Changeset 2266


Ignore:
Timestamp:
Mar 5, 2014, 11:48:50 AM (9 years ago)
Author:
Nicklas Nordborg
Message:

Revert change from [2265] which was checked in by accident.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
2 deleted
8 edited

Legend:

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

    r2265 r2266  
    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>
    6056    <servlet-name>SampleReport</servlet-name>
    6157    <servlet-class>net.sf.basedb.reggie.servlet.SampleReportServlet</servlet-class>
     
    9086  </servlet>
    9187  <servlet>
    92     <servlet-name>DemuxMerge</servlet-name>
    93     <servlet-class>net.sf.basedb.reggie.servlet.DemuxMergeServlet</servlet-class>
    94   </servlet>
    95   <servlet>
    9688    <servlet-name>CaseSummary</servlet-name>
    9789    <servlet-class>net.sf.basedb.reggie.servlet.CaseSummaryServlet</servlet-class>
  • extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

    r2265 r2266  
    229229    else if (what == 'unconfirmed-sequencing-runs')
    230230    {
    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';
     231      url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountUncomfirmedSequencingRuns';
    236232    }
    237233   
     
    408404      var count = error ? -1 : response.count;
    409405      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);
    417406    }
    418407   
     
    715704              >Confirm sequencing completed</span> <span class="counter" id="count.unconfirmed-sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
    716705           
    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>
     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>
    719708            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/demux_end.jsp?ID=<%=ID%>"
    720709              >Register demux and merge completed</span>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Library.java

    r2265 r2266  
    99import net.sf.basedb.core.BioWell;
    1010import net.sf.basedb.core.DbControl;
    11 import net.sf.basedb.core.DerivedBioAssay;
    1211import net.sf.basedb.core.Extract;
    13 import net.sf.basedb.core.Include;
    1412import net.sf.basedb.core.ItemQuery;
    1513import net.sf.basedb.core.Tag;
     
    148146    return jsonWell;
    149147  }
    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 
    169148}
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/SequencingRun.java

    r2265 r2266  
    1010import net.sf.basedb.core.DerivedBioAssay;
    1111import net.sf.basedb.core.Extract;
    12 import net.sf.basedb.core.Include;
    1312import net.sf.basedb.core.ItemQuery;
    1413import net.sf.basedb.core.Type;
     
    170169    super.initJSON(json);
    171170  }
    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   }
    189171
    190172
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

    r2265 r2266  
    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);
    209197 
    210198  /**
     
    269257  public static final Subtype SEQUENCING_PROTOCOL = new Subtype("Sequencing", Item.PROTOCOL, false);
    270258
    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      
     259 
    295260  /**
    296261    File subtype for BioAnalyzer PDF reports.
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java

    r2265 r2266  
    654654  }
    655655 
    656   public static String sequencingCycles2ReadString(String sequencingCycles)
     656  private String sequencingCycles2ReadString(String sequencingCycles)
    657657  {
    658658    StringBuilder readString = new StringBuilder();
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r2265 r2266  
    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));
    210204
    211205        // Plate geometries
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java

    r2265 r2266  
    136136        json.put("sequencingRuns", jsonRuns);
    137137      }
    138       else if ("CountUnconfirmedSequencingRuns".equals(cmd))
     138      else if ("CountUncomfirmedSequencingRuns".equals(cmd))
    139139      {
    140140        dc = sc.newDbControl();
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