diff --git a/.gitignore b/.gitignore
index 7a336e068b59b0d519d1e05eddd8a1bf89f61349..a402933690c345f2d7eaf6ce03cc8a22606b1f46 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,4 +9,6 @@ web/src/main/webapp/svnversion.txt
*.war
/target/
service/minerva-big/
-npm-debug.log
\ No newline at end of file
+npm-debug.log
+
+.idea/workspace.xml
diff --git a/.idea/.name b/.idea/.name
new file mode 100644
index 0000000000000000000000000000000000000000..25dd2a9fd672ddcee1a0dbe914393f0e0c939e7c
--- /dev/null
+++ b/.idea/.name
@@ -0,0 +1 @@
+parent
\ No newline at end of file
diff --git a/.idea/artifacts/web_war.xml b/.idea/artifacts/web_war.xml
new file mode 100644
index 0000000000000000000000000000000000000000..1a8b7b5da0bdedb9cc76511d29327e9a6f7430ca
--- /dev/null
+++ b/.idea/artifacts/web_war.xml
@@ -0,0 +1,8 @@
+<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>
\ No newline at end of file
diff --git a/.idea/artifacts/web_war_exploded.xml b/.idea/artifacts/web_war_exploded.xml
new file mode 100644
index 0000000000000000000000000000000000000000..17bd68e9d9d95599c6d9a598a6ad4297626aa0d8
--- /dev/null
+++ b/.idea/artifacts/web_war_exploded.xml
@@ -0,0 +1,175 @@
+<component name="ArtifactManager">
+ <artifact type="exploded-war" name="web:war exploded">
+ <output-path>$PROJECT_DIR$/web/target/web-1.0</output-path>
+ <root id="root">
+ <element id="directory" name="WEB-INF">
+ <element id="directory" name="classes">
+ <element id="module-output" name="web" />
+ </element>
+ <element id="directory" name="lib">
+ <element id="archive" name="service-1.0.jar">
+ <element id="module-output" name="service" />
+ </element>
+ <element id="archive" name="model-1.0.jar">
+ <element id="module-output" name="model" />
+ </element>
+ <element id="archive" name="commons-1.0.jar">
+ <element id="module-output" name="commons" />
+ </element>
+ <element id="library" level="project" name="Maven: commons-io:commons-io:2.4" />
+ <element id="library" level="project" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" />
+ <element id="library" level="project" name="Maven: commons-collections:commons-collections:3.2.1" />
+ <element id="library" level="project" name="Maven: antlr:antlr:2.7.7" />
+ <element id="library" level="project" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" />
+ <element id="library" level="project" name="Maven: dom4j:dom4j:1.6.1" />
+ <element id="library" level="project" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" />
+ <element id="library" level="project" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" />
+ <element id="library" level="project" name="Maven: org.javassist:javassist:3.15.0-GA" />
+ <element id="library" level="project" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" />
+ <element id="library" level="project" name="Maven: xml-apis:xml-apis:1.4.01" />
+ <element id="library" level="project" name="Maven: org.reflections:reflections:0.9.9-RC1" />
+ <element id="library" level="project" name="Maven: com.google.guava:guava:11.0.2" />
+ <element id="library" level="project" name="Maven: com.google.code.findbugs:jsr305:1.3.9" />
+ <element id="archive" name="persist-1.0.jar">
+ <element id="module-output" name="persist" />
+ </element>
+ <element id="library" level="project" name="Maven: commons-net:commons-net:3.5" />
+ <element id="library" level="project" name="Maven: postgresql:postgresql:9.1-901.jdbc4" />
+ <element id="archive" name="model-command-1.0.jar">
+ <element id="module-output" name="model-command" />
+ </element>
+ <element id="archive" name="annotation-1.0.jar">
+ <element id="module-output" name="annotation" />
+ </element>
+ <element id="archive" name="converter-1.0.jar">
+ <element id="module-output" name="converter" />
+ </element>
+ <element id="library" level="project" name="Maven: xerces:xercesImpl:2.11.0" />
+ <element id="library" level="project" name="Maven: uk.ac.ebi.chebi.webapps.chebiWS.client:chebiWS-client:2.2.2" />
+ <element id="library" level="project" name="Maven: com.sun.xml.ws:jaxws-rt:2.1.7" />
+ <element id="library" level="project" name="Maven: com.sun.xml.stream.buffer:streambuffer:0.9" />
+ <element id="library" level="project" name="Maven: org.codehaus.woodstox:wstx-asl:3.2.3" />
+ <element id="library" level="project" name="Maven: org.jvnet.staxex:stax-ex:1.2" />
+ <element id="library" level="project" name="Maven: javax.xml.stream:stax-api:1.0" />
+ <element id="library" level="project" name="Maven: com.sun.org.apache.xml.internal:resolver:20050927" />
+ <element id="library" level="project" name="Maven: org.jvnet:mimepull:1.3" />
+ <element id="library" level="project" name="Maven: javax.xml.ws:jaxws-api:2.1" />
+ <element id="library" level="project" name="Maven: com.sun.xml.ws:jaxws-tools:2.1.3" />
+ <element id="library" level="project" name="Maven: com.sun.xml.bind:jaxb-xjc:2.1.6" />
+ <element id="library" level="project" name="Maven: com.sun.xml.messaging.saaj:saaj-impl:1.3.2" />
+ <element id="library" level="project" name="Maven: javax.xml.soap:saaj-api:1.3" />
+ <element id="library" level="project" name="Maven: uk.ac.ebi.miriam:miriam-lib:1.1.5" />
+ <element id="library" level="project" name="Maven: axis:axis:1.4" />
+ <element id="library" level="project" name="Maven: org.apache.axis:axis-jaxrpc:1.4" />
+ <element id="library" level="project" name="Maven: org.apache.axis:axis-saaj:1.4" />
+ <element id="library" level="project" name="Maven: axis:axis-wsdl4j:1.5.1" />
+ <element id="library" level="project" name="Maven: commons-discovery:commons-discovery:0.2" />
+ <element id="library" level="project" name="Maven: javax.activation:activation:1.1" />
+ <element id="library" level="project" name="Maven: javax.mail:mail:1.4" />
+ <element id="library" level="project" name="Maven: org.apache.httpcomponents:httpclient:4.4" />
+ <element id="library" level="project" name="Maven: org.apache.httpcomponents:httpmime:4.4" />
+ <element id="library" level="project" name="Maven: org.apache.httpcomponents:httpcore:4.4" />
+ <element id="library" level="project" name="Maven: javax.xml.bind:jaxb-api:2.2.7" />
+ <element id="library" level="project" name="Maven: com.sun.xml.bind:jaxb-impl:2.2.7" />
+ <element id="library" level="project" name="Maven: com.sun.xml.bind:jaxb-core:2.2.7" />
+ <element id="library" level="project" name="Maven: com.sun.istack:istack-commons-runtime:2.16" />
+ <element id="library" level="project" name="Maven: com.sun.xml.fastinfoset:FastInfoset:1.2.12" />
+ <element id="library" level="project" name="Maven: javax.xml.bind:jsr173_api:1.0" />
+ <element id="library" level="project" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" />
+ <element id="library" level="project" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" />
+ <element id="library" level="project" name="Maven: stax:stax-api:1.0.1" />
+ <element id="archive" name="converter-CellDesigner-1.0.jar">
+ <element id="module-output" name="converter-CellDesigner" />
+ </element>
+ <element id="archive" name="converter-SBGNML-1.0.jar">
+ <element id="module-output" name="converter-SBGNML" />
+ </element>
+ <element id="library" level="project" name="Maven: org.sbgn:libsbgn:0.2" />
+ <element id="library" level="project" name="Maven: commons-cli:commons-cli:1.2" />
+ <element id="archive" name="converter-graphics-1.0.jar">
+ <element id="module-output" name="converter-graphics" />
+ </element>
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-css:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-script:1.8" />
+ <element id="library" level="project" name="Maven: xalan:xalan:2.7.0" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" />
+ <element id="library" level="project" name="Maven: xml-apis:xml-apis-ext:1.3.04" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-util:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" />
+ <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" />
+ <element id="library" level="project" name="Maven: com.itextpdf:itextpdf:5.5.6" />
+ <element id="library" level="project" name="Maven: com.google.code.gson:gson:2.2.2" />
+ <element id="library" level="project" name="Maven: org.apache.poi:poi:3.12" />
