Example usage for java.util HashMap size

List of usage examples for java.util HashMap size

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Prototype

int size

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Document

The number of key-value mappings contained in this map.

Usage

From source file:website.openeng.async.Connection.java

/**
 * Downloads any missing media files according to the mediaURL deckvar.
 *
 * @param data//from  w  ww.  j  a  v a  2  s .c  o m
 * @return The return type contains data.resultType and an array of Integer in data.data. data.data[0] is the number
 *         of total missing media, data.data[1] is the number of downloaded ones.
 */
private Payload doInBackgroundDownloadMissingMedia(Payload data) {
    Timber.i("DownloadMissingMedia");
    HashMap<String, String> missingPaths = new HashMap<String, String>();
    HashMap<String, String> missingSums = new HashMap<String, String>();

    data.result = (Decks) data.data[0]; // pass it to the return object so we close the deck in the deck picker
    String syncName = "";// deck.getDeckName();

    data.success = false;
    data.data = new Object[] { 0, 0, 0 };
    // if (!deck.hasKey("mediaURL")) {
    // data.success = true;
    // return data;
    // }
    String urlbase = "";// deck.getVar("mediaURL");
    if (urlbase.equals("")) {
        data.success = true;
        return data;
    }

    String mdir = "";// deck.mediaDir(true);
    int totalMissing = 0;
    int missing = 0;
    int grabbed = 0;

    Cursor cursor = null;
    try {
        cursor = null;// deck.getDB().getDatabase().rawQuery("SELECT filename, originalPath FROM media", null);
        String path = null;
        String f = null;
        while (cursor.moveToNext()) {
            f = cursor.getString(0);
            path = mdir + "/" + f;
            File file = new File(path);
            if (!file.exists()) {
                missingPaths.put(f, path);
                missingSums.put(f, cursor.getString(1));
                Timber.d("Missing file: %s", f);
            }
        }
    } finally {
        if (cursor != null) {
            cursor.close();
        }
    }

    totalMissing = missingPaths.size();
    data.data[0] = totalMissing;
    if (totalMissing == 0) {
        data.success = true;
        return data;
    }
    publishProgress(Boolean.FALSE, totalMissing, 0, syncName);

    URL url = null;
    HttpURLConnection connection = null;
    String path = null;
    String sum = null;
    int readbytes = 0;
    byte[] buf = new byte[4096];
    for (String file : missingPaths.keySet()) {

        try {
            android.net.Uri uri = android.net.Uri.parse(Uri.encode(urlbase, ":/@%") + Uri.encode(file));
            url = new URI(uri.toString()).toURL();
            connection = (HttpURLConnection) url.openConnection();
            connection.connect();
            if (connection.getResponseCode() == 200) {
                path = missingPaths.get(file);
                InputStream is = connection.getInputStream();
                BufferedInputStream bis = new BufferedInputStream(is, 4096);
                FileOutputStream fos = new FileOutputStream(path);
                while ((readbytes = bis.read(buf, 0, 4096)) != -1) {
                    fos.write(buf, 0, readbytes);
                    Timber.d("Downloaded %d file: %s", readbytes, path);
                }
                fos.close();

                // Verify with checksum
                sum = missingSums.get(file);
                if (true) {// sum.equals("") || sum.equals(Utils.fileChecksum(path))) {
                    grabbed++;
                } else {
                    // Download corrupted, delete file
                    Timber.i("Downloaded media file %s failed checksum.", path);
                    File f = new File(path);
                    f.delete();
                    missing++;
                }
            } else {
                Timber.e("Connection error (" + connection.getResponseCode() + ") while retrieving media file "
                        + urlbase + file);
                Timber.e("Connection message: " + connection.getResponseMessage());
                if (missingSums.get(file).equals("")) {
                    // Ignore and keep going
                    missing++;
                } else {
                    data.success = false;
                    data.data = new Object[] { file };
                    return data;
                }
            }
            connection.disconnect();
        } catch (URISyntaxException e) {
            Timber.e(e, "doInBackgroundDownloadMissingMedia URISyntaxException");
        } catch (MalformedURLException e) {
            Timber.e(e, "MalformedURLException while download media file " + path);
            if (missingSums.get(file).equals("")) {
                // Ignore and keep going
                missing++;
            } else {
                data.success = false;
                data.data = new Object[] { file };
                return data;
            }
        } catch (IOException e) {
            Timber.e(e, "IOException while download media file " + path);
            if (missingSums.get(file).equals("")) {
                // Ignore and keep going
                missing++;
            } else {
                data.success = false;
                data.data = new Object[] { file };
                return data;
            }
        } finally {
            if (connection != null) {
                connection.disconnect();
            }
        }
        publishProgress(Boolean.TRUE, totalMissing, grabbed + missing, syncName);
    }

    data.data[1] = grabbed;
    data.data[2] = missing;
    data.success = true;
    return data;
}

