diff options
Diffstat (limited to 'src/main/scala/xyz/driver')
20 files changed, 207 insertions, 67 deletions
diff --git a/src/main/scala/xyz/driver/pdsuicommon/acl/ACL.scala b/src/main/scala/xyz/driver/pdsuicommon/acl/ACL.scala index 180ebf9..3eb1a65 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/acl/ACL.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/acl/ACL.scala @@ -144,7 +144,9 @@ object ACL extends PhiLogging { object Hypothesis extends BaseACL( label = "hypothesis", - read = Set(TrialSummarizer, TrialAdmin) ++ TreatmentMatchingRoles + read = Set(TrialSummarizer, TrialAdmin) ++ TreatmentMatchingRoles, + create = Set(TrialAdmin), + delete = Set(TrialAdmin) ) object Criterion diff --git a/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala index 7366151..9962edf 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala @@ -6,6 +6,7 @@ import java.time.LocalDateTime import slick.jdbc.{JdbcProfile, PositionedParameters, SQLActionBuilder, SetParameter} import xyz.driver.pdsuicommon.db.Sorting.{Dimension, Sequential} import xyz.driver.pdsuicommon.db.SortingOrder.{Ascending, Descending} +import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import scala.concurrent.{ExecutionContext, Future} @@ -44,6 +45,18 @@ object SlickQueryBuilder { pp.setObject(v, JDBCType.BINARY.getVendorTypeNumber) } } + + implicit def setLongIdQueryParameter[T]: SetParameter[LongId[T]] = SetParameter[LongId[T]] { (v, pp) => + pp.setLong(v.id) + } + + implicit def setStringIdQueryParameter[T]: SetParameter[StringId[T]] = SetParameter[StringId[T]] { (v, pp) => + pp.setString(v.id) + } + + implicit def setUuidIdQueryParameter[T]: SetParameter[UuidId[T]] = SetParameter[UuidId[T]] { (v, pp) => + pp.setObject(v.id, JDBCType.BINARY.getVendorTypeNumber) + } } final case class SlickTableLink(keyColumnName: String, foreignTableName: String, foreignKeyColumnName: String) @@ -160,7 +173,7 @@ sealed trait SlickQueryBuilderParameters { def isNull(string: AnyRef) = Option(string).isEmpty || string.toString.toLowerCase == "null" def escapeDimension(dimension: SearchFilterExpr.Dimension) = { - s"$escapedTableName.$qs${dimension.name}$qs" + s"${dimension.tableName.map(t => s"$qs$databaseName$qs.$qs$t$qs").getOrElse(escapedTableName)}.$qs${dimension.name}$qs" } def filterToSqlMultiple(operands: Seq[SearchFilterExpr]) = operands.collect { @@ -174,9 +187,9 @@ sealed trait SlickQueryBuilderParameters { if (conditions.nonEmpty) { val condition = conditions.head if (first) { - multipleSqlToAction(false, op, conditions.tail, condition) + multipleSqlToAction(first = false, op, conditions.tail, condition) } else { - multipleSqlToAction(false, op, conditions.tail, sql concat sql" #${op} " concat condition) + multipleSqlToAction(first = false, op, conditions.tail, sql concat sql" #${op} " concat condition) } } else sql } @@ -184,9 +197,9 @@ sealed trait SlickQueryBuilderParameters { def concatenateParameters(sql: SQLActionBuilder, first: Boolean, tail: Seq[AnyRef]): SQLActionBuilder = { if (tail.nonEmpty) { if (!first) { - concatenateParameters(sql concat sql""",${tail.head}""", false, tail.tail) + concatenateParameters(sql concat sql""",${tail.head}""", first = false, tail.tail) } else { - concatenateParameters(sql"""(${tail.head}""", false, tail.tail) + concatenateParameters(sql"""(${tail.head}""", first = false, tail.tail) } } else sql concat sql")" } @@ -196,10 +209,10 @@ sealed trait SlickQueryBuilderParameters { sql"" case AllowAll => - sql"1" + sql"1=1" case DenyAll => - sql"0" + sql"1=0" case Atom.Binary(dimension, Eq, value) if isNull(value) => sql"#${escapeDimension(dimension)} is NULL" @@ -232,17 +245,19 @@ sealed trait SlickQueryBuilderParameters { case SearchFilterNAryOperation.NotIn => sql" not in " } - val formattedValues = if (values.nonEmpty) { - concatenateParameters(sql"", true, values) - } else sql"NULL" - sql"#${escapeDimension(dimension)}" concat sqlOp concat formattedValues + if (values.nonEmpty) { + val formattedValues = concatenateParameters(sql"", first = true, values) + sql"#${escapeDimension(dimension)}" concat sqlOp concat formattedValues + } else { + sql"1=0" + } case Intersection(operands) => - val filter = multipleSqlToAction(true, "and", filterToSqlMultiple(operands), sql"") + val filter = multipleSqlToAction(first = true, "and", filterToSqlMultiple(operands), sql"") sql"(" concat filter concat sql")" case Union(operands) => - val filter = multipleSqlToAction(true, "or", filterToSqlMultiple(operands), sql"") + val filter = multipleSqlToAction(first = true, "or", filterToSqlMultiple(operands), sql"") sql"(" concat filter concat sql")" } } diff --git a/src/main/scala/xyz/driver/pdsuicommon/http/Directives.scala b/src/main/scala/xyz/driver/pdsuicommon/http/Directives.scala index fd1856b..37e7687 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/http/Directives.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/http/Directives.scala @@ -3,6 +3,7 @@ package xyz.driver.pdsuicommon.http import akka.http.scaladsl.server._ import akka.http.scaladsl.server.Directives._ import akka.http.scaladsl.model._ +import xyz.driver.core.app.DriverApp import xyz.driver.core.rest.ContextHeaders import xyz.driver.entities.users.AuthUserInfo import xyz.driver.pdsuicommon.auth._ @@ -88,7 +89,7 @@ trait Directives { val text = errorsResponseJsonFormat.write(err).toString() HttpEntity(ContentTypes.`application/json`, text) } - RejectionHandler.default.mapRejectionResponse { + DriverApp.rejectionHandler.mapRejectionResponse { case res @ HttpResponse(_, _, ent: HttpEntity.Strict, _) => res.copy(entity = wrapContent(ent.data.utf8String)) case x => x // pass through all other types of responses diff --git a/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala b/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala index 85e9149..718a42d 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParser.scala @@ -1,5 +1,7 @@ package xyz.driver.pdsuicommon.parsers +import java.util.UUID + import xyz.driver.pdsuicommon.utils.Implicits.{toCharOps, toStringOps} import fastparse.all._ import fastparse.core.Parsed @@ -79,7 +81,7 @@ object SearchFilterParser { } private val numericOperatorParser: Parser[String] = { - P(IgnoreCase("eq") | ((IgnoreCase("gt") | IgnoreCase("lt")) ~ IgnoreCase("eq").?)).! + P(IgnoreCase("eq") | IgnoreCase("noteq") | ((IgnoreCase("gt") | IgnoreCase("lt")) ~ IgnoreCase("eq").?)).! } private val naryOperatorParser: Parser[String] = P(IgnoreCase("in")).! @@ -89,10 +91,8 @@ object SearchFilterParser { case _ => true } - // Exclude Unicode "digits" - private val digitsParser: Parser[String] = P(CharIn('0' to '9').rep(min = 1).!) + private val digitsParser: Parser[String] = P(CharIn('0' to '9').rep(min = 1).!) // Exclude Unicode "digits" - // @TODO Make complex checking here private val numberParser: Parser[String] = P(isPositiveParser ~ digitsParser.! ~ ("." ~ digitsParser).!.?).map { case (false, intPart, Some(fracPart)) => s"-$intPart.${fracPart.tail}" case (false, intPart, None) => s"-$intPart" @@ -107,11 +107,20 @@ object SearchFilterParser { private val booleanParser: Parser[Boolean] = P((IgnoreCase("true") | IgnoreCase("false")).!.map(_.toBoolean)) + private val hexDigit: Parser[String] = P((CharIn('a' to 'f') | CharIn('A' to 'F') | CharIn('0' to '9')).!) + + private val uuidParser: Parser[UUID] = + P( + hexDigit.rep(8).! ~ "-" ~ hexDigit.rep(4).! ~ "-" ~ hexDigit.rep(4).! ~ "-" ~ hexDigit.rep(4).! ~ "-" ~ hexDigit + .rep(12) + .!).map { + case (group1, group2, group3, group4, group5) => UUID.fromString(s"$group1-$group2-$group3-$group4-$group5") + } + private val binaryAtomParser: Parser[SearchFilterExpr.Atom.Binary] = P( - dimensionParser ~ whitespaceParser ~ ( - (numericOperatorParser.! ~ whitespaceParser ~ (longParser | booleanParser | numberParser.!)) | - (commonOperatorParser.! ~ whitespaceParser ~ AnyChar.rep(min = 1).!) - ) ~ End + dimensionParser ~ whitespaceParser ~ + ((numericOperatorParser.! ~ whitespaceParser ~ (longParser | numberParser.!) ~ End) | + (commonOperatorParser.! ~ whitespaceParser ~ (uuidParser | booleanParser | AnyChar.rep(min = 1).!) ~ End)) ).map { case BinaryAtomFromTuple(atom) => atom } @@ -119,9 +128,9 @@ object SearchFilterParser { private val nAryAtomParser: