Open Source Projects Europe

--- a/src/main/java/net/timbusproject/extractors/modules/debiansoftwareextractor/cli/CLI.java
+++ b/src/main/java/net/timbusproject/extractors/modules/debiansoftwareextractor/local/LocalCLI.java
@@ -16,78 +16,51 @@
  * See the License for the specific language governing permissions and limitation under the License.
  */
 
-package net.timbusproject.extractors.modules.debiansoftwareextractor.cli;
+package net.timbusproject.extractors.modules.debiansoftwareextractor.local;
 
-import com.jcraft.jsch.JSchException;
-import net.timbusproject.extractors.modules.debiansoftwareextractor.Engine;
-import net.timbusproject.extractors.modules.debiansoftwareextractor.ReadJSON;
-import net.timbusproject.extractors.modules.debiansoftwareextractor.SSHManager;
-import org.apache.commons.cli.*;
-import org.apache.commons.cli.ParseException;
 import org.codehaus.jettison.json.JSONArray;
 import org.codehaus.jettison.json.JSONException;
 
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
 import java.io.IOException;
-import java.text.*;
-import java.util.Scanner;
+import java.text.ParseException;
 
-public class CLI {
-    public static void main(String... args) throws ParseException, IOException, JSONException, JSchException, java.text.ParseException {
-        final Options options = new Options();
-        final CommandLineParser parser = new PosixParser();
-        //Available options
-        options.addOption("e", "extract", true, "[user@]hostname]");
-        options.addOption("h", "help", false, "Prints this help message");
-        final CommandLine line = parser.parse(options, args);
+public class LocalCLI {
 
-        //Print help if there are no arguments
-        checkOptions(options, line);
+    public static void main(String[] args) throws IOException, JSONException {
+        try {
+            CommandManager commandManager = new CommandManager();
+            JSONArray array;
 
-        if (line.hasOption("h")) {
-            printHelp(options);
-        }
-
-        String extract = getOption("e", line);
-        if (extract.isEmpty()) {
-//            printHelp(options);
-        } else {
-            String[] split = extract.split("@");
-            String user = "", fqdn = "";
-            //user@hostname
-            if (split.length == 2) {
-                user = split[0];
-                fqdn = split[1];
-                Scanner scanner = new Scanner(System.in);
-                System.out.println("Please write your pass: ");
-                String pass = scanner.nextLine();
-                SSHManager manager = new SSHManager(user, pass, fqdn, "", "");
-
-                Engine engine = new Engine();
-                JSONArray jsonArray = engine.run(manager);
-                System.out.print(jsonArray.toString(2));
+            array = commandManager.run(true);
+            if (args.length > 0) {
+                File f;
+                if (args[0].equals("y"))
+                    f = new File("extraction.json");
+                else
+                    f = new File(args[0]);
+                BufferedWriter fileWriter = new BufferedWriter(new FileWriter(f));
+                fileWriter.write(array.toString(2));
+                fileWriter.close();
+                if (args.length > 1) {
+                    String command;
+                    if (args[1].equals("y"))
+                        command = "java -jar local-deb-software-converter-1.0-SNAPSHOT.jar";
+                    else
+                        command = "java -jar " + args[1];
+                    if (args.length > 2){
+                        command = command + " " + args[2];
+                        if(args.length > 3)
+                            command = command + " " + args[3];
+                    }
+                    commandManager.doCommand(command);
+                }
             }
-            System.exit(0);
+        } catch (ParseException e) {
+            e.printStackTrace();
         }
     }
+}
 
-    public static String getOption(String option, CommandLine line) {
-        if (line.hasOption(option)) {
-            return line.getOptionValue(option);
-        }
-
-        return "";
-    }
-
-    public static void checkOptions(Options options, CommandLine line) {
-        HelpFormatter formatter = new HelpFormatter();
-        if (line.getOptions().length == 0)
-            formatter.printHelp("launch", options);
-
-    }
-
-    private static void printHelp(Options options) {
-        HelpFormatter formatter = new HelpFormatter();
-        formatter.printHelp("launch", options);
-        System.exit(0);
-    }
-}

