add jar packaging in pom.xml file and optimize the query of the sources

YayeAwa · Sep 1, 2015 · 6e13c1c · 6e13c1c
1 parent 33e9c16
commit 6e13c1c
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Showing 6 changed files with 1,346 additions and 10 deletions.
diff --git a/BasecolDAOTest/pom.xml b/BasecolDAOTest/pom.xml
@@ -40,7 +40,6 @@
     <dependency>
 		<groupId>org.apache.cayenne</groupId>
 		<artifactId>cayenne-server</artifactId>
-   		<!-- Here specify the version of Cayenne you are actually using -->
 		<version>3.1</version>
 	</dependency>
 	<dependency>

diff --git a/TAP-PLUG-BASECOL2012/pom.xml b/TAP-PLUG-BASECOL2012/pom.xml
@@ -3,6 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.vamdc.tap.plugin</groupId>
 	<artifactId>TAP-BASECOL2012</artifactId>
+	<packaging>jar</packaging>
 	<name>Basecol node plugin</name>
 	<description>Basecol plugin for VAMDC-TAP Java node software</description>
 

diff --git a/TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/builders/states/AtomicTypeBuilder.java b/TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/builders/states/AtomicTypeBuilder.java
@@ -27,7 +27,7 @@ public class AtomicTypeBuilder {
 	public static void addAtom(EnergyTables myetable, RequestInterface myrequest){
 		if (!myrequest.checkBranch(Requestable.Atoms)) 
 			return;
-		String atomID = IDs.getSpecieID(myetable.getToElements()./*getElementRel()*/getIdElement().intValue());
+		String atomID = IDs.getSpecieID(myetable.getToElements().getIdElement().intValue());
 		if (myrequest.getXsamsManager().getElement(atomID)==null)
 		{//build atom description only in case we don't have it yet, in other case just add states
 			AtomType myatom = new Atom(myetable);
@@ -64,7 +64,7 @@ public static void addAtom(EnergyTables myetable, RequestInterface myrequest){
 			}
 			//Add states to XSAMS tree
 			myrequest.getXsamsManager().addStates(
-					IDs.getSpecieID(myetable.getToElements()/*getElementRel()*/.getIdElement().intValue()),
+					IDs.getSpecieID(myetable.getToElements().getIdElement().intValue()),
 					mystates);
 		}
 

diff --git a/TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/xsams/Collision.java b/TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/xsams/Collision.java
@@ -3,7 +3,6 @@
 import java.util.List;
 import java.util.Map;
 
-import org.apache.cayenne.access.DataContext;
 import org.vamdc.BasecolTest.dao.Collisions;
 import org.vamdc.BasecolTest.dao.LevelGroups;
 import org.vamdc.BasecolTest.dao.RefsGroups;
@@ -28,11 +27,6 @@ public Collision(
 			List<RefsGroups> allRefs,List<RefsGroups> methodRefs){
 
 		this.setId(IDs.getID('P',"C"+data.getIdCollision()+levelmap.get(rates.getLevelGroupID()).getID()));
-
-		//List<RefsGroups> allRefs = data.getToRefsGroups();
-		/*allRefs.addAll(data.getToRefsMethod());
-		allRefs.addAll(data.getToRefsPES());
-		allRefs.addAll(data.getToRefsReduMass());*/
 
 		this.addSources(Source.getSources(allRefs,document,true));
 
@@ -42,7 +36,7 @@ public Collision(
 
 		int targetETable = data.getToEnergyTarget().getIdEnergyTable().intValue();
 		int colliderETable = data.getToEnergyCollider().getIdEnergyTable().intValue();
-		//LevelSet levels = rates.getMylevels();
+
 		LevelGroups lg=levelmap.get(rates.getLevelGroupID());
 
 		this.getReactants().add(