+ <element id="library" level="project" name="Maven: commons-codec:commons-codec:1.9" />
+ <element id="library" level="project" name="Maven: org.apache.poi:poi-ooxml:3.12" />
+ <element id="archive" name="rest-api-1.0.jar">
+ <element id="module-output" name="rest-api" />
+ </element>
+ <element id="library" level="project" name="Maven: com.sun.jersey:jersey-server:1.18.1" />
+ <element id="library" level="project" name="Maven: com.sun.jersey:jersey-core:1.18.1" />
+ <element id="library" level="project" name="Maven: com.sun.jersey:jersey-servlet:1.18.1" />
+ <element id="library" level="project" name="Maven: com.fasterxml.jackson.core:jackson-core:2.8.8" />
+ <element id="library" level="project" name="Maven: com.fasterxml.jackson.core:jackson-databind:2.8.8" />
+ <element id="library" level="project" name="Maven: com.fasterxml.jackson.core:jackson-annotations:2.8.0" />
+ <element id="archive" name="frontend-js-1.0.jar">
+ <element id="module-output" name="frontend-js" />
+ </element>
+ <element id="library" level="project" name="Maven: com.sun.faces:jsf-api:2.1.7" />
+ <element id="library" level="project" name="Maven: com.sun.faces:jsf-impl:2.1.7" />
+ <element id="library" level="project" name="Maven: javax.servlet:jstl:1.2" />
+ <element id="library" level="project" name="Maven: org.primefaces:primefaces:4.0" />
+ <element id="library" level="project" name="Maven: org.primefaces.themes:home:1.0.8" />
+ <element id="library" level="project" name="Maven: org.springframework.webflow:spring-faces:2.4.2.RELEASE" />
+ <element id="library" level="project" name="Maven: commons-logging:commons-logging:1.1.1" />
+ <element id="library" level="project" name="Maven: org.springframework.webflow:spring-binding:2.4.2.RELEASE" />
+ <element id="library" level="project" name="Maven: opensymphony:ognl:2.6.11" />
+ <element id="library" level="project" name="Maven: org.springframework.webflow:spring-webflow:2.4.2.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework.webflow:spring-js:2.4.2.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework.webflow:spring-js-resources:2.4.2.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: log4j:log4j:1.2.17" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework:spring-webmvc:4.2.0.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework.security:spring-security-config:4.0.2.RELEASE" />
+ <element id="library" level="project" name="Maven: aopalliance:aopalliance:1.0" />
+ <element id="library" level="project" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" />
+ <element id="library" level="project" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" />
+ <element id="library" level="project" name="Maven: c3p0:c3p0:0.9.1.2" />
+ <element id="library" level="project" name="Maven: cglib:cglib:2.2.2" />
+ <element id="library" level="project" name="Maven: asm:asm:3.3.1" />
+ <element id="library" level="project" name="Maven: commons-fileupload:commons-fileupload:1.2.2" />
+ <element id="library" level="project" name="Maven: org.primefaces.extensions:primefaces-extensions:0.7.1" />
+ <element id="library" level="project" name="Maven: org.apache.commons:commons-lang3:3.1" />
+ <element id="library" level="project" name="Maven: commons-validator:commons-validator:1.4.0" />
+ <element id="library" level="project" name="Maven: commons-beanutils:commons-beanutils:1.8.3" />
+ <element id="library" level="project" name="Maven: commons-digester:commons-digester:1.8" />
+ <element id="library" level="project" name="Maven: junit:junit:4.12" />
+ <element id="library" level="project" name="Maven: org.hamcrest:hamcrest-core:1.3" />
+ </element>
+ </element>
+ <element id="directory" name="META-INF">
+ <element id="file-copy" path="$PROJECT_DIR$/web/target/web-1.0/META-INF/MANIFEST.MF" />
+ </element>
+ <element id="javaee-facet-resources" facet="web/web/Web" />
+ </root>
+ </artifact>
+</component>
\ No newline at end of file
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
new file mode 100644
index 0000000000000000000000000000000000000000..89c969d46c57d246a74a06161a9f3675abe78a60
--- /dev/null
+++ b/.idea/compiler.xml
@@ -0,0 +1,55 @@
+<?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>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5fc2649a0dc189c09831261aff29e4931c7993b3
--- /dev/null
+++ b/.idea/encodings.xml
@@ -0,0 +1,26 @@
+<?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" />
+ <file url="file://$PROJECT_DIR$/converter-SBGNML" charset="UTF-8" />
+ <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" />
+ <file url="file://$PROJECT_DIR$/pathvisio" charset="UTF-8" />
+ <file url="file://$PROJECT_DIR$/persist" charset="UTF-8" />
+ <file url="file://$PROJECT_DIR$/quadTrees" charset="UTF-8" />
+ <file url="file://$PROJECT_DIR$/reactome" charset="UTF-8" />
+ <file url="file://$PROJECT_DIR$/rest-api" charset="UTF-8" />
+ <file url="file://$PROJECT_DIR$/service" charset="UTF-8" />
+ <file url="file://$PROJECT_DIR$/web" charset="UTF-8" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0e732d0743d1e7fdf56d6f83b8e35eb12811f3a9
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,28 @@
+<?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" />
+ <module fileurl="file://$PROJECT_DIR$/comparison/comparison.iml" filepath="$PROJECT_DIR$/comparison/comparison.iml" />
+ <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" />
+ <module fileurl="file://$PROJECT_DIR$/converter-CellDesigner/converter-CellDesigner.iml" filepath="$PROJECT_DIR$/converter-CellDesigner/converter-CellDesigner.iml" />
+ <module fileurl="file://$PROJECT_DIR$/converter-SBGNML/converter-SBGNML.iml" filepath="$PROJECT_DIR$/converter-SBGNML/converter-SBGNML.iml" />
+ <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" />
+ <module fileurl="file://$PROJECT_DIR$/model/model.iml" filepath="$PROJECT_DIR$/model/model.iml" />
+ <module fileurl="file://$PROJECT_DIR$/model-command/model-command.iml" filepath="$PROJECT_DIR$/model-command/model-command.iml" />
+ <module fileurl="file://$PROJECT_DIR$/parent.iml" filepath="$PROJECT_DIR$/parent.iml" />
+ <module fileurl="file://$PROJECT_DIR$/pathvisio/pathvisio.iml" filepath="$PROJECT_DIR$/pathvisio/pathvisio.iml" />
+ <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
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..94a25f7f4cb416c083d265558da75d457237d671
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="VcsDirectoryMappings">
+ <mapping directory="$PROJECT_DIR$" vcs="Git" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/CellDesigner-plugin/CellDesigner-plugin.iml b/CellDesigner-plugin/CellDesigner-plugin.iml
new file mode 100644
index 0000000000000000000000000000000000000000..20aff5378cd416639d08c580d7f98d6a57d45fad
--- /dev/null
+++ b/CellDesigner-plugin/CellDesigner-plugin.iml
@@ -0,0 +1,41 @@
+<?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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <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" />
+ <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
diff --git a/annotation/annotation.iml b/annotation/annotation.iml
new file mode 100644
index 0000000000000000000000000000000000000000..2c466bf93d664b135a4e39019816c9929fda81e8
--- /dev/null
+++ b/annotation/annotation.iml
@@ -0,0 +1,104 @@
+<?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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="model" />
+ <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="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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" 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="persist" />
+ <orderEntry type="library" name="Maven: commons-net:commons-net:3.5" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: postgresql:postgresql:9.1-901.jdbc4" level="project" />
+ <orderEntry type="library" name="Maven: c3p0:c3p0:0.9.1.2" level="project" />
+ <orderEntry type="library" name="Maven: cglib:cglib:2.2.2" level="project" />
+ <orderEntry type="library" name="Maven: asm:asm:3.3.1" level="project" />
+ <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
+ <orderEntry type="module" module-name="converter-CellDesigner" />
