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author | vlad <vlad@driver.xyz> | 2018-01-25 14:12:31 -0800 |
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committer | vlad <vlad@driver.xyz> | 2018-01-25 14:12:31 -0800 |
commit | a0877d81ca2844d75dc361b5ce7c99afacd6e25f (patch) | |
tree | 8fe49f45cbcddbbb9a3d167099abe7aa2625e56b /src/main/scala/xyz/driver/pdsuidomain | |
parent | 46a22e9ab324a0068a85952cdc809800f360f445 (diff) | |
download | rest-query-a0877d81ca2844d75dc361b5ce7c99afacd6e25f.tar.gz rest-query-a0877d81ca2844d75dc361b5ce7c99afacd6e25f.tar.bz2 rest-query-a0877d81ca2844d75dc361b5ce7c99afacd6e25f.zip |
Extracting query library
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain')
128 files changed, 0 insertions, 10025 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/ListResponse.scala b/src/main/scala/xyz/driver/pdsuidomain/ListResponse.scala deleted file mode 100644 index c6dce7b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/ListResponse.scala +++ /dev/null @@ -1,24 +0,0 @@ -package xyz.driver.pdsuidomain - -import java.time.LocalDateTime - -import xyz.driver.pdsuicommon.db.Pagination - -final case class ListResponse[+T](items: Seq[T], meta: ListResponse.Meta) - -object ListResponse { - - final case class Meta(itemsCount: Int, pageNumber: Int, pageSize: Int, lastUpdate: Option[LocalDateTime]) - - object Meta { - def apply(itemsCount: Int, pagination: Pagination, lastUpdate: Option[LocalDateTime]): Meta = { - Meta( - itemsCount, - pagination.pageNumber, - pagination.pageSize, - lastUpdate - ) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Arm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Arm.scala deleted file mode 100644 index 2190b8d..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Arm.scala +++ /dev/null @@ -1,20 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuicommon.logging._ - -final case class Arm(id: LongId[Arm], - name: String, - originalName: String, - trialId: StringId[Trial], - deleted: Option[LocalDateTime] = None) - -object Arm { - - implicit def toPhiString(x: Arm): PhiString = { - import x._ - phi"Arm(id=$id, name=${Unsafe(x.name)}, trialId=${Unsafe(x.trialId)})" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala deleted file mode 100644 index 26ced22..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala +++ /dev/null @@ -1,57 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.Criterion.Meta.Evidence - -final case class Criterion(id: LongId[Criterion], - trialId: StringId[Trial], - text: Option[String], - isCompound: Boolean, - meta: String, - inclusion: Option[Boolean]) { - - def isValid: Boolean = text.nonEmpty && Option(meta).isDefined -} - -object Criterion { - - final case class Meta(evidence: Evidence) - - object Meta { - final case class Evidence(pageRatio: Double, start: TextLayerPosition, end: TextLayerPosition) - final case class TextLayerPosition(page: Integer, index: Integer, offset: Integer) - } - - implicit def toPhiString(x: Criterion): PhiString = { - import x._ - phi"Criterion(id=$id, trialId=$trialId, isCompound=$isCompound)" - } -} - -final case class CriterionArm(criterionId: LongId[Criterion], armId: LongId[EligibilityArm]) - -object CriterionArm { - - implicit def toPhiString(x: CriterionArm): PhiString = { - import x._ - phi"CriterionArm(criterionId=$criterionId, armId=$armId)" - } -} - -final case class CriterionLabel(id: LongId[CriterionLabel], - labelId: Option[LongId[Label]], - criterionId: LongId[Criterion], - categoryId: Option[LongId[LabelCategory]], - value: Option[Boolean], - isDefining: Boolean) - -object CriterionLabel { - - implicit def toPhiString(x: CriterionLabel): PhiString = { - import x._ - phi"CriterionLabel(id=$id, labelId=$labelId, criterionId=$criterionId, " + - phi"categoryId=$categoryId, value=$value, isDefining=$isDefining)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala deleted file mode 100644 index f35c3fd..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala +++ /dev/null @@ -1,24 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDate - -import xyz.driver.entities.assays.AssayType -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.domain.UuidId - -object DirectReport { - implicit def toPhiString(x: DirectReport): PhiString = { - import x._ - phi"DirectReport(id=$id, patientId=$patientId, reportType=${Unsafe(reportType)}, date=${Unsafe(date)}, " + - phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, " + - phi"providerName=${Unsafe(providerName)})" - } -} - -final case class DirectReport(id: UuidId[DirectReport], - patientId: UuidId[Patient], - reportType: AssayType, - date: LocalDate, - documentType: DocumentType, - providerType: ProviderType, - providerName: String) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala deleted file mode 100644 index 0669baf..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala +++ /dev/null @@ -1,492 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.{LocalDate, LocalDateTime, ZoneId} - -import com.fasterxml.jackson.annotation.JsonIgnoreProperties -import com.fasterxml.jackson.core.{JsonGenerator, JsonParser} -import com.fasterxml.jackson.databind._ -import com.fasterxml.jackson.databind.annotation.{JsonDeserialize, JsonSerialize} -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils -import xyz.driver.pdsuicommon.validation.Validators -import xyz.driver.pdsuicommon.validation.Validators.Validator -import xyz.driver.pdsuidomain.entities.Document.Meta - -import scalaz.Equal -import scalaz.syntax.equal._ -import scalaz.Scalaz.stringInstance - -sealed trait ProviderType { - val id: LongId[ProviderType] - val name: String -} - -object ProviderType { - - case object MedicalOncology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](1) - val name: String = "Medical Oncology" - } - - case object Surgery extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](2) - val name: String = "Surgery" - } - - case object Pathology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](3) - val name: String = "Pathology" - } - - case object MolecularPathology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](4) - val name: String = "Molecular Pathology" - } - - case object LaboratoryMedicine extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](5) - val name: String = "Laboratory Medicine" - } - - case object Radiology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](6) - val name: String = "Radiology" - } - - case object InterventionalRadiology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](7) - val name: String = "Interventional Radiology" - } - - case object RadiationOncology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](8) - val name: String = "Radiation Oncology" - } - - case object PrimaryCare extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](9) - val name: String = "Primary Care" - } - - case object Cardiology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](10) - val name: String = "Cardiology" - } - - case object Dermatology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](11) - val name: String = "Dermatology" - } - - case object Ophthalmology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](12) - val name: String = "Ophthalmology" - } - - case object Gastroenterology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](13) - val name: String = "Gastroenterology" - } - - case object Neurology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](14) - val name: String = "Neurology" - } - - case object Psychiatry extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](15) - val name: String = "Psychiatry" - } - - case object Gynecology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](16) - val name: String = "Gynecology" - } - - case object InfectiousDisease extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](17) - val name: String = "Infectious Disease" - } - - case object Immunology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](18) - val name: String = "Immunology" - } - - case object Nephrology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](19) - val name: String = "Nephrology" - } - - case object Rheumatology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](20) - val name: String = "Rheumatology" - } - - case object Cytology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](21) - val name: String = "Cytology" - } - - case object Otolaryngology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](22) - val name: String = "Otolaryngology" - } - - case object Anesthesiology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](23) - val name: String = "Anesthesiology" - } - - case object Urology extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](24) - val name: String = "Urology" - } - - case object PalliativeCare extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](25) - val name: String = "Palliative Care" - } - - case object EmergencyMedicine extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](26) - val name: String = "Emergency Medicine" - } - - case object SocialWork extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](27) - val name: String = "Social Work" - } - - case object NA extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](28) - val name: String = "N/A" - } - - case object Other extends ProviderType { - val id: LongId[ProviderType] = LongId[ProviderType](29) - val name: String = "Other" - } - - val All = Seq[ProviderType]( - MedicalOncology, - Surgery, - Pathology, - MolecularPathology, - LaboratoryMedicine, - Radiology, - InterventionalRadiology, - RadiationOncology, - PrimaryCare, - Cardiology, - Dermatology, - Ophthalmology, - Gastroenterology, - Neurology, - Psychiatry, - Gynecology, - InfectiousDisease, - Immunology, - Nephrology, - Rheumatology, - Cytology, - Otolaryngology, - Anesthesiology, - Urology, - PalliativeCare, - EmergencyMedicine, - SocialWork, - NA, - Other - ) - - def fromString(txt: String): Option[ProviderType] = { - All.find(_.name === txt) - } - - implicit def toPhiString(x: ProviderType): PhiString = { - import x._ - phi"ProviderType(id=$id, category=${Unsafe(name)})" - } -} - -sealed trait DocumentType { - val id: LongId[DocumentType] - val name: String -} - -object DocumentType { - - case object OutpatientPhysicianNote extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](1) - val name: String = "Outpatient Physician Note" - } - - case object DischargeNote extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](2) - val name: String = "Discharge Note" - } - - case object LaboratoryReport extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](3) - val name: String = "Laboratory Report" - } - - case object MedicationList extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](4) - val name: String = "Medication List" - } - - case object HospitalizationNote extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](5) - val name: String = "Hospitalization Note" - } - - case object PathologyReport extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](6) - val name: String = "Pathology Report" - } - - case object RadiologyReport extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](7) - val name: String = "Radiology Report" - } - - case object OperativeProcedureReport extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](8) - val name: String = "Operative/Procedure Report" - } - - case object MedicationAdministration extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](9) - val name: String = "Medication Administration" - } - - case object SocialWorkCaseManagementNote extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](10) - val name: String = "Social Work/Case Management Note" - } - - case object NonPhysicianProviderNote extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](11) - val name: String = "Non-physician Provider Note" - } - - case object Administrative extends DocumentType { - val id: LongId[DocumentType] = LongId[DocumentType](12) - val name: String = "Administrative" - } - - val All = Seq[DocumentType]( - OutpatientPhysicianNote, - DischargeNote, - LaboratoryReport, - MedicationList, - HospitalizationNote, - PathologyReport, - RadiologyReport, - OperativeProcedureReport, - MedicationAdministration, - SocialWorkCaseManagementNote, - NonPhysicianProviderNote, - Administrative - ) - - def fromString(txt: String): Option[DocumentType] = { - All.find(_.name === txt) - } - - implicit def equal: Equal[DocumentType] = Equal.equal[DocumentType](_ == _) - - implicit def toPhiString(x: DocumentType): PhiString = { - import x._ - phi"DocumentType(id=$id, name=${Unsafe(name)})" - } -} - -object Document { - - final case class Meta(startPage: Double, endPage: Double) - - class DocumentStatusSerializer extends JsonSerializer[Status] { - def serialize(value: Status, gen: JsonGenerator, serializers: SerializerProvider): Unit = { - gen.writeString(value.toString.toUpperCase) - } - } - - class DocumentStatusDeserializer extends JsonDeserializer[Status] { - def deserialize(parser: JsonParser, context: DeserializationContext): Status = { - val value = parser.getValueAsString - Option(value).fold[Document.Status](Status.New /* Default document status */ ) { v => - Status.All.find(_.toString.toUpperCase == v) match { - case None => throw new RuntimeJsonMappingException(s"$v is not valid Document.Status") - case Some(status) => status - } - } - } - } - - // Product with Serializable fixes issue: - // Set(New, Organized) has type Set[Status with Product with Serializable] - @JsonDeserialize(using = classOf[DocumentStatusDeserializer]) - @JsonSerialize(using = classOf[DocumentStatusSerializer]) - sealed trait Status extends Product with Serializable { - - def oneOf(xs: Status*): Boolean = xs.contains(this) - - def oneOf(xs: Set[Status]): Boolean = xs.contains(this) - - } - - object Status { - case object New extends Status - case object Organized extends Status - case object Extracted extends Status - case object Done extends Status - case object Flagged extends Status - case object Archived extends Status - - val All = Set[Status](New, Organized, Extracted, Done, Flagged, Archived) - val AllPrevious = Set[Status](Organized, Extracted) - - def fromString(status: String): Option[Status] = status match { - case "New" => Some(Status.New) - case "Organized" => Some(Status.Organized) - case "Extracted" => Some(Status.Extracted) - case "Done" => Some(Status.Done) - case "Flagged" => Some(Status.Flagged) - case "Archived" => Some(Status.Archived) - case _ => None - } - - def statusToString(x: Status): String = x match { - case Status.New => "New" - case Status.Organized => "Organized" - case Status.Extracted => "Extracted" - case Status.Done => "Done" - case Status.Flagged => "Flagged" - case Status.Archived => "Archived" - } - - implicit def toPhiString(x: Status): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - sealed trait RequiredType extends Product with Serializable { - - def oneOf(xs: RequiredType*): Boolean = xs.contains(this) - - def oneOf(xs: Set[RequiredType]): Boolean = xs.contains(this) - - } - - object RequiredType { - case object OPN extends RequiredType - case object PN extends RequiredType - - val All = Set[RequiredType](OPN, PN) - - def fromString(tpe: String): Option[RequiredType] = tpe match { - case "OPN" => Some(RequiredType.OPN) - case "PN" => Some(RequiredType.PN) - case _ => None - } - - def requiredTypeToString(x: RequiredType): String = x match { - case RequiredType.OPN => "OPN" - case RequiredType.PN => "PN" - } - - implicit def toPhiString(x: RequiredType): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - implicit def toPhiString(x: Document): PhiString = { - import x._ - phi"Document(id=$id, status=$status, assignee=${Unsafe(assignee)}, " + - phi"previousAssignee=${Unsafe(previousAssignee)}, " + - phi"lastActiveUserId=${Unsafe(lastActiveUserId)}, recordId=$recordId)" - } - - val validator: Validator[Document, Document] = { input => - for { - typeId <- Validators.nonEmpty("typeId")(input.typeId).right - - providerTypeId <- Validators.nonEmpty("providerTypeId")(input.providerTypeId).right - - institutionName <- Validators.nonEmpty("institutionName")(input.institutionName).right - - meta <- Validators.nonEmpty("meta")(input.meta).right - - startDate <- Validators.nonEmpty("startDate")(input.startDate).right - - isOrderRight <- (input.endDate match { - case Some(endDate) if startDate.isAfter(endDate) => - Validators.fail("The start date should be less, than the end one") - - case _ => Validators.success(true) - }).right - - areDatesInThePast <- { - val dates = List(input.startDate, input.endDate).flatten - val now = LocalDate.now() - val hasInvalid = dates.exists(_.isAfter(now)) - - if (hasInvalid) Validators.fail("Dates should be in the past") - else Validators.success(true) - }.right - } yield input - } - -} - -@JsonIgnoreProperties(value = Array("valid")) -final case class Document(id: LongId[Document] = LongId(0L), - status: Document.Status, - previousStatus: Option[Document.Status], - assignee: Option[xyz.driver.core.Id[User]], - previousAssignee: Option[xyz.driver.core.Id[User]], - lastActiveUserId: Option[xyz.driver.core.Id[User]], - recordId: LongId[MedicalRecord], - physician: Option[String], - typeId: Option[LongId[DocumentType]], // not null - providerName: Option[String], // not null - providerTypeId: Option[LongId[ProviderType]], // not null - requiredType: Option[Document.RequiredType], - institutionName: Option[String], - meta: Option[TextJson[Meta]], // not null - startDate: Option[LocalDate], // not null - endDate: Option[LocalDate], - lastUpdate: LocalDateTime, - labelVersion: Int) { - - import Document.Status._ - - if (previousStatus.nonEmpty) { - assert(AllPrevious.contains(previousStatus.get), s"Previous status has invalid value: ${previousStatus.get}") - } - - def getRequiredType(documentTypeName: String, providerTypeName: String): Option[Document.RequiredType] = { - import DocumentType.{OutpatientPhysicianNote, PathologyReport} - import ProviderType.MedicalOncology - - (DocumentType.fromString(documentTypeName), ProviderType.fromString(providerTypeName), startDate) match { - case (Some(OutpatientPhysicianNote), Some(MedicalOncology), Some(date)) - if !(date.isAfter(LocalDate.now(ZoneId.of("Z"))) || date.isBefore( - LocalDate.now(ZoneId.of("Z")).minusMonths(6))) => - Some(Document.RequiredType.OPN) - - case (Some(PathologyReport), _, _) => Some(Document.RequiredType.PN) - - case _ => None - } - } - - // TODO: with the current business logic code this constraint sometimes harmful - // require(status match { - // case Document.Status.New if assignee.isDefined => false - // case Document.Status.Done if assignee.isDefined => false - // case _ => true - // }, "Assignee can't be defined in New or Done statuses") - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/DocumentHistory.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/DocumentHistory.scala deleted file mode 100644 index f076074..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/DocumentHistory.scala +++ /dev/null @@ -1,98 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.{LocalDateTime, ZoneId} - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils -import xyz.driver.pdsuidomain.entities.DocumentHistory.{Action, _} - -object DocumentHistory { - - implicit def toPhiString(x: DocumentHistory): PhiString = { - import x._ - phi"DocumentHistory(id=$id, executor=${Unsafe(executor)}, documentId=$documentId, state=$state, action=$action, " + - phi"created=$created)" - } - - sealed trait State - object State { - case object New extends State - case object Extract extends State - case object Review extends State - case object Done extends State - case object Flag extends State - case object Archive extends State - - val All: Set[State] = Set( - State.New, - State.Extract, - State.Review, - State.Done, - State.Flag, - State.Archive - ) - - private val stateToName: Map[State, String] = - All.map(s => s -> s.toString).toMap - - val fromString: PartialFunction[String, State] = - for ((k, v) <- stateToName) yield (v, k) - - def stateToString: State => String = stateToName - - implicit def toPhiString(x: State): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - sealed trait Action extends Product with Serializable { - - def oneOf(xs: Action*): Boolean = xs.contains(this) - - def oneOf(xs: Set[Action]): Boolean = xs.contains(this) - - } - - object Action { - case object Start extends Action - case object Submit extends Action - case object Unassign extends Action - case object Resolve extends Action - case object Flag extends Action - case object Archive extends Action - case object PostEvidence extends Action - case object CreateDocument extends Action - case object ReadDocument extends Action - - val All: Set[Action] = Set( - Action.Start, - Action.Submit, - Action.Unassign, - Action.Resolve, - Action.Flag, - Action.Archive, - Action.PostEvidence, - Action.CreateDocument, - Action.ReadDocument - ) - - private val actionToName: Map[Action, String] = - All.map(a => a -> a.toString).toMap - - val fromString: PartialFunction[String, Action] = - for ((k, v) <- actionToName) yield (v, k) - - def actionToString: Action => String = actionToName - - implicit def toPhiString(x: Action): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } -} - -final case class DocumentHistory(id: LongId[DocumentHistory], - executor: xyz.driver.core.Id[User], - documentId: LongId[Document], - state: State, - action: Action, - created: LocalDateTime = LocalDateTime.now(ZoneId.of("Z"))) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/DocumentIssue.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/DocumentIssue.scala deleted file mode 100644 index 279ef38..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/DocumentIssue.scala +++ /dev/null @@ -1,24 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ - -final case class DocumentIssue(id: LongId[DocumentIssue], - userId: xyz.driver.core.Id[User], - documentId: LongId[Document], - startPage: Option[Double], - endPage: Option[Double], - lastUpdate: LocalDateTime, - isDraft: Boolean, - text: String, - archiveRequired: Boolean) - -object DocumentIssue { - implicit def toPhiString(x: DocumentIssue): PhiString = { - import x._ - phi"DocumentIssue(id=$id, userId=${Unsafe(userId)}, documentId=$documentId)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala deleted file mode 100644 index 50b49ad..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/EligibilityArm.scala +++ /dev/null @@ -1,42 +0,0 @@ -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=$eligibilityArmDiseases)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala deleted file mode 100644 index 569375a..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala +++ /dev/null @@ -1,48 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} -import xyz.driver.pdsuicommon.domain.{LongId, TextJson} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.ExtractedData.Meta - -final case class ExtractedData(id: LongId[ExtractedData] = LongId(0L), - documentId: LongId[Document], - keywordId: Option[LongId[Keyword]], - evidenceText: Option[String], - meta: Option[TextJson[Meta]]) { - - def isValid: Boolean = evidenceText.getOrElse("") != "" && meta.nonEmpty - -} - -object ExtractedData { - - final case class Meta(keyword: Option[Meta.Keyword], evidence: Option[Meta.Evidence]) - - object Meta { - final case class Evidence(pageRatio: Double, start: TextLayerPosition, end: TextLayerPosition) - - final case class TextLayerPosition(page: Integer, index: Integer, offset: Integer) - - final case class Keyword(page: Integer, pageRatio: Option[Double], index: Integer, sortIndex: String) - } - - implicit def toPhiString(x: ExtractedData): PhiString = { - import x._ - phi"ExtractedData(id=$id, documentId=$documentId, keywordId=$keywordId)" - } -} - -object ExtractedDataLabel { - - implicit def toPhiString(x: ExtractedDataLabel): PhiString = { - import x._ - phi"ExtractedDataLabel(id=$id, dataId=$dataId, labelId=$labelId, categoryId=$categoryId, value=${Unsafe(value)})" - } -} - -final case class ExtractedDataLabel(id: LongId[ExtractedDataLabel], - dataId: LongId[ExtractedData], - labelId: Option[LongId[Label]], - categoryId: Option[LongId[LabelCategory]], - value: Option[LabelValue]) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Hypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Hypothesis.scala deleted file mode 100644 index 47b87ff..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Hypothesis.scala +++ /dev/null @@ -1,13 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuicommon.logging._ - -final case class Hypothesis(id: UuidId[Hypothesis], name: String, treatmentType: String, description: String) - -object Hypothesis { - implicit def toPhiString(x: Hypothesis): PhiString = { - import x._ - phi"Hypothesis(id=$id, name=${Unsafe(name)})" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala deleted file mode 100644 index be51e4f..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala +++ /dev/null @@ -1,215 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod -import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod._ - -import scalaz.syntax.equal._ -import scalaz.Scalaz.stringInstance - -sealed trait InterventionType { - val id: LongId[InterventionType] - val name: String - val deliveryMethods: Set[DeliveryMethod] -} - -object InterventionType { - - final case object Chemotherapy extends InterventionType { - val id: LongId[InterventionType] = LongId[InterventionType](2) - val name: String = "Chemotherapy" - val deliveryMethods: Set[DeliveryMethod] = commonMethods - } - - final case object TargetedTherapy extends InterventionType { - val id: LongId[InterventionType] = LongId[InterventionType](3) - val name: String = "Targeted therapy" - val deliveryMethods: Set[DeliveryMethod] = commonMethods - } - - final case object Immunotherapy extends InterventionType { - val id: LongId[InterventionType] = LongId[InterventionType](4) - val name: String = "Immunotherapy" - val deliveryMethods: Set[DeliveryMethod] = commonMethods - } - - final case object HormoneTherapy extends InterventionType { - val id: LongId[InterventionType] = LongId[InterventionType](6) - val name: String = "Hormone therapy" - val deliveryMethods: Set[DeliveryMethod] = commonMethods - } - - final case object Other extends InterventionType { - val id: LongId[InterventionType] = LongId[InterventionType](7) - val name: String = "Other" - val deliveryMethods: Set[DeliveryMethod] = commonMethods - } - - final case object Radiation extends InterventionType { - val id: LongId[InterventionType] = LongId[InterventionType](8) - val name: String = "Radiation" - val deliveryMethods: Set[DeliveryMethod] = Set( - ExternalRadiationTherapy, - Brachytherapy, - SystemicRadiationTherapyIV, - SystemicRadiationTherapyOral, - ProtonBeamTherapy - ) - } - - final case object SurgeryProcedure extends InterventionType { - val id: LongId[InterventionType] = LongId[InterventionType](9) - val name: String = "Surgery/Procedure" - val deliveryMethods: Set[DeliveryMethod] = Set( - RadioFrequencyAblationRFA, - Cryoablation, - TherapeuticConventionalSurgery, - RoboticAssistedLaparoscopicSurgery - ) - } - - def typeFromString(txt: String): Option[InterventionType] = { - All.values.find(_.name === txt) - } - - sealed trait DeliveryMethod - object DeliveryMethod { - case object IntravenousInfusionIV extends DeliveryMethod - case object IntramuscularInjection extends DeliveryMethod - case object SubcutaneousInjection extends DeliveryMethod - case object IntradermalInjection extends DeliveryMethod - case object SpinalInjection extends DeliveryMethod - case object Oral extends DeliveryMethod - case object Topical extends DeliveryMethod - case object TransdermalPatch extends DeliveryMethod - case object Inhalation extends DeliveryMethod - case object Rectal extends DeliveryMethod - case object ExternalRadiationTherapy extends DeliveryMethod - case object Brachytherapy extends DeliveryMethod - case object SystemicRadiationTherapyIV extends DeliveryMethod - case object SystemicRadiationTherapyOral extends DeliveryMethod - case object ProtonBeamTherapy extends DeliveryMethod - case object RadioFrequencyAblationRFA extends DeliveryMethod - case object Cryoablation extends DeliveryMethod - case object TherapeuticConventionalSurgery extends DeliveryMethod - case object RoboticAssistedLaparoscopicSurgery extends DeliveryMethod - - def fromString: PartialFunction[String, DeliveryMethod] = { - case "Intravenous Infusion (IV)" => IntravenousInfusionIV - case "Intramuscular Injection" => IntramuscularInjection - case "Subcutaneous Injection" => SubcutaneousInjection - case "Intradermal Injection" => IntradermalInjection - case "Spinal Injection" => SpinalInjection - case "Oral" => Oral - case "Topical" => Topical - case "Transdermal Patch" => TransdermalPatch - case "Inhalation" => Inhalation - case "Rectal" => Rectal - case "External Radiation Therapy" => ExternalRadiationTherapy - case "Brachytherapy" => Brachytherapy - case "Systemic Radiation Therapy (IV)" => SystemicRadiationTherapyIV - case "Systemic Radiation Therapy (Oral)" => SystemicRadiationTherapyOral - case "Proton Beam Therapy" => ProtonBeamTherapy - case "Radio-Frequency Ablation (RFA)" => RadioFrequencyAblationRFA - case "Cryoablation" => Cryoablation - case "Therapeutic Conventional Surgery" => TherapeuticConventionalSurgery - case "Robotic Assisted Laparoscopic Surgery" => RoboticAssistedLaparoscopicSurgery - } - - def methodToString(x: DeliveryMethod): String = x match { - case IntravenousInfusionIV => "Intravenous Infusion (IV)" - case IntramuscularInjection => "Intramuscular Injection" - case SubcutaneousInjection => "Subcutaneous Injection" - case IntradermalInjection => "Intradermal Injection" - case SpinalInjection => "Spinal Injection" - case Oral => "Oral" - case Topical => "Topical" - case TransdermalPatch => "Transdermal Patch" - case Inhalation => "Inhalation" - case Rectal => "Rectal" - case ExternalRadiationTherapy => "External Radiation Therapy" - case Brachytherapy => "Brachytherapy" - case SystemicRadiationTherapyIV => "Systemic Radiation Therapy (IV)" - case SystemicRadiationTherapyOral => "Systemic Radiation Therapy (Oral)" - case ProtonBeamTherapy => "Proton Beam Therapy" - case RadioFrequencyAblationRFA => "Radio-Frequency Ablation (RFA)" - case Cryoablation => "Cryoablation" - case TherapeuticConventionalSurgery => "Therapeutic Conventional Surgery" - case RoboticAssistedLaparoscopicSurgery => "Robotic Assisted Laparoscopic Surgery" - } - } - - val commonMethods: Set[DeliveryMethod] = Set[DeliveryMethod]( - IntravenousInfusionIV, - IntramuscularInjection, - SubcutaneousInjection, - IntradermalInjection, - SpinalInjection, - Oral, - Topical, - TransdermalPatch, - Inhalation, - Rectal - ) - - val All: Map[LongId[InterventionType], InterventionType] = Map[LongId[InterventionType], InterventionType]( - LongId[InterventionType](2) -> Chemotherapy, - LongId[InterventionType](3) -> TargetedTherapy, - LongId[InterventionType](4) -> Immunotherapy, - LongId[InterventionType](6) -> HormoneTherapy, - LongId[InterventionType](7) -> Other, - LongId[InterventionType](8) -> Radiation, - LongId[InterventionType](9) -> SurgeryProcedure - ) - - implicit def toPhiString(x: InterventionType): PhiString = { - import x._ - phi"InterventionType(id=$id, name=${Unsafe(name)})" - } -} - -final case class InterventionArm(armId: LongId[SlotArm], interventionId: LongId[Intervention]) - -object InterventionArm { - implicit def toPhiString(x: InterventionArm): PhiString = { - import x._ - phi"InterventionArm(armId=$armId, interventionId=$interventionId)" - } -} - -final case class Intervention(id: LongId[Intervention], - trialId: StringId[Trial], - name: String, - originalName: String, - typeId: Option[LongId[InterventionType]], - originalType: Option[String], - dosage: String, - originalDosage: String, - isActive: Boolean, - deliveryMethod: Option[String]) { - def deliveryMethodIsCorrect: Boolean = { - if (this.typeId.nonEmpty && this.deliveryMethod.nonEmpty) { - InterventionType.All - .getOrElse(this.typeId.get, throw new IllegalArgumentException(s"Not found Intervention type ${this.typeId}")) - .deliveryMethods - .contains(DeliveryMethod.fromString(this.deliveryMethod.get)) - } else true - } -} - -object Intervention { - implicit def toPhiString(x: Intervention): PhiString = { - import x._ - phi"Intervention(id=$id, trialId=$trialId, name=${Unsafe(name)}, typeId=$typeId, isActive=$isActive, deliveryMethod=${Unsafe(deliveryMethod)})" - } -} - -final case class InterventionWithArms(intervention: Intervention, arms: List[InterventionArm]) - -object InterventionWithArms { - implicit def toPhiString(x: InterventionWithArms): PhiString = { - import x._ - phi"InterventionWithArms(intervention=$intervention, arms=$arms)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Keyword.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Keyword.scala deleted file mode 100644 index a984f92..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Keyword.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ - -final case class Keyword(id: LongId[Keyword], keyword: String) - -object Keyword { - implicit def toPhiString(x: Keyword): PhiString = { - import x._ - phi"Keyword(id=$id, keyword=${Unsafe(keyword)})" - } -} - -final case class KeywordWithLabels(keyword: Keyword, labels: List[Label]) - -object KeywordWithLabels { - implicit def toPhiString(x: KeywordWithLabels): PhiString = { - import x._ - phi"KeywordWithLabels(keyword=$keyword, ${Unsafe(labels)}" - } -} - -final case class KeywordLabel(keywordId: LongId[Keyword], labelId: LongId[Label]) - -object KeywordLabel { - implicit def toPhiString(x: KeywordLabel): PhiString = { - import x._ - phi"KeywordLabel($keywordId, $labelId)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecord.scala deleted file mode 100644 index cf13d1a..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecord.scala +++ /dev/null @@ -1,164 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.nio.channels.ReadableByteChannel -import java.time.LocalDateTime - -import com.fasterxml.jackson.annotation.JsonSubTypes.Type -import com.fasterxml.jackson.annotation.{JsonProperty, JsonSubTypes, JsonTypeInfo} -import xyz.driver.core.auth.User -import xyz.driver.entities.assays.PatientCase -import xyz.driver.entities.clinic.ClinicalRecord -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils -import xyz.driver.pdsuidomain.entities.MedicalRecord.Meta -import xyz.driver.pdsuidomain.entities.MedicalRecord.Meta.{Duplicate, Reorder, Rotation} - -object MedicalRecord { - - @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, property = "type") - @JsonSubTypes( - Array( - new Type(value = classOf[Duplicate], name = "duplicate"), - new Type(value = classOf[Reorder], name = "reorder"), - new Type(value = classOf[Rotation], name = "rotation") - )) - trait Meta { - @JsonProperty("type") def metaType: String - } - - object Meta { - - final case class Duplicate(startPage: Double, - endPage: Double, - startOriginalPage: Double, - endOriginalPage: Option[Double]) - extends Meta { - override val metaType = "duplicate" - } - - object Duplicate { - implicit def toPhiString(x: Duplicate): PhiString = { - import x._ - phi"Duplicate(startPage=${Unsafe(startPage)}, endPage=${Unsafe(endPage)}, " + - phi"startOriginalPage=${Unsafe(startOriginalPage)}, endOriginalPage=${Unsafe(endOriginalPage)}" - } - } - - final case class Reorder(items: Seq[Int]) extends Meta { - override val metaType = "reorder" - } - - object Reorder { - implicit def toPhiString(x: Reorder): PhiString = { - import x._ - phi"Reorder(items=${Unsafe(items.toString)})" - } - } - - final case class Rotation(items: Map[String, Int]) extends Meta { - override val metaType = "rotation" - } - - object Rotation { - implicit def toPhiString(x: Rotation): PhiString = { - import x._ - phi"Rotation(items=${Unsafe(items.toString)})" - } - } - - implicit def toPhiString(input: Meta): PhiString = input match { - case x: Duplicate => Duplicate.toPhiString(x) - case x: Reorder => Reorder.toPhiString(x) - case x: Rotation => Rotation.toPhiString(x) - } - - } - - // Product with Serializable fixes issue: - // Set(New, Cleaned) has type Set[Status with Product with Serializable] - sealed trait Status extends Product with Serializable { - - def oneOf(xs: Status*): Boolean = xs.contains(this) - - def oneOf(xs: Set[Status]): Boolean = xs.contains(this) - - } - object Status { - case object New extends Status - case object Cleaned extends Status - case object Reviewed extends Status - case object Organized extends Status - case object Done extends Status - case object Flagged extends Status - case object Archived extends Status - - def fromString(status: String): Option[Status] = status match { - case "New" => Some(New) - case "Cleaned" => Some(Cleaned) - case "Reviewed" => Some(Reviewed) - case "Organized" => Some(Organized) - case "Done" => Some(Done) - case "Flagged" => Some(Flagged) - case "Archived" => Some(Archived) - case _ => None - } - - val All: Set[Status] = Set[Status]( - New, - Cleaned, - Reviewed, - Organized, - Done, - Flagged, - Archived - ) - - val AllPrevious: Set[Status] = Set[Status](New, Cleaned, Reviewed, Organized) - - implicit def toPhiString(x: Status): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - sealed trait PdfSource - - object PdfSource { - case object Empty extends PdfSource - - /** @param createResource Constructor of the resource which is represents the file */ - final case class Channel(createResource: () => ReadableByteChannel) extends PdfSource - } - - implicit def toPhiString(x: MedicalRecord): PhiString = { - import x._ - phi"MedicalRecord(id=$id, status=$status, assignee=${Unsafe(assignee)}, " + - phi"previousAssignee=${Unsafe(previousAssignee)}, lastActiveUserId=${Unsafe(lastActiveUserId)})" - } -} - -final case class MedicalRecord(id: LongId[MedicalRecord], - status: MedicalRecord.Status, - previousStatus: Option[MedicalRecord.Status], - assignee: Option[xyz.driver.core.Id[User]], - previousAssignee: Option[xyz.driver.core.Id[User]], - lastActiveUserId: Option[xyz.driver.core.Id[User]], - patientId: UuidId[Patient], - requestId: xyz.driver.core.Id[ClinicalRecord], - disease: String, - caseId: Option[xyz.driver.core.Id[PatientCase]], - physician: Option[String], - meta: Option[TextJson[List[Meta]]], - lastUpdate: LocalDateTime, - totalPages: Int) { - - import MedicalRecord.Status._ - - if (previousStatus.nonEmpty) { - assert(AllPrevious.contains(previousStatus.get), s"Previous status has invalid value: ${previousStatus.get}") - } - - // TODO: with the current business logic code this constraint sometimes harmful - // require(status match { - // case MedicalRecord.Status.Done if assignee.isDefined => false - // case _ => true - // }, "Assignee can't be defined in Done status") -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecordHistory.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecordHistory.scala deleted file mode 100644 index 5ed5805..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecordHistory.scala +++ /dev/null @@ -1,112 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.{LocalDateTime, ZoneId} - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils -import xyz.driver.pdsuidomain.entities.MedicalRecordHistory._ - -object MedicalRecordHistory { - - implicit def toPhiString(x: MedicalRecordHistory): PhiString = { - import x._ - phi"MedicalRecordHistory(id=$id, executor=${Unsafe(executor)}, recordId=$recordId, state=$state, action=$action, " + - phi"created=$created)" - } - - sealed trait State - - object State { - case object New extends State - case object Clean extends State - case object Organize extends State - case object Review extends State - case object Done extends State - case object Flag extends State - case object Archive extends State - - val All: Set[State] = Set( - State.New, - State.Clean, - State.Organize, - State.Review, - State.Done, - State.Flag, - State.Archive - ) - - private val stateToName: Map[State, String] = - All.map(s => s -> s.toString).toMap - - val fromString: PartialFunction[String, State] = - for ((k, v) <- stateToName) yield (v, k) - - def stateToString: State => String = stateToName - - implicit def toPhiString(x: State): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - sealed trait Action extends Product with Serializable { - def oneOf(xs: Action*): Boolean = xs.contains(this) - def oneOf(xs: Set[Action]): Boolean = xs.contains(this) - } - - object Action { - case object Start extends Action - case object Submit extends Action - case object Unassign extends Action - case object Resolve extends Action - case object Flag extends Action - case object Archive extends Action - case object SaveDuplicate extends Action - case object SaveReorder extends Action - case object SaveRotation extends Action - case object DeleteDuplicate extends Action - case object DeleteReorder extends Action - case object DeleteRotation extends Action - case object CreateDocument extends Action - case object DeleteDocument extends Action - case object CreateRecord extends Action - case object ReadRecord extends Action - - val All: Set[Action] = Set( - Action.Start, - Action.Submit, - Action.Unassign, - Action.Resolve, - Action.Flag, - Action.Archive, - Action.SaveDuplicate, - Action.SaveReorder, - Action.SaveRotation, - Action.DeleteDuplicate, - Action.DeleteReorder, - Action.DeleteRotation, - Action.CreateDocument, - Action.DeleteDocument, - Action.CreateRecord, - Action.ReadRecord - ) - - private val actionToName: Map[Action, String] = - All.map(a => a -> a.toString).toMap - - val fromString: PartialFunction[String, Action] = - for ((k, v) <- actionToName) yield (v, k) - - def actionToString: Action => String = actionToName - - implicit def toPhiString(x: Action): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } -} - -final case class MedicalRecordHistory(id: LongId[MedicalRecordHistory], - executor: xyz.driver.core.Id[User], - recordId: LongId[MedicalRecord], - state: State, - action: Action, - created: LocalDateTime = LocalDateTime.now(ZoneId.of("Z"))) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecordIssue.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecordIssue.scala deleted file mode 100644 index 6cdad49..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/MedicalRecordIssue.scala +++ /dev/null @@ -1,24 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ - -final case class MedicalRecordIssue(id: LongId[MedicalRecordIssue], - userId: xyz.driver.core.Id[User], - recordId: LongId[MedicalRecord], - startPage: Option[Double], - endPage: Option[Double], - lastUpdate: LocalDateTime, - isDraft: Boolean, - text: String, - archiveRequired: Boolean) - -object MedicalRecordIssue { - implicit def toPhiString(x: MedicalRecordIssue): PhiString = { - import x._ - phi"MedicalRecordIssue(id=$id, userId=${Unsafe(userId)}, recordId=$recordId)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Message.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Message.scala deleted file mode 100644 index 68fd5cd..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Message.scala +++ /dev/null @@ -1,35 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuicommon.logging._ - -final case class Message(id: LongId[Message], - text: String, - lastUpdate: LocalDateTime, - userId: xyz.driver.core.Id[User], - isDraft: Boolean, - recordId: Option[LongId[MedicalRecord]], - documentId: Option[LongId[Document]], - patientId: Option[UuidId[Patient]], - trialId: Option[StringId[Trial]], - startPage: Option[Double], - endPage: Option[Double], - evidence: Option[String], - archiveRequired: Option[Boolean], - meta: Option[String]) - -object Message { - implicit def toPhiString(x: Message): PhiString = { - import x._ - - val entityId: Option[String] = recordId - .map(_.toString) - .orElse(documentId.map(_.toString)) - .orElse(patientId.map(_.toString)) - - phi"Message(id=$id, userId=${Unsafe(userId)}, isDraft=$isDraft, entityId=${Unsafe(entityId)}" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala deleted file mode 100644 index c48e0d9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala +++ /dev/null @@ -1,63 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.{LocalDate, LocalDateTime} - -import xyz.driver.core.auth.User -import xyz.driver.entities.clinic.TestOrder -import xyz.driver.entities.common.FullName -import xyz.driver.entities.patient.CancerType -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils - -object Patient { - - // Product with Serizalizable fixes issue: - // Set(New, Verified) has type Set[Status with Product with Serializable] - sealed trait Status extends Product with Serializable { - def oneOf(xs: Status*): Boolean = xs.contains(this) - - def oneOf(xs: Set[Status]): Boolean = xs.contains(this) - } - - object Status { - case object New extends Status - case object Verified extends Status - case object Reviewed extends Status - case object Curated extends Status - case object Flagged extends Status - case object Done extends Status - - val AllPrevious: Set[Status] = Set[Status](New, Verified, Reviewed, Curated) - - val All: Set[Status] = Set[Status](New, Verified, Reviewed, Curated, Flagged, Done) - - implicit def toPhiString(x: Status): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - implicit def toPhiString(x: Patient): PhiString = { - import x._ - phi"Patient(id=$id, status=$status, previousStatus=$previousStatus, lastActiveUserId=${Unsafe(lastActiveUserId)}" + - phi"assignee=${Unsafe(assignee)}, previousAssignee=${Unsafe(previousAssignee)})" - } -} - -final case class Patient(id: UuidId[Patient], - status: Patient.Status, - name: FullName[Patient], - dob: LocalDate, - assignee: Option[xyz.driver.core.Id[User]], - previousStatus: Option[Patient.Status], - previousAssignee: Option[xyz.driver.core.Id[User]], - lastActiveUserId: Option[xyz.driver.core.Id[User]], - isUpdateRequired: Boolean, - disease: CancerType, - orderId: xyz.driver.core.Id[TestOrder], - lastUpdate: LocalDateTime) { - - import Patient.Status._ - - if (previousStatus.nonEmpty) { - assert(AllPrevious.contains(previousStatus.get), s"Previous status has invalid value: ${previousStatus.get}") - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala deleted file mode 100644 index e6d466a..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala +++ /dev/null @@ -1,96 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.entities.labels.{Label, LabelValue} -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuicommon.logging._ - -object PatientCriterion { - implicit def toPhiString(x: PatientCriterion): PhiString = { - import x._ - phi"PatientCriterion(id=$id, patientLabelId=$patientLabelId, trialId=${Unsafe(trialId)}, nctId=$nctId, " + - phi"criterionId=$criterionId, criterionValue=${Unsafe(criterionValue)}, " + - phi"isImplicitMatch=$criterionIsDefining), criterionIsDefining=${Unsafe(criterionIsDefining)}, " + - phi"eligibilityStatus=${Unsafe(eligibilityStatus)}, verifiedEligibilityStatus=${Unsafe(verifiedEligibilityStatus)}, " + - phi"isVerified=${Unsafe(isVerified)}, lastUpdate=${Unsafe(lastUpdate)}, inclusion=${Unsafe(inclusion)}" - } - - /** - * @see https://driverinc.atlassian.net/wiki/display/MTCH/EV+Business+Process - */ - def getEligibilityStatus(criterionValue: Option[Boolean], primaryValue: LabelValue): LabelValue = { - primaryValue match { - case LabelValue.Unknown => LabelValue.Unknown - case LabelValue.Maybe => LabelValue.Maybe - case _ if criterionValue.isEmpty => LabelValue.Maybe - case status => - LabelValue.fromBoolean( - LabelValue.fromBoolean( - criterionValue.getOrElse(throw new IllegalArgumentException("Criterion should not be empty"))) == status - ) - } - } - -} - -/** - * @param eligibilityStatus - a value, that selects an eligibility verifier (EV) - * @param verifiedEligibilityStatus - a copy of eligibilityStatus, when a patient goes to routes curator (RC) - * @param isVerified - is EV selected the eligibilityStatus? - */ -final case class PatientCriterion(id: LongId[PatientCriterion], - patientLabelId: LongId[PatientLabel], - trialId: Long, - nctId: StringId[Trial], - criterionId: LongId[Criterion], - criterionText: String, - criterionValue: Option[Boolean], - criterionIsDefining: Boolean, - eligibilityStatus: LabelValue, - verifiedEligibilityStatus: LabelValue, - isVerified: Boolean, - isVisible: Boolean, - lastUpdate: LocalDateTime, - inclusion: Option[Boolean]) { - import scalaz.syntax.equal._ - def isIneligibleForEv: Boolean = eligibilityStatus === LabelValue.No && isVerified -} - -final case class DraftPatientCriterion(id: LongId[PatientCriterion], - eligibilityStatus: Option[LabelValue], - isVerified: Option[Boolean]) { - def applyTo(orig: PatientCriterion) = { - orig.copy( - eligibilityStatus = eligibilityStatus.getOrElse(orig.eligibilityStatus), - isVerified = isVerified.getOrElse(orig.isVerified) - ) - } -} - -object DraftPatientCriterion { - implicit def toPhiString(x: DraftPatientCriterion): PhiString = { - phi"DraftPatientCriterion(id=${x.id}, eligibilityStatus=${Unsafe(x.eligibilityStatus)}, isVerified=${x.isVerified})" - } -} - -final case class RichPatientCriterion(patientCriterion: PatientCriterion, - labelId: LongId[Label], - armList: List[PatientCriterionArm]) - -object RichPatientCriterion { - implicit def toPhiString(x: RichPatientCriterion): PhiString = { - phi"RichPatientCriterion(patientCriterion=${x.patientCriterion}, labelId=${x.labelId}, arms=${x.armList})" - } -} - -object PatientCriterionArm { - - implicit def toPhiString(x: PatientCriterionArm): PhiString = { - import x._ - phi"PatientCriterionArm(patientCriterionId=$patientCriterionId, armId=$armId, armName=${Unsafe(armName)})" - } - -} - -final case class PatientCriterionArm(patientCriterionId: LongId[PatientCriterion], armId: LongId[Arm], armName: String) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala deleted file mode 100644 index 4f62a9e..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala +++ /dev/null @@ -1,94 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.entities.labels.LabelValue -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuicommon.logging._ - -object PatientTrialArm { - - implicit def toPhiString(x: PatientTrialArm): PhiString = { - import x._ - phi"PatientTrialArm(armId=$armId, trialArmGroupId=$trialArmGroupId)" - } -} - -final case class PatientTrialArm(armId: LongId[Arm], trialArmGroupId: LongId[PatientTrialArmGroup]) - -object PatientEligibleTrial { - implicit def toPhiString(x: PatientEligibleTrial): PhiString = { - import x._ - phi"PatientEligibleTrial(id=$id, patientId=$patientId, trialId=$trialId, hypothesisId=$hypothesisId)" - } -} - -final case class PatientEligibleTrial(id: UuidId[PatientEligibleTrial], - patientId: UuidId[Patient], - trialId: StringId[Trial], - hypothesisId: UuidId[Hypothesis]) - -object PatientTrialArmGroup { - - implicit def toPhiString(x: PatientTrialArmGroup): PhiString = { - import x._ - phi"PatientTrialArmGroup(id=$id, eligibleTrialId=$eligibleTrialId, " + - phi"eligibilityStatus=${Unsafe(eligibilityStatus)}, " + - phi"verifiedEligibilityStatus=${Unsafe(verifiedEligibilityStatus)}, isVerified=$isVerified)" - } - - /** - * @see https://driverinc.atlassian.net/wiki/display/DMPD/EV+Business+Process - */ - def getEligibilityStatusForRc(criterionList: TraversableOnce[PatientCriterion]): LabelValue = { - def isEligible: Boolean = criterionList.forall(_.verifiedEligibilityStatus == LabelValue.Yes) - def isIneligible: Boolean = criterionList.exists(_.verifiedEligibilityStatus == LabelValue.No) - def isUnknown: Boolean = criterionList.forall(_.verifiedEligibilityStatus == LabelValue.Unknown) - - if (isEligible) LabelValue.Yes - else if (isIneligible) LabelValue.No - else if (isUnknown) LabelValue.Unknown - else LabelValue.Maybe - } -} - -final case class PatientTrialArmGroup(id: LongId[PatientTrialArmGroup], - eligibleTrialId: UuidId[PatientEligibleTrial], - eligibilityStatus: LabelValue, - verifiedEligibilityStatus: LabelValue, - isVerified: Boolean) - -object PatientTrialArmGroupView { - - implicit def toPhiString(x: PatientTrialArmGroupView): PhiString = { - import x._ - phi"PatientTrialArmGroupView(id=$id, patientId=$patientId, trialId=$trialId, " + - phi"hypothesisId=$hypothesisId, eligibilityStatus=${Unsafe(eligibilityStatus)}, " + - phi"verifiedEligibilityStatus=${Unsafe(verifiedEligibilityStatus)}, isVerified=$isVerified)" - } -} - -final case class PatientTrialArmGroupView(id: LongId[PatientTrialArmGroup], - patientId: UuidId[Patient], - trialId: StringId[Trial], - hypothesisId: UuidId[Hypothesis], - eligibilityStatus: LabelValue, - verifiedEligibilityStatus: LabelValue, - isVerified: Boolean) { - - def applyTo(trialArmGroup: PatientTrialArmGroup) = { - trialArmGroup.copy( - eligibilityStatus = this.eligibilityStatus, - verifiedEligibilityStatus = this.verifiedEligibilityStatus, - isVerified = this.isVerified - ) - } -} - -final case class RichPatientEligibleTrial(trial: Trial, - group: PatientTrialArmGroupView, - arms: List[PatientCriterionArm]) - -object RichPatientEligibleTrial { - implicit def toPhiString(x: RichPatientEligibleTrial): PhiString = { - phi"RichPatientEligibleTrial(group=${x.group}, trial=${x.trial}, arms=${x.arms})" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHistory.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHistory.scala deleted file mode 100644 index bea2c3b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHistory.scala +++ /dev/null @@ -1,94 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.{LocalDateTime, ZoneId} - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils -import xyz.driver.pdsuidomain.entities.PatientHistory.{Action, State} - -object PatientHistory { - - implicit def toPhiString(x: PatientHistory): PhiString = { - import x._ - phi"PatientHistory(id=$id, executor=${Unsafe(executor)}, patientId=$patientId, " + - phi"state=$state, action=$action, created=$created)" - } - - sealed trait State - object State { - case object Verify extends State - case object Curate extends State - case object Review extends State - case object Flag extends State - - val All: Set[State] = Set[State](Verify, Curate, Review, Flag) - - val fromString: PartialFunction[String, State] = { - case "Verify" => State.Verify - case "Curate" => State.Curate - case "Review" => State.Review - case "Flag" => State.Flag - } - - def stateToString(x: State): String = x match { - case State.Verify => "Verify" - case State.Curate => "Curate" - case State.Review => "Review" - case State.Flag => "Flag" - } - - implicit def toPhiString(x: State): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - sealed trait Action extends Product with Serializable { - - def oneOf(xs: Action*): Boolean = xs.contains(this) - - def oneOf(xs: Set[Action]): Boolean = xs.contains(this) - - } - - object Action { - case object Start extends Action - case object Submit extends Action - case object Unassign extends Action - case object Resolve extends Action - case object Flag extends Action - case object Archive extends Action - - val All: Set[Action] = - Set[Action](Start, Submit, Unassign, Resolve, Flag, Archive) - - val fromString: PartialFunction[String, Action] = { - case "Start" => Action.Start - case "Submit" => Action.Submit - case "Unassign" => Action.Unassign - case "Resolve" => Action.Resolve - case "Flag" => Action.Flag - case "Archive" => Action.Archive - } - - def actionToString(x: Action): String = x match { - case Action.Start => "Start" - case Action.Submit => "Submit" - case Action.Unassign => "Unassign" - case Action.Resolve => "Resolve" - case Action.Flag => "Flag" - case Action.Archive => "Archive" - } - - implicit def toPhiString(x: Action): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } - -} - -final case class PatientHistory(id: LongId[PatientHistory], - executor: xyz.driver.core.Id[User], - patientId: UuidId[Patient], - state: State, - action: Action, - created: LocalDateTime = LocalDateTime.now(ZoneId.of("Z"))) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHypothesis.scala deleted file mode 100644 index 7943fb9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHypothesis.scala +++ /dev/null @@ -1,20 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import eu.timepit.refined.api.Refined -import eu.timepit.refined.numeric.NonNegative -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuicommon.logging._ - -object PatientHypothesis { - implicit def toPhiString(x: PatientHypothesis): PhiString = { - import x._ - phi"PatientHypothesis(id=$id, patientId=$patientId, hypothesisId=$hypothesisId, " + - phi"rationale=${Unsafe(rationale)}, matchedTrials=${Unsafe(matchedTrials)})" - } -} - -final case class PatientHypothesis(id: UuidId[PatientHypothesis], - patientId: UuidId[Patient], - hypothesisId: UuidId[Hypothesis], - rationale: Option[String], - matchedTrials: Long Refined NonNegative) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientIssue.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientIssue.scala deleted file mode 100644 index b60c2ea..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientIssue.scala +++ /dev/null @@ -1,22 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ - -final case class PatientIssue(id: LongId[PatientIssue], - userId: xyz.driver.core.Id[User], - patientId: UuidId[Patient], - lastUpdate: LocalDateTime, - isDraft: Boolean, - text: String, - archiveRequired: Boolean) - -object PatientIssue { - implicit def toPhiString(x: PatientIssue): PhiString = { - import x._ - phi"PatientIssue(id=$id, userId=${Unsafe(userId)}, patientId=$patientId)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala deleted file mode 100644 index 8d64389..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala +++ /dev/null @@ -1,47 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.entities.labels.{Label, LabelValue} -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuicommon.logging._ - -object PatientLabel { - implicit def toPhiString(x: PatientLabel): PhiString = { - import x._ - phi"PatientLabel(id=$id, patientId=$patientId, labelId=$labelId, " + - phi"score=${Unsafe(score)}, primaryValue=${Unsafe(primaryValue)}, " + - phi"verifiedPrimaryValue=${Unsafe(verifiedPrimaryValue)})" - } -} - -final case class PatientLabel(id: LongId[PatientLabel], - patientId: UuidId[Patient], - labelId: LongId[Label], - score: Int, - primaryValue: LabelValue, - verifiedPrimaryValue: LabelValue, - isImplicitMatch: Boolean, - isVisible: Boolean) - -final case class RichPatientLabel(patientLabel: PatientLabel, isVerified: Boolean) - -object RichPatientLabel { - implicit def toPhiString(x: RichPatientLabel): PhiString = { - phi"RichPatientLabel(patientLabel=${x.patientLabel}, isVerified=${x.isVerified})" - } -} - -object PatientLabelEvidence { - implicit def toPhiString(x: PatientLabelEvidence): PhiString = { - import x._ - phi"PatientLabelEvidence(id=$id, patientLabelId=$patientLabelId, value=${Unsafe(value)}, " + - phi"documentId=$documentId, evidenceId=$evidenceId, reportId=$reportId)" - } -} - -final case class PatientLabelEvidence(id: LongId[PatientLabelEvidence], - patientLabelId: LongId[PatientLabel], - value: LabelValue, - evidenceText: String, - reportId: Option[UuidId[DirectReport]], - documentId: Option[LongId[Document]], - evidenceId: Option[LongId[ExtractedData]]) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala deleted file mode 100644 index 6055921..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala +++ /dev/null @@ -1,29 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDate - -import xyz.driver.entities.labels.{Label, LabelValue} -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ - -object PatientLabelEvidenceView { - implicit def toPhiString(x: PatientLabelEvidenceView): PhiString = { - import x._ - phi"PatientLabelEvidenceView(id=$id, value=${Unsafe(value)}, documentId=$documentId, " + - phi"evidenceId=$evidenceId, reportId=$reportId, patientId=$patientId, labelId=$labelId, " + - phi"isImplicitMatch=$isImplicitMatch)" - } -} - -final case class PatientLabelEvidenceView(id: LongId[PatientLabelEvidence], - value: LabelValue, - evidenceText: String, - documentId: Option[LongId[Document]], - evidenceId: Option[LongId[ExtractedData]], - reportId: Option[UuidId[DirectReport]], - documentType: DocumentType, - date: Option[LocalDate], // Document.startDate is optional - providerType: ProviderType, - patientId: UuidId[Patient], - labelId: LongId[Label], - isImplicitMatch: Boolean) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientDocument.scala deleted file mode 100644 index 45cdc4e..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientDocument.scala +++ /dev/null @@ -1,30 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDate - -import xyz.driver.core.Id -import xyz.driver.entities.clinic.ClinicalRecord -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuicommon.logging._ - -final case class RawPatientDocument(disease: String, - patientId: UuidId[Patient], - requestId: Id[ClinicalRecord], - recordId: LongId[MedicalRecord], - recordStatus: MedicalRecord.Status, - documentId: LongId[Document], - documentType: String, - documentProviderType: String, - documentStartDate: LocalDate, - documentStatus: Document.Status) - -object RawPatientDocument { - - implicit def toPhiString(x: RawPatientDocument): PhiString = { - import x._ - phi"RawPatientDocument(disease=${Unsafe(disease)}, patientId=$patientId, requestId=${Unsafe(requestId)}, " + - phi"recordId=$recordId, recordStatus=$recordStatus, documentId=$documentId, " + - phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(documentProviderType)}, " + - phi"startDate=$documentStartDate, documentStatus=$documentStatus)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArmEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArmEligibilityArm.scala deleted file mode 100644 index 70114de..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArmEligibilityArm.scala +++ /dev/null @@ -1,13 +0,0 @@ -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 deleted file mode 100644 index 932de38..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/SlotArms.scala +++ /dev/null @@ -1,20 +0,0 @@ -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=${Unsafe(x.trialId)})" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala deleted file mode 100644 index fa5ed61..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala +++ /dev/null @@ -1,126 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils -import xyz.driver.pdsuidomain.entities.Trial.Status - -import scalaz.syntax.equal._ -import scalaz.Scalaz.stringInstance - -sealed trait StudyDesign { - val id: LongId[StudyDesign] - val name: String -} - -object StudyDesign { - - final case object Randomized extends StudyDesign { - val id: LongId[StudyDesign] = LongId[StudyDesign](1) - val name: String = "Randomized" - } - - final case object NonRandomized extends StudyDesign { - val id: LongId[StudyDesign] = LongId[StudyDesign](2) - val name: String = "Non-randomized" - } - - final case object SingleGroupAssignment extends StudyDesign { - val id: LongId[StudyDesign] = LongId[StudyDesign](3) - val name: String = "Single-group assignment" - } - - val All = Seq[StudyDesign]( - Randomized, - NonRandomized, - SingleGroupAssignment - ) - - def fromString(txt: String): Option[StudyDesign] = { - All.find(_.name === txt) - } - - implicit def toPhiString(x: StudyDesign): PhiString = { - import x._ - phi"StudyDesign(id=$id, category=${Unsafe(name)})" - } -} - -object TrialCreationRequest { - - implicit def toPhiString(x: TrialCreationRequest): PhiString = phi"${Unsafe(x.toString)}" -} - -final case class TrialCreationRequest(id: UuidId[Trial], nctId: String, phase: String) - -object Trial { - - sealed trait Status { - def oneOf(xs: Status*): Boolean = xs.contains(this) - def oneOf(xs: Set[Status]): Boolean = xs.contains(this) - } - - object Status { - case object New extends Status - case object ReviewSummary extends Status - case object Summarized extends Status - case object PendingUpdate extends Status - case object Update extends Status - case object ReviewCriteria extends Status - case object Done extends Status - case object Flagged extends Status - case object Archived extends Status - - val All: Set[Status] = Set[Status]( - New, - ReviewSummary, - Summarized, - PendingUpdate, - Update, - ReviewCriteria, - Done, - Flagged, - Archived - ) - - val AllPrevious: Set[Status] = Set[Status](New, ReviewSummary, Summarized, ReviewCriteria) - - implicit def toPhiString(x: Status): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - implicit def toPhiString(x: Trial): PhiString = { - import x._ - phi"Trial(id=$id, externalId=$externalId, status=$status, previousStatus=$previousStatus, " + - phi"lastActiveUserId=${Unsafe(lastActiveUserId)}, assignee=${Unsafe(assignee)}, previousAssignee=${Unsafe(previousAssignee)})" - } - - final case class Locations(locations: List[String]) -} - -final case class Trial(id: StringId[Trial], - externalId: UuidId[Trial], - status: Status, - assignee: Option[xyz.driver.core.Id[User]], - previousStatus: Option[Status], - previousAssignee: Option[xyz.driver.core.Id[User]], - lastActiveUserId: Option[xyz.driver.core.Id[User]], - lastUpdate: LocalDateTime, - phase: String, - hypothesisId: Option[UuidId[Hypothesis]], - studyDesignId: Option[LongId[StudyDesign]], - originalStudyDesign: Option[String], - isPartner: Boolean, - overview: Option[String], - overviewTemplate: String, - isUpdated: Boolean, - title: String, - originalTitle: String) { - import Trial.Status._ - - if (previousStatus.nonEmpty) { - assert(AllPrevious.contains(previousStatus.get), s"Previous status has invalid value: ${previousStatus.get}") - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/TrialHistory.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/TrialHistory.scala deleted file mode 100644 index 9210742..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/TrialHistory.scala +++ /dev/null @@ -1,100 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.{LocalDateTime, ZoneId} - -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils -import TrialHistory._ -import xyz.driver.core.auth.User - -object TrialHistory { - - implicit def toPhiString(x: TrialHistory): PhiString = { - import x._ - phi"TrialHistory(id=$id, executor=${Unsafe(executor)}, trialId=$trialId, state=$state, action=$action, created=$created)" - } - - sealed trait State - object State { - case object Summarize extends State - case object Criteriarize extends State - case object Review extends State - case object ReviewSummary extends State - case object ReviewCriteria extends State - case object Flag extends State - - val All: Set[State] = Set[State](Summarize, Criteriarize, Review, ReviewSummary, ReviewCriteria, Flag) - - val fromString: PartialFunction[String, State] = { - case "Summarize" => State.Summarize - case "Criteriarize" => State.Criteriarize - case "Review" => State.Review - case "ReviewSummary" => State.ReviewSummary - case "ReviewCriteria" => State.ReviewCriteria - case "Flag" => State.Flag - } - - def stateToString(x: State): String = x match { - case State.Summarize => "Summarize" - case State.Criteriarize => "Criteriarize" - case State.Review => "Review" - case State.ReviewSummary => "ReviewSummary" - case State.ReviewCriteria => "ReviewCriteria" - case State.Flag => "Flag" - } - - implicit def toPhiString(x: State): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - sealed trait Action extends Product with Serializable { - - def oneOf(xs: Action*): Boolean = xs.contains(this) - - def oneOf(xs: Set[Action]): Boolean = xs.contains(this) - - } - - object Action { - case object Start extends Action - case object Submit extends Action - case object Unassign extends Action - case object Resolve extends Action - case object Flag extends Action - case object Archive extends Action - - val All: Set[Action] = - Set[Action](Start, Submit, Unassign, Resolve, Flag, Archive) - - val fromString: PartialFunction[String, Action] = { - case "Start" => Action.Start - case "Submit" => Action.Submit - case "Unassign" => Action.Unassign - case "Resolve" => Action.Resolve - case "Flag" => Action.Flag - case "Archive" => Action.Archive - } - - def actionToString(x: Action): String = x match { - case Action.Start => "Start" - case Action.Submit => "Submit" - case Action.Unassign => "Unassign" - case Action.Resolve => "Resolve" - case Action.Flag => "Flag" - case Action.Archive => "Archive" - } - - implicit def toPhiString(x: Action): PhiString = - Unsafe(Utils.getClassSimpleName(x.getClass)) - } - -} - -final case class TrialHistory(id: LongId[TrialHistory], - executor: xyz.driver.core.Id[User], - trialId: StringId[Trial], - state: State, - action: Action, - created: LocalDateTime = LocalDateTime.now(ZoneId.of("Z")), - comment: Option[String] = None) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/TrialIssue.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/TrialIssue.scala deleted file mode 100644 index f69e681..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/TrialIssue.scala +++ /dev/null @@ -1,24 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.LocalDateTime - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuicommon.logging._ - -final case class TrialIssue(id: LongId[TrialIssue], - userId: xyz.driver.core.Id[User], - trialId: StringId[Trial], - lastUpdate: LocalDateTime, - isDraft: Boolean, - text: String, - evidence: String, - archiveRequired: Boolean, - meta: String) - -object TrialIssue { - implicit def toPhiString(x: TrialIssue): PhiString = { - import x._ - phi"TrialIssue(id=$id, userId=${Unsafe(userId)}, trialId=$trialId)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/UserHistory.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/UserHistory.scala deleted file mode 100644 index 6299ed4..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/UserHistory.scala +++ /dev/null @@ -1,146 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import java.time.{LocalDateTime, ZoneId} - -import xyz.driver.core.auth.User -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuicommon.utils.Utils - -final case class UserHistory(id: LongId[UserHistory], - executor: xyz.driver.core.Id[User], - recordId: Option[LongId[MedicalRecord]] = None, - documentId: Option[LongId[Document]] = None, - trialId: Option[StringId[Trial]] = None, - patientId: Option[UuidId[Patient]] = None, - state: UserHistory.State, - action: UserHistory.Action, - created: LocalDateTime = LocalDateTime.now(ZoneId.of("Z"))) - -object UserHistory { - - def forDocument(executor: xyz.driver.core.Id[User], - documentId: LongId[Document], - state: UserHistory.State, - action: UserHistory.Action): UserHistory = UserHistory( - id = LongId(0L), - executor = executor, - documentId = Some(documentId), - state = state, - action = action - ) - - def forRecord(executor: xyz.driver.core.Id[User], - recordId: LongId[MedicalRecord], - state: UserHistory.State, - action: UserHistory.Action): UserHistory = UserHistory( - id = LongId(0L), - executor = executor, - recordId = Some(recordId), - state = state, - action = action - ) - - def forPatient(executor: xyz.driver.core.Id[User], - patientId: UuidId[Patient], - state: UserHistory.State, - action: UserHistory.Action): UserHistory = UserHistory( - id = LongId(0L), - executor = executor, - patientId = Some(patientId), - state = state, - action = action - ) - - sealed trait State extends Product with Serializable { - - def oneOf(xs: State*): Boolean = xs.contains(this) - - def oneOf(xs: Set[State]): Boolean = xs.contains(this) - } - - object State { - case object Clean extends State - case object Organize extends State - case object Extract extends State - case object Summarize extends State - case object Criteriarize extends State - case object Verify extends State - case object Curate extends State - case object Review extends State - case object Flag extends State - - val All: Set[State] = Set[State](Clean, Organize, Extract, Summarize, Criteriarize, Verify, Curate, Review, Flag) - - val fromString: PartialFunction[String, State] = { - case "Clean" => State.Clean - case "Organize" => State.Organize - case "Extract" => State.Extract - case "Summarize" => State.Summarize - case "Criteriarize" => State.Criteriarize - case "Verify" => State.Verify - case "Curate" => State.Curate - case "Review" => State.Review - case "Flag" => State.Flag - } - - def stateToString(x: State): String = x match { - case State.Clean => "Clean" - case State.Organize => "Organize" - case State.Extract => "Extract" - case State.Summarize => "Summarize" - case State.Criteriarize => "Criteriarize" - case State.Verify => "Verify" - case State.Curate => "Curate" - case State.Review => "Review" - case State.Flag => "Flag" - } - - implicit def toPhiString(x: State): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - sealed trait Action extends Product with Serializable { - - def oneOf(xs: Action*): Boolean = xs.contains(this) - - def oneOf(xs: Set[Action]): Boolean = xs.contains(this) - } - - object Action { - case object Start extends Action - case object Submit extends Action - case object Unassign extends Action - case object Resolve extends Action - case object Flag extends Action - case object Archive extends Action - - val All: Set[Action] = Set[Action](Start, Submit, Unassign, Resolve, Flag, Archive) - - val fromString: PartialFunction[String, Action] = { - case "Start" => Action.Start - case "Submit" => Action.Submit - case "Unassign" => Action.Unassign - case "Resolve" => Action.Resolve - case "Flag" => Action.Flag - case "Archive" => Action.Archive - } - - def actionToString(x: Action): String = x match { - case Action.Start => "Start" - case Action.Submit => "Submit" - case Action.Unassign => "Unassign" - case Action.Resolve => "Resolve" - case Action.Flag => "Flag" - case Action.Archive => "Archive" - } - - implicit def toPhiString(x: Action): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass)) - } - - implicit def toPhiString(x: UserHistory): PhiString = { - import x._ - phi"UserHistory(id=$id, executor=${Unsafe(executor)}, recordId=$recordId, " + - phi"documentId=$documentId, trialId=$trialId, patientId=$patientId, " + - phi"state=$state, action=$action, created=$created)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/eligibility.scala deleted file mode 100644 index 9362a0c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/eligibility.scala +++ /dev/null @@ -1,68 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.core.Id -import xyz.driver.core.date.Date -import xyz.driver.entities.assays.AssayType -import xyz.driver.entities.clinic.