Merge branch '1088-allow-to-import-export-of-unit-of-information-to-sbml' into 'master'

Resolve "allow to import/export of unit of information to SBML"

Closes #1088

See merge request !1052

CHANGELOG

 minerva (15.0.0~beta.0) stable; urgency=medium
   * Feature removal: some custom fields (like transparency zoom level) are not
     exported to CellDesigner file (#1071)
+  * Small improvement: import/export to SBML of unit of information obtained
+    from SBGN source is supported (#1088)
   * Bug fix: import from SBGN assigned invalid name to species that didn't have 
     label defined (#1093)
   * Bug fix: drawing protein in SBGN-like style didn't handle properly
     dimension of the species for multimers bigger than 2 (#1091)
+  * Bug fix: drawing of structural state in SBGN-like style uses
+    RoundedRectangle insetad of Ellipse which was not SBGN-compliant (#1095)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 28 Jan 2020 13:00:00 +0200
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java

@@ -37,6 +37,12 @@ public enum BioEntityFeature {
   ABBREVIATION("Abbreviation", null, new Class<?>[] { Element.class },
       "minerva_abbreviation_"),
 
+  STATE_PREFIX("State profix", null, new Class<?>[] { Element.class },
+      "minerva_state_prefix_"),
+
+  STATE_SUFFIX("State suffix", null, new Class<?>[] { Element.class },
+      "minerva_state_suffix_"),
+
   SYMBOL("Symbol", null, new Class<?>[] { Element.class },
       "minerva_symbol_");
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java

@@ -54,6 +54,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     assignListOfSynonymsToMulti(element, multiExtension, speciesType);
     assignListOfFormerSymbolsToMulti(element, multiExtension, speciesType);
     assignSymbolToMulti(element, multiExtension, speciesType);
+    assignStatePrefixToMulti(element, multiExtension, speciesType);
+    assignStateSuffixToMulti(element, multiExtension, speciesType);
     assignFullNameToMulti(element, multiExtension, speciesType);
     assignFormulaToMulti(element, multiExtension, speciesType);
     assignDimerToMulti(element, multiExtension, speciesType);
@@ -248,6 +250,20 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     }
   }
 
+  private void assignStatePrefixToMulti(Species element, MultiSpeciesPlugin multiExtension,
+      MultiSpeciesType speciesType) {
+    if (element.getStatePrefix() != null) {
+      assignValueToFeature(element, multiExtension, speciesType, element.getStatePrefix(), BioEntityFeature.STATE_PREFIX);
+    }
+  }
+
+  private void assignStateSuffixToMulti(Species element, MultiSpeciesPlugin multiExtension,
+      MultiSpeciesType speciesType) {
+    if (element.getStateLabel() != null) {
+      assignValueToFeature(element, multiExtension, speciesType, element.getStateLabel(), BioEntityFeature.STATE_SUFFIX);
+    }
+  }
+
   private void assignFullNameToMulti(Species element, MultiSpeciesPlugin multiExtension,
       MultiSpeciesType speciesType) {
     if (element.getFullName() != null) {

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java

@@ -116,6 +116,18 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
       } else {
         minervaElement.setSymbol(featureValues.get(0));
       }
+    } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.STATE_PREFIX)) {
+      if (featureValues.size() != 1) {
+        logger.warn(warnPrefix + "State prefix must have exactly one value");
+      } else {
+        minervaElement.setStatePrefix(featureValues.get(0));
+      }
+    } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.STATE_SUFFIX)) {
+      if (featureValues.size() != 1) {
+        logger.warn(warnPrefix + "State suffix must have exactly one value");
+      } else {
+        minervaElement.setStateLabel(featureValues.get(0));
+      }
     } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.FULL_NAME)) {
       if (featureValues.size() != 1) {
         logger.warn(warnPrefix + "Full name must have exactly one value");

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExport.java

@@ -49,7 +49,7 @@ public class ElementPropertiesExport extends SbmlTestFunctions {
 
     element = createProtein();
     element.setConstant(true);
-    data.add(createTestEntry("Constatnt", element));
+    data.add(createTestEntry("Constant", element));
 
     return data;
   }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java

@@ -74,6 +74,15 @@ public class ElementPropertiesExportToMultiTest extends SbmlTestFunctions {
     element.setSynonyms(Arrays.asList(new String[] { "syn 1", "s2" }));
     data.add(createTestEntry("Synonyms", element));
 
+    element = createProtein();
+    element.setStatePrefix("prefix1");
+    data.add(createTestEntry("State prefix", element));
+
+    element = createProtein();
+    element.setStatePrefix("state_suffix");
+    data.add(createTestEntry("State suffix", element));
+
+
     return data;
   }