Merge pull request #37 from drivergroup/add-slot-eligibility-armsv0.8.1

Add slot eligibility arms

6 files changed, 100 insertions, 21 deletions

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/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,