Fixing Patients and Trials parsing, some refined to tryv0.11.1

11 files changed, 201 insertions, 20 deletions

diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHypothesis.scala
index 23bb546..7943fb9 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHypothesis.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientHypothesis.scala
@@ -1,5 +1,7 @@
 package xyz.driver.pdsuidomain.entities
 
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.numeric.NonNegative
 import xyz.driver.pdsuicommon.domain.UuidId
 import xyz.driver.pdsuicommon.logging._
 
@@ -15,4 +17,4 @@ final case class PatientHypothesis(id: UuidId[PatientHypothesis],
                                    patientId: UuidId[Patient],
                                    hypothesisId: UuidId[Hypothesis],
                                    rationale: Option[String],
-                                   matchedTrials: Long)
+                                   matchedTrials: Long Refined NonNegative)
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientIssue.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientIssue.scala
index f616754..7f17419 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientIssue.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientIssue.scala
@@ -2,6 +2,8 @@ package xyz.driver.pdsuidomain.entities
 
 import java.time.LocalDateTime
 
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.collection.NonEmpty
 import xyz.driver.pdsuicommon.domain._
 import xyz.driver.pdsuicommon.logging._
 
@@ -10,7 +12,7 @@ final case class PatientIssue(id: LongId[PatientIssue],
                               patientId: UuidId[Patient],
                               lastUpdate: LocalDateTime,
                               isDraft: Boolean,
-                              text: String,
+                              text: String Refined NonEmpty,
                               archiveRequired: Boolean)
 
 object PatientIssue {
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 94c41ff..2780526 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala
@@ -1,5 +1,6 @@
 package xyz.driver.pdsuidomain.fakes.entities
 
+import eu.timepit.refined.numeric.NonNegative
 import xyz.driver.entities.labels.Label
 import xyz.driver.fakes
 import xyz.driver.pdsuicommon.domain.{LongId, StringId, User}
@@ -9,6 +10,7 @@ import xyz.driver.pdsuidomain.services.PatientCriterionService.{DraftPatientCrit
 import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial
 import xyz.driver.pdsuidomain.services.PatientHypothesisService.RichPatientHypothesis
 import xyz.driver.pdsuidomain.services.PatientLabelService.RichPatientLabel
+import eu.timepit.refined.{refineV, refineMV}
 
 object treatmentmatching {
   import common._
@@ -163,7 +165,10 @@ object treatmentmatching {
     patientId = nextUuidId[Patient],
     hypothesisId = nextUuidId[Hypothesis],
     rationale = Option(generators.nextString()),
-    matchedTrials = generators.nextInt(Int.MaxValue).toLong
+    matchedTrials = refineV[NonNegative](generators.nextInt(Int.MaxValue).toLong) match {
+      case Left(_)            => refineMV[NonNegative](0)
+      case Right(nonNegative) => nonNegative
+    }
   )
 
   def nextRichPatientHypothesis(): RichPatientHypothesis = RichPatientHypothesis(
@@ -177,7 +182,7 @@ object treatmentmatching {
     patientId = nextUuidId[Patient],
     lastUpdate = nextLocalDateTime,
     isDraft = generators.nextBoolean(),
-    text = generators.nextString(),
+    text = generators.nextNonEmptyString(),
     archiveRequired = generators.nextBoolean()
   )
 
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
deleted file mode 100644
index 8b13789..0000000
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala
index 75eb016..0830723 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient.scala
@@ -1,9 +1,14 @@
 package xyz.driver.pdsuidomain.formats.json
 
+import java.time.{LocalDate, LocalDateTime}
+
 import spray.json._
 import xyz.driver.core.json.EnumJsonFormat
+import xyz.driver.entities.common.FullName
+import xyz.driver.entities.patient.CancerType
 import xyz.driver.formats.json.common._
 import xyz.driver.formats.json.patient._
+import xyz.driver.pdsuicommon.domain.{StringId, User, UuidId}
 import xyz.driver.pdsuidomain.entities._
 
 object patient {
@@ -11,7 +16,7 @@ object patient {
   import Patient._
   import common._
 
-  implicit val patientStatusFormat = new EnumJsonFormat[Status](
+  implicit val patientStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status](
     "New"      -> Status.New,
     "Verified" -> Status.Verified,
     "Reviewed" -> Status.Reviewed,
@@ -20,7 +25,7 @@ object patient {
     "Flagged"  -> Status.Flagged
   )
 