+ <orderEntry type="module" module-name="converter" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
+ <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi.chebi.webapps.chebiWS.client:chebiWS-client:2.2.2" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-rt:2.1.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.stream.buffer:streambuffer:0.9" level="project" />
+ <orderEntry type="library" name="Maven: org.codehaus.woodstox:wstx-asl:3.2.3" level="project" />
+ <orderEntry type="library" name="Maven: org.jvnet.staxex:stax-ex:1.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.stream:stax-api:1.0" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.org.apache.xml.internal:resolver:20050927" level="project" />
+ <orderEntry type="library" name="Maven: org.jvnet:mimepull:1.3" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.ws:jaxws-api:2.1" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-tools:2.1.3" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-xjc:2.1.6" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.messaging.saaj:saaj-impl:1.3.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.soap:saaj-api:1.3" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi.miriam:miriam-lib:1.1.5" level="project" />
+ <orderEntry type="library" name="Maven: axis:axis:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.axis:axis-jaxrpc:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.axis:axis-saaj:1.4" level="project" />
+ <orderEntry type="library" scope="RUNTIME" name="Maven: axis:axis-wsdl4j:1.5.1" level="project" />
+ <orderEntry type="library" scope="RUNTIME" name="Maven: commons-discovery:commons-discovery:0.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
+ <orderEntry type="library" name="Maven: javax.mail:mail:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.4" level="project" />
+ <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.2" level="project" />
+ <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.9" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpmime:4.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.4" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.bind:jaxb-api:2.2.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-impl:2.2.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-core:2.2.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.istack:istack-commons-runtime:2.16" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.fastinfoset:FastInfoset:1.2.12" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.bind:jsr173_api:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.poi:poi:3.12" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" level="project" />
+ <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml:3.12" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.10.19" 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
diff --git a/build.xml b/build.xml
index d07a746c62961c0896ae6bdaa13d18d65cc58e50..64e4a6d807c5db3ef9dbd169bb56f0eb10331801 100644
--- a/build.xml
+++ b/build.xml
@@ -1,114 +1,123 @@
<?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}
+ ${build.time}
+ </echo>
+ <copy file="CHANGELOG" tofile="web/src/main/webapp/CHANGELOG" overwrite="true"/>
+ </target>
+
+ <target name="debian-pkg" depends="maven-build">
+ <exec executable="debian/create-debian-pkg.sh"/>
+ </target>
</project>
diff --git a/commons/commons.iml b/commons/commons.iml
new file mode 100644
index 0000000000000000000000000000000000000000..879234cda491dcaecb6e503e2e9f2558cc7b5f8c
--- /dev/null
+++ b/commons/commons.iml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
+ <output url="file://$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$/target" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
+ <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
+ <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
+ <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/comparison/comparison.iml b/comparison/comparison.iml
new file mode 100644
index 0000000000000000000000000000000000000000..1dad1245c2b2bbd7b4dc48e7834dd3d407cf726c
--- /dev/null
+++ b/comparison/comparison.iml
@@ -0,0 +1,123 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="FacetManager">
+ <facet type="Spring" name="Spring">
+ <configuration />
+ </facet>
+ </component>
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
+ <output url="file://$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$/src/test/java" isTestSource="true" />
+ <excludeFolder url="file://$MODULE_DIR$/target" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="model" />
+ <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="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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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.reflections:reflections:0.9.9-RC1" level="project" />
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+ <orderEntry type="module" module-name="converter-CellDesigner" />
+ <orderEntry type="module" module-name="converter-graphics" />
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+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
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+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
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+ <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" 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
diff --git a/console/console.iml b/console/console.iml
new file mode 100644
index 0000000000000000000000000000000000000000..b66c7c73aa897ac2d995cded176e6f9884b22760
--- /dev/null
+++ b/console/console.iml
@@ -0,0 +1,143 @@
+<?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$/target" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="service" />
+ <orderEntry type="module" module-name="model" />
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diff --git a/converter-CellDesigner/converter-CellDesigner.iml b/converter-CellDesigner/converter-CellDesigner.iml
new file mode 100644
index 0000000000000000000000000000000000000000..4175676f92fdda11264b5f26ca1d4b6951622042
--- /dev/null
+++ b/converter-CellDesigner/converter-CellDesigner.iml
@@ -0,0 +1,39 @@
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+ <output-test url="file://$MODULE_DIR$/target/test-classes" />
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+ <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
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+ <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
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+</module>
\ No newline at end of file
diff --git a/converter-SBGNML/converter-SBGNML.iml b/converter-SBGNML/converter-SBGNML.iml
new file mode 100644
index 0000000000000000000000000000000000000000..5338a83e1a4099ce88d7d976467d602056097536
--- /dev/null
+++ b/converter-SBGNML/converter-SBGNML.iml
@@ -0,0 +1,89 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="FacetManager">
+ <facet type="Spring" name="Spring">
+ <configuration />
+ </facet>
+ </component>
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
+ <output url="file://$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$/src/main/resources" type="java-resource" />
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+ <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
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+</module>
\ No newline at end of file
diff --git a/converter-graphics/converter-graphics.iml b/converter-graphics/converter-graphics.iml
new file mode 100644
index 0000000000000000000000000000000000000000..d17adbc39b6add3f49104c7cd50581cf823b4ab6
--- /dev/null
+++ b/converter-graphics/converter-graphics.iml
@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
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+ <output-test url="file://$MODULE_DIR$/target/test-classes" />
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diff --git a/converter/converter.iml b/converter/converter.iml
new file mode 100644
index 0000000000000000000000000000000000000000..e8e77af09df2199aaad07364558052acf7416aaf
--- /dev/null
