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Example 1 with CellType

use of eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CellType in project hale by halestudio.

the class TemplateProject method onSuccess.

@Override
protected void onSuccess(Void context, String projectId, File projectFile, Project project, ReportFile reportFile) {
    super.onSuccess(context, projectId, projectFile, project, reportFile);
    // update locations in project file
    LocationUpdater updater = new LocationUpdater(project, projectFile.toURI());
    updater.updateProject(false);
    resources.clear();
    List<Path> invalidSources = new ArrayList<>();
    Path projectFolder = getProjectFolder().toPath();
    // validate resources
    for (IOConfiguration config : project.getResources()) {
        Resource resource = new IOConfigurationResource(config, getProjectFile().toURI());
        // check if file URIs are valid and inside project folder
        URI source = resource.getSource();
        if (source != null) {
            Path path = null;
            if (source.getScheme() == null) {
                // is a relative URI
                path = projectFile.toPath().resolve(source.toString()).normalize();
            } else if ("file".equals(source.getScheme())) {
                // is a file URI
                path = Paths.get(source).normalize();
            }
            if (path != null) {
                if (!path.startsWith(projectFolder) || !Files.exists(path)) {
                    // invalid source
                    invalidSources.add(path);
                }
            }
        }
        resources.put(resource.getActionId(), resource);
    }
    valid = invalidSources.isEmpty();
    if (!valid) {
        StringBuilder builder = new StringBuilder("Files referenced by the project could not be found: ");
        for (int i = 0; i < invalidSources.size(); i++) {
            if (i > 0)
                builder.append(", ");
            Path path = invalidSources.get(i);
            builder.append(path.getFileName().toString());
        }
        notValidMessage = builder.toString();
    } else {
        notValidMessage = "";
    }
    // additionally, try to find out cell count
    definedRelations = 0;
    // check if default alignment file exists
    try {
        File defAlignmentFile = new File(URI.create(projectFile.toURI().toASCIIString() + "." + AlignmentIO.PROJECT_FILE_ALIGNMENT));
        if (defAlignmentFile.exists()) {
            try (InputStream in = new BufferedInputStream(new FileInputStream(defAlignmentFile))) {
                /*
					 * Try loading the file with JAXB - only supports 2.6+
					 * projects.
					 */
                AlignmentType alignment = JaxbToAlignment.load(in, null);
                // XXX ignoring base alignments
                int count = 0;
                for (Object element : alignment.getCellOrModifier()) {
                    if (element instanceof CellType) {
                        count++;
                    }
                }
                definedRelations = count;
            } catch (Exception e) {
            // ignore
            }
        }
    } catch (Exception e) {
    // ignore
    }
}
Also used : Path(java.nio.file.Path) LocationUpdater(eu.esdihumboldt.hale.common.core.io.project.util.LocationUpdater) IOConfiguration(eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration) BufferedInputStream(java.io.BufferedInputStream) FileInputStream(java.io.FileInputStream) InputStream(java.io.InputStream) ArrayList(java.util.ArrayList) IOConfigurationResource(eu.esdihumboldt.hale.common.core.io.project.model.IOConfigurationResource) Resource(eu.esdihumboldt.hale.common.core.io.project.model.Resource) IOConfigurationResource(eu.esdihumboldt.hale.common.core.io.project.model.IOConfigurationResource) URI(java.net.URI) FileInputStream(java.io.FileInputStream) IOException(java.io.IOException) AlignmentType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AlignmentType) BufferedInputStream(java.io.BufferedInputStream) CellType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CellType) ReportFile(eu.esdihumboldt.hale.common.headless.report.ReportFile) File(java.io.File)

Example 2 with CellType

use of eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CellType in project hale by halestudio.

the class JaxbAlignmentIO method printCell.

/**
 * Print a cell to an output stream (intended for tests/debugging).
 *
 * @param cell the cell to print
 * @param out the output stream
 * @throws Exception if an error occurs trying to print the cell
 */
public static void printCell(MutableCell cell, OutputStream out) throws Exception {
    DefaultAlignment alignment = new DefaultAlignment();
    alignment.addCell(cell);
    IOReporter reporter = new DefaultIOReporter(new Locatable() {

