Examples with RegistrationManager org.gbif.ipt.service.admin.RegistrationManager used on opensource projects

Example 1 with RegistrationManager

use of org.gbif.ipt.service.admin.RegistrationManager in project ipt by gbif.

the class PublishAllResourcesActionTest method setup.

@BeforeEach
public void setup() throws IOException, ParserConfigurationException, SAXException, AlreadyExistingException, ImportException, InvalidFilenameException {
    ResourceManagerImplTest test = new ResourceManagerImplTest();
    ResourceManagerImpl mockResourceManager = test.getResourceManagerImpl();
    // prepare and add resource
    Resource resource = test.getNonRegisteredMetadataOnlyResource();
    // ensure resource has mandatory metadata filled in, meaning its EML validates and it has a valid publishing org
    Eml eml = EmlFactory.build(FileUtils.classpathStream("data/eml.xml"));
    eml.setEmlVersion(BigDecimal.valueOf(3.0));
    eml.setPreviousEmlVersion(BigDecimal.valueOf(1.0));
    resource.setEml(eml);
    // assign publishing organisation to resource
    Organisation o = new Organisation();
    o.setName("TestOrg");
    o.setKey(UUID.randomUUID().toString());
    resource.setOrganisation(o);
    // mock successful lookup for organization by key (done by RegistrationManager in EmlValidator)
    RegistrationManager mockRegistrationManager = mock(RegistrationManager.class);
    when(mockRegistrationManager.get(any(UUID.class))).thenReturn(o);
    mockResourceManager.save(resource);
    // mock generateDwca() throwing PublicationException, not actually possible, but used to test failed publications
    GenerateDwcaFactory mockDwcaFactory = mockResourceManager.getDwcaFactory();
    when(mockDwcaFactory.create(any(Resource.class), any(ReportHandler.class))).thenThrow(new PublicationException(PublicationException.TYPE.DWCA, "Mock exception"));
    // mock finding versioned EML file - not important which one
    File emlXML = File.createTempFile("eml-1.1", ".xml");
    when(test.getMockedDataDir().resourceEmlFile(anyString(), any(BigDecimal.class))).thenReturn(emlXML);
    // mock finding versioned RTF file - not important which one
    File rtf = File.createTempFile("short-1.1", ".rtf");
    when(test.getMockedDataDir().resourceRtfFile(anyString(), any(BigDecimal.class))).thenReturn(rtf);
    // mock action
    action = new PublishAllResourcesAction(mock(SimpleTextProvider.class), mock(AppConfig.class), mockRegistrationManager, mockResourceManager, mock(RegistryManager.class));
}

Example 2 with RegistrationManager

use of org.gbif.ipt.service.admin.RegistrationManager in project ipt by gbif.

the class OverviewActionOtherIT method testReuseAndReserveExistingRegisteredDoiFailsWrongTarget.

