Changeset 5697

Timestamp:

Aug 15, 2011, 8:52:47 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1153: Handling short read transcript sequence data

Re-added image import functionality to ScanImporter.

Location:

trunk/src

Files:

• core/net/sf/basedb/core/DataFileType.java (modified) (2 diffs)
• core/net/sf/basedb/core/DerivedBioAssay.java (modified) (2 diffs)
• core/net/sf/basedb/core/Install.java (modified) (2 diffs)
• plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java (modified) (7 diffs)

trunk/src/core/net/sf/basedb/core/DataFileType.java

@@ -24 +24 @@
 import java.util.Set;
 
-import net.sf.basedb.core.Transactional.Action;
 import net.sf.basedb.core.data.DataFileTypeData;
 import net.sf.basedb.core.query.Expressions;
@@ -143 +142 @@
   */
   public static final String BAM = "assembly.bam";
-  
+
+  /**
+    The external ID for the file type representing
+    scanned microarray image.
+    @since 3.0
+  */
+  public static final String MICROARRAY_IMAGE = "microarray.image";
+
   /**
     The maximum length of the file extension that can be stored in the database.

trunk/src/core/net/sf/basedb/core/DerivedBioAssay.java

@@ -23 +23 @@
 
 import java.util.Collection;
+import java.util.Collections;
 import java.util.Date;
 import java.util.HashSet;
@@ -389 +390 @@
   public Collection<FileSet> getParentFileSets()
   {
+    DerivedBioAssay parent = getParent();
     Collection<FileSet> parents = null;
-    // TODO - part of #1153
+    if (parent != null && parent.hasFileSet())
+    {
+      parents = Collections.singleton(parent.getFileSet());
+    }
     return parents;
   }

trunk/src/core/net/sf/basedb/core/Install.java

@@ -684 +684 @@
       if (progress != null) progress.display((int)(progressStep*progress_factor), "--Creating clients...");
       createClient(rootUser, "net.sf.basedb.clients.test", "Test programs", "This client is used by test programs", keyEveryoneUse);
-      createClient(rootUser, "net.sf.basedb.clients.migration", "Migration tool", "This client is used to migrate BASE 1.2.x data to BASE 2", null);
       createClient(rootUser, "net.sf.basedb.clients.jobagent", "Job agent client", "This client is used by all job agents", keyJobAgentUse);
       createClient(rootUser, "net.sf.basedb.clients.internal", "Internal", 
@@ -857 +856 @@
         Item.DERIVEDBIOASSAY, "bam", alignedType
       );
+      DataFileTypeData scanImageFile = createDataFileType(
+        DataFileType.MICROARRAY_IMAGE, "Microarray image",
+        "Scanned image from a microarray slide.",
+        Item.DERIVEDBIOASSAY, "tif", imageType
+      );
       
       // Platforms and variants

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java

@@ -22 +22 @@
 package net.sf.basedb.plugins.batchimport;
 
+import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DerivedBioAssay;
@@ -92 +93 @@
       );
   
-  protected static final PluginParameter<String> imageNameColumnMapping = new PluginParameter<String>(
-      "imageColumnMapping",
-      "Image name",
-      "Mapping that picks the name the image from the data columns. " +     
-      "Example: \\Image\\",
-      optionalColumnMapping
-      );
-  
-  protected static final PluginParameter<String> imageFormatColumnMapping = new PluginParameter<String>(
-      "imageFormatColumnMapping",
-      "Image format",
-      "Mapping that picks the format of the given image from the data columns. " +
-      "The plug-in tries to parse the given format into one of the supported in BASE. " +
-      "The image will get format 'unknown' if this isn't specified or has null-value." +
-      "The column can either be empty or has one of the values 'TIFF', 'JPEG' or 'Unknown'."+
-      "Example: \\Image format\\",
-      optionalColumnMapping
-      );
-  
-  protected static final PluginParameter<String> imagePreviewColumnMapping = new PluginParameter<String>(
-      "imagePreviewColumnMapping",
-      "Image preview",
-      "Mapping that picks the preview flag of the given image from the data columns. " +
-      "Example: \\Image preview\\",
-      optionalColumnMapping
-      );
-  
-  protected static final PluginParameter<String> imageDescriptionColumnMapping = new PluginParameter<String>(
-      "imageDescriptionColumnMapping",
-      "Image description",
-      "Mapping that picks the description of the given image from the data columns. " +
-      "Example: \\Image description\\",
-      optionalColumnMapping
-      );
-
-  
   public ScanImporter()
   {}
@@ -153 +118 @@
   private Mapper hybridizationMapper;
   private Mapper imageFileMapper;
-  private Mapper imageNameMapper;
-  private Mapper imageFormatMapper;
-  private Mapper imagePreviewMapper;
-  private Mapper imageDescriptionMapper;
   private String imagesDirectory;
   
