Changeset 4095

Timestamp:

Jan 21, 2008, 5:10:00 PM (15 years ago)

Author:

Johan Enell

Message:

Merged patch release 2.5.1 to the trunk. Delta 2.5 - 2.5.1

Location:

trunk

Files:

• build.xml (modified) (5 diffs)
• src/clients/web/net/sf/basedb/clients/web/fileupload/FileUpload.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/Page.java (modified) (1 diff)
• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/Affymetrix.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Job.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/SpotImages.java (modified) (1 diff)
• src/core/net/sf/basedb/util/BioAssaySetFilterUtil.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/IntensityCalculatorUtil.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/parser/FlatFileParser.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/zip/TarFilePacker.java (modified) (1 diff)
• src/core/net/sf/basedb/util/zip/TarUtil.java (copied) (copied from tags/2.5.1/src/core/net/sf/basedb/util/zip/TarUtil.java)
• src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java (modified) (5 diffs)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (4 diffs)
• src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java (modified) (7 diffs)
• src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/TarFileUnpacker.java (modified) (5 diffs)
• src/test/net/sf/basedb/test/FileUtil.java (modified) (3 diffs)
• src/test/net/sf/basedb/test/roles/AdminTest.java (modified) (1 diff)
• src/test/net/sf/basedb/test/roles/PowerUserTest.java (modified) (1 diff)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (1 diff)
• www/common/annotations/list_annotations.jsp (modified) (1 diff)
• www/images/plot_empty_400x300.png (copied) (copied from tags/2.5.1/www/images/plot_empty_400x300.png)
• www/images/transparent_pixel.gif (copied) (copied from tags/2.5.1/www/images/transparent_pixel.gif)
• www/views/experiments/bioassaysets/view_bioassayset.jsp (modified) (5 diffs)

trunk/build.xml

@@ -61 +61 @@
 
     Packaging:
-    package:          Create *.tar.gz files with binary, source and example distributions
+    package:          Create *.tar.gz files with binary, source and exampele distributions
     package.bin       Create binary distribution only
     package.src       Create source distribution only
@@ -772 +772 @@
   <target
     name="examples.webservices"
-    depends="examples.webservices.compile,webservices.jar"
+    depends="examples.webservices.compile,webservices.jar,webservices.wsdl"
     description="Put together the webservices examples in the examples/webservices directory"
     >
@@ -880 +880 @@
   <target
     name="web.compile"
-    depends="web.init,core.compile"
+    depends="web.init,core.compile,coreplugins.compile"
     description="Compile the web client application"
     >
@@ -966 +966 @@
   <target
     name="webservices.init"
-    depends="core.init,coreplugins.init"
+    depends="core.init,coreplugins.init,web.init"
     >
     <property name="webservices.src" location="${src}/webservices" 
@@ -1024 +1024 @@
     name="webservices.server.compile"
     description="Compile the server part of webservices"
-    depends="webservices.init,core.compile,coreplugins.compile"
+    depends="webservices.init,core.compile,coreplugins.compile,web.compile"
     >
     <mkdir dir="${webservices.build}/server" />

trunk/src/clients/web/net/sf/basedb/clients/web/fileupload/FileUpload.java

@@ -774 +774 @@
       throws IOException
     {
-      if (status.eof || status.atBoundary) return -1;
+      int available = end - start;
+      if (available == 0)
+      {
+        if (status.eof || status.atBoundary) return -1;
+        available = readMoreData();
+      }
       int result = -1;
-      int available = end - start;
-      if (available == 0) available = readMoreData();
       if (available > 0)
       {
-        result = buffer[start];
+        // Important! Mask with 0xff to get values in range (0,255), NOT (-128,127)
+        result = buffer[start] & 0xff;
         start++;
       }

trunk/src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java

@@ -468 +468 @@
     template.writeHeaders();
     
-    int numExported = 0;
+    long numExported = 0;
     ResultIterator result = null;
     try
@@ -506 +506 @@
           if (progress != null)
           {
-            int percent = (int)(100f * numExported / totalItems);
+            int percent = (int)(100L * numExported / totalItems);
             progress.display(percent, numExported + " of " + totalItems + " done.");
           }

