Examples with DefaultCell eu.esdihumboldt.hale.common.align.model.impl.DefaultCell used on opensource projects

Example 36 with DefaultCell

use of eu.esdihumboldt.hale.common.align.model.impl.DefaultCell in project hale by halestudio.

the class DefaultCellMigrator method updateCell.

@Override
public MutableCell updateCell(final Cell originalCell, final AlignmentMigration migration, final MigrationOptions options, SimpleLog log) {
    MutableCell result = new DefaultCell(originalCell);
    SimpleLog cellLog = SimpleLog.all(log, new CellLog(result, CELL_LOG_CATEGORY));
    final AtomicBoolean replacedEntities = new AtomicBoolean(false);
    EntryTransformer<String, Entity, Entity> entityTransformer = new EntryTransformer<String, Entity, Entity>() {

        @Override
        public Entity transformEntry(String key, Entity value) {
            EntityDefinition org = value.getDefinition();
            Optional<EntityDefinition> replace = migration.entityReplacement(org, cellLog);
            EntityDefinition entity = replace.orElse(org);
            if (!Objects.equal(entity, org)) {
                replacedEntities.set(true);
            }
            if (entity instanceof PropertyEntityDefinition) {
                return new DefaultProperty((PropertyEntityDefinition) entity);
            } else if (entity instanceof TypeEntityDefinition) {
                return new DefaultType((TypeEntityDefinition) entity);
            } else {
                throw new IllegalStateException("Invalid entity definition for creating entity");
            }
        }
    };
    // update source entities
    if (options.updateSource() && result.getSource() != null && !result.getSource().isEmpty()) {
        result.setSource(ArrayListMultimap.create(Multimaps.transformEntries(result.getSource(), entityTransformer)));
    }
    // update target entities
    if (options.updateTarget() && result.getTarget() != null && !result.getTarget().isEmpty()) {
        result.setTarget(ArrayListMultimap.create(Multimaps.transformEntries(result.getTarget(), entityTransformer)));
    }
    // TODO anything else?
    postUpdateCell(result, options, replacedEntities.get(), cellLog);
    return result;
}

Example 37 with DefaultCell

use of eu.esdihumboldt.hale.common.align.model.impl.DefaultCell in project hale by halestudio.

the class EffectiveMapping method expand.

/**
 * Convert an alignment into an expanded version where all effective
 * mappings are defined explicitly, i.e. mappings effective due to
 * inheritance are converted to use the respective sub-types. Also, base
 * alignment cells are converted into normal cells.
 *
 * @param alignment the alignment to convert
 * @return the expanded copy of the alignment
 */
public static MutableAlignment expand(Alignment alignment) {
    MutableAlignment result = new DefaultAlignment(alignment);
    // remove base alignment cells keeping custom functions
    MigrationUtil.removeBaseCells(result);
    // remove other cells
    result.clearCells();
    // transfer cells based on effective mapping
    // set of all cells used as they are in the resulting alignment
    Set<Cell> usedAsIs = new HashSet<>();
    for (Cell typeCell : alignment.getTypeCells()) {
        // transfer type cell unchanged
        MutableCell typeCellNew = new DefaultCell(typeCell);
        MigrationUtil.removeIdPrefix(typeCellNew, true, true);
        result.addCell(typeCellNew);
        usedAsIs.add(typeCell);
        Collection<? extends Cell> propertyCells = alignment.getPropertyCells(typeCell, true, false);
        for (Cell propertyCell : propertyCells) {
            // FIXME what does this do in case of a join where there are
            // potentially multiple cells to be handled?
            Cell reparented = AlignmentUtil.reparentCell(propertyCell, typeCell, true);
            if (reparented == propertyCell) {
                // use as is
                if (!usedAsIs.contains(propertyCell)) {
                    // only add if not done yet
                    // transfer unchanged
                    MutableCell newCell = new DefaultCell(propertyCell);
                    MigrationUtil.removeIdPrefix(newCell, true, true);
                    result.addCell(newCell);
                    usedAsIs.add(propertyCell);
                }
            } else {
                // inherited cell
                // add the reparented cell
                // TODO check if similar cell has been added already?
                MutableCell rCell = (MutableCell) reparented;
                MigrationUtil.removeIdPrefix(rCell, true, true);
                // avoid ID collision
                // no updates needed in other places because it's a property
                // cell
                rCell.setId(rCell.getId() + '_' + typeCellNew.getId());
                result.addCell(rCell);
            }
        }
    }
    return result;
}

Example 38 with DefaultCell

use of eu.esdihumboldt.hale.common.align.model.impl.DefaultCell in project hale by halestudio.

the class DefaultAlignmentIOTest method testSaveLoad.

