Examples with Path org.dishevelled.bio.assembly.gfa2.Path used on opensource projects

Example 1 with Path

use of org.dishevelled.bio.assembly.gfa2.Path in project jmulticard by ctt-gob-es.

the class SmartCafePkcs15Applet method preloadCertificates.

private void preloadCertificates() throws FileNotFoundException, Iso7816FourCardException, IOException, Asn1Exception, TlvException {
    selectMasterFile();
    // Seleccionamos el ODF, no nos devuelve FCI ni nada
    selectFileById(ODF_PATH);
    // Leemos el ODF
    final byte[] odfBytes = readBinaryComplete(162);
    final Odf odf = new Odf();
    odf.setDerValue(odfBytes);
    // Sacamos del ODF la ruta del CDF
    final Path cdfPath = odf.getCdfPath();
    // Leemos el CDF
    final Cdf cdf = new Cdf();
    try {
        selectMasterFile();
        final byte[] cdfBytes = selectFileByIdAndRead(cdfPath.getPathBytes());
        cdf.setDerValue(cdfBytes);
    } catch (final Exception e) {
        throw new ApduConnectionException(// $NON-NLS-1$
        "No se ha podido cargar el CDF de la tarjeta: " + e, // $NON-NLS-1$
        e);
    }
    if (cdf.getCertificateCount() < 1) {
        // $NON-NLS-1$
        LOGGER.warning("La tarjeta no contiene ningun certificado");
    }
    for (int i = 0; i < cdf.getCertificateCount(); i++) {
        try {
            int fileLength = -1;
            Location certLocation = new Location(cdf.getCertificatePath(i));
            while (certLocation != null) {
                final byte[] id = certLocation.getFile();
                try {
                    fileLength = selectFileById(id);
                } catch (final FileNotFoundException e) {
                    System.out.println(// $NON-NLS-1$//$NON-NLS-2$
                    "El CDF indicaba un certificado en la ruta '" + certLocation + "', pero un elemento de esta no existe, se ignorara: " + e);
                }
                certLocation = certLocation.getChild();
            }
            final byte[] certBytes;
            if (fileLength <= 0) {
                // A veces hay punteros que apuntan a localizaciones vacias
                LOGGER.warning(// $NON-NLS-1$ //$NON-NLS-2$
                "El certificado " + i + " del dispositivo esta vacio");
                continue;
            }
            certBytes = readBinaryComplete(fileLength);
            CERTS_BY_ALIAS.put(cdf.getCertificateAlias(i), CertificateUtils.generateCertificate(certBytes));
        } catch (final Exception e) {
            // Puede darse el caso de que el puntero apunte a algo que no es un certificado
            LOGGER.severe(// $NON-NLS-1$ //$NON-NLS-2$
            "Error en la lectura del certificado " + i + " del dispositivo: " + e);
            continue;
        }
    }
}

Example 2 with Path

use of org.dishevelled.bio.assembly.gfa2.Path in project policies-ui-backend by RedHatInsights.

the class OapiTest method validateOpenApi.

@Test
void validateOpenApi() throws Exception {
    OpenApi3 model = new OpenApi3Parser().parse(url, true);
    System.out.printf("OpenAPI Model at %s\n", url);
    if (!model.isValid()) {
        for (ValidationResults.ValidationItem item : model.getValidationItems()) {
            System.err.println(item);
        }
        fail("OpenAPI spec is not valid");
    }
    // 
    // Now that basic validation is done, we can add some of our own
    // 
    Map<String, Path> paths = model.getPaths();
    Map<String, Schema> schemas = model.getSchemas();
    // The base path filler. See also OASModifier.mangleName
    assertTrue(paths.containsKey("/"));
    // User config is private, so don't show it
    assertFalse(paths.containsKey("/user-config"));
    assertFalse(schemas.containsKey("SettingsValues"));
    // Check that openapi does not (again) collapse parameters
    assertEquals(9, paths.get("/policies").getOperation("get").getParameters().size());
    // Check that all properties are present ( https://github.com/smallrye/smallrye-open-api/issues/437 )
    Map<String, Schema> policyProperties = schemas.get("Policy").getProperties();
    assertEquals(9, policyProperties.size());
    assertTrue(policyProperties.containsKey("ctime"));
    assertTrue(policyProperties.containsKey("mtime"));
    // Now that the OpenAPI file has been validated, save a copy to the filesystem
    // This file is going to be uploaded in a regular CI build to know the API state
    // for a given build.
    InputStream in = url.openStream();
    Files.copy(in, Paths.get(TARGET_OPENAPI), StandardCopyOption.REPLACE_EXISTING);
}