Parser[SearchFilterExpr.Atom.NAry] = P( dimensionParser ~ whitespaceParser ~ ( naryOperatorParser ~ whitespaceParser ~ - (longParser.rep(min = 1, sep = ",") | booleanParser.rep(min = 1, sep = ",") | nAryValueParser.!.rep(min = 1, - sep = ",")) - ) ~ End + ((longParser.rep(min = 1, sep = ",") ~ End) | (booleanParser.rep(min = 1, sep = ",") ~ End) | + (nAryValueParser.!.rep(min = 1, sep = ",") ~ End)) + ) ).map { case NAryAtomFromTuple(atom) => atom } diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala index 352cf55..569375a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala @@ -17,7 +17,7 @@ final case class ExtractedData(id: LongId[ExtractedData] = LongId(0L), object ExtractedData { - final case class Meta(keyword: Meta.Keyword, evidence: Meta.Evidence) + final case class Meta(keyword: Option[Meta.Keyword], evidence: Option[Meta.Evidence]) object Meta { final case class Evidence(pageRatio: Double, start: TextLayerPosition, end: TextLayerPosition) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala index 79a19ed..7027eef 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala @@ -9,11 +9,11 @@ import xyz.driver.pdsuicommon.logging._ object PatientCriterion { implicit def toPhiString(x: PatientCriterion): PhiString = { import x._ - phi"PatientCriterion(id=$id, patientLabelId=$patientLabelId, trialId=${Unsafe(trialId)}, nctId=${Unsafe(nctId)}, " + + phi"PatientCriterion(id=$id, patientLabelId=$patientLabelId, trialId=${Unsafe(trialId)}, nctId=$nctId, " + phi"criterionId=$criterionId, criterionValue=${Unsafe(criterionValue)}, " + phi"isImplicitMatch=$criterionIsDefining), criterionIsDefining=${Unsafe(criterionIsDefining)}, " + phi"eligibilityStatus=${Unsafe(eligibilityStatus)}, verifiedEligibilityStatus=${Unsafe(verifiedEligibilityStatus)}, " + - phi"isVerified=${Unsafe(isVerified)}, lastUpdate=${Unsafe(lastUpdate)}" + phi"isVerified=${Unsafe(isVerified)}, lastUpdate=${Unsafe(lastUpdate)}, inclusion=${Unsafe(inclusion)}" } /** @@ -52,7 +52,8 @@ final case class PatientCriterion(id: LongId[PatientCriterion], verifiedEligibilityStatus: Option[LabelValue], isVerified: Boolean, isVisible: Boolean, - lastUpdate: LocalDateTime) { + lastUpdate: LocalDateTime, + inclusion: Option[Boolean]) { def isIneligibleForEv: Boolean = eligibilityStatus.contains(LabelValue.No) && isVerified } diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala index 8376e34..98bd084 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala @@ -11,13 +11,14 @@ final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion], armIds: Set[LongId[EligibilityArm]], criteria: String, isCompound: Boolean, - isDefining: Boolean) + isDefining: Boolean, + inclusion: Option[Boolean]) object ExportTrialLabelCriterion { implicit def toPhiString(x: ExportTrialLabelCriterion): PhiString = { import x._ phi"TrialLabelCriterion(criterionId=$criterionId, value=$value, labelId=$labelId, " + - phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining)" + phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining), inclusion=${Unsafe(inclusion)}" } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala index 2c7d0e0..33da392 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala @@ -28,7 +28,8 @@ object export { armIds = setOf(nextLongId[EligibilityArm]), criteria = nextString(100), isCompound = nextBoolean(), - isDefining = nextBoolean() + isDefining = nextBoolean(), + inclusion = nextOption(nextBoolean()) ) def nextExportTrialWithLabels(): ExportTrialWithLabels = diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala index 86583c1..3a018fa 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/recordprocessing.scala @@ -245,13 +245,13 @@ object recordprocessing { def nextExtractedDataMeta(): Meta = { ExtractedData.Meta( - nextExtractedDataMetaKeyword(), - nextExtractedDataMetaEvidence() + nextOption(nextExtractedDataMetaKeyword()), + nextOption(nextExtractedDataMetaEvidence()) ) } def nextExtractedDataMetaJson(): TextJson[Meta] = - nextTextJson(ExtractedData.Meta(nextExtractedDataMetaKeyword(), nextExtractedDataMetaEvidence())) + nextTextJson(nextExtractedDataMeta()) def