TRIAL-192, TRIAL-159 Trial model simplification to support Trial Synchronizer removal and the InterventionType's update for TRIAL-159

9 files changed, 59 insertions, 156 deletions

diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala
index 5e743b7..be51e4f 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala
@@ -16,12 +16,6 @@ sealed trait InterventionType {
 
 object InterventionType {
 
-  final case object RadiationTherapy extends InterventionType {
-    val id: LongId[InterventionType]         = LongId[InterventionType](1)
-    val name: String                         = "Radiation therapy"
-    val deliveryMethods: Set[DeliveryMethod] = commonMethods
-  }
-
   final case object Chemotherapy extends InterventionType {
     val id: LongId[InterventionType]         = LongId[InterventionType](2)
     val name: String                         = "Chemotherapy"
@@ -40,12 +34,6 @@ object InterventionType {
     val deliveryMethods: Set[DeliveryMethod] = commonMethods
   }
 
-  final case object Surgery extends InterventionType {
-    val id: LongId[InterventionType]         = LongId[InterventionType](5)
-    val name: String                         = "Surgery"
-    val deliveryMethods: Set[DeliveryMethod] = commonMethods
-  }
-
   final case object HormoneTherapy extends InterventionType {
     val id: LongId[InterventionType]         = LongId[InterventionType](6)
     val name: String                         = "Hormone therapy"
@@ -152,7 +140,7 @@ object InterventionType {
     }
   }
 
-  val commonMethods = Set[DeliveryMethod](
+  val commonMethods: Set[DeliveryMethod] = Set[DeliveryMethod](
     IntravenousInfusionIV,
     IntramuscularInjection,
     SubcutaneousInjection,
@@ -166,11 +154,9 @@ object InterventionType {
   )
 
   val All: Map[LongId[InterventionType], InterventionType] = Map[LongId[InterventionType], InterventionType](
-    LongId[InterventionType](1) -> RadiationTherapy,
     LongId[InterventionType](2) -> Chemotherapy,
     LongId[InterventionType](3) -> TargetedTherapy,
     LongId[InterventionType](4) -> Immunotherapy,
-    LongId[InterventionType](5) -> Surgery,
     LongId[InterventionType](6) -> HormoneTherapy,
     LongId[InterventionType](7) -> Other,
     LongId[InterventionType](8) -> Radiation,
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/ScrapedTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/ScrapedTrial.scala
deleted file mode 100644
index e7ee1cb..0000000
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/ScrapedTrial.scala
+++ /dev/null
@@ -1,81 +0,0 @@
-package xyz.driver.pdsuidomain.entities
-
-import java.time.LocalDateTime
-import java.util.UUID
-
-import xyz.driver.pdsuicommon.logging._
-import xyz.driver.pdsuicommon.domain.UuidId
-
-final case class ScrapedStudyDesign(value: String)
-
-final case class ScrapedOverall(affiliation: String,
-                                status: String,
-                                facilityName: Option[String],
-                                firstName: Option[String],
-                                lastName: Option[String],
-                                phone: Option[String],
-                                phoneExt: Option[String],
-                                email: Option[String],
-                                isBackup: Boolean)
-
-final case class ScrapedInterventionType(value: String)
-
-final case class ScrapedIntervention(name: String,
-                                     kind: ScrapedInterventionType,
-                                     description: Option[String],
-                                     isSynonym: Boolean)
-
-object ScrapedIntervention {
-
-  implicit def toPhiString(x: ScrapedIntervention): PhiString =
-    phi"ScrapedIntervention(${Unsafe(x.name)})"
-}
-
-final case class ScrapedArm(name: String, kind: Option[String], interventions: Set[ScrapedIntervention])
-
-object ScrapedArm {
-
-  implicit def toPhiString(x: ScrapedArm): PhiString = {
-    import x._
-    phi"ScrapedArm(name=${Unsafe(name)}, inverventions=$interventions)"
-  }
-}
-
-final case class ScrapedTrialChecksum(eligibilityCriteria: String,
-                                      briefSummary: String,
-                                      detailedDescription: String,
-                                      armDescription: String)
-
-object ScrapedTrialChecksum {
-
-  implicit def toPhiString(x: ScrapedTrialChecksum): PhiString = {
-    import x._
-    phi"ScrapedTrialChecksum(eligibilityCriteria=${Unsafe(eligibilityCriteria)}, briefSummary=${Unsafe(briefSummary)}, " +
-      phi"detailedDescription=${Unsafe(detailedDescription)}, armDescription=${Unsafe(armDescription)}"
-  }
-}
-
-object ScrapedTrial {
-
-  implicit def toPhiString(x: ScrapedTrial): PhiString = {
-    import x._
-    phi"ScrapedTrial(rawId=$rawId, nctId=${Unsafe(nctId)}, arms=$arms, checksum=$checksum)"
-  }
-}
-
-final case class ScrapedTrial(rawId: UuidId[ScrapedTrial],
-                              createdAt: LocalDateTime,
-                              disease: String,
-                              nctId: String,
-                              nctUuid: UUID,
-                              title: Option[String],
-                              startDate: Option[LocalDateTime],
-                              phase: String,
-                              studyDesign: Option[ScrapedStudyDesign],
-                              overall: Set[ScrapedOverall],
-                              // // see ClinicalTrialRaw
-                              // trialHtml: String,
-                              // eligibilityText: String,
-                              lastReviewed: LocalDateTime,
-                              arms: Set[ScrapedArm],
-                              checksum: ScrapedTrialChecksum)
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
index cb75803..2713b4e 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
@@ -49,6 +49,18 @@ object StudyDesign {
   }
 }
 
