From deba20326e3269fee3ef51f8e6841f17453b4155 Mon Sep 17 00:00:00 2001 From: vlad Date: Thu, 28 Sep 2017 13:12:32 -0700 Subject: Simplified Export entities for EVLS --- .../json/sprayformats/ExportFormatSuite.scala | 26 +++++++++++----------- 1 file changed, 13 insertions(+), 13 deletions(-) (limited to 'src/test/scala/xyz/driver') diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala index d0d4d1a..52c8c81 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala @@ -6,7 +6,7 @@ import java.util.UUID import spray.json._ import org.scalatest.{FlatSpec, Matchers} import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities.RecordRequestId +import xyz.driver.pdsuidomain.entities.{DocumentType, ProviderType, RecordRequestId} class ExportFormatSuite extends FlatSpec with Matchers { import export._ @@ -16,10 +16,11 @@ class ExportFormatSuite extends FlatSpec with Matchers { val document = ExportPatientLabelEvidenceDocument( documentId = LongId(101), requestId = RecordRequestId(UUID.fromString("7b54a75d-4197-4b27-9045-b9b6cb131be9")), - documentType = "document type", - providerType = "provider type", + documentType = DocumentType(LongId[DocumentType](1), "document type"), + providerType = ProviderType(LongId[ProviderType](2), "provider type"), date = LocalDate.parse("2017-08-10") ) + val labels = List( ExportPatientLabel( id = LongId(1), @@ -62,18 +63,18 @@ class ExportFormatSuite extends FlatSpec with Matchers { labels = labels ) - val writtenJson = patientWithLabelsWriter.write(patientWithLabels) + val writtenJson = patientWithLabelsFormat.write(patientWithLabels) writtenJson should be( """{"patientId":"748b5884-3528-4cb9-904b-7a8151d6e343","labelVersion":1,"labels":[{"labelId":1,"evidence":[{"evidenceId":11, "labelValue":"Yes","evidenceText":"evidence text 11","document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9", - "documentType":"document type","providerType":"provider type","date":"2017-08-10"}},{"evidenceId":12,"labelValue":"No", - "evidenceText":"evidence text 12","document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9", - "documentType":"document type","providerType":"provider type","date":"2017-08-10"}}]}, + "documentType":{"id":1,"name":"document type"},"providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}}, + {"evidenceId":12,"labelValue":"No","evidenceText":"evidence text 12","document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9", + "documentType":{"id":1,"name":"document type"},"providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}}]}, {"labelId":2,"evidence":[{"evidenceId":12,"labelValue":"Yes","evidenceText":"evidence text 12","document": - {"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":"document type", - "providerType":"provider type","date":"2017-08-10"}},{"evidenceId":13,"labelValue":"Yes","evidenceText":"evidence text 13", - "document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":"document type", - "providerType":"provider type","date":"2017-08-10"}}]}]}""".parseJson) + {"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":{"id":1,"name":"document type"}, + "providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}},{"evidenceId":13,"labelValue":"Yes","evidenceText":"evidence text 13", + "document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":{"id":1,"name":"document type"}, + "providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}}]}]}""".parseJson) } "Json format for ApiExportTrialWithLabels" should "read and write correct JSON" in { @@ -112,7 +113,7 @@ class ExportFormatSuite extends FlatSpec with Matchers { criteria = criteriaList ) - val writtenJson = trialWithLabelsWriter.write(trialWithLabels) + val writtenJson = trialWithLabelsFormat.write(trialWithLabels) writtenJson should be( """{"nctId":"NCT000001","trialId":"40892a07-c638-49d2-9795-1edfefbbcc7c","disease":"Breast","lastReviewed":"2017-08-10T18:00Z", "labelVersion":1,"arms":[{"armId":1,"armName":"arm 1"},{"armId":2,"armName":"arm 2"}],"criteria":[ @@ -120,5 +121,4 @@ class ExportFormatSuite extends FlatSpec with Matchers { {"value":"Unknown","labelId":21,"criterionId":11,"criterionText":"criteria 11 text","armIds":[2],"isCompound":true,"isDefining":false}]}""".parseJson) } - } -- cgit v1.2.3 From b5e0d5f91b52013bc11ef3ea586a54bb001577bc Mon Sep 17 00:00:00 2001 From: vlad Date: Sun, 1 Oct 2017 12:50:54 -0700 Subject: Fixing IN in filters, Model from EVLS added to common, Reusing domain model labels --- build.sbt | 4 +- .../pdsuicommon/db/SlickPostgresQueryBuilder.scala | 3 +- .../driver/pdsuicommon/db/SlickQueryBuilder.scala | 3 +- .../pdsuicommon/parsers/SearchFilterParser.scala | 23 +++-- .../utils/CustomSwaggerJsonFormats.scala | 2 +- .../driver/pdsuidomain/entities/Criterion.scala | 5 +- .../pdsuidomain/entities/ExtractedData.scala | 3 +- .../xyz/driver/pdsuidomain/entities/Keyword.scala | 3 +- .../xyz/driver/pdsuidomain/entities/Label.scala | 31 ------- .../driver/pdsuidomain/entities/PatientLabel.scala | 1 + .../entities/PatientLabelEvidenceView.scala | 1 + .../pdsuidomain/entities/RawPatientLabel.scala | 1 + .../pdsuidomain/entities/RawTrialLabel.scala | 1 + .../driver/pdsuidomain/entities/eligibility.scala | 63 +++++++++++++ .../export/patient/ExportPatientLabel.scala | 3 +- .../export/trial/ExportTrialLabelCriterion.scala | 3 +- .../driver/pdsuidomain/fakes/entities/common.scala | 41 +++++++-- .../pdsuidomain/fakes/entities/eligibility.scala | 72 +++++++++++++++ .../driver/pdsuidomain/fakes/entities/export.scala | 35 +++++++ .../pdsuidomain/fakes/entities/rep/Common.scala | 35 ------- .../fakes/entities/rep/DocumentGen.scala | 7 +- .../fakes/entities/rep/ExportPatientGen.scala | 11 +-- .../fakes/entities/rep/ExtractedDataGen.scala | 17 ++-- .../fakes/entities/rep/MedicalRecordGen.scala | 7 +- .../fakes/entities/rep/ProviderTypeGen.scala | 14 --- .../pdsuidomain/fakes/entities/trialcuration.scala | 3 +- .../formats/json/category/ApiCategory.scala | 23 ----- .../formats/json/keyword/ApiKeyword.scala | 23 ----- .../formats/json/label/ApiCriterionLabel.scala | 5 +- .../formats/json/label/ApiExtractedDataLabel.scala | 5 +- .../pdsuidomain/formats/json/label/ApiLabel.scala | 22 ----- .../json/patient/trial/ApiPatientCriterion.scala | 3 +- .../formats/json/sprayformats/criterion.scala | 3 +- .../formats/json/sprayformats/documenttype.scala | 1 - .../formats/json/sprayformats/eligibility.scala | 101 +++++++++++++++++++++ .../formats/json/sprayformats/export.scala | 3 +- .../formats/json/sprayformats/extracteddata.scala | 3 +- .../json/sprayformats/patientcriterion.scala | 1 + .../formats/json/sprayformats/providerttype.scala | 12 --- .../formats/json/sprayformats/providertype.scala | 12 +++ .../services/EligibilityVerificationService.scala | 18 ++++ .../services/PatientCriterionService.scala | 1 + .../services/PatientEligibleTrialService.scala | 1 + .../services/PatientLabelEvidenceService.scala | 1 + .../pdsuidomain/services/PatientLabelService.scala | 1 + .../fake/FakeEligibilityVerificationService.scala | 28 ++++++ .../services/fake/FakeTrialService.scala | 3 +- .../rest/RestEligibilityVerificationService.scala | 43 +++++++++ .../parsers/SearchFilterParserSuite.scala | 13 ++- 49 files changed, 494 insertions(+), 224 deletions(-) delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/entities/Label.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/entities/eligibility.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/fakes/entities/eligibility.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/Common.scala delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ProviderTypeGen.scala delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/category/ApiCategory.scala delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/keyword/ApiKeyword.scala delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiLabel.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/eligibility.scala delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providerttype.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala create mode 100644 src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala (limited to 'src/test/scala/xyz/driver') diff --git a/build.sbt b/build.sbt index 837a1f0..66c0f7b 100644 --- a/build.sbt +++ b/build.sbt @@ -18,8 +18,8 @@ lazy val core = (project in file(".")) "io.github.cloudify" %% "spdf" % "1.4.0", "org.davidbild" %% "tristate-core" % "0.2.0", "org.davidbild" %% "tristate-play" % "0.2.0" exclude ("com.typesafe.play", "play-json"), - "xyz.driver" %% "core" % "0.16.7", - "xyz.driver" %% "domain-model" % "0.12.26", + "xyz.driver" %% "core" % "1.2.1", + "xyz.driver" %% "domain-model" % "0.17.1", "ch.qos.logback" % "logback-classic" % "1.1.7", "com.fasterxml.jackson.datatype" % "jackson-datatype-jsr310" % "2.8.4", "com.github.spullara.mustache.java" % "scala-extensions-2.11" % "0.9.4", 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 4ecf915..a3f48d1 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala @@ -89,7 +89,7 @@ object CustomSwaggerJsonFormats { classOf[DocumentHistory.State] -> documenthistory.documentStateFormat.write(rep.DocumentGen.nextDocumentHistoryState()), classOf[ProviderType] -> - providertype.providerTypeFormat.write(rep.ProviderTypeGen.nextProviderType()), + providertype.providerTypeFormat.write(rep.MedicalRecordGen.nextProviderType()), classOf[TextJson[List[MedicalRecord.Meta]]] -> record.recordMetaFormat.write(rep.MedicalRecordGen.nextMedicalRecordMetasJson()), classOf[MedicalRecord] -> diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala index 0dfb33f..7f065d4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.entities +import xyz.driver.entities.labels.