Changeset 3807

Timestamp:

Oct 5, 2007, 3:36:13 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

References #721: Most things for attaching files to rw bioassays are now in place.

Location:

branches/filedb

Files:

• config/dist/raw-data-types.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/Affymetrix.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Application.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ArrayDesign.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/FileSet.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/InvalidRelationException.java (added)
• src/core/net/sf/basedb/core/Platform.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PlatformVariant.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (12 diffs)
• src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/RawDataType.java (modified) (8 diffs)
• src/core/net/sf/basedb/core/RawDataTypes.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/RawBioAssayData.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/filehandler/AffymetrixFileHandler.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/filehandler/CdfFileHandler.java (modified) (1 diff)
• src/core/net/sf/basedb/core/filehandler/CelFileHandler.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/filehandler/DataFileValidator.java (modified) (3 diffs)
• www/common/datafiles/select_files.jsp (modified) (2 diffs)
• www/include/scripts/platforms.js (modified) (1 diff)
• www/lims/arraydesigns/edit_design.jsp (modified) (6 diffs)
• www/lims/arraydesigns/list_designs.jsp (modified) (2 diffs)
• www/views/rawbioassays/edit_rawbioassay.jsp (modified) (19 diffs)
• www/views/rawbioassays/index.jsp (modified) (7 diffs)
• www/views/rawbioassays/list_rawbioassays.jsp (modified) (6 diffs)
• www/views/rawbioassays/view_rawbioassay.jsp (modified) (5 diffs)

branches/filedb/config/dist/raw-data-types.xml

@@ -649 +649 @@
     </intensity-formula>
   </raw-data-type>
-  
-  <raw-data-type
-    id="affymetrix"
-    channels="1"
-    name="Affymetrix"
-    storage="file"
-    >
-  </raw-data-type>
-  
+
   <raw-data-type
     id="agilent"

branches/filedb/src/core/net/sf/basedb/core/Affymetrix.java

@@ -27 +27 @@
 import net.sf.basedb.core.data.ReporterData;
 import net.sf.basedb.core.filehandler.CdfFileHandler;
+import net.sf.basedb.core.filehandler.CelFileHandler;
 import affymetrix.fusion.cdf.FusionCDFData;
 import affymetrix.fusion.cel.FusionCELData;
@@ -162 +163 @@
       raw data type
     @throws BaseException If there is another error
-    @deprecated
+    @deprecated Use {@link FileStoreUtil#setDataFile(DbControl, FileStoreEnabled, String, File)}
+      instead with {@link DataFileType#AFFYMETRIX_CEL} as the file
+      type
   */
   public static void setCelFile(RawBioAssay rawBioAssay, File file)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
-    // Validate raw bioassay
     if (rawBioAssay == null) throw new InvalidUseOfNullException("rawBioAssay");
-    if (!rawBioAssay.getRawDataType().isAffymetrix()) 
-    {
-      throw new InvalidDataException("Raw data type for " + rawBioAssay.getName() + 
-        " is not an Affymetrix raw data type");
-    }
     rawBioAssay.checkPermission(Permission.WRITE);
-  
+
+    if (!rawBioAssay.isPlatform(Platform.AFFYMETRIX)) 
+    {
+      throw new InvalidDataException("Raw bioassay isn't an Affymetrix chip: " + rawBioAssay.getName());
+    }
     DbControl dc = rawBioAssay.getDbControl();
-    if (file != null) 
-    {
-      // Validate array design
-      ArrayDesign design = rawBioAssay.getArrayDesign();
-      if (design == null) 
-      {
-        throw new InvalidDataException("Raw bioassay " + rawBioAssay.getName() + 
-          " must have an array design to set CEL file");
-      }
-      if (!design.isPlatform(Platform.AFFYMETRIX))
-      {
-        throw new InvalidDataException("The array design " + design.getName() + 
-          " is not an Affymterix design");
-      }
-  
-      // Verify that CEL chip type match CDF type
-      FusionCELData cel = loadCelFile(file);
-      File cdfFile = getCdfFile(design);
-      FusionCDFData cdf = loadCdfFile(cdfFile);
-      validateCelAndCdf(cel, cdf, cdfFile.getName());
-      
-      file.checkPermission(Permission.USE);
-      AnyToAny ata = AnyToAny.getNewOrExisting(dc, rawBioAssay, CEL_LINK_NAME, file, true);
-      if (!ata.isInDatabase()) dc.saveItem(ata);
-      
-      // Set headers
-      setHeader(rawBioAssay, "Algorithm", cel.getAlg());
-      for (int i = 0; i < cel.getNumberAlgorithmParameters(); ++i)
-      {
-        String name = cel.getAlgorithmParameterTag(i);
-        setHeader(rawBioAssay, "Algorithm parameter: " + name, cel.getAlgorithmParameter(name));
-      }
-      setHeader(rawBioAssay, "Dat header", cel.getDatHeader());
-      setHeader(rawBioAssay, "Chip type", cel.getChipType());
-      
-      // Set number of spots
-      rawBioAssay.getData().setHasData(true);
-      rawBioAssay.getData().setSpots(cel.getCells());
-      
-    }
-    else
-    {
-      AnyToAny.unlinkFrom(dc, rawBioAssay, CEL_LINK_NAME);
-      rawBioAssay.getData().setHasData(false);
-      rawBioAssay.getData().setSpots(0);
-    }
-  }
-  
-  private static void setHeader(RawBioAssay rba, String name, String value)
-  {
-    if (name == null || value == null) return;
-    rba.setHeader(name, value);
+    FileStoreUtil.setDataFile(dc, rawBioAssay, DataFileType.AFFYMETRIX_CEL, file);
+    if (file != null) rawBioAssay.getFileSet().validate(dc, true);
   }
   
@@ -349 +300 @@
     @throws InvalidDataException If the file is not a CEL file
     @since 2.4
+    @deprecated Use {@link CdfFileHandler#loadCdfFile(File)} instead
   */
   public static FusionCELData loadCelFile(File celFile)
     throws InvalidDataException
   {
-    if (celFile == null) throw new InvalidUseOfNullException("celFile");
-    if (celFile.getLocation() != Location.PRIMARY)
-    {
-      throw new ItemNotFoundException("File data is not online for file '" + 
-          celFile.getName() + "'; location=" + celFile.getLocation());
-    }
-    FusionCELData cel = new FusionCELData();
-    cel.setFileName(celFile.getName());
-    cel.setInputStream(celFile.getDownloadStream(0));
-    if (!cel.readHeader())
-    {
-      throw new InvalidDataException("Could not read CEL file '" +
-          celFile.getPath()+"': " + cel.getError());
-    }
-    return cel;
+    return new CelFileHandler().loadCelFile(celFile);
   }
   

branches/filedb/src/core/net/sf/basedb/core/Application.java

@@ -468 +468 @@
         Keyring.init();
         HibernateUtil.testTransactions();
+        RawDataTypes.initPlatforms();
   
         // Adding a task that cleans the session control cache at regular intervale

branches/filedb/src/core/net/sf/basedb/core/ArrayDesign.java

@@ -299 +299 @@
       write permission
     @throws InvalidDataException If platform is null
+    @since 2.5
   */
   public void setPlatform(Platform platform)
@@ -316 +317 @@
     @throws PermissionDeniedException If the logged in user doesn't have
       write permission
+    @since 2.5
   */
   public void setVariant(PlatformVariant variant)
@@ -337 +339 @@
     @return TRUE if either the variant of platform matches the
       external ID
+    @since 2.5
   */
   public boolean isPlatform(String externalId)
@@ -353 +356 @@
     If the array design has a platform variant, the setting from the 
     variant is returned, otherwise the setting from the platform.
-    @return TRUE if this array design use a file-only platform
+    @return TRUE if this array design use a file-only variant / platform
+    @since 2.5
   */
   public boolean isFileOnlyPlatform()
@@ -709 +713 @@
   }
   
+  /**
+    Set the number of features that are stored in files.
+    @param numFeatures The number of features
+    @since 2.5
+  */
   public void setNumFileFeatures(int numFeatures)
   {

branches/filedb/src/core/net/sf/basedb/core/FileSet.java

@@ -538 +538 @@
       boolean ignore = false;
       boolean isValid = true;
+      boolean invalidRelation = false;
       String errorMessage = null;
       if (handler.isValidator)
@@ -547 +548 @@
         catch (Throwable t)
         {
+          invalidRelation = t instanceof InvalidRelationException;
           ignore = t instanceof PermissionDeniedException;
           errors.add(t);
           isValid = false;
           errorMessage = t.getMessage();
-          if (!ignore) handler.resetMetadata(dc);
+          if (!ignore && !invalidRelation) handler.resetMetadata(dc);
         }
       }
-      if (extractMetadata && handler.isMetadataReader && isValid)
+      if (extractMetadata && handler.isMetadataReader && (isValid || invalidRelation))
       {
         try

branches/filedb/src/core/net/sf/basedb/core/Platform.java

@@ -378 +378 @@
     if (isFileOnly())
     {
-      // TODO - autogenerate a raw data type in a proper way
-      rdt = new RawDataType(getExternalId(), getName(), getDescription(), getData().getChannels(), 
-        "file", null, null, null);
+      rdt = RawDataTypes.getRawDataType("platform." + getExternalId());
     }
     else

branches/filedb/src/core/net/sf/basedb/core/PlatformVariant.java

@@ -408 +408 @@
     if (isFileOnly())
     {
-      // TODO - autogenerate a raw data type
-      rdt = new RawDataType(getExternalId(), getName(), getDescription(), getData().getChannels(), 
-          "file", null, null, null);
+      rdt = RawDataTypes.getRawDataType("variant." + getExternalId());
     }
     else

branches/filedb/src/core/net/sf/basedb/core/RawBioAssay.java

@@ -102 +102 @@
     throws BaseException
   {
-    Platform generic = Platform.getById(dc, SystemItems.getId(Platform.GENERIC));
+    Platform generic = Platform.getByExternalId(dc, 
+      rawDataType.isAffymetrix() ? Platform.AFFYMETRIX : Platform.GENERIC);
     return getNew(dc, generic, rawDataType);
   }
@@ -116 +117 @@
   }
   
