Merge pull request #55 from drivergroup/PDSUI-2330

PDSUI-2330 Add support for inclusion/exclusion criteria to the TM backend

10 files changed, 95 insertions, 41 deletions

diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala
index 79a19ed..7027eef 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala
@@ -9,11 +9,11 @@ import xyz.driver.pdsuicommon.logging._
 object PatientCriterion {
   implicit def toPhiString(x: PatientCriterion): PhiString = {
     import x._
-    phi"PatientCriterion(id=$id, patientLabelId=$patientLabelId, trialId=${Unsafe(trialId)}, nctId=${Unsafe(nctId)}, " +
+    phi"PatientCriterion(id=$id, patientLabelId=$patientLabelId, trialId=${Unsafe(trialId)}, nctId=$nctId, " +
       phi"criterionId=$criterionId, criterionValue=${Unsafe(criterionValue)}, " +
       phi"isImplicitMatch=$criterionIsDefining), criterionIsDefining=${Unsafe(criterionIsDefining)}, " +
       phi"eligibilityStatus=${Unsafe(eligibilityStatus)}, verifiedEligibilityStatus=${Unsafe(verifiedEligibilityStatus)}, " +
-      phi"isVerified=${Unsafe(isVerified)}, lastUpdate=${Unsafe(lastUpdate)}"
+      phi"isVerified=${Unsafe(isVerified)}, lastUpdate=${Unsafe(lastUpdate)}, inclusion=${Unsafe(inclusion)}"
   }
 
   /**
@@ -52,7 +52,8 @@ final case class PatientCriterion(id: LongId[PatientCriterion],
                                   verifiedEligibilityStatus: Option[LabelValue],
                                   isVerified: Boolean,
                                   isVisible: Boolean,
-                                  lastUpdate: LocalDateTime) {
+                                  lastUpdate: LocalDateTime,
+                                  inclusion: Option[Boolean]) {
   def isIneligibleForEv: Boolean = eligibilityStatus.contains(LabelValue.No) && isVerified
 }
 
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala
index 8376e34..98bd084 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala
@@ -11,13 +11,14 @@ final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion],
                                            armIds: Set[LongId[EligibilityArm]],
                                            criteria: String,
                                            isCompound: Boolean,
-                                           isDefining: Boolean)
+                                           isDefining: Boolean,
+                                           inclusion: Option[Boolean])
 
 object ExportTrialLabelCriterion {
 
   implicit def toPhiString(x: ExportTrialLabelCriterion): PhiString = {
     import x._
     phi"TrialLabelCriterion(criterionId=$criterionId, value=$value, labelId=$labelId, " +
-      phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining)"
+      phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining), inclusion=${Unsafe(inclusion)}"
   }
 }
diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala
index 2c7d0e0..33da392 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala
@@ -28,7 +28,8 @@ object export {
       armIds = setOf(nextLongId[EligibilityArm]),
       criteria = nextString(100),
       isCompound = nextBoolean(),
-      isDefining = nextBoolean()
+      isDefining = nextBoolean(),
+      inclusion = nextOption(nextBoolean())
     )
 
   def nextExportTrialWithLabels(): ExportTrialWithLabels =
diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala
index d5adc32..36ef3d9 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala
@@ -86,7 +86,8 @@ object treatmentmatching {
     verifiedEligibilityStatus = generators.nextOption(fakes.entities.labels.nextLabelValue()),
     isVerified = generators.nextBoolean(),
     isVisible = generators.nextBoolean(),
-    lastUpdate = nextLocalDateTime
+    lastUpdate = nextLocalDateTime,
+    inclusion = generators.nextOption(generators.nextBoolean())
   )
 
   def nextDraftPatientCriterion(): DraftPatientCriterion = DraftPatientCriterion(
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala
index b9bf772..5e44413 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala
@@ -22,7 +22,8 @@ final case class ApiPatientCriterion(id: Long,
                                      verifiedEligibilityStatus: Option[String],
                                      isVerified: Boolean,
                                      isVisible: Boolean,
-                                     lastUpdate: ZonedDateTime)
+                                     lastUpdate: ZonedDateTime,
+                                     inclusion: Option[Boolean])
 
 object ApiPatientCriterion {
 
@@ -49,7 +50,8 @@ object ApiPatientCriterion {
         }), Writes.of[String])) and
       (JsPath \ "isVerified").format[Boolean] and
       (JsPath \ "isVisible").format[Boolean] and
-      (JsPath \ "lastUpdate").format[ZonedDateTime]
+      (JsPath \ "lastUpdate").format[ZonedDateTime] and
+      (JsPath \ "inclusion").formatNullable[Boolean]
     ) (ApiPatientCriterion.apply, unlift(ApiPatientCriterion.unapply))
 
