Changeset 4972


Ignore:
Timestamp:
Sep 20, 2018, 1:42:21 PM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1054: Even more functionality in the Flagged alignment wizard

Added two new annotation types: DoNotUse and DoNotUseComment.

They should be set on any item (from Specimen all the way down to RawBioassay?) to indicate that it should not be used in the future for some reason (as indicated by the comment). The DoNotUse is a string enumeration with possible values: Specimen, Lysate, RNA, Library. The value should reflect the top-most item where there is a problem. For example, if an RNA is contaminated, then DoNotUse=RNA for the RNA and all items downstreams.

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/Annotationtype.java

    r4710 r4972  
    14261426 
    14271427  /**
     1428    The "DoNotUse" annotation type which is a flag to indicate that
     1429    a biomaterial (sample or extract) is not correct and it should
     1430    not be used. The typical problems are mixups in the QiaCube or
     1431    contamination in the lib-prep. The flag is also put on all child items.
     1432    The value is an enumeration that indicates the topmost item type.
     1433    @since 4.20
     1434  */
     1435  public static final Annotationtype DO_NOT_USE =
     1436    new Annotationtype("DoNotUse", Type.STRING, false, Item.SAMPLE, Item.EXTRACT, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
     1437 
     1438  /**
     1439    A comment that goes with the "DoNotUse" annotations.
     1440    @since 4.20
     1441  */
     1442  public static final Annotationtype DO_NOT_USE_COMMENT =
     1443    new Annotationtype("DoNotUseComment", Type.STRING, false, Item.SAMPLE, Item.EXTRACT, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY);
     1444 
     1445  /**
    14281446    The "SerialNumber" annotation, used for hardware items.
    14291447    It is a string annotation containing a typically unique
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r4712 r4972  
    587587        jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_GENOTYPE_COMMENT, 1, null, createIfMissing, effectivePermissionsUse));
    588588       
     589        jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE, 1,
     590            new ValueOptions("Specimen", "Lysate", "RNA", "Library"),
     591            createIfMissing, effectivePermissionsUse));
     592        jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE_COMMENT, 1, null, createIfMissing, effectivePermissionsUse));
     593       
    589594        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BARCODE_SEQUENCE, 1, null, createIfMissing, effectivePermissionsUse));
    590595        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SERIAL_NUMBER, 1, null, createIfMissing, effectivePermissionsUse));
     
    690695            Annotationtype.SAMPLING_DATETIME, Annotationtype.SPECIMEN_TYPE,
    691696            Annotationtype.LINKED_SPECIMEN, Annotationtype.YELLOW_LABEL,
    692             Annotationtype.COMPLETED_DATE,
     697            Annotationtype.COMPLETED_DATE,
     698            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
    693699            Annotationtype.AUTO_PROCESSING));
    694700       
     
    713719            Annotationtype.RLT_PLUS, Annotationtype.BETA_MERCA,
    714720            Annotationtype.REAGENT_DX, Annotationtype.QIA_SHREDDER,
    715             Annotationtype.RESERVED_BY, Annotationtype.AUTO_PROCESSING
     721            Annotationtype.RESERVED_BY,
     722            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
     723            Annotationtype.AUTO_PROCESSING
    716724            ));
    717725       
     
    725733            Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER,
    726734            Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL,
     735            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
    727736            Annotationtype.AUTO_PROCESSING, Annotationtype.FLAG));
    728737       
     
    746755            Annotationtype.BUFFER_AW1, Annotationtype.BUFFER_AW2,
    747756            Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER,
    748             Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL
     757            Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL,
     758            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT
    749759            ));
    750760       
     
    756766            Annotationtype.BUFFER_AW1, Annotationtype.BUFFER_AW2,
    757767            Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER,
    758             Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL
     768            Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL,
     769            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT
    759770            ));
    760771
     
    788799            Annotationtype.DILUTION_DATE, Annotationtype.DILUTION_OPERATOR,
    789800            Annotationtype.NEOPREP_DATE, Annotationtype.NEOPREP_DATE,
    790             Annotationtype.POOL_SCHEMA, Annotationtype.BARCODE_VARIANT, Annotationtype.PLATE_PROCESS_RESULT));
     801            Annotationtype.POOL_SCHEMA, Annotationtype.BARCODE_VARIANT,
     802            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
     803            Annotationtype.PLATE_PROCESS_RESULT));
    791804
    792805        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.POOLED_LIBRARY, createIfMissing,
     
    822835            Annotationtype.FRAGMENT_SIZE_AVG, Annotationtype.FRAGMENT_SIZE_STDEV,
    823836            Annotationtype.DATA_FILES_FOLDER,
     837            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
    824838            Annotationtype.AUTO_PROCESSING
    825839          ));
     
    836850            Annotationtype.QC_GENOTYPE_COUNT, Annotationtype.QC_GENOTYPE_HET_PCT,
    837851            Annotationtype.QC_GENOTYPE_STATUS, Annotationtype.QC_GENOTYPE_VERIFIED,
    838             Annotationtype.QC_GENOTYPE_COMMENT, Annotationtype.AUTO_PROCESSING
     852            Annotationtype.QC_GENOTYPE_COMMENT,
     853            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT,
     854            Annotationtype.AUTO_PROCESSING
    839855          ));
    840856       
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