-  /*
   public static RawBioAssay getNew(DbControl dc, PlatformVariant variant, RawDataType rawDataType)
   {
-    
-  }
-  */
+    RawBioAssay rba = dc.newItem(RawBioAssay.class);
+    rba.setVariant(variant);
+    RawDataType variantRdt = variant.getRawDataType();
+    rba.setRawDataType(variantRdt != null ? variantRdt : rawDataType);
+    rba.setName("New raw bioassay");
+    return rba;
+  
+  }
 
   /**
@@ -349 +354 @@
   // -------------------------------------------
 
+  /**
+    Set the platform of the raw bioassay. This method will set the variant
+    to null. Use {@link #setVariant(PlatformVariant)} if you want to
+    set a specific variant.
+    @param platform The new platform
+    @throws PermissionDeniedException If the logged in user doesn't have
+      write permission
+    @throws InvalidDataException If platform is null
+    @since 2.5
+  */
   public void setPlatform(Platform platform)
   {
@@ -357 +372 @@
   }
   
+  /**
+    Set the platform and variant of the raw bioassay. This method will 
+    automatically set the platform to {@link PlatformVariant#getPlatform()}.
+  
+    @param variant The new platform variant, or null to remove
+      the variant and keep the platform as it is
+    @throws PermissionDeniedException If the logged in user doesn't have
+      write permission
+    @since 2.5
+  */
   public void setVariant(PlatformVariant variant)
   {
@@ -370 +395 @@
     }
   } 
+  
+  /**
+    Check if the platform/variant of this raw bioassay has the
+    given external ID. 
+    @param externalId The external ID to match
+    @return TRUE if either the variant of platform matches the
+      external ID
+    @since 2.5
+  */
+  public boolean isPlatform(String externalId)
+  {
+    if (externalId == null) return false;
+    if (externalId.equals(getData().getPlatform().getExternalId())) return true;
+    if (getData().getVariant() != null)
+    {
+      if (externalId.equals(getData().getVariant().getExternalId())) return true;
+    }
+    return false;
+  }
+
+  /**
+    Check if this raw bioassay uses a file-only platform or variant.
+    If the raw bioassay has a platform variant, the setting from the 
+    variant is returned, otherwise the setting from the platform.
+    @return TRUE if this raw bioassay use a file-only variant / platform
+    @since 2.5
+  */
+  public boolean isFileOnlyPlatform()
+  {
+    if (getData().getVariant() != null)
+    {
+      return getData().getVariant().isFileOnly();
+    }
+    else
+    {
+      return getData().getPlatform().isFileOnly();
+    }
+  }
   
   /**
@@ -393 +456 @@
     checkPermission(Permission.WRITE);
     if (rawDataType == null) throw new InvalidUseOfNullException("rawDataType");
-    if (getData().getSpots() > 0) 
+    if (getData().getNumDbSpots() > 0) 
     {
       throw new PermissionDeniedException("Not allowed to change the raw data type after raw data has been added");
@@ -523 +586 @@
     checkPermission(Permission.WRITE);
     if (arrayDesign != null) arrayDesign.checkPermission(Permission.USE);
-    if (getData().getSpots() > 0) 
+    if (getData().getNumDbSpots() > 0) 
     {
       throw new PermissionDeniedException("Not allowed to change the array design after raw data has been added");
@@ -550 +613 @@
     checkPermission(Permission.WRITE);
     if (arrayDesign != null) arrayDesign.checkPermission(Permission.USE);
-    if (getData().getSpots() > 0 && arrayDesign != null) 
-    {
-      // No need to validate if there is no change
-      if (arrayDesign.getData().equals(getData().getArrayDesign())) return;
-  
-      if (getRawDataType().isAffymetrix())
-      {
-        // Verify CEL and CDF files
-        Affymetrix.validateCelAndCdf(this, arrayDesign, false);
-      }
-      else if (getRawDataType().isStoredInDb())
-      {
-        validateFeatures(getDbControl(), arrayDesign, true, progress);
-      }
+    
+    // No need to validate if there is no change
+    if (arrayDesign == null && getData().getArrayDesign() == null) return;
+    if (arrayDesign != null && arrayDesign.getData().equals(getData().getArrayDesign())) return;
+    
+    // Re-validate files
+    if (hasFileSet()) getFileSet().validate(getDbControl(), true);
+    
+    // Re-validate data in database if we already have db data
+    if (getData().getNumDbSpots() > 0 && arrayDesign != null) 
+    {
+      validateFeatures(getDbControl(), arrayDesign, true, progress);
     }
     getData().setArrayDesign(arrayDesign == null ? null : arrayDesign.getData());
@@ -581 +642 @@
     raw bioassay.
     @return The number of spots
+    @deprecated Use {@link #getNumDbSpots()} or {@link #getNumFileSpots()}
+      instead. This method first checks the database and if not 0, it
+      returns that value, otherwise it returns the number of file spots
   */
   public int getSpots()
   {
-    return getData().getSpots();
-  }
+    int dbSpots = getNumDbSpots();
+    return dbSpots > 0 ? dbSpots : getNumFileSpots();
+  }
+  
+  /**
+    Get the number of spots on this raw bioassay that are
+    stored in the database.
+    @return The number of spots in the database
+    @since 2.5
+  */
+  public int getNumDbSpots()
+  {
+    return getData().getNumDbSpots();
+  }
+  
+  /**
+    Get the number of spots on this raw bioassay that are
+    stored inside files.
+    @return The number of spots in files
+    @since 2.5
+  */
+  public int getNumFileSpots()
+  {
+    return getData().getNumFileSpots();
+  }
+  
+  /**
+    Set the number of spots that are stored in files.
+    @param numSpots The number of spots
+    @since 2.5
+  */
+  public void setNumFileSpots(int numSpots)
+  {
+    checkPermission(Permission.WRITE);
+    getData().setNumFileSpots(numSpots);
+    getData().setHasData(numSpots > 0 || getNumDbSpots() > 0);
+  }
+  
   
   /**
@@ -656 +756 @@
   {
     checkPermission(Permission.WRITE);
-    if (getData().getSpots() > 0) 
-    {
-      throw new PermissionDeniedException("Not allowed to change the headers after raw data has been added");
-    }
     if (name == null) throw new InvalidUseOfNullException("header.name");
     if (name.length() > MAX_HEADER_NAME_LENGTH) 
@@ -672 +768 @@
     getData().getHeaders().put(name, value);
   }
+  
+  public void removeHeaders()
+  {
+    checkPermission(Permission.WRITE);
+    getData().getHeaders().clear();
+  }
+
+  public void removeHeader(String name)
+  {
+    checkPermission(Permission.WRITE);
+    getData().getHeaders().remove(name);
+  }
+
   /**
     Get the names of all raw data headers. The set is sorted by name.
@@ -819 +928 @@
   private void validateFeatures(DbControl dc, ArrayDesign design, boolean update, ProgressReporter progress)
   {
-    if (design.isAffyChip())
-    {
-      throw new InvalidDataException("The array design is an Affymetrix chip: " + design.getName());
-    }
     if (design.hasFeatures())
     {

branches/filedb/src/core/net/sf/basedb/core/RawDataBatcher.java

@@ -306 +306 @@
     throws BaseException
   {
-    rawBioAssayData.setSpots(rawBioAssayData.getSpots() + getTotalInsertCount());
+    rawBioAssayData.setNumDbSpots(rawBioAssayData.getNumDbSpots() + getTotalInsertCount());
     rawBioAssayData.setBytes(rawBioAssayData.getBytes() + bytes);
-    rawBioAssayData.setHasData(rawBioAssayData.getSpots() > 0);
+    rawBioAssayData.setHasData(rawBioAssayData.getNumDbSpots() > 0);
     if (preloaded != null) preloaded.clear();
   }
@@ -441 +441 @@
       Statement s = HibernateUtil.getConnection(getDbControl().getHibernateSession()).createStatement();
       s.executeUpdate(sql);
-      rawBioAssayData.setSpots(0);
+      rawBioAssayData.setNumDbSpots(0);
       rawBioAssayData.setBytes(0);
-      rawBioAssayData.setHasData(false);
+      rawBioAssayData.setHasData(rawBioAssayData.getNumFileSpots() > 0);
     }
     catch (SQLException ex)

branches/filedb/src/core/net/sf/basedb/core/RawDataType.java

@@ -29 +29 @@
 import java.util.Collections;
 
+import net.sf.basedb.core.data.PlatformData;
+import net.sf.basedb.core.data.PlatformVariantData;
 import net.sf.basedb.core.data.RawData;
 
@@ -48 +50 @@
 {
 
-  private final boolean isAffymetrix;
   private final String id;
   private final String name;
   private final String description;
-  private final String storage;
-  private final boolean isStoredInDb;
+  private final boolean fileOnly;
+  private final boolean isAffymetrix;
   private final int channels;
-  private final String table;
-  private final List<RawDataProperty> properties;
-  private final Map<String, RawDataProperty> namedProperties;
-  private final List<IntensityFormula> formulas;
-  private final Map<String, IntensityFormula> namedFormulas;
-  
-  private final RealTable realTable;
+  private String table;
+  private RealTable realTable;
+  private List<RawDataProperty> properties;
+  private Map<String, RawDataProperty> namedProperties;
+  private List<IntensityFormula> formulas;
+  private Map<String, IntensityFormula> namedFormulas;
+  
 
   /**
@@ -67 +68 @@
     See the getter methods for a description of the parameters
   */
-  RawDataType(String id, String name, String description, int channels, String storage, 
+  RawDataType(String id, String name, String description, int channels, 
+    String table, List<RawDataProperty> properties, List<IntensityFormula> formulas)
+  {
+    this(id, name, description, channels, false, false, table, properties, formulas);
+  }
+  
+  RawDataType(PlatformData platform)
+  {
+    this("platform." + platform.getExternalId(), platform.getName(), 
+      platform.getDescription(), platform.getChannels(), true, 
+      Platform.AFFYMETRIX.equals(platform.getExternalId()),
+      null, null, null);
+  }
+
+  RawDataType(PlatformVariantData variant)
+  {
+    this("variant." + variant.getExternalId(), variant.getName(), 
+        variant.getDescription(), variant.getChannels(), true, 
+        Platform.AFFYMETRIX.equals(variant.getPlatform().getExternalId()),
+        null, null, null);    
+  }
+  
+  private RawDataType(String id, String name, String description, int channels, 
+    boolean fileOnly, boolean isAffymetrix,
     String table, List<RawDataProperty> properties, List<IntensityFormula> formulas)
   {
@@ -73 +97 @@
     this.name = name;
     this.description = description;
-    this.storage = storage;
     this.channels = channels;
-    this.isStoredInDb = "database".equals(storage);
-    this.table = isStoredInDb ? table : null;
-    this.properties = properties == null ? null : Collections.unmodifiableList(properties);
-    this.formulas = formulas;
-    this.realTable = isStoredInDb ? new RealTable(table, "raw") : null;
+    this.fileOnly = fileOnly;
+    this.isAffymetrix = isAffymetrix;
     