{ClinicalRecord, TestOrder} -import xyz.driver.entities.common.FullName -import xyz.driver.entities.labels.{Label, LabelValue} -import xyz.driver.entities.patient.CancerType -import xyz.driver.entities.process.ProcessStepExecutionStatus -import xyz.driver.entities.report.Report -import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels - -object eligibility { - - sealed trait EvidenceDocument { - val documentType: DocumentType - val providerType: ProviderType - val providerName: Option[String] - val date: Option[Date] - val isDriverDocument: Boolean - } - - final case class MolecularEvidenceDocument(documentType: DocumentType, - providerType: ProviderType, - providerName: Option[String], - date: Option[Date], - reportId: Id[Report], - reportType: AssayType, - isDriverDocument: Boolean = true) - extends EvidenceDocument - - final case class ClinicalEvidenceDocument(documentId: Id[ClinicalEvidenceDocument], - documentType: DocumentType, - providerType: ProviderType, - providerName: Option[String], - date: Option[Date], - requestId: Id[ClinicalRecord], - isDriverDocument: Boolean = false) - extends EvidenceDocument - - // Some fields are optional because they are not in the backend response - final case class Evidence(evidenceId: Option[Id[Evidence]], - evidenceText: String, - labelValue: LabelValue, - document: EvidenceDocument, - isPrimaryValue: Option[Boolean] = None) - - final case class LabelEvidence(label: Label, evidence: Seq[Evidence] = Seq.empty) - - final case class LabelMismatchRank(label: Label, - score: Int, - trials: Seq[ExportTrialWithLabels], - evidence: Seq[Evidence]) - final case class MismatchRankedLabels(data: Seq[LabelMismatchRank], labelVersion: Int) - - final case class MatchedPatient(patientId: Id[xyz.driver.entities.patient.Patient], - name: FullName[xyz.driver.entities.patient.Patient], - birthDate: Date, - orderId: Id[TestOrder], - disease: CancerType, - patientDataStatus: ProcessStepExecutionStatus) - - final case class EligibleTrial(nctId: String, arms: Seq[EligibleArm]) - final case class EligibleArm(title: String, criteria: Seq[EligibleCriterion]) - final case class EligibleCriterion(text: String, eligibilityStatus: LabelValue) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala deleted file mode 100644 index 957e607..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala +++ /dev/null @@ -1,15 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ - -final case class ExportPatientLabel(id: LongId[Label], evidences: List[ExportPatientLabelEvidence]) - -object ExportPatientLabel extends PhiLogging { - - implicit def toPhiString(x: ExportPatientLabel): PhiString = { - import x._ - phi"ExportPatientLabel(id=$id, evidences=$evidences)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala deleted file mode 100644 index 6472a6b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala +++ /dev/null @@ -1,21 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import xyz.driver.entities.labels.LabelValue -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.ExtractedData - -final case class ExportPatientLabelEvidence(id: LongId[ExtractedData], - value: LabelValue, - evidenceText: String, - document: ExportPatientLabelEvidenceDocument) - -object ExportPatientLabelEvidence { - - implicit def toPhiString(x: ExportPatientLabelEvidence): PhiString = { - import x._ - phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=${Unsafe(value)}, " + - phi"evidenceText=${Unsafe(evidenceText)}, document=$document)" - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala deleted file mode 100644 index 1b3a6d6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala +++ /dev/null @@ -1,23 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import java.time.LocalDate - -import xyz.driver.entities.clinic.ClinicalRecord -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities._ - -final case class ExportPatientLabelEvidenceDocument(documentId: LongId[Document], - requestId: xyz.driver.core.Id[ClinicalRecord], - documentType: DocumentType, - providerType: ProviderType, - date: LocalDate) - -object ExportPatientLabelEvidenceDocument extends PhiLogging { - - implicit def toPhiString(x: ExportPatientLabelEvidenceDocument): PhiString = { - import x._ - phi"ExportPatientLabelEvidenceDocument(documentId=$documentId, requestId=${Unsafe(requestId)}, " + - phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, date=$date)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala deleted file mode 100644 index 8fb2660..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala +++ /dev/null @@ -1,17 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.patient - -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.Patient - -final case class ExportPatientWithLabels(patientId: UuidId[Patient], - labelVersion: Long, - labels: List[ExportPatientLabel]) - -object ExportPatientWithLabels { - - implicit def toPhiString(x: ExportPatientWithLabels): PhiString = { - import x._ - phi"ExportPatientWithLabels(patientId=$patientId, version=${Unsafe(labelVersion)}, labels=$labels)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala deleted file mode 100644 index fbac0df..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialArm.scala +++ /dev/null @@ -1,15 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.trial - -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.EligibilityArm - -final case class ExportTrialArm(armId: LongId[EligibilityArm], armName: String, diseaseList: Seq[String]) - -object ExportTrialArm { - - implicit def toPhiString(x: ExportTrialArm): PhiString = { - import x._ - phi"ExportTrialArm(armId=$armId, armName=${Unsafe(armName)}, diseaseList=${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 deleted file mode 100644 index 98bd084..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala +++ /dev/null @@ -1,24 +0,0 @@ -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.{Criterion, EligibilityArm} - -final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion], - value: Option[Boolean], - labelId: LongId[Label], - armIds: Set[LongId[EligibilityArm]], - criteria: String, - isCompound: Boolean, - isDefining: Boolean, - inclusion: Option[Boolean]) - -object ExportTrialLabelCriterion { - - implicit def toPhiString(x: ExportTrialLabelCriterion): PhiString = { - import x._ - phi"TrialLabelCriterion(criterionId=$criterionId, value=$value, labelId=$labelId, " + - phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining), inclusion=${Unsafe(inclusion)}" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala deleted file mode 100644 index 3681945..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala +++ /dev/null @@ -1,23 +0,0 @@ -package xyz.driver.pdsuidomain.entities.export.trial - -import java.time.LocalDateTime - -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.Trial - -final case class ExportTrialWithLabels(nctId: StringId[Trial], - trialId: UuidId[Trial], - lastReviewed: LocalDateTime, - labelVersion: Long, - arms: List[ExportTrialArm], - criteria: List[ExportTrialLabelCriterion]) - -object ExportTrialWithLabels { - - implicit def toPhiString(x: ExportTrialWithLabels): PhiString = { - import x._ - phi"TrialWithLabels(nctId=$nctId, trialId=$trialId}, " + - phi"lastReviewed=$lastReviewed, labelVersion=${Unsafe(labelVersion)}, arms=$arms, criteria=$criteria)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala deleted file mode 100644 index 2aaa251..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala +++ /dev/null @@ -1,123 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities - -import java.time.{LocalDate, LocalDateTime, LocalTime} - -import xyz.driver.core.generators._ -import xyz.driver.entities.common.FullName -import xyz.driver.entities.patient.CancerType -import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue -import xyz.driver.pdsuicommon.domain.{LongId, StringId, TextJson, UuidId} -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ - -import scala.util.Random - -object common { - import xyz.driver.core.generators - - def nextUuidId[T]: UuidId[T] = UuidId[T](generators.nextUuid()) - - def nextLongId[T]: LongId[T] = LongId[T](generators.nextInt(Int.MaxValue).toLong) - - def nextStringId[T]: StringId[T] = StringId[T](generators.nextString(maxLength = 20)) - - def nextTrialStatus: Trial.Status = generators.oneOf[Trial.Status](Trial.Status.All) - - def nextPreviousTrialStatus: Trial.Status = generators.oneOf[Trial.Status](Trial.Status.AllPrevious) - - def nextLocalDateTime: LocalDateTime = LocalDateTime.of(nextLocalDate, LocalTime.MIDNIGHT) - - def nextLocalDate: LocalDate = LocalDate.of( - 1970 + Random.nextInt(68), - 1 + Random.nextInt(12), - 1 + Random.nextInt(28) // all months have at least 28 days - ) - - def nextTrialAction = generators.oneOf[TrialHistory.Action](TrialHistory.Action.All) - - def nextTrialState = generators.oneOf[TrialHistory.State](TrialHistory.State.All) - - def genBoundedRange[T](from: T, to: T)(implicit ord: Ordering[T]): (T, T) = { - if (ord.compare(from, to) > 0) { - to -> from - } else { - from -> to - } - } - - def genBoundedRangeOption[T](from: T, to: T)(implicit ord: Ordering[T]): (Option[T], Option[T]) = { - val ranges = nextOption(from).map { left => - val range = genBoundedRange(left, to) - range._1 -> nextOption(range._2) - } - - ranges.map(_._1) -> ranges.flatMap(_._2) - } - - def nextStartAndEndPagesOption: (Option[Double], Option[Double]) = - genBoundedRangeOption[Double](nextDouble(), nextDouble()) - - def nextStartAndEndPages: (Double, Double) = - genBoundedRange(nextDouble(), nextDouble()) - - def nextPatientStatus: Patient.Status = generators.oneOf[Patient.Status](Patient.Status.All) - - def nextFullName[T]: FullName[T] = FullName( - firstName = generators.nextName[T](10), - middleName = generators.nextName[T](10), - lastName = generators.nextName[T](10) - ) - - def nextCancerType: CancerType = - generators.oneOf[CancerType](CancerType.Breast, CancerType.Lung, CancerType.Prostate) - - private val maxAttemptsNumber = 100 - - def nextBridgeUploadQueueItem(): BridgeUploadQueue.Item = { - BridgeUploadQueue.Item( - kind = nextString(), - tag = nextString(), - created = nextLocalDateTime, - attempts = nextInt(maxAttemptsNumber, minValue = 0), - nextAttempt = nextLocalDateTime, - completed = nextBoolean(), - dependencyKind = nextOption(nextString()), - dependencyTag = nextOption(nextString()) - ) - } - - def nextBridgeUploadQueueItemListResponse(): ListResponse[BridgeUploadQueue.Item] = { - val xs: Seq[BridgeUploadQueue.Item] = Seq.fill(3)(nextBridgeUploadQueueItem()) - nextListResponse(xs) - } - - def nextDocumentType(): DocumentType = generators.oneOf[DocumentType](DocumentType.All: _*) - - def nextProviderType(): ProviderType = generators.oneOf[ProviderType](ProviderType.All: _*) - - def nextDocumentTypeListResponse(): ListResponse[DocumentType] = { - val xs: Seq[DocumentType] = Seq.fill(3)(nextDocumentType()) - nextListResponse(xs) - } - - def nextProviderTypeListResponse(): ListResponse[ProviderType] = { - val xs: Seq[ProviderType] = Seq.fill(3)(nextProviderType()) - nextListResponse(xs) - } - - def nextTextJson[T](obj: T): TextJson[T] = TextJson(obj) - - def nextListResponse[T](xs: Seq[T]): ListResponse[T] = { - val pageSize = generators.nextInt(xs.size, 1) - ListResponse( - items = xs, - meta = ListResponse.Meta( - itemsCount = xs.size, - pageNumber = generators.nextInt(xs.size / pageSize), - pageSize = pageSize, - lastUpdate = generators.nextOption(nextLocalDateTime) - ) - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/eligibility.scala deleted file mode 100644 index 1796fe6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/eligibility.scala +++ /dev/null @@ -1,72 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities - -import xyz.driver.core.generators -import xyz.driver.entities.clinic.{ClinicalRecord, TestOrder} -import xyz.driver.entities.patient.{CancerType, Patient} -import xyz.driver.entities.report.Report -import xyz.driver.fakes -import xyz.driver.pdsuidomain.entities.eligibility._ - -object eligibility { - import xyz.driver.core.generators._ - - def nextMolecularEvidenceDocument(): MolecularEvidenceDocument = - MolecularEvidenceDocument( - documentType = xyz.driver.pdsuidomain.fakes.entities.common.nextDocumentType(), - providerType = xyz.driver.pdsuidomain.fakes.entities.common.nextProviderType(), - providerName = nextOption(nextString(100)), - date = nextOption(nextDate()), - reportId = nextId[Report](), - reportType = fakes.entities.assays.nextAssayType(), - isDriverDocument = nextBoolean() - ) - - def nextClinicalEvidenceDocument(): ClinicalEvidenceDocument = - ClinicalEvidenceDocument( - documentType = xyz.driver.pdsuidomain.fakes.entities.common.nextDocumentType(), - providerType = xyz.driver.pdsuidomain.fakes.entities.common.nextProviderType(), - providerName = nextOption(nextString(100)), - date = nextOption(nextDate()), - documentId = nextId[ClinicalEvidenceDocument](), - requestId = nextId[ClinicalRecord](), - isDriverDocument = nextBoolean() - ) - - def nextEvidenceDocument(): EvidenceDocument = - oneOf[EvidenceDocument](nextMolecularEvidenceDocument(), - nextClinicalEvidenceDocument(), - nextClinicalEvidenceDocument()) // For more clinical documents - - def nextEvidence(): Evidence = - Evidence( - evidenceId = Option(nextId[Evidence]()), - evidenceText = nextString(100), - labelValue = xyz.driver.fakes.entities.labels.nextLabelValue(), - nextEvidenceDocument(), - isPrimaryValue = nextOption(nextBoolean()) - ) - - def nextLabelEvidence(): LabelEvidence = - LabelEvidence(label = fakes.entities.labels.nextLabel(), evidence = Seq.empty) - - def nextLabelMismatchRank(): LabelMismatchRank = - LabelMismatchRank( - label = fakes.entities.labels.nextLabel(), - score = nextInt(100), - trials = seqOf(xyz.driver.pdsuidomain.fakes.entities.export.nextExportTrialWithLabels()), - evidence = seqOf(nextEvidence()) - ) - - def nextMismatchRankedLabels(): MismatchRankedLabels = - MismatchRankedLabels(data = seqOf(nextLabelMismatchRank()), labelVersion = nextInt(100)) - - def nextMatchedPatient(): MatchedPatient = - MatchedPatient( - patientId = nextId[Patient](), - name = fakes.entities.common.nextFullName[Patient](), - birthDate = nextDate(), - orderId = nextId[TestOrder](), - disease = generators.oneOf[CancerType](CancerType.Breast, CancerType.Lung, CancerType.Prostate), - patientDataStatus = fakes.entities.process.nextProcessStepExecutionStatus() - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala deleted file mode 100644 index 12eff61..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala +++ /dev/null @@ -1,76 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities - -import xyz.driver.core.generators -import xyz.driver.entities.clinic.ClinicalRecord -import xyz.driver.entities.labels.Label -import xyz.driver.fakes -import xyz.driver.pdsuidomain.entities.export.patient._ -import xyz.driver.pdsuidomain.entities.export.trial._ -import xyz.driver.pdsuidomain.entities._ - -object export { - import common._ - import xyz.driver.core.generators._ - - def nextExportTrialArm(): ExportTrialArm = - 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[EligibilityArm]), - criteria = nextString(100), - isCompound = nextBoolean(), - isDefining = nextBoolean(), - inclusion = nextOption(nextBoolean()) - ) - - def nextExportTrialWithLabels(): ExportTrialWithLabels = - ExportTrialWithLabels( - nctId = nextStringId[Trial], - trialId = nextUuidId[Trial], - lastReviewed = nextLocalDateTime, - labelVersion = nextInt(100).toLong, - arms = listOf(nextExportTrialArm()), - criteria = listOf(nextExportTrialLabelCriterion()) - ) - - def nextExportPatientLabelEvidenceDocument(): ExportPatientLabelEvidenceDocument = { - ExportPatientLabelEvidenceDocument( - documentId = nextLongId[Document], - requestId = generators.nextId[ClinicalRecord](), - documentType = nextDocumentType(), - providerType = nextProviderType(), - date = nextLocalDate - ) - } - - def nextExportPatientLabelEvidence(): ExportPatientLabelEvidence = { - ExportPatientLabelEvidence( - id = nextLongId[ExtractedData], - value = fakes.entities.labels.nextLabelValue(), - evidenceText = nextString(), - document = nextExportPatientLabelEvidenceDocument() - ) - } - - def nextExportPatientLabel(): ExportPatientLabel = { - ExportPatientLabel( - id = nextLongId[Label], - evidences = List.fill(nextInt(10))(nextExportPatientLabelEvidence()) - ) - } - - def nextExportPatientWithLabels(): ExportPatientWithLabels = { - ExportPatientWithLabels( - patientId = nextUuidId[Patient], - labelVersion = nextInt(Int.MaxValue).toLong, - labels = List.fill(nextInt(10))(nextExportPatientLabel()) - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala deleted file mode 100644 index d3d76b8..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala +++ /dev/null @@ -1,322 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities - -import java.time.LocalDate - -import xyz.driver.core.auth.User -import xyz.driver.core.generators -import xyz.driver.core.generators._ -import xyz.driver.entities.assays.PatientCase -import xyz.driver.entities.clinic.ClinicalRecord -import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} -import xyz.driver.pdsuicommon.domain.{LongId, TextJson} -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.ExtractedData.Meta -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.fakes.entities.common._ -import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData - -object recordprocessing { - - private val maxItemsInCollectionNumber: Int = 50 - private val maxPageNumber = 100 - private val maxIndexNumber = 100 - private val maxOffsetNumber = 10 - - implicit private class LocalDateOrdering(localData: LocalDate) extends Ordered[LocalDate] { - override def compare(that: LocalDate): Int = { - this.localData.compareTo(that) - } - } - - implicit private class TextLayerPositionOrdering(textLayerPosition: ExtractedData.Meta.TextLayerPosition) - extends Ordered[ExtractedData.Meta.TextLayerPosition] { - override def compare(that: Meta.TextLayerPosition): Int = { - if (this.textLayerPosition.page < that.page) -1 - else if (this.textLayerPosition.page > that.page) 1 - else if (this.textLayerPosition.index < that.index) -1 - else if (this.textLayerPosition.index > that.index) 1 - else if (this.textLayerPosition.offset < that.offset) -1 - else if (this.textLayerPosition.offset > that.offset) 1 - else 0 - } - } - - private def nextDates(): (Option[LocalDate], Option[LocalDate]) = - genBoundedRangeOption[LocalDate](nextLocalDate, nextLocalDate) - - private val medicalRecordMeta: Set[() => MedicalRecord.Meta] = { - Set( - () => nextMedicalRecordMetaReorder(), - () => nextMedicalRecordMetaDuplicate(), - () => nextMedicalRecordMetaRotation() - ) - } - - def nextMedicalRecordMeta(count: Int): List[MedicalRecord.Meta] = - List.fill(count)(nextMedicalRecordMeta()) - - def nextMedicalRecordMetaJson(): TextJson[List[MedicalRecord.Meta]] = - TextJson(nextMedicalRecordMeta(nextInt(maxItemsInCollectionNumber))) - - private def nextDocumentList(count: Int): List[Document] = - List.fill(count)(nextDocument()) - - def nextDocumentList(recordId: LongId[MedicalRecord]): TextJson[List[Document]] = { - val documents = nextDocumentList( - nextInt(maxItemsInCollectionNumber) - ) - TextJson(documents.map(_.copy(recordId = recordId))) - } - - def nextMedicalRecordStatus(): MedicalRecord.Status = - generators.oneOf[MedicalRecord.Status](MedicalRecord.Status.All) - - def nextMedicalRecordHistoryState(): MedicalRecordHistory.State = - generators.oneOf[MedicalRecordHistory.State](MedicalRecordHistory.State.All) - - def nextMedicalRecordHistoryAction(): MedicalRecordHistory.Action = - generators.oneOf[MedicalRecordHistory.Action](MedicalRecordHistory.Action.All) - - def nextMedicalRecordMetaReorder(): MedicalRecord.Meta.Reorder = { - val itemsNumber = maxItemsInCollectionNumber - val items = scala.util.Random.shuffle(Seq.tabulate(itemsNumber)(identity)) - - MedicalRecord.Meta.Reorder(items) - } - - def nextMedicalRecordMetaDuplicate(): MedicalRecord.Meta.Duplicate = { - val startPageGen = nextInt(maxPageNumber) - val endPageGen = nextInt(maxPageNumber, startPageGen) - - MedicalRecord.Meta.Duplicate( - startPage = startPageGen.toDouble, - endPage = endPageGen.toDouble, - startOriginalPage = startPageGen.toDouble, - endOriginalPage = nextOption(endPageGen.toDouble) - ) - } - - def nextMedicalRecordMetaRotation(): MedicalRecord.Meta.Rotation = { - val items = Array.tabulate(maxItemsInCollectionNumber)(index => nextString() -> index).toMap - - MedicalRecord.Meta.Rotation(items = items) - } - - def nextMedicalRecordMeta(): MedicalRecord.Meta = generators.oneOf(medicalRecordMeta)() - - def nextMedicalRecord(): MedicalRecord = MedicalRecord( - id = nextLongId[MedicalRecord], - status = nextMedicalRecordStatus(), - previousStatus = nextOption(generators.oneOf[MedicalRecord.Status](MedicalRecord.Status.AllPrevious)), - assignee = nextOption(generators.nextId[User]), - previousAssignee = nextOption(generators.nextId[User]), - lastActiveUserId = nextOption(generators.nextId[User]), - patientId = nextUuidId[Patient], - requestId = generators.nextId[ClinicalRecord](), - disease = generators.nextString(), - caseId = nextOption(generators.nextId[PatientCase]()), - physician = nextOption(generators.nextString()), - meta = nextOption(nextMedicalRecordMetaJson()), - lastUpdate = nextLocalDateTime, - totalPages = nextInt(10) - ) - - def nextMedicalRecordHistory(): MedicalRecordHistory = MedicalRecordHistory( - id = nextLongId[MedicalRecordHistory], - executor = generators.nextId[User], - recordId = nextLongId[MedicalRecord], - state = nextMedicalRecordHistoryState(), - action = nextMedicalRecordHistoryAction(), - created = nextLocalDateTime - ) - - def nextMedicalRecordIssue(): MedicalRecordIssue = { - val (startPage, endPage) = nextStartAndEndPagesOption - - MedicalRecordIssue( - id = nextLongId[MedicalRecordIssue], - userId = generators.nextId[User], - recordId = nextLongId[MedicalRecord], - startPage = startPage, - endPage = endPage, - lastUpdate = nextLocalDateTime, - isDraft = nextBoolean(), - text = nextString(), - archiveRequired = nextBoolean() - ) - } - - def nextDocumentStatus(): Document.Status = generators.oneOf[Document.Status](Document.Status.All) - - def nextDocumentRequiredType(): Document.RequiredType = - generators.oneOf[Document.RequiredType](Document.RequiredType.All) - - def nextDocumentHistoryState(): DocumentHistory.State = - generators.oneOf[DocumentHistory.State](DocumentHistory.State.All) - - def nextDocumentHistoryAction(): DocumentHistory.Action = - generators.oneOf[DocumentHistory.Action](DocumentHistory.Action.All) - - def nextDocumentMeta(): Document.Meta = { - val (startPage, endPage) = nextStartAndEndPages - Document.Meta(startPage, endPage) - } - - def nextDocumentMetaJson(): TextJson[Document.Meta] = nextTextJson(nextDocumentMeta()) - - def nextDocument(): Document = { - val (startDate, endDate) = nextDates() - - Document( - id = nextLongId[Document], - status = nextDocumentStatus(), - previousStatus = nextOption(generators.oneOf[Document.Status](Document.Status.AllPrevious)), - assignee = nextOption(generators.nextId[User]), - previousAssignee = nextOption(generators.nextId[User]), - lastActiveUserId = nextOption(generators.nextId[User]), - recordId = nextLongId[MedicalRecord], - physician = nextOption(nextString()), - typeId = nextOption(nextLongId[DocumentType]), - providerName = nextOption(nextString()), - providerTypeId = nextOption(nextLongId[ProviderType]), - requiredType = nextOption(nextDocumentRequiredType()), - institutionName = nextOption(nextString()), - meta = nextOption(nextDocumentMetaJson()), - startDate = startDate, - endDate = endDate, - lastUpdate = nextLocalDateTime, - labelVersion = generators.nextInt(100) - ) - } - - def nextDocumentIssue(): DocumentIssue = { - val (startPage, endPage) = nextStartAndEndPagesOption - DocumentIssue( - id = nextLongId[DocumentIssue], - userId = generators.nextId[User], - documentId = nextLongId[Document], - startPage = startPage, - endPage = endPage, - lastUpdate = nextLocalDateTime, - isDraft = nextBoolean(), - text = nextString(), - archiveRequired = nextBoolean() - ) - } - - def nextDocumentHistory(): DocumentHistory = DocumentHistory( - id = nextLongId[DocumentHistory], - executor = generators.nextId[User], - documentId = nextLongId[Document], - state = nextDocumentHistoryState(), - action = nextDocumentHistoryAction(), - created = nextLocalDateTime - ) - - def nextExtractedDataMetaKeyword(): Meta.Keyword = { - ExtractedData.Meta.Keyword( - page = nextInt(maxPageNumber), - pageRatio = nextOption(nextDouble()), - index = nextInt(maxIndexNumber), - sortIndex = nextString() - ) - } - - def nextExtractedDataMetaTextLayerPosition(): Meta.TextLayerPosition = { - ExtractedData.Meta.TextLayerPosition( - page = nextInt(maxPageNumber), - index = nextInt(maxIndexNumber), - offset = nextInt(maxOffsetNumber) - ) - } - - def nextExtractedDataMetaEvidence(): Meta.Evidence = { - val (start, end) = - genBoundedRange[ExtractedData.Meta.TextLayerPosition]( - nextExtractedDataMetaTextLayerPosition(), - nextExtractedDataMetaTextLayerPosition() - ) - - ExtractedData.Meta.Evidence( - pageRatio = nextDouble(), - start = start, - end = end - ) - } - - def nextExtractedDataMeta(): Meta = { - ExtractedData.Meta( - nextOption(nextExtractedDataMetaKeyword()), - nextOption(nextExtractedDataMetaEvidence()) - ) - } - - def nextExtractedDataMetaJson(): TextJson[Meta] = - nextTextJson(nextExtractedDataMeta()) - - def nextExtractedData(): ExtractedData = { - ExtractedData( - id = nextLongId[ExtractedData], - documentId = nextLongId[Document], - keywordId = nextOption(nextLongId[Keyword]), - evidenceText = nextOption(nextString()), - meta = nextOption(nextExtractedDataMetaJson()) - ) - } - - def nextExtractedDataLabel(): ExtractedDataLabel = { - ExtractedDataLabel( - id = nextLongId[ExtractedDataLabel], - dataId = nextLongId[ExtractedData], - labelId = nextOption(nextLongId[Label]), - categoryId = nextOption(nextLongId[LabelCategory]), - value = nextOption(generators.oneOf[LabelValue](LabelValue.Yes, LabelValue.No, LabelValue.Maybe)) - ) - } - - def nextRichExtractedData(): RichExtractedData = { - val extractedData = nextExtractedData() - RichExtractedData( - extractedData = extractedData, - labels = List.fill( - nextInt(maxItemsInCollectionNumber) - )(nextExtractedDataLabel()) - ) - } - - def nextMedicalRecordListResponse(): ListResponse[MedicalRecord] = { - val xs: Seq[MedicalRecord] = Seq.fill(3)(nextMedicalRecord()) - nextListResponse(xs) - } - - def nextMedicalRecordIssueListResponse(): ListResponse[MedicalRecordIssue] = { - val xs: Seq[MedicalRecordIssue] = Seq.fill(3)(nextMedicalRecordIssue()) - nextListResponse(xs) - } - - def nextMedicalRecordHistoryListResponse(): ListResponse[MedicalRecordHistory] = { - val xs: Seq[MedicalRecordHistory] = Seq.fill(3)(nextMedicalRecordHistory()) - nextListResponse(xs) - } - - def nextDocumentListResponse(): ListResponse[Document] = { - val xs: Seq[Document] = Seq.fill(3)(nextDocument()) - nextListResponse(xs) - } - - def nextDocumentIssueListResponse(): ListResponse[DocumentIssue] = { - val xs: Seq[DocumentIssue] = Seq.fill(3)(nextDocumentIssue()) - nextListResponse(xs) - } - - def nextDocumentHistoryListResponse(): ListResponse[DocumentHistory] = { - val xs: Seq[DocumentHistory] = Seq.fill(3)(nextDocumentHistory()) - nextListResponse(xs) - } - - def nextRichExtractedDataListResponse(): ListResponse[RichExtractedData] = { - val xs: Seq[RichExtractedData] = Seq.fill(3)(nextRichExtractedData()) - nextListResponse(xs) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala deleted file mode 100644 index 8b13789..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala +++ /dev/null @@ -1 +0,0 @@ - diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala deleted file mode 100644 index 190add6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala +++ /dev/null @@ -1,233 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities - -import eu.timepit.refined.numeric.NonNegative -import xyz.driver.entities.labels.Label -import xyz.driver.fakes -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import eu.timepit.refined.{refineMV, refineV} -import xyz.driver.core.auth.User - -object treatmentmatching { - import common._ - import xyz.driver.core.generators - - final case class DraftPatientCriterionList(list: List[DraftPatientCriterion]) - object DraftPatientCriterionList { - import spray.json._ - import xyz.driver.pdsuidomain.formats.json.patientcriterion._ - - implicit val draftPatientCriterionListFormat: RootJsonFormat[DraftPatientCriterionList] = - new RootJsonFormat[DraftPatientCriterionList] { - override def write(obj: DraftPatientCriterionList): JsValue = { - JsArray(obj.list.map(_.toJson).toVector) - } - - override def read(json: JsValue): DraftPatientCriterionList = json match { - case j: JsObject => - DraftPatientCriterionList(draftPatientCriterionListReader.read(j)) - - case _ => deserializationError(s"Expected List of DraftPatientCriterion json object, but got $json") - } - } - } - - def nextPatientAction: PatientHistory.Action = - generators.oneOf[PatientHistory.Action](PatientHistory.Action.All) - - def nextPatientState: PatientHistory.State = - generators.oneOf[PatientHistory.State](PatientHistory.State.All) - - def nextPatient(): Patient = Patient( - id = nextUuidId[Patient], - status = nextPatientStatus, - name = nextFullName[Patient], - dob = nextLocalDate, - assignee = generators.nextOption(generators.nextId[User]), - previousStatus = generators.nextOption(generators.oneOf[Patient.Status](Patient.Status.AllPrevious)), - previousAssignee = generators.nextOption(generators.nextId[User]), - lastActiveUserId = generators.nextOption(generators.nextId[User]), - isUpdateRequired = generators.nextBoolean(), - disease = nextCancerType, - orderId = generators.nextId(), - lastUpdate = nextLocalDateTime - ) - - def nextPatientLabel(): PatientLabel = PatientLabel( - id = nextLongId[PatientLabel], - patientId = nextUuidId[Patient], - labelId = nextLongId[Label], - score = generators.nextInt(100), - primaryValue = fakes.entities.labels.nextLabelValue(), - verifiedPrimaryValue = fakes.entities.labels.nextLabelValue(), - isImplicitMatch = generators.nextBoolean(), - isVisible = generators.nextBoolean() - ) - - def nextRichPatientLabel(): RichPatientLabel = RichPatientLabel( - patientLabel = nextPatientLabel(), - isVerified = generators.nextBoolean() - ) - - def nextPatientCriterion(): PatientCriterion = PatientCriterion( - id = nextLongId[PatientCriterion], - patientLabelId = nextLongId[PatientLabel], - trialId = generators.nextInt(Int.MaxValue).toLong, - nctId = nextStringId[Trial], - criterionId = nextLongId[Criterion], - criterionText = generators.nextString(), - criterionValue = generators.nextOption(generators.nextBoolean()), - criterionIsDefining = generators.nextBoolean(), - eligibilityStatus = fakes.entities.labels.nextLabelValue(), - verifiedEligibilityStatus = fakes.entities.labels.nextLabelValue(), - isVerified = generators.nextBoolean(), - isVisible = generators.nextBoolean(), - lastUpdate = nextLocalDateTime, - inclusion = generators.nextOption(generators.nextBoolean()) - ) - - def nextDraftPatientCriterion(): DraftPatientCriterion = DraftPatientCriterion( - id = nextLongId[PatientCriterion], - eligibilityStatus = generators.nextOption(fakes.entities.labels.nextLabelValue()), - isVerified = generators.nextOption(generators.nextBoolean()) - ) - - def nextDraftPatientCriterionList(): DraftPatientCriterionList = { - DraftPatientCriterionList(List.fill(3)(nextDraftPatientCriterion())) - } - - def nextPatientCriterionArm(criterionId: LongId[PatientCriterion]): PatientCriterionArm = PatientCriterionArm( - patientCriterionId = criterionId, - armId = nextLongId[Arm], - armName = generators.nextString() - ) - - def nextRichPatientCriterion(): RichPatientCriterion = { - val patientCriterion = nextPatientCriterion() - RichPatientCriterion( - patientCriterion = patientCriterion, - labelId = nextLongId[Label], - armList = List( - nextPatientCriterionArm(patientCriterion.id), - nextPatientCriterionArm(patientCriterion.id), - nextPatientCriterionArm(patientCriterion.id) - ) - ) - } - - def nextPatientLabelEvidenceView(): PatientLabelEvidenceView = PatientLabelEvidenceView( - id = nextLongId[PatientLabelEvidence], - value = fakes.entities.labels.nextLabelValue(), - evidenceText = generators.nextString(), - documentId = generators.nextOption(nextLongId[Document]), - evidenceId = generators.nextOption(nextLongId[ExtractedData]), - reportId = generators.nextOption(nextUuidId[DirectReport]), - documentType = nextDocumentType(), - date = generators.nextOption(nextLocalDate), - providerType = nextProviderType(), - patientId = nextUuidId[Patient], - labelId = nextLongId[Label], - isImplicitMatch = generators.nextBoolean() - ) - - def nextPatientTrialArmGroupView(trialId: StringId[Trial]): PatientTrialArmGroupView = PatientTrialArmGroupView( - id = nextLongId[PatientTrialArmGroup], - patientId = nextUuidId[Patient], - trialId = trialId, - hypothesisId = nextUuidId[Hypothesis], - eligibilityStatus = fakes.entities.labels.nextLabelValue(), - verifiedEligibilityStatus = fakes.entities.labels.nextLabelValue(), - isVerified = generators.nextBoolean() - ) - - def nextRichPatientEligibleTrial(): RichPatientEligibleTrial = { - val patientCriterionId = nextLongId[PatientCriterion] - val trial = trialcuration.nextTrial() - RichPatientEligibleTrial( - trial = trial, - group = nextPatientTrialArmGroupView(trial.id), - arms = List( - nextPatientCriterionArm(patientCriterionId), - nextPatientCriterionArm(patientCriterionId), - nextPatientCriterionArm(patientCriterionId) - ) - ) - } - - def nextPatientHypothesis(): PatientHypothesis = PatientHypothesis( - id = nextUuidId[PatientHypothesis], - patientId = nextUuidId[Patient], - hypothesisId = nextUuidId[Hypothesis], - rationale = Option(generators.nextString()), - matchedTrials = refineV[NonNegative](generators.nextInt(Int.MaxValue).toLong) match { - case Left(_) => refineMV[NonNegative](0) - case Right(nonNegative) => nonNegative - } - ) - - def nextPatientIssue(): PatientIssue = PatientIssue( - id = nextLongId[PatientIssue], - userId = generators.nextId[User], - patientId = nextUuidId[Patient], - lastUpdate = nextLocalDateTime, - isDraft = generators.nextBoolean(), - text = generators.nextString(), - archiveRequired = generators.nextBoolean() - ) - - def nextPatientHistory(): PatientHistory = PatientHistory( - id = nextLongId[PatientHistory], - executor = generators.nextId[User], - patientId = nextUuidId[Patient], - state = nextPatientState, - action = nextPatientAction, - created = nextLocalDateTime - ) - - def nextPatientListResponse(): ListResponse[Patient] = { - val xs: Seq[Patient] = Seq.fill(3)(nextPatient()) - nextListResponse(xs) - } - - def nextRichPatientLabelListResponse(): ListResponse[RichPatientLabel] = { - val xs: Seq[RichPatientLabel] = Seq.fill(3)(nextRichPatientLabel()) - nextListResponse(xs) - } - - def nextPatientLabelListResponse(): ListResponse[PatientLabel] = { - val xs: Seq[PatientLabel] = Seq.fill(3)(nextPatientLabel()) - nextListResponse(xs) - } - - def nextRichPatientCriterionListResponse(): ListResponse[RichPatientCriterion] = { - val xs: Seq[RichPatientCriterion] = Seq.fill(3)(nextRichPatientCriterion()) - nextListResponse(xs) - } - - def nextRichPatientEligibleTrialListResponse(): ListResponse[RichPatientEligibleTrial] = { - val xs: Seq[RichPatientEligibleTrial] = Seq.fill(3)(nextRichPatientEligibleTrial()) - nextListResponse(xs) - } - - def nextPatientHypothesisListResponse(): ListResponse[PatientHypothesis] = { - val xs: Seq[PatientHypothesis] = Seq.fill(3)(nextPatientHypothesis()) - nextListResponse(xs) - } - - def nextPatientLabelEvidenceViewListResponse(): ListResponse[PatientLabelEvidenceView] = { - val xs: Seq[PatientLabelEvidenceView] = Seq.fill(3)(nextPatientLabelEvidenceView()) - nextListResponse(xs) - } - - def nextPatientIssuesListResponse(): ListResponse[PatientIssue] = { - val xs: Seq[PatientIssue] = Seq.fill(3)(nextPatientIssue()) - nextListResponse(xs) - } - - def nextPatientHistoryListResponse(): ListResponse[PatientHistory] = { - val xs: Seq[PatientHistory] = Seq.fill(3)(nextPatientHistory()) - nextListResponse(xs) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala deleted file mode 100644 index 925a019..