From 4fd983ad2280f6ab65b27397d139d585b03a204c Mon Sep 17 00:00:00 2001
From: unknown <david.hoksza@gmail.com>
Date: Wed, 19 Sep 2018 12:29:34 +0200
Subject: [PATCH] conflicting dependencies in libsbml
---
CellDesigner-plugin/.classpath | 7 ++
.../.settings/org.eclipse.jdt.core.prefs | 1 +
annotation/.classpath | 2 +
.../.settings/org.eclipse.jdt.core.prefs | 1 +
commons/.classpath | 2 +
commons/.settings/org.eclipse.jdt.core.prefs | 1 +
comparison/.classpath | 1 +
.../.settings/org.eclipse.jdt.core.prefs | 1 +
console/.classpath | 2 +
console/.settings/org.eclipse.jdt.core.prefs | 1 +
converter-CellDesigner/.classpath | 2 +
.../.settings/org.eclipse.jdt.core.prefs | 1 +
converter-SBGNML/.classpath | 2 +
.../.settings/org.eclipse.jdt.core.prefs | 1 +
converter-graphics/.classpath | 8 ++
.../.settings/org.eclipse.jdt.core.prefs | 1 +
.../org.eclipse.wst.common.component | 1 +
.../graphics/AbstractImageGenerator.java | 2 +-
converter-sbml/.classpath | 2 +
converter-sbml/.project | 4 +-
.../.settings/org.eclipse.jdt.core.prefs | 1 +
converter/.classpath | 2 +
.../.settings/org.eclipse.jdt.core.prefs | 1 +
editor/.classpath | 2 +
editor/.settings/org.eclipse.jdt.core.prefs | 1 +
frontend-js/.classpath | 1 +
.../.settings/org.eclipse.jdt.core.prefs | 1 +
model-command/.classpath | 2 +
.../.settings/org.eclipse.jdt.core.prefs | 1 +
model/.classpath | 2 +
model/.settings/org.eclipse.jdt.core.prefs | 1 +
pathvisio/.classpath | 7 ++
.../.settings/org.eclipse.jdt.core.prefs | 1 +
persist/.classpath | 2 +
persist/.settings/org.eclipse.jdt.core.prefs | 1 +
quadTrees/.classpath | 7 ++
.../.settings/org.eclipse.jdt.core.prefs | 1 +
reactome/.classpath | 2 +
reactome/.settings/org.eclipse.jdt.core.prefs | 1 +
rest-api/.classpath | 2 +
rest-api/.settings/org.eclipse.jdt.core.prefs | 1 +
.../api/convert/ConvertController.java | 26 +++-
.../api/convert/ConvertRestImpl.java | 114 ++++++++++++------
.../api/convert/ConvertRestImplTest.java | 17 ++-
service/.classpath | 2 +
service/.settings/org.eclipse.jdt.core.prefs | 1 +
web/.classpath | 3 +
web/.settings/org.eclipse.jdt.core.prefs | 1 +
.../org.eclipse.wst.common.component | 24 ++--
49 files changed, 210 insertions(+), 61 deletions(-)
diff --git a/CellDesigner-plugin/.classpath b/CellDesigner-plugin/.classpath
index 1b6e759069..2787dc1507 100644
--- a/CellDesigner-plugin/.classpath
+++ b/CellDesigner-plugin/.classpath
@@ -10,11 +10,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
@@ -27,5 +29,10 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/CellDesigner-plugin/.settings/org.eclipse.jdt.core.prefs b/CellDesigner-plugin/.settings/org.eclipse.jdt.core.prefs
index d59e09c909..f494d1de02 100644
--- a/CellDesigner-plugin/.settings/org.eclipse.jdt.core.prefs
+++ b/CellDesigner-plugin/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/annotation/.classpath b/annotation/.classpath
index 71a86ecfe6..5b0cf1c117 100644
--- a/annotation/.classpath
+++ b/annotation/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/annotation/.settings/org.eclipse.jdt.core.prefs b/annotation/.settings/org.eclipse.jdt.core.prefs
index df46a9aced..e24b722f83 100644
--- a/annotation/.settings/org.eclipse.jdt.core.prefs
+++ b/annotation/.settings/org.eclipse.jdt.core.prefs
@@ -9,4 +9,5 @@ org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/commons/.classpath b/commons/.classpath
index 08d7a50f5b..2d7c6a5d6d 100644
--- a/commons/.classpath
+++ b/commons/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/commons/.settings/org.eclipse.jdt.core.prefs b/commons/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/commons/.settings/org.eclipse.jdt.core.prefs
+++ b/commons/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/comparison/.classpath b/comparison/.classpath
index 42e0e84810..5919bb8b86 100644
--- a/comparison/.classpath
+++ b/comparison/.classpath
@@ -10,6 +10,7 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
diff --git a/comparison/.settings/org.eclipse.jdt.core.prefs b/comparison/.settings/org.eclipse.jdt.core.prefs
index d59e09c909..f494d1de02 100644
--- a/comparison/.settings/org.eclipse.jdt.core.prefs
+++ b/comparison/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/console/.classpath b/console/.classpath
index fc5f96c9fe..8ffcdca273 100644
