From 4edda6943cd9685ac9b5b851466a6d1996f5b48e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 15 Nov 2017 16:03:32 +0100
Subject: [PATCH] neutral color for data overlays is provided (by default it's
white, but it can be changed)
---
frontend-js/src/main/js/ConfigurationType.js | 1 +
frontend-js/src/main/js/Functions.js | 31 +-
frontend-js/src/main/js/ServerConnector.js | 8 +
frontend-js/src/main/js/map/data/User.js | 9 +
frontend-js/src/test/js/Functions-test.js | 189 +++---
.../src/test/js/ServerConnector-test.js | 7 +
.../configuration/token=MOCK_TOKEN_ID& | 2 +-
.../model/user/ConfigurationElementType.java | 411 ++++++------
.../java/lcsb/mapviewer/model/user/User.java | 625 +++++++++---------
persist/src/db/12.0.0/fix_db_20171115.sql | 3 +
.../mapviewer/api/users/UserRestImpl.java | 3 +
11 files changed, 676 insertions(+), 613 deletions(-)
diff --git a/frontend-js/src/main/js/ConfigurationType.js b/frontend-js/src/main/js/ConfigurationType.js
index 5e25a66b4f..5bb518bf03 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",
+ NEUTRAL_COLOR_VAL: "NEUTRAL_COLOR_VAL",
REQUEST_ACCOUNT_EMAIL: "REQUEST_ACCOUNT_EMAIL",
SIMPLE_COLOR_VAL: "SIMPLE_COLOR_VAL",
SEARCH_DISTANCE: "SEARCH_DISTANCE",
diff --git a/frontend-js/src/main/js/Functions.js b/frontend-js/src/main/js/Functions.js
index 6cbd327994..a369f12974 100644
--- a/frontend-js/src/main/js/Functions.js
+++ b/frontend-js/src/main/js/Functions.js
@@ -173,44 +173,49 @@ Functions.overlayToColor = function (elementOverlay) {
return Promise.resolve(self.intToColorString(elementOverlay.color.rgb));
} else {
var ratio = 0;
- var promiseColor = null;
+ var promiseColors;
if (elementOverlay.value !== undefined && elementOverlay.value !== null) {
if (elementOverlay.value < 0) {
ratio = -elementOverlay.value;
- promiseColor = ServerConnector.getMinOverlayColorInt();
+ promiseColors = [ServerConnector.getMinOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
} else {
ratio = elementOverlay.value;
- promiseColor = ServerConnector.getMaxOverlayColorInt();
+ promiseColors = [ServerConnector.getMaxOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
}
} else {
ratio = 1;
- promiseColor = ServerConnector.getSimpleOverlayColorInt();
+ promiseColors = [ServerConnector.getSimpleOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
}
- return promiseColor.then(function (color) {
+ return Promise.all(promiseColors).then(function (colors) {
+ var maxColor = colors[0];
+ var neutralColor = colors[1];
ratio = 1 - ratio;
var MAX_RED = 0xFF0000;
var MAX_GREEN = 0x00FF00;
var MAX_BLUE = 0x0000FF;
- var red = color & MAX_RED;
+ var red = maxColor & MAX_RED;
+ var neutralRed = neutralColor & MAX_RED;
- red = red + (MAX_RED - red) * ratio;
+ red = red + (neutralRed - red) * ratio;
red = parseInt(red);
- red = red & 0xFF0000;
+ red = red & MAX_RED;
- var green = color & MAX_GREEN;
- green = green + (MAX_GREEN - green) * ratio;
+ var green = maxColor & MAX_GREEN;
+ var neutralGreen = neutralColor & MAX_GREEN;
+ green = green + (neutralGreen - green) * ratio;
green = parseInt(green);
green = green & MAX_GREEN;
- var blue = color & MAX_BLUE;
- blue = blue + (MAX_BLUE - blue) * ratio;
+ var blue = maxColor & MAX_BLUE;
+ var neutralBlue = neutralColor & MAX_BLUE;
+ blue = blue + (neutralBlue - blue) * ratio;
blue = parseInt(blue);
blue = blue & MAX_BLUE;
- color = red | green | blue;
+ var color = red | green | blue;
return self.intToColorString(color);
});
}
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index fc63dd89a1..5dd2d408f4 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -110,6 +110,14 @@ ServerConnector.getMaxOverlayColorInt = function () {
});
};
+ServerConnector.getNeutralOverlayColorInt = function () {
+ var self = this;
+ return self.getLoggedUser().then(function (user) {
+ var userColor = user.getNeutralColor();
+ return self.returnUserOrSystemColor(userColor, self.getConfigurationParam(ConfigurationType.NEUTRAL_COLOR_VAL));
+ });
+};
+
ServerConnector.sendGetRequest = function (url, description) {
return this.sendRequest({
url: url,
diff --git a/frontend-js/src/main/js/map/data/User.js b/frontend-js/src/main/js/map/data/User.js
index b60a37cb38..2b22fadb81 100644
--- a/frontend-js/src/main/js/map/data/User.js
+++ b/frontend-js/src/main/js/map/data/User.js
@@ -22,6 +22,7 @@ function User(javaObject) {
this.setPreferences(javaObject.preferences);
this.setMinColor(javaObject.minColor);
this.setMaxColor(javaObject.maxColor);
+ this.setNeutralColor(javaObject.neutralColor);
this.setSimpleColor(javaObject.simpleColor);
}
@@ -86,6 +87,14 @@ User.prototype.getSimpleColor = function () {
return this._simpleColor;
};
+User.prototype.setNeutralColor = function (neutralColor) {
+ this._neutralColor = neutralColor;
+};
+
+User.prototype.getNeutralColor = function () {
+ return this._neutralColor;
+};
+
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 7951eb34d4..c1fb623227 100644
--- a/frontend-js/src/test/js/Functions-test.js
+++ b/frontend-js/src/test/js/Functions-test.js
@@ -1,141 +1,143 @@
"use strict";
+require('./mocha-config');
+
var functions = require('../../main/js/Functions');
var logger = require('./logger');
var assert = require('assert');
var originalNavigator = null;
-describe('functions', function() {
+describe('functions', function () {
- beforeEach(function() {
+ beforeEach(function () {
originalNavigator = global.navigator;
});
- afterEach(function() {
+ afterEach(function () {
global.navigator = originalNavigator;
});
- it('Point inside polygon 1', function() {
+ it('Point inside polygon 1', function () {
var point = {
- x : 123,
- y : 124
+ x: 123,
+ y: 124
};
var polygon = [];
polygon[0] = {
- x : 0,
- y : 0
+ x: 0,
+ y: 0
};
polygon[1] = {
- x : 100,
- y : 0
+ x: 100,
+ y: 0
};
polygon[2] = {
