Examples with TableData omero.gateway.model.TableData used on opensource projects

Example 6 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class UploadTableTest method testReferenceTable.

@Test
public void testReferenceTable() throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final GenericTable table = new DefaultGenericTable();
    final OMERORefColumn rc0 = new OMERORefColumn(OMERORef.WELL);
    final OMERORefColumn rc1 = new OMERORefColumn(OMERORef.WELL);
    final OMERORefColumn rc2 = new OMERORefColumn(OMERORef.WELL);
    rc0.fill(new long[] { 2314, 3141324, 1235 });
    rc1.fill(new long[] { 1234, 18367, 82156 });
    rc2.fill(new long[] { 3198, 968431, 5489 });
    table.add(rc0);
    table.add(rc1);
    table.add(rc2);
    final Object[][] wells = new Object[3][3];
    for (int c = 0; c < table.getColumnCount(); c++) {
        for (int r = 0; r < table.getRowCount(); r++) {
            wells[c][r] = new WellSampleData(new WellSampleI((long) table.get(c, r), false));
        }
        ((OMERORefColumn) table.get(c)).setOriginalData(wells[c]);
    }
    // Create expectations
    setUpMethodCalls();
    final long id = service.uploadTable(credentials, "table", table, 0);
    assertEquals(id, -1);
    // NB: Can only capture in a Verifications block
    new Verifications() {

        {
            TableData td;
            tablesFacility.addTable((SecurityContext) any, (ImageData) any, anyString, td = withCapture());
            tableEquals(table, td, WellSampleData.class);
        }
    };
}

Example 7 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class DownloadTableTest method downloadLongTable.

@Test
public void downloadLongTable() throws PermissionDeniedException, CannotCreateSessionException, ServerError, DSOutOfServiceException, ExecutionException, DSAccessException {
    // Setup OMERO data structures
    final TableDataColumn[] tdc = new TableDataColumn[] { new TableDataColumn("Header 1", 0, Long.class), new TableDataColumn("Header 2", 1, Long.class), new TableDataColumn("Header 3", 2, Long.class), new TableDataColumn("Header 4", 3, Long.class) };
    final Object[][] data = new Object[4][];
    data[0] = new Long[] { 0l, -9223372036854775808l, 9223372036854775807l };
    data[1] = new Long[] { 134l, 5415145l, 4775807l };
    data[2] = new Long[] { -1898l, -97234l, 75807l };
    data[3] = new Long[] { 19048l, -123l, 4l };
    final TableData table = new TableData(tdc, data);
    table.setNumberOfRows(3);
    // Create expectations
    setUpMethodCalls(table);
    final Table<?, ?> imageJTable = ((DefaultOMEROService) service).downloadTable(credentials, 0);
    // Tests
    assertTrue(LongTable.class.isInstance(imageJTable));
    assertEquals(imageJTable.getColumnCount(), 4);
    assertEquals(imageJTable.getRowCount(), 3);
    assertEquals(imageJTable.getColumnHeader(0), "Header 1");
    assertEquals(imageJTable.getColumnHeader(1), "Header 2");
    assertEquals(imageJTable.getColumnHeader(2), "Header 3");
    assertEquals(imageJTable.getColumnHeader(3), "Header 4");
    for (int r = 0; r < imageJTable.getRowCount(); r++) {
        for (int c = 0; c < imageJTable.getColumnCount(); c++) {
            assertEquals(data[c][r], imageJTable.get(c, r));
        }
    }
}

Example 8 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class DownloadTableTest method downloadMixedTable.