-    // This is an ugly hack to support affymetrix data
-    this.isAffymetrix = "affymetrix".equals(id);
-    
-    if (isStoredInDb && table == null)
+    // For database raw data types
+    if (!fileOnly)
     {
-      throw new InvalidDataException("No table specified for raw data type: " + id);
+      if (table == null)
+      {
+        throw new InvalidDataException("No table specified for raw data type: " + id);
+      }
+      this.table = table;
+      this.realTable = new RealTable(table, "raw");
+      
+      // Extended properties (=columns) of the table
+      if (properties == null)
+      {
+        this.properties = null;
+      }
+      else
+      {
+        this.properties = Collections.unmodifiableList(properties);
+        this.namedProperties = new HashMap<String, RawDataProperty>();
+        for (RawDataProperty property : properties)
+        {
+          if (namedProperties.put(property.getName(), property) != null)
+          {
+            throw new BaseException("RawDataProperty[name="+property.getName()+"] is already defined for raw data type: "+name);
+          }
+        }
+      }
+      
+      // Intensity formulas
+      this.formulas = formulas;
+      if (formulas != null)
+      {
+        this.namedFormulas = new HashMap<String, IntensityFormula>();
+        for (IntensityFormula formula : formulas)
+        {
+          if (namedFormulas.put(formula.getName(), formula) != null)
+          {
+            throw new BaseException("IntensityFormula[name="+formula.getName()+"] is already defined for raw data type: "+name);
+          }
+        }
+      }
     }
-    
-    this.namedProperties = new HashMap<String, RawDataProperty>(
-        properties == null ? 0 : properties.size());
-    if (properties != null)
-    {
-      for (RawDataProperty property : properties)
-      {
-        if (namedProperties.put(property.getName(), property) != null)
-        {
-          throw new BaseException("RawDataProperty[name="+property.getName()+"] is already defined for raw data type: "+name);
-        }
-      }
-    }
-    
-    this.namedFormulas = new HashMap<String, IntensityFormula>(
-        formulas == null ? 0 : formulas.size());
-    if (formulas != null)
-    {
-      for (IntensityFormula formula : formulas)
-      {
-        if (namedFormulas.put(formula.getName(), formula) != null)
-        {
-          throw new BaseException("IntensityFormula[name="+formula.getName()+"] is already defined for raw data type: "+name);
-        }
-      }
-    }
-  }
-
+  }
+  
   /**
     Get the id of this raw data type. This value is the same as the
@@ -129 +158 @@
   /**
     If this raw data type is the Affymetrix raw data type.
+    @deprecated Use --- instead
   */
   public boolean isAffymetrix()
@@ -177 +207 @@
 
   /**
-    If the raw data of this raw data type is stored in the database
+    If the raw data of this raw data type can be stored in the database
     or not.
     @see #getTableName()
@@ -183 +213 @@
   public boolean isStoredInDb()
   {
-    return isStoredInDb;
+    return !fileOnly;
   }
   
@@ -213 +243 @@
   
   /**
-    Get a list of {@link RawDataProperty}s with definitions for the
+    Get a list of {@link RawDataProperty}:s with definitions for the
     extra properties that has been defined for this raw data type.
 

branches/filedb/src/core/net/sf/basedb/core/RawDataTypes.java

@@ -26 +26 @@
 package net.sf.basedb.core;
 
+import net.sf.basedb.core.data.PlatformData;
+import net.sf.basedb.core.data.PlatformVariantData;
 import net.sf.basedb.core.dbengine.DbEngine;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.XMLUtil;
 
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -66 +69 @@
   private static Map<String, RawDataType> rawDataTypes = null;
 
+  private static Map<String, RawDataType> platformTypes = null;
+  
   /**
     The DTD which is used to validate the XML file.
@@ -86 +91 @@
   }
   
+  static synchronized void initPlatforms()
+  {
+    org.hibernate.Session session = null;
+    org.hibernate.Transaction tx = null;
+    
+    try
+    {
+      platformTypes = new HashMap<String, RawDataType>();
+      session = HibernateUtil.newSession();
+      tx = HibernateUtil.newTransaction(session);
+      
+      org.hibernate.Query query = HibernateUtil.createQuery(session, 
+        "FROM PlatformData pfd WHERE pfd.fileOnly = true");
+      for (PlatformData platform : HibernateUtil.loadList(PlatformData.class, query))
+      {
+        RawDataType rdt = new RawDataType(platform);
+        platformTypes.put(rdt.getId(), rdt);
+      }
+      
+      query = HibernateUtil.createQuery(session, 
+        "FROM PlatformVariantData pfv WHERE pfv.fileOnly = true");
+      for (PlatformVariantData variant : HibernateUtil.loadList(PlatformVariantData.class, query))
+      {
+        RawDataType rdt = new RawDataType(variant);
+        platformTypes.put(rdt.getId(), rdt);
+      }
+
+    }
+    finally
+    {
+      if (tx != null) HibernateUtil.commit(tx);
+      if (session != null) HibernateUtil.close(session);
+    }
+  }
+  
   /**
     Unload all settings.
@@ -94 +134 @@
     if (rawDataTypes != null) rawDataTypes.clear();
     rawDataTypes = null;
+    if (platformTypes != null) platformTypes.clear();
+    platformTypes = null;
   }
 
@@ -136 +178 @@
   public static RawDataType getRawDataType(String id)
   {
-    return id == null ? null : rawDataTypes.get(id);
+    if (id == null) return null;
+    if (id.startsWith("platform."))
+    {
+      return getPlatformRawDataType(id);
+    }
+    else if (id.startsWith("variant."))
+    {
+      return getVariantRawDataType(id);
+    }
+    else
+    {
+      return rawDataTypes.get(id);
+    }
+  }
+  
+  
+  private static RawDataType getPlatformRawDataType(String id)
+  {
+    RawDataType rdt = platformTypes.get(id);
+    if (rdt != null) return rdt;
+    
+    org.hibernate.Session session = null;
+    org.hibernate.Transaction tx = null;
+    try
+    {
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_PLATFORM_FOR_EXTERNAL_ID");
+      query.setString("externalId", id.substring(9));
+      PlatformData platform = HibernateUtil.loadData(PlatformData.class, query);
+      if (platform == null || !platform.isFileOnly()) return null;
+      rdt = new RawDataType(platform);
+      platformTypes.put(id, rdt);
+    }
+    finally
+    {
+      if (tx != null) HibernateUtil.commit(tx);
+      if (session != null) HibernateUtil.close(session);
+    }
+    return rdt;
+  }
+  
+  private static RawDataType getVariantRawDataType(String id)
+  {
+    RawDataType rdt = platformTypes.get(id);
+    if (rdt != null) return rdt;
+    
+    org.hibernate.Session session = null;
+    org.hibernate.Transaction tx = null;
+    try
+    {
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_PLATFORMVARIANT_FOR_EXTERNAL_ID");
+      query.setString("externalId", id.substring(9));
+      PlatformVariantData variant = HibernateUtil.loadData(PlatformVariantData.class, query);
+      if (variant == null || !variant.isFileOnly()) return null;
+      rdt = new RawDataType(variant);
+      platformTypes.put(id, rdt);
+    }
+    finally
+    {
+      if (tx != null) HibernateUtil.commit(tx);
+      if (session != null) HibernateUtil.close(session);
+    }
+    return rdt; 
   }
 
@@ -182 +287 @@
         usedNames.add("table:" + table);
       }
+      else
+      {
+        throw new ConfigurationException("Attribute storage='" + storage + 
+          "' is no longer supported. Please remove declaration for <rawdatatype id='" + id + 
+          "'> from " + Application.getRawDataTypesFile());
+      }
       if (channels <= 0)
       {
@@ -189 +300 @@
       List<RawDataProperty> properties = loadProperties(el, channels);
       List<IntensityFormula> formulas = loadIntensityFormulas(el, channels);
-      RawDataType rdt = new RawDataType(id, name, description, channels, storage, table, properties, formulas);
+      RawDataType rdt = new RawDataType(id, name, description, channels, 
+          table, properties, formulas);
       rawDataTypes.put(id, rdt);
     }

branches/filedb/src/core/net/sf/basedb/core/Update.java

@@ -1763 +1763 @@
       HibernateUtil.executeUpdate(query);
 
+      // Change filter with 'spots' to 'numDbSpots'
+      query = HibernateUtil.getPredefinedSQLQuery(session, 
+          "UPDATE_PROPERTY_FILTER");
+      /*
+        UPDATE PropertyFilters pf
+        SET pf.property = :newProperty
+        WHERE pf.property = :oldProperty
+       */
+      query.setString("oldProperty", "spots");
+      query.setString("newProperty", "numDbSpots");
+      HibernateUtil.executeUpdate(query);         
+      
       // Add READ permission to PLATFORM and DATAFILETYPE for all plug-ins
       // working with ARRAYDESIGN or RAWBIOASSAY

branches/filedb/src/core/net/sf/basedb/core/data/RawBioAssayData.java

@@ -83 +83 @@
     Get the platform this raw bioassay uses.
     @since 2.5
-    @hibernate.many-to-one outer-join="false" update="false"
+    @hibernate.many-to-one outer-join="false" 
     @hibernate.column name="`platform_id`" not-null="true"
   */
@@ -99 +99 @@
     Get the platform variant this raw bioassay uses, or null.
     @since 2.5
-    @hibernate.many-to-one outer-join="false" update="false"
+    @hibernate.many-to-one outer-join="false" 
     @hibernate.column name="`variant_id`"
   */
@@ -212 +212 @@
   private int spots;
   /**
-    The number of data spots in this raw bio assay. 
+    The number of data spots in this raw bio assay, that
+    are stored in the database.
     @hibernate.property column="`spots`" type="int" not-null="true"
-  */
-  public int getSpots()
+    @since 2.5
+  */
+  public int getNumDbSpots()
   {
     return spots;
   }
-  public void setSpots(int spots)
+  public void setNumDbSpots(int spots)
   {
     this.spots = spots;
   }
 