/**
 * Test reserving an existing registered DOI (reusing an existing registered DOI) using GBIF's test DataCite account.
 * </b>
 * But, make it fail by making it use the wrong target URI.
 */
@Test
public void testReuseAndReserveExistingRegisteredDoiFailsWrongTarget() throws Exception {
    // common mock AppConfig
    AppConfig mockAppConfig = mock(AppConfig.class);
    DataDir mockDataDir = mock(DataDir.class);
    when(mockAppConfig.getDataDir()).thenReturn(mockDataDir);
    // mock returning target URLs
    when(mockAppConfig.getResourceUri(anyString())).thenReturn(new URI("http://ipt.gbif-uat.org/resource?r=wrong"));
    RegistrationManager mockRegistrationManagerDataCite = mock(RegistrationManager.class);
    Organisation oDataCiteGBIF = new Organisation();
    oDataCiteGBIF.setKey(ORGANISATION_KEY.toString());
    oDataCiteGBIF.setAgencyAccountPrimary(true);
    oDataCiteGBIF.setName("GBIF");
    oDataCiteGBIF.setDoiPrefix("10.21373");
    oDataCiteGBIF.setCanHost(true);
    oDataCiteGBIF.setAgencyAccountUsername(cfg.getUser());
    oDataCiteGBIF.setAgencyAccountPassword(cfg.getPassword());
    oDataCiteGBIF.setDoiRegistrationAgency(DOIRegistrationAgency.DATACITE);
    when(mockRegistrationManagerDataCite.findPrimaryDoiAgencyAccount()).thenReturn(oDataCiteGBIF);
    when(mockRegistrationManagerDataCite.get(any(UUID.class))).thenReturn(oDataCiteGBIF);
    when(mockRegistrationManagerDataCite.getDoiService()).thenReturn(dataCiteService);
    // mock action for DataCite
    action = new OverviewAction(mock(SimpleTextProvider.class), mockAppConfig, mockRegistrationManagerDataCite, mock(ResourceManager.class), mock(UserAccountManager.class), mock(ExtensionManager.class), mock(GenerateDwcaFactory.class), mock(VocabulariesManager.class), mock(RegistryManager.class));
    LOG.info("Testing DataCite with GBIF test Prefix...");
    action.setReserveDoi("true");
    action.setResource(r);
    assertNull(r.getDoi());
    assertEquals(IdentifierStatus.UNRESERVED, r.getIdentifierStatus());
    assertNotNull(r.getEml().getCitation());
    assertNull(r.getEml().getCitation().getIdentifier());
    DOI existingDOI = new DOI("doi:10.15469/xhav6t");
    // set citation identifier equal to existing registered DOI (doi:10.15469/xhav6t) - this should get reused
    r.setCitationAutoGenerated(true);
    r.getEml().setCitation(new Citation("Replaced by auto-generated citation", existingDOI.toString()));
    // start with private resource - error: resource must be public
    r.setStatus(PublicationStatus.PUBLIC);
    action.reserveDoi();
    // 1 error is expected for the resource having wrong target URI
    assertEquals(1, action.getActionErrors().size());
    // make sure the existing DOI was NOT reused
    assertNull(r.getDoi());
    assertNull(r.getDoiOrganisationKey());
    assertEquals(IdentifierStatus.UNRESERVED, r.getIdentifierStatus());
    // alternate ids updated
    assertEquals(0, r.getEml().getAlternateIdentifiers().size());
    LOG.info("Existing DOI was NOT reused because resource was private and had wrong target URI");
}

Example 3 with RegistrationManager

use of org.gbif.ipt.service.admin.RegistrationManager in project ipt by gbif.

the class OverviewActionTest method testUndeleteButResourceOrganisationNoLongerInIPT.

@Test
public void testUndeleteButResourceOrganisationNoLongerInIPT() {
    Resource r = new Resource();
    DOI doiToUndelete = DOIUtils.mintDOI(DOIRegistrationAgency.DATACITE, Constants.TEST_DOI_PREFIX);
    BigDecimal versionToUndelete = new BigDecimal("1.0");
    VersionHistory vh = new VersionHistory(versionToUndelete, new Date(), PublicationStatus.PUBLIC);
    vh.setDoi(doiToUndelete);
    vh.setStatus(IdentifierStatus.PUBLIC);
    r.addVersionHistory(vh);
    // resource deleted!
    r.setStatus(PublicationStatus.DELETED);
    // mock organisation that is not associated to IPT
    Organisation org = new Organisation();
    org.setKey(UUID.randomUUID().toString());
    r.setOrganisation(org);
    // mock RegistrationManager returning mock DoiService
    RegistrationManager mockRegistrationManager = mock(RegistrationManager.class);
    DoiService mockDataCiteService = mock(RestJsonApiDataCiteService.class);
    when(mockRegistrationManager.getDoiService()).thenReturn(mockDataCiteService);
    // mock action
    action = new OverviewAction(mock(SimpleTextProvider.class), mock(AppConfig.class), mockRegistrationManager, mock(ResourceManager.class), mock(UserAccountManager.class), mock(ExtensionManager.class), mock(GenerateDwcaFactory.class), mock(VocabulariesManager.class), mock(RegistryManager.class));
    action.setResource(r);
    action.setUndelete("true");
    assertEquals("input", action.undelete());
    assertEquals(1, action.getActionErrors().size());
}

