Example usage for java.io StringWriter flush

List of usage examples for java.io StringWriter flush

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Introduction

In this page you can find the example usage for java.io StringWriter flush.

Prototype

public void flush()

Source Link

Document

Flush the stream.

Usage

From source file:org.jetbrains.jet.grammar.GrammarGenerator.java

private static String generate(List<Token> tokens) throws IOException {
    StringWriter result = new StringWriter();

    Set<String> declaredSymbols = new HashSet<String>();
    Set<String> usedSymbols = new HashSet<String>();
    Multimap<String, String> usages = Multimaps.newSetMultimap(Maps.<String, Collection<String>>newHashMap(),
            new Supplier<Set<String>>() {
                @Override/*from   www  . j  a v a 2s.  c  o m*/
                public Set<String> get() {
                    return Sets.newHashSet();
                }
            });

    Declaration lastDeclaration = null;
    for (Token advance : tokens) {
        if (advance instanceof Declaration) {
            Declaration declaration = (Declaration) advance;
            lastDeclaration = declaration;
            declaredSymbols.add(declaration.getName());
        } else if (advance instanceof Identifier) {
            Identifier identifier = (Identifier) advance;
            assert lastDeclaration != null;
            usages.put(identifier.getName(), lastDeclaration.getName());
            usedSymbols.add(identifier.getName());
        }
    }

    try {

        JAXBContext context = JAXBContext.newInstance(Annotation.class, Comment.class, Declaration.class,
                DocComment.class, Identifier.class, Other.class, StringToken.class, SymbolToken.class,
                Token.class, WhiteSpace.class, TokenList.class);
        Marshaller m = context.createMarshaller();
        TokenList list = new TokenList(tokens);
        list.updateUsages(usedSymbols, usages);
        m.marshal(list, result);

    } catch (PropertyException e) {
        e.printStackTrace();
    } catch (JAXBException e) {
        e.printStackTrace();
    }

    result.flush();
    result.close();
    return result.toString();
}

From source file:com.tek42.perforce.parse.AbstractPerforceTemplate.java

protected StringBuilder getPerforceResponse(String origcmd[], ResponseFilter filter) throws PerforceException {
    // TODO: Create a way to wildcard portions of the error checking.  Add method to check for these errors.
    boolean loop = false;
    boolean attemptLogin = true;

    List<String> lines = null;
    int totalLength = 0;

    do {//w  w  w.  j a  v a2s . co m
        int mesgIndex = -1, count = 0;
        Executor p4 = depot.getExecFactory().newExecutor();

        String debugCmd = "";
        // get entire cmd to execute
        String cmd[] = getExtraParams(origcmd);

        // setup information for logging...
        for (String cm : cmd) {
            debugCmd += cm + " ";
        }

        // Perform execution and IO
        p4.exec(cmd);
        BufferedReader reader = p4.getReader();
        String line = null;
        totalLength = 0;
        lines = new ArrayList<String>(1024);
        TimedStreamCloser timedStreamCloser = null;
        try {
            PerforceSCM.PerforceSCMDescriptor scmDescr = PerforceSCM.getInstance();
            p4.getWriter().close();
            int timeout = -1;
            if (scmDescr.hasP4ReadlineTimeout()) { // Implementation with timeout
                timeout = scmDescr.getP4ReadLineTimeout();
            }
            timedStreamCloser = new TimedStreamCloser(p4.getInputStream(), timeout);
            timedStreamCloser.start();

            while ((line = reader.readLine()) != null) {
                timedStreamCloser.reset();
                // only check for errors if we have not found one already
                if (mesgIndex == -1)
                    mesgIndex = checkAuthnErrors(line);
                if (filter.reject(line))
                    continue;
                lines.add(line);
                totalLength += line.length();
                count++;
            }
            if (timedStreamCloser.timedOut()) {
                throw new PerforceException("Perforce operation timed out after " + timeout + " seconds.");
            }
        } catch (IOException ioe) {
            //this is generally not anything to worry about.  The underlying
            //perforce process terminated and that causes java to be angry
            StringWriter sw = new StringWriter();
            PrintWriter pw = new PrintWriter(sw, true);
            ioe.printStackTrace(pw);
            pw.flush();
            sw.flush();
            getLogger().warn("Perforce process terminated suddenly");
            getLogger().warn(sw.toString());

            try {
                p4.getWriter().close();
            } catch (IOException e) {
                getLogger().warn("Write pipe failed to close.");
            }

            try {
                p4.getReader().close();
            } catch (IOException e) {
                getLogger().warn("Read pipe failed to close.");
            }

            p4.close();

