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

Example 6 with DefaultAlignment

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

the class AppSchemaMappingTest method testXrefJoinHandler.

@Test
public void testXrefJoinHandler() {
    DefaultCell joinCell = buildJoinCell(null);
    // create minimal alignment and pass it to JoinHandler
    DefaultCell renameCell = new DefaultCell();
    renameCell.setTransformationIdentifier(RenameFunction.ID);
    renameCell.setSource(getUnitIdSourceProperty(unitDenormType));
    renameCell.setTarget(getNestedUnitHrefTargetProperty());
    DefaultAlignment alignment = new DefaultAlignment();
    alignment.addCell(joinCell);
    alignment.addCell(renameCell);
    processJoinAlignment(alignment, null);
    // logMapping(mappingWrapper.getMainMapping());
    List<FeatureTypeMapping> ftMappings = mappingWrapper.getMainMapping().getTypeMappings().getFeatureTypeMapping();
    assertEquals(2, ftMappings.size());
    FeatureTypeMapping lcdMapping = null, lcuMapping = null;
    for (FeatureTypeMapping ftMapping : ftMappings) {
        if (SOURCE_DATASET.equals(ftMapping.getSourceType()) && "lcv:LandCoverDataset".equals(ftMapping.getTargetElement())) {
            lcdMapping = ftMapping;
        }
        if (SOURCE_UNIT_DENORM.equals(ftMapping.getSourceType()) && "lcv:LandCoverUnit".equals(ftMapping.getTargetElement())) {
            lcuMapping = ftMapping;
        }
    }
    assertNotNull(lcdMapping);
    assertNotNull(lcuMapping);
    // check feature chaining configuration
    List<AttributeMappingType> lcdAttrMappings = lcdMapping.getAttributeMappings().getAttributeMapping();
    List<AttributeMappingType> lcuAttrMappings = lcuMapping.getAttributeMappings().getAttributeMapping();
    assertNotNull(lcdAttrMappings);
    assertNotNull(lcuAttrMappings);
    assertEquals(1, lcdAttrMappings.size());
    assertEquals(1, lcuAttrMappings.size());
    AttributeMappingType containerMapping = lcdAttrMappings.get(0);
    assertEquals("lcv:member", containerMapping.getTargetAttribute());
    assertEquals("lcv:LandCoverUnit", containerMapping.getSourceExpression().getLinkElement());
    assertEquals("FEATURE_LINK[1]", containerMapping.getSourceExpression().getLinkField());
    assertEquals(SOURCE_DATASET_ID, containerMapping.getSourceExpression().getOCQL());
    assertTrue(containerMapping.isIsMultiple());
    assertNotNull(containerMapping.getClientProperty());
    assertEquals(1, containerMapping.getClientProperty().size());
    assertEquals("xlink:href", containerMapping.getClientProperty().get(0).getName());
    assertEquals(SOURCE_UNIT_ID, containerMapping.getClientProperty().get(0).getValue());
    AttributeMappingType nestedMapping = lcuAttrMappings.get(0);
    assertEquals("FEATURE_LINK[1]", nestedMapping.getTargetAttribute());
    assertEquals(SOURCE_DATASET_ID, nestedMapping.getSourceExpression().getOCQL());
    assertNull(nestedMapping.getSourceExpression().getLinkElement());
    assertNull(nestedMapping.getSourceExpression().getLinkField());
}

Example 7 with DefaultAlignment

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

the class AppSchemaMappingTest method testFeatureChainingJoin.

