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authorAleksandr <ognelisar@gmail.com>2017-10-12 10:44:54 +0700
committerAleksandr <ognelisar@gmail.com>2017-10-12 10:44:54 +0700
commitf525ab2604cc5d1366c852bdbcb4d912bbcea800 (patch)
tree4fe4b35e1f474e2dc85a8885dc4c9002f3ea46c2 /src/main/scala/xyz/driver/pdsuidomain/formats/json
parent9198729ebf3d20b650b4467daa0d484a3148f01c (diff)
parente15415d69ec990d5243e58704e232e619b80aa6f (diff)
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All merge conflicts are resolved
Diffstat (limited to 'src/main/scala/xyz/driver/pdsuidomain/formats/json')
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala4
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala2
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala4
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala57
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala33
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala23
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala3
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala12
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiPartialSlotArm.scala14
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotArm.scala35
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotCreateArm.scala20
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala6
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibilityarm.scala44
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala19
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala4
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala6
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/slotarm.scala44
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala4
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala11
19 files changed, 303 insertions, 42 deletions
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala
index 43b5494..239adb1 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala
@@ -4,7 +4,7 @@ import xyz.driver.pdsuicommon.json.Serialization.seqJsonFormat
import play.api.libs.functional.syntax._
import play.api.libs.json._
import xyz.driver.pdsuicommon.domain.{LongId, StringId}
-import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial}
+import xyz.driver.pdsuidomain.entities.{EligibilityArm, Criterion, Trial}
import xyz.driver.pdsuidomain.formats.json.label.ApiCriterionLabel
import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion
@@ -26,7 +26,7 @@ final case class ApiCriterion(id: Long,
meta.getOrElse(""),
inclusion
),
- armIds = arms.map(LongId[Arm]),
+ armIds = arms.map(LongId[EligibilityArm]),
labels = labels.map(_.toDomain(LongId[Criterion](id)))
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala
index d72a9b4..4b85f83 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala
@@ -25,7 +25,7 @@ final case class ApiNewCriterion(meta: Option[String],
text = text,
inclusion = inclusion
),
- armIds = arms.getOrElse(Seq.empty).map(LongId[Arm]),
+ armIds = arms.getOrElse(Seq.empty).map(LongId[EligibilityArm]),
labels = labels.map(_.toDomain(LongId(Long.MaxValue))) // A developer should specify right criterionId himself
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala
index 77989f0..a700309 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala
@@ -2,7 +2,7 @@ package xyz.driver.pdsuidomain.formats.json.criterion
import xyz.driver.pdsuicommon.domain.LongId
import xyz.driver.pdsuicommon.json.Serialization.seqJsonFormat
-import xyz.driver.pdsuidomain.entities.{Arm, Criterion}
+import xyz.driver.pdsuidomain.entities.{EligibilityArm, Criterion}
import org.davidbild.tristate._
import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath
import play.api.libs.functional.syntax._
@@ -19,7 +19,7 @@ final case class ApiUpdateCriterion(meta: Tristate[String],
def applyTo(orig: RichCriterion): RichCriterion = RichCriterion(
criterion = applyTo(orig.criterion),