Example 4 with RegistrationManager

use of org.gbif.ipt.service.admin.RegistrationManager in project ipt by gbif.

the class ResourceManagerImplIT method data.

public static Stream<Arguments> data() throws IOException {
    // Mock classes
    AppConfig mockAppConfig = mock(AppConfig.class);
    // mock returning resource URI in gbif-uat belong
    when(mockAppConfig.getResourceUri(anyString())).thenReturn(UriBuilder.fromPath("http://www.gbif-uat.org:7001/ipt?r=ants").build());
    when(mockAppConfig.getResourceVersionUri("ants", new BigDecimal("1.1"))).thenReturn(UriBuilder.fromPath("http://www.gbif-uat.org:7001/ipt?r=ants&v=1.1").build());
    when(mockAppConfig.getMaxThreads()).thenReturn(3);
    UserAccountManager mockUserAccountManager = mock(UserAccountManager.class);
    UserEmailConverter mockEmailConverter = new UserEmailConverter(mockUserAccountManager);
    ExtensionRowTypeConverter mockExtensionRowTypeConverter = mock(ExtensionRowTypeConverter.class);
    ExtensionManager mockExtensionManager = mock(ExtensionManager.class);
    JdbcInfoConverter mockJdbcConverter = mock(JdbcInfoConverter.class);
    SourceManager mockSourceManager = mock(SourceManager.class);
    RegistryManager mockRegistryManager = MockRegistryManager.buildMock();
    GenerateDwcaFactory mockDwcaFactory = mock(GenerateDwcaFactory.class);
    PasswordEncrypter mockPasswordEncrypter = mock(PasswordEncrypter.class);
    Eml2Rtf mockEml2Rtf = mock(Eml2Rtf.class);
    VocabulariesManager mockVocabulariesManager = mock(VocabulariesManager.class);
    SimpleTextProvider mockSimpleTextProvider = mock(SimpleTextProvider.class);
    ConceptTermConverter mockConceptTermConverter = mock(ConceptTermConverter.class);
    // persist eml file for version 1.0 (contents written later)
    TMP_EML_FILE = File.createTempFile("eml-1.0", ".xml");
    when(MOCK_DATA_DIR.resourceEmlFile("ants", new BigDecimal("1.1"))).thenReturn(TMP_EML_FILE);
    // DataCite parameters..
    RegistrationManager mockRegistrationManagerDataCite = mock(RegistrationManager.class);
    Properties p = PropertiesUtil.loadProperties("datacite.properties");
    ClientConfiguration cfg = ClientConfiguration.builder().withBaseApiUrl(p.getProperty("baseApiUrl")).withTimeOut(Long.valueOf(p.getProperty("timeOut"))).withFileCacheMaxSizeMb(Long.valueOf(p.getProperty("fileCacheMaxSizeMb"))).withUser(p.getProperty("user")).withPassword(p.getProperty("password")).build();
    // LOG.info("DataCite password (read from Maven property datacite.password)= " + dcCfg.getPassword());
    Organisation oDataCite = new Organisation();
    oDataCite.setAgencyAccountPrimary(true);
    oDataCite.setName("GBIF");
    oDataCite.setDoiPrefix(Constants.TEST_DOI_PREFIX);
    oDataCite.setCanHost(true);
    oDataCite.setAgencyAccountUsername(cfg.getUser());
    oDataCite.setAgencyAccountPassword(cfg.getPassword());
    oDataCite.setDoiRegistrationAgency(DOIRegistrationAgency.DATACITE);
    // mock returning primary DOI agency account
    when(mockRegistrationManagerDataCite.findPrimaryDoiAgencyAccount()).thenReturn(oDataCite);
    // mock returning DataCite service
    DoiService dataCiteService = new RestJsonApiDataCiteService(cfg.getBaseApiUrl(), cfg.getUser(), cfg.getPassword());
    when(mockRegistrationManagerDataCite.getDoiService()).thenReturn(dataCiteService);
    // mock ResourceManagerImpl for DataCite
    ResourceManagerImpl managerDataCite = new ResourceManagerImpl(mockAppConfig, MOCK_DATA_DIR, mockEmailConverter, new OrganisationKeyConverter(mockRegistrationManagerDataCite), mockExtensionRowTypeConverter, mockJdbcConverter, mockSourceManager, mockExtensionManager, mockRegistryManager, mockConceptTermConverter, mockDwcaFactory, mockPasswordEncrypter, mockEml2Rtf, mockVocabulariesManager, mockSimpleTextProvider, mockRegistrationManagerDataCite);
    return Stream.of(Arguments.of(managerDataCite, DOIRegistrationAgency.DATACITE, DOIUtils.mintDOI(DOIRegistrationAgency.DATACITE, Constants.TEST_DOI_PREFIX), mockRegistrationManagerDataCite));
}

