Example usage for java.io PrintWriter close

Introduction

In this page you can find the example usage for java.io PrintWriter close.

Prototype

public void close() 

Source Link

Document

Closes the stream and releases any system resources associated with it.

Usage

From source file:ch.epfl.lsir.xin.test.MostPopularTest.java

/**
 * @param args//w  w w.  j  a v  a2 s.co m
 */
public static void main(String[] args) throws Exception {
    // TODO Auto-generated method stub

    PrintWriter logger = new PrintWriter(".//results//MostPopular");
    PropertiesConfiguration config = new PropertiesConfiguration();
    config.setFile(new File(".//conf//MostPopular.properties"));
    try {
        config.load();
    } catch (ConfigurationException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + " Read rating data...");
    DataLoaderFile loader = new DataLoaderFile(".//data//MoveLens100k.txt");
    loader.readSimple();
    DataSetNumeric dataset = loader.getDataset();
    System.out.println("Number of ratings: " + dataset.getRatings().size() + " Number of users: "
            + dataset.getUserIDs().size() + " Number of items: " + dataset.getItemIDs().size());
    logger.println("Number of ratings: " + dataset.getRatings().size() + ", Number of users: "
            + dataset.getUserIDs().size() + ", Number of items: " + dataset.getItemIDs().size());
    logger.flush();

    TrainTestSplitter splitter = new TrainTestSplitter(dataset);
    splitter.splitFraction(config.getDouble("TRAIN_FRACTION"));
    ArrayList<NumericRating> trainRatings = splitter.getTrain();
    ArrayList<NumericRating> testRatings = splitter.getTest();

    HashMap<String, Integer> userIDIndexMapping = new HashMap<String, Integer>();
    HashMap<String, Integer> itemIDIndexMapping = new HashMap<String, Integer>();
    //create rating matrix
    for (int i = 0; i < dataset.getUserIDs().size(); i++) {
        userIDIndexMapping.put(dataset.getUserIDs().get(i), i);
    }
    for (int i = 0; i < dataset.getItemIDs().size(); i++) {
        itemIDIndexMapping.put(dataset.getItemIDs().get(i), i);
    }
    RatingMatrix trainRatingMatrix = new RatingMatrix(dataset.getUserIDs().size(), dataset.getItemIDs().size());
    for (int i = 0; i < trainRatings.size(); i++) {
        trainRatingMatrix.set(userIDIndexMapping.get(trainRatings.get(i).getUserID()),
                itemIDIndexMapping.get(trainRatings.get(i).getItemID()), trainRatings.get(i).getValue());
    }
    RatingMatrix testRatingMatrix = new RatingMatrix(dataset.getUserIDs().size(), dataset.getItemIDs().size());
    for (int i = 0; i < testRatings.size(); i++) {
        //only consider 5-star rating in the test set
        //         if( testRatings.get(i).getValue() < 5 )
        //            continue;
        testRatingMatrix.set(userIDIndexMapping.get(testRatings.get(i).getUserID()),
                itemIDIndexMapping.get(testRatings.get(i).getItemID()), testRatings.get(i).getValue());
    }
    System.out.println("Training: " + trainRatingMatrix.getTotalRatingNumber() + " vs Test: "
            + testRatingMatrix.getTotalRatingNumber());

    logger.println("Initialize a most popular based recommendation model.");
    MostPopular algo = new MostPopular(trainRatingMatrix);
    algo.setLogger(logger);
    algo.build();
    algo.saveModel(".//localModels//" + config.getString("NAME"));
    logger.println("Save the model.");
    logger.flush();

    HashMap<Integer, ArrayList<ResultUnit>> results = new HashMap<Integer, ArrayList<ResultUnit>>();
    for (int i = 0; i < testRatingMatrix.getRow(); i++) {
        ArrayList<ResultUnit> rec = algo.getRecommendationList(i);
        if (rec == null)
            continue;
        int total = testRatingMatrix.getUserRatingNumber(i);
        if (total == 0)//this user is ignored
            continue;
        results.put(i, rec);
    }

    RankResultGenerator generator = new RankResultGenerator(results, algo.getTopN(), testRatingMatrix,
            trainRatingMatrix);
    System.out.println("Precision@N: " + generator.getPrecisionN());
    System.out.println("Recall@N: " + generator.getRecallN());
    System.out.println("MAP@N: " + generator.getMAPN());
    System.out.println("MRR@N: " + generator.getMRRN());
    System.out.println("NDCG@N: " + generator.getNDCGN());
    System.out.println("AUC@N: " + generator.getAUC());
    logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + "\n" + "Precision@N: "
            + generator.getPrecisionN() + "\n" + "Recall@N: " + generator.getRecallN() + "\n" + "MAP@N: "
            + generator.getMAPN() + "\n" + "MRR@N: " + generator.getMRRN() + "\n" + "NDCG@N: "
            + generator.getNDCGN() + "\n" + "AUC@N: " + generator.getAUC());
    logger.flush();
    logger.close();
}

---

From source file:friendsandfollowers.DBFollowersIDs.java

public static void main(String[] args) throws ClassNotFoundException, SQLException, JSONException,
        FileNotFoundException, UnsupportedEncodingException {

    // Check arguments that passed in
    if ((args == null) || (args.length == 0)) {
        System.err.println("2 Parameters are required plus one optional " + "parameter to launch a Job.");
        System.err.println("First: String 'OUTPUT: /output/path/'");
        System.err.println("Second: (int) Number of ids to fetch. " + "Provide number which increment by 5000 "
                + "(5000, 10000, 15000 etc) " + "or -1 to fetch all ids.");
        System.err.println("Third (optional): 'screen_name / user_id_str'");
        System.err.println("If 3rd argument not provided then provide" + " Twitter users through database.");
        System.exit(-1);//from  w  w  w  .  jav  a 2s . c  o  m
    }

    MysqlDB DB = new MysqlDB();
    AppOAuth AppOAuths = new AppOAuth();
    Misc helpers = new Misc();
    String endpoint = "/followers/ids";

    String OutputDirPath = null;
    try {
        OutputDirPath = StringEscapeUtils.escapeJava(args[0]);
    } catch (Exception e) {
        System.err.println("Argument" + args[0] + " must be an String.");
        System.exit(-1);
    }

    int IDS_TO_FETCH_INT = -1;
    try {
        IDS_TO_FETCH_INT = Integer.parseInt(args[1]);
    } catch (NumberFormatException e) {
        System.err.println("Argument" + args[1] + " must be an integer.");
        System.exit(-1);
    }

    int IDS_TO_FETCH = 0;
    if (IDS_TO_FETCH_INT > 5000) {

        float IDS_TO_FETCH_F = (float) IDS_TO_FETCH_INT / 5000;
        IDS_TO_FETCH = (int) Math.ceil(IDS_TO_FETCH_F);
    } else if ((IDS_TO_FETCH_INT <= 5000) && (IDS_TO_FETCH_INT > 0)) {
        IDS_TO_FETCH = 1;
    }

    String targetedUser = "";
    if (args.length == 3) {
        try {
            targetedUser = StringEscapeUtils.escapeJava(args[2]);
        } catch (Exception e) {
            System.err.println("Argument" + args[2] + " must be an String.");
            System.exit(-1);
        }
    }

    try {

        TwitterFactory tf = AppOAuths.loadOAuthUser(endpoint);
        Twitter twitter = tf.getInstance();

        int RemainingCalls = AppOAuths.RemainingCalls;
        int RemainingCallsCounter = 0;
        System.out.println("First Time Remianing Calls: " + RemainingCalls);

        String Screen_name = AppOAuths.screen_name;
        System.out.println("First Time Loaded OAuth Screen_name: " + Screen_name);

        IDs ids;
        System.out.println("Listing followers ids.");

        // if targetedUser not provided by argument, then look into database.
        if (StringUtils.isEmpty(targetedUser)) {

            String selectQuery = "SELECT * FROM `followers_parent` WHERE " + "`targeteduser` != '' AND "
                    + "`nextcursor` != '0' AND " + "`nextcursor` != '2'";

            ResultSet results = DB.selectQ(selectQuery);

            int numRows = DB.numRows(results);
            if (numRows < 1) {
                System.err.println("No User in database to get followersIDS");
                System.exit(-1);
            }

            OUTERMOST: while (results.next()) {

                int followers_parent_id = results.getInt("id");
                targetedUser = results.getString("targeteduser");
                long cursor = results.getLong("nextcursor");
                System.out.println("Targeted User: " + targetedUser);

                int idsLoopCounter = 0;
                int totalIDs = 0;

                // put idsJSON in a file
                PrintWriter writer = new PrintWriter(OutputDirPath + "/" + targetedUser, "UTF-8");

                // call different functions for screen_name and id_str
                Boolean chckedNumaric = helpers.isNumeric(targetedUser);

                do {
                    ids = null;
                    try {

                        if (chckedNumaric) {

                            long LongValueTargetedUser = Long.valueOf(targetedUser).longValue();

                            ids = twitter.getFollowersIDs(LongValueTargetedUser, cursor);
                        } else {
                            ids = twitter.getFollowersIDs(targetedUser, cursor);
                        }

                    } catch (TwitterException te) {

                        // do not throw if user has protected tweets, 
                        // or if they deleted their account
                        if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED
                                || te.getStatusCode() == HttpResponseCode.NOT_FOUND) {