- armIds = arms.cata(_.map(LongId[Arm]), Seq.empty, orig.armIds),
+ armIds = arms.cata(_.map(LongId[EligibilityArm]), Seq.empty, orig.armIds),
labels = labels.cata(_.map(_.toDomain(orig.criterion.id)), Seq.empty, orig.labels)
)
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala
new file mode 100644
index 0000000..71423e8
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityArm.scala
@@ -0,0 +1,57 @@
+package xyz.driver.pdsuidomain.formats.json.eligibilityarm
+
+import play.api.libs.functional.syntax._
+import play.api.libs.json._
+import xyz.driver.entities.patient.CancerType
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
+import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases}
+
+final case class ApiEligibilityArm(id: Long,
+ name: String,
+ originalName: String,
+ trialId: String,
+ diseases: Seq[String]) {
+
+ def toDomain: EligibilityArmWithDiseases = {
+ val eligibilityArm = EligibilityArm(
+ id = LongId(this.id),
+ name = this.name,
+ originalName = this.originalName,
+ trialId = StringId(this.trialId),
+ deleted = None // if we have an ApiEligibilityArm object, the EligibilityArm itself has not been deleted
+ )
+
+ EligibilityArmWithDiseases(
+ eligibilityArm,
+ this.diseases.map { disease =>
+ val condition = CancerType
+ .fromString(disease)
+ .getOrElse(throw new NoSuchElementException(s"unknown condition $disease"))
+ EligibilityArmDisease(eligibilityArm.id, condition)
+ }
+ )
+ }
+}
+
+object ApiEligibilityArm {
+
+ implicit val format: Format[ApiEligibilityArm] = (
+ (JsPath \ "id").format[Long] and
+ (JsPath \ "name").format[String] and
+ (JsPath \ "originalName").format[String] and
+ (JsPath \ "trialId").format[String] and
+ (JsPath \ "diseases").format[Seq[String]]
+ )(ApiEligibilityArm.apply, unlift(ApiEligibilityArm.unapply))
+
+ def fromDomain(eligibilityArmWithDiseases: EligibilityArmWithDiseases): ApiEligibilityArm = {
+ import eligibilityArmWithDiseases.{eligibilityArm, eligibilityArmDiseases}
+
+ ApiEligibilityArm(
+ id = eligibilityArm.id.id,
+ name = eligibilityArm.name,
+ originalName = eligibilityArm.originalName,
+ trialId = eligibilityArm.trialId.id,
+ diseases = eligibilityArmDiseases.map(_.disease.toString)
+ )
+ }
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala
new file mode 100644
index 0000000..087fed5
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiEligibilityCreateArm.scala
@@ -0,0 +1,33 @@
+package xyz.driver.pdsuidomain.formats.json.eligibilityarm
+
+import play.api.libs.json.{Format, Json}
+import xyz.driver.entities.patient.CancerType
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
+import xyz.driver.pdsuidomain.entities.{EligibilityArm, EligibilityArmDisease, EligibilityArmWithDiseases}
+
+final case class ApiCreateEligibilityArm(name: String, trialId: String, diseases: Seq[String]) {
+
+ def toDomain: EligibilityArmWithDiseases = {
+ val eligibilityArm = EligibilityArm(
+ id = LongId(0),
+ name = name,
+ trialId = StringId(trialId),
+ originalName = name
+ )
+
+ EligibilityArmWithDiseases(
+ eligibilityArm,
+ diseases.map { disease =>
+ val condition = CancerType
+ .fromString(disease)
+ .getOrElse(throw new NoSuchElementException(s"unknown condition $disease"))
+ EligibilityArmDisease(eligibilityArm.id, condition)
+ }
+ )
+ }
+}
+
+object ApiCreateEligibilityArm {
+
+ implicit val format: Format[ApiCreateEligibilityArm] = Json.format[ApiCreateEligibilityArm]
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala
new file mode 100644
index 0000000..aca22ef
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/eligibilityarm/ApiPartialEligibilityArm.scala
@@ -0,0 +1,23 @@
+package xyz.driver.pdsuidomain.formats.json.eligibilityarm
+
+import play.api.libs.json.{Format, Json}
+import xyz.driver.entities.patient.CancerType
+import xyz.driver.pdsuidomain.entities.{EligibilityArmDisease, EligibilityArmWithDiseases}
+
