Examples with DatabaseAction org.molgenis.data.DatabaseAction used on opensource projects

Example 1 with DatabaseAction

use of org.molgenis.data.DatabaseAction in project molgenis by molgenis.

the class PackageWizardPage method handleRequest.

@Override
public String handleRequest(HttpServletRequest request, BindingResult result, Wizard wizard) {
    ImportWizardUtil.validateImportWizard(wizard);
    ImportWizard importWizard = (ImportWizard) wizard;
    String entityImportOption = importWizard.getEntityImportOption();
    if (entityImportOption != null) {
        try {
            // convert input to database action
            DatabaseAction entityDbAction = ImportWizardUtil.toDatabaseAction(entityImportOption);
            if (entityDbAction == null) {
                throw new IOException("unknown database action: " + entityImportOption);
            }
            RepositoryCollection repositoryCollection = fileRepositoryCollectionFactory.createFileRepositoryCollection(importWizard.getFile());
            ImportService importService = importServiceFactory.getImportService(importWizard.getFile(), repositoryCollection);
            // Do integration test only if there are no previous errors found
            if (!importWizard.getEntitiesImportable().containsValue(false)) {
                // The package name that is selected in the "package selection" page
                String selectedPackage = request.getParameter("selectedPackage");
                // The entities that can be imported
                Map<String, Boolean> entitiesImportable = importService.determineImportableEntities(metaDataService, repositoryCollection, selectedPackage);
                // The results of the attribute checks are stored in maps with the entityname as key, those need to be updated with the packagename
                updateFieldReports(importWizard, selectedPackage, entitiesImportable);
                // Set the entities that can be imported
                importWizard.setEntitiesImportable(entitiesImportable);
                // The entities that can not be imported. If even one entity can not be imported, everything fails
                List<String> entitiesNotImportable = entitiesImportable.entrySet().stream().filter(entity -> !entity.getValue()).map(Map.Entry::getKey).collect(toList());
                if (!entitiesNotImportable.isEmpty()) {
                    throw new MolgenisDataException("You are trying to upload entities that are not compatible with the already existing entities: " + entitiesNotImportable.toString());
                }
            }
        } catch (RuntimeException | IOException e) {
            ImportWizardUtil.handleException(e, importWizard, result, LOG, entityImportOption);
        }
    }
    return null;
}

Example 2 with DatabaseAction

use of org.molgenis.data.DatabaseAction in project molgenis by molgenis.

the class ValidationResultWizardPage method handleRequest.

@Override
public String handleRequest(HttpServletRequest request, BindingResult result, Wizard wizard) {
    ImportWizardUtil.validateImportWizard(wizard);
    ImportWizard importWizard = (ImportWizard) wizard;
    String entityImportOption = importWizard.getEntityImportOption();
    if (entityImportOption != null) {
        try {
            // convert input to database action
            DatabaseAction entityDbAction = ImportWizardUtil.toDatabaseAction(entityImportOption);
            if (entityDbAction == null)
                throw new IOException("unknown database action: " + entityImportOption);
            RepositoryCollection repositoryCollection = fileRepositoryCollectionFactory.createFileRepositoryCollection(importWizard.getFile());
            ImportService importService = importServiceFactory.getImportService(importWizard.getFile(), repositoryCollection);
            synchronized (this) {
                ImportRun importRun = importRunService.addImportRun(SecurityUtils.getCurrentUsername(), false);
                ((ImportWizard) wizard).setImportRunId(importRun.getId());
                asyncImportJobs.execute(new ImportJob(importService, SecurityContextHolder.getContext(), repositoryCollection, entityDbAction, importRun.getId(), importRunService, request.getSession(), importWizard.getSelectedPackage()));
            }
        } catch (RuntimeException | IOException e) {
            ImportWizardUtil.handleException(e, importWizard, result, LOG, entityImportOption);
        }
    }
    // Convert to list because it's less impossible use in FreeMarker
    if (!userAccountService.getCurrentUser().isSuperuser()) {
        String username = SecurityUtils.getCurrentUsername();
        groups = RunAsSystemAspect.runAsSystem(() -> Lists.newArrayList(userService.getUserGroups(username)));
    } else {
        groups = dataService.findAll(GROUP, Group.class).collect(toList());
    }
    ((ImportWizard) wizard).setGroups(groups);
    return null;
}

Example 3 with DatabaseAction

use of org.molgenis.data.DatabaseAction in project molgenis by molgenis.

the class ImportWizardController method importFile.

private ImportRun importFile(HttpServletRequest request, File file, String action, Boolean notify, String packageId) {
    // no action specified? default is ADD just like the importerPlugin
    ImportRun importRun;
    String fileExtension = getExtension(file.getName());
    DatabaseAction databaseAction = getDatabaseAction(file, action);
    if (fileExtension.contains("vcf") && dataService.hasRepository(getBaseName(file.getName()))) {
        throw new MolgenisDataException("A repository with name " + getBaseName(file.getName()) + " already exists");
    }
    ImportService importService = importServiceFactory.getImportService(file.getName());
    RepositoryCollection repositoryCollection = fileRepositoryCollectionFactory.createFileRepositoryCollection(file);
    importRun = importRunService.addImportRun(SecurityUtils.getCurrentUsername(), Boolean.TRUE.equals(notify));
    asyncImportJobs.execute(new ImportJob(importService, SecurityContextHolder.getContext(), repositoryCollection, databaseAction, importRun.getId(), importRunService, request.getSession(), packageId));
    return importRun;
}