        @Override
        public URI getLocation() {
            return null;
        }
    }, "Print cell", null, false);
    PathUpdate pathUpdate = new PathUpdate(null, null);
    AlignmentType at = convert(alignment, reporter, pathUpdate);
    CellType ct = (CellType) at.getCellOrModifier().get(0);
    JAXBContext jc = JAXBContext.newInstance(ALIGNMENT_CONTEXT, ObjectFactory.class.getClassLoader());
    Marshaller m = jc.createMarshaller();
    m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
    ObjectFactory of = new ObjectFactory();
    try {
        m.marshal(of.createCell(ct), out);
    } finally {
        out.flush();
        out.close();
    }
}
Also used : AlignmentType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AlignmentType) DefaultIOReporter(eu.esdihumboldt.hale.common.core.io.report.impl.DefaultIOReporter) IOReporter(eu.esdihumboldt.hale.common.core.io.report.IOReporter) Marshaller(javax.xml.bind.Marshaller) DefaultIOReporter(eu.esdihumboldt.hale.common.core.io.report.impl.DefaultIOReporter) ObjectFactory(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ObjectFactory) CellType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CellType) PathUpdate(eu.esdihumboldt.hale.common.core.io.PathUpdate) DefaultAlignment(eu.esdihumboldt.hale.common.align.model.impl.DefaultAlignment) JAXBContext(javax.xml.bind.JAXBContext) URI(java.net.URI) Locatable(eu.esdihumboldt.hale.common.core.io.supplier.Locatable)

Example 3 with CellType

use of eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CellType in project hale by halestudio.

the class JaxbToAlignment method createUnmigratedCell.