+final case class ApiPartialEligibilityArm(name: String, diseases: Seq[String]) {
+
+ def applyTo(armWithDisease: EligibilityArmWithDiseases): EligibilityArmWithDiseases = {
+ val arm = armWithDisease.eligibilityArm.copy(name = name)
+ val armDiseases = diseases.map { disease =>
+ EligibilityArmDisease(
+ armWithDisease.eligibilityArm.id,
+ CancerType.fromString(disease).getOrElse(throw new NoSuchElementException(s"unknown condition $disease")))
+ }
+ EligibilityArmWithDiseases(arm, armDiseases)
+ }
+}
+
+object ApiPartialEligibilityArm {
+
+ implicit val format: Format[ApiPartialEligibilityArm] = Json.format
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala
index 1f8c683..fd14f7c 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiCreateRecord.scala
@@ -22,7 +22,8 @@ final case class ApiCreateRecord(disease: String, patientId: String, requestId:
caseId = None,
physician = None,
meta = None,
- lastUpdate = LocalDateTime.now()
+ lastUpdate = LocalDateTime.now(),
+ totalPages = 0
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala
index fc0a2e7..00441a1 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record/ApiRecord.scala
@@ -41,7 +41,8 @@ object ApiRecord {
(JsPath \ "requestId").format[UUID] and
(JsPath \ "meta").format(Format(Reads { x =>
JsSuccess(Json.stringify(x))
- }, Writes[String](Json.parse)))
+ }, Writes[String](Json.parse))) and
+ (JsPath \ "totalPages").format[Int]
)(ApiRecord.apply, unlift(ApiRecord.unapply))
def fromDomain(record: MedicalRecord) = ApiRecord(
@@ -57,7 +58,8 @@ object ApiRecord {
previousAssignee = record.previousAssignee.map(_.id),
lastActiveUser = record.lastActiveUserId.map(_.id),
requestId = record.requestId.id,
- meta = record.meta.map(x => JsonSerializer.serialize(x.content)).getOrElse(emptyMeta)
+ meta = record.meta.map(x => JsonSerializer.serialize(x.content)).getOrElse(emptyMeta),
+ totalPages = record.totalPages
)
}
@@ -73,7 +75,8 @@ final case class ApiRecord(id: Long,
previousAssignee: Option[String],
lastActiveUser: Option[String],
requestId: UUID,
- meta: String) {
+ meta: String,
+ totalPages: Int) {
private def extractStatus(status: String): Status =
Status
@@ -101,6 +104,7 @@ final case class ApiRecord(id: Long,
Some(TextJson(JsonSerializer.deserialize[List[MedicalRecord.Meta]](this.meta)))
}
},
- lastUpdate = this.lastUpdate.toLocalDateTime()
+ lastUpdate = this.lastUpdate.toLocalDateTime,
+ totalPages = 0
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiPartialSlotArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiPartialSlotArm.scala
new file mode 100644
index 0000000..2f8e93f
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiPartialSlotArm.scala
@@ -0,0 +1,14 @@
+package xyz.driver.pdsuidomain.formats.json.slotarm
+
+import xyz.driver.pdsuidomain.entities.SlotArm
+import play.api.libs.json.{Format, Json}
+
+final case class ApiPartialSlotArm(name: String) {
+
+ def applyTo(arm: SlotArm): SlotArm = arm.copy(name = name)
+}
+
+object ApiPartialSlotArm {
+
+ implicit val format: Format[ApiPartialSlotArm] = Json.format
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotArm.scala
new file mode 100644
index 0000000..375c1a2
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotArm.scala
@@ -0,0 +1,35 @@
+package xyz.driver.pdsuidomain.formats.json.slotarm
+
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
+import xyz.driver.pdsuidomain.entities.SlotArm
+import play.api.libs.functional.syntax._
+import play.api.libs.json._
+
+final case class ApiSlotArm(id: Long, name: String, originalName: String, trialId: String) {
+
+ def toDomain: SlotArm = SlotArm(
+ id = LongId(this.id),
+ name = this.name,
+ originalName = this.originalName,
+ trialId = StringId(this.trialId),
+ deleted = None // if we have an ApiSlotArm object, the SlotArm itself has not been deleted
+ )
+
+}
+
+object ApiSlotArm {
+
+ implicit val format: Format[ApiSlotArm] = (
