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authorAleksandr <ognelisar@gmail.com>2017-10-10 16:41:33 +0700
committerAleksandr <ognelisar@gmail.com>2017-10-10 16:41:33 +0700
commit4c22afe6a34641f5b35ff4953a5821a2bc940255 (patch)
tree4f77275d4460a184cf64085e9d7597841a50fbc9
parentc32f965212481e4d26c2ae1ae5616f2d4b3e22ae (diff)
parent4f83461cba1f78e607ca2a4edb6fa26f6e16e732 (diff)
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All merge conflicts are resolved
-rw-r--r--build.sbt4
-rw-r--r--src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala25
-rw-r--r--src/main/scala/xyz/driver/pdsuicommon/domain/FuzzyValue.scala40
-rw-r--r--src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala3
-rw-r--r--src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala3
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala27
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala8
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala6
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala19
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala23
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala10
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala10
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala31
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala32
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala23
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabel.scala5
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala19
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala8
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala12
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialLabelCriterion.scala12
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala36
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala7
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala2
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExportPatientGen.scala6
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/fakes/entities/rep/ExtractedDataGen.scala5
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala3
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala7
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiCriterionLabel.scala6
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/label/ApiExtractedDataLabel.scala12
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala25
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala8
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala15
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala32
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala8
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala14
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala9
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPatientCriterion.scala18
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala10
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/export.scala1
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/extracteddata.scala7
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala4
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientcriterion.scala8
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala1
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala1
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala9
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala9
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala17
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala4
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala5
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala7
-rw-r--r--src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala9
-rw-r--r--src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExportFormatSuite.scala13
-rw-r--r--src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala11
-rw-r--r--src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala11
-rw-r--r--src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala10
-rw-r--r--src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala11
-rw-r--r--src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala22
-rw-r--r--src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala5
58 files changed, 273 insertions, 435 deletions
diff --git a/build.sbt b/build.sbt
index bebf2aa..d68a8f5 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" % "1.2.1",
- "xyz.driver" %% "domain-model" % "0.17.5",
+ "xyz.driver" %% "core" % "1.2.2",
+ "xyz.driver" %% "domain-model" % "0.17.8",
"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/SlickQueryBuilder.scala b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala
index 0daa84d..dc03a52 100644
--- a/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala
+++ b/src/main/scala/xyz/driver/pdsuicommon/db/SlickQueryBuilder.scala
@@ -1,6 +1,6 @@
package xyz.driver.pdsuicommon.db
-import java.sql.PreparedStatement
+import java.sql.{JDBCType, PreparedStatement}
import java.time.LocalDateTime
import slick.jdbc.{JdbcProfile, PositionedParameters, SQLActionBuilder, SetParameter}
@@ -38,6 +38,12 @@ object SlickQueryBuilder {
})
}
}
+
+ implicit object SetQueryParameter extends SetParameter[AnyRef] {
+ def apply(v: AnyRef, pp: PositionedParameters) = {
+ pp.setObject(v, JDBCType.BINARY.getVendorTypeNumber)
+ }
+ }
}
final case class SlickTableLink(keyColumnName: String, foreignTableName: String, foreignKeyColumnName: String)
@@ -175,6 +181,16 @@ sealed trait SlickQueryBuilderParameters {
} else sql
}
+ def concatenateParameters(sql: SQLActionBuilder, first: Boolean, tail: Seq[AnyRef]): SQLActionBuilder = {
+ if (tail.nonEmpty) {
+ if (!first) {
+ concatenateParameters(sql concat sql""",${tail.head}""", false, tail.tail)
+ } else {
+ concatenateParameters(sql"""(${tail.head}""", false, tail.tail)
+ }
+ } else sql concat sql")"
+ }
+
filter match {
case x if isEmpty(x) =>
sql""
@@ -196,7 +212,7 @@ sealed trait SlickQueryBuilderParameters {
// So, to handle NotEq for nullable fields we need to use more complex SQL expression.
// http://dev.mysql.com/doc/refman/5.7/en/working-with-null.html
val escapedColumn = escapeDimension(dimension)
- sql"(#${escapedColumn} is null or #${escapedColumn} != ${value.toString})"
+ sql"(#${escapedColumn} is null or #${escapedColumn} != $value)"
case Atom.Binary(dimension, op, value) =>
val operator = op match {
@@ -208,7 +224,7 @@ sealed trait SlickQueryBuilderParameters {
case Lt => sql"<"
case LtEq => sql"<="
}
- sql"#${escapeDimension(dimension)}" concat operator concat sql"""${value.toString}"""
+ sql"#${escapeDimension(dimension)}" concat operator concat sql"""$value"""
case Atom.NAry(dimension, op, values) =>
val sqlOp = op match {
@@ -217,8 +233,7 @@ sealed trait SlickQueryBuilderParameters {
}
val formattedValues = if (values.nonEmpty) {
- val condition = s"(${values.map(v => "'" + v.toString + "'").mkString(",")})"
- sql"#${condition}"
+ concatenateParameters(sql"", true, values)
} else sql"NULL"
sql"#${escapeDimension(dimension)}" concat sqlOp concat formattedValues
diff --git a/src/main/scala/xyz/driver/pdsuicommon/domain/FuzzyValue.scala b/src/main/scala/xyz/driver/pdsuicommon/domain/FuzzyValue.scala
deleted file mode 100644
index 36c3de7..0000000
--- a/src/main/scala/xyz/driver/pdsuicommon/domain/FuzzyValue.scala
+++ /dev/null
@@ -1,40 +0,0 @@
-package xyz.driver.pdsuicommon.domain
-
-import xyz.driver.pdsuicommon.logging._
-import xyz.driver.pdsuicommon.utils.Utils
-
-sealed trait FuzzyValue
-
-object FuzzyValue {
- case object Yes extends FuzzyValue
- case object No extends FuzzyValue
- case object Maybe extends FuzzyValue
-
- private val yes = "Yes"
- private val no = "No"
- private val maybe = "Maybe"
-
- val All: Set[FuzzyValue] =
- Set(Yes, No, Maybe)
-
- def fromBoolean(x: Boolean): FuzzyValue =
- if (x) Yes else No
-
- implicit def toPhiString(x: FuzzyValue): PhiString =
- Unsafe(Utils.getClassSimpleName(x.getClass))
-
- val fromString: PartialFunction[String, FuzzyValue] = {
- case fuzzy =>
- fuzzy.toLowerCase.capitalize match {
- case `yes` => Yes
- case `no` => No
- case `maybe` => Maybe
- }
- }
-
- def valueToString(x: FuzzyValue): String = x match {
- case Yes => `yes`
- case No => `no`
- case Maybe => `maybe`
- }
-}
diff --git a/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala b/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala
index a53f1dd..9383a1c 100644
--- a/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala
+++ b/src/main/scala/xyz/driver/pdsuicommon/json/JsonSerializer.scala
@@ -3,7 +3,7 @@ package xyz.driver.pdsuicommon.json
import java.text.SimpleDateFormat
import com.fasterxml.jackson.annotation.JsonInclude
-import com.fasterxml.jackson.databind.ObjectMapper
+import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper}
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule
import com.fasterxml.jackson.module.scala.DefaultScalaModule
import com.fasterxml.jackson.module.scala.experimental.ScalaObjectMapper
@@ -15,6 +15,7 @@ object JsonSerializer {
mapper.registerModule(new JavaTimeModule)
mapper.setDateFormat(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'"))
mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL)
+ mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
def serialize(value: Any): String = {
mapper.writeValueAsString(value)
diff --git a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala
index 83c4e6f..6d2a068 100644
--- a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala
+++ b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala
@@ -15,6 +15,7 @@ import xyz.driver.pdsuidomain.formats.json.sprayformats.trial._
import xyz.driver.pdsuidomain.formats.json.sprayformats.trialhistory._
import xyz.driver.pdsuidomain.formats.json.sprayformats.trialissue._
import xyz.driver.core.swagger.CustomSwaggerJsonConverter._
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.concurrent.BridgeUploadQueue
import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion
import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData
@@ -32,7 +33,7 @@ object CustomSwaggerJsonFormats {
)
val customTrialCurationProperties = immutable.Map[Class[_], Property](
classOf[Trial.Status] -> stringProperty(),
- classOf[Trial.Condition] -> stringProperty(),
