Changeset 1139

Timestamp:

Aug 26, 2005, 2:23:06 PM (18 years ago)

Author:

Nicklas Nordborg

Message:

Added SpotImages? and test program to create spot images

Location:

trunk

Files:

• build.xml (modified) (2 diffs)
• lib/compile/jai_codec.jar (added)
• lib/compile/jai_core.jar (added)
• lib/compile/mlibwrapper_jai.jar (added)
• src/core/net/sf/basedb/core/Item.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/ReporterBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/SpotImage.java (added)
• src/core/net/sf/basedb/core/SpotImages.java (added)
• src/test/TestAll.java (modified) (1 diff)
• src/test/TestFile.java (modified) (1 diff)
• src/test/TestRawBioAssay.java (modified) (4 diffs)
• src/test/TestSpotImages.java (added)
• src/test/spots.tif (added)

trunk/build.xml

@@ -369 +369 @@
       <fileset dir="${lib}/compile">
         <include name="**/*.jar"/>
-        <exclude name="**/jai*.jar" />
+        <exclude name="**/*jai*.jar" />
         <exclude name="**/servlet-api.jar" />
         <exclude name="**/jsp-api.jar" />
@@ -382 +382 @@
     <copy todir="${dist.classes}" file="${src}/hibernate.properties" />
     <copy todir="${dist.classes}" file="${src}/log4j.properties" />
-<!--
-    <copy todir="${dist.classes}" file="${src}/extended-properties.xml" />
-    <copy todir="${dist.classes}" file="${src}/raw-data-types.xml" />
-    <copy todir="${dist.classes}" file="${src}/mysql-queries.xml" />
-    <copy todir="${dist.classes}" file="${src}/sqlserver-queries.xml" />
--->
   </target>
 

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

@@ -304 +304 @@
   RAWBIOASSAY(264, "Raw bioassay", "rba", RawBioAssay.class, RawBioAssayData.class, DefinedPermissions.shareable),
   /**
-    The item is a {@link RawBioAssay}.
-  */
-  RAWDATA(265, "Raw data", "rdt", null, RawData.class, null),
+    The item is a {@link SpotImages}.
+  */
+  SPOTIMAGES(265, "Spot images", "spi", SpotImages.class, SpotImagesData.class, null),
+  /**
+    The item is a {@link RawData} spot.
+  */
+  RAWDATA(266, "Raw data", "rdt", null, RawData.class, null),
 
   /**

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

@@ -27 +27 @@
 import net.sf.basedb.core.data.RawBioAssayData;
 import net.sf.basedb.core.data.RawData;
+import net.sf.basedb.core.data.SpotImagesData;
 
 import net.sf.basedb.core.query.Restrictions;
@@ -355 +356 @@
   }
   
+  /**
+    Get the {@link SpotImages} item used to generate spot images
+    for this raw bio assay. If no <code>SpotImages</code> exists
+    a new one is created, and it must be saved to the database before it can
+    be used.
+
+    @return The <code>SpotImages</code> item
+  */
+  public SpotImages getSpotImages()
+    throws PermissionDeniedException, BaseException
+  {
+    SpotImagesData spi = getData().getSpotImages();
+    if (spi == null)
+    {
+      return SpotImages.getNew(getDbControl(), this);
+    }
+    else
+    {
+      return getDbControl().getItem(SpotImages.class, spi);
+    }
+  }
+
+  
   public RawDataBatcher getRawDataBatcher()
     throws PermissionDeniedException, BaseException

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

@@ -178 +178 @@
   }
   
+  public ReporterData getByExternalId(String externalId)
+    throws BaseException
+  {
+    if (findReporter == null)
+    {
+      findReporter = HibernateUtil.getPredefinedQuery(getDbControl().getHibernateSession(), "GET_REPORTER_FOR_EXTERNAL_ID");
+    }
+    findReporter.setString("externalId", externalId);
+    ReporterData r = HibernateUtil.loadData(ReporterData.class, findReporter);
+    if (r == null) throw new ItemNotFoundException("Reporter[externalId="+externalId+"]");
+    return r;
+  }
+  
 }

trunk/src/test/TestAll.java

@@ -112 +112 @@
 //    results.put("TestRawData", TestRawData.test_all());
 //    results.put("TestRawDataImport", TestRawDataImport.test_all());
-//    results.put("TestSpotImages", TestSpotImages.test_all());
+    results.put("TestSpotImages", TestSpotImages.test_all());
 
