From 3ab57631f2a608c316d7c22765552bee5ae4a418 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 25 Jul 2017 18:02:19 +0200
Subject: [PATCH] simple upload uses different color then min/max value of the
overlay
---
.../graphics/AbstractImageGenerator.java | 28 +++++++++++++++++--
.../converter/graphics/ConverterTest.java | 2 +-
.../bioEntity/BioEntityConverterImplTest.java | 2 +-
.../element/species/SpeciesConverterTest.java | 2 +-
.../reaction/ReactionConverterTest.java | 2 +-
frontend-js/src/main/js/ConfigurationType.js | 1 +
frontend-js/src/main/js/Functions.js | 20 +++++++------
frontend-js/src/main/js/ServerConnector.js | 18 ++++++++++++
frontend-js/src/main/js/map/data/User.js | 9 ++++++
frontend-js/src/test/js/Functions-test.js | 4 +--
.../commands/ClearColorModelCommand.java | 2 +-
.../mapviewer/commands/ColorExtractor.java | 13 +++++++--
.../commands/ColorModelCommandTest.java | 2 +-
.../model/user/ConfigurationElementType.java | 7 ++++-
.../java/lcsb/mapviewer/model/user/User.java | 24 ++++++++++++++++
persist/src/db/11/fix_db_20170725.sql | 2 ++
.../api/projects/ProjectRestImpl.java | 3 +-
.../mapviewer/api/users/UserRestImpl.java | 3 ++
.../services/impl/LayoutService.java | 12 ++++----
.../mapviewer/services/impl/UserService.java | 7 ++++-
.../services/utils/ColorSchemaReader.java | 2 +-
.../services/impl/LayoutServiceTest2.java | 2 +-
.../services/utils/ColorSchemaReaderTest.java | 2 +-
23 files changed, 135 insertions(+), 34 deletions(-)
create mode 100644 persist/src/db/11/fix_db_20170725.sql
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index 036d3b221f..bcd7da6eec 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -17,6 +17,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -68,7 +69,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*
*/
public abstract class AbstractImageGenerator {
-
+
/**
* Class that allows to check if element is visible (or transparent) when
* drawing. It's used to filter out invisible elements when drawing
@@ -205,6 +206,8 @@ public abstract class AbstractImageGenerator {
*/
private Color maxColor = Color.BLACK;
+ private Color simpleColor = Color.BLACK;
+
/**
* @param scale
* scale to set
@@ -533,6 +536,10 @@ public abstract class AbstractImageGenerator {
return maxColor;
}
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+
/**
* Returns {@link Color} that should be used for drawing overlays with
* minimum value.
@@ -566,6 +573,17 @@ public abstract class AbstractImageGenerator {
return this;
}
+ /**
+ * @param simpleColor
+ * simpleColor to set
+ * @return object with all parameters
+ * @see #simpleColor
+ */
+ public Params simpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ return this;
+ }
+
/**
* @return the sbgn
* @see #sbgn
@@ -585,6 +603,12 @@ public abstract class AbstractImageGenerator {
return this;
}
+ public Params colorExtractor(ColorExtractor colorExtractor) {
+ return minColor(colorExtractor.getMinColor()).//
+ maxColor(colorExtractor.getMaxColor()).//
+ simpleColor(colorExtractor.getSimpleColor());
+ }
+
}
/**
@@ -653,7 +677,7 @@ public abstract class AbstractImageGenerator {
this.level = params.getLevel();
this.scale = params.getScale();
- colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor());
+ colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
// set border frame extended by a margin
border = new Rectangle2D.Double(
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index 59f4964c75..13aac7e427 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -26,7 +26,7 @@ public class ConverterTest {
@Test
public void test() {
try {
- ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED, Color.BLUE);
new BioEntityConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
new BioEntityConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
new BioEntityConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);
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 206b3f332f..68060ae783 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
@@ -27,7 +27,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class BioEntityConverterImplTest {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@AfterClass
