List of writeProtoNetwork() Examples

Examples of writeProtoNetwork()

org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer.writeProtoNetwork()
Writes a binary-based proto network and produces a descriptor including the binary file. @param protoNetwork {@link ProtoNetwork}, the proto network, which cannot be null @param protoNetworkRootPath {@link String}, the root path where proto network files should be created @return {@link ProtoNetworkDescriptor}, the proto network descriptor @throws ProtoNetworkError , if there was an error writing the {@link ProtoNetwork}
org.openbel.framework.core.protonetwork.ProtoNetworkExternalizer.writeProtoNetwork()
Writes a proto network and produces a descriptor. @param protoNetwork {@link ProtoNetwork}, the proto network, which cannot be null @param protoNetworkRootPath {@link String}, the root path where proto network files should be created @return {@link ProtoNetworkDescriptor}, the proto network descriptor @throws ProtoNetworkError , if there was an error writing the {@link ProtoNetwork}
org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()
Writes a text table-based proto network and produces a descriptor including all of the table files. @param pn {@link ProtoNetwork}, the proto network, which cannot be null @param protoNetworkRootPath {@link String}, the root path where proto network files should be created @return {@link ProtoNetworkDescriptor}, the proto network descriptor @throws ProtoNetworkError Thrown if there was an error writing the {@link ProtoNetwork} @throws InvalidArgument Thrown if {@code protoNetwork} is null

Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()

            createDirectories(pfpath);


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

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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()


            // 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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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()

            createDirectories(ncpath);


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

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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()


            // 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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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()

            createDirectories(gpath);


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

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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()


            // 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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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()


            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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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()

            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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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()


        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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Examples of org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer.writeProtoNetwork()


        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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