- x : 100,
- y : 100
+ x: 100,
+ y: 100
};
polygon[3] = {
- x : 0,
- y : 100
+ x: 0,
+ y: 100
};
assert.equal(false, functions.pointInsidePolygon(point, polygon));
});
- it('Point inside polygon 2', function() {
+ it('Point inside polygon 2', function () {
var point = {
- x : 123,
- y : 124
+ x: 123,
+ y: 124
};
var polygon = [];
polygon[0] = {
- x : 0,
- y : 0
+ x: 0,
+ y: 0
};
polygon[1] = {
- x : 1000,
- y : 0
+ x: 1000,
+ y: 0
};
polygon[2] = {
- x : 1000,
- y : 1000
+ x: 1000,
+ y: 1000
};
polygon[3] = {
- x : 0,
- y : 1000
+ x: 0,
+ y: 1000
};
assert.ok(functions.pointInsidePolygon(point, polygon));
});
- it('Point inside polygon 3', function() {
+ it('Point inside polygon 3', function () {
var point = {
- x : 20,
- y : 50
+ x: 20,
+ y: 50
};
var polygon = [];
polygon[0] = {
- x : 0,
- y : 0
+ x: 0,
+ y: 0
};
polygon[1] = {
- x : 100,
- y : 0
+ x: 100,
+ y: 0
};
polygon[2] = {
- x : 10,
- y : 50
+ x: 10,
+ y: 50
};
polygon[3] = {
- x : 100,
- y : 100
+ x: 100,
+ y: 100
};
polygon[4] = {
- x : 0,
- y : 100
+ x: 0,
+ y: 100
};
assert.equal(false, functions.pointInsidePolygon(point, polygon));
});
- it('Point inside polygon 4', function() {
+ it('Point inside polygon 4', function () {
var point = {
- x : 5,
- y : 50
+ x: 5,
+ y: 50
};
var polygon = [];
polygon[0] = {
- x : 0,
- y : 0
+ x: 0,
+ y: 0
};
polygon[1] = {
- x : 100,
- y : 0
+ x: 100,
+ y: 0
};
polygon[2] = {
- x : 10,
- y : 50
+ x: 10,
+ y: 50
};
polygon[3] = {
- x : 100,
- y : 100
+ x: 100,
+ y: 100
};
polygon[4] = {
- x : 0,
- y : 100
+ x: 0,
+ y: 100
};
assert.ok(functions.pointInsidePolygon(point, polygon));
});
- it('Integer to html color', function() {
+ it('Integer to html color', function () {
var integer = -16711936;
var color = functions.intToColorString(integer);
assert.equal(7, color.length);
assert.equal(color.charAt(0), '#');
});
- it('isInt', function() {
+ it('isInt', function () {
assert.ok(functions.isInt(12));
assert.ok(functions.isInt(-12));
assert.ok(functions.isInt(0));
@@ -144,11 +146,11 @@ describe('functions', function() {
assert.equal(functions.isInt(""), false);
});
- it('stackTrace', function() {
+ it('stackTrace', function () {
assert.ok(functions.stackTrace());
});
- it('getPosition', function() {
+ it('getPosition', function () {
var div = document.createElement('div');
div.scrollLeft = 0;
div.scrollTop = 0;
@@ -157,7 +159,7 @@ describe('functions', function() {
assert.equal(0, pos.y);
});
- it('isDomElement', function() {
+ it('isDomElement', function () {
assert.strictEqual(false, functions.isDomElement(12));
assert.strictEqual(false, functions.isDomElement(-12));
assert.strictEqual(false, functions.isDomElement(0));
@@ -168,43 +170,44 @@ describe('functions', function() {
assert.strictEqual(true, functions.isDomElement(document.createElement('div')));
});
- it('overlayToColor', function() {
- var overlay = {
- value : 0.5,
- };
- return functions.overlayToColor(overlay).then(function(colorString) {
- // check the format of the html color
- assert.equal(colorString.charAt(0), "#");
- assert.equal(colorString.length, 7);
+ describe('overlayToColor', function () {
+ it('positive value', function () {
+ var overlay = {
+ value: 0.5
+ };
+ return functions.overlayToColor(overlay).then(function (colorString) {
+ // check the format of the html color
+ assert.equal(colorString.charAt(0), "#");
+ assert.equal(colorString.length, 7);
+ });
});
- });
-
- it('overlayToColor 2', function() {
- var overlay = {
- value : -0.5,
- };
- return functions.overlayToColor(overlay).then(function(colorString) {
- // check the format of the html color
- assert.equal(colorString.charAt(0), "#");
- assert.equal(colorString.length, 7);
+ it('negative value', function () {
+ var overlay = {
+ value: -0.5
+ };
+ return functions.overlayToColor(overlay).then(function (colorString) {
+ // check the format of the html color
+ assert.equal(colorString.charAt(0), "#");
+ assert.equal(colorString.length, 7);
+ });
});
- });
-
- it('overlayToColor with invalid arg', function() {
- return functions.overlayToColor(null).then(function(colorString) {
- throw new Error('Promise was unexpectedly fulfilled. Result: ' + colorString);
- }, function rejected(error) {
- assert.ok(error.indexOf("cannot be null") >= 0);
+ it('invalid arg', function () {
+ return functions.overlayToColor(null).then(function (colorString) {
+ throw new Error('Promise was unexpectedly fulfilled. Result: ' + colorString);
+ }, function rejected(error) {
+ assert.ok(error.indexOf("cannot be null") >= 0);
+ });
});
- });
- it('overlayToColor with invalid arg 2', function() {
- return functions.overlayToColor({}).then(function(colorString) {
- assert.ok(colorString);
+ it('invalid arg 2', function () {
+ return functions.overlayToColor({}).then(function (colorString) {
+ assert.ok(colorString);
+ });
});
});
- it('bound with null params', function() {
+
+ it('bound with null params', function () {
var value = 12;
var result = functions.bound(value, 13, null);
assert.equal(result, 13);
@@ -214,17 +217,17 @@ describe('functions', function() {
assert.equal(result2, -1);
});
- it('browser detection simulation with unsupported detection browser', function() {
+ it('browser detection simulation with unsupported detection browser', function () {
var browser = functions.browser;
browser.init();
assert.equal(browser.name, "Unknown");
assert.equal(browser.version, "Unknown");
});
- it('browser detection simulation with IE', function() {
+ it('browser detection simulation with IE', function () {
global.navigator = {
- appName : 'Microsoft Internet Explorer',
- userAgent : "MSIE 7.0",
+ appName: 'Microsoft Internet Explorer',
+ userAgent: "MSIE 7.0"
};
var browser = functions.browser;
@@ -233,10 +236,10 @@ describe('functions', function() {
