Example usage for org.apache.commons.io.input ReaderInputStream ReaderInputStream

List of usage examples for org.apache.commons.io.input ReaderInputStream ReaderInputStream

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Introduction

In this page you can find the example usage for org.apache.commons.io.input ReaderInputStream ReaderInputStream.

Prototype

public ReaderInputStream(Reader reader)

Source Link

Document

Construct a new ReaderInputStream that uses the default character encoding with a default input buffer size of 1024 characters.

Usage

From source file:org.pentaho.platform.util.versionchecker.PentahoVersionCheckReflectHelperTest.java

private void validateResult(String result) {

    try {/*from   ww w. ja  va2  s. co m*/
        DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
        DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
        StringReader stringReader = new StringReader(result);
        documentBuilder.parse(new ReaderInputStream(stringReader));
    } catch (ParserConfigurationException | SAXException | IOException e) {
        assertTrue("unexpected exception", false);
    }
}

From source file:org.pepstock.jem.gwt.server.services.JobsManager.java

/**
 * Indents JCL content, for editing//from ww  w.  ja va  2  s.  c o m
 * @param content JCL
 * @return indented JCL
 * @throws ServiceMessageException 
 * @throws Exception if any XML exception occurs
 */
public String indent(String content) throws ServiceMessageException {
    try {
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        DocumentBuilder builder = factory.newDocumentBuilder();
        Document document = builder.parse(new ReaderInputStream(new StringReader(content)));
        OutputFormat format = new OutputFormat(document);
        format.setLineWidth(65);
        format.setIndenting(true);
        format.setIndent(4);

        StringWriter writer = new StringWriter();
        XMLSerializer serializer = new XMLSerializer(writer, format);
        serializer.serialize(document);
        return writer.toString();
    } catch (ParserConfigurationException e) {
        throw new ServiceMessageException(UserInterfaceMessage.JEMG022E, e, e.getMessage());
    } catch (SAXException e) {
        throw new ServiceMessageException(UserInterfaceMessage.JEMG022E, e, e.getMessage());
    } catch (IOException e) {
        throw new ServiceMessageException(UserInterfaceMessage.JEMG022E, e, e.getMessage());
    }
}

From source file:org.pepstock.jem.node.executors.configuration.CheckHazelcastConfiguration.java

/**
 * Checks if content could be a Hazelcast configuration file
 * @return always TRUE/*w  ww.  ja v a 2s  .  c o  m*/
 * @throws ParserConfigurationException 
 * @throws IOException 
 * @throws SAXException 
 * @throws Exception occurs if errors
 */
@Override
public Boolean execute() throws ExecutorException {
    try {
        // XML syntax check
        // because Hazelcast continues if XMl error occurs
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        DocumentBuilder builder = factory.newDocumentBuilder();
        builder.parse(new ReaderInputStream(new StringReader(content)));
        return Boolean.TRUE;
    } catch (ParserConfigurationException e) {
        throw new ExecutorException(NodeMessage.JEMC241E, e, e.getMessage());
    } catch (SAXException e) {
        throw new ExecutorException(NodeMessage.JEMC241E, e, e.getMessage());
    } catch (IOException e) {
        throw new ExecutorException(NodeMessage.JEMC241E, e, e.getMessage());
    }
}

From source file:org.safs.selenium.webdriver.lib.interpreter.WDScriptFactory.java