--- a/console/.classpath
+++ b/console/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/console/.settings/org.eclipse.jdt.core.prefs b/console/.settings/org.eclipse.jdt.core.prefs
index d59e09c909..f494d1de02 100644
--- a/console/.settings/org.eclipse.jdt.core.prefs
+++ b/console/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/converter-CellDesigner/.classpath b/converter-CellDesigner/.classpath
index 8edbacf9fa..10bcdfc901 100644
--- a/converter-CellDesigner/.classpath
+++ b/converter-CellDesigner/.classpath
@@ -10,11 +10,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/converter-CellDesigner/.settings/org.eclipse.jdt.core.prefs b/converter-CellDesigner/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/converter-CellDesigner/.settings/org.eclipse.jdt.core.prefs
+++ b/converter-CellDesigner/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/converter-SBGNML/.classpath b/converter-SBGNML/.classpath
index 92bb54b5c5..214629b39b 100644
--- a/converter-SBGNML/.classpath
+++ b/converter-SBGNML/.classpath
@@ -20,11 +20,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/converter-SBGNML/.settings/org.eclipse.jdt.core.prefs b/converter-SBGNML/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/converter-SBGNML/.settings/org.eclipse.jdt.core.prefs
+++ b/converter-SBGNML/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/converter-graphics/.classpath b/converter-graphics/.classpath
index 22c865221b..e90097a5e7 100644
--- a/converter-graphics/.classpath
+++ b/converter-graphics/.classpath
@@ -10,16 +10,19 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="org.eclipse.jst.component.nondependency" value=""/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
@@ -27,5 +30,10 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/converter-graphics/.settings/org.eclipse.jdt.core.prefs b/converter-graphics/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/converter-graphics/.settings/org.eclipse.jdt.core.prefs
+++ b/converter-graphics/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/converter-graphics/.settings/org.eclipse.wst.common.component b/converter-graphics/.settings/org.eclipse.wst.common.component
index 2faa3f2b45..b5db52c6c5 100644
--- a/converter-graphics/.settings/org.eclipse.wst.common.component
+++ b/converter-graphics/.settings/org.eclipse.wst.common.component
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
<wb-module deploy-name="MapViewer-converter-graphics">
<wb-resource deploy-path="/" source-path="/src/main/java"/>
+ <wb-resource deploy-path="/" source-path="/src/main/resources"/>
</wb-module>
</project-modules>
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index 50350a9247..d3ae21c24b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -981,7 +981,7 @@ public abstract class AbstractImageGenerator {
if (!isDrawn()) {
draw();
}
- saveToOutputStream(os);
+ saveToOutputStreamImplementation(os);
}
/**
diff --git a/converter-sbml/.classpath b/converter-sbml/.classpath
index ebdb3af0aa..02b328e20b 100644
--- a/converter-sbml/.classpath
+++ b/converter-sbml/.classpath
@@ -10,11 +10,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
diff --git a/converter-sbml/.project b/converter-sbml/.project
index 6ae989581c..ec05189268 100644
--- a/converter-sbml/.project
+++ b/converter-sbml/.project
@@ -16,12 +16,12 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
+ <name>org.eclipse.wst.validation.validationbuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
- <name>org.eclipse.wst.validation.validationbuilder</name>
+ <name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
diff --git a/converter-sbml/.settings/org.eclipse.jdt.core.prefs b/converter-sbml/.settings/org.eclipse.jdt.core.prefs
index 6e80039d3b..4e4a3ada9a 100644
--- a/converter-sbml/.settings/org.eclipse.jdt.core.prefs
+++ b/converter-sbml/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/converter/.classpath b/converter/.classpath
index 9286345950..d31a016bf3 100644
--- a/converter/.classpath
+++ b/converter/.classpath
@@ -10,11 +10,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/converter/.settings/org.eclipse.jdt.core.prefs b/converter/.settings/org.eclipse.jdt.core.prefs
index df46a9aced..e24b722f83 100644
--- a/converter/.settings/org.eclipse.jdt.core.prefs
