Updates for comparment in compartments and reactions with phenotypes

.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <faceted-project>
+  <runtime name="Apache Tomcat v8.0"/>
   <installed facet="java" version="1.7"/>
   <installed facet="jst.utility" version="1.0"/>
 </faceted-project>

pom.xml

@@ -3,7 +3,7 @@
     <groupId>de.uni-rostock.sbi</groupId>
     <artifactId>BiVeS-Core</artifactId>
     <packaging>jar</packaging>
-    <version>1.9.5</version>
+    <version>1.9.8</version>
     <name>BiVeS-Core</name>
     <properties>
         <maven.compiler.source>1.6</maven.compiler.source>

src/main/java/de/unirostock/sems/bives/ds/graph/GraphTranslatorSbgnJson.java

@@ -208,7 +208,7 @@ public String translate (ReactionNetwork rn)
 		//add compartments
 		for (ReactionNetworkCompartment c : rn.getCompartments ()){
 			String path = getPath(c.getA(), c.getB(), c.getModification());
-			addCompartment(c.getId(), "null", c.getLabel(), c.getModification(), "SBO:0000290", path);
+			addCompartment(c.getId(), c.getOutsideCompartment(), c.getLabel(), c.getModification(), "SBO:0000290", path);
 		}
 
 		//add species 
@@ -238,6 +238,35 @@ public String translate (ReactionNetwork rn)
 
 			String rPath = getPath(r.getA(), r.getB(), r.getModification());
 
+			//handle phenotypes
+			//	no process node
+			// 	one or more modulation arcs
+			if (outputs.size() == 1) {
+				Collection<ReactionNetworkSubstanceRef> outs = outputs;
+				ReactionNetworkSubstanceRef o = outs.iterator().next();
+
+				String sbo = "";
+				if(o.getSubstance().getB() != null) {
+					if(o.getSubstance().getB().getAttributeValue("sboTerm") != null)
+							sbo = o.getSubstance().getB().getAttributeValue("sboTerm");
+				} else if (o.getSubstance().getA() != null) {
+					if(o.getSubstance().getA().getAttributeValue("sboTerm") != null)
+					sbo = o.getSubstance().getA().getAttributeValue("sboTerm");
+				}
+
+
+					if(sbo.equals("SBO:0000358")) {
+						for(ReactionNetworkSubstanceRef i : inputs) {
+							//allways nec. stim.
+							addEdge(i.getSubstance().getId(), o.getSubstance().getId(), "SBO:0000171", i.getModification(), i.getXPath());
+						}
+						continue;
+
+					}
+
+
+			}
+
 			//add process Node
 			String processId = r.getId();
 			String compartmentId = null;

src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkCompartment.java

@@ -23,10 +23,12 @@ public class ReactionNetworkCompartment
 	 * @param labelB the label of that compartment in the modified document
 	 * @param docA the original document
 	 * @param docB the modified document
+	 * @param outisdeA the compartment id of the containing compartment in the original document
+	 * @param outisdeB the compartment id of the containing compartment in the modified document
 	 */
-	public ReactionNetworkCompartment (ReactionNetwork rn, String labelA, String labelB, DocumentNode docA, DocumentNode docB)
+	public ReactionNetworkCompartment (ReactionNetwork rn, String labelA, String labelB, DocumentNode docA, DocumentNode docB, ReactionNetworkCompartment outsideA, ReactionNetworkCompartment outsideB)
 	{
-		super ("c" + rn.getNextCompartmentID (), labelA, labelB, docA, docB);
+		super ("c" + rn.getNextCompartmentID (), labelA, labelB, docA, docB, outsideA, outsideB);
 	}
 
 }

src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkEntity.java

@@ -32,6 +32,12 @@ public abstract class ReactionNetworkEntity
 	/** The single doc flag if in single-doc-operation-mode. */
 	protected boolean singleDoc;
 
+	/** Id of the containing compartment in original document **/
+	protected ReactionNetworkCompartment outsideA;
+
+	/** Id of the containing compartment in original document **/
+	protected ReactionNetworkCompartment outsideB;
+
 	/**
 	 * Instantiates a new entity.
 	 *
@@ -40,15 +46,19 @@ public abstract class ReactionNetworkEntity
 	 * @param labelB the label of that entity in the modified document
 	 * @param docA the original document
 	 * @param docB the modified document
+	 * @param compartmentB 
+	 * @param compartmentA 
 	 */
-	public ReactionNetworkEntity (String entityId, String labelA, String labelB, DocumentNode docA, DocumentNode docB)
+	public ReactionNetworkEntity (String entityId, String labelA, String labelB, DocumentNode docA, DocumentNode docB, ReactionNetworkCompartment compartmentA, ReactionNetworkCompartment compartmentB)
 	{
 		this.id = entityId;
 		this.labelA = labelA;
 		this.labelB = labelB;
 		this.docA = docA;
 		this.docB = docB;
 		singleDoc = false;
+		this.outsideA = compartmentA;
+		this.outsideB = compartmentB;
 	}
 