Example 3 with Path

use of org.dishevelled.bio.assembly.gfa2.Path in project dishevelled by heuermh.

the class AssemblyModel method setPaths.

/**
 * Set the paths for this assembly model to the specified GFA 1.0 paths.
 *
 * @param paths zero or more GFA 1.0 paths, must not be null
 * @param traversalsByPathName traversals keyed by path name, must not be null
 */
void setPaths(final Iterable<Path> paths, final ListMultimap<String, Traversal> traversalsByPathName) {
    checkNotNull(paths);
    checkNotNull(traversalsByPathName);
    // reset if necessary
    if (!this.paths.isEmpty()) {
        setPath(null);
        this.paths.clear();
        traversals.clear();
        traversalsByPath.clear();
    }
    // create traversals from paths if necessary
    for (Path path : paths) {
        List<Traversal> traversals = traversalsByPathName.get(path.getName());
        traversalsByPath.putAll(path, traversals.isEmpty() ? traversalsFor(path) : traversals);
    }
    if (!traversalsByPath.isEmpty()) {
        Set<Path> keys = traversalsByPath.keySet();
        paths().addAll(keys);
        setPath(keys.iterator().next());
    }
}

Example 4 with Path

use of org.dishevelled.bio.assembly.gfa2.Path in project dishevelled by heuermh.

the class ImportGfa1Task method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Import a network in Graphical Fragment Assembly (GFA) 1.0 format");
    final Map<String, Segment> segmentsById = new HashMap<String, Segment>();
    final Table<String, Orientation, Segment> segmentsByOrientation = HashBasedTable.create();
    final ListMultimap<String, Traversal> traversalsByPathName = ArrayListMultimap.create();
    taskMonitor.setStatusMessage("Reading segments from file ...");
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream segments, building cache
        stream(readable, new Gfa1Adapter() {

            @Override
            protected boolean segment(final Segment segment) {
                segmentsById.put(segment.getId(), segment);
                return true;
            }
        });
    }
    taskMonitor.setStatusMessage("Finding reverse orientation references ...");
    final List<Path> paths = new ArrayList<Path>();
    final List<Link> links = new ArrayList<Link>();
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream paths and links, looking for reverse orientation references
        stream(readable, new Gfa1Adapter() {

            private void putIfAbsent(final Reference reference) {
                Segment segment = segmentsById.get(reference.getId());
                if (segment == null) {
                    throw new RuntimeException("could not find segment by id " + reference.getId());
                }
                if (!segmentsByOrientation.contains(reference.getId(), reference.getOrientation())) {
                    segmentsByOrientation.put(reference.getId(), reference.getOrientation(), segment);
                }
            }

            @Override
            protected boolean path(final Path path) {
                for (Reference reference : path.getSegments()) {
                    putIfAbsent(reference);
                }
                if (loadPaths) {
                    paths.add(path);
                }
                return true;
            }

            @Override
            protected boolean link(final Link link) {
                putIfAbsent(link.getSource());
                putIfAbsent(link.getTarget());
                links.add(link);
                return true;
            }

