Changeset 2265


Ignore:
Timestamp:
Mar 5, 2014, 11:45:07 AM (9 years ago)
Author:
Nicklas Nordborg
Message:
 
Location:
extensions/net.sf.basedb.reggie/trunk
Files:
2 added
8 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/META-INF/servlets.xml

    r2197 r2265  
    5454  </servlet>
    5555  <servlet>
     56    <servlet-name>Software</servlet-name>
     57    <servlet-class>net.sf.basedb.reggie.servlet.SoftwareServlet</servlet-class>
     58  </servlet>
     59  <servlet>
    5660    <servlet-name>SampleReport</servlet-name>
    5761    <servlet-class>net.sf.basedb.reggie.servlet.SampleReportServlet</servlet-class>
     
    8690  </servlet>
    8791  <servlet>
     92    <servlet-name>DemuxMerge</servlet-name>
     93    <servlet-class>net.sf.basedb.reggie.servlet.DemuxMergeServlet</servlet-class>
     94  </servlet>
     95  <servlet>
    8896    <servlet-name>CaseSummary</servlet-name>
    8997    <servlet-class>net.sf.basedb.reggie.servlet.CaseSummaryServlet</servlet-class>
  • extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

    r2240 r2265  
    229229    else if (what == 'unconfirmed-sequencing-runs')
    230230    {
    231       url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountUncomfirmedSequencingRuns';
     231      url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountUnconfirmedSequencingRuns';
     232    }
     233    else if (what == 'confirmed-sequencing-runs-for-demux')
     234    {
     235      url = 'DemuxMerge.servlet?ID=<%=ID%>&cmd=CountConfirmedSequencingRuns';
    232236    }
    233237   
     
    404408      var count = error ? -1 : response.count;
    405409      setCount('count.unconfirmed-sequencing-run', count, 'sequencing runs', msg);
     410      startCounting('confirmed-sequencing-runs-for-demux');
     411    }
     412    else if (currentCount == 'confirmed-sequencing-runs-for-demux')
     413    {
     414      var msg = error || 'Number of confirmed sequencing runs waiting to be demuxed';
     415      var count = error ? -1 : response.count;
     416      setCount('count.confirmed-sequencing-run', count, 'sequencing runs', msg);
    406417    }
    407418   
     
    704715              >Confirm sequencing completed</span> <span class="counter" id="count.unconfirmed-sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
    705716           
    706             <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>"
    707               >Start demux and merge</span>
     717            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>"
     718              >Start demux and merge</span> <span class="counter" id="count.confirmed-sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
    708719            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/demux_end.jsp?ID=<%=ID%>"
    709720              >Register demux and merge completed</span>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Library.java

    r2134 r2265  
    99import net.sf.basedb.core.BioWell;
    1010import net.sf.basedb.core.DbControl;
     11import net.sf.basedb.core.DerivedBioAssay;
    1112import net.sf.basedb.core.Extract;
     13import net.sf.basedb.core.Include;
    1214import net.sf.basedb.core.ItemQuery;
    1315import net.sf.basedb.core.Tag;
     
    146148    return jsonWell;
    147149  }
     150 
     151  /**
     152    Find the next name to give a "MergedSequences" child item. This assumes that
     153    all child items are using the naming convention. foo.g, foo.g2, and
     154    so on. NOTE! The first child item have no number!
     155    @return The next unused name
     156  */
     157  public String getNextMergedSequencesName(DbControl dc)
     158  {
     159    Extract lib = getItem();
     160   
     161    ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
     162    Subtype.MERGED_SEQUENCES.addFilter(dc, query);
     163    query.setIncludes(Include.ALL);
     164    query.restrict(Restrictions.eq(Hql.property("extract"), Hql.entity(lib)));
     165    long count = query.count(dc);
     166    return lib.getName() + ".g" + (count == 0 ? "" : count+1);
     167  }
     168
    148169}
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/SequencingRun.java

    r2232 r2265  
    1010import net.sf.basedb.core.DerivedBioAssay;
    1111import net.sf.basedb.core.Extract;
     12import net.sf.basedb.core.Include;
    1213import net.sf.basedb.core.ItemQuery;
    1314import net.sf.basedb.core.Type;
     
