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author | Kseniya Tomskikh <ktomskih@datamonsters.co> | 2017-10-11 16:56:06 +0700 |
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committer | GitHub <noreply@github.com> | 2017-10-11 16:56:06 +0700 |
commit | 3375f1beeab7af9a6732d6fce8762c3a3038e1f3 (patch) | |
tree | e4f1ad85a2ea17c76bcc844420d5f97bfd116e23 /src | |
parent | bbbcaf35a6081dba24dbb9a9aeb9d25fc2ca60be (diff) | |
parent | 85c78f58f0428d13795aa0419ff42471513a34d6 (diff) | |
download | rest-query-3375f1beeab7af9a6732d6fce8762c3a3038e1f3.tar.gz rest-query-3375f1beeab7af9a6732d6fce8762c3a3038e1f3.tar.bz2 rest-query-3375f1beeab7af9a6732d6fce8762c3a3038e1f3.zip |
Merge pull request #37 from drivergroup/add-slot-eligibility-armsv0.8.1
Add slot eligibility arms
Diffstat (limited to 'src')
60 files changed, 925 insertions, 241 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala index 2432251..26ced22 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala @@ -30,7 +30,7 @@ object Criterion { } } -final case class CriterionArm(criterionId: LongId[Criterion], armId: LongId[Arm]) +final case class CriterionArm(criterionId: LongId[Criterion], armId: LongId[EligibilityArm]) object CriterionArm { diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala new file mode 100644 index 0000000..50b49ad --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala @@ -0,0 +1,42 @@ +package xyz.driver.pdsuidomain.entities + +import java.time.LocalDateTime + +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuicommon.logging._ + +final case class EligibilityArm(id: LongId[EligibilityArm], + name: String, + originalName: String, + trialId: StringId[Trial], + deleted: Option[LocalDateTime] = None) + +object EligibilityArm { + + implicit def toPhiString(x: EligibilityArm): PhiString = { + import x._ + phi"Arm(id=$id, name=${Unsafe(x.name)}, trialId=${Unsafe(x.trialId)})" + } +} + +final case class EligibilityArmDisease(eligibilityArmId: LongId[EligibilityArm], disease: CancerType) + +object EligibilityArmDisease { + + implicit def toPhiString(x: EligibilityArmDisease): PhiString = { + phi"EligibilityArmDisease(eligibilityArmId=${Unsafe(x.eligibilityArmId)}, disease=${Unsafe(x.disease)})" + } + +} + +final case class EligibilityArmWithDiseases(eligibilityArm: EligibilityArm, + eligibilityArmDiseases: Seq[EligibilityArmDisease]) + +object EligibilityArmWithDiseases { + + implicit def toPhiString(x: EligibilityArmWithDiseases): PhiString = { + import x._ + phi"EligibilityArmWithDiseases(eligibilityArm=$eligibilityArm, eligibilityArmDiseases=$eligibilityArmDiseases)" + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala index cc831cd..f02bedc 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala @@ -188,7 +188,7 @@ object InterventionType { } } -final case class InterventionArm(armId: LongId[Arm], interventionId: LongId[Intervention]) +final case class InterventionArm(armId: LongId[SlotArm], interventionId: LongId[Intervention]) object InterventionArm { implicit def toPhiString(x: InterventionArm): PhiString = { diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArmEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArmEligibilityArm.scala new file mode 100644 index 0000000..70114de --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArmEligibilityArm.scala @@ -0,0 +1,13 @@ +package xyz.driver.pdsuidomain.entities + +import xyz.driver.pdsuicommon.domain.LongId +import xyz.driver.pdsuicommon.logging._ + +final case class SlotArmEligibilityArm(slotArmId: LongId[SlotArm], eligibilityArmId: LongId[EligibilityArm]) + +object SlotArmEligibilityArm { + implicit def toPhiString(x: SlotArmEligibilityArm): PhiString = { + import x._ + phi"SlotArmEligibilityArm(slotArmId=$slotArmId, eligibilityArmId=$eligibilityArmId)" + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArms.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArms.scala new file mode 100644 index 0000000..932de38 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArms.scala @@ -0,0 +1,20 @@ +package xyz.driver.pdsuidomain.entities + +import java.time.LocalDateTime + +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuicommon.logging._ + +final case class SlotArm(id: LongId[SlotArm], + name: String, + originalName: String, + trialId: StringId[Trial], + deleted: Option[LocalDateTime] = None) + +object SlotArm { + + implicit def toPhiString(x: SlotArm): PhiString = { + import x._ + phi"Arm(id=$id, name=${Unsafe(x.name)}, trialId=${Unsafe(x.trialId)})" + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala index 7584e9c..ac5feef 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala @@ -2,7 +2,6 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDateTime -import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.domain.{LongId, StringId, User, UuidId} import xyz.driver.pdsuicommon.logging._ import xyz.driver.pdsuicommon.utils.Utils @@ -69,7 +68,6 @@ final case class Trial(id: StringId[Trial], previousAssignee: Option[StringId[User]], lastActiveUserId: Option[StringId[User]], lastUpdate: LocalDateTime, - disease: CancerType, phase: String, hypothesisId: Option[UuidId[Hypothesis]], studyDesignId: Option[LongId[StudyDesign]], diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala index 5a9a406..fbac0df 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala @@ -2,14 +2,14 @@ package xyz.driver.pdsuidomain.entities.export.trial import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.Arm +import xyz.driver.pdsuidomain.entities.EligibilityArm -final case class ExportTrialArm(armId: LongId[Arm], armName: String) +final case class ExportTrialArm(armId: LongId[EligibilityArm], armName: String, diseaseList: Seq[String]) object ExportTrialArm { implicit def toPhiString(x: ExportTrialArm): PhiString = { import x._ - phi"ExportTrialArm(armId=$armId, armName=${Unsafe(armName)})" + phi"ExportTrialArm(armId=$armId, armName=${Unsafe(armName)}, diseaseList=${Unsafe(diseaseList)})" } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala index 385bbbe..8376e34 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala @@ -3,12 +3,12 @@ package xyz.driver.pdsuidomain.entities.export.trial import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Arm, Criterion} +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm} final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion], value: Option[Boolean], labelId: LongId[Label], - armIds: Set[LongId[Arm]], + armIds: Set[LongId[EligibilityArm]], criteria: String, isCompound: Boolean, isDefining: Boolean) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala index 3a9434b..3681945 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala @@ -8,7 +8,6 @@ import xyz.driver.pdsuidomain.entities.Trial final case class ExportTrialWithLabels(nctId: StringId[Trial], trialId: UuidId[Trial], - disease: String, lastReviewed: LocalDateTime, labelVersion: Long, arms: List[ExportTrialArm], @@ -18,7 +17,7 @@ object ExportTrialWithLabels { implicit def toPhiString(x: ExportTrialWithLabels): PhiString = { import x._ - phi"TrialWithLabels(nctId=$nctId, trialId=$trialId, disease=${Unsafe(disease)}, " + + phi"TrialWithLabels(nctId=$nctId, trialId=$trialId}, " + phi"lastReviewed=$lastReviewed, labelVersion=${Unsafe(labelVersion)}, arms=$arms, criteria=$criteria)" } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala index a3ba562..1fe7533 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala @@ -1,22 +1,24 @@ package xyz.driver.pdsuidomain.fakes.entities import xyz.driver.entities.labels.Label -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial} import xyz.driver.pdsuidomain.entities.export.trial._ +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm, Trial} object export { - import xyz.driver.core.generators._ import common._ + import xyz.driver.core.generators._ def nextExportTrialArm(): ExportTrialArm = - ExportTrialArm(armId = nextLongId[Arm], armName = nextString(100)) + ExportTrialArm(armId = nextLongId[EligibilityArm], + armName = nextString(100), + diseaseList = listOf(nextString(100))) def nextExportTrialLabelCriterion(): ExportTrialLabelCriterion = ExportTrialLabelCriterion( criterionId = nextLongId[Criterion], value = nextOption[Boolean](nextBoolean()), labelId = nextLongId[Label], - armIds = setOf(nextLongId[Arm]), + armIds = setOf(nextLongId[EligibilityArm]), criteria = nextString(100), isCompound = nextBoolean(), isDefining = nextBoolean() @@ -26,7 +28,6 @@ object export { ExportTrialWithLabels( nctId = nextStringId[Trial], trialId = nextUuidId[Trial], - disease = nextString(100), lastReviewed = nextLocalDateTime, labelVersion = nextInt(100).toLong, arms = listOf(nextExportTrialArm()), diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala index 069d1f1..ade0115 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala @@ -1,14 +1,13 @@ package xyz.driver.pdsuidomain.fakes.entities import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.domain.{LongId, User} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion object trialcuration { - import xyz.driver.core.generators import common._ + import xyz.driver.core.generators import xyz.driver.pdsuidomain.entities.InterventionType._ def nextTrial(): Trial = Trial( @@ -20,7 +19,6 @@ object trialcuration { previousAssignee = Option(nextStringId[User]), lastActiveUserId = Option(nextStringId[User]), lastUpdate = nextLocalDateTime, - disease = generators.oneOf[CancerType](CancerType.Breast, CancerType.Lung, CancerType.Prostate), phase = generators.nextString(), hypothesisId = Option(nextUuidId[Hypothesis]), studyDesignId = Option(nextLongId[StudyDesign]), @@ -63,7 +61,7 @@ object trialcuration { val criterion = nextCriterion() RichCriterion( criterion = criterion, - armIds = Seq(nextLongId[Arm], nextLongId[Arm]), + armIds = Seq(nextLongId[EligibilityArm], nextLongId[EligibilityArm]), labels = Seq( nextCriterionLabel(criterion.id), nextCriterionLabel(criterion.id) @@ -86,7 +84,7 @@ object trialcuration { def nextInterventionArm(interventionId: LongId[Intervention]): InterventionArm = InterventionArm( interventionId = interventionId, - armId = nextLongId[Arm] + armId = nextLongId[SlotArm] ) def nextInterventionWithArms(): InterventionWithArms = { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala index 43b5494..239adb1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala @@ -4,7 +4,7 @@ import xyz.driver.pdsuicommon.json.Serialization.seqJsonFormat import play.api.libs.functional.syntax._ import play.api.libs.json._ import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, Criterion, Trial} import xyz.driver.pdsuidomain.formats.json.label.ApiCriterionLabel import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion @@ -26,7 +26,7 @@ final case class ApiCriterion(id: Long, meta.getOrElse(""), inclusion ), - armIds = arms.map(LongId[Arm]), + armIds = arms.map(LongId[EligibilityArm]), labels = labels.map(_.toDomain(LongId[Criterion](id))) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala index d72a9b4..4b85f83 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala @@ -25,7 +25,7 @@ final case class ApiNewCriterion(meta: Option[String], text = text, inclusion = inclusion ), - armIds = arms.getOrElse(Seq.empty).map(LongId[Arm]), + armIds = arms.getOrElse(Seq.empty).map(LongId[EligibilityArm]), labels = labels.map(_.toDomain(LongId(Long.MaxValue))) // A developer should specify right criterionId himself ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala index 77989f0..a700309 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala @@ -2,7 +2,7 @@ package xyz.driver.pdsuidomain.formats.json.criterion import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuicommon.json.Serialization.seqJsonFormat -import xyz.driver.pdsuidomain.entities.