@@ -189 +150 @@
     parameters.add(hardwareColumnMapping);
     parameters.add(imageFileColumnMapping);
-    parameters.add(imageNameColumnMapping);
-    parameters.add(imageFormatColumnMapping);
-    parameters.add(imagePreviewColumnMapping);
-    parameters.add(imageDescriptionColumnMapping);
     parameters.add(permissionTemplateColumnMapping);
   }
@@ -241 +198 @@
     hybridizationMapper = getMapper(ffp, (String)job.getValue("hybridizationColumnMapping"), null, null);
     imageFileMapper = getMapper(ffp, (String)job.getValue("imageFileColumnMapping"), null, null);
-    imageNameMapper = getMapper(ffp, (String)job.getValue("imageColumnMapping"), null, null);
-    imageFormatMapper = getMapper(ffp, (String)job.getValue("imageFormatColumnMapping"), null, null);
-    imagePreviewMapper = getMapper(ffp, (String)job.getValue("imagePreviewColumnMapping"), null, null);
-    imageDescriptionMapper = getMapper(ffp, (String)job.getValue("imageDescriptionColumnMapping"), null, null);
     imagesDirectory = (String)job.getValue("imagesDirectory");
     if (imagesDirectory != null && !imagesDirectory.startsWith("/"))
@@ -291 +244 @@
   protected void updateMultiLineItem(DbControl dc, DerivedBioAssay scan, FlatFileParser.Data data, int multiLineNum)
   {
-//    TODO (#1153)
-  //  Image image = null;
-    File imageFile = null;
-    String imageName = null;
+
     // Get the imagefile
-    if (imageFileMapper != null && imageFileMapper.getValue(data) != null)
+    if (imageFileMapper != null)
     {
       String filePath = imageFileMapper.getValue(data);
@@ -303 +253 @@
         filePath = imagesDirectory + filePath;
       }
-      imageFile = File.getByPath(dc, new Path(filePath, Path.Type.FILE), false);
-  //    image = findImage(dc, scan, imageFile);
-    }
-    if (imageNameMapper != null) 
-    {
-      imageName = imageNameMapper.getValue(data);
-    }
-    /*
-    TODO (#1153)
-    else if (image != null)
-    {
-      imageName = image.getName();
-    }
-    if (image != null)
-    {
-      image.setName(imageName != null ? imageName : scan.getName() + "." + imageFile.getName());
-      if (imageDescriptionMapper != null) image.setDescription(imageDescriptionMapper.getValue(data));
-      if (imageFormatMapper != null && imageFormatMapper.getValue(data) != null) image.setFormat(Image.Format.valueOf(imageFormatMapper.getValue(data)));
-      if (imagePreviewMapper != null) image.setPreview(Boolean.getBoolean(imagePreviewMapper.getValue(data)));
-    }
-    */
+      File imageFile = File.getByPath(dc, new Path(filePath, Path.Type.FILE), false);
+      DataFileType imageType = DataFileType.getByExternalId(dc, DataFileType.MICROARRAY_IMAGE);
+      if (imageFile != null)
+      {
+        scan.getFileSet().setMember(imageFile, imageType);
+      }
+      else
+      {
+        scan.getFileSet().removeMember(imageType);
+      }
+    }
   }
   // ------------------------------------