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Commit d08fabf3 authored by Piotr Gawron's avatar Piotr Gawron
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Merge branch 'v11.0.2'

parents 8569e97d b8bf8efa
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.gitignore
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......@@ -9,4 +9,6 @@ web/src/main/webapp/svnversion.txt
*.war
/target/
service/minerva-big/
npm-debug.log
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npm-debug.log
.idea/workspace.xml
.idea/.name 0 → 100644
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parent
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.idea/artifacts/web_war.xml 0 → 100644
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<component name="ArtifactManager">
<artifact type="war" name="web:war">
<output-path>$PROJECT_DIR$/web/target</output-path>
<root id="archive" name="web-1.0.war">
<element id="artifact" artifact-name="web:war exploded" />
</root>
</artifact>
</component>
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.idea/artifacts/web_war_exploded.xml 0 → 100644
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<component name="ArtifactManager">
<artifact type="exploded-war" name="web:war exploded">
<output-path>$PROJECT_DIR$/web/target/web-1.0</output-path>
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</artifact>
</component>
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.idea/compiler.xml 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="CompilerConfiguration">
<annotationProcessing>
<profile name="Maven default annotation processors profile" enabled="true">
<sourceOutputDir name="target/generated-sources/annotations" />
<sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
<outputRelativeToContentRoot value="true" />
<module name="annotation" />
<module name="CellDesigner-plugin" />
<module name="commons" />
<module name="comparison" />
<module name="console" />
<module name="converter" />
<module name="converter-CellDesigner" />
<module name="converter-graphics" />
<module name="converter-SBGNML" />
<module name="editor" />
<module name="frontend-js" />
<module name="model" />
<module name="model-command" />
<module name="pathvisio" />
<module name="persist" />
<module name="quadTrees" />
<module name="reactome" />
<module name="rest-api" />
<module name="service" />
<module name="web" />
</profile>
</annotationProcessing>
<bytecodeTargetLevel>
<module name="annotation" target="1.8" />
<module name="CellDesigner-plugin" target="1.8" />
<module name="commons" target="1.8" />
<module name="comparison" target="1.8" />
<module name="console" target="1.8" />
<module name="converter" target="1.8" />
<module name="converter-CellDesigner" target="1.8" />
<module name="converter-graphics" target="1.8" />
<module name="converter-SBGNML" target="1.8" />
<module name="editor" target="1.8" />
<module name="frontend-js" target="1.8" />
<module name="model" target="1.8" />
<module name="model-command" target="1.8" />
<module name="parent" target="1.5" />
<module name="pathvisio" target="1.8" />
<module name="persist" target="1.8" />
<module name="quadTrees" target="1.8" />
<module name="reactome" target="1.8" />
<module name="rest-api" target="1.8" />
<module name="service" target="1.8" />
<module name="web" target="1.8" />
</bytecodeTargetLevel>
</component>
</project>
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.idea/encodings.xml 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="Encoding">
<file url="file://$PROJECT_DIR$" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/CellDesigner-plugin" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/annotation" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/commons" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/comparison" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/console" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/converter" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/converter-CellDesigner" charset="UTF-8" />
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<file url="file://$PROJECT_DIR$/converter-graphics" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/editor" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/frontend-js" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/model" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/model-command" charset="UTF-8" />
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<file url="file://$PROJECT_DIR$/reactome" charset="UTF-8" />
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<file url="file://$PROJECT_DIR$/service" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/web" charset="UTF-8" />
</component>
</project>
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.idea/modules.xml 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectModuleManager">