    169170    super.initJSON(json);
    170171  }
     172 
     173  /**
     174    Find the next name to give a "DemuxedSequences" child item. This assumes that
     175    all child items are using the naming convention. foo.dx, foo.dx2, and
     176    so on. NOTE! The first child item have no number!
     177    @return The next unused name
     178  */
     179  public String getNextDemuxedSequencesName(DbControl dc)
     180  {
     181    DerivedBioAssay seqRun = getItem();
     182   
     183    ItemQuery<DerivedBioAssay> query = seqRun.getChildren();
     184    Subtype.DEMUXED_SEQUENCES.addFilter(dc, query);
     185    query.setIncludes(Include.ALL);
     186    long count = query.count(dc);
     187    return seqRun.getName() + ".dx" + (count == 0 ? "" : count+1);
     188  }
    171189
    172190
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

    r2109 r2265  
    195195  */
    196196  public static final Subtype SEQUENCING_RUN = new Subtype("SequencingRun", Item.DERIVEDBIOASSAY, false);
     197
     198  /**
     199    The definition of the "DemuxedSequences" derived bioassay subtype.
     200    @since 2.16
     201  */
     202  public static final Subtype DEMUXED_SEQUENCES = new Subtype("DemuxedSequences", Item.DERIVEDBIOASSAY, false);
     203
     204  /**
     205    The definition of the "MergedSequences" derived bioassay subtype.
     206    @since 2.16
     207  */
     208  public static final Subtype MERGED_SEQUENCES = new Subtype("MergedSequences", Item.DERIVEDBIOASSAY, false);
    197209 
    198210  /**
     
    257269  public static final Subtype SEQUENCING_PROTOCOL = new Subtype("Sequencing", Item.PROTOCOL, false);
    258270
    259  
     271  /**
     272    The definition of the "Demuxing" protocol subtype.
     273    @since 2.16
     274  */
     275  public static final Subtype DEMUX_PROTOCOL = new Subtype("Demuxing", Item.PROTOCOL, false);
     276
     277  /**
     278    The definition of the "Demuxing" software subtype.
     279    @since 2.16
     280  */
     281  public static final Subtype DEMUX_SOFTWARE = new Subtype("Demuxing", Item.SOFTWARE, false);
     282
     283  /**
     284    The definition of the "Merging" protocol subtype.
     285    @since 2.16
     286  */
     287  public static final Subtype MERGE_PROTOCOL = new Subtype("Merging", Item.PROTOCOL, false);
     288 
     289  /**
     290    The definition of the "Merging" software subtype.
     291    @since 2.16
     292  */
     293  public static final Subtype MERGE_SOFTWARE = new Subtype("Merging", Item.SOFTWARE, false);
     294     
    260295  /**
    261296    File subtype for BioAnalyzer PDF reports.
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java

    r2226 r2265  
    654654  }
    655655 
    656   private String sequencingCycles2ReadString(String sequencingCycles)
     656  public static String sequencingCycles2ReadString(String sequencingCycles)
    657657  {
    658658    StringBuilder readString = new StringBuilder();
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r2251 r2265  
    202202        jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_PROTOCOL, createIfMissing));
    203203        jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_RUN, createIfMissing, Subtype.FLOW_CELL, Subtype.SEQUENCER, Subtype.SEQUENCING_PROTOCOL));
     204        jsonChecks.add(checkSubtype(dc, Subtype.DEMUX_PROTOCOL, createIfMissing));
     205        jsonChecks.add(checkSubtype(dc, Subtype.DEMUX_SOFTWARE, createIfMissing));
     206        jsonChecks.add(checkSubtype(dc, Subtype.DEMUXED_SEQUENCES, createIfMissing, Subtype.SEQUENCING_RUN, Subtype.DEMUX_PROTOCOL, Subtype.DEMUX_SOFTWARE));
     207        jsonChecks.add(checkSubtype(dc, Subtype.MERGE_PROTOCOL, createIfMissing));
     208        jsonChecks.add(checkSubtype(dc, Subtype.MERGE_SOFTWARE, createIfMissing));
     209        jsonChecks.add(checkSubtype(dc, Subtype.MERGED_SEQUENCES, createIfMissing, Subtype.DEMUXED_SEQUENCES, Subtype.MERGE_PROTOCOL, Subtype.MERGE_SOFTWARE));
    204210
    205211        // Plate geometries
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java

    r2239 r2265  
    136136        json.put("sequencingRuns", jsonRuns);
    137137      }
    138       else if ("CountUncomfirmedSequencingRuns".equals(cmd))
     138      else if ("CountUnconfirmedSequencingRuns".equals(cmd))
    139139      {
    140140        dc = sc.newDbControl();
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