Java tutorial
/* * Copyright (c) 2012 Data Harmonisation Panel * * All rights reserved. This program and the accompanying materials are made * available under the terms of the GNU Lesser General Public License as * published by the Free Software Foundation, either version 3 of the License, * or (at your option) any later version. * * You should have received a copy of the GNU Lesser General Public License * along with this distribution. If not, see <http://www.gnu.org/licenses/>. * * Contributors: * HUMBOLDT EU Integrated Project #030962 * Data Harmonisation Panel <http://www.dhpanel.eu> */ package eu.esdihumboldt.hale.common.align.io.impl.internal; import java.io.IOException; import java.io.InputStream; import java.net.URI; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.LinkedHashSet; import java.util.Map; import org.exolab.castor.mapping.Mapping; import org.exolab.castor.mapping.MappingException; import org.exolab.castor.xml.MarshalException; import org.exolab.castor.xml.Unmarshaller; import org.exolab.castor.xml.ValidationException; import org.exolab.castor.xml.XMLContext; import org.xml.sax.InputSource; import com.google.common.base.Function; import com.google.common.collect.Maps; import eu.esdihumboldt.hale.common.align.extension.function.custom.CustomPropertyFunction; import eu.esdihumboldt.hale.common.align.model.Alignment; import eu.esdihumboldt.hale.common.align.model.BaseAlignmentCell; import eu.esdihumboldt.hale.common.align.model.Cell; import eu.esdihumboldt.hale.common.align.model.MutableAlignment; import eu.esdihumboldt.hale.common.align.model.MutableCell; import eu.esdihumboldt.hale.common.align.model.TransformationMode; import eu.esdihumboldt.hale.common.core.io.PathUpdate; import eu.esdihumboldt.hale.common.core.io.report.IOReporter; import eu.esdihumboldt.hale.common.schema.model.TypeIndex; /** * Alignment bean serving as model for alignment I/O * * @author Simon Templer */ public class AlignmentBean extends AbstractBaseAlignmentLoader<AlignmentBean, CellBean, ModifierBean> { private Map<String, URI> base = new HashMap<String, URI>(); private Collection<CellBean> cells = new LinkedHashSet<CellBean>(); private Collection<ModifierBean> modifiers = new ArrayList<ModifierBean>(); /** * Default constructor */ public AlignmentBean() { super(); } /** * Create a bean for the given alignment * * @param alignment the alignment * @param pathUpdate to update relative paths in case of a path change */ public AlignmentBean(Alignment alignment, final PathUpdate pathUpdate) { super(); base = new HashMap<String, URI>( Maps.transformValues(alignment.getBaseAlignments(), new Function<URI, URI>() { @Override public URI apply(URI input) { return pathUpdate.findLocation(input, true, false, true); } })); // populate bean from alignment for (Cell cell : alignment.getCells()) { generateModifier(cell); if (cell instanceof BaseAlignmentCell) continue; CellBean cellBean = new CellBean(cell); cells.add(cellBean); } } /** * Load an AlignmentBean from an input stream. The stream is closed at the * end. * * @param in the input stream * @param reporter the I/O reporter to report any errors to, may be * <code>null</code> * @return the AlignmentBean * * @throws MappingException if the mapping could not be loaded * @throws MarshalException if the alignment could not be read * @throws ValidationException if the input stream did not provide valid XML */ public static AlignmentBean load(InputStream in, IOReporter reporter) throws MappingException, MarshalException, ValidationException { Mapping mapping = new Mapping(AlignmentBean.class.getClassLoader()); mapping.loadMapping(new InputSource(AlignmentBean.class.getResourceAsStream("AlignmentBean.xml"))); XMLContext context = new XMLContext(); context.addMapping(mapping); Unmarshaller unmarshaller = context.createUnmarshaller(); try { return (AlignmentBean) unmarshaller.unmarshal(new InputSource(in)); } finally { try { in.close(); } catch (IOException e) { // ignore } } } /** * Adds the given base alignment to the given alignment. * * @param alignment the alignment to add a base alignment to * @param newBase URI of the new base alignment * @param projectLocation the project location or <code>null</code> * @param sourceTypes the source types to use for resolving definition * references * @param targetTypes the target types to use for resolving definition * references * @param reporter the I/O reporter to report any errors to, may be * <code>null</code> * @throws IOException if adding the base alignment fails */ public static void addBaseAlignment(MutableAlignment