Changeset 2265

Timestamp:

Mar 5, 2014, 11:45:07 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

 

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• META-INF/servlets.xml (modified) (2 diffs)
• resources/index.jsp (modified) (3 diffs)
• src/net/sf/basedb/reggie/dao/Library.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao/SequencingRun.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao/Subtype.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java (added)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/SoftwareServlet.java (added)

extensions/net.sf.basedb.reggie/trunk/META-INF/servlets.xml

@@ -54 +54 @@
   </servlet>
   <servlet>
+    <servlet-name>Software</servlet-name>
+    <servlet-class>net.sf.basedb.reggie.servlet.SoftwareServlet</servlet-class>
+  </servlet>
+  <servlet>
     <servlet-name>SampleReport</servlet-name>
     <servlet-class>net.sf.basedb.reggie.servlet.SampleReportServlet</servlet-class>
@@ -86 +90 @@
   </servlet>
   <servlet>
+    <servlet-name>DemuxMerge</servlet-name>
+    <servlet-class>net.sf.basedb.reggie.servlet.DemuxMergeServlet</servlet-class>
+  </servlet>
+  <servlet>
     <servlet-name>CaseSummary</servlet-name>
     <servlet-class>net.sf.basedb.reggie.servlet.CaseSummaryServlet</servlet-class>

extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

@@ -229 +229 @@
     else if (what == 'unconfirmed-sequencing-runs')
     {
-      url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountUncomfirmedSequencingRuns';
+      url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountUnconfirmedSequencingRuns';
+    }
+    else if (what == 'confirmed-sequencing-runs-for-demux')
+    {
+      url = 'DemuxMerge.servlet?ID=<%=ID%>&cmd=CountConfirmedSequencingRuns';
     }
     
@@ -404 +408 @@
       var count = error ? -1 : response.count;
       setCount('count.unconfirmed-sequencing-run', count, 'sequencing runs', msg);
+      startCounting('confirmed-sequencing-runs-for-demux');
+    }
+    else if (currentCount == 'confirmed-sequencing-runs-for-demux')
+    {
+      var msg = error || 'Number of confirmed sequencing runs waiting to be demuxed';
+      var count = error ? -1 : response.count;
+      setCount('count.confirmed-sequencing-run', count, 'sequencing runs', msg);
     }
     
@@ -704 +715 @@
               >Confirm sequencing completed</span> <span class="counter" id="count.unconfirmed-sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
             
-            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>"
-              >Start demux and merge</span> 
+            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>"
+              >Start demux and merge</span> <span class="counter" id="count.confirmed-sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
             <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/demux_end.jsp?ID=<%=ID%>"
               >Register demux and merge completed</span> 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Library.java

@@ -9 +9 @@
 import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.DerivedBioAssay;
 import net.sf.basedb.core.Extract;
+import net.sf.basedb.core.Include;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Tag;
@@ -146 +148 @@
     return jsonWell;
   }
+  
+  /**
+    Find the next name to give a "MergedSequences" child item. This assumes that
+    all child items are using the naming convention. foo.g, foo.g2, and
+    so on. NOTE! The first child item have no number!
+    @return The next unused name
+  */
+  public String getNextMergedSequencesName(DbControl dc)
+  {
+    Extract lib = getItem();
+    
+    ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
+    Subtype.MERGED_SEQUENCES.addFilter(dc, query);
+    query.setIncludes(Include.ALL);
+    query.restrict(Restrictions.eq(Hql.property("extract"), Hql.entity(lib)));
+    long count = query.count(dc);
+    return lib.getName() + ".g" + (count == 0 ? "" : count+1);
+  }
+
 }

