From 4b9a0e62a87e23ee96f868481c8bda79cb1bf859 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 25 Jan 2018 14:38:47 +0100
Subject: [PATCH] there is uniform way of storing BioEntity id in color schema
---
.../mapviewer/commands/ColorModelCommand.java | 10 +-
.../commands/ColorModelCommandTest.java | 21 +-
.../model/map/layout/ColorSchema.java | 24 +-
.../model/map/layout/ColorSchemaTest.java | 4 +-
.../services/impl/LayoutService.java | 4 +-
.../services/utils/ColorSchemaReader.java | 6 +-
.../services/utils/ColorSchemaXlsxReader.java | 6 +-
.../mapviewer/services/AllServicesTests.java | 11 +-
.../services/impl/LayoutServiceTest2.java | 419 +++++++++---------
.../services/utils/ColorSchemaReaderTest.java | 2 +-
.../utils/ColorSchemaReaderXlsTest.java | 2 +-
.../utils/ColorSchemaReaderXlsxTest.java | 2 +-
12 files changed, 243 insertions(+), 268 deletions(-)
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index e66453a029..f6ff490e8d 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -134,10 +134,6 @@ public class ColorModelCommand extends ModelCommand {
return false;
}
- if (schema.getReactionIdentifier() != null
- && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
- return true;
- }
if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
@@ -155,7 +151,7 @@ public class ColorModelCommand extends ModelCommand {
}
}
- return false;
+ return true;
}
private boolean modelMatch(ModelData model, ColorSchema schema) {
@@ -270,10 +266,6 @@ public class ColorModelCommand extends ModelCommand {
}
}
- // if we have reaction id to match then reject
- if (schema.getReactionIdentifier() != null) {
- return false;
- }
return true;
} else {
return false;
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index 252d31a3c8..d240a93b7c 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -16,6 +16,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -136,7 +137,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Reaction re1 = model.getReactionByReactionId("re1");
Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
+ schema.setElementId("re1");
schema.setColor(Color.RED);
schemas.add(schema);
@@ -161,7 +162,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Reaction re2 = model.getReactionByReactionId("re2");
Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re2");
+ schema.setElementId("re2");
schema.setValue(-1.0);
schemas.add(schema);
@@ -267,7 +268,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model model = getModelForFile("testFiles/sample.xml", false);
Collection<ColorSchema> schemas = new ArrayList<>();
ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
+ schema.setElementId("re1");
schema.setLineWidth(3.0);
schema.setColor(Color.BLUE);
schema.setName("");
@@ -289,7 +290,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model model = getModelForFile("testFiles/sample.xml", false);
Collection<ColorSchema> schemas = new ArrayList<>();
ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
+ schema.setElementId("re1");
schema.setLineWidth(3.0);
schema.setColor(Color.BLUE);
schema.setName(null);
@@ -312,13 +313,13 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testAliasMatchWithReactionId() throws Exception {
+ public void testAliasMatchWithInvalidElementId() throws Exception {
try {
GenericColorSchema colorSchema = new GenericColorSchema();
colorSchema.setName(null);
- colorSchema.setReactionIdentifier("1");
+ colorSchema.setElementId("1");
- GenericProtein protein = new GenericProtein("id");
+ BioEntity protein = new GenericProtein("id");
protein.setName("test");
List<ColorSchema> schemas = new ArrayList<>();
@@ -328,7 +329,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
assertFalse(factory.match(protein, colorSchema));
- colorSchema.setReactionIdentifier(null);
+ colorSchema.setElementId(null);
assertTrue(factory.match(protein, colorSchema));
} catch (Exception e) {
@@ -368,7 +369,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re4");
+ schema.setElementId("re4");
schema.setName(null);
schema.setModelName(model.getName() + "XXX");
@@ -391,7 +392,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re4");
+ schema.setElementId("re4");
schema.setName(null);
schema.setModelName(model.getName());
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
index 0d185c7ad4..a8628a8345 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
@@ -7,6 +7,7 @@ import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
@@ -39,10 +40,8 @@ public abstract class ColorSchema implements Serializable {
private String modelName = null;
/**
- * Identifier of the reaction to change the color.
+ * Original identifier of the {@link BioEntity} to change the color.
