Examples with EntityImportReport org.molgenis.data.importer.EntityImportReport used on opensource projects

Example 1 with EntityImportReport

use of org.molgenis.data.importer.EntityImportReport in project molgenis by molgenis.

the class OntologyImportService method doImport.

@Override
@Transactional
public EntityImportReport doImport(RepositoryCollection source, DatabaseAction databaseAction, String packageId) {
    if (databaseAction != DatabaseAction.ADD) {
        throw new IllegalArgumentException("Only ADD is supported");
    }
    EntityImportReport report = new EntityImportReport();
    for (String entityTypeId : source.getEntityTypeIds()) {
        try (Repository<Entity> sourceRepository = source.getRepository(entityTypeId)) {
            Repository<Entity> targetRepository = dataService.getRepository(entityTypeId);
            Integer count = targetRepository.add(asStream(sourceRepository));
            report.addEntityCount(entityTypeId, count);
        } catch (IOException e) {
            LOG.error("", e);
            throw new MolgenisDataException(e);
        }
    }
    return report;
}

Example 2 with EntityImportReport

use of org.molgenis.data.importer.EntityImportReport in project molgenis by molgenis.

the class VcfImporterService method doImport.

@Transactional
@Override
public EntityImportReport doImport(RepositoryCollection source, DatabaseAction databaseAction, String packageId) {
    if (databaseAction != DatabaseAction.ADD)
        throw new IllegalArgumentException("Only ADD is supported");
    List<EntityType> addedEntities = Lists.newArrayList();
    EntityImportReport report;
    Iterator<String> it = source.getEntityTypeIds().iterator();
    if (it.hasNext()) {
        try (Repository<Entity> repo = source.getRepository(it.next())) {
            report = importVcf(repo, addedEntities, packageId);
        } catch (IOException e) {
            LOG.error("", e);
            throw new MolgenisDataException(e);
        }
    } else {
        report = new EntityImportReport();
    }
    return report;
}

Example 3 with EntityImportReport

use of org.molgenis.data.importer.EntityImportReport in project molgenis by molgenis.

the class OntologyImportServiceIT method testDoImportOwl.

private void testDoImportOwl() {
    String fileName = "ontology-small.owl.zip";
    File file = getFile("/owl/" + fileName);
    FileRepositoryCollection repoCollection = fileRepositoryCollectionFactory.createFileRepositoryCollection(file);
    ImportService importService = importServiceFactory.getImportService(file, repoCollection);
    EntityImportReport importReport = importService.doImport(repoCollection, ADD, PACKAGE_DEFAULT);
    validateImportReport(importReport, ImmutableMap.of("sys_ont_OntologyTermDynamicAnnotation", 4, "sys_ont_OntologyTermSynonym", 9, "sys_ont_OntologyTermNodePath", 10, "sys_ont_Ontology", 1, "sys_ont_OntologyTerm", 9), emptySet());
    // Verify the import as system as we need write permissions on sys tables to carry out the verification
    runAsSystem(this::verifyOwlAsSystem);
}

Example 4 with EntityImportReport

use of org.molgenis.data.importer.EntityImportReport in project molgenis by molgenis.

the class VcfImportServiceIT method testDoImportVcfWithoutSamples.

private void testDoImportVcfWithoutSamples() {
    String entityTypeId = "variantsWithoutSamples";
    String fileName = entityTypeId + ".vcf";
    File file = getFile("/vcf/" + fileName);
    FileRepositoryCollection repoCollection = fileRepositoryCollectionFactory.createFileRepositoryCollection(file);
    ImportService importService = importServiceFactory.getImportService(file, repoCollection);
    EntityImportReport importReport = importService.doImport(repoCollection, ADD, PACKAGE_DEFAULT);
    validateImportReport(importReport, ImmutableMap.of(entityTypeId, 10), ImmutableSet.of(entityTypeId));
    assertVariants(entityTypeId, false);
}

Example 5 with EntityImportReport

use of org.molgenis.data.importer.EntityImportReport in project molgenis by molgenis.

the class VcfImportServiceIT method testDoImportVcfGzWithSamples.

private void testDoImportVcfGzWithSamples() {
    String entityTypeId = "variantsWithSamplesGz";
    String fileName = entityTypeId + ".vcf.gz";
    File file = getFile("/vcf/" + fileName);
    FileRepositoryCollection repoCollection = fileRepositoryCollectionFactory.createFileRepositoryCollection(file);
    ImportService importService = importServiceFactory.getImportService(file, repoCollection);
    EntityImportReport importReport = importService.doImport(repoCollection, ADD, PACKAGE_DEFAULT);
    validateImportReport(importReport, ImmutableMap.of("variantsWithSamplesGz", 10, "variantsWithSamplesGzSample", 10), ImmutableSet.of("variantsWithSamplesGz", "variantsWithSamplesGzSample"));
    assertVariants(entityTypeId, true);
}