{Label, LabelCategory} import xyz.driver.pdsuicommon.domain.{LongId, StringId} import xyz.driver.pdsuicommon.logging._ import xyz.driver.pdsuidomain.entities.Criterion.Meta.Evidence @@ -10,7 +11,7 @@ final case class Criterion(id: LongId[Criterion], isCompound: Boolean, meta: String) { - def isValid(): Boolean = text.nonEmpty && Option(meta).isDefined + def isValid: Boolean = text.nonEmpty && Option(meta).isDefined } object Criterion { @@ -41,7 +42,7 @@ object CriterionArm { final case class CriterionLabel(id: LongId[CriterionLabel], labelId: Option[LongId[Label]], criterionId: LongId[Criterion], - categoryId: Option[LongId[Category]], + categoryId: Option[LongId[LabelCategory]], value: Option[Boolean], isDefining: Boolean) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala index 32258dc..fbd468f 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.entities +import xyz.driver.entities.labels.{Label, LabelCategory} import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson} import xyz.driver.pdsuicommon.logging._ import xyz.driver.pdsuidomain.entities.ExtractedData.Meta @@ -43,5 +44,5 @@ object ExtractedDataLabel { final case class ExtractedDataLabel(id: LongId[ExtractedDataLabel], dataId: LongId[ExtractedData], labelId: Option[LongId[Label]], - categoryId: Option[LongId[Category]], + categoryId: Option[LongId[LabelCategory]], value: Option[FuzzyValue]) diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Keyword.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Keyword.scala index 3683efc..a984f92 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Keyword.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Keyword.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.entities +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuicommon.logging._ @@ -17,7 +18,7 @@ final case class KeywordWithLabels(keyword: Keyword, labels: List[Label]) object KeywordWithLabels { implicit def toPhiString(x: KeywordWithLabels): PhiString = { import x._ - phi"KeywordWithLabels(keyword=$keyword, $labels)" + phi"KeywordWithLabels(keyword=$keyword, ${Unsafe(labels)}" } } diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Label.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Label.scala deleted file mode 100644 index eea39de..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Label.scala +++ /dev/null @@ -1,31 +0,0 @@ -package xyz.driver.pdsuidomain.entities - -import xyz.driver.pdsuicommon.domain.LongId -import xyz.driver.pdsuicommon.logging._ - -final case class Category(id: LongId[Category], name: String) - -object Category { - implicit def toPhiString(x: Category): PhiString = { - import x._ - phi"Category(id=$id, name=${Unsafe(name)})" - } -} - -final case class Label(id: LongId[Label], categoryId: LongId[Category], name: String, description: String) - -object Label { - implicit def toPhiString(x: Label): PhiString = { - import x._ - phi"Label($id, categoryId=${Unsafe(categoryId)}, name=${Unsafe(name)}, description=${Unsafe(description)})" - } -} - -final case class CategoryWithLabels(category: Category, labels: List[Label]) - -object CategoryWithLabels { - implicit def toPhiString(x: CategoryWithLabels): PhiString = { - import x._ - phi"CategoryWithLabels(category=$category, labels=$labels)" - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala index 633a347..d10c7d2 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.entities +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, UuidId} import xyz.driver.pdsuicommon.logging._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala index 34e3741..3311d96 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDate +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala index 184782b..689eaa4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDate +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, UuidId} import xyz.driver.pdsuicommon.logging._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala index 9e69c87..bdbc4ea 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.entities import java.time.LocalDateTime +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} import xyz.driver.pdsuicommon.logging._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/eligibility.scala new file mode 100644 index 0000000..aa7a7d2 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/eligibility.scala @@ -0,0 +1,63 @@ +package xyz.driver.pdsuidomain.entities + +import xyz.driver.core.Id +import xyz.driver.core.date.Date +import xyz.driver.entities.assays.AssayType +import xyz.driver.entities.clinic.{ClinicalRecord, TestOrder} +import xyz.driver.entities.common.FullName +import xyz.driver.entities.labels.{Label, LabelValue} +import xyz.driver.entities.patient.CancerType +import xyz.driver.entities.process.ProcessStepExecutionStatus +import xyz.driver.entities.report.Report +import xyz.driver.pdsuidomain.entities.export.trial.ExportTrialWithLabels + +object eligibility { + + sealed trait EvidenceDocument { + val documentType: DocumentType + val providerType: ProviderType + val providerName: Option[String] + val date: Option[Date] + val isDriverDocument: Boolean + } + + final case class MolecularEvidenceDocument(documentType: DocumentType, + providerType: ProviderType, + providerName: Option[String], + date: Option[Date], + reportId: Id[Report], + reportType: AssayType, + isDriverDocument: Boolean = true) + extends EvidenceDocument + + final case class ClinicalEvidenceDocument(documentId: Id[ClinicalEvidenceDocument], + documentType: DocumentType, + providerType: ProviderType, + providerName: Option[String], + date: Option[Date], + requestId: Id[ClinicalRecord], + isDriverDocument: Boolean = false) + extends EvidenceDocument + + // Some fields are optional because they are not in the backend response + final case class Evidence(evidenceId: Option[Id[Evidence]], + evidenceText: String, + labelValue: LabelValue, + document: EvidenceDocument, + isPrimaryValue: Option[Boolean] = None) + + final case class LabelWithEvidence(label: Label, evidence: Seq[Evidence] = Seq.empty) + + final case class LabelMismatchRank(label: Label, + score: Int, + trials: Seq[ExportTrialWithLabels], + evidence: Seq[Evidence]) + final case class MismatchRankedLabels(data: Seq[LabelMismatchRank], labelVersion: Int) + + final case class MatchedPatient(patientId: Id[MatchedPatient], + name: FullName[MatchedPatient], + birthDate: Date, + orderId: Id[TestOrder], + disease: CancerType, + patientDataStatus: ProcessStepExecutionStatus) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala index c69fc09..2edd707 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala @@ -1,8 +1,9 @@ package xyz.driver.pdsuidomain.entities.export.patient +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Label, RawPatientLabel} +import xyz.driver.pdsuidomain.entities.RawPatientLabel final case class ExportPatientLabel(id: LongId[Label], evidences: List[ExportPatientLabelEvidence]) 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 7bff22c..1f06e0d 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 @@ -1,8 +1,9 @@ package xyz.driver.pdsuidomain.entities.export.trial +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain._ import xyz.driver.pdsuicommon.logging._ -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Label, RawTrialLabel} +import xyz.driver.pdsuidomain.entities.{Arm, Criterion, RawTrialLabel} final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion], value: Option[Boolean], diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala index b259b07..7318ff6 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala @@ -2,26 +2,28 @@ package xyz.driver.pdsuidomain.fakes.entities import java.time.{LocalDate, LocalDateTime, LocalTime} -import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} +import xyz.driver.core.generators.{nextDouble, nextOption} +import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId} import xyz.driver.pdsuidomain.entities.{Trial, TrialHistory} + import scala.util.Random object common { import xyz.driver.core.generators - def nextUuidId[T] = UuidId[T](generators.nextUuid()) + def nextUuidId[T]: UuidId[T] = UuidId[T](generators.nextUuid()) - def nextLongId[T] = LongId[T](generators.nextInt(Int.MaxValue).toLong) + def nextLongId[T]: LongId[T] = LongId[T](generators.nextInt(Int.MaxValue).toLong) - def nextStringId[T] = StringId[T](generators.nextString(maxLength = 20)) + def nextStringId[T]: StringId[T] = StringId[T](generators.nextString(maxLength = 20)) - def nextTrialStatus = generators.oneOf[Trial.Status](Trial.Status.All) + def nextTrialStatus: Trial.Status = generators.oneOf[Trial.Status](Trial.Status.All) - def nextPreviousTrialStatus = generators.oneOf[Trial.Status](Trial.Status.AllPrevious) + def nextPreviousTrialStatus: Trial.Status = generators.oneOf[Trial.Status](Trial.Status.AllPrevious) - def nextLocalDateTime = LocalDateTime.of(nextLocalDate, LocalTime.MIDNIGHT) + def nextLocalDateTime: LocalDateTime = LocalDateTime.of(nextLocalDate, LocalTime.MIDNIGHT) - def nextLocalDate = LocalDate.of( + def nextLocalDate: LocalDate = LocalDate.of( 1970 + Random.nextInt(68), 1 + Random.nextInt(12), 1 + Random.nextInt(28) // all months have at least 28 days @@ -33,4 +35,27 @@ object common { def nextTrialState = generators.oneOf[TrialHistory.State](TrialHistory.State.All) + def genBoundedRange[T](from: T, to: T)(implicit ord: Ordering[T]): (T, T) = { + if (ord.compare(from, to) > 0) { + to -> from + } else { + from -> to + } + } + + def genBoundedRangeOption[T](from: T, to: T)(implicit ord: Ordering[T]): (Option[T], Option[T]) = { + val ranges = nextOption(from).map { left => + val range = genBoundedRange(left, to) + range._1 -> nextOption(range._2) + } + + ranges.map(_._1) -> ranges.flatMap(_._2) + } + + def nextFuzzyValue(): FuzzyValue = + generators.oneOf[FuzzyValue](FuzzyValue.All) + + def nextStartAndEndPages: (Option[Double], Option[Double]) = + genBoundedRangeOption[Double](nextDouble(), nextDouble()) + } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/eligibility.