+++ b/converter/.settings/org.eclipse.jdt.core.prefs
@@ -9,4 +9,5 @@ org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/editor/.classpath b/editor/.classpath
index 16c89cc137..d2bc4e02a3 100644
--- a/editor/.classpath
+++ b/editor/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/editor/.settings/org.eclipse.jdt.core.prefs b/editor/.settings/org.eclipse.jdt.core.prefs
index d59e09c909..f494d1de02 100644
--- a/editor/.settings/org.eclipse.jdt.core.prefs
+++ b/editor/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/frontend-js/.classpath b/frontend-js/.classpath
index b10870e6cf..1d05ba33da 100644
--- a/frontend-js/.classpath
+++ b/frontend-js/.classpath
@@ -10,6 +10,7 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/frontend-js/.settings/org.eclipse.jdt.core.prefs b/frontend-js/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/frontend-js/.settings/org.eclipse.jdt.core.prefs
+++ b/frontend-js/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/model-command/.classpath b/model-command/.classpath
index 08d7a50f5b..2d7c6a5d6d 100644
--- a/model-command/.classpath
+++ b/model-command/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/model-command/.settings/org.eclipse.jdt.core.prefs b/model-command/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/model-command/.settings/org.eclipse.jdt.core.prefs
+++ b/model-command/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/model/.classpath b/model/.classpath
index 08d7a50f5b..2d7c6a5d6d 100644
--- a/model/.classpath
+++ b/model/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/model/.settings/org.eclipse.jdt.core.prefs b/model/.settings/org.eclipse.jdt.core.prefs
index df46a9aced..e24b722f83 100644
--- a/model/.settings/org.eclipse.jdt.core.prefs
+++ b/model/.settings/org.eclipse.jdt.core.prefs
@@ -9,4 +9,5 @@ org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/pathvisio/.classpath b/pathvisio/.classpath
index 273e16e17b..36e8b1c83a 100644
--- a/pathvisio/.classpath
+++ b/pathvisio/.classpath
@@ -10,11 +10,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
@@ -27,5 +29,10 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/pathvisio/.settings/org.eclipse.jdt.core.prefs b/pathvisio/.settings/org.eclipse.jdt.core.prefs
index d59e09c909..f494d1de02 100644
--- a/pathvisio/.settings/org.eclipse.jdt.core.prefs
+++ b/pathvisio/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/persist/.classpath b/persist/.classpath
index 08d7a50f5b..2d7c6a5d6d 100644
--- a/persist/.classpath
+++ b/persist/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/persist/.settings/org.eclipse.jdt.core.prefs b/persist/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/persist/.settings/org.eclipse.jdt.core.prefs
+++ b/persist/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/quadTrees/.classpath b/quadTrees/.classpath
index 1b6e759069..2787dc1507 100644
--- a/quadTrees/.classpath
+++ b/quadTrees/.classpath
@@ -10,11 +10,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
@@ -27,5 +29,10 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/quadTrees/.settings/org.eclipse.jdt.core.prefs b/quadTrees/.settings/org.eclipse.jdt.core.prefs
index d59e09c909..f494d1de02 100644
--- a/quadTrees/.settings/org.eclipse.jdt.core.prefs
+++ b/quadTrees/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/reactome/.classpath b/reactome/.classpath
index 16c89cc137..d2bc4e02a3 100644
--- a/reactome/.classpath
+++ b/reactome/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/reactome/.settings/org.eclipse.jdt.core.prefs b/reactome/.settings/org.eclipse.jdt.core.prefs
index d59e09c909..f494d1de02 100644
--- a/reactome/.settings/org.eclipse.jdt.core.prefs
+++ b/reactome/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/rest-api/.classpath b/rest-api/.classpath
index 3783d3d93c..7f345a678f 100644
--- a/rest-api/.classpath
+++ b/rest-api/.classpath
@@ -10,6 +10,7 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
@@ -20,6 +21,7 @@
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/rest-api/.settings/org.eclipse.jdt.core.prefs b/rest-api/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/rest-api/.settings/org.eclipse.jdt.core.prefs
+++ b/rest-api/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