   def fromDomain(patientCriterion: PatientCriterion,
@@ -70,6 +72,7 @@ object ApiPatientCriterion {
     verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(_.toString),
     isVerified = patientCriterion.isVerified,
     isVisible = patientCriterion.isVisible,
-    lastUpdate = ZonedDateTime.of(patientCriterion.lastUpdate, ZoneId.of("Z"))
+    lastUpdate = ZonedDateTime.of(patientCriterion.lastUpdate, ZoneId.of("Z")),
+    inclusion = patientCriterion.inclusion
   )
 }
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 4391453..9579288 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
@@ -3,6 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
 import spray.json._
 import xyz.driver.entities.labels.Label
 import xyz.driver.formats.json.labels._
+import xyz.driver.pdsuicommon.domain.LongId
 import xyz.driver.pdsuidomain.entities.export.patient._
 import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels}
 import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm}
@@ -13,6 +14,14 @@ object export {
   import document._
   import record._
 
+  private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = {
+    deserializationError(s"$className json object do not contain '$field' field: $json")
+  }
+
+  private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = {
+    deserializationError(s"Expected Json Object as $className, but got $json")
+  }
+
   implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] =
     jsonFormat5(ExportPatientLabelEvidenceDocument.apply)
 
@@ -29,6 +38,8 @@ object export {
 
   implicit val trialLabelCriterionFormat: RootJsonFormat[ExportTrialLabelCriterion] =
     new RootJsonFormat[ExportTrialLabelCriterion] {
+      implicit val className: String = "ExportTrialLabelCriterion"
+
       override def write(obj: ExportTrialLabelCriterion): JsValue =
         JsObject(
           "value" -> obj.value
@@ -43,40 +54,69 @@ object export {
           "criterionText" -> obj.criteria.toJson,
           "armIds"        -> obj.armIds.toJson,
           "isCompound"    -> obj.isCompound.toJson,
-          "isDefining"    -> obj.isDefining.toJson
+          "isDefining"    -> obj.isDefining.toJson,
+          "inclusion"     -> obj.inclusion.toJson
         )
 
       override def read(json: JsValue): ExportTrialLabelCriterion = {
+        json match {
+          case JsObject(fields) =>
+            val value = fields
+              .get("value")
+              .map(_.convertTo[String])
+              .map {
+                case "Yes"     => Option(true)
+                case "No"      => Option(false)
+                case "Unknown" => Option.empty[Boolean]
+              }
+              .getOrElse(deserializationErrorFieldMessage("value", json))
 
-        val fields = Seq("value", "labelId", "criterionId", "criterionText", "armIds", "isCompound", "isDefining")
-
-        json.asJsObject.getFields(fields: _*) match {
-          case Seq(JsString(valueString),
-                   labelId,
-                   criterionId,
-                   JsString(criterionText),
-                   JsArray(armIdsVector),
-                   JsBoolean(isCompound),
-                   JsBoolean(isDefining)) =>
-            val value = valueString match {
-              case "Yes"     => Option(true)
-              case "No"      => Option(false)
-              case "Unknown" => Option.empty[Boolean]
-            }
+            val labelId = fields
+              .get("labelId")
+              .map(_.convertTo[LongId[Label]])
+              .getOrElse(deserializationErrorFieldMessage("labelId", json))
+
+            val criterionId = fields
+              .get("criterionId")
+              .map(_.convertTo[LongId[Criterion]])
+              .getOrElse(deserializationErrorFieldMessage("criterionId", json))
+
+            val criterionText = fields
+              .get("criterionText")
+              .map(_.convertTo[String])
+              .getOrElse(deserializationErrorFieldMessage("criterionText", json))
+
+            val armIds = fields
+              .get("armIds")
+              .map(_.convertTo[Set[LongId[EligibilityArm]]])
+              .getOrElse(deserializationErrorFieldMessage("armIds", json))
+
+            val isCompound = fields
+              .get("isCompound")
+              .map(_.convertTo[Boolean])
+              .getOrElse(deserializationErrorFieldMessage("isCompound", json))
+
+            val isDefining = fields
+              .get("isDefining")
+              .map(_.convertTo[Boolean])
+              .getOrElse(deserializationErrorFieldMessage("isDefining", json))
+
+            val inclusion = fields
+              .get("inclusion")
+              .flatMap(_.convertTo[Option[Boolean]])
 
             ExportTrialLabelCriterion(
-              longIdFormat[Criterion].read(criterionId),
+              criterionId,
               value,
-              longIdFormat[Label].read(labelId),
-              armIdsVector.map(longIdFormat[EligibilityArm].read).toSet,
+              labelId,
+              armIds,
               criterionText,
               isCompound,
-              isDefining
+              isDefining,
+              inclusion
             )
 