private static UnmigratedCell createUnmigratedCell(CellType cell, LoadAlignmentContext context, IOReporter reporter, EntityResolver resolver, ServiceProvider serviceProvider) {
    // The sourceCell represents the cell as it was imported from the
    // XML alignment. The conversion to the resolved cell must be performed
    // later by migrating the UnmigratedCell returned from this function.
    final DefaultCell sourceCell = new DefaultCell();
    sourceCell.setTransformationIdentifier(cell.getRelation());
    final FunctionDefinition<?> cellFunction = FunctionUtil.getFunction(sourceCell.getTransformationIdentifier(), serviceProvider);
    final CellMigrator migrator;
    if (cellFunction != null) {
        migrator = cellFunction.getCustomMigrator().orElse(new DefaultCellMigrator());
    } else {
        migrator = new DefaultCellMigrator();
    }
    Map<EntityDefinition, EntityDefinition> mappings = new HashMap<>();
    try {
        // The returned Entity pair consists of
        // (1st) a dummy entity representing the entity read from JAXB
        // (2nd) the resolved entity
        ListMultimap<String, Pair<Entity, Entity>> convertedSourceEntities = convertEntities(cell.getSource(), context.getSourceTypes(), SchemaSpaceID.SOURCE, resolver);
        if (convertedSourceEntities == null) {
            sourceCell.setSource(null);
        } else {
            sourceCell.setSource(Multimaps.transformValues(convertedSourceEntities, pair -> pair.getFirst()));
            for (Pair<Entity, Entity> pair : convertedSourceEntities.values()) {
                mappings.put(pair.getFirst().getDefinition(), pair.getSecond().getDefinition());
            }
        }
        ListMultimap<String, Pair<Entity, Entity>> convertedTargetEntities = convertEntities(cell.getTarget(), context.getTargetTypes(), SchemaSpaceID.TARGET, resolver);
        if (convertedTargetEntities == null) {
            sourceCell.setTarget(null);
        } else {
            sourceCell.setTarget(Multimaps.transformValues(convertedTargetEntities, pair -> pair.getFirst()));
            for (Pair<Entity, Entity> pair : convertedTargetEntities.values()) {
                mappings.put(pair.getFirst().getDefinition(), pair.getSecond().getDefinition());
            }
        }
        if (sourceCell.getTarget() == null || sourceCell.getTarget().isEmpty()) {
            // target is mandatory for cells!
            throw new IllegalStateException("Cannot create cell without target");
        }
    } catch (Exception e) {
        if (reporter != null) {
            reporter.error(new IOMessageImpl("Could not create cell", e));
        }
        return null;
    }
    if (!cell.getAbstractParameter().isEmpty()) {
        ListMultimap<String, ParameterValue> parameters = ArrayListMultimap.create();
        for (JAXBElement<? extends AbstractParameterType> param : cell.getAbstractParameter()) {
            AbstractParameterType apt = param.getValue();
            if (apt instanceof ParameterType) {
                // treat string parameters or null parameters
                ParameterType pt = (ParameterType) apt;
                ParameterValue pv = new ParameterValue(pt.getType(), Value.of(pt.getValue()));
                parameters.put(pt.getName(), pv);
            } else if (apt instanceof ComplexParameterType) {
                // complex parameters
                ComplexParameterType cpt = (ComplexParameterType) apt;
                parameters.put(cpt.getName(), new ParameterValue(new ElementValue(cpt.getAny(), context)));
            } else
                throw new IllegalStateException("Illegal parameter type");
        }
        sourceCell.setTransformationParameters(parameters);
    }
    // annotations & documentation
    for (Object element : cell.getDocumentationOrAnnotation()) {
        if (element instanceof AnnotationType) {
            // add annotation to the cell
            AnnotationType annot = (AnnotationType) element;
            // but first load it from the DOM
            AnnotationDescriptor<?> desc = AnnotationExtension.getInstance().get(annot.getType());
            if (desc != null) {
                try {
                    Object value = desc.fromDOM(annot.getAny(), null);
                    sourceCell.addAnnotation(annot.getType(), value);
                } catch (Exception e) {
                    if (reporter != null) {
                        reporter.error(new IOMessageImpl("Error loading cell annotation", e));
                    } else
                        throw new IllegalStateException("Error loading cell annotation", e);
                }
            } else
                reporter.error(new IOMessageImpl("Cell annotation of type {0} unknown, cannot load the annotation object", null, -1, -1, annot.getType()));
        } else if (element instanceof DocumentationType) {
            // add documentation to the cell
            DocumentationType doc = (DocumentationType) element;
            sourceCell.getDocumentation().put(doc.getType(), doc.getValue());
        }
    }
    sourceCell.setId(cell.getId());
    // a default value is assured for priority
    String priorityStr = cell.getPriority().value();
    Priority priority = Priority.fromValue(priorityStr);
    if (priority != null) {
        sourceCell.setPriority(priority);
    } else {
        // used.
        throw new IllegalArgumentException();
    }
    return new UnmigratedCell(sourceCell, migrator, mappings);
}
Also used : ArrayListMultimap(com.google.common.collect.ArrayListMultimap) ListMultimap(com.google.common.collect.ListMultimap) CellMigrator(eu.esdihumboldt.hale.common.align.migrate.CellMigrator) Collections2(com.google.common.collect.Collections2) ModifierType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ModifierType) MutableAlignment(eu.esdihumboldt.hale.common.align.model.MutableAlignment) ElementValue(eu.esdihumboldt.hale.common.core.io.impl.ElementValue) HaleIO(eu.esdihumboldt.hale.common.core.io.HaleIO) DefaultCell(eu.esdihumboldt.hale.common.align.model.impl.DefaultCell) Map(java.util.Map) ParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ParameterType) Pair(eu.esdihumboldt.util.Pair) AnnotationDescriptor(eu.esdihumboldt.hale.common.align.model.AnnotationDescriptor) URI(java.net.URI) AnnotationExtension(eu.esdihumboldt.hale.common.align.extension.annotation.AnnotationExtension) Value(eu.esdihumboldt.hale.common.core.io.Value) Function(com.google.common.base.Function) Collection(java.util.Collection) UnmigratedCell(eu.esdihumboldt.hale.common.align.migrate.impl.UnmigratedCell) ParameterValue(eu.esdihumboldt.hale.common.align.model.ParameterValue) IOReporter(eu.esdihumboldt.hale.common.core.io.report.IOReporter) JAXBException(javax.xml.bind.JAXBException) LoadAlignmentContext(eu.esdihumboldt.hale.common.align.io.LoadAlignmentContext) PathUpdate(eu.esdihumboldt.hale.common.core.io.PathUpdate) SchemaSpaceID(eu.esdihumboldt.hale.common.schema.SchemaSpaceID) CustomFunctionType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CustomFunctionType) DummyEntityResolver(eu.esdihumboldt.hale.common.align.io.impl.dummy.DummyEntityResolver) List(java.util.List) Base(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AlignmentType.Base) ComplexParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ComplexParameterType) TypeIndex(eu.esdihumboldt.hale.common.schema.model.TypeIndex) CellType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CellType) Priority(eu.esdihumboldt.hale.common.align.model.Priority) StreamSource(javax.xml.transform.stream.StreamSource) AnnotationType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AnnotationType) HashMap(java.util.HashMap) DefaultCellMigrator(eu.esdihumboldt.hale.common.align.migrate.impl.DefaultCellMigrator) ArrayList(java.util.ArrayList) Multimaps(com.google.common.collect.Multimaps) JaxbAlignmentIO(eu.esdihumboldt.hale.common.align.io.impl.JaxbAlignmentIO) EntityResolver(eu.esdihumboldt.hale.common.align.io.EntityResolver) IOMessageImpl(eu.esdihumboldt.hale.common.core.io.report.impl.IOMessageImpl) MutableCell(eu.esdihumboldt.hale.common.align.model.MutableCell) DisableFor(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ModifierType.DisableFor) JAXBContext(javax.xml.bind.JAXBContext) Unmarshaller(javax.xml.bind.Unmarshaller) CustomPropertyFunction(eu.esdihumboldt.hale.common.align.extension.function.custom.CustomPropertyFunction) DocumentationType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.DocumentationType) JAXBElement(javax.xml.bind.JAXBElement) IOException(java.io.IOException) ServiceProvider(eu.esdihumboldt.hale.common.core.service.ServiceProvider) DefaultEntityResolver(eu.esdihumboldt.hale.common.align.io.impl.DefaultEntityResolver) Entity(eu.esdihumboldt.hale.common.align.model.Entity) FunctionUtil(eu.esdihumboldt.hale.common.align.extension.function.FunctionUtil) AbstractParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AbstractParameterType) TransformationMode(eu.esdihumboldt.hale.common.align.model.TransformationMode) FunctionDefinition(eu.esdihumboldt.hale.common.align.extension.function.FunctionDefinition) Element(org.w3c.dom.Element) NamedEntityType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.NamedEntityType) AlignmentType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AlignmentType) EntityDefinition(eu.esdihumboldt.hale.common.align.model.EntityDefinition) InputStream(java.io.InputStream) Entity(eu.esdihumboldt.hale.common.align.model.Entity) HashMap(java.util.HashMap) IOMessageImpl(eu.esdihumboldt.hale.common.core.io.report.impl.IOMessageImpl) CellMigrator(eu.esdihumboldt.hale.common.align.migrate.CellMigrator) DefaultCellMigrator(eu.esdihumboldt.hale.common.align.migrate.impl.DefaultCellMigrator) DefaultCellMigrator(eu.esdihumboldt.hale.common.align.migrate.impl.DefaultCellMigrator) AnnotationType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AnnotationType) UnmigratedCell(eu.esdihumboldt.hale.common.align.migrate.impl.UnmigratedCell) AbstractParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AbstractParameterType) Pair(eu.esdihumboldt.util.Pair) ParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ParameterType) ComplexParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ComplexParameterType) AbstractParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AbstractParameterType) ParameterValue(eu.esdihumboldt.hale.common.align.model.ParameterValue) Priority(eu.esdihumboldt.hale.common.align.model.Priority) ElementValue(eu.esdihumboldt.hale.common.core.io.impl.ElementValue) JAXBException(javax.xml.bind.JAXBException) IOException(java.io.IOException) ComplexParameterType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.ComplexParameterType) EntityDefinition(eu.esdihumboldt.hale.common.align.model.EntityDefinition) DocumentationType(eu.esdihumboldt.hale.common.align.io.impl.internal.generated.DocumentationType) DefaultCell(eu.esdihumboldt.hale.common.align.model.impl.DefaultCell)