+  private int fileSpots;
+  /**
+    The number of spots on this raw bioassay that are stored inside
+    files.
+    @hibernate.property column="`file_spots`" type="int" not-null="true"
+    @since 2.5
+  */
+  public int getNumFileSpots()
+  {
+    return fileSpots;
+  }
+  public void setNumFileSpots(int fileSpots)
+  {
+    this.fileSpots = fileSpots;
+  }
+  
   private long bytes;
   /**

branches/filedb/src/core/net/sf/basedb/core/filehandler/AffymetrixFileHandler.java

@@ -25 +25 @@
 
 import affymetrix.fusion.cdf.FusionCDFData;
+import affymetrix.fusion.cel.FusionCELData;
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileStoreEnabled;
@@ -92 +93 @@
   }
   
+  public FusionCELData loadCelFile(File celFile)
+  {
+    if (celFile == null) throw new InvalidUseOfNullException("celFile");
+    if (celFile.getLocation() != Location.PRIMARY)
+    {
+      throw new ItemNotFoundException("File data is not online for file '" + 
+          celFile.getName() + "'; location=" + celFile.getLocation());
+    }
+    FusionCELData cel = new FusionCELData();
+    cel.setFileName(celFile.getName());
+    cel.setInputStream(celFile.getDownloadStream(0));
+    if (!cel.readHeader())
+    {
+      throw new InvalidDataException("Could not read CEL file '" +
+          celFile.getPath()+"': " + cel.getError());
+    }
+    return cel;
+  }
 }

branches/filedb/src/core/net/sf/basedb/core/filehandler/CdfFileHandler.java

@@ -66 +66 @@
     if (!isAffymetrix(design))
     {
-      throw new InvalidDataException("Array design '" + design + 
+      throw new InvalidDataException("Array design '" + design.getName() + 
         "' is not using the Affymetrix platform");
     }

branches/filedb/src/core/net/sf/basedb/core/filehandler/CelFileHandler.java

@@ -24 +24 @@
 package net.sf.basedb.core.filehandler;
 
+import affymetrix.fusion.cdf.FusionCDFData;
+import affymetrix.fusion.cel.FusionCELData;
+import net.sf.basedb.core.ArrayDesign;
+import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.File;
+import net.sf.basedb.core.FileSetMember;
+import net.sf.basedb.core.FileStoreUtil;
+import net.sf.basedb.core.InvalidDataException;
+import net.sf.basedb.core.InvalidRelationException;
+import net.sf.basedb.core.Platform;
+import net.sf.basedb.core.RawBioAssay;
+import net.sf.basedb.core.StringUtil;
 
 /**
@@ -38 +50 @@
   implements DataFileValidator, DataFileMetadataReader
 {
+  private FusionCELData celData;
 
   public CelFileHandler()
   {}
   
+  /*
+    From the DataFileValidator interface
+    ----------------------------------------
+  */
+  /**
+    Check that the raw bioassay is using the Affymetrix platform 
+    ({@link Platform#AFFYMETRIX}) and that the file selected
+    as the CEL file really is a CEL file.
+  */
   public void validate(DbControl dc)
   {
+    RawBioAssay rba = (RawBioAssay)getItem();
+    // Check platform
+    if (!isAffymetrix(rba))
+    {
+      throw new InvalidDataException("Raw bioassay '" + rba.getName() + 
+        "' is not using the Affymetrix platform");
+    }
+    
+    // Get the member for CEL file type
+    FileSetMember celMember = getMember(DataFileType.AFFYMETRIX_CEL);
+    if (celMember != null)
+    {
+      // Verify CEL file
+      File celFile = celMember.getFile();
+      celData = loadCelFile(celFile);
+    }
+    
+    // The CEL file is valid, a failure below will result in InvalidRelationException
+    try
+    {
+      ArrayDesign design = rba.getArrayDesign();
+      if (design == null) 
+      {
+        throw new InvalidDataException("Raw bioassay " + rba.getName() + 
+          " has no array design");
+      }
+      if (!design.isPlatform(Platform.AFFYMETRIX))
+      {
+        throw new InvalidDataException("The array design " + design.getName() + 
+          " is not an Affymterix design");
+      }
+  
+      // Verify that CEL chip type match CDF type
+      File cdfFile = FileStoreUtil.getDataFile(dc, design, DataFileType.AFFYMETRIX_CDF);
+      FusionCDFData cdfData = loadCdfFile(cdfFile);
+      validateCelAndCdf(celData, cdfData, cdfFile.getName());
+    }
+    catch (Throwable t)
+    {
+      throw new InvalidRelationException(t);
+    }
     
   }
+  // -------------------------------------------
   
+  /*
+    From the DataFileMetadataReader interface
+    ----------------------------------------
+  */
   public void extractMetadata(DbControl dc)
   {
-    
+    if (celData == null)
+    {
+      FileSetMember celMember = getMember(DataFileType.AFFYMETRIX_CEL);
+      if (celMember != null) celData = loadCelFile(celMember.getFile());
+    }
+    if (celData != null)
+    {
+      RawBioAssay rba = (RawBioAssay)getItem();
+      setHeader(rba, "Algorithm", celData.getAlg());
+      for (int i = 0; i < celData.getNumberAlgorithmParameters(); ++i)
+      {
+        String name = celData.getAlgorithmParameterTag(i);
+        setHeader(rba, "Algorithm parameter: " + name, 
+            celData.getAlgorithmParameter(name));
+      }
+      setHeader(rba, "Dat header", celData.getDatHeader());
+      setHeader(rba, "Chip type", celData.getChipType());
+      
+      // Set number of spots
+      rba.setNumFileSpots(celData.getCells());
+    }
   }
   
+  /**
+    Reset the number of file spots to 0, and remove all headers.
+  */
   public void resetMetadata(DbControl dc)
   {
-    
+    RawBioAssay rba = (RawBioAssay)getItem();
+    rba.setNumFileSpots(0);
+    rba.removeHeaders();
+  }
+  // -------------------------------------------
+
+  private void setHeader(RawBioAssay rba, String name, String value)
+  {
+    if (name == null || value == null) return;
+    value = StringUtil.trimString(value, RawBioAssay.MAX_HEADER_VALUE_LENGTH);
+    rba.setHeader(name, value);
   }
 
+  private static void validateCelAndCdf(FusionCELData cel, FusionCDFData cdf, String cdfChipType)
+    throws InvalidDataException
+  {
+    String celChipType = cel.getChipType();
+    if (!cdfChipType.startsWith(celChipType))
+    {
+      throw new InvalidDataException("CEL chip type (" + celChipType + 
+        ") doesn't match CDF chip type (" + cdfChipType + ")");
+    }
+    
+    if (cel.getRows() != cdf.getHeader().getRows() || cel.getCols() != cdf.getHeader().getRows())
+    {
+      throw new InvalidDataException("CEL size (rows=" + cel.getRows() + ", cols=" + cel.getCols() +
+        ") doesn't match CDF size (rows=" + 
+        cdf.getHeader().getRows() + ", cols=" + cdf.getHeader().getCols()+")");
+    }   
+  }
+
+  
 }

branches/filedb/src/core/net/sf/basedb/core/filehandler/DataFileValidator.java

@@ -27 +27 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.InvalidDataException;
+import net.sf.basedb.core.InvalidRelationException;
 import net.sf.basedb.core.PermissionDeniedException;
 
@@ -49 +50 @@
     or a subclass if the file is not a valid file. {@link PermissionDeniedException}:s
     are ignored by the core and will not change the validation status.
+    An exception of type {@link InvalidRelationException} is thrown
+    the file itself is valid, but a related file that it depends on is not. The
+    core will still mark the file as invalid and store the error message,
+    but metadata extraction will still be performed.
     
     @param dc A DbControl object that can be used for database
@@ -54 +59 @@
     @throws InvalidDataException If the validator detects an invalid
       file
+    @throws InvalidRelationException If the validator detects that the
+      file is valid but another file that it depends on is not, metadata
+      extract will still happen
   */
   public void validate(DbControl dc)
-    throws InvalidDataException;
+    throws InvalidDataException, InvalidRelationException;
 }