@Test
public void testFeatureChainingJoin() throws Exception {
    FeatureChaining chainingConf = readFeatureChainingConfiguration(FEATURE_CHAINING_CONF_PATH);
    assertNotNull(chainingConf);
    DefaultCell joinCell = buildJoinCell(chainingConf);
    // create minimal alignment and pass it to JoinHandler
    DefaultAlignment alignment = new DefaultAlignment();
    alignment.addCell(joinCell);
    DefaultCell renameCell = new DefaultCell();
    renameCell.setTransformationIdentifier(RenameFunction.ID);
    renameCell.setSource(getUuidSourceProperty(unitType));
    renameCell.setTarget(getNestedUnitLocalIdTargetProperty());
    alignment.addCell(renameCell);
    DefaultCell renameClassCell = new DefaultCell();
    renameClassCell.setTransformationIdentifier(RenameFunction.ID);
    renameClassCell.setSource(getObservationClassSourceProperty());
    renameClassCell.setTarget(getNestedObservationClassTargetProperty());
    alignment.addCell(renameClassCell);
    processJoinAlignment(alignment, chainingConf);
    // logMapping(mappingWrapper.getMainMapping());
    // logMapping(mappingWrapper.getIncludedTypesMapping());
    List<FeatureTypeMapping> mainMappings = mappingWrapper.getMainMapping().getTypeMappings().getFeatureTypeMapping();
    assertEquals(2, mainMappings.size());
    List<FeatureTypeMapping> includedMappings = mappingWrapper.getIncludedTypesMapping().getTypeMappings().getFeatureTypeMapping();
    assertEquals(1, includedMappings.size());
    FeatureTypeMapping obsMapping = includedMappings.get(0);
    assertTrue(SOURCE_OBSERVATION.equals(obsMapping.getSourceType()) && "lcv:LandCoverObservation".equals(obsMapping.getTargetElement()));
    FeatureTypeMapping lcdMapping = null, lcuMapping = null;
    for (FeatureTypeMapping ftMapping : mainMappings) {
        if (SOURCE_DATASET.equals(ftMapping.getSourceType()) && "lcv:LandCoverDataset".equals(ftMapping.getTargetElement())) {
            lcdMapping = ftMapping;
        }
        if (SOURCE_UNIT.equals(ftMapping.getSourceType()) && "lcv:LandCoverUnit".equals(ftMapping.getTargetElement())) {
            lcuMapping = ftMapping;
        }
    }
    assertNotNull(lcdMapping);
    assertNotNull(lcuMapping);
    // check feature chaining configuration
    List<AttributeMappingType> lcdAttrMappings = lcdMapping.getAttributeMappings().getAttributeMapping();
    List<AttributeMappingType> lcuAttrMappings = lcuMapping.getAttributeMappings().getAttributeMapping();
    List<AttributeMappingType> obsAttrMappings = obsMapping.getAttributeMappings().getAttributeMapping();
    assertNotNull(lcdAttrMappings);
    assertNotNull(lcuAttrMappings);
    assertNotNull(obsAttrMappings);
    assertEquals(1, lcdAttrMappings.size());
    assertEquals(3, lcuAttrMappings.size());
    assertEquals(2, obsAttrMappings.size());
    // NOTE: the order of attribute mappings is predictable, as it follows
    // the order of join conditions
    AttributeMappingType datasetContainerMapping = lcdAttrMappings.get(0);
    assertEquals("lcv:member", datasetContainerMapping.getTargetAttribute());
    assertEquals("lcv:LandCoverUnit", datasetContainerMapping.getSourceExpression().getLinkElement());
    assertEquals("FEATURE_LINK[1]", datasetContainerMapping.getSourceExpression().getLinkField());
    assertEquals(SOURCE_DATASET_ID, datasetContainerMapping.getSourceExpression().getOCQL());
    assertTrue(datasetContainerMapping.isIsMultiple());
    AttributeMappingType unitNestedMapping = lcuAttrMappings.get(0);
    assertEquals("FEATURE_LINK[1]", unitNestedMapping.getTargetAttribute());
    assertEquals(SOURCE_DATASET_ID, unitNestedMapping.getSourceExpression().getOCQL());
    assertNull(unitNestedMapping.getSourceExpression().getLinkElement());
    assertNull(unitNestedMapping.getSourceExpression().getLinkField());
    assertNull(unitNestedMapping.isIsMultiple());
    AttributeMappingType unitContainerMapping = lcuAttrMappings.get(1);
    assertEquals("lcv:landCoverObservation", unitContainerMapping.getTargetAttribute());
    assertEquals(SOURCE_UNIT_ID, unitContainerMapping.getSourceExpression().getOCQL());
    assertEquals("lcv:LandCoverObservation", unitContainerMapping.getSourceExpression().getLinkElement());
    assertEquals("FEATURE_LINK[1]", unitContainerMapping.getSourceExpression().getLinkField());
    assertTrue(unitContainerMapping.isIsMultiple());
    AttributeMappingType unitLocalIdMapping = lcuAttrMappings.get(2);
    assertEquals(TARGET_LOCAL_ID, unitLocalIdMapping.getTargetAttribute());
    assertEquals(SOURCE_UUID_V1, unitLocalIdMapping.getSourceExpression().getOCQL());
    assertNull(unitLocalIdMapping.getSourceExpression().getLinkElement());
    assertNull(unitLocalIdMapping.getSourceExpression().getLinkField());
    assertNull(unitLocalIdMapping.isIsMultiple());
    AttributeMappingType observationNestedMapping = obsAttrMappings.get(0);
    assertEquals("FEATURE_LINK[1]", observationNestedMapping.getTargetAttribute());
    assertEquals(SOURCE_OBS_UNIT_ID, observationNestedMapping.getSourceExpression().getOCQL());
    assertNull(observationNestedMapping.getSourceExpression().getLinkElement());
    assertNull(observationNestedMapping.getSourceExpression().getLinkField());
    assertNull(observationNestedMapping.isIsMultiple());
    AttributeMappingType observationClassMapping = obsAttrMappings.get(1);
    assertEquals("lcv:class", observationClassMapping.getTargetAttribute());
    assertEquals(SOURCE_OBS_CLASS, observationClassMapping.getSourceExpression().getOCQL());
    assertNull(observationClassMapping.getSourceExpression().getLinkElement());
    assertNull(observationClassMapping.getSourceExpression().getLinkField());
    assertNull(observationClassMapping.isIsMultiple());
}

