export to CellDesigner properly handles new line characters

CHANGELOG

@@ -5,6 +5,8 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
     (#995)
   * Bug fix: clear button icon, refresh comments button and show overview 
     button icons were missing (regression 15.0.0~alpha.0)
+  * Bug fix: export to CellDesigner names with new line is properly handled
+    (#930)
 
 minerva (15.0.0~alpha.0) stable; urgency=medium
   * Improvement: logs provided for validation data model are structurized (#325)

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

@@ -33,13 +33,13 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
    * Default class logger.
    */
   @SuppressWarnings("unused")
-  private Logger logger = LogManager.getLogger(AbstractElementXmlParser.class.getName());
+  private Logger logger = LogManager.getLogger();
 
   /**
    * List of special strings in CellDesigner that should be translated into some
    * UTF characters.
    */
-  private List<Pair<String, String>> encodedStrings = new ArrayList<Pair<String, String>>();
+  private List<Pair<String, String>> encodedStrings = new ArrayList<>();
 
   /**
    * Parser of the notes that allows to extract additional structured data for the
@@ -51,61 +51,61 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
    * Default constructor.
    */
   protected AbstractElementXmlParser() {
-    encodedStrings.add(new Pair<String, String>("_underscore_", "_"));
-    encodedStrings.add(new Pair<String, String>("_BR_", "\n"));
-    encodedStrings.add(new Pair<String, String>("_br_", "\n"));
-    encodedStrings.add(new Pair<String, String>("_plus_", "+"));
-    encodedStrings.add(new Pair<String, String>("_minus_", "-"));
-    encodedStrings.add(new Pair<String, String>("_slash_", "/"));
-    encodedStrings.add(new Pair<String, String>("_space_", " "));
-    encodedStrings.add(new Pair<String, String>("_Alpha_", "Α"));
-    encodedStrings.add(new Pair<String, String>("_alpha_", "α"));
-    encodedStrings.add(new Pair<String, String>("_Beta_", "Β"));
-    encodedStrings.add(new Pair<String, String>("_beta_", "β"));
-    encodedStrings.add(new Pair<String, String>("_Gamma_", "Γ"));
-    encodedStrings.add(new Pair<String, String>("_gamma_", "γ"));
-    encodedStrings.add(new Pair<String, String>("_Delta_", "Δ"));
-    encodedStrings.add(new Pair<String, String>("_delta_", "δ"));
-    encodedStrings.add(new Pair<String, String>("_Epsilon_", "Ε"));
-    encodedStrings.add(new Pair<String, String>("_epsilon_", "ε"));
-    encodedStrings.add(new Pair<String, String>("_Zeta_", "Ζ"));
-    encodedStrings.add(new Pair<String, String>("_zeta_", "ζ"));
-    encodedStrings.add(new Pair<String, String>("_Eta_", "Η"));
-    encodedStrings.add(new Pair<String, String>("_eta_", "η"));
-    encodedStrings.add(new Pair<String, String>("_Theta_", "Θ"));
-    encodedStrings.add(new Pair<String, String>("_theta_", "θ"));
-    encodedStrings.add(new Pair<String, String>("_Iota_", "Ι"));
-    encodedStrings.add(new Pair<String, String>("_iota_", "ι"));
-    encodedStrings.add(new Pair<String, String>("_Kappa_", "Κ"));
-    encodedStrings.add(new Pair<String, String>("_kappa_", "κ"));
-    encodedStrings.add(new Pair<String, String>("_Lambda_", "Λ"));
-    encodedStrings.add(new Pair<String, String>("_lambda_", "λ"));
-    encodedStrings.add(new Pair<String, String>("_Mu_", "Μ"));
-    encodedStrings.add(new Pair<String, String>("_mu_", "μ"));
-    encodedStrings.add(new Pair<String, String>("_Nu_", "Ν"));
-    encodedStrings.add(new Pair<String, String>("_nu_", "ν"));
-    encodedStrings.add(new Pair<String, String>("_Xi_", "Ξ"));
-    encodedStrings.add(new Pair<String, String>("_xi_", "ξ"));
-    encodedStrings.add(new Pair<String, String>("_Omicron_", "Ο"));
-    encodedStrings.add(new Pair<String, String>("_omicron_", "ο"));
-    encodedStrings.add(new Pair<String, String>("_Pi_", "Π"));
-    encodedStrings.add(new Pair<String, String>("_pi_", "π"));
-    encodedStrings.add(new Pair<String, String>("_Rho_", "Ρ"));
-    encodedStrings.add(new Pair<String, String>("_rho_", "ρ"));
-    encodedStrings.add(new Pair<String, String>("_Sigma_", "Σ"));
-    encodedStrings.add(new Pair<String, String>("_sigma_", "σ"));
-    encodedStrings.add(new Pair<String, String>("_Tau_", "Τ"));
-    encodedStrings.add(new Pair<String, String>("_tau_", "τ"));
-    encodedStrings.add(new Pair<String, String>("_Upsilon_", "Υ"));
-    encodedStrings.add(new Pair<String, String>("_upsilon_", "υ"));
