Changeset 1226


Ignore:
Timestamp:
May 24, 2010, 1:45:23 PM (13 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #265: Investigate and fix issues with external files introduced in BASE 2.16

There was a check that BGX and SNP files had location=Location.PRIMARY and throwed an exception if not. It now checks isDownloadable() instead. There was also a progress reporting issue in the BeadSummaryImporter? for files with unknown size.

Location:
plugins/base2/net.sf.basedb.illumina/trunk
Files:
8 edited

Legend:

Unmodified
Added
Removed

  • plugins/base2/net.sf.basedb.illumina/trunk/INSTALL

    r1189 r1226  
    2828== Requirements ==
    2929
    30  1. BASE 2.15.0 or later.
     30 1. BASE 2.16.0 or later.
    3131
    3232

  • plugins/base2/net.sf.basedb.illumina/trunk/META-INF/base-plugins.xml

    r1189 r1226  
    44<plugins jarname="%%plugins.jar%%">
    55  <pluginclass classname="net.sf.basedb.illumina.install.Install">
    6     <minbaseversion>2.15</minbaseversion>
     6    <minbaseversion>2.16</minbaseversion>
    77    <hasconfigurations/>
    88  </pluginclass>
    99  <pluginclass classname="net.sf.basedb.illumina.plugins.BackgroundCorrection">
    10     <minbaseversion>2.15</minbaseversion>
     10    <minbaseversion>2.16</minbaseversion>
    1111    <hasconfigurations/>
    1212  </pluginclass>
    1313  <pluginclass classname="net.sf.basedb.illumina.plugins.BeadSummaryImporter">
    14     <minbaseversion>2.15</minbaseversion>
     14    <minbaseversion>2.16</minbaseversion>
    1515    <hasconfigurations/>
    1616  </pluginclass>
    1717  <pluginclass classname="net.sf.basedb.illumina.plugins.BgxFeatureImporter">
    18     <minbaseversion>2.15</minbaseversion>
     18    <minbaseversion>2.16</minbaseversion>
    1919    <hasconfigurations>yes</hasconfigurations>
    2020  </pluginclass>
    2121  <pluginclass classname="net.sf.basedb.illumina.plugins.BgxReporterImporter">
    22     <minbaseversion>2.15</minbaseversion>
     22    <minbaseversion>2.16</minbaseversion>
    2323    <hasconfigurations>yes</hasconfigurations>
    2424  </pluginclass>
    2525  <pluginclass classname="net.sf.basedb.illumina.plugins.DetectionPValue">
    26     <minbaseversion>2.15</minbaseversion>
     26    <minbaseversion>2.16</minbaseversion>
    2727    <hasconfigurations/>
    2828  </pluginclass>
    2929  <pluginclass classname="net.sf.basedb.illumina.plugins.SnpIntensityCalculator">
    30     <minbaseversion>2.15</minbaseversion>
     30    <minbaseversion>2.16</minbaseversion>
    3131    <hasconfigurations/>
    3232  </pluginclass>
    3333  <pluginclass classname="net.sf.basedb.illumina.plugins.SnpRawDataImporter">
    34     <minbaseversion>2.15</minbaseversion>
     34    <minbaseversion>2.16</minbaseversion>
    3535    <hasconfigurations/>
    3636  </pluginclass>
    3737  <pluginclass classname="net.sf.basedb.illumina.plugins.SnpReporterImporter">
    38     <minbaseversion>2.15</minbaseversion>
     38    <minbaseversion>2.16</minbaseversion>
    3939    <hasconfigurations>yes</hasconfigurations>
    4040  </pluginclass>

  • plugins/base2/net.sf.basedb.illumina/trunk/README

    r1196 r1226  
    2525== Requirements ==
    2626
    27  1. BASE 2.15.0 or later.
     27 1. BASE 2.16.0 or later.
    2828 
    2929For expression experiments:

  • plugins/base2/net.sf.basedb.illumina/trunk/build.xml

    r1223 r1226  
    2424  <property name="javac.encoding" value="UTF-8" />
    2525  <property name="depend.jars"
    26     value="http://base2.thep.lu.se/base/jars/2.15.0"
     26    value="http://base2.thep.lu.se/base/jars/2.16.0"
    2727    description="The location of the BASE core JARs that we depend on"
    2828  />

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/filehandler/BgxFileHandler.java

    r941 r1226  
    3030import net.sf.basedb.core.InvalidRelationException;
    3131import net.sf.basedb.core.InvalidUseOfNullException;
    32 import net.sf.basedb.core.Location;
    3332import net.sf.basedb.core.filehandler.AbstractDataFileHandler;
    3433import net.sf.basedb.core.filehandler.DataFileMetadataReader;
    … …  
    161160      throw new InvalidUseOfNullException("bgxFile");
    162161    }
    163     if (bgxFile.getLocation() != Location.PRIMARY)
    164     {
    165       throw new InvalidUseOfNullException("Data is not online for file " +
    166           bgxFile.getName() + " location = '" + bgxFile.getLocation() + "'");
     162    if (!bgxFile.getLocation().isDownloadable())
     163    {
     164      throw new InvalidDataException("Can't download file data for file '" +
     165          bgxFile.getName() + "'; location=" + bgxFile.getLocation());
    167166    }
    168167    InputStream in = null;

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/filehandler/SnpCvsFileHandler.java

    r941 r1226  
    3030import net.sf.basedb.core.InvalidRelationException;
    3131import net.sf.basedb.core.InvalidUseOfNullException;
    32 import net.sf.basedb.core.Location;
    3332import net.sf.basedb.core.filehandler.AbstractDataFileHandler;
    3433import net.sf.basedb.core.filehandler.DataFileMetadataReader;
    … …  
    135134      throw new InvalidUseOfNullException("manifestFile");
    136135    }
    137     if (manifestFile.getLocation() != Location.PRIMARY)
    138     {
    139       throw new InvalidUseOfNullException("Data is not online for file " +
    140           manifestFile.getName() + " location = '" + manifestFile.getLocation() + "'");
     136    if (!manifestFile.getLocation().isDownloadable())
     137    {
     138      throw new InvalidDataException("Can't download file data for file '" +
     139          manifestFile.getName() + "'; location=" + manifestFile.getLocation());
    141140    }
    142141    InputStream in = manifestFile.getDownloadStream(0);

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BeadSummaryImporter.java

    r1149 r1226  
    665665    for (File file : files)
    666666    {
    667       totalFileSize += file.getSize();
     667      long fileSize = file.getSize();
     668      if (fileSize == -1) totalFileSize = -1;
     669      if (totalFileSize != -1) totalFileSize += file.getSize();
    668670    }
    669671    // 0-40% = file parsing; 40-60% = batcher preparation; 60-100% = data insertion
    670     double factor = 40.0 / totalFileSize;
     672    double factor = totalFileSize == -1 ? 0 : 40.0 / totalFileSize;
    671673   
    672674    // For the final status report
    … …  
    704706            String message = rba.getName() + " - parsing file " + file.getName() +
    705707              "; " + lines + " lines done.";
    706             int percent = (int)(factor * (offsetFileSize + ffp.getParsedBytes()));
     708            int percent = totalFileSize == -1 ?
     709              -1 : (int)(factor * (offsetFileSize + ffp.getParsedBytes()));
    707710            progress.display(percent, message);
    708711          }

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/SnpIntensityCalculator.java

    r941 r1226  
    203203      for (RawBioAssay rba : sources)
    204204      {
    205         dc.reattachItem(rba);
     205        dc.reattachItem(rba, false);
    206206        totalProgressTicks += rba.getNumFileSpots();
    207207      }
Note: See TracChangeset for help on using the changeset viewer.