Merge branch 'master' into entity-list-responses

20 files changed, 103 insertions, 46 deletions

diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala
index 258aa03..fa5f4ce 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala
@@ -456,7 +456,8 @@ final case class Document(id: LongId[Document] = LongId(0L),
                           meta: Option[TextJson[Meta]], // not null
                           startDate: Option[LocalDate], // not null
                           endDate: Option[LocalDate],
-                          lastUpdate: LocalDateTime) {
+                          lastUpdate: LocalDateTime,
+                          labelVersion: Int) {
 
   import Document.Status._
 
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala
index f02bedc..5e743b7 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Intervention.scala
@@ -5,6 +5,9 @@ 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
@@ -78,16 +81,8 @@ object InterventionType {
     )
   }
 
-  def typeFromString: PartialFunction[String, InterventionType] = {
-    case "Radiation therapy" => RadiationTherapy
-    case "Chemotherapy"      => Chemotherapy
-    case "Targeted therapy"  => TargetedTherapy
-    case "Immunotherapy"     => Immunotherapy
-    case "Surgery"           => Surgery
-    case "Hormone therapy"   => HormoneTherapy
-    case "Other"             => Other
-    case "Radiation"         => Radiation
-    case "Surgery/Procedure" => SurgeryProcedure
+  def typeFromString(txt: String): Option[InterventionType] = {
+    All.values.find(_.name === txt)
   }
 
   sealed trait DeliveryMethod
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
index ac5feef..e734779 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
@@ -7,9 +7,41 @@ import xyz.driver.pdsuicommon.logging._
 import xyz.driver.pdsuicommon.utils.Utils
 import xyz.driver.pdsuidomain.entities.Trial.Status
 
-final case class StudyDesign(id: LongId[StudyDesign], name: String)
+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)})"
diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala
index c0c3391..86583c1 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala
@@ -183,7 +183,8 @@ object recordprocessing {
       meta = nextOption(nextDocumentMetaJson()),
       startDate = startDate,
       endDate = endDate,
-      lastUpdate = nextLocalDateTime
+      lastUpdate = nextLocalDateTime,
+      labelVersion = generators.nextInt(100)
     )
   }
 
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
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala
@@ -0,0 +1 @@
+
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 3ab50e1..eeec577 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala
@@ -132,10 +132,7 @@ object trialcuration {
     description = generators.nextString()
   )
 
-  def nextStudyDesign(): StudyDesign = StudyDesign(
-    id = nextLongId[StudyDesign],
-    name = generators.nextString()
-  )
+  def nextStudyDesign(): StudyDesign = generators.oneOf[StudyDesign](StudyDesign.All: _*)
 
   def nextInterventionType(): InterventionType = generators.oneOf[InterventionType](
     RadiationTherapy,
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 3f1ecfe..250e650 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
@@ -25,7 +25,8 @@ final case class ApiDocument(id: Long,
                              assignee: Option[String],
                              previousAssignee: Option[String],
                              lastActiveUser: Option[String],
-                             meta: Option[String]) {
+                             meta: Option[String],
+                             labelVersion: Int) {
 
   private def extractStatus(status: String): Document.Status =
     Document.Status.fromString(status).getOrElse(throw new NoSuchElementException(s"Status $status unknown"))
@@ -50,7 +51,8 @@ final case class ApiDocument(id: Long,
     meta = this.meta.map(x => TextJson(JsonSerializer.deserialize[Document.Meta](x))),
     startDate = this.startDate,
     endDate = this.endDate,
-    lastUpdate = this.lastUpdate.toLocalDateTime()
+    lastUpdate = this.lastUpdate.toLocalDateTime(),
+    labelVersion = this.labelVersion
   )
 
 }
@@ -83,7 +85,8 @@ object ApiDocument {
       (JsPath \ "lastActiveUser").formatNullable[String] and
       (JsPath \ "meta").formatNullable(Format(Reads { x =>
         JsSuccess(Json.stringify(x))
-      }, Writes[String](Json.parse)))
+      }, Writes[String](Json.parse))) and
+      (JsPath \ "labelVersion").format[Int]
   )(ApiDocument.apply, unlift(ApiDocument.unapply))
 
