TSPS-138 add cbas client integration (#49)

Co-authored-by: Jose Soto <[email protected]>

service/build.gradle

@@ -56,7 +56,8 @@ dependencies {
     // terra clients
     implementation "org.broadinstitute.dsde.workbench:sam-client_2.13:0.1-fd8ee25"
     implementation "org.broadinstitute.dsde.workbench:leonardo-client_2.13:1.3.6-66d9fcf"
-    implementation 'org.databiosphere:workspacedataservice-client-okhttp-javax:0.2.104-SNAPSHOT'
+    implementation "org.databiosphere:workspacedataservice-client-okhttp-javax:0.2.104-SNAPSHOT"
+    implementation "bio.terra:cbas-client:0.0.183"
 
     liquibaseRuntime 'org.liquibase:liquibase-core:3.10.0'
     liquibaseRuntime 'info.picocli:picocli:4.6.1'

service/src/main/java/bio/terra/pipelines/app/configuration/external/CbasConfiguration.java

@@ -0,0 +1,6 @@
+package bio.terra.pipelines.app.configuration.external;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties(prefix = "cbas")
+public record CbasConfiguration(Boolean debugApiLogging) {}

service/src/main/java/bio/terra/pipelines/app/configuration/internal/RetryConfiguration.java

@@ -26,7 +26,7 @@ public RetryTemplate listenerResetRetryTemplate() {
     FixedBackOffPolicy fixedBackOffPolicy = new FixedBackOffPolicy();
     fixedBackOffPolicy.setBackOffPeriod(1000L);
 
-    // Inner retry (assumping the classifier hits): up to 3 times
+    // Inner retry (assuming the classifier hits): up to 3 times
     SimpleRetryPolicy srp = new SimpleRetryPolicy();
     srp.setMaxAttempts(3);
 

service/src/main/java/bio/terra/pipelines/dependencies/cbas/CbasClient.java

@@ -0,0 +1,51 @@
+package bio.terra.pipelines.dependencies.cbas;
+
+import bio.terra.cbas.api.MethodsApi;
+import bio.terra.cbas.api.PublicApi;
+import bio.terra.cbas.api.RunSetsApi;
+import bio.terra.cbas.api.RunsApi;
+import bio.terra.cbas.client.ApiClient;
+import bio.terra.pipelines.app.configuration.external.CbasConfiguration;
+import org.springframework.stereotype.Component;
+
+@Component
+public class CbasClient {
+
+  private final CbasConfiguration cbasConfiguration;
+
+  public CbasClient(CbasConfiguration cbasConfiguration) {
+    this.cbasConfiguration = cbasConfiguration;
+  }
+
+  protected ApiClient getApiClient(String cbasBaseUri, String accessToken) {
+    ApiClient apiClient = new ApiClient().setBasePath(cbasBaseUri);
+    apiClient.addDefaultHeader("Authorization", "Bearer " + accessToken);
+    // By closing the connection after each request, we avoid the problem of the open connection
+    // being force-closed ungracefully by the Azure Relay/Listener infrastructure:
+    apiClient.addDefaultHeader("Connection", "close");
+    apiClient.setDebugging(cbasConfiguration.debugApiLogging());
+    return apiClient;
+  }
+
+  // used to access public endpoints like status and health
+  PublicApi publicApi(String cbasBaseUri, String accessToken) {
+    return new PublicApi(getApiClient(cbasBaseUri, accessToken));
+  }
+
+  // used to access endpoints related to methods (wdls)
+  // create, search, delete,etc.
+  MethodsApi methodsApi(String cbasBaseUri, String accessToken) {
+    return new MethodsApi(getApiClient(cbasBaseUri, accessToken));
+  }
+
+  // used to access endpoints to get information related to runs in a run set
+  RunsApi runsApi(String cbasBaseUri, String accessToken) {
+    return new RunsApi(getApiClient(cbasBaseUri, accessToken));
+  }
+
+  // used to access endpoints related to running of a submission of methods
+  // launch, abort, list run sets for a given method
+  RunSetsApi runSetsApi(String cbasBaseUri, String accessToken) {
+    return new RunSetsApi(getApiClient(cbasBaseUri, accessToken));
+  }
+}

