Changeset 5927


Ignore:
Timestamp:
Apr 29, 2020, 9:39:49 AM (5 weeks ago)
Author:
Nicklas Nordborg
Message:

References #1239: Include Single Sample Predictor models in the StringTie? pipeline

Added possibility to include a description for a model.

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

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

    r5920 r5927  
    8686      <models>
    8787        <!-- Each entry should be a filename of the *.RData object representing the model. -->
    88         <!-- Each entry should have a 'name' and an associated 'annotation-type' -->
     88        <!-- Each entry should have a 'name' and an associated 'annotation-type'. -->
     89        <!-- A 'description' is optional. -->
    8990        <!-- The annotation type need to be created manually. -->
    90         <model name="Subtype" annotation-type="SSP_Subtype">Training_Run19081Genes_noNorm_SSP.subtypeMost.Fcc15_5x5foldCV.num.rules.50_24.selRules.AIMS.GS.RData</model>
     91        <model name="Subtype" annotation-type="SSP_Subtype" description="">
     92          Training_Run19081Genes_noNorm_SSP.subtypeMost.Fcc15_5x5foldCV.num.rules.50_24.selRules.AIMS.GS.RData
     93        </model>
    9194      </models>
    9295    </ssp>
  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/ssp_start.js

    r5924 r5927  
    240240    {
    241241      var model = models[mNo];
     242      html += '<tr class="align-top">';
     243      if (mNo == 0)
     244      {
     245        html += '<td class="prompt" rowspan="'+models.length+'">Models</td>';
     246      }
     247       
     248      html += '<td class="input">';
    242249      html += '<label><input type="checkbox" checked name="model.'+mNo+'">'+Strings.encodeTags(model.name)+'</label>';
    243       html += '<br>';
     250     
     251      if (mNo == 0)
     252      {
     253        html += '<td class="status" id="models.status" rowspan="'+models.length+'"></td>';
     254      }
     255      html += '<td class="help">';
     256      if (mNo == 0)
     257      {
     258        html += '<span id="models.message" class="message"></span>';
     259      }
     260      html += Strings.encodeTags(model.description) + '</td>';
     261      html += '</tr>';
    244262    }
    245263    Doc.element('models').innerHTML = html;
     
    271289    {
    272290      Wizard.setInputStatus('models', 'valid');
     291      Doc.removeClass('models', 'invalid');
    273292    }
    274293    else
    275294    {
    276295      Wizard.setInputStatus('models', 'invalid', 'Select at least one model!');
     296      Doc.addClass('models', 'invalid');
    277297    }
    278298  }
  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/ssp_start.jsp

    r5924 r5927  
    7373
    7474      <table class="step-form">
    75       <tr class="align-top">
    76         <td class="prompt">Models</td>
    77         <td class="input" id="models">
    78          
    79         </td>
    80         <td class="status" id="models.status"></td>
    81         <td class="help">
    82           <span id="models.message" class="message"></span>
    83           Select which models to use.
    84         </td>
    85       </tr>
     75      <tbody id="models">
     76     
     77      </tbody>
    8678      </table>
    8779    </div>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SspServlet.java

    r5926 r5927  
    128128          JSONObject jsonModel = new JSONObject();
    129129          jsonModel.put("name", m.getName());
     130          jsonModel.put("description", m.getDescription());
    130131          jsonModels.add(jsonModel);
    131132        }
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/ssp/SspModel.java

    r5926 r5927  
    8383 
    8484  private final String name;
     85  private final String description;
    8586  private final String modelData;
    8687  private final String annotationTypeName;
     
    9192  {
    9293    this.name = e.getAttributeValue("name");
     94    this.description = e.getAttributeValue("description");
    9395    this.modelData = e.getTextTrim();
    9496    this.annotationTypeName = e.getAttributeValue("annotation-type");
     
    112114  }
    113115
     116  /**
     117    Get a description of the model.
     118    Configured in reggie-config.xml, "description" attribute of the "model" tag.
     119  */
     120  public String getDescription()
     121  {
     122    return description;
     123  }
    114124 
    115125  /**
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