From source file:org.openmeetings.axis.services.RoomWebService.java

/**
 * Returns a object of type RoomReturn/*from  ww  w. ja v  a 2  s  . c o  m*/
 * 
 * @param SID The SID of the User. This SID must be marked as Loggedin 
 * @param rooms_id
 * @return
 * @throws AxisFault
 */
public RoomReturn getRoomWithClientObjectsById(String SID, long rooms_id) throws AxisFault {
    try {
        Long users_id = sessionManagement.checkSession(SID);
        Long user_level = userManagement.getUserLevelByID(users_id);

        if (authLevelManagement.checkWebServiceLevel(user_level)) {

            Rooms room = roommanagement.getRoomById(user_level, rooms_id);

            RoomReturn roomReturn = new RoomReturn();

            roomReturn.setCreated(room.getStarttime());
            roomReturn.setCreator(null);
            roomReturn.setName(room.getName());
            roomReturn.setRoom_id(room.getRooms_id());

            HashMap<String, RoomClient> map = clientListManager.getClientListByRoom(room.getRooms_id());

            RoomUser[] roomUsers = new RoomUser[map.size()];

            int i = 0;
            for (Iterator<String> iter = map.keySet().iterator(); iter.hasNext();) {
                RoomClient rcl = map.get(iter.next());

                RoomUser roomUser = new RoomUser();
                roomUser.setFirstname(rcl.getFirstname());
                roomUser.setLastname(rcl.getLastname());
                roomUser.setBroadcastId(rcl.getBroadCastID());
                roomUser.setPublicSID(rcl.getPublicSID());
                roomUser.setIsBroadCasting(rcl.getIsBroadcasting());
                roomUser.setAvsettings(rcl.getAvsettings());

                roomUsers[i] = roomUser;

                i++;

            }

            roomReturn.setRoomUser(roomUsers);

            return roomReturn;
        }

        return null;

    } catch (Exception err) {
        log.error("[getRoomWithClientObjectsById]", err);
        throw new AxisFault(err.getMessage());
    }

}

From source file:com.ichi2.async.DeckTask.java

private TaskData doInBackgroundImportReplace(TaskData... params) {
    Timber.d("doInBackgroundImportReplace");
    Collection col = CollectionHelper.getInstance().getCol(mContext);
    String path = params[0].getString();
    Resources res = AnkiDroidApp.getInstance().getBaseContext().getResources();

    // extract the deck from the zip file
    String colPath = col.getPath();
    File dir = new File(new File(colPath).getParentFile(), "tmpzip");
    if (dir.exists()) {
        BackupManager.removeDir(dir);/*from  w  w  w. j  a  v  a  2 s .  c  o  m*/
    }

    publishProgress(new TaskData(res.getString(R.string.import_unpacking)));
    // from anki2.py
    String colFile = new File(dir, "collection.anki2").getAbsolutePath();
    ZipFile zip;
    try {
        zip = new ZipFile(new File(path), ZipFile.OPEN_READ);
    } catch (IOException e) {
        Timber.e(e, "doInBackgroundImportReplace - Error while unzipping");
        AnkiDroidApp.sendExceptionReport(e, "doInBackgroundImportReplace0");
        return new TaskData(false);
    }
    if (!Utils.unzipFiles(zip, dir.getAbsolutePath(), new String[] { "collection.anki2", "media" }, null)
            || !(new File(colFile)).exists()) {
        return new TaskData(-2, null, false);
    }

    Collection tmpCol = null;
    try {
        tmpCol = Storage.Collection(colFile);
        if (!tmpCol.validCollection()) {
            tmpCol.close();
            return new TaskData(-2, null, false);
        }
    } catch (Exception e) {
        Timber.e("Error opening new collection file... probably it's invalid");
        try {
            tmpCol.close();
        } catch (Exception e2) {
            // do nothing
        }
        return new TaskData(-2, null, false);
    } finally {
        if (tmpCol != null) {
            tmpCol.close();
        }
    }

    publishProgress(new TaskData(res.getString(R.string.importing_collection)));
    if (col != null) {
        // unload collection and trigger a backup
        CollectionHelper.getInstance().closeCollection(true);
        CollectionHelper.getInstance().lockCollection();
        BackupManager.performBackupInBackground(colPath, true);
    }
    // overwrite collection
    File f = new File(colFile);
    if (!f.renameTo(new File(colPath))) {
        // Exit early if this didn't work
        return new TaskData(-2, null, false);
    }
    int addedCount = -1;
    try {
        col = CollectionHelper.getInstance().reopenCollection();
        CollectionHelper.getInstance().unlockCollection();

