Merge branch '329-select-mode-export-to-celldesigner-does-not-work' into 'master'

Resolve "Select mode: Export to CellDesigner does not work"

Closes #329

See merge request piotr.gawron/minerva!237

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java

@@ -7,6 +7,9 @@ import org.apache.log4j.Logger;
 
 import lcsb.mapviewer.model.map.modifier.Catalysis;
 import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.Trigger;
 import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
 import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
 import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -14,6 +17,9 @@ import lcsb.mapviewer.model.map.reaction.Modifier;
 public enum SBOTermModifierType {
   CATALYSIS(Catalysis.class, new String[] { "SBO:0000013" }), //
   INHIBITION(Inhibition.class, new String[] { "SBO:0000537" }), //
+  MODULATION(Modulation.class, new String[] { "SBO:0000594" }), //
+  PHYSICAL_STIMULATION(PhysicalStimulation.class, new String[] { "SBO:0000459" }), //
+  TRIGGER(Trigger.class, new String[] { "SBO:0000461" }), //
   UNKNOWN_CATALYSIS(UnknownCatalysis.class, new String[] { "SBO:0000462" }), //
   UNKNOWN_INHIBITION(UnknownInhibition.class, new String[] { "SBO:0000536" }), //
   ;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java

@@ -11,6 +11,9 @@ import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
 import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
 import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
 import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
 import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
 import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
 import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
@@ -18,22 +21,31 @@ import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
 import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
 import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction;
 import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
 
 public enum SBOTermReactionType {
+  DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }), //
+  HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }), //
+  KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }), //
+  NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }), //
+  POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }), //
+  REDUCED_MODULATION(ReducedModulationReaction.class, new String[] { "SBO:0000632" }), //
+  REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000411" }), //
+  REDUCED_TRIGGER(ReducedTriggerReaction.class, new String[] { "SBO:0000461" }), //
   STATE_TRANSITION(StateTransitionReaction.class, new String[] { "SBO:0000176" }), //
   TRANSCRIPTION(TranscriptionReaction.class, new String[] { "SBO:0000183" }), //
   TRANSLATION(TranslationReaction.class, new String[] { "SBO:0000184" }), //
   TRANSPORT(TransportReaction.class, new String[] { "SBO:0000185" }), //
-  KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }), //
-  UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }), //
-  HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }), //
-  DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }), //
   TRUNCATION(TruncationReaction.class, new String[] { "SBO:0000178" }), //
-  POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }), //
-  UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000170" }), //
-  NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }), //
   UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, new String[] { "SBO:0000169" }), //
+  UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000172" }), //
+  UNKNOWN_REDUCED_MODULATION(UnknownReducedModulationReaction.class, new String[] { "SBO:0000631" }), //
+  UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000170" }), //
+  UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, new String[] { "SBO:0000533" }), //
+  UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }), //
   ;
 
   private static Logger logger = Logger.getLogger(SBOTermReactionType.class);
@@ -60,7 +72,7 @@ public enum SBOTermReactionType {
       }
     }
     if (result == null) {
-      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for modifier");
+      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for reaction");
       result = StateTransitionReaction.class;
     }
     return result;

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java

@@ -151,10 +151,11 @@ public class SbmlReactionParserTest {
 
   @Test
   public void testParseUnknownPositiveInfluence() throws FileNotFoundException, InvalidInputDataExecption {
-    Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_positive_influence.xml"));
+    Model model = parser
+        .createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_positive_influence.xml"));
     Reaction reaction = model.getReactions().iterator().next();
     assertNotNull(reaction);
-    assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+    assertTrue("Invalid class type: " + reaction.getClass(), reaction instanceof UnknownPositiveInfluenceReaction);
   }
 
   @Test
@@ -167,7 +168,8 @@ public class SbmlReactionParserTest {
 
   @Test
   public void testParseUnknownNegativeInfluence() throws FileNotFoundException, InvalidInputDataExecption {
-    Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_negative_influence.xml"));
+    Model model = parser
+        .createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_negative_influence.xml"));
     Reaction reaction = model.getReactions().iterator().next();
     assertNotNull(reaction);
     assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);

converter-sbml/testFiles/small/reaction/self_reaction.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model id="TestGEN">
+    <annotation/>
+    <listOfCompartments>
+      <compartment constant="true" id="default" name="cell" sboTerm="SBO:0000290" size="1">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#">
+              <bqbiol:isVersionOf>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+                </rdf:Bag>
+              </bqbiol:isVersionOf>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="default" initialConcentration="1" id="s1588" name="NGFR" sboTerm="SBO:0000252">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#">
+              <bqbiol:isEncodedBy>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="urn:miriam:hgnc.symbol:NGFR"/>
+                </rdf:Bag>
+              </bqbiol:isEncodedBy>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfReactions>
+<reaction reversible="false" id="r2149" sboTerm="SBO:0000170">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#">
+              <bqbiol:isDescribedBy>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="urn:miriam:pubmed:22236693 "/>
+                </rdf:Bag>
+              </bqbiol:isDescribedBy>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="s1588" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="s1588" stoichiometry="1"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

converter-sbml/testFiles/small/reaction/unknown_positive_influence.xml

@@ -26,7 +26,7 @@
       </species>
     </listOfSpecies>
     <listOfReactions>
-      <reaction id="re1" sboTerm="SBO:0000170">
+      <reaction id="re1" sboTerm="SBO:0000172">
         <listOfReactants>
           <speciesReference species="s1" stoichiometry="1"/>
         </listOfReactants>

model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java

@@ -120,10 +120,10 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
     Set<Species> elementToAlign = new HashSet<>();
     Map<Compartment, Set<Element>> elementsByStaticCompartment = new HashMap<>();
     for (Element element : elements) {
-      if (element.getWidth()==0) {
+      if (element.getWidth() == 0) {
         element.setWidth(SPECIES_WIDTH);
         element.setHeight(SPECIES_HEIGHT);
-        
+
       }
       if (element.getCompartment() == null || element.getCompartment() == parent) {
         if (element instanceof Compartment) {
@@ -218,6 +218,11 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
 
     Point2D middle = getMiddlePoint(productElement.getCenter(), reactantElement.getCenter());
 
+    //for self reactions
+    if (productElement.equals(reactantElement)) {
+      middle.setLocation(middle.getX(), middle.getY() + 50);
+    }
+
     modifyProducts(reaction, middle);
     modifyReactants(reaction, middle);
     modifyModifiers(reaction, middle);