services.PatientCriterionService.{DraftPatientCriterion, RichPatientCriterion} +import xyz.driver.formats.json.labels._ object patientcriterion { import DefaultJsonProtocol._ @@ -15,13 +15,13 @@ object patientcriterion { val eligibilityStatus = if (fields.contains("eligibilityStatus")) { fields .get("eligibilityStatus") - .map(_.convertTo[FuzzyValue]) + .map(_.convertTo[LabelValue]) } else orig.eligibilityStatus val verifiedEligibilityStatus = if (fields.contains("verifiedEligibilityStatus")) { fields .get("verifiedEligibilityStatus") - .map(_.convertTo[FuzzyValue]) + .map(_.convertTo[LabelValue]) } else orig.verifiedEligibilityStatus orig.copy( @@ -38,30 +38,27 @@ object patientcriterion { override def read(json: JsValue) = json.convertTo[List[JsValue]].map(_.convertTo[DraftPatientCriterion]) } - implicit val patientCriterionWriter: JsonWriter[(PatientCriterion, LongId[Label], List[PatientCriterionArm])] = - new JsonWriter[(PatientCriterion, LongId[Label], List[PatientCriterionArm])] { - override def write(obj: (PatientCriterion, LongId[Label], List[PatientCriterionArm])): JsValue = { - val criterion = obj._1 - val labelId = obj._2 - val arms = obj._3 + implicit val patientCriterionWriter: RootJsonWriter[RichPatientCriterion] = + new RootJsonWriter[RichPatientCriterion] { + override def write(obj: RichPatientCriterion): JsValue = { JsObject( - "id" -> criterion.id.toJson, - "labelId" -> labelId.toJson, - "nctId" -> criterion.nctId.toJson, - "criterionId" -> criterion.criterionId.toJson, - "criterionText" -> criterion.criterionText.toJson, - "criterionValue" -> criterion.criterionValue.map { + "id" -> obj.patientCriterion.id.toJson, + "labelId" -> obj.labelId.toJson, + "nctId" -> obj.patientCriterion.nctId.toJson, + "criterionId" -> obj.patientCriterion.criterionId.toJson, + "criterionText" -> obj.patientCriterion.criterionText.toJson, + "criterionValue" -> obj.patientCriterion.criterionValue.map { case true => "Yes" case false => "No" }.toJson, - "criterionIsDefining" -> criterion.criterionIsDefining.toJson, - "criterionIsCompound" -> criterion.criterionValue.isEmpty.toJson, - "arms" -> arms.map(_.armName).toJson, - "eligibilityStatus" -> criterion.eligibilityStatus.toJson, - "verifiedEligibilityStatus" -> criterion.verifiedEligibilityStatus.toJson, - "isVerified" -> criterion.isVerified.toJson, - "isVisible" -> criterion.isVisible.toJson, - "lastUpdate" -> criterion.lastUpdate.toJson + "criterionIsDefining" -> obj.patientCriterion.criterionIsDefining.toJson, + "criterionIsCompound" -> obj.patientCriterion.criterionValue.isEmpty.toJson, + "arms" -> obj.armList.map(_.armName).toJson, + "eligibilityStatus" -> obj.patientCriterion.eligibilityStatus.toJson, + "verifiedEligibilityStatus" -> obj.patientCriterion.verifiedEligibilityStatus.toJson, + "isVerified" -> obj.patientCriterion.isVerified.toJson, + "isVisible" -> obj.patientCriterion.isVisible.toJson, + "lastUpdate" -> obj.patientCriterion.lastUpdate.toJson ) } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala index b97570a..746c7b4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala @@ -2,12 +2,13 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuidomain.entities.PatientLabel +import xyz.driver.formats.json.labels._ object patientdefiningcriteria { import DefaultJsonProtocol._ import common._ - implicit val patientLabelDefiningCriteriaWriter: JsonWriter[PatientLabel] = new JsonWriter[PatientLabel] { + implicit val patientLabelDefiningCriteriaWriter: RootJsonWriter[PatientLabel] = new RootJsonWriter[PatientLabel] { override def write(obj: PatientLabel) = JsObject( "id" -> obj.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala index 894e453..342d3a8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala @@ -3,6 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial +import xyz.driver.formats.json.labels._ object patienteligibletrial { import DefaultJsonProtocol._ @@ -21,8 +22,8 @@ object patienteligibletrial { case _ => deserializationError(s"Expected Json Object as partial PatientTrialArmGroupView, but got $json") } - implicit val patientEligibleTrialWriter: JsonWriter[RichPatientEligibleTrial] = - new JsonWriter[RichPatientEligibleTrial] { + implicit val patientEligibleTrialWriter: RootJsonWriter[RichPatientEligibleTrial] = + new RootJsonWriter[RichPatientEligibleTrial] { override def write(obj: RichPatientEligibleTrial) = JsObject( "id" -> obj.group.