+++ b/converter/converter.iml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
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+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
+ <output url="file://$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$/src/test/java" isTestSource="true" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
+ <excludeFolder url="file://$MODULE_DIR$/target" />
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+ <orderEntry type="inheritedJdk" />
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+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
+ <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
+ <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
+ <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
+ <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
+ <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
+ <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/editor/editor.iml b/editor/editor.iml
new file mode 100644
index 0000000000000000000000000000000000000000..012f288c841e4be85e7f35300d9468d08b903838
--- /dev/null
+++ b/editor/editor.iml
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
+ <output url="file://$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$/src/test/resources" type="java-test-resource" />
+ <excludeFolder url="file://$MODULE_DIR$/target" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="model" />
+ <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="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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" 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="converter-graphics" />
+ <orderEntry type="module" module-name="model-command" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-script:1.8" level="project" />
+ <orderEntry type="library" name="Maven: xalan:xalan:2.7.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis-ext:1.3.04" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
+ <orderEntry type="library" name="Maven: com.itextpdf:itextpdf:5.5.6" 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: log4j:log4j:1.2.17" 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
diff --git a/frontend-js/frontend-js.iml b/frontend-js/frontend-js.iml
new file mode 100644
index 0000000000000000000000000000000000000000..a5cc752c7a0ba92b2dae51325422a7f9f2e107f1
--- /dev/null
+++ b/frontend-js/frontend-js.iml
@@ -0,0 +1,14 @@
+<?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$">
+ <excludeFolder url="file://$MODULE_DIR$/target" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <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
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index 1e05d57715704904ae833534af9e89bb1f08c29a..58f766c25d6de55f79b2739ec56671b53b511d0a 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -178,9 +178,9 @@ GuiConnector.alert = function (error) {
}
var message = error;
if (message instanceof SecurityError) {
- message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resuorce</p>";
+ message = error.message + "<p>Please <a href=\"login.xhtml?from="+encodeURI(window.location.href)+"\">login</a> to access this resource</p>";
} else if (message instanceof GuiMessageError) {
- message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resource</p>";
+ message = error.message;
} else if (message instanceof NetworkError && (error.message === "XHR error" || error.message === "Failed to fetch")) {
message = "File to big.<br>Please reduce file size or contact administrators.";
} else if (message instanceof Error) {
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index b7454ef5074a92c0c1c33437a43a4ab95854b3e1..605b8284070d6d4701c92040c72c8aba41278174 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -44,6 +44,8 @@ ServerConnector.registerListenerType("onDataLoadStart");
ServerConnector.registerListenerType("onDataLoadStop");
ServerConnector._configurationParam = [];
+ServerConnector._serverBaseUrl= undefined;
+
ServerConnector.getMinOverlayColorInt = function () {
var self = this;
@@ -273,6 +275,9 @@ ServerConnector.getApiBaseUrl = function () {
ServerConnector.getServerBaseUrl = function () {
if (this._serverBaseUrl === undefined) {
var url = "" + window.location.href;
+ if (url.indexOf("?")>=0) {
+ url = url.substr(0,url.indexOf("?"));
+ }
if (!url.endsWith("/")) {
url = url.substr(0, url.lastIndexOf("/") + 1);
}
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index 730bca8fa4bf409b466d4fc8e62d3f2e90c18eac..3231d91f5d11319b11adb5b7e58b8bce40df92c0 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -196,22 +196,32 @@ describe('ServerConnector', function() {
});
});
- describe('login', function() {
- it('try invalid credentials', function() {
- var method = ServerConnector.sendPostRequest;
- ServerConnector.sendPostRequest = function() {
- return Promise.reject(new NetworkError("xxx", {
- statusCode : HttpStatus.FORBIDDEN
- }));
- };
- return ServerConnector.login("blabla", "blablabla").then(function() {
- ServerConnector.sendPostRequest = method;
- assert.ok(false);
- }, function(error) {
- ServerConnector.sendPostRequest = method;
- assert.ok(error.message.indexOf("credentials") >= 0);
- });
+ describe('login', function() {
+ it('try invalid credentials', function() {
+ var method = ServerConnector.sendPostRequest;
+ ServerConnector.sendPostRequest = function() {
+ return Promise.reject(new NetworkError("xxx", {
+ statusCode : HttpStatus.FORBIDDEN
+ }));
+ };
+ return ServerConnector.login("blabla", "blablabla").then(function() {
+ ServerConnector.sendPostRequest = method;
+ assert.ok(false);
+ }, function(error) {
+ ServerConnector.sendPostRequest = method;
+ assert.ok(error.message.indexOf("credentials") >= 0);
+ });
+ });
+ });
+
+ describe('getServerBaseUrl', function() {
+ it('url with GET arg that looks similar to original url', function() {
+ helper.setUrl("http://localhost:8080/minerva/login.xhtml?from=http://localhost:8080/minerva/?id=sample");
+ var url = ServerConnector.getServerBaseUrl();
+ assert.ok(url.indexOf("?")===-1);
+ });
});
- });
+
+
});
diff --git a/model-command/model-command.iml b/model-command/model-command.iml
new file mode 100644
index 0000000000000000000000000000000000000000..b581f7dac6c8f5a4d3ad60214cb8e4481bc7c74e
--- /dev/null
+++ b/model-command/model-command.iml
@@ -0,0 +1,39 @@
+<?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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="model" />
+ <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="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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" 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="converter-CellDesigner" scope="TEST" />
+ <orderEntry type="module" module-name="converter" scope="TEST" />
+ <orderEntry type="library" scope="TEST" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" 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
diff --git a/model/model.iml b/model/model.iml
new file mode 100644
index 0000000000000000000000000000000000000000..3887ea7ae0ddd5e62b7040edfe2bc966c44fe0e2
--- /dev/null
+++ b/model/model.iml
@@ -0,0 +1,36 @@
+<?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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <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="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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <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="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.10.19" 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
diff --git a/parent.iml b/parent.iml
new file mode 100644
index 0000000000000000000000000000000000000000..fbe8d0356cb6f6a5a6a2872eb1e5f651afd0edb9
--- /dev/null
+++ b/parent.iml
@@ -0,0 +1,14 @@
+<?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_5">
+ <output url="file://$MODULE_DIR$/target/classes" />
+ <output-test url="file://$MODULE_DIR$/target/test-classes" />
+ <content url="file://$MODULE_DIR$">
+ <excludeFolder url="file://$MODULE_DIR$/target" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
+ <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/pathvisio/pathvisio.iml b/pathvisio/pathvisio.iml