index 01939779d1..3da7412df8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
@@ -42,18 +42,34 @@ public class ConvertController extends BaseController {
@Autowired
private ConvertRestImpl convertController;
-
- @RequestMapping(value = "/convert/{fromFormat:celldesigner|sbml|sbgn}:{toFormat:celldesigner|sbml|sbgn}",
- method = { RequestMethod.POST }, produces = {
- MediaType.TEXT_PLAIN_VALUE })
+
+ @RequestMapping(value = "/convert/{fromFormat}:{toFormat}",
+ method = { RequestMethod.POST })
public String convertInput(//
@PathVariable(value = "fromFormat") String fromFormat, //
@PathVariable(value = "toFormat") String toFormat, //
@RequestBody String body, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token //
) throws SecurityException, IOException, QueryException, SBMLException,
- InvalidInputDataExecption, InconsistentModelException, ConverterException, XMLStreamException {
+ InvalidInputDataExecption, InconsistentModelException, ConverterException, XMLStreamException,
+ DrawingException {
return convertController.convert(token, fromFormat, toFormat, body);
}
+ /*
+ @RequestMapping(value = "/convert/{fromFormat}:{toFormat}:img",
+ method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_OCTET_STREAM_VALUE })
+ public String convertInputToImage(//
+ @PathVariable(value = "fromFormat") String fromFormat, //
+ @PathVariable(value = "toFormat") String toFormat, //
+ @RequestBody String body, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException, SBMLException,
+ InvalidInputDataExecption, InconsistentModelException, ConverterException, XMLStreamException,
+ DrawingException {
+ return convertController.converToImage(token, fromFormat, toFormat, body);
+
+ }
+ */
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
index 878b1867af..a06934e249 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
@@ -1,72 +1,62 @@
package lcsb.mapviewer.api.convert;
-import java.awt.geom.PathIterator;
import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.io.OutputStream;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.sbml.jsbml.SBMLException;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
+import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.graphics.SvgImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlExporter;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlParser;
-import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlParser;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
@Transactional(value = "txManager")
public class ConvertRestImpl extends BaseRestImpl {
+
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ConvertRestImpl.class);
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ConvertRestImpl.class);
public String convert(String token, String fromFormat, String toFormat, String input)
- throws SecurityException, ObjectNotFoundException, InvalidInputDataExecption,
- SBMLException, InconsistentModelException, IOException, ConverterException, XMLStreamException {
+ throws SecurityException, InvalidInputDataExecption,
+ SBMLException, InconsistentModelException, IOException, ConverterException,
+ XMLStreamException, DrawingException, QueryException {
- Model model = loadModel(input, fromFormat);
-
- return exportModel(model, toFormat);
- }
-
- private Model loadModel(String input, String format) throws InvalidInputDataExecption {
+ ConverterParams params = createConvertParams(input);
+ Model model = getModelParser(fromFormat).createModel(params);
- switch (format) {
- case "celldesigner":
- return loadCellDesigner(input);
- case "sbml":
- return loadSbml(input);
- case "sbgn":
- return loadSbgn(input);
- default:
- return null;
- }
+ IConverter exporter = getModelParser(toFormat);
+ return IOUtils.toString(exporter.exportModelToInputStream(model));
}
private String exportModel(Model model, String format)
throws InvalidInputDataExecption, InconsistentModelException,
- IOException, ConverterException, SBMLException, XMLStreamException {
+ IOException, ConverterException, SBMLException, XMLStreamException,
+ DrawingException {
switch (format) {
case "celldesigner":
@@ -75,13 +65,19 @@ private String exportModel(Model model, String format)
return exportSbml(model);
case "sbgn":
return exportSbgn(model);
+ case "pdf":
