Package org.openbel.framework.core.protonetwork

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

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     * {@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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            final String rootpath = artifactPath.getAbsolutePath();
            final String pfpath = asPath(rootpath, PRUNED_PF_NAME);
            createDirectories(pfpath);

            try {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();
                textExternalizer.writeProtoNetwork(pfpn, pfpath);
            } catch (ProtoNetworkError e) {
                stageError(e.getUserFacingMessage());
            }
        }

        stageOutput("Merging proto-networks");
        t1 = currentTimeMillis();
        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();
                textExternalizer.writeProtoNetwork(pn, s1path);
            }
        } catch (ProtoNetworkError e) {
            stageError(e.getUserFacingMessage());
            bail(FAILED_TO_MERGE_PROTO_NETWORKS);
            return pn; // Dead code
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            final String rootpath = artifactPath.getAbsolutePath();
            final String ncpath = asPath(rootpath, PRUNED_NC_NAME);
            createDirectories(ncpath);

            try {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();
                textExternalizer.writeProtoNetwork(ncpn, ncpath);
            } catch (ProtoNetworkError e) {
                stageError(e.getUserFacingMessage());
            }
        }

        stageOutput("Merging proto-networks");

        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();
                textExternalizer.writeProtoNetwork(pn, s2path);
            }
        } catch (ProtoNetworkError e) {
            stageError(e.getUserFacingMessage());
            bail(FAILED_TO_MERGE_PROTO_NETWORKS);
            return pn; // Dead code
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            final String rootpath = artifactPath.getAbsolutePath();
            final String gpath = asPath(rootpath, PRUNED_NC_NAME);
            createDirectories(gpath);

            try {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();
                textExternalizer.writeProtoNetwork(gpn, gpath);
            } catch (ProtoNetworkError e) {
                stageError(e.getUserFacingMessage());
            }
        }

        stageOutput("Merging proto-networks");

        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();
                textExternalizer.writeProtoNetwork(pn, s3path);
            }
        } catch (ProtoNetworkError e) {
            stageError(e.getUserFacingMessage());
            bail(FAILED_TO_MERGE_PROTO_NETWORKS);
            return pn; // Dead code
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        try {
            p3.write(rootpath, pn);

            if (withDebug()) {
                try {
                    TextProtoNetworkExternalizer textExternalizer =
                            new TextProtoNetworkExternalizer();
                    textExternalizer.writeProtoNetwork(pn,
                            rootpath);
                } catch (ProtoNetworkError e) {
                    error("Could not write out equivalenced proto network.");
                }
            }
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        boolean success = true;
        try {
            p1.stage7Saving(pn, pnpathname);

            if (withDebug()) {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();
                textExternalizer.writeProtoNetwork(pn,
                        pnpathname.getAbsolutePath());
            }
        } catch (ProtoNetworkError e) {
            success = false;
            error("failed to save proto-network");
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        p2.stage4WriteEquivalentProtoNetwork(ret,
                artifactPath.getAbsolutePath() + "/merged");

        if (withDebug()) {
            try {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();
                textExternalizer.writeProtoNetwork(ret,
                        artifactPath.getAbsolutePath() + "/merged");
            } catch (ProtoNetworkError e) {
                error("Could not write out equivalenced proto network.");
            }
        }
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                p2.stage4WriteEquivalentProtoNetwork(eqNetwork,
                        artifactPath.getAbsolutePath());

        if (withDebug()) {
            try {
                TextProtoNetworkExternalizer textExternalizer =
                        new TextProtoNetworkExternalizer();
                textExternalizer.writeProtoNetwork(eqNetwork,
                        artifactPath.getAbsolutePath());
            } catch (ProtoNetworkError e) {
                error("Could not write out equivalenced proto network.");
            }
        }
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