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Page.java

@@ -278 +278 @@
     throws JspException
   {
-    StringBuilder sb = new StringBuilder();
-    sb.append("</html>\n");
-    try
-    {
-      pageContext.getOut().print(sb.toString());
-    }
-    catch (Exception ex)
-    {
-      throw new JspTagException(ex.getMessage());
+    if (type != PAGE_TYPE_INCLUDE)
+    {
+      StringBuilder sb = new StringBuilder();
+      sb.append("</html>\n");
+      try
+      {
+        pageContext.getOut().print(sb.toString());
+      }
+      catch (Exception ex)
+      {
+        throw new JspTagException(ex.getMessage());
+      }
     }
     return EVAL_PAGE;

trunk/src/core/common-queries.xml

@@ -524 +524 @@
       SELECT s
       FROM net.sf.basedb.core.data.MimeTypeData s
-      WHERE s.extension = :extension
+      WHERE LOWER(s.extension) = LOWER(:extension)
     </sql>
     <description>

trunk/src/core/net/sf/basedb/core/Affymetrix.java

@@ -357 +357 @@
       if (hasProgress && (index % progressInterval == 0))
       {
-        int percent = 5 + 90 * index / numProbesets;
+        int percent = 5 + (int)(90L * (long)index / numProbesets);
         int remain = numProbesets - index;
         String created = create ? "; " + numCreated + " created" : "";

trunk/src/core/net/sf/basedb/core/Job.java

@@ -1279 +1279 @@
     private long lastUpdate;
     
+    private int lastValue;
+    private int offset;
+    
     ProgressReporterImpl(Job job, String server, ProgressReporter chained)
       throws BaseException
@@ -1288 +1291 @@
       this.chained = chained;
       this.lastUpdate = 0;
+      this.lastValue = 0;
+      this.offset = 0;
     }
     
@@ -1299 +1304 @@
       if (System.currentTimeMillis() - lastUpdate > UPDATE_INTERVAL || percent == 100)
       {
+        // If the percent is negative and less then the last value, an offset will be calculated.
+        // This will adjust the percent to a realistic value. 
+        //Notice: It is only possible to give a value close to what expected. 
+        if (percent < lastValue && percent < 0)
+        { 
+          if (Math.abs(percent) < Math.abs(lastValue))
+          {
+            offset = offset + 2*Math.abs(lastValue);
+          }
+          else
+          { 
+            offset = offset + 2*Math.abs(percent);
+          }
+        }
+        lastValue = percent;    
+        percent = percent + offset;
+        
         lastUpdate = System.currentTimeMillis();
         DbControl dc = null;

trunk/src/core/net/sf/basedb/core/RawBioAssay.java

@@ -1164 +1164 @@
 
       DataResultIterator<RawData> result = rawQuery.iterate(dc);
-      int numValidated = 0;
+      long numValidated = 0;
       int numTotal = getNumDbSpots();
       while (result.hasNext())
@@ -1221 +1221 @@
         if (progress != null && numValidated % 100 == 0)
         {
-          int percent = 10 + (90 * numValidated) / numTotal;
+          int percent = 10 + ((int)(90L * numValidated) / numTotal);
           progress.display(percent, "Validated " + numValidated + " of " + numTotal + " spots.");
         }

trunk/src/core/net/sf/basedb/core/SpotImages.java

@@ -472 +472 @@
           if (progress != null) 
           {
-            int spotsDone = spotImagesPerImage*imageNumber;
-            int percent = 10 + 90 * spotsDone / totalSpots;
+            long spotsDone = spotImagesPerImage*imageNumber;
+            int percent = 10 + (int)(90L * spotsDone / totalSpots);
             progress.display(percent, "Generating spot images ("+spotsDone+" done)...");
           }

trunk/src/core/net/sf/basedb/util/BioAssaySetFilterUtil.java

@@ -123 +123 @@
     }
     
-    int spotsDone = 0;
+    long spotsDone = 0;
     int spotsAfter = 0;
     if (progress != null) progress.display(10, "Filtering spots (0 done; "+spotsTotal+" total)...");
@@ -139 +139 @@
       if (progress != null) 
       {
-        int percent = 10 + 90 * spotsDone / spotsTotal;
+        int percent = 10 + (int)(90L * spotsDone / spotsTotal);
         progress.display(percent, 
           "Filtering spot intensities ("+spotsDone+" done; "+spotsTotal+" total)...");
@@ -205 +205 @@
     // Prepare progress reporting
     int interval = 10;  // Update progress after this many spots >= 10
-    int spotsDone = 0;
+    long spotsDone = 0;
     int spotsAfter = 0;
     if (progress != null)
@@ -236 +236 @@
             if (spotsDone % interval == 0)
             {
-              int percent = 10 + 90 * spotsDone / spotsTotal;
+              int percent = 10 + (int)(90L * spotsDone / spotsTotal);
               progress.display(percent, 
                 "Filtering spot intensities ("+spotsDone+" done; "+spotsTotal+" total)...");

trunk/src/core/net/sf/basedb/util/IntensityCalculatorUtil.java

@@ -305 +305 @@
     int maxPosition = 0;
     
