From 28c03dc321a70266c84d6e35025d147906c69c6c Mon Sep 17 00:00:00 2001
From: Jules Jacobsen <j.jacobsen@qmul.ac.uk>
Date: Wed, 28 Feb 2024 18:26:00 +0000
Subject: [PATCH] Update logback-test.xml to remove unnecessary logging to
 \tmp\spring.log Remove logback-spring.xml from exomiser-data-genome,
 exomiser-data-phenotype

---
 .../src/main/resources/application.properties |  4 ++-
 .../src/test/resources/logback-test.xml       |  7 ++++-
 .../src/test/resources/logback-test.xml       |  8 +++--
 .../src/main/resources/logback-spring.xml     | 31 -------------------
 .../src/test/resources/logback-test.xml       |  7 ++++-
 .../src/main/resources/logback-spring.xml     | 31 -------------------
 .../src/test/resources/logback-test.xml       |  9 ++++--
 .../src/test/resources/logback-test.xml       |  7 ++++-
 .../src/test/resources/logback-test.xml       |  6 +++-
 .../src/test/resources/logback-test.xml       | 26 ----------------
 .../src/main/resources/logback-spring.xml     | 31 -------------------
 .../src/test/resources/logback-test.xml       | 26 ----------------
 12 files changed, 39 insertions(+), 154 deletions(-)
 delete mode 100644 exomiser-data-genome/src/main/resources/logback-spring.xml
 delete mode 100644 exomiser-data-phenotype/src/main/resources/logback-spring.xml
 delete mode 100644 exomiser-spring-boot-test/src/test/resources/logback-test.xml
 delete mode 100644 exomiser-web/src/main/resources/logback-spring.xml
 delete mode 100644 exomiser-web/src/test/resources/logback-test.xml

diff --git a/exomiser-cli/src/main/resources/application.properties b/exomiser-cli/src/main/resources/application.properties
index 9d6991c87..3387f3a75 100644
--- a/exomiser-cli/src/main/resources/application.properties
+++ b/exomiser-cli/src/main/resources/application.properties
@@ -79,4 +79,6 @@ exomiser.phenotype.data-version=2402
 #spring.cache.caffeine.spec=maximumSize=60000
 
 ### logging ###
-#logging.file.name=logs/exomiser.log
\ No newline at end of file
+# Logging is highly configurable - see https://docs.spring.io/spring-boot/docs/current/reference/html/features.html#features.logging.file-output
+#logging.file.name=logs/exomiser.log
+logging.level.com.zaxxer.hikari=ERROR
\ No newline at end of file
diff --git a/exomiser-cli/src/test/resources/logback-test.xml b/exomiser-cli/src/test/resources/logback-test.xml
index e74b16833..22dd5246e 100644
--- a/exomiser-cli/src/test/resources/logback-test.xml
+++ b/exomiser-cli/src/test/resources/logback-test.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" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
     <logger name="org.springframework" level="ERROR"/>
     <logger name="org.thymeleaf" level="ERROR"/>
 </configuration>
diff --git a/exomiser-core/src/test/resources/logback-test.xml b/exomiser-core/src/test/resources/logback-test.xml
index c4da0c84f..22dd5246e 100644
--- a/exomiser-core/src/test/resources/logback-test.xml
+++ b/exomiser-core/src/test/resources/logback-test.xml
@@ -20,8 +20,12 @@
   -->
 