/**
 * @param reader A Reader pointing to one of 2 possible script formats:<br>
 * a JSON stream describing a script or suite, or an HTML Fit Table.
 * @param sourceFile Optionally. the file the script was loaded from.
 * @return A list of scripts, ready to run.
 * @throws IOException If anything goes wrong with interpreting the script, or
 * with the Reader./*from  ww  w . jav  a2  s .  c  o m*/
 */
public List<Script> parse(Reader reader, File sourceFile) throws IOException {
    String message = "WDScriptFactory.parse(Reader)";
    try {
        return parse(new JSONObject(new JSONTokener(reader)), sourceFile);
    } catch (Exception x) {
        message += ", " + x.getClass().getSimpleName() + " " + x.getMessage();
        try {
            reader.close();
        } catch (Exception rc) {
        }
        try {
            reader = getUTF8Reader(sourceFile);
            return parse(getDocumentBuilder().parse(new ReaderInputStream(reader)), sourceFile,
                    stepTypeFactory);
        } catch (Exception px) {
            message += ", " + px.getClass().getSimpleName() + " " + px.getMessage();
            throw new IOException(message);
        } finally {
            try {
                reader.close();
            } catch (Exception fx) {
            }
        }
    }
}

From source file:org.sonar.plugins.resharper.ReSharperProfileImporter.java

@Override
public RulesProfile importProfile(Reader reader, ValidationMessages messages) {
    this.messages = messages;
    profile = RulesProfile.create();/*from  w ww.ja va  2 s. co m*/
    StaxParser parser = new StaxParser(new StaxParser.XmlStreamHandler() {
        @Override
        public void stream(SMHierarchicCursor rootCursor) throws XMLStreamException {
            rootCursor.advance();
            parseRootNode(rootCursor);
        }
    });
    try {
        parser.parse(new ReaderInputStream(reader));
    } catch (XMLStreamException e) {
        String errorMessage = "Error parsing content";
        messages.addErrorText(errorMessage + ": " + e);
        LOG.error(errorMessage, e);
    }
    return profile;
}

From source file:org.sonar.plugins.spcaf.SpcafProfileImporter.java

@Override
public RulesProfile importProfile(Reader reader, ValidationMessages messages) {
    this.messages = messages;
    profile = RulesProfile.create();/* w w w . ja  v a  2s. co m*/
    StaxParser parser = new StaxParser(new StaxParser.XmlStreamHandler() {
        @Override
        public void stream(SMHierarchicCursor rootCursor) throws XMLStreamException {
            rootCursor.advance();
            parseRootNode(rootCursor);
        }
    });
    try {
        parser.parse(new ReaderInputStream(reader));
    } catch (XMLStreamException e) {
        String errorMessage = "SPCAF: Error parsing content";
        messages.addErrorText(errorMessage + ": " + e);
        LOG.error(errorMessage, e);
    }
    return profile;
}

From source file:org.strasa.web.managegermplasm.view.model.Index.java

@NotifyChange({ "lstStudyGermplasm", "lstKnownGermplasm", "totalUnknownGermplasm", "totalKnownGermplasm" })
@Command("uploadGenotypeData")
public void uploadGenotypeData(@ContextParam(ContextType.BIND_CONTEXT) BindContext ctx,
        @ContextParam(ContextType.VIEW) Component view) {

    UploadEvent event = (UploadEvent) ctx.getTriggerEvent();

    String name = event.getMedia().getName();
    if (!name.endsWith(".csv")) {
        Messagebox.show("Error: File must be a text-based CSV  format", "Upload Error", Messagebox.OK,
                Messagebox.ERROR);/*from   www  . j  av  a2  s. com*/
        return;
    }
    ((Label) view.getFellow("lblFileName")).setValue(name);
    try {
        String filename = name + Encryptions.encryptStringToNumber(name, new Date().getTime());
        File tempGenoFile = File.createTempFile(filename, ".tmp");
        InputStream in = event.getMedia().isBinary() ? event.getMedia().getStreamData()
                : new ReaderInputStream(event.getMedia().getReaderData());
        FileUtilities.uploadFile(tempGenoFile.getAbsolutePath(), in);
        List<GermplasmExt> lstGermplasm = CSVToBean(tempGenoFile);