{Arm, Criterion} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, Criterion} import org.davidbild.tristate._ import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath import play.api.libs.functional.syntax._ @@ -19,7 +19,7 @@ final case class ApiUpdateCriterion(meta: Tristate[String], def applyTo(orig: RichCriterion): RichCriterion = RichCriterion( criterion = applyTo(orig.criterion), - armIds = arms.cata(_.map(LongId[Arm]), Seq.empty, orig.armIds), + armIds = arms.cata(_.map(LongId[EligibilityArm]), Seq.empty, orig.armIds), labels = labels.cata(_.map(_.toDomain(orig.criterion.id)), Seq.empty, orig.labels) ) 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 new file mode 100644 index 0000000..71423e8 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala @@ -0,0 +1,57 @@ +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} + +final case class ApiEligibilityArm(id: Long, + name: String, + originalName: String, + trialId: String, + diseases: Seq[String]) { + + 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 { + + implicit val format: Format[ApiEligibilityArm] = ( + (JsPath \ "id").format[Long] and + (JsPath \ "name").format[String] and + (JsPath \ "originalName").format[String] and + (JsPath \ "trialId").format[String] and + (JsPath \ "diseases").format[Seq[String]] + )(ApiEligibilityArm.apply, unlift(ApiEligibilityArm.unapply)) + + 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 new file mode 100644 index 0000000..087fed5 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala @@ -0,0 +1,33 @@ +package xyz.driver.pdsuidomain.formats.json.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]) { + + def toDomain: EligibilityArmWithDiseases = { + val eligibilityArm = 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 { + + implicit val format: Format[ApiCreateEligibilityArm] = Json.format[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 new file mode 100644 index 0000000..aca22ef --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala @@ -0,0 +1,23 @@ +package xyz.driver.pdsuidomain.formats.json.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, diseases: Seq[String]) { + + 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 { + + implicit val format: Format[ApiPartialEligibilityArm] = Json.format +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiPartialSlotArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiPartialSlotArm.scala new file mode 100644 index 0000000..2f8e93f --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiPartialSlotArm.scala @@ -0,0 +1,14 @@ +package xyz.driver.pdsuidomain.formats.json.slotarm + +import xyz.driver.pdsuidomain.entities.SlotArm +import play.api.libs.json.{Format, Json} + +final case class ApiPartialSlotArm(name: String) { + + def applyTo(arm: SlotArm): SlotArm = arm.copy(name = name) +} + +object ApiPartialSlotArm { + + implicit val format: Format[ApiPartialSlotArm] = Json.format +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotArm.scala new file mode 100644 index 0000000..375c1a2 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotArm.scala @@ -0,0 +1,35 @@ +package xyz.driver.pdsuidomain.formats.json.slotarm + +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.SlotArm +import play.api.libs.functional.syntax._ +import play.api.libs.json._ + +final case class ApiSlotArm(id: Long, name: String, originalName: String, trialId: String) { + + def toDomain: SlotArm = SlotArm( + id = LongId(this.id), + name = this.name, + originalName = this.originalName, + trialId = StringId(this.trialId), + deleted = None // if we have an ApiSlotArm object, the SlotArm itself has not been deleted + ) + +} + +object ApiSlotArm { + + implicit val format: Format[ApiSlotArm] = ( + (JsPath \ "id").format[Long] and + (JsPath \ "name").format[String] and + (JsPath \ "originalName").format[String] and + (JsPath \ "trialId").format[String] + )(ApiSlotArm.apply, unlift(ApiSlotArm.unapply)) + + def fromDomain(arm: SlotArm): ApiSlotArm = ApiSlotArm( + id = arm.id.id, + name = arm.name, + originalName = arm.originalName, + trialId = arm.trialId.id + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotCreateArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotCreateArm.scala new file mode 100644 index 0000000..3e52c13 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotCreateArm.scala @@ -0,0 +1,20 @@ +package xyz.driver.pdsuidomain.formats.json.slotarm + +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.SlotArm +import play.api.libs.json.{Format, Json} + +final case class ApiCreateSlotArm(name: String, trialId: String) { + + def toDomain = SlotArm( + id = LongId(0), + name = name, + trialId = StringId(trialId), + originalName = name + ) +} + +object ApiCreateSlotArm { + + implicit val format: Format[ApiCreateSlotArm] = Json.format[ApiCreateSlotArm] +} 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 89c843f..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 @@ -80,7 +80,7 @@ object criterion { val arms = fields .get("arms") - .map(_.convertTo[Option[List[LongId[Arm]]]].getOrElse(List.empty[LongId[Arm]])) + .map(_.convertTo[Option[List[LongId[EligibilityArm]]]].getOrElse(List.empty[LongId[EligibilityArm]])) .getOrElse(orig.armIds) val labels = fields @@ -143,8 +143,8 @@ object criterion { val arms = fields .get("arms") - .map(_.convertTo[List[LongId[Arm]]]) - .getOrElse(List.empty[LongId[Arm]]) + .map(_.convertTo[List[LongId[EligibilityArm]]]) + .getOrElse(List.empty[LongId[EligibilityArm]]) val labels = fields .get("labels") diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibilityarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibilityarm.scala new file mode 100644 index 0000000..acb790a --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibilityarm.scala @@ -0,0 +1,44 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import spray.json._ +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, Trial} + +object eligibilityarm { + import DefaultJsonProtocol._ + import common._ + + def applyUpdateToArm(json: JsValue, orig: EligibilityArm): EligibilityArm = json match { + case JsObject(fields) => + val name = fields + .get("name") + .map(_.convertTo[String]) + .getOrElse(deserializationError(s"Arm json object does not contain `name` field: $json")) + orig.copy(name = name) + + case _ => deserializationError(s"Expected Json Object as partial Arm, but got $json") + } + + def eligibilityArmFormat: RootJsonFormat[EligibilityArm] = new RootJsonFormat[EligibilityArm] { + override def write(obj: EligibilityArm): JsValue = + JsObject( + "id" -> obj.id.toJson, + "name" -> obj.name.toJson, + "originalName" -> obj.originalName.toJson, + "trialId" -> obj.trialId.toJson + ) + + override def read(json: JsValue): EligibilityArm = json.asJsObject.getFields("trialId", "name") match { + case Seq(trialId, name) => + EligibilityArm( + id = LongId(0), + name = name.convertTo[String], + trialId = trialId.convertTo[StringId[Trial]], + originalName = name.convertTo[String] + ) + + case _ => deserializationError(s"Expected Json Object as Arm, but got $json") + } + } + +} 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 85d614d..4391453 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 @@ -2,16 +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.formats.json.labels._ +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) @@ -25,7 +25,7 @@ object export { implicit val patientWithLabelsFormat: RootJsonFormat[ExportPatientWithLabels] = jsonFormat(ExportPatientWithLabels.apply, "patientId", "labelVersion", "labels") - implicit val trialArmFormat: RootJsonFormat[ExportTrialArm] = jsonFormat2(ExportTrialArm.apply) + implicit val trialArmFormat: RootJsonFormat[ExportTrialArm] = jsonFormat3(ExportTrialArm.apply) implicit val trialLabelCriterionFormat: RootJsonFormat[ExportTrialLabelCriterion] = new RootJsonFormat[ExportTrialLabelCriterion] { @@ -68,7 +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 @@ -82,12 +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/intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala index 62cb9fa..2ced434 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala @@ -56,7 +56,7 @@ object intervention { val arms = fields .get("arms") - .map(_.convertTo[List[LongId[Arm]]].map(x => InterventionArm(armId = x, interventionId = LongId(0)))) + .map(_.convertTo[List[LongId[SlotArm]]].map(x => InterventionArm(armId = x, interventionId = LongId(0)))) .getOrElse(List.empty[InterventionArm]) InterventionWithArms( @@ -104,7 +104,7 @@ object intervention { val origIntervention = orig.intervention val arms = fields .get("arms") - .map(_.convertTo[List[LongId[Arm]]].map(x => InterventionArm(x, orig.intervention.id))) + .map(_.convertTo[List[LongId[SlotArm]]].map(x => InterventionArm(x, orig.intervention.id))) orig.copy( intervention = origIntervention.copy( diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/slotarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/slotarm.scala new file mode 100644 index 0000000..192bd6a --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/slotarm.scala @@ -0,0 +1,44 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import spray.json._ +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.