+ return exportPdf(model);
+ case "png":
+ return exportPng(model);
+ case "svg":
+ return exportSvg(model);
default:
return null;
}
}
private Model loadCellDesigner(String input) throws InvalidInputDataExecption {
- ConverterParams params = createParams(input);
+ ConverterParams params = createConvertParams(input);
CellDesignerXmlParser parser = new CellDesignerXmlParser();
return parser.createModel(params);
}
@@ -92,7 +88,7 @@ private String exportModel(Model model, String format)
}
private Model loadSbml(String input) throws InvalidInputDataExecption {
- ConverterParams params = createParams(input);
+ ConverterParams params = createConvertParams(input);
SbmlParser parser = new SbmlParser();
return parser.createModel(params);
}
@@ -103,7 +99,7 @@ private String exportModel(Model model, String format)
}
private Model loadSbgn(String input) throws InvalidInputDataExecption {
- ConverterParams params = createParams(input);
+ ConverterParams params = createConvertParams(input);
SbgnmlXmlParser parser = new SbgnmlXmlParser();
return parser.createModel(params);
}
@@ -114,8 +110,54 @@ private String exportModel(Model model, String format)
return IOUtils.toString(converter.exportModelToInputStream(model));
}
+ private String exportPdf(Model model) throws IOException, DrawingException {
+
+ AbstractImageGenerator generator = new PdfImageGenerator(createImageParams(model));
+
+
+ // generator.saveToFile("test1.pdf");
+
+ ByteArrayOutputStream os = new ByteArrayOutputStream();
+ generator.saveToOutputStream(os);
+
+ return new String(os.toByteArray());
+ }
+
+ private String exportPng(Model model) throws IOException, DrawingException {
+
+ AbstractImageGenerator generator = new PngImageGenerator(createImageParams(model));
+
+
+ // generator.saveToFile("test1.png");
+
+ ByteArrayOutputStream os = new ByteArrayOutputStream();
+ generator.saveToOutputStream(os);
+
+ return new String(os.toByteArray());
+ }
+
+ private String exportSvg(Model model) throws IOException, DrawingException {
+
+ AbstractImageGenerator generator = new SvgImageGenerator(createImageParams(model));
+
+
+ // generator.saveToFile("test1.svg");
+
+ ByteArrayOutputStream os = new ByteArrayOutputStream();
+ generator.saveToOutputStream(os);
+
+ return new String(os.toByteArray());
+ }
+
+ private AbstractImageGenerator.Params createImageParams(Model model){
+ return new AbstractImageGenerator.Params().//
+ model(model).//
+ width(model.getWidth()).//
+ height(model.getHeight());
+ }
+
- private ConverterParams createParams(String input) {
+ private ConverterParams createConvertParams(String input) {
ConverterParams params = new ConverterParams();
InputStream is = new ByteArrayInputStream(input.getBytes());
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
index edb28075aa..31d3b00610 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
@@ -13,6 +13,10 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.model.sbml.SbmlParser;
+import lcsb.mapviewer.model.map.model.Model;
public class ConvertRestImplTest extends RestTestFunctions {
@@ -38,11 +42,14 @@ public class ConvertRestImplTest extends RestTestFunctions {
@Test
public void testCelDesigner2Sbml() throws Exception {
try {
- File file = new File("testFiles/convert/sample.sbgn");
- String content = FileUtils.readFileToString(file);
- String result = convertRestImpl.convert(token, "sbgn", "celldesigner", content);
- System.out.print(result);
- assertTrue(result.length() > 0);
+ IConverter converter = new SbmlParser();
+
+ Model model = converter.createModel(new ConverterParams().filename("testFiles/example1.xml"));
+ model.setName(null);
+
+ converter.exportModelToFile(model, "tmp.xml");
+
+
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/service/.classpath b/service/.classpath
index 08d7a50f5b..2d7c6a5d6d 100644
--- a/service/.classpath
+++ b/service/.classpath
@@ -15,11 +15,13 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
diff --git a/service/.settings/org.eclipse.jdt.core.prefs b/service/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/service/.settings/org.eclipse.jdt.core.prefs
+++ b/service/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/web/.classpath b/web/.classpath
index ace82666f2..11def0e9b1 100644
--- a/web/.classpath
+++ b/web/.classpath
