Examples with TablesFacility omero.gateway.facility.TablesFacility used on opensource projects

Example 1 with TablesFacility

use of omero.gateway.facility.TablesFacility in project imagej-omero by imagej.

the class DefaultOMEROService method uploadTable.

@Override
public long uploadTable(final OMEROCredentials credentials, final String name, final Table<?, ?> imageJTable, final long imageID) throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final TableData omeroTable = convertOMEROTable(imageJTable);
    long id = -1;
    try (final OMEROSession session = new DefaultOMEROSession(credentials)) {
        // Get image
        final BrowseFacility browseFacility = session.getGateway().getFacility(BrowseFacility.class);
        final ImageData image = browseFacility.getImage(session.getSecurityContext(), imageID);
        // attach table to image
        final TablesFacility tablesFacility = session.getGateway().getFacility(TablesFacility.class);
        final TableData stored = tablesFacility.addTable(session.getSecurityContext(), image, name, omeroTable);
        id = stored.getOriginalFileId();
    }
    return id;
}

Example 2 with TablesFacility

use of omero.gateway.facility.TablesFacility 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 3 with TablesFacility

use of omero.gateway.facility.TablesFacility in project imagej-omero by imagej.

the class DefaultOMEROService method downloadTable.

@Override
public Table<?, ?> downloadTable(final OMEROCredentials credentials, final long tableID) throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    try (final OMEROSession session = new DefaultOMEROSession(credentials)) {
        final TablesFacility tableService = session.getGateway().getFacility(TablesFacility.class);
        final TableData table = tableService.getTable(session.getSecurityContext(), tableID, 0, Integer.MAX_VALUE - 1);
        final TableDataColumn[] omeroColumns = table.getColumns();
        final Object[][] data = table.getData();
        final Table<?, ?> imageJTable = TableUtils.createImageJTable(omeroColumns);
        imageJTable.setRowCount((int) table.getNumberOfRows());
        boolean colsCreated = false;
        if (!(imageJTable instanceof GenericTable)) {
            imageJTable.appendColumns(omeroColumns.length);
            colsCreated = true;
        }
        for (int i = 0; i < omeroColumns.length; i++) {
            if (!colsCreated) {
                final Column<?> imageJCol = TableUtils.createImageJColumn(omeroColumns[i]);
                TableUtils.populateImageJColumn(omeroColumns[i].getType(), data[omeroColumns[i].getIndex()], imageJCol);
                ((GenericTable) imageJTable).add(omeroColumns[i].getIndex(), imageJCol);
            } else {
                TableUtils.populateImageJColumn(omeroColumns[i].getType(), data[omeroColumns[i].getIndex()], imageJTable.get(i));
                imageJTable.get(i).setHeader(omeroColumns[i].getName());
            }
        }
        return imageJTable;
    }
}

Example 4 with TablesFacility

use of omero.gateway.facility.TablesFacility in project imagej-omero by imagej.

the class ModuleAdapter method attachTablesToImages.

/**
 * Attaches the tables to the input images. This also adds the Table ids to
 * the omero client.
 */
private void attachTablesToImages(final List<ImageData> images, final HashMap<String, TableData> tables, final SecurityContext ctx, final DataManagerFacility dm) throws DSOutOfServiceException, DSAccessException, ExecutionException, ServerError {
    final TablesFacility tablesFacility = gateway.getFacility(TablesFacility.class);
    for (final String name : tables.keySet()) {
        final TableData t = tablesFacility.addTable(ctx, images.get(0), name, tables.get(name));
        client.setOutput(name, omero.rtypes.rlong(t.getOriginalFileId()));
    }
    // Adding tables again would create new tables on the server
    for (int i = 1; i < images.size(); i++) {
        for (final String name : tables.keySet()) {
            final OriginalFile file = new OriginalFileI(tables.get(name).getOriginalFileId(), false);
            final FileAnnotation anno = new FileAnnotationI();
            anno.setFile(file);
            FileAnnotationData annotation = new FileAnnotationData(anno);
            annotation.setDescription(name);
            annotation = (FileAnnotationData) dm.saveAndReturnObject(ctx, annotation);
            dm.attachAnnotation(ctx, annotation, images.get(i));
        }
    }
}