From b5612c1cf7cd762b418faac2ab61006ae9b86fb8 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 28 Mar 2018 19:01:52 +0200
Subject: [PATCH] data in model API doesn't include: submodels,
centerLatLng,topLeftLatLng,bottomRightLatLng + models moved to project in JS
---
frontend-js/package-lock.json | 54 +--
frontend-js/src/main/js/ServerConnector.js | 2 +-
frontend-js/src/main/js/gui/CommentDialog.js | 3 +-
.../main/js/gui/export/AbstractExportPanel.js | 7 +-
.../main/js/gui/export/ElementExportPanel.js | 365 +++++++++---------
.../main/js/gui/export/NetworkExportPanel.js | 159 ++++----
.../src/main/js/gui/leftPanel/SubmapPanel.js | 6 +-
.../src/main/js/map/AbstractCustomMap.js | 25 +-
frontend-js/src/main/js/map/CustomMap.js | 6 +-
frontend-js/src/main/js/map/Submap.js | 2 +-
frontend-js/src/main/js/map/data/MapModel.js | 80 ----
frontend-js/src/main/js/map/data/Project.js | 28 +-
.../src/main/js/map/surface/AliasSurface.js | 2 +-
frontend-js/src/main/js/minerva.js | 6 +-
.../src/main/js/plugin/MinervaPluginProxy.js | 14 +-
.../src/test/js/gui/MapContextMenu-test.js | 4 +-
.../test/js/gui/SelectionContextMenu-test.js | 4 +-
.../js/gui/leftPanel/OverlayPanel-test.js | 2 +-
frontend-js/src/test/js/helper.js | 17 +-
.../src/test/js/map/AbstractCustomMap-test.js | 4 +-
frontend-js/src/test/js/map/CustomMap-test.js | 6 +-
.../src/test/js/map/data/MapModel-test.js | 2 +-
.../js/map/overlay/SearchDbOverlay-test.js | 4 +-
frontend-js/src/test/js/minerva-test.js | 7 +-
.../test/js/plugin/MinervaPluginProxy-test.js | 6 +-
.../lcsb/mapviewer/model/map/model/Model.java | 2 +-
.../api/projects/models/ModelMetaData.java | 110 ------
.../api/projects/models/ModelRestImpl.java | 7 +-
28 files changed, 365 insertions(+), 569 deletions(-)
diff --git a/frontend-js/package-lock.json b/frontend-js/package-lock.json
index 29898ad842..378ebd3885 100644
--- a/frontend-js/package-lock.json
+++ b/frontend-js/package-lock.json
@@ -45,30 +45,38 @@
"litemol": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
},
"dependencies": {
+ "ProtVista": {
+ "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
+ "dev": true,
+ "requires": {
+ "d3": "3.5.17",
+ "file-saver": "1.3.3",
+ "jquery": "2.2.4",
+ "jszip": "3.1.4",
+ "underscore": "1.8.3"
+ },
+ "dependencies": {
+ "jquery": {
+ "version": "2.2.4",
+ "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
+ "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
+ "dev": true
+ }
+ }
+ },
"jquery": {
"version": "3.3.1",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
"integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
"dev": true
- }
- }
- },
- "ProtVista": {
- "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
- "dev": true,
- "requires": {
- "d3": "3.5.17",
- "file-saver": "1.3.3",
- "jquery": "2.2.4",
- "jszip": "3.1.4",
- "underscore": "1.8.3"
- },
- "dependencies": {
- "jquery": {
- "version": "2.2.4",
- "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
- "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
- "dev": true
+ },
+ "litemol": {
+ "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
+ "dev": true,
+ "requires": {
+ "@types/react": "15.6.14",
+ "@types/react-dom": "15.5.7"
+ }
}
}
},
@@ -2050,14 +2058,6 @@
"immediate": "3.0.6"
}
},
- "litemol": {
- "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
- "dev": true,
- "requires": {
- "@types/react": "15.6.14",
- "@types/react-dom": "15.5.7"
- }
- },
"lodash": {
"version": "4.17.4",
"resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz",
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 698bd803ef..48c374d88e 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -807,7 +807,7 @@ ServerConnector.getProject = function (projectId) {
}
project = self._projectsById[projectId];
return self.getModels(projectId).then(function (models) {
- project.setModel(models[0]);
+ project.setModels(models);
return self.getOverlays({
projectId: projectId,
publicOverlay: true
diff --git a/frontend-js/src/main/js/gui/CommentDialog.js b/frontend-js/src/main/js/gui/CommentDialog.js
index 1974a06571..86148135a6 100644
--- a/frontend-js/src/main/js/gui/CommentDialog.js
+++ b/frontend-js/src/main/js/gui/CommentDialog.js
@@ -7,6 +7,7 @@ var Promise = require("bluebird");
var AbstractGuiElement = require('./AbstractGuiElement');
var Alias = require('../map/data/Alias');
var Reaction = require('../map/data/Reaction');
+// noinspection JSUnusedLocalSymbols
var logger = require('../logger');
var Functions = require('../Functions');
@@ -18,7 +19,7 @@ function CommentDialog(params) {
autoOpen : false,
resizable : false,
width : window.innerWidth / 2,
- height : window.innerHeight / 2,
+ height : window.innerHeight / 2
});
}
diff --git a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
index 144896dd33..61eba919cc 100644
--- a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
@@ -253,12 +253,7 @@ AbstractExportPanel.prototype._getCompartmentNames = function () {
};
AbstractExportPanel.prototype.getModels = function () {
- var self = this;
- var models = [self.getProject().getModel()];
- for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
- models.push(self.getProject().getModel().getSubmodels()[i]);
- }
- return models;
+ return this.getProject().getModels();
};
AbstractExportPanel.prototype._getAllCompartments = function () {
diff --git a/frontend-js/src/main/js/gui/export/ElementExportPanel.js b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
index fc9f884e7e..e07f58e4ab 100644
--- a/frontend-js/src/main/js/gui/export/ElementExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
@@ -10,209 +10,206 @@ var logger = require('../../logger');
var Promise = require("bluebird");
function ElementExportPanel(params) {
- params.panelName = "elementExport";
- AbstractExportPanel.call(this, params);
+ params.panelName = "elementExport";
+ AbstractExportPanel.call(this, params);
}
ElementExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
ElementExportPanel.prototype.constructor = ElementExportPanel;
ElementExportPanel.prototype.init = function () {
- var self = this;
- var element = self.getElement();
- var configuration;
- return ServerConnector.getConfiguration().then(function (result) {
- configuration = result;
- var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
- element.appendChild(typeDiv);
- element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
- return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
- }).then(function (statistics) {
- return self._createMiriamTypeDiv(statistics.getElementAnnotations());
- }).then(function (div) {
- element.appendChild(div);
- return self._createSelectIncludedCompartmentDiv();
- }).then(function (div) {
- element.appendChild(div);
- return self._createSelectExcludedCompartmentDiv();