Aggregations

AlignmentType (eu.esdihumboldt.hale.common.align.io.impl.internal.generated.AlignmentType)3 CellType (eu.esdihumboldt.hale.common.align.io.impl.internal.generated.CellType)3 URI (java.net.URI)3 PathUpdate (eu.esdihumboldt.hale.common.core.io.PathUpdate)2 IOReporter (eu.esdihumboldt.hale.common.core.io.report.IOReporter)2 JAXBContext (javax.xml.bind.JAXBContext)2 Function (com.google.common.base.Function)1 ArrayListMultimap (com.google.common.collect.ArrayListMultimap)1 Collections2 (com.google.common.collect.Collections2)1 ListMultimap (com.google.common.collect.ListMultimap)1 Multimaps (com.google.common.collect.Multimaps)1 AnnotationExtension (eu.esdihumboldt.hale.common.align.extension.annotation.AnnotationExtension)1 FunctionDefinition (eu.esdihumboldt.hale.common.align.extension.function.FunctionDefinition)1 FunctionUtil (eu.esdihumboldt.hale.common.align.extension.function.FunctionUtil)1 CustomPropertyFunction (eu.esdihumboldt.hale.common.align.extension.function.custom.CustomPropertyFunction)1 EntityResolver (eu.esdihumboldt.hale.common.align.io.EntityResolver)1 LoadAlignmentContext (eu.esdihumboldt.hale.common.align.io.LoadAlignmentContext)1 DefaultEntityResolver (eu.esdihumboldt.hale.common.align.io.impl.DefaultEntityResolver)1 JaxbAlignmentIO (eu.esdihumboldt.hale.common.align.io.impl.JaxbAlignmentIO)1 DummyEntityResolver (eu.esdihumboldt.hale.common.align.io.impl.dummy.DummyEntityResolver)1