From df13abbda4c0927536cfa7e936f17be5ef44aa2b Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 9 Oct 2018 14:29:55 +0200
Subject: [PATCH] jsbml upgraded to version 1.4
---
converter-sbml/pom.xml | 65 +++++++++++++++++++++++++++++++++++-------
pom.xml | 2 ++
2 files changed, 56 insertions(+), 11 deletions(-)
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index 02b7787a01..f2d8e21147 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -76,9 +76,9 @@
<dependency>
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml</artifactId>
- <version>1.3.1</version>
+ <version>${jsbml.version}</version>
<!-- for now we use lower version of log4j and this one introduce some
- problem with tomcat loggin -->
+ problem with tomcat logging -->
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
@@ -97,24 +97,67 @@
<artifactId>slf4j-api</artifactId>
</exclusion>
<exclusion>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
</exclusion>
<exclusion>
- <groupId>commons-logging</groupId>
- <artifactId>commons-logging</artifactId>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
</exclusion>
<exclusion>
- <groupId>org.codehaus.woodstox</groupId>
- <artifactId>stax2-api</artifactId>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>stax2-api</artifactId>
+ </exclusion>
+ <!-- https://github.com/sbmlteam/jsbml/issues/156 -->
+ <exclusion>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-core</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-core</artifactId>
+ <version>${jsbml.version}</version>
+ <!-- for now we use lower version of log4j and this one introduce some
+ problem with tomcat logging -->
+ <exclusions>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-core</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-api</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-1.2-api</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>stax2-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
- <groupId>org.codehaus.woodstox</groupId>
- <artifactId>stax2-api</artifactId>
- <version>${stax2-api.version}</version>
+ <groupId>org.codehaus.woodstox</groupId>
+ <artifactId>stax2-api</artifactId>
+ <version>${stax2-api.version}</version>
</dependency>
<dependency>
diff --git a/pom.xml b/pom.xml
index 947569cfae..a8adf9f7c4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -54,6 +54,8 @@
<jaxb.version>2.2.7</jaxb.version>
<batik.version>1.8</batik.version>
+
+ <jsbml.version>1.4</jsbml.version>
<itext.version>5.5.6</itext.version>
--
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