Changeset 3492

Timestamp:

Sep 18, 2015, 9:01:00 AM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #812: Pilot report wizard

Added a pilot wizard stub. The report is more more or less a copy of the current gene report but without the validation cohort reference. The GUI and servlet is using the same code as the gene report. The plug-in is currently an independent class, but I think it is possible to refactor this code as well to make a common "Report" plug-in with multiple configurations.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• META-INF/extensions.xml (modified) (1 diff)
• META-INF/servlets.xml (modified) (1 diff)
• config/reggie-config.xml (modified) (1 diff)
• resources/analysis/gene_report.js (deleted)
• resources/analysis/gene_report.jsp (deleted)
• resources/analysis/report.js (added)
• resources/analysis/report.jsp (added)
• resources/index.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/counter/CounterService.java (modified) (4 diffs)
• src/net/sf/basedb/reggie/plugins/PilotReportPlugin.java (added)
• src/net/sf/basedb/reggie/r/PilotReport.java (added)
• src/net/sf/basedb/reggie/servlet/GeneReportServlet.java (deleted)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/ReportServlet.java (added)

extensions/net.sf.basedb.reggie/trunk/META-INF/extensions.xml

@@ -112 +112 @@
     </settings>
   </plugin-definition>
+  <plugin-definition id="PilotReportPlugin">
+    <about>
+      <name>Pilot report</name>
+      <description>
+        Plug-in for generating the pilot report in PDF format.
+      </description>
+    </about>
+    <plugin-class>net.sf.basedb.reggie.plugins.PilotReportPlugin</plugin-class>
+    <settings>
+      <property name="everyone-use">0</property>
+      <property name="immediate-execution">1</property>
+    </settings>
+  </plugin-definition>
   <plugin-definition id="GeneReportsCombinerPlugin">
     <about>

extensions/net.sf.basedb.reggie/trunk/META-INF/servlets.xml

@@ -126 +126 @@
   </servlet>
   <servlet>
-    <servlet-name>GeneReport</servlet-name>
-    <servlet-class>net.sf.basedb.reggie.servlet.GeneReportServlet</servlet-class>
+    <servlet-name>Report</servlet-name>
+    <servlet-class>net.sf.basedb.reggie.servlet.ReportServlet</servlet-class>
   </servlet>
   <servlet>

extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

@@ -23 +23 @@
       <pdf-name>genereport.pdf</pdf-name>
     </gene-report>
+    
+    <!-- options for the 'pilot report' script -->
+    <pilot-report>
+      <!-- full path to the R script -->
+      <path>/path/to/pilot-report.R</path>
+      <!-- full path to directory with SCAN-B reference data -->
+      <!-- default is same directory as the R script -->
+      <ref-dir-scanb></ref-dir-scanb>
+      <!-- full path to the PDF template -->
+      <!-- default is 'template.pdf' in the same directory as the R script -->
+      <template></template>
+      <!-- file name in BASE for storing the generated report  -->
+      <pdf-name>pilotreport.pdf</pdf-name>
+    </pilot-report>
+    
   </rscript>
 

extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

@@ -784 +784 @@
           <dd>
             <ul>
-            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/gene_report.jsp?ID=<%=ID%>"
+            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=GeneReport"
               >Gene report</span> 
             <span class="counter" data-counter="rawbioassys-without-genereport" 
                 title="Number of rawbioassays without a Gene report PDF">∙</span>
+            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/report.jsp?ID=<%=ID%>&report=PilotReport"
+              >Pilot report</span> 
+            <span class="counter" data-counter="rawbioassys-without-pilotreport" 
+                title="Number of rawbioassays without a Pilot report PDF">∙</span>
             </ul>
           </dd>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/counter/CounterService.java

@@ -38 +38 @@
 import net.sf.basedb.reggie.query.AnyToAnyRestriction;
 import net.sf.basedb.reggie.r.GeneReport;
+import net.sf.basedb.reggie.r.PilotReport;
 import net.sf.basedb.util.extensions.Extension;
 
@@ -988 +989 @@
   private void countRawBioAssays(DbControl dc, JSONObject json)
   {
-    String pdfName = Reggie.getConfig().getConfig("rscript/gene-report/pdf-name", null, GeneReport.DEFAULT_PDF_NAME);
+    String geneReportPdfName = Reggie.getConfig().getConfig("rscript/gene-report/pdf-name", null, GeneReport.DEFAULT_PDF_NAME);
+    String pilotReportPdfName = Reggie.getConfig().getConfig("rscript/pilot-report/pdf-name", null, PilotReport.DEFAULT_PDF_NAME);
 
     // Raw bioassays not confirmed
@@ -1019 +1021 @@
     query.restrict(Restrictions.eq(Hql.alias("ar"), Expressions.string(Rawbioassay.FEATURE_EXTRACTION_SUCCESSFUL)));
     // Must not have 'genereport.pdf' already (no filter on FILE! since it may be in progress if linked to JOB)
-    query.restrict(AnyToAnyRestriction.missing(pdfName, null));
+    query.restrict(AnyToAnyRestriction.missing(geneReportPdfName, null));
     query.setCacheResult(true);
     json.put("rawbioassys-without-genereport", query.count(dc));
+    // ---
+    
+    // Raw bioassays without pilot report
+    query = RawBioAssay.getQuery();
+    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    query.restrict(Restrictions.eq(Hql.property("variant.externalId"), Expressions.string(PlatformVariant.SEQUENCING_EXPRESSION)));
+    // Must have a ANALYSIS_RESULT=Successful annotation
+    query.join(Annotations.leftJoin(null, Annotationtype.ANALYSIS_RESULT.load(dc), "ar"));
+    query.restrict(Restrictions.eq(Hql.alias("ar"), Expressions.string(Rawbioassay.FEATURE_EXTRACTION_SUCCESSFUL)));
+    // Must not have 'pilotreport.pdf' already (no filter on FILE! since it may be in progress if linked to JOB)
+    query.restrict(AnyToAnyRestriction.missing(pilotReportPdfName, null));
+    query.setCacheResult(true);
+    json.put("rawbioassys-without-pilotreport", query.count(dc));
     // ---
     
@@ -1029 +1044 @@
     query.restrict(Restrictions.eq(Hql.property("variant.externalId"), Expressions.string(PlatformVariant.SEQUENCING_EXPRESSION)));
     // Must have 'genereport.pdf' FILE already
-    query.restrict(AnyToAnyRestriction.exists(pdfName, Item.FILE));
+    query.restrict(AnyToAnyRestriction.exists(geneReportPdfName, Item.FILE));
     query.setCacheResult(true);
     json.put("rawbioassys-all-with-genereport", query.count(dc));

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -84 +84 @@
 import net.sf.basedb.reggie.plugins.FlowCellSampleSheetExporter;
 import net.sf.basedb.reggie.plugins.GeneReportPlugin;
+import net.sf.basedb.reggie.plugins.PilotReportPlugin;
 import net.sf.basedb.reggie.plugins.QubitSampleNameExporter;
 import net.sf.basedb.util.EqualsHelper;
@@ -749 +750 @@
 
         jsonChecks.add(checkPlugin(dc, GeneReportPlugin.class.getName(), secondaryAnalysisUse, createIfMissing));
+        jsonChecks.add(checkPlugin(dc, PilotReportPlugin.class.getName(), secondaryAnalysisUse, createIfMissing));
         jsonChecks.add(checkPlugin(dc, GeneReportsCombinerPlugin.class.getName(), effectivePermissionsUse, createIfMissing));