diff options
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/formats/json/patient')
12 files changed, 445 insertions, 0 deletions
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 new file mode 100644 index 0000000..0a3938c --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala @@ -0,0 +1,44 @@ +package xyz.driver.pdsuidomain.formats.json.patient + +import java.time.{LocalDate, ZoneId, ZonedDateTime} + +import xyz.driver.pdsuidomain.entities.Patient +import play.api.libs.functional.syntax._ +import play.api.libs.json.{Format, JsPath} + +final case class ApiPatient(id: String, + status: String, + name: String, + dob: LocalDate, + assignee: Option[Long], + previousStatus: Option[String], + previousAssignee: Option[Long], + lastUpdate: ZonedDateTime, + condition: String) + +object ApiPatient { + + implicit val format: Format[ApiPatient] = ( + (JsPath \ "id").format[String] and + (JsPath \ "status").format[String] and + (JsPath \ "name").format[String] and + (JsPath \ "dob").format[LocalDate] and + (JsPath \ "assignee").formatNullable[Long] and + (JsPath \ "previousStatus").formatNullable[String] and + (JsPath \ "previousAssignee").formatNullable[Long] and + (JsPath \ "lastUpdate").format[ZonedDateTime] and + (JsPath \ "condition").format[String] + ) (ApiPatient.apply, unlift(ApiPatient.unapply)) + + def fromDomain(patient: Patient) = ApiPatient( + id = patient.id.toString, + status = PatientStatus.statusToString(patient.status), + name = patient.name, + dob = patient.dob, + assignee = patient.assignee.map(_.id), + previousStatus = patient.previousStatus.map(PatientStatus.statusToString), + previousAssignee = patient.previousAssignee.map(_.id), + lastUpdate = ZonedDateTime.of(patient.lastUpdate, ZoneId.of("Z")), + condition = patient.condition + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/PatientStatus.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/PatientStatus.scala new file mode 100644 index 0000000..d906fc6 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/PatientStatus.scala @@ -0,0 +1,24 @@ +package xyz.driver.pdsuidomain.formats.json.patient + +import xyz.driver.pdsuidomain.entities.Patient.Status + +object PatientStatus { + + val statusFromString: PartialFunction[String, Status] = { + case "New" => Status.New + case "Verified" => Status.Verified + case "Reviewed" => Status.Reviewed + case "Curated" => Status.Curated + case "Flagged" => Status.Flagged + case "Done" => Status.Done + } + + def statusToString(x: Status): String = x match { + case Status.New => "New" + case Status.Verified => "Verified" + case Status.Reviewed => "Reviewed" + case Status.Curated => "Curated" + case Status.Flagged => "Flagged" + case Status.Done => "Done" + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPartialPatientEligibleTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPartialPatientEligibleTrial.scala new file mode 100644 index 0000000..03ff275 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPartialPatientEligibleTrial.scala @@ -0,0 +1,18 @@ +package xyz.driver.pdsuidomain.formats.json.patient.eligible + +import xyz.driver.pdsuidomain.entities.PatientTrialArmGroupView +import play.api.libs.json.{Format, Json} + +final case class ApiPartialPatientEligibleTrial(isVerified: Option[Boolean]) { + + def applyTo(orig: PatientTrialArmGroupView): PatientTrialArmGroupView = { + orig.copy( + isVerified = isVerified.getOrElse(orig.isVerified) + ) + } +} + +object ApiPartialPatientEligibleTrial { + + implicit val format: Format[ApiPartialPatientEligibleTrial] = Json.format +} 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 new file mode 100644 index 0000000..c1a6e76 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala @@ -0,0 +1,46 @@ +package xyz.driver.pdsuidomain.formats.json.patient.eligible + +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.