Changeset 5199

Timestamp:

Dec 15, 2009, 1:58:52 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #1448: Implement BFS exporter for spot data

The exporter implementation should now be usable and it should be possible to start implementating the plug-in that will use this export.

Location:

trunk/src

Files:

• core/net/sf/basedb/util/export/spotdata/AbstractBioAssaySetExporter.java (modified) (2 diffs)
• core/net/sf/basedb/util/export/spotdata/AssayPropertyField.java (added)
• core/net/sf/basedb/util/export/spotdata/BfsExporter.java (added)
• core/net/sf/basedb/util/export/spotdata/ExportableFieldFactory.java (modified) (2 diffs)
• core/net/sf/basedb/util/export/spotdata/MatrixBfsExporter.java (added)
• core/net/sf/basedb/util/export/spotdata/SerialBfsExporter.java (added)
• test/TestBioAsssaySetExporter.java (modified) (8 diffs)

trunk/src/core/net/sf/basedb/util/export/spotdata/AbstractBioAssaySetExporter.java

@@ -272 +272 @@
   {
     RuntimeException e = null;
+    validate();
     try
     {
@@ -296 +297 @@
 
   /*
-    Export methods to be implemented by subclasses
-    ----------------------------------------------
-  */
+    Export methods that may be implemented by subclasses
+    ----------------------------------------------------
+  */
+  /**
+    Validate that all required options has been set and that other
+    options have sensible values. Subclasses that override this method
+    should call super.validate(). The default implementation will at least
+    validate that a DbControl and a source bioassay set has been set.
+    @since 2.15
+  */
+  protected void validate()
+  {
+    if (getDbControl() == null) throw new NullPointerException("getDbControl()");
+    if (getSource() == null) throw new NullPointerException("getSource()");
+  }
+  
   /**
     Make preparations for the export. Subclasses that need to initialise

trunk/src/core/net/sf/basedb/util/export/spotdata/ExportableFieldFactory.java

@@ -26 +26 @@
 import net.sf.basedb.core.ExtraValueType;
 import net.sf.basedb.core.Formula;
+import net.sf.basedb.core.Metadata;
 import net.sf.basedb.core.RawDataProperty;
 import net.sf.basedb.core.VirtualColumn;
@@ -52 +53 @@
     AnnotationAssayField field = new AnnotationAssayField();
     field.setAnnotationType(at);
+    field.setFormatter(formatter);
+    return field;
+  }
+  
+  /**
+    Create a property assay field. This field is used to export, for
+    example, name and description, from the bioassay.
+    @param property The property to export, see 
+      {@link Metadata#getPropertyValue(net.sf.basedb.core.DbControl, Object, String)}
+      for more information about the syntax of this parameter.
+    @param title The column title
+    @param formatter A formatter or null
+    @return An {@link AssayPropertyField} object
+    @since 2.15
+  */
+  public static AssayPropertyField assayProperty(String property, String title,
+    Formatter<?> formatter)
+  {
+    AssayPropertyField field = new AssayPropertyField();
+    field.setProperty(property);
+    field.setTitle(title);
     field.setFormatter(formatter);
     return field;

trunk/src/test/TestBioAsssaySetExporter.java

@@ -28 +28 @@
 import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Directory;
 import net.sf.basedb.core.Experiment;
 import net.sf.basedb.core.File;
@@ -51 +52 @@
 import net.sf.basedb.util.ConsoleProgressReporter;
 import net.sf.basedb.util.basefile.BaseFileWriter;
+import net.sf.basedb.util.bfs.AnnotationWriter;
+import net.sf.basedb.util.bfs.GenericBaseDataWriterFactory;
+import net.sf.basedb.util.bfs.MetadataWriter;
+import net.sf.basedb.util.export.spotdata.AssayField;
 import net.sf.basedb.util.export.spotdata.BaseFileExporter;
+import net.sf.basedb.util.export.spotdata.BfsExporter;
 import net.sf.basedb.util.export.spotdata.DynamicField;
 import net.sf.basedb.util.export.spotdata.ExportableFieldFactory;
 import net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter;
+import net.sf.basedb.util.export.spotdata.MatrixBfsExporter;
 import net.sf.basedb.util.export.spotdata.SerialBaseFileExporter;
+import net.sf.basedb.util.export.spotdata.SerialBfsExporter;
 import net.sf.basedb.util.parser.FlatFileParser;
 import net.sf.basedb.util.parser.FlatFileParser.Line;
@@ -106 +114 @@
     int fileMatrixNoMerge = TestFile.test_create("matrix.nomerge.txt", false, false);
     int fileMatrixMerge = TestFile.test_create("matrix.merge.txt", false, false);
+    int bfsSerialDir = TestDirectory.test_create(true, "bfs-serial");
+    int bfsMatrixDir = TestDirectory.test_create(true, "bfs-matrix");
     int bas = 0;
     if (ok)
@@ -119 +129 @@
       test_exportBaseFile(bas, fileMatrixNoMerge, true, false, true);
       test_exportBaseFile(bas, fileMatrixMerge, true, true, true);
+      
+      test_bfs_export(bas, bfsSerialDir, annotationType, false);
+      test_bfs_export(bas, bfsMatrixDir, annotationType, true);
     }
     