            // If the project was interrupted, p4 needs to be killed
            // or it will continue running. In the worst case it will
            // still synchronize gigabytes of data into the workspace
            p4.kill();
        } finally {
            if (timedStreamCloser != null)
                timedStreamCloser.interrupt();
            try {
                p4.getWriter().close();
            } catch (IOException e) {
                getLogger().warn("Write pipe failed to close.");
            }
            try {
                p4.getReader().close();
            } catch (IOException e) {
                getLogger().warn("Read pipe failed to close.");
            }
            p4.close();
        }
        loop = false;
        // If we failed to execute because of an authentication issue, try a p4 login.
        if (attemptLogin && (mesgIndex == 1 || mesgIndex == 2 || mesgIndex == 6 || mesgIndex == 9)) {
            // password is unset means that perforce isn't using the environment var P4PASSWD
            // Instead it is using tickets. We must attempt to login via p4 login, then
            // retry this cmd.
            p4.close();
            trustIfSSL();
            login();
            loop = true;
            attemptLogin = false;
            continue;
        }

        // We aren't using the exact message because we want to add the username for more info
        if (mesgIndex == 4)
            throw new PerforceException(
                    "Access for user '" + depot.getUser() + "' has not been enabled by 'p4 protect'");
        if (mesgIndex != -1)
            throw new PerforceException(p4errors[mesgIndex]);
        if (count == 0)
            throw new PerforceException("No output for: " + debugCmd);
    } while (loop);

    StringBuilder response = new StringBuilder(totalLength + lines.size());
    for (String line : lines) {
        response.append(line);
        response.append("\n");
    }

    return response;
}

From source file:edu.cornell.med.icb.goby.modes.TestDiscoverSVMethylationRatesMode.java

@Test
public void testMethylationFormatGenomicContext() throws IOException, JSAPException {
    final MethylationRateVCFOutputFormat outputFormat = new MethylationRateVCFOutputFormat();

    DiscoverVariantIterateSortedAlignments iterator = new DiscoverVariantIterateSortedAlignments(outputFormat) {
        @Override//from   w ww  .  j  ava 2 s .co  m
        public CharSequence getReferenceId(int targetIndex) {
            return Integer.toString(targetIndex);
        }
    };
    DiscoverSequenceVariantsMode mode = new DiscoverSequenceVariantsMode() {
        @Override
        public String[] getSamples() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public String[] getGroups() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public int[] getReaderIndexToGroupIndex() {
            return new int[] { 0, 1 }; // sample index is group index;
        }

        @Override
        public ArrayList<GroupComparison> getGroupComparisons() {
            ArrayList<GroupComparison> list = new ArrayList<GroupComparison>();
            list.add(new GroupComparison("methylated", "not-so", 0, 1, 0));
            return list;
        }
    };
    outputFormat.setGenome(genome);

    StringWriter writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), 1, 6, list1(), 0, 1);
    writer.flush();

    String stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("Context=CpG"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);

    final int referenceIndex = 2;
    outputFormat.setGenomeReferenceIndex(referenceIndex);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), referenceIndex, 1, list1(), 0, 1);
    writer.flush();

    String stringC = writer.getBuffer().toString();
    assertTrue(stringC, stringC.contains("Context=CpT"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    final int referenceIndex1 = 1;
    outputFormat.setGenomeReferenceIndex(referenceIndex1);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), referenceIndex1, 2, list1(), 0, 1);
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("CpT"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    final int referenceIndex4 = 4;
    outputFormat.setGenomeReferenceIndex(referenceIndex4);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), referenceIndex4, 7, list1(), 0, 1);
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("CpC"));

}

From source file:fr.xebia.confluence.gist.GistMacro.java

private String fetchGistUrl(String gistUrl, String proxyHost, String proxyPort) throws MacroException {
    StringWriter sw = new StringWriter();
    PrintWriter pw = new PrintWriter(sw);
    InputStream in = null;/*  w w w  . j  a  v a  2  s.  co  m*/
    try {
        URL url = new URL(gistUrl);
        URLConnection c;
        if (proxyHost != null) {
            int port;
            if (proxyPort == null) {
                port = 80;
            } else {
                port = Integer.parseInt(proxyPort);
            }
            Proxy proxy = new Proxy(Proxy.Type.HTTP, new InetSocketAddress(proxyHost, port));
            c = url.openConnection(proxy);
        } else {
            c = url.openConnection();
        }
        in = c.getInputStream();
        IOUtils.copy(in, pw, settingsManager.getGlobalSettings().getDefaultEncoding());
        pw.flush();
        sw.flush();
        return sw.toString();
    } catch (IOException e) {
        String message = ConfluenceActionSupport.getTextStatic(COULD_NOT_FETCH_URL_CONTENTS_ERROR_KEY,
                new String[] { gistUrl, e.getMessage() });
        throw new MacroException(message, e);
    } finally {
        Closeables.closeQuietly(pw);
        Closeables.closeQuietly(sw);
        Closeables.closeQuietly(in);
    }
}

