Changeset 5787


Ignore:
Timestamp:
Dec 13, 2019, 11:02:36 AM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1216: Finalize the "Confirm MIPs demux" wizard

Added the "MIPs alignment pipeline" item list.

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/dao/BiomaterialList.java

    r5683 r5787  
    177177      "automatically, but it is possible to also manually add items.");
    178178
    179    
     179  /**
     180    The definition of the list used for storing merged sequences that
     181    should to be processed with the MIPs alignment pipeline.
     182    @since 4.25
     183  */
     184  public static final BiomaterialList MIPS_ALIGN_PIPELINE =
     185    new BiomaterialList("MIPs Alignment Pipeline", "net.sf.basedb.reggie.pipeline.mips-align",
     186      Item.DERIVEDBIOASSAY, Subtype.MERGED_SEQUENCES,
     187      "This list contains merged sequences items that should be processed with the " +
     188      "MIPs alignment pipeline. Items are normally added and removed from this list " +
     189      "automatically, but it is possible to also manually add items.");
     190
    180191  /**
    181192    Get the bioplate type by name of the static constant defined in this class.
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r5784 r5787  
    11081108        jsonChecks.add(checkItemList(dc, BiomaterialList.MBAF_PIPELINE, effectivePermissionsWrite, createIfMissing));
    11091109        jsonChecks.add(checkItemList(dc, BiomaterialList.VARIANT_CALLING_PIPELINE, effectivePermissionsWrite, createIfMissing));
     1110        jsonChecks.add(checkItemList(dc, BiomaterialList.MIPS_ALIGN_PIPELINE, effectivePermissionsWrite, createIfMissing));
    11101111        jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_ALIGNMENT, effectivePermissionsWrite, createIfMissing));
    11111112       
     
    11501151        ItemList mBafPipeline = BiomaterialList.MBAF_PIPELINE.get(dc);
    11511152        ItemList variantCallingPipeline = BiomaterialList.VARIANT_CALLING_PIPELINE.get(dc);
     1153        ItemList mipsAlignPipeline = BiomaterialList.MIPS_ALIGN_PIPELINE.get(dc);
    11521154        AnnotationType autoProc = Annotationtype.AUTO_PROCESSING.get(dc);
    11531155        if (autoProc != null)
     
    11581160          json.put("mBafPipelineDisabled", "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, mBafPipeline)));
    11591161          json.put("variantCallingPipelineDisabled", "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, variantCallingPipeline)));
     1162          json.put("mipsAlignPipelineDisabled", "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, mipsAlignPipeline)));
    11601163        }
    11611164        dc.close();
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