@@ -126 +139 @@
     TestRawBioAssay.test_delete(rba1);
     TestRawBioAssay.test_delete(rba2);
+    TestDirectory.test_delete(bfsSerialDir, true);
+    TestDirectory.test_delete(bfsMatrixDir, true);
     TestFile.test_delete(fileSerialNoMerge);
     TestFile.test_delete(fileSerialMerge);
@@ -548 +563 @@
         }
       }
-      write("--Exporting basefile [matrix:"+matrix+", mergeReporters:"+mergeReporters+"] SUCCEEDED");
+      write("--Exporting basefile [matrix:"+matrix+", mergeReporters:"+mergeReporters+"] OK");
     }
     catch (Throwable ex)
@@ -562 +577 @@
   }
   
+  static void test_bfs_export(int bioAssaySetId, int directoryId, 
+      int annotationTypeId, boolean matrix)
+  {
+    DbControl dc = null;
+    FlatFileParser ffp = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      BioAssaySet bas = BioAssaySet.getById(dc, bioAssaySetId);
+      Directory dir = Directory.getById(dc, directoryId);
+      
+      // Create exporter
+      BfsExporter bfs = matrix ? new MatrixBfsExporter() : new SerialBfsExporter();
+      bfs.setDbControl(dc);
+      bfs.setSource(bas);
+      if (!TestUtil.getSilent()) bfs.setProgressReporter(new ConsoleProgressReporter());
+
+      // Create files and file factory
+      File metadata = createFile(dc, dir, "metadata.txt");
+      File reporter = createFile(dc, dir, "rdata.txt");
+      File assay = createFile(dc, dir, "pdata.txt");
+      bfs.setMetadataWriter(MetadataWriter.create(
+          metadata.getUploadStream(false), metadata.getName()));
+      bfs.setReporterAnnotationsWriter(AnnotationWriter.create(
+          reporter.getUploadStream(false), reporter.getName()));
+      bfs.setAssayAnnotationsWriter(AnnotationWriter.create(
+          assay.getUploadStream(false), assay.getName()));
+      bfs.setDataWriterFactory(new GenericBaseDataWriterFactory(dc, dir));
+      
+      // Parameters that go in the 'settings' section
+      bfs.setParameter("b", "some parameter");
+      bfs.setParameter("a", "some other parameter");
+      
+      // Configure the spot fields to export
+      ItemQuery<Formula> ratio = Formula.getQuery(Formula.Type.COLUMN_EXPRESSION, 
+          bas.getRawDataType(), bas.getIntensityTransform());
+      ratio.restrict(Restrictions.eq(Hql.property("name"), Expressions.string("Ratio, ch1 / ch2")));
+      if (ratio.count(dc) < 1)
+      {
+        throw new Exception("Cant find formula 'Ratio, ch1 / ch2'");
+      }
+      List<DynamicField> spotFields = new ArrayList<DynamicField>();
+      spotFields.add(ExportableFieldFactory.channel(1, "intensity1", null));
+      spotFields.add(ExportableFieldFactory.rawData("row", null, Formula.AverageMethod.NONE, null));
+      spotFields.add(ExportableFieldFactory.rawData("flags", null, Formula.AverageMethod.NONE, null));
+      spotFields.add(ExportableFieldFactory.formula(ratio.list(dc).get(0), null, null));
+      for (DynamicField field : spotFields)
+      {
+        bfs.addSpotField(field, Type.FLOAT);
+      }
+      
+      // Configure the reporter fields to export
+      List<DynamicField> reporterFields = new ArrayList<DynamicField>();
+      reporterFields.add(ExportableFieldFactory.reporter("externalId", null, Formula.AverageMethod.NONE, null));
+      reporterFields.add(ExportableFieldFactory.reporter("name", null, Formula.AverageMethod.NONE, null));
+      reporterFields.add(ExportableFieldFactory.simple(Dynamic.column(VirtualColumn.POSITION), "position", Formula.AverageMethod.NONE, null));
+      bfs.addReporterFields(reporterFields);
+
+      // Configure assay fields to export
+      List<AssayField> assayFields = new ArrayList<AssayField>();
+      assayFields.add(ExportableFieldFactory.assayProperty("name", "Name", null));
+      if (annotationTypeId != 0)
+      {
+        AnnotationType at = AnnotationType.getById(dc, annotationTypeId);
+        assayFields.add(ExportableFieldFactory.annotation(at, null));
+      }
+      bfs.addAssayFields(assayFields);
+      
+      bfs.doExport();
+      if (!TestUtil.getSilent()) write("");
+      dc.commit();
+      write("--Exporting bfs [" + (matrix ? "matrix" : "serial") + "] OK");
+    }
+    catch (Throwable ex)
+    {
+      write("--Exporting bfs [" + (matrix ? "matrix" : "serial") + "] FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+
+  }
+  
   static void write(String message)
   {
@@ -567 +668 @@
   }
   
+  static File createFile(DbControl dc, Directory dir, String name)
+  {
+    File f = File.getNew(dc, dir);
+    f.setName(name);
+    f.setCharacterSet("UTF-8");
+    f.setMimeType("text/plain");
+    dc.saveItem(f);
+    return f;
+  }
+  
 }