Examples with User io.dockstore.webservice.core.User used on opensource projects

Example 1 with User

use of io.dockstore.webservice.core.User in project dockstore by dockstore.

the class AbstractWorkflowResource method syncEntities.

/**
 * Syncs entities based on GitHub app installation, optionally limiting to orgs in the GitHub organization <code>organization</code>.
 *
 * 1. Finds all repos that have the Dockstore GitHub app installed
 * 2. For existing entities, ensures that <code>user</code> is one of the entity's users
 *
 * @param user
 * @param gitHubToken
 */
private void syncEntities(User user, Token gitHubToken) {
    GitHubSourceCodeRepo gitHubSourceCodeRepo = (GitHubSourceCodeRepo) SourceCodeRepoFactory.createSourceCodeRepo(gitHubToken);
    // Get all GitHub repositories for the user
    final Map<String, String> workflowGitUrl2Name = gitHubSourceCodeRepo.getWorkflowGitUrl2RepositoryId();
    // Filter by organization if necessary
    final Collection<String> repositories = workflowGitUrl2Name.values();
    // Add user to any services they should have access to that already exist on Dockstore
    final List<Workflow> existingWorkflows = findDockstoreWorkflowsForGitHubRepos(repositories);
    existingWorkflows.stream().filter(workflow -> !workflow.getUsers().contains(user)).forEach(workflow -> workflow.getUsers().add(user));
// No longer adds stub services, though code could be useful
// final Set<String> existingWorkflowPaths = existingWorkflows.stream()
// .map(workflow -> workflow.getWorkflowPath()).collect(Collectors.toSet());
// 
// GitHubHelper.checkJWT(gitHubAppId, gitHubPrivateKeyFile);
// 
// GitHubHelper.reposToCreateEntitiesFor(repositories, organization, existingWorkflowPaths).stream()
// .forEach(repositoryName -> {
// final T entity = initializeEntity(repositoryName, gitHubSourceCodeRepo);
// entity.addUser(user);
// final long entityId = workflowDAO.create(entity);
// final Workflow createdEntity = workflowDAO.findById(entityId);
// final Workflow updatedEntity = gitHubSourceCodeRepo.getWorkflow(repositoryName, Optional.of(createdEntity));
// updateDBWorkflowWithSourceControlWorkflow(createdEntity, updatedEntity, user);
// });
}

Example 2 with User

use of io.dockstore.webservice.core.User 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;
}

Example 3 with User

use of io.dockstore.webservice.core.User in project dockstore by dockstore.

the class CollectionResource method createCollection.

@POST
@Timed
@UnitOfWork
@Path("{organizationId}/collections")
@ApiOperation(value = "Create a collection in the given organization.", authorizations = { @Authorization(value = JWT_SECURITY_DEFINITION_NAME) }, response = Collection.class)
@Operation(operationId = "createCollection", summary = "Create a collection in the given organization.", description = "Create a collection in the given organization.", security = @SecurityRequirement(name = "bearer"))
public Collection createCollection(@ApiParam(hidden = true) @Parameter(hidden = true, name = "user") @Auth User user, @ApiParam(value = "Organization ID.", required = true) @Parameter(description = "Organization ID.", name = "organizationId", in = ParameterIn.PATH, required = true) @PathParam("organizationId") Long organizationId, @ApiParam(value = "Collection to register.", required = true) @Parameter(description = "Collection to register.", name = "collection", required = true) Collection collection) {
    // First check if the organization exists and that the user is an admin or maintainer
    boolean isUserAdminOrMaintainer = OrganizationResource.isUserAdminOrMaintainer(organizationId, user.getId(), organizationDAO);
    if (!isUserAdminOrMaintainer) {
        String msg = "Organization not found.";
        LOG.info(msg);
        throw new CustomWebApplicationException(msg, HttpStatus.SC_NOT_FOUND);
    }
    // Check if any other collections in the organization exist with that name
    Collection matchingCollection = collectionDAO.findByNameAndOrg(collection.getName(), organizationId);
    if (matchingCollection != null) {
        String msg = "A collection already exists with the name '" + collection.getName() + "' in the specified organization.";
        LOG.info(msg);
        throw new CustomWebApplicationException(msg, HttpStatus.SC_BAD_REQUEST);
    }
    // Get the organization
    Organization organization = organizationDAO.findById(organizationId);
    // Save the collection
    long id = collectionDAO.create(collection);
    organization.addCollection(collection);
    // Event for creation
    User foundUser = userDAO.findById(user.getId());
    Event createCollectionEvent = new Event.Builder().withOrganization(organization).withCollection(collection).withInitiatorUser(foundUser).withType(Event.EventType.CREATE_COLLECTION).build();
    eventDAO.create(createCollectionEvent);
    return collectionDAO.findById(id);
}

Example 4 with User

use of io.dockstore.webservice.core.User in project dockstore by dockstore.

the class CollectionResource method deleteEntryFromCollection.

