Changeset 5737
- Timestamp:
- Nov 20, 2019, 7:39:02 AM (3 years ago)
- 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 137 137 </settings> 138 138 </plugin-definition> 139 <!-- 139 140 <plugin-definition id="SingleSamplePredictorPlugin"> 140 141 <about> … … 150 151 </settings> 151 152 </plugin-definition> 152 153 --> 153 154 <plugin-definition id="SetPermissionsForDelivery"> 154 155 <about> -
extensions/net.sf.basedb.reggie/trunk/META-INF/plugin-configurations.xml
r5682 r5737 450 450 </parameter> 451 451 </configuration> 452 <!-- 452 453 <configuration pluginClassName="net.sf.basedb.reggie.plugins.GeneReportPlugin"> 453 454 <configname>SCAN-B report</configname> … … 461 462 </parameter> 462 463 </configuration> 464 --> 463 465 <configuration pluginClassName="net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin"> 464 466 <configname>Gene report</configname> … … 483 485 </parameter> 484 486 </configuration> 487 <!-- 485 488 <configuration pluginClassName="net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin"> 486 489 <configname>SCAN-B report</configname> … … 494 497 </parameter> 495 498 </configuration> 496 499 --> 497 500 </configfile> -
extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml
r5704 r5737 69 69 </pilot-report> 70 70 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>95 71 </rscript> 96 72 -
extensions/net.sf.basedb.reggie/trunk/resources/analysis/report.jsp
r3976 r5737 6 6 import="net.sf.basedb.core.SessionControl" 7 7 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" 9 10 import="net.sf.basedb.clients.web.util.HTML" 10 11 import="net.sf.basedb.clients.web.extensions.ExtensionsControl" … … 19 20 final String report = request.getParameter("report"); 20 21 22 if ("SCANB_REPORT".equals(report)) throw new PermissionDeniedException("The SCAN-B report is not yet implemented"); 21 23 22 24 DbControl dc = null; -
extensions/net.sf.basedb.reggie/trunk/resources/index.jsp
r5724 r5737 791 791 <span class="counter" data-counter="stringtie-not-confirmed" 792 792 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" 794 794 >SCAN-B report</span> 795 795 <span class="counter" data-counter="rawbioassys-without-scanbreport" 796 796 title="Number of rawbioassays without a SCAN-B report PDF">∙</span> 797 797 798 </ul> 798 799 </dd> -
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/counter/CounterService.java
r5725 r5737 1359 1359 1360 1360 // StringTie raw bioassays without SCAN-B report 1361 /* 1361 1362 query = RawBioAssay.getQuery(); 1362 1363 query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT); … … 1370 1371 query.setCacheResult(true); 1371 1372 json.put("rawbioassys-without-scanbreport", query.count(dc)); 1373 */ 1372 1374 // --- 1373 1375 -
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/pdf/PdfReportTemplate.java
r5672 r5737 3 3 import java.lang.reflect.Field; 4 4 5 import net.sf.basedb.core.PermissionDeniedException; 5 6 import net.sf.basedb.reggie.Reggie; 6 7 import net.sf.basedb.reggie.activity.ActivityDef; … … 92 93 public PdfReportWorker getWorker(String parameterSet) 93 94 { 95 if (true) throw new PermissionDeniedException("The SCAN-B report is not implemented."); 94 96 return new ScanBReportWorker(SCANB_REPORT, config, parameterSet); 95 97 } -
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/GeneReportPlugin.java
r5674 r5737 483 483 reportOptions.add("GENE_REPORT", "Gene report"); 484 484 reportOptions.add("PILOT_REPORT", "Pilot report"); 485 reportOptions.add("SCANB_REPORT", "SCAN-B report");485 // reportOptions.add("SCANB_REPORT", "SCAN-B report"); 486 486 parameters.add(new PluginParameter<String> 487 487 ( -
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/GeneReportsCombinerPlugin.java
r5673 r5737 224 224 reportOptions.add("GENE_REPORT", "Gene report"); 225 225 reportOptions.add("PILOT_REPORT", "Pilot report"); 226 reportOptions.add("SCANB_REPORT", "SCAN-B report");226 // reportOptions.add("SCANB_REPORT", "SCAN-B report"); 227 227 parameters.add(new PluginParameter<String> 228 228 ( -
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/ssp/SspPlugin.java
r5668 r5737 24 24 import net.sf.basedb.core.Type; 25 25 import net.sf.basedb.core.Job.ExecutionTime; 26 import net.sf.basedb.core.PermissionDeniedException; 26 27 import net.sf.basedb.core.StringParameterType; 27 28 import net.sf.basedb.core.plugin.AbstractPlugin; … … 54 55 55 56 public SspPlugin() 56 {} 57 { 58 throw new PermissionDeniedException("The SSP plug-in is not implemented"); 59 } 57 60 58 61 /*
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