*/
- private String reactionIdentifier = null;
-
private String elementId = null;
/**
@@ -112,7 +111,7 @@ public abstract class ColorSchema implements Serializable {
*/
protected ColorSchema(ColorSchema original) {
this.setName(original.getName());
- this.setReactionIdentifier(original.getReactionIdentifier());
+ this.setElementId(original.getElementId());
this.setReverseReaction(original.getReverseReaction());
this.setLineWidth(original.getLineWidth());
this.addCompartments(original.getCompartments());
@@ -366,23 +365,6 @@ public abstract class ColorSchema implements Serializable {
}
- /**
- * @return the reactionIdentifier
- * @see #reactionIdentifier
- */
- public String getReactionIdentifier() {
- return reactionIdentifier;
- }
-
- /**
- * @param reactionIdentifier
- * the reactionIdentifier to set
- * @see #reactionIdentifier
- */
- public void setReactionIdentifier(String reactionIdentifier) {
- this.reactionIdentifier = reactionIdentifier;
- }
-
/**
* @return the lineWidth
* @see #lineWidth
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
index afeb53d81f..717ca331c5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
@@ -62,8 +62,8 @@ public class ColorSchemaTest {
cs.setLineWidth(lineWidth);
assertEquals(lineWidth, cs.getLineWidth());
- cs.setReactionIdentifier(reactionIdentifier);
- assertEquals(reactionIdentifier, cs.getReactionIdentifier());
+ cs.setElementId(reactionIdentifier);
+ assertEquals(reactionIdentifier, cs.getElementId());
cs.setReverseReaction(reverseReaction);
assertEquals(reverseReaction, cs.getReverseReaction());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 3e56dd04c2..7177a69cbe 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -814,7 +814,7 @@ public class LayoutService implements ILayoutService {
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
- sb.append(schema.getReactionIdentifier() + "\t");
+ sb.append(schema.getElementId() + "\t");
} else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
sb.append(schema.getLineWidth() + "\t");
} else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
@@ -871,7 +871,7 @@ public class LayoutService implements ILayoutService {
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
- sb.append(schema.getReactionIdentifier() + "\t");
+ sb.append(schema.getElementId() + "\t");
} else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
sb.append(schema.getLineWidth() + "\t");
} else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 0176a0da7e..dcdacb20ab 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -638,12 +638,12 @@ public class ColorSchemaReader {
* @param schema
* {@link ColorSchema} where name should be set
* @param content
- * content of the cell where reaction identifieris stored
+ * content of the cell where reaction identifiers stored
*/
private void processReactionIdentifier(ColorSchema schema, String content) {
if (!content.isEmpty()) {
- schema.setReactionIdentifier(content);
+ schema.setElementId(content);
}
}
@@ -746,7 +746,7 @@ public class ColorSchemaReader {
if (schema.getModelName() != null) {
result.add(ColorSchemaColumn.MODEL_NAME);
}
- if (schema.getReactionIdentifier() != null) {
+ if (schema.getElementId() != null) {
result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
}
if (schema.getReverseReaction() != null) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
index be39f1a333..b1dc835219 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -224,7 +224,7 @@ public class ColorSchemaXlsxReader {
schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
}
if (reactionIdentifierColumn != null) {
- schema.setReactionIdentifier(row.getCell(reactionIdentifierColumn).getStringCellValue());
+ schema.setElementId(row.getCell(reactionIdentifierColumn).getStringCellValue());
}
if (lineWidthColumn != null) {
cell = row.getCell(lineWidthColumn);
@@ -271,7 +271,7 @@ public class ColorSchemaXlsxReader {
}
if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
- && schema.getReactionIdentifier() == null) {
+ && schema.getElementId() == null) {
throw new InvalidColorSchemaException(
"One of these columns values is obligatory: name, identifier, reactionIdentifier");
}
@@ -323,7 +323,7 @@ public class ColorSchemaXlsxReader {
if (schema.getModelName() != null) {
result.add(ColorSchemaColumn.MODEL_NAME);
}
- if (schema.getReactionIdentifier() != null) {
+ if (schema.getElementId() != null) {
result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
}
if (schema.getReverseReaction() != null) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
index 18f68071be..6b57e86398 100644
--- a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
@@ -12,12 +12,11 @@ import lcsb.mapviewer.services.view.AllViewTests;
@RunWith(Suite.class)
@SuiteClasses({ AllImplServiceTests.class, //
- AllOverlayTests.class, //
- AllSearchTests.class, //
- AllViewTests.class, //
- AllUtilsTests.class, //
+ AllOverlayTests.class, //
+ AllSearchTests.class, //
+ AllViewTests.class, //
+ AllUtilsTests.class, //
})
public class AllServicesTests {
-}
-;
\ No newline at end of file
+};
\ No newline at end of file
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index 0d39e9cb6d..1bf9bb3ab4 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -36,214 +36,215 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
import lcsb.mapviewer.services.utils.data.ColorSchemaType;
public class LayoutServiceTest2 {
- Logger logger = Logger.getLogger(LayoutServiceTest2.class);
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidPreprareTableResultForGeneric() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GenericColorSchema();
- cs.setColor(Color.CYAN);
- cs.addCompartment("BLA");
- cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
- cs.setLineWidth(3.3);
- cs.setMatches(2);
- cs.setName("UUU");
- cs.setReactionIdentifier("RE ID");
- cs.setReverseReaction(true);
- cs.addType(GenericProtein.class);
- cs.setValue(1111.1111);
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testValidPreprareTableResultForGeneVariation() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- GeneVariationColorSchema cs = new GeneVariationColorSchema();
- cs.setColor(Color.CYAN);
- cs.addCompartment("BLA");
- cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
- cs.setLineWidth(3.3);
- cs.setMatches(2);
- cs.setName("UUU");
- cs.setReactionIdentifier("RE ID");
- cs.setReverseReaction(true);
