Changeset 6475


Ignore:
Timestamp:
Nov 5, 2021, 9:20:14 AM (15 months ago)
Author:
Nicklas Nordborg
Message:

References #1346: Implement support for OncoArray? SNP data

Added GenotypeCall derived bioassay type and related file and software type.

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/Datafiletype.java

    r5827 r6475  
    8989
    9090  /**
     91    Genotype call file.
     92    @since 4.34
     93  */
     94  public static final Datafiletype GTC =
     95    new Datafiletype("GTC", "net.sf.basedb.reggie.gtc",
     96      Item.DERIVEDBIOASSAY, "gtc", Subtype.GENOTYPE_CALL_FILE,
     97      true, true,
     98      "Genotype call file");
     99
     100  /**
    91101    Get the file type by name of the static constant defined in this class.
    92102   
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Mimetype.java

    r4619 r6475  
    3838    new Mimetype("text/plain", "vcf", "Variant call format", Subtype.VARIANT_CALL_FORMAT);
    3939 
    40    
     40  /**
     41    The definition of the "GTC" type.
     42    @since 4.34
     43  */
     44  public static final Mimetype GTC =
     45    new Mimetype("application/octet-stream", "gtc", "Genotype call", Subtype.GENOTYPE_CALL_FILE);
     46 
    4147  /**
    4248    Get the MIME type by name of the static constant defined in this class.
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

    r6461 r6475  
    262262  */
    263263  public static final Subtype SCAN = new Subtype("Scan", "Scan", null, null, Item.DERIVEDBIOASSAY, false);
    264  
     264
     265  /**
     266    The definition of the "GenotypeCall" derived bioassay subtype.
     267    @since 4.34
     268  */
     269  public static final Subtype GENOTYPE_CALL = new Subtype("GenotypeCall", "GenotypeCall", null, null, Item.DERIVEDBIOASSAY, false);
     270
     271  /**
     272    The definition of the "Genotyping" software subtype.
     273    @since 4.34
     274  */
     275  public static final Subtype GENOTYPING_SOFTWARE = new Subtype("Genotyping", null, null, null, Item.SOFTWARE, false);
     276
     277  /**
     278    File subtype for genotype call files.
     279    @since 4.34
     280  */
     281  public static final Subtype GENOTYPE_CALL_FILE = new Subtype("Genotype call", null, null, null, Item.FILE, false);
     282
    265283  /**
    266284    The definition of the "SequencingRun" derived bioassay subtype.
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r6474 r6475  
    259259        JSONObject jsonSubtype_SEQUENCE_DATA = checkSubtype(dc, Subtype.SEQUENCE_DATA, null, createIfMissing);
    260260        JSONObject jsonSubtype_ALIGNED_SEQUENCE_DATA = checkSubtype(dc, Subtype.ALIGNED_SEQUENCE_DATA, null, createIfMissing);
     261        JSONObject jsonSubtype_GENOTYPE_CALL_FILE = checkSubtype(dc, Subtype.GENOTYPE_CALL_FILE, null, createIfMissing);
    261262
    262263        // Data file types
     
    265266        jsonChecks.add(checkDataFileType(dc, Datafiletype.FPKM, createIfMissing));
    266267        jsonChecks.add(checkDataFileType(dc, Datafiletype.VCF, createIfMissing));
     268        jsonChecks.add(checkDataFileType(dc, Datafiletype.GTC, createIfMissing));
    267269       
    268270        // Platforms
     
    311313        jsonChecks.add(checkSubtype(dc, Subtype.FLOW_CELL, null, createIfMissing, Subtype.POOLED_LIBRARY_ALIQUOT, Subtype.CLUSTER_GENERATOR, Subtype.CLUSTER_PROTOCOL));
    312314        jsonChecks.add(checkSubtype(dc, Subtype.BEAD_CHIP, null, createIfMissing, Subtype.BLOOD_DNA));
    313         jsonChecks.add(checkSubtype(dc, Subtype.SCAN, null, createIfMissing, Subtype.BEAD_CHIP));
     315        jsonChecks.add(checkSubtype(dc, Subtype.SCAN, null, createIfMissing, Subtype.BEAD_CHIP));
     316        jsonChecks.add(checkSubtype(dc, Subtype.GENOTYPING_SOFTWARE, null, createIfMissing));
     317        jsonChecks.add(jsonSubtype_GENOTYPE_CALL_FILE);
     318        jsonChecks.add(checkSubtype(dc, Subtype.GENOTYPE_CALL, Datafiletype.GTC, createIfMissing, Subtype.SCAN, Subtype.GENOTYPING_SOFTWARE));
    314319        jsonChecks.add(checkSubtype(dc, Subtype.BIOANALYZER_PDF, null, createIfMissing));
    315320        jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_PDF, null, createIfMissing));
     
    10591064            Annotationtype.PIPELINE
    10601065          ));
     1066
     1067        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.GENOTYPE_CALL, createIfMissing,
     1068            Annotationtype.DATA_FILES_FOLDER,
     1069            Annotationtype.ANALYSIS_RESULT,
     1070            Annotationtype.PIPELINE
     1071          ));
    10611072       
    10621073        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing,
     
    12801291        jsonChecks.add(checkMimeType(dc, Mimetype.GDX, createIfMissing));
    12811292        jsonChecks.add(checkMimeType(dc, Mimetype.VCF, createIfMissing));
     1293        jsonChecks.add(checkMimeType(dc, Mimetype.GTC, createIfMissing));
    12821294       
    12831295        // Special items
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