--- a/src/main/java/net/timbusproject/extractors/modules/debiansoftwareextractor/local/CLOption.java
+++ b/src/main/java/net/timbusproject/extractors/modules/debiansoftwareextractor/absolute/ReadJSON.java
@@ -1,135 +1,43 @@
-package net.timbusproject.extractors.modules.debiansoftwareextractor.local;
+/**
+ * Copyright (c) 2013, Caixa Magica Software Lda (CMS).
+ * The work has been developed in the TIMBUS Project and the above-mentioned are Members of the TIMBUS Consortium.
+ * TIMBUS is supported by the European Union under the 7th Framework Programme for research and technological
+ * development and demonstration activities (FP7/2007-2013) under grant agreement no. 269940.
+ *
+ * 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, including without
+ * limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTIBITLY, or FITNESS FOR A PARTICULAR
+ * PURPOSE. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise,
+ * unless required by applicable law or agreed to in writing, shall any Contributor be liable for damages, including
+ * any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this
+ * License or out of the use or inability to use the Work.
+ * See the License for the specific language governing permissions and limitation under the License.
+ */
+package net.timbusproject.extractors.modules.debiansoftwareextractor.absolute;
 
-import org.apache.commons.cli.Option;
+import org.apache.commons.io.IOUtils;
+import org.codehaus.jettison.json.JSONArray;
+import org.codehaus.jettison.json.JSONException;
 
-/**
- * Created with IntelliJ IDEA.
- * User: jorge
- * Date: 1/7/14
- * Time: 3:42 PM
- * To change this template use File | Settings | File Templates.
- */
-class CLOption {
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.StringWriter;
 
-    private final Option option;
-    private final String defaultValue;
-    private String title;
+public class ReadJSON {
 
-    private CLOption(Option option) {
-        this(option, null);
+    private JSONArray jsonArray;
+
+    public ReadJSON(String path) throws IOException, JSONException {
+        StringWriter writer = new StringWriter();
+        IOUtils.copy(new FileInputStream(new File(path)), writer);
+        this.jsonArray = new JSONArray(writer.toString());
     }
 
-    private CLOption(Option option, String defaultValue) {
-        this.option = option;
-        this.defaultValue = defaultValue;
+    public JSONArray getJsonArray() {
+        return jsonArray;
     }
 
-    static CLOption buildOption(Option option) {
-        return new CLOption(option);
-    }
-
-    static CLOption buildOption(Option option, String argName) {
-        option.setArgName(argName);
-        return new CLOption(option);
-    }
-
-    static CLOption buildOption(Option option, Class type) {
-        option.setType(type);
-        return new CLOption(option);
-    }
-
-    static CLOption buildOption(Option option, String argName, Class type) {
-        option.setArgName(argName);
-        option.setType(type);
-        return new CLOption(option);
-    }
-
-    static CLOption buildOption(Option option, String argName, Class type, String defaultValue) {
-        option.setArgName(argName);
-        option.setType(type);
-        return new CLOption(option, defaultValue);
-    }
-
-    CLOption setTitle(String title) {
-        this.title = title;
-        return this;
-    }
-
-    String getDefaultValue() {
-        return defaultValue;
-    }
-
-    String getTitle() {
-        return title;
-    }
-
-    Option getOption() {
-        return option;
-    }
-
-
-
-
-
-
-
-
-
-
-
-
-/*
-    public CLOption(String opt, String description) throws IllegalArgumentException {
-        super(opt, description);
-    }
-
-    public CLOption(String opt, boolean hasArg, String description) throws IllegalArgumentException {
-        super(opt, hasArg, description);
-    }
-
-    public CLOption(String opt, boolean hasArg, String description, Class type) throws IllegalArgumentException {
-        super(opt, hasArg, description);
-        setType(type);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description) throws IllegalArgumentException {
-        super(opt, longOpt, hasArg, description);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description, Class type) throws IllegalArgumentException {
-        super(opt, longOpt, hasArg, description);
-        setType(type);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description, String argName) throws IllegalArgumentException {
-        super(opt, longOpt, hasArg, description);
-        setArgName(argName);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description, String argName, Class type) throws IllegalArgumentException {
-        this(opt, longOpt, hasArg, description, argName);
-        setType(type);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description, int args) throws IllegalArgumentException {
-        super(opt, longOpt, hasArg, description);
-        setArgs(args);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description, int args, Class type) throws IllegalArgumentException {
-        this(opt, longOpt, hasArg, description, args);
-        setType(type);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description, String argName, int args) throws IllegalArgumentException {
-        this(opt, longOpt, hasArg, description, argName);
-        setArgs(args);
-    }
-
-    public CLOption(String opt, String longOpt, boolean hasArg, String description, String argName, int args, Class type) throws IllegalArgumentException {
-        this(opt, longOpt, hasArg, description, argName, args);
-        setType(type);
-    }
-*/
-
 }

