From 92df74ed76b7a06dbe1405fc496f3f650709e75f Mon Sep 17 00:00:00 2001 From: Jakob Odersky Date: Mon, 20 Nov 2017 20:41:50 -0800 Subject: Add formats for patient eligible trials --- .../utils/CustomSwaggerJsonFormats.scala | 2 +- .../formats/json/patienteligibletrial.scala | 21 ++---- .../rest/RestPatientEligibleTrialService.scala | 85 ++++++++++++++++++++++ .../json/PatientEligibleTrialFormatSuite.scala | 12 ++- 4 files changed, 102 insertions(+), 18 deletions(-) create mode 100644 src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala diff --git a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala index f617a20..62c9690 100644 --- a/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala +++ b/src/main/scala/xyz/driver/pdsuicommon/utils/CustomSwaggerJsonFormats.scala @@ -197,7 +197,7 @@ object CustomSwaggerJsonFormats { classOf[RichPatientCriterion] -> richPatientCriterionFormat.write(nextRichPatientCriterion()), classOf[DraftPatientCriterion] -> draftPatientCriterionFormat.write(nextDraftPatientCriterion()), classOf[PatientLabelEvidenceView] -> patientLabelEvidenceWriter.write(nextPatientLabelEvidenceView()), - classOf[RichPatientEligibleTrial] -> patientEligibleTrialWriter.write(nextRichPatientEligibleTrial()), + classOf[RichPatientEligibleTrial] -> patientEligibleTrialFormat.write(nextRichPatientEligibleTrial()), classOf[PatientHypothesis] -> patientHypothesisWriter.write(nextPatientHypothesis()), classOf[PatientHistory] -> patientHistoryFormat.write(nextPatientHistory()), classOf[PatientIssue] -> patientIssueWriter.write(nextPatientIssue()), diff --git a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala index 4c006f9..11253fc 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala @@ -8,6 +8,8 @@ import xyz.driver.pdsuidomain.services.PatientEligibleTrialService.RichPatientEl object patienteligibletrial { import DefaultJsonProtocol._ import common._ + import xyz.driver.pdsuidomain.formats.json.trial._ + import xyz.driver.pdsuidomain.formats.json.patientcriterion._ def applyUpdateToTrialArmGroup(json: JsValue, orig: PatientTrialArmGroupView): PatientTrialArmGroupView = json match { @@ -22,19 +24,10 @@ object patienteligibletrial { case _ => deserializationError(s"Expected Json Object as partial PatientTrialArmGroupView, but got $json") } - implicit val patientEligibleTrialWriter: RootJsonWriter[RichPatientEligibleTrial] = - new RootJsonWriter[RichPatientEligibleTrial] { - override def write(obj: RichPatientEligibleTrial) = - JsObject( - "id" -> obj.group.id.toJson, - "patientId" -> obj.group.patientId.toJson, - "trialId" -> obj.group.trialId.toJson, - "trialTitle" -> obj.trial.title.toJson, - "arms" -> obj.arms.map(_.armName).toJson, - "hypothesisId" -> obj.trial.hypothesisId.toJson, - "verifiedEligibilityStatus" -> obj.group.verifiedEligibilityStatus.toJson, - "isVerified" -> obj.group.isVerified.toJson - ) - } + implicit val patientEligibleArmGroupView: RootJsonFormat[PatientTrialArmGroupView] = + jsonFormat7(PatientTrialArmGroupView.apply) + + implicit val patientEligibleTrialFormat: RootJsonFormat[RichPatientEligibleTrial] = + jsonFormat3(RichPatientEligibleTrial.apply) } diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala new file mode 100644 index 0000000..f1c5f54 --- /dev/null +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala @@ -0,0 +1,85 @@ +package xyz.driver.pdsuidomain.services.rest + +import akka.http.scaladsl.marshalling.Marshal +import akka.http.scaladsl.model._ +import akka.stream.Materializer +import xyz.driver.core.rest.{Pagination => _, _} +import xyz.driver.entities.labels.Label +import xyz.driver.entities.users.AuthUserInfo +import xyz.driver.pdsuicommon.db._ +import xyz.driver.pdsuicommon.domain._ +import xyz.driver.pdsuidomain.ListResponse +import xyz.driver.pdsuidomain.entities._ +import xyz.driver.pdsuidomain.services.PatientCriterionService.RichPatientCriterion +import xyz.driver.pdsuidomain.services.{PatientEligibleTrialService, PatientLabelService} + +import scala.concurrent.