- }).then(function (div) {
- element.appendChild(div);
- element.appendChild(self._createDownloadButton());
- }).then(function () {
- $(window).trigger('resize');
- });
+ var self = this;
+ var element = self.getElement();
+ var configuration;
+ return ServerConnector.getConfiguration().then(function (result) {
+ configuration = result;
+ var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
+ element.appendChild(typeDiv);
+ element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
+ return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
+ }).then(function (statistics) {
+ return self._createMiriamTypeDiv(statistics.getElementAnnotations());
+ }).then(function (div) {
+ element.appendChild(div);
+ return self._createSelectIncludedCompartmentDiv();
+ }).then(function (div) {
+ element.appendChild(div);
+ return self._createSelectExcludedCompartmentDiv();
+ }).then(function (div) {
+ element.appendChild(div);
+ element.appendChild(self._createDownloadButton());
+ }).then(function () {
+ $(window).trigger('resize');
+ });
};
ElementExportPanel.prototype.createResponseString = function () {
- var self = this;
- var types, miriamTypes;
- var includedCompartmentIds = [];
- var excludedCompartmentIds = [];
- var models = [self.getProject().getModel()];
- for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
- models.push(self.getProject().getModel().getSubmodels()[i]);
+ var self = this;
+ var types, miriamTypes;
+ var includedCompartmentIds = [];
+ var excludedCompartmentIds = [];
+ var models = self.getProject().getModels();
+
+ var elements = [];
+ return self.getSelectedTypes().then(function (result) {
+ if (result.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one type"));
}
-
- var elements = [];
- return self.getSelectedTypes().then(function (result) {
- if (result.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one type"));
- }
- types = result;
- return self.getSelectedIncludedCompartments();
- }).then(function (result) {
- result.forEach(function (compartment) {
- includedCompartmentIds.push(compartment.getId());
- });
- return self.getSelectedExcludedCompartments();
- }).then(function (result) {
- result.forEach(function (compartment) {
- excludedCompartmentIds.push(compartment.getId());
- });
-
- var promises = [];
- for (var i = 0; i < models.length; i++) {
- promises.push(models[i].getAliases({
- type: types,
- complete: true,
- includedCompartmentIds: includedCompartmentIds,
- excludedCompartmentIds: excludedCompartmentIds,
- }));
- }
- return Promise.all(promises);
- }).then(function (aliasesByModel) {
- for (var i = 0; i < aliasesByModel.length; i++) {
- for (var j = 0; j < aliasesByModel[i].length; j++) {
- elements.push(aliasesByModel[i][j]);
- }
- }
-
- return self.getSelectedMiriamTypes();
- }).then(function (result) {
- miriamTypes = result;
- return self.getSelectedColumns();
- }).then(function (selectedColumns) {
- if (selectedColumns.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one column"));
- }
-
- var rows = [];
- rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
- for (var i = 0; i < elements.length; i++) {
- rows.push(self.createResponseRow(elements[i], selectedColumns, miriamTypes));
- }
- return rows.join("\n");
+ types = result;
+ return self.getSelectedIncludedCompartments();
+ }).then(function (result) {
+ result.forEach(function (compartment) {
+ includedCompartmentIds.push(compartment.getId());
+ });
+ return self.getSelectedExcludedCompartments();
+ }).then(function (result) {
+ result.forEach(function (compartment) {
+ excludedCompartmentIds.push(compartment.getId());
});
+
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getAliases({
+ type: types,
+ complete: true,
+ includedCompartmentIds: includedCompartmentIds,
+ excludedCompartmentIds: excludedCompartmentIds,
+ }));
+ }
+ return Promise.all(promises);
+ }).then(function (aliasesByModel) {
+ for (var i = 0; i < aliasesByModel.length; i++) {
+ for (var j = 0; j < aliasesByModel[i].length; j++) {
+ elements.push(aliasesByModel[i][j]);
+ }
+ }
+
+ return self.getSelectedMiriamTypes();
+ }).then(function (result) {
+ miriamTypes = result;
+ return self.getSelectedColumns();
+ }).then(function (selectedColumns) {
+ if (selectedColumns.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one column"));
+ }
+
+ var rows = [];
+ rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
+ for (var i = 0; i < elements.length; i++) {
+ rows.push(self.createResponseRow(elements[i], selectedColumns, miriamTypes));
+ }
+ return rows.join("\n");
+ });
};
ElementExportPanel.prototype.createResponseRow = function (alias, columns, miriamTypes) {
- var stringBuilder = [];
- var i, value;
- for (i = 0; i < columns.length; i++) {
- var column = columns[i];
- value = alias[column.method]();
- if (column.formatFunction !== undefined) {
- value = column.formatFunction(value);
- }
- if (value instanceof String || typeof value === "string") {
- value = value.replace(/[\n\r]/g, ' ');
- }
- stringBuilder.push(value);
+ var stringBuilder = [];
+ var i, value;
+ for (i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ value = alias[column.method]();
+ if (column.formatFunction !== undefined) {
+ value = column.formatFunction(value);
+ }
+ if (value instanceof String || typeof value === "string") {
+ value = value.replace(/[\n\r]/g, ' ');
}
- for (i = 0; i < miriamTypes.length; i++) {
- value = "";
- var miriamType = miriamTypes[i];
- var references = alias.getReferences();
- for (var j = 0; j < references.length; j++) {
- var reference = references[j];
- if (reference.getType() === miriamType.getName()) {
- value += reference.getResource() + ",";
- }
- }
- stringBuilder.push(value);
+ stringBuilder.push(value);
+ }
+ for (i = 0; i < miriamTypes.length; i++) {
+ value = "";
+ var miriamType = miriamTypes[i];
+ var references = alias.getReferences();
+ for (var j = 0; j < references.length; j++) {
+ var reference = references[j];
+ if (reference.getType() === miriamType.getName()) {
+ value += reference.getResource() + ",";
+ }
}
- var result = stringBuilder.join("\t");
- return result;
+ stringBuilder.push(value);
+ }
+ var result = stringBuilder.join("\t");
+ return result;
};
ElementExportPanel.prototype.getAllColumns = function () {
- return [{
- "columnName": "id",
- "method": "getId",
- "name": "Id",
- }, {
- "columnName": "name",
- "method": "getName",
- "name": "Name",
- }, {
- "columnName": "description",
- "method": "getDescription",
- "name": "Description",
- }, {
- "columnName": "modelId",
- "method": "getModelId",
- "name": "Model",
- }, {
- "columnName": "type",
- "method": "getType",
- "name": "Type",
- }, {
- "columnName": "complexId",
- "method": "getComplexId",
- "name": "Complex",
- }, {
- "columnName": "compartmentId",