--- a/src/main/java/net/timbusproject/extractors/modules/debiansoftwareextractor/local/CommonsEngine2.java
+++ b/src/main/java/net/timbusproject/extractors/modules/debiansoftwareextractor/absolute/Engine2.java
@@ -1,234 +1,224 @@
-package net.timbusproject.extractors.modules.debiansoftwareextractor.local;
+package net.timbusproject.extractors.modules.debiansoftwareextractor.absolute;
 
 import com.jcraft.jsch.JSchException;
-import net.timbusproject.extractors.core.Endpoint;
-import net.timbusproject.extractors.modules.debiansoftwareextractor.absolute.Engine;
-import net.timbusproject.extractors.modules.debiansoftwareextractor.absolute.SSHManager;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.ParseException;
 import org.codehaus.jettison.json.JSONArray;
 import org.codehaus.jettison.json.JSONException;
 import org.codehaus.jettison.json.JSONObject;
 
 import java.io.*;
-import java.util.*;
-import java.util.regex.Pattern;
-
-/**
- * Created with IntelliJ IDEA.
- * User: jorge
- * Date: 12/17/13
- * Time: 5:36 PM
- * To change this template use File | Settings | File Templates.
- */
-public class CommonsEngine2 {
-
-    private final CLI cmd = new CLI();
-    private final JSONObject request = new JSONObject();
-    private JSONObject response;
-    //    private final OutputStream out;
-    private final Log log;
-    Engine engine = new Engine();
-
-    public CommonsEngine2(String... args) throws IOException, ParseException, JSONException, JSchException, java.text.ParseException {
-        this(args, null);
-    }
-
-    public CommonsEngine2(String[] args, OutputStream out) throws IOException, ParseException, JSONException, JSchException, java.text.ParseException {
-        response = new JSONObject();
-        setOptions();
-        OutputStream o = null;
-//        cmd.parse(args);
-        try {
-            o = parse(args);
-        } catch (ParseException e) {
-            Log.out(System.out, true, true, e.getMessage());
-        }
-        log = new Log(o != null ? o : out);
-        printHelp();
-        execute();
-    }
-
-    private void execute() throws IOException, JSONException, JSchException, java.text.ParseException {
-        String result = "";
-        if(!cmd.hasOption("l") && !cmd.hasOption("s") && !cmd.hasOption("o") && !cmd.hasOption("j"))
-            printUsage(System.out);
-        if (cmd.hasOption("l")) {
-            boolean show = false;
-            if (cmd.hasOption("s"))
-                show = true;
-            result = engine.run(show).toString();
-        }
-        if (cmd.hasOption("j")) {
-            StringBuilder request = new StringBuilder();
-            String currentLine;
-            BufferedReader fileReader = new BufferedReader(new FileReader(new File(cmd.getOptionValue("j"))));
-            while ((currentLine = fileReader.readLine()) != null)
-                request.append(currentLine);
-            fileReader.close();
-            JSONObject jsonObject = new JSONObject(request.toString());
-            SSHManager manager = new SSHManager(
-                    jsonObject.optString("user"),
-                    jsonObject.optString("password"),
-                    jsonObject.optString("fqdn"),
-                    jsonObject.optString("knownHosts"),
-                    jsonObject.has("port") ? Integer.parseInt(jsonObject.getString("port")) : Endpoint.DEFAULT_SSH_PORT,
-                    jsonObject.optString("privateKey"));
-            result = engine.run(manager).toString();
-            if(cmd.hasOption("s"))
-                System.out.println(result);
-        }
-        if (cmd.hasOption("o"))
-            if (result != "") {
-                engine.writeToFile(cmd.getOptionValue("o"), result);
-            }
-    }
-
-    public boolean printHelp() throws IOException {
-        if (cmd.getParsedOptions() == null)
-            printUsage(System.out);
-        else if (cmd.hasOption("h"))
-            printUsage(System.out);
-        else
-            return false;
-        return true;
-    }
-
-    public boolean confirmInput() throws IOException, ParseException {
-        Hashtable<String, List<Object>> table = new Hashtable<>();
-        for (Option option : cmd.getParsedOptions()) {
-            String title = cmd.getOptionTitle(option);
-            if (!table.containsKey(title))
-                table.put(title, new ArrayList<>());
-            table.get(title).add(cmd.getParsedValue(option));
-        }
-/*
-        String[] values = inputToArray(cmd.getParsedValues());
-        Log.out(System.out, true, "Your input was:");