public static void tearDownAfterClass() throws Exception {
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 1bdacdc9d7..3b8f0499b3 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
@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class SpeciesConverterTest {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
index f5f2408841..6c54f92d23 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -40,7 +40,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class ReactionConverterTest extends GraphicsTestFunctions {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
diff --git a/frontend-js/src/main/js/ConfigurationType.js b/frontend-js/src/main/js/ConfigurationType.js
index defc30720f..aa792f821a 100644
--- a/frontend-js/src/main/js/ConfigurationType.js
+++ b/frontend-js/src/main/js/ConfigurationType.js
@@ -8,6 +8,7 @@ var ConfigurationType = {
LEGEND_FILES : "LEGEND_FILES",
MIN_COLOR_VAL : "MIN_COLOR_VAL",
MAX_COLOR_VAL : "MAX_COLOR_VAL",
+ SIMPLE_COLOR_VAL : "SIMPLE_COLOR_VAL",
SEARCH_DISTANCE : "SEARCH_DISTANCE",
USER_MANUAL_FILE : "USER_MANUAL_FILE",
};
diff --git a/frontend-js/src/main/js/Functions.js b/frontend-js/src/main/js/Functions.js
index 3d7acf87d5..de976d6f37 100644
--- a/frontend-js/src/main/js/Functions.js
+++ b/frontend-js/src/main/js/Functions.js
@@ -171,16 +171,22 @@ Functions.overlayToColor = function(elementOverlay) {
return Promise.reject("elementOverlay cannot be null!");
} else if (elementOverlay.color !== undefined && elementOverlay.color !== null) {
return Promise.resolve(self.intToColorString(elementOverlay.color.value));
- } else if (elementOverlay.value !== undefined && elementOverlay.value !== null) {
+ } else {
var ratio = 0;
var promiseColor = null;
- if (elementOverlay.value < 0) {
- ratio = -elementOverlay.value;
- promiseColor = ServerConnector.getMinOverlayColorInt();
+ if (elementOverlay.value !== undefined && elementOverlay.value !== null) {
+ if (elementOverlay.value < 0) {
+ ratio = -elementOverlay.value;
+ promiseColor = ServerConnector.getMinOverlayColorInt();
+ } else {
+ ratio = elementOverlay.value;
+ promiseColor = ServerConnector.getMaxOverlayColorInt();
+ }
} else {
- ratio = elementOverlay.value;
- promiseColor = ServerConnector.getMaxOverlayColorInt();
+ ratio = 1;
+ promiseColor = ServerConnector.getSimpleOverlayColorInt();
}
+
return promiseColor.then(function(color) {
ratio = 1 - ratio;
@@ -207,8 +213,6 @@ Functions.overlayToColor = function(elementOverlay) {
color = red | green | blue;
return self.intToColorString(color);
});
- } else {
- return Promise.reject(new Error("elementOverlay doesn't have neither color nor value set!"));
}
};
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 98798955d4..45af28dfb1 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -62,6 +62,24 @@ ServerConnector.getMinOverlayColorInt = function() {
});
};
+ServerConnector.getSimpleOverlayColorInt = function() {
+ var self = this;
+ var userColor;
+ return self.getLoggedUser().then(function(user) {
+ userColor = user.getSimpleColor();
+ return self.getConfigurationParam(ConfigurationType.SIMPLE_COLOR_VAL);
+ }).then(function(systemSimpleColor) {
+ var color = userColor;
+ if (userColor === null || userColor === undefined || userColor === "") {
+ color = systemSimpleColor;
+ }
+ color = parseInt(color, 16);
+ /* jslint bitwise: true */
+ color = (color & 0xFFFFFF);
+ return color;
+ });
+};
+
ServerConnector.getMaxOverlayColorInt = function() {
var self = this;
var userColor;
diff --git a/frontend-js/src/main/js/map/data/User.js b/frontend-js/src/main/js/map/data/User.js
index 48398247f9..cd41f7d7f9 100644
--- a/frontend-js/src/main/js/map/data/User.js
+++ b/frontend-js/src/main/js/map/data/User.js
@@ -13,6 +13,7 @@ function User(javaObject) {
this.setPrivileges(javaObject.privileges);
this.setMinColor(javaObject.minColor);
this.setMaxColor(javaObject.maxColor);
+ this.setSimpleColor(javaObject.simpleColor);
}
User.prototype.setLogin = function(login) {
@@ -63,6 +64,14 @@ User.prototype.getMinColor = function() {
return this._minColor;
};
+User.prototype.setSimpleColor = function(simpleColor) {