-          case _ =>
-            deserializationError(
-              s"Cannot find required fields ${fields.mkString(", ")} in ExportTrialLabelCriterion object!")
+          case _ => deserializationErrorEntityMessage(json)
         }
       }
     }
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 f41c846..2cad78c 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
@@ -56,7 +56,8 @@ object patientcriterion {
           "verifiedEligibilityStatus" -> obj.patientCriterion.verifiedEligibilityStatus.toJson,
           "isVerified"                -> obj.patientCriterion.isVerified.toJson,
           "isVisible"                 -> obj.patientCriterion.isVisible.toJson,
-          "lastUpdate"                -> obj.patientCriterion.lastUpdate.toJson
+          "lastUpdate"                -> obj.patientCriterion.lastUpdate.toJson,
+          "inclusion"                 -> obj.patientCriterion.inclusion.toJson
         )
       }
     }
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 e0efcd1..e23449c 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala
@@ -85,7 +85,8 @@ class FakeTrialService extends TrialService {
           generators.setOf(LongId[EligibilityArm](generators.nextInt(999999).toLong)),
           generators.nextName().value,
           generators.nextBoolean(),
-          generators.nextBoolean()
+          generators.nextBoolean(),
+          generators.nextOption(generators.nextBoolean())
         ))
     )
 
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala
index d78e754..767f832 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala
@@ -92,7 +92,8 @@ class ExportFormatSuite extends FlatSpec with Matchers {
         armIds = Set(LongId(1), LongId(2)),
         criteria = "criteria 10 text",
         isCompound = false,
-        isDefining = false
+        isDefining = false,
+        inclusion = Some(false)
       ),
       ExportTrialLabelCriterion(
         criterionId = LongId(11),
@@ -101,7 +102,8 @@ class ExportFormatSuite extends FlatSpec with Matchers {
         armIds = Set(LongId(2)),
         criteria = "criteria 11 text",
         isCompound = true,
-        isDefining = false
+        isDefining = false,
+        inclusion = None
       )
     )
     val trialWithLabels = ExportTrialWithLabels(
@@ -117,8 +119,10 @@ class ExportFormatSuite extends FlatSpec with Matchers {
     writtenJson should be(
       """{"nctId":"NCT000001","trialId":"40892a07-c638-49d2-9795-1edfefbbcc7c","lastReviewed":"2017-08-10T18:00Z",
         "labelVersion":1,"arms":[{"armId":1,"armName":"arm 1","diseaseList":["Breast"]},{"armId":2,"armName":"arm 2","diseaseList":["Breast"]}],"criteria":[
-        {"value":"Yes","labelId":21,"criterionId":10,"criterionText":"criteria 10 text","armIds":[1,2],"isCompound":false,"isDefining":false},
-        {"value":"Unknown","labelId":21,"criterionId":11,"criterionText":"criteria 11 text","armIds":[2],"isCompound":true,"isDefining":false}]}""".parseJson)
+        {"value":"Yes","labelId":21,"criterionId":10,"criterionText":"criteria 10 text","armIds":[1,2],"isCompound":false,
+        "isDefining":false,"inclusion":false},
+        {"value":"Unknown","labelId":21,"criterionId":11,"criterionText":"criteria 11 text","armIds":[2],"isCompound":true,
+        "isDefining":false,"inclusion":null}]}""".parseJson)
   }
 
 }
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala
index b254013..27e27c2 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala
@@ -26,7 +26,8 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers {
       verifiedEligibilityStatus = None,
       isVisible = true,
       isVerified = true,
-      lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00")
+      lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00"),
+      inclusion = Some(true)
     )
     val arms = List(
       PatientCriterionArm(patientCriterionId = LongId(1), armId = LongId(31), armName = "arm 31"),
@@ -38,7 +39,7 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers {
     writtenJson should be(
       """{"id":1,"labelId":21,"nctId":"NCT00001","criterionId":101,"criterionText":"criterion text","criterionValue":"Yes",
          "criterionIsDefining":false,"criterionIsCompound":false,"eligibilityStatus":"Yes","verifiedEligibilityStatus":null,
-         "isVisible":true,"isVerified":true,"lastUpdate":"2017-08-10T18:00Z","arms":["arm 31","arm 32"]}""".parseJson)
+         "isVisible":true,"isVerified":true,"lastUpdate":"2017-08-10T18:00Z","arms":["arm 31","arm 32"],"inclusion":true}""".parseJson)
 
     val updatePatientCriterionJson      = """{"verifiedEligibilityStatus":"No"}""".parseJson
     val expectedUpdatedPatientCriterion = orig.copy(verifiedEligibilityStatus = Some(LabelValue.No))