<modules>
<module fileurl="file://$PROJECT_DIR$/CellDesigner-plugin/CellDesigner-plugin.iml" filepath="$PROJECT_DIR$/CellDesigner-plugin/CellDesigner-plugin.iml" />
<module fileurl="file://$PROJECT_DIR$/annotation/annotation.iml" filepath="$PROJECT_DIR$/annotation/annotation.iml" />
<module fileurl="file://$PROJECT_DIR$/commons/commons.iml" filepath="$PROJECT_DIR$/commons/commons.iml" />
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<module fileurl="file://$PROJECT_DIR$/console/console.iml" filepath="$PROJECT_DIR$/console/console.iml" />
<module fileurl="file://$PROJECT_DIR$/converter/converter.iml" filepath="$PROJECT_DIR$/converter/converter.iml" />
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<module fileurl="file://$PROJECT_DIR$/converter-graphics/converter-graphics.iml" filepath="$PROJECT_DIR$/converter-graphics/converter-graphics.iml" />
<module fileurl="file://$PROJECT_DIR$/editor/editor.iml" filepath="$PROJECT_DIR$/editor/editor.iml" />
<module fileurl="file://$PROJECT_DIR$/frontend-js/frontend-js.iml" filepath="$PROJECT_DIR$/frontend-js/frontend-js.iml" />
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<module fileurl="file://$PROJECT_DIR$/parent.iml" filepath="$PROJECT_DIR$/parent.iml" />
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<module fileurl="file://$PROJECT_DIR$/persist/persist.iml" filepath="$PROJECT_DIR$/persist/persist.iml" />
<module fileurl="file://$PROJECT_DIR$/quadTrees/quadTrees.iml" filepath="$PROJECT_DIR$/quadTrees/quadTrees.iml" />
<module fileurl="file://$PROJECT_DIR$/reactome/reactome.iml" filepath="$PROJECT_DIR$/reactome/reactome.iml" />
<module fileurl="file://$PROJECT_DIR$/rest-api/rest-api.iml" filepath="$PROJECT_DIR$/rest-api/rest-api.iml" />
<module fileurl="file://$PROJECT_DIR$/service/service.iml" filepath="$PROJECT_DIR$/service/service.iml" />
<module fileurl="file://$PROJECT_DIR$/web/web.iml" filepath="$PROJECT_DIR$/web/web.iml" />
</modules>
</component>
</project>
\ No newline at end of file
.idea/vcs.xml 0 → 100644
+ 6
− 0
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="VcsDirectoryMappings">
<mapping directory="$PROJECT_DIR$" vcs="Git" />
</component>
</project>
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CellDesigner-plugin/CellDesigner-plugin.iml 0 → 100644
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− 0
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<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
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<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
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<sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
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<orderEntry type="inheritedJdk" />
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<orderEntry type="module" module-name="model" />
<orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
<orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
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<orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
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<orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
<orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
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<orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
<orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
<orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
<orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
<orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
<orderEntry type="module" module-name="commons" />
<orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
<orderEntry type="module" module-name="converter-CellDesigner" />
<orderEntry type="module" module-name="converter" />
<orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
<orderEntry type="library" name="Maven: jp.sbi:celldesigner:4.4" level="project" />
<orderEntry type="library" name="Maven: org.sbml:libsbml:1.0" level="project" />
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<orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
</component>
</module>
\ No newline at end of file
annotation/annotation.iml 0 → 100644
+ 104
− 0
View file @ d08fabf3
<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="FacetManager">
<facet type="Spring" name="Spring">
<configuration />
</facet>
</component>
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
<sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
<sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
<excludeFolder url="file://$MODULE_DIR$/target" />
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<orderEntry type="inheritedJdk" />
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<orderEntry type="module" module-name="model" />