        // because users don't have a backup of media, it's safer to import new
        // data and rely on them running a media db check to get rid of any
        // unwanted media. in the future we might also want to duplicate this step
        // import media
        HashMap<String, String> nameToNum = new HashMap<String, String>();
        HashMap<String, String> numToName = new HashMap<String, String>();
        File mediaMapFile = new File(dir.getAbsolutePath(), "media");
        if (mediaMapFile.exists()) {
            JsonReader jr = new JsonReader(new FileReader(mediaMapFile));
            jr.beginObject();
            String name;
            String num;
            while (jr.hasNext()) {
                num = jr.nextName();
                name = jr.nextString();
                nameToNum.put(name, num);
                numToName.put(num, name);
            }
            jr.endObject();
            jr.close();
        }
        String mediaDir = col.getMedia().dir();
        int total = nameToNum.size();
        int i = 0;
        for (Map.Entry<String, String> entry : nameToNum.entrySet()) {
            String file = entry.getKey();
            String c = entry.getValue();
            File of = new File(mediaDir, file);
            if (!of.exists()) {
                Utils.unzipFiles(zip, mediaDir, new String[] { c }, numToName);
            }
            ++i;
            publishProgress(new TaskData(res.getString(R.string.import_media_count, (i + 1) * 100 / total)));
        }
        zip.close();
        // delete tmp dir
        BackupManager.removeDir(dir);
        return new TaskData(true);
    } catch (RuntimeException e) {
        Timber.e(e, "doInBackgroundImportReplace - RuntimeException");
        AnkiDroidApp.sendExceptionReport(e, "doInBackgroundImportReplace1");
        return new TaskData(false);
    } catch (FileNotFoundException e) {
        Timber.e(e, "doInBackgroundImportReplace - FileNotFoundException");
        AnkiDroidApp.sendExceptionReport(e, "doInBackgroundImportReplace2");
        return new TaskData(false);
    } catch (IOException e) {
        Timber.e(e, "doInBackgroundImportReplace - IOException");
        AnkiDroidApp.sendExceptionReport(e, "doInBackgroundImportReplace3");
        return new TaskData(false);
    }
}

From source file:gov.anl.cue.arcane.engine.matrix.MatrixModel.java

/**
 * Imports a matrix model from a template spreadsheet.
 *
 * @param matrixEngine the matrix engine
 * @param fileName            the file name
 * @return the results/*from   www. j  a va 2s  .c o m*/
 */
public static MatrixModel importTemplate(MatrixEngine matrixEngine, String fileName) {

    // Declare the results storage.
    MatrixModel matrixModel = new MatrixModel(matrixEngine);

    // Try to read the template spreadsheet.
    try {

        // Find the node request counts.
        HashMap<Integer, Integer> nodeCounts = MatrixModel.importTemplateDimensions(fileName);

        // Find the node base index counts.
        HashMap<Integer, Integer> nodeBases = MatrixModel.findNodeBases(nodeCounts);

        // Find the dimensions of the template spreadsheet.
        int nodeRequests = nodeCounts.size();
        int nodeCount = 0;
        for (Integer nodeRequest : nodeCounts.values()) {
            nodeCount += nodeRequest;
        }

        // Attempt to open the template spreadsheet.
        XSSFWorkbook workbook = new XSSFWorkbook(new FileInputStream(new File(fileName)));

        // Extract the fitness function.
        Iterator<XSSFSheet> sheets = MatrixModel.importTemplateExtractFitnessInformation(matrixModel,
                nodeCounts, nodeRequests, workbook);

        // Scan the variables.
        MatrixModel.importTemplateScanVariables(matrixModel, nodeCounts, nodeBases, nodeRequests, nodeCount,
                sheets);

        // Normalize the new model.
        matrixModel.normalize();

        // Catch errors.
    } catch (Exception e) {

        // Note an error.
        matrixModel = null;

    }

    // Return the results.
    return matrixModel;

}

From source file:edu.csupomona.nlp.tool.crawler.Facebook.java

/**
 * Get all the Pages match the searching keyword.
 * @param keyword               Keyword for search
 * @param onlyVerified          Return only verified pages (currently NA)
 * @return                      HashMap of Pages
 * @throws JSONException/*from  w  w w .j  ava2s . co  m*/
 */
public HashMap<String, Page> getPages(String keyword, boolean onlyVerified) throws JSONException {
    HashMap<String, Page> fullPages = new HashMap<>();
    int totalLikes = 0;
    try {
        // search pages according to keyword
        ResponseList<Page> pages = fb_.searchPages(keyword);
        System.out.println(pages.size());
        int idx = 0;
        for (Page page : pages) {
            if (onlyVerified) {
                // TOTALLY GAVE UP DUE TO UNKNOWN REASON OF UNABLE TO 
                // ACCESS FQL WITH APP ACCESS TOKEN OR USER ACCESS TOKEN
                // is_verified field is only accessable through FQL
                //                    String query = "select is_verified from page where page_id=" 
                //                            + page.getId();
                //                    JSONObject json = fb_.executeFQL(query).getJSONObject(0);
                //                    boolean isVerified = json.getBoolean("is_verified");
                //                
                //                    // reduce speed
                //                    pause(1);
                //                    
                //                    if (!isVerified)
                //                        continue;
            }

