Changeset 3737


Ignore:
Timestamp:
Sep 17, 2007, 9:23:14 AM (14 years ago)
Author:
Nicklas Nordborg
Message:

Added modified AffxFusion?.jar that can read from InputStream? for some file formats.

Location:
trunk
Files:
4 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/3rd-party-components.txt

    r3679 r3737  
    233233Affymetrix Fusion SDK
    234234---------------------
    235 Package for reading various Affymetrix file formats.
     235Package for reading various Affymetrix file formats. We use a modified
     236version that for some file formats can read from an InputStream instead
     237of from a File object. This avoids a lot of copying and decompressing.
    236238
    237239More info: http://www.affymetrix.com/support/developer/fusion/index.affx
     240         : (original version)
     241         : http://trac.thep.lu.se/trac/basehacks/wiki/AffxFusion
     242         : (modified version)
    238243Version  : 1.09
    239244License  : LGPL (lgpl.txt)
  • trunk/src/core/net/sf/basedb/core/Affymetrix.java

    r3675 r3737  
    2525package net.sf.basedb.core;
    2626
     27import java.io.FileOutputStream;
     28
    2729import net.sf.basedb.core.data.ReporterData;
     30import net.sf.basedb.util.FileUtil;
    2831import affymetrix.fusion.cdf.FusionCDFData;
    2932import affymetrix.fusion.cel.FusionCELData;
     
    342345  {
    343346    if (cdfFile == null) throw new InvalidUseOfNullException("cdfFile");
     347    if (cdfFile.getLocation() != Location.PRIMARY)
     348    {
     349      throw new ItemNotFoundException("File data is not online for file '" +
     350        cdfFile.getName() + "'; location=" + cdfFile.getLocation());
     351    }
    344352    FusionCDFData cdf = new FusionCDFData();
    345     cdf.setFileName(File.getAbsolutePath(cdfFile.getData().getInternalName()).getPath());
    346     if (!cdf.exists())
    347     {
    348       throw new ItemNotFoundException("File data not found on server: " + cdfFile.getPath());
    349     }
     353    cdf.setFileName(cdfFile.getName());
     354    cdf.setInputStream(cdfFile.getDownloadStream(0));
    350355    if (!cdf.readHeader())
    351356    {
     
    370375  {
    371376    if (celFile == null) throw new InvalidUseOfNullException("celFile");
     377    if (celFile.getLocation() != Location.PRIMARY)
     378    {
     379      throw new ItemNotFoundException("File data is not online for file '" +
     380          celFile.getName() + "'; location=" + celFile.getLocation());
     381    }
    372382    FusionCELData cel = new FusionCELData();
    373     cel.setFileName(File.getAbsolutePath(celFile.getData().getInternalName()).getPath());
    374     if (!cel.exists())
    375     {
    376       throw new InvalidDataException("File data not found on server: " + celFile.getPath());
    377     }
     383    cel.setFileName(celFile.getName());
     384    cel.setInputStream(celFile.getDownloadStream(0));
    378385    if (!cel.readHeader())
    379386    {
     
    413420   
    414421    if (hasProgress) progress.display(5, "Reading CDF file...");
    415     cdf.clear();
    416422    if (!cdf.read())
    417423    {
  • trunk/www/filemanager/upload/upload.jsp

    r3719 r3737  
    9393  boolean writeProtected = Values.getBoolean(upload.getParameter("write_protected"), false);
    9494  Boolean compress = null; // null == auto by MIME type
    95   if (upload.getParameter("compressed") != null)
     95  if (Values.getStringOrNull(upload.getParameter("compressed")) != null)
    9696  {
    9797    compress = Values.getBoolean(upload.getParameter("compressed"));
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