From 33b5a143c83b888106c98eef56be24fb6df93ac0 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 10 May 2019 18:36:45 +0200
Subject: [PATCH] problem with not drawing images on map upload fixed
---
.../bioEntity/element/ElementConverter.java | 2 +-
.../compartment/CompartmentConverter.java | 9 +-
.../element/species/SpeciesConverter.java | 11 +-
.../bioEntity/BioEntityConverterImplTest.java | 150 +++++++++++-------
.../element/species/SpeciesConverterTest.java | 14 +-
.../model/map/layout/graphics/Glyph.java | 2 +-
.../mapviewer/model/map/species/Element.java | 4 +-
.../model/map/species/ElementTest.java | 12 ++
8 files changed, 132 insertions(+), 72 deletions(-)
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
index 9a6e85e6ec..973cf072fc 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
@@ -43,7 +43,7 @@ public abstract class ElementConverter<T extends Element> extends BioEntityConve
* @throws DrawingException
* thrown when there is a problem with drawing
*/
- private void drawGlyph(T bioEntity, Graphics2D graphics) throws DrawingException {
+ protected void drawGlyph(T bioEntity, Graphics2D graphics) throws DrawingException {
try {
Image img = ImageIO.read(new ByteArrayInputStream(bioEntity.getGlyph().getFile().getFileContent()));
graphics.drawImage(img,
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
index 2c9b32cc90..4d630b573c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
@@ -179,7 +179,14 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
@Override
public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- drawImpl(alias, graphics, params);
+ logger.debug("Draw: "+alias.getElementId());
+ if (alias.getGlyph() != null) {
+ logger.debug("as glyph");
+ drawGlyph(alias, graphics);
+ } else {
+ logger.debug("without glyph");
+ drawImpl(alias, graphics, params);
+ }
Color oldColor = graphics.getColor();
int count = 0;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index 2aca0689bd..da4c75cc04 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -496,9 +496,16 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
@Override
- public void draw(T species, Graphics2D graphics, ConverterParams params,
+ public final void draw(T species, Graphics2D graphics, ConverterParams params,
List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- drawImpl(species, graphics, params);
+ logger.debug("Draw: "+species.getElementId());
+ if (species.getGlyph() != null) {
+ logger.debug("as glyph");
+ drawGlyph(species, graphics);
+ } else {
+ logger.debug("without glyph");
+ drawImpl(species, graphics, params);
+ }
Color oldColor = graphics.getColor();
int count = 0;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
index 68060ae783..4cd4aa512c 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
@@ -1,13 +1,23 @@
package lcsb.mapviewer.converter.graphics.bioEntity;
-import static org.mockito.Matchers.any;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyInt;
+import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import java.awt.Color;
+import java.awt.Desktop;
import java.awt.Graphics2D;
+import java.awt.Image;
import java.awt.geom.GeneralPath;
import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+import java.awt.image.ImageObserver;
+import java.io.File;
+import java.nio.file.Files;
+
+import javax.imageio.ImageIO;
import org.junit.After;
import org.junit.AfterClass;
@@ -17,7 +27,10 @@ import org.mockito.Mockito;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.GraphicsTestFunctions;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.modifier.Catalysis;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -25,74 +38,103 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
-public class BioEntityConverterImplTest {
+public class BioEntityConverterImplTest extends GraphicsTestFunctions{
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndReactantOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ Reaction reaction = createReaction(1.0);
+ reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
+
+ BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(0)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndProductOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ Reaction reaction = createReaction(1.0);
+ reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
- @Before
- public void setUp() throws Exception {
- }
+ BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
- @After
- public void tearDown() throws Exception {
- }
+ verify(graphics, times(0)).draw(any(GeneralPath.class));
- @Test
- public void testDrawReactionWithSemanticZoomingAndReactantOff() throws Exception {
- try {
- Graphics2D graphics = Mockito.mock(Graphics2D.class);
- Reaction reaction = createReaction(1.0);
- reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
+ } catch (Exception e) {
+ throw e;
+ }
+ }
- BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+ @Test
+ public void testDrawAliasWithGlyph() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = Mockito.spy(bi.createGraphics());
