Changeset 1293


Ignore:
Timestamp:
Feb 24, 2011, 12:40:24 PM (11 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #278: Plug-in should suggest better job names

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

Legend:

Unmodified
Added
Removed
  • plugins/base2/net.sf.basedb.illumina/trunk/COMPILE

    r1189 r1293  
    12122. Java 1.6
    1313
    14 3. BASE 2.15.0
     143. BASE 2.17.0
    1515
    1616---------
  • plugins/base2/net.sf.basedb.illumina/trunk/INSTALL

    r1236 r1293  
    44== Requirements ==
    55
    6  1. BASE 2.16.0 or later.
     6 1. BASE 2.17.0 or later.
    77
    88
  • plugins/base2/net.sf.basedb.illumina/trunk/META-INF/base-plugins.xml

    r1226 r1293  
    44<plugins jarname="%%plugins.jar%%">
    55  <pluginclass classname="net.sf.basedb.illumina.install.Install">
    6     <minbaseversion>2.16</minbaseversion>
     6    <minbaseversion>2.17</minbaseversion>
    77    <hasconfigurations/>
    88  </pluginclass>
    99  <pluginclass classname="net.sf.basedb.illumina.plugins.BackgroundCorrection">
    10     <minbaseversion>2.16</minbaseversion>
     10    <minbaseversion>2.17</minbaseversion>
    1111    <hasconfigurations/>
    1212  </pluginclass>
    1313  <pluginclass classname="net.sf.basedb.illumina.plugins.BeadSummaryImporter">
    14     <minbaseversion>2.16</minbaseversion>
     14    <minbaseversion>2.17</minbaseversion>
    1515    <hasconfigurations/>
    1616  </pluginclass>
    1717  <pluginclass classname="net.sf.basedb.illumina.plugins.BgxFeatureImporter">
    18     <minbaseversion>2.16</minbaseversion>
     18    <minbaseversion>2.17</minbaseversion>
    1919    <hasconfigurations>yes</hasconfigurations>
    2020  </pluginclass>
    2121  <pluginclass classname="net.sf.basedb.illumina.plugins.BgxReporterImporter">
    22     <minbaseversion>2.16</minbaseversion>
     22    <minbaseversion>2.17</minbaseversion>
    2323    <hasconfigurations>yes</hasconfigurations>
    2424  </pluginclass>
    2525  <pluginclass classname="net.sf.basedb.illumina.plugins.DetectionPValue">
    26     <minbaseversion>2.16</minbaseversion>
     26    <minbaseversion>2.17</minbaseversion>
    2727    <hasconfigurations/>
    2828  </pluginclass>
    2929  <pluginclass classname="net.sf.basedb.illumina.plugins.SnpIntensityCalculator">
    30     <minbaseversion>2.16</minbaseversion>
     30    <minbaseversion>2.17</minbaseversion>
    3131    <hasconfigurations/>
    3232  </pluginclass>
    3333  <pluginclass classname="net.sf.basedb.illumina.plugins.SnpRawDataImporter">
    34     <minbaseversion>2.16</minbaseversion>
     34    <minbaseversion>2.17</minbaseversion>
    3535    <hasconfigurations/>
    3636  </pluginclass>
    3737  <pluginclass classname="net.sf.basedb.illumina.plugins.SnpReporterImporter">
    38     <minbaseversion>2.16</minbaseversion>
     38    <minbaseversion>2.17</minbaseversion>
    3939    <hasconfigurations>yes</hasconfigurations>
    4040  </pluginclass>
  • plugins/base2/net.sf.basedb.illumina/trunk/README

    r1226 r1293  
    2525== Requirements ==
    2626
    27  1. BASE 2.16.0 or later.
     27 1. BASE 2.17.0 or later.
    2828 
    2929For expression experiments:
  • plugins/base2/net.sf.basedb.illumina/trunk/build.xml

    r1276 r1293  
    1515  <property name="name" value="illumina-plugins" />
    1616  <property name="version" value="1.7pre" />
    17   <property name="minbaseversion" value="2.16"
     17  <property name="minbaseversion" value="2.17"
    1818    description="Minimal BASE version required by the plug-ins" />
    1919  <property name="src" location="src" description="Location of source files" />
     
    2626  <property name="javac.encoding" value="UTF-8" />
    2727  <property name="depend.jars"
    28     value="http://base2.thep.lu.se/base/jars/2.16.0"
     28    value="http://base2.thep.lu.se/base/jars/2.17.0"
    2929    description="The location of the BASE core JARs that we depend on"
    3030  />
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BackgroundCorrection.java

    r1258 r1293  
    266266        // Estimate execution time
    267267        Job.ExecutionTime execTime = Job.ExecutionTime.SHORT;
     268        String sourceName = "";
    268269        DbControl dc = sc.newDbControl();
    269270        try {
    270271          BioAssaySet source = getSourceBioAssaySet(dc);
     272          sourceName = source.getName();
    271273          int nofAssays = source.getBioAssays().list(dc).size();
    272274          if (nofAssays>10 && nofAssays<30)
     