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/SequencingRun.java

@@ -10 +10 @@
 import net.sf.basedb.core.DerivedBioAssay;
 import net.sf.basedb.core.Extract;
+import net.sf.basedb.core.Include;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Type;
@@ -169 +170 @@
     super.initJSON(json);
   }
+  
+  /**
+    Find the next name to give a "DemuxedSequences" child item. This assumes that
+    all child items are using the naming convention. foo.dx, foo.dx2, and
+    so on. NOTE! The first child item have no number!
+    @return The next unused name
+  */
+  public String getNextDemuxedSequencesName(DbControl dc)
+  {
+    DerivedBioAssay seqRun = getItem();
+    
+    ItemQuery<DerivedBioAssay> query = seqRun.getChildren();
+    Subtype.DEMUXED_SEQUENCES.addFilter(dc, query);
+    query.setIncludes(Include.ALL);
+    long count = query.count(dc);
+    return seqRun.getName() + ".dx" + (count == 0 ? "" : count+1);
+  }
 
 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

@@ -195 +195 @@
   */
   public static final Subtype SEQUENCING_RUN = new Subtype("SequencingRun", Item.DERIVEDBIOASSAY, false);
+
+  /**
+    The definition of the "DemuxedSequences" derived bioassay subtype.
+    @since 2.16
+  */
+  public static final Subtype DEMUXED_SEQUENCES = new Subtype("DemuxedSequences", Item.DERIVEDBIOASSAY, false);
+
+  /**
+    The definition of the "MergedSequences" derived bioassay subtype.
+    @since 2.16
+  */
+  public static final Subtype MERGED_SEQUENCES = new Subtype("MergedSequences", Item.DERIVEDBIOASSAY, false);
   
   /**
@@ -257 +269 @@
   public static final Subtype SEQUENCING_PROTOCOL = new Subtype("Sequencing", Item.PROTOCOL, false);
 
-  
+  /**
+    The definition of the "Demuxing" protocol subtype.
+    @since 2.16
+  */
+  public static final Subtype DEMUX_PROTOCOL = new Subtype("Demuxing", Item.PROTOCOL, false);
+
+  /**
+    The definition of the "Demuxing" software subtype.
+    @since 2.16
+  */
+  public static final Subtype DEMUX_SOFTWARE = new Subtype("Demuxing", Item.SOFTWARE, false);
+
+  /**
+    The definition of the "Merging" protocol subtype.
+    @since 2.16
+  */
+  public static final Subtype MERGE_PROTOCOL = new Subtype("Merging", Item.PROTOCOL, false);
+  
+  /**
+    The definition of the "Merging" software subtype.
+    @since 2.16
+  */
+  public static final Subtype MERGE_SOFTWARE = new Subtype("Merging", Item.SOFTWARE, false);
+      
   /**
     File subtype for BioAnalyzer PDF reports.

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java

@@ -654 +654 @@
   }
   
-  private String sequencingCycles2ReadString(String sequencingCycles)
+  public static String sequencingCycles2ReadString(String sequencingCycles)
   {
     StringBuilder readString = new StringBuilder();

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -202 +202 @@
         jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_PROTOCOL, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_RUN, createIfMissing, Subtype.FLOW_CELL, Subtype.SEQUENCER, Subtype.SEQUENCING_PROTOCOL));
+        jsonChecks.add(checkSubtype(dc, Subtype.DEMUX_PROTOCOL, createIfMissing));
+        jsonChecks.add(checkSubtype(dc, Subtype.DEMUX_SOFTWARE, createIfMissing));
+        jsonChecks.add(checkSubtype(dc, Subtype.DEMUXED_SEQUENCES, createIfMissing, Subtype.SEQUENCING_RUN, Subtype.DEMUX_PROTOCOL, Subtype.DEMUX_SOFTWARE));
+        jsonChecks.add(checkSubtype(dc, Subtype.MERGE_PROTOCOL, createIfMissing));
+        jsonChecks.add(checkSubtype(dc, Subtype.MERGE_SOFTWARE, createIfMissing));
+        jsonChecks.add(checkSubtype(dc, Subtype.MERGED_SEQUENCES, createIfMissing, Subtype.DEMUXED_SEQUENCES, Subtype.MERGE_PROTOCOL, Subtype.MERGE_SOFTWARE));
 
         // Plate geometries

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java

@@ -136 +136 @@
         json.put("sequencingRuns", jsonRuns);
       }
-      else if ("CountUncomfirmedSequencingRuns".equals(cmd))
+      else if ("CountUnconfirmedSequencingRuns".equals(cmd))
       {
         dc = sc.newDbControl();