branches/filedb/www/common/datafiles/select_files.jsp

@@ -180 +180 @@
 
     <form name="datafiles">
-    <table class="form" cellspacing="2" border="0" cellpadding="0" width="100%">
     <%
-    if (deniedPlatform)
+    if (fileTypes.size() == 0)
+    {
+      %>
+      <div class="error">
+        The <%=platform == null ? "" : "'" + HTML.encodeTags(platform.getName()) + "'" %>
+        platform doesn't define any file types for <%=itemType.toString() %>
+        items.
+      </div>
+      <%
+    }
+    else if (deniedPlatform)
     {
       %>
@@ -188 +197 @@
       <%
     }
-    %>
-    <%
-    for (DataFileType dft : fileTypes)
-    {
-      PlatformFileType pft = platform == null ?
-        null : platform.getFileType(dft, variant);
-      boolean isRequired = pft == null ? false : pft.isRequired();
-      FileSetMember member = fileSet == null || !fileSet.hasMember(dft) ?
-        null : fileSet.getMember(dft);
-      File file = null;
-      boolean deniedFile = false;
-      if (member != null)
+    else
+    {
+      %>
+      <table class="form" cellspacing="2" border="0" cellpadding="0" width="100%">
+      <%
+      for (DataFileType dft : fileTypes)
       {
-        try
+        PlatformFileType pft = platform == null ?
+          null : platform.getFileType(dft, variant);
+        boolean isRequired = pft == null ? false : pft.isRequired();
+        FileSetMember member = fileSet == null || !fileSet.hasMember(dft) ?
+          null : fileSet.getMember(dft);
+        File file = null;
+        boolean deniedFile = false;
+        if (member != null)
         {
-          file = member.getFile();
+          try
+          {
+            file = member.getFile();
+          }
+          catch (PermissionDeniedException ex)
+          {
+            deniedFile = true;
+          }
         }
-        catch (PermissionDeniedException ex)
+        
+        String path = "";
+        if (file != null)
         {
-          deniedFile = true;
+          path = file.getPath().toString();
         }
-      }
-      
-      String path = "";
-      if (file != null)
-      {
-        path = file.getPath().toString();
-      }
-      else if (deniedFile || deniedPlatform)
-      {
-        path = "- denied -";
-      }
-      String inputName= "datafile."+dft.getId();
-      recentFiles = (List<File>)cc.getRecent(dc, Item.FILE, dft.getExternalId());
-      %>
-      <tr>
-        <td class="prompt"><%=HTML.encodeTags(dft.getName())%></td>
-        <td>
-          <table border="0" cellspacing="0" cellpadding="0">
-          <tr>
-            <td>      
-              <input <%=isRequired ? requiredClazz : clazz%> type="text" 
-              name="<%=inputName%>" value="<%=HTML.encodeTags(path)%>"
-              size="50" title="<%=HTML.encodeTags(dft.getDescription())%>"
-              <%=deniedFile || deniedPlatform ? "disabled" : "" %>
-              onchange="fileOnChange('<%=inputName%>')">&nbsp;
-            </td>
-            <td><base:button 
-                title="Browse&hellip;"
-                onclick="<%="browseOnClick('"+inputName+"')"%>"
-                disabled="<%=deniedFile || deniedPlatform %>"
-                />
-            </td>
-          </tr>
-          </table>
-        </td>
-      </tr>
-      <tr>
-        <td align="right"></td>
-        <td>
-        <%
-        if (recentFiles != null && recentFiles.size() > 0)
+        else if (deniedFile || deniedPlatform)
         {
-          %>
-          <select name="recent.<%=inputName%>" onchange="recentOnChange('<%=inputName%>')">
-          <option value="">- recently used -
+          path = "- denied -";
+        }
+        String inputName= "datafile."+dft.getId();
+        recentFiles = (List<File>)cc.getRecent(dc, Item.FILE, dft.getExternalId());
+        %>
+        <tr>
+          <td class="prompt"><%=HTML.encodeTags(dft.getName())%></td>
+          <td>
+            <table border="0" cellspacing="0" cellpadding="0">
+            <tr>
+              <td>      
+                <input <%=isRequired ? requiredClazz : clazz%> type="text" 
+                name="<%=inputName%>" value="<%=HTML.encodeTags(path)%>"
+                size="50" title="<%=HTML.encodeTags(dft.getDescription())%>"
+                <%=deniedFile || deniedPlatform ? "disabled" : "" %>
+                onchange="fileOnChange('<%=inputName%>')">&nbsp;
+              </td>
+              <td><base:button 
+                  title="Browse&hellip;"
+                  onclick="<%="browseOnClick('"+inputName+"')"%>"
+                  disabled="<%=deniedFile || deniedPlatform %>"
+                  />
+              </td>
+            </tr>
+            </table>
+          </td>
+        </tr>
+        <tr>
+          <td align="right"></td>
+          <td>
           <%
-          for (File recent : recentFiles)
+          if (recentFiles != null && recentFiles.size() > 0)
           {
             %>
-            <option value="<%=recent.getId()%>"><%=HTML.encodeTags(recent.getPath().toString())%>
+            <select name="recent.<%=inputName%>" onchange="recentOnChange('<%=inputName%>')">
+            <option value="">- recently used -
+            <%
+            for (File recent : recentFiles)
+            {
+              %>
+              <option value="<%=recent.getId()%>"><%=HTML.encodeTags(recent.getPath().toString())%>
+              <%
+            }
+            %>
+            </select>
             <%
           }
           %>
-          </select>
-          <%
-        }
-        %>
-        </td>
+          </td>
+        </tr>
+        <%
+      }
+      %>
+      <tr>
+        <td class="prompt">Validate</td>
+        <td><input type="checkbox" value="1" name="datafiles.validate"></td>
       </tr>
+      <tr>
+        <td class="prompt">Extract metadata</td>
+        <td><input type="checkbox" value="1" name="datafiles.metadata"></td>
+      </tr>
+      </table>
       <%
     }
     %>
-    <tr>
-      <td class="prompt">Validate</td>
-      <td><input type="checkbox" value="1" name="datafiles.validate"></td>
-    </tr>
-    <tr>
-      <td class="prompt">Extract metadata</td>
-      <td><input type="checkbox" value="1" name="datafiles.metadata"></td>
-    </tr>
-    </table>
 
     </form>

branches/filedb/www/include/scripts/platforms.js

@@ -54 +54 @@
       }
     }
-  } 
+  }
+  
+  this.getPlatformById = function(id)
+  {
+    return allPlatforms['ID'+id];
+  }
+  
+  this.populateList = function(list, platformId, variantId)
+  {
+    for (var p = 0; p < allPlatforms.length; p++)
+    {
+      var platform = allPlatforms[p];
+      var option = new Option(platform.name, platform.id, false, platformId == platform.id && !variantId);
+      list[list.length] = option;
+      option.className = 'selectoptionheader';
+      for (var v = 0; v < platform.variants.length; v++)
+      {
+        var variant = platform.variants[v];
+        option = new Option(variant.name, platform.id + ':' + variant.id, false, platformId == platform.id && variantId == variant.id);
+        option.className = 'selectoptionindent';
+        list[list.length] = option;
+      }
+    }
+  }
+  
+  this.getSelectedPlatform = function(list)
+  {
+    if (list.length == 0 || list.selectedIndex < 0) return null;
+    var pv = list[list.selectedIndex].value.split(':');
+    return this.getPlatformById(pv[0]);
+  }
+
+  this.getSelectedVariant = function(list)
+  {
+    if (list.length == 0 || list.selectedIndex < 0) return null;
+    var pv = list[list.selectedIndex].value.split(':');
+    if (pv.length < 2) return null;
+    var platform = this.getPlatformById(pv[0]);
+    return platform.getVariantById(pv[1]);
+  }
+  
+}
+
+var allPlatforms = new Array();
+function Platform(id, externalId, name, fileOnly, rawDataType)
+{
+  this.id = id;
+  this.externalId = externalId;
+  this.name = name;
+  this.fileOnly = fileOnly;
+  this.rawDataType = rawDataType;
+  this.variants = new Array();
+  
+  allPlatforms[allPlatforms.length] = this;
+  allPlatforms['ID'+id] = this;
+  
+  this.getVariantById = function(id)
+  {
+    return this.variants['ID'+id];
+  }
+}
+
+function Variant(platform, id, externalId, name, fileOnly, rawDataType)
+{
+  this.platform = platform;
+  this.id = id;
+  this.externalId = externalId;
+  this.name = name;
+  this.fileOnly = fileOnly;
+  this.rawDataType = rawDataType;
+  
+  platform.variants[platform.variants.length] = this;
+  platform.variants['ID'+id] = this;
 }
 
 
 
+

branches/filedb/www/lims/arraydesigns/edit_design.jsp

@@ -37 +37 @@
   import="net.sf.basedb.core.Platform"
   import="net.sf.basedb.core.PlatformVariant"
-  import="net.sf.basedb.core.Affymetrix"
+  import="net.sf.basedb.core.RawDataType"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
@@ -153 +153 @@
     function switchTab(tabControlId, tabId)
     {
+      var frm = document.forms['design'];
       if (TabControl.setActiveTab(tabControlId, tabId))
       {
@@ -169 +170 @@
         else if (tabId == 'datafiles' && (platformChanged || !dataFilesLoaded))
         {
-          var platformId = getPlatform();
-          var variantId = getVariant();
-          Platforms.loadDataFilesFrame(frames.datafiles, '<%=ID%>', '<%=itemType.name()%>', <%=design == null ? 0 : design.getId()%>, platformId, variantId);
+          var platform = Platforms.getSelectedPlatform(frm.platform);
+          var variant = Platforms.getSelectedVariant(frm.platform);
+          Platforms.loadDataFilesFrame(frames.datafiles, '<%=ID%>', '<%=itemType.name()%>', <%=design == null ? 0 : design.getId()%>, platform == null ? 0 : platform.id, variant == null ? 0 : variant.id);
           dataFilesLoaded = true;
           platformChanged = false;
@@ -183 +184 @@
     }
     
-    function getPlatform()
-    {
-      var frm = document.forms['design'];
-      if (frm.platform.length == 0) return 0;
-      var pv = frm.platform[frm.platform.selectedIndex].value.split(':');
-      return pv[0];
-    }
-    
-    function getVariant()
-    {
-      var frm = document.forms['design'];
-      if (frm.platform.length == 0) return 0;
-      var pv = frm.platform[frm.platform.selectedIndex].value.split(':');
-      return pv.length > 1 ? pv[1] : null;
-    }
-
     function platformOnChange()
     {
@@ -221 +206 @@
     function initPlatforms(platformId, variantId)
     {
-      var platforms = new Array();
-      var variants = new Array();
       <%
       for (Platform p : platforms)
       {
+        RawDataType rdt = p.isFileOnly() ? null : p.getRawDataType();
         %>
-        platforms[platforms.length] = { name:'<%=p.getName()%>', id:<%=p.getId()%> };
-        variants['platform.<%=p.getId()%>'] = new Array();
+        var p<%=p.getId()%> = new Platform(<%=p.getId()%>, '<%=HTML.javaScriptEncode(p.getExternalId())%>', '<%=HTML.javaScriptEncode(p.getName())%>', <%=p.isFileOnly()%>, '<%=rdt == null ? "" : rdt.getId()%>');
         <%
       }
       for (PlatformVariant v : variants)
       {
+        RawDataType rdt = v.isFileOnly() ? null : v.getRawDataType();
         Platform p = v.getPlatform();
-        String index = "platform." + p.getId();
         %>
-        variants['<%=index%>'][variants['<%=index%>'].length] = { name:'<%=v.getName()%>', id:<%=v.getId()%> };
+        var v<%=v.getId()%> = new Variant(p<%=p.getId()%>, <%=v.getId()%>, '<%=HTML.javaScriptEncode(v.getExternalId())%>', '<%=HTML.javaScriptEncode(v.getName())%>', <%=v.isFileOnly()%>, '<%=rdt == null ? "" : rdt.getId()%>');
         <%
       }
       %>
       var frm = document.forms['design'];
-      for (var p = 0; p < platforms.length; p++)
-      {
-        var platform = platforms[p];
-        var index = 'platform.' + platform.id;
-        var option = new Option(platform.name, platform.id, false, platformId == platform.id && !variantId);
-        frm.platform[frm.platform.length] = option;
-        option.className = 'selectoptionheader';
-        for (var v = 0; v < variants[index].length; v++)
-        {
-          var variant = variants[index][v];
-          option = new Option(variant.name, platform.id + ':' + variant.id, false, platformId == platform.id && variantId == variant.id);
-          option.className = 'selectoptionindent';
-          frm.platform[frm.platform.length] = option;
-        }
-      }
+      Platforms.populateList(frm.platform, platformId, variantId);
     }
     </script>
@@ -278 +247 @@
         <td class="prompt">Platform</td>
         <td>
-          <select name="platform" onchange="platformOnChange()" <%=deniedPlatform ? "disabled" : "" %>>
+          <select name="platform" onchange="platformOnChange()" class="required"
+            <%=deniedPlatform ? "disabled" : "" %>>
           <%
           if (deniedPlatform)

