From fc0310de9834647a6f6bfa9c3f2230063f204136 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 20 Nov 2017 16:12:08 +0100
Subject: [PATCH] string<->species mapping is case insensitive
this is used by ColorSchemaReader
---
.../celldesigner/species/SpeciesMapping.java | 414 +++++++++---------
.../species/SpeciesMappingTest.java | 167 +++----
2 files changed, 294 insertions(+), 287 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
index 933c6486fd..20a0223130 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
@@ -1,207 +1,207 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Unknown;
-
-/**
- * This enum contains information about mapping between CellDesigner xml nodes
- * and classes that extend {@link CellDesignerSpecies}.
- *
- * @author Piotr Gawron
- *
- */
-public enum SpeciesMapping {
- /**
- * {@link Protein}.
- */
- PROTEIN(CellDesignerProtein.class, Protein.class, "PROTEIN"), //
-
- /**
- * {@link Gene}.
- */
- GENE(CellDesignerGene.class, Gene.class, "GENE"), //
-
- /**
- * {@link ComplexSpecies}.
- */
- COMPLEX(CellDesignerComplexSpecies.class, Complex.class, "COMPLEX"), //
-
- /**
- * {@link SimpleMolecule}.
- */
- SIMPLE_MOLECULE(CellDesignerSimpleMolecule.class, SimpleMolecule.class, "SIMPLE_MOLECULE"), //
-
- /**
- * {@link Ion}.
- */
- ION(CellDesignerIon.class, Ion.class, "ION"), //
-
- /**
- * {@link Phenotype}.
- */
- PHENOTYPE(CellDesignerPhenotype.class, Phenotype.class, "PHENOTYPE"), //
-
- /**
- * {@link Drug}.
- */
- DRUG(CellDesignerDrug.class, Drug.class, "DRUG"), //
-
- /**
- * {@link Rna}.
- */
- RNA(CellDesignerRna.class, Rna.class, "RNA"), //
-
- /**
- * {@link AntisenseRna}.
- */
- ANTISENSE_RNA(CellDesignerAntisenseRna.class, AntisenseRna.class, "ANTISENSE_RNA"), //
-
- /**
- * {@link Unknown}.
- */
- UNKNOWN(CellDesignerUnknown.class, Unknown.class, "UNKNOWN"), //
-
- /**
- * {@link Degraded}.
- */
- DEGRADED(CellDesignerDegraded.class, Degraded.class, "DEGRADED");
-
- /**
- * CellDesigner xml node type.
- */
- private String cellDesignerString;
-
- /**
- * Class that should be used to represent cell designer node.
- */
- private Class<? extends CellDesignerSpecies<?>> cellDesignerClazz;
-
- /**
- * Model class that represent the species.
- */
- private Class<? extends Element> modelClazz;
-
- /**
- * Default constructor.
- *
- * @param cellDesignerClazz
- * {@link #clazz}
- * @param modelClazz
- * {@link #clazz class} in model corresponding to celldesigner object
- * @param cellDesignerString
- * {@link #cellDesignerString}
- */
- SpeciesMapping(Class<?> cellDesignerClazz, Class<? extends Element> modelClazz, String cellDesignerString) {
- this.cellDesignerString = cellDesignerString;
- this.setCellDesignerClazz(cellDesignerClazz);
- this.modelClazz = modelClazz;
- }
-
- /**
- * Sets new cellDesignerClazz value.
- *
- * @param cellDesignerClazz2
- * new cellDesignerClazz value
- */
- @SuppressWarnings("unchecked")
- private void setCellDesignerClazz(Class<?> cellDesignerClazz2) {
- cellDesignerClazz = (Class<? extends CellDesignerSpecies<?>>) cellDesignerClazz2;
- }
-
- /**
- * @return the cellDesignerString
- * @see #cellDesignerString
- */
- public String getCellDesignerString() {
- return cellDesignerString;
- }
-
- /**
- * @return the clazz
- * @see #clazz
- */
- public Class<? extends CellDesignerSpecies<?>> getCellDesignerClazz() {
- return cellDesignerClazz;
- }
-
- /**
- * Returns model class that represent the species.
- *
- * @return model class that represent the species
- */
- public Class<? extends Element> getModelClazz() {
- return modelClazz;
- }
-
- /**
- * Creates instance of {@link CellDesignerSpecies} specific for this
- * {@link SpeciesMapping}.
- *
- * @param result
- * parameter that should be passed to the constructor
- * @return new instance of {@link CellDesignerSpecies} specific for this
- * {@link SpeciesMapping}.
- */
- public CellDesignerSpecies<?> createSpecies(CellDesignerSpecies<?> result) {
- try {
- return cellDesignerClazz.getConstructor(result.getClass()).newInstance(result);
- } catch (Exception e) {
- throw new InvalidStateException(e);
- }
- }
-
- /**
- * Returns {@link SpeciesMapping} for given CellDesigner xml node name.
