Changeset 6077

Timestamp:

Aug 3, 2012, 12:53:22 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1706: External program executor and BASE 1 plug-in executor doesn't remove temporary working files

Location:

trunk

Files:

• doc/src/docbook/appendix/incompatible.xml (modified) (1 diff)
• src/core/net/sf/basedb/util/export/spotdata/BaseFileExporter.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/importer/spotdata/BaseFileImporter.java (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (1 diff)

trunk/doc/src/docbook/appendix/incompatible.xml

@@ -35 +35 @@
     and backwards compatible.
   </para>
+  
+  <sect1 id="appendix.incompatible.3.2">
+    <title>BASE 3.2 release</title>
+
+    <bridgehead>BASEfile exporter automatically closes the output stream</bridgehead>
+    <para>
+      The implementation of the BASEfile exporter has been changed to
+      automatically close the provided output stream when the export
+      is complete. Clients that need the old behavior should call
+      <code>BaseFileExporter.setAutoCloseWriters(false)</code> before
+      using it.
+    </para>
+  </sect1>
   
   <sect1 id="appendix.incompatible.3.1">

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

@@ -69 +69 @@
   private Map<String, String> parameters;
   private BaseFileWriter out;
+  private boolean autoCloseWriters;
   
   protected BaseFileExporter()
   {
     this.parameters = new LinkedHashMap<String, String>();
+    this.autoCloseWriters = true;
   }
   
@@ -87 +89 @@
   {
     this.out = out;
+  }
+  
+  /**
+    If this option is set then all writers are automatically closed
+    when all data has been writted to them. This setting is enabled by default.
+    @since 3.2
+  */
+  public void setAutoCloseWriters(boolean autoClose)
+  {
+    this.autoCloseWriters = autoClose;
   }
   
@@ -246 +258 @@
     exportAssaysSectionData();
     return true;
+  }
+  
+  @Override
+  protected void endExport(RuntimeException e) 
+  {
+    if (out != null && autoCloseWriters) out.close();
+    super.endExport(e);
   }
   // -------------------------------------------  

