Examples with CustomWebApplicationException io.dockstore.webservice.CustomWebApplicationException used on opensource projects

Example 1 with CustomWebApplicationException

use of io.dockstore.webservice.CustomWebApplicationException in project dockstore by dockstore.

the class LimitedCRUDClientIT method generateSourceFiles.

private List<SourceFile> generateSourceFiles(DescriptorLanguage descriptorLanguage) throws IOException {
    String resourceFilePath;
    String dockstorePath;
    SourceFile.TypeEnum type;
    if (descriptorLanguage == CWL) {
        resourceFilePath = "tar-param.cwl";
        dockstorePath = "/Dockstore.cwl";
        type = SourceFile.TypeEnum.DOCKSTORE_CWL;
    } else if (descriptorLanguage == WDL) {
        resourceFilePath = "hello.wdl";
        dockstorePath = "/Dockstore.wdl";
        type = SourceFile.TypeEnum.DOCKSTORE_WDL;
    } else {
        throw new CustomWebApplicationException("Only WDL and CWL are an option", HttpStatus.SC_BAD_REQUEST);
    }
    SourceFile descriptorFile = new SourceFile();
    descriptorFile.setContent(FileUtils.readFileToString(new File(ResourceHelpers.resourceFilePath(resourceFilePath)), StandardCharsets.UTF_8));
    descriptorFile.setType(type);
    descriptorFile.setPath(dockstorePath);
    descriptorFile.setAbsolutePath(dockstorePath);
    SourceFile dockerfile = new SourceFile();
    dockerfile.setContent("FROM ubuntu:latest");
    dockerfile.setType(SourceFile.TypeEnum.DOCKERFILE);
    dockerfile.setPath("/Dockerfile");
    dockerfile.setAbsolutePath("/Dockerfile");
    return Lists.newArrayList(descriptorFile, dockerfile);
}

Example 2 with CustomWebApplicationException

use of io.dockstore.webservice.CustomWebApplicationException in project dockstore by dockstore.

the class NextflowHandler method getContent.

@Override
public Optional<String> getContent(String mainDescName, String mainDescriptor, Set<SourceFile> secondarySourceFiles, Type type, ToolDAO dao) {
    // This may change later (ex. tool, workflow)
    String callType = "call";
    String toolType = "tool";
    // Write main descriptor to file
    // The use of temporary files is not needed here and might cause new problems
    // Iterate over each call, grab docker containers
    // nextflow uses the main script from the manifest as the main descriptor
    // add the Nextflow scripts
    Configuration configuration = null;
    try {
        configuration = NextflowUtilities.grabConfig(mainDescriptor);
    } catch (NextflowUtilities.NextflowParsingException e) {
        throw new CustomWebApplicationException(e.getMessage(), HttpStatus.SC_UNPROCESSABLE_ENTITY);
    }
    String mainScriptPath = "main.nf";
    if (configuration.containsKey("manifest.mainScript")) {
        mainScriptPath = configuration.getString("manifest.mainScript");
    }
    final String finalMainScriptPath = mainScriptPath;
    mainDescriptor = secondarySourceFiles.stream().filter(sf -> sf.getPath().equals(finalMainScriptPath)).findFirst().map(sf -> sf.getContent()).orElse(null);
    // Get default container (process.container takes precedence over params.container)
    String defaultContainer = null;
    if (configuration.containsKey("params.container")) {
        defaultContainer = configuration.getString("params.container");
    }
    if (configuration.containsKey("process.container")) {
        defaultContainer = configuration.getString("process.container");
    }
    Map<String, String> callToDockerMap = new HashMap<>();
    String finalDefaultContainer = defaultContainer;
    // Add all DockerMap from each secondary sourcefile
    if (!secondarySourceFiles.isEmpty()) {
        secondarySourceFiles.forEach(sourceFile -> callToDockerMap.putAll(this.getCallsToDockerMap(sourceFile.getContent(), finalDefaultContainer)));
    }
    callToDockerMap.putAll(this.getCallsToDockerMap(mainDescriptor, defaultContainer));
    // Iterate over each call, determine dependencies
    // Mapping of stepId -> array of dependencies for the step
    Map<String, List<String>> callToDependencies = this.getCallsToDependencies(mainDescriptor);
    // Get import files
    Map<String, String> namespaceToPath = this.getImportMap(mainDescriptor);
    Map<String, ToolInfo> toolInfoMap = WDLHandler.mapConverterToToolInfo(WDLHandler.convertToDockerParameter(callToDockerMap), callToDependencies);
    return convertMapsToContent(mainScriptPath, type, dao, callType, toolType, toolInfoMap, namespaceToPath);
}

Example 3 with CustomWebApplicationException

use of io.dockstore.webservice.CustomWebApplicationException in project dockstore by dockstore.

the class AbstractWorkflowResource method getSourceCodeRepoInterface.

protected SourceCodeRepoInterface getSourceCodeRepoInterface(String gitUrl, User user) {
    List<Token> tokens = getAndRefreshTokens(user, tokenDAO, client, bitbucketClientID, bitbucketClientSecret);
    final String bitbucketTokenContent = getToken(tokens, TokenType.BITBUCKET_ORG);
    Token gitHubToken = Token.extractToken(tokens, TokenType.GITHUB_COM);
    final String gitlabTokenContent = getToken(tokens, TokenType.GITLAB_COM);
    final SourceCodeRepoInterface sourceCodeRepo = SourceCodeRepoFactory.createSourceCodeRepo(gitUrl, bitbucketTokenContent, gitlabTokenContent, gitHubToken);
    if (sourceCodeRepo == null) {
        throw new CustomWebApplicationException("Git tokens invalid, please re-link your git accounts.", HttpStatus.SC_BAD_REQUEST);
    }
    return sourceCodeRepo;
}

Example 4 with CustomWebApplicationException

use of io.dockstore.webservice.CustomWebApplicationException in project dockstore by dockstore.

the class AbstractWorkflowResource method createServicesAndVersionsFromDockstoreYml.