                            System.out.println(targetedUser + " is protected or account is deleted");
                        } else {
                            System.out.println("Followers Get Exception: " + te.getMessage());
                        }

                        // If rate limit reached then switch Auth user
                        RemainingCallsCounter++;
                        if (RemainingCallsCounter >= RemainingCalls) {

                            // load auth user
                            tf = AppOAuths.loadOAuthUser(endpoint);
                            twitter = tf.getInstance();

                            System.out.println(
                                    "New User Loaded OAuth" + " Screen_name: " + AppOAuths.screen_name);

                            RemainingCalls = AppOAuths.RemainingCalls;
                            RemainingCallsCounter = 0;

                            System.out.println("New Remianing Calls: " + RemainingCalls);
                        }

                        // update cursor in "followers_parent"
                        String fieldValues = "`nextcursor` = 2";
                        String where = "id = " + followers_parent_id;
                        DB.Update("`followers_parent`", fieldValues, where);

                        // If error then switch to next user
                        continue OUTERMOST;
                    }

                    if (ids.getIDs().length > 0) {

                        idsLoopCounter++;
                        totalIDs += ids.getIDs().length;
                        System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length);

                        JSONObject responseDetailsJson = new JSONObject();
                        JSONArray jsonArray = new JSONArray();
                        for (long id : ids.getIDs()) {
                            jsonArray.put(id);
                        }
                        Object idsJSON = responseDetailsJson.put("ids", jsonArray);

                        writer.println(idsJSON);
                    }

                    // If rate limit reached then switch Auth user
                    RemainingCallsCounter++;
                    if (RemainingCallsCounter >= RemainingCalls) {

                        // load auth user
                        tf = AppOAuths.loadOAuthUser(endpoint);
                        twitter = tf.getInstance();

                        System.out.println("New User Loaded OAuth " + "Screen_name: " + AppOAuths.screen_name);

                        RemainingCalls = AppOAuths.RemainingCalls;
                        RemainingCallsCounter = 0;

                        System.out.println("New Remianing Calls: " + RemainingCalls);
                    }

                    if (IDS_TO_FETCH_INT != -1) {
                        if (idsLoopCounter == IDS_TO_FETCH) {
                            break;
                        }
                    }

                } while ((cursor = ids.getNextCursor()) != 0);
                writer.close();
                System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs);
                System.out.println();

                // update cursor in "followers_parent"
                String fieldValues = "`nextcursor` = " + cursor;
                String where = "id = " + followers_parent_id;
                DB.Update("`followers_parent`", fieldValues, where);

            } // loop through every result found in db
        } else {

            // Second Argument Set, so we are here.
            System.out.println("screen_name / user_id_str passed by argument");

            int idsLoopCounter = 0;
            int totalIDs = 0;

            // put idsJSON in a file
            PrintWriter writer = new PrintWriter(
                    OutputDirPath + "/" + targetedUser + "_ids_" + helpers.getUnixTimeStamp(), "UTF-8");

            // call different functions for screen_name and id_str
            Boolean chckedNumaric = helpers.isNumeric(targetedUser);
            long cursor = -1;

            do {
                ids = null;
                try {

                    if (chckedNumaric) {

                        long LongValueTargetedUser = Long.valueOf(targetedUser).longValue();

                        ids = twitter.getFollowersIDs(LongValueTargetedUser, cursor);
                    } else {
                        ids = twitter.getFollowersIDs(targetedUser, cursor);
                    }

                } catch (TwitterException te) {

                    // do not throw if user has protected tweets, or if they deleted their account
                    if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED
                            || te.getStatusCode() == HttpResponseCode.NOT_FOUND) {

                        System.out.println(targetedUser + " is protected or account is deleted");
                    } else {
                        System.out.println("Followers Get Exception: " + te.getMessage());
                    }
                    System.exit(-1);
                }

                if (ids.getIDs().length > 0) {

                    idsLoopCounter++;
                    totalIDs += ids.getIDs().length;
                    System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length);

                    JSONObject responseDetailsJson = new JSONObject();
                    JSONArray jsonArray = new JSONArray();

                    for (long id : ids.getIDs()) {
                        jsonArray.put(id);
                    }

                    Object idsJSON = responseDetailsJson.put("ids", jsonArray);
                    writer.println(idsJSON);
                }

                // If rate limit reach then switch Auth user
                RemainingCallsCounter++;
                if (RemainingCallsCounter >= RemainingCalls) {

                    // load auth user
                    tf = AppOAuths.loadOAuthUser(endpoint);
                    twitter = tf.getInstance();

                    System.out.println("New User Loaded OAuth Screen_name: " + AppOAuths.screen_name);

                    RemainingCalls = AppOAuths.RemainingCalls;
                    RemainingCallsCounter = 0;

                    System.out.println("New Remianing Calls: " + RemainingCalls);
                }

                if (IDS_TO_FETCH_INT != -1) {
                    if (idsLoopCounter == IDS_TO_FETCH) {
                        break;
                    }
                }

            } while ((cursor = ids.getNextCursor()) != 0);
            writer.close();

            System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs);
            System.out.println();
        }

    } catch (TwitterException te) {
        // te.printStackTrace();
        System.err.println("Failed to get followers' ids: " + te.getMessage());
        System.exit(-1);
    }
    System.out.println("!!!! DONE !!!!");
}

---

From source file:friendsandfollowers.DBFriendsIDs.java

public static void main(String[] args) throws ClassNotFoundException, SQLException, JSONException,
        FileNotFoundException, UnsupportedEncodingException {

    // Check arguments that passed in
    if ((args == null) || (args.length == 0)) {
        System.err.println("2 Parameters are required plus one optional " + "parameter to launch a Job.");
        System.err.println("First: String 'OUTPUT: /output/path/'");
        System.err.println("Second: (int) Number of ids to fetch. " + "Provide number which increment by 5000 "
                + "(5000, 10000, 15000 etc) " + "or -1 to fetch all ids.");
        System.err.println("Third (optional): 'screen_name / user_id_str'");
        System.err.println("If 3rd argument not provided then provide" + " Twitter users through database.");
        System.exit(-1);// w  ww .  ja va 2  s  .  c o  m
    }

    MysqlDB DB = new MysqlDB();
    AppOAuth AppOAuths = new AppOAuth();
    Misc helpers = new Misc();
    String endpoint = "/friends/ids";

    String OutputDirPath = null;
    try {
        OutputDirPath = StringEscapeUtils.escapeJava(args[0]);
    } catch (Exception e) {
        System.err.println("Argument" + args[0] + " must be an String.");
        System.exit(-1);
    }

    int IDS_TO_FETCH_INT = -1;
    try {
        IDS_TO_FETCH_INT = Integer.parseInt(args[1]);
    } catch (NumberFormatException e) {
        System.err.println("Argument" + args[1] + " must be an integer.");
        System.exit(-1);
    }

    int IDS_TO_FETCH = 0;
    if (IDS_TO_FETCH_INT > 5000) {

        float IDS_TO_FETCH_F = (float) IDS_TO_FETCH_INT / 5000;
        IDS_TO_FETCH = (int) Math.ceil(IDS_TO_FETCH_F);
    } else if ((IDS_TO_FETCH_INT <= 5000) && (IDS_TO_FETCH_INT > 0)) {
        IDS_TO_FETCH = 1;
    }

    String targetedUser = "";
    if (args.length == 3) {
        try {
            targetedUser = StringEscapeUtils.escapeJava(args[2]);
        } catch (Exception e) {
            System.err.println("Argument" + args[2] + " must be an String.");
            System.exit(-1);
        }
    }

    try {

        TwitterFactory tf = AppOAuths.loadOAuthUser(endpoint);
        Twitter twitter = tf.getInstance();

        int RemainingCalls = AppOAuths.RemainingCalls;
        int RemainingCallsCounter = 0;
        System.out.println("First Time Remianing Calls: " + RemainingCalls);

        String Screen_name = AppOAuths.screen_name;
        System.out.println("First Time Loaded OAuth Screen_name: " + Screen_name);

        IDs ids;
        System.out.println("Listing friends ids.");

        // if targetedUser not provided by argument, then look into database.
        if (StringUtils.isEmpty(targetedUser)) {

            String selectQuery = "SELECT * FROM `followings_parent` WHERE " + "`targeteduser` != '' AND "
                    + "`nextcursor` != '0' AND " + "`nextcursor` != '2'";

            ResultSet results = DB.selectQ(selectQuery);

            int numRows = DB.numRows(results);
            if (numRows < 1) {
                System.err.println("No User in database to get friendsIDS");
                System.exit(-1);
            }

            OUTERMOST: while (results.next()) {

                int following_parent_id = results.getInt("id");
                targetedUser = results.getString("targeteduser");
                long cursor = results.getLong("nextcursor");
                System.out.println("Targeted User: " + targetedUser);

                int idsLoopCounter = 0;
                int totalIDs = 0;

                // put idsJSON in a file
                PrintWriter writer = new PrintWriter(OutputDirPath + "/" + targetedUser, "UTF-8");

                // call different functions for screen_name and id_str
                Boolean chckedNumaric = helpers.isNumeric(targetedUser);

                do {
                    ids = null;
                    try {

                        if (chckedNumaric) {

                            long LongValueTargetedUser = Long.valueOf(targetedUser).longValue();

