Example usage for java.io FileInputStream available

List of usage examples for java.io FileInputStream available

Introduction

In this page you can find the example usage for java.io FileInputStream available.

Prototype

public int available() throws IOException 

Source Link

Document

Returns an estimate of the number of remaining bytes that can be read (or skipped over) from this input stream without blocking by the next invocation of a method for this input stream.

Usage

From source file:gov.nih.nci.rembrandt.web.taglib.PCAPlotTag.java

public int doStartTag() {
    chart = null;// w ww .  j a v a 2 s  .c o  m
    pcaResults = null;
    pcaData.clear();

    ServletRequest request = pageContext.getRequest();
    HttpSession session = pageContext.getSession();
    Object o = request.getAttribute(beanName);
    JspWriter out = pageContext.getOut();
    ServletResponse response = pageContext.getResponse();

    try {
        //retrieve the Finding from cache and build the list of PCAData points
        PrincipalComponentAnalysisFinding principalComponentAnalysisFinding = (PrincipalComponentAnalysisFinding) businessTierCache
                .getSessionFinding(session.getId(), taskId);

        Collection<ClinicalFactorType> clinicalFactors = new ArrayList<ClinicalFactorType>();
        List<String> sampleIds = new ArrayList<String>();
        Map<String, PCAresultEntry> pcaResultMap = new HashMap<String, PCAresultEntry>();
        if (principalComponentAnalysisFinding != null) {
            pcaResults = principalComponentAnalysisFinding.getResultEntries();
            for (PCAresultEntry pcaEntry : pcaResults) {
                sampleIds.add(pcaEntry.getSampleId());
                pcaResultMap.put(pcaEntry.getSampleId(), pcaEntry);
            }

            Collection<SampleResultset> validatedSampleResultset = ClinicalDataValidator
                    .getValidatedSampleResultsetsFromSampleIDs(sampleIds, clinicalFactors);

            if (validatedSampleResultset != null) {
                String id;
                PCAresultEntry entry;

                for (SampleResultset rs : validatedSampleResultset) {
                    id = rs.getBiospecimen().getSpecimenName();
                    entry = pcaResultMap.get(id);
                    PrincipalComponentAnalysisDataPoint pcaPoint = new PrincipalComponentAnalysisDataPoint(id,
                            entry.getPc1(), entry.getPc2(), entry.getPc3());
                    String diseaseName = rs.getDisease().getValueObject();
                    if (diseaseName != null) {
                        pcaPoint.setDiseaseName(diseaseName);
                    } else {
                        pcaPoint.setDiseaseName(DiseaseType.NON_TUMOR.name());
                    }
                    GenderDE genderDE = rs.getGenderCode();
                    if (genderDE != null && genderDE.getValue() != null) {
                        String gt = genderDE.getValueObject().trim();
                        if (gt != null) {
                            GenderType genderType = GenderType.valueOf(gt);
                            if (genderType != null) {
                                pcaPoint.setGender(genderType);
                            }
                        }
                    }
                    Long survivalLength = rs.getSurvivalLength();
                    if (survivalLength != null) {
                        //survival length is stored in days in the DB so divide by 30 to get the 
                        //approx survival in months
                        double survivalInMonths = survivalLength.doubleValue() / 30.0;
                        pcaPoint.setSurvivalInMonths(survivalInMonths);
                    }
                    pcaData.add(pcaPoint);
                }
            }

            PCAcomponent pone = PCAcomponent.PC1;
            PCAcomponent ptwo = PCAcomponent.PC2;
            //check the components to see which graph to get
            if (components.equalsIgnoreCase("PC1vsPC2")) {
                pone = PCAcomponent.PC2;
                ptwo = PCAcomponent.PC1;
                //chart = (JFreeChart) CaIntegratorChartFactory.getPrincipalComponentAnalysisGraph(pcaData,PCAcomponent.PC2,PCAcomponent.PC1,PCAcolorByType.valueOf(PCAcolorByType.class,colorBy));
            }
            if (components.equalsIgnoreCase("PC1vsPC3")) {
                pone = PCAcomponent.PC3;
                ptwo = PCAcomponent.PC1;
                //chart = (JFreeChart) CaIntegratorChartFactory.getPrincipalComponentAnalysisGraph(pcaData,PCAcomponent.PC3,PCAcomponent.PC1,PCAcolorByType.valueOf(PCAcolorByType.class,colorBy));
            }
            if (components.equalsIgnoreCase("PC2vsPC3")) {
                pone = PCAcomponent.PC2;
                ptwo = PCAcomponent.PC3;
                //chart = (JFreeChart) CaIntegratorChartFactory.getPrincipalComponentAnalysisGraph(pcaData,PCAcomponent.PC3,PCAcomponent.PC2,PCAcolorByType.valueOf(PCAcolorByType.class,colorBy));
            }