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala +++ /dev/null @@ -1,239 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities - -import xyz.driver.core.auth.User -import xyz.driver.core.generators._ -import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion - -object trialcuration { - - import common._ - import xyz.driver.core.generators - import xyz.driver.pdsuidomain.entities.InterventionType._ - - private val maxItemsInCollectionNumber: Int = 5 - - def nextTrial(): Trial = Trial( - id = nextStringId[Trial], - externalId = nextUuidId[Trial], - status = nextTrialStatus, - assignee = Option(generators.nextId[User]), - previousStatus = Option(nextPreviousTrialStatus), - previousAssignee = Option(generators.nextId[User]), - lastActiveUserId = Option(generators.nextId[User]), - lastUpdate = nextLocalDateTime, - phase = generators.nextString(), - hypothesisId = Option(nextUuidId[Hypothesis]), - studyDesignId = Option(nextLongId[StudyDesign]), - originalStudyDesign = Option(generators.nextString()), - isPartner = generators.nextBoolean(), - overview = Option(generators.nextString()), - overviewTemplate = generators.nextString(), - isUpdated = generators.nextBoolean(), - title = generators.nextString(), - originalTitle = generators.nextString() - ) - - def nextArm(): Arm = Arm( - id = nextLongId[Arm], - name = generators.nextString(), - originalName = generators.nextString(), - trialId = nextStringId[Trial], - deleted = Option(nextLocalDateTime) - ) - - def nextCriterion(): Criterion = Criterion( - id = nextLongId[Criterion], - trialId = nextStringId[Trial], - text = Option(generators.nextString()), - isCompound = generators.nextBoolean(), - meta = generators.nextString(), - inclusion = Option(generators.nextBoolean()) - ) - - def nextCriterionLabel(criterionId: LongId[Criterion]): CriterionLabel = CriterionLabel( - id = nextLongId[CriterionLabel], - labelId = Option(nextLongId[Label]), - criterionId = criterionId, - categoryId = Option(nextLongId[LabelCategory]), - value = Option(generators.nextBoolean()), - isDefining = generators.nextBoolean() - ) - - def nextRichCriterion(): RichCriterion = { - val criterion = nextCriterion() - RichCriterion( - criterion = criterion, - armIds = Seq(nextLongId[EligibilityArm], nextLongId[EligibilityArm]), - labels = Seq( - nextCriterionLabel(criterion.id), - nextCriterionLabel(criterion.id) - ) - ) - } - - def nextIntervention(): Intervention = Intervention( - id = nextLongId[Intervention], - trialId = nextStringId[Trial], - name = generators.nextString(), - originalName = generators.nextString(), - typeId = Option(nextLongId[InterventionType]), - originalType = Option(generators.nextString()), - dosage = generators.nextString(), - originalDosage = generators.nextString(), - isActive = generators.nextBoolean(), - deliveryMethod = Option(generators.nextString()) - ) - - def nextInterventionArm(interventionId: LongId[Intervention]): InterventionArm = InterventionArm( - interventionId = interventionId, - armId = nextLongId[SlotArm] - ) - - def nextInterventionWithArms(): InterventionWithArms = { - val intervention = nextIntervention() - InterventionWithArms( - intervention = intervention, - arms = List( - nextInterventionArm(intervention.id), - nextInterventionArm(intervention.id), - nextInterventionArm(intervention.id) - ) - ) - } - - def nextTrialIssue(): TrialIssue = TrialIssue( - id = nextLongId[TrialIssue], - userId = generators.nextId[User], - trialId = nextStringId[Trial], - lastUpdate = nextLocalDateTime, - isDraft = generators.nextBoolean(), - text = generators.nextString(), - evidence = generators.nextString(), - archiveRequired = generators.nextBoolean(), - meta = generators.nextString() - ) - - def nextTrialHistory(): TrialHistory = TrialHistory( - id = nextLongId[TrialHistory], - executor = generators.nextId[User], - trialId = nextStringId[Trial], - state = nextTrialState, - action = nextTrialAction, - created = nextLocalDateTime, - comment = generators.nextOption(generators.nextString()) - ) - - def nextHypothesis(): Hypothesis = Hypothesis( - id = nextUuidId[Hypothesis], - name = generators.nextString(), - treatmentType = generators.nextString(), - description = generators.nextString() - ) - - def nextStudyDesign(): StudyDesign = generators.oneOf[StudyDesign](StudyDesign.All: _*) - - def nextInterventionType(): InterventionType = generators.oneOf[InterventionType]( - Chemotherapy, - TargetedTherapy, - Immunotherapy, - HormoneTherapy, - Other, - Radiation, - SurgeryProcedure - ) - - def nextEligibilityArm(): EligibilityArm = EligibilityArm( - id = nextLongId, - name = nextString(), - originalName = nextString(), - trialId = nextStringId - ) - - def nextEligibilityArmDisease(): EligibilityArmDisease = EligibilityArmDisease( - eligibilityArmId = nextLongId, - disease = nextCancerType - ) - - private def nextEligibilityArmDiseaseCollection(count: Int): Seq[EligibilityArmDisease] = - Seq.fill(count)(nextEligibilityArmDisease()) - - def nextEligibilityArmWithDiseases(): EligibilityArmWithDiseases = { - val entity = nextEligibilityArm() - val id = entity.id - val collection = nextEligibilityArmDiseaseCollection( - nextInt(maxItemsInCollectionNumber, minValue = 0) - ).map(_.copy(eligibilityArmId = id)) - - EligibilityArmWithDiseases( - entity, - collection - ) - } - - def nextSlotArm(): SlotArm = SlotArm( - id = nextLongId, - name = nextString(), - originalName = nextString(), - trialId = nextStringId - ) - - def nextTrialListResponse(): ListResponse[Trial] = { - val xs: Seq[Trial] = Seq.fill(3)(nextTrial()) - nextListResponse(xs) - } - - def nextTrialIssueListResponse(): ListResponse[TrialIssue] = { - val xs: Seq[TrialIssue] = Seq.fill(3)(nextTrialIssue()) - nextListResponse(xs) - } - - def nextTrialHistoryListResponse(): ListResponse[TrialHistory] = { - val xs: Seq[TrialHistory] = Seq.fill(3)(nextTrialHistory()) - nextListResponse(xs) - } - - def nextArmListResponse(): ListResponse[Arm] = { - val xs: Seq[Arm] = Seq.fill(3)(nextArm()) - nextListResponse(xs) - } - - def nextInterventionWithArmsListResponse(): ListResponse[InterventionWithArms] = { - val xs: Seq[InterventionWithArms] = Seq.fill(3)(nextInterventionWithArms()) - nextListResponse(xs) - } - - def nextEligibilityArmWithDiseasesListResponse(): ListResponse[EligibilityArmWithDiseases] = { - val xs: Seq[EligibilityArmWithDiseases] = Seq.fill(3)(nextEligibilityArmWithDiseases()) - nextListResponse(xs) - } - - def nextSlotArmListResponse(): ListResponse[SlotArm] = { - val xs: Seq[SlotArm] = Seq.fill(3)(nextSlotArm()) - nextListResponse(xs) - } - - def nextRichCriterionListResponse(): ListResponse[RichCriterion] = { - val xs: Seq[RichCriterion] = Seq.fill(3)(nextRichCriterion()) - nextListResponse(xs) - } - - def nextInterventionTypeListResponse(): ListResponse[InterventionType] = { - val xs: Seq[InterventionType] = Seq.fill(3)(nextInterventionType()) - nextListResponse(xs) - } - - def nextStudyDesignListResponse(): ListResponse[StudyDesign] = { - val xs: Seq[StudyDesign] = Seq.fill(3)(nextStudyDesign()) - nextListResponse(xs) - } - - def nextHypothesesListResponse(): ListResponse[Hypothesis] = { - val xs: Seq[Hypothesis] = Seq.fill(3)(nextHypothesis()) - nextListResponse(xs) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/arm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/arm.scala deleted file mode 100644 index 69029b6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/arm.scala +++ /dev/null @@ -1,44 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ - -object arm { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToArm(json: JsValue, orig: Arm): Arm = 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") - } - - implicit val armFormat: RootJsonFormat[Arm] = new RootJsonFormat[Arm] { - override def write(obj: Arm): JsValue = - JsObject( - "id" -> obj.id.toJson, - "name" -> obj.name.toJson, - "originalName" -> obj.originalName.toJson, - "trialId" -> obj.trialId.toJson - ) - - override def read(json: JsValue): Arm = json.asJsObject.getFields("trialId", "name") match { - case Seq(trialId, name) => - Arm( - id = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[Arm]]]).getOrElse(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/bridgeuploadqueue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/bridgeuploadqueue.scala deleted file mode 100644 index 6725a15..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/bridgeuploadqueue.scala +++ /dev/null @@ -1,68 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue -import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue.Item - -object bridgeuploadqueue { - import DefaultJsonProtocol._ - import common._ - - implicit val queueUploadItemFormat: RootJsonFormat[BridgeUploadQueue.Item] = new RootJsonFormat[Item] { - override def write(obj: Item) = - JsObject( - "kind" -> obj.kind.toJson, - "tag" -> obj.tag.toJson, - "created" -> obj.created.toJson, - "attempts" -> obj.attempts.toJson, - "nextAttempt" -> obj.nextAttempt.toJson, - "completed" -> obj.completed.toJson - ) - - override def read(json: JsValue): Item = json match { - case JsObject(fields) => - val kind = fields - .get("kind") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"BridgeUploadQueue.Item json object does not contain `kind` field: $json")) - - val tag = fields - .get("tag") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"BridgeUploadQueue.Item json object does not contain `tag` field: $json")) - - val created = fields - .get("created") - .map(_.convertTo[LocalDateTime]) - .getOrElse( - deserializationError(s"BridgeUploadQueue.Item json object does not contain `created` field: $json")) - - val attempts = fields - .get("attempts") - .map(_.convertTo[Int]) - .getOrElse( - deserializationError(s"BridgeUploadQueue.Item json object does not contain `attempts` field: $json")) - - val nextAttempt = fields - .get("nextAttempt") - .map(_.convertTo[LocalDateTime]) - .getOrElse( - deserializationError(s"BridgeUploadQueue.Item json object does not contain `nextAttempt` field: $json")) - - BridgeUploadQueue.Item( - kind = kind, - tag = tag, - created = created, - attempts = attempts, - nextAttempt = nextAttempt, - completed = true, - dependencyKind = None, - dependencyTag = None - ) - - case _ => deserializationError(s"Expected Json Object as BridgeUploadQueue.Item, but got $json") - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/common.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/common.scala deleted file mode 100644 index 26adb9c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/common.scala +++ /dev/null @@ -1,66 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDate, LocalDateTime, ZoneId, ZonedDateTime} - -import spray.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} - -object common { - - implicit def longIdFormat[T] = new RootJsonFormat[LongId[T]] { - override def write(id: LongId[T]): JsNumber = JsNumber(id.id) - override def read(json: JsValue): LongId[T] = json match { - case JsNumber(value) => LongId(value.toLong) - case _ => deserializationError(s"Expected number as LongId, but got $json") - } - } - - implicit def stringIdFormat[T] = new RootJsonFormat[StringId[T]] { - override def write(id: StringId[T]): JsString = JsString(id.toString) - override def read(json: JsValue): StringId[T] = json match { - case JsString(value) => StringId(value) - case _ => deserializationError(s"Expected string as StringId, but got $json") - } - } - - implicit def uuidIdFormat[T] = new RootJsonFormat[UuidId[T]] { - override def write(id: UuidId[T]): JsString = JsString(id.toString) - override def read(json: JsValue): UuidId[T] = json match { - case JsString(value) => UuidId(value) - case _ => deserializationError(s"Expected string as UuidId, but got $json") - } - } - - implicit def dateTimeFormat = new RootJsonFormat[LocalDateTime] { - override def write(date: LocalDateTime): JsString = JsString(ZonedDateTime.of(date, ZoneId.of("Z")).toString) - override def read(json: JsValue): LocalDateTime = json match { - case JsString(value) => ZonedDateTime.parse(value).toLocalDateTime - case _ => deserializationError(s"Expected date as LocalDateTime, but got $json") - } - } - - implicit def zonedDateTimeFormat = new RootJsonFormat[ZonedDateTime] { - override def write(date: ZonedDateTime): JsString = JsString(date.toString) - override def read(json: JsValue): ZonedDateTime = json match { - case JsString(value) => ZonedDateTime.parse(value) - case _ => deserializationError(s"Expected date as ZonedDateTime, but got $json") - } - } - - implicit def dateFormat = new RootJsonFormat[LocalDate] { - override def write(date: LocalDate): JsString = JsString(date.toString) - override def read(json: JsValue): LocalDate = json match { - case JsString(value) => LocalDate.parse(value) - case _ => deserializationError(s"Expected date as LocalDate, but got $json") - } - } - - implicit val integerFormat: RootJsonFormat[Integer] = new RootJsonFormat[Integer] { - override def write(obj: Integer): JsNumber = JsNumber(obj.intValue()) - override def read(json: JsValue): Integer = json match { - case JsNumber(value) => value.toInt - case _ => deserializationError(s"Expected number as Integer, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion.scala deleted file mode 100644 index c4e89f0..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion.scala +++ /dev/null @@ -1,175 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.{Label, LabelCategory} -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion - -object criterion { - import DefaultJsonProtocol._ - import common._ - - implicit val criterionLabelWriter: RootJsonWriter[CriterionLabel] = new RootJsonWriter[CriterionLabel] { - override def write(obj: CriterionLabel) = JsObject( - "labelId" -> obj.labelId.toJson, - "categoryId" -> obj.categoryId.toJson, - "value" -> obj.value.map { - case true => "Yes" - case false => "No" - }.toJson, - "isDefining" -> obj.isDefining.toJson - ) - } - - def jsValueToCriterionLabel(json: JsValue, criterionId: LongId[Criterion]): CriterionLabel = json match { - case JsObject(fields) => - val labelId = fields - .get("labelId") - .flatMap(_.convertTo[Option[LongId[Label]]]) - - val categoryId = fields - .get("categoryId") - .flatMap(_.convertTo[Option[LongId[LabelCategory]]]) - - val value = fields - .get("value") - .flatMap(_.convertTo[Option[String]]) - .map { - case "Yes" => true - case "No" => false - case other => - deserializationError(s"Unknown `value` of CriterionLabel object: expected `yes` or `no`, but got $other") - } - - val isDefining = fields - .get("isDefining") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"CriterionLabel json object does not contain `isDefining` field: $json")) - - CriterionLabel( - id = LongId(0L), - labelId = labelId, - criterionId = criterionId, - categoryId = categoryId, - value = value, - isDefining = isDefining - ) - - case _ => deserializationError(s"Expected Json Object as CriterionLabel, but got $json") - } - - def applyUpdateToCriterion(json: JsValue, orig: RichCriterion): RichCriterion = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - - val isCompound = fields - .get("isCompound") - .exists(_.convertTo[Boolean]) - - val meta = fields - .get("meta") - .map(_.convertTo[Option[String]].getOrElse("{}")) - .getOrElse(orig.criterion.meta) - - val inclusion = fields - .get("inclusion") - .map(_.convertTo[Option[Boolean]]) - .getOrElse(orig.criterion.inclusion) - - val arms = fields - .get("arms") - .map(_.convertTo[Option[List[LongId[EligibilityArm]]]].getOrElse(List.empty[LongId[EligibilityArm]])) - .getOrElse(orig.armIds) - - val labels = fields - .get("labels") - .map(_.convertTo[Option[List[JsValue]]].getOrElse(List.empty[JsValue])) - .map(_.map(l => jsValueToCriterionLabel(l, orig.criterion.id))) - .getOrElse(orig.labels) - - orig.copy( - criterion = orig.criterion.copy( - meta = meta, - text = text, - isCompound = isCompound, - inclusion = inclusion - ), - armIds = arms, - labels = labels - ) - - case _ => deserializationError(s"Expected Json Object as partial Criterion, but got $json") - } - - implicit val richCriterionFormat: RootJsonFormat[RichCriterion] = new RootJsonFormat[RichCriterion] { - override def write(obj: RichCriterion): JsValue = - JsObject( - "id" -> obj.criterion.id.toJson, - "meta" -> Option(obj.criterion.meta).toJson, - "arms" -> obj.armIds.toJson, - "text" -> obj.criterion.text.toJson, - "isCompound" -> obj.criterion.isCompound.toJson, - "labels" -> obj.labels.map(_.toJson).toJson, - "trialId" -> obj.criterion.trialId.toJson, - "inclusion" -> obj.criterion.inclusion.toJson - ) - - override def read(json: JsValue): RichCriterion = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[Criterion]]]) - - val trialId = fields - .get("trialId") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationError(s"Criterion json object does not contain `trialId` field: $json")) - - val text = fields - .get("text") - .flatMap(_.convertTo[Option[String]]) - - val isCompound = fields - .get("isCompound") - .exists(_.convertTo[Boolean]) - - val meta = fields - .get("meta") - .flatMap(_.convertTo[Option[String]]) - - val inclusion = fields - .get("inclusion") - .flatMap(_.convertTo[Option[Boolean]]) - - val arms = fields - .get("arms") - .map(_.convertTo[Seq[LongId[EligibilityArm]]]) - .getOrElse(Seq.empty[LongId[EligibilityArm]]) - - val labels = fields - .get("labels") - .map(_.convertTo[Seq[JsValue]]) - .map(_.map(l => jsValueToCriterionLabel(l, LongId(0)))) - .getOrElse(Seq.empty[CriterionLabel]) - - RichCriterion( - criterion = Criterion( - id = id.getOrElse(LongId(0)), - trialId = trialId, - text = text, - isCompound = isCompound, - meta = meta.getOrElse(""), - inclusion = inclusion - ), - armIds = arms, - labels = labels - ) - - case _ => deserializationError(s"Expected Json Object as Criterion, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document.scala deleted file mode 100644 index 66e95f3..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document.scala +++ /dev/null @@ -1,221 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDate, LocalDateTime} - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, TextJson} -import xyz.driver.pdsuidomain.entities._ - -object document { - import DefaultJsonProtocol._ - import Document._ - import common._ - - implicit val documentStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "Organized" -> Status.Organized, - "Extracted" -> Status.Extracted, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged, - "Archived" -> Status.Archived - ) - - implicit val requiredTypeFormat: RootJsonFormat[RequiredType] = new EnumJsonFormat[RequiredType]( - "OPN" -> RequiredType.OPN, - "PN" -> RequiredType.PN - ) - - implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat2(Meta.apply) - - implicit val documentTypeFormat: RootJsonFormat[DocumentType] = new RootJsonFormat[DocumentType] { - override def read(json: JsValue): DocumentType = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Document type json object does not contain `name` field: $json")) - - DocumentType - .fromString(name) - .getOrElse(deserializationError(s"Unknown document type: $name")) - - case _ => deserializationError(s"Expected Json Object as Document type, but got $json") - } - - override def write(obj: DocumentType) = - JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) - } - - implicit val fullDocumentMetaFormat = new RootJsonFormat[TextJson[Meta]] { - override def write(obj: TextJson[Meta]): JsValue = obj.content.toJson - override def read(json: JsValue) = TextJson(documentMetaFormat.read(json)) - } - - def applyUpdateToDocument(json: JsValue, orig: Document): Document = json match { - case JsObject(fields) => - val physician = fields - .get("physician") - .map(_.convertTo[String]) - - val typeId = fields - .get("typeId") - .map(_.convertTo[Option[LongId[DocumentType]]]) - .getOrElse(orig.typeId) - - val provider = fields - .get("provider") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.providerName) - - val providerTypeId = fields - .get("providerTypeId") - .map(_.convertTo[Option[LongId[ProviderType]]]) - .getOrElse(orig.providerTypeId) - - val institutionName = fields - .get("institutionName") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.institutionName) - - val meta = fields - .get("meta") - .map(_.convertTo[Option[TextJson[Meta]]]) - .getOrElse(orig.meta) - - val startDate = fields - .get("startDate") - .map(_.convertTo[Option[LocalDate]]) - .getOrElse(orig.startDate) - - val endDate = fields - .get("endDate") - .map(_.convertTo[Option[LocalDate]]) - .getOrElse(orig.endDate) - - orig.copy( - physician = physician.orElse(orig.physician), - typeId = typeId, - providerName = provider, - providerTypeId = providerTypeId, - institutionName = institutionName, - meta = meta, - startDate = startDate, - endDate = endDate - ) - - case _ => deserializationError(s"Expected Json Object as partial Document, but got $json") - } - - implicit val documentFormat: RootJsonFormat[Document] = new RootJsonFormat[Document] { - override def write(document: Document): JsValue = - JsObject( - "id" -> document.id.toJson, - "recordId" -> document.recordId.toJson, - "physician" -> document.physician.toJson, - "typeId" -> document.typeId.toJson, - "provider" -> document.providerName.toJson, - "providerTypeId" -> document.providerTypeId.toJson, - "requiredType" -> document.requiredType.toJson, - "institutionName" -> document.institutionName.toJson, - "startDate" -> document.startDate.toJson, - "endDate" -> document.endDate.toJson, - "status" -> document.status.toJson, - "previousStatus" -> document.previousStatus.toJson, - "assignee" -> document.assignee.toJson, - "previousAssignee" -> document.previousAssignee.toJson, - "meta" -> document.meta.toJson, - "lastActiveUser" -> document.lastActiveUserId.toJson, - "lastUpdate" -> document.lastUpdate.toJson, - "labelVersion" -> document.labelVersion.toJson - ) - - override def read(json: JsValue): Document = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[Document]]]) - - val recordId = fields - .get("recordId") - .map(_.convertTo[LongId[MedicalRecord]]) - .getOrElse(deserializationError(s"Document create json object does not contain `recordId` field: $json")) - - val status = fields - .get("status") - .flatMap(_.convertTo[Option[Document.Status]]) - - val previousStatus = fields - .get("previousStatus") - .flatMap(_.convertTo[Option[Document.Status]]) - - val physician = fields - .get("physician") - .flatMap(_.convertTo[Option[String]]) - - val typeId = fields - .get("typeId") - .flatMap(_.convertTo[Option[LongId[DocumentType]]]) - - val requiredType = fields - .get("requiredType") - .flatMap(_.convertTo[Option[Document.RequiredType]]) - - val provider = fields - .get("provider") - .flatMap(_.convertTo[Option[String]]) - - val providerTypeId = fields - .get("providerTypeId") - .flatMap(_.convertTo[Option[LongId[ProviderType]]]) - - val institutionName = fields - .get("institutionName") - .flatMap(_.convertTo[Option[String]]) - - val meta = fields - .get("meta") - .flatMap(_.convertTo[Option[TextJson[Meta]]]) - - val startDate = fields - .get("startDate") - .flatMap(_.convertTo[Option[LocalDate]]) - - val endDate = fields - .get("endDate") - .flatMap(_.convertTo[Option[LocalDate]]) - - val lastUpdate = fields - .get("lastUpdate") - .flatMap(_.convertTo[Option[LocalDateTime]]) - - val labelVersion = fields - .get("labelVersion") - .flatMap(_.convertTo[Option[Int]]) - - Document( - id = id.getOrElse(LongId(0)), - recordId = recordId, - status = status.getOrElse(Document.Status.New), - physician = physician, - typeId = typeId, - startDate = startDate, - endDate = endDate, - providerName = provider, - providerTypeId = providerTypeId, - requiredType = requiredType, - institutionName = institutionName, - meta = meta, - previousStatus = previousStatus, - assignee = None, - previousAssignee = None, - lastActiveUserId = None, - lastUpdate = lastUpdate.getOrElse(LocalDateTime.MIN), - labelVersion = labelVersion.getOrElse(0) - ) - - case _ => deserializationError(s"Expected Json Object as Document, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documenthistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/documenthistory.scala deleted file mode 100644 index 1652f7b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documenthistory.scala +++ /dev/null @@ -1,35 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object documenthistory { - import DefaultJsonProtocol._ - import DocumentHistory._ - import common._ - - implicit val documentStateFormat = new EnumJsonFormat[State]( - "New" -> State.New, - "Extract" -> State.Extract, - "Done" -> State.Done, - "Review" -> State.Review, - "Flag" -> State.Flag, - "Archive" -> State.Archive - ) - - implicit val documentActionFormat = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive, - "PostEvidence" -> Action.PostEvidence, - "CreateDocument" -> Action.CreateDocument, - "ReadDocument" -> Action.ReadDocument - ) - - implicit val documentHistoryFormat: RootJsonFormat[DocumentHistory] = jsonFormat6(DocumentHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documentissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/documentissue.scala deleted file mode 100644 index 037a3ad..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/documentissue.scala +++ /dev/null @@ -1,72 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities._ - -object documentissue { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToDocumentIssue(json: JsValue, orig: DocumentIssue): DocumentIssue = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"DocumentIssue json object does not contain `text` field: $json")) - - val archiveRequired = fields - .get("archiveRequired") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"DocumentIssue json object does not contain `archiveRequired` field: $json")) - - val startPage = fields.get("startPage").map(_.convertTo[Option[Double]]) - val endPage = fields.get("endPage").map(_.convertTo[Option[Double]]) - - orig.copy( - text = text, - archiveRequired = archiveRequired, - startPage = startPage.getOrElse(orig.startPage), - endPage = endPage.getOrElse(orig.endPage) - ) - - case _ => deserializationError(s"Expected Json Object as partial DocumentIssue, but got $json") - - } - - def jsValueToDocumentIssue(json: JsValue, - documentId: LongId[Document], - userId: xyz.driver.core.Id[User]): DocumentIssue = - json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"DocumentIssue json object does not contain `text` field: $json")) - - val id = fields.get("id").map(_.convertTo[LongId[DocumentIssue]]) - val startPage = fields.get("startPage").flatMap(_.convertTo[Option[Double]]) - val endPage = fields.get("endPage").flatMap(_.convertTo[Option[Double]]) - - DocumentIssue( - id = id.getOrElse(LongId(0)), - userId = userId, - documentId = documentId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text, - archiveRequired = false, - startPage = startPage, - endPage = endPage - ) - - case _ => deserializationError(s"Expected Json Object as DocumentIssue, but got $json") - } - - implicit val documentIssueFormat: RootJsonFormat[DocumentIssue] = jsonFormat9(DocumentIssue.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibility.scala deleted file mode 100644 index 925ba65..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibility.scala +++ /dev/null @@ -1,108 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json.DefaultJsonProtocol._ -import spray.json._ -import DefaultJsonProtocol._ -import xyz.driver.core.Id -import xyz.driver.core.json._ -import xyz.driver.entities.labels.LabelValue -import xyz.driver.pdsuidomain.entities.eligibility._ - -object eligibility { - import export._ - import xyz.driver.formats.json.assay._ - import xyz.driver.formats.json.common._ - import xyz.driver.formats.json.labels._ - import xyz.driver.formats.json.process._ - import xyz.driver.pdsuidomain.formats.json.document._ - import xyz.driver.pdsuidomain.formats.json.record._ - import xyz.driver.pdsuidomain.formats.json.export._ - - implicit val molecularDocumentFormat: RootJsonFormat[MolecularEvidenceDocument] = jsonFormat7( - MolecularEvidenceDocument) - implicit val clinicalDocumentFormat: RootJsonFormat[ClinicalEvidenceDocument] = jsonFormat7(ClinicalEvidenceDocument) - - implicit val evidenceDocumentFormat: RootJsonFormat[EvidenceDocument] = - GadtJsonFormat.create[EvidenceDocument]("evidenceDocumentType") { - case _: MolecularEvidenceDocument => "Molecular" - case _: ClinicalEvidenceDocument => "Clinical" - } { - case "Molecular" => molecularDocumentFormat - case "Clinical" => clinicalDocumentFormat - } - - implicit object evidenceFormat extends RootJsonFormat[Evidence] { - - override def write(evidence: Evidence): JsValue = { - JsObject( - "evidenceId" -> evidence.evidenceId.toJson, - "evidenceText" -> evidence.evidenceText.toJson, - "labelValue" -> evidence.labelValue.toJson, - "document" -> evidence.document.toJson, - "isPrimaryValue" -> evidence.isPrimaryValue.toJson - ) - } - - override def read(json: JsValue): Evidence = { - json match { - case JsObject(fields) => - val evidenceId = fields - .get("evidenceId") - .map(_.convertTo[Id[Evidence]]) - - val evidenceText = fields - .get("evidenceText") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Evidence json object do not contain 'evidenceText' field: $json")) - - val labelValue = fields - .get("labelValue") - .map(_.convertTo[LabelValue]) - .getOrElse(deserializationError(s"Evidence json object do not contain 'labelValue' field: $json")) - - val isDriverDocument = fields - .get("document") - .flatMap { - case JsObject(fieldMap) => - fieldMap - .get("isDriverDocument") - .map(_.convertTo[Boolean]) - case _ => deserializationError(s"Expected Json Object as 'isDriverDocument', but got $json") - } - .getOrElse(deserializationError(s"Evidence json object do not contain 'document' field: $json")) - - val document = customDocumentParser(isDriverDocument, fields, json) - - val isPrimaryValue = fields - .get("isPrimaryValue") - .map(_.convertTo[Option[Boolean]]) - .getOrElse(deserializationError(s"Evidence json object do not contain 'isPrimaryValue' field: $json")) - - Evidence(evidenceId, evidenceText, labelValue, document, isPrimaryValue) - case _ => deserializationError(s"Expected Json Object as 'Evidence', but got $json") - } - } - - def customDocumentParser(isDriverDocument: Boolean, - fields: Map[String, JsValue], - json: JsValue): EvidenceDocument = { - fields.get("document").fold { deserializationError(s"Expected Json Object as 'Document', but got $json") } { - document => - if (isDriverDocument) document.convertTo[MolecularEvidenceDocument] - else document.convertTo[ClinicalEvidenceDocument] - } - } - } - - implicit def labelWithEvidenceJsonFormat: RootJsonFormat[LabelEvidence] = jsonFormat2(LabelEvidence) - - implicit def labelRankingFormat: RootJsonFormat[LabelMismatchRank] = jsonFormat4(LabelMismatchRank) - implicit def labelRankingsFormat: RootJsonFormat[MismatchRankedLabels] = jsonFormat2(MismatchRankedLabels) - - implicit def matchedPatientFormat: RootJsonFormat[MatchedPatient] = jsonFormat6(MatchedPatient) - - implicit lazy val eligibleTrialFormat: RootJsonFormat[EligibleTrial] = jsonFormat2(EligibleTrial.apply) - implicit lazy val eligibleArmFormat: RootJsonFormat[EligibleArm] = jsonFormat2(EligibleArm.apply) - implicit lazy val eligibleCriterionFormat: RootJsonFormat[EligibleCriterion] = jsonFormat2(EligibleCriterion.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm.scala deleted file mode 100644 index 5827f62..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm.scala +++ /dev/null @@ -1,107 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.patient.CancerType -import xyz.driver.formats.json.patient._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ - -object eligibilityarm { - - import DefaultJsonProtocol._ - import common._ - - private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = { - deserializationError(s"$className json object do not contain '$field' field: $json") - } - - private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = { - deserializationError(s"Expected Json Object as $className, but got $json") - } - - implicit def eligibilityArmWithDiseasesWriter: RootJsonWriter[EligibilityArmWithDiseases] = - new RootJsonWriter[EligibilityArmWithDiseases] { - override def write(obj: EligibilityArmWithDiseases): JsValue = { - JsObject( - "id" -> obj.eligibilityArm.id.toJson, - "name" -> obj.eligibilityArm.name.toJson, - "originalName" -> obj.eligibilityArm.originalName.toJson, - "trialId" -> obj.eligibilityArm.trialId.toJson, - "diseases" -> obj.eligibilityArmDiseases.map(_.disease.toJson).toJson - ) - } - } - - implicit def eligibilityArmWithDiseasesReader: RootJsonReader[EligibilityArmWithDiseases] = { - new RootJsonReader[EligibilityArmWithDiseases] { - implicit val className: String = "create EligibilityArmWithDiseases" - - override def read(json: JsValue): EligibilityArmWithDiseases = { - json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[EligibilityArm]]]) - - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("name", json)) - - val trialId = fields - .get("trialId") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationErrorFieldMessage("trialId", json)) - - val diseases = fields - .get("diseases") - .map(_.convertTo[Seq[String]]) - .getOrElse(deserializationErrorFieldMessage("diseases", json)) - - val eligibilityArm = EligibilityArm( - id = id.getOrElse(LongId(0)), - name = name, - trialId = trialId, - originalName = name - ) - - EligibilityArmWithDiseases( - eligibilityArm, - diseases.map { disease => - val condition = CancerType - .fromString(disease) - .getOrElse(throw new NoSuchElementException(s"unknown condition $disease")) - EligibilityArmDisease(eligibilityArm.id, condition) - } - ) - case _ => deserializationErrorEntityMessage(json) - } - } - } - } - - def applyUpdateToEligibilityArmWithDiseases(json: JsValue, - orig: EligibilityArmWithDiseases): EligibilityArmWithDiseases = { - implicit val className: String = "update EligibilityArmWithDiseases" - json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(orig.eligibilityArm.name) - - val diseases = fields - .get("diseases") - .map(_.convertTo[Seq[CancerType]].map(x => EligibilityArmDisease(orig.eligibilityArm.id, x))) - .getOrElse(orig.eligibilityArmDiseases) - - orig.copy( - eligibilityArm = orig.eligibilityArm - .copy(name = name), - eligibilityArmDiseases = diseases - ) - - case _ => deserializationErrorEntityMessage(json) - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala deleted file mode 100644 index 8fb7d03..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala +++ /dev/null @@ -1,127 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json.idFormat -import xyz.driver.entities.labels.Label -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.export.patient._ -import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} -import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm} - -object export { - import DefaultJsonProtocol._ - import common._ - import document._ - import record._ - - private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = { - deserializationError(s"$className json object do not contain '$field' field: $json") - } - - private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = { - deserializationError(s"Expected Json Object as $className, but got $json") - } - - implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] = - jsonFormat5(ExportPatientLabelEvidenceDocument.apply) - - implicit val patientLabelEvidenceFormat: RootJsonFormat[ExportPatientLabelEvidence] = - jsonFormat(ExportPatientLabelEvidence.apply, "evidenceId", "labelValue", "evidenceText", "document") - - implicit val patientLabelFormat: RootJsonFormat[ExportPatientLabel] = - jsonFormat(ExportPatientLabel.apply, "labelId", "evidence") - - implicit val patientWithLabelsFormat: RootJsonFormat[ExportPatientWithLabels] = - jsonFormat(ExportPatientWithLabels.apply, "patientId", "labelVersion", "labels") - - implicit val trialArmFormat: RootJsonFormat[ExportTrialArm] = jsonFormat3(ExportTrialArm.apply) - - implicit val trialLabelCriterionFormat: RootJsonFormat[ExportTrialLabelCriterion] = - new RootJsonFormat[ExportTrialLabelCriterion] { - implicit val className: String = "ExportTrialLabelCriterion" - - override def write(obj: ExportTrialLabelCriterion): JsValue = - JsObject( - "value" -> obj.value - .map { - case true => "Yes" - case false => "No" - } - .getOrElse("Unknown") - .toJson, - "labelId" -> obj.labelId.toJson, - "criterionId" -> obj.criterionId.toJson, - "criterionText" -> obj.criteria.toJson, - "armIds" -> obj.armIds.toJson, - "isCompound" -> obj.isCompound.toJson, - "isDefining" -> obj.isDefining.toJson, - "inclusion" -> obj.inclusion.toJson - ) - - override def read(json: JsValue): ExportTrialLabelCriterion = { - json match { - case JsObject(fields) => - val value = fields - .get("value") - .map(_.convertTo[String]) - .map { - case "Yes" => Option(true) - case "No" => Option(false) - case "Unknown" => Option.empty[Boolean] - } - .getOrElse(deserializationErrorFieldMessage("value", json)) - - val labelId = fields - .get("labelId") - .map(_.convertTo[LongId[Label]]) - .getOrElse(deserializationErrorFieldMessage("labelId", json)) - - val criterionId = fields - .get("criterionId") - .map(_.convertTo[LongId[Criterion]]) - .getOrElse(deserializationErrorFieldMessage("criterionId", json)) - - val criterionText = fields - .get("criterionText") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("criterionText", json)) - - val armIds = fields - .get("armIds") - .map(_.convertTo[Set[LongId[EligibilityArm]]]) - .getOrElse(deserializationErrorFieldMessage("armIds", json)) - - val isCompound = fields - .get("isCompound") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("isCompound", json)) - - val isDefining = fields - .get("isDefining") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("isDefining", json)) - - val inclusion = fields - .get("inclusion") - .flatMap(_.convertTo[Option[Boolean]]) - - ExportTrialLabelCriterion( - criterionId, - value, - labelId, - armIds, - criterionText, - isCompound, - isDefining, - inclusion - ) - - case _ => deserializationErrorEntityMessage(json) - } - } - } - - implicit val trialWithLabelsFormat: RootJsonFormat[ExportTrialWithLabels] = - jsonFormat(ExportTrialWithLabels.apply, "nctId", "trialId", "lastReviewed", "labelVersion", "arms", "criteria") -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/extracteddata.