/**
 * Test saving and loading an example alignment
 *
 * @throws Exception if an error occurs
 */
@Test
public void testSaveLoad() throws Exception {
    // populate alignment
    MutableAlignment align = new DefaultAlignment();
    DefaultSchema source = new DefaultSchema("", null);
    DefaultSchema target = new DefaultSchema("", null);
    // cell 1
    MutableCell cell1 = new DefaultCell();
    String id1;
    cell1.setTransformationIdentifier(id1 = "trans1");
    ListMultimap<String, ParameterValue> parameters1 = LinkedListMultimap.create();
    parameters1.put("test", new ParameterValue("1"));
    parameters1.put("test", new ParameterValue("2"));
    parameters1.put("t", new ParameterValue("3"));
    cell1.setTransformationParameters(parameters1);
    if (supportsTransformationModes()) {
        cell1.setTransformationMode(TransformationMode.passive);
    }
    ListMultimap<String, Type> source1 = ArrayListMultimap.create();
    QName source1TypeName;
    String source1EntityName;
    TypeDefinition sourceType1 = new DefaultTypeDefinition(source1TypeName = new QName("source1Type"));
    String filterText = "someproperty > 12";
    Filter filter = new FilterGeoCqlImpl(filterText);
    source1.put(source1EntityName = null, new DefaultType(new TypeEntityDefinition(sourceType1, SchemaSpaceID.SOURCE, filter)));
    cell1.setSource(source1);
    source.addType(sourceType1);
    ListMultimap<String, Type> target1 = ArrayListMultimap.create();
    QName target1TypeName;
    String target1EntityName;
    TypeDefinition targetType1 = new DefaultTypeDefinition(target1TypeName = new QName("http://some.name.space/t1", "target1Type"));
    target1.put(target1EntityName = "Some name", new DefaultType(new TypeEntityDefinition(targetType1, SchemaSpaceID.TARGET, null)));
    cell1.setTarget(target1);
    target.addType(targetType1);
    align.addCell(cell1);
    // cell 2
    MutableCell cell2 = new DefaultCell();
    String id2;
    cell2.setTransformationIdentifier(id2 = "trans2");
    ListMultimap<String, ParameterValue> parameters2 = LinkedListMultimap.create();
    parameters2.put("test", new ParameterValue("4"));
    parameters2.put("tx", new ParameterValue("5"));
    parameters2.put("tx", new ParameterValue("6"));
    // complex parameter value
    if (supportsComplexParameters()) {
        TestAnnotation commentParam = new TestAnnotation();
        commentParam.setAuthor("Gerd");
        commentParam.setComment("Should a comment really be used as parameter?");
        parameters2.put("comment", new ParameterValue(Value.complex(commentParam)));
    }
    cell2.setTransformationParameters(parameters2);
    ListMultimap<String, Type> target2 = ArrayListMultimap.create();
    TypeDefinition targetType2 = new DefaultTypeDefinition(new QName("target2Type"));
    target2.put("Some other name", new DefaultType(new TypeEntityDefinition(targetType2, SchemaSpaceID.TARGET, null)));
    cell2.setTarget(target2);
    target.addType(targetType2);
    align.addCell(cell2);
    TestAnnotation ann1 = null;
    TestAnnotation ann2 = null;
    if (supportsAnnotations()) {
        // add some annotations
        ann1 = (TestAnnotation) cell2.addAnnotation("test");
        ann1.setAuthor("Simon");
        ann1.setComment("I have really no idea what I did here");
        ann2 = (TestAnnotation) cell2.addAnnotation("test");
        ann2.setAuthor("Hans");
        ann2.setComment("Me neither");
    }
    String doc1 = "This cell was created in memory of...\nSorry, forgotten.";
    String tag1 = "This is a tag";
    String tag2 = "awesome";
    if (supportsDocumentation()) {
        cell1.getDocumentation().put(null, doc1);
        cell1.getDocumentation().put("tag", tag1);
        cell1.getDocumentation().put("tag", tag2);
    }
    // write alignment
    File alignmentFile = tmp.newFile("alignment.xml");
    System.out.println(alignmentFile.getAbsolutePath());
    saveAlignment(align, new BufferedOutputStream(new FileOutputStream(alignmentFile)));
    // load alignment
    // TODO use and check reporter?
    MutableAlignment align2 = loadAlignment(new FileInputStream(alignmentFile), source, target);
    // compare loaded alignment
    Collection<? extends Cell> cells = align2.getCells();
    assertFalse(cells.isEmpty());
    Iterator<? extends Cell> it = cells.iterator();
    // cell 1
    Cell ncell1 = it.next();
    assertNotNull(ncell1);
    assertEquals(id1, ncell1.getTransformationIdentifier());
    // documentation
    if (supportsDocumentation()) {
        assertEquals(3, ncell1.getDocumentation().size());
        assertEquals(doc1, ncell1.getDocumentation().get(null).get(0));
        assertEquals(tag1, ncell1.getDocumentation().get("tag").get(0));
        assertEquals(tag2, ncell1.getDocumentation().get("tag").get(1));
    }
    if (supportsTransformationModes()) {
        assertEquals(TransformationMode.passive, ncell1.getTransformationMode());
    }
    // source 1
    ListMultimap<String, ? extends Entity> source1Entities = ncell1.getSource();
    assertEquals(1, source1Entities.size());
    List<? extends Entity> s1list = source1Entities.get(source1EntityName);
    assertFalse(s1list.isEmpty());
    assertEquals(source1TypeName, s1list.get(0).getDefinition().getDefinition().getName());
    // filter
    assertEquals(filter, s1list.get(0).getDefinition().getFilter());
    // target 1
    ListMultimap<String, ? extends Entity> target1Entities = ncell1.getTarget();
    assertEquals(1, target1Entities.size());
    List<? extends Entity> t1list = target1Entities.get(target1EntityName);
    assertFalse(t1list.isEmpty());
    assertEquals(target1TypeName, t1list.get(0).getDefinition().getDefinition().getName());
    // cell 2
    Cell ncell2 = it.next();
    assertNotNull(ncell2);
    assertEquals(id2, ncell2.getTransformationIdentifier());
    // parameters
    ListMultimap<String, ParameterValue> param2 = ncell2.getTransformationParameters();
    if (!supportsComplexParameters()) {
        assertEquals(2, param2.keySet().size());
        assertEquals(3, param2.values().size());
    } else {
        assertEquals(3, param2.keySet().size());
        assertEquals(4, param2.values().size());
        ParameterValue complexParam = param2.get("comment").get(0);
        assertTrue(complexParam.getValue() instanceof TestAnnotation);
    }
    // annotations
    if (supportsAnnotations()) {
        List<?> annotations = ncell2.getAnnotations("test");
        assertEquals(2, annotations.size());
        TestAnnotation nann1 = (TestAnnotation) annotations.get(0);
        assertEquals(ann1, nann1);
        TestAnnotation nann2 = (TestAnnotation) annotations.get(1);
        assertEquals(ann2, nann2);
    }
}