{SlotArm, Trial} + +object slotarm { + import DefaultJsonProtocol._ + import common._ + + def applyUpdateToArm(json: JsValue, orig: SlotArm): SlotArm = json match { + case JsObject(fields) => + val name = fields + .get("name") + .map(_.convertTo[String]) + .getOrElse(deserializationError(s"Arm json object does not contain `name` field: $json")) + orig.copy(name = name) + + case _ => deserializationError(s"Expected Json Object as partial Arm, but got $json") + } + + def slotArmFormat: RootJsonFormat[SlotArm] = new RootJsonFormat[SlotArm] { + override def write(obj: SlotArm): JsValue = + JsObject( + "id" -> obj.id.toJson, + "name" -> obj.name.toJson, + "originalName" -> obj.originalName.toJson, + "trialId" -> obj.trialId.toJson + ) + + override def read(json: JsValue): SlotArm = json.asJsObject.getFields("trialId", "name") match { + case Seq(trialId, name) => + SlotArm( + id = LongId(0), + name = name.convertTo[String], + trialId = trialId.convertTo[StringId[Trial]], + originalName = name.convertTo[String] + ) + + case _ => deserializationError(s"Expected Json Object as Arm, but got $json") + } + } + +} 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 d851c2c..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 @@ -6,12 +6,11 @@ import spray.json._ import xyz.driver.core.json.EnumJsonFormat import xyz.driver.pdsuicommon.domain.{LongId, UuidId} import xyz.driver.pdsuidomain.entities._ -import xyz.driver.formats.json.patient._ object trial { import DefaultJsonProtocol._ - import common._ import Trial._ + import common._ implicit val trialStatusFormat = new EnumJsonFormat[Status]( "New" -> Status.New, @@ -36,7 +35,6 @@ object trial { "previousStatus" -> obj.previousStatus.toJson, "previousAssignee" -> obj.previousAssignee.toJson, "lastActiveUser" -> obj.lastActiveUserId.toJson, - "disease" -> obj.disease.toJson, "phase" -> obj.phase.toJson, "hypothesisId" -> obj.hypothesisId.toJson, "studyDesignId" -> obj.studyDesignId.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 a2a1ca9..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 @@ -3,11 +3,10 @@ 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.entities.patient.CancerType +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} +import xyz.driver.pdsuidomain.entities.Trial final case class ApiTrial(id: String, externalId: UUID, @@ -17,7 +16,6 @@ final case class ApiTrial(id: String, previousStatus: Option[String], previousAssignee: Option[String], lastActiveUser: Option[String], - disease: String, phase: String, hypothesisId: Option[UUID], studyDesignId: Option[Long], @@ -38,9 +36,6 @@ final case class ApiTrial(id: String, previousAssignee = this.previousAssignee.map(id => StringId(id)), lastActiveUserId = this.lastActiveUser.map(id => StringId(id)), lastUpdate = this.lastUpdate.toLocalDateTime, - disease = CancerType - .fromString(this.disease) - .getOrElse(throw new NoSuchElementException(s"Unknown disease ${this.disease}")), phase = this.phase, hypothesisId = this.hypothesisId.map(id => UuidId(id)), studyDesignId = this.studyDesignId.map(id => LongId(id)), @@ -66,7 +61,6 @@ object ApiTrial { (JsPath \ "previousStatus").formatNullable[String] and (JsPath \ "previousAssignee").formatNullable[String] and (JsPath \ "lastActiveUser").formatNullable[String] and - (JsPath \ "disease").format[String] and (JsPath \ "phase").format[String] and (JsPath \ "hypothesisId").formatNullable[UUID] and (JsPath \ "studyDesignId").formatNullable[Long] and @@ -88,7 +82,6 @@ object ApiTrial { previousAssignee = trial.previousAssignee.map(_.id), lastActiveUser = trial.lastActiveUserId.map(_.id), lastUpdate = ZonedDateTime.of(trial.lastUpdate, ZoneId.of("Z")), - disease = trial.disease.toString, phase = trial.phase, hypothesisId = trial.hypothesisId.map(_.id), studyDesignId = trial.studyDesignId.map(_.id), diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/CriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/CriterionService.scala index fd9268b..7dbf0d9 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/CriterionService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/CriterionService.scala @@ -21,7 +21,9 @@ object CriterionService { def userMessage: String = "Access denied" } - final case class RichCriterion(criterion: Criterion, armIds: Seq[LongId[Arm]], labels: Seq[CriterionLabel]) + final case class RichCriterion(criterion: Criterion, + armIds: Seq[LongId[EligibilityArm]], + labels: Seq[CriterionLabel]) object RichCriterion { implicit def toPhiString(x: RichCriterion): PhiString = { import x._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala new file mode 100644 index 0000000..1e0f65e --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala @@ -0,0 +1,139 @@ +package xyz.driver.pdsuidomain.services + +import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext +import xyz.driver.pdsuicommon.db._ +import xyz.driver.pdsuicommon.domain.LongId +import xyz.driver.pdsuicommon.error.DomainError +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmWithDiseases, SlotArm} + +import scala.concurrent.Future + +object EligibilityArmService { + + trait DefaultAccessDeniedError { + def userMessage: String = "Access denied" + } + + trait DefaultNotFoundError { + def userMessage: String = "EligibilityArm not found" + } + + trait SlotArmNotFoundError { + def userMessage: String = "SlotArm not found" + } + + sealed trait GetByIdReply + object GetByIdReply { + + final case class Entity(x: EligibilityArmWithDiseases) extends GetByIdReply + + type Error = GetByIdReply with DomainError + + case object NotFoundError extends GetByIdReply with DefaultNotFoundError with DomainError.NotFoundError + + case object AuthorizationError + extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError + + final case class CommonError(userMessage: String)(implicit requestContext: AuthenticatedRequestContext) + extends GetByIdReply with DomainError + } + + sealed trait GetListReply + object GetListReply { + type Error = GetListReply with DomainError + + final case class EntityList(xs: Seq[EligibilityArmWithDiseases], totalFound: Int) extends GetListReply + + case object AuthorizationError + extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError + } + + sealed trait UpdateReply + object UpdateReply { + + final case class Updated(updated: EligibilityArmWithDiseases) extends UpdateReply + + type Error = UpdateReply with DomainError + + case object NotFoundError extends UpdateReply with DefaultNotFoundError with DomainError.NotFoundError + + case object AuthorizationError + extends UpdateReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + final case class CommonError(userMessage: String) extends UpdateReply with DomainError + + final case class AlreadyExistsError(x: EligibilityArmWithDiseases) extends UpdateReply with DomainError { + val userMessage = s"The arm with such name of trial already exists." + } + + implicit def toPhiString(reply: UpdateReply): PhiString = reply match { + case Updated(x) => phi"Updated($x)" + case x: Error => DomainError.toPhiString(x) + } + } + + sealed trait CreateReply + object CreateReply { + final case class Created(x: EligibilityArmWithDiseases) extends CreateReply + + type Error = CreateReply with DomainError + + case object AuthorizationError + extends CreateReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + case object NotFoundError extends CreateReply with SlotArmNotFoundError with DomainError.NotFoundError + + final case class CommonError(userMessage: String) extends CreateReply with DomainError + + final case class AlreadyExistsError(x: EligibilityArmWithDiseases) extends CreateReply with DomainError { + val userMessage = s"The arm with this name of trial already exists." + } + + implicit def toPhiString(reply: CreateReply): PhiString = reply match { + case Created(x) => phi"Created($x)" + case x: Error => DomainError.toPhiString(x) + } + } + + sealed trait DeleteReply + object DeleteReply { + case object Deleted extends DeleteReply + + type Error = DeleteReply with DomainError + + case object NotFoundError extends DeleteReply with DefaultNotFoundError with DomainError.NotFoundError + + case object AuthorizationError + extends DeleteReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + final case class CommonError(userMessage: String) extends DeleteReply with DomainError + } +} + +trait EligibilityArmService { + + import EligibilityArmService._ + + def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, + sorting: Option[Sorting] = None, + pagination: Option[Pagination] = None)( + implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] + + def getByEligibilityId(armId: LongId[EligibilityArm])( + implicit requestContext: AuthenticatedRequestContext): Future[GetByIdReply] + + def getBySlotId(armId: LongId[SlotArm], + filter: SearchFilterExpr = SearchFilterExpr.Empty, + sorting: Option[Sorting] = None, + pagination: Option[Pagination] = None)( + implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] + + def create(slotArmId: LongId[SlotArm], draftEligibilityArm: EligibilityArmWithDiseases)( + implicit requestContext: AuthenticatedRequestContext): Future[CreateReply] + + def update(origEligibilityArm: EligibilityArmWithDiseases, draftEligibilityArm: EligibilityArmWithDiseases)( + implicit requestContext: AuthenticatedRequestContext): Future[UpdateReply] + + def delete(id: LongId[EligibilityArm])(implicit requestContext: AuthenticatedRequestContext): Future[DeleteReply] +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/SlotArmService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/SlotArmService.scala new file mode 100644 index 0000000..af7084b --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/services/SlotArmService.scala @@ -0,0 +1,125 @@ +package xyz.driver.pdsuidomain.services + +import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext +import xyz.driver.pdsuicommon.db._ +import xyz.driver.pdsuicommon.domain.LongId +import xyz.driver.pdsuicommon.error.DomainError +import xyz.driver.pdsuicommon.logging._ +import xyz.driver.pdsuidomain.entities.SlotArm + +import scala.concurrent.Future + +object SlotArmService { + + trait DefaultAccessDeniedError { + def userMessage: String = "Access denied" + } + + trait DefaultNotFoundError { + def userMessage: String = "SlotArm not found" + } + + sealed trait GetByIdReply + object GetByIdReply { + + final case class Entity(x: SlotArm) extends GetByIdReply + + type Error = GetByIdReply with DomainError + + case object NotFoundError extends GetByIdReply with DefaultNotFoundError with DomainError.NotFoundError + + case object AuthorizationError + extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError + + final case class CommonError(userMessage: String)(implicit requestContext: AuthenticatedRequestContext) + extends GetByIdReply with DomainError + } + + sealed trait GetListReply + object GetListReply { + type Error = GetListReply with DomainError + + final case class EntityList(xs: Seq[SlotArm], totalFound: Int) extends GetListReply + + case object AuthorizationError + extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError + } + + sealed trait UpdateReply + object UpdateReply { + + final case class Updated(updated: SlotArm) extends UpdateReply + + type Error = UpdateReply with DomainError + + case object NotFoundError extends UpdateReply with DefaultNotFoundError with DomainError.NotFoundError + + case object AuthorizationError + extends UpdateReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + final case class CommonError(userMessage: String) extends UpdateReply with DomainError + + final case class AlreadyExistsError(x: SlotArm) extends UpdateReply with DomainError { + val userMessage = s"The arm with such name of trial already exists." + } + + implicit def toPhiString(reply: UpdateReply): PhiString = reply match { + case Updated(x) => phi"Updated($x)" + case x: Error => DomainError.toPhiString(x) + } + } + + sealed trait CreateReply + object CreateReply { + final case class Created(x: SlotArm) extends CreateReply + + type Error = CreateReply with DomainError + + case object AuthorizationError + extends CreateReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + final case class CommonError(userMessage: String) extends CreateReply with DomainError + + final case class AlreadyExistsError(x: SlotArm) extends CreateReply with DomainError { + val userMessage = s"The arm with this name of trial already exists." + } + + implicit def toPhiString(reply: CreateReply): PhiString = reply match { + case Created(x) => phi"Created($x)" + case x: Error => DomainError.toPhiString(x) + } + } + + sealed trait DeleteReply + object DeleteReply { + case object Deleted extends DeleteReply + + type Error = DeleteReply with DomainError + + case object NotFoundError extends DeleteReply with DefaultNotFoundError with DomainError.NotFoundError + + case object AuthorizationError + extends DeleteReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + final case class CommonError(userMessage: String) extends DeleteReply with DomainError + } +} + +trait SlotArmService { + + import SlotArmService._ + + def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, + sorting: Option[Sorting] = None, + pagination: Option[Pagination] = None)( + implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] + + def getById(armId: LongId[SlotArm])(implicit requestContext: AuthenticatedRequestContext): Future[GetByIdReply] + + def create(draftSlotArm: SlotArm)(implicit requestContext: AuthenticatedRequestContext): Future[CreateReply] + + def update(origSlotArm: SlotArm, draftSlotArm: SlotArm)( + implicit requestContext: AuthenticatedRequestContext): Future[UpdateReply] + + def delete(id: LongId[SlotArm])(implicit requestContext: AuthenticatedRequestContext): Future[DeleteReply] +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala index a1efdac..e0efcd1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala @@ -11,8 +11,8 @@ import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial} import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} +import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm, Trial} import xyz.driver.pdsuidomain.services.TrialService import scala.concurrent.Future @@ -30,7 +30,6 @@ class FakeTrialService extends TrialService { previousAssignee = None, lastActiveUserId = None, lastUpdate = LocalDateTime.now(), - disease = CancerType.Breast, phase = "", hypothesisId = None, studyDesignId = None, @@ -70,20 +69,20 @@ class FakeTrialService extends TrialService { ExportTrialWithLabels( StringId[Trial]("NCT" + generators.nextInt(999999).toString), UuidId[Trial](generators.nextUuid()), - generators.oneOf("adenocarcinoma", "breast", "prostate"), LocalDateTime.now(), labelVersion = 1L, generators.listOf( new ExportTrialArm( - LongId[Arm](generators.nextInt(999999).toLong), - generators.nextName().value + LongId[EligibilityArm](generators.nextInt(999999).toLong), + generators.nextName().value, + generators.listOf(generators.oneOf("adenocarcinoma", "breast", "prostate")) )), generators.listOf( new ExportTrialLabelCriterion( LongId[Criterion](generators.nextInt(999999).toLong), generators.nextOption(generators.nextBoolean()), LongId[Label](generators.nextInt(999999).toLong), - generators.setOf(LongId[Arm](generators.nextInt(999999).toLong)), + generators.setOf(LongId[EligibilityArm](generators.nextInt(999999).toLong)), generators.nextName().value, generators.nextBoolean(), generators.nextBoolean() diff --git a/src/test/scala/xyz/driver/pdsuicommon/parsers/PaginationParserSuite.scala b/src/test/scala/xyz/driver/pdsuicommon/parsers/PaginationParserSuite.scala index 48fc99b..609c8c8 100644 --- a/src/test/scala/xyz/driver/pdsuicommon/parsers/PaginationParserSuite.scala +++ b/src/test/scala/xyz/driver/pdsuicommon/parsers/PaginationParserSuite.scala @@ -11,36 +11,40 @@ class PaginationParserSuite extends FreeSpecLike with MustMatchers { "parse" - { "pageSize" - { "should parse positive value" in { - val pagination = PaginationParser.parse(Seq( - "pageSize" -> "10", - "pageNumber" -> "1" - )) + val pagination = PaginationParser.parse( + Seq( + "pageSize" -> "10", + "pageNumber" -> "1" + )) pagination must success pagination.get.pageSize mustBe 10 } "should return a default value if there is no one" in { - val pagination = PaginationParser.parse(Seq( - "pageNumber" -> "1" - )) + val pagination = PaginationParser.parse( + Seq( + "pageNumber" -> "1" + )) pagination must success pagination.get.pageSize mustBe 100 } "should return a error for zero value" in { - val pagination = PaginationParser.parse(Seq( - "pageSize" -> "0", - "pageNumber" -> "1" - )) + val pagination = PaginationParser.parse( + Seq( + "pageSize" -> "0", + "pageNumber" -> "1" + )) checkFailedValidationOnlyOn(pagination, "pageSize") } "should return a error for negative value" in { - val pagination = PaginationParser.parse(Seq( - "pageSize" -> "-10", - "pageNumber" -> "1" - )) + val pagination = PaginationParser.parse( + Seq( + "pageSize" -> "-10", + "pageNumber" -> "1" + )) checkFailedValidationOnlyOn(pagination, "pageSize") } @@ -48,36 +52,40 @@ class PaginationParserSuite extends FreeSpecLike with MustMatchers { "pageNumber" - { "should parse positive value" in { - val pagination = PaginationParser.parse(Seq( - "pageSize" -> "1", - "pageNumber" -> "1" - )) + val pagination = PaginationParser.parse( + Seq( + "pageSize" -> "1", + "pageNumber" -> "1" + )) pagination must success pagination.get.pageSize mustBe 1 } "should return a default value if there is no one" in { - val pagination = PaginationParser.parse(Seq( - "pageSize" -> "1" - )) + val pagination = PaginationParser.parse( + Seq( + "pageSize" -> "1" + )) pagination must success pagination.get.pageNumber mustBe 1 } "should return a error for zero value" in { - val pagination = PaginationParser.parse(Seq( - "pageSize" -> "1", - "pageNumber" -> "0" - )) + val pagination = PaginationParser.parse( + Seq( + "pageSize" -> "1", + "pageNumber" -> "0" + )) checkFailedValidationOnlyOn(pagination, "pageNumber") } "should return a error for negative value" in { - val pagination = PaginationParser.parse(Seq( - "pageSize" -> "1", - "pageNumber" -> "-1" - )) + val pagination = PaginationParser.parse( + Seq( + "pageSize" -> "1", + "pageNumber" -> "-1" + )) checkFailedValidationOnlyOn(pagination, "pageNumber") } diff --git a/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala b/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala index 5deaecb..02243aa 100644 --- a/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala +++ b/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala @@ -30,16 +30,20 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { "should convert column names to snake case" in { import SearchFilterBinaryOperation._ - val filter = SearchFilterParser.parse(Seq( - "filters" -> "status IN Summarized,ReviewCriteria,Flagged,Done", - "filters" -> "previousStatus NOTEQ New", - "filters" -> "previousStatus NOTEQ ReviewSummary" - )) - - assert(filter === Success(SearchFilterExpr.Intersection(List( - SearchFilterExpr.Atom.NAry(Dimension(None, "status"), In, Seq("Summarized", "ReviewCriteria", "Flagged", "Done")), - SearchFilterExpr.Atom.Binary(Dimension(None, "previous_status"), NotEq, "New"), - SearchFilterExpr.Atom.Binary(Dimension(None, "previous_status"), NotEq, "ReviewSummary"))))) + val filter = SearchFilterParser.parse( + Seq( + "filters" -> "status IN Summarized,ReviewCriteria,Flagged,Done", + "filters" -> "previousStatus NOTEQ New", + "filters" -> "previousStatus NOTEQ ReviewSummary" + )) + + assert( + filter === Success(SearchFilterExpr.Intersection(List( + SearchFilterExpr.Atom + .NAry(Dimension(None, "status"), In, Seq("Summarized", "ReviewCriteria", "Flagged", "Done")), + SearchFilterExpr.Atom.Binary(Dimension(None, "previous_status"), NotEq, "New"), + SearchFilterExpr.Atom.Binary(Dimension(None, "previous_status"), NotEq, "ReviewSummary") + )))) } "dimensions" - { "with table name" in check { @@ -50,11 +54,11 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { Prop.forAllNoShrink(dimensionGen) { case (left, right) => val raw = s"$left.