diff options
Diffstat (limited to 'src/main/scala')
24 files changed, 220 insertions, 93 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala index eccb254..168eb38 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala @@ -419,6 +419,8 @@ object Document { providerTypeId <- Validators.nonEmpty("providerTypeId")(input.providerTypeId) + institutionName <- Validators.nonEmpty("institutionName")(input.institutionName) + meta <- Validators.nonEmpty("meta")(input.meta) startDate <- Validators.nonEmpty("startDate")(input.startDate) @@ -456,6 +458,7 @@ final case class Document(id: LongId[Document] = LongId(0L), 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], 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 index 1ac75ab..94eb029 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala @@ -68,6 +68,7 @@ object DocumentGen { providerName = nextOption(nextString()), providerTypeId = nextOption(nextLongId[ProviderType]), requiredType = nextOption(nextDocumentRequiredType()), + institutionName = nextOption(nextString()), meta = nextOption(nextDocumentMetaJson()), startDate = dates._1, endDate = dates._2, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala index 1869ff3..3f1ecfe 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocument.scala @@ -2,7 +2,6 @@ package xyz.driver.pdsuidomain.formats.json.document import java.time.{LocalDate, ZoneId, ZonedDateTime} import xyz.driver.pdsuicommon.domain.{LongId, StringId, TextJson} -import xyz.driver.pdsuicommon.json.JsonSerializer import xyz.driver.pdsuidomain.entities._ import play.api.data.validation.ValidationError @@ -20,6 +19,7 @@ final case class ApiDocument(id: Long, provider: Option[String], providerTypeId: Option[Long], requiredType: Option[String], + institutionName: Option[String], status: Option[String], previousStatus: Option[String], assignee: Option[String], @@ -46,6 +46,7 @@ final case class ApiDocument(id: Long, providerName = this.provider, providerTypeId = this.providerTypeId.map(LongId(_)), requiredType = this.requiredType.map(extractRequiredType), + institutionName = this.institutionName, meta = this.meta.map(x => TextJson(JsonSerializer.deserialize[Document.Meta](x))), startDate = this.startDate, endDate = this.endDate, @@ -74,6 +75,7 @@ object ApiDocument { (JsPath \ "provider").formatNullable[String] and (JsPath \ "providerTypeId").formatNullable[Long] and (JsPath \ "requiredType").formatNullable[String] and + (JsPath \ "institutionName").formatNullable[String] and (JsPath \ "status").formatNullable(statusFormat) and (JsPath \ "previousStatus").formatNullable(statusFormat) and (JsPath \ "assignee").formatNullable[String] and @@ -96,6 +98,7 @@ object ApiDocument { provider = document.providerName, providerTypeId = document.providerTypeId.map(_.id), requiredType = document.requiredType.map(Document.RequiredType.requiredTypeToString), + institutionName = document.institutionName, status = Option(Document.Status.statusToString(document.status)), previousStatus = document.previousStatus.map(Document.Status.statusToString), assignee = document.assignee.map(_.id), diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala index eae0c62..032ddf6 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala @@ -23,6 +23,7 @@ final case class ApiPartialDocument(recordId: Option[Long], endDate: Tristate[LocalDate], provider: Tristate[String], providerTypeId: Tristate[Long], + institutionName: Tristate[String], status: Option[String], assignee: Tristate[String], meta: Tristate[String]) { @@ -42,6 +43,7 @@ final case class ApiPartialDocument(recordId: Option[Long], providerName = provider.cata(Some(_), None, orig.providerName), providerTypeId = providerTypeId.map(LongId[ProviderType]).cata(Some(_), None, orig.providerTypeId), requiredType = orig.requiredType, + institutionName = institutionName.cata(Some(_), None, orig.institutionName), meta = meta.cata(x => Some(TextJson(JsonSerializer.deserialize[Meta](x))), None, orig.meta), startDate = startDate.cata(Some(_), None, orig.startDate), endDate = endDate.cata(Some(_), None, orig.endDate), @@ -67,6 +69,7 @@ final case class ApiPartialDocument(recordId: Option[Long], providerName = provider.toOption, providerTypeId = providerTypeId.map(LongId[ProviderType]).toOption, requiredType = None, + institutionName = institutionName.toOption, meta = meta.map(x => TextJson(JsonSerializer.deserialize[Meta](x))).toOption, previousStatus = None, assignee = None, @@ -90,6 +93,7 @@ object ApiPartialDocument { (JsPath \ "endDate").readTristate[LocalDate] and (JsPath \ "provider").readTristate[String] and (JsPath \ "providerTypeId").readTristate[Long] and + (JsPath \ "institutionName").readTristate[String] and (JsPath \ "status").readNullable[String]( Reads .of[String] @@ -115,6 +119,7 @@ object ApiPartialDocument { (JsPath \ "endDate").writeTristate[LocalDate] and (JsPath \ "provider").writeTristate[String] and (JsPath \ "providerTypeId").writeTristate[Long] and + (JsPath \ "institutionName").writeTristate[String] and (JsPath \ "status").writeNullable[String] and (JsPath \ "assignee").writeTristate[String] and (JsPath \ "meta").writeTristate(Writes[String](Json.parse)) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala new file mode 100644 index 0000000..2a670c4 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ListResponse.scala @@ -0,0 +1,39 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import java.time.LocalDateTime + +import spray.json.{RootJsonFormat, _} +import xyz.driver.pdsuicommon.db.Pagination +import xyz.driver.pdsuidomain.formats.json.sprayformats.common._ + +final case class ListResponse[+T](items: Seq[T], meta: ListResponse.Meta) + +object ListResponse extends DefaultJsonProtocol { + private val itemsField = "items" + private val metaField = "meta" + + final case class Meta(itemsCount: Int, pageNumber: Int, pageSize: Int, lastUpdate: Option[LocalDateTime]) + + object Meta { + def apply(itemsCount: Int, pagination: Pagination, lastUpdate: Option[LocalDateTime]): Meta = { + Meta( + itemsCount, + pagination.pageNumber, + pagination.pageSize, + lastUpdate + ) + } + } + + implicit val listResponseMetaFormat: RootJsonFormat[Meta] = jsonFormat4(Meta.apply) + + implicit def listResponseMetaWriter[T: JsonWriter]: RootJsonWriter[ListResponse[T]] = + new RootJsonWriter[ListResponse[T]] { + override def write(listResponse: ListResponse[T]): JsValue = { + JsObject( + itemsField -> listResponse.items.map(_.toJson).toJson, + metaField -> listResponse.meta.toJson + ) + } + } +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala index 7526d9c..a43e92a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala @@ -10,7 +10,7 @@ object criterion { import DefaultJsonProtocol._ import common._ - implicit val criterionLabelWriter = new JsonWriter[CriterionLabel] { + implicit val criterionLabelWriter = new RootJsonWriter[CriterionLabel] { override def write(obj: CriterionLabel) = JsObject( "labelId" -> obj.labelId.toJson, "categoryId" -> obj.categoryId.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala index e3f6a9c..6c33fe5 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala @@ -40,7 +40,7 @@ object document { .fromString(name) .getOrElse(deserializationError(s"Unknown document type: $name")) - case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json") + case _ => deserializationError(s"Expected Json Object as Document type, but got $json") } override def write(obj: DocumentType) = @@ -73,6 +73,11 @@ object document { .map(_.convertTo[Option[LongId[ProviderType]]]) .getOrElse(orig.providerTypeId) + val institutionName = fields + .get("institutionName") + .map(_.convertTo[Option[String]]) + .getOrElse(orig.institutionName) + val meta = fields .get("meta") .map(_.convertTo[Option[TextJson[Meta]]]) @@ -93,6 +98,7 @@ object document { typeId = typeId, providerName = provider, providerTypeId = providerTypeId, + institutionName = institutionName, meta = meta, startDate = startDate, endDate = endDate @@ -111,6 +117,7 @@ object document { "provider" -> document.providerName.toJson, "providerTypeId" -> document.providerTypeId.toJson, "requiredType" -> document.requiredType.toJson, + "institutionName" -> document.institutionName.toJson, "startDate" -> document.startDate.toJson, "endDate" -> document.endDate.toJson, "status" -> document.status.toJson, @@ -145,6 +152,10 @@ object document { .get("providerTypeId") .map(_.convertTo[LongId[ProviderType]]) + val institutionName = fields + .get("institutionName") + .map(_.convertTo[String]) + val