Merge branch '1204-compartment-identifier-alias' into 'devel_14.0.x'

Resolve "compartment alias identifiers in CD must have at least 2 characters"

See merge request !1095

CHANGELOG

@@ -3,6 +3,8 @@ minerva (14.0.11) stable; urgency=medium
     installations (#1207)
   * Bug fix: complex with no border was inproperly imported from CellDesigner 
     (#1198)
+  * Bug fix: export to CellDesigner deal with CellDesigner issue that does not
+    allow complex species alias to be shorter than 2 characters (#1204)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 30 Mar 2020 10:00:00 +0200
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java

@@ -8,6 +8,7 @@ import org.apache.logging.log4j.Logger;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@@ -268,4 +269,14 @@ public class CellDesignerElementCollection {
     return getModificationResidueId(mr.createModificationResidue(new Gene("X")), number);
   }
 
+  public String getCompartmentAliasId(Compartment ca) {
+    if (ca == null) {
+      return null;
+    }
+    if (ca.getElementId().length() >= 2) {
+      return ca.getElementId();
+    }
+    return "ca_prefix_issue_" + ca.getElementId();
+  }
+
 }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java

@@ -130,7 +130,7 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
     StringBuilder sb = new StringBuilder("");
 
     sb.append("<celldesigner:compartmentAlias ");
-    sb.append("id=\"" + compartment.getElementId() + "\" ");
+    sb.append("id=\"" + elements.getCompartmentAliasId(compartment) + "\" ");
     sb.append("compartment=\"" + elements.getElementId(compartment) + "\">\n");
 
     boolean bounds = true;

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java

@@ -139,7 +139,8 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
     } else if (state.equalsIgnoreCase("complexparentbrief")) {
       view = briefView;
     } else {
-      throw new InvalidXmlSchemaException(new ElementUtils().getElementTag(result)+"Don't know how to process state: " + state);
+      throw new InvalidXmlSchemaException(
+          new ElementUtils().getElementTag(result) + "Don't know how to process state: " + state);
     }
 
     if (view != null) {
@@ -195,10 +196,8 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
 
     Complex complexAlias = alias.getComplex();
 
-    String compartmentAliasId = null;
-    if (ca != null) {
-      compartmentAliasId = ca.getElementId();
-    }
+    String compartmentAliasId = elements.getCompartmentAliasId(ca);
+
     StringBuilder sb = new StringBuilder("");
     sb.append("<celldesigner:complexSpeciesAlias ");
     sb.append("id=\"" + alias.getElementId() + "\" ");

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java

@@ -179,10 +179,8 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
 
     Complex complex = species.getComplex();
 
-    String compartmentAliasId = null;
-    if (ca != null) {
-      compartmentAliasId = ca.getElementId();
-    }
+    String compartmentAliasId = elements.getCompartmentAliasId(ca);
+
     StringBuilder sb = new StringBuilder("");
     sb.append("<celldesigner:speciesAlias ");
     sb.append("id=\"" + species.getElementId() + "\" ");

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java

 package lcsb.mapviewer.converter.model.celldesigner.compartment;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.*;
 
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
 
 public class CompartmentParserTests extends CellDesignerTestFunctions {
   Logger logger = LogManager.getLogger(CompartmentParserTests.class);
@@ -48,4 +54,42 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
     assertEquals(1, model.getElements().size());
   }
 
+  @Test
+  public void testToXmlWithCompartmentIdNotRecognizedByCellDesigner() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    Compartment compartment = new SquareCompartment("c");
+    compartment.setName("xyz");
+    model.addElement(compartment);
+
+    Model model2 = super.serializeModel(model);
+    assertTrue(model2.getCompartments().get(0).getElementId().length() >= 2);
+  }
+
+  @Test
+  public void testToXmlWithCompartmentIdNotRecognizedByCellDesignerAndChildren() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    Compartment compartment = new SquareCompartment("c");
+    compartment.setName("xyz");
+    model.addElement(compartment);
+
+    Complex complex = new Complex("comp");
+    GenericProtein protein = new GenericProtein("prot1");
+    complex.addSpecies(protein);
+
+    model.addElement(complex);
+    model.addElement(protein);
+
+    compartment.addElement(complex);
+
+    GenericProtein protein2 = new GenericProtein("prot2");
+    compartment.addElement(protein2);
+    model.addElement(protein2);
+
+    Model model2 = super.serializeModel(model);
+    Compartment compartment2 = model2.getCompartments().get(0);
+
+    assertEquals(compartment2, model2.getElementByElementId("prot2").getCompartment());
+    assertEquals(compartment2, model2.getElementByElementId("comp").getCompartment());
+  }
+
 }