Example 5 with RegistrationManager

use of org.gbif.ipt.service.admin.RegistrationManager in project ipt by gbif.

the class GenerateDwcaEventTest method getResource.

/**
 * Generates a test sampling event resource having an event core with occurrence extension.
 */
private Resource getResource(@NotNull File resourceXML, @NotNull File eventSourceFile, @NotNull File occurrenceSourceFile) throws IOException, SAXException, ParserConfigurationException, AlreadyExistingException, ImportException, InvalidFilenameException {
    UserAccountManager mockUserAccountManager = mock(UserAccountManager.class);
    UserEmailConverter mockEmailConverter = new UserEmailConverter(mockUserAccountManager);
    RegistrationManager mockRegistrationManager = mock(RegistrationManager.class);
    OrganisationKeyConverter mockOrganisationKeyConverter = new OrganisationKeyConverter(mockRegistrationManager);
    RegistryManager mockRegistryManager = MockRegistryManager.buildMock();
    GenerateDwcaFactory mockDwcaFactory = mock(GenerateDwcaFactory.class);
    Eml2Rtf mockEml2Rtf = mock(Eml2Rtf.class);
    VocabulariesManager mockVocabulariesManager = mock(VocabulariesManager.class);
    SimpleTextProvider mockSimpleTextProvider = mock(SimpleTextProvider.class);
    mockHandler = mock(ResourceManagerImpl.class);
    resourceDir = FileUtils.createTempDir();
    BaseAction baseAction = new BaseAction(mockSimpleTextProvider, mockAppConfig, mockRegistrationManager);
    // construct ExtensionFactory using injected parameters
    Injector injector = Guice.createInjector(new ServletModule(), new Struts2GuicePluginModule(), new IPTModule());
    HttpClient httpClient = injector.getInstance(HttpClient.class);
    ThesaurusHandlingRule thesaurusRule = new ThesaurusHandlingRule(mock(VocabulariesManagerImpl.class));
    SAXParserFactory saxf = injector.getInstance(SAXParserFactory.class);
    ExtensionFactory extensionFactory = new ExtensionFactory(thesaurusRule, saxf, httpClient);
    JdbcSupport support = injector.getInstance(JdbcSupport.class);
    PasswordEncrypter passwordEncrypter = injector.getInstance(PasswordEncrypter.class);
    JdbcInfoConverter jdbcConverter = new JdbcInfoConverter(support);
    ExtensionManager extensionManager = mock(ExtensionManager.class);
    // construct event core Extension
    InputStream eventCoreIs = GenerateDwcaTest.class.getResourceAsStream("/extensions/dwc_event_2015-04-24.xml");
    Extension eventCore = extensionFactory.build(eventCoreIs);
    // construct occurrence core Extension
    InputStream occurrenceCoreIs = GenerateDwcaTest.class.getResourceAsStream("/extensions/dwc_occurrence_2015-04-24.xml");
    Extension occurrenceCore = extensionFactory.build(occurrenceCoreIs);
    // mock ExtensionManager returning occurrence core Extension
    when(extensionManager.get("http://rs.tdwg.org/dwc/terms/Occurrence")).thenReturn(occurrenceCore);
    when(extensionManager.get("http://rs.tdwg.org/dwc/terms/Event")).thenReturn(eventCore);
    ExtensionRowTypeConverter extensionRowTypeConverter = new ExtensionRowTypeConverter(extensionManager);
    ConceptTermConverter conceptTermConverter = new ConceptTermConverter(extensionRowTypeConverter);
    // mock finding resource.xml file
    when(mockDataDir.resourceFile(anyString(), anyString())).thenReturn(resourceXML);
    // retrieve sample zipped resource folder