new file mode 100644
index 0000000000000000000000000000000000000000..51f177eb5c0dc0826ea3f5ac591dbaf96889b194
--- /dev/null
+++ b/pathvisio/pathvisio.iml
@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="FacetManager">
+ <facet type="Osmorc" name="OSGi">
+ <configuration manifestGenerationMode="OsmorcControlled" manifestLocation="" jarfileLocation="pathvisio-1.0.jar" outputPathType="CompilerOutputPath" bndFileLocation="" bundlorFileLocation="" bundleActivator="lcsb.mapviewer.wikipathway.Activator" bundleSymbolicName="lcsb.mapviewer.pathvisio" bundleVersion="1.0.0" ignoreFilePattern="" useProjectDefaultManifestFileLocation="true" alwaysRebuildBundleJAR="false" doNotSynchronizeWithMaven="false">
+ <additionalProperties>
+ <property key="Bundle-Name" value="CellDesigner plugin v.${svnversion}" />
+ <property key="Embed-Transitive" value="true" />
+ <property key="Embed-Dependency" value="*;scope=compile|runtime;inline=false" />
+ <property key="Import-Package" value="!org.relaxng.datatype,!org.slf4j,!org.slf4j.spi,!com.fasterxml.classmate,!com.fasterxml.classmate.members,!com.ibm.uvm.tools,!com.sun.jdi,!com.sun.jdi.connect,!com.sun.jdi.event,!com.sun.jdi.request,!com.sun.jdmk.comm,!com.sun.msv.datatype,!com.sun.msv.datatype.xsd,!com.google.gson,!javax.imageio,!javax.jmdns,!javax.jms,!javax.mail,!javax.mail.internet,!javax.management,!javax.naming,!javax.naming.event,!javax.naming.spi,!javax.security.auth,!javax.security.jacc,!javax.sql,!javax.swing,!javax.swing.border,!javax.swing.event,!javax.swing.filechooser,!javax.swing.plaf,!javax.swing.table,!javax.swing.text,!javax.swing.text.html,!javax.swing.tree,!javax.validation,!javax.validation.constraints,!javax.validation.groups,!javax.validation.metadata,!javax.xml,!javax.xml.bind,!javax.xml.bind.annotation,!javax.xml.bind.annotation.adapters,!javax.xml.namespace,!javax.xml.parsers,!javax.xml.stream,!javax.xml.stream.events,!javax.xml.stream.util,!javax.xml.transform,!javax.xml.transform.dom,!javax.xml.transform.sax,!javax.xml.transform.stream,!javax.xml.validation,!oracle.xml.parser,!oracle.xml.parser.v2,!org.apache.batik.dom,!org.apache.batik.svggen,!org.apache.batik.transcoder,!org.apache.batik.transcoder.image,!org.apache.commons.math,!org.apache.commons.math.stat,!org.apache.commons.math.stat.inference,!org.apache.commons.vfs2,!org.apache.fop.svg,!org.apache.tools.ant,!org.apache.tools.ant.taskdefs,!org.apache.tools.ant.types,!org.bridgedb,!org.bridgedb.bio,!org.bridgedb.gui,!org.bridgedb.rdb.construct,!org.gjt.xpp,!org.jaxen,!org.jaxen.jdom,!org.jaxen.dom4j,!org.jaxen.pattern,!org.jaxen.saxpath,!org.jboss.jandex,!org.jboss.logmanager,!org.jdom,!org.jdom.input,!org.jdom.output,!org.pathvisio.data,!org.w3c.dom,!org.w3c.dom.events,!org.w3c.dom.ranges,!org.w3c.dom.traversal,!org.xml.sax,!org.xml.sax.ext,!org.xml.sax.helpers,!org.xmlpull.v1,!sun.io,!sun.misc,org.osgi.framework;version=1.3.0,*" />
+ <property key="Require-Bundle" value="org.pathvisio.core;bundle-version=3.0.0,org.pathvisio.desktop;bundle-version=3.0.0,org.pathvisio.gui;bundle-version=3.0.0" />
+ <property key="Bundle-ClassPath" value=".,javassist-3.15.0-GA.jar,log4j-1.2.17.jar,jsr305-1.3.9.jar,reflections-0.9.9-RC1.jar,converter-CellDesigner-1.0.jar,javassist-3.16.1-GA.jar,jboss-logging-3.1.0.CR2.jar,junit-4.12.jar,hibernate-core-4.1.0.Final.jar,dom4j-1.6.1.jar,jboss-transaction-api_1.1_spec-1.0.0.Final.jar,commons-collections-3.2.1.jar,desktop-3.2.0.jar,hibernate-commons-annotations-4.0.1.Final.jar,model-1.0.jar,core-3.2.0.jar,hibernate-jpa-2.0-api-1.0.1.Final.jar,xml-apis-1.3.04.jar,gui-3.2.0.jar,converter-1.0.jar,commons-lang3-3.1.jar,guava-11.0.2.jar,org.osgi.core-1.0.0.jar,commons-1.0.jar,xercesImpl-2.11.0.jar,hamcrest-core-1.3.jar,commons-io-2.4.jar,xml-apis-1.0.b2.jar,xml-apis-1.4.01.jar,antlr-2.7.7.jar" />
+ <property key="Include-Resource" value="javassist-3.15.0-GA.jar=$MAVEN_REPOSITORY$/org/javassist/javassist/3.15.0-GA/javassist-3.15.0-GA.jar,log4j-1.2.17.jar=$MAVEN_REPOSITORY$/log4j/log4j/1.2.17/log4j-1.2.17.jar,jsr305-1.3.9.jar=$MAVEN_REPOSITORY$/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar,reflections-0.9.9-RC1.jar=$MAVEN_REPOSITORY$/org/reflections/reflections/0.9.9-RC1/reflections-0.9.9-RC1.jar,converter-CellDesigner-1.0.jar=$MODULE_DIR$/../converter-CellDesigner/pom.xml,javassist-3.16.1-GA.jar=$MAVEN_REPOSITORY$/org/javassist/javassist/3.16.1-GA/javassist-3.16.1-GA.jar,jboss-logging-3.1.0.CR2.jar=$MAVEN_REPOSITORY$/org/jboss/logging/jboss-logging/3.1.0.CR2/jboss-logging-3.1.0.CR2.jar,junit-4.12.jar=$MAVEN_REPOSITORY$/junit/junit/4.12/junit-4.12.jar,hibernate-core-4.1.0.Final.jar=$MAVEN_REPOSITORY$/org/hibernate/hibernate-core/4.1.0.Final/hibernate-core-4.1.0.Final.jar,dom4j-1.6.1.jar=$MAVEN_REPOSITORY$/dom4j/dom4j/1.6.1/dom4j-1.6.1.jar,jboss-transaction-api_1.1_spec-1.0.0.Final.jar=$MAVEN_REPOSITORY$/org/jboss/spec/javax/transaction/jboss-transaction-api_1.1_spec/1.0.0.Final/jboss-transaction-api_1.1_spec-1.0.0.Final.jar,commons-collections-3.2.1.jar=$MAVEN_REPOSITORY$/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.jar,desktop-3.2.0.jar=$MAVEN_REPOSITORY$/org/pathvisio/desktop/3.2.0/desktop-3.2.0.jar,hibernate-commons-annotations-4.0.1.Final.jar=$MAVEN_REPOSITORY$/org/hibernate/common/hibernate-commons-annotations/4.0.1.Final/hibernate-commons-annotations-4.0.1.Final.jar,model-1.0.jar=$MODULE_DIR$/../model/pom.xml,core-3.2.0.jar=$MAVEN_REPOSITORY$/org/pathvisio/core/3.2.0/core-3.2.0.jar,hibernate-jpa-2.0-api-1.0.1.Final.jar=$MAVEN_REPOSITORY$/org/hibernate/javax/persistence/hibernate-jpa-2.0-api/1.0.1.Final/hibernate-jpa-2.0-api-1.0.1.Final.jar,xml-apis-1.3.04.jar=$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.3.04/xml-apis-1.3.04.jar,gui-3.2.0.jar=$MAVEN_REPOSITORY$/org/pathvisio/gui/3.2.0/gui-3.2.0.jar,converter-1.0.jar=$MODULE_DIR$/../converter/pom.xml,commons-lang3-3.1.jar=$MAVEN_REPOSITORY$/org/apache/commons/commons-lang3/3.1/commons-lang3-3.1.jar,guava-11.0.2.jar=$MAVEN_REPOSITORY$/com/google/guava/guava/11.0.2/guava-11.0.2.jar,org.osgi.core-1.0.0.jar=$MAVEN_REPOSITORY$/org/apache/felix/org.osgi.core/1.0.0/org.osgi.core-1.0.0.jar,commons-1.0.jar=$MODULE_DIR$/../commons/pom.xml,xercesImpl-2.11.0.jar=$MAVEN_REPOSITORY$/xerces/xercesImpl/2.11.0/xercesImpl-2.11.0.jar,hamcrest-core-1.3.jar=$MAVEN_REPOSITORY$/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar,commons-io-2.4.jar=$MAVEN_REPOSITORY$/commons-io/commons-io/2.4/commons-io-2.4.jar,xml-apis-1.0.b2.jar=$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2.jar,xml-apis-1.4.01.jar=$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.4.01/xml-apis-1.4.01.jar,antlr-2.7.7.jar=$MAVEN_REPOSITORY$/antlr/antlr/2.7.7/antlr-2.7.7.jar" />
+ <property key="Embedded-Artifacts" value="javassist-3.15.0-GA.jar;g="org.javassist";a="javassist";v="3.15.0-GA",log4j-1.2.17.jar;g="log4j";a="log4j";v="1.2.17",jsr305-1.3.9.jar;g="com.google.code.findbugs";a="jsr305";v="1.3.9",reflections-0.9.9-RC1.jar;g="org.reflections";a="reflections";v="0.9.9-RC1",converter-CellDesigner-1.0.jar;g="lcsb.mapviewer";a="converter-CellDesigner";v="1.0",javassist-3.16.1-GA.jar;g="org.javassist";a="javassist";v="3.16.1-GA",jboss-logging-3.1.0.CR2.jar;g="org.jboss.logging";a="jboss-logging";v="3.1.0.CR2",junit-4.12.jar;g="junit";a="junit";v="4.12",hibernate-core-4.1.0.Final.jar;g="org.hibernate";a="hibernate-core";v="4.1.0.Final",dom4j-1.6.1.jar;g="dom4j";a="dom4j";v="1.6.1",jboss-transaction-api_1.1_spec-1.0.0.Final.jar;g="org.jboss.spec.javax.transaction";a="jboss-transaction-api_1.1_spec";v="1.0.0.Final",commons-collections-3.2.1.jar;g="commons-collections";a="commons-collections";v="3.2.1",desktop-3.2.0.jar;g="org.pathvisio";a="desktop";v="3.2.0",hibernate-commons-annotations-4.0.1.Final.jar;g="org.hibernate.common";a="hibernate-commons-annotations";v="4.0.1.Final",model-1.0.jar;g="lcsb.mapviewer";a="model";v="1.0",core-3.2.0.jar;g="org.pathvisio";a="core";v="3.2.0",hibernate-jpa-2.0-api-1.0.1.Final.jar;g="org.hibernate.javax.persistence";a="hibernate-jpa-2.0-api";v="1.0.1.Final",xml-apis-1.3.04.jar;g="xml-apis";a="xml-apis";v="1.3.04",gui-3.2.0.jar;g="org.pathvisio";a="gui";v="3.2.0",converter-1.0.jar;g="lcsb.mapviewer";a="converter";v="1.0",commons-lang3-3.1.jar;g="org.apache.commons";a="commons-lang3";v="3.1",guava-11.0.2.jar;g="com.google.guava";a="guava";v="11.0.2",org.osgi.core-1.0.0.jar;g="org.apache.felix";a="org.osgi.core";v="1.0.0",commons-1.0.jar;g="lcsb.mapviewer";a="commons";v="1.0",xercesImpl-2.11.0.jar;g="xerces";a="xercesImpl";v="2.11.0",hamcrest-core-1.3.jar;g="org.hamcrest";a="hamcrest-core";v="1.3",commons-io-2.4.jar;g="commons-io";a="commons-io";v="2.4",xml-apis-1.0.b2.jar;g="xml-apis";a="xml-apis";v="1.0.b2",xml-apis-1.4.01.jar;g="xml-apis";a="xml-apis";v="1.4.01",antlr-2.7.7.jar;g="antlr";a="antlr";v="2.7.7"" />