 	/**
@@ -91,6 +101,16 @@ public void setLabelB (String labelB)
 		this.labelB = labelB;
 	}
 
+	public void setOutsideA(ReactionNetworkCompartment compartmentA) {
+		this.outsideA = compartmentA;
+
+	}
+
+	public void setOutsideB(ReactionNetworkCompartment compartmentB) {
+		this.outsideB = compartmentB;
+	}
+
+
 	/**
 	 * Gets the original document node.
 	 *
@@ -157,6 +177,20 @@ public int getModification ()
 			return MODIFIED;
 		return UNMODIFIED;
 	}
+
+	public String getOutsideCompartment() {
+		if(outsideA == outsideB) {
+			if(outsideA == null) return null;
+			return outsideB.getId();
+		}
+		if(outsideA != null && outsideB != null)
+			return outsideB.getId();
+		if(outsideA == null && outsideB != null)
+			return outsideB.getId();
+		if(outsideA != null)
+			return outsideA.getId();
+		return null;
+	}
 
 	/**
 	 * Sets the single document flag.

src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkReaction.java

@@ -51,7 +51,7 @@ public class ReactionNetworkReaction
 	 */
 	public ReactionNetworkReaction (ReactionNetwork rn, String labelA, String labelB, DocumentNode docA, DocumentNode docB, ReactionNetworkCompartment compartmentA, ReactionNetworkCompartment compartmentB, boolean reversible)
 	{
-		super ("r" + rn.getNextReactionID (), labelA, labelB, docA, docB);
+		super ("r" + rn.getNextReactionID (), labelA, labelB, docA, docB, compartmentA, compartmentB);
 		in = new HashMap<ReactionNetworkSubstance, ReactionNetworkSubstanceRef> ();
 		out = new HashMap<ReactionNetworkSubstance, ReactionNetworkSubstanceRef> ();
 		mod = new Vector<ReactionNetworkSubstanceRef> ();
@@ -213,17 +213,19 @@ public void addModA (ReactionNetworkSubstance subst, SBOTerm sbo, String xPath)
 	 *
 	 * @param subst the substance
 	 * @param sbo the SBOTerm describing the interaction
+	 * @throws BivesUnsupportedException when SBO terms don't match
 	 */
-	public void addInputB (ReactionNetworkSubstance subst, SBOTerm sbo, String xPath)
+	public void addInputB (ReactionNetworkSubstance subst, SBOTerm sbo, String xPath) throws BivesUnsupportedException
 	{
 		ReactionNetworkSubstanceRef r = in.get (subst);
 		if (r == null)
 			try{
-				in.put (subst, new ReactionNetworkSubstanceRef (subst, false, true, null, sbo, xPath)); //checken
+				in.put (subst, new ReactionNetworkSubstanceRef (subst, false, true, null, sbo, xPath));
 			}catch (BivesUnsupportedException e){}
 		else
 		{
 			r.setFlagB (true);
+			r.setSboB(sbo);
 		}
 	}
 
@@ -232,8 +234,9 @@ public void addInputB (ReactionNetworkSubstance subst, SBOTerm sbo, String xPath
 	 *
 	 * @param subst the substance
 	 * @param sbo the SBOTerm describing the interaction
+	 * @throws BivesUnsupportedException when sbo terms don't match
 	 */
-	public void addOutputB (ReactionNetworkSubstance subst, SBOTerm sbo, String xPath)
+	public void addOutputB (ReactionNetworkSubstance subst, SBOTerm sbo, String xPath) throws BivesUnsupportedException
 	{
 		ReactionNetworkSubstanceRef r = out.get (subst);
 		if (r == null)
@@ -243,6 +246,7 @@ public void addOutputB (ReactionNetworkSubstance subst, SBOTerm sbo, String xPat
 		else
 		{
 			r.setFlagB (true);
+			r.setSboB(sbo);
 		}
 	}
 

src/main/java/de/unirostock/sems/bives/ds/rn/ReactionNetworkSubstance.java

@@ -30,7 +30,7 @@ public class ReactionNetworkSubstance
 	 */
 	public ReactionNetworkSubstance (ReactionNetwork rn, String labelA, String labelB, DocumentNode docA, DocumentNode docB, ReactionNetworkCompartment compartmentA, ReactionNetworkCompartment compartmentB)
 	{
-		super ("s" + rn.getNextSubstanceID (), labelA, labelB, docA, docB);
+		super ("s" + rn.getNextSubstanceID (), labelA, labelB, docA, docB, compartmentA, compartmentB);
 		this.compartmentA = compartmentA;
 		this.compartmentB = compartmentB;
 		singleDoc = false;