service/src/main/java/bio/terra/pipelines/dependencies/cbas/CbasService.java

@@ -0,0 +1,53 @@
+package bio.terra.pipelines.dependencies.cbas;
+
+import bio.terra.cbas.client.ApiException;
+import bio.terra.cbas.model.MethodListResponse;
+import bio.terra.cbas.model.SystemStatus;
+import bio.terra.pipelines.dependencies.common.HealthCheckWorkspaceApps;
+import org.springframework.retry.support.RetryTemplate;
+import org.springframework.stereotype.Service;
+
+@Service
+public class CbasService implements HealthCheckWorkspaceApps {
+  private final CbasClient cbasClient;
+  private final RetryTemplate listenerResetRetryTemplate;
+
+  public CbasService(CbasClient cbasClient, RetryTemplate listenerResetRetryTemplate) {
+    this.cbasClient = cbasClient;
+    this.listenerResetRetryTemplate = listenerResetRetryTemplate;
+  }
+
+  public MethodListResponse getAllMethods(String cbasBaseUri, String accesstoken) {
+    return executionWithRetryTemplate(
+        listenerResetRetryTemplate,
+        () -> cbasClient.methodsApi(cbasBaseUri, accesstoken).getMethods(null, null, null));
+  }
+
+  @Override
+  public Result checkHealth(String wdsBaseUri, String accessToken) {
+    try {
+      SystemStatus result = cbasClient.publicApi(wdsBaseUri, accessToken).getStatus();
+      return new Result(result.isOk(), result.toString());
+    } catch (ApiException e) {
+      return new Result(false, e.getMessage());
+    }
+  }
+
+  interface CbasAction<T> {
+    T execute() throws ApiException;
+  }
+
+  static <T> T executionWithRetryTemplate(
+      RetryTemplate retryTemplate, CbasService.CbasAction<T> action)
+      throws CbasServiceApiException {
+
+    return retryTemplate.execute(
+        context -> {
+          try {
+            return action.execute();
+          } catch (ApiException e) {
+            throw new CbasServiceApiException(e);
+          }
+        });
+  }
+}

service/src/main/java/bio/terra/pipelines/dependencies/cbas/CbasServiceApiException.java

@@ -0,0 +1,10 @@
+package bio.terra.pipelines.dependencies.cbas;
+
+import bio.terra.cbas.client.ApiException;
+
+public class CbasServiceApiException extends CbasServiceException {
+
+  public CbasServiceApiException(ApiException exception) {
+    super("Cbas returned an unsuccessful status code", exception);
+  }
+}

service/src/main/java/bio/terra/pipelines/dependencies/cbas/CbasServiceException.java

@@ -0,0 +1,11 @@
+package bio.terra.pipelines.dependencies.cbas;
+
+import bio.terra.common.exception.ErrorReportException;
+import java.util.ArrayList;
+import org.springframework.http.HttpStatus;
+
+public class CbasServiceException extends ErrorReportException {
+  protected CbasServiceException(String message, Throwable cause) {
+    super(message, cause, new ArrayList<>(), HttpStatus.INTERNAL_SERVER_ERROR);
+  }
+}

service/src/main/java/bio/terra/pipelines/dependencies/leonardo/LeonardoService.java

@@ -15,7 +15,6 @@
 public class LeonardoService implements HealthCheck {
 
   private final LeonardoClient leonardoClient;
-
   private final AppUtils appUtils;
   private final RetryTemplate listenerResetRetryTemplate;
 
@@ -49,6 +48,10 @@ public String getWdsUrlFromApps(String workspaceId, String authToken, boolean cr
     return appUtils.findUrlForWds(getApps(workspaceId, authToken, creatorOnly), workspaceId);
   }
 
+  public String getCbasUrlFromApps(String workspaceId, String authToken, boolean creatorOnly) {
+    return appUtils.findUrlForCbas(getApps(workspaceId, authToken, creatorOnly), workspaceId);
+  }
+
   @Override
   public Result checkHealth() {
     try {

service/src/main/java/bio/terra/pipelines/service/ImputationService.java

@@ -7,6 +7,8 @@
 import bio.terra.pipelines.db.exception.DuplicateObjectException;
 import bio.terra.pipelines.db.repositories.ImputationJobsRepository;
 import bio.terra.pipelines.db.repositories.PipelineInputsRepository;
+import bio.terra.pipelines.dependencies.cbas.CbasService;
+import bio.terra.pipelines.dependencies.cbas.CbasServiceException;
 import bio.terra.pipelines.dependencies.leonardo.LeonardoService;
 import bio.terra.pipelines.dependencies.leonardo.LeonardoServiceException;
 import bio.terra.pipelines.dependencies.sam.SamService;
@@ -38,6 +40,7 @@ public class ImputationService {
   private LeonardoService leonardoService;
   private SamService samService;
   private WdsService wdsService;
+  private CbasService cbasService;
   private final JobService jobService;
   private ImputationConfiguration imputationConfiguration;
 
@@ -48,13 +51,15 @@ public class ImputationService {
       LeonardoService leonardoService,
       SamService samService,
       WdsService wdsService,
+      CbasService cbasService,
       JobService jobService,
       ImputationConfiguration imputationConfiguration) {
     this.imputationJobsRepository = imputationJobsRepository;
     this.pipelineInputsRepository = pipelineInputsRepository;
     this.leonardoService = leonardoService;
     this.samService = samService;
     this.wdsService = wdsService;
+    this.cbasService = cbasService;
     this.jobService = jobService;
     this.imputationConfiguration = imputationConfiguration;
   }
@@ -118,6 +123,7 @@ public UUID writeJobToDb(
   public List<ListAppResponse> queryForWorkspaceApps() {
     String workspaceId = imputationConfiguration.workspaceId();
     try {
+      // leonardo related calls
       List<ListAppResponse> getAppsResponse =
           leonardoService.getApps(workspaceId, samService.getTspsServiceAccountToken(), false);
 
@@ -126,6 +132,7 @@ public List<ListAppResponse> queryForWorkspaceApps() {
           imputationConfiguration.workspaceId(),
           getAppsResponse);
 