            // retrieve full information of the page 
            Page fullPage = fb_.getPage(page.getId());

            fullPages.put(fullPage.getId(), fullPage);

            // records number of likes
            totalLikes += fullPage.getLikes();

            // to reduce speed
            //                pause(1);

            System.out.println(idx++);
        }
    } catch (FacebookException ex) {
        Logger.getLogger(Facebook.class.getName()).log(Level.SEVERE, null, ex);
    }

    // post processing. only keep pages with number of likes above average 
    int average = totalLikes / fullPages.size();
    System.out.println("Average=" + average);
    List<String> removePageIds = new ArrayList<>();
    for (String pageId : fullPages.keySet())
        if (fullPages.get(pageId).getLikes() < average) {
            System.out.println("RM: " + fullPages.get(pageId).getName() + " [L="
                    + fullPages.get(pageId).getLikes().toString() + "]");
            removePageIds.add(pageId);
        }

    for (String pageId : removePageIds)
        fullPages.remove(pageId);

    return fullPages;
}

From source file:org.taverna.server.master.localworker.SecurityContextDelegate.java

/**
 * Builds and transfers a keystore with suitable credentials to the back-end
 * workflow execution engine.// w  w  w  .  java  2s .  co  m
 * 
 * @throws GeneralSecurityException
 *             If the manipulation of the keystore, keys or certificates
 *             fails.
 * @throws IOException
 *             If there are problems building the data (should not happen).
 * @throws RemoteException
 *             If the conveyancing fails.
 */
@Override
public final void conveySecurity() throws GeneralSecurityException, IOException, ImplementationException {
    RemoteSecurityContext rc = run.run.getSecurityContext();

    synchronized (lock) {
        if (credentials.isEmpty() && trusted.isEmpty())
            return;
    }
    char[] password = null;
    try {
        password = generateNewPassword();

        log.info("constructing merged keystore");
        Truststore truststore = new Truststore(password);
        Keystore keystore = new Keystore(password);
        HashMap<URI, String> uriToAliasMap = new HashMap<URI, String>();
        int trustedCount = 0, keyCount = 0;

        synchronized (lock) {
            try {
                for (Trust t : trusted)
                    for (Certificate cert : t.loadedCertificates) {
                        truststore.addCertificate(cert);
                        trustedCount++;
                    }

                this.uriToAliasMap = uriToAliasMap;
                this.keystore = keystore;
                for (Credential c : credentials) {
                    addCredentialToKeystore(c);
                    keyCount++;
                }
            } finally {
                this.uriToAliasMap = null;
                this.keystore = null;
                credentials.clear();
                trusted.clear();
                flushToDB();
            }
        }

        byte[] trustbytes = null, keybytes = null;
        try {
            trustbytes = truststore.serialize();
            keybytes = keystore.serialize();

            // Now we've built the security information, ship it off...

            log.info("transfering merged truststore with " + trustedCount + " entries");
            rc.setTruststore(trustbytes);

            log.info("transfering merged keystore with " + keyCount + " entries");
            rc.setKeystore(keybytes);
        } finally {
            if (trustbytes != null)
                fill(trustbytes, (byte) 0);
            if (keybytes != null)
                fill(keybytes, (byte) 0);
        }
        rc.setPassword(password);

        log.info("transferring serviceURL->alias map with " + uriToAliasMap.size() + " entries");
        rc.setUriToAliasMap(uriToAliasMap);
    } finally {
        if (password != null)
            fill(password, ' ');
    }

    synchronized (lock) {
        conveyExtraSecuritySettings(rc);
    }
}

From source file:fr.cirad.mgdb.exporting.markeroriented.EigenstratExportHandler.java

@Override
public void exportData(OutputStream outputStream, String sModule, List<SampleId> sampleIDs,
        ProgressIndicator progress, DBCursor markerCursor, Map<Comparable, Comparable> markerSynonyms,
        int nMinimumGenotypeQuality, int nMinimumReadDepth, Map<String, InputStream> readyToExportFiles)
        throws Exception {
    // long before = System.currentTimeMillis();