            PrincipalComponentAnalysisPlot plot = new RBTPrincipalComponentAnalysisPlot(pcaData, pone, ptwo,
                    PCAcolorByType.valueOf(PCAcolorByType.class, colorBy));
            if (plot != null) {
                chart = (JFreeChart) plot.getChart();
            }

            RembrandtImageFileHandler imageHandler = new RembrandtImageFileHandler(session.getId(), "png", 650,
                    600);
            //The final complete path to be used by the webapplication
            String finalPath = imageHandler.getSessionTempFolder();
            String finalURLpath = imageHandler.getFinalURLPath();
            /*
             * Create the actual charts, writing it to the session temp folder
            */
            ChartRenderingInfo info = new ChartRenderingInfo(new StandardEntityCollection());
            String mapName = imageHandler.createUniqueMapName();
            //PrintWriter writer = new PrintWriter(new FileWriter(mapName));
            ChartUtilities.writeChartAsPNG(new FileOutputStream(finalPath), chart, 650, 600, info);
            //ImageMapUtil.writeBoundingRectImageMap(writer,"PCAimageMap",info,true);
            //writer.close();

            /*   This is here to put the thread into a loop while it waits for the
             *   image to be available.  It has an unsophisticated timer but at 
             *   least it is something to avoid an endless loop.
             **/
            boolean imageReady = false;
            int timeout = 1000;
            FileInputStream inputStream = null;
            while (!imageReady) {
                timeout--;
                try {
                    inputStream = new FileInputStream(finalPath);
                    inputStream.available();
                    imageReady = true;
                    inputStream.close();
                } catch (IOException ioe) {
                    imageReady = false;
                    if (inputStream != null) {
                        inputStream.close();
                    }
                }
                if (timeout <= 1) {

                    break;
                }
            }

            out.print(ImageMapUtil.getBoundingRectImageMapTag(mapName, false, info));
            finalURLpath = finalURLpath.replace("\\", "/");
            long randomness = System.currentTimeMillis(); //prevent image caching
            out.print("<img id=\"geneChart\" name=\"geneChart\" alt=\"geneChart\" src=\"" + finalURLpath + "?"
                    + randomness + "\" usemap=\"#" + mapName + "\" border=\"0\" />");

            //(imageHandler.getImageTag(mapFileName));
        }
    } catch (IOException e) {
        logger.error(e);
    } catch (Exception e) {
        logger.error(e);
    } catch (Throwable t) {
        logger.error(t);
    }

    return EVAL_BODY_INCLUDE;
}

From source file:net.urlgrey.mythpodcaster.transcode.FeedFileAccessorImpl.java

/**
 * @param series//w  w  w. j a v a  2  s . c om
 * @param program
 * @param channel
 * @param feed
 * @param transcoderProfile
 */
@SuppressWarnings({ "unchecked", "rawtypes" })
public void addProgramToFeed(RecordedSeries series, RecordedProgram program, Channel channel, SyndFeed feed,
        String transcodingProfileId) {
    LOGGER.info("Transcoding new feed entry: programId[" + program.getProgramId() + "], key[" + program.getKey()
            + "], title[" + program.getTitle() + "], channel[" + (channel != null ? channel.getName() : "")
            + "], transcodingProfileId[" + transcodingProfileId + "]");
    final SyndEntryImpl entry = new SyndEntryImpl();
    entry.setUri(program.getKey());
    entry.setPublishedDate(program.getRecordedProgramKey().getStartTime());

    // set author info from the channel if available
    if (channel != null) {
        entry.setAuthor(channel.getName());
    }

    entry.setTitle(program.getProgramTitle());

    final SyndContentImpl description = new SyndContentImpl();
    description.setType("text/plain");
    description.setValue(program.getDescription());
    entry.setDescription(description);

    // apply thumbnail for clip to the feed
    final String feedImageUrl;
    final File originalClipThumbnail = clipLocator.locateThumbnailForOriginalClip(program.getFilename());
    if (originalClipThumbnail != null) {
        final String seriesId = series.getSeriesId();
        final File encodingDirectory = new File(feedFilePath, transcodingProfileId);
        final File feedThumbnailFile = new File(encodingDirectory, seriesId + PNG_EXTENSION);
        feedImageUrl = this.applicationURL + PATH_SEPARATOR + transcodingProfileId + PATH_SEPARATOR + seriesId
                + PNG_EXTENSION;

        try {
            FileOperations.copy(originalClipThumbnail, feedThumbnailFile);

            final SyndImageImpl feedImage = new SyndImageImpl();
            feedImage.setUrl(feedImageUrl);
            feedImage.setTitle(series.getTitle());
            feed.setImage(feedImage);

            // include iTunes-specific metadata
            final Module module = feed.getModule("http://www.itunes.com/dtds/podcast-1.0.dtd");
            final FeedInformation itunesFeedMetadata;
            if (module == null) {
                itunesFeedMetadata = new FeedInformationImpl();
                feed.getModules().add(itunesFeedMetadata);
            } else {
                itunesFeedMetadata = (FeedInformation) module;
            }

            itunesFeedMetadata.setImage(new URL(feedImageUrl));

            LOGGER.info("Applied clip thumbnail to feed: thumbnail[" + feedThumbnailFile.getAbsolutePath()
                    + "], url[" + feedImage.getUrl() + "]");
        } catch (IOException e) {
            if (feedThumbnailFile.canWrite()) {
                feedThumbnailFile.delete();
                feed.setImage(null);
            }
        }
    } else {
        feedImageUrl = null;
    }

    // transcode
    final File originalClip = clipLocator.locateOriginalClip(program.getFilename());
    if (originalClip != null) {
        final TranscodingProfile profile = transcodingProfilesDao.findAllProfiles().get(transcodingProfileId);
        if (profile != null) {

            final File outputFile = profile.generateOutputFilePath(feedFilePath, program.getKey());
            try {

                LOGGER.info("Transcode STARTING: profile[" + profile.getId() + "]");
                transcodingController.transcode(profile, program.getKey(), series.getTitle(),
                        program.getProgramTitle(), originalClip, outputFile);
                LOGGER.info("Transcode FINISHED: profile[" + profile.getId() + "]");

                if (outputFile.canRead()) {
                    // get the file-size in bytes
                    FileInputStream in = new FileInputStream(outputFile);
                    final int fileSize = in.available();
                    in.close();

                    final String link = profile.generateOutputFileURL(this.applicationURL, outputFile);
                    final SyndEnclosure enclosure = new SyndEnclosureImpl();
                    enclosure.setUrl(link);
                    enclosure.setType(profile.getEncodingMimeType());
                    enclosure.setLength(fileSize);
                    final List enclosures = new ArrayList();
                    enclosures.add(enclosure);
                    entry.setEnclosures(enclosures);

                    // include iTunes-specific metadata
                    final Module itunesModule = entry.getModule("http://www.itunes.com/dtds/podcast-1.0.dtd");
                    if (itunesModule != null) {
                        entry.getModules().remove(itunesModule);
                    }
                    final EntryInformation itunesEntryMetadata = new EntryInformationImpl();
                    final Duration duration = new Duration(program.getEndTime().getTime()
                            - program.getRecordedProgramKey().getStartTime().getTime());
                    itunesEntryMetadata.setDuration(duration);
                    itunesEntryMetadata.setSummary(program.getDescription());
                    if (program.getCategory() != null) {
                        itunesEntryMetadata.setKeywords(new String[] { program.getCategory() });
                    }
                    if (channel != null) {
                        itunesEntryMetadata.setAuthor(channel.getName());
                    }

                    entry.getModules().add(itunesEntryMetadata);

                    // include Media RSS metadata
                    final MediaContent[] contents = new MediaContent[1];
                    final MediaContent mrssContent = new MediaContent(new UrlReference(link));
                    mrssContent.setFileSize(Long.valueOf(fileSize));
                    mrssContent.setType(profile.getEncodingMimeType());
                    final long durationInSeconds = (long) Math.ceil(duration.getMilliseconds() / 1000);
                    mrssContent.setDuration(durationInSeconds);
                    contents[0] = mrssContent;
                    Metadata md = new Metadata();
                    if (feedImageUrl != null) {
                        Thumbnail[] thumbs = new Thumbnail[1];
                        thumbs[0] = new Thumbnail(new URI(feedImageUrl));
                        md.setThumbnail(thumbs);
                    }
                    md.setDescription(program.getDescription());
                    md.setCategories(new Category[] { new Category(program.getCategory()) });
                    mrssContent.setMetadata(md);
                    MediaEntryModuleImpl mrssModule = new MediaEntryModuleImpl();
                    mrssModule.setMediaContents(contents);
                    entry.getModules().add(mrssModule);
                } else {
                    LOGGER.warn("Transcoded output file cannot be read, setting link to null: path["
                            + outputFile.getAbsolutePath() + "]");
                    entry.setLink(null);
                }
            } catch (Exception e) {
                LOGGER.error("Error while transcoding, setting link to null", e);
                entry.setLink(null);
                if (outputFile != null && outputFile.canWrite()) {
                    outputFile.delete();
                }
            }
        } else {
            final String msg = "Unable to locate transcoding profile with given id: [" + transcodingProfileId
                    + "]";
            LOGGER.error(msg);
        }
    } else {
        LOGGER.warn("Original clip could not be found in content paths");
        entry.setLink(null);
    }

    feed.getEntries().add(entry);
}

From source file:org.geoserver.wfs.response.SpatiaLiteOutputFormatDev.java

protected void write(List<SimpleFeatureCollection> collections, Charset charset, OutputStream output,
        GetFeatureType request) throws IOException, ServiceException {

    Connection conn = null;/*ww w .  java2  s.  c om*/

    /**
     * Get the necessary JDBC object.
     */
    try {
        Class.forName(this.driverClassName);
    } catch (ClassNotFoundException e) {
        System.out.println(e);
    }
    /**
     * base location to temporally store spatialite database files
     */
    File tempDir = File.createTempFile("spatialitemp", ".sqlite");

    /**
     * enables load extension
     */
    SQLiteConfig config = new SQLiteConfig();
    config.enableLoadExtension(true);

    /**
     * the Url for the temporally sqlite file
     */
    String JDBCFileUrl = tempDir.getAbsolutePath();

    try {
        //create a connection to database
        conn = DriverManager.getConnection("jdbc:sqlite:" + JDBCFileUrl, config.toProperties());
        Statement stmt = conn.createStatement();
        stmt.setQueryTimeout(30);

        /**
         * A string to store the statements to run to create the Spatialite DataBase 
         */
        String sql = null;
        conn.setAutoCommit(false);
        // FIXME: we are now working on PATH - we will define different JAR files to change this as required by platform
        sql = "SELECT load_extension('/tmp/libspatialite-2-4.dll');";
        stmt.execute(sql);
        sql = "SELECT InitSpatialMetaData();";
        stmt.execute(sql);
        conn.commit();

        /**
         * A string to store the names of the columns that will be used to populate the table 
         */
        String column_names = null;

        //We might get multiple feature collections in our response (multiple queries?) so we need to
        //write out multiple tables, one for each query response.
        for (SimpleFeatureCollection fc : collections) {

            //get the current feature
            SimpleFeatureType ft = fc.getSchema();

            //To check if the current feature has a geometry.
            String the_geom = null;
            if (ft.getGeometryDescriptor() != null) {
                the_geom = ft.getGeometryDescriptor().getLocalName();
            }

            //Get the table name for the current feature
            String tbl_name = ft.getName().getLocalPart();

            /**
             * Create the table for the current feature as follows:
             * - first get the statement for create the table
             * - execute the statement
             * - second get the statement for add the geometry (if has one) 
             * - execute the statement
             */

            //Initialize the "create table" query.
            column_names = "";
            int column_cnt = 0;
            sql = "CREATE TABLE " + tbl_name;
            sql += " ( PK_UID INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT";

            //Get the columns names for the table tbl_name
            for (int i = 0; i < ft.getAttributeCount(); i++) {
                AttributeDescriptor ad = ft.getDescriptor(i);
                if (ad.getLocalName() != the_geom) {
                    sql += ", " + prepareColumnHeader(ad);
                    column_names += ad.getLocalName();
                    column_cnt++;
                    if (i < ft.getAttributeCount() - 1) {
                        column_names += ", ";
                    }

