From 586260b9f877e0954513fcffb0aa27eaddc5d0ff Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 10 May 2022 12:26:35 +0100
Subject: [PATCH] JWS-128 patch out log4j references in the compbio.FileUtil
 class, and corresponding calls to methods in the JABAWS
 client and engine code.

---
 compbio-utils/compbio/util/FileUtil.java           |   34 +++++++-------------
 engine/compbio/engine/client/ConfExecutable.java   |    2 +-
 engine/compbio/engine/client/EngineUtil.java       |    4 +--
 engine/compbio/engine/client/Util.java             |    4 +--
 engine/compbio/engine/local/ExecutableWrapper.java |    4 +--
 5 files changed, 19 insertions(+), 29 deletions(-)

diff --git a/compbio-utils/compbio/util/FileUtil.java b/compbio-utils/compbio/util/FileUtil.java
index 7456a05..dc10637 100644
--- a/compbio-utils/compbio/util/FileUtil.java
+++ b/compbio-utils/compbio/util/FileUtil.java
@@ -204,7 +204,7 @@ public class FileUtil {
 		try {
 			out.close();
 		} finally {
-			closeSilently(log, out);
+			closeSilently(out);
 		}
 		return file;
 	}
@@ -228,9 +228,9 @@ public class FileUtil {
 			bis.close();
 			inStream.close();
 		} finally {
-			closeSilently(log, out);
-			closeSilently(log, bis);
-			closeSilently(log, inStream);
+			closeSilently(out);
+			closeSilently(bis);
+			closeSilently(inStream);
 		}
 		return result;
 	}
@@ -245,7 +245,7 @@ public class FileUtil {
 		try {
 			contentStr.close();
 		} finally {
-			closeSilently(log, contentStr);
+			closeSilently(contentStr);
 		}
 		return content;
 	}
@@ -287,8 +287,8 @@ public class FileUtil {
 				br.close();
 				reader.close();
 			} finally {
-				closeSilently(log, br);
-				closeSilently(log, reader);
+				closeSilently(br);
+				closeSilently(reader);
 			}
 		}
 		return fileStr;
@@ -313,8 +313,8 @@ public class FileUtil {
 			bw.close();
 			fwriter.close();
 		} finally {
-			closeSilently(log, bw);
-			closeSilently(log, fwriter);
+			closeSilently(bw);
+			closeSilently(fwriter);
 		}
 	}
 
@@ -337,8 +337,8 @@ public class FileUtil {
 			bw.close();
 			outStream.close();
 		} finally {
-			closeSilently(log, bw);
-			closeSilently(log, outStream);
+			closeSilently(bw);
+			closeSilently(outStream);
 		}
 	}
 
@@ -366,23 +366,13 @@ public class FileUtil {
 		return Arrays.asList(new File(path).list(filter));
 	}
 
-	public final static void closeSilently(Logger log, Closeable stream) {
-		if (stream != null) {
-			try {
-				stream.close();
-			} catch (IOException e) {
-				log.warning(e.getLocalizedMessage() + " Cause \n"+e.getCause());
-			}
-		}
-	}
-
 
 	public final static void closeSilently(Closeable stream) {
 		if (stream != null) {
 			try {
 				stream.close();
 			} catch (IOException e) {
-				log.warning(e.getLocalizedMessage()+" Cause \n"+e.getCause());
+				System.err.println(e.getLocalizedMessage()+" Cause \n"+e.getCause());
 			}
 		}
 	}
diff --git a/engine/compbio/engine/client/ConfExecutable.java b/engine/compbio/engine/client/ConfExecutable.java
index dcce7d2..bd24840 100644
--- a/engine/compbio/engine/client/ConfExecutable.java
+++ b/engine/compbio/engine/client/ConfExecutable.java
@@ -276,7 +276,7 @@ public class ConfExecutable<T> implements ConfiguredExecutable<T> {
 		} catch (JAXBException e) {
 			log.warning(e.getLocalizedMessage()+" Caused by\n"+e.getCause());
 		} finally {
-			FileUtil.closeSilently(log, confFileStream);
+			FileUtil.closeSilently(confFileStream);
 		}
 		return rconf;
 	}
diff --git a/engine/compbio/engine/client/EngineUtil.java b/engine/compbio/engine/client/EngineUtil.java
index d5c30af..906745f 100644
--- a/engine/compbio/engine/client/EngineUtil.java
+++ b/engine/compbio/engine/client/EngineUtil.java
@@ -99,7 +99,7 @@ public final class EngineUtil {
 					+ workDirectory + " for local execution! Ignoring... "
 					+ e.getMessage());
 		} finally {
-			FileUtil.closeSilently(log, writer);
+			FileUtil.closeSilently(writer);
 		}
 	}
 
@@ -376,7 +376,7 @@ public final class EngineUtil {
 					"Could not load run configuration!" + e.getMessage()+"\n"+
 					e.getCause());
 		} finally {
-			FileUtil.closeSilently(log, fileInStream);
+			FileUtil.closeSilently(fileInStream);
 		}
 		return exec;
 	}
diff --git a/engine/compbio/engine/client/Util.java b/engine/compbio/engine/client/Util.java
index c57596c..f558153 100644
--- a/engine/compbio/engine/client/Util.java
+++ b/engine/compbio/engine/client/Util.java
@@ -99,7 +99,7 @@ public final class Util {
 					+ workDirectory + " for local execution! Ignoring... "
 					+ e.getMessage());
 		} finally {
-			FileUtil.closeSilently(log, writer);
+			FileUtil.closeSilently(writer);
 		}
 	}
 
@@ -376,7 +376,7 @@ public final class Util {
 					"Could not load run configuration!" + e.getMessage(),
 					e.getCause());
 		} finally {
-			FileUtil.closeSilently(log, fileInStream);
+			FileUtil.closeSilently(fileInStream);
 		}
 		return exec;
 	}
diff --git a/engine/compbio/engine/local/ExecutableWrapper.java b/engine/compbio/engine/local/ExecutableWrapper.java
index 1cdf9a4..dbf12ae 100644
--- a/engine/compbio/engine/local/ExecutableWrapper.java
+++ b/engine/compbio/engine/local/ExecutableWrapper.java
@@ -209,8 +209,8 @@ public final class ExecutableWrapper implements
 			}
 			// hack - we probably lost log messages here.
 			java.util.logging.Logger logger = java.util.logging.Logger.getLogger(this.getClass().getCanonicalName());
-			FileUtil.closeSilently(logger, errorStream);
-			FileUtil.closeSilently(logger, outStream);
+			FileUtil.closeSilently(errorStream);
+			FileUtil.closeSilently(outStream);
 		}
 		return confExec;
 	}
-- 
1.7.10.2