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala index 4f2783c..b8c0058 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientHypothesisService.RichPatientHypothesis object patienthypothesis { import DefaultJsonProtocol._ @@ -18,18 +19,29 @@ object patienthypothesis { case _ => deserializationError(s"Expected Json Object as partial PatientHypothesis, but got $json") } - implicit val patientHypothesisWriter: JsonWriter[(PatientHypothesis, Boolean)] = - new JsonWriter[(PatientHypothesis, Boolean)] { - override def write(obj: (PatientHypothesis, Boolean)): JsValue = { - val patientHypothesis = obj._1 - val isRationaleRequired = obj._2 + implicit val richPatientHypothesisWriter: RootJsonWriter[RichPatientHypothesis] = + new RootJsonWriter[RichPatientHypothesis] { + override def write(obj: RichPatientHypothesis): JsValue = { JsObject( - "id" -> patientHypothesis.id.toJson, - "patientId" -> patientHypothesis.patientId.toJson, - "hypothesisId" -> patientHypothesis.hypothesisId.toJson, - "matchedTrials" -> patientHypothesis.matchedTrials.toJson, - "rationale" -> patientHypothesis.rationale.toJson, - "isRationaleRequired" -> isRationaleRequired.toJson + "id" -> obj.patientHypothesis.id.toJson, + "patientId" -> obj.patientHypothesis.patientId.toJson, + "hypothesisId" -> obj.patientHypothesis.hypothesisId.toJson, + "matchedTrials" -> obj.patientHypothesis.matchedTrials.toJson, + "rationale" -> obj.patientHypothesis.rationale.toJson, + "isRationaleRequired" -> obj.isRequired.toJson + ) + } + } + + implicit val patientHypothesisWriter: RootJsonWriter[PatientHypothesis] = + new RootJsonWriter[PatientHypothesis] { + override def write(obj: PatientHypothesis): JsValue = { + JsObject( + "id" -> obj.id.toJson, + "patientId" -> obj.patientId.toJson, + "hypothesisId" -> obj.hypothesisId.toJson, + "matchedTrials" -> obj.matchedTrials.toJson, + "rationale" -> obj.rationale.toJson ) } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala index 7d35bd1..d325a53 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala @@ -40,7 +40,7 @@ object patientissue { } - implicit val patientIssueWriter = new JsonWriter[PatientIssue] { + implicit val patientIssueWriter = new RootJsonWriter[PatientIssue] { override def write(obj: PatientIssue) = JsObject( "id" -> obj.id.toJson, "text" -> obj.text.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala index 3b52833..57dca1e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala @@ -1,8 +1,12 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ -import xyz.driver.pdsuicommon.domain.FuzzyValue +import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientLabelService.RichPatientLabel +import xyz.driver.formats.json.labels._ +import xyz.driver.pdsuidomain.formats.json.sprayformats.record._ +import xyz.driver.pdsuidomain.formats.json.sprayformats.document._ object patientlabel { import DefaultJsonProtocol._ @@ -12,12 +16,12 @@ object patientlabel { case JsObject(fields) => val primaryValue = fields .get("primaryValue") - .map(_.convertTo[Option[FuzzyValue]]) + .map(_.convertTo[Option[LabelValue]]) .getOrElse(orig.primaryValue) val verifiedPrimaryValue = fields .get("verifiedPrimaryValue") - .map(_.convertTo[Option[FuzzyValue]]) + .map(_.convertTo[Option[LabelValue]]) .getOrElse(orig.verifiedPrimaryValue) orig.copy( @@ -28,25 +32,23 @@ object patientlabel { case _ => deserializationError(s"Expected Json Object as PatientLabel, but got $json") } - implicit val patientLabelWriter: JsonWriter[(PatientLabel, Boolean)] = new JsonWriter[(PatientLabel, Boolean)] { - override def write(obj: (PatientLabel, Boolean)): JsValue = { - val patientLabel = obj._1 - val isVerified = obj._2 + implicit val richPatientLabelWriter: RootJsonWriter[RichPatientLabel] = new RootJsonWriter[RichPatientLabel] { + override def write(obj: RichPatientLabel): JsValue = { JsObject( - "id" -> patientLabel.id.toJson, - "labelId" -> patientLabel.labelId.toJson, - "primaryValue" -> patientLabel.primaryValue.toJson, - "verifiedPrimaryValue" -> patientLabel.verifiedPrimaryValue.toJson, - "score" -> patientLabel.score.toJson, - "isImplicitMatch" -> patientLabel.isImplicitMatch.toJson, - "isVisible" -> patientLabel.isVisible.toJson, - "isVerified" -> isVerified.toJson + "id" -> obj.patientLabel.id.toJson, + "labelId" -> obj.patientLabel.labelId.toJson, + "primaryValue" -> obj.patientLabel.primaryValue.toJson, + "verifiedPrimaryValue" -> obj.patientLabel.verifiedPrimaryValue.toJson, + "score" -> obj.patientLabel.score.toJson, + "isImplicitMatch" -> obj.patientLabel.isImplicitMatch.toJson, + "isVisible" -> obj.patientLabel.isVisible.toJson, + "isVerified" -> obj.isVerified.toJson ) } } - implicit val patientLabelEvidenceWriter: JsonWriter[PatientLabelEvidenceView] = - new JsonWriter[PatientLabelEvidenceView] { + implicit val patientLabelEvidenceWriter: RootJsonWriter[PatientLabelEvidenceView] = + new RootJsonWriter[PatientLabelEvidenceView] { override def write(evidence: PatientLabelEvidenceView): JsValue = JsObject( "id" -> evidence.