branches/filedb/www/lims/arraydesigns/list_designs.jsp

@@ -252 +252 @@
         exportable="true"
         show="always" 
-      />
-      <tbl:columndef 
-        id="affyChip"
-        property="affyChip"
-        datatype="boolean"
-        title="Affy chip"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
-      />
-      <tbl:columndef 
-        id="cdfFile"
-        title="CDF file"
       />
       <tbl:columndef 
@@ -549 +536 @@
                     enablePropertyLink="<%=mode.hasPropertyLink()%>"
                   /></tbl:cell>
-                <tbl:cell column="affyChip"><%=item.isAffyChip()%></tbl:cell>
-                <tbl:cell column="cdfFile">
-                <%
-                if (item.isAffyChip())
-                {
-                  File cdfFile = null;
-                  boolean readCdfFile = true;
-                  try
-                  {
-                    cdfFile = Affymetrix.getCdfFile(item);
-                  }
-                  catch (PermissionDeniedException ex)
-                  {
-                    readCdfFile = false;
-                  }
-                  %>
-                  <%=Base.getLinkedFile(ID, cdfFile, !readCdfFile, true, true, root)%>
-                  <%
-                }
-                %>
-                </tbl:cell>
                 <tbl:cell column="hasFeatures"><%=item.hasFeatures() ? "yes" : "no"%></tbl:cell>
                 <tbl:cell column="numDbFeatures"><%=item.getNumDbFeatures()%></tbl:cell>

branches/filedb/www/views/rawbioassays/edit_rawbioassay.jsp

@@ -36 +36 @@
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.RawBioAssay"
-  import="net.sf.basedb.core.Affymetrix"
+  import="net.sf.basedb.core.Platform"
+  import="net.sf.basedb.core.PlatformVariant"
   import="net.sf.basedb.core.Scan"
   import="net.sf.basedb.core.Protocol"
@@ -52 +53 @@
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.BaseException"
+  import="net.sf.basedb.core.query.Orders"
+  import="net.sf.basedb.core.query.Hql"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.util.HTML"
@@ -74 +77 @@
   RawBioAssay rawBioAssay = null;
   String name = null;
-  boolean readCurrentCelFile = true;
-  File currentCelFile = null; 
+  boolean hasDbSpots = false;
+
+  boolean deniedPlatform = false;
+  Platform currentPlatform = null;
+  PlatformVariant currentVariant = null;
+  
   boolean readCurrentScan = true;
   Scan currentScan = null;
@@ -131 +138 @@
     title = "Create raw bioassay";
     cc.removeObject("item");
+    
+    int currentPlatformId = Values.getInt(cc.getPropertyValue("platform"), 0);
+    if (currentPlatformId == 0)
+    {
+      currentPlatformId = Values.getInt(cc.getRecent(Item.PLATFORM.name(), 0), 0);
+    }
+    if (currentPlatformId != 0) currentPlatform = Platform.getById(dc, currentPlatformId);
+    
     currentRawDataType = RawDataTypes.getRawDataType(cc.getPropertyValue("rawDataType"));
     if (currentRawDataType == null)
@@ -182 +197 @@
   {
     rawBioAssay = RawBioAssay.getById(dc, itemId);
+    rawBioAssay.checkPermission(Permission.WRITE);
+    hasDbSpots = rawBioAssay.getNumDbSpots() > 0;
     cc.setObject("item", rawBioAssay);
     name = rawBioAssay.getName();
@@ -187 +204 @@
     title = "Edit raw bioassay -- " + HTML.encodeTags(rawBioAssay.getName());
     
-    if (currentRawDataType.isAffymetrix())
-    {
-      try
-      {
-        currentCelFile = Affymetrix.getCelFile(rawBioAssay);
-      }
-      catch (PermissionDeniedException ex)
-      {
-        readCurrentCelFile = false;
-      }
-    }
-    
     try
     {
+      currentPlatform = rawBioAssay.getPlatform();
+      currentVariant = rawBioAssay.getVariant();
+    }
+    catch (PermissionDeniedException ex)
+    {
+      deniedPlatform = true;
+    }
+    
+    try
+    {
       currentScan = rawBioAssay.getScan();
     }
@@ -232 +247 @@
     }
   }
-  if (rawBioAssay != null) rawBioAssay.checkPermission(Permission.WRITE);
+  
+  ItemQuery<Platform> platformQuery = Platform.getQuery();
+  platformQuery.order(Orders.asc(Hql.property("name")));
+  platformQuery.setCacheResult(true);
+  ItemResultList<Platform> platforms = platformQuery.list(dc);
+
+  ItemQuery<PlatformVariant> variantQuery = PlatformVariant.getQuery();
+  variantQuery.order(Orders.asc(Hql.property("name")));
+  variantQuery.setCacheResult(true);
+  ItemResultList<PlatformVariant> variants = variantQuery.list(dc);
+  
   final String clazz = "class=\"text\"";
   final String requiredClazz = "class=\"text required\"";
@@ -238 +263 @@
 
   <base:page type="popup" title="<%=title%>">
-  <base:head scripts="tabcontrol.js,annotations.js" styles="tabcontrol.css">
+  <base:head scripts="tabcontrol.js,annotations.js,platforms.js" styles="tabcontrol.css">
     <script language="JavaScript">
     // Validate the "RawBioAssay" tab
@@ -249 +274 @@
         frm.name.focus();
         return false;
-      }
-      if (frm.rawdatatype)
-      {
-        var rawDataType = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
-        if (isAffymetrix[rawDataType])
-        {
-          var celFileId = frm.celfile_id[frm.celfile_id.selectedIndex].value;
-          var arrayDesignId = frm.arraydesign_id[frm.arraydesign_id.selectedIndex].value;
-          if (celFileId != 0 && arrayDesignId == 0)
-          {
-            alert('You must select an array design if a CEL file is specified');
-            return false;
-          }
-        }
       }
       return true;
@@ -281 +292 @@
           Annotations.addInheritedAnnotationsToForm(frames.inheritedAnnotations, frm);
         }
+        if (dataFilesLoaded)
+        {
+          Platforms.addDataFilesToForm(frames.datafiles, frm);
+        }
         frm.submit();
       }
@@ -289 +304 @@
     var parentsChanged = false;
     var protocolChanged = false;
+    var dataFilesLoaded = false;
+    var platformChanged = false;
     function switchTab(tabControlId, tabId)
     {
+      var frm = document.forms['rawbioassay'];
       if (TabControl.setActiveTab(tabControlId, tabId))
       {
@@ -306 +324 @@
           parentsChanged = false;
         }
-      }
-    }
-    
+        else if (tabId == 'datafiles' && (platformChanged || !dataFilesLoaded))
+        {
+          var platform = Platforms.getSelectedPlatform(frm.platform);
+          var variant = Platforms.getSelectedVariant(frm.platform);
+          Platforms.loadDataFilesFrame(frames.datafiles, '<%=ID%>', '<%=itemType.name()%>', <%=rawBioAssay == null ? 0 : rawBioAssay.getId()%>, platform == null ? 0 : platform.id, variant == null ? 0 : variant.id);
+          dataFilesLoaded = true;
+          platformChanged = false;
+        }
+      }
+    }
+
+    function platformOnChange()
+    {
+      var frm = document.forms['rawbioassay'];
+      platformChanged = true;
+      var platform = Platforms.getSelectedPlatform(frm.platform);
+      var variant = Platforms.getSelectedVariant(frm.platform);
+      var fileOnly = (variant != null && variant.fileOnly) || 
+        (variant == null && platform.fileOnly);
+      var rawDataType = variant == null ? platform.rawDataType : variant.rawDataType;
+      if (frm.rawdatatype[frm.rawdatatype.length - 1].value == '')
+      {
+        frm.rawdatatype[frm.rawdatatype.length - 1] = null;
+      }
+      if (fileOnly)
+      {
+        frm.rawdatatype.disabled = true;
+        Main.removeClass(frm.rawdatatype, 'required');
+        frm.rawdatatype[frm.rawdatatype.length] = new Option('- file only -', '');
+        frm.rawdatatype.selectedIndex = frm.rawdatatype.length - 1;
+      }
+      else if (rawDataType)
+      {
+        frm.rawdatatype.disabled = true;
+        Main.removeClass(frm.rawdatatype, 'required');
+        Forms.selectListOption(frm.rawdatatype, rawDataType);
+      }
+      else
+      {
+        frm.rawdatatype.disabled = false;
+        Main.addClass(frm.rawdatatype, 'required');
+      }
+    }
+
     function getProtocolId()
     {
@@ -426 +485 @@
     {
       var frm = document.forms['rawbioassay'];
-      var url = '../../lims/arraydesigns/index.jsp?ID=<%=ID%>&mode=selectone&callback=setArrayDesignCallback';
+      var url = '../../lims/arraydesigns/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setArrayDesignCallback';
       if (frm.arraydesign_id.length > 1) 
       {
@@ -432 +491 @@
         url += '&item_id='+id;
       }
+      var platform = Platforms.getSelectedPlatform(frm.platform);
+      url += '&filter:INT:platform='+platform.id;
       Main.openPopup(url, 'SelectArrayDesign', 1000, 700);
     }
@@ -448 +509 @@
     }
     