                            ids = twitter.getFriendsIDs(LongValueTargetedUser, cursor);
                        } else {
                            ids = twitter.getFriendsIDs(targetedUser, cursor);
                        }

                    } catch (TwitterException te) {

                        // do not throw if user has protected tweets, 
                        // or if they deleted their account
                        if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED
                                || te.getStatusCode() == HttpResponseCode.NOT_FOUND) {

                            System.out.println(targetedUser + " is protected or account is deleted");
                        } else {
                            System.out.println("Friends Get Exception: " + te.getMessage());
                        }

                        // If rate limit reached then switch Auth user
                        RemainingCallsCounter++;
                        if (RemainingCallsCounter >= RemainingCalls) {

                            // load auth user
                            tf = AppOAuths.loadOAuthUser(endpoint);
                            twitter = tf.getInstance();

                            System.out.println(
                                    "New User Loaded OAuth" + " Screen_name: " + AppOAuths.screen_name);

                            RemainingCalls = AppOAuths.RemainingCalls;
                            RemainingCallsCounter = 0;

                            System.out.println("New Remianing Calls: " + RemainingCalls);
                        }

                        // update cursor in "followings_parent"
                        String fieldValues = "`nextcursor` = 2";
                        String where = "id = " + following_parent_id;
                        DB.Update("`followings_parent`", fieldValues, where);

                        // If error then switch to next user
                        continue OUTERMOST;
                    }

                    if (ids.getIDs().length > 0) {

                        idsLoopCounter++;
                        totalIDs += ids.getIDs().length;
                        System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length);

                        JSONObject responseDetailsJson = new JSONObject();
                        JSONArray jsonArray = new JSONArray();
                        for (long id : ids.getIDs()) {
                            jsonArray.put(id);
                        }
                        Object idsJSON = responseDetailsJson.put("ids", jsonArray);

                        writer.println(idsJSON);
                    }

                    // If rate limit reached then switch Auth user.
                    RemainingCallsCounter++;
                    if (RemainingCallsCounter >= RemainingCalls) {

                        // load auth user
                        tf = AppOAuths.loadOAuthUser(endpoint);
                        twitter = tf.getInstance();

                        System.out.println("New User Loaded OAuth " + "Screen_name: " + AppOAuths.screen_name);

                        RemainingCalls = AppOAuths.RemainingCalls;
                        RemainingCallsCounter = 0;

                        System.out.println("New Remianing Calls: " + RemainingCalls);
                    }

                    if (IDS_TO_FETCH_INT != -1) {
                        if (idsLoopCounter == IDS_TO_FETCH) {
                            break;
                        }
                    }

                } while ((cursor = ids.getNextCursor()) != 0);
                writer.close();
                System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs);
                System.out.println();

                // update cursor in "followings_parent"
                String fieldValues = "`nextcursor` = " + cursor;
                String where = "id = " + following_parent_id;
                DB.Update("`followings_parent`", fieldValues, where);

            } // loop through every result found in db
        } else {

            // Second Argument Sets, so we are here.
            System.out.println("screen_name / user_id_str " + "passed by argument");

            int idsLoopCounter = 0;
            int totalIDs = 0;

            // put idsJSON in a file
            PrintWriter writer = new PrintWriter(
                    OutputDirPath + "/" + targetedUser + "_ids_" + helpers.getUnixTimeStamp(), "UTF-8");

            // call different functions for screen_name and id_str
            Boolean chckedNumaric = helpers.isNumeric(targetedUser);
            long cursor = -1;

            do {
                ids = null;
                try {

                    if (chckedNumaric) {

                        long LongValueTargetedUser = Long.valueOf(targetedUser).longValue();

                        ids = twitter.getFriendsIDs(LongValueTargetedUser, cursor);
                    } else {
                        ids = twitter.getFriendsIDs(targetedUser, cursor);
                    }

                } catch (TwitterException te) {

                    // do not throw if user has protected tweets, 
                    // or if they deleted their account
                    if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED
                            || te.getStatusCode() == HttpResponseCode.NOT_FOUND) {

                        System.out.println(targetedUser + " is protected or account is deleted");
                    } else {
                        System.out.println("Friends Get Exception: " + te.getMessage());
                    }
                    System.exit(-1);
                }

                if (ids.getIDs().length > 0) {

                    idsLoopCounter++;
                    totalIDs += ids.getIDs().length;
                    System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length);

                    JSONObject responseDetailsJson = new JSONObject();
                    JSONArray jsonArray = new JSONArray();
                    for (long id : ids.getIDs()) {
                        jsonArray.put(id);
                    }
                    Object idsJSON = responseDetailsJson.put("ids", jsonArray);

                    writer.println(idsJSON);

                }

                // If rate limit reach then switch Auth user
                RemainingCallsCounter++;
                if (RemainingCallsCounter >= RemainingCalls) {

                    // load auth user
                    tf = AppOAuths.loadOAuthUser(endpoint);
                    twitter = tf.getInstance();

                    System.out.println("New User Loaded OAuth Screen_name: " + AppOAuths.screen_name);

                    RemainingCalls = AppOAuths.RemainingCalls;
                    RemainingCallsCounter = 0;

                    System.out.println("New Remianing Calls: " + RemainingCalls);
                }

                if (IDS_TO_FETCH_INT != -1) {
                    if (idsLoopCounter == IDS_TO_FETCH) {
                        break;
                    }
                }

            } while ((cursor = ids.getNextCursor()) != 0);
            writer.close();
            System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs);
            System.out.println();

        }

    } catch (TwitterException te) {
        // te.printStackTrace();
        System.err.println("Failed to get friends' ids: " + te.getMessage());
        System.exit(-1);
    }
    System.out.println("!!!! DONE !!!!");
}

---

From source file:friendsandfollowers.FilesThreaderFriendsIDsParser.java

public static void main(String[] args) throws ClassNotFoundException, SQLException, JSONException,
        FileNotFoundException, UnsupportedEncodingException {

    // Check how many arguments were passed in
    if ((args == null) || (args.length < 5)) {
        System.err.println("5 Parameters are required  plus one optional " + "parameter to launch a Job.");
        System.err.println("First: String 'INPUT: DB or /input/path/'");
        System.err.println("Second: String 'OUTPUT: /output/path/'");
        System.err.println("Third: (int) Total Number Of Jobs");
        System.err.println("Fourth: (int) This Job Number");
        System.err.println("Fifth: (int) Number of seconds to pause");
        System.err.println("Sixth: (int) Number of ids to fetch" + "Provide number which increment by 5000 "
                + "(5000, 10000, 15000 etc) " + "or -1 to fetch all ids.");
        System.err.println("Example: fileToRun /input/path/ " + "/output/path/ 10 1 3 75000");
        System.exit(-1);//from  ww w  . j  a  va2 s  . com
    }

    // TODO documentation for command line
    AppOAuth AppOAuths = new AppOAuth();
    Misc helpers = new Misc();
    String endpoint = "/friends/ids";

    String inputPath = null;
    try {
        inputPath = StringEscapeUtils.escapeJava(args[0]);
    } catch (Exception e) {
        System.err.println("Argument " + args[0] + " must be an String.");
        System.exit(-1);
    }

    String outputPath = null;
    try {
        outputPath = StringEscapeUtils.escapeJava(args[1]);
    } catch (Exception e) {
        System.err.println("Argument " + args[1] + " must be an String.");
        System.exit(-1);
    }

    int TOTAL_JOBS = 0;
    try {
        TOTAL_JOBS = Integer.parseInt(args[2]);
    } catch (NumberFormatException e) {
        System.err.println("Argument " + args[2] + " must be an integer.");
        System.exit(1);
    }

    int JOB_NO = 0;
    try {
        JOB_NO = Integer.parseInt(args[3]);
    } catch (NumberFormatException e) {
        System.err.println("Argument " + args[3] + " must be an integer.");
        System.exit(1);
    }

    int secondsToPause = 0;
    try {
        secondsToPause = Integer.parseInt(args[4]);
    } catch (NumberFormatException e) {
        System.err.println("Argument" + args[4] + " must be an integer.");
        System.exit(-1);
    }

    int IDS_TO_FETCH_INT = -1;
    if (args.length == 6) {
        try {
            IDS_TO_FETCH_INT = Integer.parseInt(args[5]);
        } catch (NumberFormatException e) {
            System.err.println("Argument" + args[5] + " must be an integer.");
            System.exit(-1);
        }
    }

    int IDS_TO_FETCH = 0;
    if (IDS_TO_FETCH_INT > 5000) {

        float IDS_TO_FETCH_F = (float) IDS_TO_FETCH_INT / 5000;
        IDS_TO_FETCH = (int) Math.ceil(IDS_TO_FETCH_F);
    } else if ((IDS_TO_FETCH_INT <= 5000) && (IDS_TO_FETCH_INT > 0)) {
        IDS_TO_FETCH = 1;
    }

    secondsToPause = (TOTAL_JOBS * secondsToPause) - (JOB_NO * secondsToPause);
    System.out.println("secondsToPause: " + secondsToPause);
    helpers.pause(secondsToPause);

    try {

        int TotalWorkLoad = 0;
        ArrayList<String> allFiles = null;
        try {
            final File folder = new File(inputPath);
            allFiles = helpers.listFilesForSingleFolder(folder);
            TotalWorkLoad = allFiles.size();
        } catch (Exception e) {

            System.err.println("Input folder is not exists: " + e.getMessage());
            System.exit(-1);
        }

