diff options
author | Marvin Bertin <marvin.bertin@gmail.com> | 2017-10-10 11:54:20 -0700 |
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committer | Marvin Bertin <marvin.bertin@gmail.com> | 2017-10-10 11:54:20 -0700 |
commit | 19a70318ecee81872fffe23c03d83e725610911d (patch) | |
tree | 984510310c95856fcdcb463d9a242f9773795266 /src/main/scala/xyz/driver/pdsuidomain/formats/json | |
parent | 05aa114cfd22228f0457b6457ce441af5eabfc60 (diff) | |
parent | 4f83461cba1f78e607ca2a4edb6fa26f6e16e732 (diff) | |
download | rest-query-19a70318ecee81872fffe23c03d83e725610911d.tar.gz rest-query-19a70318ecee81872fffe23c03d83e725610911d.tar.bz2 rest-query-19a70318ecee81872fffe23c03d83e725610911d.zip |
fix merge conflicts with master
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/formats/json')
28 files changed, 148 insertions, 151 deletions
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 4d6d0a2..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 @@ -2,10 +2,15 @@ package xyz.driver.pdsuidomain.formats.json.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, Trial} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases} -final case class ApiEligibilityArm(id: Long, name: String, originalName: String, trialId: String, diseases: Seq[String]) { +final case class ApiEligibilityArm(id: Long, + name: String, + originalName: String, + trialId: String, + diseases: Seq[String]) { def toDomain: EligibilityArmWithDiseases = { val eligibilityArm = EligibilityArm( @@ -16,11 +21,15 @@ final case class ApiEligibilityArm(id: Long, name: String, originalName: String, deleted = None // if we have an ApiEligibilityArm object, the EligibilityArm itself has not been deleted ) - EligibilityArmWithDiseases(eligibilityArm, this.diseases.map { disease => - val condition = Trial.Condition.fromString(disease) - .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) - EligibilityArmDisease(eligibilityArm.id, condition) - }) + EligibilityArmWithDiseases( + eligibilityArm, + this.diseases.map { disease => + val condition = CancerType + .fromString(disease) + .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) + EligibilityArmDisease(eligibilityArm.id, condition) + } + ) } } 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 6cf71a2..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 @@ -1,8 +1,9 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases, Trial} 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]) { @@ -14,11 +15,15 @@ final case class ApiCreateEligibilityArm(name: String, trialId: String, diseases originalName = name ) - EligibilityArmWithDiseases(eligibilityArm, diseases.map { disease => - val condition = Trial.Condition.fromString(disease) - .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) - EligibilityArmDisease(eligibilityArm.id, condition) - }) + EligibilityArmWithDiseases( + eligibilityArm, + diseases.map { disease => + val condition = CancerType + .fromString(disease) + .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) + EligibilityArmDisease(eligibilityArm.id, condition) + } + ) } } 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 3d9445f..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 @@ -1,7 +1,8 @@ package xyz.driver.pdsuidomain.formats.json.eligibilityarm import play.api.libs.json.{Format, Json} -import xyz.driver.pdsuidomain.entities.{EligibilityArmDisease, EligibilityArmWithDiseases, Trial} +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuidomain.entities.{EligibilityArmDisease, EligibilityArmWithDiseases} final case class ApiPartialEligibilityArm(name: String, diseases: Seq[String]) { @@ -10,9 +11,9 @@ final case class ApiPartialEligibilityArm(name: String, diseases: Seq[String]) { val armDiseases = diseases.map { disease => EligibilityArmDisease( armWithDisease.eligibilityArm.id, - Trial.Condition.fromString(disease).getOrElse(throw new NoSuchElementException(s"unknown condition $disease"))) + CancerType.fromString(disease).getOrElse(throw new NoSuchElementException(s"unknown condition $disease"))) } - EligibilityArmWithDiseases(arm ,armDiseases) + EligibilityArmWithDiseases(arm, armDiseases) } } 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/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/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala index 6c33fe5..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 { 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..85d614d 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 @@ -5,6 +5,7 @@ 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} +import xyz.driver.formats.json.labels._ object export { import DefaultJsonProtocol._ 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 95c0674..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._ @@ -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 affb346..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 @@ -1,9 +1,10 @@ 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.PatientCriterionService.{DraftPatientCriterion, RichPatientCriterion} +import xyz.driver.formats.json.labels._ object patientcriterion { import DefaultJsonProtocol._ @@ -14,13 +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( 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 0520ef2..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 @@ -2,6 +2,7 @@ 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._ 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 041d9da..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._ 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 b36949e..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 @@ -1,9 +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._ @@ -13,12 +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( 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 aeec90f..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, @@ -24,12 +24,6 @@ object trial { "Archived" -> Status.Archived ) - implicit val conditionFormat = new EnumJsonFormat[Condition]( - "Breast" -> Condition.Breast, - "Lung" -> Condition.Lung, - "Prostate" -> Condition.Prostate - ) - implicit val trialWriter: RootJsonWriter[Trial] = new RootJsonWriter[Trial] { override def write(obj: Trial) = JsObject( 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, |