-    int spotsDone = 0; // Number of calculated spots
+    long spotsDone = 0; // Number of calculated spots
     int totalSpots = 0; // Total number of spots
     int interval = 0; // Interval between reporter to the progress reporter
@@ -426 +426 @@
           if (spotsDone % interval == 0)
           {
-            int percent = 10 + 90 * spotsDone / totalSpots;
+            int percent = 10 + (int)((90L * spotsDone) / totalSpots);
             progress.display(percent, "Calculating spot intensities ("+spotsDone+" done)...");
           }

trunk/src/core/net/sf/basedb/util/parser/FlatFileParser.java

@@ -47 +47 @@
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.Config;
+import net.sf.basedb.util.InputStreamTracker;
 
 /**
@@ -176 +177 @@
 
   /**
+    For keeping track of the number of bytes parsed.
+  */
+  private InputStreamTracker tracker;
+  
+  /**
     The regular expression for matching a header line.
   */
@@ -522 +528 @@
   {
     Charset cs = Charset.forName(charsetName == null ? Config.getCharset() : charsetName);
-    this.reader = new BufferedReader(new InputStreamReader(in, cs));
+    this.tracker = new InputStreamTracker(in);
+    this.reader = new BufferedReader(new InputStreamReader(tracker, cs));
   }
 
@@ -1116 +1123 @@
     correspond to the number of parsed bytes depending on the character
     set of the file.
+    @see #getParsedBytes()
   */
   public long getParsedCharacters()
   {
     return parsedCharacters;
+  }
+  
+  /**
+    Get the number of parsed bytes so far. This value may or may not
+    correspond to the number of parsed characters depending on the character
+    set of the file.
+    @since 2.5.1
+    @see #getParsedCharacters()
+  */
+  public long getParsedBytes()
+  {
+    return tracker == null ? 0 : tracker.getNumRead();
   }
   

trunk/src/core/net/sf/basedb/util/zip/TarFilePacker.java

@@ -97 +97 @@
     if (lastModified > 0) entry.setModTime(lastModified);
     entry.setSize(size);
-    tar.putNextEntry(entry);
+    TarUtil.putNextEntry(entry, tar);
     if (!isDirectory) FileUtil.copy(in, tar);
     tar.closeEntry();

trunk/src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java

@@ -542 +542 @@
         if (section != null && section.type() == FlatFileParser.LineType.SECTION)
         {
-          if (progress != null) progress.display(getProgress(ffp.getParsedCharacters()), "Parsing section "+section.name()+"...");
+          if (progress != null) progress.display(getProgress(ffp), "Parsing section "+section.name()+"...");
           try
           {
@@ -571 +571 @@
         else
         {
-          if (progress != null) progress.display(getProgress(ffp.getParsedCharacters()), "Parsing headers...");
+          if (progress != null) progress.display(getProgress(ffp), "Parsing headers...");
         }
         FlatFileParser.LineType result = ffp.parseHeaders();
@@ -609 +609 @@
             " on line " + (line == null ? "-1" : line.lineNo() + ": " + StringUtil.trimString(line.line(), 20)), t);      
         }
-        if (progress != null) progress.display(getProgress(ffp.getParsedCharacters()), "Parsing data...");
+        if (progress != null) progress.display(getProgress(ffp), "Parsing data...");
         int progressLine = 0;
         
@@ -640 +640 @@
               if (progress != null)
               {
-                progress.display(getProgress(ffp.getParsedCharacters()), "Parsing data... (" + ffp.getParsedLines() + " lines so far)");
+                progress.display(getProgress(ffp), "Parsing data... (" + ffp.getParsedLines() + " lines so far)");
               }
             }
@@ -685 +685 @@
   // -------------------------------------------
 
-  private int getProgress(long parsedCharacters)
-  {
-    return (int) (100 * parsedCharacters / fileSize);
+  private int getProgress(FlatFileParser ffp)
+  {
+    return (int) (100 * ffp.getParsedBytes() / fileSize);
   }
 