        System.out.println("Total Workload is: " + TotalWorkLoad);

        if (TotalWorkLoad < 1) {
            System.err.println("No screen names file exists in: " + inputPath);
            System.exit(-1);
        }

        if (TOTAL_JOBS > TotalWorkLoad) {
            System.err.println("Number of jobs are more than total work"
                    + " load. Please reduce 'Number of jobs' to launch.");
            System.exit(-1);
        }

        float TotalWorkLoadf = TotalWorkLoad;
        float TOTAL_JOBSf = TOTAL_JOBS;
        float res = (TotalWorkLoadf / TOTAL_JOBSf);

        int chunkSize = (int) Math.ceil(res);
        int offSet = JOB_NO * chunkSize;
        int chunkSizeToGet = (JOB_NO + 1) * chunkSize;

        System.out.println("My Share is " + chunkSize);
        System.out.println();

        // Load OAuh User
        TwitterFactory tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO);
        Twitter twitter = tf.getInstance();

        int RemainingCalls = AppOAuths.RemainingCalls;
        int RemainingCallsCounter = 0;
        System.out.println("First Time OAuth Remianing Calls: " + RemainingCalls);

        String Screen_name = AppOAuths.screen_name;
        System.out.println("First Time Loaded OAuth Screen_name: " + Screen_name);
        System.out.println();

        IDs ids;
        System.out.println("Going to get friends ids.");

        // to write output in a file
        System.out.flush();

        if (JOB_NO + 1 == TOTAL_JOBS) {
            chunkSizeToGet = TotalWorkLoad;
        }

        List<String> myFilesShare = allFiles.subList(offSet, chunkSizeToGet);

        for (String myFile : myFilesShare) {
            System.out.println("Going to parse file: " + myFile);

            try (BufferedReader br = new BufferedReader(new FileReader(inputPath + "/" + myFile))) {
                String line;
                OUTERMOST: while ((line = br.readLine()) != null) {
                    // process the line.

                    System.out.println("Going to get friends ids of Screen-name / user_id: " + line);
                    System.out.println();

                    String targetedUser = line.trim(); // tmp
                    long cursor = -1;
                    int idsLoopCounter = 0;
                    int totalIDs = 0;

                    PrintWriter writer = new PrintWriter(outputPath + "/" + targetedUser, "UTF-8");

                    // call different functions for screen_name and id_str
                    Boolean chckedNumaric = helpers.isNumeric(targetedUser);

                    do {
                        ids = null;
                        try {

                            if (chckedNumaric) {

                                long LongValueTargetedUser = Long.valueOf(targetedUser).longValue();

                                ids = twitter.getFriendsIDs(LongValueTargetedUser, cursor);
                            } else {
                                ids = twitter.getFriendsIDs(targetedUser, cursor);
                            }

                        } catch (TwitterException te) {

                            // do not throw if user has protected tweets, or
                            // if they deleted their account
                            if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED
                                    || te.getStatusCode() == HttpResponseCode.NOT_FOUND) {

                                System.out.println(targetedUser + " is protected or account is deleted");
                            } else {
                                System.out.println("Friends Get Exception: " + te.getMessage());
                            }

                            // If rate limit reached then switch Auth user
                            RemainingCallsCounter++;
                            if (RemainingCallsCounter >= RemainingCalls) {

                                // load auth user
                                tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO);
                                twitter = tf.getInstance();

                                System.out.println(
                                        "New Loaded OAuth User " + " Screen_name: " + AppOAuths.screen_name);

                                RemainingCalls = AppOAuths.RemainingCalls;
                                RemainingCallsCounter = 0;

                                System.out.println("New OAuth Remianing Calls: " + RemainingCalls);
                            }

                            // Remove file if ids not found
                            if (totalIDs == 0) {

                                System.out.println("No ids fetched so removing " + "file " + targetedUser);

                                File fileToDelete = new File(outputPath + "/" + targetedUser);
                                fileToDelete.delete();
                            }
                            System.out.println();

                            // If error then switch to next user
                            continue OUTERMOST;
                        }

                        if (ids.getIDs().length > 0) {

                            idsLoopCounter++;
                            totalIDs += ids.getIDs().length;
                            System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length);

                            JSONObject responseDetailsJson = new JSONObject();
                            JSONArray jsonArray = new JSONArray();
                            for (long id : ids.getIDs()) {
                                jsonArray.put(id);
                            }
                            Object idsJSON = responseDetailsJson.put("ids", jsonArray);

                            writer.println(idsJSON);

                        }

                        // If rate limit reached then switch Auth user
                        RemainingCallsCounter++;
                        if (RemainingCallsCounter >= RemainingCalls) {

                            // load auth user
                            tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO);
                            twitter = tf.getInstance();

                            System.out.println("New Loaded OAuth User Screen_name: " + AppOAuths.screen_name);

                            RemainingCalls = AppOAuths.RemainingCalls;
                            RemainingCallsCounter = 0;

                            System.out.println("New OAuth Remianing Calls: " + RemainingCalls);
                        }

                        if (IDS_TO_FETCH_INT != -1) {
                            if (idsLoopCounter == IDS_TO_FETCH) {
                                break;
                            }
                        }

                    } while ((cursor = ids.getNextCursor()) != 0);

                    writer.close();
                    System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs);

                    // Remove file if ids not found
                    if (totalIDs == 0) {

                        System.out.println("No ids fetched so removing " + "file " + targetedUser);

                        File fileToDelete = new File(outputPath + "/" + targetedUser);
                        fileToDelete.delete();
                    }
                    System.out.println();

                } // while get records from single file
            } // read my single file
            catch (IOException e) {
                System.err.println("Failed to read lines from " + myFile);
            }

            // to write output in a file
            System.out.flush();
        } // all my files share

    } catch (TwitterException te) {
        // te.printStackTrace();
        System.err.println("Failed to get friends' ids: " + te.getMessage());
        System.exit(-1);
    }
    System.out.println("!!!! DONE !!!!");

    // Close System.out for this thread which will
    // flush and close this thread.
    System.out.close();
}

---

From source file:friendsandfollowers.FilesThreaderFollowersIDsParser.java

public static void main(String[] args) throws ClassNotFoundException, SQLException, JSONException,
        FileNotFoundException, UnsupportedEncodingException {

    // Check how many arguments were passed in
    if ((args == null) || (args.length < 5)) {
        System.err.println("5 Parameters are required  plus one optional " + "parameter to launch a Job.");
        System.err.println("First: String 'INPUT: DB or /input/path/'");
        System.err.println("Second: String 'OUTPUT: /output/path/'");
        System.err.println("Third: (int) Total Number Of Jobs");
        System.err.println("Fourth: (int) This Job Number");
        System.err.println("Fifth: (int) Number of seconds to pause");
        System.err.println("Sixth: (int) Number of ids to fetch" + "Provide number which increment by 5000 "
                + "(5000, 10000, 15000 etc) " + "or -1 to fetch all ids.");
        System.err.println("Example: fileToRun /input/path/ " + "/output/path/ 10 1 3 75000");
        System.exit(-1);// w  w  w .  java  2  s  .  c o  m
    }

    // TODO documentation for command line
    AppOAuth AppOAuths = new AppOAuth();
    Misc helpers = new Misc();
    String endpoint = "/followers/ids";

    String inputPath = null;
    try {
        inputPath = StringEscapeUtils.escapeJava(args[0]);
    } catch (Exception e) {
        System.err.println("Argument " + args[0] + " must be an String.");
        System.exit(-1);
    }

    String outputPath = null;
    try {
        outputPath = StringEscapeUtils.escapeJava(args[1]);
    } catch (Exception e) {
        System.err.println("Argument " + args[1] + " must be an String.");
        System.exit(-1);
    }

    int TOTAL_JOBS = 0;
    try {
        TOTAL_JOBS = Integer.parseInt(args[2]);
    } catch (NumberFormatException e) {
        System.err.println("Argument " + args[2] + " must be an integer.");
        System.exit(1);
    }

    int JOB_NO = 0;
    try {
        JOB_NO = Integer.parseInt(args[3]);
    } catch (NumberFormatException e) {
        System.err.println("Argument " + args[3] + " must be an integer.");
        System.exit(1);
    }

    int secondsToPause = 0;
    try {
        secondsToPause = Integer.parseInt(args[4]);
    } catch (NumberFormatException e) {
        System.err.println("Argument" + args[4] + " must be an integer.");
        System.exit(-1);
    }

    int IDS_TO_FETCH_INT = -1;
    if (args.length == 6) {
        try {
            IDS_TO_FETCH_INT = Integer.parseInt(args[5]);
        } catch (NumberFormatException e) {
            System.err.println("Argument" + args[5] + " must be an integer.");
            System.exit(-1);
        }
    }

    int IDS_TO_FETCH = 0;
    if (IDS_TO_FETCH_INT > 5000) {

        float IDS_TO_FETCH_F = (float) IDS_TO_FETCH_INT / 5000;
        IDS_TO_FETCH = (int) Math.ceil(IDS_TO_FETCH_F);
    } else if ((IDS_TO_FETCH_INT <= 5000) && (IDS_TO_FETCH_INT > 0)) {
        IDS_TO_FETCH = 1;
    }

    secondsToPause = (TOTAL_JOBS * secondsToPause) - (JOB_NO * secondsToPause);
    System.out.println("secondsToPause: " + secondsToPause);
    helpers.pause(secondsToPause);

    try {

        int TotalWorkLoad = 0;
        ArrayList<String> allFiles = null;
        try {
            final File folder = new File(inputPath);
            allFiles = helpers.listFilesForSingleFolder(folder);
            TotalWorkLoad = allFiles.size();
        } catch (Exception e) {