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<orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
<orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
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<orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
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<orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
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<orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" level="project" />
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</component>
</module>
\ No newline at end of file
build.xml
+ 120
− 111
View file @ d08fabf3
<?xml version="1.0" encoding="UTF-8"?>
<project name="minerva" default="main" basedir=".">
<property environment="env"/>
<property name="build.dir" value="web/target" />
<property name="war.file" value="web-1.0.war" />
<property name="tomcat.home" value="${env.CATALINA_HOME}" />
<property name="tomcat.deploy.dir" value="${tomcat.home}/webapps" />
<condition property="isWindows">
<os family="windows" />
</condition>
<condition property="isUnix">
<os family="unix" />
</condition>
<target name="war-exists">
<available file="${tomcat.deploy.dir}/${ant.project.name}.war" property="war.exists"/>
</target>
<target name="remove-war" depends="war-exists" if="war.exists">
<delete file="${tomcat.deploy.dir}/${ant.project.name}.war" />
</target>
<target name="war-dir-exists">
<available file="${tomcat.deploy.dir}/${ant.project.name}" property="war-dir.exists" type="dir"/>
</target>
<target name="remove-war-dir" depends="war-dir-exists" if="war-dir.exists">
<delete dir="${tomcat.deploy.dir}/${ant.project.name}" />
</target>
<target name="deploy" depends="remove-war,remove-war-dir">
<copy file="${build.dir}/${war.file}" todir="${tomcat.deploy.dir}" />
<move file="${tomcat.deploy.dir}/${war.file}" tofile="${tomcat.deploy.dir}/${ant.project.name}.war"/>
</target>
<target name="main" depends="tomcat-stop,maven-build,deploy,tomcat-start">
</target>
<target name="all" depends="main">
</target>
<target name="tomcat-start">
<exec executable="${tomcat.home}/bin/startup.bat">
</exec>
</target>
<target name="tomcat-stop">
<exec executable="${tomcat.home}/bin/shutdown.bat">
</exec>
</target>
<target name="maven-build" depends="gitversion, maven-build-windows, maven-build-unix"/>
<target name="maven-build-windows" if="isWindows">
<exec dir="." executable="cmd" >
<arg line="/c mvn -Dmaven.test.skip=true clean install -pl web -am" />
</exec>
</target>
<target name="maven-build-unix" if="isUnix">
<exec dir="." executable="sh" >
<arg line="-c 'mvn -Dmaven.test.skip=true clean install -pl web -am'" />
</exec>
</target>
<target name="maven-test" depends="maven-test-windows, maven-test-unix"/>
<target name="maven-test-windows" depends="maven-build" if="isWindows">
<exec dir="." executable="cmd" >
<arg line="/c mvn test -fn" />
<!-- <arg line="/c mvn surefire-report:report" /> -->
</exec>
</target>
<target name="maven-test-unix" depends="maven-build" if="isUnix">
<exec dir="." executable="sh" >
<arg line="-c 'mvn test -fn'" />
<!-- <arg line="-c 'mvn surefire-report:report'" /> -->
</exec>
</target>
<target name="deployMapFiles">
<copy todir="${tomcat.deploy.dir}/map_images">
<fileset dir="map_images" />
</copy>
</target>
<target name="gitversion">
<exec executable="git" outputproperty="gitversion">
<arg value="rev-parse"/>
<arg value="HEAD"/>
</exec>
<tstamp>
<format property="build.time" pattern="dd/MM/yyyy HH:mm"
unit="hour"/>
</tstamp>
<echo >GIT Version: ${gitversion}
Build timestamp: ${build.time}</echo>
<echo file="web/src/main/webapp/version.txt">${gitversion}
${build.time}</echo>
<copy file="CHANGELOG" tofile="web/src/main/webapp/CHANGELOG" overwrite="true"/>
</target>
<target name="debian-pkg" depends="maven-build">
<exec executable="debian/create-debian-pkg.sh"/>
</target>
<property environment="env"/>
<property name="build.dir" value="web/target"/>
<property name="war.file" value="web-1.0.war"/>
<property name="tomcat.home" value="${env.CATALINA_HOME}"/>
<property name="tomcat.deploy.dir" value="${tomcat.home}/webapps"/>
<condition property="isWindows">
<os family="windows"/>
</condition>
<condition property="isUnix">
<os family="unix"/>
</condition>
<target name="war-exists">
<available file="${tomcat.deploy.dir}/${ant.project.name}.war" property="war.exists"/>
</target>
<target name="remove-war" depends="war-exists" if="war.exists">
<delete file="${tomcat.deploy.dir}/${ant.project.name}.war"/>
</target>
<target name="war-dir-exists">
<available file="${tomcat.deploy.dir}/${ant.project.name}" property="war-dir.exists" type="dir"/>
</target>
<target name="remove-war-dir" depends="war-dir-exists" if="war-dir.exists">
<delete dir="${tomcat.deploy.dir}/${ant.project.name}"/>
</target>
<target name="deploy" depends="remove-war,remove-war-dir">
