Merge branch 'master' into synch-refactor

4 files changed, 93 insertions, 16 deletions

diff --git a/src/main/scala/xyz/driver/pdsuicommon/db/SlickPostgresQueryBuilder.scala b/src/main/scala/xyz/driver/pdsuicommon/db/SlickPostgresQueryBuilder.scala
index f882441..a56ab9a 100644
--- a/src/main/scala/xyz/driver/pdsuicommon/db/SlickPostgresQueryBuilder.scala
+++ b/src/main/scala/xyz/driver/pdsuicommon/db/SlickPostgresQueryBuilder.scala
@@ -2,8 +2,7 @@ package xyz.driver.pdsuicommon.db
 
 import java.time.{LocalDateTime, ZoneOffset}
 
-import slick.driver.JdbcProfile
-import slick.jdbc.GetResult
+import slick.jdbc.{JdbcProfile, GetResult}
 import xyz.driver.core.database.SlickDal
 import xyz.driver.pdsuicommon.logging._
 
diff --git a/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala
index ab2757b..0daa84d 100644
--- a/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala
+++ b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala
@@ -3,8 +3,7 @@ package xyz.driver.pdsuicommon.db
 import java.sql.PreparedStatement
 import java.time.LocalDateTime
 
-import slick.driver.JdbcProfile
-import slick.jdbc.{PositionedParameters, SQLActionBuilder, SetParameter}
+import slick.jdbc.{JdbcProfile, PositionedParameters, SQLActionBuilder, SetParameter}
 import xyz.driver.pdsuicommon.db.Sorting.{Dimension, Sequential}
 import xyz.driver.pdsuicommon.db.SortingOrder.{Ascending, Descending}
 
diff --git a/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala b/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala
index e0adeb8..e46e11c 100644
--- a/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala
+++ b/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala
@@ -15,10 +15,7 @@ object SearchFilterParser {
   private object BinaryAtomFromTuple {
     def unapply(input: (SearchFilterExpr.Dimension, (String, Any))): Option[SearchFilterExpr.Atom.Binary] = {
       val (dimensionName, (strOperation, value)) = input
-      val updatedValue = value match {
-        case s: String => s.safeTrim
-        case a         => a
-      }
+      val updatedValue                           = trimIfString(value)
 
       parseOperation(strOperation.toLowerCase).map { op =>
         SearchFilterExpr.Atom.Binary(dimensionName, op, updatedValue.asInstanceOf[AnyRef])
@@ -30,15 +27,24 @@ object SearchFilterParser {
     // Compiler warning: unchecked since it is eliminated by erasure, if we user Seq[String]
     def unapply(input: (SearchFilterExpr.Dimension, (String, Seq[_]))): Option[SearchFilterExpr.Atom.NAry] = {
       val (dimensionName, (strOperation, xs)) = input
+      val updatedValues                       = xs.map(trimIfString)
+
       if (strOperation.toLowerCase == "in") {
-        val values = xs.asInstanceOf[Seq[String]].map(_.safeTrim)
-        Some(SearchFilterExpr.Atom.NAry(dimensionName, SearchFilterNAryOperation.In, values))
+        Some(
+          SearchFilterExpr.Atom
+            .NAry(dimensionName, SearchFilterNAryOperation.In, updatedValues.map(_.asInstanceOf[AnyRef])))
       } else {
         None
       }
     }
   }
 
+  private def trimIfString(value: Any) =
+    value match {
+      case s: String => s.safeTrim
+      case a         => a
+    }
+
   private val operationsMapping = {
     import xyz.driver.pdsuicommon.db.SearchFilterBinaryOperation._
 
@@ -96,7 +102,7 @@ object SearchFilterParser {
 
   private val nAryValueParser: Parser[String] = P(CharPred(_ != ',').rep(min = 1).!)
 