Example 39 with DefaultCell

use of eu.esdihumboldt.hale.common.align.model.impl.DefaultCell in project hale by halestudio.

the class DefaultAlignmentIOTest method testCellDisableSaveLoad.

/**
 * Tests cell disable save and load.
 *
 * @throws Exception if an error occurs
 */
@Test
public void testCellDisableSaveLoad() throws Exception {
    DefaultAlignment baseAlignment = new DefaultAlignment();
    MutableAlignment alignment = new DefaultAlignment();
    Schema schema = TestUtil.loadSchema(getClass().getResource("/testdata/simple/t1.xsd").toURI());
    Iterator<? extends TypeDefinition> iter = schema.getMappingRelevantTypes().iterator();
    TypeDefinition t = iter.next();
    if (!t.getName().getLocalPart().equals("T1")) {
        t = iter.next();
    }
    // generate base alignment
    DefaultCell cell1 = new DefaultCell();
    cell1.setTransformationIdentifier("trans1");
    ListMultimap<String, Type> source = ArrayListMultimap.create();
    source.put(null, new DefaultType(new TypeEntityDefinition(t, SchemaSpaceID.SOURCE, null)));
    cell1.setSource(source);
    ListMultimap<String, Type> target = ArrayListMultimap.create();
    target.put(null, new DefaultType(new TypeEntityDefinition(t, SchemaSpaceID.TARGET, null)));
    cell1.setTarget(target);
    DefaultCell cell2 = new DefaultCell();
    cell2.setTransformationIdentifier("trans2");
    List<ChildContext> childContext2 = new ArrayList<ChildContext>();
    PropertyDefinition child2 = DefinitionUtil.getChild(t, new QName("a1")).asProperty();
    childContext2.add(new ChildContext(child2));
    ListMultimap<String, Property> source2 = ArrayListMultimap.create();
    source2.put(null, new DefaultProperty(new PropertyEntityDefinition(t, childContext2, SchemaSpaceID.SOURCE, null)));
    cell2.setSource(source2);
    ListMultimap<String, Property> target2 = ArrayListMultimap.create();
    target2.put(null, new DefaultProperty(new PropertyEntityDefinition(t, childContext2, SchemaSpaceID.TARGET, null)));
    cell2.setTarget(target2);
    DefaultCell cell3 = new DefaultCell();
    cell3.setTransformationIdentifier("trans3");
    List<ChildContext> childContext3 = new ArrayList<ChildContext>();
    PropertyDefinition child3 = DefinitionUtil.getChild(t, new QName("b1")).asProperty();
    childContext3.add(new ChildContext(child3));
    ListMultimap<String, Property> source3 = ArrayListMultimap.create();
    source3.put(null, new DefaultProperty(new PropertyEntityDefinition(t, childContext3, SchemaSpaceID.SOURCE, null)));
    cell3.setSource(source3);
    ListMultimap<String, Property> target3 = ArrayListMultimap.create();
    target3.put(null, new DefaultProperty(new PropertyEntityDefinition(t, childContext3, SchemaSpaceID.TARGET, null)));
    cell3.setTarget(target3);
    baseAlignment.addCell(cell1);
    baseAlignment.addCell(cell2);
    String baseDisableCellId = cell2.getId();
    baseAlignment.addCell(cell3);
    String extendedDisableCellId = cell3.getId();
    assertEquals(3, baseAlignment.getCells().size());
    Cell typeCell = baseAlignment.getTypeCells().iterator().next();
    assertEquals(2, baseAlignment.getPropertyCells(typeCell).size());
    // test disable, it should not be with the related property cells