$right" - val l = toSnakeCase(left) - val r = toSnakeCase(right) - SearchFilterParser.dimensionParser.parse(raw) match { + val l = toSnakeCase(left) + val r = toSnakeCase(right) + SearchFilterParser.dimensionParser.parse(raw) match { case Parsed.Success(Dimension(Some(`l`), `r`), _) => true - case _ => false + case _ => false } } } @@ -63,7 +67,7 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { val databaseS = Utils.toSnakeCase(s) SearchFilterParser.dimensionParser.parse(s) match { case Parsed.Success(Dimension(None, `databaseS`), _) => true - case _ => false + case _ => false } } } @@ -81,10 +85,11 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { ) Prop.forAllNoShrink(testQueryGen) { query => - SearchFilterParser.parse(Seq("filters" -> query)) + SearchFilterParser + .parse(Seq("filters" -> query)) .map { case SearchFilterExpr.Atom.Binary(_, Eq | NotEq | Like, _) => true - case x => throw new UnexpectedSearchFilterExprException(x) + case x => throw new UnexpectedSearchFilterExprException(x) } .successProp } @@ -96,7 +101,9 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { val testQueryGen = queryGen( dimensionGen = Gen.identifier, opGen = numericBinaryOpsGen, - valueGen = nonEmptyString.filter { s => !s.matches("^\\d+$") } + valueGen = nonEmptyString.filter { s => + !s.matches("^\\d+$") + } ) Prop.forAllNoShrink(testQueryGen) { query => @@ -121,10 +128,11 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { ) Prop.forAllNoShrink(testQueryGen) { query => - SearchFilterParser.parse(Seq("filters" -> query)) + SearchFilterParser + .parse(Seq("filters" -> query)) .map { case _: SearchFilterExpr.Atom.Binary => true - case x => throw new UnexpectedSearchFilterExprException(x) + case x => throw new UnexpectedSearchFilterExprException(x) } .successProp } @@ -140,7 +148,8 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { case Success(_) => () case Failure(t) => t.printStackTrace() } - assert(filter === Success(SearchFilterExpr.Atom.NAry(Dimension(None, "id"), In, Seq(Long.box(1), Long.box(5))))) + assert( + filter === Success(SearchFilterExpr.Atom.NAry(Dimension(None, "id"), In, Seq(Long.box(1), Long.box(5))))) } } @@ -152,10 +161,11 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { ) Prop.forAllNoShrink(testQueryGen) { query => - SearchFilterParser.parse(Seq("filters" -> query)) + SearchFilterParser + .parse(Seq("filters" -> query)) .map { case SearchFilterExpr.Atom.NAry(_, SearchFilterNAryOperation.In, _) => true - case x => throw new UnexpectedSearchFilterExprException(x) + case x => throw new UnexpectedSearchFilterExprException(x) } .successProp } @@ -189,16 +199,19 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { } } - private val CommonBinaryOps = Seq("eq", "noteq", "like") + private val CommonBinaryOps = Seq("eq", "noteq", "like") private val NumericBinaryOps = Seq("gt", "gteq", "lt", "lteq") - private val allBinaryOpsGen: Gen[String] = Gen.oneOf(CommonBinaryOps ++ NumericBinaryOps).flatMap(randomCapitalization) - private val commonBinaryOpsGen: Gen[String] = Gen.oneOf(CommonBinaryOps).flatMap(randomCapitalization) + private val allBinaryOpsGen: Gen[String] = + Gen.oneOf(CommonBinaryOps ++ NumericBinaryOps).flatMap(randomCapitalization) + private val commonBinaryOpsGen: Gen[String] = Gen.oneOf(CommonBinaryOps).flatMap(randomCapitalization) private val numericBinaryOpsGen: Gen[String] = Gen.oneOf(NumericBinaryOps).flatMap(randomCapitalization) private val inValueCharsGen: Gen[Char] = arbitrary[Char].filter(_ != ',') - private val nonEmptyString = arbitrary[String].filter { s => !s.safeTrim.isEmpty } + private val nonEmptyString = arbitrary[String].filter { s => + !s.safeTrim.isEmpty + } private val numericBinaryAtomValuesGen: Gen[String] = arbitrary[Long].map(_.toString) private val inValueGen: Gen[String] = { @@ -208,18 +221,22 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { Gen.containerOfN[Seq, String](size, inValueGen).map(_.mkString(",")) } - private def queryGen(dimensionGen: Gen[String], opGen: Gen[String], valueGen: Gen[String]): Gen[String] = for { - dimension <- dimensionGen - op <- opGen - value <- valueGen - } yield s"$dimension $op $value" + private def queryGen(dimensionGen: Gen[String], opGen: Gen[String], valueGen: Gen[String]): Gen[String] = + for { + dimension <- dimensionGen + op <- opGen + value <- valueGen + } yield s"$dimension $op $value" private def randomCapitalization(input: String): Gen[String] = { Gen.containerOfN[Seq, Boolean](input.length, arbitrary[Boolean]).map { capitalize => - input.view.zip(capitalize).map { - case (currChar, true) => currChar.toUpper - case (currChar, false) => currChar - }.mkString + input.view + .zip(capitalize) + .map { + case (currChar, true) => currChar.toUpper + case (currChar, false) => currChar + } + .mkString } } diff --git a/src/test/scala/xyz/driver/pdsuicommon/parsers/SortingParserSuite.scala b/src/test/scala/xyz/driver/pdsuicommon/parsers/SortingParserSuite.scala index e46015c..f34f8e1 100644 --- a/src/test/scala/xyz/driver/pdsuicommon/parsers/SortingParserSuite.scala +++ b/src/test/scala/xyz/driver/pdsuicommon/parsers/SortingParserSuite.scala @@ -12,7 +12,7 @@ class SortingParserSuite extends FreeSpecLike with MustMatchers with Checkers { "single dimension" - commonTests(singleSortingQueryGen) "multiple dimensions in one query" - commonTests(multipleSortingQueryGen) "multiple queries" in { - val r = SortingParser.parse(Set("foo", "bar"), Seq("sort" -> "foo", "sort" ->"bar")) + val r = SortingParser.parse(Set("foo", "bar"), Seq("sort" -> "foo", "sort" -> "bar")) r must failWith[ParseQueryArgException] } } @@ -21,7 +21,7 @@ class SortingParserSuite extends FreeSpecLike with MustMatchers with Checkers { "valid" in check { val inputGen: Gen[(Set[String], String)] = for { validDimensions <- dimensionsGen - sorting <- queryGen(validDimensions) + sorting <- queryGen(validDimensions) } yield (validDimensions, sorting) Prop.forAllNoShrink(inputGen) { @@ -33,7 +33,9 @@ class SortingParserSuite extends FreeSpecLike with MustMatchers with Checkers { "invalid" in check { val inputGen: Gen[(Set[String], String)] = for { validDimensions <- dimensionsGen - invalidDimensions <- dimensionsGen.filter { xs => xs.intersect(validDimensions).isEmpty } + invalidDimensions <- dimensionsGen.filter { xs => + xs.intersect(validDimensions).isEmpty + } sorting <- queryGen(invalidDimensions) } yield (validDimensions, sorting) @@ -46,12 +48,12 @@ class SortingParserSuite extends FreeSpecLike with MustMatchers with Checkers { private val dimensionsGen: Gen[Set[String]] = for { unPrefixedSize <- Gen.choose(0, 3) - prefixedSize <- Gen.choose(0, 3) + prefixedSize <- Gen.choose(0, 3) if (unPrefixedSize + prefixedSize) > 0 unPrefixedDimensions <- Gen.containerOfN[Set, String](unPrefixedSize, Gen.identifier) - prefixes <- Gen.containerOfN[Set, String](prefixedSize, Gen.identifier) + prefixes <- Gen.containerOfN[Set, String](prefixedSize, Gen.identifier) dimensions <- Gen.containerOfN[Set, String](prefixedSize, Gen.identifier) } yield { val prefixedDimensions = prefixes.zip(dimensions).map { @@ -62,30 +64,33 @@ class SortingParserSuite extends FreeSpecLike with MustMatchers with Checkers { private def multipleSortingQueryGen(validDimensions: Set[String]): Gen[String] = { val validDimensionsSeq = validDimensions.toSeq - val indexGen = Gen.oneOf(validDimensionsSeq.indices) + val indexGen = Gen.oneOf(validDimensionsSeq.indices) val multipleDimensionsGen = Gen.nonEmptyContainerOf[Set, Int](indexGen).filter(_.size >= 2).map { indices => indices.map(validDimensionsSeq.apply) } for { - dimensions <- multipleDimensionsGen + dimensions <- multipleDimensionsGen isAscending <- Gen.containerOfN[Seq, Boolean](dimensions.size, arbitrary[Boolean]) } yield { - isAscending.zip(dimensions) + isAscending + .zip(dimensions) .map { - case (true, dimension) => dimension + case (true, dimension) => dimension case (false, dimension) => "-" + dimension } .mkString(",") } } - private def singleSortingQueryGen(validDimensions: Set[String]): Gen[String] = for { - isAscending <- arbitrary[Boolean] - dimensions <- Gen.oneOf(validDimensions.toSeq) - } yield isAscending match { - case true => dimensions - case false => "-" + dimensions - } + private def singleSortingQueryGen(validDimensions: Set[String]): Gen[String] = + for { + isAscending <- arbitrary[Boolean] + dimensions <- Gen.oneOf(validDimensions.toSeq) + } yield + isAscending match { + case true => dimensions + case false => "-" + dimensions + } } diff --git a/src/test/scala/xyz/driver/pdsuicommon/parsers/TestUtils.scala b/src/test/scala/xyz/driver/pdsuicommon/parsers/TestUtils.scala index 4892b95..09b60ed 100644 --- a/src/test/scala/xyz/driver/pdsuicommon/parsers/TestUtils.scala +++ b/src/test/scala/xyz/driver/pdsuicommon/parsers/TestUtils.scala @@ -22,8 +22,9 @@ object TestUtils { left.isFailure && left.failed.get.getClass == ct.runtimeClass, left match { case Success(x) => s"$left did not fail" - case Failure(e) => s"$left did fail with ${Utils.getClassSimpleName(e.getClass)}, " + - s"not ${Utils.getClassSimpleName(ct.runtimeClass)}" + case Failure(e) => + s"$left did fail with ${Utils.getClassSimpleName(e.getClass)}, " + + s"not ${Utils.getClassSimpleName(ct.runtimeClass)}" }, left match { case Success(_) => s"$left failed with ${Utils.getClassSimpleName(ct.runtimeClass)}" @@ -33,7 +34,7 @@ object TestUtils { } } - def failWith[ThrowableT <:Throwable](implicit ct: ClassTag[ThrowableT]) = new FailWith[ThrowableT] + def failWith[ThrowableT <: Throwable](implicit ct: ClassTag[ThrowableT]) = new FailWith[ThrowableT] final implicit class TryPropOps(val self: Try[Any]) extends AnyVal { diff --git a/src/test/scala/xyz/driver/pdsuicommon/utils/StringOpsSuite.scala b/src/test/scala/xyz/driver/pdsuicommon/utils/StringOpsSuite.scala index 9bd4382..bd0bd2b 100644 --- a/src/test/scala/xyz/driver/pdsuicommon/utils/StringOpsSuite.scala +++ b/src/test/scala/xyz/driver/pdsuicommon/utils/StringOpsSuite.scala @@ -30,4 +30,4 @@ class StringOpsSuite extends FreeSpecLike { assert("foo".safeTrim == "foo") } } -}