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -1806 +1806 @@
         case STRING:
         {
-          StringParameterType t = new StringParameterType(255, defaultValue, false, 1, new Integer(options), 1);
+          StringParameterType t = new StringParameterType(65535, defaultValue, false, 1, new Integer(options), 1);
           parameter = new PluginParameter<String>(name, commonName, "", t);
           break;
@@ -1827 +1827 @@
         case HIDDEN_STRING:
         {
-          StringParameterType t = new StringParameterType(255, defaultValue, false, 1, 0, 1);
+          StringParameterType t = new StringParameterType(65535, defaultValue, false, 1, 0, 1);
           parameter = new PluginParameter<String>(name, null, "", t);
           break;
@@ -1855 +1855 @@
             enums.add(at.getName(), at.getName());
           }
-          StringParameterType t = new StringParameterType(255, null, false, 1, Values.getInt(options, 30), 1, enums);
+          StringParameterType t = new StringParameterType(65535, null, false, 1, Values.getInt(options, 30), 1, enums);
           parameter = new PluginParameter<String>(name, commonName, "", t);
           break;
@@ -1861 +1861 @@
         case ENUMERATION:
         {
-          StringParameterType t = new StringParameterType(255, defaultValue, false, 1, Values.getInt(options, 30), 1, enumOptions);
+          StringParameterType t = new StringParameterType(65535, defaultValue, false, 1, Values.getInt(options, 30), 1, enumOptions);
           parameter = new PluginParameter<String>(name, commonName, "", t);
           break;

trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -685 +685 @@
     int nof_reporters=bioassayset.getNumReporters();
     int progress_report_interval=nof_reporters/10;
-    int nof_processed_reporters=0;
+    long nof_processed_reporters=0;
     while (spotData.hasNext())
     {
       if (progress != null && (nof_processed_reporters%progress_report_interval == 0))
       {
-        progress.display(100 * nof_processed_reporters / nof_reporters,
+        progress.display((int)(100L * nof_processed_reporters / nof_reporters),
                          "Exporting ... " + nof_processed_reporters + " of " +
                          nof_reporters + " done.");
@@ -781 +781 @@
     int nof_spots=bioassayset.getNumSpots();
     int progress_spot_interval=nof_spots/10;
-    int nof_processed_spots=0;
+    long nof_processed_spots=0;
     while (spotData.hasNext())
     {
@@ -791 +791 @@
           (nof_processed_spots%progress_spot_interval == 0))
         {
-          progress.display(100 * nof_processed_spots / nof_spots,
+          progress.display((int)(100L * nof_processed_spots / nof_spots),
                            "Exporting ..." + nof_processed_spots + " of " +
                            nof_spots + " done.");

trunk/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java

@@ -88 +88 @@
 import net.sf.basedb.util.parser.FlatFileParser.Data;
 import net.sf.basedb.util.parser.FlatFileParser.Line;
+import net.sf.basedb.util.parser.FlatFileParser.LineType;
 
 /**
@@ -165 +166 @@
         Arrays.asList(new String[] {"COORDINATE", "POSITION", "FEATURE_ID" } ))
     );
-
   
   private static final PluginParameter<String> invalidColumnsErrorParameter = new PluginParameter<String>(
@@ -290 +290 @@
         storeValue(job, request, fileParameter);
         storeValue(job, request, ri.getParameter(CHARSET));
+        storeValue(job, request, ri.getParameter(DECIMAL_SEPARATOR));
         
         // Associations
@@ -343 +344 @@
     Create a FlatFileParser that can parse Illumina data files:
     <ul>
-    <li>Data splitter: ,
+    <li>Data splitter: (,|\t)
     <li>Header regexp: (.+)=(.*?),*
-    <li>Data header: TargetId,.*
+    <li>Data header: TargetID(,|\t).*
     </ul>
+    NOTE! To begin with we support both comma and tab as column splitter but
+    later on (in {@link #isImportable(FlatFileParser)}) when we know which one is actually
+    used, we change this in the parser. We need to do this since numbers may
+    use comma as decimal separator.
   */
   @Override
@@ -352 +357 @@
     throws BaseException
   {
+    String separator = "(,|\\t)";
     FlatFileParser ffp = new FlatFileParser();
-    ffp.setDataSplitterRegexp(Pattern.compile(","));
-    ffp.setDataHeaderRegexp(Pattern.compile("TargetID,.*"));
+    ffp.setDataSplitterRegexp(Pattern.compile(separator));
+    ffp.setDataHeaderRegexp(Pattern.compile("TargetID"+separator + ".*"));
     ffp.setHeaderRegexp(Pattern.compile("(.+)=(.*?),*"));
     return ffp;
   }
   /**
-    @return Always "dot"
+    @return As specified by job parameter or "dot" if not
   */
   @Override
   protected String getDecimalSeparator()
   {
-    return "dot";
+    String separator = super.getDecimalSeparator();
+    if (separator == null) separator = "dot";
+    return separator;
   }
 
