AJ-1496: remove /api/duos/consent/orsp/{orspId} API (#1249)

local-dev/templates/firecloud-orchestration.conf.ctmpl

@@ -122,7 +122,6 @@ elasticsearch {
 }
 
 duos {
-    baseConsentUrl = "https://consent.dsde-dev.broadinstitute.org"
     baseOntologyUrl = "https://consent-ontology.dsde-dev.broadinstitute.org"
     dulvn = 4
 }

src/main/resources/swagger/api-docs.yaml

@@ -5540,42 +5540,6 @@ paths:
           content: {}
       x-passthrough: false
       x-codegen-request-body-name: body
-  /api/duos/consent/orsp/{orspId}:
-    get:
-      tags:
-        - Library
-      summary: Find Consent by ORSP ID
-      operationId: duosConsentOrspId
-      parameters:
-        - name: orspId
-          in: path
-          description: Finds the consent for the provided ORSP ID.
-          required: true
-          schema:
-            type: string
-      responses:
-        200:
-          description: Consent
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/Consent'
-        400:
-          description: The consent associated with the provided name has not been
-            approved.
-          content: {}
-        401:
-          description: Invalid authorization, must be a Terra user.
-          content: {}
-        404:
-          description: The consent associated with the provided name could not be
-            found.
-          content: {}
-        500:
-          description: Internal Server Error
-          content: {}
-      x-passthrough: true
-      x-passthrough-target: consent
   /error:
     get:
       tags:

src/main/scala/org/broadinstitute/dsde/firecloud/Application.scala

@@ -9,7 +9,6 @@ import org.broadinstitute.dsde.firecloud.dataaccess._
 case class Application(agoraDAO: AgoraDAO,
                        googleServicesDAO: GoogleServicesDAO,
                        ontologyDAO: OntologyDAO,
-                       consentDAO: ConsentDAO,
                        rawlsDAO: RawlsDAO,
                        samDAO: SamDAO,
                        searchDAO: SearchDAO,

src/main/scala/org/broadinstitute/dsde/firecloud/Boot.scala

@@ -31,14 +31,13 @@ object Boot extends App with LazyLogging {
     val thurloeDAO:ThurloeDAO = new HttpThurloeDAO
     val googleServicesDAO:GoogleServicesDAO = new HttpGoogleServicesDAO(FireCloudConfig.GoogleCloud.priceListUrl, GooglePriceList(GooglePrices(FireCloudConfig.GoogleCloud.defaultStoragePriceList, UsTieredPriceItem(FireCloudConfig.GoogleCloud.defaultEgressPriceList)), "v1", "1"))
     val ontologyDAO:OntologyDAO = new ElasticSearchOntologyDAO(elasticSearchClient, FireCloudConfig.ElasticSearch.ontologyIndexName)
-    val consentDAO:ConsentDAO = new HttpConsentDAO
     val researchPurposeSupport:ResearchPurposeSupport = new ESResearchPurposeSupport(ontologyDAO)
     val searchDAO:SearchDAO = new ElasticSearchDAO(elasticSearchClient, FireCloudConfig.ElasticSearch.indexName, researchPurposeSupport)
     val shareLogDAO:ShareLogDAO = new ElasticSearchShareLogDAO(elasticSearchClient, FireCloudConfig.ElasticSearch.shareLogIndexName)
     val importServiceDAO:ImportServiceDAO = new HttpImportServiceDAO
     val shibbolethDAO:ShibbolethDAO = new HttpShibbolethDAO
 