            System.err.println("Input folder is not exists: " + e.getMessage());
            System.exit(-1);
        }

        System.out.println("Total Workload is: " + TotalWorkLoad);

        if (TotalWorkLoad < 1) {
            System.err.println("No screen names file exists in: " + inputPath);
            System.exit(-1);
        }

        if (TOTAL_JOBS > TotalWorkLoad) {
            System.err.println("Number of jobs are more than total work"
                    + " load. Please reduce 'Number of jobs' to launch.");
            System.exit(-1);
        }

        float TotalWorkLoadf = TotalWorkLoad;
        float TOTAL_JOBSf = TOTAL_JOBS;
        float res = (TotalWorkLoadf / TOTAL_JOBSf);

        int chunkSize = (int) Math.ceil(res);
        int offSet = JOB_NO * chunkSize;
        int chunkSizeToGet = (JOB_NO + 1) * chunkSize;

        System.out.println("My Share is " + chunkSize);
        System.out.println();

        // Load OAuh User
        TwitterFactory tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO);
        Twitter twitter = tf.getInstance();

        int RemainingCalls = AppOAuths.RemainingCalls;
        int RemainingCallsCounter = 0;
        System.out.println("First Time OAuth Remianing Calls: " + RemainingCalls);

        String Screen_name = AppOAuths.screen_name;
        System.out.println("First Time Loaded OAuth Screen_name: " + Screen_name);
        System.out.println();

        IDs ids;
        System.out.println("Going to get followers ids.");

        // to write output in a file
        System.out.flush();

        if (JOB_NO + 1 == TOTAL_JOBS) {
            chunkSizeToGet = TotalWorkLoad;
        }

        List<String> myFilesShare = allFiles.subList(offSet, chunkSizeToGet);

        for (String myFile : myFilesShare) {
            System.out.println("Going to parse file: " + myFile);

            try (BufferedReader br = new BufferedReader(new FileReader(inputPath + "/" + myFile))) {
                String line;
                OUTERMOST: while ((line = br.readLine()) != null) {
                    // process the line.

                    System.out.println("Going to get followers ids of Screen-name / user_id: " + line);
                    System.out.println();

                    String targetedUser = line.trim(); // tmp
                    long cursor = -1;
                    int idsLoopCounter = 0;
                    int totalIDs = 0;

                    PrintWriter writer = new PrintWriter(outputPath + "/" + targetedUser, "UTF-8");

                    // call different functions for screen_name and id_str
                    Boolean chckedNumaric = helpers.isNumeric(targetedUser);

                    do {
                        ids = null;
                        try {

                            if (chckedNumaric) {

                                long LongValueTargetedUser = Long.valueOf(targetedUser).longValue();

                                ids = twitter.getFollowersIDs(LongValueTargetedUser, cursor);
                            } else {
                                ids = twitter.getFollowersIDs(targetedUser, cursor);
                            }

                        } catch (TwitterException te) {

                            // do not throw if user has protected tweets, or
                            // if they deleted their account
                            if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED
                                    || te.getStatusCode() == HttpResponseCode.NOT_FOUND) {

                                System.out.println(targetedUser + " is protected or account is deleted");
                            } else {
                                System.out.println("Followers Get Exception: " + te.getMessage());
                            }

                            // If rate limit reached then switch Auth user
                            RemainingCallsCounter++;
                            if (RemainingCallsCounter >= RemainingCalls) {

                                // load auth user
                                tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO);
                                twitter = tf.getInstance();

                                System.out.println(
                                        "New Loaded OAuth User " + " Screen_name: " + AppOAuths.screen_name);

                                RemainingCalls = AppOAuths.RemainingCalls;
                                RemainingCallsCounter = 0;

                                System.out.println("New OAuth Remianing Calls: " + RemainingCalls);
                            }

                            // Remove file if ids not found
                            if (totalIDs == 0) {

                                System.out.println("No ids fetched so removing " + "file " + targetedUser);

                                File fileToDelete = new File(outputPath + "/" + targetedUser);
                                fileToDelete.delete();
                            }
                            System.out.println();

                            // If error then switch to next user
                            continue OUTERMOST;
                        }

                        if (ids.getIDs().length > 0) {

                            idsLoopCounter++;
                            totalIDs += ids.getIDs().length;
                            System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length);

                            JSONObject responseDetailsJson = new JSONObject();
                            JSONArray jsonArray = new JSONArray();
                            for (long id : ids.getIDs()) {
                                jsonArray.put(id);
                            }
                            Object idsJSON = responseDetailsJson.put("ids", jsonArray);

                            writer.println(idsJSON);

                        }

                        // If rate limit reached then switch Auth user
                        RemainingCallsCounter++;
                        if (RemainingCallsCounter >= RemainingCalls) {

                            // load auth user
                            tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO);
                            twitter = tf.getInstance();

                            System.out.println("New Loaded OAuth User Screen_name: " + AppOAuths.screen_name);

                            RemainingCalls = AppOAuths.RemainingCalls;
                            RemainingCallsCounter = 0;

                            System.out.println("New OAuth Remianing Calls: " + RemainingCalls);
                        }

                        if (IDS_TO_FETCH_INT != -1) {
                            if (idsLoopCounter == IDS_TO_FETCH) {
                                break;
                            }
                        }

                    } while ((cursor = ids.getNextCursor()) != 0);

                    writer.close();
                    System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs);

                    // Remove file if ids not found
                    if (totalIDs == 0) {

                        System.out.println("No ids fetched so removing " + "file " + targetedUser);

                        File fileToDelete = new File(outputPath + "/" + targetedUser);
                        fileToDelete.delete();
                    }
                    System.out.println();

                } // while get records from single file
            } // read my single file
            catch (IOException e) {
                System.err.println("Failed to read lines from " + myFile);
            }

            // to write output in a file
            System.out.flush();
        } // all my files share

    } catch (TwitterException te) {
        // te.printStackTrace();
        System.err.println("Failed to get followers' ids: " + te.getMessage());
        System.exit(-1);
    }
    System.out.println("!!!! DONE !!!!");

    // Close System.out for this thread which will
    // flush and close this thread.
    System.out.close();
}

---

From source file:edu.harvard.med.iccbl.screensaver.soaputils.PubchemChembankQueryUtility.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws IOException, InterruptedException {
    final PubchemChembankQueryUtility app = new PubchemChembankQueryUtility(args);

    String[] option = LIBRARY_NAME;
    app.addCommandLineOption(//from  w w w  . j  a  v  a 2s  . c  om
            OptionBuilder.hasArg().withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX])
                    .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX]));

    option = QUERY_ALL_LIBRARIES;
    app.addCommandLineOption(
            OptionBuilder.withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX])
                    .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX]));

    option = OUTPUT_FILE;
    app.addCommandLineOption(
            OptionBuilder.hasArg().withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX])
                    .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX]));

    option = TRY_LIMIT;
    app.addCommandLineOption(
            OptionBuilder.hasArg().withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX])
                    .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX]));

    option = INTERVAL_BETWEEN_TRIES;
    app.addCommandLineOption(
            OptionBuilder.hasArg().withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX])
                    .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX]));

    option = QUERY_PUBCHEM;
    app.addCommandLineOption(
            OptionBuilder.withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX])
                    .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX]));

    option = QUERY_CHEMBANK;
    app.addCommandLineOption(
            OptionBuilder.withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX])
                    .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX]));
    try {
        if (!app.processOptions(/* acceptDatabaseOptions= */true, /* showHelpOnError= */true)) {
            return;
        }

        final boolean queryPubchem = app.isCommandLineFlagSet(QUERY_PUBCHEM[SHORT_OPTION_INDEX]);
        final boolean queryChembank = app.isCommandLineFlagSet(QUERY_CHEMBANK[SHORT_OPTION_INDEX]);

        if (!(queryPubchem || queryChembank)) {
            log.error("Must specify either " + QUERY_PUBCHEM[LONG_OPTION_INDEX] + " or "
                    + QUERY_CHEMBANK[LONG_OPTION_INDEX]);
            app.showHelp();
            return;
        }
        if (!app.isCommandLineFlagSet(LIBRARY_NAME[SHORT_OPTION_INDEX])
                && !app.isCommandLineFlagSet(QUERY_ALL_LIBRARIES[SHORT_OPTION_INDEX])) {
            log.error("Must specify either " + LIBRARY_NAME[LONG_OPTION_INDEX] + " or "
                    + QUERY_ALL_LIBRARIES[LONG_OPTION_INDEX]);
            app.showHelp();
            return;
        }
        if (app.isCommandLineFlagSet(LIBRARY_NAME[SHORT_OPTION_INDEX])
                && app.isCommandLineFlagSet(QUERY_ALL_LIBRARIES[SHORT_OPTION_INDEX])) {
            log.error("Must specify either " + LIBRARY_NAME[LONG_OPTION_INDEX] + " or "
                    + QUERY_ALL_LIBRARIES[LONG_OPTION_INDEX]);
            app.showHelp();
            return;
        }
        if (app.isCommandLineFlagSet(QUERY_ALL_LIBRARIES[SHORT_OPTION_INDEX])
                && app.isCommandLineFlagSet(OUTPUT_FILE[SHORT_OPTION_INDEX])) {
            log.error("option \"" + OUTPUT_FILE[LONG_OPTION_INDEX] + "\" not allowed with \""
                    + QUERY_ALL_LIBRARIES[LONG_OPTION_INDEX] + "\" option.");
            app.showHelp();
            return;
        }
        //      if(app.isCommandLineFlagSet(LIBRARY_NAME[SHORT_OPTION_INDEX])
        //        && !app.isCommandLineFlagSet(OUTPUT_FILE[SHORT_OPTION_INDEX])) {
        //        log.error("option \"" + OUTPUT_FILE[LONG_OPTION_INDEX] + "\" must be specified with \"" + LIBRARY_NAME[LONG_OPTION_INDEX] + "\" option.");
        //        app.showHelp();
        //        return;
        //      }