-    var isAffymetrix = new Array();
-    <%
-    for (RawDataType rdt : RawDataTypes.getRawDataTypes())
-    {
-      %>
-      isAffymetrix['<%=rdt.getId()%>'] = <%=rdt.isAffymetrix() ? "true" : "false" %>;
-      <%
-    }
-    %>
-    
-    function selectCelFileOnClick()
-    {
-      var frm = document.forms['rawbioassay'];
-      
-      if (frm.rawdatatype)
-      {
-        var rawDataType = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
-        if (!isAffymetrix[rawDataType])
-        {
-          alert('CEL-files are only used for Affymetrix data types.');
-          return;
-        }
-      }
-
-      var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&callback=setCelFileCallback';
-      if (frm.celfile_id.length > 1) 
-      {
-        var id = Math.abs(parseInt(frm.celfile_id[1].value));       
-        url += '&item_id='+id;
-      }
-      url += '&filter:STRING:name=%25.cel';
-      Main.openPopup(url, 'SelectFile', 1000, 700);
-    }
-    function setCelFileCallback(id, name)
-    {
-      var frm = document.forms['rawbioassay'];
-      var list = frm.celfile_id;
-      if (list.length < 2 || list[1].value == '0') // >
-      {
-        Forms.addListOption(list, 1, new Option());
-      }
-      list[1].value = id;
-      list[1].text = name;
-      list.selectedIndex = 1;
-    }
-
-    function rawDataTypeOnChange()
-    {
-      var frm = document.forms['rawbioassay'];
-      if (frm.rawdatatype)
-      {
-        var rawDataType = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
-        if (isAffymetrix[rawDataType])
-        {
-          frm.celfile_id.disabled = false;
-        }
-        else
-        {
-          frm.celfile_id.disabled = true;
-        }
-      }
-    }
-
     function init()
     {
@@ -523 +521 @@
       }
       %>
-      rawDataTypeOnChange();
+      initPlatforms(<%=currentPlatform == null ? 0 : currentPlatform.getId()%>, <%=currentVariant == null ? 0 : currentVariant.getId()%>);
+      platformOnChange();
+    }
+    
+    function initPlatforms(platformId, variantId)
+    {
+      <%
+      for (Platform p : platforms)
+      {
+        RawDataType rdt = p.isFileOnly() ? null : p.getRawDataType();
+        %>
+        var p<%=p.getId()%> = new Platform(<%=p.getId()%>, '<%=HTML.javaScriptEncode(p.getExternalId())%>', '<%=HTML.javaScriptEncode(p.getName())%>', <%=p.isFileOnly()%>, '<%=rdt == null ? "" : rdt.getId()%>');
+        <%
+      }
+      for (PlatformVariant v : variants)
+      {
+        RawDataType rdt = v.isFileOnly() ? null : v.getRawDataType();
+        Platform p = v.getPlatform();
+        %>
+        var v<%=v.getId()%> = new Variant(p<%=p.getId()%>, <%=v.getId()%>, '<%=HTML.javaScriptEncode(v.getExternalId())%>', '<%=HTML.javaScriptEncode(v.getName())%>', <%=v.isFileOnly()%>, '<%=rdt == null ? "" : rdt.getId()%>');
+        <%
+      }
+      %>
+      var frm = document.forms['rawbioassay'];
+      Platforms.populateList(frm.platform, platformId, variantId);
     }
     </script>
@@ -544 +566 @@
       </tr>
       <tr>
-        <td class="prompt">Raw data type</td>
+        <td class="prompt">Platform</td>
         <td>
+          <select name="platform" onchange="platformOnChange()" class="required"
+            <%=deniedPlatform || hasDbSpots ? "disabled" : "" %>>
           <%
-          if (rawBioAssay == null || !rawBioAssay.hasData())
+          if (deniedPlatform)
           {
             %>
-            <select name="rawdatatype" class="required" onchange="rawDataTypeOnChange()">
-            <%
-            for (RawDataType rdt : RawDataTypes.getRawDataTypes())
-            {
-              String selected = rdt.equals(currentRawDataType) ? "selected" : "";
-              %>
-              <option value="<%=rdt.getId()%>" <%=selected%>><%=HTML.encodeTags(rdt.getName())%>
-              <%
-            }
-            %>
-            </select>
-            <%
-          }
-          else
-          {
-            %>
-            <%=HTML.encodeTags(currentRawDataType.getName())%>
+            <option value="-1">- denied -
             <%
           }
           %>
-        
+          </select>
+        </td>
+      </tr>
+      <tr>
+        <td class="prompt">Raw data type</td>
+        <td>
+          <select name="rawdatatype" class="required"
+            <%=hasDbSpots ? "disabled" : "" %>>
+          <%
+          for (RawDataType rdt : RawDataTypes.getRawDataTypes())
+          {
+            String selected = rdt.equals(currentRawDataType) ? "selected" : "";
+            %>
+            <option value="<%=rdt.getId()%>" <%=selected%>><%=HTML.encodeTags(rdt.getName())%>
+            <%
+          }
+          %>
+          </select>
         </td>
       </tr>
@@ -577 +602 @@
         <td class="prompt">Array design</td>
         <td>
-          <%
-          //if (rawBioAssay == null || !rawBioAssay.hasData())
-          {
-            %>
-            <base:select 
-              id="arraydesign_id"
-              clazz="selectionlist"
-              required="false"
-              current="<%=currentArrayDesign%>"
-              denied="<%=!readCurrentArrayDesign%>"
-              recent="<%=recentArrayDesigns%>"
-              defaultitem="<%=defaultArrayDesign%>"
-              newitem="<%=rawBioAssay == null%>"
-              onselect="selectArrayDesignOnClick()"
-              onchange="arrayDesignOnChange()"
-            />
-            <%
-          }
-          /*
-          else
-          {
-            %>
-            <%=readCurrentArrayDesign ? 
-              (currentArrayDesign != null ? HTML.encodeTags(currentArrayDesign.getName()) : "<i>- none -</i>") 
-              : "<i>- denied - </i>"%>
-            <%
-          }
-          */
-          %>
+          <base:select 
+            id="arraydesign_id"
+            clazz="selectionlist"
+            required="false"
+            current="<%=currentArrayDesign%>"
+            denied="<%=!readCurrentArrayDesign%>"
+            recent="<%=recentArrayDesigns%>"
+            defaultitem="<%=defaultArrayDesign%>"
+            newitem="<%=rawBioAssay == null%>"
+            onselect="selectArrayDesignOnClick()"
+            onchange="arrayDesignOnChange()"
+          />
         </td>
       </tr>
-      <% 
-      if (rawBioAssay == null || !rawBioAssay.hasData() || rawBioAssay.getRawDataType().isAffymetrix())
-      {
-        %>
-        <tr id="celFile">
-          <td class="prompt">CEL file</td>
-          <td>
-            <base:select 
-              id="celfile_id"
-              clazz="selectionlist"
-              required="false"
-              current="<%=currentCelFile%>"
-              denied="<%=!readCurrentCelFile%>"
-              recent="<%=recentFiles%>"
-              newitem="<%=rawBioAssay == null%>"
-              onselect="selectCelFileOnClick()"
-            />
-          </td>
-        </tr>
-        <%
-      }
-      %>
 
       <tr>
@@ -691 +677 @@
       <div align=right>&nbsp;<i><base:icon image="required.gif" /> = required information</i></div>
     </t:tab>
+    
+    <t:tab id="datafiles" title="Data files" helpid="datafiles.edit">
+      <iframe name="datafiles" id="idDatafiles" src="../../common/datafiles/wait.jsp" 
+        width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
+        marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>
+    </t:tab>
 
     <t:tab id="annotations" title="Annotations &amp; parameters" 

branches/filedb/www/views/rawbioassays/index.jsp

@@ -43 +43 @@
   import="net.sf.basedb.core.RawDataType"
   import="net.sf.basedb.core.RawDataTypes"
+  import="net.sf.basedb.core.Platform"
+  import="net.sf.basedb.core.PlatformVariant"
   import="net.sf.basedb.core.User"
   import="net.sf.basedb.core.Path"
@@ -78 +80 @@
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 <%!
-  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,rawDataType,spots,description");
+  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,platform,variant,hasData,description");
   private static final Item itemType = Item.RAWBIOASSAY;
   
@@ -214 +216 @@
     dc = sc.newDbControl();
     RawBioAssay rba = (RawBioAssay)cc.getObject("item");
+    
+    Platform platform = null;
+    PlatformVariant variant = null;
+    if (request.getParameter("platform") != null)
+    {
+      String[] pv = request.getParameter("platform").split(":");
+      int platformId = Values.getInt(pv[0], -1);
+      int variantId = pv.length > 1 ? Values.getInt(pv[1], -1) : -1;
+      if (platformId > 0) platform = Platform.getById(dc, platformId);
+      if (variantId > 0) variant = PlatformVariant.getById(dc, variantId);
+    }
+    
     RawDataType rdt = RawDataTypes.getRawDataType(Values.getStringOrNull(request.getParameter("rawdatatype")));
     if (rdt != null) cc.setRecent("RawDataType", rdt.getId(), maxRecent);
@@ -219 +233 @@
     if (rba == null)
     {
-      rba = RawBioAssay.getNew(dc, rdt);
+      if (variant != null)
+      {
+        rba = RawBioAssay.getNew(dc, variant, rdt);
+      }
+      else
+      {
+        rba = RawBioAssay.getNew(dc, platform, rdt);
+      }
       message = "Raw bioassay created";
       dc.saveItem(rba);
@@ -225 +246 @@
     else
     {
+      dc.reattachItem(rba);
       if (rdt != null) rba.setRawDataType(rdt);
-      dc.reattachItem(rba);
+      if (variant != null)
+      {
+        rba.setVariant(variant);
+      }
+      else if (platform != null)
+      {
+        rba.setPlatform(platform);
+      }
       message = "Raw bioassay updated";
     }
@@ -258 +287 @@
     {
       ad = arrayDesignId == 0 ? null : ArrayDesign.getById(dc, arrayDesignId);
-      if (rba.getSpots() > 0)
+      if (rba.hasData())
       {
         if (rba.getRawDataType().isStoredInDb() && ad != null && ad.hasFeatures())
@@ -280 +309 @@
       if (ad != null) cc.setRecent(ad, maxRecent);
     }
-    rdt = rba.getRawDataType();
-    if (rdt.isAffymetrix())
-    {
-      int celFileId = Values.getInt(request.getParameter("celfile_id"), -1);
-      if (celFileId >= 0) // < 0 = denied or unchanged
-      {
-        File celFile = celFileId == 0 ? null : File.getById(dc, celFileId);
-        Affymetrix.setCelFile(rba, celFile);
-      }
-    }
-
+
+    // Data files tab
+    boolean validate = Values.getBoolean(request.getParameter("datafiles.validate"));
+    boolean metadata = Values.getBoolean(request.getParameter("datafiles.metadata"));
+    Base.updateFiles(dc, rba, request, validate, metadata, cc, maxRecent);
+    
     // Annotations tab
     Base.updateAnnotations(dc, rba, rba, request);

branches/filedb/www/views/rawbioassays/list_rawbioassays.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.RawBioAssay"
+  import="net.sf.basedb.core.Platform"
   import="net.sf.basedb.core.RawDataType"
   import="net.sf.basedb.core.RawDataTypes"
@@ -89 +90 @@
 {
   final ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
-  final ItemQuery<RawBioAssay> query = Base.getConfiguredQuery(cc, true, RawBioAssay.getQuery(), mode);
 
