Fixing IN in filters, Model from EVLS added to common, Reusing domain model labelsv0.5.1

7 files changed, 108 insertions, 4 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 732bcad..743f885 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
@@ -1,6 +1,7 @@
 package xyz.driver.pdsuidomain.formats.json.sprayformats
 
 import spray.json._
+import xyz.driver.entities.labels.{Label, LabelCategory}
 import xyz.driver.pdsuicommon.domain.{LongId, StringId}
 import xyz.driver.pdsuidomain.entities._
 import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion
@@ -29,7 +30,7 @@ object criterion {
 
       val categoryId = fields
         .get("categoryId")
-        .map(_.convertTo[LongId[Category]])
+        .map(_.convertTo[LongId[LabelCategory]])
 
       val value = fields
         .get("value")
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala
index 8119d35..7ec6ef5 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala
@@ -1,7 +1,6 @@
 package xyz.driver.pdsuidomain.formats.json.sprayformats
 
 import spray.json._
-import xyz.driver.pdsuidomain.entities._
 import xyz.driver.pdsuidomain.entities.DocumentType
 
 object documenttype {
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala
new file mode 100644
index 0000000..30ceae2
--- /dev/null
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala
@@ -0,0 +1,101 @@
+package xyz.driver.pdsuidomain.formats.json.sprayformats
+
+import spray.json._
+import DefaultJsonProtocol._
+import xyz.driver.core.Id
+import xyz.driver.core.json._
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.pdsuidomain.entities.eligibility._
+
+object eligibility {
+  import xyz.driver.formats.json.assay._
+  import xyz.driver.formats.json.common._
+  import xyz.driver.formats.json.labels._
+  import xyz.driver.formats.json.process._
+  import xyz.driver.pdsuidomain.formats.json.sprayformats.document._
+  import xyz.driver.pdsuidomain.formats.json.sprayformats.record._
+  import xyz.driver.pdsuidomain.formats.json.sprayformats.export._
+
+  implicit val molecularDocumentFormat: RootJsonFormat[MolecularEvidenceDocument] = jsonFormat7(
+    MolecularEvidenceDocument)
+  implicit val clinicalDocumentFormat: RootJsonFormat[ClinicalEvidenceDocument] = jsonFormat7(ClinicalEvidenceDocument)
+
+  implicit val evidenceDocumentFormat: RootJsonFormat[EvidenceDocument] =
+    GadtJsonFormat.create[EvidenceDocument]("documentType") {
+      case _: MolecularEvidenceDocument => "Molecular"
+      case _: ClinicalEvidenceDocument  => "Clinical"
+    } {
+      case "Molecular" => molecularDocumentFormat
+      case "Clinical"  => clinicalDocumentFormat
+    }
+
+  implicit object evidenceFormat extends RootJsonFormat[Evidence] {
+
+    override def write(evidence: Evidence): JsValue = {
+      JsObject(
+        "evidenceId"     -> evidence.evidenceId.toJson,
+        "evidenceText"   -> evidence.evidenceText.toJson,
+        "labelValue"     -> evidence.labelValue.toJson,
+        "document"       -> evidence.document.toJson,
+        "isPrimaryValue" -> evidence.isPrimaryValue.toJson
+      )
+    }
+
+    override def read(json: JsValue): Evidence = {
+      json match {
+        case JsObject(fields) =>
+          val evidenceId = fields
+            .get("evidenceId")
+            .map(_.convertTo[Id[Evidence]])
+
+          val evidenceText = fields
+            .get("evidenceText")
+            .map(_.convertTo[String])
+            .getOrElse(deserializationError(s"Evidence json object do not contain 'evidenceText' field: $json"))
+
+          val labelValue = fields
+            .get("labelValue")
+            .map(_.convertTo[LabelValue])
+            .getOrElse(deserializationError(s"Evidence json object do not contain 'labelValue' field: $json"))
+
+          val isDriverDocument = fields
+            .get("document")
+            .flatMap {
+              case JsObject(fieldMap) =>
+                fieldMap
+                  .get("isDriverDocument")
+                  .map(_.convertTo[Boolean])
+              case _ => deserializationError(s"Expected Json Object as 'isDriverDocument', but got $json")
+            }
+            .getOrElse(deserializationError(s"Evidence json object do not contain 'document' field: $json"))
+
+          val document = customDocumentParser(isDriverDocument, fields, json)
+
+          val isPrimaryValue = fields
+            .get("isPrimaryValue")
+            .map(_.convertTo[Option[Boolean]])
+            .getOrElse(deserializationError(s"Evidence json object do not contain 'isPrimaryValue' field: $json"))
+
+          Evidence(evidenceId, evidenceText, labelValue, document, isPrimaryValue)
+        case _ => deserializationError(s"Expected Json Object as 'Evidence', but got $json")
+      }
+    }
+
+    def customDocumentParser(isDriverDocument: Boolean,
+                             fields: Map[String, JsValue],
+                             json: JsValue): EvidenceDocument = {
+      fields.get("document").fold { deserializationError(s"Expected Json Object as 'Document', but got $json") } {
+        document =>
+          if (isDriverDocument) document.convertTo[MolecularEvidenceDocument]
+          else document.convertTo[ClinicalEvidenceDocument]
+      }
+    }
+  }
+
+  implicit def labelWithEvidenceJsonFormat: RootJsonFormat[LabelWithEvidence] = jsonFormat2(LabelWithEvidence)
+
+  implicit def labelRankingFormat: RootJsonFormat[LabelMismatchRank]     = jsonFormat4(LabelMismatchRank)
+  implicit def labelRankingsFormat: RootJsonFormat[MismatchRankedLabels] = jsonFormat2(MismatchRankedLabels)
+
+  implicit def matchedPatientFormat: RootJsonFormat[MatchedPatient] = jsonFormat6(MatchedPatient)
+}
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 2a1fe46..39d5c59 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
@@ -1,7 +1,8 @@
 package xyz.driver.pdsuidomain.formats.json.sprayformats
 
 import spray.json._
-import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Label}
+import xyz.driver.entities.labels.Label
+import xyz.driver.pdsuidomain.entities.{Arm, Criterion}
 import xyz.driver.pdsuidomain.entities.export.patient._
 import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels}
 
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala
index 42473bc..d6eadbd 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala
@@ -1,6 +1,7 @@
 package xyz.driver.pdsuidomain.formats.json.sprayformats
 
 import spray.json._
+import xyz.driver.entities.labels.{Label, LabelCategory}
 import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson}
 import xyz.driver.pdsuidomain.entities._
 import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData
@@ -39,7 +40,7 @@ object extracteddata {
 
       val categoryId = fields
         .get("categoryId")
-        .map(_.convertTo[LongId[Category]])
+        .map(_.convertTo[LongId[LabelCategory]])
 
       val value = fields
         .get("value")
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 53e927d..b091746 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
@@ -1,6 +1,7 @@
 package xyz.driver.pdsuidomain.formats.json.sprayformats
 
 import spray.json._
+import xyz.driver.entities.labels.Label
 import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId}
 import xyz.driver.pdsuidomain.entities._
 import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providerttype.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala
index 385feb2..385feb2 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providerttype.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala