Changeset 589


Ignore:
Timestamp:
Feb 20, 2008, 3:49:58 PM (13 years ago)
Author:
Martin Svensson
Message:

References #100 Installation is now including SNP platform-variant and data file types but metadata-extractor and validator are not being set for the data file types. Depends on #93
New SNP-specific columns have been added to extended-properties.

Location:
trunk/net/sf/basedb/illumina
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/net/sf/basedb/illumina/config/illumina-extended-properties.xml

    r580 r589  
    33<!--
    44  Extended properties file with definitions for reporter annotations
    5   that are specific to the Illumina platform. You should manually
    6   copy the annotations that you want from this file into your main
    7   extended-properties.xml file.
     5  that are specific to the Illumina platform. You should manually 
     6  add/remove wanted columns and copy this file into your
     7  [base2home]/www/WEB-INF/classes/extended-properties/ directory
    88-->
    99<extended-properties>
     
    9797      length="255"
    9898    />
     99    <property
     100      name="ilmnStrand"
     101      title="Ilmn strand"
     102      description="Strand definition of the SNP"
     103      column="ilmnStrand"
     104      type="string"
     105      length="255"
     106    />
     107    <property
     108      name="snp"
     109      title="SNP"
     110      description="Type of SNP"
     111      column="snp"
     112      type="string"
     113      length="255"
     114    />
    99115  </class>
    100116</extended-properties>
  • trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/Illumina.java

    r572 r589  
    6565    <code>PlatformVariant.getByExternalId(dc, Illumina.SNP_VARIANT_ID)<code>
    6666    to load this item.
    67   *//*TODO
     67  */
    6868  public static final String SNP_VARIANT_ID = "illumina.snp";
    69   */
     69 
     70  /**
     71    The ID for Illumina SNP manifest file types. Use
     72    <code>DataFileType.getByExternalId(dc, Illumina.SNP_MANIFEST_FILE_ID)</code>
     73    to load this item.
     74   */
     75  public static final String SNP_MANIFEST_FILE_ID = "illumina.snp.manifest";
     76 
     77  /**
     78    The ID for Illumina SNP split data file type. Use
     79    <code>DataFileType.getByExternalId(dc, Illumina.SNP_SPLITDATA_FILE_ID)</code>
     80    to load this item.
     81   */
     82  public static final String SNP_SPLITDATA_FILE_ID = "illumina.snp.splitdata";
     83 
     84  /**
     85    The ID for Illumina SNP orginal data file type. Use
     86    <code>DataFileType.getByExternalId(dc, Illumina.SNP_DATA_FILE_ID)</code>
     87    to load this item.
     88   */
     89  public static final String SNP_DATA_FILE_ID = "illumina.snp.data";
    7090 
    7191  /**
     
    85105    Class name of the BGX validator and meta data extractor
    86106   */
    87   public static final String BGX_VALIDATOR_METADATAREADER = "net.sf.basedb.illumina.filehandler.BgxFileHandler"; 
    88  
     107  public static final String BGX_VALIDATOR_METADATAREADER = "net.sf.basedb.illumina.filehandler.BgxFileHandler";
    89108 
    90109  /**
  • trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/install/Install.java

    r587 r589  
    113113  private static final Set<Permissions> permissions = new HashSet<Permissions>();
    114114
    115   /*TODO SNP
    116   private static final PluginParameter<Boolean> installSnpVariantParameter
    117   */   
     115  private PluginParameter<String> installSnpVariantParameter;
    118116  private PluginParameter<String> installExp1VariantParameter;
    119117  private PluginParameter<String> installExp2VariantParameter;
     
    160158  private static final String BGX_FILEYTPE_EXTENSION = "bgx";
    161159  private static final String BEAD_SUMMARY_FILETYPE_EXTENSION = "csv";
    162   /*
    163   TODO
    164   private static final String SNP_FILETYPE_EXTENSION = "";
    165   */
     160  private static final String SNP_MF_FILETYPE_EXTENSION = "csv";
     161  private static final String SNP_SPLITDATA_FILETYPE_EXTENSION = "split";
     162 
    166163  private static final PluginParameter<String> alreadyInstalledErrorParameter = new PluginParameter<String>(
    167164    "alreadyInstalledError",
     
    221218      try
    222219      {
    223         /*TODO SNP
    224         boolean installSnp = (Boolean)job.getValue("installSnp");
    225         */
    226220        boolean installExp1 = YES_OPTION.equals(job.getValue("installExp1"));
    227         boolean installExp2 = YES_OPTION.equals(job.getValue("installExp2"));       
     221        boolean installExp2 = YES_OPTION.equals(job.getValue("installExp2"));
     222        boolean installSnp = YES_OPTION.equals(job.getValue("installSnp"));
    228223        boolean installScanner = YES_OPTION.equals(job.getValue("installScanner"));
    229224        boolean installSoftware = YES_OPTION.equals(job.getValue("installSoftware"));
     
    245240        }
    246241       
    247         installIlluminaItems(dc, false, expressionTypes, ignoreExisingItems, progress);
     242        installIlluminaItems(dc, installSnp, expressionTypes, ignoreExisingItems, progress);
    248243        if (installScanner)
    249244        {
     
    342337      storeValue(job, request, installExp1VariantParameter);
    343338      storeValue(job, request, installExp2VariantParameter);
    344       /*TODO SNP
    345339      storeValue(job, request, installSnpVariantParameter);
    346       */
    347340     
    348341      storeValue(job, request, installScannerParameter);
     
    409402    String jarPath = PluginDefinition.getByClassName(dc, this.getClass().getName()).getJarPath();
    410403
    411     /*TODO SNP
    412     String snpVariantExternalId = "illumina.snp";
    413     */
    414404    String expExternalIdPrefix = "illumina.exp";
    415405    String beadSummaryTypePrefix = "illlumina.ibs.";
     
    445435      dataFileTypes.put(dft.getExternalId(), dft);
    446436    }
    447     //TODO Create data file type for SNP filer.
     437   
     438    //TODO Define each filetype's validatorclass, metadatareaderclass.
     439    DataFileType snpManifestType = createDataFileType(dc,
     440        Illumina.SNP_MANIFEST_FILE_ID, "SNP manifest file", "Manifest file for Illumina SNP",
     441        Item.ARRAYDESIGN, SNP_MF_FILETYPE_EXTENSION, reporterMapType, null, null,
     442        jarPath, ignoreExistingItems);
     443    DataFileType snpSplitDataType = createDataFileType(dc,
     444        Illumina.SNP_SPLITDATA_FILE_ID, "SNP split data file", "Data file for Illumina SNP. Contains data for only one sample",
     445        Item.RAWBIOASSAY, SNP_SPLITDATA_FILETYPE_EXTENSION, rawDataType,
     446        null, null, jarPath, ignoreExistingItems);
     447    DataFileType snpDataType = createDataFileType(dc,
     448        Illumina.SNP_DATA_FILE_ID, "SNP original data file", "The original data file exported from Illumina BeadStudio",
     449        Item.RAWBIOASSAY, null, rawDataType,
     450        null, null, jarPath, ignoreExistingItems);
    448451   
    449452    //Platform and variants
     
    472475    }
    473476   
    474     /*TODO SNP
     477   
    475478    if (installSNP != null && installSNP)
    476479    {
    477480      PlatformVariant pfv = createPlatformVariant(dc, Illumina.SNP_VARIANT_ID,
    478           "Illumina SNP", illuminaPlatform, 2, ignoreExistingItems);
     481          "SNP", illuminaPlatform, 3, ignoreExistingItems);
    479482      if (pfv.getDescription() == null || pfv.getDescription().equals(""))
    480483      {
    481         pfv.setDescription("Platform variant to be used with Illumina SNP data.");
    482       }
    483       //TODO Add data file types to the SNP variant.
     484        pfv.setDescription("Platform variant to use with Illumina SNP data.");
     485      }
     486      pfv.addFileType(snpManifestType, true);
     487      pfv.addFileType(snpSplitDataType, true);
     488      pfv.addFileType(snpDataType, false);
    484489      platformVariants.add(pfv);       
    485     }
    486     */ 
     490    }
    487491  }
    488492
     
    517521          installOptionType
    518522        );
     523     
     524      installSnpVariantParameter = new PluginParameter<String>
     525      (
     526        "installSnp",
     527        "Create SNP",
     528        "Select '" + YES_OPTION + "' to create an Illumina SNP variant.",
     529        installOptionType
     530      );
    519531     
    520532      installScannerParameter = new PluginParameter<String>
     
    617629     
    618630      List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
    619       /*TODO SNP
    620       parameters.add(installSnpVariantParameter);
    621       */
     631     
    622632      parameters.add(variantSection);
    623633      parameters.add(installExp1VariantParameter);
    624634      parameters.add(installExp2VariantParameter);
     635      parameters.add(installSnpVariantParameter);
    625636     
    626637      parameters.add(hardwareSection);
     
    814825 
    815826  /*
    816     TODO SNP
    817827    Creates file-only platform variants, eg. SNP
    818    *
     828   */
    819829  private PlatformVariant createPlatformVariant(DbControl dc, String externalId,
    820830      String name, Platform platform, int channels, boolean ignoreExistingItems)
     
    841851    }
    842852    return variant;
    843   }*/
     853  }
    844854}
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