assert.equal(browser.version, "7.0");
});
- it('browser detection simulation with other', function() {
+ it('browser detection simulation with other', function () {
global.navigator = {
- appName : 'Netscape',
- userAgent : "Mozilla/5.0 (Windows NT 6.3; Trident/7.0; rv 11.0) like Gecko",
+ appName: 'Netscape',
+ userAgent: "Mozilla/5.0 (Windows NT 6.3; Trident/7.0; rv 11.0) like Gecko"
};
var browser = functions.browser;
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index c45b1b0ef2..754d45cfdc 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -363,4 +363,11 @@ describe('ServerConnector', function () {
});
});
+ it('getNeutralOverlayColorInt', function () {
+ return ServerConnector.getNeutralOverlayColorInt().then(function (color) {
+ assert.ok(color);
+ });
+ });
+
+
});
diff --git a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
index ef9880cdb9..0511d724fa 100644
--- a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"modelFormats":[{"handler":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser","extension":"xml","name":"CellDesigner SBML"},{"handler":"lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter","extension":"sbgn","name":"SBGN-ML"}],"elementTypes":[{"name":"Degraded","className":"lcsb.mapviewer.model.map.species.Degraded","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.IonChannelProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.TopSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Ion","className":"lcsb.mapviewer.model.map.species.Ion","parentClass":"lcsb.mapviewer.model.map.species.Chemical"},{"name":"Species","className":"lcsb.mapviewer.model.map.species.Species","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.RightSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Drug","className":"lcsb.mapviewer.model.map.species.Drug","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.Protein","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.TruncatedProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.PathwayCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"RNA","className":"lcsb.mapviewer.model.map.species.Rna","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Chemical","className":"lcsb.mapviewer.model.map.species.Chemical","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.Compartment","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.OvalCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.SquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Unknown","className":"lcsb.mapviewer.model.map.species.Unknown","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Element","className":"lcsb.mapviewer.model.map.species.Element","parentClass":"lcsb.mapviewer.model.map.BioEntity"},{"name":"Phenotype","className":"lcsb.mapviewer.model.map.species.Phenotype","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Complex","className":"lcsb.mapviewer.model.map.species.Complex","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Antisense RNA","className":"lcsb.mapviewer.model.map.species.AntisenseRna","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.ReceptorProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Simple molecule","className":"lcsb.mapviewer.model.map.species.SimpleMolecule","parentClass":"lcsb.mapviewer.model.map.species.Chemical"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.GenericProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Gene","className":"lcsb.mapviewer.model.map.species.Gene","parentClass":"lcsb.mapviewer.model.map.species.Species"}],"modificationStateTypes":{"PHOSPHORYLATED":{"commonName":"phosphorylated","abbreviation":"P"},"METHYLATED":{"commonName":"methylated","abbreviation":"Me"},"PALMYTOYLATED":{"commonName":"palmytoylated","abbreviation":"Pa"},"ACETYLATED":{"commonName":"acetylated","abbreviation":"Ac"},"SULFATED":{"commonName":"sulfated","abbreviation":"S"},"GLYCOSYLATED":{"commonName":"glycosylated","abbreviation":"G"},"PRENYLATED":{"commonName":"prenylated","abbreviation":"Pr"},"UBIQUITINATED":{"commonName":"ubiquitinated","abbreviation":"Ub"},"PROTONATED":{"commonName":"protonated","abbreviation":"H"},"HYDROXYLATED":{"commonName":"hydroxylated","abbreviation":"OH"},"MYRISTOYLATED":{"commonName":"myristoylated","abbreviation":"My"},"UNKNOWN":{"commonName":"unknown","abbreviation":"?"},"EMPTY":{"commonName":"empty","abbreviation":""},"DONT_CARE":{"commonName":"don't care","abbreviation":"*"}},"imageFormats":[{"handler":"lcsb.mapviewer.converter.graphics.PngImageGenerator","extension":"png","name":"PNG image"},{"handler":"lcsb.mapviewer.converter.graphics.PdfImageGenerator","extension":"pdf","name":"PDF"},{"handler":"lcsb.mapviewer.converter.graphics.SvgImageGenerator","extension":"svg","name":"SVG image"}],"plugins":[{"load-on-start":false,"url":"resources/js/plugins/empty.js"}],"annotators":[{"name":"Biocompendium","className":"lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://biocompendium.embl.de/"},{"name":"Chebi","className":"lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Chemical"],"url":"http://www.ebi.ac.uk/chebi/"},{"name":"Uniprot","className":"lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://www.uniprot.org/"},{"name":"Gene Ontology","className":"lcsb.mapviewer.annotation.services.annotators.GoAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Phenotype","lcsb.mapviewer.model.map.compartment.Compartment","lcsb.mapviewer.model.map.species.Complex"],"url":"http://amigo.geneontology.org/amigo"},{"name":"HGNC","className":"lcsb.mapviewer.annotation.services.annotators.HgncAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"http://www.genenames.org"},{"name":"Protein Data Bank","className":"lcsb.mapviewer.annotation.services.annotators.PdbAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"http://www.pdbe.org/"},{"name":"Recon 