-    val app:Application = Application(agoraDAO, googleServicesDAO, ontologyDAO, consentDAO, rawlsDAO, samDAO, searchDAO, researchPurposeSupport, thurloeDAO, shareLogDAO, importServiceDAO, shibbolethDAO);
+    val app:Application = Application(agoraDAO, googleServicesDAO, ontologyDAO, rawlsDAO, samDAO, searchDAO, researchPurposeSupport, thurloeDAO, shareLogDAO, importServiceDAO, shibbolethDAO);
 
     val agoraPermissionServiceConstructor: (UserInfo) => AgoraPermissionService = AgoraPermissionService.constructor(app)
     val exportEntitiesByTypeActorConstructor: (ExportEntitiesByTypeArguments) => ExportEntitiesByTypeActor = ExportEntitiesByTypeActor.constructor(app, system)

src/main/scala/org/broadinstitute/dsde/firecloud/FireCloudConfig.scala

@@ -183,7 +183,6 @@ object FireCloudConfig {
 
   object Duos {
     private val duos = config.getConfig("duos")
-    val baseConsentUrl = duos.getString("baseConsentUrl")
     val baseOntologyUrl = duos.getString("baseOntologyUrl")
     val dulvn = duos.getInt("dulvn")
   }

src/main/scala/org/broadinstitute/dsde/firecloud/HealthChecks.scala

@@ -22,7 +22,6 @@ class HealthChecks(app: Application, registerSAs: Boolean = true)
   def healthMonitorChecks: () => Map[Subsystem, Future[SubsystemStatus]] = () => {
     Map(
       Agora -> app.agoraDAO.status,
-      Consent -> app.consentDAO.status,
       GoogleBuckets -> app.googleServicesDAO.status,
       LibraryIndex -> app.searchDAO.status,
       OntologyIndex -> app.ontologyDAO.status,

src/main/scala/org/broadinstitute/dsde/firecloud/dataaccess/ReportsSubsystemStatus.scala

@@ -1,18 +1,9 @@
 package org.broadinstitute.dsde.firecloud.dataaccess
 
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport
-import akka.http.scaladsl.model.HttpResponse
-import akka.http.scaladsl.unmarshalling.Unmarshal
-import akka.http.scaladsl.unmarshalling._
-import akka.stream.Materializer
-import org.broadinstitute.dsde.firecloud.model.DUOS.ConsentStatus
-import org.broadinstitute.dsde.firecloud.model.DropwizardHealth
-import org.broadinstitute.dsde.firecloud.model.ModelJsonProtocol.{impDuosConsentStatus, impDropwizardHealth}
 import org.broadinstitute.dsde.workbench.util.health.SubsystemStatus
-import spray.json.DefaultJsonProtocol._
-import spray.json._
 
-import scala.concurrent.{ExecutionContext, Future}
+import scala.concurrent.Future
 
 /**
   * Created by anichols on 4/21/17.
@@ -22,32 +13,4 @@ trait ReportsSubsystemStatus extends SprayJsonSupport {
   def status: Future[SubsystemStatus]
 
   def serviceName: String
-
-  def getStatusFromDropwizardChecks(response: Future[HttpResponse])(implicit ec: ExecutionContext, materializer: Materializer): Future[SubsystemStatus] = {
-    response flatMap { resp =>
-      Unmarshal(resp).to[ConsentStatus].map { status =>
-        val ok = status.ok.get
-        val errors = status.systems.get.
-          filter(dw => !dw._2.healthy).
-          map(dw => s"Error in ${dw._1}: ${dw._2.message.getOrElse("unspecified error")}").toList
-        if (ok)
-          SubsystemStatus(ok, None)
-        else
-          SubsystemStatus(ok, Some(errors))
-      }.recoverWith {
-        case _: Throwable =>
-          Unmarshal(resp).to[Map[String, DropwizardHealth]].map { dwStatus =>
-            val ok = dwStatus.values.forall(_.healthy)
-            val errors = dwStatus.
-              filter(dw => !dw._2.healthy).
-              map(dw => s"Error in ${dw._1}: ${dw._2.message.getOrElse("unspecified error")}").toList
-            if (ok)
-              SubsystemStatus(ok, None)
-            else
-              SubsystemStatus(ok, Some(errors))
-          }
-      }
-    }
-  }
-
 }