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/extracteddata.scala deleted file mode 100644 index 232bb39..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/extracteddata.scala +++ /dev/null @@ -1,155 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue} -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuicommon.domain.{LongId, TextJson} -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData - -object extracteddata { - import DefaultJsonProtocol._ - import ExtractedData._ - import common._ - - implicit val metaKeywordFormat: RootJsonFormat[Meta.Keyword] = jsonFormat4(Meta.Keyword) - implicit val metaTextLayerPositionFormat: RootJsonFormat[Meta.TextLayerPosition] = jsonFormat3( - Meta.TextLayerPosition) - implicit val metaEvidenceFormat: RootJsonFormat[Meta.Evidence] = jsonFormat3(Meta.Evidence) - - implicit val extractedDataMetaFormat: RootJsonFormat[Meta] = jsonFormat2(Meta.apply) - implicit val fullExtractedDataMetaFormat = new RootJsonFormat[TextJson[Meta]] { - override def write(obj: TextJson[Meta]): JsValue = obj.content.toJson - override def read(json: JsValue): TextJson[Meta] = TextJson(extractedDataMetaFormat.read(json)) - } - - implicit val extractedDataLabelWriter: JsonWriter[ExtractedDataLabel] = new JsonWriter[ExtractedDataLabel] { - override def write(label: ExtractedDataLabel): JsObject = { - JsObject( - "id" -> label.labelId.toJson, - "categoryId" -> label.categoryId.toJson, - "value" -> label.value.toJson - ) - } - } - - def applyLabelsForExtractedData(json: JsValue, dataId: LongId[ExtractedData]): ExtractedDataLabel = json match { - case JsObject(fields) => - val labelId = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[Label]]]) - - val categoryId = fields - .get("categoryId") - .flatMap(_.convertTo[Option[LongId[LabelCategory]]]) - - val value = fields - .get("value") - .flatMap(_.convertTo[Option[LabelValue]]) - - ExtractedDataLabel( - id = LongId(0), - dataId = dataId, - labelId = labelId, - categoryId = categoryId, - value = value - ) - - case _ => deserializationError(s"Expected Json Object as ExtractedDataLabel, but got $json") - } - - def applyUpdateToExtractedData(json: JsValue, orig: RichExtractedData): RichExtractedData = json match { - case JsObject(fields) => - val keywordId = fields - .get("keywordId") - .map(_.convertTo[Option[LongId[Keyword]]]) - .getOrElse(orig.extractedData.keywordId) - - val evidence = fields - .get("evidence") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.extractedData.evidenceText) - - val meta = fields - .get("meta") - .map(_.convertTo[Option[TextJson[Meta]]]) - .getOrElse(orig.extractedData.meta) - - val labels = fields - .get("labels") - .map( - _.convertTo[Option[List[JsValue]]] - .getOrElse(List.empty[JsValue]) - .map(l => applyLabelsForExtractedData(l, orig.extractedData.id))) - .getOrElse(orig.labels) - - val extractedData = orig.extractedData.copy( - keywordId = keywordId, - evidenceText = evidence, - meta = meta - ) - - orig.copy( - extractedData = extractedData, - labels = labels - ) - - case _ => deserializationError(s"Expected Json Object as partial ExtractedData, but got $json") - } - - implicit val extractedDataFormat: RootJsonFormat[RichExtractedData] = new RootJsonFormat[RichExtractedData] { - override def write(richData: RichExtractedData): JsValue = - JsObject( - "id" -> richData.extractedData.id.toJson, - "documentId" -> richData.extractedData.documentId.toJson, - "keywordId" -> richData.extractedData.keywordId.toJson, - "evidence" -> richData.extractedData.evidenceText.toJson, - "meta" -> richData.extractedData.meta.toJson, - "labels" -> richData.labels.map(_.toJson).toJson - ) - - override def read(json: JsValue): RichExtractedData = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[ExtractedData]]]) - - val documentId = fields - .get("documentId") - .map(_.convertTo[LongId[Document]]) - .getOrElse( - deserializationError(s"ExtractedData create json object does not contain `documentId` field: $json")) - - val keywordId = fields - .get("keywordId") - .flatMap(_.convertTo[Option[LongId[Keyword]]]) - - val evidence = fields - .get("evidence") - .flatMap(_.convertTo[Option[String]]) - - val meta = fields - .get("meta") - .flatMap(_.convertTo[Option[TextJson[Meta]]]) - - val labels = fields - .get("labels") - .map(_.convertTo[List[JsValue]]) - .getOrElse(List.empty[JsValue]) - .map(l => applyLabelsForExtractedData(l, LongId(0))) - - val extractedData = ExtractedData( - id = id.getOrElse(LongId(0L)), - documentId = documentId, - keywordId = keywordId, - evidenceText = evidence, - meta = meta - ) - - RichExtractedData(extractedData, labels) - - case _ => deserializationError(s"Expected Json Object as ExtractedData, but got $json") - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/hypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/hypothesis.scala deleted file mode 100644 index c5f6141..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/hypothesis.scala +++ /dev/null @@ -1,12 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuidomain.entities._ - -object hypothesis { - import DefaultJsonProtocol._ - import common._ - - implicit val hypothesisFormat: RootJsonFormat[Hypothesis] = jsonFormat4(Hypothesis.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala deleted file mode 100644 index bf528e6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala +++ /dev/null @@ -1,147 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities.InterventionType.DeliveryMethod -import xyz.driver.pdsuidomain.entities._ - -object intervention { - import DefaultJsonProtocol._ - import common._ - - implicit def interventionFormat: RootJsonFormat[InterventionWithArms] = new RootJsonFormat[InterventionWithArms] { - override def write(obj: InterventionWithArms) = - JsObject( - "id" -> obj.intervention.id.toJson, - "name" -> obj.intervention.name.toJson, - "typeId" -> obj.intervention.typeId.toJson, - "dosage" -> obj.intervention.dosage.toJson, - "isActive" -> obj.intervention.isActive.toJson, - "arms" -> obj.arms.map(_.armId).toJson, - "trialId" -> obj.intervention.trialId.toJson, - "deliveryMethod" -> obj.intervention.deliveryMethod.toJson, - "originalName" -> obj.intervention.originalName.toJson, - "originalDosage" -> obj.intervention.originalDosage.toJson, - "originalType" -> obj.intervention.originalType.toJson - ) - - override def read(json: JsValue): InterventionWithArms = json match { - case JsObject(fields) => - val trialId = fields - .get("trialId") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationError(s"Intervention json object does not contain `trialId` field: $json")) - - val typeId = fields - .get("typeId") - .flatMap(_.convertTo[Option[LongId[InterventionType]]]) - - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse("") - - val dosage = fields - .get("dosage") - .map(_.convertTo[String]) - - val isActive = fields - .get("isActive") - .exists(_.convertTo[Boolean]) - - val deliveryMethod = fields - .get("deliveryMethod") - .flatMap(_.convertTo[Option[String]]) - - val arms = fields - .get("arms") - .map(_.convertTo[List[LongId[SlotArm]]]) - .map(_ map (x => InterventionArm(armId = x, interventionId = LongId(0L)))) - .getOrElse(List.empty[InterventionArm]) - - InterventionWithArms( - intervention = Intervention( - id = LongId(0L), - trialId = trialId, - name = name, - originalName = name, - typeId = typeId, - originalType = None, - dosage = dosage.getOrElse(""), - originalDosage = dosage.getOrElse(""), - isActive = isActive, - deliveryMethod = deliveryMethod - ), - arms = arms - ) - - case _ => deserializationError(s"Expected Json Object as create Intervention json, but got $json") - } - } - - def applyUpdateToInterventionWithArms(json: JsValue, orig: InterventionWithArms): InterventionWithArms = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - - val typeId = fields - .get("typeId") - .map(_.convertTo[Option[LongId[InterventionType]]]) - - val dosage = fields - .get("dosage") - .map(_.convertTo[String]) - - val isActive = fields - .get("isActive") - .map(_.convertTo[Boolean]) - - val deliveryMethod = fields - .get("deliveryMethod") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.intervention.deliveryMethod) - - val origIntervention = orig.intervention - val arms = fields - .get("arms") - .map(_.convertTo[List[LongId[SlotArm]]].map(x => InterventionArm(x, orig.intervention.id))) - - orig.copy( - intervention = origIntervention.copy( - name = name.getOrElse(origIntervention.name), - typeId = typeId.getOrElse(origIntervention.typeId), - dosage = dosage.getOrElse(origIntervention.dosage), - isActive = isActive.getOrElse(origIntervention.isActive), - deliveryMethod = deliveryMethod - ), - arms = arms.getOrElse(orig.arms) - ) - - case _ => deserializationError(s"Expected Json Object as partial Intervention, but got $json") - } - - implicit def interventionTypeFormat: JsonFormat[InterventionType] = new RootJsonFormat[InterventionType] { - override def read(json: JsValue): InterventionType = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Intervention type json object does not contain `name` field: $json")) - - InterventionType - .typeFromString(name) - .getOrElse(deserializationError(s"Unknown intervention type: $name")) - - case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json") - } - - override def write(obj: InterventionType) = - JsObject( - "id" -> obj.id.toJson, - "name" -> obj.name.toJson, - "deliveryMethods" -> obj.deliveryMethods.map(DeliveryMethod.methodToString).toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/listresponse.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/listresponse.scala deleted file mode 100644 index 1e359d6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/listresponse.scala +++ /dev/null @@ -1,45 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json.DefaultJsonProtocol._ -import spray.json._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.formats.json.common._ - -object listresponse { - private val itemsField = "items" - private val metaField = "meta" - - implicit val listResponseMetaFormat: RootJsonFormat[ListResponse.Meta] = jsonFormat4(ListResponse.Meta.apply) - - implicit def listResponseWriter[T: JsonWriter]: RootJsonWriter[ListResponse[T]] = - new RootJsonWriter[ListResponse[T]] { - override def write(listResponse: ListResponse[T]): JsValue = { - JsObject( - itemsField -> listResponse.items.map(_.toJson).toJson, - metaField -> listResponse.meta.toJson - ) - } - } - - implicit def listResponseReader[T: JsonReader]: RootJsonReader[ListResponse[T]] = - new RootJsonReader[ListResponse[T]] { - override def read(json: JsValue): ListResponse[T] = json match { - case JsObject(fields) => - val items = fields - .get(itemsField) - .map { - case JsArray(elements) => elements.map(_.convertTo[T])(collection.breakOut) - case x => deserializationError(s"Expected Array as JsArray, but got $x") - } - .getOrElse(deserializationError(s"ListResponse json object does not contain `$itemsField` field: $json")) - - val meta = fields - .get(metaField) - .map(_.convertTo[ListResponse.Meta]) - .getOrElse(deserializationError(s"ListResponse json object does not contain `$metaField` field: $json")) - - ListResponse(items, meta) - case _ => deserializationError(s"Expected ListResponse json object, but got $json") - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala deleted file mode 100644 index 774a1ff..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala +++ /dev/null @@ -1,118 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDate, LocalDateTime} - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.entities.clinic.TestOrder -import xyz.driver.entities.common.FullName -import xyz.driver.entities.patient.CancerType -import xyz.driver.formats.json.common._ -import xyz.driver.formats.json.patient._ -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.entities._ - -object patient { - import DefaultJsonProtocol._ - import Patient._ - import common._ - - implicit val patientStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "Verified" -> Status.Verified, - "Reviewed" -> Status.Reviewed, - "Curated" -> Status.Curated, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged - ) - - implicit val patientFormat: RootJsonFormat[Patient] = new RootJsonFormat[Patient] { - override def write(patient: Patient): JsValue = - JsObject( - "id" -> patient.id.toJson, - "status" -> patient.status.toJson, - "name" -> patient.name.toJson, - "dob" -> patient.dob.toJson, - "assignee" -> patient.assignee.toJson, - "previousStatus" -> patient.previousStatus.toJson, - "previousAssignee" -> patient.previousAssignee.toJson, - "lastActiveUser" -> patient.lastActiveUserId.toJson, - "lastUpdate" -> patient.lastUpdate.toJson, - "disease" -> patient.disease.toJson, - "orderId" -> patient.orderId.toJson - ) - - override def read(json: JsValue): Patient = { - json match { - case JsObject(fields) => - val id = fields - .get("id") - .map(_.convertTo[UuidId[Patient]]) - .getOrElse(deserializationError(s"Patient create json object does not contain `id` field: $json")) - - val status = fields - .get("status") - .map(_.convertTo[Patient.Status]) - .getOrElse(deserializationError(s"Patient create json object does not contain `status` field: $json")) - - val name = fields - .get("name") - .map(_.convertTo[FullName[Patient]]) - .getOrElse(deserializationError(s"Patient create json object does not contain `name` field: $json")) - - val dob = fields - .get("dob") - .map(_.convertTo[LocalDate]) - .getOrElse(deserializationError(s"Patient create json object does not contain `dob` field: $json")) - - val assignee = fields - .get("assignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - - val previousStatus = fields - .get("previousStatus") - .flatMap(_.convertTo[Option[Patient.Status]]) - - val previousAssignee = fields - .get("previousAssignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - - val lastActiveUser = fields - .get("lastActiveUser") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - - val disease = fields - .get("disease") - .map(_.convertTo[CancerType]) - .getOrElse(deserializationError(s"Patient create json object does not contain `disease` field: $json")) - - val orderId = fields - .get("orderId") - .map(_.convertTo[xyz.driver.core.Id[TestOrder]]) - .getOrElse(deserializationError(s"Patient create json object does not contain `orderId` field: $json")) - - val lastUpdate = fields - .get("lastUpdate") - .map(_.convertTo[LocalDateTime]) - .getOrElse(deserializationError(s"Patient create json object does not contain `lastUpdate` field: $json")) - - Patient(id, - status, - name, - dob, - assignee, - previousStatus, - previousAssignee, - lastActiveUser, - isUpdateRequired = false, - disease, - orderId, - lastUpdate) - - case _ => deserializationError(s"Expected Json Object as Trial, but got $json") - } - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala deleted file mode 100644 index 035310b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala +++ /dev/null @@ -1,65 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.{Label, LabelValue} -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities._ - -object patientcriterion { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToPatientCriterion(json: JsValue, orig: PatientCriterion): PatientCriterion = json match { - case JsObject(fields) => - val eligibilityStatus = fields - .get("eligibilityStatus") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.eligibilityStatus) - - val verifiedEligibilityStatus = fields - .get("verifiedEligibilityStatus") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.verifiedEligibilityStatus) - - orig.copy( - eligibilityStatus = eligibilityStatus, - verifiedEligibilityStatus = verifiedEligibilityStatus - ) - - case _ => deserializationError(s"Expected Json Object as partial PatientCriterion, but got $json") - } - - implicit val draftPatientCriterionFormat: RootJsonFormat[DraftPatientCriterion] = jsonFormat3( - DraftPatientCriterion.apply) - implicit val draftPatientCriterionListReader = new JsonReader[List[DraftPatientCriterion]] { - override def read(json: JsValue) = json.convertTo[List[JsValue]].map(_.convertTo[DraftPatientCriterion]) - } - - implicit val patientCriterionFormat: RootJsonFormat[PatientCriterion] = jsonFormat14(PatientCriterion.apply) - implicit val patientCriterionArmFormat: RootJsonFormat[PatientCriterionArm] = jsonFormat3(PatientCriterionArm.apply) - - implicit val richPatientCriterionFormat: RootJsonFormat[RichPatientCriterion] = - new RootJsonFormat[RichPatientCriterion] { - override def read(json: JsValue): RichPatientCriterion = { - val fields = json.asJsObject.fields - val labelId = fields.getOrElse("labelId", deserializationError("field 'labelId' is missing")) - val arms = fields.getOrElse("armList", deserializationError("field 'arms' is missing")) - RichPatientCriterion( - json.convertTo[PatientCriterion], - labelId.convertTo[LongId[Label]], - arms.convertTo[List[PatientCriterionArm]] - ) - } - override def write(obj: RichPatientCriterion): JsValue = { - JsObject( - obj.patientCriterion.toJson.asJsObject.fields ++ - Map( - "labelId" -> obj.labelId.toJson, - "armList" -> obj.armList.toJson - ) - ) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientdefiningcriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientdefiningcriteria.scala deleted file mode 100644 index a67115c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientdefiningcriteria.scala +++ /dev/null @@ -1,18 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.entities.PatientLabel - -object patientdefiningcriteria { - import common._ - - implicit val patientLabelDefiningCriteriaWriter: RootJsonWriter[PatientLabel] = new RootJsonWriter[PatientLabel] { - override def write(obj: PatientLabel) = - JsObject( - "id" -> obj.id.toJson, - "value" -> obj.verifiedPrimaryValue.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala deleted file mode 100644 index d719c5c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala +++ /dev/null @@ -1,39 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.entities._ - -object patienteligibletrial { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToTrialArmGroup(json: JsValue, orig: PatientTrialArmGroupView): PatientTrialArmGroupView = - json match { - case JsObject(fields) => - val isVerified = fields - .get("isVerified") - .map(_.convertTo[Boolean]) - .getOrElse(orig.isVerified) - - orig.copy(isVerified = isVerified) - - case _ => deserializationError(s"Expected Json Object as partial PatientTrialArmGroupView, but got $json") - } - - implicit val patientEligibleTrialWriter: RootJsonWriter[RichPatientEligibleTrial] = - new RootJsonWriter[RichPatientEligibleTrial] { - override def write(obj: RichPatientEligibleTrial) = - JsObject( - "id" -> obj.group.id.toJson, - "patientId" -> obj.group.patientId.toJson, - "trialId" -> obj.group.trialId.toJson, - "trialTitle" -> obj.trial.title.toJson, - "arms" -> obj.arms.map(_.armName).toJson, - "hypothesisId" -> obj.trial.hypothesisId.toJson, - "verifiedEligibilityStatus" -> obj.group.verifiedEligibilityStatus.toJson, - "isVerified" -> obj.group.isVerified.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthistory.scala deleted file mode 100644 index c9cdc63..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthistory.scala +++ /dev/null @@ -1,30 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object patienthistory { - import DefaultJsonProtocol._ - import PatientHistory._ - import common._ - - implicit val patientStateFormat: RootJsonFormat[State] = new EnumJsonFormat[State]( - "Verify" -> State.Verify, - "Curate" -> State.Curate, - "Review" -> State.Review, - "Flag" -> State.Flag - ) - - implicit val patientActionFormat: RootJsonFormat[Action] = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive - ) - - implicit val patientHistoryFormat: RootJsonFormat[PatientHistory] = jsonFormat6(PatientHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala deleted file mode 100644 index da991a4..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala +++ /dev/null @@ -1,35 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuidomain.entities._ - -object patienthypothesis { - import DefaultJsonProtocol._ - import common._ - import xyz.driver.core.json._ - - def applyUpdateToPatientHypothesis(json: JsValue, orig: PatientHypothesis): PatientHypothesis = json match { - case JsObject(fields) => - val rationale = if (fields.contains("rationale")) { - fields.get("rationale").map(_.convertTo[String]) - } else orig.rationale - - orig.copy(rationale = rationale) - - case _ => deserializationError(s"Expected Json Object as partial PatientHypothesis, but got $json") - } - - implicit val patientHypothesisWriter: RootJsonWriter[PatientHypothesis] = - new RootJsonWriter[PatientHypothesis] { - override def write(obj: PatientHypothesis): JsValue = { - JsObject( - "id" -> obj.id.toJson, - "patientId" -> obj.patientId.toJson, - "hypothesisId" -> obj.hypothesisId.toJson, - "matchedTrials" -> obj.matchedTrials.toJson, - "rationale" -> obj.rationale.toJson - ) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala deleted file mode 100644 index ed05325..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala +++ /dev/null @@ -1,58 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuidomain.entities._ - -object patientissue { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToPatientIssue(json: JsValue, orig: PatientIssue): PatientIssue = { - json.asJsObject.getFields("text", "archiveRequired") match { - case Seq(text, archiveRequired) => - orig.copy( - text = text.convertTo[String], - archiveRequired = archiveRequired.convertTo[Boolean] - ) - - case _ => deserializationError(s"Expected Json Object as partial PatientIssue, but got $json") - } - } - - def jsValueToPatientIssue(json: JsValue, - patientId: UuidId[Patient], - userId: xyz.driver.core.Id[User]): PatientIssue = { - json.asJsObject.getFields("text") match { - case Seq(text) => - PatientIssue( - id = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[PatientIssue]]]).getOrElse(LongId(0)), - userId = userId, - patientId = patientId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text.convertTo[String], - archiveRequired = false - ) - - case _ => deserializationError(s"Expected Json Object as PatientIssue, but got $json") - } - - } - - implicit val patientIssueWriter: RootJsonWriter[PatientIssue] = new RootJsonWriter[PatientIssue] { - override def write(obj: PatientIssue) = JsObject( - "id" -> obj.id.toJson, - "text" -> obj.text.toJson, - "lastUpdate" -> obj.lastUpdate.toJson, - "userId" -> obj.userId.toJson, - "isDraft" -> obj.isDraft.toJson, - "archiveRequired" -> obj.archiveRequired.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientlabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientlabel.scala deleted file mode 100644 index 615b3a2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientlabel.scala +++ /dev/null @@ -1,65 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.entities.labels.LabelValue -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.formats.json.labels._ -import xyz.driver.pdsuidomain.formats.json.record._ -import xyz.driver.pdsuidomain.formats.json.document._ - -object patientlabel { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToPatientLabel(json: JsValue, orig: PatientLabel): PatientLabel = json match { - case JsObject(fields) => - val primaryValue = fields - .get("primaryValue") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.primaryValue) - - val verifiedPrimaryValue = fields - .get("verifiedPrimaryValue") - .map(_.convertTo[LabelValue]) - .getOrElse(orig.verifiedPrimaryValue) - - orig.copy( - primaryValue = primaryValue, - verifiedPrimaryValue = verifiedPrimaryValue - ) - - case _ => deserializationError(s"Expected Json Object as PatientLabel, but got $json") - } - - implicit val patientLabelFormat: RootJsonFormat[PatientLabel] = jsonFormat8(PatientLabel.apply) - - implicit val richPatientLabelFormat: RootJsonFormat[RichPatientLabel] = new RootJsonFormat[RichPatientLabel] { - override def read(json: JsValue): RichPatientLabel = { - val isVerified = - json.asJsObject.fields.getOrElse("isVerified", deserializationError("isVerified field is missing")) - RichPatientLabel(json.convertTo[PatientLabel], isVerified.convertTo[Boolean]) - } - override def write(obj: RichPatientLabel): JsValue = { - val labelFields = obj.patientLabel.toJson.asJsObject.fields - JsObject(labelFields ++ Map("isVerified" -> obj.isVerified.toJson)) - } - } - - implicit val patientLabelEvidenceWriter: RootJsonWriter[PatientLabelEvidenceView] = - new RootJsonWriter[PatientLabelEvidenceView] { - override def write(evidence: PatientLabelEvidenceView): JsValue = - JsObject( - "id" -> evidence.id.toJson, - "value" -> evidence.value.toJson, - "evidenceText" -> evidence.evidenceText.toJson, - "documentId" -> evidence.documentId.toJson, - "evidenceId" -> evidence.evidenceId.toJson, - "reportId" -> evidence.reportId.toJson, - "documentType" -> evidence.documentType.toJson, - "date" -> evidence.date.toJson, - "providerType" -> evidence.providerType.toJson - ) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala deleted file mode 100644 index d3fe2c9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala +++ /dev/null @@ -1,213 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.Id -import xyz.driver.core.json._ -import xyz.driver.entities.clinic.ClinicalRecord -import xyz.driver.pdsuicommon.domain.{LongId, TextJson, UuidId} -import xyz.driver.pdsuidomain.entities.MedicalRecord.Meta._ -import xyz.driver.pdsuidomain.entities._ - -object record { - import DefaultJsonProtocol._ - import MedicalRecord._ - import common._ - - implicit val recordStatusFormat: EnumJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "Cleaned" -> Status.Cleaned, - "Reviewed" -> Status.Reviewed, - "Organized" -> Status.Organized, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged, - "Archived" -> Status.Archived - ) - - implicit val providerTypeFormat: RootJsonFormat[ProviderType] = new RootJsonFormat[ProviderType] { - override def read(json: JsValue): ProviderType = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Provider type json object does not contain `name` field: $json")) - - ProviderType - .fromString(name) - .getOrElse(deserializationError(s"Unknown provider type: $name")) - - case _ => deserializationError(s"Expected Json Object as Provider type, but got $json") - } - - override def write(obj: ProviderType) = - JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) - } - - implicit val duplicateMetaFormat: RootJsonFormat[Duplicate] = new RootJsonFormat[Duplicate] { - override def write(obj: Duplicate) = - JsObject( - "type" -> "duplicate".toJson, - "startPage" -> obj.startPage.toJson, - "endPage" -> obj.endPage.toJson, - "startOriginalPage" -> obj.startOriginalPage.toJson, - "endOriginalPage" -> obj.endOriginalPage.toJson - ) - - override def read(json: JsValue): Duplicate = json match { - case JsObject(fields) => - val startPage = fields - .get("startPage") - .map(_.convertTo[Double]) - .getOrElse(deserializationError(s"Duplicate meta json object does not contain `startPage` field: $json")) - - val endPage = fields - .get("endPage") - .map(_.convertTo[Double]) - .getOrElse(deserializationError(s"Duplicate meta json object does not contain `endPage` field: $json")) - - val startOriginalPage = fields - .get("startOriginalPage") - .map(_.convertTo[Double]) - .getOrElse( - deserializationError(s"Duplicate meta json object does not contain `startOriginalPage` field: $json")) - - val endOriginalPage = fields - .get("endOriginalPage") - .flatMap(_.convertTo[Option[Double]]) - - Duplicate( - startPage = startPage, - endPage = endPage, - startOriginalPage = startOriginalPage, - endOriginalPage = endOriginalPage - ) - - case _ => deserializationError(s"Expected JsObject as Duplicate meta of medical record, but got $json") - } - } - - implicit val reorderMetaFormat: RootJsonFormat[Reorder] = new RootJsonFormat[Reorder] { - override def write(obj: Reorder) = - JsObject("type" -> "reorder".toJson, "items" -> obj.items.toJson) - - override def read(json: JsValue): Reorder = json match { - case JsObject(fields) => - val items = fields - .get("items") - .map(_.convertTo[Seq[Int]]) - .getOrElse(deserializationError(s"Reorder meta json object does not contain `items` field: $json")) - - Reorder(items) - - case _ => deserializationError(s"Expected JsObject as Reorder meta of medical record, but got $json") - } - } - - implicit val rotateMetaFormat: RootJsonFormat[Rotation] = new RootJsonFormat[Rotation] { - override def write(obj: Rotation) = - JsObject("type" -> "rotation".toJson, "items" -> obj.items.toJson) - - override def read(json: JsValue): Rotation = json match { - case JsObject(fields) => - val items = fields - .get("items") - .map(_.convertTo[Map[String, Int]]) - .getOrElse(deserializationError(s"Rotation meta json object does not contain `items` field: $json")) - - Rotation(items = items) - - case _ => deserializationError(s"Expected JsObject as Rotation meta of medical record, but got $json") - } - } - - implicit val recordMetaTypeFormat: GadtJsonFormat[MedicalRecord.Meta] = { - GadtJsonFormat.create[Meta]("type")({ case m => m.metaType }) { - case "duplicate" => duplicateMetaFormat - case "reorder" => reorderMetaFormat - case "rotation" => rotateMetaFormat - } - } - - implicit val recordMetaFormat: RootJsonFormat[TextJson[List[Meta]]] = new RootJsonFormat[TextJson[List[Meta]]] { - override def write(obj: TextJson[List[Meta]]): JsArray = JsArray(obj.content.map(_.toJson).toVector) - override def read(json: JsValue): TextJson[List[Meta]] = json match { - case JsArray(values) => TextJson[List[Meta]](values.map(_.convertTo[Meta]).toList) - case _ => deserializationError(s"Expected array as Meta, but got $json") - } - } - - implicit val recordFormat: RootJsonFormat[MedicalRecord] = - new RootJsonFormat[MedicalRecord] { - override def write(record: MedicalRecord): JsValue = - JsObject( - "id" -> record.id.toJson, - "patientId" -> record.patientId.toJson, - "caseId" -> record.caseId.toJson, - "disease" -> record.disease.toJson, - "physician" -> record.physician.toJson, - "status" -> record.status.toJson, - "previousStatus" -> record.previousStatus.toJson, - "assignee" -> record.assignee.toJson, - "previousAssignee" -> record.previousAssignee.toJson, - "requestId" -> record.requestId.toJson, - "meta" -> record.meta.getOrElse(TextJson[List[Meta]](List.empty)).toJson, - "lastActiveUser" -> record.lastActiveUserId.toJson, - "lastUpdate" -> record.lastUpdate.toJson, - "totalPages" -> record.totalPages.toJson - ) - - override def read(json: JsValue): MedicalRecord = json match { - case JsObject(fields) => - val id = fields - .get("id") - .flatMap(_.convertTo[Option[LongId[MedicalRecord]]]) - - val disease = fields - .get("disease") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"MedicalRecord json object does not contain `disease` field: $json")) - - val patientId = fields - .get("patientId") - .map(_.convertTo[UuidId[Patient]]) - .getOrElse(deserializationError(s"MedicalRecord json object does not contain `patientId` field: $json")) - - val requestId = fields - .get("requestId") - .map(_.convertTo[Id[ClinicalRecord]]) - .getOrElse(deserializationError(s"MedicalRecord json object does not contain `requestId` field: $json")) - - MedicalRecord( - id = id.getOrElse(LongId(0)), - status = MedicalRecord.Status.New, - previousStatus = None, - assignee = None, - previousAssignee = None, - lastActiveUserId = None, - patientId = patientId, - requestId = requestId, - disease = disease, - caseId = None, - physician = None, - meta = None, - lastUpdate = LocalDateTime.now(), - totalPages = 0 - ) - - case _ => deserializationError(s"Expected Json Object as MedicalRecord, but got $json") - } - } - - def applyUpdateToMedicalRecord(json: JsValue, orig: MedicalRecord): MedicalRecord = json match { - case JsObject(fields) => - val meta = fields - .get("meta") - .map(_.convertTo[Option[TextJson[List[Meta]]]]) - .getOrElse(orig.meta) - orig.copy(meta = meta) - - case _ => deserializationError(s"Expected Json Object as partial MedicalRecord, but got $json") - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordhistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordhistory.scala deleted file mode 100644 index be9dae9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordhistory.scala +++ /dev/null @@ -1,43 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object recordhistory { - import DefaultJsonProtocol._ - import MedicalRecordHistory._ - import common._ - - implicit val recordStateFormat = new EnumJsonFormat[State]( - "New" -> State.New, - "Clean" -> State.Clean, - "Organize" -> State.Organize, - "Review" -> State.Review, - "Done" -> State.Done, - "Flag" -> State.Flag, - "Archive" -> State.Archive - ) - - implicit val recordActionFormat = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive, - "SaveDuplicate" -> Action.SaveDuplicate, - "SaveReorder" -> Action.SaveReorder, - "SaveRotation" -> Action.SaveRotation, - "DeleteDuplicate" -> Action.DeleteDuplicate, - "DeleteReorder" -> Action.DeleteReorder, - "DeleteRotation" -> Action.DeleteRotation, - "CreateDocument" -> Action.CreateDocument, - "DeleteDocument" -> Action.DeleteDocument, - "CreateRecord" -> Action.CreateRecord, - "ReadRecord" -> Action.ReadRecord - ) - - implicit val recordHistoryFormat: RootJsonFormat[MedicalRecordHistory] = jsonFormat6(MedicalRecordHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordissue.scala deleted file mode 100644 index e7f2f65..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/recordissue.scala +++ /dev/null @@ -1,72 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities._ - -object recordissue { - import DefaultJsonProtocol._ - import common._ - - def applyUpdateToRecordIssue(json: JsValue, orig: MedicalRecordIssue): MedicalRecordIssue = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"MedicalRecordIssue json object does not contain `text` field: $json")) - - val archiveRequired = fields - .get("archiveRequired") - .map(_.convertTo[Boolean]) - .getOrElse( - deserializationError(s"MedicalRecordIssue json object does not contain `archiveRequired` field: $json")) - - val startPage = fields.get("startPage").map(_.convertTo[Double]) - val endPage = fields.get("endPage").map(_.convertTo[Double]) - - orig.copy( - text = text, - archiveRequired = archiveRequired, - startPage = startPage, - endPage = endPage - ) - - case _ => deserializationError(s"Expected Json Object as partial MedicalRecordIssue, but got $json") - - } - - def jsValueToRecordIssue(json: JsValue, - recordId: LongId[MedicalRecord], - userId: xyz.driver.core.Id[User]): MedicalRecordIssue = json match { - case JsObject(fields) => - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"MedicalRecordIssue json object does not contain `text` field: $json")) - - val id = fields.get("id").flatMap(_.convertTo[Option[LongId[MedicalRecordIssue]]]).getOrElse(LongId(0)) - val startPage = fields.get("startPage").map(_.convertTo[Double]) - val endPage = fields.get("endPage").map(_.convertTo[Double]) - - MedicalRecordIssue( - id = id, - userId = userId, - recordId = recordId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text, - archiveRequired = false, - startPage = startPage, - endPage = endPage - ) - - case _ => deserializationError(s"Expected Json Object as MedicalRecordIssue, but got $json") - } - - implicit val recordIssueFormat: RootJsonFormat[MedicalRecordIssue] = jsonFormat9(MedicalRecordIssue.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm.scala deleted file mode 100644 index 60d6521..