Examples with OMEROCredentials net.imagej.omero.OMEROCredentials used on opensource projects

Example 1 with OMEROCredentials

use of net.imagej.omero.OMEROCredentials in project imagej-omero by imagej.

the class OpenTableFromOMERO method run.

@Override
public void run() {
    final OMEROCredentials credentials = new OMEROCredentials();
    credentials.setServer(getServer());
    credentials.setPort(getPort());
    credentials.setUser(getUser());
    credentials.setPassword(getPassword());
    try {
        table = ((DefaultOMEROService) omeroService).downloadTable(credentials, tableID);
    } catch (ServerError exc) {
        log.error(exc);
        exc.printStackTrace();
        cancel("Error talking to OMERO: " + exc.getMessage());
    } catch (PermissionDeniedException exc) {
        log.error(exc);
        exc.printStackTrace();
        cancel("Error talking to OMERO: " + exc.getMessage());
    } catch (CannotCreateSessionException exc) {
        log.error(exc);
        exc.printStackTrace();
        cancel("Error talking to OMERO: " + exc.getMessage());
    } catch (DSOutOfServiceException exc) {
        log.error(exc);
        exc.printStackTrace();
        cancel("Error talking to OMERO: " + exc.getMessage());
    } catch (ExecutionException exc) {
        log.error(exc);
        exc.printStackTrace();
        cancel("Error talking to OMERO: " + exc.getMessage());
    } catch (DSAccessException exc) {
        log.error(exc);
        exc.printStackTrace();
        cancel("Error talking to OMERO: " + exc.getMessage());
    }
}

Example 2 with OMEROCredentials

use of net.imagej.omero.OMEROCredentials in project imagej-omero by imagej.

the class SaveTableToOMERO method run.

@Override
public void run() {
    final OMEROCredentials credentials = new OMEROCredentials();
    credentials.setServer(getServer());
    credentials.setPort(getPort());
    credentials.setUser(getUser());
    credentials.setPassword(getPassword());
    final Table<?, ?> table = tableDisplay.get(0);
    try {
        ((DefaultOMEROService) omeroService).uploadTable(credentials, name, table, imageID);
    } catch (ServerError exc) {
        log.error(exc);
        cancel("Error talking to OMERO: " + exc.message);
    } catch (PermissionDeniedException exc) {
        log.error(exc);
        cancel("Error talking to OMERO: " + exc.getMessage());
    } catch (CannotCreateSessionException exc) {
        log.error(exc);
        cancel("Error talking to OMERO: " + exc.getMessage());
    } catch (ExecutionException exc) {
        log.error(exc);
        cancel("Error attaching table to OMERO image: " + exc.getMessage());
    } catch (DSOutOfServiceException exc) {
        log.error(exc);
        cancel("Error attaching table to OMERO image: " + exc.getMessage());
    } catch (DSAccessException exc) {
        log.error(exc);
        cancel("Error attaching table to OMERO image: " + exc.getMessage());
    }
}

Example 3 with OMEROCredentials

use of net.imagej.omero.OMEROCredentials in project imagej-omero by imagej.

the class OmeroIT method testUploadTable.

@Test
public void testUploadTable() throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final byte[][] d = new byte[][] { { 127, 0, -128 }, { -1, -6, -23 }, { 100, 87, 4 } };
    final ByteTable table = new DefaultByteTable(3, 3);
    for (int c = 0; c < table.getColumnCount(); c++) {
        table.setColumnHeader(c, "Heading " + (c + 1));
        for (int r = 0; r < table.getRowCount(); r++) table.set(c, r, d[c][r]);
    }
    final long tableId = omero.uploadTable(cred, "test-table-upload", table, 1);
    // When upload table was called it created a session, which cleared out
    // the username and password from the credentials. The credentials must
    // have a username and password to create security contexts.
    final OMEROCredentials tc = new OMEROCredentials();
    tc.setServer(OMERO_SERVER);
    tc.setPort(OMERO_PORT);
    tc.setUser(OMERO_USER);
    tc.setPassword(OMERO_PASSWORD);
    try (final OMEROSession session = new DefaultOMEROSession(tc)) {
        final TablesFacility tablesFacility = session.getGateway().getFacility(TablesFacility.class);
        final TableData td = tablesFacility.getTableInfo(session.getSecurityContext(), tableId);
        assertEquals(td.getColumns().length, 3);
        assertEquals(td.getColumns()[0].getName(), "Heading 1");
        assertEquals(td.getColumns()[1].getName(), "Heading 2");
        assertEquals(td.getColumns()[2].getName(), "Heading 3");
        assertEquals(td.getNumberOfRows(), 3);
    }
}

Example 4 with OMEROCredentials

use of net.imagej.omero.OMEROCredentials in project imagej-omero by imagej.

the class OmeroIT method setup.

@Before
public void setup() {
    client = new omero.client(OMERO_SERVER, OMERO_PORT);
    cred = new OMEROCredentials();
    cred.setServer(OMERO_SERVER);
    cred.setPort(OMERO_PORT);
    cred.setUser(OMERO_USER);
    cred.setPassword(OMERO_PASSWORD);
    context = new Context();
    omero = context.getService(OMEROService.class);
}

Example 5 with OMEROCredentials

use of net.imagej.omero.OMEROCredentials in project imagej-omero by imagej.

the class OmeroIT method testDownloadThenUploadTable.

@Test
public void testDownloadThenUploadTable() throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final long originalId = 83;
    final Table<?, ?> ijTable = omero.downloadTable(cred, originalId);
    // When download table was called it created a session, which cleared out
    // the username and password from the credentials. The credentials must
    // have a username and password to create security contexts.
    final OMEROCredentials tc = new OMEROCredentials();
    tc.setServer(OMERO_SERVER);
    tc.setPort(OMERO_PORT);
    tc.setUser(OMERO_USER);
    tc.setPassword(OMERO_PASSWORD);
    final long newId = omero.uploadTable(tc, "table-version2", ijTable, 1);
    assertTrue(originalId != newId);
}