\ No newline at end of file +} diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ArmFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ArmFormatSuite.scala index e7d37a0..35b0fad 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ArmFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ArmFormatSuite.scala @@ -17,19 +17,20 @@ class ArmFormatSuite extends FlatSpec with Matchers { ) val writtenJson = armFormat.write(arm) - writtenJson should be("""{"id":10,"trialId":"NCT000001","name":"arm name","originalName":"orig arm name"}""".parseJson) + writtenJson should be( + """{"id":10,"trialId":"NCT000001","name":"arm name","originalName":"orig arm name"}""".parseJson) val createArmJson = """{"trialId":"NCT000001","name":"arm name"}""".parseJson - val parsedArm = armFormat.read(createArmJson) + val parsedArm = armFormat.read(createArmJson) val expectedCreatedArm = arm.copy( id = LongId(0), originalName = "arm name" ) parsedArm should be(expectedCreatedArm) - val updateArmJson = """{"name":"new arm name"}""".parseJson + val updateArmJson = """{"name":"new arm name"}""".parseJson val expectedUpdatedArm = arm.copy(name = "new arm name") - val parsedUpdateArm = applyUpdateToArm(updateArmJson, arm) + val parsedUpdateArm = applyUpdateToArm(updateArmJson, arm) parsedUpdateArm should be(expectedUpdatedArm) } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala index 708aed9..51665d2 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala @@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import org.scalatest.{FlatSpec, Matchers} import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, CriterionLabel} +import xyz.driver.pdsuidomain.entities.{EligibilityArm, Criterion, CriterionLabel} import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion class CriterionFormatSuite extends FlatSpec with Matchers { @@ -36,7 +36,7 @@ class CriterionFormatSuite extends FlatSpec with Matchers { isDefining = true ) ) - val arms = List(LongId[Arm](20), LongId[Arm](21), LongId[Arm](21)) + val arms = List(LongId[EligibilityArm](20), LongId[EligibilityArm](21), LongId[EligibilityArm](21)) val richCriterion = RichCriterion( criterion = criterion, armIds = arms, diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala index 193e066..e6dd4a1 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala @@ -32,7 +32,7 @@ class DocumentFormatSuite extends FlatSpec with Matchers { ) val writtenJson = documentFormat.write(orig) - writtenJson should be ( + writtenJson should be( """{"id":1,"recordId":101,"physician":"physician","typeId":10,"provider":"provider 21","providerTypeId":21, "requiredType":"OPN","institutionName":"institution name","startDate":null,"endDate":null,"status":"New","assignee":null,"previousStatus":null, "previousAssignee":null,"lastActiveUser":null,"lastUpdate":"2017-08-10T18:00Z","meta":null}""".parseJson) @@ -60,11 +60,11 @@ class DocumentFormatSuite extends FlatSpec with Matchers { } "Json format for Document.Meta" should "read and write correct JSON" in { - val meta = Document.Meta(startPage = 1.0, endPage = 2.0) + val meta = Document.Meta(startPage = 1.0, endPage = 2.0) val writtenJson = documentMetaFormat.write(meta) - writtenJson should be ("""{"startPage":1.0,"endPage":2.0}""".parseJson) + writtenJson should be("""{"startPage":1.0,"endPage":2.0}""".parseJson) - val metaJson = """{"startPage":1.0,"endPage":2.0}""".parseJson + val metaJson = """{"startPage":1.0,"endPage":2.0}""".parseJson val parsedMeta = documentMetaFormat.read(metaJson) parsedMeta should be(meta) } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentHistoryFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentHistoryFormatSuite.scala index ddbda1d..5975919 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentHistoryFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentHistoryFormatSuite.scala @@ -21,8 +21,7 @@ class DocumentHistoryFormatSuite extends FlatSpec with Matchers { ) val writtenJson = documentHistoryFormat.write(documentHistory) - writtenJson should be( - """{"id":10,"executor":"userId-001","documentId":1,"state":"Extract", + writtenJson should be("""{"id":10,"executor":"userId-001","documentId":1,"state":"Extract", "action":"Start","created":"2017-08-10T18:00Z"}""".parseJson) val parsedDocumentHistory = documentHistoryFormat.read(writtenJson) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentIssueFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentIssueFormatSuite.scala index c4c9f7c..54cfe90 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentIssueFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentIssueFormatSuite.scala @@ -29,7 +29,8 @@ class DocumentIssueFormatSuite extends FlatSpec with Matchers { "text":"message text","archiveRequired":false,"startPage":1.0,"endPage":2.0}""".parseJson) val createDocumentIssueJson = """{"text":"message text","startPage":1.0,"endPage":2.0}""".parseJson - val expectedCreatedDocumentIssue = documentIssue.copy(id = LongId(0), lastUpdate = LocalDateTime.MIN, isDraft = true) + val expectedCreatedDocumentIssue = + documentIssue.copy(id = LongId(0), lastUpdate = LocalDateTime.MIN, isDraft = true) val parsedCreateDocumentIssue = jsValueToDocumentIssue(createDocumentIssueJson, LongId(1), StringId("userId-001")) parsedCreateDocumentIssue should be(expectedCreatedDocumentIssue) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/EligibilityArmFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/EligibilityArmFormatSuite.scala new file mode 100644 index 0000000..bcfb977 --- /dev/null +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/EligibilityArmFormatSuite.scala @@ -0,0 +1,36 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import spray.json._ +import org.scalatest.{FlatSpec, Matchers} +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.EligibilityArm + +class EligibilityArmFormatSuite extends FlatSpec with Matchers { + import eligibilityarm._ + + "Json format for EligibilityArm" should "read and write correct JSON" in { + val arm = EligibilityArm( + id = LongId(10), + trialId = StringId("NCT000001"), + name = "arm name", + originalName = "orig arm name" + ) + val writtenJson = eligibilityArmFormat.write(arm) + + writtenJson should be( + """{"id":10,"trialId":"NCT000001","name":"arm name","originalName":"orig arm name"}""".parseJson) + + val createArmJson = """{"trialId":"NCT000001","name":"arm name"}""".parseJson + val parsedArm = eligibilityArmFormat.read(createArmJson) + val expectedCreatedArm = arm.copy( + id = LongId(0), + originalName = "arm name" + ) + parsedArm should be(expectedCreatedArm) + + val updateArmJson = """{"name":"new arm name"}""".parseJson + val expectedUpdatedArm = arm.copy(name = "new arm name") + val parsedUpdateArm = applyUpdateToArm(updateArmJson, arm) + parsedUpdateArm should be(expectedUpdatedArm) + } +} diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala index 402e893..d78e754 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala @@ -3,8 +3,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.{LocalDate, LocalDateTime} import java.util.UUID -import spray.json._ import org.scalatest.{FlatSpec, Matchers} +import spray.json._ import xyz.driver.entities.labels.LabelValue import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.{DocumentType, ProviderType, RecordRequestId} @@ -81,8 +81,8 @@ class ExportFormatSuite extends FlatSpec with Matchers { "Json format for ApiExportTrialWithLabels" should "read and write correct JSON" in { import xyz.driver.pdsuidomain.entities.export.trial._ val arms = List( - ExportTrialArm(armId = LongId(1), armName = "arm 1"), - ExportTrialArm(armId = LongId(2), armName = "arm 2") + ExportTrialArm(armId = LongId(1), armName = "arm 1", diseaseList = Seq("Breast")), + ExportTrialArm(armId = LongId(2), armName = "arm 2", diseaseList = Seq("Breast")) ) val criteriaList = List( ExportTrialLabelCriterion( @@ -107,7 +107,6 @@ class ExportFormatSuite extends FlatSpec with Matchers { val trialWithLabels = ExportTrialWithLabels( nctId = StringId("NCT000001"), trialId = UuidId("40892a07-c638-49d2-9795-1edfefbbcc7c"), - disease = "Breast", lastReviewed = LocalDateTime.parse("2017-08-10T18:00:00"), labelVersion = 1L, arms = arms, @@ -116,8 +115,8 @@ class ExportFormatSuite extends FlatSpec with Matchers { val writtenJson = trialWithLabelsFormat.write(trialWithLabels) writtenJson should be( - """{"nctId":"NCT000001","trialId":"40892a07-c638-49d2-9795-1edfefbbcc7c","disease":"Breast","lastReviewed":"2017-08-10T18:00Z", - "labelVersion":1,"arms":[{"armId":1,"armName":"arm 1"},{"armId":2,"armName":"arm 2"}],"criteria":[ + """{"nctId":"NCT000001","trialId":"40892a07-c638-49d2-9795-1edfefbbcc7c","lastReviewed":"2017-08-10T18:00Z", + "labelVersion":1,"arms":[{"armId":1,"armName":"arm 1","diseaseList":["Breast"]},{"armId":2,"armName":"arm 2","diseaseList":["Breast"]}],"criteria":[ {"value":"Yes","labelId":21,"criterionId":10,"criterionText":"criteria 10 text","armIds":[1,2],"isCompound":false,"isDefining":false}, {"value":"Unknown","labelId":21,"criterionId":11,"criterionText":"criteria 11 text","armIds":[2],"isCompound":true,"isDefining":false}]}""".parseJson) } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala index aa82b98..1feca6a 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala @@ -41,7 +41,7 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers { ) val writtenJson = extractedDataFormat.write(origRichExtractedData) - writtenJson should be ( + writtenJson should be( """{"id":1,"documentId":101,"keywordId":201,"evidence":"evidence text","meta":null, "labels":[{"id":null,"categoryId":null,"value":"Yes"},{"id":12,"categoryId":1,"value":"No"}]}""".parseJson) @@ -78,14 +78,15 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers { val expectedUpdatedExtractedData = origRichExtractedData.copy( extractedData = extractedData.copy( evidenceText = Some("new evidence text"), - meta = Some(TextJson(Meta( - keyword = Meta.Keyword(page = 1, pageRatio = None, index = 2, sortIndex = "ASC"), - evidence = Meta.Evidence( - pageRatio = 1.0, - start = Meta.TextLayerPosition(page = 1, index = 3, offset = 2), - end = Meta.TextLayerPosition(page = 2, index = 3, offset = 10) - ) - ))) + meta = Some( + TextJson(Meta( + keyword = Meta.Keyword(page = 1, pageRatio = None, index = 2, sortIndex = "ASC"), + evidence = Meta.Evidence( + pageRatio = 1.0, + start = Meta.TextLayerPosition(page = 1, index = 3, offset = 2), + end = Meta.TextLayerPosition(page = 2, index = 3, offset = 10) + ) + ))) ), labels = updatedExtractedDataLabels ) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/HypothesisFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/HypothesisFormatSuite.scala index 306fb17..76d90f5 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/HypothesisFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/HypothesisFormatSuite.scala @@ -17,8 +17,7 @@ class HypothesisFormatSuite extends FlatSpec with Matchers { ) val writtenJson = hypothesisFormat.write(hypothesis) - writtenJson should be( - """{"id":"3b80b2e2-5372-4cf5-a342-6e4ebe10fafd","name":"hypothesis name", + writtenJson should be("""{"id":"3b80b2e2-5372-4cf5-a342-6e4ebe10fafd","name":"hypothesis name", "treatmentType":"treatment type","description":"descr"}""".parseJson) val parsedHypothesis = hypothesisFormat.read(writtenJson) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala index dad39c8..5891e1c 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala @@ -60,7 +60,7 @@ class InterventionFormatSuite extends FlatSpec with Matchers { "Json format for InterventionType" should "read and write correct JSON" in { val interventionType = InterventionType.typeFromString("Surgery/Procedure") - val writtenJson = interventionTypeFormat.write(interventionType) + val writtenJson = interventionTypeFormat.write(interventionType) writtenJson should be( """{"id":9,"name":"Surgery/Procedure","deliveryMethods":["Radio-Frequency Ablation (RFA)", diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponseSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponseSuite.scala index 65024a3..d7f1a9b 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponseSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponseSuite.scala @@ -10,10 +10,9 @@ import xyz.driver.pdsuidomain.entities.MedicalRecord.Status import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.formats.json.sprayformats.record.recordFormat - class ListResponseSuite extends FlatSpec with Matchers { - private val lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00") + private val lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00") private val lastUpdateToLocal = "2017-08-10T18:00Z" private def metaJsonObjectAsString(meta: ListResponse.Meta) = { @@ -25,7 +24,6 @@ class ListResponseSuite extends FlatSpec with Matchers { s"""{"itemsCount":$itemsCount,"pageNumber":$pageNumber,"pageSize":$pageSize$lastUpdate}""" } - "Json format for ListResponse.Meta" should "read and write correct JSON" in { val meta1 = ListResponse.Meta( @@ -38,15 +36,13 @@ class ListResponseSuite extends FlatSpec with Matchers { val writtenJson1 = ListResponse.listResponseMetaFormat.write(meta1) - writtenJson1 should be( - metaJsonObjectAsString(meta1).parseJson) + writtenJson1 should be(metaJsonObjectAsString(meta1).parseJson) val parsedItem1: ListResponse.Meta = ListResponse.listResponseMetaFormat.read(writtenJson1) meta1 shouldBe parsedItem1 - val meta2 = ListResponse.Meta( itemsCount = 1, @@ -58,8 +54,7 @@ class ListResponseSuite extends FlatSpec with Matchers { val writtenJson2 = ListResponse.listResponseMetaFormat.write(meta2) - writtenJson2 should be( - metaJsonObjectAsString(meta2).parseJson) + writtenJson2 should be(metaJsonObjectAsString(meta2).parseJson) val parsedItem2: ListResponse.Meta = ListResponse.listResponseMetaFormat.read(writtenJson2) @@ -67,7 +62,6 @@ class ListResponseSuite extends FlatSpec with Matchers { meta2 shouldBe parsedItem2 } - "Json format for ListResponse" should "write correct JSON" in { val orig = MedicalRecord( @@ -102,11 +96,10 @@ class ListResponseSuite extends FlatSpec with Matchers { val listResponse = ListResponse(Seq(orig), meta) - val writtenJson = ListResponse.listResponseMetaWriter.write(listResponse) + val writtenJson = ListResponse.listResponseMetaWriter.write(listResponse) val expectedJson = s"""{"items":[$recordJsonAsString],"meta":${metaJsonObjectAsString(meta)}}""" - writtenJson should be( - expectedJson.parseJson) + writtenJson should be(expectedJson.parseJson) } } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala index 90d5b6e..9616e70 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordFormatSuite.scala @@ -31,7 +31,7 @@ class MedicalRecordFormatSuite extends FlatSpec with Matchers { ) val writtenJson = recordFormat.write(orig) - writtenJson should be ( + writtenJson should be( """{"id":1,"status":"New","assignee":null,"previousStatus":null,"previousAssignee":null,"lastActiveUser":null, "lastUpdate":"2017-08-10T18:00Z","meta":[],"patientId":"748b5884-3528-4cb9-904b-7a8151d6e343","caseId":null, "requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","disease":"Breast","physician":"physician","totalPages":10}""".parseJson) @@ -62,11 +62,13 @@ class MedicalRecordFormatSuite extends FlatSpec with Matchers { {"type":"reorder","items":[1,2]}, {"type":"rotation","items":{"item1":1,"item2":2}}]}""".parseJson val expectedUpdatedRecord = orig.copy( - meta = Some(TextJson(List( - Meta.Duplicate(startPage = 1.0, endPage = 2.0, startOriginalPage = 1.0, endOriginalPage = None), - Meta.Reorder(Seq(1, 2)), - Meta.Rotation(Map("item1" -> 1, "item2" -> 2)) - ))) + meta = Some( + TextJson( + List( + Meta.Duplicate(startPage = 1.0, endPage = 2.0, startOriginalPage = 1.0, endOriginalPage = None), + Meta.Reorder(Seq(1, 2)), + Meta.Rotation(Map("item1" -> 1, "item2" -> 2)) + ))) ) val parsedUpdatedRecord = applyUpdateToMedicalRecord(updateRecordJson, orig) parsedUpdatedRecord should be(expectedUpdatedRecord) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordHistoryFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordHistoryFormatSuite.scala index 5cd6c8d..a8634d9 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordHistoryFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordHistoryFormatSuite.scala @@ -21,8 +21,7 @@ class MedicalRecordHistoryFormatSuite extends FlatSpec with Matchers { ) val writtenJson = recordHistoryFormat.write(recordHistory) - writtenJson should be( - """{"id":10,"executor":"userId-001","recordId":1,"state":"Clean", + writtenJson should be("""{"id":10,"executor":"userId-001","recordId":1,"state":"Clean", "action":"Start","created":"2017-08-10T18:00Z"}""".parseJson) val parsedRecordHistory = recordHistoryFormat.read(writtenJson) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordIssueFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordIssueFormatSuite.scala index c23ca37..5fa740b 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordIssueFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/MedicalRecordIssueFormatSuite.scala @@ -28,9 +28,9 @@ class MedicalRecordIssueFormatSuite extends FlatSpec with Matchers { """{"id":10,"recordId":1,"userId":"userId-001","lastUpdate":"2017-08-10T18:00Z","isDraft":false, "text":"message text","archiveRequired":false,"startPage":1.0,"endPage":2.0}""".parseJson) - val createRecordIssueJson = """{"text":"message text","startPage":1.0,"endPage":2.0}""".parseJson + val createRecordIssueJson = """{"text":"message text","startPage":1.0,"endPage":2.0}""".parseJson val expectedCreatedRecordIssue = recordIssue.copy(id = LongId(0), lastUpdate = LocalDateTime.MIN, isDraft = true) - val parsedCreateRecordIssue = jsValueToRecordIssue(createRecordIssueJson, LongId(1), StringId("userId-001")) + val parsedCreateRecordIssue = jsValueToRecordIssue(createRecordIssueJson, LongId(1), StringId("userId-001")) parsedCreateRecordIssue should be(expectedCreatedRecordIssue) val updateRecordIssueJson = diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala index fc206c7..b254013 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala @@ -33,19 +33,20 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers { PatientCriterionArm(patientCriterionId = LongId(1), armId = LongId(32), armName = "arm 32") ) val richPatientCriterion = RichPatientCriterion(orig, LongId(21), arms) - val writtenJson = patientCriterionWriter.write(richPatientCriterion) + val writtenJson = patientCriterionWriter.write(richPatientCriterion) - writtenJson should be ( + writtenJson should be( """{"id":1,"labelId":21,"nctId":"NCT00001","criterionId":101,"criterionText":"criterion text","criterionValue":"Yes", "criterionIsDefining":false,"criterionIsCompound":false,"eligibilityStatus":"Yes","verifiedEligibilityStatus":null, "isVisible":true,"isVerified":true,"lastUpdate":"2017-08-10T18:00Z","arms":["arm 31","arm 32"]}""".parseJson) - val updatePatientCriterionJson = """{"verifiedEligibilityStatus":"No"}""".parseJson + val updatePatientCriterionJson = """{"verifiedEligibilityStatus":"No"}""".parseJson val expectedUpdatedPatientCriterion = orig.copy(verifiedEligibilityStatus = Some(LabelValue.No)) - val parsedUpdatePatientCriterion = applyUpdateToPatientCriterion(updatePatientCriterionJson, orig) + val parsedUpdatePatientCriterion = applyUpdateToPatientCriterion(updatePatientCriterionJson, orig) parsedUpdatePatientCriterion should be(expectedUpdatedPatientCriterion) - val updateBulkPatientCriterionJson = """[{"id":1,"eligibilityStatus":"No"},{"id":2,"isVerified":false}]""".parseJson + val updateBulkPatientCriterionJson = + """[{"id":1,"eligibilityStatus":"No"},{"id":2,"isVerified":false}]""".parseJson val expectedDraftPatientCriterionList = List( DraftPatientCriterion(id = LongId(1), eligibilityStatus = Some(LabelValue.No), isVerified = None), DraftPatientCriterion(id = LongId(2), eligibilityStatus = None, isVerified = Some(false)) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala index 31f541f..b8f6f8e 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala @@ -2,10 +2,9 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.LocalDateTime -import spray.json._ import org.scalatest.{FlatSpec, Matchers} +import spray.json._ import xyz.driver.entities.labels.LabelValue -import xyz.driver.entities.patient.CancerType import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.{PatientCriterionArm, PatientTrialArmGroupView, Trial} import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial @@ -23,7 +22,6 @@ class PatientEligibleTrialFormatSuite extends FlatSpec with Matchers { previousAssignee = None, lastActiveUserId = None, lastUpdate = LocalDateTime.parse("2017-08-10T18:16:19"), - disease = CancerType.Breast, phase = "", hypothesisId = Some(UuidId("e76e2fc4-a29c-44fb-a81b-8856d06bb1d4")), studyDesignId = Some(LongId(321)), @@ -48,16 +46,16 @@ class PatientEligibleTrialFormatSuite extends FlatSpec with Matchers { PatientCriterionArm(patientCriterionId = LongId(1), armId = LongId(31), armName = "arm 31"), PatientCriterionArm(patientCriterionId = LongId(1), armId = LongId(32), armName = "arm 32") ) - val orig = RichPatientEligibleTrial(trial, group, arms) + val orig = RichPatientEligibleTrial(trial, group, arms) val writtenJson = patientEligibleTrialWriter.write(orig) - writtenJson should be ( + writtenJson should be( """{"id":1,"patientId":"748b5884-3528-4cb9-904b-7a8151d6e343","trialId":"NCT000001","trialTitle":"trial title", "hypothesisId":"e76e2fc4-a29c-44fb-a81b-8856d06bb1d4","verifiedEligibilityStatus":"Yes","isVerified":false,"arms":["arm 31","arm 32"]}""".parseJson) - val updatePatientEligibleTrialJson = """{"isVerified":true}""".parseJson + val updatePatientEligibleTrialJson = """{"isVerified":true}""".parseJson val expectedUpdatedPatientTrialArmGroup = group.copy(isVerified = true) - val parsedUpdatePatientTrialArmGroup = applyUpdateToTrialArmGroup(updatePatientEligibleTrialJson, group) + val parsedUpdatePatientTrialArmGroup = applyUpdateToTrialArmGroup(updatePatientEligibleTrialJson, group) parsedUpdatePatientTrialArmGroup should be(expectedUpdatedPatientTrialArmGroup) } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala index ad12b3b..128cad1 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala @@ -29,7 +29,7 @@ class PatientFormatSuite extends FlatSpec with Matchers { ) val writtenJson = patientWriter.write(orig) - writtenJson should be ( + writtenJson should