Example 8 with DefaultAlignment

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

the class GenerateDefaults method generateMapping.

private void generateMapping() {
    System.out.println("Generating default value mapping cells for");
    // collect all ADE feature types
    List<TypeDefinition> featureTypes = BGISAppUtil.getADEFeatureTypes(schema);
    // visit ADE properties and create cells
    DefaultsVisitor defs = new DefaultsVisitor(defaultValues);
    for (TypeDefinition type : featureTypes) {
        System.out.println(type.getDisplayName() + "...");
        defs.accept(new TypeEntityDefinition(type, SchemaSpaceID.TARGET, null));
    }
    if (defs.getCells().isEmpty()) {
        System.out.println("WARNING: no cells were created");
    } else {
        System.out.println(defs.getCells().size() + " cells were created.");
    }
    // create alignment
    MutableAlignment align = new DefaultAlignment();
    for (MutableCell cell : defs.getCells()) {
        align.addCell(cell);
    }
    this.alignment = align;
}

Example 9 with DefaultAlignment

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

the class GenerateDuplicates method generateMapping.

private void generateMapping() {
    System.out.println("Indexing example cells...");
    // index all cells based on the target property name
    SetMultimap<String, Cell> exampleCells = HashMultimap.create();
    for (Cell cell : examples.getCells()) {
        if (cell.getTarget().size() == 1) {
            // only supports cells with one target
            EntityDefinition entityDef = CellUtil.getFirstEntity(cell.getTarget()).getDefinition();
            if (entityDef.getDefinition() instanceof PropertyDefinition) {
                if (ADE_NS.equals(entityDef.getDefinition().getName().getNamespaceURI())) {
                    exampleCells.put(entityDef.getDefinition().getName().getLocalPart(), cell);
                } else
                    System.out.println("WARNING: ignoring cell with non-ADE target property");
            } else
                System.out.println("WARNING: ignoring type cell");
        } else
            System.out.println("WARNING: ignoring cell with multiple or no targets");
    }
    // collect all ADE feature types
    List<TypeDefinition> featureTypes = BGISAppUtil.getADEFeatureTypes(targetSchema);
    // visit ADE properties and create cells
    System.out.println("Generating mapping from example cells for");
    String cellNote = MessageFormat.format("Generated through duplication of example cells on BGIS ADE feature types.\n" + "{0,date,medium}", new Date());
    DuplicateVisitor visitor = new DuplicateVisitor(exampleCells, cellNote);
    for (TypeDefinition type : featureTypes) {
        System.out.println(type.getDisplayName() + "...");
        visitor.accept(new TypeEntityDefinition(type, SchemaSpaceID.TARGET, null));
    }
    if (visitor.getCells().isEmpty()) {
        System.out.println("WARNING: no cells were created");
    } else {
        System.out.println(visitor.getCells().size() + " cells were created.");
    }
    // create alignment
    MutableAlignment align = new DefaultAlignment();
    for (MutableCell cell : visitor.getCells()) {
        align.addCell(cell);
    }
    this.alignment = align;
}

Example 10 with DefaultAlignment

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

the class DefaultAlignmentMigrator method updateAligmment.

@Override
public MutableAlignment updateAligmment(Alignment originalAlignment, AlignmentMigration migration, MigrationOptions options, SimpleLog log) {
    MutableAlignment result = new DefaultAlignment(originalAlignment);
    // XXX TODO adapt custom functions?!
    // result.getCustomPropertyFunctions();
    Collection<? extends Cell> cellList = new ArrayList<>(result.getCells());
    for (Cell cell : cellList) {
        // XXX
        if (cell instanceof MutableCell) {
            CellMigrator cm = getCellMigrator(cell.getTransformationIdentifier());
            MutableCell newCell = cm.updateCell(cell, migration, options, log);
            MigrationUtil.removeIdPrefix(newCell, options.transferBase(), options.transferBase());
            result.removeCell(cell);
            if (newCell != null) {
                result.addCell(newCell);
            }
        } else {
            // XXX can we deal with other cases? (Base alignment cells)
            if (options.transferBase()) {
                // include base alignment cell as mutable mapping cell
                CellMigrator cm = getCellMigrator(cell.getTransformationIdentifier());
                MutableCell newCell = cm.updateCell(cell, migration, options, log);
                MigrationUtil.removeIdPrefix(newCell, true, true);
                result.removeCell(cell);
                if (newCell != null) {
                    result.addCell(newCell);
                }
            }
        }
    }
    if (options.transferBase()) {
        MigrationUtil.removeBaseCells(result);
    } else {
    // does something need to be done to correctly retain base
    // alignments?
    }
    return result;
}