reactome api url changed

reactome/src/main/java/lcsb/mapviewer/reactome/package-info.java

@@ -2,7 +2,7 @@
  * This package provides interface to access data in <a
  * href="http://www.reactome.org/">Reactome</a> database. Information from this
  * database are retrieved using <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * > Reactome RESTful API</a>. Reactome model was implemented in
  * {@link lcsb.mapviewer.reactome.model model} subpackage. By design all
  * reactome objects inherit from

reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java

@@ -136,7 +136,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp
 	/**
 	 * Url used for accessing Reactome RestFULL API.
 	 */
-	private static final String									 REACTOME_URL			= "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/RESTfulWS/";
+	private static final String									 REACTOME_URL			= "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/";
 
 	@Override
 	public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException {
@@ -752,7 +752,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp
 	@Override
 	public ExternalServiceStatus getServiceStatus() {
 		ExternalServiceStatus status = new ExternalServiceStatus(
-				"Reactome RESTful API", "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html");
+				"Reactome RESTful API", "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html");
 
 		GeneralCacheInterface cacheCopy = getCache();
 		this.setCache(null);

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAbstractModifiedResidueParser.java

@@ -4,9 +4,9 @@ import lcsb.mapviewer.reactome.model.ReactomeAbstractModifiedResidue;
 import lcsb.mapviewer.reactome.xml.columnParser.AbstractModifiedResidueColumnParser;
 
 /**
- * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
- * >Reactome API</a> for <a href=
+ * Parser for reactome xml retrieved from
+ * <a href= "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html" >
+ * Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=AbstractModifiedResidue"
  * >AbstractModifiedResidue</a> object.
  * 

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeAffiliationParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.AffiliationColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Affiliation"
  * >Affiliation</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.BlackBoxEventColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=BlackBoxEvent"
  * >BlackBoxEvent</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeBookParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.BookColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Book"
  * >Book</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CandidateSetColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=CandidateSet"
  * >CandidateSet</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CatalystActivityColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=CatalystActivity"
  * >CatalystActivity</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCellTypeParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CellTypeColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=CellType"
  * >CellType</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeCompartmentParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.CompartmentColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Compartment"
  * >Compartment</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeComplexParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ComplexColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Complex"
  * >Complex</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeConcurrentEventSetParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.ConcurrentEventSetColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ConcurrentEventSet"
  * >ConcurrentEventSet</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseIdentifierParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DatabaseIdentifierColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=DatabaseIdentifier"
  * >DatabaseIdentifier</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDatabaseObjectParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DatabaseObjectColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=DatabaseObject"
  * >DatabaseObject</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DefinedSetColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=DefinedSet"
  * >DefinedSet</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDepolymerisationParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DepolymerisationColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Depolymerisation"
  * >Depolymerisation</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeDiseaseParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.DiseaseColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=Disease"
  * >Disease</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityCompartmentParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EntityCompartmentColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EntityCompartment"
  * >EntityCompartment</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntityFunctionalStatusParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EntityFunctionalStatusColumnPars
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EntityFunctionalStatus"
  * >EntityFunctionalStatus</a> object.

reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeEntitySetParser.java

@@ -5,7 +5,7 @@ import lcsb.mapviewer.reactome.xml.columnParser.EntitySetColumnParser;
 
 /**
  * Parser for reactome xml retrieved from <a href=
- * "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
+ * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
  * >Reactome API</a> for <a href=
  * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=EntitySet"
  * >EntitySet</a> object.