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/eligibility.scala new file mode 100644 index 0000000..7dc50be --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/eligibility.scala @@ -0,0 +1,72 @@ +package xyz.driver.pdsuidomain.fakes.entities + +import xyz.driver.core.generators +import xyz.driver.entities.clinic.{ClinicalRecord, TestOrder} +import xyz.driver.entities.patient.CancerType +import xyz.driver.entities.report.Report +import xyz.driver.fakes +import xyz.driver.pdsuidomain.entities.eligibility._ + +object eligibility { + import xyz.driver.core.generators._ + + def nextMolecularEvidenceDocument(): MolecularEvidenceDocument = + MolecularEvidenceDocument( + documentType = xyz.driver.pdsuidomain.fakes.entities.rep.DocumentGen.nextDocumentType(), + providerType = xyz.driver.pdsuidomain.fakes.entities.rep.MedicalRecordGen.nextProviderType(), + providerName = nextOption(nextString(100)), + date = nextOption(nextDate()), + reportId = nextId[Report](), + reportType = fakes.entities.assays.nextAssayType(), + isDriverDocument = nextBoolean() + ) + + def nextClinicalEvidenceDocument(): ClinicalEvidenceDocument = + ClinicalEvidenceDocument( + documentType = xyz.driver.pdsuidomain.fakes.entities.rep.DocumentGen.nextDocumentType(), + providerType = xyz.driver.pdsuidomain.fakes.entities.rep.MedicalRecordGen.nextProviderType(), + providerName = nextOption(nextString(100)), + date = nextOption(nextDate()), + documentId = nextId[ClinicalEvidenceDocument](), + requestId = nextId[ClinicalRecord](), + isDriverDocument = nextBoolean() + ) + + def nextEvidenceDocument(): EvidenceDocument = + oneOf[EvidenceDocument](nextMolecularEvidenceDocument(), + nextClinicalEvidenceDocument(), + nextClinicalEvidenceDocument()) // For more clinical documents + + def nextEvidence(): Evidence = + Evidence( + evidenceId = Option(nextId[Evidence]()), + evidenceText = nextString(100), + labelValue = xyz.driver.fakes.entities.labels.nextLabelValue(), + nextEvidenceDocument(), + isPrimaryValue = nextOption(nextBoolean()) + ) + + def nextLabelWithEvidence(): LabelWithEvidence = + LabelWithEvidence(label = fakes.entities.labels.nextLabel(), evidence = Seq.empty) + + def nextLabelMismatchRank(): LabelMismatchRank = + LabelMismatchRank( + label = fakes.entities.labels.nextLabel(), + score = nextInt(100), + trials = seqOf(xyz.driver.pdsuidomain.fakes.entities.export.nextExportTrialWithLabels()), + evidence = seqOf(nextEvidence()) + ) + + def nextMismatchRankedLabels(): MismatchRankedLabels = + MismatchRankedLabels(data = seqOf(nextLabelMismatchRank()), labelVersion = nextInt(100)) + + def nextMatchedPatient(): MatchedPatient = + MatchedPatient( + patientId = nextId[MatchedPatient](), + name = fakes.entities.common.nextFullName[MatchedPatient](), + birthDate = nextDate(), + orderId = nextId[TestOrder](), + disease = generators.oneOf[CancerType](CancerType.Breast, CancerType.Lung, CancerType.Prostate), + patientDataStatus = fakes.entities.process.nextProcessStepExecutionStatus() + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala new file mode 100644 index 0000000..7f3c410 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala @@ -0,0 +1,35 @@ +package xyz.driver.pdsuidomain.fakes.entities + +import xyz.driver.entities.labels.Label +import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial} +import xyz.driver.pdsuidomain.entities.export.trial._ + +object export { + import xyz.driver.core.generators._ + import common._ + + def nextExportTrialArm(): ExportTrialArm = + ExportTrialArm(armId = nextLongId[Arm], armName = nextString(100)) + + def nextExportTrialLabelCriterion(): ExportTrialLabelCriterion = + ExportTrialLabelCriterion( + criterionId = nextLongId[Criterion], + value = nextOption[Boolean](nextBoolean()), + labelId = nextLongId[Label], + armIds = setOf(nextLongId[Arm]), + criteria = nextString(100), + isCompound = nextBoolean(), + isDefining = nextBoolean() + ) + + def nextExportTrialWithLabels(): ExportTrialWithLabels = + ExportTrialWithLabels( + nctId = nextStringId[Trial], + trialId = nextUuidId[Trial], + condition = nextString(100), + lastReviewed = nextLocalDateTime, + labelVersion = nextInt(100).toLong, + arms = listOf(nextExportTrialArm()), + criteria = listOf(nextExportTrialLabelCriterion()) + ) +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/Common.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/Common.scala deleted file mode 100644 index 9618eed..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/Common.scala +++ /dev/null @@ -1,35 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities.rep - -import xyz.driver.core.generators -import xyz.driver.core.generators._ -import xyz.driver.pdsuicommon.domain.FuzzyValue - -private[rep] object Common { - def genBoundedRange[T](from: T, to: T)(implicit ord: Ordering[T]): (T, T) = { - if (ord.compare(from, to) > 0) { - to -> from - } else { - from -> to - } - } - - def genBoundedRangeOption[T](from: T, to: T)(implicit ord: Ordering[T]): (Option[T], Option[T]) = { - val ranges = nextOption(from) - .map(left => genBoundedRange(left, to)) - .map { - case (left, right) => - left -> nextOption(right) - } - - ranges.map(_._1) -> ranges.flatMap(_._2) - } - - def nextFuzzyValue(): FuzzyValue = { - generators.oneOf[FuzzyValue](FuzzyValue.All) - } - - def nextStartAndEndPages: (Option[Double], Option[Double]) = { - genBoundedRangeOption[Double](nextDouble(), nextDouble()) - } - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala index 10349bb..6d5330e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala @@ -4,6 +4,7 @@ import java.time.LocalDate import xyz.driver.core.generators import xyz.driver.core.generators.{nextBoolean, nextDouble, nextOption, nextString} +import xyz.driver.pdsuidomain.fakes.entities.common._ import xyz.driver.pdsuicommon.domain.{LongId, TextJson, User} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.fakes.entities.common.{nextLocalDate, nextLocalDateTime, nextLongId, nextStringId} @@ -17,13 +18,13 @@ object DocumentGen { } private def nextDates() = - Common.genBoundedRangeOption[LocalDate](nextLocalDate, nextLocalDate) + genBoundedRangeOption[LocalDate](nextLocalDate, nextLocalDate) private def nextStartAndEndPagesOption() = - Common.nextStartAndEndPages + nextStartAndEndPages private def nextStartAndEndPage() = - Common.genBoundedRange(nextDouble(), nextDouble()) + genBoundedRange(nextDouble(), nextDouble()) def nextDocumentStatus(): Document.Status = Document.Status.New diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala index c2909f3..e3ef6bc 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala @@ -1,14 +1,11 @@ package xyz.driver.pdsuidomain.fakes.entities.rep import xyz.driver.core.generators._ +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.domain.{LongId, UuidId} +import xyz.driver.pdsuidomain.fakes.entities.common._ import xyz.driver.pdsuidomain.entities._ -import xyz.driver.pdsuidomain.entities.export.patient.{ - ExportPatientLabel, - ExportPatientLabelEvidence, - ExportPatientLabelEvidenceDocument, - ExportPatientWithLabels -} +import xyz.driver.pdsuidomain.entities.export.patient._ import xyz.driver.pdsuidomain.fakes.entities.common.{nextLocalDate, nextLongId} object ExportPatientGen { @@ -41,7 +38,7 @@ object ExportPatientGen { def nextExportPatientLabelEvidence(documentId: LongId[Document]): ExportPatientLabelEvidence = { ExportPatientLabelEvidence( id = nextLongId[ExtractedData], - value = Common.nextFuzzyValue(), + value = nextFuzzyValue(), evidenceText = nextString(), document = nextExportPatientLabelEvidenceDocument(documentId) ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala index 8ac07d0..8e77445 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala @@ -1,6 +1,7 @@ package xyz.driver.pdsuidomain.fakes.entities.rep import xyz.driver.core.generators._ +import xyz.driver.entities.labels.{Label, LabelCategory} import xyz.driver.pdsuicommon.domain.{LongId, TextJson} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.entities.ExtractedData.Meta @@ -46,7 +47,7 @@ object ExtractedDataGen { def nextExtractedDataMetaEvidence(): Meta.Evidence = { val layersPosition = - Common.genBoundedRange[ExtractedData.Meta.TextLayerPosition]( + genBoundedRange[ExtractedData.Meta.TextLayerPosition]( nextExtractedDataMetaTextLayerPosition(), nextExtractedDataMetaTextLayerPosition() ) @@ -65,14 +66,8 @@ object ExtractedDataGen { ) } - def nextExtractedDataMetaJson(): TextJson[Meta] = { - TextJson( - ExtractedData.Meta( - nextExtractedDataMetaKeyword(), - nextExtractedDataMetaEvidence() - ) - ) - } + def nextExtractedDataMetaJson(): TextJson[Meta] = + TextJson(ExtractedData.Meta(nextExtractedDataMetaKeyword(), nextExtractedDataMetaEvidence())) def nextExtractedData(documentId: LongId[Document]): ExtractedData = { ExtractedData( @@ -89,8 +84,8 @@ object ExtractedDataGen { id = nextLongId[ExtractedDataLabel], dataId = nextLongId[ExtractedData], labelId = nextOption(nextLongId[Label]), - categoryId = nextOption(nextLongId[Category]), - value = nextOption(Common.nextFuzzyValue()) + categoryId = nextOption(nextLongId[LabelCategory]), + value = nextOption(nextFuzzyValue()) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala index 7221e66..023dc00 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala @@ -4,7 +4,7 @@ import xyz.driver.pdsuidomain.entities._ import xyz.driver.core.generators import xyz.driver.core.generators._ import xyz.driver.pdsuicommon.domain.