Merge branch '702-plugin-functionalities' into 'master'

Resolve "plugin functionalities"

Closes #702

See merge request !690

CHANGELOG

 minerva (12.3.0~alpha.0) unstable; urgency=low
-  * Feature: annotators are more flexible - you can define set of input and outputs used by
-    annotator (#617)
-  * Small improvement: added current username next to logout button in admin panel (#660)
-  * Small improvement: New comment dialog does not contain content of previous comment dialog (#680)
+  * Feature: annotators are more flexible - you can define set of input and 
+    outputs used by annotator (#617)
+  * Small improvement: added current username next to logout button in admin 
+    panel (#660)
+  * Small improvement: New comment dialog does not contain content of previous 
+    comment dialog (#680)
   * Small improvement: Left logo is configurable (#731)
-  * Bug fix: progress bar of gene genome mapping upload is refreshing properly (#728)
+  * Small improvement: Plugin API provides list of overview images (#702)
+  * Small improvement: Plugin API allows to show/hide overview images (#702)
+  * Small improvement: Plugin API allows to trigger search on the map (#702)
+  * Small improvement: Plugin API allows to clear search results on map (#702)
+  * Bug fix: progress bar of gene genome mapping upload is refreshing properly 
+    (#728)
 
 minerva (12.2.0~beta.2) unstable; urgency=medium
   * Bug fix: order of the overlays is defined explicitly also for general

frontend-js/src/main/js/gui/OverviewDialog.js

@@ -255,7 +255,17 @@ OverviewDialog.prototype.drawClickableShapes = function (canvas, ratio) {
  *
  */
 OverviewDialog.prototype.destroy = function () {
-  $(this.getElement()).dialog("destroy");
+  var div = $(this.getElement());
+  if (div.hasClass("ui-dialog-content")) {
+    div.dialog("destroy");
+  }
+};
+
+/**
+ *
+ */
+OverviewDialog.prototype.close = function () {
+  $(this.getElement()).dialog('close');
 };
 
 module.exports = OverviewDialog;

frontend-js/src/main/js/gui/topMenu/TopMenu.js

@@ -192,7 +192,7 @@ TopMenu.prototype.init = function () {
   var commentCheckbox = self.getControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX);
   var refreshCommentButton = self.getControlElement(PanelControlElementType.MENU_REFRESH_COMMENTS_BUTTON);
   commentCheckbox.onclick = function () {
-    ServerConnector.getSessionData(project).setShowComments(commentCheckbox.checked);
+    self.getServerConnector().getSessionData(project).setShowComments(commentCheckbox.checked);
     if (commentCheckbox.checked) {
       $(refreshCommentButton).css("display", "inline");
     } else {
@@ -228,9 +228,10 @@ TopMenu.prototype.init = function () {
       return self._overviewDialog.showOverview();
     };
     $(showOverviewButton).css("display", "inline-block");
+    self.getMap().setOverviewDialog(self._overviewDialog);
   }
 
-  if (ServerConnector.getSessionData().getShowComments()) {
+  if (self.getServerConnector().getSessionData().getShowComments()) {
     self.getControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX).checked = true;
     return self.getMap().refreshComments();
   } else {

frontend-js/src/main/js/map/AbstractCustomMap.js

@@ -882,7 +882,7 @@ AbstractCustomMap.prototype.setElement = function (element) {
  *
  * @param {Point} coordinates
  *          new center point on map
- * @returns {PromiseLike}
+ * @returns {Promise|PromiseLike}
  */
 AbstractCustomMap.prototype.setCenter = function (coordinates) {
   if (!(coordinates instanceof Point)) {
@@ -916,6 +916,7 @@ AbstractCustomMap.prototype.getBounds = function () {
  *
  * @param {number} zoom
  *          new zoom level on map
+ * @return {Promise|PromiseLike}
  */
 AbstractCustomMap.prototype.setZoom = function (zoom) {
   var self = this;

frontend-js/src/main/js/map/CustomMap.js

@@ -10,8 +10,9 @@ var Alias = require('./data/Alias');
 var CommentDialog = require('../gui/CommentDialog');
 var ConfigurationType = require('../ConfigurationType');
 var CustomMapOptions = require('./CustomMapOptions');
-var IdentifiedElement = require('./data/IdentifiedElement');
 var DataOverlay = require('./data/DataOverlay');
+var IdentifiedElement = require('./data/IdentifiedElement');
+var OverviewDialog = require('../gui/OverviewDialog');
 var Reaction = require('./data/Reaction');
 var ReferenceGenome = require('./data/ReferenceGenome');
 var SecurityError = require('../SecurityError');
@@ -354,7 +355,7 @@ CustomMap.prototype.refreshComments = function () {
       return commentDbOverlay.clear();
     }
   }
-  throw new Error("comment DbOverlay not found");
+  return Promise.reject(new Error("comment DbOverlay not found"));
 };
 