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial + +final case class ApiPatientEligibleTrial(id: Long, + patientId: String, + trialId: String, + trialTitle: String, + arms: List[String], + hypothesisId: UUID, + eligibilityStatus: Option[String], + isVerified: Boolean) + +object ApiPatientEligibleTrial { + + implicit val apiEligibleTrialJsonFormat: Format[ApiPatientEligibleTrial] = ( + (JsPath \ "id").format[Long] and + (JsPath \ "patientId").format[String] and + (JsPath \ "trialId").format[String] and + (JsPath \ "trialTitle").format[String] and + (JsPath \ "arms").format[List[String]] and + (JsPath \ "hypothesisId").format[UUID] and + (JsPath \ "eligibilityStatus").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown eligibility status"))({ + case x if FuzzyValue.fromString.isDefinedAt(x) => true + case _ => false + }), Writes.of[String])) and + (JsPath \ "isVerified").format[Boolean] + ) (ApiPatientEligibleTrial.apply, unlift(ApiPatientEligibleTrial.unapply)) + + def fromDomain(eligibleTrialWithTrial: RichPatientEligibleTrial) = ApiPatientEligibleTrial( + id = eligibleTrialWithTrial.group.id.id, + patientId = eligibleTrialWithTrial.group.patientId.toString, + trialId = eligibleTrialWithTrial.group.trialId.id, + trialTitle = eligibleTrialWithTrial.trial.title, + arms = eligibleTrialWithTrial.arms.map(_.name), + hypothesisId = eligibleTrialWithTrial.group.hypothesisId.id, + eligibleTrialWithTrial.group.eligibilityStatus.map(FuzzyValue.valueToString), + eligibleTrialWithTrial.group.isVerified + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/hypothesis/ApiPartialPatientHypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/hypothesis/ApiPartialPatientHypothesis.scala new file mode 100644 index 0000000..0858ce1 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/hypothesis/ApiPartialPatientHypothesis.scala @@ -0,0 +1,27 @@ +package xyz.driver.pdsuidomain.formats.json.patient.hypothesis + +import xyz.driver.pdsuidomain.entities.PatientHypothesis +import org.davidbild.tristate.Tristate +import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath +import play.api.libs.functional.syntax._ +import play.api.libs.json._ + +final case class ApiPartialPatientHypothesis(rationale: Tristate[String]) { + + def applyTo(orig: PatientHypothesis): PatientHypothesis = { + orig.copy( + rationale = rationale.cata(Some(_), None, orig.rationale) + ) + } +} + +object ApiPartialPatientHypothesis { + + implicit val reads: Reads[ApiPartialPatientHypothesis] = + (__ \ "rationale").readTristate[String].map(x => ApiPartialPatientHypothesis(x)) + + implicit val writes: Writes[ApiPartialPatientHypothesis] = + (__ \ "rationale").writeTristate[String].contramap(_.rationale) + + implicit val format: Format[ApiPartialPatientHypothesis] = Format(reads, writes) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/hypothesis/ApiPatientHypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/hypothesis/ApiPatientHypothesis.scala new file mode 100644 index 0000000..1b0767d --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/hypothesis/ApiPatientHypothesis.scala @@ -0,0 +1,32 @@ +package xyz.driver.pdsuidomain.formats.json.patient.hypothesis + +import java.util.UUID + +import xyz.driver.pdsuidomain.entities.PatientHypothesis +import play.api.libs.functional.syntax._ +import play.api.libs.json._ + +final case class ApiPatientHypothesis(id: UUID, + patientId: String, + hypothesisId: UUID, + matchedTrials: Long, + rationale: Option[String]) + +object ApiPatientHypothesis { + + implicit val apiPatientHypothesisJsonFormat: Format[ApiPatientHypothesis] = ( + (JsPath \ "id").format[UUID] and + (JsPath \ "patientId").format[String] and + (JsPath \ "hypothesisId").format[UUID] and + (JsPath \ "matchedTrials").format[Long] and + (JsPath \ "rationale").formatNullable[String] + ) (ApiPatientHypothesis.apply, unlift(ApiPatientHypothesis.unapply)) + + def fromDomain(patientHypothesis: PatientHypothesis) = ApiPatientHypothesis( + id = patientHypothesis.id.id, + patientId = patientHypothesis.patientId.toString, + hypothesisId = patientHypothesis.hypothesisId.id, + matchedTrials = patientHypothesis.matchedTrials, + rationale = patientHypothesis.rationale + ) +} 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 new file mode 100644 index 0000000..82e3a3f --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala @@ -0,0 +1,38 @@ +package xyz.driver.pdsuidomain.formats.json.patient.label + +import xyz.driver.pdsuidomain.entities.PatientLabel +import org.davidbild.tristate.Tristate +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 + +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) + ) + } + +} + +object ApiPartialPatientLabel { + + implicit val format: Format[ApiPartialPatientLabel] = ( + (JsPath \ "primaryValue").formatNullable[String](Format( + Reads.of[String].filter(ValidationError("unknown primary value"))({ + case x if FuzzyValue.fromString.isDefinedAt(x) => true + case _ => false + }), Writes.of[String])) and + (JsPath \ "verifiedPrimaryValue").formatTristate[String](Format( + Reads.of[String].filter(ValidationError("unknown verified primary value"))({ + case x if FuzzyValue.fromString.isDefinedAt(x) => true + case _ => false + }), Writes.of[String])) + ) (ApiPartialPatientLabel.apply, unlift(ApiPartialPatientLabel.unapply)) + +} 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 new file mode 100644 index 0000000..fc8687b --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala @@ -0,0 +1,47 @@ +package xyz.driver.pdsuidomain.formats.json.patient.label + +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 + +final case class ApiPatientLabel(id: Long, + labelId: Long, + primaryValue: Option[String], + verifiedPrimaryValue: Option[String], + score: Int, + isImplicitMatch: Boolean, + isVisible: Boolean, + isVerified: Boolean) + +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 \ "score").format[Int] and + (JsPath \ "isImplicitMatch").format[Boolean] and + (JsPath \ "isVisible").format[Boolean] and + (JsPath \ "isVerified").format[Boolean] + ) (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), + score = patientLabel.score, + isImplicitMatch = patientLabel.isImplicitMatch, + isVisible = patientLabel.isVisible, + isVerified = isVerified + ) +} 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 new file mode 100644 index 0000000..3fe135e --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala @@ -0,0 +1,25 @@ +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.pdsuidomain.entities.PatientLabel + +final case class ApiPatientLabelDefiningCriteria(labelId: Long, value: Option[String]) + +object ApiPatientLabelDefiningCriteria { + + implicit val format: Format[ApiPatientLabelDefiningCriteria] = ( + (JsPath \ "labelId").format[Long] and + (JsPath \ "value").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({ + case x if FuzzyValue.fromString.isDefinedAt(x) => 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) + ) +} 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 new file mode 100644 index 0000000..b68dad5 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala @@ -0,0 +1,40 @@ +package xyz.driver.pdsuidomain.formats.json.patient.trial + +import xyz.driver.pdsuidomain.entities.PatientCriterion +import org.davidbild.tristate.Tristate +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 + +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), + verifiedEligibilityStatus = verifiedEligibilityStatus.cata(x => + Some(FuzzyValue.fromString(x)), + None, + orig.verifiedEligibilityStatus + ) + ) + } +} + +object ApiPartialPatientCriterion { + + implicit val format: Format[ApiPartialPatientCriterion] = ( + (JsPath \ "eligibilityStatus").formatNullable[String](Format( + Reads.of[String].filter(ValidationError("unknown eligibility status"))({ + case x if FuzzyValue.fromString.isDefinedAt(x) => true + case _ => false + }), Writes.of[String])) and + (JsPath \ "verifiedEligibilityStatus").formatTristate[String](Format( + Reads.of[String].filter(ValidationError("unknown verified eligibility status"))({ + case x if FuzzyValue.fromString.isDefinedAt(x) => true + case _ => false + }), Writes.of[String])) + ) (ApiPartialPatientCriterion.apply, unlift(ApiPartialPatientCriterion.unapply)) +} 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 new file mode 100644 index 0000000..71cb58f --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala @@ -0,0 +1,32 @@ +package xyz.driver.pdsuidomain.formats.json.patient.trial + +import xyz.driver.pdsuicommon.domain.