@@ -376 +384 @@
   {
     String firstLine = ffp.getLineCount() >= 1 ? ffp.getLine(0).line() : null;
-    return firstLine != null && firstLine.contains("Illumina") ;
+    boolean isIllumina = firstLine != null && firstLine.contains("Illumina");
+    if (isIllumina)
+    {
+      String separator = ",";
+      FlatFileParser.Line lastLine = ffp.getLine(ffp.getLineCount()-1);
+      if (lastLine.type() == LineType.DATA_HEADER)
+      {
+        int firstTab = lastLine.line().indexOf("\t");
+        if (firstTab > 0 && firstTab < lastLine.line().indexOf(","))
+        {
+          separator = "\\t";
+        }
+        ffp.setDataSplitterRegexp(Pattern.compile(separator));
+      }
+    }
+    return isIllumina;
   }
   
@@ -649 +672 @@
         parameters.add(fileParameter);
         parameters.add(getCharsetParameter(null, null, null));
+        parameters.add(getDecimalSeparatorParameter(null, null, (String)job.getValue(DECIMAL_SEPARATOR)));
   
         // parameters for scan, protocol, software and array design

trunk/src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java

@@ -408 +408 @@
     query.restrict(intensityRestriction);
     long numSpots = query.count(dc);
-    int normalizedSpots = 0;
+    long normalizedSpots = 0;
     if (progress != null) progress.display((int)(normalizedSpots / numSpots * 100), normalizedSpots + " spots normalized");
     
@@ -504 +504 @@
             }
             normalizedSpots += smoothCurve.size();
-            if (progress != null) progress.display((int)((normalizedSpots * 100) / numSpots), normalizedSpots + " spots normalized");
+            if (progress != null) progress.display((int)((normalizedSpots * 100L) / numSpots), normalizedSpots + " spots normalized");
           }
           fromBlock = toBlock + 1;

trunk/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -349 +349 @@
     query.restrict(intensityRestriction);
     long numSpots = query.count(dc);
-    int normalizedSpots = 0;
+    long normalizedSpots = 0;
     if (progress != null) progress.display((int)(normalizedSpots / numSpots * 100), normalizedSpots + " spots normalized");
     
@@ -441 +441 @@
             }
             normalizedSpots += toIndex - fromIndex;
-            if (progress != null) progress.display((int)((normalizedSpots * 100) / numSpots), normalizedSpots + " spots normalized");
+            if (progress != null) progress.display((int)((normalizedSpots * 100L) / numSpots), normalizedSpots + " spots normalized");
           }
           fromBlock = toBlock + 1;

trunk/src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java

@@ -356 +356 @@
     // Get parameters
     Directory rootDir = (Directory)job.getValue("root");
+    rootDir = Directory.getById(dc, rootDir.getId());
     List<Integer> files = (List<Integer>)job.getValues("files");        
     List<Integer> directories = (List<Integer>)job.getValues("directories");

trunk/src/plugins/core/net/sf/basedb/plugins/TarFileUnpacker.java

@@ -24 +24 @@
 package net.sf.basedb.plugins;
 
+import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -53 +54 @@
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.zip.AbstractFileUnpacker;
+import net.sf.basedb.util.zip.TarUtil;
 