@Test
@SuppressWarnings("unchecked")
public void downloadMixedTable() throws PermissionDeniedException, CannotCreateSessionException, ServerError, DSOutOfServiceException, ExecutionException, DSAccessException {
    // / Setup OMERO data structures
    final TableDataColumn[] tdc = new TableDataColumn[] { new TableDataColumn("Header 1", 0, String.class), new TableDataColumn("Header 2", 1, Boolean.class), new TableDataColumn("Header 3", 2, Double[].class), new TableDataColumn("Header 4", 3, Long.class) };
    final Object[][] data = new Object[4][];
    data[0] = new String[] { "abc", "123", "hi!" };
    data[1] = new Boolean[] { false, true, false };
    data[2] = new Double[][] { { 0.125, 3879123.5, -93.25 }, { 0d, -123353.03125, -5.5 }, { 100.25, 0.125, -9000.5 } };
    data[3] = new Long[] { -9028131908l, 0l, 12l };
    final TableData table = new TableData(tdc, data);
    table.setNumberOfRows(3);
    // Create expectations
    setUpMethodCalls(table);
    final Table<?, ?> imageJTable = ((DefaultOMEROService) service).downloadTable(credentials, 0);
    // Tests
    assertTrue(GenericTable.class.isInstance(imageJTable));
    assertTrue(DefaultColumn.class.isInstance(imageJTable.get(0)));
    assertTrue(imageJTable.get(0).getType() == String.class);
    assertTrue(BoolColumn.class.isInstance(imageJTable.get(1)));
    assertTrue(DefaultColumn.class.isInstance(imageJTable.get(2)));
    assertTrue(imageJTable.get(2).getType() == DoubleArray.class);
    assertTrue(LongColumn.class.isInstance(imageJTable.get(3)));
    assertEquals(imageJTable.getColumnCount(), 4);
    assertEquals(imageJTable.getRowCount(), 3);
    assertEquals(imageJTable.getColumnHeader(0), "Header 1");
    assertEquals(imageJTable.getColumnHeader(1), "Header 2");
    assertEquals(imageJTable.getColumnHeader(2), "Header 3");
    assertEquals(imageJTable.getColumnHeader(3), "Header 4");
    for (int r = 0; r < imageJTable.getRowCount(); r++) assertEquals(data[0][r], ((DefaultColumn<String>) imageJTable.get(0)).get(r));
    for (int r = 0; r < imageJTable.getRowCount(); r++) assertEquals(data[1][r], ((BoolColumn) imageJTable.get(1)).getValue(r));
    for (int r = 0; r < imageJTable.getRowCount(); r++) assertArrayEquals((Double[]) data[2][r], ((DefaultColumn<DoubleArray>) imageJTable.get(2)).get(r).toArray());
    for (int r = 0; r < imageJTable.getRowCount(); r++) assertEquals(data[3][r], ((LongColumn) imageJTable.get(3)).getValue(r));
}

Example 9 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class DownloadTableTest method downloadDoubleTable.

@Test
public void downloadDoubleTable() throws PermissionDeniedException, CannotCreateSessionException, ServerError, DSOutOfServiceException, ExecutionException, DSAccessException {
    // Setup OMERO data structures
    final TableDataColumn[] tdc = new TableDataColumn[] { new TableDataColumn("Header 1", 0, Double.class), new TableDataColumn("Header 2", 1, Double.class) };
    final Object[][] data = new Object[2][];
    data[0] = new Double[] { 0.125, -0.5, 923014712408917.25, -241.03125, 0.0 };
    data[1] = new Double[] { 1002.125, 908082.5, 59871249.0625, -7.25, 4.5 };
    final TableData table = new TableData(tdc, data);
    table.setNumberOfRows(5);
    // Create expectations
    setUpMethodCalls(table);
    final Table<?, ?> imageJTable = ((DefaultOMEROService) service).downloadTable(credentials, 0);
    // Tests
    assertTrue(ResultsTable.class.isInstance(imageJTable));
    assertEquals(imageJTable.getColumnCount(), 2);
    assertEquals(imageJTable.getRowCount(), 5);
    assertEquals(imageJTable.getColumnHeader(0), "Header 1");
    assertEquals(imageJTable.getColumnHeader(1), "Header 2");
    for (int r = 0; r < imageJTable.getRowCount(); r++) {
        for (int c = 0; c < imageJTable.getColumnCount(); c++) {
            assertEquals((double) data[c][r], ((ResultsTable) imageJTable).get(c, r), 0);
        }
    }
}

Example 10 with TableData

use of omero.gateway.model.TableData 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);
    }
}