Examples with WorkflowDAO io.dockstore.webservice.jdbi.WorkflowDAO used on opensource projects

Example 1 with WorkflowDAO

use of io.dockstore.webservice.jdbi.WorkflowDAO in project dockstore by dockstore.

the class WorkflowIT method setup.

@Before
public void setup() {
    DockstoreWebserviceApplication application = SUPPORT.getApplication();
    SessionFactory sessionFactory = application.getHibernate().getSessionFactory();
    this.workflowDAO = new WorkflowDAO(sessionFactory);
    this.workflowVersionDAO = new WorkflowVersionDAO(sessionFactory);
    this.fileDAO = new FileDAO(sessionFactory);
    // used to allow us to use workflowDAO outside of the web service
    Session session = application.getHibernate().getSessionFactory().openSession();
    ManagedSessionContext.bind(session);
}

Example 2 with WorkflowDAO

use of io.dockstore.webservice.jdbi.WorkflowDAO in project dockstore by dockstore.

the class UserResource method deleteSelfFromEntries.

private void deleteSelfFromEntries(User user) {
    user.getEntries().stream().filter(e -> e.getUsers().size() == 1 && !e.getIsPublished()).forEach(entry -> {
        EntryDAO entryDAO;
        if (entry instanceof Workflow) {
            entryDAO = workflowDAO;
        } else if (entry instanceof Tool) {
            entryDAO = toolDAO;
        } else {
            throw new CustomWebApplicationException(MessageFormat.format("Unexpected entry type {0}", entry.getClass().toString()), HttpStatus.SC_INTERNAL_SERVER_ERROR);
        }
        eventDAO.deleteEventByEntryID(entry.getId());
        entryDAO.delete(entry);
    });
}

Example 3 with WorkflowDAO

use of io.dockstore.webservice.jdbi.WorkflowDAO in project dockstore by dockstore.

the class ServiceIT method setup.

@Before
public void setup() {
    DockstoreWebserviceApplication application = SUPPORT.getApplication();
    SessionFactory sessionFactory = application.getHibernate().getSessionFactory();
    this.workflowDAO = new WorkflowDAO(sessionFactory);
    this.serviceDAO = new ServiceDAO(sessionFactory);
    this.userDAO = new UserDAO(sessionFactory);
    this.fileDAO = new FileDAO(sessionFactory);
    // non-confidential test database sequences seem messed up and need to be iterated past, but other tests may depend on ids
    testingPostgres.runUpdateStatement("alter sequence enduser_id_seq increment by 50 restart with 100");
    testingPostgres.runUpdateStatement("alter sequence token_id_seq increment by 50 restart with 100");
    // used to allow us to use tokenDAO outside of the web service
    this.session = application.getHibernate().getSessionFactory().openSession();
    ManagedSessionContext.bind(session);
}

Example 4 with WorkflowDAO

use of io.dockstore.webservice.jdbi.WorkflowDAO in project dockstore by dockstore.

the class DockstoreWebserviceApplication method run.