- "method": "getCompartmentId",
- "name": "Compartment",
- }, {
- "columnName": "charge",
- "method": "getCharge",
- "name": "Charge",
- }, {
- "columnName": "symbol",
- "method": "getSymbol",
- "name": "Symbol",
- }, {
- "columnName": "fullName",
- "method": "getFullName",
- "name": "Full name",
- }, {
- "columnName": "abbreviation",
- "method": "getAbbreviation",
- "name": "Abbreviation",
- }, {
- "columnName": "formula",
- "method": "getFormula",
- "name": "Formula",
- }, {
- "columnName": "synonyms",
- "method": "getSynonyms",
- "name": "Synonyms",
- }, {
- "columnName": "formerSymbols",
- "method": "getFormerSymbols",
- "name": "Former symbols",
- }, {
- "columnName": "references",
- "method": "getReferences",
- "name": "References",
- "formatFunction": function (references) {
- var stringBuilder = [];
- for (var i = 0; i < references.length; i++) {
- var reference = references[i];
- stringBuilder.push(reference.getType() + ":" + reference.getResource());
- }
- return stringBuilder.join(",");
- },
- }, {
- "columnName": "linkedSubmodelId",
- "method": "getLinkedSubmodelId",
- "name": "Linked submodel",
- }, {
- "columnName": "elementId",
- "method": "getElementId",
- "name": "Element external id",
- },];
+ return [{
+ "columnName": "id",
+ "method": "getId",
+ "name": "Id",
+ }, {
+ "columnName": "name",
+ "method": "getName",
+ "name": "Name",
+ }, {
+ "columnName": "description",
+ "method": "getDescription",
+ "name": "Description",
+ }, {
+ "columnName": "modelId",
+ "method": "getModelId",
+ "name": "Model",
+ }, {
+ "columnName": "type",
+ "method": "getType",
+ "name": "Type",
+ }, {
+ "columnName": "complexId",
+ "method": "getComplexId",
+ "name": "Complex",
+ }, {
+ "columnName": "compartmentId",
+ "method": "getCompartmentId",
+ "name": "Compartment",
+ }, {
+ "columnName": "charge",
+ "method": "getCharge",
+ "name": "Charge",
+ }, {
+ "columnName": "symbol",
+ "method": "getSymbol",
+ "name": "Symbol",
+ }, {
+ "columnName": "fullName",
+ "method": "getFullName",
+ "name": "Full name",
+ }, {
+ "columnName": "abbreviation",
+ "method": "getAbbreviation",
+ "name": "Abbreviation",
+ }, {
+ "columnName": "formula",
+ "method": "getFormula",
+ "name": "Formula",
+ }, {
+ "columnName": "synonyms",
+ "method": "getSynonyms",
+ "name": "Synonyms",
+ }, {
+ "columnName": "formerSymbols",
+ "method": "getFormerSymbols",
+ "name": "Former symbols",
+ }, {
+ "columnName": "references",
+ "method": "getReferences",
+ "name": "References",
+ "formatFunction": function (references) {
+ var stringBuilder = [];
+ for (var i = 0; i < references.length; i++) {
+ var reference = references[i];
+ stringBuilder.push(reference.getType() + ":" + reference.getResource());
+ }
+ return stringBuilder.join(",");
+ },
+ }, {
+ "columnName": "linkedSubmodelId",
+ "method": "getLinkedSubmodelId",
+ "name": "Linked submodel",
+ }, {
+ "columnName": "elementId",
+ "method": "getElementId",
+ "name": "Element external id",
+ },];
};
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
index d93fdebae2..8409f17553 100644
--- a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -17,43 +17,43 @@ function NetworkExportPanel(params) {
NetworkExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
NetworkExportPanel.prototype.constructor = NetworkExportPanel;
-NetworkExportPanel.prototype.init = function() {
+NetworkExportPanel.prototype.init = function () {
var self = this;
var element = self.getElement();
var configuration;
- return ServerConnector.getConfiguration().then(function(result) {
+ return ServerConnector.getConfiguration().then(function (result) {
configuration = result;
var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
element.appendChild(typeDiv);
element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
- }).then(function(statistics) {
+ }).then(function (statistics) {
return self._createMiriamTypeDiv(statistics.getReactionAnnotations());
- }).then(function(div) {
+ }).then(function (div) {
element.appendChild(div);
return self._createSelectIncludedCompartmentDiv();
- }).then(function(div) {
+ }).then(function (div) {
element.appendChild(div);
return self._createSelectExcludedCompartmentDiv();
- }).then(function(div) {
+ }).then(function (div) {
element.appendChild(div);
element.appendChild(self._createDownloadButton());
- }).then(function() {
+ }).then(function () {
$(window).trigger('resize');
});
};
-NetworkExportPanel.prototype.getAllColumns = function() {
- return [ {
- "columnName" : "elements",
- "method" : "getElements",
- "name" : "Elements",
- "formatFunction" : function(elements, reaction, elementIds) {
+NetworkExportPanel.prototype.getAllColumns = function () {
+ return [{
+ "columnName": "elements",
+ "method": "getElements",
+ "name": "Elements",
+ "formatFunction": function (elements, reaction, elementIds) {
var stringBuilder = [];
var type;
- var elementFormat = function(element) {
+ var elementFormat = function (element) {
if (elementIds[element.getId()]) {
stringBuilder.push(type + ":" + element.getId());
}
@@ -68,42 +68,42 @@ NetworkExportPanel.prototype.getAllColumns = function() {
return stringBuilder.join(",");
},
}, {
- "columnName" : "id",
- "method" : "getId",
- "name" : "Id",
+ "columnName": "id",
+ "method": "getId",
+ "name": "Id",
}, {
- "columnName" : "description",
- "method" : "getDescription",
- "name" : "Description",
+ "columnName": "description",
+ "method": "getDescription",
+ "name": "Description",
}, {
- "columnName" : "modelId",
- "method" : "getModelId",
- "name" : "Model",
+ "columnName": "modelId",
+ "method": "getModelId",
+ "name": "Model",
}, {
- "columnName" : "type",
- "method" : "getType",
- "name" : "Type",
+ "columnName": "type",
+ "method": "getType",
+ "name": "Type",
}, {
- "columnName" : "symbol",
- "method" : "getSymbol",
- "name" : "Symbol",
+ "columnName": "symbol",
+ "method": "getSymbol",
+ "name": "Symbol",
}, {
- "columnName" : "abbreviation",
- "method" : "getAbbreviation",
- "name" : "Abbreviation",
+ "columnName": "abbreviation",
+ "method": "getAbbreviation",
+ "name": "Abbreviation",
}, {
- "columnName" : "formula",
- "method" : "getFormula",
- "name" : "Formula",
+ "columnName": "formula",
+ "method": "getFormula",
+ "name": "Formula",
}, {
- "columnName" : "synonyms",
- "method" : "getSynonyms",
- "name" : "Synonyms",
+ "columnName": "synonyms",
+ "method": "getSynonyms",
+ "name": "Synonyms",
}, {
- "columnName" : "references",
- "method" : "getReferences",
- "name" : "References",
- "formatFunction" : function(references) {
+ "columnName": "references",
+ "method": "getReferences",
+ "name": "References",
+ "formatFunction": function (references) {
var stringBuilder = [];
for (var i = 0; i < references.length; i++) {
var reference = references[i];