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala index 8eef44a..65687c1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala @@ -67,7 +67,6 @@ object record { override def write(obj: Duplicate) = JsObject( "type" -> "duplicate".toJson, - "predicted" -> obj.predicted.toJson, "startPage" -> obj.startPage.toJson, "endPage" -> obj.endPage.toJson, "startOriginalPage" -> obj.startOriginalPage.toJson, @@ -76,10 +75,6 @@ object record { override def read(json: JsValue): Duplicate = json match { case JsObject(fields) => - val predicted = fields - .get("predicted") - .map(_.convertTo[Boolean]) - val startPage = fields .get("startPage") .map(_.convertTo[Double]) @@ -101,7 +96,6 @@ object record { .map(_.convertTo[Double]) Duplicate( - predicted = predicted, startPage = startPage, endPage = endPage, startOriginalPage = startOriginalPage, @@ -114,27 +108,16 @@ object record { implicit val reorderMetaFormat: RootJsonFormat[Reorder] = new RootJsonFormat[Reorder] { override def write(obj: Reorder) = - JsObject( - "type" -> "reorder".toJson, - "predicted" -> obj.predicted.toJson, - "items" -> obj.items.toJson - ) + JsObject("type" -> "reorder".toJson, "items" -> obj.items.toJson) override def read(json: JsValue): Reorder = json match { case JsObject(fields) => - val predicted = fields - .get("predicted") - .map(_.convertTo[Boolean]) - val items = fields .get("items") .map(_.convertTo[Seq[Int]]) .getOrElse(deserializationError(s"Reorder meta json object does not contain `items` field: $json")) - Reorder( - predicted = predicted, - items = items - ) + Reorder(items) case _ => deserializationError(s"Expected JsObject as Reorder meta of medical record, but got $json") } @@ -142,27 +125,16 @@ object record { implicit val rotateMetaFormat: RootJsonFormat[Rotation] = new RootJsonFormat[Rotation] { override def write(obj: Rotation) = - JsObject( - "type" -> "rotation".toJson, - "predicted" -> obj.predicted.toJson, - "items" -> obj.items.toJson - ) + JsObject("type" -> "rotation".toJson, "items" -> obj.items.toJson) override def read(json: JsValue): Rotation = json match { case JsObject(fields) => - val predicted = fields - .get("predicted") - .map(_.convertTo[Boolean]) - val items = fields .get("items") .map(_.convertTo[Map[String, Int]]) .getOrElse(deserializationError(s"Rotation meta json object does not contain `items` field: $json")) - Rotation( - predicted = predicted, - items = items - ) + Rotation(items = items) case _ => deserializationError(s"Expected JsObject as Rotation meta of medical record, but got $json") } @@ -233,8 +205,6 @@ object record { caseId = None, physician = None, meta = None, - predictedMeta = None, - predictedDocuments = None, lastUpdate = LocalDateTime.now() ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala index a778000..b25ed1d 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala @@ -9,8 +9,8 @@ import xyz.driver.pdsuidomain.entities._ object trial { import DefaultJsonProtocol._ - import common._ import Trial._ + import common._ implicit val trialStatusFormat = new EnumJsonFormat[Status]( "New" -> Status.New, @@ -24,13 +24,7 @@ object trial { "Archived" -> Status.Archived ) - implicit val conditionFormat = new EnumJsonFormat[Condition]( - "Breast" -> Condition.Breast, - "Lung" -> Condition.Lung, - "Prostate" -> Condition.Prostate - ) - - implicit val trialWriter: JsonWriter[Trial] = new JsonWriter[Trial] { + implicit val trialWriter: RootJsonWriter[Trial] = new RootJsonWriter[Trial] { override def write(obj: Trial) = JsObject( "id" -> obj.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala index 572f44d..d1ca191 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala @@ -44,7 +44,7 @@ object trialissue { } - implicit val trialIssueWriter = new JsonWriter[TrialIssue] { + implicit val trialIssueWriter = new RootJsonWriter[TrialIssue] { override def write(obj: TrialIssue) = JsObject( "id" -> obj.id.toJson, "text" -> obj.text.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala index fbf506b..133a2c8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala @@ -2,11 +2,11 @@ package xyz.driver.pdsuidomain.formats.json.trial import java.time.{ZoneId, ZonedDateTime} import java.util.UUID -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities.Trial import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} +import xyz.driver.pdsuidomain.entities.Trial final case class ApiTrial(id: String, externalId: UUID, |