meta = fields .get("meta") .map(_.convertTo[TextJson[Meta]]) @@ -168,6 +179,7 @@ object document { providerName = provider, providerTypeId = providerTypeId, requiredType = None, + institutionName = institutionName, meta = meta, previousStatus = None, assignee = None, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala index b836e1c..3c2465f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala @@ -21,7 +21,7 @@ object eligibility { implicit val clinicalDocumentFormat: RootJsonFormat[ClinicalEvidenceDocument] = jsonFormat7(ClinicalEvidenceDocument) implicit val evidenceDocumentFormat: RootJsonFormat[EvidenceDocument] = - GadtJsonFormat.create[EvidenceDocument]("documentType") { + GadtJsonFormat.create[EvidenceDocument]("evidenceDocumentType") { case _: MolecularEvidenceDocument => "Molecular" case _: ClinicalEvidenceDocument => "Clinical" } { diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala index 724c391..95c0674 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala @@ -26,7 +26,7 @@ object patient { } } - implicit val patientWriter: JsonWriter[Patient] = new JsonWriter[Patient] { + implicit val patientWriter: RootJsonWriter[Patient] = new RootJsonWriter[Patient] { override def write(patient: Patient): JsValue = JsObject( "id" -> patient.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala index b091746..affb346 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala @@ -1,10 +1,9 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ -import xyz.driver.entities.labels.Label -import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} +import xyz.driver.pdsuicommon.domain.FuzzyValue import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion +import xyz.driver.pdsuidomain.services.PatientCriterionService.{DraftPatientCriterion, RichPatientCriterion} object patientcriterion { import DefaultJsonProtocol._ @@ -38,30 +37,27 @@ object patientcriterion { override def read(json: JsValue) = json.convertTo[List[JsValue]].map(_.convertTo[DraftPatientCriterion]) } - implicit val patientCriterionWriter: JsonWriter[(PatientCriterion, LongId[Label], List[PatientCriterionArm])] = - new JsonWriter[(PatientCriterion, LongId[Label], List[PatientCriterionArm])] { - override def write(obj: (PatientCriterion, LongId[Label], List[PatientCriterionArm])): JsValue = { - val criterion = obj._1 - val labelId = obj._2 - val arms = obj._3 + implicit val patientCriterionWriter: RootJsonWriter[RichPatientCriterion] = + new RootJsonWriter[RichPatientCriterion] { + override def write(obj: RichPatientCriterion): JsValue = { JsObject( - "id" -> criterion.id.toJson, - "labelId" -> labelId.toJson, - "nctId" -> criterion.nctId.toJson, - "criterionId" -> criterion.criterionId.toJson, - "criterionText" -> criterion.criterionText.toJson, - "criterionValue" -> criterion.criterionValue.map { + "id" -> obj.patientCriterion.id.toJson, + "labelId" -> obj.labelId.toJson, + "nctId" -> obj.patientCriterion.nctId.toJson, + "criterionId" -> obj.patientCriterion.criterionId.toJson, + "criterionText" -> obj.patientCriterion.criterionText.toJson, + "criterionValue" -> obj.patientCriterion.criterionValue.map { case true => "Yes" case false => "No" }.toJson, - "criterionIsDefining" -> criterion.criterionIsDefining.toJson, - "criterionIsCompound" -> criterion.criterionValue.isEmpty.toJson, - "arms" -> arms.map(_.armName).toJson, - "eligibilityStatus" -> criterion.eligibilityStatus.toJson, - "verifiedEligibilityStatus" -> criterion.verifiedEligibilityStatus.toJson, - "isVerified" -> criterion.isVerified.toJson, - "isVisible" -> criterion.isVisible.toJson, - "lastUpdate" -> criterion.lastUpdate.toJson + "criterionIsDefining" -> obj.patientCriterion.criterionIsDefining.toJson, + "criterionIsCompound" -> obj.patientCriterion.criterionValue.isEmpty.toJson, + "arms" -> obj.armList.map(_.armName).toJson, + "eligibilityStatus" -> obj.patientCriterion.eligibilityStatus.toJson, + "verifiedEligibilityStatus" -> obj.patientCriterion.verifiedEligibilityStatus.toJson, + "isVerified" -> obj.patientCriterion.isVerified.toJson, + "isVisible" -> obj.patientCriterion.isVisible.toJson, + "lastUpdate" -> obj.patientCriterion.lastUpdate.toJson ) } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala index b97570a..0520ef2 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala @@ -7,7 +7,7 @@ object patientdefiningcriteria { import DefaultJsonProtocol._ import common._ - implicit val patientLabelDefiningCriteriaWriter: JsonWriter[PatientLabel] = new JsonWriter[PatientLabel] { + implicit val patientLabelDefiningCriteriaWriter: RootJsonWriter[PatientLabel] = new RootJsonWriter[PatientLabel] { override def write(obj: PatientLabel) = JsObject( "id" -> obj.