Examples with CLIHandler org.vcell.cli.CLIHandler used on opensource projects

Example 1 with CLIHandler

use of org.vcell.cli.CLIHandler in project vcell by virtualcell.

the class VcmlOmexConverter method parseArgsAndConvert.

public static void parseArgsAndConvert(String[] args) throws IOException {
    File input = null;
    try {
        // TODO: handle if it's not valid PATH
        input = new File(args[1]);
    } catch (Exception e1) {
        e1.printStackTrace();
    }
    args = parseArgs(args);
    // if (bHasDataOnly) {
    try {
        conFactory = DatabaseService.getInstance().createConnectionFactory();
        adminDbTopLevel = new AdminDBTopLevel(conFactory);
    } catch (SQLException e) {
        System.err.println("\n\n\n=====>>>>EXPORT FAILED: connection to database failed");
        e.printStackTrace();
    }
    // }
    VCInfoContainer vcic;
    try {
        vcic = adminDbTopLevel.getPublicOracleVCInfoContainer(false);
        if (vcic != null) {
            User user = vcic.getUser();
            BioModelInfo[] bioModelInfos = vcic.getBioModelInfos();
            // int count = 0;
            for (BioModelInfo bi : bioModelInfos) {
                // if(bi.getPublicationInfos() != null && bi.getPublicationInfos().length > 0) {
                // // let's see what has PublicationInfo
                // System.out.println(bi.getVersion().getName());
                // count++;
                // }
                // build the biomodel id / biomodel info map
                String biomodelId = "biomodel_" + bi.getVersion().getVersionKey();
                String biomodelName = bi.getVersion().getName();
                // String biomodelId2 = "biomodel_" + bi.getModelKey();
                bioModelInfoMap.put(biomodelId, bi);
                bioModelInfoMap2.put(biomodelName, bi);
            }
        // System.out.println("User: " + user.getName() + "   count published biomodels: " + count);
        }
    } catch (SQLException | DataAccessException e1) {
        System.err.println("\n\n\n=====>>>>EXPORT FAILED: failed to retrieve metadata");
        e1.printStackTrace();
    }
    System.out.println("Found " + bioModelInfoMap.size() + " public BioNodelInfo objects");
    if (input != null && input.isDirectory()) {
        FilenameFilter filterVcmlFiles = (f, name) -> name.endsWith(".vcml");
        // jusr a list of vcml names, like biomodel-185577495.vcml, ...
        String[] inputFiles = input.list(filterVcmlFiles);
        if (inputFiles == null) {
            System.err.println("No VCML files found in the directory `" + input + "`");
        }
        // full directory name, like C:\TEMP\biomodel\omex\native
        String outputDir = args[3];
        CLIStandalone.writeSimErrorList(outputDir, "hasDataOnly is " + bHasDataOnly);
        CLIStandalone.writeSimErrorList(outputDir, "makeLogsOnly is " + bMakeLogsOnly);
        // assert inputFiles != null;
        for (String inputFile : inputFiles) {
            File file = new File(input, inputFile);
            System.out.println(" ============== start: " + inputFile);
            args[1] = file.toString();
            cliHandler = new CLIHandler(args);
            try {
                if (inputFile.endsWith(".vcml")) {
                    boolean isCreated = vcmlToOmexConversion(outputDir);
                    if (isCreated) {
                        System.out.println("Combine archive created for file(s) `" + input + "`");
                    } else {
                        System.err.println("Failed converting VCML to OMEX archive for `" + input + "`");
                    }
                } else {
                    System.err.println("No VCML files found in the directory `" + input + "`");
                }
            } catch (Exception e) {
                // e.printStackTrace(System.err);
                System.out.println("\n\n\n=====>>>>EXPORT FAILED: " + inputFile + "\n\n\n");
                CLIStandalone.writeDetailedErrorList(outputDir, inputFile + ",   " + e.getMessage());
            // System.exit(1);
            }
        }
    } else {
        try {
            assert input != null;
            if (input.toString().endsWith(".vcml")) {
                cliHandler = new CLIHandler(args);
                boolean isCreated = vcmlToOmexConversion(null);
                if (isCreated)
                    System.out.println("Combine archive created for `" + input + "`");
                else
                    System.err.println("Failed converting VCML to OMEX archive for `" + input + "`");
            } else
                System.err.println("No input files found in the directory `" + input + "`");
        } catch (Exception e) {
            // e.printStackTrace();
            System.out.println("\n\n\n=====>>>>EXPORT FAILED: " + input + "\n\n\n");
        // System.exit(1);
        }
    }
}