Groups make now use of the new SBO term "subsystem". For documentation

purposes, an overview html file has been created and the POM file was slightly updated.
draeger-lab · Apr 30, 2016 · 152150e · 152150e
1 parent 917577e
commit 152150e
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Showing 3 changed files with 16 additions and 6 deletions.
diff --git a/pom.xml b/pom.xml
@@ -61,11 +61,11 @@
   <!-- Repositories                                                        -->
   <!-- =================================================================== -->
   <repositories>
-		<repository>
-    		<id>in-project</id>
-    		<name>In project repository</name>
-    		<url>file://${project.basedir}/lib</url>
-		</repository>
+    <repository>
+      <id>in-project</id>
+      <name>In project repository</name>
+      <url>file://${project.basedir}/lib</url>
+    </repository>
   </repositories>
 
   <!-- =================================================================== -->
@@ -82,7 +82,7 @@
       <scope>compile</scope>
     </dependency>
     <dependency>
-      <!-- mvn install:install-file -Dfile=/path/to/sysbio.jar -DgroupId=de.zbit -DartifactId=SysBio -Dversion=REVISION_NUMBER -Dpackaging=jar -->
+      <!-- mvn install:install-file -Dfile=./lib/sysbio.jar -DgroupId=de.zbit -DartifactId=SysBio -Dversion=REVISION_NUMBER -Dpackaging=jar -DlocalRepositoryPath=./lib/ && rm ./lib/sysbio.jar -->
       <groupId>de.zbit</groupId>
       <artifactId>SysBio</artifactId>
       <version>1390</version> <!-- SVN revision -->

diff --git a/src/edu/ucsd/sbrg/bigg/SBMLPolisher.java b/src/edu/ucsd/sbrg/bigg/SBMLPolisher.java
@@ -719,6 +719,7 @@ public boolean polish(Reaction r) {
             group = groupsModelPlugin.createGroup("g" + (groupsModelPlugin.getGroupCount() + 1));
             group.setName(subsystem);
             group.setKind(Group.Kind.partonomy);
+            group.setSBOTerm(633); // subsystem
             groupForName.put(subsystem, group);
           }
           Member member = group.createMember();

diff --git a/src/overview.html b/src/overview.html
@@ -0,0 +1,9 @@
+<html>
+
+  <head>
+  </head>
+
+  <body>
+  </body>
+
+</html>
-Original file line number
+Diff line change
@@ -0,0 +1,9 @@
+    <html>
+      <head>
+      </head>
+      <body>
+      </body>
+    </html>