-    encodedStrings.add(new Pair<String, String>("_Phi_", "Φ"));
-    encodedStrings.add(new Pair<String, String>("_phi_", "φ"));
-    encodedStrings.add(new Pair<String, String>("_Chi_", "Χ"));
-    encodedStrings.add(new Pair<String, String>("_chi_", "χ"));
-    encodedStrings.add(new Pair<String, String>("_Psi_", "Ψ"));
-    encodedStrings.add(new Pair<String, String>("_psi_", "ψ"));
-    encodedStrings.add(new Pair<String, String>("_Omega_", "Ω"));
-    encodedStrings.add(new Pair<String, String>("_omega_", "ω"));
+    encodedStrings.add(new Pair<>("_underscore_", "_"));
+    encodedStrings.add(new Pair<>("_br_", "\n"));
+    encodedStrings.add(new Pair<>("_BR_", "\n"));
+    encodedStrings.add(new Pair<>("_plus_", "+"));
+    encodedStrings.add(new Pair<>("_minus_", "-"));
+    encodedStrings.add(new Pair<>("_slash_", "/"));
+    encodedStrings.add(new Pair<>("_space_", " "));
+    encodedStrings.add(new Pair<>("_Alpha_", "Α"));
+    encodedStrings.add(new Pair<>("_alpha_", "α"));
+    encodedStrings.add(new Pair<>("_Beta_", "Β"));
+    encodedStrings.add(new Pair<>("_beta_", "β"));
+    encodedStrings.add(new Pair<>("_Gamma_", "Γ"));
+    encodedStrings.add(new Pair<>("_gamma_", "γ"));
+    encodedStrings.add(new Pair<>("_Delta_", "Δ"));
+    encodedStrings.add(new Pair<>("_delta_", "δ"));
+    encodedStrings.add(new Pair<>("_Epsilon_", "Ε"));
+    encodedStrings.add(new Pair<>("_epsilon_", "ε"));
+    encodedStrings.add(new Pair<>("_Zeta_", "Ζ"));
+    encodedStrings.add(new Pair<>("_zeta_", "ζ"));
+    encodedStrings.add(new Pair<>("_Eta_", "Η"));
+    encodedStrings.add(new Pair<>("_eta_", "η"));
+    encodedStrings.add(new Pair<>("_Theta_", "Θ"));
+    encodedStrings.add(new Pair<>("_theta_", "θ"));
+    encodedStrings.add(new Pair<>("_Iota_", "Ι"));
+    encodedStrings.add(new Pair<>("_iota_", "ι"));
+    encodedStrings.add(new Pair<>("_Kappa_", "Κ"));
+    encodedStrings.add(new Pair<>("_kappa_", "κ"));
+    encodedStrings.add(new Pair<>("_Lambda_", "Λ"));
+    encodedStrings.add(new Pair<>("_lambda_", "λ"));
+    encodedStrings.add(new Pair<>("_Mu_", "Μ"));
+    encodedStrings.add(new Pair<>("_mu_", "μ"));
+    encodedStrings.add(new Pair<>("_Nu_", "Ν"));
+    encodedStrings.add(new Pair<>("_nu_", "ν"));
+    encodedStrings.add(new Pair<>("_Xi_", "Ξ"));
+    encodedStrings.add(new Pair<>("_xi_", "ξ"));
+    encodedStrings.add(new Pair<>("_Omicron_", "Ο"));
+    encodedStrings.add(new Pair<>("_omicron_", "ο"));
+    encodedStrings.add(new Pair<>("_Pi_", "Π"));
+    encodedStrings.add(new Pair<>("_pi_", "π"));
+    encodedStrings.add(new Pair<>("_Rho_", "Ρ"));
+    encodedStrings.add(new Pair<>("_rho_", "ρ"));
+    encodedStrings.add(new Pair<>("_Sigma_", "Σ"));
+    encodedStrings.add(new Pair<>("_sigma_", "σ"));
+    encodedStrings.add(new Pair<>("_Tau_", "Τ"));
+    encodedStrings.add(new Pair<>("_tau_", "τ"));
+    encodedStrings.add(new Pair<>("_Upsilon_", "Υ"));
+    encodedStrings.add(new Pair<>("_upsilon_", "υ"));
+    encodedStrings.add(new Pair<>("_Phi_", "Φ"));
+    encodedStrings.add(new Pair<>("_phi_", "φ"));
+    encodedStrings.add(new Pair<>("_Chi_", "Χ"));
+    encodedStrings.add(new Pair<>("_chi_", "χ"));
+    encodedStrings.add(new Pair<>("_Psi_", "Ψ"));
+    encodedStrings.add(new Pair<>("_psi_", "ψ"));
+    encodedStrings.add(new Pair<>("_Omega_", "Ω"));
+    encodedStrings.add(new Pair<>("_omega_", "ω"));
   }
 
   /**

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParserTest.java

+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertTrue;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+
+public class AbstractElementXmlParserTest extends CellDesignerTestFunctions {
+  Logger logger = LogManager.getLogger();
+
+  AbstractElementXmlParser<?, ?> parser = new ProteinXmlParser(null);
+  
+  @Test
+  public void testEncode() {
+    String encoded = parser.encodeName("\n");
+    assertTrue(encoded.contains("_br_"));
+  }
+
+}

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java

@@ -4,7 +4,9 @@ import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 
 @RunWith(Suite.class)
-@Suite.SuiteClasses({ AntisenseRnaXmlParserTest.class,
+@Suite.SuiteClasses({
+    AbstractElementXmlParserTest.class,
+    AntisenseRnaXmlParserTest.class,
     ComplexParserTest.class,
     GeneXmlParserTest.class,
     InternalModelSpeciesDataTest.class,
@@ -17,6 +19,7 @@ import org.junit.runners.Suite;
     SpeciesMappingTest.class,
     SpeciesSbmlParserTest.class,
 })
+
 public class AllSpeciesTests {
 
 }