nextExtractedData(): ExtractedData = { ExtractedData( 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 2a06998..94c41ff 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/treatmentmatching.scala @@ -86,7 +86,8 @@ object treatmentmatching { verifiedEligibilityStatus = generators.nextOption(fakes.entities.labels.nextLabelValue()), isVerified = generators.nextBoolean(), isVisible = generators.nextBoolean(), - lastUpdate = nextLocalDateTime + lastUpdate = nextLocalDateTime, + inclusion = generators.nextOption(generators.nextBoolean()) ) def nextDraftPatientCriterion(): DraftPatientCriterion = DraftPatientCriterion( 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 new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiPartialDocument.scala @@ -0,0 +1 @@ + diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala index 6b72cb8..d70ce6f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/export.scala @@ -3,6 +3,7 @@ package xyz.driver.pdsuidomain.formats.json import spray.json._ import xyz.driver.entities.labels.Label import xyz.driver.formats.json.labels._ +import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.export.patient._ import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} import xyz.driver.pdsuidomain.entities.{Criterion, EligibilityArm} @@ -13,6 +14,14 @@ object export { import document._ import record._ + private def deserializationErrorFieldMessage(field: String, json: JsValue)(implicit className: String) = { + deserializationError(s"$className json object do not contain '$field' field: $json") + } + + private def deserializationErrorEntityMessage(json: JsValue)(implicit className: String) = { + deserializationError(s"Expected Json Object as $className, but got $json") + } + implicit val patientLabelEvidenceDocumentFormat: RootJsonFormat[ExportPatientLabelEvidenceDocument] = jsonFormat5(ExportPatientLabelEvidenceDocument.apply) @@ -29,6 +38,8 @@ object export { implicit val trialLabelCriterionFormat: RootJsonFormat[ExportTrialLabelCriterion] = new RootJsonFormat[ExportTrialLabelCriterion] { + implicit val className: String = "ExportTrialLabelCriterion" + override def write(obj: ExportTrialLabelCriterion): JsValue = JsObject( "value" -> obj.value @@ -43,40 +54,69 @@ object export { "criterionText" -> obj.criteria.toJson, "armIds" -> obj.armIds.toJson, "isCompound" -> obj.isCompound.toJson, - "isDefining" -> obj.isDefining.toJson + "isDefining" -> obj.isDefining.toJson, + "inclusion" -> obj.inclusion.toJson ) override def read(json: JsValue): ExportTrialLabelCriterion = { + json match { + case JsObject(fields) => + val value = fields + .get("value") + .map(_.convertTo[String]) + .map { + case "Yes" => Option(true) + case "No" => Option(false) + case "Unknown" => Option.empty[Boolean] + } + .getOrElse(deserializationErrorFieldMessage("value", json)) - val fields = Seq("value", "labelId", "criterionId", "criterionText", "armIds", "isCompound", "isDefining") - - json.asJsObject.getFields(fields: _*) match { - case Seq(JsString(valueString), - labelId, - criterionId, - JsString(criterionText), - JsArray(armIdsVector), - JsBoolean(isCompound), - JsBoolean(isDefining)) => - val value = valueString match { - case "Yes" => Option(true) - case "No" => Option(false) - case "Unknown" => Option.empty[Boolean] - } + val labelId = fields + .get("labelId") + .map(_.convertTo[LongId[Label]]) + .getOrElse(deserializationErrorFieldMessage("labelId", json)) + + val criterionId = fields + .get("criterionId") + .map(_.convertTo[LongId[Criterion]]) + .getOrElse(deserializationErrorFieldMessage("criterionId", json)) + + val criterionText = fields + .get("criterionText") + .map(_.convertTo[String]) + .getOrElse(deserializationErrorFieldMessage("criterionText", json)) + + val armIds = fields + .get("armIds") + .map(_.convertTo[Set[LongId[EligibilityArm]]]) + .getOrElse(deserializationErrorFieldMessage("armIds", json)) + + val isCompound = fields + .get("isCompound") + .map(_.convertTo[Boolean]) + .getOrElse(deserializationErrorFieldMessage("isCompound", json)) + + val isDefining = fields + .get("isDefining") + .map(_.convertTo[Boolean]) + .getOrElse(deserializationErrorFieldMessage("isDefining", json)) + + val inclusion = fields + .get("inclusion") + .flatMap(_.convertTo[Option[Boolean]]) ExportTrialLabelCriterion( - longIdFormat[Criterion].read(criterionId), + criterionId, value, - longIdFormat[Label].read(labelId), - armIdsVector.map(longIdFormat[EligibilityArm].read).toSet, + labelId, + armIds, criterionText, isCompound, - isDefining + isDefining, + inclusion ) - case _ => - deserializationError( - s"Cannot find required fields ${fields.mkString(", ")} in ExportTrialLabelCriterion object!") + case _ => deserializationErrorEntityMessage(json) } } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala index 5cd7527..14edd5d 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/intervention.scala @@ -99,7 +99,8 @@ object intervention { val deliveryMethod = fields .get("deliveryMethod") - .map(_.convertTo[String]) + .map(_.convertTo[Option[String]]) + .getOrElse(orig.intervention.deliveryMethod) val origIntervention = orig.intervention val arms = fields @@ -112,7 +113,7 @@ object intervention { typeId = typeId.orElse(origIntervention.typeId), dosage = dosage.getOrElse(origIntervention.dosage), isActive = isActive.getOrElse(origIntervention.isActive), - deliveryMethod = deliveryMethod.orElse(origIntervention.deliveryMethod) + deliveryMethod = deliveryMethod ), arms = arms.getOrElse(orig.arms) ) 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 new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala @@ -0,0 +1 @@ + diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala index fc0b725..fbefd33 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patientcriterion.scala @@ -56,7 +56,8 @@ object patientcriterion { "verifiedEligibilityStatus" -> obj.patientCriterion.verifiedEligibilityStatus.toJson, "isVerified" -> obj.patientCriterion.isVerified.toJson, "isVisible" -> obj.patientCriterion.isVisible.toJson, - "lastUpdate" -> obj.patientCriterion.lastUpdate.toJson + "lastUpdate" -> obj.patientCriterion.lastUpdate.toJson, + "inclusion" -> obj.patientCriterion.inclusion.toJson ) } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala index 9a8dc9c..b6ed103 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/record.scala @@ -15,6 +15,7 @@ object record { import common._ implicit val recordStatusFormat = new EnumJsonFormat[Status]( + "PreCleaning" -> Status.PreCleaning, "Unprocessed" -> Status.Unprocessed, "PreOrganized" -> Status.PreOrganized, "New" -> Status.New, @@ -93,7 +94,7 @@ object record { val endOriginalPage = fields .get("endOriginalPage") - .map(_.convertTo[Double]) + .flatMap(_.convertTo[Option[Double]]) Duplicate( startPage = startPage, diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/HypothesisService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/HypothesisService.scala index 52cd6c8..572edb6 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/HypothesisService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/HypothesisService.scala @@ -2,12 +2,21 @@ package xyz.driver.pdsuidomain.services import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db.Sorting +import xyz.driver.pdsuicommon.domain.UuidId import xyz.driver.pdsuicommon.error.DomainError import xyz.driver.pdsuidomain.entities.Hypothesis import scala.concurrent.Future object HypothesisService { + trait DefaultNotFoundError { + def userMessage: String = "Hypothesis not found" + } + + trait DefaultAccessDeniedError { + def userMessage: String = "Access denied" + } + sealed trait GetListReply object GetListReply { final case class EntityList(xs: Seq[Hypothesis], totalFound: Int) extends GetListReply @@ -16,6 +25,32 @@ object HypothesisService { def userMessage: String = "Access denied" } } + + sealed trait CreateReply + object CreateReply { + final case class Created(x: Hypothesis) extends CreateReply + + type Error = CreateReply with DomainError + + case object AuthorizationError + extends CreateReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + final case class CommonError(userMessage: String) extends CreateReply with DomainError + } + + sealed trait DeleteReply + object DeleteReply { + case object Deleted extends DeleteReply + + type Error = DeleteReply with DomainError + + case object NotFoundError extends DeleteReply with DefaultNotFoundError with DomainError.NotFoundError + + case object AuthorizationError + extends DeleteReply with DefaultAccessDeniedError with DomainError.AuthorizationError + + final case class CommonError(userMessage: String) extends DeleteReply with DomainError + } } trait HypothesisService { @@ -24,4 +59,8 @@ trait HypothesisService { def getAll(sorting: Option[Sorting] = None)( implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] + + def create(draftHypothesis: Hypothesis)(implicit requestContext: AuthenticatedRequestContext): Future[CreateReply] + + def delete(id: UuidId[Hypothesis])(implicit requestContext: AuthenticatedRequestContext): Future[DeleteReply] } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala index e0efcd1..e23449c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala @@ -85,7 +85,8 @@ class FakeTrialService extends TrialService { generators.setOf(LongId[EligibilityArm](generators.nextInt(999999).toLong)), generators.nextName().value, generators.nextBoolean(), - generators.nextBoolean() + generators.nextBoolean(), + generators.nextOption(generators.nextBoolean()) )) ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHelper.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHelper.scala index bf42f40..8e75c76 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHelper.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHelper.scala @@ -59,9 +59,9 @@ trait RestHelper { def exprToQuery(expr: SearchFilterExpr): Seq[(String, String)] = expr match { case SearchFilterExpr.Empty => Seq.empty case SearchFilterExpr.Atom.Binary(dimension, op, value) => - Seq("filters" -> s"${dimension.name} ${opToString(op)} $value") + Seq("filters" -> s"${dimension.tableName.fold("")(t => s"$t.") + dimension.name} ${opToString(op)} $value") case SearchFilterExpr.Atom.NAry(dimension, SearchFilterNAryOperation.In, values) => - Seq("filters" -> s"${dimension.name} in ${values.mkString(",")}") + Seq("filters" -> s"${dimension.tableName.fold("")(t => s"$t.") + dimension.name} in ${values.mkString(",")}") case SearchFilterExpr.Intersection(ops) => ops.flatMap(op => exprToQuery(op)) case expr => sys.error(s"No parser available for filter expression $expr.") diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHypothesisService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHypothesisService.scala index a352053..73abb0e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHypothesisService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestHypothesisService.scala @@ -1,11 +1,14 @@ package xyz.driver.pdsuidomain.services.rest +import akka.http.scaladsl.marshalling.Marshal + import scala.concurrent.{ExecutionContext, Future} import akka.http.scaladsl.model._ import akka.stream.Materializer import xyz.driver.core.rest._ import xyz.driver.pdsuicommon.auth._ import xyz.driver.pdsuicommon.db._ +import xyz.driver.pdsuicommon.domain.UuidId import xyz.driver.pdsuidomain.ListResponse import xyz.driver.pdsuidomain.entities.Hypothesis import xyz.driver.pdsuidomain.services.HypothesisService @@ -31,4 +34,25 @@ class RestHypothesisService(transport: ServiceTransport, baseUri: Uri)( } } + def create(draftHypothesis: Hypothesis)(implicit requestContext: AuthenticatedRequestContext): Future[CreateReply] = { + for { + entity <- Marshal(draftHypothesis).to[RequestEntity] + request = HttpRequest(HttpMethods.POST, endpointUri(baseUri, "/v1/hypothesis")).withEntity(entity) + response <- transport.sendRequestGetResponse(requestContext)(request) + reply <- apiResponse[Hypothesis](response) + } yield { + CreateReply.Created(reply) + } + } + + def delete(id: UuidId[Hypothesis])(implicit requestContext: AuthenticatedRequestContext): Future[DeleteReply] = { + val request = HttpRequest(HttpMethods.DELETE, endpointUri(baseUri, s"/v1/hypothesis/$id")) + for { + response <- transport.sendRequestGetResponse(requestContext)(request) + _ <- apiResponse[HttpEntity](response) + } yield { + DeleteReply.Deleted + } + } + } |