+ this._simpleColor = simpleColor;
+};
+
+User.prototype.getSimpleColor = function() {
+ return this._simpleColor;
+};
+
User.prototype.setMaxColor = function(maxColor) {
this._maxColor = maxColor;
};
diff --git a/frontend-js/src/test/js/Functions-test.js b/frontend-js/src/test/js/Functions-test.js
index c1c9dc2c3d..7951eb34d4 100644
--- a/frontend-js/src/test/js/Functions-test.js
+++ b/frontend-js/src/test/js/Functions-test.js
@@ -200,9 +200,7 @@ describe('functions', function() {
it('overlayToColor with invalid arg 2', function() {
return functions.overlayToColor({}).then(function(colorString) {
- throw new Error('Promise was unexpectedly fulfilled. Result: ' + colorString);
- }, function rejected(error) {
- assert.ok(error.message.indexOf("elementOverlay doesn't have neither color nor value set") >= 0);
+ assert.ok(colorString);
});
});
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
index 891434f015..64a211a664 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
@@ -26,7 +26,7 @@ public class ClearColorModelCommand extends ModelCommand {
*/
public ClearColorModelCommand(Model model) {
super(model);
- colorModelCommand = new ColorModelCommand(model, new ArrayList<>(), new ColorExtractor(Color.WHITE, Color.WHITE));
+ colorModelCommand = new ColorModelCommand(model, new ArrayList<>(), new ColorExtractor(Color.WHITE, Color.WHITE, Color.WHITE));
}
@Override
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
index 1a6d5d5d31..0638978854 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
@@ -24,6 +24,8 @@ public class ColorExtractor {
*/
private Color maxColor;
+ private Color simpleColor;
+
/**
* Default constructor.
*
@@ -34,12 +36,13 @@ public class ColorExtractor {
* Color that should be used for max values of
* {@link ColorSchema#value}
*/
- public ColorExtractor(Color minColor, Color maxColor) {
- if (minColor == null || maxColor == null) {
+ public ColorExtractor(Color minColor, Color maxColor, Color simpleColor) {
+ if (minColor == null || maxColor == null || simpleColor == null) {
throw new InvalidArgumentException("Parameters cannot be null");
}
this.minColor = minColor;
this.maxColor = maxColor;
+ this.simpleColor = simpleColor;
}
/**
@@ -53,6 +56,8 @@ public class ColorExtractor {
public Color getNormalizedColor(ColorSchema colorSchema) {
if (colorSchema.getColor() != null) {
return colorSchema.getColor();
+ } else if (colorSchema.getValue() == null) {
+ return simpleColor;
} else {
return getColorForValue(colorSchema.getValue());
}
@@ -93,4 +98,8 @@ public class ColorExtractor {
public Color getMaxColor() {
return maxColor;
}
+
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
}
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 14d934650b..8bc1cd05cb 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -31,7 +31,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class ColorModelCommandTest extends CommandTestFunctions {
Logger logger = Logger.getLogger(ColorModelCommandTest.class);
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index 71e8845ee3..8ff0f95344 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -126,7 +126,12 @@ public enum ConfigurationElementType {
/**
* Color used for positive overlay values.
*/
- MAX_COLOR_VAL("Overlay color for postive values", "0000FF", ConfigurationElementEditType.COLOR, false);
+ MAX_COLOR_VAL("Overlay color for postive values", "0000FF", ConfigurationElementEditType.COLOR, false),
+
+ /**
+ * Color used for undefined overlay values.
+ */
+ SIMPLE_COLOR_VAL("Overlay color when no values are defined", "00FF00", ConfigurationElementEditType.COLOR, false);
/**
* Default value of the configuration parameter (it will be used only when
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/User.java b/model/src/main/java/lcsb/mapviewer/model/user/User.java
index 3cc421f8f5..216c7837db 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -80,6 +80,13 @@ public class User implements Serializable {
*/
private Color maxColor;
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#SIMPLE_COLOR_VAL}. Used for coloring
+ * overlays without values and colors.
+ */
+ private Color simpleColor;
+
/**
* Is the user removed.