   // Query for experiments relatated to the current raw bioassay
@@ -98 +98 @@
   experimentQuery.order(Orders.asc(Hql.property("name"))); 
   
+  // Get all platforms
+  final ItemQuery<Platform> platformQuery = Platform.getQuery();
+  platformQuery.order(Orders.asc(Hql.property("name")));
+  platformQuery.setCacheResult(true);
+  Enumeration<String, String> platforms = new Enumeration<String, String>();
+  for (Platform p : platformQuery.list(dc))
+  {
+    platforms.add(Integer.toString(p.getId()), p.getName());
+  }
+  
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
   annotationTypes = annotationTypeQuery.list(dc);
   try
   {
+    final ItemQuery<RawBioAssay> query = Base.getConfiguredQuery(cc, true, RawBioAssay.getQuery(), mode);
     rawBioAssays = query.iterate(dc);
   }
   catch (Throwable t)
   {
+    t.printStackTrace();
     cc.setMessage(t.getMessage());
   }
@@ -250 +262 @@
         show="always" 
       />
-      <%
+      <tbl:columndef 
+        id="platform"
+        property="platform"
+        sortproperty="platform.name"
+        exportproperty="platform.name"
+        datatype="int"
+        enumeration="<%=platforms%>"
+        title="Platform"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />  
+      <tbl:columndef 
+        id="variant"
+        property="variant.name"
+        datatype="string"
+        title="Variant"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />        <%
       Enumeration<String, String> rawEnumeration = new Enumeration<String, String>();
       for (RawDataType rdt : RawDataTypes.getRawDataTypes())
@@ -277 +309 @@
       />
       <tbl:columndef 
-        id="spots"
-        property="spots"
+        id="numDbSpots"
+        property="numDbSpots"
         datatype="int"
-        title="Spots"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
-      />
-      <tbl:columndef 
-        id="celFile"
-        title="CEL file"
-      />
+        title="Db spots"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
+        id="numFileSpots"
+        property="numFileSpots"
+        datatype="int"
+        title="File spots"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />      
       <tbl:columndef 
         id="bytes"
@@ -560 +597 @@
                   onclick="itemOnClick(<%=writePermission ? "event" : null%>, <%=itemId%>)" 
                   title="<%=tooltip%>"><%=name%></div></tbl:cell>
-                <tbl:cell column="spots"><%=item.getSpots()%></tbl:cell>
+                <tbl:cell column="numDbSpots"><%=item.getNumDbSpots()%></tbl:cell>
+                <tbl:cell column="numFileSpots"><%=item.getNumFileSpots()%></tbl:cell>
                 <tbl:cell column="bytes"><%=Values.formatBytes(item.getBytes())%></tbl:cell>
-                <tbl:cell column="rawDataType"><%=HTML.encodeTags(rdt.getName())%></tbl:cell>
-                <tbl:cell column="celFile">
-                <%
-                if (rdt.isAffymetrix())
-                {
-                  File celFile = null;
-                  boolean readCelFile = true;
-                  try
-                  {
-                    celFile = Affymetrix.getCelFile(item);
-                  }
-                  catch (PermissionDeniedException ex)
-                  {
-                    readCelFile = false;
-                  }
-                  %>
-                  <%=Base.getLinkedFile(ID, celFile, !readCelFile, true, true, root)%>
-                  <%
-                }
-                %>
-                </tbl:cell>
+                <tbl:cell column="platform"
+                  ><base:propertyvalue 
+                    item="<%=item%>" 
+                    property="platform"
+                    enableEditLink="<%=mode.hasEditLink()%>" 
+                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
+                  /></tbl:cell>
+                <tbl:cell column="variant"
+                  ><base:propertyvalue 
+                    item="<%=item%>" 
+                    property="variant"
+                    enableEditLink="<%=mode.hasEditLink()%>" 
+                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
+                  /></tbl:cell>               <tbl:cell column="rawDataType"><%=HTML.encodeTags(rdt.getName())%></tbl:cell>
                 <tbl:cell column="hasData"><%=item.hasData()%></tbl:cell>
                 <tbl:cell column="scan"

branches/filedb/www/views/rawbioassays/view_rawbioassay.jsp

@@ -265 +265 @@
       </tr>
       <tr>
+        <td class="prompt">Platform</td>
+        <td><base:propertyvalue item="<%=rawBioAssay%>" property="platform" /></td>
+      </tr>
+      <tr>
+        <td class="prompt">Variant</td>
+        <td><base:propertyvalue item="<%=rawBioAssay%>" property="variant" /></td>
+      </tr>
+      <tr>
         <td class="prompt">Raw data type</td>
         <td><%=HTML.encodeTags(rawDataType.getName())%></td>
       </tr>
       <tr>
-        <td class="prompt">Has data</td>
-        <td><%=rawBioAssay.hasData() ? "yes" : "no" %></td>
-      </tr>
-      <tr>
         <td class="prompt">Spots</td>
-        <td><%=rawBioAssay.getSpots()%></td>
-      </tr>
-      <%
-      if (rawDataType.isAffymetrix())
-      {
-        boolean readCurrentCelFile = true;
-        File currentCelFile = null; 
-        try
-        {
-          currentCelFile = Affymetrix.getCelFile(rawBioAssay);
-        }
-        catch (PermissionDeniedException ex)
-        {
-          readCurrentCelFile = false;
-        }
-        %>
-        <tr>
-          <td class="prompt">CEL file</td>
-          <td><%=Base.getLinkedFile(ID, currentCelFile, !readCurrentCelFile, true, true, root)%></td>
-        </tr>
-        <%
-      }
-      %>
+        <td><%=rawBioAssay.hasData() ? "yes (db: " + rawBioAssay.getNumDbSpots() + 
+            "; file: " + rawBioAssay.getNumFileSpots() + ")" : "no"%></td>
+      </tr>
       <tr>
         <td class="prompt">Protocol</td>
@@ -388 +372 @@
       </table>
       
-      <h4>Raw data headers</h4>
-      <table class="form" cellspacing="0">
+      <jsp:include page="../../common/datafiles/list_files.jsp">
+        <jsp:param name="item_type" value="<%=itemType.name()%>" />
+        <jsp:param name="item_id" value="<%=itemId%>" />
+        <jsp:param name="ID" value="<%=ID%>" />
+      </jsp:include>
+      
       <%
       Set<String> names = rawBioAssay.getHeaderNames();
-      boolean needsTr = true;
-      if (names != null)
-      {
-        for (String name : names)
+      %>
+      <base:section 
+        id="headers"
+        title="<%="Raw data headers (" + (names == null ? 0 : names.size()) + ")"%>"
+        context="<%=cc%>"
+        >
+        <table class="form" cellspacing="0">
+        <%
+        boolean needsTr = true;
+        if (names != null)
         {
+          for (String name : names)
+          {
+            %>
+            <%=needsTr ? "<tr valign=\"top\">" : "" %>
+              <td class="prompt"><%=HTML.encodeTags(name)%></td>
+              <td><%=HTML.encodeTags(rawBioAssay.getHeader(name))%></td>
+              <td>&nbsp;&nbsp;</td>
+            <%=needsTr ? "" : "</tr>"%>
+            <%
+            needsTr = !needsTr;
+          }
           %>
-          <%=needsTr ? "<tr valign=\"top\">" : "" %>
-            <td class="prompt"><%=HTML.encodeTags(name)%></td>
-            <td><%=HTML.encodeTags(rawBioAssay.getHeader(name))%></td>
-            <td>&nbsp;&nbsp;</td>
           <%=needsTr ? "" : "</tr>"%>
           <%
-          needsTr = !needsTr;
         }
         %>
-        <%=needsTr ? "" : "</tr>"%>
-        <%
-      }
-      %>
-      </table>
+        </table>
+      </base:section>
 
       <%
@@ -429 +426 @@
       {
         %>
-        <h4 class="docked">Experiments</h4>
-        <tbl:table
+        <base:section 
           id="experiments"
-          clazz="itemlist"
-          columns="all"
+          title="<%="Experiments (" + experiments.size() + ")"%>"
+          context="<%=cc%>"
           >
-        <tbl:columndef 
-          id="name"
-          title="Name"
-        />
-        <tbl:columndef 
-          id="description"
-          title="Description"
-        />
-        <tbl:data>
-          <tbl:columns>
-          </tbl:columns>
-          <tbl:rows>
-          <%
-          for (Experiment item : experiments)
-          {
+          <h4 class="docked">Experiments</h4>
+          <tbl:table
+            id="experiments"
+            clazz="itemlist"
+            columns="all"
+            >
+          <tbl:columndef 
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef 
+            id="description"
+            title="Description"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            for (Experiment item : experiments)
+            {
+              %>
+              <tbl:row>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
+                <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
+              </tbl:row>
+              <%
+            }
             %>
-            <tbl:row>
-              <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
-              <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
-            </tbl:row>
-            <%
-          }
-          %>
-          </tbl:rows>
-        </tbl:data>
-        </tbl:table>
+            </tbl:rows>
+          </tbl:data>
+          </tbl:table>
+        </base:section>
         <%
       }     
@@ -473 +476 @@
       {
         %>
-        <h4 class="docked">Shared to</h4>
+        <base:section 
+          id="sharedTo" 
+          title="Shared to"
+          context="<%=cc%>">
         <tbl:table 
           id="itemsSharedTo"
@@ -542 +548 @@
           </tbl:data>
         </tbl:table>
+        </base:section>
         <%
       }