            @Override
            protected boolean traversal(final Traversal traversal) {
                traversalsByPathName.put(traversal.getPathName(), traversal);
                return true;
            }
        });
    }
    logger.info("read {} segments, {} links, {} paths, and {} traversals from {}", new Object[] { segmentsById.size(), links.size(), paths.size(), traversalsByPathName.size(), inputFile });
    segmentsById.clear();
    taskMonitor.setStatusMessage("Building Cytoscape nodes from segments ...");
    final CyNetwork network = applicationManager.getCurrentNetwork();
    final Map<String, CyNode> nodes = new HashMap<String, CyNode>(segmentsByOrientation.size());
    for (Table.Cell<String, Orientation, Segment> c : segmentsByOrientation.cellSet()) {
        String id = c.getRowKey();
        Orientation orientation = c.getColumnKey();
        Segment segment = c.getValue();
        String name = id + (orientation.isForward() ? "+" : "-");
        if (!nodes.containsKey(name)) {
            CyNode node = network.addNode();
            CyTable nodeTable = network.getDefaultNodeTable();
            CyRow nodeRow = nodeTable.getRow(node.getSUID());
            Integer length = segment.getLengthOpt().orElse(null);
            Integer readCount = segment.getReadCountOpt().orElse(null);
            Integer fragmentCount = segment.getFragmentCountOpt().orElse(null);
            Integer kmerCount = segment.getKmerCountOpt().orElse(null);
            String sequenceChecksum = segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : null;
            String sequenceUri = segment.getSequenceUriOpt().orElse(null);
            setValue(nodeTable, nodeRow, "name", String.class, name);
            setValue(nodeTable, nodeRow, "length", Integer.class, length);
            setValue(nodeTable, nodeRow, "readCount", Integer.class, readCount);
            setValue(nodeTable, nodeRow, "fragmentCount", Integer.class, fragmentCount);
            setValue(nodeTable, nodeRow, "kmerCount", Integer.class, kmerCount);
            setValue(nodeTable, nodeRow, "sequenceChecksum", String.class, sequenceChecksum);
            setValue(nodeTable, nodeRow, "sequenceUri", String.class, sequenceUri);
            // default display length to length
            Integer displayLength = length;
            String sequence = orientation.isForward() ? segment.getSequence() : reverseComplement(segment.getSequence());
            if (sequence != null) {
                Integer sequenceLength = sequence.length();
                String displaySequence = trimFromMiddle(sequence, displaySequenceLimit);
                Integer displaySequenceLength = displaySequence.length();
                if (loadSequences) {
                    setValue(nodeTable, nodeRow, "sequence", String.class, sequence);
                }
                setValue(nodeTable, nodeRow, "sequenceLength", Integer.class, sequenceLength);
                setValue(nodeTable, nodeRow, "displaySequence", String.class, displaySequence);
                setValue(nodeTable, nodeRow, "displaySequenceLength", Integer.class, displaySequenceLength);
                // override display length with sequence length if necessary
                if (length == null || length != sequenceLength) {
                    displayLength = sequenceLength;
                }
            }
            StringBuilder sb = new StringBuilder();
            sb.append(name);
            if (displayLength != null) {
                sb.append("  ");
                sb.append(displayLength);
                sb.append(" bp");
            }
            String displayName = sb.toString();
            if (readCount != null) {
                sb.append(" ");
                sb.append(readCount);
                sb.append(" reads");
            }
            if (fragmentCount != null) {
                sb.append(" ");
                sb.append(fragmentCount);
                sb.append(" fragments");
            }
            if (kmerCount != null) {
                sb.append(" ");
                sb.append(kmerCount);
                sb.append(" kmers");
            }
            String displayLabel = sb.toString();
            setValue(nodeTable, nodeRow, "displayName", String.class, displayName);
            setValue(nodeTable, nodeRow, "displayLength", Integer.class, displayLength);
            setValue(nodeTable, nodeRow, "displayLabel", String.class, displayLabel);
            nodes.put(name, node);
        }
    }
    logger.info("converted segments and orientation to " + nodes.size() + " nodes");
    segmentsByOrientation.clear();
    taskMonitor.setStatusMessage("Building Cytoscape edges from links ...");
    for (Link link : links) {
        String sourceId = link.getSource().getId();
        String sourceOrientation = link.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = link.getTarget().getId();
        String targetOrientation = link.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge edge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(edge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, link.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "edge");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "overlap", String.class, link.getOverlapOpt().orElse(null));
        setValue(edgeTable, edgeRow, "readCount", Integer.class, link.getReadCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "fragmentCount", Integer.class, link.getFragmentCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "kmerCount", Integer.class, link.getKmerCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mappingQuality", Integer.class, link.getMappingQualityOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mismatchCount", Integer.class, link.getMismatchCountOpt().orElse(null));
    }
    logger.info("converted links to " + links.size() + " edges");
    nodes.clear();
    links.clear();
    // pass paths to AssemblyApp if requested
    if (loadPaths && !paths.isEmpty()) {
        taskMonitor.setStatusMessage("Loading paths in path view ...");
        assemblyModel.setInputFileName(inputFile.toString());
        assemblyModel.setPaths(paths, traversalsByPathName);
    }
}