-        Log.out(System.out, true, values);
-*/
-        List<String> list = new ArrayList<>();
-        list.add("Your input was:");
-        for (Map.Entry<String, List<Object>> entry : table.entrySet()) {
-            list.add(formatString(4, cmd.getOptionsTab(), ':', entry.getKey(), String.valueOf(entry.getValue()).replaceAll("\\[|\\]", "")));
-        }
-        Log.out(System.out, true, list.toArray(new String[list.size()]));
-        Log.out(System.out, "Proceed using this information? [y/n] ");
-        switch (new Scanner(System.in).nextLine().trim().toLowerCase()) {
-            case "y":
-            case "":
-                list.add("");
-                log.out(true, list.toArray(new String[list.size()]));
-                Log.out(System.out, true, "");
-                return true;
-        }
-        return false;
-    }
-
-/*
-    private String[] inputToArray(Hashtable<String, List<Object>> table) {
-        List<String> list = new ArrayList<>();
-        for (Map.Entry<String, List<Object>> entry : table.entrySet()) {
-            list.add(formatString(4, cmd.getOptionsTab(), ':', entry.getKey(), String.valueOf(entry.getValue()).replaceAll("\\[|\\]", "")));
-        }
-        return list.toArray(new String[list.size()]);
-    }
-*/
-
-    public boolean convert() throws JSONException, IOException, ParseException {
+import java.text.ParseException;
+import java.util.LinkedList;
+import java.util.Scanner;
+
+public class Engine2 {
+
+    public JSONArray run(SSHManager instance) throws JSchException, IOException, JSONException {
+        String dpkgStatus = "less /var/lib/dpkg/status";
+        String result;
+        if (instance != null) {
+            instance.connect();
+            result = instance.sendCommand(dpkgStatus);
+        } else
+            result = doLocalCommand(dpkgStatus);
+
+        StringBuilder stringBuilder = new StringBuilder(result);
+        Scanner scanner = new Scanner(stringBuilder.toString());
+        LinkedList<String> packgeList = buildList(scanner);
+        JSONArray array = parseList(packgeList);
+
+        // printList(packgeList);
+
+        writeToFile(array.toString(2));
+        if (instance != null)
+            instance.close();
+
+        return array;
+    }
+
+    public JSONArray run() throws ParseException, JSchException, JSONException, IOException {
+        return run(null);
+    }
+
+    public String doLocalCommand(String command) throws IOException {
+        StringBuilder outputBuffer = new StringBuilder();
+        InputStream commandOutput;
+        ProcessBuilder processBuilder = new ProcessBuilder("/bin/sh", "-c", command);
+        Process p = processBuilder.start();
+        commandOutput = p.getInputStream();
+
+        int readByte = commandOutput.read();
+        while (readByte != 0xffffffff) {
+            outputBuffer.append((char) readByte);
+            readByte = commandOutput.read();
+        }
+        commandOutput.close();
+        p.destroy();
+        return outputBuffer.toString();
+    }
+
+
+    private void printList(LinkedList<String> packgeList) throws IOException {
+        StringBuilder stringBuilder = new StringBuilder();
+        for (String str : packgeList)
+            stringBuilder.append(str);
+
+        writeToFile(stringBuilder.toString());
+
+    }
+
+    private JSONArray parseList(LinkedList<String> packgeList) throws JSONException {
+
+        JSONArray array = new JSONArray();
+        for (String str : packgeList) {
+            array.put(parser(str));
+        }
+        return array;
+    }
+
+    private void writeToFile(String result) throws IOException {
+        File file = new File("intel-extraction.json");
+        if (file.exists())
+            file.createNewFile();
+
+        FileWriter fileWriter = new FileWriter(file.getAbsoluteFile());
+        BufferedWriter bufWriter = new BufferedWriter(fileWriter);
+        bufWriter.write(result);
+        bufWriter.close();
+
+    }
+
+    private LinkedList<String> buildList(Scanner scanner) {
+        LinkedList<String> linkedList = new LinkedList<>();
+        StringBuilder stringBuilder = new StringBuilder();
+        String tmp;
+        while (scanner.hasNextLine()) {
+            tmp = scanner.nextLine();
+            stringBuilder.append(tmp + "\n");
+
+            if (tmp.isEmpty()) {
+                linkedList.add(stringBuilder.toString());
+                stringBuilder = new StringBuilder();
+            }
+        }
+        return linkedList;
+    }
+
+
+    public JSONObject parser(String pkg) throws JSONException {
+        Scanner scanner = new Scanner(pkg);