        KeyCharacteristicManagerImpl keyMan = new KeyCharacteristicManagerImpl();
        List<KeyBiotic> lstKeyBiotics = keyMan.getAllBiotic();
        List<KeyAbiotic> lstKeyAbioitc = keyMan.getAllAbiotic();
        List<KeyMajorGenes> lstKeyMajorGenes = keyMan.getAllMajorGenes();
        List<KeyGrainQuality> lstKeyGrainQuality = keyMan.getAllGrainQuality();
        ArrayList<GermplasmDeepInfoModel> tempKnown = new ArrayList<GermplasmDeepInfoModel>();
        ArrayList<GermplasmDeepInfoModel> lstInvalidCharacteristics = new ArrayList<GermplasmDeepInfoModel>();

        for (GermplasmExt germData : lstGermplasm) {
            if (!StringUtils.isNullOrEmpty(germData.getGermplasmname())) {
                // System.out.println(germData.toString());
                if (lstKnownGermplasm.containsKey(germData.getGermplasmname())) {

                    tempKnown.add(lstKnownGermplasm.get(germData.getGermplasmname()));
                    if (lstKnownGermplasm.get(germData.getGermplasmname())
                            .setGermplasmExCharacteristic(germData) == false) {
                        lstInvalidCharacteristics.add(lstKnownGermplasm.get(germData.getGermplasmname()));
                    }
                } else {

                    GermplasmDeepInfoModel newData = new GermplasmDeepInfoModel();

                    newData.setGermplasmtypeid(getGermplasmTypeById(germData.getGermplasmtype()));
                    newData.setGermplasmname(germData.getGermplasmname());
                    newData.setValueFromeGermplasmEx(germData, lstGermplasmType);
                    newData.setBiotic(lstKeyBiotics);
                    newData.setAbiotic(lstKeyAbioitc);
                    newData.setMajorGenes(lstKeyMajorGenes);
                    newData.setUserid(this.userID);
                    newData.setGrainQuality(lstKeyGrainQuality);
                    newData.setKnown(false);
                    if (!newData.setGermplasmExCharacteristic(germData)) {
                        lstInvalidCharacteristics.add(newData);
                    }
                    lstStudyGermplasm.put(newData.getGermplasmname(), newData);

                }
            }
        }

        lstKnownGermplasm.clear();
        for (GermplasmDeepInfoModel germData : tempKnown) {
            lstKnownGermplasm.put(germData.getGermplasmname(), germData);
        }

        gbUnknownGermplasm.setVisible(true);
        gbKnownGermplasm.setVisible(true);
        view.getFellow("divUploadOption").setVisible(true);
        view.getFellow("uploadGenotypeData").setVisible(false);
        resetSize();
        if (!lstInvalidCharacteristics.isEmpty()) {
            Map<String, Object> params = new HashMap<String, Object>();

            params.put("germplasmList", lstInvalidCharacteristics);
            params.put("parent", view);
            Window popup = (Window) Executions.createComponents(ValidateGermplasmCharacteristics.ZUL_PATH, view,
                    params);

            popup.doModal();
        }

        // gbKnownGermplasm.invalidate();
        // gbUnknownGermplasm.invalidate();
    } catch (IOException e1) {
        // TODO Auto-generated catch block
    }

}

From source file:org.strasa.web.updatestudy.view.DerivedDataView.java

@NotifyChange("*")
@Command("uploadCSV")
public void uploadCSV(@ContextParam(ContextType.BIND_CONTEXT) BindContext ctx,
        @ContextParam(ContextType.VIEW) Component view) {

    UploadEvent event = (UploadEvent) ctx.getTriggerEvent();

    // System.out.println(event.getMedia().getStringData());

    String name = event.getMedia().getName();
    if (tempFile == null)
        try {/*  w  w w. j ava  2  s .c o  m*/
            tempFile = File.createTempFile(name, ".tmp");
        } catch (IOException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }

    if (!name.endsWith(".csv")) {
        Messagebox.show("Error: File must be a text-based csv format", "Upload Error", Messagebox.OK,
                Messagebox.ERROR);
        return;
    }

