From 14091acefc7125b96aec2d1c33ac495e09779d64 Mon Sep 17 00:00:00 2001
From: Jules Jacobsen <j.jacobsen@qmul.ac.uk>
Date: Tue, 27 Feb 2024 10:33:21 +0000
Subject: [PATCH] Fix for #541 - update logback-spring.xml to use
 org/springframework/boot/logging/logback/defaults.xml rather than
 org/springframework/boot/logging/logback/base.xml in order to not create the
 /tmp/spring.log file

---
 exomiser-cli/src/main/resources/logback-spring.xml    |  8 +++++++-
 .../src/main/resources/logback-spring.xml             |  9 +++++++--
 .../src/main/resources/logback-spring.xml             | 11 +++++++++--
 .../src/main/resources/logback-spring.xml             | 11 +++++++++--
 exomiser-web/src/main/resources/logback-spring.xml    | 11 +++++++++--
 5 files changed, 41 insertions(+), 9 deletions(-)

diff --git a/exomiser-cli/src/main/resources/logback-spring.xml b/exomiser-cli/src/main/resources/logback-spring.xml
index 9c18cdcce..c8020061d 100644
--- a/exomiser-cli/src/main/resources/logback-spring.xml
+++ b/exomiser-cli/src/main/resources/logback-spring.xml
@@ -20,6 +20,12 @@
   -->
 
 <configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml"/>
+    <include resource="org/springframework/boot/logging/logback/defaults.xml" />
+    <include resource="org/springframework/boot/logging/logback/console-appender.xml" />
+    <include resource="org/springframework/boot/logging/logback/file-appender.xml" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+        <appender-ref ref="FILE" />
+    </root>
     <logger name="com.zaxxer.hikari" level="ERROR"/>
 </configuration>
\ No newline at end of file
diff --git a/exomiser-data-genome/src/main/resources/logback-spring.xml b/exomiser-data-genome/src/main/resources/logback-spring.xml
index f69a24573..c8020061d 100644
--- a/exomiser-data-genome/src/main/resources/logback-spring.xml
+++ b/exomiser-data-genome/src/main/resources/logback-spring.xml
@@ -20,7 +20,12 @@
   -->
 
 <configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml"/>
+    <include resource="org/springframework/boot/logging/logback/defaults.xml" />
+    <include resource="org/springframework/boot/logging/logback/console-appender.xml" />
+    <include resource="org/springframework/boot/logging/logback/file-appender.xml" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+        <appender-ref ref="FILE" />
+    </root>
     <logger name="com.zaxxer.hikari" level="ERROR"/>
-    <logger name="de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser" level="ERROR"/>
 </configuration>
\ No newline at end of file
diff --git a/exomiser-data-phenotype/src/main/resources/logback-spring.xml b/exomiser-data-phenotype/src/main/resources/logback-spring.xml
index 558b0cb5a..c8020061d 100644
--- a/exomiser-data-phenotype/src/main/resources/logback-spring.xml
+++ b/exomiser-data-phenotype/src/main/resources/logback-spring.xml
@@ -2,7 +2,7 @@
 <!--
   ~ The Exomiser - A tool to annotate and prioritize genomic variants
   ~
-  ~ Copyright (c) 2016-2017 Queen Mary University of London.
+  ~ Copyright (c) 2016-2020 Queen Mary University of London.
   ~ Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
   ~
   ~ This program is free software: you can redistribute it and/or modify
@@ -20,5 +20,12 @@
   -->
 
 <configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml"/>
+    <include resource="org/springframework/boot/logging/logback/defaults.xml" />
+    <include resource="org/springframework/boot/logging/logback/console-appender.xml" />
+    <include resource="org/springframework/boot/logging/logback/file-appender.xml" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+        <appender-ref ref="FILE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
 </configuration>
\ No newline at end of file
diff --git a/exomiser-rest-prioritiser/src/main/resources/logback-spring.xml b/exomiser-rest-prioritiser/src/main/resources/logback-spring.xml
index 558b0cb5a..c8020061d 100644
--- a/exomiser-rest-prioritiser/src/main/resources/logback-spring.xml
+++ b/exomiser-rest-prioritiser/src/main/resources/logback-spring.xml
@@ -2,7 +2,7 @@
 <!--
   ~ The Exomiser - A tool to annotate and prioritize genomic variants
   ~
-  ~ Copyright (c) 2016-2017 Queen Mary University of London.
+  ~ Copyright (c) 2016-2020 Queen Mary University of London.
   ~ Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
   ~
   ~ This program is free software: you can redistribute it and/or modify
@@ -20,5 +20,12 @@
   -->
 
 <configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml"/>
+    <include resource="org/springframework/boot/logging/logback/defaults.xml" />
+    <include resource="org/springframework/boot/logging/logback/console-appender.xml" />
+    <include resource="org/springframework/boot/logging/logback/file-appender.xml" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+        <appender-ref ref="FILE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
 </configuration>
\ No newline at end of file
diff --git a/exomiser-web/src/main/resources/logback-spring.xml b/exomiser-web/src/main/resources/logback-spring.xml
index 558b0cb5a..c8020061d 100644
--- a/exomiser-web/src/main/resources/logback-spring.xml
+++ b/exomiser-web/src/main/resources/logback-spring.xml
@@ -2,7 +2,7 @@
 <!--
   ~ The Exomiser - A tool to annotate and prioritize genomic variants
   ~
-  ~ Copyright (c) 2016-2017 Queen Mary University of London.
+  ~ Copyright (c) 2016-2020 Queen Mary University of London.
   ~ Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
   ~
   ~ This program is free software: you can redistribute it and/or modify
@@ -20,5 +20,12 @@
   -->
 
 <configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml"/>
+    <include resource="org/springframework/boot/logging/logback/defaults.xml" />
+    <include resource="org/springframework/boot/logging/logback/console-appender.xml" />
+    <include resource="org/springframework/boot/logging/logback/file-appender.xml" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+        <appender-ref ref="FILE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
 </configuration>
\ No newline at end of file