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modulation","className":"lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Translation","className":"lcsb.mapviewer.model.map.reaction.type.TranslationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Heterodimer association","className":"lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Transcription","className":"lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced trigger","className":"lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown negative influence","className":"lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Truncation","className":"lcsb.mapviewer.model.map.reaction.type.TruncationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Transport","className":"lcsb.mapviewer.model.map.reaction.type.TransportReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced trigger","className":"lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"State transition","className":"lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Positive influence","className":"lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced physical stimulation","className":"lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Boolean logic gate","className":"lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced modulation","className":"lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown transition","className":"lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Dissociation","className":"lcsb.mapviewer.model.map.reaction.type.DissociationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"}],"version":"11.0.4","mapTypes":[{"name":"Downstream 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(English)","uris":["urn:miriam:wikipedia.en"],"homepage":"http://en.wikipedia.org/wiki/Main_Page","registryIdentifier":"MIR:00000384"},"CHEBI":{"commonName":"Chebi","uris":["urn:miriam:obo.chebi","urn:miriam:chebi"],"homepage":"http://www.ebi.ac.uk/chebi/","registryIdentifier":"MIR:00000002"},"WIKIDATA":{"commonName":"Wikidata","uris":["urn:miriam:wikidata"],"homepage":"https://www.wikidata.org/","registryIdentifier":"MIR:00000549"},"REACTOME":{"commonName":"Reactome","uris":["urn:miriam:reactome"],"homepage":"http://www.reactome.org/","registryIdentifier":"MIR:00000018"},"EC":{"commonName":"Enzyme Nomenclature","uris":["urn:miriam:ec-code"],"homepage":"http://www.enzyme-database.org/","registryIdentifier":"MIR:00000004"},"UNIPROT_ISOFORM":{"commonName":"UniProt Isoform","uris":["urn:miriam:uniprot.isoform"],"homepage":"http://www.uniprot.org/","registryIdentifier":"MIR:00000388"},"OMIM":{"commonName":"Online Mendelian Inheritance in 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"},{"idObject":2,"type":"GOOGLE_ANALYTICS_IDENTIFIER","value":"","valueType":"STRING","commonName":"Google Analytics tracking ID used for statistics"},{"idObject":5,"type":"LOGO_TEXT","value":"University of Luxembourg","valueType":"STRING","commonName":"Logo description"},{"idObject":56,"type":"X_FRAME_DOMAIN","value":"http://localhost:8080/","valueType":"URL","commonName":"Domain allowed to connect via x-frame technology"},{"idObject":131,"type":"BIG_FILE_STORAGE_DIR","value":"minerva-big/","valueType":"STRING","commonName":"Path to store big files"},{"idObject":138,"type":"LEGEND_FILE_1","value":"resources/images/legend_a.png","valueType":"URL","commonName":"Legend 1 image file"},{"idObject":139,"type":"LEGEND_FILE_2","value":"resources/images/legend_b.png","valueType":"URL","commonName":"Legend 2 image file"},{"idObject":140,"type":"LEGEND_FILE_3","value":"resources/images/legend_c.png","valueType":"URL","commonName":"Legend 3 image file"},{"idObject":141,"type":"LEGEND_FILE_4","value":"resources/images/legend_d.png","valueType":"URL","commonName":"Legend 4 image file"},{"idObject":142,"type":"USER_MANUAL_FILE","value":"resources/other/user_guide.pdf","valueType":"URL","commonName":"User manual file"},{"idObject":205,"type":"MIN_COLOR_VAL","value":"FF0000","valueType":"COLOR","commonName":"Overlay color for negative values"},{"idObject":206,"type":"MAX_COLOR_VAL","value":"fbff00","valueType":"COLOR","commonName":"Overlay color for postive values"},{"idObject":218,"type":"SIMPLE_COLOR_VAL","value":"00ff40","valueType":"COLOR","commonName":"Overlay color when no values are defined"},{"idObject":239,"type":"NEUTRAL_COLOR_VAL","value":"0400ff","valueType":"COLOR","commonName":"Overlay color for value=0"}],"privilegeTypes":{"VIEW_PROJECT":{"commonName":"View project","valueType":"boolean","objectType":"Project"},"LAYOUT_MANAGEMENT":{"commonName":"Manage layouts","valueType":"boolean","objectType":"Project"},"PROJECT_MANAGEMENT":{"commonName":"Map management","valueType":"boolean","objectType":null},"CUSTOM_LAYOUTS":{"commonName":"Custom layouts","valueType":"int","objectType":null},"ADD_MAP":{"commonName":"Add project","valueType":"boolean","objectType":null},"LAYOUT_VIEW":{"commonName":"View layout","valueType":"boolean","objectType":"Layout"},"MANAGE_GENOMES":{"commonName":"Manage genomes","valueType":"boolean","objectType":null},"EDIT_COMMENTS_PROJECT":{"commonName":"Manage comments","valueType":"boolean","objectType":"Project"},"CONFIGURATION_MANAGE":{"commonName":"Manage configuration","valueType":"boolean","objectType":null},"USER_MANAGEMENT":{"commonName":"User management","valueType":"boolean","objectType":null}},"overlayTypes":[{"name":"GENERIC"},{"name":"GENETIC_VARIANT"}]}
\ No newline at end of file
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 fa8fb2c6d1..bd0d5a4c40 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -1,212 +1,221 @@
package lcsb.mapviewer.model.user;
/**
- * This enum defines all possible configuration parameter that are configurable
- * by the user.