{FuzzyValue, 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.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion + +final case class ApiPartialPatientCriterionList(id: Long, + eligibilityStatus: Option[String], + isVerified: Option[Boolean]) { + + def toDomain: DraftPatientCriterion = DraftPatientCriterion( + id = LongId[PatientCriterion](id), + eligibilityStatus = eligibilityStatus.map(FuzzyValue.fromString), + isVerified = isVerified + ) +} + +object ApiPartialPatientCriterionList { + + implicit val format: Format[ApiPartialPatientCriterionList] = ( + (JsPath \ "id").format[Long] and + (JsPath \ "eligibilityStatus").formatNullable[String](Format( + Reads.of[String].filter(ValidationError("unknown eligibility status"))({ + case x if FuzzyValue.fromString.isDefinedAt(x) => true + case _ => false + }), Writes.of[String])) and + (JsPath \ "isVerified").formatNullable[Boolean] + ) (ApiPartialPatientCriterionList.apply, unlift(ApiPartialPatientCriterionList.unapply)) +} 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 new file mode 100644 index 0000000..3e2de99 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala @@ -0,0 +1,72 @@ +package xyz.driver.pdsuidomain.formats.json.patient.trial + +import java.time.{ZoneId, ZonedDateTime} + +import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuidomain.entities.{Arm, Label, PatientCriterion} +import play.api.data.validation.ValidationError +import play.api.libs.functional.syntax._ +import play.api.libs.json.{Format, JsPath, Reads, Writes} + +final case class ApiPatientCriterion(id: Long, + labelId: Long, + nctId: String, + criterionText: String, + criterionValue: Option[String], + criterionIsDefining: Boolean, + criterionIsCompound: Boolean, + arms: List[String], + eligibilityStatus: Option[String], + verifiedEligibilityStatus: Option[String], + isVerified: Boolean, + isVisible: Boolean, + lastUpdate: ZonedDateTime) + +object ApiPatientCriterion { + + implicit val format: Format[ApiPatientCriterion] = ( + (JsPath \ "id").format[Long] and + (JsPath \ "labelId").format[Long] and + (JsPath \ "nctId").format[String] and + (JsPath \ "criterionText").format[String] and + (JsPath \ "criterionValue").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({ x => + x == "Yes" || x == "No" + }), Writes.of[String])) and + (JsPath \ "criterionIsDefining").format[Boolean] and + (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 + }), 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 + }), Writes.of[String])) and + (JsPath \ "isVerified").format[Boolean] and + (JsPath \ "isVisible").format[Boolean] and + (JsPath \ "lastUpdate").format[ZonedDateTime] + ) (ApiPatientCriterion.apply, unlift(ApiPatientCriterion.unapply)) + + def fromDomain(patientCriterion: PatientCriterion, + labelId: LongId[Label], + arms: List[Arm], + criterionIsCompound: Boolean) = ApiPatientCriterion( + id = patientCriterion.id.id, + labelId = labelId.id, + nctId = patientCriterion.nctId.id, + criterionText = patientCriterion.criterionText, + criterionValue = patientCriterion.criterionValue.map { x => + FuzzyValue.valueToString(FuzzyValue.fromBoolean(x)) + }, + criterionIsDefining = patientCriterion.criterionIsDefining, + criterionIsCompound = criterionIsCompound, + arms = arms.map(_.name), + eligibilityStatus = patientCriterion.eligibilityStatus.map(FuzzyValue.valueToString), + verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(FuzzyValue.valueToString), + isVerified = patientCriterion.isVerified, + isVisible = patientCriterion.isVisible, + lastUpdate = ZonedDateTime.of(patientCriterion.lastUpdate, ZoneId.of("Z")) + ) +} |