<copy file="${build.dir}/${war.file}" todir="${tomcat.deploy.dir}"/>
<move file="${tomcat.deploy.dir}/${war.file}" tofile="${tomcat.deploy.dir}/${ant.project.name}.war"/>
</target>
<target name="main" depends="tomcat-stop,maven-build,deploy,tomcat-start">
</target>
<target name="all" depends="main">
</target>
<target name="tomcat-start" depends="tomcat-start-windows, tomcat-start-unix"/>
<target name="tomcat-start-windows" if="isWindows">
<exec executable="${tomcat.home}/bin/startup.bat"/>
</target>
<target name="tomcat-start-unix" if="isUnix">
<exec executable="${tomcat.home}/bin/startup.sh"/>
</target>
<target name="tomcat-stop" depends="tomcat-stop-windows, tomcat-stop-unix"/>
<target name="tomcat-stop-windows" if="isWindows">
<exec executable="${tomcat.home}/bin/shutdown.bat"/>
</target>
<target name="tomcat-stop-unix" if="isUnix">
<exec executable="${tomcat.home}/bin/shutdown.sh"/>
</target>
<target name="maven-build" depends="gitversion, maven-build-windows, maven-build-unix"/>
<target name="maven-build-windows" if="isWindows">
<exec dir="." executable="cmd">
<arg line="/c mvn -Dmaven.test.skip=true clean install -pl web -am"/>
</exec>
</target>
<target name="maven-build-unix" if="isUnix">
<exec dir="." executable="sh">
<arg line="-c 'mvn -Dmaven.test.skip=true clean install -pl web -am'"/>
</exec>
</target>
<target name="maven-test" depends="maven-test-windows, maven-test-unix"/>
<target name="maven-test-windows" depends="maven-build" if="isWindows">
<exec dir="." executable="cmd">
<arg line="/c mvn test -fn"/>
<!-- <arg line="/c mvn surefire-report:report" /> -->
</exec>
</target>
<target name="maven-test-unix" depends="maven-build" if="isUnix">
<exec dir="." executable="sh">
<arg line="-c 'mvn test -fn'"/>
<!-- <arg line="-c 'mvn surefire-report:report'" /> -->
</exec>
</target>
<target name="deployMapFiles">
<copy todir="${tomcat.deploy.dir}/map_images">
<fileset dir="map_images"/>
</copy>
</target>
<target name="gitversion">
<exec executable="git" outputproperty="gitversion">
<arg value="rev-parse"/>
<arg value="HEAD"/>
</exec>
<tstamp>
<format property="build.time" pattern="dd/MM/yyyy HH:mm"
unit="hour"/>
</tstamp>
<echo>GIT Version: ${gitversion}
Build timestamp: ${build.time}
</echo>
<echo file="web/src/main/webapp/version.txt">${gitversion}
${build.time}
</echo>
<copy file="CHANGELOG" tofile="web/src/main/webapp/CHANGELOG" overwrite="true"/>
</target>
<target name="debian-pkg" depends="maven-build">
<exec executable="debian/create-debian-pkg.sh"/>
</target>
</project>
commons/commons.iml 0 → 100644
+ 23
− 0
View file @ d08fabf3
<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
<sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
<sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
<excludeFolder url="file://$MODULE_DIR$/target" />
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<orderEntry type="inheritedJdk" />
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<orderEntry type="library" scope="TEST" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
<orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
<orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
</component>
</module>
\ No newline at end of file
comparison/comparison.iml 0 → 100644
+ 123
− 0
View file @ d08fabf3
<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="FacetManager">
<facet type="Spring" name="Spring">
<configuration />
</facet>
</component>
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
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<orderEntry type="inheritedJdk" />
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<orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
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converter-CellDesigner/converter-CellDesigner.iml 0 → 100644
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converter-SBGNML/converter-SBGNML.iml 0 → 100644
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View file @ d08fabf3
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converter-graphics/converter-graphics.iml 0 → 100644
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View file @ d08fabf3
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converter/converter.iml 0 → 100644
+ 36
− 0
View file @ d08fabf3
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editor/editor.iml 0 → 100644
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View file @ d08fabf3
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frontend-js/frontend-js.iml 0 → 100644
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View file @ d08fabf3
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<orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
<orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
</component>
</module>
\ No newline at end of file
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