@DELETE
@Timed
@UnitOfWork
@Path("{organizationId}/collections/{collectionId}/entry")
@ApiOperation(value = "Delete an entry from a collection.", authorizations = { @Authorization(value = JWT_SECURITY_DEFINITION_NAME) }, response = Collection.class)
@Operation(operationId = "deleteEntryFromCollection", summary = "Delete an entry to a collection.", description = "Delete an entry to a collection.", security = @SecurityRequirement(name = "bearer"))
public Collection deleteEntryFromCollection(@ApiParam(hidden = true) @Parameter(hidden = true, name = "user") @Auth User user, @ApiParam(value = "Organization ID.", required = true) @Parameter(description = "Organization ID.", name = "organizationId", in = ParameterIn.PATH, required = true) @PathParam("organizationId") Long organizationId, @ApiParam(value = "Collection ID.", required = true) @Parameter(description = "Collection ID.", name = "collectionId", in = ParameterIn.PATH, required = true) @PathParam("collectionId") Long collectionId, @ApiParam(value = "Entry ID", required = true) @Parameter(description = "Entry ID.", name = "entryId", in = ParameterIn.QUERY, required = true) @QueryParam("entryId") Long entryId, @ApiParam(value = "Version ID", required = false) @Parameter(description = "Version ID.", name = "versionId", in = ParameterIn.QUERY, required = false) @QueryParam("versionName") String versionName) {
    // Call common code to check if entry and collection exist and return them
    ImmutablePair<Entry, Collection> entryAndCollection = commonModifyCollection(organizationId, entryId, collectionId, user);
    Long versionId = null;
    if (versionName != null) {
        Set<Version> workflowVersions = entryAndCollection.getLeft().getWorkflowVersions();
        Optional<Version> first = workflowVersions.stream().filter(version -> version.getName().equals(versionName)).findFirst();
        if (first.isPresent()) {
            versionId = first.get().getId();
        } else {
            throw new CustomWebApplicationException("Version not found", HttpStatus.SC_NOT_FOUND);
        }
    }
    // Remove the entry from the organization,
    // This silently fails if the user somehow manages to give a non-existent entryId and versionId pair
    entryAndCollection.getRight().removeEntry(entryAndCollection.getLeft().getId(), versionId);
    // Event for deletion
    Organization organization = organizationDAO.findById(organizationId);
    Event.Builder eventBuild = new Event.Builder().withOrganization(organization).withCollection(entryAndCollection.getRight()).withInitiatorUser(user).withType(Event.EventType.REMOVE_FROM_COLLECTION);
    if (entryAndCollection.getLeft() instanceof BioWorkflow) {
        eventBuild = eventBuild.withBioWorkflow((BioWorkflow) entryAndCollection.getLeft());
    } else if (entryAndCollection.getLeft() instanceof Service) {
        eventBuild = eventBuild.withService((Service) entryAndCollection.getLeft());
    } else if (entryAndCollection.getLeft() instanceof Tool) {
        eventBuild = eventBuild.withTool((Tool) entryAndCollection.getLeft());
    }
    Event removeFromCollectionEvent = eventBuild.build();
    eventDAO.create(removeFromCollectionEvent);
    return collectionDAO.findById(collectionId);
}

Example 5 with User

use of io.dockstore.webservice.core.User in project dockstore by dockstore.

the class SamPermissionsImpl method getApiClient.

private ApiClient getApiClient(User user) {
    ApiClient apiClient = new ApiClient() {

        @Override
        protected void performAdditionalClientConfiguration(ClientConfig clientConfig) {
            // Calling ResourcesApi.addUserToPolicy invokes PUT without a body, which will fail
            // without this:
            clientConfig.property(ClientProperties.SUPPRESS_HTTP_COMPLIANCE_VALIDATION, true);
        }
    };
    apiClient.setBasePath(config.getSamConfiguration().getBasepath());
    return googleAccessToken(user).map(credentials -> {
        apiClient.setAccessToken(credentials);
        return apiClient;
    }).orElseThrow(() -> new CustomWebApplicationException("Could not get Google access token. Try relinking your Google account.", HttpStatus.SC_UNAUTHORIZED));
}