-  implicit val patientOrderIdFormat = new RootJsonFormat[PatientOrderId] {
+  implicit val patientOrderIdFormat: RootJsonFormat[PatientOrderId] = new RootJsonFormat[PatientOrderId] {
     override def write(orderId: PatientOrderId): JsString = JsString(orderId.toString)
     override def read(json: JsValue): PatientOrderId = json match {
       case JsString(value) => PatientOrderId(value)
@@ -44,7 +49,76 @@ object patient {
         "orderId"          -> patient.orderId.toJson
       )
 
-    override def read(json: JsValue): Patient = jsonReader[Patient].read(json)
+    override def read(json: JsValue): Patient = {
+      json match {
+        case JsObject(fields) =>
+          val id = fields
+            .get("id")
+            .map(_.convertTo[UuidId[Patient]])
+            .getOrElse(deserializationError(s"Patient create json object does not contain `id` field: $json"))
+
+          val status = fields
+            .get("status")
+            .map(_.convertTo[Patient.Status])
+            .getOrElse(deserializationError(s"Patient create json object does not contain `status` field: $json"))
+
+          val name = fields
+            .get("name")
+            .map(_.convertTo[FullName[Patient]])
+            .getOrElse(deserializationError(s"Patient create json object does not contain `name` field: $json"))
+
+          val dob = fields
+            .get("dob")
+            .map(_.convertTo[LocalDate])
+            .getOrElse(deserializationError(s"Patient create json object does not contain `dob` field: $json"))
+
+          val assignee = fields
+            .get("assignee")
+            .flatMap(_.convertTo[Option[StringId[User]]])
+
+          val previousStatus = fields
+            .get("previousStatus")
+            .flatMap(_.convertTo[Option[Patient.Status]])
+
+          val previousAssignee = fields
+            .get("previousAssignee")
+            .flatMap(_.convertTo[Option[StringId[User]]])
+
+          val lastActiveUser = fields
+            .get("lastActiveUser")
+            .flatMap(_.convertTo[Option[StringId[User]]])
+
+          val disease = fields
+            .get("disease")
+            .map(_.convertTo[CancerType])
+            .getOrElse(deserializationError(s"Patient create json object does not contain `disease` field: $json"))
+
+          val orderId = fields
+            .get("orderId")
+            .map(_.convertTo[PatientOrderId])
+            .getOrElse(deserializationError(s"Patient create json object does not contain `orderId` field: $json"))
+
+          val lastUpdate = fields
+            .get("lastUpdate")
+            .map(_.convertTo[LocalDateTime])
+            .getOrElse(deserializationError(s"Patient create json object does not contain `lastUpdate` field: $json"))
+
+          Patient(id,
+                  status,
+                  name,
+                  dob,
+                  assignee,
+                  previousStatus,
+                  previousAssignee,
+                  lastActiveUser,
+                  isUpdateRequired = false,
+                  disease,
+                  orderId,
+                  lastUpdate)
+
+        case _ => deserializationError(s"Expected Json Object as Trial, but got $json")
+      }
+    }
   }
 
 }
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
deleted file mode 100644
index 8b13789..0000000
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala
index a36bac2..a459158 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienthypothesis.scala
@@ -7,6 +7,7 @@ import xyz.driver.pdsuidomain.services.PatientHypothesisService.RichPatientHypot
 object patienthypothesis {
   import DefaultJsonProtocol._
   import common._
+  import xyz.driver.core.json._
 
   def applyUpdateToPatientHypothesis(json: JsValue, orig: PatientHypothesis): PatientHypothesis = json match {
     case JsObject(fields) =>
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala
index 5a2955f..bf1c0fd 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientissue.scala
@@ -2,6 +2,8 @@ package xyz.driver.pdsuidomain.formats.json
 
 import java.time.LocalDateTime
 
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.collection.NonEmpty
 import spray.json._
 import xyz.driver.pdsuicommon.domain.{LongId, StringId, User, UuidId}
 import xyz.driver.pdsuidomain.entities._
@@ -9,12 +11,13 @@ import xyz.driver.pdsuidomain.entities._
 object patientissue {
   import DefaultJsonProtocol._
   import common._
+  import xyz.driver.core.json._
 
   def applyUpdateToPatientIssue(json: JsValue, orig: PatientIssue): PatientIssue = {
     json.asJsObject.getFields("text", "archiveRequired") match {
       case Seq(text, archiveRequired) =>
         orig.copy(
-          text = text.convertTo[String],
+          text = text.convertTo[String Refined NonEmpty],
           archiveRequired = archiveRequired.convertTo[Boolean]
         )
 