+ </additionalProperties>
+ <additionalJARContents />
+ </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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="Maven: org.pathvisio:core:3.2.0" level="project" />
+ <orderEntry type="library" name="Maven: org.pathvisio:desktop:3.2.0" level="project" />
+ <orderEntry type="library" name="Maven: org.pathvisio:gui:3.2.0" level="project" />
+ <orderEntry type="module" module-name="model" />
+ <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="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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" 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="converter-CellDesigner" />
+ <orderEntry type="module" module-name="converter" />
+ <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
+ <orderEntry type="module" module-name="converter-graphics" scope="TEST" />
+ <orderEntry type="module" module-name="model-command" scope="TEST" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-script:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: xalan:xalan:2.7.0" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: xml-apis:xml-apis-ext:1.3.04" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: com.itextpdf:itextpdf:5.5.6" level="project" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.felix:org.osgi.core:1.0.0" 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
diff --git a/persist/persist.iml b/persist/persist.iml
new file mode 100644
index 0000000000000000000000000000000000000000..1fee876a338b84c30dbc946192cd9c29d091f8b1
--- /dev/null
+++ b/persist/persist.iml
@@ -0,0 +1,63 @@
+<?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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="model" />
+ <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="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="library" name="Maven: commons-net:commons-net:3.5" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <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.springframework:spring-core:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.2" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: postgresql:postgresql:9.1-901.jdbc4" level="project" />
+ <orderEntry type="library" name="Maven: c3p0:c3p0:0.9.1.2" level="project" />
+ <orderEntry type="library" name="Maven: cglib:cglib:2.2.2" level="project" />
+ <orderEntry type="library" name="Maven: asm:asm:3.3.1" level="project" />
+ <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" 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
diff --git a/quadTrees/quadTrees.iml b/quadTrees/quadTrees.iml
new file mode 100644
index 0000000000000000000000000000000000000000..ae2a802e417e33733afa7a5e03c8d5d677093218
--- /dev/null
+++ b/quadTrees/quadTrees.iml
@@ -0,0 +1,19 @@
+<?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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
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+ <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
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\ No newline at end of file
diff --git a/reactome/reactome.iml b/reactome/reactome.iml
new file mode 100644
index 0000000000000000000000000000000000000000..719ba8dc8171605a90ba1729fa1d77f790a72c8b
--- /dev/null
+++ b/reactome/reactome.iml
@@ -0,0 +1,111 @@
+<?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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diff --git a/rest-api/rest-api.iml b/rest-api/rest-api.iml
new file mode 100644
index 0000000000000000000000000000000000000000..fa783be2e59f854b10836e188bf7cd63ecdd98c7
--- /dev/null
+++ b/rest-api/rest-api.iml
@@ -0,0 +1,146 @@
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+ <component name="FacetManager">
+ <facet type="Spring" name="Spring">
+ <configuration />
+ </facet>
+ </component>
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
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+ <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.webflow:spring-binding:2.4.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: opensymphony:ognl:2.6.11" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.webflow:spring-webflow:2.4.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.webflow:spring-js:2.4.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.webflow:spring-js-resources:2.4.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-webmvc:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: com.fasterxml.jackson.core:jackson-core:2.8.8" level="project" />
+ <orderEntry type="library" name="Maven: com.fasterxml.jackson.core:jackson-databind:2.8.8" level="project" />
+ <orderEntry type="library" name="Maven: com.fasterxml.jackson.core:jackson-annotations:2.8.0" level="project" />
+ <orderEntry type="library" scope="PROVIDED" name="Maven: javax.servlet:servlet-api:2.5" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.10.19" 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
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index d85484790e2f2380db8344c9dd8418d38ae340f2..2e9f2635975fd8858d385de89e0af2dbcb46c6cf 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -11,12 +11,7 @@ import javax.servlet.http.HttpServletResponse;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.*;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.ObjectNotFoundException;
@@ -41,9 +36,9 @@ public class UserController extends BaseController {
@RequestMapping(value = "/doLogin", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> login(//
- @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login, //
- @RequestParam(value = "password", required = false) String password, //
- HttpServletResponse response //
+ @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login, //
+ @RequestParam(value = "password", required = false) String password, //
+ HttpServletResponse response //
) throws SecurityException, IOException {
AuthenticationToken token = userService.login(login, password);
if (token == null) {
@@ -84,10 +79,10 @@ public class UserController extends BaseController {
userService.logout(token);
Map<String, String> result = new HashMap<>();
result.put("status", "OK");
-
+
final Boolean useSecureCookie = false;
final String cookiePath = "/";
-
+
Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
cookie.setSecure(useSecureCookie);
diff --git a/service/service.iml b/service/service.iml
new file mode 100644
index 0000000000000000000000000000000000000000..b4677809e8144a2d4b938dc6b27fdea3c60f350f
--- /dev/null
+++ b/service/service.iml
@@ -0,0 +1,130 @@
+<?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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="model" />
+ <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="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" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <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" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" 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="persist" />
+ <orderEntry type="library" name="Maven: commons-net:commons-net:3.5" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.2" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: postgresql:postgresql:9.1-901.jdbc4" level="project" />
+ <orderEntry type="library" name="Maven: c3p0:c3p0:0.9.1.2" level="project" />
+ <orderEntry type="library" name="Maven: cglib:cglib:2.2.2" level="project" />
+ <orderEntry type="library" name="Maven: asm:asm:3.3.1" level="project" />
