Example usage for java.io FileReader close

List of usage examples for java.io FileReader close

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Introduction

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

Prototype

public void close() throws IOException

Source Link

Usage

From source file:org.kuali.kfs.gl.document.service.impl.CorrectionDocumentServiceImpl.java

public String createOutputFileForProcessing(String docId, java.util.Date today) {
    File outputFile = new File(glcpDirectoryName + File.separator + docId + OUTPUT_ORIGIN_ENTRIES_FILE_SUFFIX);
    String newFileName = batchFileDirectoryName + File.separator + GLCP_OUTPUT_PREFIX + "." + docId
            + buildFileExtensionWithDate(today);
    File newFile = new File(newFileName);
    FileReader inputFileReader;
    FileWriter newFileWriter;// ww w . j  a  va  2s.co m

    try {
        // copy output file and put in OriginEntryInformation directory
        inputFileReader = new FileReader(outputFile);
        newFileWriter = new FileWriter(newFile);
        int c;
        while ((c = inputFileReader.read()) != -1) {
            newFileWriter.write(c);
        }

        inputFileReader.close();
        newFileWriter.close();

        // create done file, after successfully copying output file
        String doneFileName = newFileName.replace(GeneralLedgerConstants.BatchFileSystem.EXTENSION,
                GeneralLedgerConstants.BatchFileSystem.DONE_FILE_EXTENSION);
        File doneFile = new File(doneFileName);
        if (!doneFile.exists()) {
            doneFile.createNewFile();
        }

    } catch (IOException e) {
        throw new RuntimeException(e);
    }

    return newFileName;
}

From source file:org.corpus_tools.pepper.connectors.impl.MavenAccessor.java

/**
 * This method tries to read the blacklist file, if it already exists
 */// ww  w.  j  a  va2s  . co m
private void init() {
    /* init Maven utils */
    /* read/write dependency blacklist */
    File blacklistFile = new File(BLACKLIST_PATH);
    if (blacklistFile.exists()) {
        try {
            FileReader fR = new FileReader(blacklistFile);
            BufferedReader reader = new BufferedReader(fR);
            String line = reader.readLine();
            while (line != null) {
                forbiddenFruits.add(line);
                line = reader.readLine();
            }
            reader.close();
            fR.close();
        } catch (IOException e) {
            logger.debug("Could not read blacklist file.", e);
        }
    }
}

From source file:com.spike.tg4w.htmlunit.XmlTestResultImpl.java

private String outputFileAsHtml(String filename) {
    FileReader fr = null;
    try {//from  ww w . j  a  v  a  2 s  .  c o  m
        fr = new FileReader(filename);
        BufferedReader reader = new BufferedReader(fr);
        String line;
        int lineNum = 0;
        String outfile = (new File(filename)).getName() + "_rec.html";
        Writer writer = new FileWriter(this.writeDir + File.separator + outfile);
        writer.write(
                "<html><head><style>.highlight {background-color:lightblue; }</style> <script> function highlight() { var line = location.search.substring(6); if (line) document.getElementById(line).setAttribute(\"class\", \"highlight\"); } </script> </head><body onload='javascript:highlight();' style='font-size:90%;font-family:courier'><table cellpadding='0' cellspacing='0'>");
        while ((line = reader.readLine()) != null) {
            lineNum++;
            line = line.replace(" ", "&nbsp;").replace("\t", "&nbsp;").replace(">", "&gt;").replace("<",
                    "&lt;");
            writer.write("<tr><td id='" + lineNum + "'>");
            writer.write("<a name='" + lineNum + "'/> &nbsp;" + lineNum + "&nbsp;&nbsp;&nbsp;&nbsp;" + line
                    + "<br/>\n");
            writer.write("</td></tr>");
        }
        writer.write("</table></body></html>");
        writer.close();
        fr.close();
        reader.close();
        return outfile;
    } catch (Exception e) {
        e.printStackTrace();
        return null;
    } finally {
        try {
            if (fr != null) {
                fr.close();
            }
        } catch (IOException ex) {
            // ignore
        }
    }
}