 /**
@@ -138 +140 @@
     if (isGzip)
     {
-      tarStream = new TarInputStream(new GZIPInputStream(pin));
+      tarStream = new TarInputStream(new GZIPInputStream(new BufferedInputStream(pin)));
     }
     else if (isBzip)
@@ -145 +147 @@
       pin.read();
       pin.read();
-      tarStream = new TarInputStream(new CBZip2InputStream(pin));
+      tarStream = new TarInputStream(new CBZip2InputStream(new BufferedInputStream(pin)));
     }
     else
@@ -160 +162 @@
     long totalUnpacked = 0;
     int numFiles = 0;
-    
-    while ((entry = tarStream.getNextEntry()) != null)
+    while ((entry = TarUtil.getNextEntry(tarStream)) != null)
     {
       String subPath = entry.getName();

trunk/src/test/net/sf/basedb/test/FileUtil.java

@@ -27 +27 @@
 
 import org.apache.tools.bzip2.CBZip2InputStream;
+
+import com.ice.tar.TarInputStream;
 
 import net.sf.basedb.core.DbControl;
@@ -66 +68 @@
     
     boolean isBzip = false;
+    boolean isTar = false;
     if (filename.endsWith(".bz2"))
     {
       isBzip = true;
       filename = filename.substring(0, filename.length()-4);
+    }
+    if (filename.endsWith(".tar"))
+    {
+      isTar = true;
+      filename = filename.substring(0, filename.length() - 4);
     }
   
@@ -96 +104 @@
           toUpload = new CBZip2InputStream(toUpload);
         }
+        if (isTar)
+        {
+          // Assume that the TAR only contains a single file
+          TarInputStream tar = new TarInputStream(toUpload);
+          tar.getNextEntry();
+          toUpload = tar;
+        }
         file.upload(toUpload, false, true);
       }

trunk/src/test/net/sf/basedb/test/roles/AdminTest.java

@@ -120 +120 @@
       dc = TestUtil.getDbControl();
       File reporters = FileUtil.uploadFile(dc, "/mouse", "plates_and_reporters.mouse.v4.37k.txt", FileType.PLATE);
-      File affyReporters = FileUtil.uploadFile(dc, "/affymetrix/annotations", "MG_U74Av2_annot.csv.bz2", FileType.REPORTER);
+      File affyReporters = FileUtil.uploadFile(dc, "/affymetrix/annotations", "MG_U74Av2_annot.csv.tar.bz2", FileType.REPORTER);
       dc.commit();
       

trunk/src/test/net/sf/basedb/test/roles/PowerUserTest.java

@@ -161 +161 @@
       File plates = FileUtil.uploadFile(dc, "/mouse", "plates_and_reporters.mouse.v4.37k.txt", FileType.PLATE);     
       File printMap = FileUtil.uploadFile(dc, "/mouse", "printmap.mouse.v4.37k.tam", FileType.PRINT_MAP);
-      File cdfFile = FileUtil.uploadFile(dc, "/affymetrix/cdf", "MG_U74Av2.cdf.bz2", FileType.REPORTER_MAP);
+      File cdfFile = FileUtil.uploadFile(dc, "/affymetrix/cdf", "MG_U74Av2.cdf.tar.bz2", FileType.REPORTER_MAP);
       dc.commit();
       

trunk/src/test/net/sf/basedb/test/roles/UserTest.java

@@ -142 +142 @@
       File rawData2DyeSwap = FileUtil.uploadFile(dc, "/mouse", "genepix.mouse.v4.37k.24h.dyeswap.gpr", FileType.RAW_DATA);
       
-      File affy1 = FileUtil.uploadFile(dc, "/affymetrix/E-TEST-1.ebi.ac.uk", "jos1761.cel.bz2", FileType.RAW_DATA);
-      File affy2 = FileUtil.uploadFile(dc, "/affymetrix/E-TEST-1.ebi.ac.uk", "jos1762.cel.bz2", FileType.RAW_DATA);
-      File affy3 = FileUtil.uploadFile(dc, "/affymetrix/E-TEST-1.ebi.ac.uk", "jos1763.cel.bz2", FileType.RAW_DATA);
+      File affy1 = FileUtil.uploadFile(dc, "/affymetrix/E-TEST-1.ebi.ac.uk", "jos1761.cel.tar.bz2", FileType.RAW_DATA);
+      File affy2 = FileUtil.uploadFile(dc, "/affymetrix/E-TEST-1.ebi.ac.uk", "jos1762.cel.tar.bz2", FileType.RAW_DATA);
+      File affy3 = FileUtil.uploadFile(dc, "/affymetrix/E-TEST-1.ebi.ac.uk", "jos1763.cel.tar.bz2", FileType.RAW_DATA);
       dc.commit();
       