@@ -15,16 +15,19 @@
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
+ <attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/web/.settings/org.eclipse.jdt.core.prefs b/web/.settings/org.eclipse.jdt.core.prefs
index 1ab2bb53af..991da2c903 100644
--- a/web/.settings/org.eclipse.jdt.core.prefs
+++ b/web/.settings/org.eclipse.jdt.core.prefs
@@ -5,4 +5,5 @@ org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/web/.settings/org.eclipse.wst.common.component b/web/.settings/org.eclipse.wst.common.component
index 9694299231..0d4deb4b31 100644
--- a/web/.settings/org.eclipse.wst.common.component
+++ b/web/.settings/org.eclipse.wst.common.component
@@ -1,40 +1,40 @@
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
- <wb-module deploy-name="MapViewer-web">
+ <wb-module deploy-name="web-1.0">
<wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
<wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
- <dependent-module archiveName="service-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/service/service">
+ <dependent-module archiveName="service-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-service/MapViewer-service">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="model-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/model/model">
+ <dependent-module archiveName="model-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-model/MapViewer-model">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="commons-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/commons/commons">
+ <dependent-module archiveName="commons-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-commons/MapViewer-commons">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="persist-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/persist/persist">
+ <dependent-module archiveName="persist-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-persist/MapViewer-persist">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="model-command-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/model-command/model-command">
+ <dependent-module archiveName="model-command-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-model-command/MapViewer-model-command">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="annotation-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/annotation/annotation">
+ <dependent-module archiveName="annotation-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-annotation/MapViewer-annotation">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="converter-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter/converter">
+ <dependent-module archiveName="converter-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-converter/MapViewer-converter">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="converter-CellDesigner-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter-CellDesigner/converter-CellDesigner">
+ <dependent-module archiveName="converter-CellDesigner-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-converter-CellDesigner/MapViewer-converter-CellDesigner">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="converter-SBGNML-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter-SBGNML/converter-SBGNML">
+ <dependent-module archiveName="converter-SBGNML-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-converter-SBGNML/MapViewer-converter-SBGNML">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="converter-graphics-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter-graphics/converter-graphics">
+ <dependent-module archiveName="converter-graphics-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-converter-graphics/MapViewer-converter-graphics">
<dependency-type>uses</dependency-type>
</dependent-module>
- <dependent-module archiveName="rest-api-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/rest-api/rest-api">
+ <dependent-module archiveName="rest-api-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/MapViewer-rest-api/MapViewer-rest-api">
<dependency-type>uses</dependency-type>
</dependent-module>
<dependent-module archiveName="converter-sbml-1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/converter-sbml/converter-sbml">
--
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