+        JSONObject jsonObject = new JSONObject();
+        String key = "";
+        while (scanner.hasNextLine()) {
+            String tmp = "";
+
+            if (scanner.hasNext())
+                tmp = scanner.next();
+
+            if (tmp.endsWith(":")) {
+                key = tmp.replace(':', ' ').trim();
+            }
+
+            switch (key.toLowerCase()) {
+                    case "conffiles":
+                        getConffiles(scanner, jsonObject, tmp, key);
+                        break;
+
+                // fields with |
+                case "pre-depends":
+                case "recommends":
+                case "suggests":
+                case "depends":
+                    // fields without |
+                case "provides":
+                case "conflicts":
+                case "replaces":
+                    JSONArray jsonArrayAnd = getDepends(scanner);
+                    jsonObject.put(key, jsonArrayAnd);
+                    break;
+                default:
+                    if (scanner.hasNextLine())
+                        jsonObject.put(key, scanner.nextLine().trim());
+                    break;
+            }
+
+        }
+        return jsonObject;
+    }
+
+    private JSONArray getDepends(Scanner scanner) throws JSONException {
+        String[] depends = scanner.nextLine().trim().split(",");
+        // main array
+        JSONArray jsonArrayAnd = new JSONArray();
+        for (String s : depends) {
+            JSONArray jsonArrayOr = new JSONArray();
+
+            if (s.contains("|")) {
+                JSONArray result = orDependency(s);
+                jsonArrayOr.put(result);
+//                System.out.println("Result " + result.toString());
+            } else {
+                String[] temp = s.trim().split(" ");
+                JSONObject jsonDependency = new JSONObject();
+                for (String pkgOr : temp) {
+                    String[] split = pkgOr.trim().split(" ");
+                    for (String string : split) {
+                        if (string.contains("(")) {
+                            jsonDependency.put("Comparator", string.replace("(", ""));
+                        } else if (string.contains(")")) {
+                            jsonDependency.put("Version", string.replace(")", ""));
+                        } else if (string.length() > 0) {
+                            jsonDependency.put("Package", string.trim());
+                        }
+//                    System.out.println("STRING" + string);
+                    }
+                }
+                jsonArrayOr.put(jsonDependency);
+            }
+            if (jsonArrayOr.length() == 1)
+                jsonArrayAnd.put(jsonArrayOr.get(0));
+            else
+                jsonArrayAnd.put(jsonArrayOr);
+        }
+        return jsonArrayAnd;
+    }
+
+    private JSONArray orDependency(String s) throws JSONException {
+        String[] temp = s.trim().split("\\|");
+        JSONArray orDependencies = new JSONArray();
+        for (String pkgOr : temp) {
+            JSONObject jsonDependency = new JSONObject();
+            String[] split = pkgOr.trim().split(" ");
+            for (String string : split) {
+                if (string.contains("(")) {
+                    jsonDependency.put("Comparator", string.replace("(", ""));
+                } else if (string.contains(")")) {
+                    jsonDependency.put("Version", string.replace(")", ""));
+                } else if (string.length() > 0) {
+                    jsonDependency.put("Package", string.trim());
+                }
+            }
+            orDependencies.put(jsonDependency);
+        }
+        return orDependencies;
+    }
+
+
+    private void getConffiles(Scanner scanner, JSONObject jsonObject, String tmp, String key) throws JSONException {
         JSONArray jsonArray = new JSONArray();
-        for (Object o : cmd.getAllParsedValues("f")) {
-            if (!(o instanceof File) || !((File) o).isFile()) {
-                Log.out(System.out, true, true, "Invalid file" + (o != null ? ": " + o : "."));
-                return false;
-            }
-            Scanner scanner = new Scanner((File) o);
-            JSONObject jsonObject = new JSONObject();
-            while (scanner.hasNextLine()) {
-                Map.Entry<String, String> entry = new AbstractMap.SimpleImmutableEntry<>(
-                        scanner.findInLine(Pattern.compile("[\\p{L}|\\p{N}]+")),
-                        scanner.nextLine().substring(1).trim()
-                );
