Changeset 4124


Ignore:
Timestamp:
Feb 4, 2008, 2:36:46 PM (15 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #915: NullPointerException? when a raw data type is missing

Use RawDataTypes?.getSafeRawDataType() instead, which throws an exception immediately.

Location:
trunk/src
Files:
22 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ExperimentTransfer.java

    r3683 r4124  
    116116    }
    117117    Experiment experiment = Experiment.getNew(
    118         dc, RawDataTypes.getRawDataType("genepix"));
     118        dc, RawDataTypes.getSafeRawDataType("genepix"));
    119119    setCommonItemData(dc, (CommonItem) experiment, rs);
    120120    experiment.setAuthors(rs.getString(9));

  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java

    r3824 r4124  
    129129    if (generic == null) generic = Platform.getByExternalId(dc, Platform.GENERIC);
    130130    RawBioAssay rawBioAssay = RawBioAssay.getNew(
    131         dc, generic, RawDataTypes.getRawDataType("genepix"));
     131        dc, generic, RawDataTypes.getSafeRawDataType("genepix"));
    132132    setCommonItemData(dc, rawBioAssay, rs);
    133133    File file = uploadFT.getRawBioAssayFileById(dc, rs.getInt(1));

  • trunk/src/core/net/sf/basedb/core/BioAssay.java

    r4011 r4124  
    338338  public RawDataType getRawDataType()
    339339  {
    340     return RawDataTypes.getRawDataType(getData().getBioAssaySet().getExperiment().getRawDataType());
     340    return RawDataTypes.getSafeRawDataType(getData().getBioAssaySet().getExperiment().getRawDataType());
    341341  }
    342342

  • trunk/src/core/net/sf/basedb/core/BioAssaySet.java

    r4011 r4124  
    417417  public RawDataType getRawDataType()
    418418  {
    419     return RawDataTypes.getRawDataType(getData().getExperiment().getRawDataType());
     419    return RawDataTypes.getSafeRawDataType(getData().getExperiment().getRawDataType());
    420420  }
    421421 

  • trunk/src/core/net/sf/basedb/core/DataCube.java

    r3679 r4124  
    223223  public RawDataType getRawDataType()
    224224  {
    225     return RawDataTypes.getRawDataType(getData().getVirtualDb().getExperiment().getRawDataType());
     225    return RawDataTypes.getSafeRawDataType(getData().getVirtualDb().getExperiment().getRawDataType());
    226226  }
    227227 

  • trunk/src/core/net/sf/basedb/core/Experiment.java

    r3974 r4124  
    292292  public RawDataType getRawDataType()
    293293  {
    294     return RawDataTypes.getRawDataType(getData().getRawDataType());
     294    return RawDataTypes.getSafeRawDataType(getData().getRawDataType());
    295295  }
    296296 

  • trunk/src/core/net/sf/basedb/core/ExtraValue.java

    r4017 r4124  
    261261  public RawDataType getRawDataType()
    262262  {
    263     return RawDataTypes.getRawDataType(getData().getBioAssaySet().getExperiment().getRawDataType());
     263    return RawDataTypes.getSafeRawDataType(getData().getBioAssaySet().getExperiment().getRawDataType());
    264264  }
    265265

  • trunk/src/core/net/sf/basedb/core/RawBioAssay.java

    r4095 r4124  
    571571  public RawDataType getRawDataType()
    572572  {
    573     return RawDataTypes.getRawDataType(getData().getRawDataType());
     573    return RawDataTypes.getSafeRawDataType(getData().getRawDataType());
    574574  }
    575575 

  • trunk/src/core/net/sf/basedb/core/RawDataTypes.java

    r4096 r4124  
    227227      return rawDataTypes.get(id);
    228228    }
     229  }
     230 
     231  /**
     232    Get a information about a raw data type or throw an exception if the
     233    raw data type is not found.
     234 
     235    @param id The id of the raw data type
     236    @return A <code>RawDataType</code> object with information about the
     237      raw data type
     238    @throws ItemNotFoundException If the specified raw data type is not found
     239    @since 2.6
     240  */
     241  public static RawDataType getSafeRawDataType(String id)
     242  {
     243    RawDataType rdt = getRawDataType(id);
     244    if (rdt == null) throw new ItemNotFoundException("RawDataType[id=" + id + "]");
     245    return rdt;
    229246  }
    230247 

  • trunk/src/core/net/sf/basedb/core/VirtualDb.java

    r4119 r4124  
    170170  public RawDataType getRawDataType()
    171171  {
    172     return RawDataTypes.getRawDataType(getData().getExperiment().getRawDataType());
     172    return RawDataTypes.getSafeRawDataType(getData().getExperiment().getRawDataType());
    173173  }
    174174