@Override
public void run(DockstoreWebserviceConfiguration configuration, Environment environment) {
    BeanConfig beanConfig = new BeanConfig();
    beanConfig.setSchemes(new String[] { configuration.getExternalConfig().getScheme() });
    String portFragment = configuration.getExternalConfig().getPort() == null ? "" : ":" + configuration.getExternalConfig().getPort();
    beanConfig.setHost(configuration.getExternalConfig().getHostname() + portFragment);
    beanConfig.setBasePath(MoreObjects.firstNonNull(configuration.getExternalConfig().getBasePath(), "/"));
    beanConfig.setResourcePackage("io.dockstore.webservice.resources,io.swagger.api,io.openapi.api");
    beanConfig.setScan(true);
    final DefaultPluginManager languagePluginManager = LanguagePluginManager.getInstance(getFilePluginLocation(configuration));
    describeAvailableLanguagePlugins(languagePluginManager);
    LanguageHandlerFactory.setLanguagePluginManager(languagePluginManager);
    final PublicStateManager publicStateManager = PublicStateManager.getInstance();
    publicStateManager.setConfig(configuration);
    final TRSListener trsListener = new TRSListener();
    publicStateManager.addListener(trsListener);
    environment.jersey().property(CommonProperties.FEATURE_AUTO_DISCOVERY_DISABLE, true);
    environment.jersey().register(new JsonProcessingExceptionMapper(true));
    final TemplateHealthCheck healthCheck = new TemplateHealthCheck(configuration.getTemplate());
    environment.healthChecks().register("template", healthCheck);
    final ElasticSearchHealthCheck elasticSearchHealthCheck = new ElasticSearchHealthCheck(new ToolsExtendedApi());
    environment.healthChecks().register("elasticSearch", elasticSearchHealthCheck);
    environment.lifecycle().manage(new ElasticSearchHelper(configuration.getEsConfiguration()));
    final UserDAO userDAO = new UserDAO(hibernate.getSessionFactory());
    final TokenDAO tokenDAO = new TokenDAO(hibernate.getSessionFactory());
    final DeletedUsernameDAO deletedUsernameDAO = new DeletedUsernameDAO(hibernate.getSessionFactory());
    final ToolDAO toolDAO = new ToolDAO(hibernate.getSessionFactory());
    final FileDAO fileDAO = new FileDAO(hibernate.getSessionFactory());
    final WorkflowDAO workflowDAO = new WorkflowDAO(hibernate.getSessionFactory());
    final TagDAO tagDAO = new TagDAO(hibernate.getSessionFactory());
    final EventDAO eventDAO = new EventDAO(hibernate.getSessionFactory());
    final VersionDAO versionDAO = new VersionDAO(hibernate.getSessionFactory());
    final BioWorkflowDAO bioWorkflowDAO = new BioWorkflowDAO(hibernate.getSessionFactory());
    LOG.info("Cache directory for OkHttp is: " + cache.directory().getAbsolutePath());
    LOG.info("This is our custom logger saying that we're about to load authenticators");
    // setup authentication to allow session access in authenticators, see https://github.com/dropwizard/dropwizard/pull/1361
    SimpleAuthenticator authenticator = new UnitOfWorkAwareProxyFactory(getHibernate()).create(SimpleAuthenticator.class, new Class[] { TokenDAO.class, UserDAO.class }, new Object[] { tokenDAO, userDAO });
    CachingAuthenticator<String, User> cachingAuthenticator = new CachingAuthenticator<>(environment.metrics(), authenticator, configuration.getAuthenticationCachePolicy());
    environment.jersey().register(new AuthDynamicFeature(new OAuthCredentialAuthFilter.Builder<User>().setAuthenticator(cachingAuthenticator).setAuthorizer(new SimpleAuthorizer()).setPrefix("Bearer").setRealm("Dockstore User Authentication").buildAuthFilter()));
    environment.jersey().register(new AuthValueFactoryProvider.Binder<>(User.class));
    environment.jersey().register(RolesAllowedDynamicFeature.class);
    final HttpClient httpClient = new HttpClientBuilder(environment).using(configuration.getHttpClientConfiguration()).build(getName());
    final PermissionsInterface authorizer = PermissionsFactory.createAuthorizer(tokenDAO, configuration);
    final EntryResource entryResource = new EntryResource(tokenDAO, toolDAO, versionDAO, userDAO, configuration);
    environment.jersey().register(entryResource);
    final WorkflowResource workflowResource = new WorkflowResource(httpClient, hibernate.getSessionFactory(), authorizer, entryResource, configuration);
    environment.jersey().register(workflowResource);