+ classOf[CancerType] -> stringProperty(),
classOf[TrialHistory.Action] -> stringProperty(),
classOf[TrialHistory.State] -> stringProperty()
) ++ customCommonProperties
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala
index 42ac55b..f35c3fd 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/DirectReport.scala
@@ -2,31 +2,14 @@ package xyz.driver.pdsuidomain.entities
import java.time.LocalDate
+import xyz.driver.entities.assays.AssayType
import xyz.driver.pdsuicommon.logging._
import xyz.driver.pdsuicommon.domain.UuidId
-import xyz.driver.pdsuicommon.utils.Utils
-import xyz.driver.pdsuidomain.entities.DirectReport.ReportType
object DirectReport {
-
- sealed trait ReportType extends Product with Serializable {
- def oneOf(xs: ReportType*): Boolean = xs.contains(this)
-
- def oneOf(xs: Set[ReportType]): Boolean = xs.contains(this)
- }
-
- object ReportType {
- case object IHC extends ReportType
- case object DNA extends ReportType
- case object CFDNA extends ReportType
-
- val All = Set(IHC, DNA, CFDNA)
- implicit def toPhiString(x: ReportType): PhiString = Unsafe(Utils.getClassSimpleName(x.getClass))
- }
-
implicit def toPhiString(x: DirectReport): PhiString = {
import x._
- phi"DirectReport(id=$id, patientId=$patientId, reportType=$reportType, date=${Unsafe(date)}, " +
+ phi"DirectReport(id=$id, patientId=$patientId, reportType=${Unsafe(reportType)}, date=${Unsafe(date)}, " +
phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, " +
phi"providerName=${Unsafe(providerName)})"
}
@@ -34,8 +17,8 @@ object DirectReport {
final case class DirectReport(id: UuidId[DirectReport],
patientId: UuidId[Patient],
- reportType: ReportType,
+ reportType: AssayType,
date: LocalDate,
- documentType: String,
- providerType: String,
+ documentType: DocumentType,
+ providerType: ProviderType,
providerName: String)
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala
index fbd468f..352cf55 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/ExtractedData.scala
@@ -1,7 +1,7 @@
package xyz.driver.pdsuidomain.entities
-import xyz.driver.entities.labels.{Label, LabelCategory}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson}
+import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue}
+import xyz.driver.pdsuicommon.domain.{LongId, TextJson}
import xyz.driver.pdsuicommon.logging._
import xyz.driver.pdsuidomain.entities.ExtractedData.Meta
@@ -37,7 +37,7 @@ object ExtractedDataLabel {
implicit def toPhiString(x: ExtractedDataLabel): PhiString = {
import x._
- phi"ExtractedDataLabel(id=$id, dataId=$dataId, labelId=$labelId, categoryId=$categoryId, value=$value)"
+ phi"ExtractedDataLabel(id=$id, dataId=$dataId, labelId=$labelId, categoryId=$categoryId, value=${Unsafe(value)})"
}
}
@@ -45,4 +45,4 @@ final case class ExtractedDataLabel(id: LongId[ExtractedDataLabel],
dataId: LongId[ExtractedData],
labelId: Option[LongId[Label]],
categoryId: Option[LongId[LabelCategory]],
- value: Option[FuzzyValue])
+ value: Option[LabelValue])
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala
index 6be0b88..598b11e 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Patient.scala
@@ -2,6 +2,8 @@ package xyz.driver.pdsuidomain.entities
import java.time.{LocalDate, LocalDateTime}
+import xyz.driver.entities.common.FullName
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.domain._
import xyz.driver.pdsuicommon.logging._
import xyz.driver.pdsuicommon.utils.Utils
@@ -52,14 +54,14 @@ object Patient {
final case class Patient(id: UuidId[Patient],
status: Patient.Status,
- name: String,
+ name: FullName[Patient],
dob: LocalDate,
assignee: Option[StringId[User]],
previousStatus: Option[Patient.Status],
previousAssignee: Option[StringId[User]],
lastActiveUserId: Option[StringId[User]],
isUpdateRequired: Boolean,
- condition: String,
+ disease: CancerType,
orderId: PatientOrderId,
lastUpdate: LocalDateTime) {
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala
index 469b21c..79a19ed 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientCriterion.scala
@@ -2,7 +2,8 @@ package xyz.driver.pdsuidomain.entities
import java.time.LocalDateTime
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId}
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
import xyz.driver.pdsuicommon.logging._
object PatientCriterion {
@@ -18,15 +19,15 @@ object PatientCriterion {
/**
* @see https://driverinc.atlassian.net/wiki/display/MTCH/EV+Business+Process
*/
- def getEligibilityStatus(criterionValue: Option[Boolean], primaryValue: Option[FuzzyValue]): Option[FuzzyValue] = {
+ def getEligibilityStatus(criterionValue: Option[Boolean], primaryValue: Option[LabelValue]): Option[LabelValue] = {
primaryValue match {
case None => None
- case Some(FuzzyValue.Maybe) => Some(FuzzyValue.Maybe)
- case Some(_) if criterionValue.isEmpty => Some(FuzzyValue.Maybe)
+ case Some(LabelValue.Maybe) => Some(LabelValue.Maybe)
+ case Some(_) if criterionValue.isEmpty => Some(LabelValue.Maybe)
case Some(status) =>
Some(
- FuzzyValue.fromBoolean(
- FuzzyValue.fromBoolean(
+ LabelValue.fromBoolean(
+ LabelValue.fromBoolean(
criterionValue.getOrElse(throw new IllegalArgumentException("Criterion should not be empty"))) == status
))
}
@@ -47,12 +48,12 @@ final case class PatientCriterion(id: LongId[PatientCriterion],
criterionText: String,
criterionValue: Option[Boolean],
criterionIsDefining: Boolean,
- eligibilityStatus: Option[FuzzyValue],
- verifiedEligibilityStatus: Option[FuzzyValue],
+ eligibilityStatus: Option[LabelValue],
+ verifiedEligibilityStatus: Option[LabelValue],
isVerified: Boolean,
isVisible: Boolean,
lastUpdate: LocalDateTime) {
- def isIneligibleForEv: Boolean = eligibilityStatus.contains(FuzzyValue.No) && isVerified
+ def isIneligibleForEv: Boolean = eligibilityStatus.contains(LabelValue.No) && isVerified
}
object PatientCriterionArm {
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala
index 8ee5b3c..ff272a8 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientEligibleTrial.scala
@@ -1,6 +1,7 @@
package xyz.driver.pdsuidomain.entities
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId}
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
import xyz.driver.pdsuicommon.logging._
object PatientTrialArm {
@@ -37,22 +38,22 @@ object PatientTrialArmGroup {
/**
* @see https://driverinc.atlassian.net/wiki/display/DMPD/EV+Business+Process
*/
- def getEligibilityStatusForRc(criterionList: TraversableOnce[PatientCriterion]): Option[FuzzyValue] = {
- def isEligible: Boolean = criterionList.forall(_.verifiedEligibilityStatus.contains(FuzzyValue.Yes))
- def isIneligible: Boolean = criterionList.exists(_.verifiedEligibilityStatus.contains(FuzzyValue.No))
+ def getEligibilityStatusForRc(criterionList: TraversableOnce[PatientCriterion]): Option[LabelValue] = {
+ def isEligible: Boolean = criterionList.forall(_.verifiedEligibilityStatus.contains(LabelValue.Yes))
+ def isIneligible: Boolean = criterionList.exists(_.verifiedEligibilityStatus.contains(LabelValue.No))
def isUnknown: Boolean = criterionList.forall(_.verifiedEligibilityStatus.isEmpty)
- if (isEligible) Some(FuzzyValue.Yes)
- else if (isIneligible) Some(FuzzyValue.No)
+ if (isEligible) Some(LabelValue.Yes)
+ else if (isIneligible) Some(LabelValue.No)
else if (isUnknown) None
- else Some(FuzzyValue.Maybe)
+ else Some(LabelValue.Maybe)
}
}
final case class PatientTrialArmGroup(id: LongId[PatientTrialArmGroup],
eligibleTrialId: UuidId[PatientEligibleTrial],
- eligibilityStatus: Option[FuzzyValue],
- verifiedEligibilityStatus: Option[FuzzyValue],
+ eligibilityStatus: Option[LabelValue],
+ verifiedEligibilityStatus: Option[LabelValue],
isVerified: Boolean)
object PatientTrialArmGroupView {
@@ -69,8 +70,8 @@ final case class PatientTrialArmGroupView(id: LongId[PatientTrialArmGroup],
patientId: UuidId[Patient],
trialId: StringId[Trial],
hypothesisId: UuidId[Hypothesis],
- eligibilityStatus: Option[FuzzyValue],
- verifiedEligibilityStatus: Option[FuzzyValue],
+ eligibilityStatus: Option[LabelValue],
+ verifiedEligibilityStatus: Option[LabelValue],
isVerified: Boolean) {
def applyTo(trialArmGroup: PatientTrialArmGroup) = {
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala
index d10c7d2..4c0f4ef 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabel.scala
@@ -1,7 +1,7 @@
package xyz.driver.pdsuidomain.entities
-import xyz.driver.entities.labels.Label
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, UuidId}
+import xyz.driver.entities.labels.{Label, LabelValue}
+import xyz.driver.pdsuicommon.domain.{LongId, UuidId}
import xyz.driver.pdsuicommon.logging._
object PatientLabel {
@@ -17,8 +17,8 @@ final case class PatientLabel(id: LongId[PatientLabel],
patientId: UuidId[Patient],
labelId: LongId[Label],
score: Int,
- primaryValue: Option[FuzzyValue],
- verifiedPrimaryValue: Option[FuzzyValue],
+ primaryValue: Option[LabelValue],
+ verifiedPrimaryValue: Option[LabelValue],
isImplicitMatch: Boolean,
isVisible: Boolean)
@@ -32,7 +32,7 @@ object PatientLabelEvidence {
final case class PatientLabelEvidence(id: LongId[PatientLabelEvidence],
patientLabelId: LongId[PatientLabel],
- value: FuzzyValue,
+ value: LabelValue,
evidenceText: String,
reportId: Option[UuidId[DirectReport]],
documentId: Option[LongId[Document]],
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala
index 3311d96..6055921 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/PatientLabelEvidenceView.scala
@@ -2,28 +2,28 @@ package xyz.driver.pdsuidomain.entities
import java.time.LocalDate
-import xyz.driver.entities.labels.Label
+import xyz.driver.entities.labels.{Label, LabelValue}
import xyz.driver.pdsuicommon.domain._
import xyz.driver.pdsuicommon.logging._
object PatientLabelEvidenceView {
implicit def toPhiString(x: PatientLabelEvidenceView): PhiString = {
import x._
- phi"PatientLabelEvidenceView(id=$id, value=$value, documentId=$documentId, " +
+ phi"PatientLabelEvidenceView(id=$id, value=${Unsafe(value)}, documentId=$documentId, " +
phi"evidenceId=$evidenceId, reportId=$reportId, patientId=$patientId, labelId=$labelId, " +
phi"isImplicitMatch=$isImplicitMatch)"
}
}
final case class PatientLabelEvidenceView(id: LongId[PatientLabelEvidence],
- value: FuzzyValue,
+ value: LabelValue,
evidenceText: String,