{LongId, TextJson, User} -import xyz.driver.pdsuidomain.fakes.entities.common.{nextLocalDateTime, nextLongId, nextStringId, nextUuidId} +import xyz.driver.pdsuidomain.fakes.entities.common._ object MedicalRecordGen { private val maxItemsInCollectionNumber: Int = 50 @@ -126,7 +126,7 @@ object MedicalRecordGen { } def nextMedicalRecordIssue(): MedicalRecordIssue = { - val pages = Common.nextStartAndEndPages + val pages = nextStartAndEndPages MedicalRecordIssue( id = nextLongId[MedicalRecordIssue], @@ -141,4 +141,7 @@ object MedicalRecordGen { ) } + def nextProviderType(): ProviderType = + ProviderType(id = nextLongId[ProviderType], name = nextString()) + } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ProviderTypeGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ProviderTypeGen.scala deleted file mode 100644 index 168f7af..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ProviderTypeGen.scala +++ /dev/null @@ -1,14 +0,0 @@ -package xyz.driver.pdsuidomain.fakes.entities.rep - -import xyz.driver.core.generators.nextString -import xyz.driver.pdsuidomain.entities.ProviderType -import xyz.driver.pdsuidomain.fakes.entities.common.nextLongId - -object ProviderTypeGen { - def nextProviderType(): ProviderType = { - ProviderType( - id = nextLongId[ProviderType], - name = nextString() - ) - } -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala index fe5bf09..fcd833a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.fakes.entities +import xyz.driver.entities.labels.{Label, LabelCategory} import xyz.driver.pdsuicommon.domain.{LongId, User} import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion @@ -51,7 +52,7 @@ object trialcuration { id = nextLongId[CriterionLabel], labelId = Option(nextLongId[Label]), criterionId = criterionId, - categoryId = Option(nextLongId[Category]), + categoryId = Option(nextLongId[LabelCategory]), value = Option(generators.nextBoolean()), isDefining = generators.nextBoolean() ) diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/category/ApiCategory.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/category/ApiCategory.scala deleted file mode 100644 index f1e15f3..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/category/ApiCategory.scala +++ /dev/null @@ -1,23 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.category - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuidomain.entities.CategoryWithLabels -import xyz.driver.pdsuidomain.formats.json.label.ApiLabel - -final case class ApiCategory(id: Long, name: String, labels: List[ApiLabel]) - -object ApiCategory { - - implicit val format: Format[ApiCategory] = ( - (JsPath \ "id").format[Long] and - (JsPath \ "name").format[String] and - (JsPath \ "labels").format[List[ApiLabel]] - )(ApiCategory.apply, unlift(ApiCategory.unapply)) - - def fromDomain(categoryWithLabels: CategoryWithLabels) = ApiCategory( - id = categoryWithLabels.category.id.id, - name = categoryWithLabels.category.name, - labels = categoryWithLabels.labels.map(x => ApiLabel(x.id.id, x.name, x.categoryId.id)) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/keyword/ApiKeyword.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/keyword/ApiKeyword.scala deleted file mode 100644 index a9d02fc..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/keyword/ApiKeyword.scala +++ /dev/null @@ -1,23 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.keyword - -import xyz.driver.pdsuidomain.entities.KeywordWithLabels -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuidomain.formats.json.label.ApiLabel - -final case class ApiKeyword(id: Long, keyword: String, labels: List[ApiLabel]) - -object ApiKeyword { - - implicit val format: Format[ApiKeyword] = ( - (JsPath \ "id").format[Long] and - (JsPath \ "keyword").format[String] and - (JsPath \ "labels").format[List[ApiLabel]] - )(ApiKeyword.apply, unlift(ApiKeyword.unapply)) - - def fromDomain(keywordWithLabels: KeywordWithLabels) = ApiKeyword( - id = keywordWithLabels.keyword.id.id, - keyword = keywordWithLabels.keyword.keyword, - labels = keywordWithLabels.labels.map(x => ApiLabel(x.id.id, x.name, x.categoryId.id)) - ) -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala index 7a65af8..d486749 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.{Category, Criterion, CriterionLabel, Label} +import xyz.driver.pdsuidomain.entities.{Criterion, CriterionLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.entities.labels.{Label, LabelCategory} /** * @param value Yes|No @@ -18,7 +19,7 @@ final case class ApiCriterionLabel(labelId: Option[Long], id = LongId(0L), labelId = labelId.map(LongId[Label]), criterionId = criterionId, - categoryId = categoryId.map(LongId[Category]), + categoryId = categoryId.map(LongId[LabelCategory]), value = value.map { case "Yes" => true case "No" => false diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala index cb45025..f8161af 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala @@ -1,10 +1,11 @@ package xyz.driver.pdsuidomain.formats.json.label import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.{Category, ExtractedData, ExtractedDataLabel, Label} +import xyz.driver.pdsuidomain.entities.{ExtractedData, ExtractedDataLabel} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json._ +import xyz.driver.entities.labels.{Label, LabelCategory} final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long], value: Option[String]) { @@ -12,7 +13,7 @@ final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long id = LongId(0), dataId = dataId, labelId = id.map(LongId[Label]), - categoryId = categoryId.map(LongId[Category]), + categoryId = categoryId.map(LongId[LabelCategory]), value = value.map(FuzzyValue.fromString) ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiLabel.scala deleted file mode 100644 index 042b380..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiLabel.scala +++ /dev/null @@ -1,22 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.label - -import play.api.libs.functional.syntax._ -import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuidomain.entities.Label - -final case class ApiLabel(id: Long, name: String, categoryId: Long) - -object ApiLabel { - - implicit val format: Format[ApiLabel] = ( - (JsPath \ "id").format[Long] and - (JsPath \ "name").format[String] and - (JsPath \ "categoryId").format[Long] - )(ApiLabel.apply, unlift(ApiLabel.unapply)) - - def fromDomain(x: Label) = ApiLabel( - id = x.id.id, - name = x.name, - categoryId = x.categoryId.id - ) -} 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 index 75347f4..6eeb40b 100644 --- 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 @@ -3,10 +3,11 @@ package xyz.driver.pdsuidomain.formats.json.patient.trial import java.time.{ZoneId, ZonedDateTime} import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId} -import xyz.driver.pdsuidomain.entities.{Label, PatientCriterion, PatientCriterionArm} +import xyz.driver.pdsuidomain.entities.{PatientCriterion, PatientCriterionArm} import play.api.data.validation.ValidationError import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath, Reads, Writes} +import xyz.driver.entities.labels.Label final case class ApiPatientCriterion(id: Long, labelId: Long, 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/providerttype.scala deleted file mode 100644 index 385feb2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providerttype.scala +++ /dev/null @@ -1,12 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.sprayformats - -import spray.json._ -import xyz.driver.pdsuidomain.entities.ProviderType - -object providertype { - import DefaultJsonProtocol._ - import common._ - - implicit val providerTypeFormat: RootJsonFormat[ProviderType] = jsonFormat2(ProviderType.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala new file mode 100644 index 0000000..385feb2 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala @@ -0,0 +1,12 @@ +package xyz.driver.pdsuidomain.formats.json.sprayformats + +import spray.json._ +import xyz.driver.pdsuidomain.entities.ProviderType + +object providertype { + import DefaultJsonProtocol._ + import common._ + + implicit val providerTypeFormat: RootJsonFormat[ProviderType] = jsonFormat2(ProviderType.apply) + +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala new file mode 100644 index 0000000..d3e977e --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/services/EligibilityVerificationService.scala @@ -0,0 +1,18 @@ +package xyz.driver.pdsuidomain.services + +import xyz.driver.core.Id +import xyz.driver.core.rest.ServiceRequestContext +import xyz.driver.entities.patient.CancerType +import xyz.driver.pdsuidomain.entities.eligibility.{MatchedPatient, MismatchRankedLabels} +import xyz.driver.pdsuidomain.entities.{Arm, Patient} + +import scala.concurrent.Future +import scalaz.ListT + +trait EligibilityVerificationService { + + def getMatchedPatients()(implicit ctx: ServiceRequestContext): ListT[Future, MatchedPatient] + + def getMismatchRankedLabels(patientId: Id[Patient], cancerType: CancerType, excludedArms: Seq[Id[Arm]])( + implicit ctx: ServiceRequestContext): Future[MismatchRankedLabels] +} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala index 9ff3879..6d85f85 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala @@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.services import java.time.LocalDateTime +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala index 2c17f74..abb3f8a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientEligibleTrialService.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.services +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db.