Example 5 with Path

use of org.dishevelled.bio.assembly.gfa2.Path in project dishevelled-bio by heuermh.

the class Gfa1ToGfa2 method call.

@Override
public Integer call() throws Exception {
    PrintWriter writer = null;
    try {
        writer = writer(outputGfa2File);
        final PrintWriter w = writer;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean header(final Header header) {
                // convert VN:Z:1.0 to VN:Z:2.0 annotation if present
                if (header.getAnnotations().containsKey("VN")) {
                    if (!"1.0".equals(header.getAnnotations().get("VN").getValue())) {
                        throw new RuntimeException("cannot convert input as GFA 1.0, was " + header.getAnnotations().get("VN").getValue());
                    }
                    Map<String, Annotation> annotations = new HashMap<String, Annotation>();
                    annotations.put("VN", new Annotation("VN", "Z", "2.0"));
                    for (Annotation annotation : header.getAnnotations().values()) {
                        if (!"VN".equals(annotation.getName())) {
                            annotations.put(annotation.getName(), annotation);
                        }
                    }
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(annotations), w);
                } else {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(header.getAnnotations()), w);
                }
                return true;
            }

            @Override
            public boolean segment(final Segment segment) {
                if (segment.getSequence() != null) {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), segment.getSequence().length(), segment.getSequence(), segment.getAnnotations()), w);
                } else if (segment.getAnnotations().containsKey("LN")) {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), Integer.parseInt(segment.getAnnotations().get("LN").getValue()), segment.getSequence(), segment.getAnnotations()), w);
                } else {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), 0, segment.getSequence(), segment.getAnnotations()), w);
                }
                return true;
            }

            @Override
            public boolean link(final Link link) {
                Position unknown = new Position(0, false);
                Alignment alignment = link.getOverlap() == null ? null : Alignment.valueOf(link.getOverlap());
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(link.getSource()), toGfa2Reference(link.getTarget()), unknown, unknown, unknown, unknown, alignment, link.getAnnotations()), w);
                return true;
            }

            @Override
            public boolean containment(final Containment containment) {
                Position unknown = new Position(0, false);
                Position targetStart = new Position(containment.getPosition(), false);
                Alignment alignment = containment.getOverlap() == null ? null : Alignment.valueOf(containment.getOverlap());
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(containment.getContainer()), toGfa2Reference(containment.getContained()), unknown, unknown, targetStart, unknown, alignment, containment.getAnnotations()), w);
                return true;
            }

            @Override
            public boolean path(final Path path) {
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Path(path.getName(), toGfa2References(path.getSegments()), path.getAnnotations()), w);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            writer.close();
        } catch (Exception e) {
        // empty
        }
    }
}