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 ++++++++++++++++++++++ 3 files changed, 93 insertions(+), 15 deletions(-) create mode 100644 src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala (limited to 'src/main') 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) + } + } + +} -- cgit v1.2.3 From 5c50fd8f9eb4588e8f2c7ea5b84822e224b222e5 Mon Sep 17 00:00:00 2001 From: Jakob Odersky Date: Mon, 20 Nov 2017 21:04:06 -0800 Subject: Nest format --- .../xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala | 5 ++--- .../pdsuidomain/formats/json/PatientEligibleTrialFormatSuite.scala | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) (limited to 'src/main') 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 11253fc..f21b0cb 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/formats/json/patienteligibletrial.scala @@ -14,9 +14,8 @@ object patienteligibletrial { def applyUpdateToTrialArmGroup(json: JsValue, orig: PatientTrialArmGroupView): PatientTrialArmGroupView = json match { case JsObject(fields) => - val isVerified = fields - .get("isVerified") - .map(_.convertTo[Boolean]) + val isVerified = fields.get("group").map(_.asJsObject) + .flatMap(_.fields.get("isVerified")).map(_.convertTo[Boolean]) .getOrElse(orig.isVerified) orig.copy(isVerified = isVerified) 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 0a83c62..9695c2d 100644 --- a/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientEligibleTrialFormatSuite.scala +++ b/src/test/scala/xyz/driver/pdsuidomain/formats/json/PatientEligibleTrialFormatSuite.scala @@ -59,7 +59,7 @@ class PatientEligibleTrialFormatSuite extends FlatSpec with Matchers { "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 updatePatientEligibleTrialJson = """{"group":{"isVerified":true}}""".parseJson val expectedUpdatedPatientTrialArmGroup = group.copy(isVerified = true) val parsedUpdatePatientTrialArmGroup = applyUpdateToTrialArmGroup(updatePatientEligibleTrialJson, group) parsedUpdatePatientTrialArmGroup should be(expectedUpdatedPatientTrialArmGroup) -- cgit v1.2.3 From f58eeb490fc8f829a5c8f727ee354bfad51c721a Mon Sep 17 00:00:00 2001 From: Jakob Odersky Date: Mon, 20 Nov 2017 21:49:42 -0800 Subject: Fix trial ID in update route --- .../pdsuidomain/services/rest/RestPatientEligibleTrialService.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/main') diff --git a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala index f1c5f54..9cc01d1 100644 --- a/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala +++ b/src/main/scala/xyz/driver/pdsuidomain/services/rest/RestPatientEligibleTrialService.scala @@ -73,7 +73,7 @@ class RestPatientEligibleTrialService(transport: ServiceTransport, baseUri: Uri) entity <- Marshal(draftPatientTrialArmGroup).to[RequestEntity] request = HttpRequest( HttpMethods.PATCH, - endpointUri(baseUri, s"/v1/patient/${origEligibleTrialWithTrial.group.patientId}/trial/${origEligibleTrialWithTrial.trial.id}")) + endpointUri(baseUri, s"/v1/patient/${origEligibleTrialWithTrial.group.patientId}/trial/${origEligibleTrialWithTrial.group.id}")) .withEntity(entity) response <- transport.sendRequestGetResponse(requestContext)(request) reply <- apiResponse[RichPatientEligibleTrial](response) -- cgit v1.2.3