Changeset 1566


Ignore:
Timestamp:
Mar 16, 2012, 11:08:08 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #366: Import annotations and other information from Caliper output

Use CA_RQS as annotation for Caliper instead of BA_RIN which is for Bioanalyzer

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/Reggie.java

    r1565 r1566  
    229229  */
    230230  public static final String ANNOTATION_BA_RIN = "BA_RIN";
     231
     232  /**
     233    The name of the "CA_RQS" annotation, used
     234    for extract (RNAQC). It is a float annotation type
     235    @since 2.4
     236  */
     237  public static final String ANNOTATION_CA_RQS = "CA_RQS";
     238
    231239 
    232240  /**
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/BioplateType.java

    r1552 r1566  
    77import net.sf.basedb.core.BioPlateType;
    88import net.sf.basedb.core.BioWell.LockMode;
    9 import net.sf.basedb.core.BioSource;
    109import net.sf.basedb.core.DbControl;
    1110import net.sf.basedb.core.Include;
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r1549 r1566  
    189189        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_BA_RIN, Item.EXTRACT, Type.FLOAT, 1,
    190190            null, effectiveOptions, createIfMissing));
     191        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_CA_RQS, Item.EXTRACT, Type.FLOAT, 1,
     192            null, effectiveOptions, createIfMissing));
    191193        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_ND_CONC, Item.EXTRACT, Type.FLOAT, 1,
    192194            null, effectiveOptions, createIfMissing));
     
    224226
    225227        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RNAQC, createIfMissing,
    226             Reggie.ANNOTATION_BA_RIN, Reggie.ANNOTATION_QC_HISENSE));
     228            Reggie.ANNOTATION_BA_RIN, Reggie.ANNOTATION_CA_RQS, Reggie.ANNOTATION_QC_HISENSE));
    227229       
    228230        json.put("checks", jsonChecks);
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/RnaQcServlet.java

    r1564 r1566  
    429429        AnnotationType qcRunDate = Reggie.findAnnotationType(dc, Item.BIOPLATE, Reggie.ANNOTATION_QC_RUN_DATE, true);
    430430        AnnotationType qcOperator = Reggie.findAnnotationType(dc, Item.BIOPLATE, Reggie.ANNOTATION_QC_OPERATOR, true);
    431         AnnotationType rin = Reggie.findAnnotationType(dc, Item.EXTRACT, Reggie.ANNOTATION_BA_RIN, true);
     431        AnnotationType rqs = Reggie.findAnnotationType(dc, Item.EXTRACT, Reggie.ANNOTATION_CA_RQS, true);
    432432       
    433433        File csv = File.getById(dc, csvId.intValue());
    434434       
    435435        CaliperPlateImporter cpi = new CaliperPlateImporter();
    436         cpi.setAnnotationMapping("RNA Quality Score", rin);
     436        cpi.setAnnotationMapping("RNA Quality Score", rqs);
    437437       
    438438        if (cpi.doImport(dc, csv.getDownloadStream(0)))
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