    279281            dc.close();
    280282        }
     283        response.setSuggestedJobName("Background correction on bioassay set '" + sourceName + "'");
    281284        response.setDone("Job configuration complete", execTime);
    282285      }
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BeadSummaryImporter.java

    r1258 r1293  
    407407        storeValue(job, request, ri.getParameter(Parameters.NUMBER_OUT_OF_RANGE_ERROR));
    408408       
     409        if (context.getItem() == Item.RAWBIOASSAY)
     410        {
     411          RawBioAssay rba = (RawBioAssay)job.getValue("rawBioAssay");
     412          File file = (File)job.getValue("file");
     413          response.setSuggestedJobName("Import bead summary data to raw bioassay '" + rba.getName() + "'");
     414        }
     415        else
     416        {
     417          Experiment exp = (Experiment)job.getValue("experiment");
     418          response.setSuggestedJobName("Import bead summary data to experiment '" + exp.getName() + "'");
     419        }
    409420        response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
    410421        // TODO - maybe check file size to make a better estimate
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BgxFeatureImporter.java

    r1146 r1293  
    2323package net.sf.basedb.illumina.plugins;
    2424
     25import net.sf.basedb.core.ArrayDesign;
    2526import net.sf.basedb.core.BaseException;
    2627import net.sf.basedb.core.FeatureIdentificationMethod;
     28import net.sf.basedb.core.File;
    2729import net.sf.basedb.core.InvalidDataException;
    2830import net.sf.basedb.core.Job;
     
    3436import net.sf.basedb.core.plugin.About;
    3537import net.sf.basedb.core.plugin.AboutImpl;
     38import net.sf.basedb.core.plugin.GuiContext;
    3639import net.sf.basedb.core.plugin.InteractivePlugin;
    3740import net.sf.basedb.core.plugin.ParameterValues;
     41import net.sf.basedb.core.plugin.Request;
     42import net.sf.basedb.core.plugin.Response;
    3843import net.sf.basedb.illumina.Illumina;
    3944import net.sf.basedb.plugins.ReporterMapFlatFileImporter;
     
    147152  }
    148153 
     154  @Override
     155  public void configure(GuiContext context, Request request, Response response)
     156  {
     157    super.configure(context, request, response);
     158    String command = request.getCommand();
     159    if (command.equals(Request.COMMAND_CONFIGURE_JOB))
     160    {
     161      ArrayDesign design = (ArrayDesign)job.getValue("arrayDesign");
     162      File file = (File)job.getValue("file");
     163      response.setSuggestedJobName("Import features for array design '" + design.getName() +
     164          "' from BGX file '" + file.getName() + "'");
     165    }
     166  }
     167
    149168  /**
    150169    Get the number of byte from the compressed file.
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java

    r1258 r1293  
    244244        // Estimate execution time
    245245        Job.ExecutionTime execTime = Job.ExecutionTime.SHORT;
     246        String sourceName = "";
    246247        DbControl dc = sc.newDbControl();
    247248        try
    248249        {
    249250          BioAssaySet source = getSourceBioAssaySet(dc);
     251          sourceName = source.getName();
    250252          int nofAssays = source.getBioAssays().list(dc).size();
    251253          if (nofAssays>10 && nofAssays<30)
     
    262264          if (dc != null) dc.close();
    263265        }
     266        response.setSuggestedJobName("P-value calculation on bioassay set '" + sourceName + "'");
    264267        response.setDone("Job configuration complete", execTime);
    265268      }
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/SnpIntensityCalculator.java

    r1258 r1293  
    245245      }
    246246      spotBatcher.close();     
    247       if (progress != null) progress.display(100, "Committing transactio...");
     247      if (progress != null) progress.display(100, "Committing transaction...");
    248248      dc.commit();
    249249      if (progress != null) progress.display(100, "Done");
     
    365365
    366366        Job.ExecutionTime execTime = Job.ExecutionTime.MEDIUM; 
     367       
     368        response.setSuggestedJobName("Create root bioassay set in experiment '" + experiment.getName() + "'");
     369
    367370        response.setDone("Job configuration complete", execTime);
    368371      }
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/SnpRawDataImporter.java

    r1204 r1293  
    269269        storeValue(job, request, defaultErrorParameter);
    270270       
     271        File file = (File)job.getValue("file");
     272        response.setSuggestedJobName("Create Illumina SNP raw bioassays from file '" + file.getName() + "'");
    271273        response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
    272274      }
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