                }
            }
            sql += ");";
            // Finish creating the table

            System.out.println(sql);
            stmt.execute(sql);
            conn.commit();

            int srid = 0;
            //If the table : "tbl_name" has a geometry, then i write the sql to add the geometry
            if (the_geom != null) {
                sql = "SELECT AddGeometryColumn('" + tbl_name + "', ";
                //get the geometry type
                sql += "'" + the_geom + "', ";
                //get the SRID.
                srid = getSpatialSRID(ft.getCoordinateReferenceSystem());
                sql += srid + ", ";
                //get the Geometry type.
                String geom_type = getSpatialGeometryType(ft);
                if (geom_type == null) {
                    throw new WFSException("Error while adding the geometry column in table " + tbl_name
                            + ", unrecognized geometry type");
                }
                sql += "'" + geom_type + "', ";
                //get Dimensions, we only works whit 2 dimensions. 
                String dimension = "XY";
                sql += "'" + dimension + "'";
                sql += " );";
            }
            //finish creating the geometry column.
            System.out.println(sql);
            stmt.execute(sql);
            conn.commit();

            /**
             * Populates the table for the current feature as follows:
             * For each row
             *      - first: configure the statement with the appropriates fields.
             *      - second: add to the statement the field the_geom if has a geometry.
             *      - third: configure the statement with the appropriates values.
             *      (if has a geometry i add that value) 
             *      - execute the statement
             * Finally commit.
             */
            //Start populating the table: tbl_name.
            SimpleFeatureIterator i = fc.features();
            try {
                while (i.hasNext()) {
                    SimpleFeature row = i.next();
                    sql = "INSERT INTO " + tbl_name + " (" + column_names;
                    //if has a geometry, i add the field the_geom.
                    if (the_geom != null)
                        if (column_cnt > 0) {
                            sql += ", " + the_geom + " ) ";
                        } else {
                            sql += the_geom + ") ";
                        }

                    else {
                        sql += ") ";
                    }

                    //I store the default geometry value, so i can omit it and add at the end.
                    Object geom_data = row.getDefaultGeometry();
                    sql += "VALUES (";
                    for (int j = 0; j < row.getAttributeCount(); j++) {
                        Object rowAtt = row.getAttribute(j);
                        if (!rowAtt.equals(geom_data)) {
                            if (rowAtt != null) {
                                //We just transform all content to String.
                                sql += "'" + rowAtt.toString() + "'";
                            }
                            if (j < row.getAttributeCount() - 1) {
                                sql += ", ";
                            }
                        }
                    }

                    //Finally if has geometry, insert the geometry data.
                    if (the_geom != null) {
                        if (column_cnt > 0) {
                            sql += ", ";
                        }
                        sql += "GeomFromText('" + prepareGeom(geom_data.toString()) + "', " + srid + ")";
                    }
                    sql += ");";
                    System.out.println(sql);
                    stmt.executeUpdate(sql);
                }
                conn.commit();
            } finally {
                fc.close(i);
            }
        }
    } catch (SQLException e) {
        System.out.println(e);
    }

    /**
     * A FileInputStream to read the tempDir in a byte array
     * so i can write this in the OutputStream output and flush it.
     */
    FileInputStream JDBCIn = new FileInputStream(tempDir);
    int longitud = JDBCIn.available();
    byte[] datos = new byte[longitud];
    JDBCIn.read(datos);
    output.write(datos);

    System.out.println(tempDir.getAbsolutePath());

}

From source file:gov.nih.nci.rembrandt.web.taglib.ClinicalPlotTag.java

public int doStartTag() {
    chart = null;//w  w  w  .j  a v  a2  s . c  o m
    clinicalData.clear();

