Commit 1deccb1f authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch '930-uppercase-line-break-tags-in-sbgn-export' into 'master'

Resolve "Uppercase line break tags in SBGN export"

Closes #930

See merge request minerva/core!996
parents 8fd36e0a 0ea35cb7
......@@ -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)
......
......@@ -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"));
}
/**
......
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_"));
}
}
......@@ -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 {
}
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