Changeset 5774


Ignore:
Timestamp:
Dec 4, 2019, 12:59:44 PM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1209: Add support for storing TMA specimen

Added new subtype for TMASpecimen and annotation types TMABlock and TMABlockPos.

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

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

    r5721 r5774  
    414414    new Annotationtype("LinkedSpecimen", Type.STRING, false, Item.SAMPLE);
    415415
     416  /**
     417    Name of TMA block were a TMASpecimen is located.
     418    @since 4.25
     419   */
     420  public static final Annotationtype TMA_BLOCK =
     421    new Annotationtype("TMABlock", Type.STRING, false, Item.SAMPLE);
     422 
     423  /**
     424    Position on TMA block were a TMASpecimen is located.
     425    @since 4.25
     426   */
     427  public static final Annotationtype TMA_BLOCK_POS =
     428    new Annotationtype("TMABlockPos", Type.STRING, false, Item.SAMPLE);
    416429 
    417430  /**
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

    r5772 r5774  
    9292  public static final Subtype NO_SPECIMEN = new Subtype("NoSpecimen", null, null, "S", Item.SAMPLE, false);
    9393
    94  
     94  /**
     95    The definition of the "TMASpecimen" subtype.
     96    @since 4.25
     97  */
     98  public static final Subtype TMA_SPECIMEN = new Subtype("TMASpecimen", null, "tma", "T", Item.SAMPLE, false);
     99
    95100  /**
    96101    The definition of the "Histology" subtype.
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r5772 r5774  
    272272        jsonChecks.add(checkSubtype(dc, Subtype.SPECIMEN,null, createIfMissing, Subtype.CASE));
    273273        jsonChecks.add(checkSubtype(dc, Subtype.NO_SPECIMEN,null, createIfMissing, Subtype.CASE));
     274        jsonChecks.add(checkSubtype(dc, Subtype.TMA_SPECIMEN,null, createIfMissing, Subtype.CASE));
    274275        jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY_PROTOCOL, null, createIfMissing));
    275276        jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY, null, createIfMissing, Subtype.SPECIMEN, Subtype.HISTOLOGY_PROTOCOL));
     
    439440        jsonChecks.add(checkAnnotationType(dc, Annotationtype.PARTITION_DATE, 1, null, createIfMissing, effectivePermissionsUse));
    440441
     442        jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK, 1, null, createIfMissing, effectivePermissionsUse));
     443        jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK_POS, 1, null, createIfMissing, effectivePermissionsUse));
     444
    441445        jsonChecks.add(checkAnnotationType(dc, Annotationtype.RLT_PLUS, 1, null, createIfMissing, effectivePermissionsUse));
    442446        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BETA_MERCA, 1, null, createIfMissing, effectivePermissionsUse));
     
    769773            Annotationtype.LINKED_SPECIMEN, Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT
    770774            ));
     775
     776        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.TMA_SPECIMEN, createIfMissing,
     777            Annotationtype.TMA_BLOCK, Annotationtype.TMA_BLOCK_POS,
     778            Annotationtype.PAD
     779            ));
    771780       
    772781        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.HISTOLOGY, createIfMissing,
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