Changeset 5737


Ignore:
Timestamp:
Nov 20, 2019, 7:39:02 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1186 and #1190. Disabling code related to the SSP plug-in and SCAN-B report. They will be postponed to a later release.

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

Legend:

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

    r5628 r5737  
    137137    </settings>
    138138  </plugin-definition>
     139  <!--
    139140  <plugin-definition id="SingleSamplePredictorPlugin">
    140141    <about>
     
    150151    </settings>
    151152  </plugin-definition>
    152  
     153  -->
    153154  <plugin-definition id="SetPermissionsForDelivery">
    154155    <about>
  • extensions/net.sf.basedb.reggie/trunk/META-INF/plugin-configurations.xml

    r5682 r5737  
    450450    </parameter>
    451451  </configuration>
     452  <!--
    452453  <configuration pluginClassName="net.sf.basedb.reggie.plugins.GeneReportPlugin">
    453454    <configname>SCAN-B report</configname>
     
    461462    </parameter>
    462463  </configuration>
     464  -->
    463465  <configuration pluginClassName="net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin">
    464466    <configname>Gene report</configname>
     
    483485    </parameter>
    484486  </configuration>
     487  <!--
    485488  <configuration pluginClassName="net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin">
    486489    <configname>SCAN-B report</configname>
     
    494497    </parameter>
    495498  </configuration>
    496  
     499  -->
    497500</configfile>
  • extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

    r5704 r5737  
    6969    </pilot-report>
    7070   
    71     <!-- options for the 'SCAN-B report' script -->
    72     <scanb-report>
    73       <!-- full path to the PDF template -->
    74       <!-- default is 'template.pdf' in the same directory as the SSP R script -->
    75       <template></template>
    76    
    77       <!-- file name in BASE for storing the generated report  -->
    78       <pdf-name>scanbreport.pdf</pdf-name>
    79     </scanb-report>
    80    
    81     <ssp>
    82       <!-- full path to the directory with SSP scripts -->
    83       <path>/path/to/ssp-dir</path>
    84       <!-- full path to directory with models -->
    85       <!-- default is 'models' directory inside -->
    86       <!-- the same directory as the R scripts -->
    87       <models-dir></models-dir>
    88      
    89       <!-- Maps training models to annotation types -->
    90       <models>
    91         <model name="Subtype" annotation-type="SSP_Subtype">Training_Run19081Genes_noNorm_SSP.subtypeMost.Fcc15_5x5foldCV.num.rules.50_24.selRules.AIMS.GS.RData</model>
    92       </models>
    93      
    94     </ssp>
    9571  </rscript>
    9672
  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/report.jsp

    r3976 r5737  
    66  import="net.sf.basedb.core.SessionControl"
    77  import="net.sf.basedb.core.Application"
    8   import="net.sf.basedb.clients.web.Base"
     8  import="net.sf.basedb.core.PermissionDeniedException"
     9  import="net.sf.basedb.clients.web.Base"
    910  import="net.sf.basedb.clients.web.util.HTML" 
    1011  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
     
    1920final String report = request.getParameter("report");
    2021
     22if ("SCANB_REPORT".equals(report)) throw new PermissionDeniedException("The SCAN-B report is not yet implemented");
    2123
    2224DbControl dc = null;
  • extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

    r5724 r5737  
    791791                <span class="counter" data-counter="stringtie-not-confirmed"
    792792                  title="Number of StringTie jobs waiting for confirmation">∙</span>
    793               <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=SCANB_REPORT"
     793              <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=SCANB_REPORT"
    794794                >SCAN-B report</span>
    795795                <span class="counter" data-counter="rawbioassys-without-scanbreport"
    796796                  title="Number of rawbioassays without a SCAN-B report PDF">∙</span>
     797             
    797798              </ul>
    798799            </dd>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/counter/CounterService.java

    r5725 r5737  
    13591359   
    13601360    // StringTie raw bioassays without SCAN-B report
     1361    /*
    13611362    query = RawBioAssay.getQuery();
    13621363    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
     
    13701371    query.setCacheResult(true);
    13711372    json.put("rawbioassys-without-scanbreport", query.count(dc));
     1373    */
    13721374    // ---
    13731375   
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/pdf/PdfReportTemplate.java

    r5672 r5737  
    33import java.lang.reflect.Field;
    44
     5import net.sf.basedb.core.PermissionDeniedException;
    56import net.sf.basedb.reggie.Reggie;
    67import net.sf.basedb.reggie.activity.ActivityDef;
     
    9293    public PdfReportWorker getWorker(String parameterSet)
    9394    {
     95      if (true) throw new PermissionDeniedException("The SCAN-B report is not implemented.");
    9496      return new ScanBReportWorker(SCANB_REPORT, config, parameterSet);
    9597    }
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/GeneReportPlugin.java

    r5674 r5737  
    483483    reportOptions.add("GENE_REPORT", "Gene report");
    484484    reportOptions.add("PILOT_REPORT", "Pilot report");
    485     reportOptions.add("SCANB_REPORT", "SCAN-B report");
     485//    reportOptions.add("SCANB_REPORT", "SCAN-B report");
    486486    parameters.add(new PluginParameter<String>
    487487    (
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/GeneReportsCombinerPlugin.java

    r5673 r5737  
    224224    reportOptions.add("GENE_REPORT", "Gene report");
    225225    reportOptions.add("PILOT_REPORT", "Pilot report");
    226     reportOptions.add("SCANB_REPORT", "SCAN-B report");
     226//    reportOptions.add("SCANB_REPORT", "SCAN-B report");
    227227    parameters.add(new PluginParameter<String>
    228228    (
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/ssp/SspPlugin.java

    r5668 r5737  
    2424import net.sf.basedb.core.Type;
    2525import net.sf.basedb.core.Job.ExecutionTime;
     26import net.sf.basedb.core.PermissionDeniedException;
    2627import net.sf.basedb.core.StringParameterType;
    2728import net.sf.basedb.core.plugin.AbstractPlugin;
     
    5455 
    5556  public SspPlugin()
    56   {}
     57  {
     58    throw new PermissionDeniedException("The SSP plug-in is not implemented");
     59  }
    5760 
    5861  /*
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