+ * This enumerate defines all possible configuration parameter that are
+ * configurable by the user.
*
* @author Piotr Gawron
*
*/
public enum ConfigurationElementType {
- /**
- * Email address used for sending email from the system.
- */
- EMAIL_ADDRESS("E-mail address", "your.account@domain.com", ConfigurationElementEditType.EMAIL, true), //
-
- /**
- * Login for the email account.
- */
- EMAIL_LOGIN("E-mail server login", "your@login", ConfigurationElementEditType.STRING, true), //
-
- /**
- * Password for the email account.
- */
- EMAIL_PASSWORD("E-mail server password", "email.secret.password", ConfigurationElementEditType.PASSWORD, true), //
-
- /**
- * Address of the imap server.
- */
- EMAIL_IMAP_SERVER("IMAP server", "your.imap.domain.com", ConfigurationElementEditType.STRING, true), //
-
- /**
- * Address of the smtp server.
- */
- EMAIL_SMTP_SERVER("SMTP server", "your.smtp.domain.com", ConfigurationElementEditType.STRING, true), //
-
- /**
- * Port used for smtp connection (sending e-mails).
- */
- EMAIL_SMTP_PORT("SMTP port", "25", ConfigurationElementEditType.INTEGER, true), //
-
- /**
- * Default map that should be presented if no map is selected by user side.
- */
- DEFAULT_MAP("Default Project Id", "empty", ConfigurationElementEditType.STRING, false), //
-
- /**
- * Logo presented in the system.
- */
- LOGO_IMG("Logo icon", "udl.png", ConfigurationElementEditType.URL, false), //
-
- /**
- * Address connected to the logo.
- */
- LOGO_LINK("Logo link (after click)", "http://wwwen.uni.lu/", ConfigurationElementEditType.URL, false), //
-
- /**
- * Maximum distance (in pixels) that is allowed during finding closest element
- * on the map.
- */
- SEARCH_DISTANCE("Max distance for clicking on element (px)", "10", ConfigurationElementEditType.DOUBLE, false),
-
- /**
- * Email used for requesting an account (in client side).
- */
- REQUEST_ACCOUNT_EMAIL("Email used for requesting an account", "your.email@domain.com", ConfigurationElementEditType.EMAIL, false),
-
- /**
- * Max number of results in search box.
- */
- SEARCH_RESULT_NUMBER("Max number of results in search box. ", "100", ConfigurationElementEditType.INTEGER, false),
-
- /**
- * Google Analytics tracking ID used for statistics. This tracking ID should
- * look like "UA-000000-01". More information about tracking ID can be found
- * <a href="https://support.google.com/analytics/answer/1032385?hl=en"> here
- * </a>.
- */
- GOOGLE_ANALYTICS_IDENTIFIER("Google Analytics tracking ID used for statistics", "", ConfigurationElementEditType.STRING, false),
-
- /**
- * Description of the logo presented in the system.
- */
- LOGO_TEXT("Logo description", "University of Luxembourg", ConfigurationElementEditType.STRING, false),
-
- /**
- * Domain allowed to connect via x-frame technology.
- */
- X_FRAME_DOMAIN("Domain allowed to connect via x-frame technology", "", ConfigurationElementEditType.URL, false),
-
- /**
- * Relative directory (in webapps folder) where big files will be stored.
- */
- BIG_FILE_STORAGE_DIR("Path to store big files", "minerva-big/", ConfigurationElementEditType.STRING, false),
-
- /**
- * File where legend 1/4 is stored.
- */
- LEGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png", ConfigurationElementEditType.URL, false),
-
- /**
- * File where legend 2/4 is stored.
- */
- LEGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png", ConfigurationElementEditType.URL, false),
-
- /**
- * File where legend 3/4 is stored.
- */
- LEGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png", ConfigurationElementEditType.URL, false),
-
- /**
- * File where legend 4/4 is stored.
- */
- LEGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png", ConfigurationElementEditType.URL, false),
-
- /**
- * File where legend 4/4 is stored.
- */
- USER_MANUAL_FILE("User manual file", "resources/other/user_guide.pdf", ConfigurationElementEditType.URL, false),
-
- /**
- * Color used for negative overlay values.
- */
- MIN_COLOR_VAL("Overlay color for negative values", "FF0000", ConfigurationElementEditType.COLOR, false),
-
- /**
- * Color used for positive overlay values.
- */
- 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
- * value doesn't exist in the DAO).
- */
- private String defaultValue = "";
-
- /**
- * Common name used for visualization (query user).
- */
- private String commonName = "";
-
- /**
- * How we want to edit specific param.
- */
- private ConfigurationElementEditType editType = null;
-
- private boolean serverSide = true;
-
- /**
- * Default constructor.