    cell2.setDisabledFor(cell1, true);
    assertEquals(1, baseAlignment.getPropertyCells(typeCell).size());
    assertTrue(cell2.getDisabledFor().contains(cell1.getId()));
    cell2.setDisabledFor(cell1, false);
    assertFalse(cell2.getDisabledFor().contains(cell1.getId()));
    cell2.setDisabledFor(cell1, true);
    assertEquals(1, baseAlignment.getPropertyCells(typeCell).size());
    // save base alignment
    File baseAlignmentFile = tmp.newFile("alignment_base.xml");
    System.out.println(baseAlignmentFile.getAbsolutePath());
    saveAlignment(baseAlignment, new BufferedOutputStream(new FileOutputStream(baseAlignmentFile)));
    // load base alignment
    MutableAlignment baseAlignment2 = loadAlignment(new FileInputStream(baseAlignmentFile), schema, schema);
    typeCell = baseAlignment2.getTypeCells().iterator().next();
    assertEquals(3, baseAlignment2.getCells().size());
    // test again that it is still disabled
    assertEquals(1, baseAlignment2.getPropertyCells(typeCell).size());
    // disable the remaining enabled cell in extended alignment
    addBaseAlignment(alignment, baseAlignmentFile.toURI(), schema, schema);
    assertEquals(1, alignment.getBaseAlignments().size());
    String usedPrefix = alignment.getBaseAlignments().keySet().iterator().next();
    File alignmentFile = tmp.newFile("alignment_extended.xml");
    // check cells
    typeCell = alignment.getTypeCells().iterator().next();
    assertEquals(3, alignment.getCells().size());
    assertEquals(1, alignment.getPropertyCells(typeCell).size());
    // disable remaining cell
    ((ModifiableCell) alignment.getPropertyCells(typeCell, false, false).iterator().next()).setDisabledFor(typeCell, true);
    assertEquals(0, alignment.getPropertyCells(typeCell).size());
    // save / load extended alignment
    System.out.println(alignmentFile.getAbsolutePath());
    saveAlignment(alignment, new BufferedOutputStream(new FileOutputStream(alignmentFile)));
    // load extended
    MutableAlignment alignment2 = loadAlignment(new FileInputStream(alignmentFile), schema, schema);
    typeCell = alignment2.getTypeCells().iterator().next();
    // test disabled again
    assertEquals(3, alignment2.getCells().size());
    // test again that it is still disabled
    assertEquals(0, alignment2.getPropertyCells(typeCell).size());
    // more specifically test whether the disables come from base alignment
    // or extended alignment
    Cell baseDisableCell = alignment2.getCell(usedPrefix + ":" + baseDisableCellId);
    Cell extendedDisableCell = alignment2.getCell(usedPrefix + ":" + extendedDisableCellId);
    assertTrue(baseDisableCell instanceof BaseAlignmentCell);
    assertEquals(1, baseDisableCell.getDisabledFor().size());
    assertEquals(1, ((BaseAlignmentCell) baseDisableCell).getBaseDisabledFor().size());
    assertEquals(0, ((BaseAlignmentCell) baseDisableCell).getAdditionalDisabledFor().size());
    assertTrue(extendedDisableCell instanceof BaseAlignmentCell);
    assertEquals(1, extendedDisableCell.getDisabledFor().size());
    assertEquals(0, ((BaseAlignmentCell) extendedDisableCell).getBaseDisabledFor().size());
    assertEquals(1, ((BaseAlignmentCell) extendedDisableCell).getAdditionalDisabledFor().size());
}