@@ -112,35 +112,35 @@ NetworkExportPanel.prototype.getAllColumns = function() {
return stringBuilder.join(",");
},
}, {
- "columnName" : "reactionId",
- "method" : "getReactionId",
- "name" : "Element external id",
+ "columnName": "reactionId",
+ "method": "getReactionId",
+ "name": "Element external id",
}, {
- "columnName" : "mechanicalConfidenceScore",
- "method" : "getMechanicalConfidenceScore",
- "name" : "Mechanical Confidence Score",
+ "columnName": "mechanicalConfidenceScore",
+ "method": "getMechanicalConfidenceScore",
+ "name": "Mechanical Confidence Score",
}, {
- "columnName" : "lowerBound",
- "method" : "getLowerBound",
- "name" : "Lower Bound",
+ "columnName": "lowerBound",
+ "method": "getLowerBound",
+ "name": "Lower Bound",
}, {
- "columnName" : "upperBound",
- "method" : "getUpperBound",
- "name" : "Upper Bound",
+ "columnName": "upperBound",
+ "method": "getUpperBound",
+ "name": "Upper Bound",
}, {
- "columnName" : "geneProteinReaction",
- "method" : "getGeneProteinReaction",
- "name" : "Gene Protein Reaction",
+ "columnName": "geneProteinReaction",
+ "method": "getGeneProteinReaction",
+ "name": "Gene Protein Reaction",
}, {
- "columnName" : "subsystem",
- "method" : "getSubsystem",
- "name" : "Subsystem",
- }, ];
+ "columnName": "subsystem",
+ "method": "getSubsystem",
+ "name": "Subsystem",
+ },];
};
function matchReaction(reaction, elementIds) {
var count = 0;
- reaction.getElements().forEach(function(element) {
+ reaction.getElements().forEach(function (element) {
if (elementIds[element.getId()]) {
count++;
}
@@ -148,45 +148,42 @@ function matchReaction(reaction, elementIds) {
return count > 1;
}
-NetworkExportPanel.prototype.createResponseString = function() {
+NetworkExportPanel.prototype.createResponseString = function () {
var self = this;
var types, miriamTypes;
var includedCompartmentIds = [];
var excludedCompartmentIds = [];
- var models = [ self.getProject().getModel() ];
- for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
- models.push(self.getProject().getModel().getSubmodels()[i]);
- }
+ var models = self.getProject().getModels();
var elementIds = [];
var reactions = [];
- return self.getSelectedTypes().then(function(result) {
+ return self.getSelectedTypes().then(function (result) {
if (result.length === 0) {
return Promise.reject(new GuiMessageError("You must select at least one type"));
}
types = result;
return self.getSelectedIncludedCompartments();
- }).then(function(result) {
- result.forEach(function(compartment) {
+ }).then(function (result) {
+ result.forEach(function (compartment) {
includedCompartmentIds.push(compartment.getId());
});
return self.getSelectedExcludedCompartments();
- }).then(function(result) {
- result.forEach(function(compartment) {
+ }).then(function (result) {
+ result.forEach(function (compartment) {
excludedCompartmentIds.push(compartment.getId());
});
var promises = [];
for (var i = 0; i < models.length; i++) {
promises.push(models[i].getAliases({
- type : types,
- complete : true,
- includedCompartmentIds : includedCompartmentIds,
- excludedCompartmentIds : excludedCompartmentIds,
+ type: types,
+ complete: true,
+ includedCompartmentIds: includedCompartmentIds,
+ excludedCompartmentIds: excludedCompartmentIds,
}));
}
return Promise.all(promises);
- }).then(function(aliasesByModel) {
+ }).then(function (aliasesByModel) {
var promises = [];
for (var i = 0; i < models.length; i++) {
promises.push(models[i].getReactionsForElements(aliasesByModel[i], true));
@@ -195,7 +192,7 @@ NetworkExportPanel.prototype.createResponseString = function() {
}
}
return Promise.all(promises);
- }).then(function(reactionsByModel) {
+ }).then(function (reactionsByModel) {
for (var i = 0; i < models.length; i++) {
for (var j = 0; j < reactionsByModel[i].length; j++) {
var reaction = reactionsByModel[i][j];
@@ -205,10 +202,10 @@ NetworkExportPanel.prototype.createResponseString = function() {
}
}
return self.getSelectedMiriamTypes();
- }).then(function(result) {
+ }).then(function (result) {
miriamTypes = result;
return self.getSelectedColumns();
- }).then(function(selectedColumns) {
+ }).then(function (selectedColumns) {
if (selectedColumns.length === 0) {
return Promise.reject(new GuiMessageError("You must select at least one column"));
}
@@ -222,7 +219,7 @@ NetworkExportPanel.prototype.createResponseString = function() {
});
};
-NetworkExportPanel.prototype.createResponseRow = function(reaction, columns, miriamTypes, elementIds) {
+NetworkExportPanel.prototype.createResponseRow = function (reaction, columns, miriamTypes, elementIds) {
var stringBuilder = [];
var i, value;
for (i = 0; i < columns.length; i++) {
diff --git a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
index 66b39646be..fb3bcf711f 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
@@ -85,11 +85,11 @@ SubmapPanel.prototype.init = function () {
return new Promise(function (resolve) {
var div = self.getControlElement(PanelControlElementType.SUBMAP_DIV);
div.innerHTML = "";
- var models = self.getMap().getProject().getModel().getSubmodels();
+ var models = self.getMap().getProject().getModels();
var modelsByType = [];
var types = [];
var i;
- for (i = 0; i < models.length; i++) {
+ for (i = 1; i < models.length; i++) {
var model = models[i];
if (modelsByType[model.getSubmodelType()] === undefined) {
modelsByType[model.getSubmodelType()] = [];
@@ -105,7 +105,7 @@ SubmapPanel.prototype.init = function () {
}
div.appendChild(self.createTable(modelsByType[type], tableName));
}
- if (models.length === 0) {
+ if (models.length <= 1) {
self.getParent().hideTab(self);
}
return resolve();
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index 3af752ca1a..e906e76f6a 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -113,13 +113,14 @@ AbstractCustomMap.prototype.createMapOptions = function () {
var self = this;
var model = self.getModel();
- var centerPoint = this.getModel().getCenterLatLng();
var zoom = ServerConnector.getSessionData(self.getProject()).getZoomLevel(model);
if (zoom === undefined) {
zoom = this.getMinZoom();
}
+ var centerPoint;
+
// if we have coordinate data stored in session then restore it
var point = ServerConnector.getSessionData(self.getProject()).getCenter(model);
if (point !== undefined) {
@@ -134,6 +135,8 @@ AbstractCustomMap.prototype.createMapOptions = function () {
centerPoint = self.fromPointToLatLng(new google.maps.Point(model.getDefaultCenterX(), model.getDefaultCenterY()));
zoom = model.getDefaultZoomLevel();
+ } else {
+ centerPoint = self.fromPointToLatLng(new google.maps.Point(model.getWidth() / 2, model.getHeight() / 2));
}
return {
@@ -413,36 +416,36 @@ AbstractCustomMap.prototype.registerMapClickEvents = function () {
});
};
-function activateMolStarLink(coordinates, map){