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm.scala +++ /dev/null @@ -1,44 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -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") - } - - implicit 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 = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[SlotArm]]]).getOrElse(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/studydesign.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign.scala deleted file mode 100644 index 60c7e70..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign.scala +++ /dev/null @@ -1,29 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.pdsuidomain.entities._ - -object studydesign { - import DefaultJsonProtocol._ - import common._ - - implicit val studyDesignFormat: RootJsonFormat[StudyDesign] = new RootJsonFormat[StudyDesign] { - override def read(json: JsValue): StudyDesign = json match { - case JsObject(fields) => - val name = fields - .get("name") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Study design json object does not contain `name` field: $json")) - - StudyDesign - .fromString(name) - .getOrElse(deserializationError(s"Unknown study design: $name")) - - case _ => deserializationError(s"Expected Json Object as Study design, but got $json") - } - - override def write(obj: StudyDesign) = - JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala deleted file mode 100644 index cdc52d9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala +++ /dev/null @@ -1,187 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.{LocalDateTime, ZoneId, ZonedDateTime} - -import spray.json._ -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities._ - -object trial { - import DefaultJsonProtocol._ - import Trial._ - import common._ - - implicit val trialStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status]( - "New" -> Status.New, - "ReviewSummary" -> Status.ReviewSummary, - "Summarized" -> Status.Summarized, - "PendingUpdate" -> Status.PendingUpdate, - "Update" -> Status.Update, - "ReviewCriteria" -> Status.ReviewCriteria, - "Done" -> Status.Done, - "Flagged" -> Status.Flagged, - "Archived" -> Status.Archived - ) - - implicit val trialFormat: RootJsonFormat[Trial] = new RootJsonFormat[Trial] { - override def write(obj: Trial) = - JsObject( - "id" -> obj.id.toJson, - "externalid" -> obj.externalId.toJson, - "lastUpdate" -> ZonedDateTime.of(obj.lastUpdate, ZoneId.of("Z")).toJson, - "status" -> obj.status.toJson, - "assignee" -> obj.assignee.toJson, - "previousStatus" -> obj.previousStatus.toJson, - "previousAssignee" -> obj.previousAssignee.toJson, - "lastActiveUser" -> obj.lastActiveUserId.toJson, - "phase" -> obj.phase.toJson, - "hypothesisId" -> obj.hypothesisId.toJson, - "studyDesignId" -> obj.studyDesignId.toJson, - "originalStudyDesignId" -> obj.originalStudyDesign.toJson, - "isPartner" -> obj.isPartner.toJson, - "overview" -> obj.overview.toJson, - "overviewTemplate" -> obj.overviewTemplate.toJson, - "isUpdated" -> obj.isUpdated.toJson, - "title" -> obj.title.toJson, - "originalTitle" -> obj.originalTitle.toJson - ) - - override def read(json: JsValue): Trial = { - json match { - case JsObject(fields) => - val id = fields - .get("id") - .map(_.convertTo[StringId[Trial]]) - .getOrElse(deserializationError(s"Trial create json object does not contain `id` field: $json")) - val externalid = fields - .get("externalid") - .map(_.convertTo[UuidId[Trial]]) - .getOrElse(deserializationError(s"Trial create json object does not contain `externalid` field: $json")) - val status = fields - .get("status") - .map(_.convertTo[Trial.Status]) - .getOrElse(deserializationError(s"Trial create json object does not contain `status` field: $json")) - val assignee = fields - .get("assignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - val previousStatus = fields - .get("previousStatus") - .flatMap(_.convertTo[Option[Trial.Status]]) - val previousAssignee = fields - .get("previousAssignee") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - val lastActiveUser = fields - .get("lastActiveUser") - .flatMap(_.convertTo[Option[xyz.driver.core.Id[User]]]) - val lastUpdate = fields - .get("lastUpdate") - .map(_.convertTo[LocalDateTime]) - .getOrElse(deserializationError(s"Trial create json object does not contain `lastUpdate` field: $json")) - val phase = fields - .get("phase") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Trial create json object does not contain `phase` field: $json")) - val hypothesisId = fields - .get("hypothesisId") - .flatMap(_.convertTo[Option[UuidId[Hypothesis]]]) - val studyDesignId = fields - .get("studyDesignId") - .flatMap(_.convertTo[Option[LongId[StudyDesign]]]) - val originalStudyDesignId = fields - .get("originalStudyDesignId") - .flatMap(_.convertTo[Option[String]]) - val isPartner = fields - .get("isPartner") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"Trial create json object does not contain `isPartner` field: $json")) - val overview = fields - .get("overview") - .flatMap(_.convertTo[Option[String]]) - val overviewTemplate = fields - .get("overviewTemplate") - .map(_.convertTo[String]) - .getOrElse( - deserializationError(s"Trial create json object does not contain `overviewTemplate` field: $json")) - val isUpdated = fields - .get("isUpdated") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationError(s"Trial create json object does not contain `isUpdated` field: $json")) - val title = fields - .get("title") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Trial create json object does not contain `title` field: $json")) - val originalTitle = fields - .get("originalTitle") - .map(_.convertTo[String]) - .getOrElse(deserializationError(s"Trial create json object does not contain `originalTitle` field: $json")) - - Trial( - id, - externalid, - status, - assignee, - previousStatus, - previousAssignee, - lastActiveUser, - lastUpdate, - phase, - hypothesisId, - studyDesignId, - originalStudyDesignId, - isPartner, - overview, - overviewTemplate, - isUpdated, - title, - originalTitle - ) - - case _ => deserializationError(s"Expected Json Object as Trial, but got $json") - } - } - } - - def applyUpdateToTrial(json: JsValue, orig: Trial): Trial = json match { - case JsObject(fields) => - val hypothesisId = fields - .get("hypothesisId") - .map(_.convertTo[Option[UuidId[Hypothesis]]]) - .getOrElse(orig.hypothesisId) - - val studyDesignId = fields - .get("studyDesignId") - .map(_.convertTo[Option[LongId[StudyDesign]]]) - .getOrElse(orig.studyDesignId) - - val overview = fields - .get("overview") - .map(_.convertTo[Option[String]]) - .getOrElse(orig.overview) - - val title = fields - .get("title") - .map(_.convertTo[Option[String]].getOrElse("")) - .getOrElse(orig.title) - - val originalTitle = fields - .get("originalTitle") - .flatMap(_.convertTo[Option[String]]) - .getOrElse(orig.originalTitle) - - orig.copy( - hypothesisId = hypothesisId, - studyDesignId = studyDesignId, - overview = overview, - title = title, - originalTitle = originalTitle - ) - - case _ => deserializationError(s"Expected Json Object as Trial, but got $json") - } - - implicit val trialCreationRequestFormat: RootJsonFormat[TrialCreationRequest] = - jsonFormat3(TrialCreationRequest.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialhistory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialhistory.scala deleted file mode 100644 index f71ec12..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialhistory.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import spray.json._ -import xyz.driver.core.json._ -import xyz.driver.pdsuidomain.entities._ - -object trialhistory { - import DefaultJsonProtocol._ - import TrialHistory._ - import common._ - - implicit val trialStateFormat = new EnumJsonFormat[State]( - "Summarize" -> State.Summarize, - "Criteriarize" -> State.Criteriarize, - "Review" -> State.Review, - "ReviewSummary" -> State.ReviewSummary, - "ReviewCriteria" -> State.ReviewCriteria, - "Flag" -> State.Flag - ) - - implicit val trialActionFormat = new EnumJsonFormat[Action]( - "Start" -> Action.Start, - "Submit" -> Action.Submit, - "Unassign" -> Action.Unassign, - "Resolve" -> Action.Resolve, - "Flag" -> Action.Flag, - "Archive" -> Action.Archive - ) - - implicit val trialHistoryFormat: RootJsonFormat[TrialHistory] = jsonFormat7(TrialHistory.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialissue.scala deleted file mode 100644 index 79882c2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trialissue.scala +++ /dev/null @@ -1,134 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json - -import java.time.LocalDateTime - -import spray.json.{RootJsonReader, _} -import xyz.driver.core.{Id, auth} -import xyz.driver.core.auth.User -import xyz.driver.core.json._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.entities._ - -object trialissue { - - import DefaultJsonProtocol._ - import common._ - - private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = { - deserializationError(s"$className json object do not contain '$field' field: $json") - } - - private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = { - deserializationError(s"Expected Json Object as $className, but got $json") - } - - def applyUpdateToTrialIssue(json: JsValue, orig: TrialIssue): TrialIssue = { - json.asJsObject.getFields("text", "evidence", "archiveRequired", "meta") match { - case Seq(text, evidence, archiveRequired, meta) => - orig.copy( - text = text.convertTo[String], - evidence = evidence.convertTo[String], - archiveRequired = archiveRequired.convertTo[Boolean], - meta = meta.convertTo[String] - ) - - case _ => deserializationError(s"Expected Json Object as partial TrialIssue, but got $json") - } - } - - def jsValueToTrialIssue(json: JsValue, trialId: StringId[Trial], userId: xyz.driver.core.Id[User]): TrialIssue = { - json.asJsObject.getFields("text", "evidence", "meta") match { - case Seq(text, evidence, meta) => - TrialIssue( - id = json.asJsObject.fields.get("id").flatMap(_.convertTo[Option[LongId[TrialIssue]]]).getOrElse(LongId(0)), - userId = userId, - trialId = trialId, - lastUpdate = LocalDateTime.MIN, - isDraft = true, - text = text.convertTo[String], - evidence = evidence.convertTo[String], - archiveRequired = false, - meta = meta.convertTo[String] - ) - - case _ => deserializationError(s"Expected Json Object as TrialIssue, but got $json") - } - - } - - implicit val trialIssueWriter = new RootJsonWriter[TrialIssue] { - override def write(obj: TrialIssue) = JsObject( - "id" -> obj.id.toJson, - "text" -> obj.text.toJson, - "lastUpdate" -> obj.lastUpdate.toJson, - "userId" -> obj.userId.toJson, - "isDraft" -> obj.isDraft.toJson, - "evidence" -> obj.evidence.toJson, - "archiveRequired" -> obj.archiveRequired.toJson, - "meta" -> obj.meta.toJson - ) - } - - def trialIssueReader(trialId: StringId[Trial]): RootJsonReader[TrialIssue] = - new RootJsonReader[TrialIssue] { - implicit val className: String = "TrialIssue" - - override def read(json: JsValue): TrialIssue = json match { - case JsObject(fields) => - val id = fields - .get("id") - .map(_.convertTo[LongId[TrialIssue]]) - .getOrElse(deserializationErrorFieldMessage("id", json)) - - val text = fields - .get("text") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("text", json)) - - val lastUpdate = fields - .get("lastUpdate") - .map(_.convertTo[LocalDateTime]) - .getOrElse(deserializationErrorFieldMessage("lastUpdate", json)) - - val userId = fields - .get("userId") - .map(_.convertTo[Id[auth.User]]) - .getOrElse(deserializationErrorFieldMessage("userId", json)) - - val isDraft = fields - .get("isDraft") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("isDraft", json)) - - val evidence = fields - .get("evidence") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("evidence", json)) - - val archiveRequired = fields - .get("archiveRequired") - .map(_.convertTo[Boolean]) - .getOrElse(deserializationErrorFieldMessage("archiveRequired", json)) - - val meta = fields - .get("meta") - .map(_.convertTo[String]) - .getOrElse(deserializationErrorFieldMessage("meta", json)) - - TrialIssue( - id = id, - userId = userId, - trialId = trialId, - lastUpdate = lastUpdate, - isDraft = isDraft, - text = text, - evidence = evidence, - archiveRequired = archiveRequired, - meta = meta - ) - - case _ => deserializationErrorEntityMessage(json) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/ArmService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/ArmService.scala deleted file mode 100644 index d4ff62b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/ArmService.scala +++ /dev/null @@ -1,130 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -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.Arm - -import scala.concurrent.Future - -object ArmService { - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - trait DefaultNotFoundError { - def userMessage: String = "Arm not found" - } - - sealed trait GetByIdReply - object GetByIdReply { - - final case class Entity(x: Arm) 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: AuthorizedServiceRequestContext[AuthUserInfo]) - extends GetByIdReply with DomainError - } - - sealed trait GetListReply - object GetListReply { - type Error = GetListReply with DomainError - - final case class EntityList(xs: Seq[Arm], totalFound: Int) extends GetListReply - - case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait UpdateReply - object UpdateReply { - - final case class Updated(updated: Arm) 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: Arm) 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: Arm) 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: Arm) 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 ArmService { - - import ArmService._ - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def getById(armId: LongId[Arm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def create(draftArm: Arm)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def update(origArm: Arm, draftArm: Arm)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(id: LongId[Arm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/CriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/CriterionService.scala deleted file mode 100644 index 9c6341c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/CriterionService.scala +++ /dev/null @@ -1,126 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -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._ - -import scala.concurrent.Future - -object CriterionService { - - trait DefaultNotFoundError { - def userMessage: String = "Criterion not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - final case class RichCriterion(criterion: Criterion, - armIds: Seq[LongId[EligibilityArm]], - labels: Seq[CriterionLabel]) - object RichCriterion { - implicit def toPhiString(x: RichCriterion): PhiString = { - import x._ - phi"RichCriterion(criterion=$criterion, armIds=$armIds, labels=$labels)" - } - } - - sealed trait CreateReply - object CreateReply { - type Error = CreateReply with DomainError - - final case class Created(x: RichCriterion) extends CreateReply - - case object AuthorizationError - extends CreateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait GetByIdReply - object GetByIdReply { - final case class Entity(x: RichCriterion) 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: AuthorizedServiceRequestContext[AuthUserInfo]) - extends GetByIdReply with DomainError - - implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x) => phi"GetByIdReply.Entity($x)" - } - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[RichCriterion], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListReply - - case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - - final case class Updated(updated: RichCriterion) extends UpdateReply - - 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 - } - - 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 CriterionService { - - import CriterionService._ - - def create(draftRichCriterion: RichCriterion)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def getById(id: LongId[Criterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def update(origRichCriterion: RichCriterion, draftRichCriterion: RichCriterion)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(id: LongId[Criterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentHistoryService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/DocumentHistoryService.scala deleted file mode 100644 index d209b39..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentHistoryService.scala +++ /dev/null @@ -1,45 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.{Document, DocumentHistory} - -import scala.concurrent.Future - -object DocumentHistoryService { - - trait DefaultNotFoundError { - def userMessage: String = "Document history not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[DocumentHistory], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListReply - - final case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - -} - -trait DocumentHistoryService { - - import DocumentHistoryService._ - - def getListByDocumentId(id: LongId[Document], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentIssueService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/DocumentIssueService.scala deleted file mode 100644 index f7fc7b2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentIssueService.scala +++ /dev/null @@ -1,95 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.{Document, DocumentIssue} - -import scala.concurrent.Future - -object DocumentIssueService { - - trait DefaultNotFoundError { - def userMessage: String = "DocumentIssue not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait CreateReply - object CreateReply { - type Error = CreateReply with DomainError - final case class Created(x: DocumentIssue) extends CreateReply - case object AuthorizationError - extends CreateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait GetByIdReply - object GetByIdReply { - type Error = GetByIdReply with DomainError - final case class Entity(x: DocumentIssue) extends GetByIdReply - case object NotFoundError extends GetByIdReply with DomainError.NotFoundError with DefaultNotFoundError - final case class CommonError(userMessage: String) extends GetByIdReply with DomainError - case object AuthorizationError - extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetListByDocumentIdReply - object GetListByDocumentIdReply { - type Error = GetListByDocumentIdReply with DomainError - final case class EntityList(xs: Seq[DocumentIssue], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListByDocumentIdReply - case object NotFoundError extends GetListByDocumentIdReply with DomainError.NotFoundError with DefaultNotFoundError - case object AuthorizationError - extends GetListByDocumentIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - final case class Updated(updated: DocumentIssue) extends UpdateReply - case object AuthorizationError - extends UpdateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - final case class CommonError(userMessage: String) extends UpdateReply with DomainError - } - - sealed trait DeleteReply - object DeleteReply { - type Error = DeleteReply with DomainError - case object Deleted extends DeleteReply - case object AuthorizationError - extends DeleteReply with DomainError.AuthorizationError with DefaultAccessDeniedError - case object NotFoundError extends DeleteReply with DomainError.NotFoundError with DefaultNotFoundError - final case class CommonError(userMessage: String) extends DeleteReply with DomainError - } -} - -trait DocumentIssueService { - - import DocumentIssueService._ - - def create(draft: DocumentIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def getById(documentId: LongId[Document], id: LongId[DocumentIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getListByDocumentId(documentId: LongId[Document], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListByDocumentIdReply] - - def update(orig: DocumentIssue, draft: DocumentIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(documentId: LongId[Document], id: LongId[DocumentIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/DocumentService.scala deleted file mode 100644 index a16ac9c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentService.scala +++ /dev/null @@ -1,147 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -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._ - -import scala.concurrent.Future - -object DocumentService { - - trait DefaultNotFoundError { - def userMessage: String = "Can not find the document" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetByIdReply - object GetByIdReply { - final case class Entity(x: Document) 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: AuthorizedServiceRequestContext[AuthUserInfo]) - extends GetByIdReply with DomainError - - implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x) => phi"GetByIdReply.Entity($x)" - } - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[Document], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListReply - - type Error = GetListReply with DomainError - - case object AuthorizationError - extends GetListReply with DefaultAccessDeniedError with DomainError.AuthorizationError - - final case class CommonError(userMessage: String) extends GetListReply with DomainError - } - - sealed trait CreateReply - object CreateReply { - final case class Created(x: Document) extends CreateReply - - type Error = CreateReply with DomainError - - case object NotFoundError extends CreateReply with DefaultNotFoundError with DomainError.NotFoundError - - case object AuthorizationError - extends CreateReply with DefaultAccessDeniedError with DomainError.AuthorizationError - - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait UpdateReply - object UpdateReply { - final case class Updated(updated: Document) 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 - - implicit def toPhiString(reply: UpdateReply): PhiString = reply match { - case Updated(x) => phi"Updated($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 DocumentService { - - import DocumentService._ - - def getById(id: LongId[Document])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def create(draftDocument: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def update(orig: Document, draft: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(id: LongId[Document])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] - - def start(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def submit(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def restart(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def flag(orig: Document)(implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def resolve(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def unassign(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def archive(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentTypeService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/DocumentTypeService.scala deleted file mode 100644 index ccaed22..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/DocumentTypeService.scala +++ /dev/null @@ -1,26 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.Sorting -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.DocumentType -import xyz.driver.pdsuidomain.services.DocumentTypeService.GetListReply - -import scala.concurrent.Future - -object DocumentTypeService { - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[DocumentType], totalFound: Int) extends GetListReply - case object AuthorizationError extends GetListReply with DomainError.AuthorizationError { - def userMessage: String = "Access denied" - } - } -} - -trait DocumentTypeService { - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala deleted file mode 100644 index 8e67627..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityArmService.scala +++ /dev/null @@ -1,145 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -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: AuthorizedServiceRequestContext[AuthUserInfo]) - 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: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def getByEligibilityId(armId: LongId[EligibilityArm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def deleteByEligibilityIdSlotArmId(armId: LongId[EligibilityArm], slotArmId: LongId[SlotArm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] - - def getBySlotId(armId: LongId[SlotArm], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def create(slotArmId: LongId[SlotArm], draftEligibilityArm: EligibilityArmWithDiseases)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def update(origEligibilityArm: EligibilityArmWithDiseases, draftEligibilityArm: EligibilityArmWithDiseases)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(id: LongId[EligibilityArm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilitySnapshotService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilitySnapshotService.scala deleted file mode 100644 index b3e6673..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilitySnapshotService.scala +++ /dev/null @@ -1,16 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.entities.{Patient => PdsuiPatient} -import xyz.driver.pdsuidomain.entities.eligibility.EligibleTrial - -import scala.concurrent.Future - -trait EligibilitySnapshotService { - - def eligibilitySnapshot(patientId: UuidId[PdsuiPatient])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Seq[EligibleTrial]] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala deleted file mode 100644 index 3788617..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala +++ /dev/null @@ -1,22 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.Id -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.patient.{CancerType, Patient} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.eligibility.{MatchedPatient, MismatchRankedLabels} -import xyz.driver.pdsuidomain.entities.EligibilityArm - -import scala.concurrent.Future -import scalaz.ListT - -trait EligibilityVerificationService { - - def getMatchedPatients()(implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): ListT[Future, MatchedPatient] - - def getMismatchRankedLabels(patientId: Id[Patient], - cancerType: CancerType, - excludedArms: Seq[LongId[EligibilityArm]])( - implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): Future[MismatchRankedLabels] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/ExtractedDataService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/ExtractedDataService.scala deleted file mode 100644 index fbfb1d2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/ExtractedDataService.scala +++ /dev/null @@ -1,126 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.entities.export.patient.ExportPatientWithLabels - -import scala.concurrent.Future - -object ExtractedDataService { - - trait DefaultNotFoundError { - def userMessage: String = "Extracted data hasn't been found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - final case class RichExtractedData(extractedData: ExtractedData, labels: List[ExtractedDataLabel]) - - object RichExtractedData { - implicit def toPhiString(x: RichExtractedData): PhiString = { - import x._ - phi"RichExtractedData(extractedData=$extractedData, labels=$labels)" - } - } - - sealed trait GetByIdReply - object GetByIdReply { - type Error = GetByIdReply with DomainError - final case class Entity(x: RichExtractedData) extends GetByIdReply - - case object AuthorizationError - extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - - case object NotFoundError extends GetByIdReply with DefaultNotFoundError with DomainError.NotFoundError - - final case class CommonError(userMessage: String) extends GetByIdReply with DomainError - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[RichExtractedData], totalFound: Int) extends GetListReply - - case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetPatientLabelsReply - object GetPatientLabelsReply { - type Error = GetPatientLabelsReply with DomainError - - final case class Entity(x: ExportPatientWithLabels) extends GetPatientLabelsReply - - case object NotFoundError extends GetPatientLabelsReply with DomainError.NotFoundError { - def userMessage: String = "Patient not found" - } - } - - sealed trait CreateReply - object CreateReply { - type Error = CreateReply with DomainError - final case class Created(x: RichExtractedData) extends CreateReply - - case object AuthorizationError - extends CreateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - final case class Updated(updated: RichExtractedData) extends UpdateReply - - case object AuthorizationError - extends UpdateReply with DefaultAccessDeniedError with DomainError.AuthorizationError - - case object NotFoundError extends UpdateReply with DefaultNotFoundError with DomainError.NotFoundError - - final case class CommonError(userMessage: String) extends UpdateReply with DomainError - } - - sealed trait DeleteReply - object DeleteReply { - type Error = DeleteReply with DomainError - case object Deleted extends DeleteReply - - case object AuthorizationError - extends DeleteReply with DefaultAccessDeniedError with DomainError.AuthorizationError - - case object NotFoundError extends DeleteReply with DefaultNotFoundError with DomainError.NotFoundError - - final case class CommonError(userMessage: String) extends DeleteReply with DomainError - } -} - -trait ExtractedDataService { - - import ExtractedDataService._ - - def getById(id: LongId[ExtractedData])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getPatientLabels(id: UuidId[Patient])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetPatientLabelsReply] - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def create(draftRichExtractedData: RichExtractedData)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def update(origRichExtractedData: RichExtractedData, draftRichExtractedData: RichExtractedData)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(id: LongId[ExtractedData])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/HypothesisService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/HypothesisService.scala deleted file mode 100644 index 929dd58..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/HypothesisService.scala +++ /dev/null @@ -1,69 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.Sorting -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.Hypothesis - -import scala.concurrent.Future - -object HypothesisService { - trait DefaultNotFoundError { - def userMessage: String = "Hypothesis not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[Hypothesis], totalFound: Int) extends GetListReply - - case object AuthorizationError extends GetListReply with DomainError.AuthorizationError { - def userMessage: String = "Access denied" - } - } - - sealed trait CreateReply - object CreateReply { - final case class Created(x: Hypothesis) 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 - } - - 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 HypothesisService { - - import HypothesisService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def create(draftHypothesis: Hypothesis)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def delete(id: UuidId[Hypothesis])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/InterventionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/InterventionService.scala deleted file mode 100644 index 85e557a..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/InterventionService.scala +++ /dev/null @@ -1,119 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities._ - -import scala.concurrent.Future - -object InterventionService { - - trait DefaultNotFoundError { - def userMessage: String = "Intervention not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[InterventionWithArms], totalFound: Int) extends GetListReply - - case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetByIdReply - object GetByIdReply { - final case class Entity(x: InterventionWithArms) 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: AuthorizedServiceRequestContext[AuthUserInfo]) - extends GetByIdReply with DomainError - - implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x) => phi"GetByIdReply.Entity($x)" - } - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - - final case class Updated(updated: InterventionWithArms) extends UpdateReply - - case object NotFoundError extends UpdateReply with DefaultNotFoundError with DomainError.NotFoundError - - case object AuthorizationError - extends UpdateReply with DefaultAccessDeniedError with DomainError.AuthorizationError - - final case class CommonError(userMessage: String) extends UpdateReply with DomainError - } - - sealed trait CreateReply - object CreateReply { - final case class Created(x: InterventionWithArms) extends CreateReply - - type Error = CreateReply with DomainError - - case object AuthorizationError - extends CreateReply with DefaultAccessDeniedError with DomainError.AuthorizationError - - final case class CommonError(userMessage: String) extends CreateReply with DomainError - - implicit def toPhiString(reply: CreateReply): PhiString = reply match { - case Created(x) => phi"Created($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 InterventionService { - - import InterventionService._ - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def getById(id: LongId[Intervention])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def update(origIntervention: InterventionWithArms, draftIntervention: InterventionWithArms)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def create(draftIntervention: InterventionWithArms)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def delete(id: LongId[Intervention])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/InterventionTypeService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/InterventionTypeService.scala deleted file mode 100644 index 58f336d..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/InterventionTypeService.scala +++ /dev/null @@ -1,28 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.Sorting -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.InterventionType - -import scala.concurrent.Future - -object InterventionTypeService { - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[InterventionType], totalFound: Int) extends GetListReply - - case object AuthorizationError extends GetListReply with DomainError.AuthorizationError { - def userMessage: String = "Access denied" - } - } -} - -trait InterventionTypeService { - - import InterventionTypeService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordHistoryService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordHistoryService.scala deleted file mode 100644 index 42285b1..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordHistoryService.scala +++ /dev/null @@ -1,45 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.{MedicalRecord, MedicalRecordHistory} - -import scala.concurrent.Future - -object MedicalRecordHistoryService { - - trait DefaultNotFoundError { - def userMessage: String = "Medical record history not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[MedicalRecordHistory], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListReply - - final case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - -} - -trait MedicalRecordHistoryService { - - import MedicalRecordHistoryService._ - - def getListByRecordId(id: LongId[MedicalRecord], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordIssueService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordIssueService.scala deleted file mode 100644 index dc10a93..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordIssueService.scala +++ /dev/null @@ -1,95 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.