-  private val longParser: Parser[Long] = P(CharIn('0' to '9').rep(1).!.map(_.toLong))
+  private val longParser: Parser[Long] = P(CharIn('0' to '9').rep(min = 1).!.map(_.toLong))
 
   private val binaryAtomParser: Parser[SearchFilterExpr.Atom.Binary] = P(
     dimensionParser ~ whitespaceParser ~ (
@@ -109,7 +115,8 @@ object SearchFilterParser {
 
   private val nAryAtomParser: Parser[SearchFilterExpr.Atom.NAry] = P(
     dimensionParser ~ whitespaceParser ~ (
-      naryOperatorParser ~/ whitespaceParser ~/ nAryValueParser.!.rep(min = 1, sep = ",")
+      naryOperatorParser ~ whitespaceParser ~
+        (longParser.rep(min = 1, sep = ",") | nAryValueParser.!.rep(min = 1, sep = ","))
     ) ~ End
   ).map {
     case NAryAtomFromTuple(atom) => atom
diff --git a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala
index 6c87858..83c4e6f 100644
--- a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala
+++ b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala
@@ -4,7 +4,7 @@ import java.time.{LocalDate, LocalDateTime}
 
 import io.swagger.models.properties.Property
 import spray.json.JsValue
-import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, TextJson, UuidId}
 import xyz.driver.pdsuidomain.entities._
 import xyz.driver.pdsuidomain.formats.json.sprayformats.arm._
 import xyz.driver.pdsuidomain.formats.json.sprayformats.criterion._
@@ -15,25 +15,29 @@ import xyz.driver.pdsuidomain.formats.json.sprayformats.trial._
 import xyz.driver.pdsuidomain.formats.json.sprayformats.trialhistory._
 import xyz.driver.pdsuidomain.formats.json.sprayformats.trialissue._
 import xyz.driver.core.swagger.CustomSwaggerJsonConverter._
+import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue
 import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion
+import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData
+
+import scala.collection.immutable
 
 object CustomSwaggerJsonFormats {
 
-  val customCommonProperties = Map[Class[_], Property](
+  val customCommonProperties = immutable.Map[Class[_], Property](
     classOf[LocalDateTime] -> stringProperty(example = Some("2010-12-31'T'18:59:59Z")),
     classOf[LocalDate]     -> stringProperty(example = Some("2010-12-31")),
     classOf[UuidId[_]]     -> stringProperty(example = Some("370b0450-35cb-4aab-ba74-0145be75add5")),
     classOf[StringId[_]]   -> stringProperty(),
     classOf[LongId[_]]     -> stringProperty()
   )
-  val customTrialCurationProperties = Map[Class[_], Property](
+  val customTrialCurationProperties = immutable.Map[Class[_], Property](
     classOf[Trial.Status]        -> stringProperty(),
     classOf[Trial.Condition]     -> stringProperty(),
     classOf[TrialHistory.Action] -> stringProperty(),
     classOf[TrialHistory.State]  -> stringProperty()
   ) ++ customCommonProperties
 
-  val customTrialCurationObjectsExamples = Map[Class[_], JsValue](
+  val customTrialCurationObjectsExamples = immutable.Map[Class[_], JsValue](
     classOf[Trial] -> trialWriter.write(xyz.driver.pdsuidomain.fakes.entities.trialcuration.nextTrial()),
     classOf[Arm]   -> armFormat.write(xyz.driver.pdsuidomain.fakes.entities.trialcuration.nextArm()),
     classOf[TrialHistory] -> trialHistoryFormat.write(
@@ -52,4 +56,72 @@ object CustomSwaggerJsonFormats {
       xyz.driver.pdsuidomain.fakes.entities.trialcuration.nextStudyDesign())
   )
 