+ <orderEntry type="module" module-name="model-command" />
+ <orderEntry type="module" module-name="annotation" />
+ <orderEntry type="module" module-name="converter" />
+ <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi.chebi.webapps.chebiWS.client:chebiWS-client:2.2.2" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-rt:2.1.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.stream.buffer:streambuffer:0.9" level="project" />
+ <orderEntry type="library" name="Maven: org.codehaus.woodstox:wstx-asl:3.2.3" level="project" />
+ <orderEntry type="library" name="Maven: org.jvnet.staxex:stax-ex:1.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.stream:stax-api:1.0" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.org.apache.xml.internal:resolver:20050927" level="project" />
+ <orderEntry type="library" name="Maven: org.jvnet:mimepull:1.3" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.ws:jaxws-api:2.1" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-tools:2.1.3" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-xjc:2.1.6" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.messaging.saaj:saaj-impl:1.3.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.soap:saaj-api:1.3" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi.miriam:miriam-lib:1.1.5" level="project" />
+ <orderEntry type="library" name="Maven: axis:axis:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.axis:axis-jaxrpc:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.axis:axis-saaj:1.4" level="project" />
+ <orderEntry type="library" scope="RUNTIME" name="Maven: axis:axis-wsdl4j:1.5.1" level="project" />
+ <orderEntry type="library" scope="RUNTIME" name="Maven: commons-discovery:commons-discovery:0.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
+ <orderEntry type="library" name="Maven: javax.mail:mail:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpmime:4.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.4" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.bind:jaxb-api:2.2.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-impl:2.2.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-core:2.2.7" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.istack:istack-commons-runtime:2.16" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.xml.fastinfoset:FastInfoset:1.2.12" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.bind:jsr173_api:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" level="project" />
+ <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+ <orderEntry type="module" module-name="converter-CellDesigner" />
+ <orderEntry type="module" module-name="converter-SBGNML" />
+ <orderEntry type="library" name="Maven: org.sbgn:libsbgn:0.2" level="project" />
+ <orderEntry type="library" name="Maven: commons-cli:commons-cli:1.2" level="project" />
+ <orderEntry type="module" module-name="converter-graphics" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-script:1.8" level="project" />
+ <orderEntry type="library" name="Maven: xalan:xalan:2.7.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis-ext:1.3.04" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
+ <orderEntry type="library" name="Maven: com.itextpdf:itextpdf:5.5.6" level="project" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
+ <orderEntry type="library" name="Maven: org.primefaces:primefaces:4.0" level="project" />
+ <orderEntry type="library" name="Maven: com.sun.faces:jsf-api:2.1.7" level="project" />
+ <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.poi:poi:3.12" level="project" />
+ <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.9" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml:3.12" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.10.19" 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
diff --git a/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java b/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java
index d825bf694a48943afab0792cf10dfefcfe18bbbe..4ded409599de634a960e5aff7d9febf39c33aaf4 100644
--- a/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java
+++ b/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java
@@ -15,53 +15,54 @@ import org.springframework.security.web.savedrequest.SavedRequest;
/**
* Implementation of Spring Authentication Success Handler. When authentication
- * is success, it will redirect user to the webpage that had accessed befor
+ * is success, it will redirect user to the web page that had accessed before
* authentication took place.
- *
+ *
* @author Piotr Gawron
- *
*/
public class MvAuthenticationSuccessHandler extends SavedRequestAwareAuthenticationSuccessHandler {
- /**
- * Default session expire time in seconds (120 minutes).
- */
- private static final Integer MAX_INACTIVE_INTERVAL = 120 * 60;
+ /**
+ * Default session expire time in seconds (120 minutes).
+ */
+ private static final Integer MAX_INACTIVE_INTERVAL = 120 * 60;
- @Override
- public void onAuthenticationSuccess(HttpServletRequest request, HttpServletResponse response, Authentication authentication) throws IOException,
- ServletException {
+ @Override
+ public void onAuthenticationSuccess(HttpServletRequest request, HttpServletResponse response, Authentication authentication) throws IOException,
+ ServletException {
- request.getSession().setMaxInactiveInterval(MAX_INACTIVE_INTERVAL);
+ request.getSession().setMaxInactiveInterval(MAX_INACTIVE_INTERVAL);
- SavedRequest savedRequest = new HttpSessionRequestCache().getRequest(request, response);
- String url = "";
+ SavedRequest savedRequest = new HttpSessionRequestCache().getRequest(request, response);
+ String url = request.getParameter("from");
- // if we are not redirecting from somewhere then
- if (savedRequest == null) {
- logger.debug(request.getRequestURL());
- logger.debug(request.getQueryString());
- //redirect to the main page
- url = request.getRequestURL().toString().replace(request.getServletPath(), "") + Configuration.MAIN_PAGE;
- String queryString = request.getQueryString();
- // and don't forget about parameters
- if (queryString != null) {
- url += "?" + queryString;
- }
- } else {
- url = savedRequest.getRedirectUrl();
- }
+ // if we are not redirecting from somewhere then
+ if ((url != null && !url.isEmpty())) {
+ logger.debug("Found redirect URL");
+ } else if (savedRequest == null) {
+ logger.debug(request.getRequestURL());
+ //redirect to the main page
+ url = request.getRequestURL().toString().replace(request.getServletPath(), "") + Configuration.MAIN_PAGE;
- logger.debug("Redirecting: " + url);
+ String queryString = request.getQueryString();
+ // and don't forget about parameters
+ if (queryString != null) {
+ url += "?" + queryString;
+ }
+ } else {
+ url = savedRequest.getRedirectUrl();
+ }
- if (!response.isCommitted()) {
- response.sendRedirect(url);
- return;
- } else {
- logger.warn("If you see this then something is wrong...");
- }
+ logger.debug("Redirecting: " + url);
- super.onAuthenticationSuccess(request, response, authentication);
- }
+ if (!response.isCommitted()) {
+ response.sendRedirect(url);
+ return;
+ } else {
+ logger.warn("If you see this then something is wrong...");
+ }
+
+ super.onAuthenticationSuccess(request, response, authentication);
+ }
}
diff --git a/web/src/main/webapp/login.xhtml b/web/src/main/webapp/login.xhtml
index fe3cd2fb52295528dcf0a984524703af05bf6d20..0f59d45952dded9f3f842730297bf43419f7fa14 100644
--- a/web/src/main/webapp/login.xhtml
+++ b/web/src/main/webapp/login.xhtml
@@ -1,112 +1,120 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:ui="http://java.sun.com/jsf/facelets"
- >
+ xmlns:h="http://java.sun.com/jsf/html"
+ xmlns:f="http://java.sun.com/jsf/core"
+ xmlns:ui="http://java.sun.com/jsf/facelets"
+>
<h:head>
- <title>#{mapMB.currentProject.name} - Authorization form</title>
- <link rel="shortcut icon" href="./resources/images/favicon.png" type="image/png" />
- <ui:include src="/WEB-INF/components/admin/statistics.xhtml" />
-
- <script src="https://maps.google.com/maps/api/js?libraries=drawing&v=3.26" type="text/javascript"/>
-
-
- <script src="https://code.jquery.com/jquery-1.12.1.min.js"></script>
