Changeset 6461


Ignore:
Timestamp:
Nov 1, 2021, 2:16:43 PM (15 months ago)
Author:
Nicklas Nordborg
Message:

References #1346: Implement support for OncoArray? SNP data

Added BeadChip and Scan item subtype and several new annotation types related to those items (BeadChipID, BeadChipType, BeadChipPosition and ScanDate).

DNA/Genotyping is a new value for the Pipeline annotation.

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

Legend:

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

    r6421 r6461  
    13011301
    13021302  /**
     1303    The "BeadChipID" annotation, used for physical bioassays (BeadChip).
     1304    @since 4.34
     1305  */
     1306  public static final Annotationtype BEADCHIP_ID =
     1307    new Annotationtype("BeadChipID", Type.STRING, false, Item.PHYSICALBIOASSAY);
     1308 
     1309  /**
     1310    The "BeadChipType" annotation, used for physical bioassays (BeadChip).
     1311    @since 4.34
     1312  */
     1313  public static final Annotationtype BEADCHIP_TYPE =
     1314    new Annotationtype("BeadChipType", Type.STRING, false, Item.PHYSICALBIOASSAY);
     1315
     1316  /**
     1317    The "BeadChipPosition" annotation, used for extracts (BloodDNA).
     1318    @since 4.34
     1319  */
     1320  public static final Annotationtype BEADCHIP_POSITION =
     1321    new Annotationtype("BeadChipPosition", Type.STRING, false, Item.EXTRACT);
     1322
     1323  /**
     1324    The "ScanDate" annotation, used for derived bioassays (Scan). It is
     1325    a timestamp annotation.
     1326    @since 4.34
     1327  */
     1328  public static final Annotationtype SCAN_DATE =
     1329    new Annotationtype("ScanDate", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
     1330 
     1331  /**
    13031332    The "ClusterStart" annotation, used for physical bioassays (FlowCell).
    13041333    The date the flow cell was clustered.
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Pipeline.java

    r5865 r6461  
    6464  public static final Pipeline RNASEQ_HISAT_VARIANTCALL = new Pipeline("RNASEQ_HISAT_VARIANTCALL", "RNAseq/Hisat/VariantCall");
    6565 
     66  /**
     67    Pipeline for genotyping from blood DNA.
     68    @since 4.34
     69  */
     70  public static final Pipeline DNA_GENOTYPING = new Pipeline("DNA_GENOTYPING", "DNA/Genotyping");
    6671 
    6772  /**
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

    r6389 r6461  
    251251  public static final Subtype FLOW_CELL = new Subtype("FlowCell", "FlowCell", null, null, Item.PHYSICALBIOASSAY, false);
    252252 
     253  /**
     254    The definition of the "BeadChip" physical bioassay subtype.
     255    @since 4.34
     256  */
     257  public static final Subtype BEAD_CHIP = new Subtype("BeadChip", "BeadChip", null, null, Item.PHYSICALBIOASSAY, false);
     258 
     259  /**
     260    The definition of the "Scan" derived bioassay subtype.
     261    @since 4.34
     262  */
     263  public static final Subtype SCAN = new Subtype("Scan", "Scan", null, null, Item.DERIVEDBIOASSAY, false);
    253264 
    254265  /**
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r6421 r6461  
    310310        jsonChecks.add(checkSubtype(dc, Subtype.CLUSTER_GENERATOR, null, createIfMissing));
    311311        jsonChecks.add(checkSubtype(dc, Subtype.FLOW_CELL, null, createIfMissing, Subtype.POOLED_LIBRARY_ALIQUOT, Subtype.CLUSTER_GENERATOR, Subtype.CLUSTER_PROTOCOL));
     312        jsonChecks.add(checkSubtype(dc, Subtype.BEAD_CHIP, null, createIfMissing, Subtype.BLOOD_DNA));
     313        jsonChecks.add(checkSubtype(dc, Subtype.SCAN, null, createIfMissing, Subtype.BEAD_CHIP));
    312314        jsonChecks.add(checkSubtype(dc, Subtype.BIOANALYZER_PDF, null, createIfMissing));
    313315        jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_PDF, null, createIfMissing));
     
    516518            new ValueOptions(Pipeline.RNA_SEQ.getName(), Pipeline.MIPS.getName(),
    517519              Pipeline.RNASEQ_LEGACY.getName(), Pipeline.RNASEQ_HISAT_STRINGTIE.getName(),
    518               Pipeline.RNASEQ_HISAT_VARIANTCALL.getName()),
     520              Pipeline.RNASEQ_HISAT_VARIANTCALL.getName(), Pipeline.DNA_GENOTYPING.getName()),
    519521            createIfMissing, effectivePermissionsUse));
    520522       
     
    611613        jsonChecks.add(checkAnnotationType(dc, Annotationtype.FAILED_LANES, 0, null, createIfMissing, effectivePermissionsUse));
    612614
     615        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_ID, 1, null, createIfMissing, effectivePermissionsUse));
     616        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_TYPE, 1,
     617            new ValueOptions("OncoArray500K"),
     618            createIfMissing, effectivePermissionsUse));
     619        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_POSITION, 1, null, createIfMissing, effectivePermissionsUse));
     620        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCAN_DATE, 1, null, createIfMissing, effectivePermissionsUse));
     621       
    613622        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_START, 1, null, createIfMissing, effectivePermissionsUse));
    614623        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_TURN_AROUND, 1, null, createIfMissing, effectivePermissionsUse));
     
    846855
    847856        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BLOOD_DNA, createIfMissing,
    848             Annotationtype.ND_CONC, Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT));
     857            Annotationtype.ND_CONC, Annotationtype.BEADCHIP_POSITION,
     858            Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT));
    849859
    850860        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SPECIMEN, createIfMissing,
     
    10361046            Annotationtype.PIPELINE,
    10371047            Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.SEQUENCING_RESULT));
     1048       
     1049        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BEAD_CHIP, createIfMissing,
     1050            Annotationtype.BEADCHIP_ID, Annotationtype.BEADCHIP_TYPE,
     1051            Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.PIPELINE
     1052          ));
     1053       
     1054        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SCAN, createIfMissing,
     1055            Annotationtype.DATA_FILES_FOLDER, Annotationtype.SCAN_DATE,
     1056            Annotationtype.ANALYSIS_RESULT,
     1057            Annotationtype.PIPELINE
     1058          ));
    10381059       
    10391060        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing,
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