From source file:com.apifest.doclet.integration.tests.DocletTest.java

@Test
public void check_what_doclet_will_generate_correct_stream_result_parameters() throws Exception {
    // GIVEN//from w w w. ja  va  2 s.  com
    String parserFilePath = "./all-mappings-docs.json";
    Map<String, ResultParamDocumentation> resNameToTypeMap = new HashMap<String, ResultParamDocumentation>();
    addResultParamToMap("tw_id", "integer", "The ** tw_id ** description", true, resNameToTypeMap);
    addResultParamToMap("in_reply_to_screen_name", "string", "The ** in_reply_to_screen_name ** description",
            true, resNameToTypeMap);
    addResultParamToMap("request_handle", "string", "The ** request_handle ** description", true,
            resNameToTypeMap);
    addResultParamToMap("in_reply_to_status_id", "string", "The ** in_reply_to_status_id ** description", true,
            resNameToTypeMap);
    addResultParamToMap("channel", "string", "The ** channel ** description", true, resNameToTypeMap);
    // WHEN
    runDoclet();
    // THEN
    JSONParser parser = new JSONParser();
    FileReader fileReader = null;
    try {
        fileReader = new FileReader(parserFilePath);
        JSONObject json = (JSONObject) parser.parse(fileReader);
        JSONArray arr = (JSONArray) json.get("endpoints");
        JSONObject obj = (JSONObject) arr.get(0);

        JSONArray resParam = (JSONArray) obj.get("resultParams");
        for (int i = 0; i < resParam.size(); i++) {
            JSONObject currentParam = (JSONObject) resParam.get(i);
            String currentName = (String) currentParam.get("name");
            ResultParamDocumentation correctCurrentParam = resNameToTypeMap.get(currentName);
            Assert.assertEquals((String) currentParam.get("type"), correctCurrentParam.getType());
            Assert.assertEquals((String) currentParam.get("name"), correctCurrentParam.getName());
            Assert.assertEquals((String) currentParam.get("description"), correctCurrentParam.getDescription());
            Assert.assertEquals(currentParam.get("required"), correctCurrentParam.isRequired());
        }
    } finally {
        if (fileReader != null) {
            fileReader.close();
        }
        deleteJsonFile(parserFilePath);
    }
}

From source file:org.fhcrc.cpl.viewer.ms2.commandline.PostProcessPepXMLCLM.java

/**
 *
 * @param featureFile/*  ww  w  . j  a va 2 s  . c  o  m*/
 * @param outputFile
 * @throws CommandLineModuleExecutionException
 */
protected void handleFeatureFile(File featureFile, File outputFile) throws CommandLineModuleExecutionException {
    ApplicationContext.infoMessage("Handling file " + featureFile.getAbsolutePath() + "...");

    if (maxFDR < Float.MAX_VALUE) {
        minPeptideProphet = (float) calcMinPeptideProphetForMaxFDR(featureFile);
        ApplicationContext.infoMessage("Minimum PeptideProphet for FDR " + maxFDR + ": " + minPeptideProphet);
    }

    try {
        Iterator<FeatureSet> featureSetIterator = new PepXMLFeatureFileHandler.PepXMLFeatureSetIterator(
                featureFile);

        List<File> tempFeatureFiles = new ArrayList<File>();
        int numSetsProcessed = 0;
        while (featureSetIterator.hasNext()) {
            FeatureSet featureSet = featureSetIterator.next();

            ApplicationContext.infoMessage("\tProcessing fraction " + (numSetsProcessed + 1) + "...");

            processFeatureSet(featureSet);
            String baseName = MS2ExtraInfoDef.getFeatureSetBaseName(featureSet);
            if (baseName == null) {
                baseName = featureFile.getName();
                if (numSetsProcessed > 0 || featureSetIterator.hasNext())
                    baseName = baseName + "_" + numSetsProcessed;
            }
            //if PeptideProphet was run from a directory below the directory containing the
            //mzXML files, we may have ../ in the baseName, which causes trouble in saving
            //the temporary files
            //                while (baseName.contains(".." + File.separator))
            //                    baseName.replaceFirst(".." + File.separator, "");
            if (baseName.contains(File.separator))
                baseName = baseName.substring(baseName.lastIndexOf(File.separator) + 1);