-                if (entry.getValue() != null && entry.getValue().length() > 0)
-                    jsonObject.put(entry.getKey(), entry.getValue());
-            }
-            jsonArray.put(jsonObject);
-        }
-        request.put("extractions", jsonArray);
-        return true;
-    }
-
-    public void printRequest() throws JSONException, IOException {
-        log.out(true, request.toString(2));
-        Log.out(System.out, true, "Input generated.");
-    }
-
-    /*public StatusLine submit() throws IOException, JSONException {
-        HttpPost post = new HttpPost("/api/extract");
-        post.setHeader("Content-Type", "application/json");
-        post.setEntity(new StringEntity(request.toString()));
-        HttpResponse httpResponse = new DefaultHttpClient().execute(post);
-
-        if (httpResponse.getFirstHeader("Content-Type").getValue().equals("application/json")) {
-            ByteArrayOutputStream stream = new ByteArrayOutputStream();
-            httpResponse.getEntity().writeTo(stream);
-            response = new JSONObject(new String(stream.toByteArray()));
-        }
-        return httpResponse.getStatusLine();
-    }*/
-
-    public void printResponse() throws JSONException, IOException {
-        log.out(true, response.toString(2));
-    }
-
-    private void setOptions() {
-        cmd.addOption(
-                CLOption.buildOption(new Option("h", "help", false, "print help")),
-                CLOption.buildOption(new Option("l", "local-extraction", false, "Do local extraction")),
-                CLOption.buildOption(new Option("s", "show-extraction", false, "Show extraction in stdout")),
-                CLOption.buildOption(new Option("f", "text-file", true, "load request from text file"), "path-to-file", File.class).setTitle("Text files"),
-                CLOption.buildOption(new Option("j", "json-file", true, "load request from json file"), "path-to-file", File.class).setTitle("JSON files"),
-                CLOption.buildOption(new Option("o", "out", true, "file to save output to"), "path-to-file", File.class).setTitle("Output file")
-        );
-    }
-
-    private OutputStream parse(String[] args) throws ParseException, FileNotFoundException {
-        try {
-            cmd.parse(args);
-            if (cmd.hasOption("o"))
-                return new FileOutputStream((File) cmd.getParsedValue("o"));
-        } catch (ParseException e) {
-            throw new ParseException(e.getMessage() + "\n");
-        }
-        return null;
-    }
-
-    private Properties readManifest() throws IOException {
-        Properties manifest = new Properties();
-        Scanner scan = new Scanner(getClass().getClassLoader().getResourceAsStream("META-INF/MANIFEST.MF"));
-        manifest.setProperty("title",
-                scan.findWithinHorizon(Pattern.compile("Implementation-Title:", Pattern.CASE_INSENSITIVE), 0) != null
-                        ? scan.nextLine().trim()
-                        : "Context Population CLI");
-        scan.reset();
-        manifest.setProperty("version",
-                scan.findWithinHorizon(Pattern.compile("Implementation-Version:", Pattern.CASE_INSENSITIVE), 0) != null
-                        ? scan.nextLine().trim()
-                        : "0.0.1-SNAPSHOT");
-        return manifest;
-    }
-
-    private void printUsage(OutputStream out) throws IOException {
-        Properties mf = readManifest();
-        new HelpFormatter().printHelp(new PrintWriter(out, true), 120, "extraction", "", cmd.getOptions(), 2, 4,
-                "\nRunning version " + mf.getProperty("version") + " of the " + mf.getProperty("title") + ".", true);
-    }
-
-    private String formatString(int indentation, int tabSize, char separator, String string1, String string2) {
-        return (indentation > 0 ? String.format("%" + indentation + "s", ' ') : "") + string1 +
-                (separator != '\0' ? separator : "")
-                + (tabSize > 0 ? String.format("%" + Math.max(tabSize - string1.length(), 1) + "s", ' ') : "") + string2;
-    }
-
+        JSONObject jsonObject1 = new JSONObject();
+        String line = "";
+        if (scanner.hasNextLine())
+            line = scanner.nextLine().trim();
+
+        if (!tmp.contains(key)) {
+            jsonObject1.put("file", tmp);
+            jsonObject1.put("hash", line);
+            jsonArray.put(jsonObject1);
+            if (jsonObject.has(key)) {
+                jsonObject.getJSONArray(key).put(jsonObject1);
+            } else {
+                jsonObject.put(key, jsonArray);
+            }
+        }
+    }
 }