+object TrialCreationRequest {
+
+  implicit def toPhiString(x: TrialCreationRequest): PhiString = phi"${Unsafe(x.toString)}"
+}
+
+final case class TrialCreationRequest(id: UuidId[Trial],
+                                      nctId: String,
+                                      title: Option[String],
+                                      phase: String,
+                                      studyDesign: Option[StudyDesign],
+                                      lastReviewed: LocalDateTime)
+
 object Trial {
 
   sealed trait Status {
@@ -67,7 +79,7 @@ object Trial {
     case object Flagged        extends Status
     case object Archived       extends Status
 
-    val All = Set[Status](
+    val All: Set[Status] = Set[Status](
       New,
       ReviewSummary,
       Summarized,
@@ -79,7 +91,7 @@ object Trial {
       Archived
     )
 
-    val AllPrevious = Set[Status](New, ReviewSummary, Summarized, ReviewCriteria)
+    val AllPrevious: Set[Status] = Set[Status](New, ReviewSummary, Summarized, ReviewCriteria)
 
     implicit def toPhiString(x: Status): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass))
   }
diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala
index 1e4ad51..925a019 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala
@@ -137,11 +137,9 @@ object trialcuration {
   def nextStudyDesign(): StudyDesign = generators.oneOf[StudyDesign](StudyDesign.All: _*)
 
   def nextInterventionType(): InterventionType = generators.oneOf[InterventionType](
-    RadiationTherapy,
     Chemotherapy,
     TargetedTherapy,
     Immunotherapy,
-    Surgery,
     HormoneTherapy,
     Other,
     Radiation,
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala
index 0b5de6b..7bbdda2 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala
@@ -12,6 +12,7 @@ object trial {
   import DefaultJsonProtocol._
   import Trial._
   import common._
+  import studydesign._
 
   implicit val trialStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status](
     "New"            -> Status.New,
@@ -181,4 +182,7 @@ object trial {
     case _ => deserializationError(s"Expected Json Object as Trial, but got $json")
   }
 
