Merge branch 'master' into PDSUI-2336

6 files changed, 119 insertions, 18 deletions

diff --git a/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala b/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala
index ac5eec1..0209222 100644
--- a/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala
@@ -1,5 +1,7 @@
 package xyz.driver.pdsuicommon.parsers
 
+import java.util.UUID
+
 import xyz.driver.pdsuicommon.db.SearchFilterExpr.Dimension
 import xyz.driver.pdsuicommon.db.{SearchFilterBinaryOperation, SearchFilterExpr, SearchFilterNAryOperation}
 import xyz.driver.pdsuicommon.utils.Implicits.toStringOps
@@ -126,6 +128,14 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers {
           }
         }
 
+        "actual patientId uuid" - {
+          "should parse the full UUID as java.util.UUID type" in {
+            val filter = SearchFilterParser.parse(Seq("filters" -> "patientId EQ 4b4879f7-42b3-4b7c-a685-5c97d9e69e7c"))
+            assert(filter === Success(SearchFilterExpr.Atom.Binary(
+              Dimension(None, "patient_id"), Eq, UUID.fromString("4b4879f7-42b3-4b7c-a685-5c97d9e69e7c"))))
+          }
+        }
+
         "all operators" - {
           "should be parsed with numeric values" in check {
             val testQueryGen = queryGen(
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/ExportFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/ExportFormatSuite.scala
index 1f024c3..c976243 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/ExportFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/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/ExtractedDataFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/ExtractedDataFormatSuite.scala
index bc20280..d1d8d44 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/ExtractedDataFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/ExtractedDataFormatSuite.scala
@@ -17,8 +17,18 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers {
       documentId = LongId(101),
       keywordId = Some(LongId(201)),
       evidenceText = Some("evidence text"),
-      meta = None
-    )
+      meta = Option(TextJson(Meta(
+        evidence = None,
+        keyword =
+          Some(Meta.Keyword(
+            page = 1,
+            pageRatio = Some(1.6161616161616161d),
+            index = 0,
+            sortIndex = "1080000"
+          ))
+      )
+    )))
+
     val extractedDataLabels = List(
       ExtractedDataLabel(
         id = LongId(1),
@@ -43,11 +53,13 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers {
 
     writtenJson should be(
       """{"id":1,"documentId":101,"keywordId":201,"evidence":"evidence text","meta":null,
-        "labels":[{"id":null,"categoryId":null,"value":"Yes"},{"id":12,"categoryId":1,"value":"No"}]}""".parseJson)
+        "labels":[{"id":null,"categoryId":null,"value":"Yes"},{"id":12,"categoryId":1,"value":"No"}],
+        "meta":{"keyword":{"index":0,"page":1,"pageRatio":1.6161616161616161,"sortIndex":"1080000"}}}""".parseJson)
 
     val createExtractedDataJson =
       """{"documentId":101,"keywordId":201,"evidence":"evidence text",
-        "labels":[{"value":"Yes"},{"id":12,"categoryId":1,"value":"No"}]}""".parseJson
+        "labels":[{"value":"Yes"},{"id":12,"categoryId":1,"value":"No"}],
+        "meta":{"keyword":{"index":0,"page":1,"pageRatio":1.6161616161616161,"sortIndex":"1080000"}}}""".parseJson
     val expectedCreatedExtractedData = origRichExtractedData.copy(
       extractedData = extractedData.copy(id = LongId(0)),
       labels = extractedDataLabels.map(_.copy(id = LongId(0), dataId = LongId(0)))
@@ -80,12 +92,12 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers {
         evidenceText = Some("new evidence text"),
         meta = Some(
           TextJson(Meta(
-            keyword = Meta.Keyword(page = 1, pageRatio = None, index = 2, sortIndex = "ASC"),
-            evidence = Meta.Evidence(
+            keyword = Some(Meta.Keyword(page = 1, pageRatio = None, index = 2, sortIndex = "ASC")),
+            evidence = Some(Meta.Evidence(
               pageRatio = 1.0,
               start = Meta.TextLayerPosition(page = 1, index = 3, offset = 2),
               end = Meta.TextLayerPosition(page = 2, index = 3, offset = 10)
-            )
+            ))
           )))
       ),
       labels = updatedExtractedDataLabels
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/InterventionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/InterventionFormatSuite.scala
index ac01c34..015c7b5 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/InterventionFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/InterventionFormatSuite.scala
@@ -19,7 +19,7 @@ class InterventionFormatSuite extends FlatSpec with Matchers {
       dosage = "",
       originalDosage = "",
       isActive = true,
-      deliveryMethod = Some("pill")
+      deliveryMethod = Some("Inhalation")
     )
     val arms = List(
       InterventionArm(interventionId = intervention.id, armId = LongId(20)),
@@ -34,11 +34,11 @@ class InterventionFormatSuite extends FlatSpec with Matchers {
 
