Changeset 2030


Ignore:
Timestamp:
Sep 30, 2013, 2:42:45 PM (8 years ago)
Author:
Nicklas Nordborg
Message:

References #499: Export sample sheet for flow cell

The exporter now uses the ReadString? stored as an annotation to the Flow cell instead of asking for it as a job parameter.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
3 edited

Legend:

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

    r2021 r2030  
    127127  </configuration>
    128128  <configuration pluginClassName="net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter">
    129     <configname>SCAN-B 2x50</configname>
    130     <description>Configuration for the default SCAN-B setup. Read string is Y54N1I6J1Y53N1.</description>
     129    <configname>SCAN-B</configname>
     130    <description>Configuration for the default SCAN-B setup.</description>
    131131    <parameter>
    132132      <name>SequencingCenter</name>
     
    135135      <class>java.lang.String</class>
    136136      <value>LuBMC</value>
    137     </parameter>
    138     <parameter>
    139       <name>ReadString</name>
    140       <label>Read string</label>
    141       <description>Pattern describing how each sequencing cycle is used.
    142 
    143 Y = the cycle should be used as part of an insert read
    144 N = the cycle should be skipped
    145 I = the cycle should be used as part of the index (barcode)
    146 J = the cycle is part of the index but should not be used in demultiplexing
    147 
    148 A number means repeat the preceding letter this many times.
    149 
    150 The person responsible for the library should enter the requested pattern of sequencing cycles here. Checked and corrected by the operator who loads the libraries on the flowcell.</description>
    151       <class>java.lang.String</class>
    152       <value>Y54N1I6J1Y53N1</value>
    153137    </parameter>
    154138    <parameter>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java

    r2021 r2030  
    164164        }
    165165
    166         String readString = (String)request.getParameterValue("ReadString");
    167         if (!isValidReadString(readString))
    168         {
    169           response.setError("Not a valid ReadString: '"+readString + "'", null);
    170           return;
    171         }
    172        
    173166        storeValue(configuration, request, ri.getParameter("Project"));
    174167        storeValue(configuration, request, ri.getParameter("SequencingCenter"));
    175         storeValue(configuration, request, ri.getParameter("ReadString"));
    176168        storeValue(configuration, request, ri.getParameter("Width"));
    177169        response.setDone("Plugin configuration complete");
     
    187179          return;
    188180        }       
    189         String readString = (String)request.getParameterValue("ReadString");
    190         if (!isValidReadString(readString))
    191         {
    192           response.setError("Not a valid ReadString: '"+readString + "'", null);
    193           return;
    194         }
    195181
    196182        storeValue(job, request, ri.getParameter("flowCell"));
    197183        storeValue(job, request, ri.getParameter("Project"));
    198184        storeValue(job, request, ri.getParameter("SequencingCenter"));
    199         storeValue(job, request, ri.getParameter("ReadString"));
    200185        storeValue(job, request, ri.getParameter("Width"));
    201186
     
    290275      parameters.add(getProjectParameter(dc));
    291276      parameters.add(getSequencingCenterParameter());
    292       parameters.add(getReadStringParameter());
    293277      parameters.add(getWidthParameter());
    294278    }
     
    343327        parameters.add(getProjectParameter(dc));
    344328        parameters.add(getSequencingCenterParameter());
    345         parameters.add(getReadStringParameter());
    346329        parameters.add(getWidthParameter());
    347330       
     
    406389    // Some info is global on the flow cell
    407390    info[0] = Annotationtype.FLOWCELL_ID.getAnnotationValue(dc, flowCell); // Flow cell ID
    408     info[2] = getParameter(parameters, "ReadString", DEFAULT_READ_STRING); // Read string
     391    info[2] = Annotationtype.READ_STRING.getAnnotationValue(dc, flowCell); // Read string
    409392    info[3] = getParameter(parameters, "Project", projectName); // Project name
    410393    info[9] = getParameter(parameters, "Width", DEFAULT_LIBRARY_WIDTH); // Width
     
    521504 
    522505  /**
    523     Check that the value is a sequence of Y, N, I, J followed by a number
    524   */
    525   private boolean isValidReadString(String value)
    526   {
    527     return value != null && value.matches("([YNIJ]\\d+)+");
    528   }
    529  
    530   /**
    531506    Convert to lower case and remove all characters not in [a-z0-9_]
    532507  */
     
    564539  }
    565540 
    566   private PluginParameter<String> getReadStringParameter()
    567   {
    568     PluginParameter<String> parameter = new PluginParameter<String>("ReadString", "Read string",
    569         "Pattern describing how each sequencing cycle is used.\n\n"+
    570         "Y = the cycle should be used as part of an insert read\n"+
    571         "N = the cycle should be skipped\n"+
    572         "I = the cycle should be used as part of the index (barcode)\n"+
    573         "J = the cycle is part of the index but should not be used in demultiplexing\n\n"+
    574         "A number means repeat the preceding letter this many times.\n\n"+
    575         "The person responsible for the library should enter the requested pattern of sequencing cycles here. Checked and corrected by the operator who loads the libraries on the flowcell.",
    576         new StringParameterType(255, DEFAULT_READ_STRING, true)
    577         );
    578     return parameter;
    579   }
    580  
     541
    581542  private PluginParameter<Integer> getWidthParameter()
    582543  {
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r2028 r2030  
    372372       
    373373        jsonChecks.add(checkPlugin(dc, FlowCellSampleSheetExporter.class, effectiveOptions, createIfMissing));
    374         jsonChecks.add(checkPluginConfiguration(dc, FlowCellSampleSheetExporter.class, "SCAN-B 2x50", effectiveOptions, createIfMissing));
     374        jsonChecks.add(checkPluginConfiguration(dc, FlowCellSampleSheetExporter.class, "SCAN-B", effectiveOptions, createIfMissing));
    375375
    376376        // Biomaterial lists
Note: See TracChangeset for help on using the changeset viewer.