     // Experiments

trunk/src/test/TestFile.java

@@ -88 +88 @@
       }
       dc.saveItem(file);
-      in = new FileInputStream(filename);
-      file.upload(in, true);
+      if (new java.io.File(filename).exists())
+      {
+        in = new FileInputStream(filename);
+        file.upload(in, true);
+      }
       dc.commit();
       id = file.getId();

trunk/src/test/TestRawBioAssay.java

@@ -25 +25 @@
 import net.sf.basedb.core.*;
 import net.sf.basedb.core.data.RawData;
+import net.sf.basedb.util.FlatFileParser;
+import net.sf.basedb.util.FileUtil;
 import java.util.Date;
 import java.util.List;
 import java.util.Map;
+import java.util.regex.Pattern;
 
 public class TestRawBioAssay
@@ -58 +61 @@
     test_load(id);
     
+    // Test adding raw data
     test_add_rawdata(id, 50);
+    TestReporter.test_import_from_file("test.rawdata.import.txt");
+    test_import_from_file(id2, "test.rawdata.import.txt");
+    
     test_list(-1);
-    
     test_list_raw_data(id, -1);
 
@@ -66 +72 @@
     test_delete(id);
     test_delete(id2);
-    
+    TestReporter.test_delete();
+
     TestScan.test_delete(scanId);
     TestHybridization.test_delete(hybridizationId);
@@ -343 +350 @@
     }
   }
+  
+  static void test_import_from_file(int rawBioAssayId, String filename)
+  {
+    if (rawBioAssayId == 0) return;
+    write("--Start import raw data from file (" + filename + ")");
+    DbControl dc = null;
+    long time;
+    int i = 0;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      RawBioAssay rba = RawBioAssay.getById(dc, rawBioAssayId);
+      RawDataBatcher rawDataBatcher = rba.getRawDataBatcher();
+      ReporterBatcher reporterBatcher = ReporterBatcher.getNew(dc);
+    
+      FlatFileParser parser = new FlatFileParser();
+      parser.setDataHeaderRegexp(Pattern.compile("\"Block\"\\t\"Column\"\\t\"Row\"\\t\"Name\"\\t\"ID\".*"));
+      parser.setDataSplitterRegexp(Pattern.compile("\"?\\t\"?"));
+      parser.setInputStream(FileUtil.getInputStream(filename));
+      parser.parseHeaders();
+      
+      time = System.currentTimeMillis();
+      while (parser.hasMoreData())
+      {
+        FlatFileParser.Data parsedData = parser.nextData();
+        RawData rawData = rawDataBatcher.newRawData();
+        rawData.setBlock(Integer.valueOf(parsedData.get(0)));
+        rawData.setRow(Integer.valueOf(parsedData.get(2)));
+        rawData.setColumn(Integer.valueOf(parsedData.get(1)));
+        rawData.setX(Integer.valueOf(parsedData.get(5)));
+        rawData.setY(Integer.valueOf(parsedData.get(6)));
+        rawData.setReporter(reporterBatcher.getByExternalId(parsedData.get(4)));
+        
+        Map<String, Object> extraData = rawData.getAllExtended();
+        extraData.put("diameter", Float.valueOf(parsedData.get(7)));
+        extraData.put("ch1FgMedian", Float.valueOf(parsedData.get(8)));
+        extraData.put("ch1FgMean", Float.valueOf(parsedData.get(9)));
+        extraData.put("ch1FgSd", Float.valueOf(parsedData.get(10)));
+        extraData.put("ch1BgMedian", Float.valueOf(parsedData.get(11)));
+        extraData.put("ch1BgMean", Float.valueOf(parsedData.get(12)));
+        extraData.put("ch1BgSd", Float.valueOf(parsedData.get(13)));
+        extraData.put("ch1PercSd1", Integer.valueOf(parsedData.get(14)));
+        extraData.put("ch1PercSd2", Integer.valueOf(parsedData.get(15)));
+        extraData.put("ch1PercSat", Integer.valueOf(parsedData.get(16)));
+        extraData.put("ch2FgMedian", Float.valueOf(parsedData.get(17)));
+        extraData.put("ch2FgMean", Float.valueOf(parsedData.get(18)));
+        extraData.put("ch2FgSd", Float.valueOf(parsedData.get(19)));
+        extraData.put("ch2BgMedian", Float.valueOf(parsedData.get(20)));
+        extraData.put("ch2BgMean", Float.valueOf(parsedData.get(21)));
+        extraData.put("ch2BgSd", Float.valueOf(parsedData.get(22)));
+        extraData.put("ch2PercSd1", Integer.valueOf(parsedData.get(23)));
+        extraData.put("ch2PercSd2", Integer.valueOf(parsedData.get(24)));
+        extraData.put("ch2PercSat", Integer.valueOf(parsedData.get(25)));
+
+        rawDataBatcher.insert(rawData);
+        i++;
+      }
+      dc.commit();
+      time = System.currentTimeMillis()-time;
+
+      write("--Import raw data from file OK ("+i+", time="+time+" ms)");
+    }
+    catch (Throwable ex)
+    {
+      write("--Import raw data from file FAILED ("+i+")");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
 }