Changeset 6004


Ignore:
Timestamp:
Sep 16, 2020, 8:44:25 AM (13 months ago)
Author:
Nicklas Nordborg
Message:

References #1266: Run prepDE.py in the StringTie? pipeline

Added a wizard for running prepDE.py on all existing StringTie? rawbioassays that doesn't have count data files. Only the GUI has been implemented so far.

Location:
extensions/net.sf.basedb.reggie/branches/4.27-stable
Files:
2 added
3 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/branches/4.27-stable/resources/index.js

    r5922 r6004  
    211211      Doc.show('more-boxes-are-needed', 'inline-block');
    212212    }
     213   
     214    if (counts['stringtie-without-prepde']) Doc.show('prepde-wizard', 'list-item');
    213215   
    214216    index.displayCounterAge();
  • extensions/net.sf.basedb.reggie/branches/4.27-stable/resources/index.jsp

    r5922 r6004  
    838838                  title="Number of rawbioassays without a SCAN-B report PDF">∙</span>
    839839             
     840              <li id="prepde-wizard" style="display: none;"><span class="require-permission" data-role="Administrator" data-link="analysis/prepde.jsp?ID=<%=ID%>"
     841                >Run prepDE.py</span>
     842                <span class="counter" data-counter="stringtie-without-prepde"
     843                  title="Number of StringTie rawbioassays that is missing prepDE data">∙</span>
     844             
    840845              </ul>
    841846            </dd>
  • extensions/net.sf.basedb.reggie/branches/4.27-stable/src/net/sf/basedb/reggie/counter/CounterService.java

    r5922 r6004  
    13851385    // ---
    13861386   
     1387    // StringTie raw bioassays without prepDE results
     1388    query = RawBioAssay.getQuery();
     1389    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
     1390    Rawdatatype.STRINGTIE.addFilter(dc, query);
     1391    Pipeline.RNASEQ_HISAT_STRINGTIE.addFilter(dc, query);
     1392    // Must have a ANALYSIS_RESULT=Successful annotation
     1393    query.join(Annotations.leftJoin(null, Annotationtype.ANALYSIS_RESULT.load(dc), "ar"));
     1394    query.restrict(Restrictions.eq(Hql.alias("ar"), Expressions.string(Rawbioassay.FEATURE_EXTRACTION_SUCCESSFUL)));
     1395    // Must not have 'gene_count.csv' already
     1396    query.restrict(AnyToAnyRestriction.missing("gene_count.csv", null));
     1397    query.setCacheResult(true);
     1398    json.put("stringtie-without-prepde", query.count(dc));
     1399    // ---
     1400   
    13871401    // All Cufflinks raw bioassays with a gene report pdf
    13881402    query = RawBioAssay.getQuery();
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