Fix windows file renaming issue

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/TextFile.java

@@ -62,13 +62,18 @@ public class TextFile {
 		List<String> result = new ArrayList<String>();
 		
 		File file = new CSFile(path);
-		BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file),"UTF-8"));
+		FileInputStream fs = new FileInputStream(file);
+		try {
+		  BufferedReader reader = new BufferedReader(new InputStreamReader(fs,"UTF-8"));
 
 		  while( reader.ready() )
 		    result.add(reader.readLine());
 
 		  reader.close();
 		  return result;
+		} finally {
+		  fs.close();
+		}
 	}
 	
 	public static void writeAllLines(String path, List<String> lines) throws IOException
@@ -141,11 +146,21 @@ public class TextFile {
   }
 
   public static String fileToString(File f) throws FileNotFoundException, IOException {
-    return streamToString(new FileInputStream(f));
+    FileInputStream fs = new FileInputStream(f);
+    try {
+      return streamToString(fs);
+    } finally {
+      fs.close();
+    }
   }
   
   public static String fileToString(String src) throws FileNotFoundException, IOException  {
-    return streamToString(new FileInputStream(new CSFile(src)));
+    FileInputStream fs = new FileInputStream(new CSFile(src));
+    try {
+      return streamToString(fs);
+    } finally {
+      fs.close();
+    }
   }
 
   public static String streamToString(InputStream input) throws IOException  {
@@ -205,7 +220,12 @@ public class TextFile {
   }
 
   public static byte[] fileToBytes(String srcFile) throws FileNotFoundException, IOException {
-    return streamToBytes(new FileInputStream(new CSFile(srcFile)));
+    FileInputStream fs = new FileInputStream(new CSFile(srcFile));
+    try {
+      return streamToBytes(fs);
+    } finally {
+      fs.close();
+    }
   }
 
   /**
@@ -218,11 +238,21 @@ public class TextFile {
    * @throws IOException
    */
   public static byte[] fileToBytesNCS(String srcFile) throws FileNotFoundException, IOException {
-    return streamToBytes(new FileInputStream(new File(srcFile)));
+    FileInputStream fs = new FileInputStream(new File(srcFile));
+    try {
+      return streamToBytes(fs);
+    } finally {
+      fs.close();
+    }
   }
 
   public static byte[] fileToBytes(File file) throws FileNotFoundException, IOException {
-    return streamToBytes(new FileInputStream(file));
+    FileInputStream fs = new FileInputStream(file);
+    try {
+      return streamToBytes(fs);
+    } finally {
+      fs.close();
+    }
   }
 
   public static String bytesToString(byte[] bs) throws IOException {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java

@@ -2033,4 +2033,30 @@ public class Utilities {
     return i == 0 ? "" : s.substring(0, i+1);
   }
 
+public static void renameDirectory(String source, String dest) throws FHIRException, IOException {
+	File src = new File(source);
+	File dst = new File(dest);
+	if (!src.renameTo(dst)) {
+	  int i = 0;
+	  do {
+	    try {
+		  Thread.sleep(20);
+        } catch (Exception e) {
+          // nothing
+        }
+		System.gc();
+		i++;
+	  } while (!src.renameTo(dst) && i < 10);
+	  if (src.exists()) {
+		copyDirectory(source, dest, null);
+		try {
+		  src.delete();	
+		} catch (Exception e) {
+		  // nothing
+		}
+	  }
+	}
+	
+}
+
 }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java

@@ -453,7 +453,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
           } catch (Throwable t) {
             log("Unable to clear directory: "+packRoot+": "+t.getMessage()+" - this may cause problems later");
           }
-          new File(tempDir).renameTo(new File(packRoot));
+          Utilities.renameDirectory(tempDir, packRoot);          
 
           IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
           ini.setTimeStampFormat("yyyyMMddhhmmss");