+  implicit val trialCreationRequestFormat: RootJsonFormat[TrialCreationRequest] =
+    jsonFormat6(TrialCreationRequest.apply)
+
 }
diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/ScrapedTrialsService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/ScrapedTrialsService.scala
deleted file mode 100644
index 233495e..0000000
--- a/src/main/scala/xyz/driver/pdsuidomain/services/ScrapedTrialsService.scala
+++ /dev/null
@@ -1,53 +0,0 @@
-package xyz.driver.pdsuidomain.services
-
-import xyz.driver.pdsuicommon.error.DomainError
-import xyz.driver.pdsuidomain.entities.ScrapedTrial
-
-import scala.concurrent.Future
-
-object ScrapedTrialsService {
-
-  sealed trait GetRawTrialReply
-  object GetRawTrialReply {
-    type Error = GetRawTrialReply with DomainError
-
-    final case class TrialRawEntity(rawTrial: ScrapedTrial) extends GetRawTrialReply
-
-    case object NotFoundError extends GetRawTrialReply with DomainError.NotFoundError {
-      override def userMessage: String = "Raw clinical trial not found"
-    }
-  }
-
-  sealed trait GetRawTrialOptReply
-  object GetRawTrialOptReply {
-    final case class TrialRawEntity(rawTrial: Option[ScrapedTrial]) extends GetRawTrialOptReply
-  }
-
-  sealed trait GetAllRawTrialsExceptReply
-  object GetAllRawTrialsExceptReply {
-    final case class MultipleRawTrials(rawTrials: Seq[ScrapedTrial]) extends GetAllRawTrialsExceptReply
-  }
-
-  sealed trait GetHtmlForReply
-  object GetHtmlForReply {
-    type TrialHtmlMap = Map[String, String]
-
-    /**
-      * @param trialHtmlMap nctId -> html
-      */
-    final case class HtmlMap(trialHtmlMap: TrialHtmlMap) extends GetHtmlForReply
-  }
-}
-
-trait ScrapedTrialsService {
-
-  import ScrapedTrialsService._
-
-  def getRawTrial(nctId: String): Future[GetRawTrialReply]
-
-  def getRawTrialOpt(nctId: String): Future[GetRawTrialOptReply]
-
-  def getAllRawTrialsExcept(nctIds: Seq[String], limit: Int): Future[GetAllRawTrialsExceptReply]
-
-  def getHtmlFor(nctIds: Set[String]): Future[GetHtmlForReply]
-}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala
index 4d61342..9ae1c10 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala
@@ -12,7 +12,7 @@ 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
+import xyz.driver.pdsuidomain.entities.{Trial, TrialCreationRequest}
 import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels
 
 import scala.concurrent.Future
@@ -121,6 +121,9 @@ trait TrialService {
   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)(
@@ -150,4 +153,6 @@ trait TrialService {
   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/FakeTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala
index 7d44309..221e56c 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala
@@ -13,7 +13,7 @@ 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.{Criterion, EligibilityArm, Trial}
+import xyz.driver.pdsuidomain.entities._
 import xyz.driver.pdsuidomain.services.TrialService
 
 import scala.concurrent.Future
@@ -52,7 +52,12 @@ class FakeTrialService extends TrialService {
   def getPdfSource(trialId: StringId[Trial])(
           implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]
   ): Future[Source[ByteString, NotUsed]] =
-    Future.failed(new NotImplementedError("fake pdf download is not implemented"))
+    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,
@@ -125,4 +130,7 @@ class FakeTrialService extends TrialService {
           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/RestTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala
index 6650d51..94e1c63 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala
@@ -73,6 +73,18 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote
     }
   }
 
+  def getHtmlSource(trialId: StringId[Trial])(
+          implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]
+  ): Future[Source[ByteString, NotUsed]] = {
+    val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/trial/$trialId/source.html"))
+    for {
+      response <- transport.sendRequestGetResponse(requestContext)(request)
+      reply    <- apiResponse[HttpEntity](response)
+    } yield {
+      reply.dataBytes.mapMaterializedValue(_ => NotUsed)
+    }
+  }
+
   def getAll(filter: SearchFilterExpr = SearchFilterExpr.Empty,
              sorting: Option[Sorting] = None,
              pagination: Option[Pagination] = None)(
@@ -146,4 +158,16 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote
   def unassign(origTrial: Trial)(
           implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] =
     singleAction(origTrial, "unassign")
+
+  override def addTrial(trial: TrialCreationRequest)(
+    implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[Trial] = {
+    for {
+      entity   <- Marshal(trial).to[RequestEntity]
+      request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, s"/v1/trial/${trial.nctId}")).withEntity(entity)
+      response <- transport.sendRequestGetResponse(requestContext)(request)
+      reply    <- apiResponse[Trial](response)
+    } yield {
+      reply
+    }
+  }
 }