documentId: Option[LongId[Document]],
evidenceId: Option[LongId[ExtractedData]],
reportId: Option[UuidId[DirectReport]],
- documentType: String,
+ documentType: DocumentType,
date: Option[LocalDate], // Document.startDate is optional
- providerType: String,
+ providerType: ProviderType,
patientId: UuidId[Patient],
labelId: LongId[Label],
isImplicitMatch: Boolean)
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala
deleted file mode 100644
index 689eaa4..0000000
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/RawPatientLabel.scala
+++ /dev/null
@@ -1,31 +0,0 @@
-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._
-
-final case class RawPatientLabel(patientId: UuidId[Patient],
- labelId: LongId[Label],
- value: FuzzyValue,
- evidenceId: LongId[ExtractedData],
- evidenceText: String,
- disease: String,
- documentId: LongId[Document],
- requestId: RecordRequestId,
- documentType: DocumentType,
- providerType: ProviderType,
- startDate: LocalDate,
- endDate: Option[LocalDate])
-
-object RawPatientLabel {
-
- implicit def toPhiString(x: RawPatientLabel): PhiString = {
- import x._
- phi"RawPatientLabel(patientId=$patientId, labelId=$labelId, value=$value, evidenceId=${Unsafe(evidenceId)}, " +
- phi"evidenceText=${Unsafe(evidenceText)}, documentId=$documentId, requestId=${Unsafe(requestId)}, " +
- phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, " +
- phi"startDate=$startDate, endDate=$endDate)"
- }
-}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala
deleted file mode 100644
index bdbc4ea..0000000
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/RawTrialLabel.scala
+++ /dev/null
@@ -1,32 +0,0 @@
-package xyz.driver.pdsuidomain.entities
-
-import java.time.LocalDateTime
-
-import xyz.driver.entities.labels.Label
-import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
-import xyz.driver.pdsuicommon.logging._
-
-final case class RawTrialLabel(nctId: StringId[Trial],
- trialId: UuidId[Trial],
- condition: String,
- lastReviewed: LocalDateTime,
- armName: String,
- armId: LongId[Arm],
- labelId: LongId[Label],
- value: Option[Boolean],
- criterionId: LongId[Criterion],
- criteria: String,
- criterionArmId: LongId[Arm],
- isCompound: Boolean,
- isDefining: Boolean)
-
-object RawTrialLabel {
-
- implicit def toPhiString(x: RawTrialLabel): PhiString = {
- import x._
- phi"RawTrialLabel(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, lastReviewed=$lastReviewed, " +
- phi"armId=$armId, armName=${Unsafe(armName)}, labelId=$labelId, value=$value, " +
- phi"criterionId=$criterionId, criteria=${Unsafe(criteria)}, criterionArmId=$criterionArmId, " +
- phi"isCompound=$isCompound, isDefining=$isDefining)"
- }
-}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
index db4def2..7584e9c 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/Trial.scala
@@ -2,10 +2,11 @@ package xyz.driver.pdsuidomain.entities
import java.time.LocalDateTime
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.domain.{LongId, StringId, User, UuidId}
import xyz.driver.pdsuicommon.logging._
import xyz.driver.pdsuicommon.utils.Utils
-import xyz.driver.pdsuidomain.entities.Trial.{Condition, Status}
+import xyz.driver.pdsuidomain.entities.Trial.Status
final case class StudyDesign(id: LongId[StudyDesign], name: String)
@@ -58,24 +59,6 @@ object Trial {
}
final case class Locations(locations: List[String])
-
- sealed trait Condition
-
- object Condition {
-
- case object Breast extends Condition
- case object Lung extends Condition
- case object Prostate extends Condition
-
- def fromString(condition: String): Option[Condition] = condition match {
- case "Breast" => Some(Breast)
- case "Lung" => Some(Lung)
- case "Prostate" => Some(Prostate)
- case _ => None
- }
-
- val All: Set[Condition] = Set(Breast, Lung, Prostate)
- }
}
final case class Trial(id: StringId[Trial],
@@ -86,7 +69,7 @@ final case class Trial(id: StringId[Trial],
previousAssignee: Option[StringId[User]],
lastActiveUserId: Option[StringId[User]],
lastUpdate: LocalDateTime,
- condition: Condition,
+ disease: CancerType,
phase: String,
hypothesisId: Option[UuidId[Hypothesis]],
studyDesignId: Option[LongId[StudyDesign]],
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 2edd707..957e607 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
@@ -3,7 +3,6 @@ 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.RawPatientLabel
final case class ExportPatientLabel(id: LongId[Label], evidences: List[ExportPatientLabelEvidence])
@@ -13,8 +12,4 @@ object ExportPatientLabel extends PhiLogging {
import x._
phi"ExportPatientLabel(id=$id, evidences=$evidences)"
}
-
- def fromRaw(labelId: LongId[Label], rawPatientLabels: List[RawPatientLabel]): ExportPatientLabel = {
- ExportPatientLabel(id = labelId, evidences = rawPatientLabels.map(ExportPatientLabelEvidence.fromRaw))
- }
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala
index fb40339..6472a6b 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidence.scala
@@ -1,11 +1,12 @@
package xyz.driver.pdsuidomain.entities.export.patient
+import xyz.driver.entities.labels.LabelValue
import xyz.driver.pdsuicommon.domain._
import xyz.driver.pdsuicommon.logging._
-import xyz.driver.pdsuidomain.entities.{ExtractedData, RawPatientLabel}
+import xyz.driver.pdsuidomain.entities.ExtractedData
final case class ExportPatientLabelEvidence(id: LongId[ExtractedData],
- value: FuzzyValue,
+ value: LabelValue,
evidenceText: String,
document: ExportPatientLabelEvidenceDocument)
@@ -13,20 +14,8 @@ object ExportPatientLabelEvidence {
implicit def toPhiString(x: ExportPatientLabelEvidence): PhiString = {
import x._
- phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=$value, " +
+ phi"ExportPatientLabelEvidence(id=${Unsafe(id)}, value=${Unsafe(value)}, " +
phi"evidenceText=${Unsafe(evidenceText)}, document=$document)"
}
- def fromRaw(x: RawPatientLabel) = ExportPatientLabelEvidence(
- id = x.evidenceId,
- value = x.value,
- evidenceText = x.evidenceText,
- document = ExportPatientLabelEvidenceDocument(
- x.documentId,
- x.requestId,
- x.documentType,
- x.providerType,
- x.startDate
- )
- )
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala
index 7003615..467170b 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientLabelEvidenceDocument.scala
@@ -19,12 +19,4 @@ object ExportPatientLabelEvidenceDocument extends PhiLogging {
phi"ExportPatientLabelEvidenceDocument(documentId=$documentId, requestId=$requestId, " +
phi"documentType=${Unsafe(documentType)}, providerType=${Unsafe(providerType)}, date=$date)"
}
-
- def fromRaw(x: RawPatientLabel) = ExportPatientLabelEvidenceDocument(
- documentId = x.documentId,
- requestId = x.requestId,
- documentType = x.documentType,
- providerType = x.providerType,
- date = x.startDate
- )
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala
index bd6173b..8fb2660 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/patient/ExportPatientWithLabels.scala
@@ -2,9 +2,7 @@ package xyz.driver.pdsuidomain.entities.export.patient
import xyz.driver.pdsuicommon.domain._
import xyz.driver.pdsuicommon.logging._
-import xyz.driver.pdsuidomain.entities.{Patient, RawPatientLabel}
-
-import scala.collection.breakOut
+import xyz.driver.pdsuidomain.entities.Patient
final case class ExportPatientWithLabels(patientId: UuidId[Patient],
labelVersion: Long,
@@ -16,12 +14,4 @@ object ExportPatientWithLabels {
import x._
phi"ExportPatientWithLabels(patientId=$patientId, version=${Unsafe(labelVersion)}, labels=$labels)"
}
-
- def fromRaw(patientId: UuidId[Patient], rawPatientRefs: List[RawPatientLabel]) = ExportPatientWithLabels(
- patientId = patientId,
- labelVersion = 1L, // TODO It is needed to replace this mock label version.
- labels = rawPatientRefs
- .groupBy(_.labelId)
- .map(Function.tupled(ExportPatientLabel.fromRaw))(breakOut)
- )
}
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 1f06e0d..385bbbe 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
@@ -3,7 +3,7 @@ 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, RawTrialLabel}
+import xyz.driver.pdsuidomain.entities.{Arm, Criterion}
final case class ExportTrialLabelCriterion(criterionId: LongId[Criterion],
value: Option[Boolean],
@@ -20,14 +20,4 @@ object ExportTrialLabelCriterion {
phi"TrialLabelCriterion(criterionId=$criterionId, value=$value, labelId=$labelId, " +
phi"criteria=${Unsafe(criteria)}, isCompound=$isCompound, isDefining=$isDefining)"
}
-
- def fromRaw(x: RawTrialLabel, armIds: Set[LongId[Arm]]) = ExportTrialLabelCriterion(
- criterionId = x.criterionId,
- value = x.value,
- labelId = x.labelId,
- armIds = armIds,
- criteria = x.criteria,
- isCompound = x.isCompound,
- isDefining = x.isDefining
- )
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala
index cf55694..3a9434b 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/entities/export/trial/ExportTrialWithLabels.scala
@@ -4,13 +4,11 @@ import java.time.LocalDateTime
import xyz.driver.pdsuicommon.domain._
import xyz.driver.pdsuicommon.logging._
-import xyz.driver.pdsuidomain.entities.{RawTrialLabel, Trial}
-
-import scala.collection.breakOut
+import xyz.driver.pdsuidomain.entities.Trial
final case class ExportTrialWithLabels(nctId: StringId[Trial],
trialId: UuidId[Trial],
- condition: String,
+ disease: String,
lastReviewed: LocalDateTime,
labelVersion: Long,
arms: List[ExportTrialArm],
@@ -20,35 +18,7 @@ object ExportTrialWithLabels {
implicit def toPhiString(x: ExportTrialWithLabels): PhiString = {
import x._
- phi"TrialWithLabels(nctId=$nctId, trialId=$trialId, condition=${Unsafe(condition)}, " +
+ phi"TrialWithLabels(nctId=$nctId, trialId=$trialId, disease=${Unsafe(disease)}, " +
phi"lastReviewed=$lastReviewed, labelVersion=${Unsafe(labelVersion)}, arms=$arms, criteria=$criteria)"
}
-
- def fromRaw(rawData: List[RawTrialLabel]): ExportTrialWithLabels = {
- val trials: Set[StringId[Trial]] = rawData.map(_.nctId)(breakOut)
-
- assert(trials.size == 1, "There are more than one trial in the rawData")
- val trial = rawData.head
-
- ExportTrialWithLabels(
- nctId = trial.nctId,
- trialId = trial.trialId,
- condition = trial.condition,
- lastReviewed = trial.lastReviewed,
- labelVersion = 1, // TODO It is needed to replace this mock label version.