    ServletRequest request = pageContext.getRequest();
    HttpSession session = pageContext.getSession();
    Object o = request.getAttribute(beanName);
    JspWriter out = pageContext.getOut();
    ServletResponse response = pageContext.getResponse();

    try {

        //
        //retrieve the Finding from cache and build the list of  Clinical Data points
        //ClinicalFinding clinicalFinding = (ClinicalFinding)businessTierCache.getSessionFinding(session.getId(),taskId);
        ReportBean clincalReportBean = presentationTierCache.getReportBean(session.getId(), taskId);
        Resultant clinicalResultant = clincalReportBean.getResultant();
        ResultsContainer resultsContainer = clinicalResultant.getResultsContainer();
        SampleViewResultsContainer sampleViewContainer = null;
        if (resultsContainer instanceof DimensionalViewContainer) {
            DimensionalViewContainer dimensionalViewContainer = (DimensionalViewContainer) resultsContainer;
            sampleViewContainer = dimensionalViewContainer.getSampleViewResultsContainer();
        }
        if (sampleViewContainer != null) {
            Collection<ClinicalFactorType> clinicalFactors = new ArrayList<ClinicalFactorType>();
            clinicalFactors.add(ClinicalFactorType.AgeAtDx);
            //clinicalFactors.add(ClinicalFactorType.Survival);
            Collection<SampleResultset> samples = sampleViewContainer.getSampleResultsets();

            if (samples != null) {
                int numDxvsKa = 0;
                int numDxvsSl = 0;
                for (SampleResultset rs : samples) {
                    //String id = rs.getBiospecimen().getValueObject();
                    String id = rs.getSampleIDDE().getValueObject();
                    ClinicalDataPoint clinicalDataPoint = new ClinicalDataPoint(id);

                    String diseaseName = rs.getDisease().getValueObject();
                    if (diseaseName != null) {
                        clinicalDataPoint.setDiseaseName(diseaseName);
                    } else {
                        clinicalDataPoint.setDiseaseName(DiseaseType.NON_TUMOR.name());
                    }

                    Long sl = rs.getSurvivalLength();
                    double survivalDays = -1.0;
                    double survivalMonths = -1.0;
                    if (sl != null) {
                        survivalDays = sl.doubleValue();
                        survivalMonths = survivalDays / 30.0;
                        //if ((survivalMonths > 0.0)&&(survivalMonths < 1000.0)) {
                        clinicalDataPoint.setSurvival(survivalDays);
                        //}
                    }

                    Long dxAge = rs.getAge();
                    if (dxAge != null) {
                        clinicalDataPoint.setAgeAtDx(dxAge.doubleValue());
                    }

                    KarnofskyClinicalEvalDE ka = rs.getKarnofskyClinicalEvalDE();
                    if (ka != null) {
                        String kaStr = ka.getValueObject();
                        if (kaStr != null) {
                            if (kaStr.contains("|")) {
                                kaStr = kaStr.trim();
                                String[] kaStrArray = kaStr.split("\\|");
                                for (int i = 0; i < kaStrArray.length; i++) {
                                    if (i == 0) {
                                        //first score is baseline just use this for now
                                        //later we will need to use all score in a series for each patient
                                        double kaVal = Double.parseDouble(kaStrArray[i].trim());
                                        clinicalDataPoint.setKarnofskyScore(kaVal);
                                    }
                                }
                            } else {
                                double kaVal = Double.parseDouble(kaStr);
                                clinicalDataPoint.setKarnofskyScore(kaVal);
                            }

                        }
                    }

                    if ((dxAge != null) && (ka != null)) {
                        numDxvsKa++;
                    }

                    if ((dxAge != null) && (sl != null)) {
                        numDxvsSl++;
                    }

                    //                        Object dx = rs.getAgeGroup();
                    //                            if(sl !=null && dx !=null){
                    //                                clinicalDataPoint.setSurvival(new Double(sl.toString()));
                    //                                clinicalDataPoint.setAgeAtDx(new Double(dx.toString()));
                    //                            }
                    //                        Object ks = rs.getKarnofskyClinicalEvalDE();
                    //                        Object dx = rs.getAgeGroup();
                    //                            if(ks !=null && dx !=null){
                    //                                clinicalDataPoint.setNeurologicalAssessment(new Double(ks.toString()));
                    //                                clinicalDataPoint.setAgeAtDx(new Double(dx.toString()));
                    //                            }

                    clinicalData.add(clinicalDataPoint);
                }
            }
        }

        System.out.println("Done creating points!");

        //-------------------------------------------------------------
        //GET THE CLINICAL DATA AND POPULATE THE clinicalData list
        //Note the ClinicalFinding is currently an empty class
        //----------------------------------------------------------

