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Upgrading to slf4j2 #1094

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merged 3 commits into from May 22, 2024
Merged

Upgrading to slf4j2 #1094

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1be0260
Bumping up to slf4j2 and log4j2. Logging doesn't work correctly yet, …
josemduarte Apr 24, 2024
e7d09d0
Fixing logging clash in structure module
josemduarte Apr 25, 2024
d019fb3
Merge branch 'master' into slf4j2
josemduarte Apr 26, 2024
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2 changes: 1 addition & 1 deletion biojava-aa-prop/pom.xml
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Expand Up @@ -86,7 +86,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-alignment/pom.xml
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Expand Up @@ -63,7 +63,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-core/pom.xml
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Expand Up @@ -63,7 +63,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-genome/pom.xml
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Expand Up @@ -103,7 +103,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-integrationtest/pom.xml
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Expand Up @@ -50,7 +50,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-modfinder/pom.xml
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Expand Up @@ -43,7 +43,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-ontology/pom.xml
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Expand Up @@ -33,7 +33,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-protein-comparison-tool/pom.xml
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Expand Up @@ -67,7 +67,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-protein-disorder/pom.xml
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Expand Up @@ -74,7 +74,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-structure-gui/pom.xml
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Expand Up @@ -53,7 +53,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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9 changes: 8 additions & 1 deletion biojava-structure/pom.xml
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Expand Up @@ -40,6 +40,13 @@
<artifactId>mmtf-codec</artifactId>
<version>${mmtf.version}</version>
<scope>compile</scope>
<exclusions>
<!-- This is needed because mmtf uses slf4j 1.7 and the log4j2 slf4j1 binding, somehow clashing with slf4j2 in this repo -->
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
Expand Down Expand Up @@ -91,7 +98,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-survival/pom.xml
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Expand Up @@ -37,7 +37,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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2 changes: 1 addition & 1 deletion biojava-ws/pom.xml
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Expand Up @@ -41,7 +41,7 @@
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
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6 changes: 3 additions & 3 deletions pom.xml
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Expand Up @@ -40,8 +40,8 @@
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<maxmem>512M</maxmem>
<mmtf.version>1.0.11</mmtf.version>
<slf4j.version>1.7.36</slf4j.version>
<log4j.version>2.22.0</log4j.version>
<slf4j.version>2.0.12</slf4j.version>
<log4j.version>2.23.1</log4j.version>
<junit-jupiter.version>5.10.1</junit-jupiter.version>
<ciftools.artifact>ciftools-java</ciftools.artifact>
<ciftools.version>5.0.1</ciftools.version>
Expand Down Expand Up @@ -436,7 +436,7 @@
<!-- binding for log4j 2 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<artifactId>log4j-slf4j2-impl</artifactId>
<version>${log4j.version}</version>
<!-- runtime scope includes the test scope as well -->
<scope>runtime</scope>
Expand Down