From source file:org.apache.olingo.fit.utils.AbstractUtilities.java

public InputStream writeEntitySet(final Accept accept, final ResWrap<EntityCollection> container)
        throws ODataSerializerException, IOException {

    final StringWriter writer = new StringWriter();
    if (accept == Accept.ATOM || accept == Accept.XML) {
        atomSerializer.write(writer, container);
    } else {/*from  w  ww.  j  a  va 2 s.c  om*/
        jsonSerializer.write(writer, container);
    }
    writer.flush();
    writer.close();

    return IOUtils.toInputStream(writer.toString(), Constants.ENCODING);
}

From source file:org.nuxeo.ecm.platform.ui.web.component.list.UIJavascriptList.java

/**
 * Renders an element using rowIndex -2 and client side marker {@link #TEMPLATE_INDEX_MARKER}.
 * <p>//from   w w  w .j  a va  2 s.  c o m
 * This element will be used on client side by js code to handle addition of a new element.
 */
protected void encodeTemplate(FacesContext context) throws IOException {
    int oldIndex = getRowIndex();
    Object requestMapValue = saveRequestMapModelValue();
    Map<String, Object> requestMap = getFacesContext().getExternalContext().getRequestMap();
    boolean hasVar = false;
    if (requestMap.containsKey(IS_LIST_TEMPLATE_VAR)) {
        hasVar = true;
    }
    Object oldIsTemplateBoolean = requestMap.remove(IS_LIST_TEMPLATE_VAR);

    try {
        setRowIndex(-2);

        // expose a boolean that can be used on client side to hide this element without disturbing the DOM
        requestMap.put(IS_LIST_TEMPLATE_VAR, Boolean.TRUE);

        // render the template as escaped html
        ResponseWriter oldResponseWriter = context.getResponseWriter();
        StringWriter cacheingWriter = new StringWriter();

        ResponseWriter newResponseWriter = context.getResponseWriter().cloneWithWriter(cacheingWriter);

        context.setResponseWriter(newResponseWriter);

        if (getChildCount() > 0) {
            for (UIComponent kid : getChildren()) {
                if (!kid.isRendered()) {
                    continue;
                }
                try {
                    ComponentSupport.encodeRecursive(context, kid);
                } catch (IOException err) {
                    log.error("Error while rendering component " + kid);
                }
            }
        }

        cacheingWriter.flush();
        cacheingWriter.close();

        context.setResponseWriter(oldResponseWriter);

        String html = Functions.htmlEscape(cacheingWriter.toString());
        ResponseWriter writer = context.getResponseWriter();
        writer.write("<script type=\"text/x-html-template\">");
        writer.write(html);
        writer.write("</script>");

    } finally {
        setRowIndex(oldIndex);

        // restore
        if (hasVar) {
            requestMap.put(IS_LIST_TEMPLATE_VAR, oldIsTemplateBoolean);
        } else {
            requestMap.remove(IS_LIST_TEMPLATE_VAR);
        }
        restoreRequestMapModelValue(requestMapValue);
    }
}

From source file:edu.harvard.hul.ois.fits.tools.exiftool.Exiftool.java

private Document createXml(String execOut) throws FitsToolException {
    StringWriter out = new StringWriter();

    out.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
    out.write("\n");
    out.write("<exiftool>");
    out.write("\n");

    out.write("<rawOutput>\n" + StringEscapeUtils.escapeXml(execOut));
    out.write("</rawOutput>");
    out.write("\n");

    String[] lines = execOut.split("\n");
    for (String line : lines) {
        String[] parts = line.split("\t");
        String field = parts[0].trim();
        if (parts.length > 1) {
            String value = parts[1].trim();
            out.write("<" + field + ">" + StringEscapeUtils.escapeXml(value) + "</" + field + ">");
            out.write("\n");
        }/*from  w  w w. j a v  a2s. c  o m*/
    }
    out.write("</exiftool>");
    out.write("\n");

    out.flush();
    try {
        out.close();
    } catch (IOException e) {
        throw new FitsToolException("Error closing Exiftool XML output stream", e);
    }
    Document doc = null;
    try {
        doc = saxBuilder.build(new StringReader(out.toString()));
    } catch (Exception e) {
        throw new FitsToolException("Error parsing Exiftool XML Output", e);
    }
    return doc;
}

From source file:edu.cornell.med.icb.goby.modes.TestDiscoverSVMethylationRatesMode.java