- <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
- <script src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
-
-
- <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.13/css/jquery.dataTables.min.css"/>
- <link rel="stylesheet" type="text/css" href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css"/>
-
-
- <h:outputScript library="js" name="minerva.js" />
-
- <h:outputStylesheet library="css" name="style.css"/>
- <h:outputStylesheet library="css" name="minerva.css" />
- <h:outputStylesheet library="css" name="admin.css"/>
-
-
- <script type="text/javascript">
-//<![CDATA[
-
-var loggedIn = false;
-
-minerva.GuiConnector.init();
-minerva.ServerConnector.getSessionData(null);
-minerva.ServerConnector.login().then(function(){
- return minerva.ServerConnector.getProject()
-});
-
-
-function login(){
- var loginString = document.getElementById('username').value;
- var passwordString = document.getElementById('password').value;
- minerva.GuiConnector.init();
- minerva.ServerConnector.getSessionData(null);
- return minerva.ServerConnector.login(loginString, passwordString);
-}
-
-function init() {
- $('#login').click(function(e){
- if (!loggedIn) {
- e.preventDefault();
- return login().then(function(){
- loggedIn = true;
- $('#login').click();
- }, function(error){
- if (error.constructor.name=== "InvalidCredentialsError" ) {
- minerva.GuiConnector.alert("invalid credentials");
- } else {
- minerva.GuiConnector.alert(error);
- }
- });
- }
- });
-}
-
-//]]>
- </script>
+ <title>minerva - Authorization form</title>
+ <link rel="shortcut icon" href="./resources/images/favicon.png" type="image/png"/>
+ <ui:include src="/WEB-INF/components/admin/statistics.xhtml"/>
+
+ <script src="https://maps.google.com/maps/api/js?libraries=drawing&v=3.26" type="text/javascript"/>
+
+
+ <script src="https://code.jquery.com/jquery-1.12.1.min.js"></script>
+ <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
+ <script src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
+
+
+ <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.13/css/jquery.dataTables.min.css"/>
+ <link rel="stylesheet" type="text/css" href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css"/>
+
+
+ <h:outputScript library="js" name="minerva.js"/>
+
+ <h:outputStylesheet library="css" name="style.css"/>
+ <h:outputStylesheet library="css" name="minerva.css"/>
+ <h:outputStylesheet library="css" name="admin.css"/>
+
+
+ <script type="text/javascript">
+ //<![CDATA[
+
+ var loggedIn = false;
+
+ minerva.GuiConnector.init();
+ minerva.ServerConnector.getSessionData(null);
+ minerva.ServerConnector.login().then(function () {
+ return minerva.ServerConnector.getProject()
+ });
+
+
+ function login() {
+ var loginString = document.getElementById('username').value;
+ var passwordString = document.getElementById('password').value;
+ minerva.GuiConnector.init();
+ minerva.ServerConnector.getSessionData(null);
+ return minerva.ServerConnector.login(loginString, passwordString);
+ }
+
+ function init() {
+ var fromPage = minerva.GuiConnector.getParams["from"];
+ if (fromPage !== undefined && fromPage !== null && fromPage !== "") {
+ $("#from")[0].value = minerva.GuiConnector.getParams["from"];
+ }
+ $('#login').click(function (e) {
+ if (!loggedIn) {
+ e.preventDefault();
+ return login().then(function () {
+ loggedIn = true;
+ $('#login').click();
+ }, function (error) {
+ if (error.constructor.name === "InvalidCredentialsError") {
+ minerva.GuiConnector.alert("invalid credentials");
+ } else {
+ minerva.GuiConnector.alert(error);
+ }
+ });
+ }
+ });
+ }
+
+ //]]>
+ </script>
</h:head>
<h:body onload="init();">
- <ui:include src="/WEB-INF/components/admin/header.xhtml" />
-
- <center>
- <h:form name="loginForm" prependId="false" class="loginPanel" style="text-align:left">
-
- <div class="headerFormTitle">AUTHORIZATION FORM</div>
-
- <h:panelGrid columns="2" styleClass="loginDataPanelGrid" >
- <label for="username" class="labelText">LOGIN: </label>
- <h:inputText id="username" name="username" value="#{userMB.login}" class="minerva-input-text"/>
-
- <label for="password" class="labelText">PASSWORD: </label>
- <h:inputSecret id="password" name="password" value="#{userMB.password}" type="password" class="minerva-input-password"/>
-
- <label class="labelText"> </label>
- <h:commandButton type="submit" id="login" action="#{userMB.doLogin}" ajax="false"
- value="LOGIN" styleClass="labelText" update="loginMessages"/>
- </h:panelGrid>
-
-
- <br />
-<br />
-<a href="javascript:;" id="register_button" onClick="window.location.href='#{request.contextPath}/?id=#{mapMB.currentMapId}';" class="adminLink"><i class="fa fa-chevron-right"></i> BACK TO MAP</a>
-<br />
-
- <a href="javascript:;" id="register_button" onClick="window.location.href='mailto:#{userMB.requestAccountEmail}?subject=MINERVA account request'; return false;" class="adminLink"><i class="fa fa-chevron-right"></i> REQUEST AN ACCOUNT</a>
-
- </h:form>
- </center>
-
- <ui:include src="/WEB-INF/components/admin/footer.xhtml" />
+ <center>
+ <h:form name="loginForm" prependId="false" class="loginPanel" style="text-align:left">
+
+ <div class="headerFormTitle">AUTHORIZATION FORM</div>
+
+ <h:panelGrid columns="2" styleClass="loginDataPanelGrid">
+ <label for="username" class="labelText">LOGIN: </label>
+ <h:inputText id="username" name="username" value="#{userMB.login}" class="minerva-input-text"/>
+
+ <label for="password" class="labelText">PASSWORD: </label>
+ <h:inputSecret id="password" name="password" value="#{userMB.password}" type="password"
+ class="minerva-input-password"/>
+
+ <label class="labelText"> </label>
+ <h:commandButton type="submit" id="login" action="#{userMB.doLogin}" ajax="false"
+ value="LOGIN" styleClass="labelText" update="loginMessages"/>
+ </h:panelGrid>
+
+ <input type="hidden" name="from" id="from" value=""/>
+
+ <br/>
+ <br/>
+ <a href="javascript:;" id="go_to_map_button"
+ onClick="window.location.href='#{request.contextPath}/?id=#{mapMB.currentMapId}';" class="adminLink"><i
+ class="fa fa-chevron-right"></i> BACK TO MAP</a>
+ <br/>
+
+ <a href="javascript:;" id="register_button"
+ onClick="window.location.href='mailto:#{userMB.requestAccountEmail}?subject=MINERVA account request'; return false;"
+ class="adminLink"><i class="fa fa-chevron-right"></i> REQUEST AN ACCOUNT</a>
+
+ </h:form>
+ </center>
+
+ <ui:include src="/WEB-INF/components/admin/footer.xhtml"/>
</h:body>
</html>
diff --git a/web/web.iml b/web/web.iml
new file mode 100644
index 0000000000000000000000000000000000000000..4f93374d1f69d16cade014ff7eee93de8b19a5c5
--- /dev/null
+++ b/web/web.iml
@@ -0,0 +1,170 @@
+<?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>
+ <facet type="web" name="Web">
+ <configuration>
+ <descriptors>
+ <deploymentDescriptor name="web.xml" url="file://$MODULE_DIR$/src/main/webapp/WEB-INF/web.xml" />
+ </descriptors>
+ <webroots>
+ <root url="file://$MODULE_DIR$/src/main/webapp" relative="/" />
+ </webroots>
+ <sourceRoots>
+ <root url="file://$MODULE_DIR$/src/main/java" />
+ <root url="file://$MODULE_DIR$/src/main/resources" />
+ </sourceRoots>
+ </configuration>
+ </facet>
+ </component>
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
+ <output url="file://$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" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="service" />
+ <orderEntry type="module" module-name="model" />
+ <orderEntry type="module" module-name="commons" />
+ <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
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+ <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
+ <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
+ <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
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+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
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+ <orderEntry type="module" module-name="annotation" />
+ <orderEntry type="module" module-name="converter" />
+ <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
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\ No newline at end of file