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala index 894e453..041d9da 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala @@ -21,8 +21,8 @@ object patienteligibletrial { case _ => deserializationError(s"Expected Json Object as partial PatientTrialArmGroupView, but got $json") } - implicit val patientEligibleTrialWriter: JsonWriter[RichPatientEligibleTrial] = - new JsonWriter[RichPatientEligibleTrial] { + implicit val patientEligibleTrialWriter: RootJsonWriter[RichPatientEligibleTrial] = + new RootJsonWriter[RichPatientEligibleTrial] { override def write(obj: RichPatientEligibleTrial) = JsObject( "id" -> obj.group.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala index 4f2783c..b8c0058 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienthypothesis.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientHypothesisService.RichPatientHypothesis object patienthypothesis { import DefaultJsonProtocol._ @@ -18,18 +19,29 @@ object patienthypothesis { case _ => deserializationError(s"Expected Json Object as partial PatientHypothesis, but got $json") } - implicit val patientHypothesisWriter: JsonWriter[(PatientHypothesis, Boolean)] = - new JsonWriter[(PatientHypothesis, Boolean)] { - override def write(obj: (PatientHypothesis, Boolean)): JsValue = { - val patientHypothesis = obj._1 - val isRationaleRequired = obj._2 + implicit val richPatientHypothesisWriter: RootJsonWriter[RichPatientHypothesis] = + new RootJsonWriter[RichPatientHypothesis] { + override def write(obj: RichPatientHypothesis): JsValue = { JsObject( - "id" -> patientHypothesis.id.toJson, - "patientId" -> patientHypothesis.patientId.toJson, - "hypothesisId" -> patientHypothesis.hypothesisId.toJson, - "matchedTrials" -> patientHypothesis.matchedTrials.toJson, - "rationale" -> patientHypothesis.rationale.toJson, - "isRationaleRequired" -> isRationaleRequired.toJson + "id" -> obj.patientHypothesis.id.toJson, + "patientId" -> obj.patientHypothesis.patientId.toJson, + "hypothesisId" -> obj.patientHypothesis.hypothesisId.toJson, + "matchedTrials" -> obj.patientHypothesis.matchedTrials.toJson, + "rationale" -> obj.patientHypothesis.rationale.toJson, + "isRationaleRequired" -> obj.isRequired.toJson + ) + } + } + + implicit val patientHypothesisWriter: RootJsonWriter[PatientHypothesis] = + new RootJsonWriter[PatientHypothesis] { + override def write(obj: PatientHypothesis): JsValue = { + JsObject( + "id" -> obj.id.toJson, + "patientId" -> obj.patientId.toJson, + "hypothesisId" -> obj.hypothesisId.toJson, + "matchedTrials" -> obj.matchedTrials.toJson, + "rationale" -> obj.rationale.toJson ) } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala index 7d35bd1..d325a53 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientissue.scala @@ -40,7 +40,7 @@ object patientissue { } - implicit val patientIssueWriter = new JsonWriter[PatientIssue] { + implicit val patientIssueWriter = new RootJsonWriter[PatientIssue] { override def write(obj: PatientIssue) = JsObject( "id" -> obj.id.toJson, "text" -> obj.text.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala index 3b52833..b36949e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala @@ -3,6 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats import spray.json._ import xyz.driver.pdsuicommon.domain.FuzzyValue import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientLabelService.RichPatientLabel object patientlabel { import DefaultJsonProtocol._ @@ -28,25 +29,23 @@ object patientlabel { case _ => deserializationError(s"Expected Json Object as PatientLabel, but got $json") } - implicit val patientLabelWriter: JsonWriter[(PatientLabel, Boolean)] = new JsonWriter[(PatientLabel, Boolean)] { - override def write(obj: (PatientLabel, Boolean)): JsValue = { - val patientLabel = obj._1 - val isVerified = obj._2 + implicit val richPatientLabelWriter: RootJsonWriter[RichPatientLabel] = new RootJsonWriter[RichPatientLabel] { + override def write(obj: RichPatientLabel): JsValue = { JsObject( - "id" -> patientLabel.id.toJson, - "labelId" -> patientLabel.labelId.toJson, - "primaryValue" -> patientLabel.primaryValue.toJson, - "verifiedPrimaryValue" -> patientLabel.verifiedPrimaryValue.toJson, - "score" -> patientLabel.score.toJson, - "isImplicitMatch" -> patientLabel.isImplicitMatch.toJson, - "isVisible" -> patientLabel.isVisible.toJson, - "isVerified" -> isVerified.toJson + "id" -> obj.patientLabel.id.toJson, + "labelId" -> obj.patientLabel.labelId.toJson, + "primaryValue" -> obj.patientLabel.primaryValue.toJson, + "verifiedPrimaryValue" -> obj.patientLabel.verifiedPrimaryValue.toJson, + "score" -> obj.patientLabel.score.toJson, + "isImplicitMatch" -> obj.patientLabel.isImplicitMatch.toJson, + "isVisible" -> obj.patientLabel.isVisible.toJson, + "isVerified" -> obj.isVerified.toJson ) } } - implicit val patientLabelEvidenceWriter: JsonWriter[PatientLabelEvidenceView] = - new JsonWriter[PatientLabelEvidenceView] { + implicit val patientLabelEvidenceWriter: RootJsonWriter[PatientLabelEvidenceView] = + new RootJsonWriter[PatientLabelEvidenceView] { override def write(evidence: PatientLabelEvidenceView): JsValue = JsObject( "id" -> evidence.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala index a778000..aeec90f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala @@ -30,7 +30,7 @@ object trial { "Prostate" -> Condition.Prostate ) - implicit val trialWriter: JsonWriter[Trial] = new JsonWriter[Trial] { + implicit val trialWriter: RootJsonWriter[Trial] = new RootJsonWriter[Trial] { override def write(obj: Trial) = JsObject( "id" -> obj.id.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala index 572f44d..d1ca191 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trialissue.scala @@ -44,7 +44,7 @@ object trialissue { } - implicit val trialIssueWriter = new JsonWriter[TrialIssue] { + implicit val trialIssueWriter = new RootJsonWriter[TrialIssue] { override def write(obj: TrialIssue) = JsObject( "id" -> obj.id.toJson, "text" -> obj.text.toJson, diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala index 6d85f85..a07eed8 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala @@ -37,13 +37,21 @@ object PatientCriterionService { def userMessage: String = "Access denied" } + 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})" + } + } + sealed trait GetListReply object GetListReply { type Error = GetListReply with DomainError - final case class EntityList(xs: Seq[(PatientCriterion, LongId[Label], List[PatientCriterionArm])], - totalFound: Int, - lastUpdate: Option[LocalDateTime]) + final case class EntityList(xs: Seq[RichPatientCriterion], totalFound: Int, lastUpdate: Option[LocalDateTime]) extends GetListReply case object AuthorizationError @@ -60,8 +68,7 @@ object PatientCriterionService { object GetByIdReply { type Error = GetByIdReply with DomainError - final case class Entity(x: PatientCriterion, labelId: LongId[Label], armList: List[PatientCriterionArm]) - extends GetByIdReply + final case class Entity(x: RichPatientCriterion) extends GetByIdReply case object AuthorizationError extends GetByIdReply with DomainError.AuthorizationError with DefaultAccessDeniedError @@ -74,8 +81,8 @@ object PatientCriterionService { final case class CommonError(userMessage: String) extends GetByIdReply with DomainError implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x, labelId, armList) => phi"GetByIdReply.Entity(entity=$x, labelId=$labelId, armList=$armList)" + case x: DomainError => phi"GetByIdReply.Error($x)" + case Entity(x) => phi"GetByIdReply.Entity($x)" } } @@ -83,8 +90,7 @@ object PatientCriterionService { object UpdateReply { type Error = UpdateReply with DomainError - final case class Updated(x: PatientCriterion, labelId: LongId[Label], armList: List[PatientCriterionArm]) - extends UpdateReply + final case class Updated(x: RichPatientCriterion) extends UpdateReply case object UpdatedList extends UpdateReply diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala index abb3f8a..d9013c6 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala @@ -1,12 +1,12 @@ package xyz.driver.pdsuidomain.services -import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext 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.