src/main/scala/org/broadinstitute/dsde/firecloud/model/ModelJsonProtocol.scala

@@ -5,7 +5,6 @@ import akka.http.scaladsl.model.StatusCode
 import akka.http.scaladsl.model.StatusCodes._
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.{MalformedRequestContentRejection, RejectionHandler}
-import org.broadinstitute.dsde.firecloud.model.DUOS._
 import org.broadinstitute.dsde.firecloud.model.DataUse._
 import org.broadinstitute.dsde.firecloud.model.ManagedGroupRoles.ManagedGroupRole
 import org.broadinstitute.dsde.firecloud.model.OrchMethodRepository._
@@ -20,7 +19,7 @@ import org.broadinstitute.dsde.rawls.model._
 import org.broadinstitute.dsde.workbench.model.ValueObjectFormat
 import org.broadinstitute.dsde.workbench.model.WorkbenchIdentityJsonSupport._
 import org.broadinstitute.dsde.workbench.model.google.GoogleModelJsonSupport.InstantFormat
-import spray.json.{JsString, _}
+import spray.json._
 
 import scala.util.{Failure, Success, Try}
 
@@ -279,38 +278,11 @@ object ModelJsonProtocol extends WorkspaceJsonSupport with SprayJsonSupport {
   implicit val impStructuredDataRequest: RootJsonFormat[StructuredDataRequest] = jsonFormat12(StructuredDataRequest)
   implicit val impStructuredDataResponse: RootJsonFormat[StructuredDataResponse] = jsonFormat4(StructuredDataResponse)
 
-  implicit object impDuosDataUse extends RootJsonFormat[DuosDataUse] {
-    override def write(ddu: DuosDataUse): JsValue = {
-      val existingProps: Seq[(String, JsValue)] = Try(ddu.getClass.getDeclaredFields.map { f =>
-        f.setAccessible(true)
-        f.get(ddu) match {
-          case Some(x: Boolean) => f.getName -> x.toJson
-          case Some(y: String) => f.getName -> y.toJson
-          case Some((h: String) :: tail) => f.getName -> (h +: tail.collect { case z: String => z }).toJson
-          case _ => f.getName -> JsNull
-        }
-      }) match {
-        case Success(props) => props.toIndexedSeq.filterNot(_._2 == JsNull)
-        case Failure(ex) => serializationError(ex.getMessage)
-      }
-      JsObject(existingProps.toMap)
-    }
-    override def read(json: JsValue): DuosDataUse = {
-      Try(DuosDataUse.apply(json.asJsObject.fields)) match {
-        case Success(ddu) => ddu
-        case Failure(ex) => deserializationError(s"Could not read DuosDataUse value: $json", ex)
-      }
-    }
-  }
-  implicit val impDuosConsent: RootJsonFormat[Consent] = jsonFormat11(Consent)
-  implicit val impDuosConsentError: RootJsonFormat[ConsentError] = jsonFormat2(ConsentError)
   implicit val impOntologyTermParent: RootJsonFormat[TermParent] = jsonFormat5(TermParent)
   implicit val impOntologyTermResource: RootJsonFormat[TermResource] = jsonFormat7(TermResource)
   implicit val impOntologyESTermParent: RootJsonFormat[ESTermParent] = jsonFormat2(ESTermParent)
 
   implicit val impThurloeStatus: RootJsonFormat[ThurloeStatus] = jsonFormat2(ThurloeStatus)
-  implicit val impDropwizardHealth: RootJsonFormat[DropwizardHealth] = jsonFormat2(DropwizardHealth)
-  implicit val impDuosConsentStatus: RootJsonFormat[ConsentStatus] = jsonFormat3(ConsentStatus)
 
   // don't make this implicit! It would be pulled in by anything including ModelJsonProtocol._
   val entityExtractionRejectionHandler = RejectionHandler.newBuilder().handle {

src/main/scala/org/broadinstitute/dsde/firecloud/model/SystemStatus.scala

@@ -4,4 +4,3 @@ package org.broadinstitute.dsde.firecloud.model
   * Created by anichols on 4/7/17.
   */
 case class ThurloeStatus(status: String, error: Option[String])
-case class DropwizardHealth(healthy: Boolean, message: Option[String])