{Pagination, SearchFilterExpr, Sorting} import xyz.driver.pdsuicommon.domain.{LongId, UuidId} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelEvidenceService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelEvidenceService.scala index 56e2e3d..6871f3e 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelEvidenceService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelEvidenceService.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.services +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain.{LongId, UuidId} diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala index 71b8bd4..2a4d7fc 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientLabelService.scala @@ -1,5 +1,6 @@ package xyz.driver.pdsuidomain.services +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain._ diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala new file mode 100644 index 0000000..c5531f9 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeEligibilityVerificationService.scala @@ -0,0 +1,28 @@ +package xyz.driver.pdsuidomain.services.fake + +import xyz.driver.core.rest.ServiceRequestContext +import xyz.driver.core.{Id, generators} +import xyz.driver.entities.patient +import xyz.driver.pdsuidomain.entities.eligibility.MismatchRankedLabels +import xyz.driver.pdsuidomain.entities.{Arm, Patient, eligibility} +import xyz.driver.pdsuidomain.services.EligibilityVerificationService + +import scala.concurrent.Future +import scalaz.ListT + +class FakeEligibilityVerificationService extends EligibilityVerificationService { + + override def getMatchedPatients()(implicit ctx: ServiceRequestContext): ListT[Future, eligibility.MatchedPatient] = + ListT.listT[Future]( + Future.successful(List(xyz.driver.pdsuidomain.fakes.entities.eligibility.nextMatchedPatient()))) + + override def getMismatchRankedLabels( + patientId: Id[Patient], + cancerType: patient.CancerType, + excludedArms: Seq[Id[Arm]])(implicit ctx: ServiceRequestContext): Future[eligibility.MismatchRankedLabels] = + Future.successful( + MismatchRankedLabels( + generators.seqOf(xyz.driver.pdsuidomain.fakes.entities.eligibility.nextLabelMismatchRank()), + labelVersion = generators.nextInt(10) + )) +} 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 3793c1f..9aeb820 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala @@ -6,10 +6,11 @@ import akka.NotUsed import akka.stream.scaladsl.Source import akka.util.ByteString import xyz.driver.core.generators +import xyz.driver.entities.labels.Label import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext import xyz.driver.pdsuicommon.db._ import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId} -import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Label, Trial} +import xyz.driver.pdsuidomain.entities.{Arm, Criterion, Trial} import xyz.driver.pdsuidomain.entities.export.trial.{ExportTrialArm, ExportTrialLabelCriterion, ExportTrialWithLabels} import xyz.driver.pdsuidomain.services.TrialService diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala new file mode 100644 index 0000000..07757e3 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestEligibilityVerificationService.scala @@ -0,0 +1,43 @@ +package xyz.driver.pdsuidomain.services.rest + +import akka.http.scaladsl.model.Uri +import akka.stream.Materializer +import spray.json.DefaultJsonProtocol +import xyz.driver.core.Id +import xyz.driver.core.rest.{RestService, ServiceRequestContext, ServiceTransport} +import xyz.driver.entities.patient +import xyz.driver.pdsuidomain.entities.eligibility.{MatchedPatient, MismatchRankedLabels} +import xyz.driver.pdsuidomain.entities.{Arm, Patient, eligibility} +import xyz.driver.pdsuidomain.services.EligibilityVerificationService + +import scala.concurrent.{ExecutionContext, Future} +import scalaz.ListT +import scalaz.Scalaz.futureInstance + +class RestEligibilityVerificationService(transport: ServiceTransport, baseUri: Uri)( + implicit protected val materializer: Materializer, + protected val exec: ExecutionContext +) extends EligibilityVerificationService with RestService { + + import DefaultJsonProtocol._ + import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ + import xyz.driver.pdsuidomain.formats.json.sprayformats.eligibility._ + + override def getMatchedPatients()(implicit ctx: ServiceRequestContext): ListT[Future, eligibility.MatchedPatient] = { + val request = get(baseUri, s"/v1/patients") + listResponse[MatchedPatient](transport.sendRequest(ctx)(request)) + } + + override def getMismatchRankedLabels(patientId: Id[Patient], + cancerType: patient.CancerType, + excludedArms: Seq[Id[Arm]])( + implicit ctx: ServiceRequestContext): Future[eligibility.MismatchRankedLabels] = { + + val query = + Seq("disease" -> cancerType.toString.toUpperCase, "ineligible_arms" -> excludedArms.map(_.value).mkString(",")) + + val request = get(baseUri, s"/v1/patients/$patientId/labels", query) + optionalResponse[MismatchRankedLabels](transport.sendRequest(ctx)(request)) + .getOrElse(throw new Exception(s"The data of patient $patientId is not ready yet")) + } +} diff --git a/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala b/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala index ba67d13..5deaecb 100644 --- a/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala +++ b/src/test/scala/xyz/driver/pdsuicommon/parsers/SearchFilterParserSuite.scala @@ -14,7 +14,7 @@ import xyz.driver.pdsuicommon.db.SearchFilterNAryOperation.In import xyz.driver.pdsuicommon.utils.Utils import xyz.driver.pdsuicommon.utils.Utils._ -import scala.util.Success +import scala.util._ object SearchFilterParserSuite { @@ -133,6 +133,17 @@ class SearchFilterParserSuite extends FreeSpecLike with Checkers { } "n-ary" - { + "actual record Ids" - { + "should not be parsed with text values" in { + val filter = SearchFilterParser.parse(Seq("filters" -> "id IN 1,5")) + filter match { + case Success(_) => () + case Failure(t) => t.printStackTrace() + } + assert(filter === Success(SearchFilterExpr.Atom.NAry(Dimension(None, "id"), In, Seq(Long.box(1), Long.box(5))))) + } + } + "in" in check { val testQueryGen = queryGen( dimensionGen = Gen.identifier, -- cgit v1.2.3 From d0482b45b6f9149f050c5e5a6dbab6f059229282 Mon Sep 17 00:00:00 2001 From: vlad Date: Mon, 2 Oct 2017 01:05:42 -0700 Subject: DocumentType and ProviderType as enums --- .../utils/CustomSwaggerJsonFormats.scala | 3 +- .../xyz/driver/pdsuidomain/entities/Document.scala | 364 +++++++++++++++------ .../fakes/entities/rep/DocumentGen.scala | 8 +- .../fakes/entities/rep/ExportPatientGen.scala | 16 +- .../fakes/entities/rep/MedicalRecordGen.scala | 2 +- .../formats/json/document/ApiDocumentType.scala | 9 +- .../formats/json/document/ApiProviderType.scala | 9 +- .../formats/json/sprayformats/document.scala | 19 +- .../formats/json/sprayformats/documenttype.scala | 12 - .../formats/json/sprayformats/providertype.scala | 12 - .../formats/json/sprayformats/record.scala | 19 +- .../json/sprayformats/ExportFormatSuite.scala | 16 +- 12 files changed, 326 insertions(+), 163 deletions(-) delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala delete mode 100644 src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala (limited to 'src/test/scala/xyz/driver') diff --git a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala index a3f48d1..83c4e6f 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala @@ -62,7 +62,6 @@ object CustomSwaggerJsonFormats { 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.providertype import xyz.driver.pdsuidomain.formats.json.sprayformats.record import xyz.driver.pdsuidomain.formats.json.sprayformats.recordissue import xyz.driver.pdsuidomain.formats.json.sprayformats.recordhistory @@ -89,7 +88,7 @@ object CustomSwaggerJsonFormats { classOf[DocumentHistory.State] -> documenthistory.documentStateFormat.write(rep.DocumentGen.nextDocumentHistoryState()), classOf[ProviderType] -> - providertype.providerTypeFormat.write(rep.MedicalRecordGen.nextProviderType()), + record.providerTypeFormat.write(rep.MedicalRecordGen.nextProviderType()), classOf[TextJson[List[MedicalRecord.Meta]]] -> record.recordMetaFormat.write(rep.MedicalRecordGen.nextMedicalRecordMetasJson()), classOf[MedicalRecord] -> diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala index 839fead..eccb254 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Document.scala @@ -15,74 +15,195 @@ import xyz.driver.pdsuicommon.validation.Validators.Validator import xyz.driver.pdsuidomain.entities.Document.Meta import scalaz.Equal +import scalaz.syntax.equal._ +import scalaz.Scalaz.stringInstance -final case class ProviderType(id: LongId[ProviderType], name: String) +sealed trait ProviderType { + val id: LongId[ProviderType] + val name: String +} object ProviderType { - sealed trait ProviderTypeName - case object MedicalOncology extends ProviderTypeName - case object Surgery extends ProviderTypeName - case object Pathology extends ProviderTypeName - case object MolecularPathology extends ProviderTypeName - case object LaboratoryMedicine extends ProviderTypeName - case object Radiology extends ProviderTypeName - case object InterventionalRadiology extends ProviderTypeName - case object RadiationOncology extends ProviderTypeName - case object PrimaryCare extends ProviderTypeName - case object Cardiology extends ProviderTypeName - case object Dermatology extends ProviderTypeName - case object Ophthalmology extends ProviderTypeName - case object Gastroenterology extends ProviderTypeName - case object Neurology extends ProviderTypeName - case object Psychiatry extends ProviderTypeName - case object Gynecology extends ProviderTypeName - case object InfectiousDisease