- cs.addType(GenericProtein.class);
- cs.setValue(1111.1111);
- GeneVariation gv = new GeneVariation();
- gv.setModifiedDna("C");
- gv.setContig("chr1");
- gv.setOriginalDna("T");
- gv.setPosition(12);
- gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
- gv.setReferenceGenomeVersion("hg19");
- cs.addGeneVariation(gv);
- GeneVariation gv2 = new GeneVariation();
- gv2.setModifiedDna("CC");
- gv2.setContig("chr2");
- gv2.setOriginalDna("TT");
- gv2.setPosition(124);
- gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
- gv2.setReferenceGenomeVersion("hg18");
- gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
- cs.addGeneVariation(gv2);
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyPreprareTableResultForGeneric() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GenericColorSchema();
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GeneVariationColorSchema();
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetLayoutAliasesForInvalidAlias() throws Exception {
- try {
-
- Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
-
- FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(fis).//
- async(false);
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader
- .readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
-
- ColorModelCommand command = new ColorModelCommand(model, schemas, colorExtractor);
- command.execute();
-
- command.getModifiedElements();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSchemaWithCompartments() throws Exception {
- try {
- FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
- for (ColorSchema colorSchema : schemas) {
- for (String string : colorSchema.getCompartments()) {
- assertNotNull(string);
- assertFalse(string.isEmpty());
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(LayoutServiceTest2.class);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidPreprareTableResultForGeneric() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GenericColorSchema();
+ cs.setColor(Color.CYAN);
+ cs.addCompartment("BLA");
+ cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+ cs.setLineWidth(3.3);
+ cs.setMatches(2);
+ cs.setName("UUU");
+ cs.setElementId("RE ID");
+ cs.setReverseReaction(true);
+ cs.addType(GenericProtein.class);
+ cs.setValue(1111.1111);
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testValidPreprareTableResultForGeneVariation() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ GeneVariationColorSchema cs = new GeneVariationColorSchema();
+ cs.setColor(Color.CYAN);
+ cs.addCompartment("BLA");
+ cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+ cs.setLineWidth(3.3);
+ cs.setMatches(2);
+ cs.setName("UUU");
+ cs.setElementId("RE ID");
+ cs.setReverseReaction(true);
+ cs.addType(GenericProtein.class);
+ cs.setValue(1111.1111);
+ GeneVariation gv = new GeneVariation();
+ gv.setModifiedDna("C");
+ gv.setContig("chr1");
+ gv.setOriginalDna("T");
+ gv.setPosition(12);
+ gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+ gv.setReferenceGenomeVersion("hg19");
+ cs.addGeneVariation(gv);
+ GeneVariation gv2 = new GeneVariation();
+ gv2.setModifiedDna("CC");
+ gv2.setContig("chr2");
+ gv2.setOriginalDna("TT");
+ gv2.setPosition(124);
+ gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+ gv2.setReferenceGenomeVersion("hg18");
+ gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
+ cs.addGeneVariation(gv2);
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyPreprareTableResultForGeneric() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GenericColorSchema();
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GeneVariationColorSchema();
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetLayoutAliasesForInvalidAlias() throws Exception {
+ try {
+
+ Model model = new CellDesignerXmlParser()
+ .createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
+
+ FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").//
+ directory("testDir").//
+ model(model).//
+ colorInputStream(fis).//
+ async(false);
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
+ TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
+
+ ColorModelCommand command = new ColorModelCommand(model, schemas, colorExtractor);
+ command.execute();
+
+ command.getModifiedElements();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSchemaWithCompartments() throws Exception {
+ try {
+ FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
+ for (ColorSchema colorSchema : schemas) {
+ for (String string : colorSchema.getCompartments()) {
+ assertNotNull(string);
+ assertFalse(string.isEmpty());
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 6b90443325..d5cc32a208 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -200,7 +200,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/reactionSchema.txt");
assertEquals(1, collection.size());
ColorSchema schema = collection.iterator().next();
- assertEquals("re1", schema.getReactionIdentifier());
+ assertEquals("re1", schema.getElementId());
assertEquals(3.0, schema.getLineWidth(), EPSILON);
assertEquals(Color.RED, schema.getColor());
} catch (Exception e) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
index 0c14891425..bcca8eab38 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
@@ -107,7 +107,7 @@ public class ColorSchemaReaderXlsTest extends ServiceTestFunctions {
Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xls", "reactionSchema");
assertEquals(1, collection.size());
ColorSchema schema = collection.iterator().next();
- assertEquals("re1", schema.getReactionIdentifier());
+ assertEquals("re1", schema.getElementId());
assertEquals(3.0, schema.getLineWidth(), EPSILON);
assertEquals(Color.RED, schema.getColor());
} catch (Exception e) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
index 05bec4e138..e80d01d43b 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
@@ -107,7 +107,7 @@ public class ColorSchemaReaderXlsxTest extends ServiceTestFunctions {
Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "reactionSchema");
assertEquals(1, collection.size());
ColorSchema schema = collection.iterator().next();
- assertEquals("re1", schema.getReactionIdentifier());
+ assertEquals("re1", schema.getElementId());
assertEquals(3.0, schema.getLineWidth(), EPSILON);
assertEquals(Color.RED, schema.getColor());
} catch (Exception e) {
--
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