Package org.openbel.framework.core.protonetwork

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

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     * {@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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     */
    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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        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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        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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        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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        phaseOutput(format("=== %s ===", getApplicationName()));

        ProtoNetworkDescriptor pnd = new BinaryProtoNetworkDescriptor(
                protoNetwork);

        BinaryProtoNetworkExternalizer bpne =
                new BinaryProtoNetworkExternalizer();
        ProtoNetwork gpn = null;
        try {
            gpn = bpne.readProtoNetwork(pnd);
        } catch (ProtoNetworkError e) {
            error("Unable to read merged network.");
            exit(ExitCode.NO_GLOBAL_PROTO_NETWORK);
        }
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Related Classes of org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer

  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.common.protonetwork.model.ProtoNetwork
  • org.openbel.framework.common.protonetwork.model.ProtoNetworkError
  • org.openbel.framework.core.protonetwork.BinaryProtoNetworkIOTest
  • org.openbel.framework.tools.PhaseFourApplication
  • org.openbel.framework.tools.PhaseThreeApplication
  • java.io.FileInputStream
  • java.io.ObjectOutputStream
  • java.io.FileOutputStream
  • java.io.ObjectInputStream
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