+function activateMolStarLink(coordinates, map) {
ServerConnector.getClosestElementsByCoordinates({
modelId: map.getId(),
coordinates: coordinates,
count: 1
- }).then(function(identifiedElements){
+ }).then(function (identifiedElements) {
return map.getDistance({
modelId: map.getId(),
coordinates: coordinates,
element: identifiedElements[0]
- }).then(function(distance){
+ }).then(function (distance) {
if (distance == 0) return identifiedElements;
else return Promise.reject(new Error());
})
- }).then(function(identifiedElements) {
+ }).then(function (identifiedElements) {
if (identifiedElements[0].type !== 'ALIAS') return Promise.reject(new Error());
return map.getModel().getAliasById(identifiedElements[0].id, true)
- }).then (function(element){
+ }).then(function (element) {
var uniprotIds = [];
- for (var i =0; i < element.references.length; i++) {
+ for (var i = 0; i < element.references.length; i++) {
var ref = element.references[i];
if (ref.constructor.name === 'Annotation' && ref.getType() === 'UNIPROT') {
- uniprotIds.push(ref.getResource());
+ uniprotIds.push(ref.getResource());
}
}
if (uniprotIds.length > 0) map.getContextMenu().getMolStar().activateInContextMenu(uniprotIds);
else map.getContextMenu().getMolStar().deactivateInContextMenu();
- }, function(){
+ }, function () {
map.getContextMenu().getMolStar().deactivateInContextMenu();
});
}
@@ -1078,11 +1081,11 @@ AbstractCustomMap.prototype.isDebug = function () {
};
AbstractCustomMap.prototype.getTopLeftLatLng = function () {
- return this.getModel().getTopLeftLatLng();
+ return this.fromPointToLatLng(new google.maps.Point(0, 0))
};
AbstractCustomMap.prototype.getBottomRightLatLng = function () {
- return this.getModel().getBottomRightLatLng();
+ return this.fromPointToLatLng(new google.maps.Point(this.getModel().getWidth(), this.getModel().getHeight()));
};
AbstractCustomMap.prototype.getElement = function () {
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 86759aabad..241812f49f 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -33,7 +33,7 @@ function CustomMap(options) {
if (!(options instanceof CustomMapOptions)) {
options = new CustomMapOptions(options);
}
- AbstractCustomMap.call(this, options.getProject().getModel(), options);
+ AbstractCustomMap.call(this, options.getProject().getModels()[0], options);
this.registerListenerType("onBioEntityClick");
this.registerListenerType("onShowOverlay");
@@ -113,8 +113,8 @@ CustomMap.prototype.init = function () {
*/
CustomMap.prototype.createSubmaps = function () {
this.submaps = [];
- for (var i = 0; i < this.getModel().getSubmodels().length; i++) {
- this.submaps.push(new Submap(this, this.getModel().getSubmodels()[i]));
+ for (var i = 1; i < this.getProject().getModels().length; i++) {
+ this.submaps.push(new Submap(this, this.getProject().getModels()[i]));
}
};
diff --git a/frontend-js/src/main/js/map/Submap.js b/frontend-js/src/main/js/map/Submap.js
index 859628cea3..9926d7ffb1 100644
--- a/frontend-js/src/main/js/map/Submap.js
+++ b/frontend-js/src/main/js/map/Submap.js
@@ -91,7 +91,7 @@ Submap.prototype.open = function (htmlTag) {
self.registerMapClickEvents();
- var centerPoint = self.getModel().getCenterLatLng();
+ var centerPoint = self.fromPointToLatLng(new google.maps.Point(self.getModel().getWidth() / 2, self.getModel().getHeight() / 2));
self.getGoogleMap().setCenter(centerPoint);
self.addCenterButton();
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index da98828014..63f81fcdc4 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -39,8 +39,6 @@ function MapModel(configuration) {
// but it can be extended)
this._pointsData = [];
- this._submodels = [];
-
this._sbmlFunctions = [];
this._sbmlParameters = [];
@@ -54,10 +52,6 @@ function MapModel(configuration) {
this.setHeight(configuration.getHeight());
this.setMinZoom(configuration.getMinZoom());
this.setMaxZoom(configuration.getMaxZoom());
- this.addSubmodels(configuration.getSubmodels());
- this.setCenterLatLng(configuration.getCenterLatLng());
- this.setTopLeftLatLng(configuration.getTopLeftLatLng());
- this.setBottomRightLatLng(configuration.getBottomRightLatLng());
this.setSubmodelType(configuration.getSubmodelType());
this.setDefaultCenterX(configuration.getDefaultCenterX());
this.setDefaultCenterY(configuration.getDefaultCenterY());
@@ -70,10 +64,6 @@ function MapModel(configuration) {
this.setHeight(configuration.height);
this.setMinZoom(configuration.minZoom);
this.setMaxZoom(configuration.maxZoom);
- this.addSubmodels(configuration.submodels);
- this.setCenterLatLng(configuration.centerLatLng);
- this.setTopLeftLatLng(configuration.topLeftLatLng);
- this.setBottomRightLatLng(configuration.bottomRightLatLng);
this.setSubmodelType(configuration.submodelType);
this.setDefaultCenterX(configuration.defaultCenterX);
this.setDefaultCenterY(configuration.defaultCenterY);
@@ -485,45 +475,6 @@ function createLatLng(param) {
}
}
-MapModel.prototype.setCenterLatLng = function (centerLatLng) {
- var newVal = createLatLng(centerLatLng);
- if (newVal === null) {
- logger.warn("centerLatLng is invalid");
- } else {
- this._centerLatLng = newVal;
- }
-};
-
-MapModel.prototype.getCenterLatLng = function () {
- return this._centerLatLng;
-};
-
-MapModel.prototype.setTopLeftLatLng = function (topLeftLatLng) {
- var newVal = createLatLng(topLeftLatLng);
- if (newVal === null) {
- logger.warn("topLeftLatLng is invalid");
- } else {
- this._topLeftLatLng = newVal;
- }
-};
-
-MapModel.prototype.getTopLeftLatLng = function () {
- return this._topLeftLatLng;
-};
-
-MapModel.prototype.setBottomRightLatLng = function (bottomRightLatLng) {
- var newVal = createLatLng(bottomRightLatLng);
- if (newVal === null) {
- logger.warn("bottomRightLatLng is invalid");
- } else {
- this._bottomRightLatLng = newVal;
- }
-};
-
-MapModel.prototype.getBottomRightLatLng = function () {
- return this._bottomRightLatLng;
-};
-
MapModel.prototype.getMaxZoom = function () {
return this._maxZoom;
};
@@ -544,37 +495,6 @@ MapModel.prototype.setTileSize = function (tileSize) {
this._tileSize = tileSize;
};
-MapModel.prototype.addSubmodels = function (submodels) {
- if (submodels !== undefined) {
- for (var i = 0; i < submodels.length; i++) {
- this.addSubmodel(submodels[i]);
- }
- }
-};
-
-MapModel.prototype.addSubmodel = function (submodel) {
- if (!(submodel instanceof MapModel)) {
- submodel = new MapModel(submodel);
- }
- this._submodels.push(submodel);
-};
-
-MapModel.prototype.getSubmodels = function () {
- return this._submodels;
-};
-
-MapModel.prototype.getSubmodelById = function (id) {
- if (this.getId() === id) {
- return this;
- }
- for (var i = 0; i < this._submodels.length; i++) {
- if (this._submodels[i].getId() === id) {
- return this._submodels[i];
- }
- }
- return null;