src/test/java/de/unirostock/sems/bives/TestGraphs.java

@@ -75,9 +75,9 @@ public ReactionNetworkCompartment addCompartment (DocumentNode node, String labe
 	{
 		ReactionNetworkCompartment compartment = null;
 		if (a)
-			compartment = new ReactionNetworkCompartment (crn, label, null, node, null);
+			compartment = new ReactionNetworkCompartment (crn, label, null, node, null, null, null);
 		else
-			compartment = new ReactionNetworkCompartment (crn, null, label, null, node);
+			compartment = new ReactionNetworkCompartment (crn, null, label, null, node, null, null);
 
 		crn.setCompartment (node, compartment);
 		return compartment;
@@ -183,8 +183,16 @@ public void testCrn ()
 		reaction1.setCompartmentB (compartment1);
 		reaction1.setLabelB ("reaction in A");
 		reaction1.setDocB (dummy);
-		reaction1.addInputB (substrate1, null, null);
-		reaction1.addOutputB (substrate1, null, null);
+		try {
+			reaction1.addInputB (substrate1, null, null);
+			reaction1.addOutputB (substrate1, null, null);
+		} 		
+		catch (BivesUnsupportedException e)
+		{
+			LOGGER.error (e, "this error wasn't expected!?");
+			fail ("this error wasn't expected!?");
+		}
+
 
 		assertEquals ("unexpected label in compartment", "compartment in A", compartment1.getLabel ());
 		assertEquals ("expected no modification", GraphEntity.UNMODIFIED, compartment1.getModification ());
@@ -209,8 +217,17 @@ public void testCrn ()
 		reaction1.setCompartmentB (compartment1);
 		reaction1.setLabelB ("reaction in N");
 		reaction1.setDocB (dummy);
-		reaction1.addInputB (substrate1, null, null);
-		reaction1.addOutputB (substrate1, null, null);
+
+		try 
+		{
+			reaction1.addInputB (substrate1, null, null);
+			reaction1.addOutputB (substrate1, null, null);
+		} 		
+		catch (BivesUnsupportedException e)
+		{
+			LOGGER.error (e, "this error wasn't expected!?");
+			fail ("this error wasn't expected!?");
+		}
 
 
 		assertFalse ("unexpected label in compartment", "compartment in A".equals (compartment1.getLabel ()));
@@ -233,8 +250,17 @@ public void testCrn ()
 		reaction1.setCompartmentB (compartment2);
 		reaction1.setLabelB ("reaction in N");
 		reaction1.setDocB (dummy);
-		reaction1.addInputB (substrate1, null, null);
-		reaction1.addOutputB (substrate1, null, null);
+
+		try
+		{
+			reaction1.addInputB (substrate1, null, null);
+			reaction1.addOutputB (substrate1, null, null);
+		} 		
+		catch (BivesUnsupportedException e)
+		{
+			LOGGER.error (e, "this error wasn't expected!?");
+			fail ("this error wasn't expected!?");
+		}
 
 
 		assertFalse ("unexpected label in substrate", "substrate in A".equals (substrate1.getLabel ()));
@@ -263,8 +289,17 @@ public void testCrn ()
 		reaction1.setCompartmentB (compartment1);
 		reaction1.setLabelB ("reaction in A");
 		reaction1.setDocB (dummy);
-		reaction1.addInputB (substrate1, null, null);
-		reaction1.addOutputB (substrate1, null, null);
+
+		try
+		{
+			reaction1.addInputB (substrate1, null, null);
+			reaction1.addOutputB (substrate1, null, null);
+		}		
+		catch (BivesUnsupportedException e)
+		{
+			LOGGER.error (e, "this error wasn't expected!?");
+			fail ("this error wasn't expected!?");
+		}
 
 		assertEquals ("unexpected label in compartment", "compartment in A", compartment1.getLabel ());
 		assertEquals ("expected no modification", GraphEntity.UNMODIFIED, compartment1.getModification ());
@@ -280,7 +315,16 @@ public void testCrn ()
 
 
 		// different i/o?
-		reaction1.addInputB (substrate2, null, null);
+		try
+		{
+			reaction1.addInputB (substrate2, null, null);
+		} 		
+		catch (BivesUnsupportedException e)
+		{
+			LOGGER.error (e, "this error wasn't expected!?");
+			fail ("this error wasn't expected!?");
+		}
+
 		reaction1.addOutputA (substrate2, null, null);
 		assertEquals ("unexpected label in compartment", "compartment in A", compartment1.getLabel ());
 		assertEquals ("expected no modification", GraphEntity.UNMODIFIED, compartment1.getModification ());