  • trunk/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java

    r4107 r4124  
    252252      }
    253253      Experiment experiment = (Experiment)item;
    254       RawDataType illumina = RawDataTypes.getRawDataType("illumina");
     254      RawDataType illumina = RawDataTypes.getSafeRawDataType("illumina");
    255255      if (illumina != experiment.getRawDataType())
    256256      {
    … …  
    409409    super.begin(ffp);
    410410    this.ffp = ffp;
    411     this.illumina = RawDataTypes.getRawDataType("illumina");
     411    this.illumina = RawDataTypes.getSafeRawDataType("illumina");
    412412    this.numberFormat = ffp.getDefaultNumberFormat();
    413413    this.headerLines = new LinkedList<Line>();

  • trunk/src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java

    r4107 r4124  
    398398    else if(command.equals(COMMAND_CONFIGURE_PARSER))
    399399    {
    400       RawDataType rdt = RawDataTypes.getRawDataType((String)configuration.getValue("rawDataType"));
     400      RawDataType rdt = RawDataTypes.getSafeRawDataType((String)configuration.getValue("rawDataType"));
    401401      requestInformation = getConfigureParserParameters(rdt);
    402402    }
    … …  
    435435      else if (command.equals(COMMAND_CONFIGURE_PARSER))
    436436      {
    437         RawDataType rdt = RawDataTypes.getRawDataType((String)configuration.getValue("rawDataType"));
     437        RawDataType rdt = RawDataTypes.getSafeRawDataType((String)configuration.getValue("rawDataType"));
    438438        RequestInformation ri = getConfigureParserParameters(rdt);
    439439        List<Throwable> errors = validateRequestParameters(ri.getParameters(), request);

  • trunk/src/test/TestAnalyzePluginUtil.java

    r4093 r4124  
    5454    {
    5555      dc = TestUtil.getDbControl();
    56       Experiment e = Experiment.getNew(dc, RawDataTypes.getRawDataType("genepix"));
     56      Experiment e = Experiment.getNew(dc, RawDataTypes.getSafeRawDataType("genepix"));
    5757      e.setName("TestAnalyze");
    5858      e.setDescription("Experiment created by TestAnalyzePluginUtil.");

  • trunk/src/test/TestBioAsssaySetExporter.java

    r4093 r4124  
    279279      dc = TestUtil.getDbControl();
    280280      Platform generic = Platform.getByExternalId(dc, Platform.GENERIC);
    281       RawBioAssay rba = RawBioAssay.getNew(dc, generic, RawDataTypes.getRawDataType("genepix"));
     281      RawBioAssay rba = RawBioAssay.getNew(dc, generic, RawDataTypes.getSafeRawDataType("genepix"));
    282282      AnnotationType at = AnnotationType.getById(dc, annotationTypeId);
    283283     

  • trunk/src/test/TestExperiment.java

    r3973 r4124  
    164164    {
    165165      dc = TestUtil.getDbControl();
    166       Experiment e = Experiment.getNew(dc, RawDataTypes.getRawDataType(rawDataType));
     166      Experiment e = Experiment.getNew(dc, RawDataTypes.getSafeRawDataType(rawDataType));
    167167      if (setAll)
    168168      {

  • trunk/src/test/TestJep.java

    r3679 r4124  
    7979    try
    8080    {
    81       Jep.newJep(formula, new RawFunction(null, RawDataTypes.getRawDataType("genepix"), true));
     81      Jep.newJep(formula, new RawFunction(null, RawDataTypes.getSafeRawDataType("genepix"), true));
    8282      write("--Parse formula: "+formula+" OK");
    8383    }
    … …  
    9494    try
    9595    {
    96       Expression e = Jep.formulaToExpression(formula, new RawFunction(null, RawDataTypes.getRawDataType("genepix"), true));
     96      Expression e = Jep.formulaToExpression(formula, new RawFunction(null, RawDataTypes.getSafeRawDataType("genepix"), true));
    9797      write(e);
    9898      write("--Jep to Expression: "+formula+" OK");
    … …  
    111111    {
    112112      Restriction r = Jep.formulaToRestriction(formula,
    113         new RawFunction(null, RawDataTypes.getRawDataType("genepix"), true));
     113        new RawFunction(null, RawDataTypes.getSafeRawDataType("genepix"), true));
    114114      write(r);
    115115      write("--Jep to Restriction: "+formula+" OK");