        final GenericEntityDAO dao = (GenericEntityDAO) app.getSpringBean("genericEntityDao");
        dao.doInTransaction(new DAOTransaction() {
            public void runTransaction() {
                PrintWriter writer = null;
                PrintWriter errorWriter = null;
                try {

                    int intervalMs = PugSoapUtil.INTERVAL_BETWEEN_TRIES_MS;
                    if (app.isCommandLineFlagSet(INTERVAL_BETWEEN_TRIES[SHORT_OPTION_INDEX])) {
                        intervalMs = app.getCommandLineOptionValue(INTERVAL_BETWEEN_TRIES[SHORT_OPTION_INDEX],
                                Integer.class);
                    }

                    int numberOfTries = PugSoapUtil.TRY_LIMIT;
                    if (app.isCommandLineFlagSet(TRY_LIMIT[SHORT_OPTION_INDEX])) {
                        numberOfTries = app.getCommandLineOptionValue(TRY_LIMIT[SHORT_OPTION_INDEX],
                                Integer.class);
                    }

                    List<Library> libraries = Lists.newArrayList();
                    if (app.isCommandLineFlagSet(LIBRARY_NAME[SHORT_OPTION_INDEX])) {
                        String temp = app.getCommandLineOptionValue(LIBRARY_NAME[SHORT_OPTION_INDEX]);
                        for (String libraryName : temp.split(",")) {
                            Library library = dao.findEntityByProperty(Library.class, "shortName",
                                    libraryName.trim());
                            if (library == null) {
                                throw new IllegalArgumentException(
                                        "no library with short name: " + libraryName);
                            }
                            libraries.add(library);
                        }

                        // if there is only one library to query, then set these values from the command line option
                        if (libraries.size() == 1) {
                            String outputFilename = app
                                    .getCommandLineOptionValue(OUTPUT_FILE[SHORT_OPTION_INDEX]);
                            writer = app.getOutputFile(outputFilename);
                            errorWriter = app.getOutputFile(outputFilename + ".errors");
                        }
                    } else if (app.isCommandLineFlagSet(QUERY_ALL_LIBRARIES[SHORT_OPTION_INDEX])) {
                        libraries = dao.findEntitiesByProperty(Library.class, "screenType",
                                ScreenType.SMALL_MOLECULE);
                        for (Iterator<Library> iter = libraries.iterator(); iter.hasNext();) {
                            Library library = iter.next();
                            if (library.getLibraryType() == LibraryType.ANNOTATION
                                    || library.getLibraryType() == LibraryType.NATURAL_PRODUCTS) {
                                iter.remove();
                            }
                        }
                    }

                    Collections.sort(libraries, new NullSafeComparator<Library>() {
                        @Override
                        protected int doCompare(Library o1, Library o2) {
                            return o1.getShortName().compareTo(o2.getShortName());
                        }

                    });

                    List<String> libraryNames = Lists.transform(libraries, new Function<Library, String>() {
                        @Override
                        public String apply(Library from) {
                            return from.getShortName();
                        }
                    });
                    log.info("libraries to process:\n" + libraryNames);

                    int i = 0;
                    for (Library library : libraries) {
                        if (writer == null || i > 0) {
                            writer = app.getOutputFile(library.getShortName());
                        }
                        if (errorWriter == null || i > 0) {
                            errorWriter = app.getOutputFile(library.getShortName() + ".errors");
                        }
                        log.info("\nProcessing the library: " + library.getShortName() + "\nlong name: "
                                + library.getLibraryName() + "\noutput file: " + library.getShortName()
                                + ".csv");
                        app.query(library, queryPubchem, queryChembank, dao, intervalMs, numberOfTries, writer,
                                errorWriter);
                        i++;
                    }
                } catch (Exception e) {
                    throw new DAOTransactionRollbackException(e);
                } finally {
                    if (writer != null)
                        writer.close();
                    if (errorWriter != null)
                        errorWriter.close();
                }
            }

        });
        System.exit(0);
    } catch (ParseException e) {
        log.error("error parsing command line options: " + e.getMessage());
    }
}

---

From source file:eu.fbk.utils.lsa.util.Anvur.java

public static void main(String[] args) throws Exception {
    String logConfig = System.getProperty("log-config");
    if (logConfig == null) {
        logConfig = "log-config.txt";
    }/*from w w  w .  j  av a 2 s. c  o m*/

    PropertyConfigurator.configure(logConfig);
    /*
    if (args.length != 2)
    {
    log.println("Usage: java -mx512M eu.fbk.utils.lsa.util.Anvur in-file out-dir");
    System.exit(1);
    }
            
    File l = new File(args[1]);
    if (!l.exists())
    {
    l.mkdir();
    }
    List<String[]> list = readText(new File(args[0]));
    String oldCategory = "";
    for (int i=0;i<list.size();i++)
    {
    String[] s = list.get(i);
    if (!oldCategory.equals(s[0]))
    {
    File f = new File(args[1] + File.separator + s[0]);
    boolean b = f.mkdir();
    logger.debug(f + " created " + b);
    }
            
    File g = new File(args[1] + File.separator + s[0] + File.separator + s[1] + ".txt");
    logger.debug("writing " + g + "...");
    PrintWriter pw = new PrintWriter(new FileWriter(g));
    //pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2]));
    if (s.length == 5)
    {
    pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2] + " " + s[4].replace('_', ' ')));
    }
    else
    {
    pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2]));
    }
    pw.flush();
    pw.close();
            
    } // end for i
    */

    if (args.length != 7) {
        System.out.println(args.length);
        System.out.println(
                "Usage: java -mx2G eu.fbk.utils.lsa.util.Anvur input threshold size dim idf in-file-csv fields\n\n");
        System.exit(1);
    }

    //
    DecimalFormat dec = new DecimalFormat("#.00");

    File Ut = new File(args[0] + "-Ut");
    File Sk = new File(args[0] + "-S");
    File r = new File(args[0] + "-row");
    File c = new File(args[0] + "-col");
    File df = new File(args[0] + "-df");
    double threshold = Double.parseDouble(args[1]);
    int size = Integer.parseInt(args[2]);
    int dim = Integer.parseInt(args[3]);
    boolean rescaleIdf = Boolean.parseBoolean(args[4]);

    //"author_check"0,   "authors"1,   "title"2,   "year"3,   "pubtype"4,   "publisher"5,   "journal"6,   "volume"7,   "number"8,   "pages"9,   "abstract"10,   "nauthors",   "citedby"
    String[] labels = { "author_check", "authors", "title", "year", "pubtype", "publisher", "journal", "volume",
            "number", "pages", "abstract", "nauthors", "citedby"
            //author_id   authors   title   year   pubtype   publisher   journal   volume   number   pages   abstract   nauthors   citedby

    };
    String name = buildName(labels, args[6]);

    File bwf = new File(args[5] + name + "-bow.txt");
    PrintWriter bw = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bwf), "UTF-8")));
    File bdf = new File(args[5] + name + "-bow.csv");
    PrintWriter bd = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bdf), "UTF-8")));
    File lwf = new File(args[5] + name + "-ls.txt");
    PrintWriter lw = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(lwf), "UTF-8")));
    File ldf = new File(args[5] + name + "-ls.csv");
    PrintWriter ld = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(ldf), "UTF-8")));
    File blwf = new File(args[5] + name + "-bow+ls.txt");
    PrintWriter blw = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(blwf), "UTF-8")));
    File bldf = new File(args[5] + name + "-bow+ls.csv");
    PrintWriter bld = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bldf), "UTF-8")));
    File logf = new File(args[5] + name + ".log");
    PrintWriter log = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(logf), "UTF-8")));

    //System.exit(0);
    LSM lsm = new LSM(Ut, Sk, r, c, df, dim, rescaleIdf);
    LSSimilarity lss = new LSSimilarity(lsm, size);

    List<String[]> list = readText(new File(args[5]));

    // author_check   authors   title   year   pubtype   publisher   journal   volume   number   pages   abstract   nauthors   citedby

    //header
    for (int i = 0; i < list.size(); i++) {
        String[] s1 = list.get(i);
        String t1 = s1[0].toLowerCase();
        bw.print("\t");
        lw.print("\t");
        blw.print("\t");
        bw.print(i + "(" + s1[0] + ")");
        lw.print(i + "(" + s1[0] + ")");
        blw.print(i + "(" + s1[0] + ")");
    } // end for i

    bw.print("\n");
    lw.print("\n");
    blw.print("\n");
    for (int i = 0; i < list.size(); i++) {
        logger.info(i + "\t");
        String[] s1 = list.get(i);
        String t1 = buildText(s1, args[6]);
        BOW bow1 = new BOW(t1);
        logger.info(bow1);

