ubc.pavlab.aspiredb.cli.DecipherVariantUploadCLI.java Source code

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Here is the source code for ubc.pavlab.aspiredb.cli.DecipherVariantUploadCLI.java

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/*
 * The aspiredb project
 * 
 * Copyright (c) 2012 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
 * the License. You may obtain a copy of the License at
 * 
 * http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
 * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations under the License.
 */
package ubc.pavlab.aspiredb.cli;

import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.Statement;

import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.springframework.beans.factory.BeanFactory;

import ubc.pavlab.aspiredb.server.fileupload.VariantUploadService;
import ubc.pavlab.aspiredb.server.fileupload.VariantUploadServiceResult;
import ubc.pavlab.aspiredb.server.project.ProjectManager;

/**
 * modified VariantUploadCLI hack for unfortunately formatted file(since modified) that we got from DECIPHER not
 * intended to be used for anything other than that file
 * 
 * @version $Id: DecipherVariantUploadCLI.java
 */
public class DecipherVariantUploadCLI extends AbstractCLI {

    private static ProjectManager projectManager;

    /**
     * @param args
     */
    public static void main(String[] args) {
        ConsoleAppender console = new ConsoleAppender(); // create appender
        // configure the appender
        String PATTERN = "%d [%p|%c|%C{1}] %m%n";
        console.setLayout(new PatternLayout(PATTERN));
        console.setThreshold(Level.DEBUG);
        console.activateOptions();
        Logger.getRootLogger().addAppender(console);

        applicationContext = SpringContextUtil.getApplicationContext(false);

        projectManager = (ProjectManager) applicationContext.getBean("projectManager");

        DecipherVariantUploadCLI p = new DecipherVariantUploadCLI();
        try {
            Exception ex = p.doWork(args);
            if (ex != null) {
                ex.printStackTrace();
            }
            System.exit(0);
        } catch (Exception e) {
            throw new RuntimeException(e);
        }
    }

    private String directory = "";
    private String filename = "";

    private String projectName = "";

    private boolean deleteProject = true;

    private boolean dryRun = false;

    private static BeanFactory applicationContext;

    @Override
    public String getLogger() {
        return "ubc.pavlab.aspiredb.cli.DecipherVariantUploadCLI";
    }

    @Override
    public String getShortDesc() {
        return "Upload a variant data file and create / assign it to a project";
    }

    @Override
    protected void buildOptions() {
        OptionBuilder.isRequired();
        OptionBuilder.hasArg();
        OptionBuilder.withArgName("Directory");
        OptionBuilder.withDescription("Directory containing csv files");
        OptionBuilder.withLongOpt("directory");
        Option d = OptionBuilder.create('d');

        OptionBuilder.isRequired();
        OptionBuilder.hasArg();
        OptionBuilder.withArgName("File name");
        OptionBuilder.withDescription("The file to parse");
        OptionBuilder.withLongOpt("filename");
        Option f = OptionBuilder.create('f');

        OptionBuilder.isRequired();
        OptionBuilder.hasArg();
        OptionBuilder.withArgName("Project name");
        OptionBuilder.withDescription(
                "The project where this data will reside. Project will be deleted if existingproject option is not specified,"
                        + "Acceptable values = 'DECIPHER");
        // Decipher will reside in a 'Special project' and are all CNVs
        Option project = OptionBuilder.create("project");

        addOption("existingproject", false, "You must use this option if you are adding to an existing project");

        addOption("dryrun", false, "Use this option to validate your data before uploading");

        addOption(d);
        addOption(f);

        addOption(project);

    }

    @Override
    protected Exception doWork(String[] args) {
        Exception err = processCommandLine("Upload Variant file", args);
        authenticate(applicationContext);
        if (err != null) {
            return err;
        }

        if (directory == null || filename == null) {
            return err;
        }

        try {
            Class.forName("org.relique.jdbc.csv.CsvDriver");

            // create a connection
            // arg[0] is the directory in which the .csv files are held
            Connection conn = DriverManager.getConnection("jdbc:relique:csv:" + directory);

            Statement stmt = conn.createStatement();
            ResultSet results = stmt.executeQuery("SELECT * FROM " + filename);

            System.out.println("getting value objects");
            VariantUploadServiceResult result = VariantUploadService
                    .makeVariantValueObjectsFromDecipherResultSet(results);

            results.close();
            stmt.close();
            conn.close();

            if (result.getErrorMessages().isEmpty() && !dryRun) {

                System.out
                        .println("inserting " + result.getVariantsToAdd().size() + " value objects into database");

                // should probably batch this up to speed it up a bit

                projectManager.addSubjectVariantsToSpecialProject(projectName, deleteProject,
                        result.getVariantsToAdd(), false);

            } else if (result.getErrorMessages().isEmpty()) {
                System.out.println("No errors are detected in your data file");

            } else {
                for (String errorMessage : result.getErrorMessages()) {
                    System.out.println(errorMessage);
                }

            }

        } catch (Exception e) {
            return e;
        }

        return null;
    }

    @Override
    protected void processOptions() {
        if (this.hasOption('d')) {
            directory = this.getOptionValue('d');
        }
        if (this.hasOption('f')) {
            filename = this.getOptionValue('f');
        }

        if (this.hasOption("project")) {
            projectName = this.getOptionValue("project");
        }

        if (this.hasOption("existingproject")) {
            deleteProject = false;
        } else {
            deleteProject = true;
        }

        if (this.hasOption("dryrun")) {
            dryRun = true;
        }

    }

}