    File warningFile = File.createTempFile("export_warnings_", "");
    FileWriter warningFileWriter = new FileWriter(warningFile);
    File snpFile = null;//from w  w  w .  j  av  a  2s.co m

    try {
        snpFile = File.createTempFile("snpFile", "");
        FileWriter snpFileWriter = new FileWriter(snpFile);

        ZipOutputStream zos = new ZipOutputStream(outputStream);
        if (ByteArrayOutputStream.class.isAssignableFrom(outputStream.getClass()))
            zos.setLevel(ZipOutputStream.STORED);

        if (readyToExportFiles != null)
            for (String readyToExportFile : readyToExportFiles.keySet()) {
                zos.putNextEntry(new ZipEntry(readyToExportFile));
                InputStream inputStream = readyToExportFiles.get(readyToExportFile);
                byte[] dataBlock = new byte[1024];
                int count = inputStream.read(dataBlock, 0, 1024);
                while (count != -1) {
                    zos.write(dataBlock, 0, count);
                    count = inputStream.read(dataBlock, 0, 1024);
                }
            }

        MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule);
        int markerCount = markerCursor.count();

        List<Individual> individuals = getIndividualsFromSamples(sModule, sampleIDs);

        ArrayList<String> individualList = new ArrayList<String>();
        StringBuffer indFileContents = new StringBuffer();

        for (int i = 0; i < sampleIDs.size(); i++) {
            Individual individual = individuals.get(i);
            if (!individualList.contains(individual.getId())) {
                individualList.add(individual.getId());
                indFileContents
                        .append(individual.getId() + "\t" + getIndividualGenderCode(sModule, individual.getId())
                                + "\t" + (individual.getPopulation() == null ? "." : individual.getPopulation())
                                + LINE_SEPARATOR);
            }
        }

        String exportName = sModule + "_" + markerCount + "variants_" + individualList.size() + "individuals";
        zos.putNextEntry(new ZipEntry(exportName + ".ind"));
        zos.write(indFileContents.toString().getBytes());

        zos.putNextEntry(new ZipEntry(exportName + ".eigenstratgeno"));

        int avgObjSize = (Integer) mongoTemplate
                .getCollection(mongoTemplate.getCollectionName(VariantRunData.class)).getStats()
                .get("avgObjSize");
        int nChunkSize = nMaxChunkSizeInMb * 1024 * 1024 / avgObjSize;
        short nProgress = 0, nPreviousProgress = 0;
        long nLoadedMarkerCount = 0;

        while (markerCursor.hasNext()) {
            int nLoadedMarkerCountInLoop = 0;
            Map<Comparable, String> markerChromosomalPositions = new LinkedHashMap<Comparable, String>();
            boolean fStartingNewChunk = true;
            markerCursor.batchSize(nChunkSize);
            while (markerCursor.hasNext()
                    && (fStartingNewChunk || nLoadedMarkerCountInLoop % nChunkSize != 0)) {
                DBObject exportVariant = markerCursor.next();
                DBObject refPos = (DBObject) exportVariant.get(VariantData.FIELDNAME_REFERENCE_POSITION);
                markerChromosomalPositions.put((Comparable) exportVariant.get("_id"),
                        refPos.get(ReferencePosition.FIELDNAME_SEQUENCE) + ":"
                                + refPos.get(ReferencePosition.FIELDNAME_START_SITE));
                nLoadedMarkerCountInLoop++;
                fStartingNewChunk = false;
            }

            List<Comparable> currentMarkers = new ArrayList<Comparable>(markerChromosomalPositions.keySet());
            LinkedHashMap<VariantData, Collection<VariantRunData>> variantsAndRuns = MgdbDao.getSampleGenotypes(
                    mongoTemplate, sampleIDs, currentMarkers, true,
                    null /*new Sort(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ChromosomalPosition.FIELDNAME_SEQUENCE).and(new Sort(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ChromosomalPosition.FIELDNAME_START_SITE))*/); // query mongo db for matching genotypes
            for (VariantData variant : variantsAndRuns.keySet()) // read data and write results into temporary files (one per sample)
            {
                Comparable variantId = variant.getId();

                List<String> chromAndPos = Helper.split(markerChromosomalPositions.get(variantId), ":");
                if (chromAndPos.size() == 0)
                    LOG.warn("Chromosomal position not found for marker " + variantId);
                // LOG.debug(marker + "\t" + (chromAndPos.length == 0 ? "0" : chromAndPos[0]) + "\t" + 0 + "\t" + (chromAndPos.length == 0 ? 0l : Long.parseLong(chromAndPos[1])) + LINE_SEPARATOR);
                if (markerSynonyms != null) {
                    Comparable syn = markerSynonyms.get(variantId);
                    if (syn != null)
                        variantId = syn;
                }
                snpFileWriter.write(variantId + "\t" + (chromAndPos.size() == 0 ? "0" : chromAndPos.get(0))
                        + "\t" + 0 + "\t" + (chromAndPos.size() == 0 ? 0l : Long.parseLong(chromAndPos.get(1)))
                        + LINE_SEPARATOR);