{MedicalRecord, MedicalRecordIssue} - -import scala.concurrent.Future - -object MedicalRecordIssueService { - - trait DefaultNotFoundError { - def userMessage: String = "MedicalRecordIssue not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait CreateReply - object CreateReply { - type Error = CreateReply with DomainError - final case class Created(x: MedicalRecordIssue) extends CreateReply - case object AuthorizationError - extends CreateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait GetByIdReply - object GetByIdReply { - type Error = GetByIdReply with DomainError - final case class Entity(x: MedicalRecordIssue) extends GetByIdReply - case object NotFoundError extends GetByIdReply with DomainError.NotFoundError with DefaultNotFoundError - final case class CommonError(userMessage: String) extends GetByIdReply with DomainError - case object AuthorizationError - extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetListByRecordIdReply - object GetListByRecordIdReply { - type Error = GetListByRecordIdReply with DomainError - final case class EntityList(xs: Seq[MedicalRecordIssue], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListByRecordIdReply - case object NotFoundError extends GetListByRecordIdReply with DomainError.NotFoundError with DefaultNotFoundError - case object AuthorizationError - extends GetListByRecordIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - final case class Updated(updated: MedicalRecordIssue) extends UpdateReply - case object AuthorizationError - extends UpdateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - final case class CommonError(userMessage: String) extends UpdateReply with DomainError - } - - sealed trait DeleteReply - object DeleteReply { - type Error = DeleteReply with DomainError - case object Deleted extends DeleteReply - case object AuthorizationError - extends DeleteReply with DomainError.AuthorizationError with DefaultAccessDeniedError - case object NotFoundError extends DeleteReply with DomainError.NotFoundError with DefaultNotFoundError - final case class CommonError(userMessage: String) extends DeleteReply with DomainError - } -} - -trait MedicalRecordIssueService { - - import MedicalRecordIssueService._ - - def create(draft: MedicalRecordIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def getById(recordId: LongId[MedicalRecord], id: LongId[MedicalRecordIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getListByRecordId(recordId: LongId[MedicalRecord], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListByRecordIdReply] - - def update(orig: MedicalRecordIssue, draft: MedicalRecordIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(recordId: LongId[MedicalRecord], id: LongId[MedicalRecordIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordService.scala deleted file mode 100644 index 0d2c58b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/MedicalRecordService.scala +++ /dev/null @@ -1,126 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import akka.NotUsed -import akka.stream.scaladsl.Source -import akka.util.ByteString -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.error._ -import xyz.driver.pdsuidomain.entities.MedicalRecord.PdfSource -import xyz.driver.pdsuidomain.entities._ - -import scala.concurrent.Future - -object MedicalRecordService { - - type PdfSourceFetcher = (String, String) => Future[PdfSource] - - trait DefaultNotFoundError { - def userMessage: String = "Medical record hasn't been found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetByIdReply - object GetByIdReply { - final case class Entity(x: MedicalRecord) extends GetByIdReply - - type Error = GetByIdReply with DomainError - - case object NotFoundError extends GetByIdReply with DomainError.NotFoundError with DefaultNotFoundError - - final case class CommonError(userMessage: String) extends GetByIdReply with DomainError - - case object AuthorizationError - extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[MedicalRecord], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListReply - - type Error = GetListReply with DomainError - - case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - - case object NotFoundError extends GetListReply with DomainError.NotFoundError { - def userMessage: String = "Patient wasn't found" - } - } - - sealed trait CreateReply - object CreateReply { - type Error = CreateReply with DomainError - - final case class Created(x: MedicalRecord) extends CreateReply - - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - - final case class Updated(updated: MedicalRecord) extends UpdateReply - - 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 Settings(pdfSourceBucket: String) -} - -trait MedicalRecordService { - - import MedicalRecordService._ - - def getById(recordId: LongId[MedicalRecord])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getPdfSource(recordId: LongId[MedicalRecord])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Source[ByteString, NotUsed]] - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def create(draft: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def update(origRecord: MedicalRecord, draftRecord: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def start(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def submit(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def restart(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def flag(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def resolve(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def unassign(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def archive(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala deleted file mode 100644 index 915dc20..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala +++ /dev/null @@ -1,28 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ - -import scala.concurrent.Future - -trait PatientCriterionService { - - def getAll(patientId: UuidId[Patient], - origFilter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[RichPatientCriterion]] - - def getById(patientId: UuidId[Patient], id: LongId[PatientCriterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[RichPatientCriterion]] - - def updateList(patientId: UuidId[Patient], draftEntities: List[DraftPatientCriterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Unit] - - def update(origEntity: PatientCriterion, draftEntity: PatientCriterion, patientId: UuidId[Patient])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[RichPatientCriterion] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala deleted file mode 100644 index e73d537..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala +++ /dev/null @@ -1,29 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ - -import scala.concurrent.Future - -trait PatientEligibleTrialService { - - def getAll(patientId: UuidId[Patient], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[RichPatientEligibleTrial]] - - def getById(patientId: UuidId[Patient], id: LongId[PatientTrialArmGroup])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[RichPatientEligibleTrial]] - - def getCriterionListByGroupId(patientId: UuidId[Patient], id: LongId[PatientTrialArmGroup])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[RichPatientCriterion]] - - def update(origEligibleTrialWithTrial: RichPatientEligibleTrial, draftPatientTrialArmGroup: PatientTrialArmGroupView)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[RichPatientEligibleTrial] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHistoryService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientHistoryService.scala deleted file mode 100644 index 3f44e58..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHistoryService.scala +++ /dev/null @@ -1,20 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.{Patient, PatientHistory} - -import scala.concurrent.Future - -trait PatientHistoryService { - - def getListByPatientId(id: UuidId[Patient], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[PatientHistory]] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala deleted file mode 100644 index 0191b5a..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala +++ /dev/null @@ -1,25 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.{Hypothesis, Patient, PatientHypothesis} - -import scala.concurrent.Future - -trait PatientHypothesisService { - - def getAll(patientId: UuidId[Patient], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[PatientHypothesis]] - - def getById(patientId: UuidId[Patient], hypothesisId: UuidId[Hypothesis])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[PatientHypothesis]] - - def update(origPatientHypothesis: PatientHypothesis, draftPatientHypothesis: PatientHypothesis)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[PatientHypothesis] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientIssueService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientIssueService.scala deleted file mode 100644 index b2ba357..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientIssueService.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.{Patient, PatientIssue} - -import scala.concurrent.Future - -trait PatientIssueService { - - def create(draft: PatientIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[PatientIssue] - - def getById(patientId: UuidId[Patient], id: LongId[PatientIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[PatientIssue]] - - def getListByPatientId(patientId: UuidId[Patient], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[PatientIssue]] - - def update(orig: PatientIssue, draft: PatientIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[PatientIssue] - - def delete(patientId: UuidId[Patient], id: LongId[PatientIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Unit] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelEvidenceService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelEvidenceService.scala deleted file mode 100644 index a999bf9..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelEvidenceService.scala +++ /dev/null @@ -1,24 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.labels.Label -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain.{LongId, UuidId} -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ - -import scala.concurrent.Future - -trait PatientLabelEvidenceService { - - def getById(patientId: UuidId[Patient], labelId: LongId[Label], id: LongId[PatientLabelEvidence])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[PatientLabelEvidenceView]] - - def getAll(patientId: UuidId[Patient], - labelId: LongId[Label], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[PatientLabelEvidenceView]] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala deleted file mode 100644 index 0eeac53..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala +++ /dev/null @@ -1,31 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.labels.Label -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ - -import scala.concurrent.Future - -trait PatientLabelService { - - def getAll(patientId: UuidId[Patient], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[RichPatientLabel]] - - def getDefiningCriteriaList(patientId: UuidId[Patient], - hypothesisId: UuidId[Hypothesis], - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[PatientLabel]] - - def getByLabelIdOfPatient(patientId: UuidId[Patient], labelId: LongId[Label])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[RichPatientLabel]] - - def update(origPatientLabel: PatientLabel, draftPatientLabel: PatientLabel)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[RichPatientLabel] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientService.scala deleted file mode 100644 index 6f95fdb..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientService.scala +++ /dev/null @@ -1,39 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ - -import scala.concurrent.Future - -trait PatientService { - - def getById(id: UuidId[Patient])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[Patient]] - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[Patient]] - - def unassign(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] - - def start(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] - - def submit(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] - - def restart(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] - - def flag(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] - - def resolve(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/ProviderTypeService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/ProviderTypeService.scala deleted file mode 100644 index ab936d6..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/ProviderTypeService.scala +++ /dev/null @@ -1,27 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.Sorting -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.ProviderType - -import scala.concurrent.Future - -object ProviderTypeService { - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[ProviderType], totalFound: Int) extends GetListReply - case object AuthorizationError extends GetListReply with DomainError.AuthorizationError { - def userMessage: String = "Access denied" - } - } -} - -trait ProviderTypeService { - - import ProviderTypeService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/QueueUploadService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/QueueUploadService.scala deleted file mode 100644 index 6cb2051..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/QueueUploadService.scala +++ /dev/null @@ -1,80 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.error.DomainError - -import scala.concurrent.Future - -object QueueUploadService { - trait DefaultNotFoundError { - def userMessage: String = "Message not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait CreateReply - object CreateReply { - type Error = CreateReply with DomainError - - final case class Created(x: BridgeUploadQueue.Item) extends CreateReply - case object AuthorizationError - extends CreateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait GetByIdReply - object GetByIdReply { - type Error = GetByIdReply with DomainError - - final case class Entity(x: BridgeUploadQueue.Item) extends GetByIdReply - case object AuthorizationError - extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - case object NotFoundError extends GetByIdReply with DomainError.NotFoundError with DefaultNotFoundError - final case class CommonError(userMessage: String) extends GetByIdReply with DomainError - } - - sealed trait GetListReply - object GetListReply { - type Error = GetListReply with DomainError - - final case class EntityList(xs: Seq[BridgeUploadQueue.Item], totalFound: Int) extends GetListReply - - case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait ResetReply - object ResetReply { - type Error = ResetReply with DomainError - - final case class Updated(updated: BridgeUploadQueue.Item) extends ResetReply - case object AuthorizationError extends ResetReply with DomainError.AuthorizationError with DefaultAccessDeniedError - case object NotFoundError extends ResetReply with DefaultNotFoundError with DomainError.NotFoundError - final case class CommonError(userMessage: String) extends ResetReply with DomainError - } -} - -trait QueueUploadService { - - import QueueUploadService._ - - def create(kind: String, tag: String)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def getById(kind: String, tag: String)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def reset(kind: String, tag: String)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ResetReply] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/SlotArmService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/SlotArmService.scala deleted file mode 100644 index 44e50da..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/SlotArmService.scala +++ /dev/null @@ -1,130 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -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: AuthorizedServiceRequestContext[AuthUserInfo]) - 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: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def getById(armId: LongId[SlotArm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def create(draftSlotArm: SlotArm)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def update(origSlotArm: SlotArm, draftSlotArm: SlotArm)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(id: LongId[SlotArm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/StudyDesignService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/StudyDesignService.scala deleted file mode 100644 index 8af159d..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/StudyDesignService.scala +++ /dev/null @@ -1,28 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.Sorting -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.StudyDesign - -import scala.concurrent.Future - -object StudyDesignService { - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[StudyDesign], totalFound: Int) extends GetListReply - - case object AuthorizationError extends GetListReply with DomainError.AuthorizationError { - def userMessage: String = "Access denied" - } - } -} - -trait StudyDesignService { - - import StudyDesignService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/TrialHistoryService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/TrialHistoryService.scala deleted file mode 100644 index 96ff96d..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/TrialHistoryService.scala +++ /dev/null @@ -1,45 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.StringId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.{Trial, TrialHistory} - -import scala.concurrent.Future - -object TrialHistoryService { - - trait DefaultNotFoundError { - def userMessage: String = "Trial not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[TrialHistory], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListReply - - final case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - -} - -trait TrialHistoryService { - - import TrialHistoryService._ - - def getListByTrialId(id: StringId[Trial], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/TrialIssueService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/TrialIssueService.scala deleted file mode 100644 index 433c1bc..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/TrialIssueService.scala +++ /dev/null @@ -1,95 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuidomain.entities.{Trial, TrialIssue} - -import scala.concurrent.Future - -object TrialIssueService { - - trait DefaultNotFoundError { - def userMessage: String = "TrialIssue not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait CreateReply - object CreateReply { - type Error = CreateReply with DomainError - final case class Created(x: TrialIssue) extends CreateReply - case object AuthorizationError - extends CreateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - final case class CommonError(userMessage: String) extends CreateReply with DomainError - } - - sealed trait GetByIdReply - object GetByIdReply { - type Error = GetByIdReply with DomainError - final case class Entity(x: TrialIssue) extends GetByIdReply - case object NotFoundError extends GetByIdReply with DomainError.NotFoundError with DefaultNotFoundError - final case class CommonError(userMessage: String) extends GetByIdReply with DomainError - case object AuthorizationError - extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetListByTrialIdReply - object GetListByTrialIdReply { - type Error = GetListByTrialIdReply with DomainError - final case class EntityList(xs: Seq[TrialIssue], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListByTrialIdReply - case object NotFoundError extends GetListByTrialIdReply with DomainError.NotFoundError with DefaultNotFoundError - case object AuthorizationError - extends GetListByTrialIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - final case class Updated(updated: TrialIssue) extends UpdateReply - case object AuthorizationError - extends UpdateReply with DomainError.AuthorizationError with DefaultAccessDeniedError - final case class CommonError(userMessage: String) extends UpdateReply with DomainError - } - - sealed trait DeleteReply - object DeleteReply { - type Error = DeleteReply with DomainError - case object Deleted extends DeleteReply - case object AuthorizationError - extends DeleteReply with DomainError.AuthorizationError with DefaultAccessDeniedError - case object NotFoundError extends DeleteReply with DomainError.NotFoundError with DefaultNotFoundError - final case class CommonError(userMessage: String) extends DeleteReply with DomainError - } -} - -trait TrialIssueService { - - import TrialIssueService._ - - def create(draft: TrialIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] - - def getById(trialId: StringId[Trial], id: LongId[TrialIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getListByTrialId(trialId: StringId[Trial], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListByTrialIdReply] - - def update(orig: TrialIssue, draft: TrialIssue)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def delete(trialId: StringId[Trial], id: LongId[TrialIssue])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala deleted file mode 100644 index 9ae1c10..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala +++ /dev/null @@ -1,158 +0,0 @@ -package xyz.driver.pdsuidomain.services - -import java.time.LocalDateTime - -import akka.NotUsed -import akka.stream.scaladsl.Source -import akka.util.ByteString -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.patient.CancerType -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain.StringId -import xyz.driver.pdsuicommon.error.DomainError -import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Trial, TrialCreationRequest} -import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels - -import scala.concurrent.Future - -object TrialService { - - trait DefaultNotFoundError { - def userMessage: String = "Trial not found" - } - - trait DefaultAccessDeniedError { - def userMessage: String = "Access denied" - } - - sealed trait GetListReply - object GetListReply { - final case class EntityList(xs: Seq[Trial], totalFound: Int, lastUpdate: Option[LocalDateTime]) - extends GetListReply - - case object AuthorizationError - extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetByIdReply - object GetByIdReply { - final case class Entity(x: Trial) 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: AuthorizedServiceRequestContext[AuthUserInfo]) - extends GetByIdReply with DomainError - - implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x) => phi"GetByIdReply.Entity($x)" - } - } - - sealed trait GetTrialWithLabelsReply - object GetTrialWithLabelsReply { - type Error = GetTrialWithLabelsReply with DomainError - - final case class Entity(x: ExportTrialWithLabels) extends GetTrialWithLabelsReply - - case object NotFoundError extends GetTrialWithLabelsReply with DomainError.NotFoundError { - def userMessage: String = "Trial not found" - } - - case object AuthorizationError - extends GetTrialWithLabelsReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait GetTrialsWithLabelsReply - object GetTrialsWithLabelsReply { - type Error = GetTrialsWithLabelsReply with DomainError - - final case class EntityList(xs: Seq[ExportTrialWithLabels]) extends GetTrialsWithLabelsReply - - case object NotFoundError extends GetTrialsWithLabelsReply with DomainError.NotFoundError { - def userMessage: String = "Trials for disease are not found" - } - - case object AuthorizationError - extends GetTrialsWithLabelsReply with DomainError.AuthorizationError with DefaultAccessDeniedError - } - - sealed trait UpdateReply - object UpdateReply { - type Error = UpdateReply with DomainError - - final case class Updated(updated: Trial) extends UpdateReply - - 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 - - implicit def toPhiString(reply: UpdateReply): PhiString = reply match { - case Updated(x) => phi"Updated($x)" - case x: Error => DomainError.toPhiString(x) - } - } -} - -trait TrialService { - - import TrialService._ - - def getById(id: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] - - def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetTrialWithLabelsReply] - - def getTrialsWithLabels(cancerType: CancerType)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetTrialsWithLabelsReply] - - def getPdfSource(trialId: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Source[ByteString, NotUsed]] - - def getHtmlSource(trialId: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Source[ByteString, NotUsed]] - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] - - def update(origTrial: Trial, draftTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def start(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def submit(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def restart(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def flag(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def resolve(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def archive(origTrial: Trial, comment: Option[String])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def unassign(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] - - def addTrial(trial: TrialCreationRequest)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Trial] -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala deleted file mode 100644 index 35c518c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala +++ /dev/null @@ -1,32 +0,0 @@ -package xyz.driver.pdsuidomain.services.fake - -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.core.{Id, generators} -import xyz.driver.entities.patient -import xyz.driver.entities.patient.Patient -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.eligibility.MismatchRankedLabels -import xyz.driver.pdsuidomain.entities.{EligibilityArm, eligibility} -import xyz.driver.pdsuidomain.services.EligibilityVerificationService - -import scala.concurrent.Future -import scalaz.ListT - -class FakeEligibilityVerificationService extends EligibilityVerificationService { - - override def getMatchedPatients()( - implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): ListT[Future, eligibility.MatchedPatient] = - ListT.listT[Future]( - Future.successful(List(xyz.driver.pdsuidomain.fakes.entities.eligibility.nextMatchedPatient()))) - - override def getMismatchRankedLabels(patientId: Id[Patient], - cancerType: patient.CancerType, - excludedArms: Seq[LongId[EligibilityArm]])( - implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): Future[eligibility.MismatchRankedLabels] = - Future.successful( - MismatchRankedLabels( - generators.seqOf(xyz.driver.pdsuidomain.fakes.entities.eligibility.nextLabelMismatchRank()), - labelVersion = generators.nextInt(10) - )) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala deleted file mode 100644 index 221e56c..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala +++ /dev/null @@ -1,136 +0,0 @@ -package xyz.driver.pdsuidomain.services.fake - -import java.time.LocalDateTime - -import akka.NotUsed -import akka.stream.scaladsl.Source -import akka.util.ByteString -import xyz.driver.core.generators -import xyz.driver.core.rest.AuthorizedServiceRequestContext -import xyz.driver.entities.labels.Label -import xyz.driver.entities.patient.CancerType -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.TrialService - -import scala.concurrent.Future - -class FakeTrialService extends TrialService { - - import TrialService._ - - private val trial = Trial( - id = StringId(""), - externalId = UuidId(), - status = Trial.Status.New, - assignee = None, - previousStatus = None, - previousAssignee = None, - lastActiveUserId = None, - lastUpdate = LocalDateTime.now(), - phase = "", - hypothesisId = None, - studyDesignId = None, - originalStudyDesign = None, - isPartner = false, - overview = None, - overviewTemplate = "", - isUpdated = false, - title = "", - originalTitle = "" - ) - - def getById(id: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = - Future.successful( - GetByIdReply.Entity(trial) - ) - - def getPdfSource(trialId: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo] - ): Future[Source[ByteString, NotUsed]] = - Future.failed(new NotImplementedError("fake PDF download is not implemented")) - - def getHtmlSource(trialId: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo] - ): Future[Source[ByteString, NotUsed]] = - Future.failed(new NotImplementedError("fake HTML download is not implemented")) - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = - Future.successful(GetListReply.EntityList(Seq(trial), 1, None)) - - override def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetTrialWithLabelsReply] = - Future.successful(GetTrialWithLabelsReply.Entity(nextExportTrialWithLabels())) - - override def getTrialsWithLabels(cancerType: CancerType)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetTrialsWithLabelsReply] = - Future.successful(GetTrialsWithLabelsReply.EntityList(generators.seqOf(nextExportTrialWithLabels()))) - - private def nextExportTrialWithLabels() = - ExportTrialWithLabels( - StringId[Trial]("NCT" + generators.nextInt(999999).toString), - UuidId[Trial](generators.nextUuid()), - LocalDateTime.now(), - labelVersion = 1L, - generators.listOf( - new ExportTrialArm( - 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[EligibilityArm](generators.nextInt(999999).toLong)), - generators.nextName().value, - generators.nextBoolean(), - generators.nextBoolean(), - generators.nextOption(generators.nextBoolean()) - )) - ) - - def update(origTrial: Trial, draftTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - Future.successful(UpdateReply.Updated(draftTrial)) - - def start(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - update(origTrial, origTrial) - - def submit(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - update(origTrial, origTrial) - - def restart(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - update(origTrial, origTrial) - - def flag(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - update(origTrial, origTrial) - - def resolve(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - update(origTrial, origTrial) - - def archive(origTrial: Trial, comment: Option[String])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - update(origTrial, origTrial) - - def unassign(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - update(origTrial, origTrial) - - def addTrial(newTrial: TrialCreationRequest)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Trial] = - Future.successful(trial) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestArmService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestArmService.scala deleted file mode 100644 index 87e2bab..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestArmService.scala +++ /dev/null @@ -1,85 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.ArmService - -class RestArmService(transport: ServiceTransport, baseUri: Uri)(implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends ArmService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.arm._ - import xyz.driver.pdsuidomain.services.ArmService._ - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest( - HttpMethods.GET, - endpointUri(baseUri, "/v1/arm", filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[Arm]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount) - } - } - - def getById(armId: LongId[Arm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/arm/$armId")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Arm](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - def create(draftArm: Arm)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] = { - for { - entity <- Marshal(draftArm).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/arm")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Arm](response) - } yield { - CreateReply.Created(reply) - } - } - - def update(origArm: Arm, draftArm: Arm)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = origArm.id - val request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/arm/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Arm](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def delete(id: LongId[Arm])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] = { - val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/arm/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[HttpEntity](response) - } yield { - DeleteReply.Deleted - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestCriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestCriterionService.scala deleted file mode 100644 index 33be27e..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestCriterionService.scala +++ /dev/null @@ -1,88 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.CriterionService - -class RestCriterionService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends CriterionService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.criterion._ - import xyz.driver.pdsuidomain.services.CriterionService._ - - def create(draftRichCriterion: RichCriterion)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] = { - for { - entity <- Marshal(draftRichCriterion).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/criterion")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[RichCriterion](response) - } yield { - CreateReply.Created(reply) - } - } - - def getById(id: LongId[Criterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/criterion/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[RichCriterion](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, - endpointUri(baseUri, - s"/v1/criterion", - filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[RichCriterion]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount, reply.meta.lastUpdate) - } - } - - def update(origRichCriterion: RichCriterion, draftRichCriterion: RichCriterion)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = origRichCriterion.criterion.id - for { - entity <- Marshal(draftRichCriterion).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/criterion/$id")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[RichCriterion](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def delete(id: LongId[Criterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] = { - val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/criterion/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[HttpEntity](response) - } yield { - DeleteReply.Deleted - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestDocumentService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestDocumentService.scala deleted file mode 100644 index bfe5e8f..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestDocumentService.scala +++ /dev/null @@ -1,121 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.DocumentService - -class RestDocumentService(transport: ServiceTransport, baseUri: Uri)(implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends DocumentService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.document._ - import xyz.driver.pdsuidomain.services.DocumentService._ - - def getById(id: LongId[Document])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/document/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Document](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - - val request = HttpRequest(HttpMethods.GET, - endpointUri(baseUri, - "/v1/document", - filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[Document]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount, reply.meta.lastUpdate) - } - } - - def create(draftDocument: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] = { - for { - entity <- Marshal(draftDocument).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/document")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Document](response) - } yield { - CreateReply.Created(reply) - } - } - - def update(orig: Document, draft: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - for { - entity <- Marshal(draft).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/document/${orig.id}")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Document](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def delete(id: LongId[Document])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] = { - val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/document/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[HttpEntity](response) - } yield { - DeleteReply.Deleted - } - } - - private def editAction(orig: Document, action: String)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = orig.id.toString - val request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, s"/v1/document/$id/$action")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Document](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def start(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "start") - def submit(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "submit") - def restart(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "restart") - def flag(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "flag") - def resolve(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "resolve") - def unassign(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "unassign") - def archive(orig: Document)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "archive") - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestDocumentTypeService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestDocumentTypeService.scala deleted file mode 100644 index 6157cc3..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestDocumentTypeService.scala +++ /dev/null @@ -1,33 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.DocumentType -import xyz.driver.pdsuidomain.services.DocumentTypeService - -class RestDocumentTypeService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends DocumentTypeService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.document.documentTypeFormat - import xyz.driver.pdsuidomain.services.DocumentTypeService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, "/v1/document-type", sortingQuery(sorting))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[DocumentType]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount) - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilitySnapshotService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilitySnapshotService.scala deleted file mode 100644 index 2187ec2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilitySnapshotService.scala +++ /dev/null @@ -1,34 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import akka.http.scaladsl.model.