+ (JsPath \ "id").format[Long] and
+ (JsPath \ "name").format[String] and
+ (JsPath \ "originalName").format[String] and
+ (JsPath \ "trialId").format[String]
+ )(ApiSlotArm.apply, unlift(ApiSlotArm.unapply))
+
+ def fromDomain(arm: SlotArm): ApiSlotArm = ApiSlotArm(
+ id = arm.id.id,
+ name = arm.name,
+ originalName = arm.originalName,
+ trialId = arm.trialId.id
+ )
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotCreateArm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotCreateArm.scala
new file mode 100644
index 0000000..3e52c13
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/slotarm/ApiSlotCreateArm.scala
@@ -0,0 +1,20 @@
+package xyz.driver.pdsuidomain.formats.json.slotarm
+
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
+import xyz.driver.pdsuidomain.entities.SlotArm
+import play.api.libs.json.{Format, Json}
+
+final case class ApiCreateSlotArm(name: String, trialId: String) {
+
+ def toDomain = SlotArm(
+ id = LongId(0),
+ name = name,
+ trialId = StringId(trialId),
+ originalName = name
+ )
+}
+
+object ApiCreateSlotArm {
+
+ implicit val format: Format[ApiCreateSlotArm] = Json.format[ApiCreateSlotArm]
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala
index 89c843f..a43e92a 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/criterion.scala
@@ -80,7 +80,7 @@ object criterion {
val arms = fields
.get("arms")
- .map(_.convertTo[Option[List[LongId[Arm]]]].getOrElse(List.empty[LongId[Arm]]))
+ .map(_.convertTo[Option[List[LongId[EligibilityArm]]]].getOrElse(List.empty[LongId[EligibilityArm]]))
.getOrElse(orig.armIds)
val labels = fields
@@ -143,8 +143,8 @@ object criterion {
val arms = fields
.get("arms")
- .map(_.convertTo[List[LongId[Arm]]])
- .getOrElse(List.empty[LongId[Arm]])
+ .map(_.convertTo[List[LongId[EligibilityArm]]])
+ .getOrElse(List.empty[LongId[EligibilityArm]])
val labels = fields
.get("labels")
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibilityarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibilityarm.scala
new file mode 100644
index 0000000..acb790a
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibilityarm.scala
@@ -0,0 +1,44 @@
+package xyz.driver.pdsuidomain.formats.json.sprayformats
+
+import spray.json._
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
+import xyz.driver.pdsuidomain.entities.{EligibilityArm, Trial}
+
+object eligibilityarm {
+ import DefaultJsonProtocol._
+ import common._
+
+ def applyUpdateToArm(json: JsValue, orig: EligibilityArm): EligibilityArm = json match {
+ case JsObject(fields) =>
+ val name = fields
+ .get("name")
+ .map(_.convertTo[String])
+ .getOrElse(deserializationError(s"Arm json object does not contain `name` field: $json"))
+ orig.copy(name = name)
+
+ case _ => deserializationError(s"Expected Json Object as partial Arm, but got $json")
+ }
+
+ def eligibilityArmFormat: RootJsonFormat[EligibilityArm] = new RootJsonFormat[EligibilityArm] {
+ override def write(obj: EligibilityArm): JsValue =
+ JsObject(
+ "id" -> obj.id.toJson,
+ "name" -> obj.name.toJson,
+ "originalName" -> obj.originalName.toJson,
+ "trialId" -> obj.trialId.toJson
+ )
+
+ override def read(json: JsValue): EligibilityArm = json.asJsObject.getFields("trialId", "name") match {
+ case Seq(trialId, name) =>
+ EligibilityArm(
+ id = LongId(0),
+ name = name.convertTo[String],
+ trialId = trialId.convertTo[StringId[Trial]],
+ originalName = name.convertTo[String]
+ )
+
+ case _ => deserializationError(s"Expected Json Object as Arm, but got $json")
+ }
+ }
+
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala
index 85d614d..4391453 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala
@@ -2,16 +2,16 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
import spray.json._
import xyz.driver.entities.labels.Label
-import xyz.driver.pdsuidomain.entities.{Arm, Criterion}
+import xyz.driver.formats.json.labels._