                Map<String, List<String>> individualGenotypes = new LinkedHashMap<String, List<String>>();
                Collection<VariantRunData> runs = variantsAndRuns.get(variant);
                if (runs != null)
                    for (VariantRunData run : runs)
                        for (Integer sampleIndex : run.getSampleGenotypes().keySet()) {
                            SampleGenotype sampleGenotype = run.getSampleGenotypes().get(sampleIndex);
                            String individualId = individuals
                                    .get(sampleIDs
                                            .indexOf(new SampleId(run.getId().getProjectId(), sampleIndex)))
                                    .getId();

                            Integer gq = null;
                            try {
                                gq = (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_GQ);
                            } catch (Exception ignored) {
                            }
                            if (gq != null && gq < nMinimumGenotypeQuality)
                                continue;

                            Integer dp = null;
                            try {
                                dp = (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_DP);
                            } catch (Exception ignored) {
                            }
                            if (dp != null && dp < nMinimumReadDepth)
                                continue;

                            String gtCode = sampleGenotype.getCode();
                            List<String> storedIndividualGenotypes = individualGenotypes.get(individualId);
                            if (storedIndividualGenotypes == null) {
                                storedIndividualGenotypes = new ArrayList<String>();
                                individualGenotypes.put(individualId, storedIndividualGenotypes);
                            }
                            storedIndividualGenotypes.add(gtCode);
                        }

                for (int j = 0; j < individualList
                        .size(); j++ /* we use this list because it has the proper ordering*/) {
                    String individualId = individualList.get(j);
                    List<String> genotypes = individualGenotypes.get(individualId);
                    HashMap<Object, Integer> genotypeCounts = new HashMap<Object, Integer>(); // will help us to keep track of missing genotypes
                    int highestGenotypeCount = 0;
                    String mostFrequentGenotype = null;
                    if (genotypes != null)
                        for (String genotype : genotypes) {
                            if (genotype.length() == 0)
                                continue; /* skip missing genotypes */

                            int gtCount = 1 + MgdbDao.getCountForKey(genotypeCounts, genotype);
                            if (gtCount > highestGenotypeCount) {
                                highestGenotypeCount = gtCount;
                                mostFrequentGenotype = genotype;
                            }
                            genotypeCounts.put(genotype, gtCount);
                        }

                    List<String> alleles = mostFrequentGenotype == null ? new ArrayList<String>()
                            : variant.getAllelesFromGenotypeCode(mostFrequentGenotype);

                    int nOutputCode = 0;
                    if (mostFrequentGenotype == null)
                        nOutputCode = 9;
                    else
                        for (String all : Helper.split(mostFrequentGenotype, "/"))
                            if ("0".equals(all))
                                nOutputCode++;
                    if (j == 0 && variant.getKnownAlleleList().size() > 2)
                        warningFileWriter.write("- Variant " + variant.getId()
                                + " is multi-allelic. Make sure Eigenstrat genotype encoding specifications are suitable for you.\n");
                    zos.write(("" + nOutputCode).getBytes());

                    if (genotypeCounts.size() > 1 || alleles.size() > 2) {
                        if (genotypeCounts.size() > 1)
                            warningFileWriter.write("- Dissimilar genotypes found for variant "
                                    + (variantId == null ? variant.getId() : variantId) + ", individual "
                                    + individualId + ". Exporting most frequent: " + nOutputCode + "\n");
                        if (alleles.size() > 2)
                            warningFileWriter.write("- More than 2 alleles found for variant "
                                    + (variantId == null ? variant.getId() : variantId) + ", individual "
                                    + individualId + ". Exporting only the first 2 alleles.\n");
                    }
                }
                zos.write((LINE_SEPARATOR).getBytes());
            }

            if (progress.hasAborted())
                return;

            nLoadedMarkerCount += nLoadedMarkerCountInLoop;
            nProgress = (short) (nLoadedMarkerCount * 100 / markerCount);
            if (nProgress > nPreviousProgress) {
                // if (nProgress%5 == 0)
                //    LOG.info("============= exportData: " + nProgress + "% =============" + (System.currentTimeMillis() - before)/1000 + "s");
                progress.setCurrentStepProgress(nProgress);
                nPreviousProgress = nProgress;
            }
        }

        snpFileWriter.close();
        zos.putNextEntry(new ZipEntry(exportName + ".snp"));
        BufferedReader in = new BufferedReader(new FileReader(snpFile));
        String sLine;
        while ((sLine = in.readLine()) != null)
            zos.write((sLine + "\n").getBytes());
        in.close();