-};
-
MapModel.prototype.getByIdentifiedElement = function (ie, complete) {
var self = this;
if (ie.getType() === "ALIAS") {
diff --git a/frontend-js/src/main/js/map/data/Project.js b/frontend-js/src/main/js/map/data/Project.js
index adda342238..47432a6b43 100644
--- a/frontend-js/src/main/js/map/data/Project.js
+++ b/frontend-js/src/main/js/map/data/Project.js
@@ -19,6 +19,7 @@ function Project(data) {
this.registerListenerType("onreload");
this._dataOverlays = [];
+ this._models = [];
this._elementsPointingToSubmap = [];
if (data !== undefined) {
@@ -77,8 +78,11 @@ Project.prototype.update = function (data) {
self.setHasWarnings(data.hasWarnings());
self.setHasErrors(data.hasErrors());
- if (data.getModel() !== undefined) {
- self.setModel(new Model(data.getModel()));
+ if (data.getModels() !== undefined) {
+ var models = data.getModels();
+ for (var i = 0; i < models.length; i++) {
+ self.addModel(new Model(models[i]));
+ }
}
self.callListeners("onreload");
@@ -138,11 +142,23 @@ Project.prototype.getName = function () {
Project.prototype.setName = function (name) {
this._name = name;
};
-Project.prototype.getModel = function () {
- return this._model;
+Project.prototype.getModels = function () {
+ return this._models;
+};
+Project.prototype.getModelById = function (modelId) {
+ for (var i = 0; i < this._models.length; i++) {
+ if (this._models[i].getId() === modelId) {
+ return this._models[i];
+ }
+ }
+ return null;
+};
+Project.prototype.setModels = function (models) {
+ this._models = models;
};
-Project.prototype.setModel = function (model) {
- this._model = model;
+
+Project.prototype.addModel = function (model) {
+ this._models.push(model);
};
Project.prototype.getOverviewImages = function () {
diff --git a/frontend-js/src/main/js/map/surface/AliasSurface.js b/frontend-js/src/main/js/map/surface/AliasSurface.js
index 2aba79b1b4..c38438102c 100644
--- a/frontend-js/src/main/js/map/surface/AliasSurface.js
+++ b/frontend-js/src/main/js/map/surface/AliasSurface.js
@@ -121,7 +121,7 @@ AliasSurface.create = function (params) {
AliasSurface.createFromIdentifiedElement = function (params) {
var element = params.element;
var map = params.map;
- var model = map.getModel().getSubmodelById(element.getModelId());
+ var model = map.getProject().getModelById(element.getModelId());
var fillOpacity;
return ServerConnector.getConfigurationParam(ConfigurationType.OVERLAY_OPACITY).then(function (result) {
fillOpacity = result;
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 7f0a8f6e64..0cffc5c390 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -35,12 +35,14 @@ function processUrlGetParams(params) {
var project = params.getProject();
var sessionData = ServerConnector.getSessionData(project);
- var modelId = project.getModel().getId();
+ var modelId;
if (GuiConnector.getParams["submap"] !== undefined) {
modelId = parseInt(GuiConnector.getParams["submap"]);
+ } else {
+ modelId = project.getModels()[0].getId()
}
- var model = project.getModel().getSubmodelById(modelId);
+ var model = project.getModelById(modelId);
if (GuiConnector.getParams["x"] !== undefined && GuiConnector.getParams["y"] !== undefined) {
var point = new google.maps.Point(GuiConnector.getParams["x"], GuiConnector.getParams["y"]);
diff --git a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
index 18bb5a27a3..6cd40e9835 100644
--- a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
+++ b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
@@ -61,7 +61,7 @@ function getElements(elementIdentifiers, customMap) {
var modelScopePromises = [];
for (var key in elementsByModelId) {
if (elementsByModelId.hasOwnProperty(key)) {
- var model = customMap.getModel().getSubmodelById(parseInt(key));
+ var model = customMap.getProject().getModelById(parseInt(key));
modelScopePromises.push(model.getByIdentifiedElements(elementsByModelId[key], true));
}
}
@@ -71,7 +71,7 @@ function getElements(elementIdentifiers, customMap) {
var elementPromises = [];
for (var i = 0; i < identifiedElements.length; i++) {
var element = identifiedElements[i];
- var model = customMap.getModel().getSubmodelById(element.getModelId());
+ var model = customMap.getProject().getModelById(element.getModelId());
var promise = model.getByIdentifiedElement(element, true);
elementPromises.push(promise);
}
@@ -98,14 +98,10 @@ function createProjectData(options) {
});
},
getAllBioEntities: function () {
- var models = [map.getModel()];
+ var models = map.getProject().getModels();
var result = [];
- var i;
- for (i = 0; i < map.getModel().getSubmodels().length; i++) {
- models.push(map.getModel().getSubmodels()[i]);
- }
var promises = [];
- for (i = 0; i < models.length; i++) {
+ for (var i = 0; i < models.length; i++) {
promises.push(models[i].getAliases({
type: map.getConfiguration().getSimpleElementTypeNames(),
complete: true
@@ -187,7 +183,7 @@ function getReactionsForElements(elementIdentifiers, customMap) {
var modelScopePromises = [];
for (var key in elementsByModelId) {
if (elementsByModelId.hasOwnProperty(key)) {
- var model = customMap.getModel().getSubmodelById(parseInt(key));
+ var model = customMap.getProject().getModelById(parseInt(key));
var promise = model.getReactionsForElements(elementsByModelId[key], true);
modelScopePromises.push(promise);
}
diff --git a/frontend-js/src/test/js/gui/MapContextMenu-test.js b/frontend-js/src/test/js/gui/MapContextMenu-test.js
index 42c576cd05..b80cb3e41e 100644
--- a/frontend-js/src/test/js/gui/MapContextMenu-test.js
+++ b/frontend-js/src/test/js/gui/MapContextMenu-test.js
@@ -41,7 +41,7 @@ describe('MapContextMenu', function () {
element: testDiv,
customMap: map
});
- map.setActiveSubmapId(map.getProject().getModel().getId());
+ map.setActiveSubmapId(map.getProject().getModels()[0].getId());
map.setActiveSubmapClickCoordinates(new google.maps.Point(2, 12));
var handler = $($("a:contains('comment')", $(testDiv))[0]).data("handler");
@@ -60,7 +60,7 @@ describe('MapContextMenu', function () {
element: testDiv,
customMap: map
});
- map.setActiveSubmapId(map.getProject().getModel().getId());
+ map.setActiveSubmapId(map.getProject().getModels()[0].getId());
map.setActiveSubmapClickCoordinates(new google.maps.Point(2, 12));
assert.ok(!map.isDrawingOn());
diff --git a/frontend-js/src/test/js/gui/SelectionContextMenu-test.js b/frontend-js/src/test/js/gui/SelectionContextMenu-test.js
index 693b76345a..ed613d4947 100644
--- a/frontend-js/src/test/js/gui/SelectionContextMenu-test.js
+++ b/frontend-js/src/test/js/gui/SelectionContextMenu-test.js
@@ -33,7 +33,7 @@ describe('SelectionContextMenu', function () {
});
return contextMenu.init();
}).then(function () {
- map.setActiveSubmapId(map.getProject().getModel().getId());
+ map.setActiveSubmapId(map.getProject().getModels()[0].getId());
