Changeset 5064


Ignore:
Timestamp:
Oct 31, 2018, 8:44:21 AM (4 years ago)
Author:
Nicklas Nordborg
Message:

References #1068: Add mBAF analysis step to the Hisat/StringTie? pipeline

File links should be created 'soft' links so that they can be easier removed or replaced if we want to.

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

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MBafJobCreator.java

    r5057 r5064  
    182182      if (autoConfirm)
    183183      {
    184         AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, "mbaf_genotype.vcf", mBafJob, true);
     184        AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, "mbaf_genotype.vcf", mBafJob, false);
    185185        if (!link.isInDatabase()) dc.saveItem(link);
    186186      }
     
    322322          }
    323323         
    324           AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, f.getName(), f, true);
     324          AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, f.getName(), f, false);
    325325          if (!link.isInDatabase()) dc.saveItem(link);
    326326         
     
    331331            {
    332332              link.setDescription("Created with " + software.getName());
    333               AnyToAny swLink = AnyToAny.getNewOrExisting(dc, f, "software", software, true);
     333              AnyToAny swLink = AnyToAny.getNewOrExisting(dc, f, "software", software, false);
    334334              if (!swLink.isInDatabase()) dc.saveItem(swLink);
    335335            }
     
    365365                png.setMimeTypeAuto("image/png", null);
    366366                if (!png.isInDatabase()) dc.saveItem(png);
    367                 AnyToAny pngLink = AnyToAny.getNewOrExisting(dc, aligned, png.getName(), png, true);
     367                AnyToAny pngLink = AnyToAny.getNewOrExisting(dc, aligned, png.getName(), png, false);
    368368                if (!pngLink.isInDatabase()) dc.saveItem(pngLink);
    369369
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/MBafPlotterPlugin.java

    r5057 r5064  
    545545  private void linkFileAndSoftware(DbControl dc, DerivedBioAssay alignment, File file, Software software)
    546546  {
    547     AnyToAny link = AnyToAny.getNewOrExisting(dc, alignment, file.getName(), file, true);
     547    AnyToAny link = AnyToAny.getNewOrExisting(dc, alignment, file.getName(), file, false);
    548548    if (!link.isInDatabase()) dc.saveItem(link);
    549549   
     
    551551    {
    552552      link.setDescription("Created with " + software.getName());
    553       AnyToAny swLink = AnyToAny.getNewOrExisting(dc, file, "software", software, true);
     553      AnyToAny swLink = AnyToAny.getNewOrExisting(dc, file, "software", software, false);
    554554      if (!swLink.isInDatabase()) dc.saveItem(swLink);
    555555    }
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