trunk/www/common/annotations/list_annotations.jsp

@@ -389 +389 @@
       }
       %>
-      </div>
 
   </base:body>

trunk/www/views/experiments/bioassaysets/view_bioassayset.jsp

@@ -174 +174 @@
       }
     }
-    function changeImage(imageId, url)
-    {
+    function runItemPlugin(cmd)
+    {
+      Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&experiment_id=<%=experimentId%>&item_id=<%=itemId%>', 'RunPlugin'+cmd, 740, 540);
+    }
+    var imageQueue = new Array();
+    var nextImage = 0;
+    function addImage(imageId, url)
+    {
+      imageQueue[imageQueue.length] = imageId;
       var img = document.getElementById(imageId);
-      img.src = url;
-    }
-    function runItemPlugin(cmd)
-    {
-      Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&experiment_id=<%=experimentId%>&item_id=<%=itemId%>', 'RunPlugin'+cmd, 740, 540);
+      img.realSrc = url;
+    }
+    function imageLoaded()
+    {
+      nextImage++;
+      prepareNextImage();
+    }
+    function prepareNextImage()
+    {
+      if (imageQueue.length > nextImage)
+      {
+        var imageId = imageQueue[nextImage];
+        var img = document.getElementById(imageId);
+        img.src = '../../../images/plot_generating_400x300.gif';
+        setTimeout('loadNextImage()', 100);
+      }
+    }
+    function loadNextImage()
+    {
+      if (imageQueue.length > nextImage)
+      {
+        var imageId = imageQueue[nextImage];
+        var img = document.getElementById(imageId);
+        img.onload = imageLoaded;
+        img.src = img.realSrc;
+      }
     }
     </script>
+    <style>
+    .plot {
+      border: 1px solid #666666; 
+      background-image: url('../../../images/plot_empty_400x300.png');
+    }
+    </style>
   </base:head>
-  <base:body>
+  <base:body onload="loadNextImage()">
     <p>
     <p:path>
@@ -481 +515 @@
         ItemQuery<BioAssay> bioAssayQuery = bioAssaySet.getBioAssays();
         bioAssayQuery.order(Orders.asc(Hql.property("name")));
+        StringBuilder script = new StringBuilder();
         for (BioAssay bioAssay : bioAssayQuery.list(dc))
         {
@@ -488 +523 @@
           url += "&filter="+filter;
           url += "&title="+HTML.urlEncode(bioAssay.getName());
+          script.append("addImage('MA").append(bioAssay.getId()).append("','").
+              append(url).append("');\n");
           %>
           <img id="MA<%=bioAssay.getId()%>" 
-            src="../../../images/plot_generating_400x300.gif" 
-            width="400" height="300" 
+            src="../../../images/transparent_pixel.gif" 
+            width="400" height="300"
             alt="MA-plot for bioassay <%=HTML.encodeTags(bioAssay.getName())%>"
-            style="border: 1px solid #666666;">
-          <script language="JavaScript">
-          setTimeout("changeImage('MA<%=bioAssay.getId()%>', '<%=url%>')", 100);
-          </script>
+            class="plot"
+            >
           <%
         }
+        %>
+        <script language="JavaScript">
+        <%=script%>
+        </script>
+        <%
       }
       %>
@@ -513 +553 @@
         String xLabel = HTML.urlEncode("A, log10(ch1 * ch2) / 2");
         String yLabel = HTML.urlEncode("M, log2(ch1 / ch2)");
+        StringBuilder script = new StringBuilder();
         for (BioAssay bioAssay : bioAssayQuery.list(dc))
         {
@@ -519 +560 @@
           url += "&xLabel="+xLabel+"&yLabel="+yLabel;
           url += "&title="+HTML.urlEncode(bioAssay.getName());
+          script.append("addImage('CF").append(bioAssay.getId()).append("','").
+          append(url).append("');\n");
           %>
           <img id="CF<%=bioAssay.getId()%>" 
-            src="../../../images/plot_generating_400x300.gif" 
-            width="400" height="300" 
+            src="../../../images/transparent_pixel.gif" 
+            width="400" height="300"
             alt="Correction factor plot for bioassay <%=HTML.encodeTags(bioAssay.getName())%>"
-            style="border: 1px solid #666666;">
-          <script language="JavaScript">
-          setTimeout("changeImage('CF<%=bioAssay.getId()%>', '<%=url%>')", 100);
-          </script>
+            class="plot"
+            >
           <%
         }
+        %>
+        <script language="JavaScript">
+        <%=script%>
+        </script>
+        <%
       }
       %>