extends ProviderTypeName - case object Immunology extends ProviderTypeName - case object Nephrology extends ProviderTypeName - case object Rheumatology extends ProviderTypeName - case object Cytology extends ProviderTypeName - case object Otolaryngology extends ProviderTypeName - case object Anesthesiology extends ProviderTypeName - case object Urology extends ProviderTypeName - case object PalliativeCare extends ProviderTypeName - case object EmergencyMedicine extends ProviderTypeName - case object SocialWork extends ProviderTypeName - case object NA extends ProviderTypeName - case object Other extends ProviderTypeName - - def fromString(txt: String): Option[ProviderTypeName] = { - txt match { - case "Medical Oncology" => Some(MedicalOncology) - case "Surgery" => Some(Surgery) - case "Pathology" => Some(Pathology) - case "Molecular Pathology" => Some(MolecularPathology) - case "LaboratoryMedicine" => Some(LaboratoryMedicine) - case "Radiology" => Some(Radiology) - case "Interventional Radiology" => Some(InterventionalRadiology) - case "Radiation Oncology" => Some(RadiationOncology) - case "Primary Care" => Some(PrimaryCare) - case "Cardiology" => Some(Cardiology) - case "Dermatology" => Some(Dermatology) - case "Ophthalmology" => Some(Ophthalmology) - case "Gastroenterology" => Some(Gastroenterology) - case "Neurology" => Some(Neurology) - case "Psychiatry" => Some(Psychiatry) - case "Gynecology" => Some(Gynecology) - case "Infectious Disease" => Some(InfectiousDisease) - case "Immunology" => Some(Immunology) - case "Nephrology" => Some(Nephrology) - case "Rheumatology" => Some(Rheumatology) - case "Cytology" => Some(Cytology) - case "Otolaryngology" => Some(Otolaryngology) - case "Anesthesiology" => Some(Anesthesiology) - case "Urology" => Some(Urology) - case "Palliative Care" => Some(PalliativeCare) - case "Emergency Medicine" => Some(EmergencyMedicine) - case "Social Work" => Some(SocialWork) - case "N/A" => Some(NA) - case "Other" => Some(Other) - case _ => None - } + + case object MedicalOncology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](1) + val name: String = "Medical Oncology" + } + + case object Surgery extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](2) + val name: String = "Surgery" + } + + case object Pathology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](3) + val name: String = "Pathology" + } + + case object MolecularPathology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](4) + val name: String = "Molecular Pathology" + } + + case object LaboratoryMedicine extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](5) + val name: String = "Laboratory Medicine" + } + + case object Radiology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](6) + val name: String = "Radiology" + } + + case object InterventionalRadiology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](7) + val name: String = "Interventional Radiology" + } + + case object RadiationOncology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](8) + val name: String = "Radiation Oncology" + } + + case object PrimaryCare extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](9) + val name: String = "Primary Care" + } + + case object Cardiology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](10) + val name: String = "Cardiology" + } + + case object Dermatology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](11) + val name: String = "Dermatology" + } + + case object Ophthalmology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](12) + val name: String = "Ophthalmology" + } + + case object Gastroenterology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](13) + val name: String = "Gastroenterology" + } + + case object Neurology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](14) + val name: String = "Neurology" + } + + case object Psychiatry extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](15) + val name: String = "Psychiatry" + } + + case object Gynecology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](16) + val name: String = "Gynecology" + } + + case object InfectiousDisease extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](17) + val name: String = "Infectious Disease" + } + + case object Immunology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](18) + val name: String = "Immunology" + } + + case object Nephrology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](19) + val name: String = "Nephrology" + } + + case object Rheumatology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](20) + val name: String = "Rheumatology" + } + + case object Cytology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](21) + val name: String = "Cytology" + } + + case object Otolaryngology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](22) + val name: String = "Otolaryngology" + } + + case object Anesthesiology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](23) + val name: String = "Anesthesiology" + } + + case object Urology extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](24) + val name: String = "Urology" + } + + case object PalliativeCare extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](25) + val name: String = "Palliative Care" + } + + case object EmergencyMedicine extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](26) + val name: String = "Emergency Medicine" + } + + case object SocialWork extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](27) + val name: String = "Social Work" + } + + case object NA extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](28) + val name: String = "N/A" + } + + case object Other extends ProviderType { + val id: LongId[ProviderType] = LongId[ProviderType](29) + val name: String = "Other" + } + + val All = Seq[ProviderType]( + MedicalOncology, + Surgery, + Pathology, + MolecularPathology, + LaboratoryMedicine, + Radiology, + InterventionalRadiology, + RadiationOncology, + PrimaryCare, + Cardiology, + Dermatology, + Ophthalmology, + Gastroenterology, + Neurology, + Psychiatry, + Gynecology, + InfectiousDisease, + Immunology, + Nephrology, + Rheumatology, + Cytology, + Otolaryngology, + Anesthesiology, + Urology, + PalliativeCare, + EmergencyMedicine, + SocialWork, + NA, + Other + ) + + def fromString(txt: String): Option[ProviderType] = { + All.find(_.name === txt) } implicit def toPhiString(x: ProviderType): PhiString = { @@ -91,39 +212,90 @@ object ProviderType { } } -final case class DocumentType(id: LongId[DocumentType], name: String) +sealed trait DocumentType { + val id: LongId[DocumentType] + val name: String +} object DocumentType { - sealed trait DocumentTypeName - case object OutpatientPhysicianNote extends DocumentTypeName - case object DischargeNote extends DocumentTypeName - case object LaboratoryReport extends DocumentTypeName - case object MedicationList extends DocumentTypeName - case object HospitalizationNote extends DocumentTypeName - case object PathologyReport extends DocumentTypeName - case object RadiologyReport extends DocumentTypeName - case object OperativeProcedureReport extends DocumentTypeName - case object MedicationAdministration extends DocumentTypeName - case object SocialWorkCaseManagementNote extends DocumentTypeName - case object NonPhysicianProviderNote extends DocumentTypeName - case object Administrative extends DocumentTypeName - - def fromString(txt: String): Option[DocumentTypeName] = { - txt match { - case "Outpatient Physician Note" => Some(OutpatientPhysicianNote) - case "Discharge Note" => Some(DischargeNote) - case "Laboratory Report" => Some(LaboratoryReport) - case "Medication List" => Some(MedicationList) - case "Hospitalization Note" => Some(HospitalizationNote) - case "Pathology Report" => Some(PathologyReport) - case "Radiology Report" => Some(RadiologyReport) - case "Operative/Procedure Report" => Some(OperativeProcedureReport) - case "Medication Administration" => Some(MedicationAdministration) - case "Social Work/Case Management Note" => Some(SocialWorkCaseManagementNote) - case "Non-physician Provider Note" => Some(NonPhysicianProviderNote) - case "Administrative" => Some(Administrative) - case _ => None - } + + case object OutpatientPhysicianNote extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](1) + val name: String = "Outpatient Physician Note" + } + + case object DischargeNote extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](2) + val name: String = "Discharge Note" + } + + case object LaboratoryReport extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](3) + val name: String = "Laboratory Report" + } + + case object MedicationList extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](4) + val name: String = "Medication List" + } + + case object HospitalizationNote extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](5) + val name: String = "Hospitalization Note" + } + + case object PathologyReport extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](6) + val name: String = "Pathology Report" + } + + case object RadiologyReport extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](7) + val name: String = "Radiology Report" + } + + case object OperativeProcedureReport extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](8) + val name: String = "Operative/Procedure Report" + } + + case object MedicationAdministration extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](9) + val name: String = "Medication Administration" + } + + case object SocialWorkCaseManagementNote extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](10) + val name: String = "Social Work/Case Management Note" + } + + case object NonPhysicianProviderNote extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](11) + val name: String = "Non-physician Provider Note" + } + + case object Administrative extends DocumentType { + val id: LongId[DocumentType] = LongId[DocumentType](12) + val name: String = "Administrative" + } + + val All = Seq[DocumentType]( + OutpatientPhysicianNote, + DischargeNote, + LaboratoryReport, + MedicationList, + HospitalizationNote, + PathologyReport, + RadiologyReport, + OperativeProcedureReport, + MedicationAdministration, + SocialWorkCaseManagementNote, + NonPhysicianProviderNote, + Administrative + ) + + def fromString(txt: String): Option[DocumentType] = { + All.find(_.name === txt) } implicit def equal: Equal[DocumentType] = Equal.equal[DocumentType](_ == _) diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala index 6d5330e..1ac75ab 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/DocumentGen.scala @@ -75,12 +75,8 @@ object DocumentGen { ) } - def nextDocumentType(): DocumentType = { - DocumentType( - id = nextLongId[DocumentType], - name = nextString() - ) - } + def nextDocumentType(): DocumentType = + generators.oneOf(DocumentType.All: _*) def nextDocumentIssue(documentId: LongId[Document] = nextLongId): DocumentIssue = { val pages = nextStartAndEndPagesOption() diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala index e3ef6bc..3fcc4cb 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala @@ -7,24 +7,12 @@ import xyz.driver.pdsuidomain.fakes.entities.common._ import xyz.driver.pdsuidomain.entities._ import xyz.driver.pdsuidomain.entities.export.patient._ import xyz.driver.pdsuidomain.fakes.entities.common.{nextLocalDate, nextLongId} +import xyz.driver.pdsuidomain.fakes.entities.rep.DocumentGen._ +import xyz.driver.pdsuidomain.fakes.entities.rep.MedicalRecordGen._ object ExportPatientGen { private val maxItemsInCollectionNumber = 3 - def nextDocumentType(documentTypeId: LongId[DocumentType] = nextLongId): DocumentType = { - DocumentType( - documentTypeId, - nextString() - ) - } - - def nextProviderType(providerTypeId: LongId[ProviderType] = nextLongId): ProviderType = { - ProviderType( - providerTypeId, - nextString() - ) - } - def nextExportPatientLabelEvidenceDocument(documentId: LongId[Document]): ExportPatientLabelEvidenceDocument = { ExportPatientLabelEvidenceDocument( documentId = documentId, diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala index 023dc00..2777116 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/MedicalRecordGen.scala @@ -142,6 +142,6 @@ object MedicalRecordGen { } def nextProviderType(): ProviderType = - ProviderType(id = nextLongId[ProviderType], name = nextString()) + generators.oneOf(ProviderType.All: _*) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala index 8b4974f..22bea6b 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiDocumentType.scala @@ -2,15 +2,14 @@ package xyz.driver.pdsuidomain.formats.json.document import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.DocumentType final case class ApiDocumentType(id: Long, name: String) { - def toDomain = DocumentType( - id = LongId(this.id), - name = this.name - ) + def toDomain: DocumentType = + DocumentType + .fromString(name) + .getOrElse(throw new IllegalArgumentException(s"Unknown document type name $name")) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala index c0eddad..9c0c216 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/document/ApiProviderType.scala @@ -2,15 +2,14 @@ package xyz.driver.pdsuidomain.formats.json.document import play.api.libs.functional.syntax._ import play.api.libs.json.{Format, JsPath} -import xyz.driver.pdsuicommon.domain.LongId import xyz.driver.pdsuidomain.entities.ProviderType final case class ApiProviderType(id: Long, name: String) { - def toDomain = ProviderType( - id = LongId(this.id), - name = this.name - ) + def toDomain: ProviderType = + ProviderType + .fromString(name) + .getOrElse(throw new IllegalArgumentException(s"Unknown provider type name $name")) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala index ff0603a..e3f6a9c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/document.scala @@ -28,7 +28,24 @@ object document { implicit val documentMetaFormat: RootJsonFormat[Meta] = jsonFormat3(Meta.apply) - implicit val documentTypeFormat: RootJsonFormat[DocumentType] = jsonFormat2(DocumentType.apply) + implicit val documentTypeFormat: RootJsonFormat[DocumentType] = new RootJsonFormat[DocumentType] { + override def read(json: JsValue): DocumentType = json match { + case JsObject(fields) => + val name = fields + .get("name") + .map(_.convertTo[String]) + .getOrElse(deserializationError(s"Intervention type json object does not contain `name` field: $json")) + + DocumentType + .fromString(name) + .getOrElse(deserializationError(s"Unknown document type: $name")) + + case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json") + } + + override def write(obj: DocumentType) = + JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) + } implicit val fullDocumentMetaFormat = new RootJsonFormat[TextJson[Meta]] { override def write(obj: TextJson[Meta]): JsValue = obj.content.toJson 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 deleted file mode 100644 index 7ec6ef5..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/documenttype.scala +++ /dev/null @@ -1,12 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.sprayformats - -import spray.json._ -import xyz.driver.pdsuidomain.entities.DocumentType - -object documenttype { - import DefaultJsonProtocol._ - import common._ - - implicit val format: RootJsonFormat[DocumentType] = jsonFormat2(DocumentType.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala deleted file mode 100644 index 385feb2..0000000 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/providertype.scala +++ /dev/null @@ -1,12 +0,0 @@ -package xyz.driver.pdsuidomain.formats.json.sprayformats - -import spray.json._ -import xyz.driver.pdsuidomain.entities.ProviderType - -object providertype { - import DefaultJsonProtocol._ - import common._ - - implicit val providerTypeFormat: RootJsonFormat[ProviderType] = jsonFormat2(ProviderType.apply) - -} diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala index 6b69873..8eef44a 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/record.scala @@ -36,7 +36,24 @@ object record { } } - implicit val providerTypeFormat = jsonFormat2(ProviderType.apply) + implicit val providerTypeFormat: RootJsonFormat[ProviderType] = new RootJsonFormat[ProviderType] { + override def read(json: JsValue): ProviderType = json match { + case JsObject(fields) => + val name = fields + .get("name") + .map(_.convertTo[String]) + .getOrElse(deserializationError(s"Intervention type json object does not contain `name` field: $json")) + + ProviderType + .fromString(name) + .getOrElse(deserializationError(s"Unknown provider type: $name")) + + case _ => deserializationError(s"Expected Json Object as Intervention type, but got $json") + } + + override def write(obj: ProviderType) = + JsObject("id" -> obj.id.toJson, "name" -> obj.name.toJson) + } implicit val caseIdFormat = new RootJsonFormat[CaseId] { override def write(caseId: CaseId): JsString = JsString(caseId.toString) diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala index 52c8c81..a451905 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala @@ -16,8 +16,8 @@ class ExportFormatSuite extends FlatSpec with Matchers { val document = ExportPatientLabelEvidenceDocument( documentId = LongId(101), requestId = RecordRequestId(UUID.fromString("7b54a75d-4197-4b27-9045-b9b6cb131be9")), - documentType = DocumentType(LongId[DocumentType](1), "document type"), - providerType = ProviderType(LongId[ProviderType](2), "provider type"), + documentType = DocumentType.OutpatientPhysicianNote, + providerType = ProviderType.Surgery, date = LocalDate.parse("2017-08-10") ) @@ -67,14 +67,14 @@ class ExportFormatSuite extends FlatSpec with Matchers { writtenJson should be( """{"patientId":"748b5884-3528-4cb9-904b-7a8151d6e343","labelVersion":1,"labels":[{"labelId":1,"evidence":[{"evidenceId":11, "labelValue":"Yes","evidenceText":"evidence text 11","document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9", - "documentType":{"id":1,"name":"document type"},"providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}}, + "documentType":{"id":1,"name":"Outpatient Physician Note"},"providerType":{"id":2,"name":"Surgery"},"date":"2017-08-10"}}, {"evidenceId":12,"labelValue":"No","evidenceText":"evidence text 12","document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9", - "documentType":{"id":1,"name":"document type"},"providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}}]}, + "documentType":{"id":1,"name":"Outpatient Physician Note"},"providerType":{"id":2,"name":"Surgery"},"date":"2017-08-10"}}]}, {"labelId":2,"evidence":[{"evidenceId":12,"labelValue":"Yes","evidenceText":"evidence text 12","document": - {"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":{"id":1,"name":"document type"}, - "providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}},{"evidenceId":13,"labelValue":"Yes","evidenceText":"evidence text 13", - "document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":{"id":1,"name":"document type"}, - "providerType":{"id":2,"name":"provider type"},"date":"2017-08-10"}}]}]}""".parseJson) + {"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":{"id":1,"name":"Outpatient Physician Note"}, + "providerType":{"id":2,"name":"Surgery"},"date":"2017-08-10"}},{"evidenceId":13,"labelValue":"Yes","evidenceText":"evidence text 13", + "document":{"documentId":101,"requestId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","documentType":{"id":1,"name":"Outpatient