Example 40 with DefaultCell

use of eu.esdihumboldt.hale.common.align.model.impl.DefaultCell in project hale by halestudio.

the class MarkdownCellExplanationTest method createTestCell.

@SuppressWarnings("unused")
private Cell createTestCell() {
    // cell 1
    MutableCell cell1 = new DefaultCell();
    String id1;
    // must be an existing function
    cell1.setTransformationIdentifier(id1 = "eu.esdihumboldt.hale.align.formattedstring");
    ListMultimap<String, ParameterValue> parameters1 = LinkedListMultimap.create();
    // parameter that does not exist (for parameter list testing)
    parameters1.put("test", new ParameterValue("1"));
    parameters1.put("test", new ParameterValue("2"));
    // existing parameter
    parameters1.put("pattern", new ParameterValue("3"));
    cell1.setTransformationParameters(parameters1);
    ListMultimap<String, Type> source1 = ArrayListMultimap.create();
    QName source1TypeName;
    String source1EntityName;
    TypeDefinition sourceType1 = new DefaultTypeDefinition(source1TypeName = new QName("source1Type"));
    Filter filter = null;
    source1.put(source1EntityName = "var", new DefaultType(new TypeEntityDefinition(sourceType1, SchemaSpaceID.SOURCE, filter)));
    cell1.setSource(source1);
    ListMultimap<String, Type> target1 = ArrayListMultimap.create();
    QName target1TypeName;
    String target1EntityName;
    TypeDefinition targetType1 = new DefaultTypeDefinition(target1TypeName = new QName("http://some.name.space/t1", "target1Type"));
    target1.put(target1EntityName = null, new DefaultType(new TypeEntityDefinition(targetType1, SchemaSpaceID.TARGET, null)));
    cell1.setTarget(target1);
    return cell1;
}