- *
- * @param commonName
- * common name used for this parameter
- * @param editType
- * type defining how we want to edit this configuration param
- * @param defaultVal
- * default value assigned to this parameter
- */
- ConfigurationElementType(String commonName, String defaultVal, ConfigurationElementEditType editType, boolean serverSide) {
- this.defaultValue = defaultVal;
- this.commonName = commonName;
- this.editType = editType;
- this.serverSide = true;
- }
-
- /**
- * @return the defaultValue
- * @see #defaultValue
- */
- public String getDefaultValue() {
- return defaultValue;
- }
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * @return the editType
- * @see #editType
- */
- public ConfigurationElementEditType getEditType() {
- return editType;
- }
-
- /**
- * @return the serverSide
- * @see #serverSide
- */
- public boolean isServerSide() {
- return serverSide;
- }
-
- /**
- * @param serverSide
- * the serverSide to set
- * @see #serverSide
- */
- public void setServerSide(boolean serverSide) {
- this.serverSide = serverSide;
- }
+ /**
+ * Email address used for sending email from the system.
+ */
+ EMAIL_ADDRESS("E-mail address", "your.account@domain.com", ConfigurationElementEditType.EMAIL, true), //
+
+ /**
+ * Login for the email account.
+ */
+ EMAIL_LOGIN("E-mail server login", "your@login", ConfigurationElementEditType.STRING, true), //
+
+ /**
+ * Password for the email account.
+ */
+ EMAIL_PASSWORD("E-mail server password", "email.secret.password", ConfigurationElementEditType.PASSWORD, true), //
+
+ /**
+ * Address of the IMAP server.
+ */
+ EMAIL_IMAP_SERVER("IMAP server", "your.imap.domain.com", ConfigurationElementEditType.STRING, true), //
+
+ /**
+ * Address of the SMTP server.
+ */
+ EMAIL_SMTP_SERVER("SMTP server", "your.smtp.domain.com", ConfigurationElementEditType.STRING, true), //
+
+ /**
+ * Port used for SMTP connection (sending e-mails).
+ */
+ EMAIL_SMTP_PORT("SMTP port", "25", ConfigurationElementEditType.INTEGER, true), //
+
+ /**
+ * Default map that should be presented if no map is selected by user side.
+ */
+ DEFAULT_MAP("Default Project Id", "empty", ConfigurationElementEditType.STRING, false), //
+
+ /**
+ * Logo presented in the system.
+ */
+ LOGO_IMG("Logo icon", "udl.png", ConfigurationElementEditType.URL, false), //
+
+ /**
+ * Address connected to the logo.
+ */
+ LOGO_LINK("Logo link (after click)", "http://wwwen.uni.lu/", ConfigurationElementEditType.URL, false), //
+
+ /**
+ * Maximum distance (in pixels) that is allowed during finding closest element
+ * on the map.
+ */
+ SEARCH_DISTANCE("Max distance for clicking on element (px)", "10", ConfigurationElementEditType.DOUBLE, false),
+
+ /**
+ * Email used for requesting an account (in client side).
+ */
+ REQUEST_ACCOUNT_EMAIL("Email used for requesting an account", "your.email@domain.com",
+ ConfigurationElementEditType.EMAIL, false),
+
+ /**
+ * Max number of results in search box.
+ */
+ SEARCH_RESULT_NUMBER("Max number of results in search box. ", "100", ConfigurationElementEditType.INTEGER, false),
+
+ /**
+ * Google Analytics tracking ID used for statistics. This tracking ID should
+ * look like "UA-000000-01". More information about tracking ID can be found
+ * <a href="https://support.google.com/analytics/answer/1032385?hl=en"> here
+ * </a>.
+ */
+ GOOGLE_ANALYTICS_IDENTIFIER("Google Analytics tracking ID used for statistics", "",
+ ConfigurationElementEditType.STRING, false),
+
+ /**
+ * Description of the logo presented in the system.
+ */
+ LOGO_TEXT("Logo description", "University of Luxembourg", ConfigurationElementEditType.STRING, false),
+
+ /**
+ * Domain allowed to connect via x-frame technology.
+ */
+ X_FRAME_DOMAIN("Domain allowed to connect via x-frame technology", "", ConfigurationElementEditType.URL, false),
+
+ /**
+ * Relative directory (in webapps folder) where big files will be stored.
+ */
+ BIG_FILE_STORAGE_DIR("Path to store big files", "minerva-big/", ConfigurationElementEditType.STRING, false),
+
+ /**
+ * File where legend 1/4 is stored.
+ */
+ LEGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png", ConfigurationElementEditType.URL, false),
+
+ /**
+ * File where legend 2/4 is stored.
+ */
+ LEGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png", ConfigurationElementEditType.URL, false),
+
+ /**
+ * File where legend 3/4 is stored.
+ */
+ LEGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png", ConfigurationElementEditType.URL, false),
+
+ /**
+ * File where legend 4/4 is stored.
+ */
+ LEGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png", ConfigurationElementEditType.URL, false),
+
+ /**
+ * File where legend 4/4 is stored.
+ */
+ USER_MANUAL_FILE("User manual file", "resources/other/user_guide.pdf", ConfigurationElementEditType.URL, false),
+
+ /**
+ * Color used for negative overlay values.
+ */
+ MIN_COLOR_VAL("Overlay color for negative values", "FF0000", ConfigurationElementEditType.COLOR, false),
+
+ /**
+ * Color used for positive overlay values.
+ */
+ 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),
+
+ /**
+ *
+ * Color used for 0 overlay value.
+ */
+ NEUTRAL_COLOR_VAL("Overlay color for value=0", "FFFFFF", ConfigurationElementEditType.COLOR, false);
+
+ /**
+ * Default value of the configuration parameter (it will be used only when value
+ * doesn't exist in the DAO).
+ */
+ private String defaultValue = "";
+
+ /**
+ * Common name used for visualization (query user).
+ */
+ private String commonName = "";
+
+ /**
+ * How we want to edit specific parameter.
+ */
+ private ConfigurationElementEditType editType = null;
+
+ private boolean serverSide = true;
+
+ /**
+ * Default constructor.
