Examples of ProtoNetworkExternalizer

org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer
ProtoNetworkExternalizer represents an externalizable {@link ProtoNetwork}. This approach was necessary because the {@link Externalizable} and readObject/writeObjectmethods only supports a single output stream and the {@link TextProtoNetworkExternalizer}requires writing a {@link ProtoNetwork} to multiple table files. @author Anthony Bargnesi {@code }

Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer

     * Testcase - Test the roundtrip input/output of a binary
     * {@link ProtoNetwork}.
     */
    @Test
    public void testProtoNetworkIO() {
        ProtoNetworkExternalizer protoNetworkExternalizer =
                new BinaryProtoNetworkExternalizer();


        try {
            // test write
            protoNetworkDescriptor =
                    protoNetworkExternalizer.writeProtoNetwork(protoNetwork,
                            System.getProperty("user.dir"));


            // test read
            ProtoNetwork serializedProtoNetwork =
                    protoNetworkExternalizer
                            .readProtoNetwork(protoNetworkDescriptor);


            Assert.assertEquals(protoNetwork, serializedProtoNetwork);
        } catch (ProtoNetworkError e) {
            e.printStackTrace();

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer

     * Testcase - Dummy test to see output of text table-based
     * {@link ProtoNetwork}.
     */
    @Test
    public void testProtoNetworkIO() {
        ProtoNetworkExternalizer protoNetworkExternalizer =
                new TextProtoNetworkExternalizer();


        try {
            protoNetworkDescriptor =
                    (TextProtoNetworkDescriptor) protoNetworkExternalizer
                            .writeProtoNetwork(protoNetwork,
                                    System.getProperty("user.dir"));


            for (final File symt : protoNetworkDescriptor.getSymbolTables()) {
                FileUtils.readFileToString(symt);

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer

     */
    private void reconstituteNetwork(final File file) {


        BinaryProtoNetworkDescriptor inputProtoNetworkDesc =
                new BinaryProtoNetworkDescriptor(file);
        ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
        ProtoNetwork global = null;


        try {
            global = pne.readProtoNetwork(inputProtoNetworkDesc);
        } catch (ProtoNetworkError e) {
            error(e.getUserFacingMessage());
            final ExitCode ec = ExitCode.NO_GLOBAL_PROTO_NETWORK;
            exit(ec);
        }

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer

        try {


            p3.merge(pn, pfpn);


            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s1path = asPath(artpath, STAGE1_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE1_OUTPUT);
            pne.writeProtoNetwork(pn, s1path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer

        t1 = currentTimeMillis();
        try {
            p3.merge(pn, ncpn);


            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s2path = asPath(artpath, STAGE2_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE2_OUTPUT);
            pne.writeProtoNetwork(pn, s2path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

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Examples of org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer

        t1 = currentTimeMillis();
        try {
            p3.merge(pn, gpn);


            // Change the input proto-network descriptor to merged network
            ProtoNetworkExternalizer pne = new BinaryProtoNetworkExternalizer();
            final String artpath = artifactPath.getAbsolutePath();
            final String s3path = asPath(artpath, STAGE3_OUTPUT);
            createDirectoryArtifact(artifactPath, STAGE3_OUTPUT);
            pne.writeProtoNetwork(pn, s3path);


            // if debug, then save the text-based merged network
            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();

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