+      // wds related calls
       String wdsUri =
           leonardoService.getWdsUrlFromApps(
               workspaceId, samService.getTspsServiceAccountToken(), false);
@@ -141,13 +148,29 @@ public List<ListAppResponse> queryForWorkspaceApps() {
               samService.getTspsServiceAccountToken(),
               imputationConfiguration.workspaceId()));
 
+      // cbas related calls
+      String cbasUri =
+          leonardoService.getCbasUrlFromApps(
+              workspaceId, samService.getTspsServiceAccountToken(), false);
+      logger.info(
+          "cbas uri for workspace id {}: {}", imputationConfiguration.workspaceId(), cbasUri);
+      logger.info(
+          "Cbas health: {}",
+          cbasService.checkHealth(cbasUri, samService.getTspsServiceAccountToken()));
+      logger.info(
+          "list of methods available: {}",
+          cbasService.getAllMethods(cbasUri, samService.getTspsServiceAccountToken()));
+
       return getAppsResponse;
     } catch (LeonardoServiceException e) {
       logger.error("Get Apps called for workspace id {} failed", workspaceId);
       return Collections.emptyList();
     } catch (WdsServiceException e) {
       logger.error("Calls to Wds for workspace id {} failed", workspaceId);
       return Collections.emptyList();
+    } catch (CbasServiceException e) {
+      logger.error("Calls to Cbas for workspace id {} failed", workspaceId);
+      return Collections.emptyList();
     }
   }
 

service/src/main/resources/application.yml

@@ -132,10 +132,13 @@ leonardo:
   # The below appTypeNames are in priority order for the named app type. This order is necessary for
   # the appComparisonFunction() located in AppUtils.java for selecting the best app for each app type.
   wdsAppTypeNames: ['WDS']
-  cbasAppTypeNames: ['CROMWELL']
+  cbasAppTypeNames: ['WORKFLOWS_APP', 'CROMWELL']
   dependencyUrlCacheTtlSeconds: 300 # Refresh every 5 minutes
   debugApiLogging: false
 
 wds:
   apiV: "v0.2"
   debugApiLogging: false
+
+cbas:
+  debugApiLogging: false

service/src/test/java/bio/terra/pipelines/configuration/external/CbasConfigurationTest.java

@@ -0,0 +1,18 @@
+package bio.terra.pipelines.configuration.external;
+
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import bio.terra.pipelines.app.configuration.external.CbasConfiguration;
+import bio.terra.pipelines.testutils.BaseEmbeddedDbTest;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+class CbasConfigurationTest extends BaseEmbeddedDbTest {
+  /** test reading Cbas config from application yml */
+  @Autowired CbasConfiguration cbasConfiguration;
+
+  @Test
+  void verifyCbasServerConfig() {
+    assertTrue(cbasConfiguration.debugApiLogging());
+  }
+}

service/src/test/java/bio/terra/pipelines/configuration/external/SamConfigurationTest.java

@@ -12,7 +12,7 @@ class SamConfigurationTest extends BaseEmbeddedDbTest {
   @Autowired SamConfiguration samConfiguration;
 
   @Test
-  void verifyLeonardoServerConfig() {
+  void verifySamServerConfig() {
     assertEquals("testSamUri", samConfiguration.baseUri());
   }
 }

service/src/test/java/bio/terra/pipelines/dependencies/cbas/CbasClientTest.java

@@ -0,0 +1,42 @@
+package bio.terra.pipelines.dependencies.cbas;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import bio.terra.cbas.api.MethodsApi;
+import bio.terra.cbas.api.PublicApi;
+import bio.terra.cbas.api.RunSetsApi;
+import bio.terra.cbas.api.RunsApi;
+import bio.terra.pipelines.testutils.BaseEmbeddedDbTest;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+class CbasClientTest extends BaseEmbeddedDbTest {
+  @Autowired CbasClient cbasClient;
+  String cbasBaseUri = "cbasBaseUri";
+  String authToken = "authToken";
+
+  @Test
+  void TestWdsClientApis() {
+
+    PublicApi publicApi = cbasClient.publicApi(cbasBaseUri, authToken);
+
+    assertEquals(cbasBaseUri, publicApi.getApiClient().getBasePath());
+    assertTrue(publicApi.getApiClient().isDebugging());
+
+    MethodsApi methodsApi = cbasClient.methodsApi(cbasBaseUri, authToken);
+
+    assertEquals(cbasBaseUri, methodsApi.getApiClient().getBasePath());
+    assertTrue(methodsApi.getApiClient().isDebugging());
+
+    RunsApi runsApi = cbasClient.runsApi(cbasBaseUri, authToken);
+
+    assertEquals(cbasBaseUri, runsApi.getApiClient().getBasePath());
+    assertTrue(runsApi.getApiClient().isDebugging());
+
+    RunSetsApi runSetsApi = cbasClient.runSetsApi(cbasBaseUri, authToken);
+
+    assertEquals(cbasBaseUri, runSetsApi.getApiClient().getBasePath());
+    assertTrue(runSetsApi.getApiClient().isDebugging());
+  }
+}