   def fromDomain(document: Document): ApiDocument = {
@@ -104,7 +107,8 @@ object ApiDocument {
       assignee = document.assignee.map(_.id),
       previousAssignee = document.previousAssignee.map(_.id),
       lastActiveUser = document.lastActiveUserId.map(_.id),
-      meta = document.meta.map(meta => JsonSerializer.serialize(meta.content))
+      meta = document.meta.map(meta => JsonSerializer.serialize(meta.content)),
+      labelVersion = document.labelVersion
     )
   }
 }
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 032ddf6..ecbdaed 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
@@ -47,7 +47,8 @@ final case class ApiPartialDocument(recordId: Option[Long],
     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),
-    lastUpdate = LocalDateTime.MIN // Should update internally in a business logic module
+    lastUpdate = LocalDateTime.MIN, // Should update internally in a business logic module,
+    labelVersion = orig.labelVersion
   )
 
   def toDomain: Try[Document] = Try {
@@ -75,7 +76,8 @@ final case class ApiPartialDocument(recordId: Option[Long],
         assignee = None,
         previousAssignee = None,
         lastActiveUserId = None,
-        lastUpdate = LocalDateTime.MIN
+        lastUpdate = LocalDateTime.MIN,
+        labelVersion = 0
       )
     } else {
       throw new JsonValidationException(validationErrors)
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 e05e841..c584b96 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
@@ -34,7 +34,7 @@ object document {
         val name = fields
           .get("name")
           .map(_.convertTo[String])
-          .getOrElse(deserializationError(s"Intervention type json object does not contain `name` field: $json"))
+          .getOrElse(deserializationError(s"Document type json object does not contain `name` field: $json"))
 
         DocumentType
           .fromString(name)
@@ -126,7 +126,8 @@ object document {
         "previousAssignee" -> document.previousAssignee.toJson,
         "meta"             -> document.meta.toJson,
         "lastActiveUser"   -> document.lastActiveUserId.toJson,
-        "lastUpdate"       -> document.lastUpdate.toJson
+        "lastUpdate"       -> document.lastUpdate.toJson,
+        "labelVersion"     -> document.labelVersion.toJson
       )
 
     override def read(json: JsValue): Document = json match {
@@ -185,7 +186,8 @@ object document {
           assignee = None,
           previousAssignee = None,
           lastActiveUserId = None,
-          lastUpdate = LocalDateTime.MIN
+          lastUpdate = LocalDateTime.MIN,
+          labelVersion = 0
         )
 
       case _ => deserializationError(s"Expected Json Object as Document, but got $json")
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 bd68566..e557e47 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
@@ -128,7 +128,9 @@ object intervention {
           .map(_.convertTo[String])
           .getOrElse(deserializationError(s"Intervention type json object does not contain `name` field: $json"))
 
-        InterventionType.typeFromString(name)
+        InterventionType
+          .typeFromString(name)
+          .getOrElse(deserializationError(s"Unknown intervention type: $name"))
 
       case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json")
     }
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 eac5ea7..09517e6 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
@@ -42,13 +42,13 @@ object record {
         val name = fields
           .get("name")
           .map(_.convertTo[String])
-          .getOrElse(deserializationError(s"Intervention type json object does not contain `name` field: $json"))
+          .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 Intervention type, but got $json")
+      case _ => deserializationError(s"Expected Json Object as Provider type, but got $json")
     }
 
     override def write(obj: ProviderType) =
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/studydesign.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/studydesign.scala
index e801666..3002b38 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/studydesign.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/studydesign.scala
@@ -7,6 +7,23 @@ object studydesign {
   import DefaultJsonProtocol._
   import common._
 
-  implicit val studyDesignFormat: RootJsonFormat[StudyDesign] = jsonFormat2(StudyDesign.apply)
+  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/studydesign/ApiStudyDesign.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign/ApiStudyDesign.scala
index 1e9a226..12d40df 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign/ApiStudyDesign.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/studydesign/ApiStudyDesign.scala
@@ -3,11 +3,10 @@ package xyz.driver.pdsuidomain.formats.json.studydesign
 import xyz.driver.pdsuidomain.entities.StudyDesign
 import play.api.libs.functional.syntax._
 import play.api.libs.json.{Format, JsPath}
-import xyz.driver.pdsuicommon.domain.LongId
 
 final case class ApiStudyDesign(id: Long, name: String) {
 
-  def toDomain = StudyDesign(id = LongId[StudyDesign](id), name = name)
+  def toDomain: Option[StudyDesign] = StudyDesign.fromString(name)
 }
 
 object ApiStudyDesign {
diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala
index d727d70..93ee2ab 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala
@@ -37,8 +37,14 @@ class RestEligibilityVerificationService(transport: ServiceTransport, baseUri: U
                                        excludedArms: Seq[LongId[EligibilityArm]])(
           implicit ctx: AuthorizedServiceRequestContext[AuthUserInfo]): Future[eligibility.MismatchRankedLabels] = {
 