{ExecutionContext, Future} + +class RestPatientEligibleTrialService(transport: ServiceTransport, baseUri: Uri)( + implicit protected val materializer: Materializer, + protected val exec: ExecutionContext) + extends PatientEligibleTrialService with RestHelper { + + import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._ + import xyz.driver.pdsuidomain.formats.json.listresponse._ + import xyz.driver.pdsuidomain.formats.json.patienteligibletrial._ + import xyz.driver.pdsuidomain.formats.json.patientcriterion._ + import PatientEligibleTrialService._ + + def getAll(patientId: UuidId[Patient], + filter: SearchFilterExpr = SearchFilterExpr.Empty, + sorting: Option[Sorting] = None, + pagination: Option[Pagination] = None)( + implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetListReply] = { + val request = HttpRequest(HttpMethods.GET, + endpointUri(baseUri, + s"/v1/patient/$patientId/label", + filterQuery(filter) ++ sortingQuery(sorting) ++ paginationQuery(pagination))) + for { + response <- transport.sendRequestGetResponse(requestContext)(request) + reply <- apiResponse[ListResponse[RichPatientEligibleTrial]](response) + } yield { + GetListReply.EntityList(reply.items, reply.meta.itemsCount) + } + } + + + def getById(patientId: UuidId[Patient], id: LongId[PatientTrialArmGroup])( + implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetByIdReply] = { + val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/patient/$patientId/trial/$id")) + for { + response <- transport.sendRequestGetResponse(requestContext)(request) + reply <- apiResponse[RichPatientEligibleTrial](response) + } yield { + GetByIdReply.Entity(reply) + } + } + + def getCriterionListByGroupId(patientId: UuidId[Patient], id: LongId[PatientTrialArmGroup])( + implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[GetCriterionListOfGroupReply] = { + val request = HttpRequest(HttpMethods.GET, endpointUri(baseUri, s"/v1/patient/$patientId/trial/$id/criterion")) + for { + response <- transport.sendRequestGetResponse(requestContext)(request) + reply <- apiResponse[ListResponse[RichPatientCriterion]](response) + } yield { + GetCriterionListOfGroupReply.EntityList(reply.items, reply.meta.itemsCount) + } + } + + def update(origEligibleTrialWithTrial: RichPatientEligibleTrial, + draftPatientTrialArmGroup: PatientTrialArmGroupView)( + implicit requestContext: AuthorizedServiceRequestContext[AuthUserInfo]): Future[UpdateReply] = { + for { + entity <- Marshal(draftPatientTrialArmGroup).to[RequestEntity] + request = HttpRequest( + HttpMethods.PATCH, + endpointUri(baseUri, s"/v1/patient/${origEligibleTrialWithTrial.group.patientId}/trial/${origEligibleTrialWithTrial.trial.id}")) + .withEntity(entity) + response <- transport.sendRequestGetResponse(requestContext)(request) + reply <- apiResponse[RichPatientEligibleTrial](response) + } yield { + UpdateReply.Updated(reply) + } + } + +} diff --git a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientEligibleTrialFormatSuite.scala b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientEligibleTrialFormatSuite.scala index faef0f6..0a83c62 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientEligibleTrialFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientEligibleTrialFormatSuite.scala @@ -47,11 +47,17 @@ class PatientEligibleTrialFormatSuite extends FlatSpec with Matchers { PatientCriterionArm(patientCriterionId = LongId(1), armId = LongId(32), armName = "arm 32") ) val orig = RichPatientEligibleTrial(trial, group, arms) - val writtenJson = patientEligibleTrialWriter.write(orig) + val writtenJson = patientEligibleTrialFormat.write(orig) writtenJson should be( - """{"id":1,"patientId":"748b5884-3528-4cb9-904b-7a8151d6e343","trialId":"NCT000001","trialTitle":"trial title", - "hypothesisId":"e76e2fc4-a29c-44fb-a81b-8856d06bb1d4","verifiedEligibilityStatus":"Yes","isVerified":false,"arms":["arm 31","arm 32"]}""".parseJson) + """{"trial":{"isPartner":false,"assignee":null,"lastUpdate":"2017-08-10T18:16:19Z","previousStatus":null, + "isUpdated":false,"overviewTemplate":"","phase":"","originalStudyDesignId":null, + "hypothesisId":"e76e2fc4-a29c-44fb-a81b-8856d06bb1d4","originalTitle":"orig trial title","studyDesignId":321, + "lastActiveUser":null,"externalid":"40892a07-c638-49d2-9795-1edfefbbcc7c","id":"NCT000001","status":"Done", + "overview":null,"previousAssignee":null,"title":"trial title"},"group":{"isVerified":false + ,"patientId":"748b5884-3528-4cb9-904b-7a8151d6e343","hypothesisId":"e76e2fc4-a29c-44fb-a81b-8856d06bb1d4", + "verifiedEligibilityStatus":"Yes","trialId":"NCT000001","eligibilityStatus":"Yes","id":1}, + "arms":[{"patientCriterionId":1,"armId":31,"armName":"arm 31"},{"patientCriterionId":1,"armId":32,"armName":"arm 32"}]}""".parseJson) val updatePatientEligibleTrialJson = """{"isVerified":true}""".parseJson val expectedUpdatedPatientTrialArmGroup = group.copy(isVerified = true) -- cgit v1.2.3