        Vector d1 = lsm.mapDocument(bow1);
        d1.normalize();
        log.println("d1:" + d1);

        Vector pd1 = lsm.mapPseudoDocument(d1);
        pd1.normalize();
        log.println("pd1:" + pd1);

        Vector m1 = merge(pd1, d1);
        log.println("m1:" + m1);

        // write the orginal line
        for (int j = 0; j < s1.length; j++) {
            bd.print(s1[j]);
            bd.print("\t");
            ld.print(s1[j]);
            ld.print("\t");
            bld.print(s1[j]);
            bld.print("\t");

        }
        // write the bow, ls, and bow+ls vectors
        bd.println(d1);
        ld.println(pd1);
        bld.println(m1);

        bw.print(i + "(" + s1[0] + ")");
        lw.print(i + "(" + s1[0] + ")");
        blw.print(i + "(" + s1[0] + ")");
        for (int j = 0; j < i + 1; j++) {
            bw.print("\t");
            lw.print("\t");
            blw.print("\t");
        } // end for j

        for (int j = i + 1; j < list.size(); j++) {
            logger.info(i + "\t" + j);
            String[] s2 = list.get(j);

            String t2 = buildText(s2, args[6]);
            BOW bow2 = new BOW(t2);

            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t1:" + t1);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t2:" + t2);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow1:" + bow1);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow2:" + bow2);

            Vector d2 = lsm.mapDocument(bow2);
            d2.normalize();
            log.println("d2:" + d2);

            Vector pd2 = lsm.mapPseudoDocument(d2);
            pd2.normalize();
            log.println("pd2:" + pd2);

            Vector m2 = merge(pd2, d2);
            log.println("m2:" + m2);

            float cosVSM = d1.dotProduct(d2) / (float) Math.sqrt(d1.dotProduct(d1) * d2.dotProduct(d2));
            float cosLSM = pd1.dotProduct(pd2) / (float) Math.sqrt(pd1.dotProduct(pd1) * pd2.dotProduct(pd2));
            float cosBOWLSM = m1.dotProduct(m2) / (float) Math.sqrt(m1.dotProduct(m1) * m2.dotProduct(m2));
            bw.print("\t");
            bw.print(dec.format(cosVSM));
            lw.print("\t");
            lw.print(dec.format(cosLSM));
            blw.print("\t");
            blw.print(dec.format(cosBOWLSM));

            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow\t" + cosVSM);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") ls:\t" + cosLSM);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow+ls:\t" + cosBOWLSM);
        }
        bw.print("\n");
        lw.print("\n");
        blw.print("\n");
    } // end for i

    logger.info("wrote " + bwf);
    logger.info("wrote " + bwf);
    logger.info("wrote " + bdf);
    logger.info("wrote " + lwf);
    logger.info("wrote " + ldf);
    logger.info("wrote " + blwf);
    logger.info("wrote " + bldf);
    logger.info("wrote " + logf);

    ld.close();
    bd.close();
    bld.close();
    bw.close();
    lw.close();
    blw.close();

    log.close();

}

---

From source file:ch.epfl.lsir.xin.test.GlobalMeanTest.java

/**
 * @param args//from w ww  . j  av a 2s.c om
 */
public static void main(String[] args) throws Exception {
    // TODO Auto-generated method stub

    PrintWriter logger = new PrintWriter(".//results//GlobalMean");

    PropertiesConfiguration config = new PropertiesConfiguration();
    config.setFile(new File("conf//GlobalMean.properties"));
    try {
        config.load();
    } catch (ConfigurationException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + " Read rating data...");
    DataLoaderFile loader = new DataLoaderFile(".//data//MoveLens100k.txt");
    loader.readSimple();
    DataSetNumeric dataset = loader.getDataset();
    System.out.println("Number of ratings: " + dataset.getRatings().size() + " Number of users: "
            + dataset.getUserIDs().size() + " Number of items: " + dataset.getItemIDs().size());
    logger.println("Number of ratings: " + dataset.getRatings().size() + ", Number of users: "
            + dataset.getUserIDs().size() + ", Number of items: " + dataset.getItemIDs().size());

    double totalMAE = 0;
    double totalRMSE = 0;
    int F = 5;
    logger.println(F + "- folder cross validation.");
    logger.flush();
    ArrayList<ArrayList<NumericRating>> folders = new ArrayList<ArrayList<NumericRating>>();
    for (int i = 0; i < F; i++) {
        folders.add(new ArrayList<NumericRating>());
    }
    while (dataset.getRatings().size() > 0) {
        int index = new Random().nextInt(dataset.getRatings().size());
        int r = new Random().nextInt(F);
        folders.get(r).add(dataset.getRatings().get(index));
        dataset.getRatings().remove(index);
    }
    for (int folder = 1; folder <= F; folder++) {
        System.out.println("Folder: " + folder);
        logger.println("Folder: " + folder);
        ArrayList<NumericRating> trainRatings = new ArrayList<NumericRating>();
        ArrayList<NumericRating> testRatings = new ArrayList<NumericRating>();
        for (int i = 0; i < folders.size(); i++) {
            if (i == folder - 1)//test data
            {
                testRatings.addAll(folders.get(i));
            } else {//training data
                trainRatings.addAll(folders.get(i));
            }
        }

        //create rating matrix
        HashMap<String, Integer> userIDIndexMapping = new HashMap<String, Integer>();
        HashMap<String, Integer> itemIDIndexMapping = new HashMap<String, Integer>();
        for (int i = 0; i < dataset.getUserIDs().size(); i++) {
            userIDIndexMapping.put(dataset.getUserIDs().get(i), i);
        }
        for (int i = 0; i < dataset.getItemIDs().size(); i++) {
            itemIDIndexMapping.put(dataset.getItemIDs().get(i), i);
        }
        RatingMatrix trainRatingMatrix = new RatingMatrix(dataset.getUserIDs().size(),
                dataset.getItemIDs().size());
        for (int i = 0; i < trainRatings.size(); i++) {
            trainRatingMatrix.set(userIDIndexMapping.get(trainRatings.get(i).getUserID()),
                    itemIDIndexMapping.get(trainRatings.get(i).getItemID()), trainRatings.get(i).getValue());
        }
        RatingMatrix testRatingMatrix = new RatingMatrix(dataset.getUserIDs().size(),
                dataset.getItemIDs().size());
        for (int i = 0; i < testRatings.size(); i++) {
            testRatingMatrix.set(userIDIndexMapping.get(testRatings.get(i).getUserID()),
                    itemIDIndexMapping.get(testRatings.get(i).getItemID()), testRatings.get(i).getValue());
        }
        System.out.println("Training: " + trainRatingMatrix.getTotalRatingNumber() + " vs Test: "
                + testRatingMatrix.getTotalRatingNumber());

        logger.println("Initialize a recommendation model based on global average method.");
        GlobalAverage algo = new GlobalAverage(trainRatingMatrix);
        algo.setLogger(logger);
        algo.build();
        algo.saveModel(".//localModels//" + config.getString("NAME"));
        logger.println("Save the model.");
        logger.flush();

        System.out.println(trainRatings.size() + " vs. " + testRatings.size());

        double RMSE = 0;
        double MAE = 0;
        int count = 0;
        for (int i = 0; i < testRatings.size(); i++) {
            NumericRating rating = testRatings.get(i);
            double prediction = algo.predict(rating.getUserID(), rating.getItemID());
            if (Double.isNaN(prediction)) {
                System.out.println("no prediction");
                continue;
            }
            MAE = MAE + Math.abs(rating.getValue() - prediction);
            RMSE = RMSE + Math.pow((rating.getValue() - prediction), 2);
            count++;
        }
        MAE = MAE / count;
        RMSE = Math.sqrt(RMSE / count);

        //         System.out.println("MAE: " + MAE + " RMSE: " + RMSE);
        logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + " MAE: " + MAE
                + " RMSE: " + RMSE);
        logger.flush();
        totalMAE = totalMAE + MAE;
        totalRMSE = totalRMSE + RMSE;
    }

    System.out.println("MAE: " + totalMAE / F + " RMSE: " + totalRMSE / F);
    logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + " Final results: MAE: "
            + totalMAE / F + " RMSE: " + totalRMSE / F);
    logger.flush();
    logger.close();
    //MAE: 0.9338607074893257 RMSE: 1.1170971131112037 (MovieLens1M)
    //MAE: 0.9446876509332618 RMSE: 1.1256517870920375 (MovieLens100K)

}

---

From source file:ch.epfl.lsir.xin.test.UserAverageTest.java

/**
 * @param args/* w  w  w . ja  v a  2  s. c om*/
 */
public static void main(String[] args) throws Exception {
    // TODO Auto-generated method stub