- verify(graphics, times(0)).draw(any(GeneralPath.class));
+ GenericProtein alias = createProtein();
+ Glyph glyph = new Glyph();
+ UploadedFileEntry file = new UploadedFileEntry();
+ file.setOriginalFileName("test");
+ byte[] fileContent = Files.readAllBytes(new File("testFiles/glyph.png").toPath());
- } catch (Exception e) {
- throw e;
- }
- }
+ file.setFileContent(fileContent);
+ glyph.setFile(file);
+ alias.setGlyph(glyph);
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(alias, false, colorExtractor);
+ converter.draw(alias, graphics, new ConverterParams());
- @Test
- public void testDrawReactionWithSemanticZoomingAndProductOff() throws Exception {
- try {
- Graphics2D graphics = Mockito.mock(Graphics2D.class);
- Reaction reaction = createReaction(1.0);
- reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
- BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+ verify(graphics, times(1)).drawImage(any(Image.class), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(),
+ anyInt(), anyInt(), nullable(ImageObserver.class));
- verify(graphics, times(0)).draw(any(GeneralPath.class));
- } catch (Exception e) {
- throw e;
- }
- }
+ } catch (Exception e) {
+ throw e;
+ }
+ }
- private Reaction createReaction(double lineWidth) {
- Reaction result = new Reaction();
+ private Reaction createReaction(double lineWidth) {
+ Reaction result = new Reaction();
- Modifier modifier = new Catalysis(new GenericProtein("s1"));
- modifier.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 80)));
- modifier.getLine().setWidth(lineWidth);
+ Modifier modifier = new Catalysis(new GenericProtein("s1"));
+ modifier.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 80)));
+ modifier.getLine().setWidth(lineWidth);
- Reactant reactant = new Reactant(new GenericProtein("s2"));
- reactant.setLine(new PolylineData(new Point2D.Double(90, 90), new Point2D.Double(10, 90)));
- reactant.getLine().setWidth(lineWidth);
- Product product = new Product(new GenericProtein("s3"));
- product.setLine(new PolylineData(new Point2D.Double(200, 90), new Point2D.Double(110, 90)));
- product.getLine().setWidth(lineWidth);
- result.addModifier(modifier);
- result.addProduct(product);
- result.addReactant(reactant);
- return result;
- }
+ Reactant reactant = new Reactant(new GenericProtein("s2"));
+ reactant.setLine(new PolylineData(new Point2D.Double(90, 90), new Point2D.Double(10, 90)));
+ reactant.getLine().setWidth(lineWidth);
+ Product product = new Product(new GenericProtein("s3"));
+ product.setLine(new PolylineData(new Point2D.Double(200, 90), new Point2D.Double(110, 90)));
+ product.getLine().setWidth(lineWidth);
+ result.addModifier(modifier);
+ result.addProduct(product);
+ result.addReactant(reactant);
+ return result;
+ }
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index 50fabb870e..12c1aa6efc 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -33,6 +33,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.GraphicsTestFunctions;
import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -49,7 +50,7 @@ import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
-public class SpeciesConverterTest {
+public class SpeciesConverterTest extends GraphicsTestFunctions{
Logger logger = Logger.getLogger(SpeciesConverterTest.class);
ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@@ -405,15 +406,4 @@ public class SpeciesConverterTest {
}
}
- private GenericProtein createProtein() {
- GenericProtein protein = new GenericProtein("id");
- protein.setName("NAME_OF_THE_ELEMENT");
- protein.setX(10);
- protein.setY(20);
- protein.setWidth(100);
- protein.setHeight(80);
- protein.setColor(Color.WHITE);
-
- return protein;
- }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java
index cbf530889c..d23576df24 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java
@@ -73,7 +73,7 @@ public class Glyph implements Serializable {
*/
public Glyph(Glyph original) {
// we should reference to the same file
- setFile(file);
+ setFile(original.getFile());
}
public UploadedFileEntry getFile() {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 6a4db28730..1d3ac88910 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -302,7 +302,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.formula = original.getFormula();
setVisibilityLevel(original.getVisibilityLevel());
setTransparencyLevel(original.getTransparencyLevel());
- setGlyph(new Glyph(original.getGlyph()));
+ if (original.getGlyph() != null) {
+ setGlyph(new Glyph(original.getGlyph()));
+ }
}
/**
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
index 29c629c7a0..0806862ac6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
@@ -130,6 +130,18 @@ public class ElementTest extends ModelTestFunctions {
}
}
+ @Test
+ public void testCopyWithoutGlyph() {
+ try {
+ GenericProtein protein = new GenericProtein();
+ Element copy = new GenericProtein(protein);
+ assertNull(copy.getGlyph());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testIncreaseBorder() {
try {
--
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