- arms = rawData
- .groupBy(_.armId)
- .map {
- case (armId, rawTrials) =>
- ExportTrialArm(armId, rawTrials.head.armName)
- }(breakOut),
- criteria = rawData
- .groupBy(x => (x.criterionId, x.labelId))
- .map {
- case (_, rawTrialLabels) =>
- val armIds = rawTrialLabels.map(_.criterionArmId).toSet
- ExportTrialLabelCriterion.fromRaw(rawTrialLabels.head, armIds)
- }(breakOut)
- )
- }
}
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 7318ff6..f77c2e0 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/common.scala
@@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.fakes.entities
import java.time.{LocalDate, LocalDateTime, LocalTime}
import xyz.driver.core.generators.{nextDouble, nextOption}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId}
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
import xyz.driver.pdsuidomain.entities.{Trial, TrialHistory}
import scala.util.Random
@@ -29,8 +29,6 @@ object common {
1 + Random.nextInt(28) // all months have at least 28 days
)
- def nextCondition = generators.oneOf[Trial.Condition](Trial.Condition.All)
-
def nextTrialAction = generators.oneOf[TrialHistory.Action](TrialHistory.Action.All)
def nextTrialState = generators.oneOf[TrialHistory.State](TrialHistory.State.All)
@@ -52,9 +50,6 @@ object common {
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/export.scala b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala
index 7f3c410..a3ba562 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/export.scala
@@ -26,7 +26,7 @@ object export {
ExportTrialWithLabels(
nctId = nextStringId[Trial],
trialId = nextUuidId[Trial],
- condition = nextString(100),
+ disease = nextString(100),
lastReviewed = nextLocalDateTime,
labelVersion = nextInt(100).toLong,
arms = listOf(nextExportTrialArm()),
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 3fcc4cb..85bab8c 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
@@ -1,9 +1,9 @@
package xyz.driver.pdsuidomain.fakes.entities.rep
+import xyz.driver.core.generators
import xyz.driver.core.generators._
-import xyz.driver.entities.labels.Label
+import xyz.driver.entities.labels.{Label, LabelValue}
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._
import xyz.driver.pdsuidomain.fakes.entities.common.{nextLocalDate, nextLongId}
@@ -26,7 +26,7 @@ object ExportPatientGen {
def nextExportPatientLabelEvidence(documentId: LongId[Document]): ExportPatientLabelEvidence = {
ExportPatientLabelEvidence(
id = nextLongId[ExtractedData],
- value = nextFuzzyValue(),
+ value = generators.oneOf[LabelValue](LabelValue.Yes, LabelValue.No, LabelValue.Maybe),
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 8e77445..70ddd10 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
@@ -1,7 +1,8 @@
package xyz.driver.pdsuidomain.fakes.entities.rep
+import xyz.driver.core.generators
import xyz.driver.core.generators._
-import xyz.driver.entities.labels.{Label, LabelCategory}
+import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue}
import xyz.driver.pdsuicommon.domain.{LongId, TextJson}
import xyz.driver.pdsuidomain.entities._
import xyz.driver.pdsuidomain.entities.ExtractedData.Meta
@@ -85,7 +86,7 @@ object ExtractedDataGen {
dataId = nextLongId[ExtractedData],
labelId = nextOption(nextLongId[Label]),
categoryId = nextOption(nextLongId[LabelCategory]),
- value = nextOption(nextFuzzyValue())
+ value = nextOption(generators.oneOf[LabelValue](LabelValue.Yes, LabelValue.No, LabelValue.Maybe))
)
}
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 9a5022c..069d1f1 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/fakes/entities/trialcuration.scala
@@ -1,6 +1,7 @@
package xyz.driver.pdsuidomain.fakes.entities
import xyz.driver.entities.labels.{Label, LabelCategory}
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.domain.{LongId, User}
import xyz.driver.pdsuidomain.entities._
import xyz.driver.pdsuidomain.services.CriterionService.RichCriterion
@@ -19,7 +20,7 @@ object trialcuration {
previousAssignee = Option(nextStringId[User]),
lastActiveUserId = Option(nextStringId[User]),
lastUpdate = nextLocalDateTime,
- condition = nextCondition,
+ disease = generators.oneOf[CancerType](CancerType.Breast, CancerType.Lung, CancerType.Prostate),
phase = generators.nextString(),
hypothesisId = Option(nextUuidId[Hypothesis]),
studyDesignId = Option(nextLongId[StudyDesign]),
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala
index e0f23e3..c7a6de9 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/evidence/ApiPatientLabelEvidence.scala
@@ -3,7 +3,6 @@ package xyz.driver.pdsuidomain.formats.json.evidence
import java.time.LocalDate
import play.api.libs.json._
-import xyz.driver.pdsuicommon.domain.FuzzyValue
import xyz.driver.pdsuidomain.entities.PatientLabelEvidenceView
final case class ApiPatientLabelEvidence(id: Long,
@@ -22,13 +21,13 @@ object ApiPatientLabelEvidence {
def fromDomain(x: PatientLabelEvidenceView) = ApiPatientLabelEvidence(
id = x.id.id,
- value = FuzzyValue.valueToString(x.value),
+ value = x.value.toString,
evidenceText = x.evidenceText,
documentId = x.documentId.map(_.id),
evidenceId = x.evidenceId.map(_.id),
reportId = x.reportId.map(_.toString),
- documentType = x.documentType,
+ documentType = x.documentType.name,
date = x.date.get,
- providerType = x.providerType
+ providerType = x.providerType.name
)
}
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 d486749..edb0603 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
@@ -1,11 +1,11 @@
package xyz.driver.pdsuidomain.formats.json.label
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId}
+import xyz.driver.pdsuicommon.domain.LongId
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}
+import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue}
/**
* @param value Yes|No
@@ -34,7 +34,7 @@ object ApiCriterionLabel {
labelId = x.labelId.map(_.id),
categoryId = x.categoryId.map(_.id),
value = x.value.map { x =>
- FuzzyValue.valueToString(FuzzyValue.fromBoolean(x))
+ LabelValue.fromBoolean(x).toString
},
isDefining = x.isDefining
)
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 f8161af..1497679 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
@@ -1,11 +1,11 @@
package xyz.driver.pdsuidomain.formats.json.label
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId}
+import xyz.driver.pdsuicommon.domain.LongId
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}
+import xyz.driver.entities.labels.{Label, LabelCategory, LabelValue}
final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long], value: Option[String]) {
@@ -14,7 +14,7 @@ final case class ApiExtractedDataLabel(id: Option[Long], categoryId: Option[Long
dataId = dataId,
labelId = id.map(LongId[Label]),
categoryId = categoryId.map(LongId[LabelCategory]),
- value = value.map(FuzzyValue.fromString)
+ value = value.flatMap(LabelValue.fromString)
)
}
@@ -27,8 +27,8 @@ object ApiExtractedDataLabel {
Format(Reads
.of[String]
.filter(ValidationError("unknown value"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String]))
)(ApiExtractedDataLabel.apply, unlift(ApiExtractedDataLabel.unapply))
@@ -36,6 +36,6 @@ object ApiExtractedDataLabel {
def fromDomain(dataLabel: ExtractedDataLabel) = ApiExtractedDataLabel(
id = dataLabel.labelId.map(_.id),
categoryId = dataLabel.categoryId.map(_.id),
- value = dataLabel.value.map(FuzzyValue.valueToString)
+ value = dataLabel.value.map(_.toString)
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala
index db430ae..585d4ed 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/ApiPatient.scala
@@ -7,6 +7,8 @@ import xyz.driver.pdsuicommon.domain.{StringId, UuidId}
import xyz.driver.pdsuidomain.entities.{Patient, PatientOrderId}
import play.api.libs.functional.syntax._
import play.api.libs.json.{Format, JsPath}
+import xyz.driver.entities.common.FullName
+import xyz.driver.entities.patient
final case class ApiPatient(id: String,
status: String,
@@ -17,24 +19,35 @@ final case class ApiPatient(id: String,
previousAssignee: Option[String],
lastActiveUser: Option[String],
lastUpdate: ZonedDateTime,
- condition: String,
+ disease: String,
orderId: UUID) {
private def extractStatus(status: String): Patient.Status =
PatientStatus.statusFromString
.applyOrElse(status, (s: String) => throw new NoSuchElementException(s"Unknown status $s"))
+ private def parseName(name: String): FullName[Patient] =
+ name.split(" ") match {
+ case Array() => throw new NoSuchElementException(s"Patient's name cannot be empty")
+ case Array(first) => FullName.fromStrings[Patient](first, "", "")
+ case Array(first, last) => FullName.fromStrings[Patient](first, "", last)
+ case Array(first, middle, last) => FullName.fromStrings[Patient](first, middle, last)
+ case _ => throw new NoSuchElementException(s"Patient's name is ambiguous")
+ }
+
def toDomain = Patient(
id = UuidId(this.id),
status = extractStatus(this.status),
- name = this.name,
+ name = parseName(this.name),
dob = this.dob,
assignee = this.assignee.map(StringId(_)),
previousStatus = this.previousStatus.map(extractStatus),
previousAssignee = this.previousAssignee.map(StringId(_)),
lastActiveUserId = this.lastActiveUser.map(StringId(_)),
isUpdateRequired = false,
- condition = this.condition,
+ disease = patient.CancerType
+ .fromString(this.disease)
+ .getOrElse(throw new IllegalArgumentException(s"Unknown cancer type ${this.disease}")),
orderId = PatientOrderId(this.orderId),
lastUpdate = this.lastUpdate.toLocalDateTime
)
@@ -53,21 +66,21 @@ object ApiPatient {
(JsPath \ "previousAssignee").formatNullable[String] and
(JsPath \ "lastActiveUser").formatNullable[String] and
(JsPath \ "lastUpdate").format[ZonedDateTime] and
- (JsPath \ "condition").format[String] and
+ (JsPath \ "disease").format[String] and
(JsPath \ "orderId").format[UUID]
)(ApiPatient.apply, unlift(ApiPatient.unapply))
def fromDomain(patient: Patient) = ApiPatient(
id = patient.id.toString,
status = PatientStatus.statusToString(patient.status),
- name = patient.name,
+ name = patient.name.toString(),
dob = patient.dob,
assignee = patient.assignee.map(_.id),
previousStatus = patient.previousStatus.map(PatientStatus.statusToString),
previousAssignee = patient.previousAssignee.map(_.id),
lastActiveUser = patient.lastActiveUserId.map(_.id),
lastUpdate = ZonedDateTime.of(patient.lastUpdate, ZoneId.of("Z")),
- condition = patient.condition,
+ disease = patient.disease.toString,
orderId = patient.orderId.id
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala
index 4136715..55c8149 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/eligible/ApiPatientEligibleTrial.scala
@@ -5,7 +5,7 @@ import java.util.UUID
import play.api.data.validation.ValidationError
import play.api.libs.functional.syntax._
import play.api.libs.json._
-import xyz.driver.pdsuicommon.domain.FuzzyValue
+import xyz.driver.entities.labels.LabelValue
import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial
final case class ApiPatientEligibleTrial(id: Long,
@@ -30,8 +30,8 @@ object ApiPatientEligibleTrial {
Reads
.of[String]
.filter(ValidationError("unknown eligibility status"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String]
)) and
@@ -45,7 +45,7 @@ object ApiPatientEligibleTrial {
trialTitle = eligibleTrialWithTrial.trial.title,
arms = eligibleTrialWithTrial.arms.map(_.armName),
hypothesisId = eligibleTrialWithTrial.group.hypothesisId.id,
- eligibleTrialWithTrial.group.verifiedEligibilityStatus.map(FuzzyValue.valueToString),
+ eligibleTrialWithTrial.group.verifiedEligibilityStatus.map(_.toString),
eligibleTrialWithTrial.group.isVerified
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala
index 91d0a0e..d92872c 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPartialPatientLabel.scala
@@ -6,15 +6,14 @@ import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath
import play.api.data.validation.ValidationError
import play.api.libs.functional.syntax._
import play.api.libs.json._
-import xyz.driver.pdsuicommon.domain.FuzzyValue
+import xyz.driver.entities.labels.LabelValue
final case class ApiPartialPatientLabel(primaryValue: Option[String], verifiedPrimaryValue: Tristate[String]) {
def applyTo(orig: PatientLabel): PatientLabel = {
orig.copy(
- primaryValue = primaryValue.map(FuzzyValue.fromString).orElse(orig.primaryValue),
- verifiedPrimaryValue =
- verifiedPrimaryValue.cata(x => Some(FuzzyValue.fromString(x)), None, orig.verifiedPrimaryValue)
+ primaryValue = primaryValue.flatMap(LabelValue.fromString).orElse(orig.primaryValue),
+ verifiedPrimaryValue = verifiedPrimaryValue.cata(x => LabelValue.fromString(x), None, orig.verifiedPrimaryValue)
)
}
}
@@ -26,8 +25,8 @@ object ApiPartialPatientLabel {
Format(Reads
.of[String]
.filter(ValidationError("unknown primary value"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String])) and
(JsPath \ "verifiedPrimaryValue").formatTristate[String](
@@ -35,8 +34,8 @@ object ApiPartialPatientLabel {
Reads
.of[String]
.filter(ValidationError("unknown verified primary value"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String]
))
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala
index fc8687b..cc8532d 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabel.scala
@@ -4,7 +4,7 @@ import xyz.driver.pdsuidomain.entities.PatientLabel
import play.api.data.validation.ValidationError
import play.api.libs.functional.syntax._
import play.api.libs.json._
-import xyz.driver.pdsuicommon.domain.FuzzyValue
+import xyz.driver.entities.labels.LabelValue
final case class ApiPatientLabel(id: Long,
labelId: Long,
@@ -20,25 +20,33 @@ object ApiPatientLabel {
implicit val apiPatientLabelJsonFormat: Format[ApiPatientLabel] = (
(JsPath \ "id").format[Long] and
(JsPath \ "labelId").format[Long] and
- (JsPath \ "primaryValue").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
- }), Writes.of[String])) and
- (JsPath \ "verifiedPrimaryValue").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown value"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
- }), Writes.of[String])) and
+ (JsPath \ "primaryValue").formatNullable[String](
+ Format(Reads
+ .of[String]
+ .filter(ValidationError("unknown value"))({
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
+ }),
+ Writes.of[String])) and
+ (JsPath \ "verifiedPrimaryValue").formatNullable[String](
+ Format(Reads
+ .of[String]
+ .filter(ValidationError("unknown value"))({
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
+ }),
+ Writes.of[String])) and
(JsPath \ "score").format[Int] and
(JsPath \ "isImplicitMatch").format[Boolean] and
(JsPath \ "isVisible").format[Boolean] and
(JsPath \ "isVerified").format[Boolean]
- ) (ApiPatientLabel.apply, unlift(ApiPatientLabel.unapply))
+ )(ApiPatientLabel.apply, unlift(ApiPatientLabel.unapply))
def fromDomain(patientLabel: PatientLabel, isVerified: Boolean): ApiPatientLabel = ApiPatientLabel(
id = patientLabel.id.id,
labelId = patientLabel.labelId.id,
- primaryValue = patientLabel.primaryValue.map(FuzzyValue.valueToString),
- verifiedPrimaryValue = patientLabel.verifiedPrimaryValue.map(FuzzyValue.valueToString),
+ primaryValue = patientLabel.primaryValue.map(_.toString),
+ verifiedPrimaryValue = patientLabel.verifiedPrimaryValue.map(_.toString),
score = patientLabel.score,
isImplicitMatch = patientLabel.isImplicitMatch,
isVisible = patientLabel.isVisible,
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala
index ae64c33..16b9cc9 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/label/ApiPatientLabelDefiningCriteria.scala
@@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.patient.label
import play.api.data.validation.ValidationError
import play.api.libs.functional.syntax._
import play.api.libs.json._
-import xyz.driver.pdsuicommon.domain.FuzzyValue
+import xyz.driver.entities.labels.LabelValue
import xyz.driver.pdsuidomain.entities.PatientLabel
final case class ApiPatientLabelDefiningCriteria(labelId: Long, value: Option[String])
@@ -16,14 +16,14 @@ object ApiPatientLabelDefiningCriteria {
Format(Reads
.of[String]
.filter(ValidationError("unknown value"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String]))
)(ApiPatientLabelDefiningCriteria.apply, unlift(ApiPatientLabelDefiningCriteria.unapply))
def fromDomain(x: PatientLabel) = ApiPatientLabelDefiningCriteria(
labelId = x.labelId.id,
- value = x.verifiedPrimaryValue.map(FuzzyValue.valueToString)
+ value = x.verifiedPrimaryValue.map(_.toString)
)
}
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala
index 399bc7d..09538b8 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterion.scala
@@ -6,16 +6,16 @@ import org.davidbild.tristate.contrib.play.ToJsPathOpsFromJsPath
import play.api.data.validation.ValidationError
import play.api.libs.functional.syntax._
import play.api.libs.json.{Format, JsPath, Reads, Writes}
-import xyz.driver.pdsuicommon.domain.FuzzyValue
+import xyz.driver.entities.labels.LabelValue
final case class ApiPartialPatientCriterion(eligibilityStatus: Option[String],
verifiedEligibilityStatus: Tristate[String]) {
def applyTo(orig: PatientCriterion): PatientCriterion = {
orig.copy(
- eligibilityStatus = eligibilityStatus.map(FuzzyValue.fromString).orElse(orig.eligibilityStatus),
+ eligibilityStatus = eligibilityStatus.flatMap(LabelValue.fromString).orElse(orig.eligibilityStatus),
verifiedEligibilityStatus =
- verifiedEligibilityStatus.cata(x => Some(FuzzyValue.fromString(x)), None, orig.verifiedEligibilityStatus)
+ verifiedEligibilityStatus.cata(x => LabelValue.fromString(x), None, orig.verifiedEligibilityStatus)
)
}
}
@@ -28,8 +28,8 @@ object ApiPartialPatientCriterion {
Reads
.of[String]
.filter(ValidationError("unknown eligibility status"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String]
)) and
@@ -38,8 +38,8 @@ object ApiPartialPatientCriterion {
Reads
.of[String]
.filter(ValidationError("unknown verified eligibility status"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String]
))
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala
index 4b08970..b7616a1 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patient/trial/ApiPartialPatientCriterionList.scala
@@ -1,10 +1,11 @@
package xyz.driver.pdsuidomain.formats.json.patient.trial
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId}
+import xyz.driver.pdsuicommon.domain.LongId
import xyz.driver.pdsuidomain.entities.PatientCriterion
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.LabelValue
import xyz.driver.pdsuidomain.services.PatientCriterionService.DraftPatientCriterion
final case class ApiPartialPatientCriterionList(id: Long,
@@ -13,7 +14,7 @@ final case class ApiPartialPatientCriterionList(id: Long,
def toDomain: DraftPatientCriterion = DraftPatientCriterion(
id = LongId[PatientCriterion](id),
- eligibilityStatus = eligibilityStatus.map(FuzzyValue.fromString),
+ eligibilityStatus = eligibilityStatus.flatMap(LabelValue.fromString),
isVerified = isVerified
)
}
@@ -26,8 +27,8 @@ object ApiPartialPatientCriterionList {
Reads
.of[String]
.filter(ValidationError("unknown eligibility status"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}),
Writes.of[String]
)) and
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 6eeb40b..b9bf772 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
@@ -2,12 +2,12 @@ package xyz.driver.pdsuidomain.formats.json.patient.trial
import java.time.{ZoneId, ZonedDateTime}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId}
+import xyz.driver.pdsuicommon.domain.LongId
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
+import xyz.driver.entities.labels.{Label, LabelValue}
final case class ApiPatientCriterion(id: Long,
labelId: Long,
@@ -39,13 +39,13 @@ object ApiPatientCriterion {
(JsPath \ "criterionIsCompound").format[Boolean] and
(JsPath \ "arms").format[List[String]] and
(JsPath \ "eligibilityStatus").formatNullable[String](Format(Reads.of[String].filter(ValidationError("unknown status"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}), Writes.of[String])) and
(JsPath \ "verifiedEligibilityStatus").formatNullable[String](Format(
Reads.of[String].filter(ValidationError("unknown status"))({
- case x if FuzzyValue.fromString.isDefinedAt(x) => true
- case _ => false
+ case x if LabelValue.fromString(x).isDefined => true
+ case _ => false
}), Writes.of[String])) and
(JsPath \ "isVerified").format[Boolean] and
(JsPath \ "isVisible").format[Boolean] and
@@ -61,13 +61,13 @@ object ApiPatientCriterion {
criterionId = patientCriterion.criterionId.id,
criterionText = patientCriterion.criterionText,
criterionValue = patientCriterion.criterionValue.map { x =>
- FuzzyValue.valueToString(FuzzyValue.fromBoolean(x))
+ LabelValue.fromBoolean(x).toString
},
criterionIsDefining = patientCriterion.criterionIsDefining,
criterionIsCompound = patientCriterion.criterionValue.isEmpty,
arms = arms.map(_.armName),
- eligibilityStatus = patientCriterion.eligibilityStatus.map(FuzzyValue.valueToString),
- verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(FuzzyValue.valueToString),
+ eligibilityStatus = patientCriterion.eligibilityStatus.map(_.toString),
+ verifiedEligibilityStatus = patientCriterion.verifiedEligibilityStatus.map(_.toString),
isVerified = patientCriterion.isVerified,
isVisible = patientCriterion.isVisible,
lastUpdate = ZonedDateTime.of(patientCriterion.lastUpdate, ZoneId.of("Z"))
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala
index dbd0a43..61e0e7f 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/common.scala
@@ -3,7 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
import java.time.{LocalDate, LocalDateTime, ZoneId, ZonedDateTime}
import spray.json._
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId}
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
object common {
@@ -55,14 +55,6 @@ object common {
}
}
- implicit def fuzzyValueFormat: RootJsonFormat[FuzzyValue] = new RootJsonFormat[FuzzyValue] {
- override def write(value: FuzzyValue): JsString = JsString(FuzzyValue.valueToString(value))
- override def read(json: JsValue): FuzzyValue = json match {
- case JsString(value) => FuzzyValue.fromString(value)
- case _ => deserializationError(s"Expected value as FuzzyValue, but got $json")
- }
- }
-
implicit val integerFormat: RootJsonFormat[Integer] = new RootJsonFormat[Integer] {
override def write(obj: Integer): JsNumber = JsNumber(obj.intValue())
override def read(json: JsValue): Integer = json match {
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 39d5c59..85d614d 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
@@ -5,6 +5,7 @@ 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}
+import xyz.driver.formats.json.labels._
object export {
import DefaultJsonProtocol._
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 d6eadbd..5d5585a 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
@@ -1,10 +1,11 @@
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.entities.labels.{Label, LabelCategory, LabelValue}
+import xyz.driver.pdsuicommon.domain.{LongId, TextJson}
import xyz.driver.pdsuidomain.entities._
import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData
+import xyz.driver.formats.json.labels._
object extracteddata {
import DefaultJsonProtocol._
@@ -44,7 +45,7 @@ object extracteddata {
val value = fields
.get("value")
- .map(_.convertTo[FuzzyValue])
+ .map(_.convertTo[LabelValue])
ExtractedDataLabel(
id = LongId(0),
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala
index 95c0674..2b0dfe5 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patient.scala
@@ -3,6 +3,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
import spray.json._
import xyz.driver.core.json.EnumJsonFormat
import xyz.driver.pdsuidomain.entities._
+import xyz.driver.formats.json.common._
+import xyz.driver.formats.json.patient._
object patient {
import DefaultJsonProtocol._
@@ -38,7 +40,7 @@ object patient {
"previousAssignee" -> patient.previousAssignee.toJson,
"lastActiveUser" -> patient.lastActiveUserId.toJson,
"lastUpdate" -> patient.lastUpdate.toJson,
- "condition" -> patient.condition.toJson,
+ "disease" -> patient.disease.toJson,
"orderId" -> patient.orderId.toJson
)
}
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 87e2a3a..f4d8e90 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
@@ -1,9 +1,10 @@
package xyz.driver.pdsuidomain.formats.json.sprayformats
import spray.json._
-import xyz.driver.pdsuicommon.domain.FuzzyValue
+import xyz.driver.entities.labels.LabelValue
import xyz.driver.pdsuidomain.entities._
import xyz.driver.pdsuidomain.services.PatientCriterionService.{DraftPatientCriterion, RichPatientCriterion}
+import xyz.driver.formats.json.labels._
object patientcriterion {
import DefaultJsonProtocol._
@@ -13,14 +14,15 @@ object patientcriterion {
case JsObject(fields) =>
val eligibilityStatus = fields
.get("eligibilityStatus")
- .map(_.convertTo[Option[FuzzyValue]])
+ .map(_.convertTo[Option[LabelValue]])
.getOrElse(orig.eligibilityStatus)
val verifiedEligibilityStatus = fields
.get("verifiedEligibilityStatus")
- .map(_.convertTo[Option[FuzzyValue]])
+ .map(_.convertTo[Option[LabelValue]])
.getOrElse(orig.verifiedEligibilityStatus)
+
orig.copy(
eligibilityStatus = eligibilityStatus,
verifiedEligibilityStatus = verifiedEligibilityStatus
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala
index 0520ef2..746c7b4 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientdefiningcriteria.scala
@@ -2,6 +2,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
import spray.json._
import xyz.driver.pdsuidomain.entities.PatientLabel
+import xyz.driver.formats.json.labels._
object patientdefiningcriteria {
import DefaultJsonProtocol._
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala
index 041d9da..342d3a8 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patienteligibletrial.scala
@@ -3,6 +3,7 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
import spray.json._
import xyz.driver.pdsuidomain.entities._
import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial
+import xyz.driver.formats.json.labels._
object patienteligibletrial {
import DefaultJsonProtocol._
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala
index b36949e..57dca1e 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/patientlabel.scala
@@ -1,9 +1,12 @@
package xyz.driver.pdsuidomain.formats.json.sprayformats
import spray.json._
-import xyz.driver.pdsuicommon.domain.FuzzyValue
+import xyz.driver.entities.labels.LabelValue
import xyz.driver.pdsuidomain.entities._
import xyz.driver.pdsuidomain.services.PatientLabelService.RichPatientLabel
+import xyz.driver.formats.json.labels._
+import xyz.driver.pdsuidomain.formats.json.sprayformats.record._
+import xyz.driver.pdsuidomain.formats.json.sprayformats.document._
object patientlabel {
import DefaultJsonProtocol._
@@ -13,12 +16,12 @@ object patientlabel {
case JsObject(fields) =>
val primaryValue = fields
.get("primaryValue")
- .map(_.convertTo[Option[FuzzyValue]])
+ .map(_.convertTo[Option[LabelValue]])
.getOrElse(orig.primaryValue)
val verifiedPrimaryValue = fields
.get("verifiedPrimaryValue")
- .map(_.convertTo[Option[FuzzyValue]])
+ .map(_.convertTo[Option[LabelValue]])
.getOrElse(orig.verifiedPrimaryValue)
orig.copy(
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala
index 8000a27..d851c2c 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/trial.scala
@@ -6,6 +6,7 @@ import spray.json._
import xyz.driver.core.json.EnumJsonFormat
import xyz.driver.pdsuicommon.domain.{LongId, UuidId}
import xyz.driver.pdsuidomain.entities._
+import xyz.driver.formats.json.patient._
object trial {
import DefaultJsonProtocol._
@@ -24,12 +25,6 @@ object trial {
"Archived" -> Status.Archived
)
- implicit val conditionFormat = new EnumJsonFormat[Condition](
- "Breast" -> Condition.Breast,
- "Lung" -> Condition.Lung,
- "Prostate" -> Condition.Prostate
- )
-
implicit val trialWriter: RootJsonWriter[Trial] = new RootJsonWriter[Trial] {
override def write(obj: Trial) =
JsObject(
@@ -41,7 +36,7 @@ object trial {
"previousStatus" -> obj.previousStatus.toJson,
"previousAssignee" -> obj.previousAssignee.toJson,
"lastActiveUser" -> obj.lastActiveUserId.toJson,
- "condition" -> obj.condition.toJson,
+ "disease" -> obj.disease.toJson,
"phase" -> obj.phase.toJson,
"hypothesisId" -> obj.hypothesisId.toJson,
"studyDesignId" -> obj.studyDesignId.toJson,
diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala
index 1b4ac64..a2a1ca9 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/trial/ApiTrial.scala
@@ -2,11 +2,12 @@ package xyz.driver.pdsuidomain.formats.json.trial
import java.time.{ZoneId, ZonedDateTime}
import java.util.UUID
-import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
import xyz.driver.pdsuidomain.entities.Trial
import play.api.libs.functional.syntax._
import play.api.libs.json._
+import xyz.driver.entities.patient.CancerType
final case class ApiTrial(id: String,
externalId: UUID,
@@ -16,7 +17,7 @@ final case class ApiTrial(id: String,
previousStatus: Option[String],
previousAssignee: Option[String],
lastActiveUser: Option[String],
- condition: String,
+ disease: String,
phase: String,
hypothesisId: Option[UUID],
studyDesignId: Option[Long],
@@ -37,11 +38,9 @@ final case class ApiTrial(id: String,
previousAssignee = this.previousAssignee.map(id => StringId(id)),
lastActiveUserId = this.lastActiveUser.map(id => StringId(id)),
lastUpdate = this.lastUpdate.toLocalDateTime,
- condition = Trial.Condition
- .fromString(this.condition)
- .getOrElse(
- throw new NoSuchElementException(s"unknown condition ${this.condition}")
- ),
+ disease = CancerType
+ .fromString(this.disease)
+ .getOrElse(throw new NoSuchElementException(s"Unknown disease ${this.disease}")),
phase = this.phase,
hypothesisId = this.hypothesisId.map(id => UuidId(id)),
studyDesignId = this.studyDesignId.map(id => LongId(id)),
@@ -67,7 +66,7 @@ object ApiTrial {
(JsPath \ "previousStatus").formatNullable[String] and
(JsPath \ "previousAssignee").formatNullable[String] and
(JsPath \ "lastActiveUser").formatNullable[String] and
- (JsPath \ "condition").format[String] and
+ (JsPath \ "disease").format[String] and
(JsPath \ "phase").format[String] and
(JsPath \ "hypothesisId").formatNullable[UUID] and
(JsPath \ "studyDesignId").formatNullable[Long] and
@@ -89,7 +88,7 @@ object ApiTrial {
previousAssignee = trial.previousAssignee.map(_.id),
lastActiveUser = trial.lastActiveUserId.map(_.id),
lastUpdate = ZonedDateTime.of(trial.lastUpdate, ZoneId.of("Z")),
- condition = trial.condition.toString,
+ disease = trial.disease.toString,
phase = trial.phase,
hypothesisId = trial.hypothesisId.map(_.id),
studyDesignId = trial.studyDesignId.map(_.id),
diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala
index a07eed8..4d0e188 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/PatientCriterionService.scala
@@ -2,7 +2,7 @@ package xyz.driver.pdsuidomain.services
import java.time.LocalDateTime
-import xyz.driver.entities.labels.Label
+import xyz.driver.entities.labels.{Label, LabelValue}
import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext
import xyz.driver.pdsuicommon.db._
import xyz.driver.pdsuicommon.domain._
@@ -15,7 +15,7 @@ import scala.concurrent.Future
object PatientCriterionService {
final case class DraftPatientCriterion(id: LongId[PatientCriterion],
- eligibilityStatus: Option[FuzzyValue],
+ eligibilityStatus: Option[LabelValue],
isVerified: Option[Boolean]) {
def applyTo(orig: PatientCriterion) = {
orig.copy(
diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala
index c6ab2d2..92233e4 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/TrialService.scala
@@ -5,6 +5,7 @@ import java.time.LocalDateTime
import akka.NotUsed
import akka.stream.scaladsl.Source
import akka.util.ByteString
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext
import xyz.driver.pdsuicommon.db._
import xyz.driver.pdsuicommon.domain.StringId
@@ -108,10 +109,10 @@ trait TrialService {
def getById(id: StringId[Trial])(implicit requestContext: AuthenticatedRequestContext): Future[GetByIdReply]
- def getTrialWithLabels(trialId: StringId[Trial], condition: String)(
+ def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)(
implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply]
- def getTrialsWithLabels(condition: String)(
+ def getTrialsWithLabels(cancerType: CancerType)(
implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply]
def getPdfSource(trialId: StringId[Trial])(
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 cd62d48..a1efdac 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/fake/FakeTrialService.scala
@@ -7,6 +7,7 @@ import akka.stream.scaladsl.Source
import akka.util.ByteString
import xyz.driver.core.generators
import xyz.driver.entities.labels.Label
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.auth.AuthenticatedRequestContext
import xyz.driver.pdsuicommon.db._
import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
@@ -29,7 +30,7 @@ class FakeTrialService extends TrialService {
previousAssignee = None,
lastActiveUserId = None,
lastUpdate = LocalDateTime.now(),
- condition = Trial.Condition.Breast,
+ disease = CancerType.Breast,
phase = "",
hypothesisId = None,
studyDesignId = None,
@@ -57,11 +58,11 @@ class FakeTrialService extends TrialService {
implicit requestContext: AuthenticatedRequestContext): Future[GetListReply] =
Future.successful(GetListReply.EntityList(Seq(trial), 1, None))
- override def getTrialWithLabels(trialId: StringId[Trial], condition: String)(
+ override def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)(
implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] =
Future.successful(GetTrialWithLabelsReply.Entity(nextExportTrialWithLabels()))
- override def getTrialsWithLabels(condition: String)(
+ override def getTrialsWithLabels(cancerType: CancerType)(
implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] =
Future.successful(GetTrialsWithLabelsReply.EntityList(generators.seqOf(nextExportTrialWithLabels())))
diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala
index 42f32fc..ea719e1 100644
--- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala
+++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestTrialService.scala
@@ -18,6 +18,7 @@ import xyz.driver.pdsuidomain.formats.json.trial.ApiTrial
import xyz.driver.pdsuidomain.services.TrialService
import spray.json.DefaultJsonProtocol._
import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuidomain.formats.json.sprayformats.export._
class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit protected val materializer: Materializer,
@@ -37,9 +38,9 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote
}
}
- def getTrialWithLabels(trialId: StringId[Trial], disease: String)(
+ def getTrialWithLabels(trialId: StringId[Trial], cancerType: CancerType)(
implicit requestContext: AuthenticatedRequestContext): Future[GetTrialWithLabelsReply] = {
- val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$disease/$trialId"))
+ val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$cancerType/$trialId"))
for {
response <- transport.sendRequestGetResponse(requestContext)(request)
reply <- apiResponse[ExportTrialWithLabels](response)
@@ -48,9 +49,9 @@ class RestTrialService(transport: ServiceTransport, baseUri: Uri)(implicit prote
}
}
- def getTrialsWithLabels(disease: String)(
+ def getTrialsWithLabels(cancerType: CancerType)(
implicit requestContext: AuthenticatedRequestContext): Future[GetTrialsWithLabelsReply] = {
- val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$disease"))
+ val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/export/trial/$cancerType"))
for {
response <- transport.sendRequestGetResponse(requestContext)(request)
reply <- apiResponse[Seq[ExportTrialWithLabels]](response)
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 a451905..402e893 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
@@ -5,7 +5,8 @@ import java.util.UUID
import spray.json._
import org.scalatest.{FlatSpec, Matchers}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId}
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
import xyz.driver.pdsuidomain.entities.{DocumentType, ProviderType, RecordRequestId}
class ExportFormatSuite extends FlatSpec with Matchers {
@@ -27,13 +28,13 @@ class ExportFormatSuite extends FlatSpec with Matchers {
evidences = List(
ExportPatientLabelEvidence(
id = LongId(11),
- value = FuzzyValue.Yes,
+ value = LabelValue.Yes,
evidenceText = "evidence text 11",
document = document
),
ExportPatientLabelEvidence(
id = LongId(12),
- value = FuzzyValue.No,
+ value = LabelValue.No,
evidenceText = "evidence text 12",
document = document
)
@@ -44,13 +45,13 @@ class ExportFormatSuite extends FlatSpec with Matchers {
evidences = List(
ExportPatientLabelEvidence(
id = LongId(12),
- value = FuzzyValue.Yes,
+ value = LabelValue.Yes,
evidenceText = "evidence text 12",
document = document
),
ExportPatientLabelEvidence(
id = LongId(13),
- value = FuzzyValue.Yes,
+ value = LabelValue.Yes,
evidenceText = "evidence text 13",
document = document
)
@@ -106,7 +107,7 @@ class ExportFormatSuite extends FlatSpec with Matchers {
val trialWithLabels = ExportTrialWithLabels(
nctId = StringId("NCT000001"),
trialId = UuidId("40892a07-c638-49d2-9795-1edfefbbcc7c"),
- condition = "Breast",
+ disease = "Breast",
lastReviewed = LocalDateTime.parse("2017-08-10T18:00:00"),
labelVersion = 1L,
arms = arms,
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala
index a4b8bab..aa82b98 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/ExtractedDataFormatSuite.scala
@@ -2,7 +2,8 @@ package xyz.driver.pdsuidomain.formats.json.sprayformats
import spray.json._
import org.scalatest.{FlatSpec, Matchers}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, TextJson}
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.pdsuicommon.domain.{LongId, TextJson}
import xyz.driver.pdsuidomain.entities.ExtractedData.Meta
import xyz.driver.pdsuidomain.entities.{ExtractedData, ExtractedDataLabel}
import xyz.driver.pdsuidomain.services.ExtractedDataService.RichExtractedData
@@ -24,14 +25,14 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers {
dataId = extractedData.id,
labelId = None,
categoryId = None,
- value = Some(FuzzyValue.Yes)
+ value = Some(LabelValue.Yes)
),
ExtractedDataLabel(
id = LongId(2),
dataId = extractedData.id,
labelId = Some(LongId(12)),
categoryId = Some(LongId(1)),
- value = Some(FuzzyValue.No)
+ value = Some(LabelValue.No)
)
)
val origRichExtractedData = RichExtractedData(
@@ -64,14 +65,14 @@ class ExtractedDataFormatSuite extends FlatSpec with Matchers {
dataId = extractedData.id,
labelId = Some(LongId(20)),
categoryId = Some(LongId(1)),
- value = Some(FuzzyValue.Yes)
+ value = Some(LabelValue.Yes)
),
ExtractedDataLabel(
id = LongId(0),
dataId = extractedData.id,
labelId = Some(LongId(12)),
categoryId = Some(LongId(1)),
- value = Some(FuzzyValue.No)
+ value = Some(LabelValue.No)
)
)
val expectedUpdatedExtractedData = origRichExtractedData.copy(
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala
index 054a1df..fc206c7 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientCriterionFormatSuite.scala
@@ -4,7 +4,8 @@ import java.time.LocalDateTime
import spray.json._
import org.scalatest.{FlatSpec, Matchers}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId}
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.pdsuicommon.domain.{LongId, StringId}
import xyz.driver.pdsuidomain.entities.{PatientCriterion, PatientCriterionArm}
