From 5b984acbabc173ccaf6b49d4363c6ab1189f2392 Mon Sep 17 00:00:00 2001
From: Alex Aiezza <Alex Aiezza@AAEIZZA1W7D.urmc-sh.rochester.edu>
Date: Tue, 3 May 2016 17:20:42 -0400
Subject: [PATCH] Fix bug where FASTQ inflation caused crash

---
 .../rit/flick/genetics/FastFileDeflator.java  |  2 +-
 .../rit/flick/genetics/FastFileInflator.java  | 42 ++++++++++++++-----
 .../rit/flick/genetics/FastaFileInflator.java |  3 +-
 .../rit/flick/genetics/FastqFileInflator.java |  9 ++--
 4 files changed, 41 insertions(+), 15 deletions(-)

diff --git a/src/edu/rit/flick/genetics/FastFileDeflator.java b/src/edu/rit/flick/genetics/FastFileDeflator.java
index c8222df..e68c2a8 100644
--- a/src/edu/rit/flick/genetics/FastFileDeflator.java
+++ b/src/edu/rit/flick/genetics/FastFileDeflator.java
@@ -164,7 +164,7 @@ public File deflate( final Configuration configuration, final File fileIn, final
                 } catch ( final Exception e )
                 {
                     if ( !interrupted )
-                        e.printStackTrace();
+                        System.err.println( e.getMessage() );
                 }
             }, "Default_Deflation_Thread" );
 
diff --git a/src/edu/rit/flick/genetics/FastFileInflator.java b/src/edu/rit/flick/genetics/FastFileInflator.java
index dc37499..5d5a9d7 100644
--- a/src/edu/rit/flick/genetics/FastFileInflator.java
+++ b/src/edu/rit/flick/genetics/FastFileInflator.java
@@ -6,8 +6,8 @@
  */
 package edu.rit.flick.genetics;
 
-import static edu.rit.flick.config.DefaultOptionSet.VERBOSE_FLAG;
 import static edu.rit.flick.config.DefaultOptionSet.DELETE_FLAG;
+import static edu.rit.flick.config.DefaultOptionSet.VERBOSE_FLAG;
 import static org.apache.commons.io.FileUtils.getFile;
 
 import java.io.File;
@@ -107,6 +107,9 @@ protected void beforeSequence() throws IOException
 
     protected void close() throws IOException, InterruptedException
     {
+        if ( fastOut == null )
+            return;
+
         fastOut.close();
         iupacfile.close();
         datahcf.close();
@@ -227,7 +230,10 @@ protected Properties getProperties( final File propertiesFile ) throws IOExcepti
     }
 
     @Override
-    public File inflate( final Configuration configuration, final File fileIn, final File fileOut )
+    public synchronized File inflate(
+            final Configuration configuration,
+            final File fileIn,
+            final File fileOut )
     {
         assert fileIn.exists();
 
@@ -264,7 +270,7 @@ public File inflate( final Configuration configuration, final File fileIn, final
                 } catch ( final Exception e )
                 {
                     if ( !interrupted )
-                        e.printStackTrace();
+                        System.err.println( e.getMessage() );
                 }
             }, "Default_Inflation_Thread" );
 
@@ -275,19 +281,32 @@ public File inflate( final Configuration configuration, final File fileIn, final
                 configuration.setFlag( DELETE_FLAG, false );
                 try
                 {
+                    if ( inflateToDirectoryThread.isAlive() )
+                        inflateToDirectoryThread.interrupt();
+
                     // Clean up IO
                     close();
                     System.gc();
                     Thread.sleep( 100 );
 
-                    // Clean up temporary directory
-                    FileUtils.deleteDirectory( tmpOutputDirectory );
-                    // Clean up INCOMPLETE output file
-                    FileUtils.deleteQuietly( fileOut );
+                    synchronized ( this )
+                    {
+                        while ( inflateToDirectoryThread.isAlive() )
+                            this.wait();
+                    }
+
                 } catch ( final IOException | InterruptedException e )
                 {
                     e.printStackTrace();
+                } finally
+                {
+                    // Clean up temporary directory
+                    FileUtils.deleteQuietly( tmpOutputDirectory );
+                    // Clean up INCOMPLETE output file
+                    FileUtils.deleteQuietly( fileOut );
+                    System.out.println();
                 }
+
             }, "Inflation_Cleaning_Thread" );
 
             cleanHookAtomic.set( cleanHook );
@@ -342,7 +361,8 @@ protected File inflateFromFile( final File fileIn, final File tmpOutputDirectory
             zipFile.extractAll( tmpOutputDirectory.getPath() );
         } catch ( final ZipException e )
         {
-            e.printStackTrace();
+            if ( !interrupted )
+                System.err.println( e.getMessage() );
         }
 
         return tmpOutputDirectory;
@@ -423,7 +443,8 @@ protected final void writeNextHeader()
             seqDnaPosition.set( 0 );
         } catch ( final IOException e )
         {
-            e.printStackTrace();
+            if ( !interrupted )
+                e.printStackTrace();
         }
     }
 
@@ -454,7 +475,8 @@ protected void writeNucleotide( final byte base )
             fastOut.write( nucleotide );
         } catch ( final IOException e )
         {
-            e.printStackTrace();
+            if ( !interrupted )
+                System.err.println( e.getMessage() );
         }
         dnaPosition.increment();
     }
diff --git a/src/edu/rit/flick/genetics/FastaFileInflator.java b/src/edu/rit/flick/genetics/FastaFileInflator.java
index 88e3b62..37db442 100644
--- a/src/edu/rit/flick/genetics/FastaFileInflator.java
+++ b/src/edu/rit/flick/genetics/FastaFileInflator.java
@@ -52,7 +52,8 @@ protected void afterWriteNucleotide()
     protected void close() throws IOException, InterruptedException
     {
         super.close();
-        tandemFile.close();
+        if ( tandemFile != null )
+            tandemFile.close();
     }
 
     @SuppressWarnings ( "resource" )
diff --git a/src/edu/rit/flick/genetics/FastqFileInflator.java b/src/edu/rit/flick/genetics/FastqFileInflator.java
index 4f0ef64..ad2edd4 100644
--- a/src/edu/rit/flick/genetics/FastqFileInflator.java
+++ b/src/edu/rit/flick/genetics/FastqFileInflator.java
@@ -48,9 +48,12 @@ protected void beforeSequence() throws IOException
     @Override
     protected void close() throws IOException, InterruptedException
     {
-        lengthfile.close();
-        commentsfile.close();
-        scorefile.close();
+        if ( lengthfile != null )
+            lengthfile.close();
+        if ( commentsfile != null )
+            commentsfile.close();
+        if ( scorefile != null )
+            scorefile.close();
 
         scorefile = null;