    PrintWriter logger = new PrintWriter(".//results//UserAverage");
    PropertiesConfiguration config = new PropertiesConfiguration();
    config.setFile(new File(".//conf//UserAverage.properties"));
    try {
        config.load();
    } catch (ConfigurationException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + " Read rating data...");
    DataLoaderFile loader = new DataLoaderFile(".//data//MoveLens100k.txt");
    loader.readSimple();
    DataSetNumeric dataset = loader.getDataset();
    System.out.println("Number of ratings: " + dataset.getRatings().size() + " Number of users: "
            + dataset.getUserIDs().size() + " Number of items: " + dataset.getItemIDs().size());
    logger.println("Number of ratings: " + dataset.getRatings().size() + " Number of users: "
            + dataset.getUserIDs().size() + " Number of items: " + dataset.getItemIDs().size());
    logger.flush();

    double totalMAE = 0;
    double totalRMSE = 0;
    int F = 5;
    logger.println(F + "- folder cross validation.");
    ArrayList<ArrayList<NumericRating>> folders = new ArrayList<ArrayList<NumericRating>>();
    for (int i = 0; i < F; i++) {
        folders.add(new ArrayList<NumericRating>());
    }
    while (dataset.getRatings().size() > 0) {
        int index = new Random().nextInt(dataset.getRatings().size());
        int r = new Random().nextInt(F);
        folders.get(r).add(dataset.getRatings().get(index));
        dataset.getRatings().remove(index);
    }
    for (int folder = 1; folder <= F; folder++) {
        logger.println("Folder: " + folder);
        System.out.println("Folder: " + folder);
        ArrayList<NumericRating> trainRatings = new ArrayList<NumericRating>();
        ArrayList<NumericRating> testRatings = new ArrayList<NumericRating>();
        for (int i = 0; i < folders.size(); i++) {
            if (i == folder - 1)//test data
            {
                testRatings.addAll(folders.get(i));
            } else {//training data
                trainRatings.addAll(folders.get(i));
            }
        }

        //create rating matrix
        HashMap<String, Integer> userIDIndexMapping = new HashMap<String, Integer>();
        HashMap<String, Integer> itemIDIndexMapping = new HashMap<String, Integer>();
        for (int i = 0; i < dataset.getUserIDs().size(); i++) {
            userIDIndexMapping.put(dataset.getUserIDs().get(i), i);
        }
        for (int i = 0; i < dataset.getItemIDs().size(); i++) {
            itemIDIndexMapping.put(dataset.getItemIDs().get(i), i);
        }
        RatingMatrix trainRatingMatrix = new RatingMatrix(dataset.getUserIDs().size(),
                dataset.getItemIDs().size());
        for (int i = 0; i < trainRatings.size(); i++) {
            trainRatingMatrix.set(userIDIndexMapping.get(trainRatings.get(i).getUserID()),
                    itemIDIndexMapping.get(trainRatings.get(i).getItemID()), trainRatings.get(i).getValue());
        }
        trainRatingMatrix.calculateGlobalAverage();
        RatingMatrix testRatingMatrix = new RatingMatrix(dataset.getUserIDs().size(),
                dataset.getItemIDs().size());
        for (int i = 0; i < testRatings.size(); i++) {
            testRatingMatrix.set(userIDIndexMapping.get(testRatings.get(i).getUserID()),
                    itemIDIndexMapping.get(testRatings.get(i).getItemID()), testRatings.get(i).getValue());
        }
        System.out.println("Training: " + trainRatingMatrix.getTotalRatingNumber() + " vs Test: "
                + testRatingMatrix.getTotalRatingNumber());

        logger.println("Initialize a recommendation model based on user average method.");
        UserAverage algo = new UserAverage(trainRatingMatrix);
        algo.setLogger(logger);
        algo.build();
        algo.saveModel(".//localModels//" + config.getString("NAME"));
        logger.println("Save the model.");
        System.out.println(trainRatings.size() + " vs. " + testRatings.size());

        double RMSE = 0;
        double MAE = 0;
        int count = 0;
        for (int i = 0; i < testRatings.size(); i++) {
            NumericRating rating = testRatings.get(i);
            double prediction = algo.predict(userIDIndexMapping.get(rating.getUserID()),
                    itemIDIndexMapping.get(rating.getItemID()));
            if (Double.isNaN(prediction)) {
                System.out.println("no prediction");
                continue;
            }
            MAE = MAE + Math.abs(rating.getValue() - prediction);
            RMSE = RMSE + Math.pow((rating.getValue() - prediction), 2);
            count++;
        }
        MAE = MAE / count;
        RMSE = Math.sqrt(RMSE / count);

        logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + " MAE: " + MAE
                + " RMSE: " + RMSE);
        logger.flush();
        totalMAE = totalMAE + MAE;
        totalRMSE = totalRMSE + RMSE;
    }

    System.out.println("MAE: " + totalMAE / F + " RMSE: " + totalRMSE / F);
    logger.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss").format(new Date()) + " Final results: MAE: "
            + totalMAE / F + " RMSE: " + totalRMSE / F);
    logger.flush();
    logger.close();
    //MAE: 0.8353035962363073 RMSE: 1.0422971886952053 (MovieLens 100k)
}

---

From source file:edu.msu.cme.rdp.multicompare.Reprocess.java

/**
 * This class reprocesses the classification results (allrank output) and print out hierarchy output file, based on the confidence cutoff;
 * and print out only the detail classification results with assignment at certain rank with confidence above the cutoff or/and matching a given taxon.
 * @param args/*  www.  ja  v  a  2s  .co  m*/
 * @throws Exception 
 */
public static void main(String[] args) throws Exception {

    PrintWriter assign_out = new PrintWriter(new NullWriter());
    float conf = 0.8f;
    PrintStream heir_out = null;
    String hier_out_filename = null;
    ClassificationResultFormatter.FORMAT format = ClassificationResultFormatter.FORMAT.allRank;
    String rank = null;
    String taxonFilterFile = null;
    String train_propfile = null;
    String gene = null;
    List<MCSample> samples = new ArrayList();

    try {
        CommandLine line = new PosixParser().parse(options, args);
        if (line.hasOption(CmdOptions.HIER_OUTFILE_SHORT_OPT)) {
            hier_out_filename = line.getOptionValue(CmdOptions.HIER_OUTFILE_SHORT_OPT);
            heir_out = new PrintStream(hier_out_filename);
        } else {
            throw new Exception(
                    "It make sense to provide output filename for " + CmdOptions.HIER_OUTFILE_LONG_OPT);
        }
        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            assign_out = new PrintWriter(line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT));
        }

        if (line.hasOption(CmdOptions.RANK_SHORT_OPT)) {
            rank = line.getOptionValue(CmdOptions.RANK_SHORT_OPT);
        }
        if (line.hasOption(CmdOptions.TAXON_SHORT_OPT)) {
            taxonFilterFile = line.getOptionValue(CmdOptions.TAXON_SHORT_OPT);
        }

        if (line.hasOption(CmdOptions.BOOTSTRAP_SHORT_OPT)) {
            conf = Float.parseFloat(line.getOptionValue(CmdOptions.BOOTSTRAP_SHORT_OPT));
            if (conf < 0 || conf > 1) {
                throw new IllegalArgumentException("Confidence must be in the range [0,1]");
            }
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else {
                throw new IllegalArgumentException(
                        "Not valid output format, only allrank, fixrank, filterbyconf and db allowed");
            }
        }
        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                train_propfile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (train_propfile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE) && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_warcup_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_unite_GENE)) {
                throw new IllegalArgumentException(gene + " is NOT valid, only allows "
                        + ClassifierFactory.RRNA_16S_GENE + ", " + ClassifierFactory.FUNGALLSU_GENE + ", "
                        + ClassifierFactory.FUNGALITS_warcup_GENE + " and "
                        + ClassifierFactory.FUNGALITS_unite_GENE);
            }
        }
        args = line.getArgs();
        if (args.length < 1) {
            throw new Exception("Incorrect number of command line arguments");
        }

        for (String arg : args) {
            String[] inFileNames = arg.split(",");
            String inputFile = inFileNames[0];
            File idmappingFile = null;

            if (inFileNames.length == 2) {
                idmappingFile = new File(inFileNames[1]);
                if (!idmappingFile.exists()) {
                    System.err.println("Failed to find input file \"" + inFileNames[1] + "\"");
                    return;
                }
            }

            MCSample nextSample = new MCSampleResult(inputFile, idmappingFile);
            samples.add(nextSample);

        }
    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(120,
                "Reprocess [options] <Classification_allrank_result>[,idmappingfile] ...", "", options, "");
        return;
    }

    if (train_propfile == null && gene == null) {
        gene = ClassifierFactory.RRNA_16S_GENE;
    }

    HashSet<String> taxonFilter = null;
    if (taxonFilterFile != null) {
        taxonFilter = readTaxonFilterFile(taxonFilterFile);
    }

    MultiClassifier multiClassifier = new MultiClassifier(train_propfile, gene);
    DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(heir_out, samples);
    MultiClassifierResult result = multiClassifier.multiClassificationParser(samples, conf, assign_out, format,
            rank, taxonFilter);

    result.getRoot().topDownVisit(printVisitor);

    assign_out.close();
    heir_out.close();
    if (multiClassifier.hasCopyNumber()) {
        // print copy number corrected counts
        File cn_corrected_s = new File(new File(hier_out_filename).getParentFile(),
                "cncorrected_" + hier_out_filename);
        PrintStream cn_corrected_hier_out = new PrintStream(cn_corrected_s);
        printVisitor = new DefaultPrintVisitor(cn_corrected_hier_out, samples, true);
        result.getRoot().topDownVisit(printVisitor);
        cn_corrected_hier_out.close();
    }

}

---

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