Physician Note"}, + "providerType":{"id":2,"name":"Surgery"},"date":"2017-08-10"}}]}]}""".parseJson) } "Json format for ApiExportTrialWithLabels" should "read and write correct JSON" in { -- cgit v1.2.3 From 14b460edbebb1d5c39809dbc591b786edec9fa8e Mon Sep 17 00:00:00 2001 From: Kseniya Tomskikh Date: Mon, 2 Oct 2017 15:21:58 +0700 Subject: TRIAL-17 Added 'inclusion' field to Criterion --- .../xyz/driver/pdsuidomain/entities/Criterion.scala | 3 ++- .../pdsuidomain/fakes/entities/trialcuration.scala | 3 ++- .../formats/json/criterion/ApiCriterion.scala | 12 ++++++++---- .../formats/json/criterion/ApiNewCriterion.scala | 9 ++++++--- .../formats/json/criterion/ApiUpdateCriterion.scala | 6 +++++- .../formats/json/sprayformats/criterion.scala | 19 ++++++++++++++++--- .../json/sprayformats/CriterionFormatSuite.scala | 17 ++++++++++++----- 7 files changed, 51 insertions(+), 18 deletions(-) (limited to 'src/test/scala/xyz/driver') diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala index 7f065d4..2432251 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Criterion.scala @@ -9,7 +9,8 @@ final case class Criterion(id: LongId[Criterion], trialId: StringId[Trial], text: Option[String], isCompound: Boolean, - meta: String) { + meta: String, + inclusion: Option[Boolean]) { def isValid: Boolean = text.nonEmpty && Option(meta).isDefined } diff --git a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala index fcd833a..9a5022c 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala @@ -45,7 +45,8 @@ object trialcuration { trialId = nextStringId[Trial], text = Option(generators.nextString()), isCompound = generators.nextBoolean(), - meta = generators.nextString() + meta = generators.nextString(), + inclusion = Option(generators.nextBoolean()) ) def nextCriterionLabel(criterionId: LongId[Criterion]): CriterionLabel = CriterionLabel( diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala index 4986b17..43b5494 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiCriterion.scala @@ -14,7 +14,8 @@ final case class ApiCriterion(id: Long, text: Option[String], isCompound: Boolean, labels: Seq[ApiCriterionLabel], - trialId: String) { + trialId: String, + inclusion: Option[Boolean]) { def toDomain = RichCriterion( criterion = Criterion( @@ -22,7 +23,8 @@ final case class ApiCriterion(id: Long, trialId = StringId[Trial](trialId), text, isCompound, - meta.getOrElse("") + meta.getOrElse(""), + inclusion ), armIds = arms.map(LongId[Arm]), labels = labels.map(_.toDomain(LongId[Criterion](id))) @@ -40,7 +42,8 @@ object ApiCriterion { (JsPath \ "text").formatNullable[String] and (JsPath \ "isCompound").format[Boolean] and (JsPath \ "labels").format(seqJsonFormat[ApiCriterionLabel]) and - (JsPath \ "trialId").format[String] + (JsPath \ "trialId").format[String] and + (JsPath \ "inclusion").formatNullable[Boolean] )(ApiCriterion.apply, unlift(ApiCriterion.unapply)) def fromDomain(richCriterion: RichCriterion) = ApiCriterion( @@ -50,6 +53,7 @@ object ApiCriterion { text = richCriterion.criterion.text, isCompound = richCriterion.criterion.isCompound, labels = richCriterion.labels.map(ApiCriterionLabel.fromDomain), - trialId = richCriterion.criterion.trialId.id + trialId = richCriterion.criterion.trialId.id, + inclusion = richCriterion.criterion.inclusion ) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala index ab7641f..d72a9b4 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiNewCriterion.scala @@ -13,7 +13,8 @@ final case class ApiNewCriterion(meta: Option[String], text: Option[String], isCompound: Option[Boolean], labels: Seq[ApiCriterionLabel], - trialId: String) { + trialId: String, + inclusion: Option[Boolean]) { def toDomain = RichCriterion( criterion = Criterion( @@ -21,7 +22,8 @@ final case class ApiNewCriterion(meta: Option[String], meta = meta.getOrElse(""), trialId = StringId(trialId), isCompound = isCompound.getOrElse(false), - text = text + text = text, + inclusion = inclusion ), armIds = arms.getOrElse(Seq.empty).map(LongId[Arm]), labels = labels.map(_.toDomain(LongId(Long.MaxValue))) // A developer should specify right criterionId himself @@ -38,6 +40,7 @@ object ApiNewCriterion { (JsPath \ "text").formatNullable[String] and (JsPath \ "isCompound").formatNullable[Boolean] and (JsPath \ "labels").format(seqJsonFormat[ApiCriterionLabel]) and - (JsPath \ "trialId").format[String] + (JsPath \ "trialId").format[String] and + (JsPath \ "inclusion").formatNullable[Boolean] )(ApiNewCriterion.apply, unlift(ApiNewCriterion.unapply)) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala index 2bcda56..77989f0 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/criterion/ApiUpdateCriterion.scala @@ -14,6 +14,7 @@ final case class ApiUpdateCriterion(meta: Tristate[String], arms: Tristate[Seq[Long]], text: Option[String], isCompound: Option[Boolean], + inclusion: Tristate[Boolean], labels: Tristate[Seq[ApiCriterionLabel]]) { def applyTo(orig: RichCriterion): RichCriterion = RichCriterion( @@ -27,7 +28,8 @@ final case class ApiUpdateCriterion(meta: Tristate[String], meta = meta.cata(identity, "{}", orig.meta), text = text.orElse(orig.text), isCompound = isCompound.getOrElse(orig.isCompound), - trialId = orig.trialId + trialId = orig.trialId, + inclusion = inclusion.cata(x => Some(x), None, orig.inclusion) ) } @@ -45,6 +47,7 @@ object ApiUpdateCriterion { (JsPath \ "arms").readTristate(seqJsonFormat[Long]) and (JsPath \ "text").readNullable[String] and (JsPath \ "isCompound").readNullable[Boolean] and + (JsPath \ "inclusion").readTristate[Boolean] and (JsPath \ "labels").readTristate(seqJsonFormat[ApiCriterionLabel]) )(ApiUpdateCriterion.apply _) @@ -53,6 +56,7 @@ object ApiUpdateCriterion { (JsPath \ "arms").writeTristate(seqJsonFormat[Long]) and (JsPath \ "text").writeNullable[String] and (JsPath \ "isCompound").writeNullable[Boolean] and + (JsPath \ "inclusion").writeTristate[Boolean] and (JsPath \ "labels").writeTristate(seqJsonFormat[ApiCriterionLabel]) )(unlift(ApiUpdateCriterion.unapply)) 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 743f885..8da719c 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 @@ -73,6 +73,11 @@ object criterion { .map(_.convertTo[Option[String]].getOrElse("{}")) .getOrElse(orig.criterion.meta) + val inclusion = fields + .get("inclusion") + .map(_.convertTo[Option[Boolean]]) + .getOrElse(orig.criterion.inclusion) + val arms = fields .get("arms") .map(_.convertTo[Option[List[LongId[Arm]]]].getOrElse(List.empty[LongId[Arm]])) @@ -88,7 +93,8 @@ object criterion { criterion = orig.criterion.copy( meta = meta, text = text, - isCompound = isCompound + isCompound = isCompound, + inclusion = inclusion ), armIds = arms, labels = labels @@ -106,7 +112,8 @@ object criterion { "text" -> obj.criterion.text.toJson, "isCompound" -> obj.criterion.isCompound.toJson, "labels" -> obj.labels.map(_.toJson).toJson, - "trialId" -> obj.criterion.trialId.toJson + "trialId" -> obj.criterion.trialId.toJson, + "inclusion" -> obj.criterion.inclusion.toJson ) override def read(json: JsValue): RichCriterion = json match { @@ -129,6 +136,11 @@ object criterion { .map(_.convertTo[String]) .getOrElse("") + val inclusion = fields + .get("inclusion") + .map(_.convertTo[Option[Boolean]]) + .getOrElse(None) + val arms = fields .get("arms") .map(_.convertTo[List[LongId[Arm]]]) @@ -146,7 +158,8 @@ object criterion { trialId = trialId, text = text, isCompound = isCompound, - meta = meta + meta = meta, + inclusion = inclusion ), armIds = arms, labels = labels diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala index d24c4c1..708aed9 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/CriterionFormatSuite.scala @@ -15,7 +15,8 @@ class CriterionFormatSuite extends FlatSpec with Matchers { trialId = StringId("NCT000001"), text = Some("text"), isCompound = false, - meta = "{}" + meta = "{}", + inclusion = None ) val labels = List( CriterionLabel( @@ -44,12 +45,12 @@ class CriterionFormatSuite extends FlatSpec with Matchers { val writtenJson = richCriterionFormat.write(richCriterion) writtenJson should be( - """{"text":"text","isCompound":false,"trialId":"NCT000001","arms":[20,21,21],"id":10,"meta":"{}", + """{"text":"text","isCompound":false,"trialId":"NCT000001","inclusion":null,"arms":[20,21,21],"id":10,"meta":"{}", "labels":[{"labelId":101,"categoryId":3,"value":"Yes","isDefining":true}, {"labelId":102,"categoryId":3,"value":"No","isDefining":true}]}""".parseJson) val createCriterionJson = - """{"text":"text","isCompound":false,"trialId":"NCT000001", + """{"text":"text","isCompound":false,"trialId":"NCT000001","inclusion":null, "arms":[20,21,21],"meta":"{}","labels":[{"labelId":101,"categoryId":3,"value":"Yes","isDefining":true}, {"labelId":102,"categoryId":3,"value":"No","isDefining":true}]}""".parseJson val parsedRichCriterion = richCriterionFormat.read(createCriterionJson) @@ -59,8 +60,14 @@ class CriterionFormatSuite extends FlatSpec with Matchers { ) parsedRichCriterion should be(expectedRichCriterion) - val updateCriterionJson = """{"meta":null,"text":"new text","isCompound":true}""".parseJson - val expectedUpdatedCriterion = richCriterion.copy(criterion = criterion.copy(text = Some("new text"), isCompound = true, meta = "{}")) + val updateCriterionJson = """{"meta":null,"text":"new text","isCompound":true,"inclusion":true}""".parseJson + val expectedUpdatedCriterion = richCriterion.copy( + criterion = criterion.copy( + text = Some("new text"), + isCompound = true, + meta = "{}", + inclusion = Some(true) + )) val parsedUpdateCriterion = applyUpdateToCriterion(updateCriterionJson, richCriterion) parsedUpdateCriterion should be(expectedUpdatedCriterion) } -- cgit v1.2.3