        //check the components to see which graph to get
        if (components.equalsIgnoreCase("SurvivalvsAgeAtDx")) {
            chart = (JFreeChart) CaIntegratorChartFactory.getClinicalGraph(clinicalData,
                    ClinicalFactorType.SurvivalLength, "Survival Length (Months)", ClinicalFactorType.AgeAtDx,
                    "Age At Diagnosis (Years)");
        }
        if (components.equalsIgnoreCase("KarnofskyScorevsAgeAtDx")) {
            chart = (JFreeChart) CaIntegratorChartFactory.getClinicalGraph(clinicalData,
                    ClinicalFactorType.KarnofskyAssessment, "Karnofsky Score", ClinicalFactorType.AgeAtDx,
                    "Age At Diagnosis (Years)");
        }

        RembrandtImageFileHandler imageHandler = new RembrandtImageFileHandler(session.getId(), "png", 600,
                500);
        //The final complete path to be used by the webapplication
        String finalPath = imageHandler.getSessionTempFolder();
        String finalURLpath = imageHandler.getFinalURLPath();
        /*
         * Create the actual charts, writing it to the session temp folder
        */
        ChartRenderingInfo info = new ChartRenderingInfo(new StandardEntityCollection());
        String mapName = imageHandler.createUniqueMapName();

        ChartUtilities.writeChartAsPNG(new FileOutputStream(finalPath), chart, 600, 500, info);

        /*   This is here to put the thread into a loop while it waits for the
         *   image to be available.  It has an unsophisticated timer but at 
         *   least it is something to avoid an endless loop.
         **/
        boolean imageReady = false;
        int timeout = 1000;
        FileInputStream inputStream = null;
        while (!imageReady) {
            timeout--;
            try {
                inputStream = new FileInputStream(finalPath);
                inputStream.available();
                imageReady = true;
                inputStream.close();
            } catch (IOException ioe) {
                imageReady = false;
                if (inputStream != null) {
                    inputStream.close();
                }
            }
            if (timeout <= 1) {

                break;
            }
        }

        out.print(ImageMapUtil.getBoundingRectImageMapTag(mapName, false, info));
        //finalURLpath = finalURLpath.replace("\\", "/");
        finalURLpath = finalURLpath.replace("\\", "/");
        long randomness = System.currentTimeMillis(); //prevent image caching
        out.print("<img id=\"geneChart\" alt=\"geneChart\" name=\"geneChart\" src=\"" + finalURLpath + "?"
                + randomness + "\" usemap=\"#" + mapName + "\" border=\"0\" />");

        //out.print("<img id=\"geneChart\" name=\"geneChart\" src=\""+finalURLpath+"\" usemap=\"#"+mapName + "\" border=\"0\" />");

    } catch (IOException e) {
        logger.error(e);
    } catch (Exception e) {
        logger.error(e);
    } catch (Throwable t) {
        logger.error(t);
    }

    return EVAL_BODY_INCLUDE;
}

From source file:com.digitalpersona.onetouch.ui.swing.sample.Enrollment.Dashboard.java

private void verify() {
    FileInputStream stream = null;
    try {//  w  w  w  .  j  a v  a 2  s  .  co  m
        File file = new File("C:\\Users\\Guinness\\Documents\\10.jpg");

        stream = new FileInputStream(file);
        byte[] data = new byte[stream.available()];
        stream.read(data);
        stream.close();
        DPFPTemplate t = DPFPGlobal.getTemplateFactory().createTemplate();
        t.deserialize(data);
        setTemplate(t);
        init();
        DPFPFeatureSet features = extractFeatures(aw.getSample(), DPFPDataPurpose.DATA_PURPOSE_VERIFICATION);

        // Check quality of the sample and start verification if it's good
        if (features != null) {
            // Compare the feature set with our template
            DPFPVerificationResult result = verificator.verify(features, t);

            if (result.isVerified()) {
                System.out.println("Verified!..");
                makeReport("The fingerprint was VERIFIED.");
            } else {
                System.out.println("Did not match");
                makeReport("The fingerprint was NOT VERIFIED.");
            }
        }

    } catch (FileNotFoundException ex) {
        Logger.getLogger(Dlg_test.class.getName()).log(Level.SEVERE, null, ex);
    } catch (IOException ex) {
        Logger.getLogger(Dlg_test.class.getName()).log(Level.SEVERE, null, ex);
    } finally {
        try {
            stream.close();
        } catch (IOException ex) {
            Logger.getLogger(Dlg_test.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
}