  • trunk/src/test/net/sf/basedb/test/merge/MergeTest.java

    r4093 r4124  
    116116      // Raw bioassays
    117117      dc = TestUtil.getDbControl();
    118       RawDataType genepix = RawDataTypes.getRawDataType("genepix");
     118      RawDataType genepix = RawDataTypes.getSafeRawDataType("genepix");
    119119      RawBioAssay rba1 = createRawBioAssay(dc, generic, genepix, "Raw bioassay for merge test #1", design);
    120120      RawBioAssay rba2 = createRawBioAssay(dc, generic, genepix, "Raw bioassay for merge test #2", design);
    … …  
    134134      // Root bioassayset's
    135135      dc = TestUtil.getDbControl();
    136       Formula formula = Util.findFormula(dc, RawDataTypes.getRawDataType("genepix"), Formula.Type.INTENSITY_EXPRESSION, "Mean FG");
     136      Formula formula = Util.findFormula(dc, RawDataTypes.getSafeRawDataType("genepix"), Formula.Type.INTENSITY_EXPRESSION, "Mean FG");
    137137      dc.commit();
    138138      BioAssaySet root = createRootBioAssaySet(experiment, "Root", formula);
    … …  
    266266  {
    267267    TestUtil.write("--Creating experiment: " + name + "\n");
    268     Experiment experiment = Experiment.getNew(dc, RawDataTypes.getRawDataType("genepix"));
     268    Experiment experiment = Experiment.getNew(dc, RawDataTypes.getSafeRawDataType("genepix"));
    269269    experiment.setName(name);
    270270   

  • trunk/src/test/net/sf/basedb/test/performance/RawDataTest.java

    r3820 r4124  
    6767      dc = TestUtil.getDbControl();
    6868      Platform generic = Platform.getByExternalId(dc, Platform.GENERIC);
    69       RawDataType genepix = RawDataTypes.getRawDataType("genepix");
     69      RawDataType genepix = RawDataTypes.getSafeRawDataType("genepix");
    7070     
    7171      // Load prepared items

  • trunk/src/test/net/sf/basedb/test/performance/Util.java

    r3820 r4124  
    6969  {
    7070    TestUtil.write("--Creating experiment: " + name + "\n");
    71     Experiment experiment = Experiment.getNew(dc, RawDataTypes.getRawDataType("genepix"));
     71    Experiment experiment = Experiment.getNew(dc, RawDataTypes.getSafeRawDataType("genepix"));
    7272    experiment.setName(name);
    7373    dc.saveItem(experiment);

  • trunk/src/test/net/sf/basedb/test/roles/AnalysisTest.java

    r4025 r4124  
    9191        activeProject, options, 2);
    9292     
    93       Formula formula = Util.findFormula(dc, RawDataTypes.getRawDataType("genepix"), Formula.Type.INTENSITY_EXPRESSION, "Mean FG - Mean BG");
     93      Formula formula = Util.findFormula(dc, RawDataTypes.getSafeRawDataType("genepix"), Formula.Type.INTENSITY_EXPRESSION, "Mean FG - Mean BG");
    9494      dc.close();
    9595     

  • trunk/src/test/net/sf/basedb/test/roles/PowerUserTest.java

    r4095 r4124  
    178178     
    179179      dc = TestUtil.getDbControl();
    180       RawDataType genepix = RawDataTypes.getRawDataType("genepix");
     180      RawDataType genepix = RawDataTypes.getSafeRawDataType("genepix");
    181181      p = Project.getById(dc, p.getId());
    182182      p.setDefaultItem(dc, genericPlatform, Project.Default.PLATFORM);

  • trunk/src/test/net/sf/basedb/test/roles/UserTest.java

    r4095 r4124  
    153153      ArrayDesign genericDesign = Util.findArrayDesign(dc, "Array design A");
    154154      ArrayDesign affymetrixDesign = Util.findArrayDesign(dc, "Affymetrix A");
    155       RawDataType genepix = RawDataTypes.getRawDataType("genepix");
     155      RawDataType genepix = RawDataTypes.getSafeRawDataType("genepix");
    156156      RawBioAssay rba1 = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.00h", sc1, genericDesign);
    157157      RawBioAssay rba2 = createRawBioAssay(dc, genericPlatform, genepix, "Raw bioassay A.24h", sc2, genericDesign);
    … …  
    194194      dc = TestUtil.getDbControl();
    195195      Experiment exp1 = createExperiment(dc, "Experiment A",
    196         RawDataTypes.getRawDataType("genepix"), rba1, rba2, rba1DyeSwap, rba2DyeSwap);
     196        RawDataTypes.getSafeRawDataType("genepix"), rba1, rba2, rba1DyeSwap, rba2DyeSwap);
    197197      Experiment affyExperiment = createExperiment(dc, "Affymetrix A",
    198198        affymetrixPlatform.getRawDataType(), affyRaw1, affyRaw2, affyRaw3);
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