{HttpMethods, HttpRequest, Uri} -import akka.stream.Materializer -import xyz.driver.core.rest.{AuthorizedServiceRequestContext, ServiceTransport} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.entities.eligibility.EligibleTrial -import xyz.driver.pdsuidomain.entities.{Patient, eligibility} -import xyz.driver.pdsuidomain.services.EligibilitySnapshotService - -import scala.concurrent.{ExecutionContext, Future} - -class RestEligibilitySnapshotService(transport: ServiceTransport, baseUrl: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) extends EligibilitySnapshotService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import spray.json.DefaultJsonProtocol._ - import xyz.driver.pdsuidomain.formats.json.eligibility._ - - override def eligibilitySnapshot(patientId: UuidId[Patient]) - (implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): - Future[Seq[eligibility.EligibleTrial]] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUrl, s"/v1/patient/$patientId/eligibilitySnapshot")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Seq[EligibleTrial]](response) - } yield { - reply - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala deleted file mode 100644 index e057c55..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala +++ /dev/null @@ -1,53 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import akka.http.scaladsl.model.Uri -import akka.stream.Materializer -import spray.json.DefaultJsonProtocol -import xyz.driver.core.Id -import xyz.driver.core.rest.{AuthorizedServiceRequestContext, RestService, ServiceTransport} -import xyz.driver.entities.patient -import xyz.driver.entities.patient.Patient -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuidomain.entities.eligibility.{MatchedPatient, MismatchRankedLabels} -import xyz.driver.pdsuidomain.entities.{EligibilityArm, eligibility} -import xyz.driver.pdsuidomain.services.EligibilityVerificationService - -import scala.concurrent.{ExecutionContext, Future} -import scalaz.ListT -import scalaz.Scalaz.futureInstance - -class RestEligibilityVerificationService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext -) extends EligibilityVerificationService with RestService { - - import DefaultJsonProtocol._ - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.eligibility._ - - override def getMatchedPatients()( - implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): ListT[Future, eligibility.MatchedPatient] = { - val request = get(baseUri, s"/v1/patients") - listResponse[MatchedPatient](transport.sendRequest(ctx)(request)) - } - - override def getMismatchRankedLabels(patientId: Id[Patient], - cancerType: patient.CancerType, - excludedArms: Seq[LongId[EligibilityArm]])( - implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): Future[eligibility.MismatchRankedLabels] = { - - val query = Seq("disease" -> cancerType.toString.toUpperCase) ++ (if (excludedArms.nonEmpty) { - Seq( - "ineligible_arms" -> excludedArms - .map(_.id) - .mkString(",")) - } else { - Seq.empty[(String, String)] - }) - - val request = get(baseUri, s"/v1/patients/$patientId/labels", query) - optionalResponse[MismatchRankedLabels](transport.sendRequest(ctx)(request)) - .getOrElse(throw new Exception(s"The data of patient $patientId is not ready yet")) - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestExtractedDataService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestExtractedDataService.scala deleted file mode 100644 index 24c5436..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestExtractedDataService.scala +++ /dev/null @@ -1,100 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.entities.export.patient.ExportPatientWithLabels -import xyz.driver.pdsuidomain.services.ExtractedDataService -import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.formats.json.export._ - -class RestExtractedDataService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends ExtractedDataService with RestHelper { - - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.extracteddata._ - import xyz.driver.pdsuidomain.services.ExtractedDataService._ - - def getById(id: LongId[ExtractedData])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/extracted-data/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[RichExtractedData](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, - endpointUri(baseUri, - "/v1/extracted-data", - filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[RichExtractedData]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount) - } - } - - def create(draftRichExtractedData: RichExtractedData)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] = { - for { - entity <- Marshal(draftRichExtractedData).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/extracted-data")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[RichExtractedData](response) - } yield { - CreateReply.Created(reply) - } - } - def update(origRichExtractedData: RichExtractedData, draftRichExtractedData: RichExtractedData)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = origRichExtractedData.extractedData.id - for { - entity <- Marshal(draftRichExtractedData).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/extracted-data/$id")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[RichExtractedData](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def delete(id: LongId[ExtractedData])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] = { - val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/export-data/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[HttpEntity](response) - } yield { - DeleteReply.Deleted - } - } - - def getPatientLabels(id: UuidId[Patient])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetPatientLabelsReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/patient/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ExportPatientWithLabels](response) - } yield { - GetPatientLabelsReply.Entity(reply) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHelper.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHelper.scala deleted file mode 100644 index 8ed2651..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHelper.scala +++ /dev/null @@ -1,107 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.model.{HttpResponse, ResponseEntity, StatusCodes, Uri} -import akka.http.scaladsl.unmarshalling.{Unmarshal, Unmarshaller} -import akka.stream.Materializer -import xyz.driver.core.rest.errors.{InvalidActionException, InvalidInputException, ResourceNotFoundException} -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterBinaryOperation, SearchFilterExpr, SearchFilterNAryOperation, Sorting, SortingOrder} -import xyz.driver.pdsuicommon.error._ - -trait RestHelper { - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import ErrorsResponse._ - - implicit protected val materializer: Materializer - implicit protected val exec: ExecutionContext - - protected def endpointUri(baseUri: Uri, path: String) = - baseUri.withPath(Uri.Path(path)) - - protected def endpointUri(baseUri: Uri, path: String, query: Seq[(String, String)]) = - baseUri.withPath(Uri.Path(path)).withQuery(Uri.Query(query: _*)) - - def sortingQuery(sorting: Option[Sorting]): Seq[(String, String)] = { - def dimensionQuery(dimension: Sorting.Dimension) = { - val ord = dimension.order match { - case SortingOrder.Ascending => "" - case SortingOrder.Descending => "-" - } - s"$ord${dimension.name}" - } - - sorting match { - case None => Seq.empty - case Some(dimension: Sorting.Dimension) => Seq("sort" -> dimensionQuery(dimension)) - case Some(Sorting.Sequential(dimensions)) => Seq("sort" -> dimensions.map(dimensionQuery).mkString(",")) - } - } - - def filterQuery(expr: SearchFilterExpr): Seq[(String, String)] = { - def opToString(op: SearchFilterBinaryOperation) = op match { - case SearchFilterBinaryOperation.Eq => "eq" - case SearchFilterBinaryOperation.NotEq => "ne" - case SearchFilterBinaryOperation.Like => "like" - case SearchFilterBinaryOperation.Gt => "gt" - case SearchFilterBinaryOperation.GtEq => "ge" - case SearchFilterBinaryOperation.Lt => "lt" - case SearchFilterBinaryOperation.LtEq => "le" - } - - def exprToQuery(expr: SearchFilterExpr): Seq[(String, String)] = expr match { - case SearchFilterExpr.Empty => Seq.empty - case SearchFilterExpr.Atom.Binary(dimension, op, value) => - Seq("filters" -> s"${dimension.tableName.fold("")(t => s"$t.") + dimension.name} ${opToString(op)} $value") - case SearchFilterExpr.Atom.NAry(dimension, SearchFilterNAryOperation.In, values) => - Seq("filters" -> s"${dimension.tableName.fold("")(t => s"$t.") + dimension.name} in ${values.mkString(",")}") - case SearchFilterExpr.Intersection(ops) => - ops.flatMap(op => exprToQuery(op)) - case expr => sys.error(s"No parser available for filter expression $expr.") - } - - exprToQuery(expr) - } - - def paginationQuery(pagination: Option[Pagination]): Seq[(String, String)] = pagination match { - case None => Seq.empty - case Some(pp) => - Seq( - "pageNumber" -> pp.pageNumber.toString, - "pageSize" -> pp.pageSize.toString - ) - } - - /** Utility method to parse responses from records-acquisition-server. - * - * Non-2xx HTTP error codes will be cause the returned future to fail with a corresponding - * `DomainException`. - * @tparam ApiReply The type of the serialized reply object, contained in the HTTP entity - * @param response The HTTP response to parse. - * @param unmarshaller An unmarshaller that converts a successful response to an api reply. - */ - def apiResponse[ApiReply](response: HttpResponse)( - implicit unmarshaller: Unmarshaller[ResponseEntity, ApiReply]): Future[ApiReply] = { - - def extractErrorMessage(response: HttpResponse): Future[String] = { - Unmarshal(response.entity) - .to[ErrorsResponse] - .transform( - response => response.errors.map(_.message).mkString(", "), - ex => InvalidInputException(s"Response has invalid format: ${ex.getMessage}") - ) - } - - if (response.status.isSuccess) { - Unmarshal(response.entity).to[ApiReply] - } else { - extractErrorMessage(response).flatMap { message => - Future.failed(response.status match { - case StatusCodes.Forbidden => InvalidActionException(message) - case StatusCodes.NotFound => ResourceNotFoundException(message) - case other => - InvalidInputException(s"Unhandled domain error for HTTP status ${other.value}. $message") - }) - } - } - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHypothesisService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHypothesisService.scala deleted file mode 100644 index 11adb8f..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHypothesisService.scala +++ /dev/null @@ -1,60 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import akka.http.scaladsl.marshalling.Marshal - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest._ -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain.UuidId -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.Hypothesis -import xyz.driver.pdsuidomain.services.HypothesisService - -class RestHypothesisService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends HypothesisService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.hypothesis._ - import xyz.driver.pdsuidomain.services.HypothesisService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, "/v1/hypothesis", sortingQuery(sorting))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[Hypothesis]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount) - } - } - - def create(draftHypothesis: Hypothesis)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] = { - for { - entity <- Marshal(draftHypothesis).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/hypothesis")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Hypothesis](response) - } yield { - CreateReply.Created(reply) - } - } - - def delete(id: UuidId[Hypothesis])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] = { - val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/hypothesis/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[HttpEntity](response) - } yield { - DeleteReply.Deleted - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionService.scala deleted file mode 100644 index c4add4a..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionService.scala +++ /dev/null @@ -1,88 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.InterventionService - -class RestInterventionService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends InterventionService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.intervention._ - import xyz.driver.pdsuidomain.services.InterventionService._ - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, - endpointUri(baseUri, - "/v1/intervention", - filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[InterventionWithArms]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount) - } - } - - def getById(id: LongId[Intervention])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/intervention/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[InterventionWithArms](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - def update(origIntervention: InterventionWithArms, draftIntervention: InterventionWithArms)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = origIntervention.intervention.id - for { - entity <- Marshal(draftIntervention).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/intervention/$id")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[InterventionWithArms](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def create(draftIntervention: InterventionWithArms)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] = { - for { - entity <- Marshal(draftIntervention).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/intervention")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[InterventionWithArms](response) - } yield { - CreateReply.Created(reply) - } - } - - def delete(id: LongId[Intervention])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[DeleteReply] = { - val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/intervention/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[HttpEntity](response) - } yield { - DeleteReply.Deleted - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionTypeService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionTypeService.scala deleted file mode 100644 index 825b936..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionTypeService.scala +++ /dev/null @@ -1,37 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest._ -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.InterventionType -import xyz.driver.pdsuidomain.services.InterventionTypeService - -class RestInterventionTypeService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends InterventionTypeService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.intervention.interventionTypeFormat - import xyz.driver.pdsuidomain.services.InterventionTypeService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, "/v1/intervention-type", sortingQuery(sorting))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[InterventionType]](response) - } yield { - { - val domain = reply.items - GetListReply.EntityList(domain.toList, reply.meta.itemsCount) - } - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestMedicalRecordService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestMedicalRecordService.scala deleted file mode 100644 index 6af6707..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestMedicalRecordService.scala +++ /dev/null @@ -1,129 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import akka.NotUsed -import akka.stream.scaladsl.Source -import akka.util.ByteString - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.MedicalRecordService - -class RestMedicalRecordService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends MedicalRecordService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.record._ - import xyz.driver.pdsuidomain.services.MedicalRecordService._ - - def getById(recordId: LongId[MedicalRecord])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/record/$recordId")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[MedicalRecord](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - def getPdfSource(recordId: LongId[MedicalRecord])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo] - ): Future[Source[ByteString, NotUsed]] = { - - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/record/$recordId/source")) - - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[HttpEntity](response) - } yield { - reply.dataBytes.mapMaterializedValue(_ => NotUsed) - } - } - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - - val request = HttpRequest( - HttpMethods.GET, - endpointUri(baseUri, "/v1/record", filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[MedicalRecord]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount, reply.meta.lastUpdate) - } - } - - def create(draftRecord: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[CreateReply] = { - for { - entity <- Marshal(draftRecord).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/record")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[MedicalRecord](response) - } yield { - CreateReply.Created(reply) - } - } - - def update(origRecord: MedicalRecord, draftRecord: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = origRecord.id.toString - for { - entity <- Marshal(draftRecord).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/record/$id")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[MedicalRecord](response) - } yield { - UpdateReply.Updated(reply) - } - } - - private def editAction(orig: MedicalRecord, action: String)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = orig.id.toString - val request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, s"/v1/record/$id/$action")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[MedicalRecord](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def start(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "start") - def submit(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "submit") - def restart(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "restart") - def flag(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "flag") - def resolve(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "resolve") - def unassign(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "unassign") - def archive(orig: MedicalRecord)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - editAction(orig, "archive") - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientCriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientCriterionService.scala deleted file mode 100644 index cc66142..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientCriterionService.scala +++ /dev/null @@ -1,81 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, _} -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.PatientCriterionService - -import scala.concurrent.{ExecutionContext, Future} - -class RestPatientCriterionService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends PatientCriterionService with RestHelper { - - import spray.json.DefaultJsonProtocol._ - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.patientcriterion._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - - def getAll(patientId: UuidId[Patient], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[RichPatientCriterion]] = { - val request = HttpRequest(HttpMethods.GET, - endpointUri(baseUri, - s"/v1/patient/$patientId/criterion", - filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(Some(pagination)))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[RichPatientCriterion]](response) - } yield { - reply - } - } - - def getById(patientId: UuidId[Patient], id: LongId[PatientCriterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[RichPatientCriterion]] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/patient/$patientId/criterion/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - entity <- apiResponse[RichPatientCriterion](response) - } yield { - Option(entity) - } - } - - def updateList(patientId: UuidId[Patient], draftEntities: List[DraftPatientCriterion])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Unit] = { - for { - entity <- Marshal(draftEntities).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/patient/$patientId/criterion")) - .withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[RichPatientCriterion](response) - } yield { - () - } - } - - def update(origEntity: PatientCriterion, draftEntity: PatientCriterion, patientId: UuidId[Patient])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[RichPatientCriterion] = { - for { - entity <- Marshal(draftEntity).to[RequestEntity] - request = HttpRequest( - HttpMethods.PATCH, - endpointUri(baseUri, s"/v1/patient/$patientId/criterion/${origEntity.criterionId}")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - entity <- apiResponse[RichPatientCriterion](response) - } yield { - entity - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientLabelService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientLabelService.scala deleted file mode 100644 index 932e123..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientLabelService.scala +++ /dev/null @@ -1,84 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.labels.Label -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, _} -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.PatientLabelService - -import scala.concurrent.{ExecutionContext, Future} - -class RestPatientLabelService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends PatientLabelService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.patientlabel._ - - def getAll(patientId: UuidId[Patient], - filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[RichPatientLabel]] = { - val request = HttpRequest(HttpMethods.GET, - endpointUri(baseUri, - s"/v1/patient/$patientId/label", - filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(Some(pagination)))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[RichPatientLabel]](response) - } yield { - reply - } - } - - def getDefiningCriteriaList(patientId: UuidId[Patient], - hypothesisId: UuidId[Hypothesis], - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo] - ): Future[ListResponse[PatientLabel]] = { - val request = HttpRequest(HttpMethods.GET, - endpointUri(baseUri, s"/patient/$patientId/hypothesis", paginationQuery(Some(pagination)))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[PatientLabel]](response) - } yield { - reply - } - } - - def getByLabelIdOfPatient(patientId: UuidId[Patient], labelId: LongId[Label])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[RichPatientLabel]] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/patient/$patientId/label/$labelId")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - entity <- apiResponse[RichPatientLabel](response) - } yield { - Option(entity) - } - } - - def update(origPatientLabel: PatientLabel, draftPatientLabel: PatientLabel)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[RichPatientLabel] = { - for { - entity <- Marshal(draftPatientLabel).to[RequestEntity] - request = HttpRequest( - HttpMethods.PATCH, - endpointUri(baseUri, s"/v1/patient/${origPatientLabel.patientId}/label/${origPatientLabel.labelId}")) - .withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - entity <- apiResponse[RichPatientLabel](response) - } yield { - entity - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientService.scala deleted file mode 100644 index 67f4e38..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientService.scala +++ /dev/null @@ -1,78 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db.{Pagination, _} -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.PatientService - -class RestPatientService(transport: ServiceTransport, baseUri: Uri)(implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends PatientService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.patient._ - - def getById(id: UuidId[Patient])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Option[Patient]] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/patient/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - entity <- apiResponse[Patient](response) - } yield { - Option(entity) - } - } - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Pagination = Pagination.Default)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[ListResponse[Patient]] = { - val request = HttpRequest( - HttpMethods.GET, - endpointUri(baseUri, "/v1/patient", filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(Some(pagination)))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[Patient]](response) - } yield { - reply - } - } - - private def editAction(orig: Patient, action: String)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] = { - val id = orig.id.toString - val request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, s"/v1/patient/$id/$action")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - entity <- apiResponse[Patient](response) - } yield { - entity - } - } - - def unassign(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] = - editAction(origPatient, "unassign") - def start(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] = - editAction(origPatient, "start") - def submit(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] = - editAction(origPatient, "submit") - def restart(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] = - editAction(origPatient, "restart") - def flag(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] = - editAction(origPatient, "flag") - def resolve(origPatient: Patient)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Patient] = - editAction(origPatient, "resolve") -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestProviderTypeService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestProviderTypeService.scala deleted file mode 100644 index ffde086..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestProviderTypeService.scala +++ /dev/null @@ -1,34 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.ProviderType -import xyz.driver.pdsuidomain.services.ProviderTypeService - -class RestProviderTypeService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends ProviderTypeService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.record.providerTypeFormat - import xyz.driver.pdsuidomain.services.ProviderTypeService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, "/v1/provider-type", sortingQuery(sorting))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[ProviderType]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestStudyDesignService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestStudyDesignService.scala deleted file mode 100644 index f8ce502..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestStudyDesignService.scala +++ /dev/null @@ -1,34 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest._ -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.StudyDesign -import xyz.driver.pdsuidomain.services.StudyDesignService - -class RestStudyDesignService(transport: ServiceTransport, baseUri: Uri)( - implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends StudyDesignService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.studydesign._ - import xyz.driver.pdsuidomain.services.StudyDesignService._ - - def getAll(sorting: Option[Sorting] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, "/v1/study-design", sortingQuery(sorting))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[StudyDesign]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount) - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialIssueService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialIssueService.scala deleted file mode 100644 index b14d35b..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialIssueService.scala +++ /dev/null @@ -1,103 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import spray.json.RootJsonReader -import xyz.driver.core.rest.{AuthorizedServiceRequestContext, ServiceTransport} -import xyz.driver.entities.users -import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} -import xyz.driver.pdsuicommon.domain.{LongId, StringId} -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.entities.{Trial, TrialIssue} -import xyz.driver.pdsuidomain.services.TrialIssueService - -import scala.concurrent.ExecutionContext - -class RestTrialIssueService(transport: ServiceTransport, baseUri: Uri) - (implicit - protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends TrialIssueService with RestHelper{ - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.trialissue._ - import xyz.driver.pdsuidomain.services.TrialIssueService._ - - override def create(draft: TrialIssue) - (implicit requestContext: AuthorizedServiceRequestContext[users.AuthUserInfo]) = { - val trialId = draft.trialId - - implicit val jsonReader: RootJsonReader[TrialIssue] = trialIssueReader(trialId) - - for { - entity <- Marshal(draft).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, s"/v1/trial/$trialId/issue")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[TrialIssue](response) - } yield { - CreateReply.Created(reply) - } - } - - override def getListByTrialId(trialId: StringId[Trial], - filter: SearchFilterExpr, - sorting: Option[Sorting], - pagination: Option[Pagination]) - (implicit requestContext: AuthorizedServiceRequestContext[users.AuthUserInfo]) = { - implicit val jsonReader: RootJsonReader[TrialIssue] = trialIssueReader(trialId) - - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/issue", - filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination)) - ) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[TrialIssue]](response) - } yield { - GetListByTrialIdReply.EntityList(reply.items, reply.meta.itemsCount, reply.meta.lastUpdate) - } - } - - override def getById(trialId: StringId[Trial], id: LongId[TrialIssue]) - (implicit requestContext: AuthorizedServiceRequestContext[users.AuthUserInfo]) = { - implicit val jsonReader: RootJsonReader[TrialIssue] = trialIssueReader(trialId) - - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/issue/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[TrialIssue](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - override def update(orig: TrialIssue, draft: TrialIssue) - (implicit requestContext: AuthorizedServiceRequestContext[users.AuthUserInfo]) = { - val trialId = draft.trialId - val id = orig.id.id - - implicit val jsonReader: RootJsonReader[TrialIssue] = trialIssueReader(trialId) - - for { - entity <- Marshal(draft).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/trial/$trialId/issue/$id")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[TrialIssue](response) - } yield { - UpdateReply.Updated(reply) - } - } - - override def delete(trialId: StringId[Trial], id: LongId[TrialIssue]) - (implicit requestContext: AuthorizedServiceRequestContext[users.AuthUserInfo]) = { - val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/trial/$trialId/issue/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - _ <- apiResponse[HttpEntity](response) - } yield { - DeleteReply.Deleted - } - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala deleted file mode 100644 index 94e1c63..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala +++ /dev/null @@ -1,173 +0,0 @@ -package xyz.driver.pdsuidomain.services.rest - -import scala.concurrent.{ExecutionContext, Future} -import akka.NotUsed -import akka.stream.scaladsl.Source -import akka.util.ByteString -import akka.http.scaladsl.marshalling.Marshal -import akka.http.scaladsl.model._ -import akka.stream.Materializer -import xyz.driver.core.rest.{Pagination => _, _} -import xyz.driver.pdsuicommon.db._ -import xyz.driver.pdsuicommon.domain._ -import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels -import xyz.driver.pdsuidomain.services.TrialService -import spray.json.DefaultJsonProtocol._ -import xyz.driver.entities.patient.CancerType -import xyz.driver.entities.users.AuthUserInfo -import xyz.driver.pdsuidomain.ListResponse -import xyz.driver.pdsuidomain.formats.json.export._ - -class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit protected val materializer: Materializer, - protected val exec: ExecutionContext) - extends TrialService with RestHelper { - - import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ - import xyz.driver.pdsuidomain.formats.json.listresponse._ - import xyz.driver.pdsuidomain.formats.json.trial._ - import xyz.driver.pdsuidomain.services.TrialService._ - - def getById(id: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$id")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Trial](response) - } yield { - GetByIdReply.Entity(reply) - } - } - - def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetTrialWithLabelsReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$cancerType/$trialId")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ExportTrialWithLabels](response) - } yield { - GetTrialWithLabelsReply.Entity(reply) - } - } - - def getTrialsWithLabels(cancerType: CancerType)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetTrialsWithLabelsReply] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$cancerType")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Seq[ExportTrialWithLabels]](response) - } yield { - GetTrialsWithLabelsReply.EntityList(reply) - } - } - - def getPdfSource(trialId: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo] - ): Future[Source[ByteString, NotUsed]] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/source")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[HttpEntity](response) - } yield { - reply.dataBytes.mapMaterializedValue(_ => NotUsed) - } - } - - def getHtmlSource(trialId: StringId[Trial])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo] - ): Future[Source[ByteString, NotUsed]] = { - val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/source.html")) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[HttpEntity](response) - } yield { - reply.dataBytes.mapMaterializedValue(_ => NotUsed) - } - } - - def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty, - sorting: Option[Sorting] = None, - pagination: Option[Pagination] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { - val request = HttpRequest( - HttpMethods.GET, - endpointUri(baseUri, "/v1/trial", filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[ListResponse[Trial]](response) - } yield { - GetListReply.EntityList(reply.items, reply.meta.itemsCount, reply.meta.lastUpdate) - } - } - - def update(origTrial: Trial, draftTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - val id = origTrial.id.id - for { - entity <- Marshal(draftTrial).to[RequestEntity] - request = HttpRequest(HttpMethods.PATCH, endpointUri(baseUri, s"/v1/trial/$id")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Trial](response) - } yield { - UpdateReply.Updated(reply) - } - } - - private def singleAction(origTrial: Trial, action: String, comment: Option[String] = None)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { - - val query = comment match { - case Some(s) => Seq("comment" -> s) - case None => Seq.empty[(String, String)] - } - - val id = origTrial.id.id - val request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, s"/v1/trial/$id/$action", query)) - for { - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Trial](response) - } yield { - UpdateReply.Updated(reply) - } - } - - def start(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - singleAction(origTrial, "start") - - def submit(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - singleAction(origTrial, "submit") - - def restart(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - singleAction(origTrial, "restart") - - def flag(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - singleAction(origTrial, "flag") - - def resolve(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - singleAction(origTrial, "resolve") - - def archive(origTrial: Trial, comment: Option[String])( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - singleAction(origTrial, "archive", comment) - - def unassign(origTrial: Trial)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = - singleAction(origTrial, "unassign") - - override def addTrial(trial: TrialCreationRequest)( - implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Trial] = { - for { - entity <- Marshal(trial).to[RequestEntity] - request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, s"/v1/trial/${trial.nctId}")).withEntity(entity) - response <- transport.sendRequestGetResponse(requestContext)(request) - reply <- apiResponse[Trial](response) - } yield { - reply - } - } -} |