alignment, URI newBase, URI projectLocation, TypeIndex sourceTypes, TypeIndex targetTypes, IOReporter reporter) throws IOException { new AlignmentBean().internalAddBaseAlignment(alignment, newBase, projectLocation, sourceTypes, targetTypes, reporter); } /** * Generates and adds a modifier for the given cell if necessary. * * @param cell the cell to generate a modifier for */ private void generateModifier(Cell cell) { Collection<String> disabledFor; if (cell instanceof BaseAlignmentCell) disabledFor = ((BaseAlignmentCell) cell).getAdditionalDisabledFor(); else disabledFor = cell.getDisabledFor(); if (!disabledFor.isEmpty()) { ModifierBean modifier = new ModifierBean(cell.getId()); modifier.setDisableForRelation(disabledFor); modifiers.add(modifier); } } /** * Create an alignment from the information in the bean. * * @param reporter the I/O reporter to report any errors to, may be * <code>null</code> * @param sourceTypes the source types to use for resolving definition * references * @param targetTypes the target types to use for resolving definition * references * @param updater the path updater to use for base alignments * @return the alignment * @throws IOException if creating the alignment fails */ public MutableAlignment createAlignment(IOReporter reporter, TypeIndex sourceTypes, TypeIndex targetTypes, PathUpdate updater) throws IOException { return super.createAlignment(this, sourceTypes, targetTypes, updater, reporter); } /** * Get the defined cells * * @return the cells */ public Collection<CellBean> getCells() { return cells; } /** * Set the defined cells * * @param cells the cells to set */ public void setCells(Collection<CellBean> cells) { this.cells = cells; } /** * Get the alignment modifiers * * @return the modifiers */ public Collection<ModifierBean> getModifiers() { return modifiers; } /** * Set the alignment modifiers * * @param modifiers the modifiers to set */ public void setModifiers(Collection<ModifierBean> modifiers) { this.modifiers = modifiers; } /** * @return the base */ public Map<String, URI> getBase() { return base; } /** * @param base the base to set */ public void setBase(Map<String, URI> base) { this.base = base; } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#loadAlignment(java.io.InputStream, * eu.esdihumboldt.hale.common.core.io.report.IOReporter) */ @Override protected AlignmentBean loadAlignment(InputStream in, IOReporter reporter) throws IOException { try { return load(in, reporter); } catch (MarshalException e) { throw new IOException(e); } catch (ValidationException e) { throw new IOException(e); } catch (MappingException e) { throw new IOException(e); } } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#getBases(java.lang.Object) */ @Override protected Map<String, URI> getBases(AlignmentBean alignment) { return alignment.base; } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#getCells(java.lang.Object) */ @Override protected Collection<CellBean> getCells(AlignmentBean alignment) { return alignment.cells; } @Override protected Collection<CustomPropertyFunction> getPropertyFunctions(AlignmentBean alignment, TypeIndex sourceTypes, TypeIndex targetTypes) { // not supported return Collections.emptyList(); } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#createCell(java.lang.Object, * eu.esdihumboldt.hale.common.schema.model.TypeIndex, * eu.esdihumboldt.hale.common.schema.model.TypeIndex, * eu.esdihumboldt.hale.common.core.io.report.IOReporter) */ @Override protected MutableCell createCell(CellBean cell, TypeIndex sourceTypes, TypeIndex targetTypes, IOReporter reporter) { return cell.createCell(reporter, sourceTypes, targetTypes); } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#getModifiers(java.lang.Object) */ @Override protected Collection<ModifierBean> getModifiers(AlignmentBean alignment) { return alignment.modifiers; } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#getModifiedCell(java.lang.Object) */ @Override protected String getModifiedCell(ModifierBean modifier) { return modifier.getCell(); } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#getDisabledForList(java.lang.Object) */ @Override protected Collection<String> getDisabledForList(ModifierBean modifier) { return modifier.getDisableForRelation(); } @Override protected TransformationMode getTransformationMode(ModifierBean modifier) { // not supported return null; } /** * @see eu.esdihumboldt.hale.common.align.io.impl.internal.AbstractBaseAlignmentLoader#getCellId(java.lang.Object) */ @Override protected String getCellId(CellBean cell) { return cell.getId(); } }