    InputStream in = event.getMedia().isBinary() ? event.getMedia().getStreamData()
            : new ReaderInputStream(event.getMedia().getReaderData());
    FileUtilities.uploadFile(tempFile.getAbsolutePath(), in);
    BindUtils.postNotifyChange(null, null, this, "*");

    ArrayList<String> invalidHeader = new ArrayList<String>();
    boolean isHeaderValid = true;
    try {
        StudyVariableManagerImpl studyVarMan = new StudyVariableManagerImpl();
        CSVReader reader = new CSVReader(new FileReader(tempFile.getAbsolutePath()));
        String[] header = reader.readNext();
        for (String column : header) {
            if (!studyVarMan.hasVariable(column)) {
                invalidHeader.add(column);
                isHeaderValid = false;
            }
        }
        System.out.println(invalidHeader.size());

    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    isVariableDataVisible = true;
    dataFileName = name;
    if (!isHeaderValid)
        openCSVHeaderValidator(tempFile.getAbsolutePath(), false);
    else {
        refreshCsv();
        if (this.isUpdateMode)
            isNewDataSet = true;

    }

}

From source file:org.strasa.web.updatestudy.view.DerivedDataView.java

@NotifyChange("genotypeFileList")
@Command("uploadGenotypeData")
public void uploadGenotypeData(@ContextParam(ContextType.BIND_CONTEXT) BindContext ctx,
        @ContextParam(ContextType.VIEW) Component view) {

    UploadEvent event = (UploadEvent) ctx.getTriggerEvent();

    // System.out.println(event.getMedia().getStringData());

    String name = event.getMedia().getName();
    if (!name.endsWith(".txt")) {
        Messagebox.show("Error: File must be a text-based  format", "Upload Error", Messagebox.OK,
                Messagebox.ERROR);/*from   www .j av  a 2  s .c o  m*/
        return;
    }

    try {
        String filename = name + Encryptions.encryptStringToNumber(name, new Date().getTime());
        File tempGenoFile = File.createTempFile(filename, ".tmp");
        InputStream in = event.getMedia().isBinary() ? event.getMedia().getStreamData()
                : new ReaderInputStream(event.getMedia().getReaderData());
        FileUtilities.uploadFile(tempGenoFile.getAbsolutePath(), in);

        GenotypeFileModel newGenotypeFile = new GenotypeFileModel(name, tempGenoFile);
        genotypeFileList.add(newGenotypeFile);
    } catch (IOException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }

}

From source file:org.strasa.web.updatestudy.view.GenotypicData.java

@NotifyChange("*")
@Command("uploadGenotypeData")
public void uploadGenotypeData(@ContextParam(ContextType.BIND_CONTEXT) BindContext ctx,
        @ContextParam(ContextType.VIEW) Component view) {

    UploadEvent event = (UploadEvent) ctx.getTriggerEvent();

    // System.out.println(event.getMedia().getStringData());

    String name = event.getMedia().getName();
    if (!name.endsWith(".txt")) {
        Messagebox.show("Error: File must be a text-based  format", "Upload Error", Messagebox.OK,
                Messagebox.ERROR);//from w  ww. j  ava2 s .  co  m
        return;
    }

    try {
        String filename = name + Encryptions.encryptStringToNumber(name, new Date().getTime());
        File tempGenoFile = File.createTempFile(filename, ".tmp");
        InputStream in = event.getMedia().isBinary() ? event.getMedia().getStreamData()
                : new ReaderInputStream(event.getMedia().getReaderData());
        FileUtilities.uploadFile(tempGenoFile.getAbsolutePath(), in);

        GenotypeFileModel newGenotypeFile = new GenotypeFileModel(name, tempGenoFile);
        UserFileManager fileMan = new UserFileManager();
        fileMan.createNewFileFromUpload(1, studyid, newGenotypeFile.getName(), newGenotypeFile.getFilepath(),
                "gd");
        setGenotypicFiles(studyFileMan.getFileByStudyIdAndDataType(studyid, dataType));
    } catch (IOException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }

}