+ *
+ * @param commonName
+ * common name used for this parameter
+ * @param editType
+ * type defining how we want to edit this configuration param
+ * @param defaultVal
+ * default value assigned to this parameter
+ */
+ ConfigurationElementType(String commonName, String defaultVal, ConfigurationElementEditType editType,
+ boolean serverSide) {
+ this.defaultValue = defaultVal;
+ this.commonName = commonName;
+ this.editType = editType;
+ this.serverSide = true;
+ }
+
+ /**
+ * @return the defaultValue
+ * @see #defaultValue
+ */
+ public String getDefaultValue() {
+ return defaultValue;
+ }
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * @return the editType
+ * @see #editType
+ */
+ public ConfigurationElementEditType getEditType() {
+ return editType;
+ }
+
+ /**
+ * @return the serverSide
+ * @see #serverSide
+ */
+ public boolean isServerSide() {
+ return serverSide;
+ }
+
+ /**
+ * @param serverSide
+ * the serverSide to set
+ * @see #serverSide
+ */
+ public void setServerSide(boolean serverSide) {
+ this.serverSide = serverSide;
+ }
}
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 6c7b603a06..f9634def04 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -27,310 +27,325 @@ import javax.persistence.Table;
@Table(name = "user_table")
public class User implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * User login.
- */
- private String login;
-
- /**
- * Password in encrypted form. For the encryption PasswordEncoder spring bean
- * is used.
- */
- private String cryptedPassword;
-
- /**
- * Name of the user.
- */
- private String name;
-
- /**
- * Family name of the user.
- */
- private String surname;
-
- /**
- * Email address of the user.
- */
- private String email;
-
- /**
- * User defined color overriding system
- * {@link ConfigurationElementType#MIN_COLOR_VAL}. Used for coloring minimum
- * values in overlays.
- */
- private Color minColor;
-
- /**
- * User defined color overriding system
- * {@link ConfigurationElementType#MAX_COLOR_VAL}. Used for coloring maximum
- * values in overlays.
- */
- 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.
- */
- private boolean removed = false;
-
- /**
- * Set of user privileges.
- */
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "user", orphanRemoval = true, cascade = CascadeType.ALL)
- private Set<BasicPrivilege> privileges = new HashSet<>();
-
- /**
- * Default annotations schema used by this user.
- */
- @OneToOne(cascade = CascadeType.ALL)
- @JoinColumn(nullable = true)
- private UserAnnotationSchema annotationSchema;
-
- /**
- * Default constructor.
- */
- public User() {
- }
-
- /**
- * Adds privilege to the user.
- *
- * @param privilege
- * privilege to add
- */
- public void addPrivilege(BasicPrivilege privilege) {
- privileges.add(privilege);
- }
-
- /**
- * @return the id
- * @see #id
- */
- public Integer getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(Integer id) {
- this.id = id;
- }
-
- /**
- * @return the login
- * @see #login
- */
- public String getLogin() {
- return login;
- }
-
- /**
- * @param login
- * the login to set
- * @see #login
- */
- public void setLogin(String login) {
- this.login = login;
- }
-
- /**
- * @return the cryptedPassword
- * @see #cryptedPassword
- */
- public String getCryptedPassword() {
- return cryptedPassword;
- }
-
- /**
- * @param cryptedPassword
- * the cryptedPassword to set
- * @see #cryptedPassword
- */
- public void setCryptedPassword(String cryptedPassword) {
- this.cryptedPassword = cryptedPassword;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the surname
- * @see #surname
- */
- public String getSurname() {
- return surname;
- }
-
- /**
- * @param surname
- * the surname to set
- * @see #surname
- */
- public void setSurname(String surname) {
- this.surname = surname;
- }
-
- /**
- * @return the email
- * @see #email
- */
- public String getEmail() {
- return email;
- }
-
- /**
- * @param email
- * the email to set
- * @see #email
- */
- public void setEmail(String email) {
- this.email = email;
- }
-
- /**
- * @return the privileges
- * @see #privileges
- */
- public Set<BasicPrivilege> getPrivileges() {
- return privileges;
- }
-
- /**
- * @param privileges
- * the privileges to set
- * @see #privileges
- */
- public void setPrivileges(Set<BasicPrivilege> privileges) {
- this.privileges = privileges;
- }
-
- /**
- * @return the removed
- * @see #removed
- */
- public boolean isRemoved() {
- return removed;
- }
-
- /**
- * @param removed
- * the removed to set
- * @see #removed
- */
- public void setRemoved(boolean removed) {
- this.removed = removed;
- }
-
- /**
- * @return the annotationSchema
- * @see #annotationSchema
- */
- public UserAnnotationSchema getAnnotationSchema() {
- return annotationSchema;
- }
-
- /**
- * @param annotationSchema
- * the annotationSchema to set
- * @see #annotationSchema
- */
- public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
- this.annotationSchema = annotationSchema;
- if (!this.equals(annotationSchema.getUser())) {
- annotationSchema.setUser(this);
- }
- }
-
- @Override
- public String toString() {
- return "[" + this.getClass().getSimpleName() + "] " + getName() + " " + getSurname();
- }
-
- /**
- * @return the minColor
- * @see #minColor
- */
- public Color getMinColor() {
- return minColor;
- }
-
- /**
- * @param minColor
- * the minColor to set
- * @see #minColor
- */
- public void setMinColor(Color minColor) {
- this.minColor = minColor;
- }
-
- /**
- * @return the maxColor
- * @see #maxColor
- */
- public Color getMaxColor() {
- return maxColor;
- }
-
- /**
- * @param maxColor
- * the maxColor to set
- * @see #maxColor
- */
- public void setMaxColor(Color maxColor) {
- 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;
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * User login.
+ */
+ private String login;
+
+ /**
+ * Password in encrypted form. For the encryption PasswordEncoder spring bean is
+ * used.
+ */
+ private String cryptedPassword;
+
+ /**
+ * Name of the user.