            File thisFractionFile = TempFileManager.createTempFile(baseName + ".pep.xml", this);

            featureSet.savePepXml(thisFractionFile);

            _log.debug("Saved fraction file as " + thisFractionFile.getAbsolutePath());
            tempFeatureFiles.add(thisFractionFile);

            numSetsProcessed++;
        }

        ApplicationContext.infoMessage("Saving output file " + outputFile.getAbsolutePath() + " ...");

        if (numSetsProcessed == 1) {
            FileReader in = new FileReader(tempFeatureFiles.get(0));
            FileWriter out = new FileWriter(outputFile);
            int c;

            while ((c = in.read()) != -1)
                out.write(c);

            in.close();
            out.close();
        } else {
            ApplicationContext.infoMessage(
                    "\tCombining individual fraction files... " + outputFile.getAbsolutePath() + "...");
            new PepXMLFeatureFileHandler().combinePepXmlFiles(tempFeatureFiles, outputFile);
        }
        ApplicationContext.infoMessage("Done.");
    } catch (IOException e) {
        throw new CommandLineModuleExecutionException(
                "Failed to process features from file " + featureFile.getAbsolutePath(), e);
    } finally {
        TempFileManager.deleteTempFiles(this);
    }
}

From source file:com.apifest.doclet.integration.tests.DocletTest.java

@Test
public void check_what_doclet_will_generate_correct_stream_request_parameters() throws Exception {
    // GIVEN/* w  w w. j a  v  a  2  s.com*/
    String parserFilePath = "./all-mappings-docs.json";
    Map<String, RequestParamDocumentation> correctNameToTypeMap = new HashMap<String, RequestParamDocumentation>();
    addRequestParamToMap("ids", "string", "** user ids goes here **", true, correctNameToTypeMap);
    addRequestParamToMap("fields", "list", "** The keys from result json can be added as filter**", false,
            correctNameToTypeMap);
    addRequestParamToMap("since", "integer", "** since is optional parameter**", false, correctNameToTypeMap);
    addRequestParamToMap("until", "integer", "** until is optional parameter**", false, correctNameToTypeMap);
    // WHEN
    runDoclet();
    // THEN
    JSONParser parser = new JSONParser();
    FileReader fileReader = null;
    try {
        fileReader = new FileReader(parserFilePath);
        JSONObject json = (JSONObject) parser.parse(fileReader);
        JSONArray arr = (JSONArray) json.get("endpoints");
        JSONObject obj = (JSONObject) arr.get(0);

        JSONArray reqParam = (JSONArray) obj.get("requestParams");

        for (int i = 0; i < reqParam.size(); i++) {
            JSONObject currentParam = (JSONObject) reqParam.get(i);
            String currentName = (String) currentParam.get("name");
            RequestParamDocumentation correctCurrentParam = correctNameToTypeMap.get(currentName);
            Assert.assertEquals((String) currentParam.get("type"), correctCurrentParam.getType());
            Assert.assertEquals((String) currentParam.get("name"), correctCurrentParam.getName());
            Assert.assertEquals((String) currentParam.get("description"), correctCurrentParam.getDescription());
            Assert.assertEquals(currentParam.get("required"), correctCurrentParam.isRequired());
        }
    } finally {
        if (fileReader != null) {
            fileReader.close();
        }
        deleteJsonFile(parserFilePath);
    }
}