 <configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml" />
-    <logger name="org.monarchinitiative.exomiser.core.genome.VariantFactoryImpl" level="ERROR"/>
+    <include resource="org/springframework/boot/logging/logback/defaults.xml" />
+    <include resource="org/springframework/boot/logging/logback/console-appender.xml" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
     <logger name="org.springframework" level="ERROR"/>
     <logger name="org.thymeleaf" level="ERROR"/>
 </configuration>
diff --git a/exomiser-data-genome/src/main/resources/logback-spring.xml b/exomiser-data-genome/src/main/resources/logback-spring.xml
deleted file mode 100644
index c8020061d..000000000
--- a/exomiser-data-genome/src/main/resources/logback-spring.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ The Exomiser - A tool to annotate and prioritize genomic variants
-  ~
-  ~ 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
-  ~ it under the terms of the GNU Affero General Public License as
-  ~ published by the Free Software Foundation, either version 3 of the
-  ~ License, or (at your option) any later version.
-  ~
-  ~ This program is distributed in the hope that it will be useful,
-  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
-  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  ~ GNU Affero General Public License for more details.
-  ~
-  ~ You should have received a copy of the GNU Affero General Public License
-  ~ along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  -->
-
-<configuration>
-    <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/test/resources/logback-test.xml b/exomiser-data-genome/src/test/resources/logback-test.xml
index e74b16833..22dd5246e 100644
--- a/exomiser-data-genome/src/test/resources/logback-test.xml
+++ b/exomiser-data-genome/src/test/resources/logback-test.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" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
     <logger name="org.springframework" level="ERROR"/>
     <logger name="org.thymeleaf" level="ERROR"/>
 </configuration>
diff --git a/exomiser-data-phenotype/src/main/resources/logback-spring.xml b/exomiser-data-phenotype/src/main/resources/logback-spring.xml
deleted file mode 100644
index c8020061d..000000000
--- a/exomiser-data-phenotype/src/main/resources/logback-spring.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ The Exomiser - A tool to annotate and prioritize genomic variants
-  ~
-  ~ 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
-  ~ it under the terms of the GNU Affero General Public License as
-  ~ published by the Free Software Foundation, either version 3 of the
-  ~ License, or (at your option) any later version.
-  ~
-  ~ This program is distributed in the hope that it will be useful,
-  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
-  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  ~ GNU Affero General Public License for more details.
-  ~
-  ~ You should have received a copy of the GNU Affero General Public License
-  ~ along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  -->
-
-<configuration>
-    <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-phenotype/src/test/resources/logback-test.xml b/exomiser-data-phenotype/src/test/resources/logback-test.xml
index e74b16833..ed3780b39 100644
--- a/exomiser-data-phenotype/src/test/resources/logback-test.xml
+++ b/exomiser-data-phenotype/src/test/resources/logback-test.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" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
     <logger name="org.springframework" level="ERROR"/>
     <logger name="org.thymeleaf" level="ERROR"/>
-</configuration>
+</configuration>
\ No newline at end of file
diff --git a/exomiser-rest-prioritiser/src/test/resources/logback-test.xml b/exomiser-rest-prioritiser/src/test/resources/logback-test.xml
index e74b16833..22dd5246e 100644
--- a/exomiser-rest-prioritiser/src/test/resources/logback-test.xml
+++ b/exomiser-rest-prioritiser/src/test/resources/logback-test.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" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+    </root>
+    <logger name="com.zaxxer.hikari" level="ERROR"/>
     <logger name="org.springframework" level="ERROR"/>
     <logger name="org.thymeleaf" level="ERROR"/>
 </configuration>
diff --git a/exomiser-spring-boot-autoconfigure/src/test/resources/logback-test.xml b/exomiser-spring-boot-autoconfigure/src/test/resources/logback-test.xml
index 8cd51eb67..eb327cc4b 100644
--- a/exomiser-spring-boot-autoconfigure/src/test/resources/logback-test.xml
+++ b/exomiser-spring-boot-autoconfigure/src/test/resources/logback-test.xml
@@ -20,7 +20,11 @@
   -->
 
 <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" />
+    <root level="INFO">
+        <appender-ref ref="CONSOLE" />
+    </root>
     <logger name="org.springframework" level="ERROR"/>
     <logger name="org.thymeleaf" level="ERROR"/>
     <logger name="org.flywaydb" level="ERROR"/>
diff --git a/exomiser-spring-boot-test/src/test/resources/logback-test.xml b/exomiser-spring-boot-test/src/test/resources/logback-test.xml
deleted file mode 100644
index e74b16833..000000000
--- a/exomiser-spring-boot-test/src/test/resources/logback-test.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ The Exomiser - A tool to annotate and prioritize genomic variants
-  ~
-  ~ Copyright (c) 2016-2018 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
-  ~ it under the terms of the GNU Affero General Public License as
-  ~ published by the Free Software Foundation, either version 3 of the
-  ~ License, or (at your option) any later version.
-  ~
-  ~ This program is distributed in the hope that it will be useful,
-  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
-  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  ~ GNU Affero General Public License for more details.
-  ~
-  ~ You should have received a copy of the GNU Affero General Public License
-  ~ along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  -->
-
-<configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml" />
-    <logger name="org.springframework" level="ERROR"/>
-    <logger name="org.thymeleaf" level="ERROR"/>
-</configuration>
diff --git a/exomiser-web/src/main/resources/logback-spring.xml b/exomiser-web/src/main/resources/logback-spring.xml
deleted file mode 100644
index c8020061d..000000000
--- a/exomiser-web/src/main/resources/logback-spring.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ The Exomiser - A tool to annotate and prioritize genomic variants
-  ~
-  ~ 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
-  ~ it under the terms of the GNU Affero General Public License as
-  ~ published by the Free Software Foundation, either version 3 of the
-  ~ License, or (at your option) any later version.
-  ~
-  ~ This program is distributed in the hope that it will be useful,
-  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
-  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  ~ GNU Affero General Public License for more details.
-  ~
-  ~ You should have received a copy of the GNU Affero General Public License
-  ~ along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  -->
-
-<configuration>
-    <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/test/resources/logback-test.xml b/exomiser-web/src/test/resources/logback-test.xml
deleted file mode 100644
index e74b16833..000000000
--- a/exomiser-web/src/test/resources/logback-test.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ The Exomiser - A tool to annotate and prioritize genomic variants
-  ~
-  ~ Copyright (c) 2016-2018 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
-  ~ it under the terms of the GNU Affero General Public License as
-  ~ published by the Free Software Foundation, either version 3 of the
-  ~ License, or (at your option) any later version.
-  ~
-  ~ This program is distributed in the hope that it will be useful,
-  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
-  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  ~ GNU Affero General Public License for more details.
-  ~
-  ~ You should have received a copy of the GNU Affero General Public License
-  ~ along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  -->
-
-<configuration>
-    <include resource="org/springframework/boot/logging/logback/base.xml" />
-    <logger name="org.springframework" level="ERROR"/>
-    <logger name="org.thymeleaf" level="ERROR"/>
-</configuration>