map.setActiveSubmapClickCoordinates(new google.maps.Point(2, 12));
var handler = $($("a:contains('PNG')", $(testDiv))[0]).data("handler");
@@ -54,7 +54,7 @@ describe('SelectionContextMenu', function () {
});
return contextMenu.init();
}).then(function () {
- map.setActiveSubmapId(map.getProject().getModel().getId());
+ map.setActiveSubmapId(map.getProject().getModels()[0].getId());
map.setActiveSubmapClickCoordinates(new google.maps.Point(2, 12));
var handler = $($("a:contains('CellDesigner')", $(testDiv))[0]).data("handler");
return handler();
diff --git a/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js b/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
index a646cce3f5..eaf001bb28 100644
--- a/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
@@ -159,7 +159,7 @@ describe('OverlayPanel', function () {
return panel.init().then(function () {
return panel.openAddOverlayDialog();
}).then(function () {
- var overlay = helper.createOverlay(panel.getProject().getModel());
+ var overlay = helper.createOverlay(panel.getProject().getModels()[0]);
return panel._addOverlayDialog.callListeners("onAddOverlay", overlay);
}).then(function () {
return panel.destroy();
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index a63b23d414..cbb33ed033 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -151,7 +151,7 @@ Helper.prototype.createProject = function () {
var result = new Project();
result.setProjectId("testId");
result.setId(this.idCounter++);
- result.setModel(this.createModel());
+ result.addModel(this.createModel());
var overlay = this.createOverlay(result);
result.addDataOverlay(overlay);
return result;
@@ -309,19 +309,6 @@ Helper.prototype.createModel = function () {
result.setHeight(800);
result.setMaxZoom(8);
result.setMinZoom(2);
- result.setCenterLatLng({
- lat: 10,
- lng: 20
- });
- result.setTopLeftLatLng({
- lat: 8,
- lng: 8
- });
- result.setBottomRightLatLng({
- lat: 30,
- lng: 30
- });
-
return result;
};
@@ -366,7 +353,7 @@ Helper.prototype.createCustomMapOptions = function (project) {
Helper.prototype.createAbstractCustomMap = function () {
var options = this.createCustomMapOptions();
- return new AbstractCustomMap(options.getProject().getModel(), options);
+ return new AbstractCustomMap(options.getProject().getModels()[0], options);
};
diff --git a/frontend-js/src/test/js/map/AbstractCustomMap-test.js b/frontend-js/src/test/js/map/AbstractCustomMap-test.js
index 011d3a7157..31aa1fc307 100644
--- a/frontend-js/src/test/js/map/AbstractCustomMap-test.js
+++ b/frontend-js/src/test/js/map/AbstractCustomMap-test.js
@@ -41,7 +41,7 @@ describe('AbstractCustomMap', function () {
var layout = project.getDataOverlays()[0];
var options = helper.createCustomMapOptions(project);
- var mockObject = new AbstractCustomMap(project.getModel(), options);
+ var mockObject = new AbstractCustomMap(project.getModels()[0], options);
var googleMap = helper.createGoogleMap();
@@ -76,7 +76,7 @@ describe('AbstractCustomMap', function () {
var options = helper.createCustomMapOptions(project);
- var mockObject = new AbstractCustomMap(project.getModel(), options);
+ var mockObject = new AbstractCustomMap(project.getModels()[0], options);
var result = mockObject.createTypeOptions(layoutDataObj);
diff --git a/frontend-js/src/test/js/map/CustomMap-test.js b/frontend-js/src/test/js/map/CustomMap-test.js
index 1400b236af..b360261aba 100644
--- a/frontend-js/src/test/js/map/CustomMap-test.js
+++ b/frontend-js/src/test/js/map/CustomMap-test.js
@@ -34,7 +34,7 @@ describe('CustomMap', function () {
it("with submaps", function () {
var options = helper.createCustomMapOptions();
- options.getProject().getModel().addSubmodel(helper.createModel());
+ options.getProject().addModel(helper.createModel());
var map = new CustomMap(options);
assert.ok(map);
@@ -805,7 +805,7 @@ describe('CustomMap', function () {
var options = helper.createCustomMapOptions();
var submodel = helper.createModel();
- options.getProject().getModel().addSubmodel(submodel);
+ options.getProject().addModel(submodel);
var map = new CustomMap(options);
@@ -827,7 +827,7 @@ describe('CustomMap', function () {
var options = helper.createCustomMapOptions();
var submodel = helper.createModel();
- options.getProject().getModel().addSubmodel(submodel);
+ options.getProject().addModel(submodel);
var map = new CustomMap(options);
map.openSubmap(submodel.getId());
diff --git a/frontend-js/src/test/js/map/data/MapModel-test.js b/frontend-js/src/test/js/map/data/MapModel-test.js
index 5f0880a965..7006c3f0e5 100644
--- a/frontend-js/src/test/js/map/data/MapModel-test.js
+++ b/frontend-js/src/test/js/map/data/MapModel-test.js
@@ -133,7 +133,7 @@ describe('MapModel', function () {
var model;
return ServerConnector.getProject().then(function (project) {
- model = project.getModel();
+ model = project.getModels()[0];
var ie = new IdentifiedElement({
modelId: 15781,
type: "ALIAS",
diff --git a/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js b/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
index cd228e1aa3..5e9a3e006b 100644
--- a/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
+++ b/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
@@ -197,7 +197,7 @@ describe('SearchDbOverlay', function () {
var searchParams = new IdentifiedElement({
type: "ALIAS",
id: 329177,
- modelId: project.getModel().getId()
+ modelId: project.getModels()[0].getId()
});
return searchDb.getDetailDataByIdentifiedElement(searchParams);
}).then(function (result) {
@@ -213,7 +213,7 @@ describe('SearchDbOverlay', function () {
var searchParams = new IdentifiedElement({
type: "POINT",
id: "2,3",
- modelId: project.getModel().getId()
+ modelId: project.getModels()[0].getId()
});
return searchDb.getDetailDataByIdentifiedElement(searchParams);
}).then(function (result) {
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index 1a149f451c..9e9e54d499 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -93,7 +93,7 @@ describe('minerva global', function () {
return minerva.create(options);
}).then(function (result) {
var sessionData = ServerConnectorMock.getSessionData(options.getProject());
- assert.equal(sessionData.getZoomLevel(options.getProject().getModel()), 5);
+ assert.equal(sessionData.getZoomLevel(options.getProject().getModels()[0]), 5);
return result.destroy();
});
});
@@ -105,7 +105,7 @@ describe('minerva global', function () {
options = helper.createCustomMapOptions(project);
return minerva.create(options);
}).then(function (result) {
- var center = ServerConnectorMock.getSessionData(options.getProject()).getCenter(options.getProject().getModel());
+ var center = ServerConnectorMock.getSessionData(options.getProject()).getCenter(options.getProject().getModels()[0]);