    File zippedResourceFolder = FileUtils.getClasspathFile("resources/event/event.zip");
    // retrieve sample eml.xml file
    File emlXML = FileUtils.getClasspathFile("resources/event/eml.xml");
    // mock finding eml.xml file
    when(mockDataDir.resourceEmlFile(anyString())).thenReturn(emlXML);
    // mock finding dwca.zip file that does not exist
    when(mockDataDir.resourceDwcaFile(anyString())).thenReturn(new File("dwca.zip"));
    // create SourceManagerImpl
    mockSourceManager = new SourceManagerImpl(mock(AppConfig.class), mockDataDir);
    // create temp directory
    File tmpDataDir = FileUtils.createTempDir();
    when(mockDataDir.tmpDir()).thenReturn(tmpDataDir);
    // publication log file
    File publicationLogFile = new File(resourceDir, DataDir.PUBLICATION_LOG_FILENAME);
    when(mockDataDir.resourcePublicationLogFile(RESOURCE_SHORTNAME)).thenReturn(publicationLogFile);
    // create ResourceManagerImpl
    ResourceManagerImpl resourceManager = new ResourceManagerImpl(mockAppConfig, mockDataDir, mockEmailConverter, mockOrganisationKeyConverter, extensionRowTypeConverter, jdbcConverter, mockSourceManager, extensionManager, mockRegistryManager, conceptTermConverter, mockDwcaFactory, passwordEncrypter, mockEml2Rtf, mockVocabulariesManager, mockSimpleTextProvider, mockRegistrationManager);
    // create user
    User creator = new User();
    creator.setFirstname("Leonardo");
    creator.setLastname("Pisano");
    creator.setEmail("fi@liberabaci.com");
    creator.setLastLoginToNow();
    creator.setRole(User.Role.Manager);
    creator.setPassword("011235813");
    // create a new resource.
    resource = resourceManager.create(RESOURCE_SHORTNAME, Resource.CoreRowType.SAMPLINGEVENT.toString(), zippedResourceFolder, creator, baseAction);
    // copy event source file to tmp folder
    File copiedEvent = new File(resourceDir, "event.txt");
    // mock file to which event source file gets copied to
    when(mockDataDir.sourceFile(any(Resource.class), any(FileSource.class))).thenReturn(copiedEvent);
    // mock log file
    when(mockDataDir.sourceLogFile(anyString(), anyString())).thenReturn(new File(resourceDir, "log.txt"));
    // add event fileSource to test Resource
    FileSource eventFileSource = mockSourceManager.add(resource, eventSourceFile, "event.txt");
    resource.getMappings().get(0).setSource(eventFileSource);
    // copy occurrence source file to tmp folder
    File copiedOccurrence = new File(resourceDir, "occurrence.txt");
    // mock file to which occurrence source file gets copied to
    when(mockDataDir.sourceFile(any(Resource.class), any(FileSource.class))).thenReturn(copiedOccurrence);
    // add occurrence fileSource to test Resource
    FileSource occurrenceFileSource = mockSourceManager.add(resource, occurrenceSourceFile, "occurrence.txt");
    resource.getMappings().get(1).setSource(occurrenceFileSource);
    // mock creation of zipped dwca in temp directory - this later becomes the actual archive generated
    when(mockDataDir.tmpFile(anyString(), anyString())).thenReturn(new File(tmpDataDir, "dwca.zip"));
    // mock creation of versioned zipped dwca in resource directory
    when(mockDataDir.resourceDwcaFile(anyString(), any(BigDecimal.class))).thenReturn(new File(resourceDir, VERSIONED_ARCHIVE_FILENAME));
    return resource;
}