From source file:com.apifest.doclet.integration.tests.DocletTest.java

@Test
public void check_what_doclet_will_generate_correct_metrics_result_parameters() throws Exception {
    // GIVEN//from w  ww .  ja  v a2  s  . c  o m
    String parserFilePath = "./all-mappings-docs.json";
    Map<String, ResultParamDocumentation> resNameToTypeMap = new HashMap<String, ResultParamDocumentation>();
    addResultParamToMap("channel", "string", "The **channel** description", true, resNameToTypeMap);
    addResultParamToMap("updated_time", "string", "The **updated_time** description", true, resNameToTypeMap);
    addResultParamToMap("request_handle", "string", "The **request_handle** description", true,
            resNameToTypeMap);
    addResultParamToMap("sentiment.score", "string", "The **sentiment_score** description", true,
            resNameToTypeMap);
    addResultParamToMap("sentiment.positive", "string", "The **sentiment_positive** description", true,
            resNameToTypeMap);
    addResultParamToMap("sentiment.neutral", "string", "The **sentiment_neutral** description", true,
            resNameToTypeMap);
    addResultParamToMap("sentiment.negative", "string", "The **sentiment_negative** description", true,
            resNameToTypeMap);
    addResultParamToMap("engagement.replies", "integer", "The **engagement_replies** description", true,
            resNameToTypeMap);
    addResultParamToMap("engagement.tweets", "integer", "The **engagement_tweets** description", true,
            resNameToTypeMap);
    // WHEN
    runDoclet();
    // THEN
    JSONParser parser = new JSONParser();
    FileReader fileReader = null;
    try {
        fileReader = new FileReader(parserFilePath);
        JSONObject json = (JSONObject) parser.parse(fileReader);
        JSONArray arr = (JSONArray) json.get("endpoints");
        JSONObject obj = (JSONObject) arr.get(1);

        JSONArray resParam = (JSONArray) obj.get("resultParams");
        for (int i = 0; i < resParam.size(); i++) {
            JSONObject currentParam = (JSONObject) resParam.get(i);
            String currentName = (String) currentParam.get("name");
            ResultParamDocumentation correctCurrentParam = resNameToTypeMap.get(currentName);
            Assert.assertEquals((String) currentParam.get("type"), correctCurrentParam.getType());
            Assert.assertEquals((String) currentParam.get("name"), correctCurrentParam.getName());
            Assert.assertEquals((String) currentParam.get("description"), correctCurrentParam.getDescription());
            Assert.assertEquals(currentParam.get("required"), correctCurrentParam.isRequired());

        }
    } finally {
        if (fileReader != null) {
            fileReader.close();
        }
        deleteJsonFile(parserFilePath);
    }
}

From source file:com.apifest.doclet.integration.tests.DocletTest.java

@Test
public void check_what_doclet_will_generate_correct_metric_exceptions() throws Exception {
    // GIVEN//from  w  w  w .  j a v  a  2s  . c o  m
    String parserFilePath = "./all-mappings-docs.json";
    Map<String, ExceptionDocumentation> exsNameToDescriptionMap = new HashMap<String, ExceptionDocumentation>();
    addException("invalid_parameter", "Please add valid parameter", 400, "The parameter is invalid",
            exsNameToDescriptionMap);
    // WHEN
    runDoclet();
    // THEN
    JSONParser parser = new JSONParser();
    FileReader fileReader = null;
    try {
        fileReader = new FileReader(parserFilePath);
        JSONObject json = (JSONObject) parser.parse(fileReader);
        JSONArray arr = (JSONArray) json.get("endpoints");
        JSONObject obj = (JSONObject) arr.get(1);

        JSONArray exsParam = (JSONArray) obj.get("exceptions");
        for (int i = 0; i < exsParam.size(); i++) {
            JSONObject currentParam = (JSONObject) exsParam.get(i);
            String currentName = (String) currentParam.get("name");
            ExceptionDocumentation correctCurrentParam = exsNameToDescriptionMap.get(currentName);
            Assert.assertEquals((String) currentParam.get("name"), correctCurrentParam.getName());
            Assert.assertEquals((String) currentParam.get("condition"), correctCurrentParam.getCondition());
            Assert.assertEquals((String) currentParam.get("description"), correctCurrentParam.getDescription());
            Assert.assertEquals(currentParam.get("code"), new Long(correctCurrentParam.getCode()));
        }
    } finally {
        if (fileReader != null) {
            fileReader.close();
        }
        deleteJsonFile(parserFilePath);
    }
}