import xyz.driver.pdsuidomain.entities.export.patient._
import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels}
-import xyz.driver.formats.json.labels._
+import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm}
object export {
import DefaultJsonProtocol._
import common._
- import record._
import document._
+ import record._
implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] =
jsonFormat5(ExportPatientLabelEvidenceDocument.apply)
@@ -25,7 +25,7 @@ object export {
implicit val patientWithLabelsFormat: RootJsonFormat[ExportPatientWithLabels] =
jsonFormat(ExportPatientWithLabels.apply, "patientId", "labelVersion", "labels")
- implicit val trialArmFormat: RootJsonFormat[ExportTrialArm] = jsonFormat2(ExportTrialArm.apply)
+ implicit val trialArmFormat: RootJsonFormat[ExportTrialArm] = jsonFormat3(ExportTrialArm.apply)
implicit val trialLabelCriterionFormat: RootJsonFormat[ExportTrialLabelCriterion] =
new RootJsonFormat[ExportTrialLabelCriterion] {
@@ -68,7 +68,7 @@ object export {
longIdFormat[Criterion].read(criterionId),
value,
longIdFormat[Label].read(labelId),
- armIdsVector.map(longIdFormat[Arm].read).toSet,
+ armIdsVector.map(longIdFormat[EligibilityArm].read).toSet,
criterionText,
isCompound,
isDefining
@@ -82,12 +82,5 @@ object export {
}
implicit val trialWithLabelsFormat: RootJsonFormat[ExportTrialWithLabels] =
- jsonFormat(ExportTrialWithLabels.apply,
- "nctId",
- "trialId",
- "disease",
- "lastReviewed",
- "labelVersion",
- "arms",
- "criteria")
+ jsonFormat(ExportTrialWithLabels.apply, "nctId", "trialId", "lastReviewed", "labelVersion", "arms", "criteria")
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala
index 62cb9fa..2ced434 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/intervention.scala
@@ -56,7 +56,7 @@ object intervention {
val arms = fields
.get("arms")
- .map(_.convertTo[List[LongId[Arm]]].map(x => InterventionArm(armId = x, interventionId = LongId(0))))
+ .map(_.convertTo[List[LongId[SlotArm]]].map(x => InterventionArm(armId = x, interventionId = LongId(0))))
.getOrElse(List.empty[InterventionArm])
InterventionWithArms(
@@ -104,7 +104,7 @@ object intervention {
val origIntervention = orig.intervention
val arms = fields
.get("arms")
- .map(_.convertTo[List[LongId[Arm]]].map(x => InterventionArm(x, orig.intervention.id)))
+ .map(_.convertTo[List[LongId[SlotArm]]].map(x => InterventionArm(x, orig.intervention.id)))
orig.copy(
intervention = origIntervention.copy(
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala
index 65687c1..e8c0b94 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala
@@ -172,7 +172,8 @@ object record {
"requestId" -> record.requestId.toJson,
"meta" -> record.meta.getOrElse(TextJson[List[Meta]](List.empty)).toJson,
"lastActiveUser" -> record.lastActiveUserId.toJson,
- "lastUpdate" -> record.lastUpdate.toJson
+ "lastUpdate" -> record.lastUpdate.toJson,
+ "totalPages" -> record.totalPages.toJson
)
override def read(json: JsValue): MedicalRecord = json match {
@@ -205,7 +206,8 @@ object record {
caseId = None,
physician = None,
meta = None,
- lastUpdate = LocalDateTime.now()
+ lastUpdate = LocalDateTime.now(),
+ totalPages = 0
)
case _ => deserializationError(s"Expected Json Object as MedicalRecord, but got $json")
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/slotarm.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/slotarm.scala
new file mode 100644
index 0000000..192bd6a
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/slotarm.scala
@@ -0,0 +1,44 @@
+package xyz.driver.pdsuidomain.formats.json.sprayformats
+
+import spray.json._
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
+import xyz.driver.pdsuidomain.entities.{SlotArm, Trial}
+
+object slotarm {
+ import DefaultJsonProtocol._
+ import common._
+
+ def applyUpdateToArm(json: JsValue, orig: SlotArm): SlotArm = json match {
+ case JsObject(fields) =>
+ val name = fields
+ .get("name")