{Trial, _} +import xyz.driver.pdsuidomain.services.PatientCriterionService.RichPatientCriterion import scala.concurrent.Future @@ -71,8 +71,7 @@ object PatientEligibleTrialService { sealed trait GetCriterionListOfGroupReply object GetCriterionListOfGroupReply { - final case class EntityList(xs: Seq[(PatientCriterion, LongId[Label], List[PatientCriterionArm])], totalFound: Int) - extends GetCriterionListOfGroupReply + final case class EntityList(xs: Seq[RichPatientCriterion], totalFound: Int) extends GetCriterionListOfGroupReply type Error = GetCriterionListOfGroupReply with DomainError diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala index f782cab..07734ed 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientHypothesisService.scala @@ -23,9 +23,17 @@ object PatientHypothesisService { def userMessage: String = "Access denied" } + final case class RichPatientHypothesis(patientHypothesis: PatientHypothesis, isRequired: Boolean) + + object RichPatientHypothesis { + implicit def toPhiString(x: RichPatientHypothesis): PhiString = { + phi"RichPatientHypothesis(patientHypothesis=${x.patientHypothesis}, isRequired=${x.isRequired})" + } + } + sealed trait GetListReply object GetListReply { - final case class EntityList(xs: Seq[(PatientHypothesis, Boolean)], totalFound: Int) extends GetListReply + final case class EntityList(xs: Seq[RichPatientHypothesis], totalFound: Int) extends GetListReply case object AuthorizationError extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError @@ -38,7 +46,7 @@ object PatientHypothesisService { sealed trait GetByIdReply object GetByIdReply { - final case class Entity(x: PatientHypothesis, isRequired: Boolean) extends GetByIdReply + final case class Entity(x: RichPatientHypothesis) extends GetByIdReply type Error = GetByIdReply with DomainError @@ -53,8 +61,8 @@ object PatientHypothesisService { final case class CommonError(userMessage: String) extends GetByIdReply with DomainError implicit def toPhiString(reply: GetByIdReply): PhiString = reply match { - case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x, isRequired) => phi"GetByIdReply.Entity($x, $isRequired)" + case x: DomainError => phi"GetByIdReply.Error($x)" + case Entity(x) => phi"GetByIdReply.Entity($x)" } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala index 2a4d7fc..cede890 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala @@ -24,9 +24,17 @@ object PatientLabelService { def userMessage: String = "Access denied" } + final case class RichPatientLabel(patientLabel: PatientLabel, isVerified: Boolean) + + object RichPatientLabel { + implicit def toPhiString(x: RichPatientLabel): PhiString = { + phi"RichPatientLabel(patientLabel=${x.patientLabel}, isVerified=${x.isVerified})" + } + } + sealed trait GetListReply object GetListReply { - final case class EntityList(xs: Seq[(PatientLabel, Boolean)], totalFound: Int) extends GetListReply + final case class EntityList(xs: Seq[RichPatientLabel], totalFound: Int) extends GetListReply case object AuthorizationError extends GetListReply with DomainError.AuthorizationError with DefaultAccessDeniedError @@ -52,7 +60,7 @@ object PatientLabelService { sealed trait GetByLabelIdReply object GetByLabelIdReply { - final case class Entity(x: PatientLabel, isVerified: Boolean) extends GetByLabelIdReply + final case class Entity(x: RichPatientLabel) extends GetByLabelIdReply type Error = GetByLabelIdReply with DomainError @@ -68,7 +76,7 @@ object PatientLabelService { implicit def toPhiString(reply: GetByLabelIdReply): PhiString = reply match { case x: DomainError => phi"GetByIdReply.Error($x)" - case Entity(x, y) => phi"GetByIdReply.Entity($x, $y)" + case Entity(x) => phi"GetByIdReply.Entity($x)" } } @@ -76,7 +84,7 @@ object PatientLabelService { object UpdateReply { type Error = UpdateReply with DomainError - final case class Updated(updated: PatientLabel, isVerified: Boolean) extends UpdateReply + final case class Updated(updated: RichPatientLabel) extends UpdateReply case object NotFoundError extends UpdateReply with DefaultNotFoundError with DomainError.NotFoundError @@ -89,8 +97,8 @@ object PatientLabelService { final case class CommonError(userMessage: String) extends UpdateReply with DomainError implicit def toPhiString(reply: UpdateReply): PhiString = reply match { - case Updated(x, y) => phi"Updated($x, $y)" - case x: Error => DomainError.toPhiString(x) + case Updated(x) => phi"Updated($x)" + case x: Error => DomainError.toPhiString(x) } } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala index 5bd99a8..c6ab2d2 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala @@ -68,6 +68,20 @@ object TrialService { 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 @@ -97,6 +111,9 @@ trait TrialService { def getTrialWithLabels(trialId: StringId[Trial], condition: String)( implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] + def getTrialsWithLabels(condition: String)( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] + def getPdfSource(trialId: StringId[Trial])( implicit requestContext: AuthenticatedRequestContext): Future[Source[ByteString, NotUsed]] diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala index 9253f88..59f300b 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala @@ -57,19 +57,27 @@ class FakeTrialService extends TrialService { Future.successful(GetListReply.EntityList(Seq(trial), 1, None)) override def getTrialWithLabels(trialId: StringId[Trial], condition: String)( - implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] = { - Future.successful( - GetTrialWithLabelsReply.Entity(ExportTrialWithLabels( - StringId[Trial]("NCT" + generators.nextInt(999999).toString), - UuidId[Trial](generators.nextUuid()), - generators.oneOf("adenocarcinoma", "breast", "prostate"), - LocalDateTime.now(), - labelVersion = 1L, - generators.listOf(new ExportTrialArm( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] = + Future.successful(GetTrialWithLabelsReply.Entity(nextExportTrialWithLabels())) + + override def getTrialsWithLabels(condition: String)( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] = + Future.successful(GetTrialsWithLabelsReply.EntityList(generators.seqOf(nextExportTrialWithLabels()))) + + private def nextExportTrialWithLabels() = + ExportTrialWithLabels( + StringId[Trial]("NCT" + generators.nextInt(999999).toString), + UuidId[Trial](generators.nextUuid()), + generators.oneOf("adenocarcinoma", "breast", "prostate"), + LocalDateTime.now(), + labelVersion = 1L, + generators.listOf( + new ExportTrialArm( LongId[Arm](generators.nextInt(999999).toLong), generators.nextName().value )), - generators.listOf(new ExportTrialLabelCriterion( + generators.listOf( + new ExportTrialLabelCriterion( LongId[Criterion](generators.nextInt(999999).toLong), generators.nextOption(generators.nextBoolean()), LongId[Label](generators.nextInt(999999).toLong), @@ -78,8 +86,7 @@ class FakeTrialService extends TrialService { generators.nextBoolean(), generators.nextBoolean() )) - ))) - } + ) def update(origTrial: Trial, draftTrial: Trial)( implicit requestContext: AuthenticatedRequestContext): Future[UpdateReply] = diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala index 7e33919..42f32fc 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala @@ -16,6 +16,7 @@ import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels import xyz.driver.pdsuidomain.formats.json.ListResponse import xyz.driver.pdsuidomain.formats.json.trial.ApiTrial import xyz.driver.pdsuidomain.services.TrialService +import spray.json.DefaultJsonProtocol._ import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ import xyz.driver.pdsuidomain.formats.json.sprayformats.export._ @@ -47,6 +48,17 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote } } + def getTrialsWithLabels(disease: String)( + implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] = { + val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$disease")) + for { + response <- transport.sendRequestGetResponse(requestContext)(request) + reply <- apiResponse[Seq[ExportTrialWithLabels]](response) + } yield { + GetTrialsWithLabelsReply.EntityList(reply) + } + } + def getPdfSource(trialId: StringId[Trial])( implicit requestContext: AuthenticatedRequestContext): Future[Source[ByteString, NotUsed]] = { val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/source")) |