     writtenJson should be(
       """{"id":1,"name":"intervention name","typeId":10,"dosage":"","isActive":true,"arms":[20,21,22],
-        "trialId":"NCT000001","deliveryMethod":"pill","originalName":"orig name","originalDosage":"","originalType":"orig type"}""".parseJson)
+        "trialId":"NCT000001","deliveryMethod":"Inhalation","originalName":"orig name","originalDosage":"","originalType":"orig type"}""".parseJson)
 
     val createInterventionJson =
       """{"id":1,"name":"intervention name","typeId":10,"dosage":"","isActive":true,"arms":[20,21,22],
-        "trialId":"NCT000001","deliveryMethod":"pill"}""".parseJson
+        "trialId":"NCT000001","deliveryMethod":"Inhalation"}""".parseJson
     val parsedCreateIntervention = interventionFormat.read(createInterventionJson)
     val expectedCreateIntervention = parsedCreateIntervention.copy(
       intervention = intervention.copy(id = LongId(0), originalType = None, originalName = "intervention name"),
@@ -46,9 +46,9 @@ class InterventionFormatSuite extends FlatSpec with Matchers {
     )
     parsedCreateIntervention should be(expectedCreateIntervention)
 
-    val updateInterventionJson = """{"dosage":"descr","arms":[21,22]}""".parseJson
+    val updateInterventionJson = """{"dosage":"descr","deliveryMethod":null,"arms":[21,22]}""".parseJson
     val expectedUpdatedIntervention = orig.copy(
-      intervention = intervention.copy(dosage = "descr"),
+      intervention = intervention.copy(dosage = "descr", deliveryMethod = None),
       arms = List(
         InterventionArm(interventionId = intervention.id, armId = LongId(21)),
         InterventionArm(interventionId = intervention.id, armId = LongId(22))
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/MedicalRecordFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/MedicalRecordFormatSuite.scala
index e811a29..b4e37a2 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/MedicalRecordFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/MedicalRecordFormatSuite.scala
@@ -12,6 +12,80 @@ class MedicalRecordFormatSuite extends FlatSpec with Matchers {
   import xyz.driver.pdsuidomain.formats.json.record._
   import MedicalRecord._
 
+  "Json format for MedicalRecord.Meta" should "read and write correct JSON" in {
+    val duplicate1 = Meta.Duplicate(
+      startPage = 1.0d,
+      endPage = 2.0d,
+      startOriginalPage = 1.0d,
+      endOriginalPage = Some(2.0d)
+    )
+
+    val duplicate2 = Meta.Duplicate(
+      startPage = 1.0d,
+      endPage = 2.0d,
+      startOriginalPage = 1.0d,
+      endOriginalPage = None
+    )
+
+    val reorder = Meta.Reorder(
+      Seq(1, 2)
+    )
+
+    val rotation = Meta.Rotation(
+      Map("item1" -> 1, "item2" -> 2)
+    )
+
+    val writtenDuplicateJson1 =
+      duplicateMetaFormat.write(duplicate1)
+
+    val writtenDuplicateJson2 =
+      duplicateMetaFormat.write(duplicate2)
+
+    val writtenReorderJson =
+      reorderMetaFormat.write(reorder)
+
+    val writtenRotationJson =
+      rotateMetaFormat.write(rotation)
+
+    writtenDuplicateJson1 should be(
+      """{"startOriginalPage":1.0,"endPage":2.0,"startPage":1.0,"type":"duplicate","endOriginalPage":2.0}""".parseJson)
+
+    writtenDuplicateJson2 should be(
+      """{"startOriginalPage":1.0,"endPage":2.0,"startPage":1.0,"type":"duplicate","endOriginalPage":null}""".parseJson)
+
+    writtenReorderJson should be(
+      """{"type":"reorder","items":[1,2]}""".parseJson)
+
+    writtenRotationJson should be(
+      """{"type":"rotation","items":{"item1":1,"item2":2}}""".parseJson)
+
+    val parsedDuplicateJson1 =
+      duplicateMetaFormat.read(writtenDuplicateJson1)
+
+    val parsedDuplicateJson2 =
+      duplicateMetaFormat.read(writtenDuplicateJson2)
+
+    val parsedReorderJson =
+      reorderMetaFormat.read(writtenReorderJson)
+
+    val parsedRotationJson =
+      rotateMetaFormat.read(writtenRotationJson)
+
+    duplicate1 should be(parsedDuplicateJson1)
+
+    duplicate2 should be(parsedDuplicateJson2)
+
+    reorder should be(parsedReorderJson)
+
+    rotation should be(parsedRotationJson)
+
+    duplicate1 should be(recordMetaTypeFormat.read(recordMetaTypeFormat.write(duplicate1)))
+    duplicate2 should be(recordMetaTypeFormat.read(recordMetaTypeFormat.write(duplicate2)))
+    reorder should be(recordMetaTypeFormat.read(recordMetaTypeFormat.write(reorder)))
+    rotation should be(recordMetaTypeFormat.read(recordMetaTypeFormat.write(rotation)))
+  }
+
+
   "Json format for MedicalRecord" should "read and write correct JSON" in {
     val orig = MedicalRecord(
       id = LongId(1),
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientCriterionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientCriterionFormatSuite.scala
index 2e193c7..93284d9 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientCriterionFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/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))