From b7067b12d72af52e771d35b483b2077fbc9df871 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 7 Jun 2019 13:52:00 +0200
Subject: [PATCH] allow empty type for data overlay
---
CHANGELOG | 1 +
.../services/utils/ColorSchemaReader.java | 22 ++++----
.../services/utils/ColorSchemaReaderTest.java | 50 ++++++-------------
3 files changed, 27 insertions(+), 46 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 34e4b4e661..bd089b970b 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -19,6 +19,7 @@ minerva (12.3.1~beta.1) unstable; urgency=low
info/submap panel (#824)
* Bug fix: when changing data in edit user dialog there was a need to click
close button twice (#818)
+ * Bug fix: empty type for data overlay is allowed (#827)
minerva (13.1.0~beta.0) unstable; urgency=low
* Feature: annotators are more flexible - you can define set of input and
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 3b2eb71dc6..40a7e31684 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -591,21 +591,23 @@ public class ColorSchemaReader {
return result;
}
- private List<Class<? extends Element>> parseSpeciesTypes(String typesString, String errorPrefix)
+ List<Class<? extends Element>> parseSpeciesTypes(String typesString, String errorPrefix)
throws InvalidColorSchemaException {
List<Class<? extends Element>> result = new ArrayList<>();
String[] types = typesString.split(",");
for (String string : types) {
- SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
- if (mapping != null) {
- result.add(mapping.getModelClazz());
- } else {
- String validStrings = "";
- for (SpeciesMapping speciesMapping : SpeciesMapping.values()) {
- validStrings += speciesMapping.getCellDesignerString() + ", ";
+ if (!string.isEmpty()) {
+ SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
+ if (mapping != null) {
+ result.add(mapping.getModelClazz());
+ } else {
+ String validStrings = "";
+ for (SpeciesMapping speciesMapping : SpeciesMapping.values()) {
+ validStrings += speciesMapping.getCellDesignerString() + ", ";
+ }
+ throw new InvalidColorSchemaException(
+ errorPrefix + "Unknown class type: " + string + ". Valid values are: " + validStrings);
}
- throw new InvalidColorSchemaException(
- errorPrefix + "Unknown class type: " + string + ". Valid values are: " + validStrings);
}
}
return result;
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 119fb25312..2f02c86852 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -17,6 +17,7 @@ import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.Collection;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import org.apache.commons.io.output.ByteArrayOutputStream;
@@ -28,19 +29,24 @@ import org.junit.Test;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GeneVariation;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
public class ColorSchemaReaderTest extends ServiceTestFunctions {
Logger logger = Logger.getLogger(ColorSchemaReaderTest.class);
+ ColorSchemaReader reader;
+
@Before
public void setUp() throws Exception {
+ reader = new ColorSchemaReader();
}
@After
@@ -50,8 +56,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testReadSchema() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/enricoData/ageing.txt");
assertNotNull(schemas);
@@ -81,8 +85,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
ByteArrayInputStream bin = new ByteArrayInputStream(data);
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema(bin,
TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
@@ -101,8 +103,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
ByteArrayInputStream bin = new ByteArrayInputStream(data);
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema(bin,
TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
@@ -140,8 +140,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
ByteArrayInputStream bin = new ByteArrayInputStream(data);
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema(bin,
TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
@@ -168,8 +166,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
ByteArrayInputStream bin = new ByteArrayInputStream(data);
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema(bin,
TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
@@ -188,8 +184,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
ByteArrayInputStream bin = new ByteArrayInputStream(data);
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema(bin,
TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
@@ -203,8 +197,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testReadInvalidGeneVariantsSchema() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
-
reader.readColorSchema("testFiles/coloring/gene_variants_invalid_genome.txt");
fail("Exception expected");
} catch (InvalidColorSchemaException e) {
@@ -217,8 +209,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testReadSchema2() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/goodSchema.txt");
assertNotNull(schemas);
@@ -234,7 +224,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
public void testReadSchema3() throws Exception {
try {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
reader.readColorSchema("testFiles/coloring/wrongSchema.txt");
fail("Excepion expected");
} catch (InvalidColorSchemaException e) {
@@ -248,7 +237,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testProblematicStephanSchema3() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
reader.readColorSchema("testFiles/coloring/problematicSchema.txt");
} catch (Exception e) {
e.printStackTrace();
@@ -259,7 +247,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testReadReactionSchema() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/reactionSchema.txt");
assertEquals(1, collection.size());
ColorSchema schema = collection.iterator().next();
@@ -275,8 +262,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test(timeout = 15000)
public void testNextVersionReadSchema() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/goodLayout.v=1.0.txt");
assertNotNull(schemas);
@@ -295,8 +280,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Model model = getModelForFile("testFiles/coloring/protein_to_color.xml", false);
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/problematicSchema.txt");
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
factory.execute();
@@ -312,7 +295,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testColoringWithValueOrColor() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
Map<String, String> params = new HashMap<>();
params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
@@ -331,7 +313,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testElementsByType() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
Map<String, String> params = new HashMap<>();
params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
@@ -349,7 +330,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testColoringWithInvalidValueAndColor() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
Map<String, String> params = new HashMap<>();
params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
@@ -366,7 +346,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testColoringWithEmptyColor() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
Map<String, String> params = new HashMap<>();
params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
@@ -383,7 +362,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testColoringWithInvalidValueAndColor2() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
Map<String, String> params = new HashMap<>();
params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
@@ -398,8 +376,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testSchemasWithId() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schemaWithIdentifiers.txt");
for (ColorSchema colorSchema : schemas) {
for (MiriamData md : colorSchema.getMiriamData()) {
@@ -417,9 +393,8 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testSchemasWithIdSnakeCase() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
-
- Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schema_with_identifiers_in_snake_case.txt");
+ Collection<ColorSchema> schemas = reader
+ .readColorSchema("testFiles/coloring/schema_with_identifiers_in_snake_case.txt");
for (ColorSchema colorSchema : schemas) {
for (MiriamData md : colorSchema.getMiriamData()) {
assertNotNull(md.getResource());
@@ -436,8 +411,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testSchemasWithEmptyNameAndId() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
-
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schemaIdWithoutName.txt");
for (ColorSchema colorSchema : schemas) {
for (MiriamData md : colorSchema.getMiriamData()) {
@@ -455,7 +428,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testSimpleNameSchemas() throws Exception {
try {
- ColorSchemaReader reader = new ColorSchemaReader();
String input = "#header\ns1\ns2\n";
Collection<ColorSchema> schemas = reader
.readSimpleNameColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
@@ -466,4 +438,10 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testParseSpeciesTypesForEmptyString() throws Exception {
+ List<Class<? extends Element>> classes = reader.parseSpeciesTypes("", null);
+ assertEquals(0, classes.size());
+ }
+
}
--
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