+ .map(_.convertTo[String])
+ .getOrElse(deserializationError(s"Arm json object does not contain `name` field: $json"))
+ orig.copy(name = name)
+
+ case _ => deserializationError(s"Expected Json Object as partial Arm, but got $json")
+ }
+
+ def slotArmFormat: RootJsonFormat[SlotArm] = new RootJsonFormat[SlotArm] {
+ override def write(obj: SlotArm): JsValue =
+ JsObject(
+ "id" -> obj.id.toJson,
+ "name" -> obj.name.toJson,
+ "originalName" -> obj.originalName.toJson,
+ "trialId" -> obj.trialId.toJson
+ )
+
+ override def read(json: JsValue): SlotArm = json.asJsObject.getFields("trialId", "name") match {
+ case Seq(trialId, name) =>
+ SlotArm(
+ id = LongId(0),
+ name = name.convertTo[String],
+ trialId = trialId.convertTo[StringId[Trial]],
+ originalName = name.convertTo[String]
+ )
+
+ case _ => deserializationError(s"Expected Json Object as Arm, but got $json")
+ }
+ }
+
+}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala
index d851c2c..b25ed1d 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala
@@ -6,12 +6,11 @@ import spray.json._
import xyz.driver.core.json.EnumJsonFormat
import xyz.driver.pdsuicommon.domain.{LongId, UuidId}
import xyz.driver.pdsuidomain.entities._
-import xyz.driver.formats.json.patient._
object trial {
import DefaultJsonProtocol._
- import common._
import Trial._
+ import common._
implicit val trialStatusFormat = new EnumJsonFormat[Status](
"New" -> Status.New,
@@ -36,7 +35,6 @@ object trial {
"previousStatus" -> obj.previousStatus.toJson,
"previousAssignee" -> obj.previousAssignee.toJson,
"lastActiveUser" -> obj.lastActiveUserId.toJson,
- "disease" -> obj.disease.toJson,
"phase" -> obj.phase.toJson,
"hypothesisId" -> obj.hypothesisId.toJson,
"studyDesignId" -> obj.studyDesignId.toJson,
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala
index a2a1ca9..133a2c8 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala
@@ -3,11 +3,10 @@ package xyz.driver.pdsuidomain.formats.json.trial
import java.time.{ZoneId, ZonedDateTime}
import java.util.UUID
-import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
-import xyz.driver.pdsuidomain.entities.Trial
import play.api.libs.functional.syntax._
import play.api.libs.json._
-import xyz.driver.entities.patient.CancerType
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
+import xyz.driver.pdsuidomain.entities.Trial
final case class ApiTrial(id: String,
externalId: UUID,
@@ -17,7 +16,6 @@ final case class ApiTrial(id: String,
previousStatus: Option[String],
previousAssignee: Option[String],
lastActiveUser: Option[String],
- disease: String,
phase: String,
hypothesisId: Option[UUID],
studyDesignId: Option[Long],
@@ -38,9 +36,6 @@ final case class ApiTrial(id: String,
previousAssignee = this.previousAssignee.map(id => StringId(id)),
lastActiveUserId = this.lastActiveUser.map(id => StringId(id)),
lastUpdate = this.lastUpdate.toLocalDateTime,
- disease = CancerType
- .fromString(this.disease)
- .getOrElse(throw new NoSuchElementException(s"Unknown disease ${this.disease}")),
phase = this.phase,
hypothesisId = this.hypothesisId.map(id => UuidId(id)),
studyDesignId = this.studyDesignId.map(id => LongId(id)),
@@ -66,7 +61,6 @@ object ApiTrial {
(JsPath \ "previousStatus").formatNullable[String] and
(JsPath \ "previousAssignee").formatNullable[String] and
(JsPath \ "lastActiveUser").formatNullable[String] and
- (JsPath \ "disease").format[String] and
(JsPath \ "phase").format[String] and
(JsPath \ "hypothesisId").formatNullable[UUID] and
(JsPath \ "studyDesignId").formatNullable[Long] and
@@ -88,7 +82,6 @@ object ApiTrial {
previousAssignee = trial.previousAssignee.map(_.id),
lastActiveUser = trial.lastActiveUserId.map(_.id),
lastUpdate = ZonedDateTime.of(trial.lastUpdate, ZoneId.of("Z")),
- disease = trial.disease.toString,
phase = trial.phase,
hypothesisId = trial.hypothesisId.map(_.id),
studyDesignId = trial.studyDesignId.map(_.id),