        warningFileWriter.close();
        if (warningFile.length() > 0) {
            zos.putNextEntry(new ZipEntry(exportName + "-REMARKS.txt"));
            int nWarningCount = 0;
            in = new BufferedReader(new FileReader(warningFile));
            while ((sLine = in.readLine()) != null) {
                zos.write((sLine + "\n").getBytes());
                nWarningCount++;
            }
            LOG.info("Number of Warnings for export (" + exportName + "): " + nWarningCount);
            in.close();
        }
        warningFile.delete();

        zos.close();
        progress.setCurrentStepProgress((short) 100);
    } finally {
        if (snpFile != null && snpFile.exists())
            snpFile.delete();
    }
}

From source file:com.intellectualcrafters.plot.database.SQLManager.java

@Override
public void createAllSettingsAndHelpers(final ArrayList<Plot> plots) {

    // TODO SEVERE [ More than 5000 plots will fail in a single SQLite
    // query./*from   w  w w.j a v  a 2 s  .co m*/

    final HashMap<String, HashMap<PlotId, Integer>> stored = new HashMap<>();
    final HashMap<Integer, ArrayList<UUID>> helpers = new HashMap<>();
    try {
        final PreparedStatement stmt = connection.prepareStatement(GET_ALL_PLOTS);
        final ResultSet result = stmt.executeQuery();
        while (result.next()) {
            final int id = result.getInt("id");
            final int idx = result.getInt("plot_id_x");
            final int idz = result.getInt("plot_id_z");
            final String world = result.getString("world");

            if (!stored.containsKey(world)) {
                stored.put(world, new HashMap<PlotId, Integer>());
            }
            stored.get(world).put(new PlotId(idx, idz), id);
        }
    } catch (final SQLException e) {
        e.printStackTrace();
    }

    for (final Plot plot : plots) {
        final String world = Bukkit.getWorld(plot.world).getName();
        if (stored.containsKey(world)) {
            final Integer id = stored.get(world).get(plot.id);
            if (id != null) {
                helpers.put(id, plot.helpers);
            }
        }
    }

    if (helpers.size() == 0) {
        return;
    }

    // add plot settings
    final Integer[] ids = helpers.keySet().toArray(new Integer[helpers.keySet().size()]);
    StringBuilder statement = new StringBuilder(CREATE_SETTINGS);
    for (int i = 0; i < (ids.length - 1); i++) {
        statement.append("(?),");
    }
    statement.append("(?)");
    PreparedStatement stmt = null;
    try {
        stmt = connection.prepareStatement(statement.toString());
        for (int i = 0; i < ids.length; i++) {
            stmt.setInt(i + 1, ids[i]);
        }
        stmt.executeUpdate();
        stmt.close();
    } catch (final SQLException e) {
        e.printStackTrace();
    }

    // add plot helpers
    String prefix = "";
    statement = new StringBuilder(CREATE_HELPERS);
    for (final Integer id : helpers.keySet()) {
        for (final UUID helper : helpers.get(id)) {
            statement.append(prefix + "(?, ?)");
            prefix = ",";
        }
    }
    if (prefix.equals("")) {
        return;
    }
    try {
        stmt = connection.prepareStatement(statement.toString());
        int counter = 0;
        for (final Integer id : helpers.keySet()) {
            for (final UUID helper : helpers.get(id)) {

                stmt.setInt((counter * 2) + 1, id);
                stmt.setString((counter * 2) + 2, helper.toString());
                counter++;
            }
        }
        stmt.executeUpdate();
        stmt.close();
    } catch (final SQLException e) {
        Logger.add(LogLevel.WARNING, "Failed to set helper for plots");
        e.printStackTrace();
    }
}