@@ -31,7 +34,7 @@ object patientissue {
           patientId = patientId,
           lastUpdate = LocalDateTime.MIN,
           isDraft = true,
-          text = text.convertTo[String],
+          text = text.convertTo[String Refined NonEmpty],
           archiveRequired = false
         )
 
@@ -40,7 +43,7 @@ object patientissue {
 
   }
 
-  implicit val patientIssueWriter = new RootJsonWriter[PatientIssue] {
+  implicit val patientIssueWriter: RootJsonWriter[PatientIssue] = new RootJsonWriter[PatientIssue] {
     override def write(obj: PatientIssue) = JsObject(
       "id"              -> obj.id.toJson,
       "text"            -> obj.text.toJson,
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 6cc2560..dc9c5e0 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial.scala
@@ -1,10 +1,10 @@
 package xyz.driver.pdsuidomain.formats.json
 
-import java.time.{ZoneId, ZonedDateTime}
+import java.time.{LocalDateTime, ZoneId, ZonedDateTime}
 
 import spray.json._
 import xyz.driver.core.json.EnumJsonFormat
-import xyz.driver.pdsuicommon.domain.{LongId, UuidId}
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, User, UuidId}
 import xyz.driver.pdsuidomain.entities._
 
 object trial {
@@ -12,7 +12,7 @@ object trial {
   import Trial._
   import common._
 
-  implicit val trialStatusFormat = new EnumJsonFormat[Status](
+  implicit val trialStatusFormat: RootJsonFormat[Status] = new EnumJsonFormat[Status](
     "New"            -> Status.New,
     "ReviewSummary"  -> Status.ReviewSummary,
     "Summarized"     -> Status.Summarized,
@@ -47,7 +47,99 @@ object trial {
         "originalTitle"         -> obj.originalTitle.toJson
       )
 
-    override def read(json: JsValue): Trial = jsonReader[Trial].read(json)
+    override def read(json: JsValue): Trial = {
+      json match {
+        case JsObject(fields) =>
+          val id = fields
+            .get("id")
+            .map(_.convertTo[StringId[Trial]])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `id` field: $json"))
+          val externalid = fields
+            .get("externalid")
+            .map(_.convertTo[UuidId[Trial]])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `externalid` field: $json"))
+          val status = fields
+            .get("status")
+            .map(_.convertTo[Trial.Status])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `status` field: $json"))
+          val assignee = fields
+            .get("assignee")
+            .flatMap(_.convertTo[Option[StringId[User]]])
+          val previousStatus = fields
+            .get("previousStatus")
+            .flatMap(_.convertTo[Option[Trial.Status]])
+          val previousAssignee = fields
+            .get("previousAssignee")
+            .flatMap(_.convertTo[Option[StringId[User]]])
+          val lastActiveUser = fields
+            .get("lastActiveUser")
+            .flatMap(_.convertTo[Option[StringId[User]]])
+          val lastUpdate = fields
+            .get("lastUpdate")
+            .map(_.convertTo[LocalDateTime])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `lastUpdate` field: $json"))
+          val phase = fields
+            .get("phase")
+            .map(_.convertTo[String])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `phase` field: $json"))
+          val hypothesisId = fields
+            .get("hypothesisId")
+            .flatMap(_.convertTo[Option[UuidId[Hypothesis]]])
+          val studyDesignId = fields
+            .get("studyDesignId")
+            .flatMap(_.convertTo[Option[LongId[StudyDesign]]])
+          val originalStudyDesignId = fields
+            .get("originalStudyDesignId")
+            .flatMap(_.convertTo[Option[String]])
+          val isPartner = fields
+            .get("isPartner")
+            .map(_.convertTo[Boolean])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `isPartner` field: $json"))
+          val overview = fields
+            .get("overview")
+            .flatMap(_.convertTo[Option[String]])
+          val overviewTemplate = fields
+            .get("overviewTemplate")
+            .map(_.convertTo[String])
+            .getOrElse(
+              deserializationError(s"Trial create json object does not contain `overviewTemplate` field: $json"))
+          val isUpdated = fields
+            .get("isUpdated")
+            .map(_.convertTo[Boolean])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `isUpdated` field: $json"))
+          val title = fields
+            .get("title")
+            .map(_.convertTo[String])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `title` field: $json"))
+          val originalTitle = fields
+            .get("originalTitle")
+            .map(_.convertTo[String])
+            .getOrElse(deserializationError(s"Trial create json object does not contain `originalTitle` field: $json"))
+
+          Trial(
+            id,
+            externalid,
+            status,
+            assignee,
+            previousStatus,
+            previousAssignee,
+            lastActiveUser,
+            lastUpdate,
+            phase,
+            hypothesisId,
+            studyDesignId,
+            originalStudyDesignId,
+            isPartner,
+            overview,
+            overviewTemplate,
+            isUpdated,
+            title,
+            originalTitle
+          )
+
+        case _ => deserializationError(s"Expected Json Object as Trial, but got $json")
+      }
+    }
   }
 