*/
@@ -309,4 +316,21 @@ public class User implements Serializable {
this.maxColor = maxColor;
}
+ /**
+ * @return the simpleColor
+ * @see #simpleColor
+ */
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+
+ /**
+ * @param simpleColor
+ * the simpleColor to set
+ * @see #simpleColor
+ */
+ public void setSimpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ }
+
}
diff --git a/persist/src/db/11/fix_db_20170725.sql b/persist/src/db/11/fix_db_20170725.sql
new file mode 100644
index 0000000000..37a66ace4e
--- /dev/null
+++ b/persist/src/db/11/fix_db_20170725.sql
@@ -0,0 +1,2 @@
+--simple color for coloring
+alter table user_table add column simplecolor bytea;
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index cba3a43808..41af2e14c2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -313,8 +313,7 @@ public class ProjectRestImpl extends BaseRestImpl {
level(level - Configuration.MIN_ZOOM_LEVEL).//
nested(false).// automatically set nested view as invalid
scale(scale).//
- minColor(colorExtractor.getMinColor()).//
- maxColor(colorExtractor.getMaxColor()).//
+ colorExtractor(colorExtractor).//
sbgn(topModel.getProject().isSbgnFormat()).//
model(colorModel);
if (overlay != null) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index 1aef78c3c4..bcd07b094b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -76,6 +76,7 @@ public class UserRestImpl {
columnsSet.add("email");
columnsSet.add("minColor");
columnsSet.add("maxColor");
+ columnsSet.add("simpleColor");
columnsSet.add("removed");
columnsSet.add("privileges");
} else {
@@ -105,6 +106,8 @@ public class UserRestImpl {
value = user.getMinColor();
} else if (column.equals("maxcolor")) {
value = user.getMaxColor();
+ } else if (column.equals("simplecolor")) {
+ value = user.getSimpleColor();
} else if (column.equals("removed")) {
value = user.isRemoved();
} else if (column.equals("privileges") && admin) {
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 d1b2df719b..78513655c6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -935,7 +935,7 @@ public class LayoutService implements ILayoutService {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
List<LightLayoutAliasView> result = new ArrayList<>();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -957,7 +957,7 @@ public class LayoutService implements ILayoutService {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
List<LightLayoutReactionView> result = new ArrayList<>();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -980,7 +980,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
return command.getModifiedElements();
} catch (InvalidColorSchemaException e) {
throw new InvalidStateException(e);
@@ -1002,7 +1002,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
List<FullLayoutAliasView> result = new ArrayList<>();
@@ -1059,7 +1059,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -1085,7 +1085,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
FullLayoutReactionViewFactory factory = new FullLayoutReactionViewFactory();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
index 15e752a460..25fa736447 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
@@ -473,11 +473,13 @@ public class UserService implements IUserService {
public ColorExtractor getColorExtractorForUser(User loggedUser) {
Color colorMin = null;
Color colorMax = null;
+ Color colorSimple = null;
if (loggedUser != null) {
User dbUser = getUserById(loggedUser.getId());
if (dbUser != null) {
colorMin = dbUser.getMinColor();
colorMax = dbUser.getMaxColor();
+ colorSimple = dbUser.getSimpleColor();
}
}
ColorParser parser = new ColorParser();
@@ -488,7 +490,10 @@ public class UserService implements IUserService {
if (colorMax == null) {
colorMax = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MAX_COLOR_VAL));
}
- return new ColorExtractor(colorMin, colorMax);
+ if (colorSimple == null) {
+ colorSimple = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.SIMPLE_COLOR_VAL));
+ }
+ return new ColorExtractor(colorMin, colorMax, colorSimple);
}
/**
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 94efeff004..3d856d3868 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -573,7 +573,7 @@ public class ColorSchemaReader {
String[] values = line.split("\t", -1);
ColorSchema schema = new GenericColorSchema();
processNameColumn(schema, values[0]);
- schema.setValue(1.0);
+ schema.setDescription("");
result.add(schema);
line = br.readLine();
}
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 3d409a1875..0d39e9cb6d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -37,7 +37,7 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaType;
public class LayoutServiceTest2 {
Logger logger = Logger.getLogger(LayoutServiceTest2.class);
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
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 38c9407b57..4553b58724 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -224,7 +224,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testColoring3() throws Exception {
try {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
Model model = getModelForFile("testFiles/coloring/protein_to_color.xml", false);
--
GitLab