From source file:com.pari.reports.request.handlers.ManageExportHandlerImpl.java

@SuppressWarnings("unchecked")
private ServiceContainer getSetUpWorkflowApprovalDetails(ColumnDefinition[] colDef,
        TableDefinition childTableDef, HashMap<String, Object> paramFilters) {
    ServiceImpl service = null;/*from  w w w.j a v  a  2 s.  c om*/
    ServiceContainerImpl serviceContainer = null;
    String customerName = getRequestDetails().getCustomer();
    int customerId = -1;
    if (customerName != null && customerName.trim().length() > 0) {
        try {
            customerId = getRequestDetails().getServerIf().getCustomerIf().getCustomerIdByName(customerName);
        } catch (Exception e) {
            logger.error("Exception while Exporting Setup Workflow", e);
        }
    }
    Map<Integer, ApprovalDefinition> approvalDefMap = null;
    try {
        if (paramFilters != null && paramFilters.size() > 0) {
            approvalDefMap = new HashMap<Integer, ApprovalDefinition>();
            ArrayList<String> grpNames = new ArrayList<String>();
            Object grpIdObj = paramFilters.get("DeviceGroup");
            if (grpIdObj instanceof String) {
                grpNames.add((String) grpIdObj);
            } else if (grpIdObj instanceof ArrayList) {
                grpNames = (ArrayList<String>) grpIdObj;
            }
            for (String grpName : grpNames) {
                int grpId = GroupingService.getInstance().getGroupIdFromName(grpName);
                ApprovalDefinition approvalDef = getRequestDetails().getServerIf().getApprovalIf()
                        .getWorkflowApprovalDefsWithLevels(grpId, customerId);
                approvalDefMap.put(grpId, approvalDef);
            }
        } else {
            approvalDefMap = getRequestDetails().getServerIf().getApprovalIf()
                    .getAllWorkflowApprovalDefsWithLevels(customerId);
        }
    } catch (PariException e) {
        e.printStackTrace();
    }
    if (null == approvalDefMap) {
        return null;
    }
    SimpleDateFormat formatter = new SimpleDateFormat("EEE, MMM dd, yyyy HH:mm:ss Z");
    serviceContainer = new ServiceContainerImpl();

    for (Map.Entry<Integer, ApprovalDefinition> map : approvalDefMap.entrySet()) {
        service = new ServiceImpl();
        ApprovalDefinition approvalDefinition = map.getValue();
        String creationTime = (0 == approvalDefinition.getCreationTime()) ? ""
                : getTimeBasedOnZone(approvalDefinition.getCreationTime());
        String modifierTime = (0 == approvalDefinition.getModifierTime()) ? ""
                : formatter.format(new Date(approvalDefinition.getModifierTime()));

        service.put(colDef[0].getId(), approvalDefinition.getGroupName());
        service.put(colDef[1].getId(), approvalDefinition.getWorkFlowName());
        service.put(colDef[2].getId(), approvalDefinition.getCreatorLogin());
        service.put(colDef[3].getId(), creationTime);
        service.put(colDef[4].getId(), approvalDefinition.getModifierLogin());
        service.put(colDef[5].getId(), modifierTime);

        if (childTableDef != null) {
            ColumnDefinition[] chidlColDef = childTableDef.getColumnDefs();
            Map<Integer, ApprovalLevelDefination> approvalLevels = approvalDefinition.getApprovalLevels();

            if (approvalLevels != null && approvalLevels.size() > 0) {

                ServiceContainerImpl approvalLevelSrvCont = new ServiceContainerImpl();
                for (Integer level : approvalLevels.keySet()) {
                    ApprovalLevelDefination approvalLevel = approvalLevels.get(level);
                    Map<Integer, String> approverLogins = approvalLevel.getApproverLogins();
                    if (approverLogins != null && approverLogins.size() > 0) {
                        for (Integer id : approverLogins.keySet()) {
                            ServiceImpl srvImpl = new ServiceImpl();
                            srvImpl.put(chidlColDef[0].getId(), approvalDefinition.getGroupName());
                            srvImpl.put(chidlColDef[1].getId(), level);
                            srvImpl.put(chidlColDef[2].getId(), approverLogins.get(id));
                            srvImpl.put(chidlColDef[3].getId(),
                                    approvalLevel.getApprovalComplType().getActionString());
                            approvalLevelSrvCont.addManageServices(srvImpl);
                        }
                    }

                    HashMap<Integer, ApprovalGroupDefinition> approvalUsrGrps = approvalLevel
                            .getApprovalUserGrps();
                    if (approvalUsrGrps != null && approvalUsrGrps.size() > 0) {
                        for (ApprovalGroupDefinition approvalUsrGrp : approvalUsrGrps.values()) {
                            approverLogins = approvalUsrGrp.getApproverLogins();
                            if (approverLogins != null && approverLogins.size() > 0) {
                                for (Integer id : approverLogins.keySet()) {
                                    ServiceImpl srvImpl = new ServiceImpl();
                                    srvImpl.put(chidlColDef[0].getId(), approvalDefinition.getGroupName());
                                    srvImpl.put(chidlColDef[1].getId(), level);
                                    srvImpl.put(chidlColDef[2].getId(), approverLogins.get(id));
                                    srvImpl.put(chidlColDef[3].getId(),
                                            approvalLevel.getApprovalComplType().getActionString());
                                    approvalLevelSrvCont.addManageServices(srvImpl);
                                }
                            }
                        }
                    }
                }
                service.put("ApprovalLevelDefs", approvalLevelSrvCont);
            }
        }

        serviceContainer.addManageServices(service);
    }
    return serviceContainer;
}