-    val query =
-      Seq("disease" -> cancerType.toString.toUpperCase, "ineligible_arms" -> excludedArms.map(_.id).mkString(","))
+    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))
diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionTypeService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionTypeService.scala
index 87f32ec..ce7ac10 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionTypeService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestInterventionTypeService.scala
@@ -27,7 +27,7 @@ class RestInterventionTypeService(transport: ServiceTransport, baseUri: Uri)(
       reply    <- apiResponse[ListResponse[ApiInterventionType]](response)
     } yield {
       {
-        val domain = reply.items.map(_.toDomain)
+        val domain = reply.items.flatMap(_.toDomain)
         GetListReply.EntityList(domain.toList, 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
index 98b397d..b1684eb 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestStudyDesignService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestStudyDesignService.scala
@@ -26,7 +26,7 @@ class RestStudyDesignService(transport: ServiceTransport, baseUri: Uri)(
       response <- transport.sendRequestGetResponse(requestContext)(request)
       reply    <- apiResponse[ListResponse[ApiStudyDesign]](response)
     } yield {
-      GetListReply.EntityList(reply.items.map(_.toDomain), reply.meta.itemsCount)
+      GetListReply.EntityList(reply.items.flatMap(_.toDomain), reply.meta.itemsCount)
     }
   }
 
diff --git a/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala
index 7d8a418..915e4e7 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/DocumentSuite.scala
@@ -82,7 +82,8 @@ class DocumentSuite extends BaseSuite {
       startDate = Some(lastUpdate.toLocalDate.minusDays(2)),
       endDate = None,
       lastUpdate = lastUpdate,
-      meta = Some(TextJson(Document.Meta(1.1, 2.2)))
+      meta = Some(TextJson(Document.Meta(1.1, 2.2))),
+      labelVersion = 1
     )
   }
 }
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala
index e6dd4a1..111da6e 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/DocumentFormatSuite.scala
@@ -28,14 +28,15 @@ class DocumentFormatSuite extends FlatSpec with Matchers {
       requiredType = Some(Document.RequiredType.OPN),
       meta = None,
       startDate = None,
-      endDate = None
+      endDate = None,
+      labelVersion = 0
     )
     val writtenJson = documentFormat.write(orig)
 
     writtenJson should be(
       """{"id":1,"recordId":101,"physician":"physician","typeId":10,"provider":"provider 21","providerTypeId":21,
          "requiredType":"OPN","institutionName":"institution name","startDate":null,"endDate":null,"status":"New","assignee":null,"previousStatus":null,
-         "previousAssignee":null,"lastActiveUser":null,"lastUpdate":"2017-08-10T18:00Z","meta":null}""".parseJson)
+         "previousAssignee":null,"lastActiveUser":null,"lastUpdate":"2017-08-10T18:00Z","meta":null,"labelVersion":0}""".parseJson)
 
     val createDocumentJson =
       """{"recordId":101,"physician":"physician","typeId":10,"provider":"provider 21","providerTypeId":21}""".parseJson
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala
index 5891e1c..4532da4 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/InterventionFormatSuite.scala
@@ -59,7 +59,7 @@ class InterventionFormatSuite extends FlatSpec with Matchers {
   }
 
   "Json format for InterventionType" should "read and write correct JSON" in {
-    val interventionType = InterventionType.typeFromString("Surgery/Procedure")
+    val interventionType = InterventionType.SurgeryProcedure
     val writtenJson      = interventionTypeFormat.write(interventionType)
 
     writtenJson should be(
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/StudyDesignFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/StudyDesignFormatSuite.scala
index 9cf9b5f..e847445 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/StudyDesignFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/StudyDesignFormatSuite.scala
@@ -2,20 +2,16 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
 
 import spray.json._
 import org.scalatest.{FlatSpec, Matchers}
-import xyz.driver.pdsuicommon.domain.LongId
 import xyz.driver.pdsuidomain.entities.StudyDesign
 
 class StudyDesignFormatSuite extends FlatSpec with Matchers {
   import studydesign._
 
   "Json format for StudyDesign" should "read and write correct JSON" in {
-    val studyDesign = StudyDesign(
-      id = LongId(10),
-      name = "study design name"
-    )
+    val studyDesign = StudyDesign.Randomized
     val writtenJson = studyDesignFormat.write(studyDesign)
 
-    writtenJson should be("""{"id":10,"name":"study design name"}""".parseJson)
+    writtenJson should be("""{"id":1,"name":"Randomized"}""".parseJson)
 
     val parsedStudyDesign = studyDesignFormat.read(writtenJson)
     parsedStudyDesign should be(studyDesign)