assert.ok(center instanceof google.maps.Point);
assert.equal(center.x, 5);
assert.equal(center.y, 6);
@@ -231,9 +231,6 @@ describe('minerva global', function () {
it('create with show submodel GET param', function () {
helper.setUrl("http://test/?submap=15781");
- var project = helper.createProject();
- project.getModel().setId(15781);
-
return ServerConnectorMock.getProject().then(function (project) {
var options = helper.createCustomMapOptions(project);
diff --git a/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js b/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
index 10cf351524..b701ce3b01 100644
--- a/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
+++ b/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
@@ -70,7 +70,7 @@ describe('MinervaPluginProxy', function () {
var params = {
coordinates: new google.maps.Point(184.79, 365.76),
zoom: 2,
- modelId: map.getProject().getModel().getId()
+ modelId: map.getProject().getModels()[0].getId()
};
return map.getOverlayByName("search").searchByCoordinates(params);
}).then(function () {
@@ -304,7 +304,7 @@ describe('MinervaPluginProxy', function () {
});
}).then(function () {
var sessionData = ServerConnector.getSessionData(map.getProject());
- var center = sessionData.getCenter(map.getProject().getModel());
+ var center = sessionData.getCenter(map.getProject().getModels()[0]);
assert.ok(center instanceof google.maps.Point);
assert.closeTo(parseFloat(center.x), 10, helper.EPSILON);
assert.closeTo(parseFloat(center.y), 20, helper.EPSILON);
@@ -344,7 +344,7 @@ describe('MinervaPluginProxy', function () {
});
}).then(function () {
var sessionData = ServerConnector.getSessionData(map.getProject());
- var zoom = sessionData.getZoomLevel(map.getProject().getModel());
+ var zoom = sessionData.getZoomLevel(map.getProject().getModels()[0]);
assert.equal(zoom, 10);
}).then(function () {
map.destroy();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index c489420b26..82bf729814 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -502,7 +502,7 @@ public interface Model {
*
* @param identifier
* identifier of the model
- * @return submodel identified by identifiere
+ * @return submodel identified by identifier
*/
Model getSubmodelById(String identifier);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
index c8f7f601e0..4fedb0ff45 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
@@ -1,18 +1,11 @@
package lcsb.mapviewer.api.projects.models;
-import java.awt.geom.Point2D;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.primefaces.model.map.LatLng;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
public class ModelMetaData implements Serializable {
@@ -59,26 +52,6 @@ public class ModelMetaData implements Serializable {
*/
private Integer maxZoom;
- /**
- * List of submodels in the model.
- */
- private List<ModelMetaData> submodels = new ArrayList<>();
-
- /**
- * Where is the center of the map in latitude, longitude format.
- */
- private LatLng centerLatLng;
-
- /**
- * Top-Left corner of the map (0,0) as a latLng coordinates.
- */
- private LatLng topLeftLatLng;
-
- /**
- * Bottom-Right corner of the map (width,height) as a latLng coordinates.
- */
- private LatLng bottomRightLatLng;
-
/**
* Type of the submodel.
*/
@@ -100,25 +73,10 @@ public class ModelMetaData implements Serializable {
this.setTileSize(model.getTileSize());
this.setWidth((int) (double) model.getWidth());
this.setHeight((int) (double) model.getHeight());
- int size = Math.max(width, height);
- CoordinationConverter cConverter = new CoordinationConverter(model);
- this.setCenterLatLng(cConverter.toLatLng(new Point2D.Double(size / 2, size / 2)));
- this.setBottomRightLatLng(cConverter.toLatLng(new Point2D.Double(model.getWidth(), model.getHeight())));
- this.setTopLeftLatLng(cConverter.toLatLng(new Point2D.Double(0, 0)));
this.setDefaultCenterX(model.getDefaultCenterX());
this.setDefaultCenterY(model.getDefaultCenterY());
this.setDefaultZoomLevel(model.getDefaultZoomLevel());
- List<ModelMetaData> submodels = new ArrayList<>();
- List<ModelSubmodelConnection > submodelLinks = new ArrayList<>();
- submodelLinks.addAll(model.getSubmodels());
- submodelLinks.sort(ModelSubmodelConnection.ID_COMPARATOR);
- for (ModelSubmodelConnection connection : submodelLinks) {
- ModelMetaData submodelData = new ModelMetaData(connection.getSubmodel());
- submodelData.setSubmodelType(connection.getType());
- submodels.add(submodelData);
- }
- this.setSubmodels(submodels);
}
protected ModelMetaData() {
@@ -192,23 +150,6 @@ public class ModelMetaData implements Serializable {
this.maxZoom = maxZoom;
}
- /**
- * @return the centerLatLng
- * @see #centerLatLng
- */
- public LatLng getCenterLatLng() {
- return centerLatLng;
- }
-
- /**
- * @param centerLatLng
- * the centerLatLng to set
- * @see #centerLatLng
- */
- public void setCenterLatLng(LatLng centerLatLng) {
- this.centerLatLng = centerLatLng;
- }
-
/**
* @return the name
* @see #name
@@ -226,40 +167,6 @@ public class ModelMetaData implements Serializable {
this.name = name;
}
- /**
- * @return the topLeftLatLng
- * @see #topLeftLatLng
- */
- public LatLng getTopLeftLatLng() {
- return topLeftLatLng;
- }
-
- /**
- * @param topLeftLatLng
- * the topLeftLatLng to set
- * @see #topLeftLatLng
- */
- public void setTopLeftLatLng(LatLng topLeftLatLng) {
- this.topLeftLatLng = topLeftLatLng;
- }
-
- /**
- * @return the bottomRightLatLng
- * @see #bottomRightLatLng
- */
- public LatLng getBottomRightLatLng() {
- return bottomRightLatLng;
- }
-
- /**
- * @param bottomRightLatLng
- * the bottomRightLatLng to set
- * @see #bottomRightLatLng
- */
- public void setBottomRightLatLng(LatLng bottomRightLatLng) {
- this.bottomRightLatLng = bottomRightLatLng;
- }
-
/**
* @return the width
* @see #width
@@ -294,23 +201,6 @@ public class ModelMetaData implements Serializable {
this.height = height;
}
- /**
- * @return the submodels
- * @see #submodels
- */
- public List<ModelMetaData> getSubmodels() {
- return submodels;
- }
-
- /**
- * @param submodels
- * the submodels to set
- * @see #submodels
- */
- public void setSubmodels(List<ModelMetaData> submodels) {
- this.submodels = submodels;
- }
-
/**
* @return the idObject
* @see #idObject
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
index b59b1e7903..238d0a36a9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -43,12 +43,7 @@ public class ModelRestImpl extends BaseRestImpl {
if (submodel == null) {
return null;
} else {
- ModelMetaData result = new ModelMetaData(submodel);
-
- List<ModelMetaData> metaDataToProcess = new ArrayList<>();
- metaDataToProcess.add(result);
- metaDataToProcess.addAll(result.getSubmodels());
- return result;
+ return new ModelMetaData(submodel);
}
}
--
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