- *
- * @param string
- * CellDesigner xml node name
- * @return {@link SpeciesMapping} for given CellDesigner xml node name
- */
- public static SpeciesMapping getMappingByString(String string) {
- for (SpeciesMapping mapping : SpeciesMapping.values()) {
- if (mapping.getCellDesignerString().equals(string)) {
- return mapping;
- }
- }
- return null;
- }
-
- /**
- * Returns {@link SpeciesMapping} for given {@link CellDesignerSpecies} class.
- *
- * @param searchClazz
- * {@link CellDesignerSpecies} class
- * @return {@link SpeciesMapping} for given {@link CellDesignerSpecies} class
- */
- public static SpeciesMapping getMappingByModelClass(Class<? extends Element> searchClazz) {
- for (SpeciesMapping mapping : SpeciesMapping.values()) {
- if (mapping.getModelClazz().isAssignableFrom(searchClazz)) {
- return mapping;
- }
- }
- return null;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+/**
+ * This enum contains information about mapping between CellDesigner xml nodes
+ * and classes that extend {@link CellDesignerSpecies}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum SpeciesMapping {
+ /**
+ * {@link Protein}.
+ */
+ PROTEIN(CellDesignerProtein.class, Protein.class, "PROTEIN"), //
+
+ /**
+ * {@link Gene}.
+ */
+ GENE(CellDesignerGene.class, Gene.class, "GENE"), //
+
+ /**
+ * {@link ComplexSpecies}.
+ */
+ COMPLEX(CellDesignerComplexSpecies.class, Complex.class, "COMPLEX"), //
+
+ /**
+ * {@link SimpleMolecule}.
+ */
+ SIMPLE_MOLECULE(CellDesignerSimpleMolecule.class, SimpleMolecule.class, "SIMPLE_MOLECULE"), //
+
+ /**
+ * {@link Ion}.
+ */
+ ION(CellDesignerIon.class, Ion.class, "ION"), //
+
+ /**
+ * {@link Phenotype}.
+ */
+ PHENOTYPE(CellDesignerPhenotype.class, Phenotype.class, "PHENOTYPE"), //
+
+ /**
+ * {@link Drug}.
+ */
+ DRUG(CellDesignerDrug.class, Drug.class, "DRUG"), //
+
+ /**
+ * {@link Rna}.
+ */
+ RNA(CellDesignerRna.class, Rna.class, "RNA"), //
+
+ /**
+ * {@link AntisenseRna}.
+ */
+ ANTISENSE_RNA(CellDesignerAntisenseRna.class, AntisenseRna.class, "ANTISENSE_RNA"), //
+
+ /**
+ * {@link Unknown}.
+ */
+ UNKNOWN(CellDesignerUnknown.class, Unknown.class, "UNKNOWN"), //
+
+ /**
+ * {@link Degraded}.
+ */
+ DEGRADED(CellDesignerDegraded.class, Degraded.class, "DEGRADED");
+
+ /**
+ * CellDesigner xml node type.
+ */
+ private String cellDesignerString;
+
+ /**
+ * Class that should be used to represent cell designer node.
+ */
+ private Class<? extends CellDesignerSpecies<?>> cellDesignerClazz;
+
+ /**
+ * Model class that represent the species.
+ */
+ private Class<? extends Element> modelClazz;
+
+ /**
+ * Default constructor.
+ *
+ * @param cellDesignerClazz
+ * {@link #clazz}
+ * @param modelClazz
+ * {@link #clazz class} in model corresponding to CellDesigner object
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ */
+ SpeciesMapping(Class<?> cellDesignerClazz, Class<? extends Element> modelClazz, String cellDesignerString) {
+ this.cellDesignerString = cellDesignerString;
+ this.setCellDesignerClazz(cellDesignerClazz);
+ this.modelClazz = modelClazz;
+ }
+
+ /**
+ * Sets new cellDesignerClazz value.
+ *
+ * @param cellDesignerClazz2
+ * new cellDesignerClazz value
+ */
+ @SuppressWarnings("unchecked")
+ private void setCellDesignerClazz(Class<?> cellDesignerClazz2) {
+ cellDesignerClazz = (Class<? extends CellDesignerSpecies<?>>) cellDesignerClazz2;
+ }
+
+ /**
+ * @return the cellDesignerString
+ * @see #cellDesignerString
+ */
+ public String getCellDesignerString() {
+ return cellDesignerString;
+ }
+
+ /**
+ * @return the clazz
+ * @see #clazz
+ */
+ public Class<? extends CellDesignerSpecies<?>> getCellDesignerClazz() {
+ return cellDesignerClazz;
+ }
+
+ /**
+ * Returns model class that represent the species.
+ *
+ * @return model class that represent the species
+ */
+ public Class<? extends Element> getModelClazz() {
+ return modelClazz;
+ }
+
+ /**
+ * Creates instance of {@link CellDesignerSpecies} specific for this
+ * {@link SpeciesMapping}.