From source file:net.sourceforge.squirrel_sql.fw.datasetviewer.cellcomponent.DataTypeBigDecimal.java

/**
 * Read a file and construct a valid object from its contents.
 * Errors are returned by throwing an IOException containing the
 * cause of the problem as its message.//from   w  ww . ja v  a2 s.  c o m
 * <P>
 * DataType is responsible for validating that the imported
 * data can be converted to an object, and then must return
 * a text string that can be used in the Popup window text area.
 * This object-to-text conversion is the same as is done by
 * the DataType object internally in the getJTextArea() method.
 * 
 * <P>
 * File is assumed to be and ASCII string of digits
 * representing a value of this data type.
 */
public String importObject(FileInputStream inStream) throws IOException {

    InputStreamReader inReader = new InputStreamReader(inStream);

    int fileSize = inStream.available();

    char charBuf[] = new char[fileSize];

    int count = inReader.read(charBuf, 0, fileSize);

    if (count != fileSize)
        throw new IOException("Could read only " + count + " chars from a total file size of " + fileSize
                + ". Import failed.");

    // convert file text into a string
    // Special case: some systems tack a newline at the end of
    // the text read.  Assume that if last char is a newline that
    // we want everything else in the line.
    String fileText;
    if (charBuf[count - 1] == KeyEvent.VK_ENTER)
        fileText = new String(charBuf, 0, count - 1);
    else
        fileText = new String(charBuf);

    // test that the string is valid by converting it into an
    // object of this data type
    StringBuffer messageBuffer = new StringBuffer();
    validateAndConvertInPopup(fileText, null, messageBuffer);
    if (messageBuffer.length() > 0) {
        ;
        // convert number conversion issue into IO issue for consistancy
        throw new IOException(
                "Text does not represent data of type " + getClassName() + ".  Text was:\n" + fileText);
    }

    // return the text from the file since it does
    // represent a valid value of this data type
    return fileText;
}

From source file:org.sogrey.frame.utils.FileUtil.java

/**
 * ??//ww w. j a v  a  2s  .c om
 *
 * @param file
 *
 * @return
 *
 * @throws Exception
 */
private static long getFileSize(File file) throws Exception {
    long size = 0;
    if (file.exists()) {
        FileInputStream fis = null;
        fis = new FileInputStream(file);
        size = fis.available();
    } else {
        file.createNewFile();
        LogUtil.e("??", "?!");
    }
    return size;
}

From source file:org.nuxeo.ecm.automation.server.test.AbstractAutomationClientTest.java

@Test
public void testUploadSmallFile() throws Exception {
    DigestMockInputStream source = new DigestMockInputStream(100);
    FileInputStream in = new UploadFileSupport(session, automationTestFolder.getPath()).testUploadFile(source);
    byte[] sentSum = source.digest.digest();
    while (in.available() > 0) {
        source.digest.update((byte) in.read());
    }/* ww  w.j ava2 s. c o  m*/
    byte[] receivedSum = source.digest.digest();
    assertTrue("Expected (sent) bytes array: " + Arrays.toString(sentSum) + " - Actual (received) bytes array: "
            + Arrays.toString(receivedSum), MessageDigest.isEqual(sentSum, receivedSum));
}

From source file:com.krawler.portal.tools.FileImpl.java

public String read(File file, boolean raw) throws IOException {
    FileInputStream fis = new FileInputStream(file);

    byte[] bytes = new byte[fis.available()];

    fis.read(bytes);//from   ww  w .  j  a  v  a2 s  . c  o m

    fis.close();

    String s = new String(bytes, StringPool.UTF8);

    if (raw) {
        return s;
    } else {
        return StringUtil.replace(s, StringPool.RETURN_NEW_LINE, StringPool.NEW_LINE);
    }
}

From source file:com.freecast.LudoCast.MainActivity.java

public void readFileData(String fileName) {

    String res = "";

    try {//from   ww  w .jav  a 2 s .c om

        FileInputStream fin = openFileInput(fileName);

        int length = fin.available();

        byte[] buffer = new byte[length];

        fin.read(buffer);

        res = EncodingUtils.getString(buffer, "UTF-8");

        fin.close();

    }

    catch (Exception e) {

        e.printStackTrace();

    }

    if (res.equals("")) {
    } else {
        editText.setText(res);
        username = editText.getText().toString();
    }

}