/**
 * Create or retrieve services based on Dockstore.yml, add or update tag version
 * ONLY WORKS FOR v1.1
 * @param repository Repository path (ex. dockstore/dockstore-ui2)
 * @param gitReference Git reference from GitHub (ex. refs/tags/1.0)
 * @param installationId installation id needed to set up GitHub Apps
 * @param user User that triggered action
 * @param dockstoreYml
 * @return List of new and updated services
 */
private List<Workflow> createServicesAndVersionsFromDockstoreYml(Service12 service, String repository, String gitReference, String installationId, User user, final SourceFile dockstoreYml) {
    GitHubSourceCodeRepo gitHubSourceCodeRepo = (GitHubSourceCodeRepo) SourceCodeRepoFactory.createGitHubAppRepo(gitHubAppSetup(installationId));
    final List<Workflow> updatedServices = new ArrayList<>();
    if (service != null) {
        if (!DockstoreYamlHelper.filterGitReference(Path.of(gitReference), service.getFilters())) {
            return updatedServices;
        }
        final DescriptorLanguageSubclass subclass = service.getSubclass();
        final Boolean publish = service.getPublish();
        final var defaultVersion = service.getLatestTagAsDefault();
        final List<YamlAuthor> yamlAuthors = service.getAuthors();
        Workflow workflow = createOrGetWorkflow(Service.class, repository, user, "", subclass.getShortName(), gitHubSourceCodeRepo);
        addDockstoreYmlVersionToWorkflow(repository, gitReference, dockstoreYml, gitHubSourceCodeRepo, workflow, defaultVersion, yamlAuthors);
        if (publish != null && workflow.getIsPublished() != publish) {
            LambdaEvent lambdaEvent = createBasicEvent(repository, gitReference, user.getUsername(), LambdaEvent.LambdaEventType.PUBLISH);
            try {
                workflow = publishWorkflow(workflow, publish);
            } catch (CustomWebApplicationException ex) {
                LOG.warn("Could not set publish state from YML.", ex);
                lambdaEvent.setSuccess(false);
                lambdaEvent.setMessage(ex.getMessage());
            }
            lambdaEventDAO.create(lambdaEvent);
        }
        updatedServices.add(workflow);
    }
    return updatedServices;
}

Example 5 with CustomWebApplicationException

use of io.dockstore.webservice.CustomWebApplicationException in project dockstore by dockstore.

the class AbstractWorkflowResource method githubWebhookDelete.

/**
 * Handle webhooks from GitHub apps after branch deletion (redirected from AWS Lambda)
 * - Delete version for corresponding service and workflow
 * @param repository Repository path (ex. dockstore/dockstore-ui2)
 * @param gitReference Git reference from GitHub (ex. refs/tags/1.0)
 * @param username Git user who triggered the event
 * @param installationId GitHub App installation ID
 * @return List of updated workflows
 */
protected List<Workflow> githubWebhookDelete(String repository, String gitReference, String username, String installationId) {
    // Retrieve name from gitReference
    Optional<String> gitReferenceName = GitHelper.parseGitHubReference(gitReference);
    if (gitReferenceName.isEmpty()) {
        String msg = "Reference " + gitReference + " is not of the valid form";
        LOG.error(msg);
        sessionFactory.getCurrentSession().clear();
        LambdaEvent lambdaEvent = createBasicEvent(repository, gitReference, username, LambdaEvent.LambdaEventType.DELETE);
        lambdaEvent.setMessage(msg);
        lambdaEvent.setSuccess(false);
        lambdaEventDAO.create(lambdaEvent);
        sessionFactory.getCurrentSession().getTransaction().commit();
        throw new CustomWebApplicationException(msg, LAMBDA_FAILURE);
    }
    // Find all workflows and services that are github apps and use the given repo
    List<Workflow> workflows = workflowDAO.findAllByPath("github.com/" + repository, false).stream().filter(workflow -> Objects.equals(workflow.getMode(), DOCKSTORE_YML)).collect(Collectors.toList());
    // When the git reference to delete is the default version, set it to the next latest version
    workflows.forEach(workflow -> {
        if (workflow.getActualDefaultVersion() != null && workflow.getActualDefaultVersion().getName().equals(gitReferenceName.get())) {
            Optional<WorkflowVersion> max = workflow.getWorkflowVersions().stream().filter(v -> !Objects.equals(v.getName(), gitReferenceName.get())).max(Comparator.comparingLong(ver -> ver.getDate().getTime()));
            workflow.setActualDefaultVersion(max.orElse(null));
        }
    });
    // Delete all non-frozen versions that have the same git reference name and then update the file formats of the entry.
    workflows.forEach(workflow -> {
        workflow.getWorkflowVersions().removeIf(workflowVersion -> Objects.equals(workflowVersion.getName(), gitReferenceName.get()) && !workflowVersion.isFrozen());
        FileFormatHelper.updateEntryLevelFileFormats(workflow);
    });
    LambdaEvent lambdaEvent = createBasicEvent(repository, gitReference, username, LambdaEvent.LambdaEventType.DELETE);
    lambdaEventDAO.create(lambdaEvent);
    return workflows;
}