+  // records-processing-service
+  object Rep {
+    import xyz.driver.pdsuidomain.fakes.entities.rep
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.document
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.documentissue
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.documenthistory
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.record
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.recordissue
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.recordhistory
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.bridgeuploadqueue
+    import xyz.driver.pdsuidomain.formats.json.sprayformats.extracteddata
+
+    val customRepObjectsExamples = immutable.Map[Class[_], JsValue](
+      classOf[Document] ->
+        document.documentFormat.write(rep.DocumentGen.nextDocument()),
+      classOf[Document.Meta] ->
+        document.documentMetaFormat.write(rep.DocumentGen.nextDocumentMeta()),
+      classOf[TextJson[Document.Meta]] ->
+        document.fullDocumentMetaFormat.write(rep.DocumentGen.nextDocumentMetaJson()),
+      classOf[Document.RequiredType] ->
+        document.requiredTypeFormat.write(rep.DocumentGen.nextDocumentRequiredType()),
+      classOf[Document.Status] ->
+        document.documentStatusFormat.write(rep.DocumentGen.nextDocumentStatus()),
+      classOf[DocumentIssue] ->
+        documentissue.documentIssueFormat.write(rep.DocumentGen.nextDocumentIssue()),
+      classOf[DocumentHistory] ->
+        documenthistory.documentHistoryFormat.write(rep.DocumentGen.nextDocumentHistory()),
+      classOf[DocumentHistory.Action] ->
+        documenthistory.documentActionFormat.write(rep.DocumentGen.nextDocumentHistoryAction()),
+      classOf[DocumentHistory.State] ->
+        documenthistory.documentStateFormat.write(rep.DocumentGen.nextDocumentHistoryState()),
+      classOf[ProviderType] ->
+        record.providerTypeFormat.write(rep.MedicalRecordGen.nextProviderType()),
+      classOf[TextJson[List[MedicalRecord.Meta]]] ->
+        record.recordMetaFormat.write(rep.MedicalRecordGen.nextMedicalRecordMetasJson()),
+      classOf[MedicalRecord] ->
+        record.recordFormat.write(rep.MedicalRecordGen.nextMedicalRecord()),
+      classOf[MedicalRecord.Meta] ->
+        record.recordMetaTypeFormat.write(rep.MedicalRecordGen.nextMedicalRecordMeta()),
+      classOf[MedicalRecord.Status] ->
+        record.recordStatusFormat.write(rep.MedicalRecordGen.nextMedicalRecordStatus()),
+      classOf[MedicalRecordIssue] ->
+        recordissue.recordIssueFormat.write(rep.MedicalRecordGen.nextMedicalRecordIssue()),
+      classOf[MedicalRecordHistory] ->
+        recordhistory.recordHistoryFormat.write(rep.MedicalRecordGen.nextMedicalRecordHistory()),
+      classOf[MedicalRecordHistory.Action] ->
+        recordhistory.recordActionFormat.write(rep.MedicalRecordGen.nextMedicalRecordHistoryAction()),
+      classOf[MedicalRecordHistory.State] ->
+        recordhistory.recordStateFormat.write(rep.MedicalRecordGen.nextMedicalRecordHistoryState()),
+      classOf[BridgeUploadQueue.Item] ->
+        bridgeuploadqueue.queueUploadItemFormat.write(rep.BridgeUploadQueueGen.nextBridgeUploadQueueItem()),
+      classOf[ExtractedData.Meta] ->
+        extracteddata.extractedDataMetaFormat.write(rep.ExtractedDataGen.nextExtractedDataMeta()),
+      classOf[ExtractedData.Meta.Evidence] ->
+        extracteddata.metaEvidenceFormat.write(rep.ExtractedDataGen.nextExtractedDataMetaEvidence()),
+      classOf[ExtractedData.Meta.Keyword] ->
+        extracteddata.metaKeywordFormat.write(rep.ExtractedDataGen.nextExtractedDataMetaKeyword()),
+      classOf[ExtractedData.Meta.TextLayerPosition] ->
+        extracteddata.metaTextLayerPositionFormat.write(rep.ExtractedDataGen.nextExtractedDataMetaTextLayerPosition()),
+      classOf[TextJson[ExtractedData.Meta]] ->
+        extracteddata.fullExtractedDataMetaFormat.write(rep.ExtractedDataGen.nextExtractedDataMetaJson()),
+      classOf[RichExtractedData] ->
+        extracteddata.extractedDataFormat.write(rep.ExtractedDataGen.nextRichExtractedData()),
+      classOf[ExtractedDataLabel] ->
+        extracteddata.extractedDataLabelWriter.write(rep.ExtractedDataGen.nextExtractedDataLabel())
+    )
+  }
+
 }