Changeset 2075


Ignore:
Timestamp:
Oct 16, 2013, 1:42:55 PM (9 years ago)
Author:
Nicklas Nordborg
Message:

References #499: Export sample sheet for flow cell

Removed hardcoded concentration of "12pM" and made it a job/configuration parameter instead.

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

Legend:

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

    r2030 r2075  
    150150      <value>100</value>
    151151    </parameter>
     152    <parameter>
     153      <name>Concentration</name>
     154      <label>Concentration</label>
     155      <description>The final molarity of the pool as it is being clustered.</description>
     156      <class>java.lang.String</class>
     157      <value>12pM</value>
     158    </parameter>
    152159  </configuration>
    153160</configfile>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java

    r2030 r2075  
    7171 
    7272  public static final String DEFAULT_SEQUENCING_CENTER = "LuOnk";
     73
     74  public static final String DEFAULT_CONCENTRATION = "12pM";
    7375 
    7476  public static final int DEFAULT_LIBRARY_WIDTH = 100;
     
    167169        storeValue(configuration, request, ri.getParameter("SequencingCenter"));
    168170        storeValue(configuration, request, ri.getParameter("Width"));
     171        storeValue(configuration, request, ri.getParameter("Concentration"));
    169172        response.setDone("Plugin configuration complete");
    170173       
     
    184187        storeValue(job, request, ri.getParameter("SequencingCenter"));
    185188        storeValue(job, request, ri.getParameter("Width"));
     189        storeValue(job, request, ri.getParameter("Concentration"));
    186190
    187191        if (request.getParameterValue(SAVE_AS) == null)
     
    276280      parameters.add(getSequencingCenterParameter());
    277281      parameters.add(getWidthParameter());
     282      parameters.add(getConcentrationParameter());
    278283    }
    279284    finally
     
    328333        parameters.add(getSequencingCenterParameter());
    329334        parameters.add(getWidthParameter());
     335        parameters.add(getConcentrationParameter());
    330336       
    331337      }
     
    394400    info[13] = "N"; // Control
    395401    info[14] = getParameter(parameters, "Operator", operator); // Operator
    396     info[15] = "12pM"; // Concentration
     402    info[15] = getParameter(parameters, "Concentration", DEFAULT_CONCENTRATION); // Concentration
    397403    info[17] = getParameter(parameters, "SequencingCenter", DEFAULT_SEQUENCING_CENTER); // Sequencing center
    398404    info[18] = flowCell.getName();  // Description
     
    548554    return parameter;
    549555  }
     556 
     557  private PluginParameter<String> getConcentrationParameter()
     558  {
     559    PluginParameter<String> parameter = new PluginParameter<String>("Concentration", "Concentration",
     560        "The final molarity of the pool as it is being clustered.",
     561        new StringParameterType(255, DEFAULT_CONCENTRATION, true)
     562        );
     563    return parameter;
     564  }
    550565}
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