trunk/src/core/net/sf/basedb/util/importer/spotdata/BaseFileImporter.java

@@ -23 +23 @@
 
 import java.io.IOException;
+import java.io.InputStream;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -52 +53 @@
 import net.sf.basedb.core.signal.ThreadSignalHandler;
 import net.sf.basedb.util.ChainedProgressReporter;
+import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.basefile.BaseFileParser;
 import net.sf.basedb.util.importer.FileWrapper;
@@ -282 +284 @@
       parser.setProgressReporter(new SimpleAbsoluteProgressReporter(chainedProgress, srcFile.getSize()));
     }
-    FlatFileParser ffp = parser.parse(srcFile.getInputStream(), srcFile.getCharacterSet());
-    int totalLines = ffp.getParsedLines();
-    
-    // If the BASEfile didn't have any 'spots' sections we don't 
-    // create a child bioassay set
-    if (parser.getSectionCount("spots") == 0) return null;
-
-    // Create the child bioassay set and bioassays
-    boolean useNewDataCube = info.getAssaysHaveParentAssaysMapping() 
-      || info.getChildHasDifferentReporterPositionMapping();
-    BioAssaySet child = createChildBioAssaySet(dc, info, t, useNewDataCube);
-    child.setIntensityTransform(transform);
-    createChildBioAssays(dc, child, info, useNewDataCube);
-    
-    // Create the position/reporter mapping if needed
-    if (useNewDataCube)
-    {
-      if (chainedProgress != null) chainedProgress.setRange(30, 40);
-      createChildPositionReporterMapping(child, info, chainedProgress);
-      if (!info.getChildHasDifferentReporterPositionMapping() && child.getRawDataType().isStoredInDb())
-      {
-        // If the child and parent has identical position/reporter mapping
-        // we can "calculate" new raw data mappings.
-        if (chainedProgress != null) chainedProgress.setRange(40, 50);
-        createChildRawDataMapping(child, parent, info, chainedProgress);
-      }
-    }
-    
-    // Second parser pass: progress=50-100%
-    SecondPassSectionSpotsParser spotParser2 = 
-      new SecondPassSectionSpotsParser(dc, info, child, totalLines);
-    BaseFileParser secondParser = new BaseFileParser();
-    secondParser.copyRedefinedColumnNames(parser);
-    secondParser.setSectionParser("spots", spotParser2);
-    if (chainedProgress != null)
-    {
-      chainedProgress.setRange(50, 100);
-      secondParser.setProgressReporter(new SimpleAbsoluteProgressReporter(chainedProgress, totalLines));
-    }
-    secondParser.parse(srcFile.getInputStream(), srcFile.getCharacterSet());
-    return child;
+    InputStream srcIn = srcFile.getInputStream();
+    try
+    {
+      FlatFileParser ffp = parser.parse(srcIn, srcFile.getCharacterSet());
+      int totalLines = ffp.getParsedLines();
+      
+      // If the BASEfile didn't have any 'spots' sections we don't 
+      // create a child bioassay set
+      if (parser.getSectionCount("spots") == 0) return null;
+  
+      // Create the child bioassay set and bioassays
+      boolean useNewDataCube = info.getAssaysHaveParentAssaysMapping() 
+        || info.getChildHasDifferentReporterPositionMapping();
+      BioAssaySet child = createChildBioAssaySet(dc, info, t, useNewDataCube);
+      child.setIntensityTransform(transform);
+      createChildBioAssays(dc, child, info, useNewDataCube);
+      
+      // Create the position/reporter mapping if needed
+      if (useNewDataCube)
+      {
+        if (chainedProgress != null) chainedProgress.setRange(30, 40);
+        createChildPositionReporterMapping(child, info, chainedProgress);
+        if (!info.getChildHasDifferentReporterPositionMapping() && child.getRawDataType().isStoredInDb())
+        {
+          // If the child and parent has identical position/reporter mapping
+          // we can "calculate" new raw data mappings.
+          if (chainedProgress != null) chainedProgress.setRange(40, 50);
+          createChildRawDataMapping(child, parent, info, chainedProgress);
+        }
+      }
+      FileUtil.close(srcIn);
+      
+      // Second parser pass: progress=50-100%
+      SecondPassSectionSpotsParser spotParser2 = 
+        new SecondPassSectionSpotsParser(dc, info, child, totalLines);
+      BaseFileParser secondParser = new BaseFileParser();
+      secondParser.copyRedefinedColumnNames(parser);
+      secondParser.setSectionParser("spots", spotParser2);
+      if (chainedProgress != null)
+      {
+        chainedProgress.setRange(50, 100);
+        secondParser.setProgressReporter(new SimpleAbsoluteProgressReporter(chainedProgress, totalLines));
+      }
+      srcIn = srcFile.getInputStream();
+      secondParser.parse(srcIn, srcFile.getCharacterSet());
+      return child;
+    }
+    finally
+    {
+      FileUtil.close(srcIn);
+    }
   }
 

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -1484 +1484 @@
         if (!File.exists(dc, d, f.getName()))
         {
+          ThreadSignalHandler.checkInterrupted();
           File newFile = File.getNew(dc, d);
           newFile.setName(f.getName());
           newFile.setMimeTypeAuto(null, null);
           dc.saveItem(newFile);
+          InputStream tmpIn = null;
           try
           {
-            ThreadSignalHandler.checkInterrupted();
-            newFile.upload(new FileInputStream(f), true);
+            tmpIn = new FileInputStream(f);
+            newFile.upload(tmpIn, true);
           }
           catch (FileNotFoundException e)
           {
             continue;
+          }
+          finally
+          {
+            FileUtil.close(tmpIn);
           }
         }