import xyz.driver.pdsuidomain.services.PatientCriterionService.{DraftPatientCriterion, RichPatientCriterion}
@@ -21,7 +22,7 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers {
criterionText = "criterion text",
criterionValue = Some(true),
criterionIsDefining = false,
- eligibilityStatus = Some(FuzzyValue.Yes),
+ eligibilityStatus = Some(LabelValue.Yes),
verifiedEligibilityStatus = None,
isVisible = true,
isVerified = true,
@@ -39,14 +40,14 @@ class PatientCriterionFormatSuite extends FlatSpec with Matchers {
"criterionIsDefining":false,"criterionIsCompound":false,"eligibilityStatus":"Yes","verifiedEligibilityStatus":null,
"isVisible":true,"isVerified":true,"lastUpdate":"2017-08-10T18:00Z","arms":["arm 31","arm 32"]}""".parseJson)
- val updatePatientCriterionJson = """{"verifiedEligibilityStatus":"No","eligibilityStatus":null}""".parseJson
- val expectedUpdatedPatientCriterion = orig.copy(verifiedEligibilityStatus = Some(FuzzyValue.No),eligibilityStatus = None)
+ val updatePatientCriterionJson = """{"verifiedEligibilityStatus":"No"}""".parseJson
+ val expectedUpdatedPatientCriterion = orig.copy(verifiedEligibilityStatus = Some(LabelValue.No))
val parsedUpdatePatientCriterion = applyUpdateToPatientCriterion(updatePatientCriterionJson, orig)
parsedUpdatePatientCriterion should be(expectedUpdatedPatientCriterion)
val updateBulkPatientCriterionJson = """[{"id":1,"eligibilityStatus":"No"},{"id":2,"isVerified":false}]""".parseJson
val expectedDraftPatientCriterionList = List(
- DraftPatientCriterion(id = LongId(1), eligibilityStatus = Some(FuzzyValue.No), isVerified = None),
+ DraftPatientCriterion(id = LongId(1), eligibilityStatus = Some(LabelValue.No), isVerified = None),
DraftPatientCriterion(id = LongId(2), eligibilityStatus = None, isVerified = Some(false))
)
val parsedDraftPatientCriterionList = draftPatientCriterionListReader.read(updateBulkPatientCriterionJson)
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala
index ad54946..31f541f 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientEligibleTrialFormatSuite.scala
@@ -4,7 +4,9 @@ import java.time.LocalDateTime
import spray.json._
import org.scalatest.{FlatSpec, Matchers}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, StringId, UuidId}
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.entities.patient.CancerType
+import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
import xyz.driver.pdsuidomain.entities.{PatientCriterionArm, PatientTrialArmGroupView, Trial}
import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEligibleTrial
@@ -21,7 +23,7 @@ class PatientEligibleTrialFormatSuite extends FlatSpec with Matchers {
previousAssignee = None,
lastActiveUserId = None,
lastUpdate = LocalDateTime.parse("2017-08-10T18:16:19"),
- condition = Trial.Condition.Breast,
+ disease = CancerType.Breast,
phase = "",
hypothesisId = Some(UuidId("e76e2fc4-a29c-44fb-a81b-8856d06bb1d4")),
studyDesignId = Some(LongId(321)),
@@ -38,8 +40,8 @@ class PatientEligibleTrialFormatSuite extends FlatSpec with Matchers {
patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"),
trialId = StringId("NCT000001"),
hypothesisId = UuidId("e76e2fc4-a29c-44fb-a81b-8856d06bb1d4"),
- eligibilityStatus = Some(FuzzyValue.Yes),
- verifiedEligibilityStatus = Some(FuzzyValue.Yes),
+ eligibilityStatus = Some(LabelValue.Yes),
+ verifiedEligibilityStatus = Some(LabelValue.Yes),
isVerified = false
)
val arms = List(
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala
index 2761d6a..ad12b3b 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientFormatSuite.scala
@@ -4,6 +4,8 @@ import java.time.{LocalDate, LocalDateTime}
import spray.json._
import org.scalatest.{FlatSpec, Matchers}
+import xyz.driver.entities.common.FullName
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.domain.UuidId
import xyz.driver.pdsuidomain.entities.{Patient, PatientOrderId}
@@ -14,23 +16,24 @@ class PatientFormatSuite extends FlatSpec with Matchers {
val orig = Patient(
id = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"),
status = Patient.Status.New,
- name = "John Doe",
+ name = FullName.fromStrings("John", "", "Doe"),
dob = LocalDate.parse("1980-06-30"),
assignee = None,
previousStatus = None,
previousAssignee = None,
lastActiveUserId = None,
isUpdateRequired = false,
- condition = "breast",
+ disease = CancerType.Breast,
orderId = PatientOrderId("7b54a75d-4197-4b27-9045-b9b6cb131be9"),
lastUpdate = LocalDateTime.parse("2017-08-10T18:00:00")
)
val writtenJson = patientWriter.write(orig)
writtenJson should be (
- """{"id":"748b5884-3528-4cb9-904b-7a8151d6e343","dob":"1980-06-30","name":"John Doe","status":"New","assignee":null,
+ """{"id":"748b5884-3528-4cb9-904b-7a8151d6e343","dob":"1980-06-30",
+ "name":{"firstName":"John","middleName":"","lastName":"Doe"},"status":"New","assignee":null,
"previousStatus":null,"previousAssignee":null,"lastActiveUser":null,"lastUpdate":"2017-08-10T18:00Z",
- "orderId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","condition":"breast"}""".parseJson)
+ "orderId":"7b54a75d-4197-4b27-9045-b9b6cb131be9","disease":"Breast"}""".parseJson)
}
}
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala
index 3ef286d..e837861 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/PatientLabelFormatSuite.scala
@@ -4,8 +4,9 @@ import java.time.LocalDate
import spray.json._
import org.scalatest.{FlatSpec, Matchers}
-import xyz.driver.pdsuicommon.domain.{FuzzyValue, LongId, UuidId}
-import xyz.driver.pdsuidomain.entities.{PatientLabel, PatientLabelEvidenceView}
+import xyz.driver.entities.labels.LabelValue
+import xyz.driver.pdsuicommon.domain.{LongId, UuidId}
+import xyz.driver.pdsuidomain.entities._
import xyz.driver.pdsuidomain.services.PatientLabelService.RichPatientLabel
class PatientLabelFormatSuite extends FlatSpec with Matchers {
@@ -16,7 +17,7 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers {
id = LongId(1),
patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"),
labelId = LongId(20),
- primaryValue = Some(FuzzyValue.Yes),
+ primaryValue = Some(LabelValue.Yes),
verifiedPrimaryValue = None,
isVisible = true,
score = 1,
@@ -29,7 +30,7 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers {
"score":1,"isImplicitMatch":false}""".parseJson)
val updatePatientLabelJson = """{"verifiedPrimaryValue":"No"}""".parseJson
- val expectedUpdatedPatientLabel = orig.copy(verifiedPrimaryValue = Some(FuzzyValue.No))
+ val expectedUpdatedPatientLabel = orig.copy(verifiedPrimaryValue = Some(LabelValue.No))
val parsedUpdatePatientLabel = applyUpdateToPatientLabel(updatePatientLabelJson, orig)
parsedUpdatePatientLabel should be(expectedUpdatedPatientLabel)
}
@@ -38,14 +39,14 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers {
import patientlabel._
val orig = PatientLabelEvidenceView(
id = LongId(1),
- value = FuzzyValue.Maybe,
+ value = LabelValue.Maybe,
evidenceText = "evidence text",
documentId = Some(LongId(21)),
evidenceId = Some(LongId(10)),
reportId = None,
- documentType = "document type",
+ documentType = DocumentType.LaboratoryReport,
date = Some(LocalDate.parse("2017-08-10")),
- providerType = "provider type",
+ providerType = ProviderType.EmergencyMedicine,
patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"),
labelId = LongId(20),
isImplicitMatch = false
@@ -54,7 +55,8 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers {
writtenJson should be (
"""{"id":1,"value":"Maybe","evidenceText":"evidence text","documentId":21,"evidenceId":10,"reportId":null,
- "documentType":"document type","date":"2017-08-10","providerType":"provider type"}""".parseJson)
+ "documentType":{"id":3,"name":"Laboratory Report"},"date":"2017-08-10",
+ "providerType":{"id":26,"name":"Emergency Medicine"}}""".parseJson)
}
"Json format for PatientLabelDefiningCriteria" should "read and write correct JSON" in {
@@ -63,8 +65,8 @@ class PatientLabelFormatSuite extends FlatSpec with Matchers {
id = LongId(1),
patientId = UuidId("748b5884-3528-4cb9-904b-7a8151d6e343"),
labelId = LongId(20),
- primaryValue = Some(FuzzyValue.Yes),
- verifiedPrimaryValue = Some(FuzzyValue.Yes),
+ primaryValue = Some(LabelValue.Yes),
+ verifiedPrimaryValue = Some(LabelValue.Yes),
isVisible = true,
score = 1,
isImplicitMatch = false
diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala
index 59cf779..beb69c4 100644
--- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala
+++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/sprayformats/TrialFormatSuite.scala
@@ -4,6 +4,7 @@ import java.time.LocalDateTime
import spray.json._
import org.scalatest.{FlatSpec, Matchers}
+import xyz.driver.entities.patient.CancerType
import xyz.driver.pdsuicommon.domain.{LongId, StringId, UuidId}
import xyz.driver.pdsuidomain.entities.Trial
@@ -20,7 +21,7 @@ class TrialFormatSuite extends FlatSpec with Matchers {
previousAssignee = None,
lastActiveUserId = None,
lastUpdate = LocalDateTime.parse("2017-08-10T18:16:19"),
- condition = Trial.Condition.Breast,
+ disease = CancerType.Breast,
phase = "",
hypothesisId = Some(UuidId("3b80b2e2-5372-4cf5-a342-6e4ebe10fafd")),
studyDesignId = Some(LongId(321)),
@@ -39,7 +40,7 @@ class TrialFormatSuite extends FlatSpec with Matchers {
"isUpdated":false,"overviewTemplate":"","phase":"","originalStudyDesignId":null,
"hypothesisId":"3b80b2e2-5372-4cf5-a342-6e4ebe10fafd","originalTitle":"orig trial title",
"studyDesignId":321,"lastActiveUser":null,"externalid":"40892a07-c638-49d2-9795-1edfefbbcc7c",
- "id":"NCT000001","condition":"Breast","status":"New","overview":null,"previousAssignee":null,"title":"trial title"}""".parseJson)
+ "id":"NCT000001","disease":"Breast","status":"New","overview":null,"previousAssignee":null,"title":"trial title"}""".parseJson)
val updateTrialJson = """{"hypothesisId":null,"overview":"new overview"}""".parseJson
val expectedUpdatedTrial = orig.copy(hypothesisId = None, overview = Some("new overview"))