be( """{"id":"748b5884-3528-4cb9-904b-7a8151d6e343","dob":"1980-06-30", "name":{"firstName":"John","middleName":"","lastName":"Doe"},"status":"New","assignee":null, "previousStatus":null,"previousAssignee":null,"lastActiveUser":null,"lastUpdate":"2017-08-10T18:00Z", diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala index fbb5213..71cbbad 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientHypothesisFormatSuite.scala @@ -19,13 +19,13 @@ class PatientHypothesisFormatSuite extends FlatSpec with Matchers { ) val writtenJson = richPatientHypothesisWriter.write(RichPatientHypothesis(orig, isRequired = true)) - writtenJson should be ( + writtenJson should be( """{"id":"815d9715-1089-4775-b120-3afb983b9a97","patientId":"748b5884-3528-4cb9-904b-7a8151d6e343", "hypothesisId":"e76e2fc4-a29c-44fb-a81b-8856d06bb1d4","rationale":null,"matchedTrials":1,"isRationaleRequired":true}""".parseJson) - val updatePatientHypothesisJson = """{"rationale":"rationale"}""".parseJson + val updatePatientHypothesisJson = """{"rationale":"rationale"}""".parseJson val expectedUpdatedPatientHypothesis = orig.copy(rationale = Some("rationale")) - val parsedUpdatePatientHypothesis = applyUpdateToPatientHypothesis(updatePatientHypothesisJson, orig) + val parsedUpdatePatientHypothesis = applyUpdateToPatientHypothesis(updatePatientHypothesisJson, orig) parsedUpdatePatientHypothesis should be(expectedUpdatedPatientHypothesis) } @@ -39,7 +39,7 @@ class PatientHypothesisFormatSuite extends FlatSpec with Matchers { ) val writtenJson = patientHypothesisWriter.write(orig) - writtenJson should be ( + writtenJson should be( """{"id":"815d9715-1089-4775-b120-3afb983b9a97","patientId":"748b5884-3528-4cb9-904b-7a8151d6e343", "hypothesisId":"e76e2fc4-a29c-44fb-a81b-8856d06bb1d4","rationale":null,"matchedTrials":1}""".parseJson) } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientIssueFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientIssueFormatSuite.scala index 1e2a11e..2776dcc 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientIssueFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientIssueFormatSuite.scala @@ -22,13 +22,14 @@ class PatientIssueFormatSuite extends FlatSpec with Matchers { ) val writtenJson = patientIssueWriter.write(patientIssue) - writtenJson should be( - """{"id":10,"userId":"userId-001","lastUpdate":"2017-08-10T18:00Z","isDraft":false, + writtenJson should be("""{"id":10,"userId":"userId-001","lastUpdate":"2017-08-10T18:00Z","isDraft":false, "text":"message text","archiveRequired":false}""".parseJson) - val createPatientIssueJson = """{"text":"message text"}""".parseJson + val createPatientIssueJson = """{"text":"message text"}""".parseJson val expectedCreatedPatientIssue = patientIssue.copy(id = LongId(0), lastUpdate = LocalDateTime.MIN, isDraft = true) - val parsedCreatePatientIssue = jsValueToPatientIssue(createPatientIssueJson, UuidId("40892a07-c638-49d2-9795-1edfefbbcc7c"), StringId("userId-001")) + val parsedCreatePatientIssue = jsValueToPatientIssue(createPatientIssueJson, + UuidId("40892a07-c638-49d2-9795-1edfefbbcc7c"), + StringId("userId-001")) parsedCreatePatientIssue should be(expectedCreatedPatientIssue) val updatePatientIssueJson = diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala index e837861..2122777 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala @@ -25,13 +25,13 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers { ) val writtenJson = richPatientLabelWriter.write(RichPatientLabel(orig, isVerified = true)) - writtenJson should be ( + writtenJson should be( """{"id":1,"labelId":20,"primaryValue":"Yes","verifiedPrimaryValue":null,"isVisible":true,"isVerified":true, "score":1,"isImplicitMatch":false}""".parseJson) - val updatePatientLabelJson = """{"verifiedPrimaryValue":"No"}""".parseJson + val updatePatientLabelJson = """{"verifiedPrimaryValue":"No"}""".parseJson val expectedUpdatedPatientLabel = orig.copy(verifiedPrimaryValue = Some(LabelValue.No)) - val parsedUpdatePatientLabel = applyUpdateToPatientLabel(updatePatientLabelJson, orig) + val parsedUpdatePatientLabel = applyUpdateToPatientLabel(updatePatientLabelJson, orig) parsedUpdatePatientLabel should be(expectedUpdatedPatientLabel) } @@ -53,7 +53,7 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers { ) val writtenJson = patientLabelEvidenceWriter.write(orig) - writtenJson should be ( + writtenJson should be( """{"id":1,"value":"Maybe","evidenceText":"evidence text","documentId":21,"evidenceId":10,"reportId":null, "documentType":{"id":3,"name":"Laboratory Report"},"date":"2017-08-10", "providerType":{"id":26,"name":"Emergency Medicine"}}""".parseJson) @@ -73,7 +73,7 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers { ) val writtenJson = patientLabelDefiningCriteriaWriter.write(orig) - writtenJson should be ("""{"id":1,"value":"Yes"}""".parseJson) + writtenJson should be("""{"id":1,"value":"Yes"}""".parseJson) } } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/SlotArmFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/SlotArmFormatSuite.scala new file mode 100644 index 0000000..7dd085c --- /dev/null +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/SlotArmFormatSuite.scala @@ -0,0 +1,36 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import spray.json._ +import org.scalatest.{FlatSpec, Matchers} +import xyz.driver.pdsuicommon.domain.{LongId, StringId} +import xyz.driver.pdsuidomain.entities.SlotArm + +class SlotArmFormatSuite extends FlatSpec with Matchers { + import slotarm._ + + "Json format for SlotArm" should "read and write correct JSON" in { + val arm = SlotArm( + id = LongId(10), + trialId = StringId("NCT000001"), + name = "arm name", + originalName = "orig arm name" + ) + val writtenJson = slotArmFormat.write(arm) + + writtenJson should be( + """{"id":10,"trialId":"NCT000001","name":"arm name","originalName":"orig arm name"}""".parseJson) + + val createArmJson = """{"trialId":"NCT000001","name":"arm name"}""".parseJson + val parsedArm = slotArmFormat.read(createArmJson) + val expectedCreatedArm = arm.copy( + id = LongId(0), + originalName = "arm name" + ) + parsedArm should be(expectedCreatedArm) + + val updateArmJson = """{"name":"new arm name"}""".parseJson + val expectedUpdatedArm = arm.copy(name = "new arm name") + val parsedUpdateArm = applyUpdateToArm(updateArmJson, arm) + parsedUpdateArm should be(expectedUpdatedArm) + } +} diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala index beb69c4..c9dc85f 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala @@ -2,9 +2,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import java.time.LocalDateTime -import spray.json._ import org.scalatest.{FlatSpec, Matchers} -import xyz.driver.entities.patient.CancerType +import spray.json._ import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.Trial @@ -21,7 +20,6 @@ class TrialFormatSuite extends FlatSpec with Matchers { previousAssignee = None, lastActiveUserId = None, lastUpdate = LocalDateTime.parse("2017-08-10T18:16:19"), - disease = CancerType.Breast, phase = "", hypothesisId = Some(UuidId("3b80b2e2-5372-4cf5-a342-6e4ebe10fafd")), studyDesignId = Some(LongId(321)), @@ -35,16 +33,16 @@ class TrialFormatSuite extends FlatSpec with Matchers { ) val writtenJson = trialWriter.write(orig) - writtenJson should be ( + writtenJson should be( """{"isPartner":false,"assignee":null,"lastUpdate":"2017-08-10T18:16:19Z","previousStatus":null, "isUpdated":false,"overviewTemplate":"","phase":"","originalStudyDesignId":null, "hypothesisId":"3b80b2e2-5372-4cf5-a342-6e4ebe10fafd","originalTitle":"orig trial title", "studyDesignId":321,"lastActiveUser":null,"externalid":"40892a07-c638-49d2-9795-1edfefbbcc7c", - "id":"NCT000001","disease":"Breast","status":"New","overview":null,"previousAssignee":null,"title":"trial title"}""".parseJson) + "id":"NCT000001","status":"New","overview":null,"previousAssignee":null,"title":"trial title"}""".parseJson) - val updateTrialJson = """{"hypothesisId":null,"overview":"new overview"}""".parseJson + val updateTrialJson = """{"hypothesisId":null,"overview":"new overview"}""".parseJson val expectedUpdatedTrial = orig.copy(hypothesisId = None, overview = Some("new overview")) - val parsedUpdateTrial = applyUpdateToTrial(updateTrialJson, orig) + val parsedUpdateTrial = applyUpdateToTrial(updateTrialJson, orig) parsedUpdateTrial should be(expectedUpdatedTrial) } diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialHistoryFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialHistoryFormatSuite.scala index dbb143c..d5ad2ec 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialHistoryFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialHistoryFormatSuite.scala @@ -21,8 +21,7 @@ class TrialHistoryFormatSuite extends FlatSpec with Matchers { ) val writtenJson = trialHistoryFormat.write(trialHistory) - writtenJson should be( - """{"id":10,"executor":"userId-001","trialId":"NCT000001","state":"Summarize", + writtenJson should be("""{"id":10,"executor":"userId-001","trialId":"NCT000001","state":"Summarize", "action":"Start","created":"2017-08-10T18:00Z"}""".parseJson) val parsedTrialHistory = trialHistoryFormat.read(writtenJson) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialIssueFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialIssueFormatSuite.scala index 02e14ba..4a9ea4f 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialIssueFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialIssueFormatSuite.scala @@ -24,13 +24,13 @@ class TrialIssueFormatSuite extends FlatSpec with Matchers { ) val writtenJson = trialIssueWriter.write(trialIssue) - writtenJson should be( - """{"id":10,"userId":"userId-001","lastUpdate":"2017-08-10T18:00Z","isDraft":false, + writtenJson should be("""{"id":10,"userId":"userId-001","lastUpdate":"2017-08-10T18:00Z","isDraft":false, "text":"message text","evidence":"evidence","archiveRequired":false,"meta":"{}"}""".parseJson) - val createTrialIssueJson = """{"text":"message text","evidence":"evidence","meta":"{}"}""".parseJson + val createTrialIssueJson = """{"text":"message text","evidence":"evidence","meta":"{}"}""".parseJson val expectedCreatedTrialIssue = trialIssue.copy(id = LongId(0), lastUpdate = LocalDateTime.MIN, isDraft = true) - val parsedCreateTrialIssue = jsValueToTrialIssue(createTrialIssueJson, StringId("NCT000001"), StringId("userId-001")) + val parsedCreateTrialIssue = + jsValueToTrialIssue(createTrialIssueJson, StringId("NCT000001"), StringId("userId-001")) parsedCreateTrialIssue should be(expectedCreatedTrialIssue) val updateTrialIssueJson = |