@Test
public void testMethylationFormat() throws IOException, JSAPException {
    final MethylationRateVCFOutputFormat outputFormat = new MethylationRateVCFOutputFormat();
    DiscoverVariantIterateSortedAlignments iterator = new DiscoverVariantIterateSortedAlignments(outputFormat) {
        @Override/*from w ww.  ja va  2s  .co m*/
        public CharSequence getReferenceId(int targetIndex) {
            return "ref-id";
        }
    };
    DiscoverSequenceVariantsMode mode = new DiscoverSequenceVariantsMode() {
        @Override
        public String[] getSamples() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public String[] getGroups() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public int[] getReaderIndexToGroupIndex() {
            return new int[] { 0, 1 }; // sample index is group index;
        }

        @Override
        public ArrayList<GroupComparison> getGroupComparisons() {
            ArrayList<GroupComparison> list = new ArrayList<GroupComparison>();
            list.add(new GroupComparison("methylated", "not-so", 0, 1, 0));
            return list;
        }
    };
    StringWriter writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.setGenome(genome);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), 0, 0, list1(), 0, 1);
    writer.flush();

    String stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("#Cm_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#Cm_Group[not-so]=0;"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);

    final SampleCountInfo[] sampleCounts = makeTwoSampleCounts();
    sampleCounts[0].referenceBase = 'G';
    outputFormat.writeRecord(iterator, sampleCounts, 0, 0, list2(), 0, 1);
    writer.flush();
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("#Cm_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#Cm_Group[not-so]=0;"));
    assertTrue(stringB, stringB.contains("MR[methylated]=100.0;"));
    assertTrue(stringB, stringB.contains("MR[not-so]=NaN;"));

    writer = new StringWriter();

    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);

    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), 0, 0, list3(), 0, 1);
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("#Cm_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#C_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#Cm_Group[not-so]=0;"));
    assertTrue(stringB, stringB.contains("#C_Group[not-so]=0;"));

    /*  org.junit.Assert.assertEquals("content must match", header+
        "ref-id\t1\t\tC\tA,T,N\t\t\tBIOMART_COORDS=ref-id:1:1;Strand=+;LOD[methylated/not-so]=NaN;LOD_SE[methylated/not-so]=NaN;LOD_Z[methylated/not-so]=NaN;FisherP[methylated/not-so]=NaN;#C Group[methylated]=0;#Cm Group[methylated]=1;#C Group[not-so]=0;#Cm Group[not-so]=0;DP=1\tMR:GT:BC:GB:FB\t100:0/1/2/3:A=5,T=1,C=9,G=0,N=1:16:0\t0:1/2/3:A=10,T=4,C=0,G=0,N=2:16:0",
        buffer.toString());
    */
}

From source file:org.yamj.api.common.http.AbstractPoolingHttpClient.java

protected DigestedResponse readContent(final HttpResponse response, final Charset charset) throws IOException {
    StringWriter content = new StringWriter(SW_BUFFER_10K);
    InputStream is = response.getEntity().getContent();
    InputStreamReader isr = null;
    BufferedReader br = null;//from w  w  w. j a  v  a  2  s  .c  o  m

    final DigestedResponse digestedResponse = new DigestedResponse();
    digestedResponse.setStatusCode(response.getStatusLine().getStatusCode());

    try {
        if (charset == null) {
            isr = new InputStreamReader(is, Charset.defaultCharset());
        } else {
            isr = new InputStreamReader(is, charset);
        }
        br = new BufferedReader(isr);

        String line = br.readLine();
        while (line != null) {
            content.write(line);
            line = br.readLine();
        }

        content.flush();
        digestedResponse.setContent(content.toString());
        return digestedResponse;
    } finally {
        if (br != null) {
            try {
                br.close();
            } catch (IOException ex) {
                LOG.trace("Failed to close BufferedReader", ex);
            }
        }
        if (isr != null) {
            try {
                isr.close();
            } catch (IOException ex) {
                LOG.trace("Failed to close InputStreamReader", ex);
            }
        }
        try {
            content.close();
        } catch (IOException ex) {
            LOG.trace("Failed to close StringWriter", ex);
        }
        try {
            is.close();
        } catch (IOException ex) {
            LOG.trace("Failed to close InputStream", ex);
        }
    }
}

From source file:de.qucosa.webapi.v1.DocumentResource.java

private void debugDump(DigitalObjectDocument dod) {
    try {/*from   ww  w  . j av  a2s.  c o m*/
        StringWriter stringWriter = new StringWriter();
        dod.save(stringWriter, new XmlOptions().setSavePrettyPrint());
        stringWriter.flush();
        log.debug(stringWriter.toString());
    } catch (IOException e) {
        log.warn("Debug error: {}", e.getMessage());
    }
}