+ */
+ private String name;
+
+ /**
+ * Family name of the user.
+ */
+ private String surname;
+
+ /**
+ * Email address of the user.
+ */
+ private String email;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#MIN_COLOR_VAL}. Used for coloring minimum
+ * values in overlays.
+ */
+ private Color minColor;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#MAX_COLOR_VAL}. Used for coloring maximum
+ * values in overlays.
+ */
+ private Color maxColor;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#NEUTRAL_COLOR_VAL}. Used for coloring neutral
+ * values (0) in overlays.
+ */
+ private Color neutralColor;
+
+ /**
+ * 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.
+ */
+ private boolean removed = false;
+
+ /**
+ * Set of user privileges.
+ */
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "user", orphanRemoval = true, cascade = CascadeType.ALL)
+ private Set<BasicPrivilege> privileges = new HashSet<>();
+
+ /**
+ * Default annotations schema used by this user.
+ */
+ @OneToOne(cascade = CascadeType.ALL)
+ @JoinColumn(nullable = true)
+ private UserAnnotationSchema annotationSchema;
+
+ /**
+ * Default constructor.
+ */
+ public User() {
+ }
+
+ /**
+ * Adds privilege to the user.
+ *
+ * @param privilege
+ * privilege to add
+ */
+ public void addPrivilege(BasicPrivilege privilege) {
+ privileges.add(privilege);
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the login
+ * @see #login
+ */
+ public String getLogin() {
+ return login;
+ }
+
+ /**
+ * @param login
+ * the login to set
+ * @see #login
+ */
+ public void setLogin(String login) {
+ this.login = login;
+ }
+
+ /**
+ * @return the cryptedPassword
+ * @see #cryptedPassword
+ */
+ public String getCryptedPassword() {
+ return cryptedPassword;
+ }
+
+ /**
+ * @param cryptedPassword
+ * the cryptedPassword to set
+ * @see #cryptedPassword
+ */
+ public void setCryptedPassword(String cryptedPassword) {
+ this.cryptedPassword = cryptedPassword;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the surname
+ * @see #surname
+ */
+ public String getSurname() {
+ return surname;
+ }
+
+ /**
+ * @param surname
+ * the surname to set
+ * @see #surname
+ */
+ public void setSurname(String surname) {
+ this.surname = surname;
+ }
+
+ /**
+ * @return the email
+ * @see #email
+ */
+ public String getEmail() {
+ return email;
+ }
+
+ /**
+ * @param email
+ * the email to set
+ * @see #email
+ */
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ /**
+ * @return the privileges
+ * @see #privileges
+ */
+ public Set<BasicPrivilege> getPrivileges() {
+ return privileges;
+ }
+
+ /**
+ * @param privileges
+ * the privileges to set
+ * @see #privileges
+ */
+ public void setPrivileges(Set<BasicPrivilege> privileges) {
+ this.privileges = privileges;
+ }
+
+ /**
+ * @return the removed
+ * @see #removed
+ */
+ public boolean isRemoved() {
+ return removed;
+ }
+
+ /**
+ * @param removed
+ * the removed to set
+ * @see #removed
+ */
+ public void setRemoved(boolean removed) {
+ this.removed = removed;
+ }
+
+ /**
+ * @return the annotationSchema
+ * @see #annotationSchema
+ */
+ public UserAnnotationSchema getAnnotationSchema() {
+ return annotationSchema;
+ }
+
+ /**
+ * @param annotationSchema
+ * the annotationSchema to set
+ * @see #annotationSchema
+ */
+ public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
+ this.annotationSchema = annotationSchema;
+ if (!this.equals(annotationSchema.getUser())) {
+ annotationSchema.setUser(this);
+ }
+ }
+
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + "] " + getName() + " " + getSurname();
+ }
+
+ /**
+ * @return the minColor
+ * @see #minColor
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @param minColor
+ * the minColor to set
+ * @see #minColor
+ */
+ public void setMinColor(Color minColor) {
+ this.minColor = minColor;
+ }
+
+ /**
+ * @return the maxColor
+ * @see #maxColor
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+
+ /**
+ * @param maxColor
+ * the maxColor to set
+ * @see #maxColor
+ */
+ public void setMaxColor(Color maxColor) {
+ 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;
+ }
+
+ public Color getNeutralColor() {
+ return neutralColor;
+ }
+
+ public void setNeutralColor(Color neutralColor) {
+ this.neutralColor = neutralColor;
+ }
}
diff --git a/persist/src/db/12.0.0/fix_db_20171115.sql b/persist/src/db/12.0.0/fix_db_20171115.sql
index 62d0d3dd86..4ad3a91d6f 100644
--- a/persist/src/db/12.0.0/fix_db_20171115.sql
+++ b/persist/src/db/12.0.0/fix_db_20171115.sql
@@ -1,2 +1,5 @@
-- clear invalid urls from miriam connector
delete from cachequery where type = (select iddb from cache_type where classname='lcsb.mapviewer.annotation.services.MiriamConnector') and value = 'INVALID';
+
+-- argument for neutral color scheme
+alter table user_table add column neutralcolor bytea;
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 1adae6c2ba..a845b33e09 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
@@ -70,6 +70,7 @@ public class UserRestImpl extends BaseRestImpl {
columnsSet.add("email");
columnsSet.add("minColor");
columnsSet.add("maxColor");
+ columnsSet.add("neutralColor");
columnsSet.add("simpleColor");
columnsSet.add("removed");
columnsSet.add("privileges");
@@ -101,6 +102,8 @@ public class UserRestImpl extends BaseRestImpl {
value = user.getMinColor();
} else if (column.equals("maxcolor")) {
value = user.getMaxColor();
+ } else if (column.equals("neutralcolor")) {
+ value = user.getNeutralColor();
} else if (column.equals("simplecolor")) {
value = user.getSimpleColor();
} else if (column.equals("removed")) {
--
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