+ *
+ * @param result
+ * parameter that should be passed to the constructor
+ * @return new instance of {@link CellDesignerSpecies} specific for this
+ * {@link SpeciesMapping}.
+ */
+ public CellDesignerSpecies<?> createSpecies(CellDesignerSpecies<?> result) {
+ try {
+ return cellDesignerClazz.getConstructor(result.getClass()).newInstance(result);
+ } catch (Exception e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ /**
+ * Returns {@link SpeciesMapping} for given CellDesigner xml node name.
+ *
+ * @param string
+ * CellDesigner xml node name
+ * @return {@link SpeciesMapping} for given CellDesigner xml node name
+ */
+ public static SpeciesMapping getMappingByString(String string) {
+ for (SpeciesMapping mapping : SpeciesMapping.values()) {
+ if (mapping.getCellDesignerString().equalsIgnoreCase(string)) {
+ return mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns {@link SpeciesMapping} for given {@link CellDesignerSpecies} class.
+ *
+ * @param searchClazz
+ * {@link CellDesignerSpecies} class
+ * @return {@link SpeciesMapping} for given {@link CellDesignerSpecies} class
+ */
+ public static SpeciesMapping getMappingByModelClass(Class<? extends Element> searchClazz) {
+ for (SpeciesMapping mapping : SpeciesMapping.values()) {
+ if (mapping.getModelClazz().isAssignableFrom(searchClazz)) {
+ return mapping;
+ }
+ }
+ return null;
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
index 2b76440dfc..75f64f4d76 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
@@ -1,80 +1,87 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.*;
-
-import java.lang.reflect.Field;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.model.map.species.Protein;
-
-public class SpeciesMappingTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
-
- @Test
- public void testAllValues() {
- for (SpeciesMapping value : SpeciesMapping.values()) {
- assertNotNull(SpeciesMapping.valueOf(value.toString()));
- }
- }
-
- @Test
- public void testCreateInvalidSpeciesImpl() throws Exception {
- // artificial implementation of Species that is invalid
- class InvalidSpecies extends CellDesignerSpecies<Protein> {
- private static final long serialVersionUID = 1L;
-
- @SuppressWarnings("unused")
- public InvalidSpecies() {
- throw new NotImplementedException();
- }
- }
-
- // mopdify one of the elements of SpeciesMapping so it will have invalid
- // implementation
- SpeciesMapping typeToModify = SpeciesMapping.ANTISENSE_RNA;
- Class<? extends CellDesignerSpecies<?>> clazz = typeToModify.getCellDesignerClazz();
-
- try {
- Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
- field.setAccessible(true);
- field.set(typeToModify, InvalidSpecies.class);
-
- // and check if we catch properly information about problematic
- // implementation
- typeToModify.createSpecies(new CellDesignerSpecies<Protein>());
- fail("Exceptione expected");
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore correct values for the modified type (if not then other test
- // might fail...)
- Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
- field.setAccessible(true);
- field.set(typeToModify, clazz);
- }
-
- }
-
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.lang.reflect.Field;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class SpeciesMappingTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAllValues() {
+ for (SpeciesMapping value : SpeciesMapping.values()) {
+ assertNotNull(SpeciesMapping.valueOf(value.toString()));
+ }
+ }
+
+ @Test
+ public void testGetMappingByStringCaseInsensitive() throws Exception {
+ SpeciesMapping mapping = SpeciesMapping.getMappingByString("PHENOTYPE");
+ assertNotNull(mapping);
+ mapping = SpeciesMapping.getMappingByString("phenotype");
+ assertNotNull(mapping);
+ }
+
+ @Test
+ public void testCreateInvalidSpeciesImpl() throws Exception {
+ // artificial implementation of Species that is invalid
+ class InvalidSpecies extends CellDesignerSpecies<Protein> {
+ private static final long serialVersionUID = 1L;
+
+ @SuppressWarnings("unused")
+ public InvalidSpecies() {
+ throw new NotImplementedException();
+ }
+ }
+
+ // modify one of the elements of SpeciesMapping so it will have invalid
+ // implementation
+ SpeciesMapping typeToModify = SpeciesMapping.ANTISENSE_RNA;
+ Class<? extends CellDesignerSpecies<?>> clazz = typeToModify.getCellDesignerClazz();
+
+ try {
+ Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
+ field.setAccessible(true);
+ field.set(typeToModify, InvalidSpecies.class);
+
+ // and check if we catch properly information about problematic
+ // implementation
+ typeToModify.createSpecies(new CellDesignerSpecies<Protein>());
+ fail("Exceptione expected");
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore correct values for the modified type (if not then other test
+ // might fail...)
+ Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
+ field.setAccessible(true);
+ field.set(typeToModify, clazz);
+ }
+
+ }
+
+}
--
GitLab