From source file:com.apifest.doclet.integration.tests.DocletTest.java

@Test
public void check_what_doclet_will_generate_correct_stream_exceptions() throws Exception {
    // GIVEN/*from www. jav a2 s  .  co  m*/
    String parserFilePath = "./all-mappings-docs.json";
    Map<String, ExceptionDocumentation> exsNameToDescriptionMap = new HashMap<String, ExceptionDocumentation>();
    addException("invalid_since_until", "Since/until parameter must be within the last 30 days", 400,
            "The period is invalid", exsNameToDescriptionMap);
    // WHEN
    runDoclet();
    // THEN
    JSONParser parser = new JSONParser();
    FileReader fileReader = null;
    try {
        fileReader = new FileReader(parserFilePath);
        JSONObject json = (JSONObject) parser.parse(fileReader);
        JSONArray arr = (JSONArray) json.get("endpoints");
        JSONObject obj = (JSONObject) arr.get(0);

        JSONArray exsParam = (JSONArray) obj.get("exceptions");
        for (int i = 0; i < exsParam.size(); i++) {
            JSONObject currentParam = (JSONObject) exsParam.get(i);
            String currentName = (String) currentParam.get("name");
            ExceptionDocumentation correctCurrentParam = exsNameToDescriptionMap.get(currentName);
            Assert.assertEquals((String) currentParam.get("name"), correctCurrentParam.getName());
            Assert.assertEquals((String) currentParam.get("condition"), correctCurrentParam.getCondition());
            Assert.assertEquals((String) currentParam.get("description"), correctCurrentParam.getDescription());
            Assert.assertEquals(currentParam.get("code"), new Long(correctCurrentParam.getCode()));
        }
    } finally {
        if (fileReader != null) {
            fileReader.close();
        }
        deleteJsonFile(parserFilePath);
    }
}

From source file:com.datatorrent.contrib.hdht.HDHTWriter.java

/**
 * Flush changes from write cache to disk. New data files will be written and meta data replaced atomically. The flush
 * frequency determines availability of changes to external readers.
 *
 * @throws IOException//from w  ww.jav a  2s . c  o  m
 */
private void writeDataFiles(Bucket bucket) throws IOException {
    BucketIOStats ioStats = getOrCretaStats(bucket.bucketKey);
    LOG.debug("Writing data files in bucket {}", bucket.bucketKey);
    // copy meta data on write
    BucketMeta bucketMetaCopy = kryo.copy(getMeta(bucket.bucketKey));

    /** Process purge requests before flushing data from cache to maintain
     * the oder or purge and put operations. This makes sure that purged data
     * removed from file, before new data is added to the files */
    HashSet<String> filesToDelete = Sets.newHashSet();
    bucketMetaCopy = processPurge(bucket, bucketMetaCopy, filesToDelete);

    // bucket keys by file
    TreeMap<Slice, BucketFileMeta> bucketSeqStarts = bucketMetaCopy.files;
    Map<BucketFileMeta, Map<Slice, Slice>> modifiedFiles = Maps.newHashMap();

    for (Map.Entry<Slice, byte[]> entry : bucket.frozenWriteCache.entrySet()) {
        // find file for key
        Map.Entry<Slice, BucketFileMeta> floorEntry = bucketSeqStarts.floorEntry(entry.getKey());
        BucketFileMeta floorFile;
        if (floorEntry != null) {
            floorFile = floorEntry.getValue();
        } else {
            floorEntry = bucketSeqStarts.firstEntry();
            if (floorEntry == null || floorEntry.getValue().name != null) {
                // no existing file or file with higher key
                floorFile = new BucketFileMeta();
            } else {
                // placeholder for new keys, move start key
                floorFile = floorEntry.getValue();
                bucketSeqStarts.remove(floorEntry.getKey());
            }
            floorFile.startKey = entry.getKey();
            if (floorFile.startKey.length != floorFile.startKey.buffer.length) {
                // normalize key for serialization
                floorFile.startKey = new Slice(floorFile.startKey.toByteArray());
            }
            bucketSeqStarts.put(floorFile.startKey, floorFile);
        }