   def applyUpdateToTrial(json: JsValue, orig: Trial): Trial = json match {
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientHypothesisFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientHypothesisFormatSuite.scala
index 270a04d..7ff1109 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientHypothesisFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientHypothesisFormatSuite.scala
@@ -1,10 +1,12 @@
 package xyz.driver.pdsuidomain.formats.json
 
+import eu.timepit.refined.numeric.NonNegative
 import spray.json._
 import org.scalatest.{FlatSpec, Matchers}
 import xyz.driver.pdsuicommon.domain.UuidId
 import xyz.driver.pdsuidomain.entities.PatientHypothesis
 import xyz.driver.pdsuidomain.services.PatientHypothesisService.RichPatientHypothesis
+import eu.timepit.refined.refineMV
 
 class PatientHypothesisFormatSuite extends FlatSpec with Matchers {
   import xyz.driver.pdsuidomain.formats.json.patienthypothesis._
@@ -15,7 +17,7 @@ class PatientHypothesisFormatSuite extends FlatSpec with Matchers {
       patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"),
       hypothesisId = UuidId("e76e2fc4-a29c-44fb-a81b-8856d06bb1d4"),
       rationale = None,
-      matchedTrials = 1
+      matchedTrials = refineMV[NonNegative](1)
     )
     val writtenJson = richPatientHypothesisWriter.write(RichPatientHypothesis(orig, isRequired = true))
 
@@ -35,7 +37,7 @@ class PatientHypothesisFormatSuite extends FlatSpec with Matchers {
       patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"),
       hypothesisId = UuidId("e76e2fc4-a29c-44fb-a81b-8856d06bb1d4"),
       rationale = None,
-      matchedTrials = 1
+      matchedTrials = refineMV[NonNegative](1)
     )
     val writtenJson = patientHypothesisWriter.write(orig)
 
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientIssueFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientIssueFormatSuite.scala
index 0d56918..d904150 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientIssueFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientIssueFormatSuite.scala
@@ -2,10 +2,12 @@ package xyz.driver.pdsuidomain.formats.json
 
 import java.time.LocalDateTime
 
+import eu.timepit.refined.collection.NonEmpty
 import spray.json._
 import org.scalatest.{FlatSpec, Matchers}
 import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
 import xyz.driver.pdsuidomain.entities.PatientIssue
+import eu.timepit.refined.refineMV
 
 class PatientIssueFormatSuite extends FlatSpec with Matchers {
   import xyz.driver.pdsuidomain.formats.json.patientissue._
@@ -17,7 +19,7 @@ class PatientIssueFormatSuite extends FlatSpec with Matchers {
       userId = StringId("userId-001"),
       lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00"),
       isDraft = false,
-      text = "message text",
+      text = refineMV[NonEmpty]("message text"),
       archiveRequired = false
     )
     val writtenJson = patientIssueWriter.write(patientIssue)
@@ -35,7 +37,7 @@ class PatientIssueFormatSuite extends FlatSpec with Matchers {
     val updatePatientIssueJson =
       """{"text":"new issue text","evidence":"issue evidence","archiveRequired":true}""".parseJson
     val expectedUpdatedPatientIssue = patientIssue.copy(
-      text = "new issue text",
+      text = refineMV[NonEmpty]("new issue text"),
       archiveRequired = true
     )
     val parsedUpdatePatientIssue = applyUpdateToPatientIssue(updatePatientIssueJson, patientIssue)