    final ServiceResource serviceResource = new ServiceResource(httpClient, hibernate.getSessionFactory(), entryResource, configuration);
    environment.jersey().register(serviceResource);
    // Note workflow resource must be passed to the docker repo resource, as the workflow resource refresh must be called for checker workflows
    final DockerRepoResource dockerRepoResource = new DockerRepoResource(httpClient, hibernate.getSessionFactory(), configuration, workflowResource, entryResource);
    environment.jersey().register(dockerRepoResource);
    environment.jersey().register(new DockerRepoTagResource(toolDAO, tagDAO, eventDAO, versionDAO));
    environment.jersey().register(new TokenResource(tokenDAO, userDAO, deletedUsernameDAO, httpClient, cachingAuthenticator, configuration));
    environment.jersey().register(new UserResource(httpClient, getHibernate().getSessionFactory(), workflowResource, serviceResource, dockerRepoResource, cachingAuthenticator, authorizer, configuration));
    MetadataResourceHelper.init(configuration);
    environment.jersey().register(new UserResourceDockerRegistries(getHibernate().getSessionFactory()));
    environment.jersey().register(new MetadataResource(getHibernate().getSessionFactory(), configuration));
    environment.jersey().register(new HostedToolResource(getHibernate().getSessionFactory(), authorizer, configuration.getLimitConfig()));
    environment.jersey().register(new HostedWorkflowResource(getHibernate().getSessionFactory(), authorizer, configuration.getLimitConfig()));
    environment.jersey().register(new OrganizationResource(getHibernate().getSessionFactory()));
    environment.jersey().register(new LambdaEventResource(getHibernate().getSessionFactory()));
    environment.jersey().register(new NotificationResource(getHibernate().getSessionFactory()));
    environment.jersey().register(new CollectionResource(getHibernate().getSessionFactory()));
    environment.jersey().register(new EventResource(eventDAO, userDAO));
    environment.jersey().register(new ToolTesterResource(configuration));
    environment.jersey().register(new CloudInstanceResource(getHibernate().getSessionFactory()));
    // disable odd extra endpoints showing up
    final SwaggerConfiguration swaggerConfiguration = new SwaggerConfiguration().prettyPrint(true);
    swaggerConfiguration.setIgnoredRoutes(Lists.newArrayList("/application.wadl", "/pprof"));
    BaseOpenApiResource openApiResource = new OpenApiResource().openApiConfiguration(swaggerConfiguration);
    environment.jersey().register(openApiResource);
    final AliasResource aliasResource = new AliasResource(hibernate.getSessionFactory(), workflowResource);
    environment.jersey().register(aliasResource);
    // attach the container dao statically to avoid too much modification of generated code
    ToolsApiServiceImpl.setToolDAO(toolDAO);
    ToolsApiServiceImpl.setWorkflowDAO(workflowDAO);
    ToolsApiServiceImpl.setBioWorkflowDAO(bioWorkflowDAO);
    ToolsApiServiceImpl.setFileDAO(fileDAO);
    ToolsApiServiceImpl.setConfig(configuration);
    ToolsApiServiceImpl.setTrsListener(trsListener);
    ToolsApiExtendedServiceImpl.setStateManager(publicStateManager);
    ToolsApiExtendedServiceImpl.setToolDAO(toolDAO);
    ToolsApiExtendedServiceImpl.setWorkflowDAO(workflowDAO);
    ToolsApiExtendedServiceImpl.setConfig(configuration);
    DOIGeneratorFactory.setConfig(configuration);
    GoogleHelper.setConfig(configuration);
    registerAPIsAndMisc(environment);
    // optional CORS support
    // Enable CORS headers
    // final FilterRegistration.Dynamic cors = environment.servlets().addFilter("CORS", CrossOriginFilter.class);
    final FilterHolder filterHolder = environment.getApplicationContext().addFilter(CrossOriginFilter.class, "/*", EnumSet.of(REQUEST));
    filterHolder.setInitParameter(ACCESS_CONTROL_ALLOW_METHODS_HEADER, "GET,POST,DELETE,PUT,OPTIONS,PATCH");
    filterHolder.setInitParameter(ALLOWED_ORIGINS_PARAM, "*");
    filterHolder.setInitParameter(ALLOWED_METHODS_PARAM, "GET,POST,DELETE,PUT,OPTIONS,PATCH");
    filterHolder.setInitParameter(ALLOWED_HEADERS_PARAM, "Authorization, X-Auth-Username, X-Auth-Password, X-Requested-With,Content-Type,Accept,Origin,Access-Control-Request-Headers,cache-control");
    // Initialize GitHub App Installation Access Token cache
    CacheConfigManager cacheConfigManager = CacheConfigManager.getInstance();
    cacheConfigManager.initCache();
}