        Map<Slice, Slice> fileUpdates = modifiedFiles.get(floorFile);
        if (fileUpdates == null) {
            modifiedFiles.put(floorFile, fileUpdates = Maps.newHashMap());
        }
        fileUpdates.put(entry.getKey(), new Slice(entry.getValue()));
    }

    // write modified files
    for (Map.Entry<BucketFileMeta, Map<Slice, Slice>> fileEntry : modifiedFiles.entrySet()) {
        BucketFileMeta fileMeta = fileEntry.getKey();
        TreeMap<Slice, Slice> fileData = new TreeMap<Slice, Slice>(getKeyComparator());

        if (fileMeta.name != null) {
            // load existing file
            long start = System.currentTimeMillis();
            FileReader reader = store.getReader(bucket.bucketKey, fileMeta.name);
            reader.readFully(fileData);
            ioStats.dataBytesRead += store.getFileSize(bucket.bucketKey, fileMeta.name);
            ioStats.dataReadTime += System.currentTimeMillis() - start;
            /* these keys are re-written */
            ioStats.dataKeysRewritten += fileData.size();
            ioStats.filesReadInCurrentWriteCycle++;
            ioStats.dataFilesRead++;
            reader.close();
            filesToDelete.add(fileMeta.name);
        }

        // apply updates
        fileData.putAll(fileEntry.getValue());
        // new file
        writeFile(bucket, bucketMetaCopy, fileData);
    }

    LOG.debug("Files written {} files read {}", ioStats.filesWroteInCurrentWriteCycle,
            ioStats.filesReadInCurrentWriteCycle);
    // flush meta data for new files
    try {
        LOG.debug("Writing {} with {} file entries", FNAME_META, bucketMetaCopy.files.size());
        OutputStream os = store.getOutputStream(bucket.bucketKey, FNAME_META + ".new");
        Output output = new Output(os);
        bucketMetaCopy.committedWid = bucket.committedLSN;
        bucketMetaCopy.recoveryStartWalPosition = bucket.recoveryStartWalPosition;
        kryo.writeClassAndObject(output, bucketMetaCopy);
        output.close();
        os.close();
        store.rename(bucket.bucketKey, FNAME_META + ".new", FNAME_META);
    } catch (IOException e) {
        throw new RuntimeException("Failed to write bucket meta data " + bucket.bucketKey, e);
    }

    // clear pending changes
    ioStats.dataKeysWritten += bucket.frozenWriteCache.size();
    // switch to new version
    this.metaCache.put(bucket.bucketKey, bucketMetaCopy);

    // delete old files
    for (String fileName : filesToDelete) {
        store.delete(bucket.bucketKey, fileName);
    }
    invalidateReader(bucket.bucketKey, filesToDelete);
    // clearing cache after invalidating readers
    bucket.frozenWriteCache.clear();

    // cleanup WAL files which are not needed anymore.
    minimumRecoveryWalPosition = bucketMetaCopy.recoveryStartWalPosition;
    for (Long bucketId : this.bucketKeys) {
        BucketMeta meta = getMeta(bucketId);
        if (meta.recoveryStartWalPosition.fileId < minimumRecoveryWalPosition.fileId
                || (meta.recoveryStartWalPosition.fileId == minimumRecoveryWalPosition.fileId
                        && meta.recoveryStartWalPosition.offset < minimumRecoveryWalPosition.offset)) {
            minimumRecoveryWalPosition = meta.recoveryStartWalPosition;
        }
    }
    this.wal.cleanup(minimumRecoveryWalPosition.fileId);
    ioStats.filesReadInCurrentWriteCycle = 0;
    ioStats.filesWroteInCurrentWriteCycle = 0;
}