gov.nasa.jpl.celgene.labkey.LabkeyDumper.java Source code

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Here is the source code for gov.nasa.jpl.celgene.labkey.LabkeyDumper.java

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/**
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You 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 gov.nasa.jpl.celgene.labkey;

import java.io.IOException;
import java.net.URL;
import java.util.List;
import java.util.Map;

import org.labkey.remoteapi.CommandException;
import org.labkey.remoteapi.Connection;
import org.labkey.remoteapi.query.ContainerFilter;
import org.labkey.remoteapi.query.SelectRowsCommand;
import org.labkey.remoteapi.query.SelectRowsResponse;

import org.json.simple.JSONObject;

public class LabkeyDumper {

    private Connection connection = null;

    private URL labkeyUrl;

    public LabkeyDumper(URL labkeyUrl, String username, String password) {
        this.connection = new Connection(labkeyUrl.toString(), username, password);
        this.labkeyUrl = labkeyUrl;

    }

    public void generateJSON(List<Map<String, Object>> studyData) {

        // loop over the returned rows
        System.out.println("{\"studies\":[");
        for (int i = 0; i < studyData.size(); i++) {
            Map<String, Object> study = studyData.get(i);
            System.out.println("{");
            String[] keySet = study.keySet().toArray(new String[] {});
            for (int j = 0; j < keySet.length; j++) {
                String key = keySet[j];
                if (j + 1 >= keySet.length) {
                    System.out.println(
                            "\"" + key + "\" : \"" + JSONObject.escape(String.valueOf(study.get(key))) + "\"");
                } else {
                    System.out.println(
                            "\"" + key + "\" : \"" + JSONObject.escape(String.valueOf(study.get(key))) + "\",");
                }
            }
            if (i + 1 >= studyData.size()) {
                System.out.println("}");
            } else {
                System.out.println("},");
            }
        }
        System.out.println("]}");
    }

    public List<Map<String, Object>> dumpStudies(String projectName) throws IOException, CommandException {
        // create a SelectRowsCommand to call the selectRows.api
        SelectRowsCommand cmd = new SelectRowsCommand("study", "Study");
        cmd.setContainerFilter(ContainerFilter.CurrentAndSubfolders);

        // execute the command against the connection
        // within the Api Test project folder
        SelectRowsResponse resp = cmd.execute(this.connection, projectName);
        System.err.println(resp.getRowCount() + " rows were returned.");
        return resp.getRows();
    }

    public static void main(String[] args) throws Exception {
        String url = null;
        String user = null;
        String pass = null;
        String projectName = null;

        String usage = "java LabkeyDumper [--url <url>] [--user <user/email>] [--pass <pass>] [--project <Project Name>]\n";

        for (int i = 0; i < args.length; i++) {
            if (args[i].equals("--url")) {
                url = args[++i];
            } else if (args[i].equals("--user")) {
                user = args[++i];
            } else if (args[i].equals("--pass")) {
                pass = args[++i];
            } else if (args[i].equals("--project")) {
                projectName = args[++i];
            }
        }

        if (isEmpty(url) || isEmpty(user) || isEmpty(pass) || isEmpty(projectName)) {
            System.err.println(usage);
            System.exit(1);
        }

        LabkeyDumper dumper = new LabkeyDumper(new URL(url), user, pass);
        dumper.generateJSON(dumper.dumpStudies(projectName));
    }

    private static boolean isEmpty(String string) {
        return string == null || (string != null && string.equals(""));
    }
}