 /**
@@ -1153,6 +1154,34 @@ CustomMap.prototype.getSelectedPolygon = function () {
   return this._selectedPolygon;
 };
 
+/**
+ *
+ * @param {OverviewDialog} overviewDialog
+ */
+CustomMap.prototype.setOverviewDialog = function (overviewDialog) {
+  this._overviewDialog = overviewDialog;
+};
+
+/**
+ *
+ * @returns {OverviewDialog}
+ */
+CustomMap.prototype.getOverviewDialog = function () {
+  var self = this;
+  if (this._overviewDialog === undefined) {
+    logger.warn("OverviewDialog is not defined");
+    var overviewDialogDiv = Functions.createElement({type: "div"});
+    self.getElement().appendChild(overviewDialogDiv);
+    this._overviewDialog = new OverviewDialog({
+      customMap: self,
+      configuration: self.getConfiguration(),
+      project: self.getProject(),
+      element: overviewDialogDiv
+    });
+  }
+  return this._overviewDialog;
+};
+
 /**
  *
  * @param {number} params.modelId
@@ -1244,6 +1273,13 @@ CustomMap.prototype.destroy = function () {
   if (self.getSelectionContextMenu() !== undefined) {
     self.getSelectionContextMenu().destroy();
   }
+
+  if (self._overviewDialog !== undefined) {
+    var div = $(self._overviewDialog.getElement());
+    if (div.hasClass("ui-dialog-content")) {
+      div.dialog("destroy");
+    }
+  }
 };
 
 /**

frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerCanvas.js

@@ -348,7 +348,7 @@ OpenLayerCanvas.prototype.fitBounds = function (bounds) {
 };
 
 OpenLayerCanvas.prototype.setCenter = function (center) {
-  this.getOpenLayersMap().getView().setCenter(this.fromPointToProjection(center));
+  return Promise.resolve(this.getOpenLayersMap().getView().setCenter(this.fromPointToProjection(center)));
 };
 
 /**

frontend-js/src/main/js/map/data/Chemical.js

@@ -3,20 +3,38 @@
 var Annotation = require("./Annotation");
 var TargettingStructure = require("./TargettingStructure");
 
+/**
+ * @typedef {TargettingStructureOptions} ChemicalOptions
+ * @property {Annotation[]} references
+ * @property {string[]} synonyms
+ * @property {string} description
+ * @property {string} directEvidence
+ * @property {Annotation[]} directEvidenceReferences
+ */
+
 /**
  *
- * @param javaObject
+ * @param {ChemicalOptions|Chemical} javaObject
  * @constructor
  */
 function Chemical(javaObject) {
   TargettingStructure.call(this, javaObject);
   if (javaObject !== undefined) {
-    this.setReferences(javaObject.references);
-    this.setDescription(javaObject.description);
-    this.setSynonyms(javaObject.synonyms);
-
-    this.setDirectEvidence(javaObject.directEvidence);
-    this.setDirectEvidenceReferences(javaObject.directEvidenceReferences);
+    if (javaObject instanceof Chemical) {
+      this.setReferences(javaObject.getReferences());
+      this.setDescription(javaObject.getDescription());
+      this.setSynonyms(javaObject.getSynonyms());
+
+      this.setDirectEvidence(javaObject.getDirectEvidence());
+      this.setDirectEvidenceReferences(javaObject.getDirectEvidenceReferences());
+    } else {
+      this.setReferences(javaObject.references);
+      this.setDescription(javaObject.description);
+      this.setSynonyms(javaObject.synonyms);
+
+      this.setDirectEvidence(javaObject.directEvidence);
+      this.setDirectEvidenceReferences(javaObject.directEvidenceReferences);
+    }
   }
 }
 

frontend-js/src/main/js/map/data/Drug.js

@@ -3,19 +3,36 @@
 var Annotation = require("./Annotation");
 var TargettingStructure = require("./TargettingStructure");
 
+/**
+ * @typedef {TargettingStructureOptions} DrugOptions
+ * @property {string[]} brandNames
+ * @property {Annotation[]} references
+ * @property {string[]} synonyms
+ * @property {string} description
+ * @property {string} bloodBrainBarrier
+ */
+
 /**
  *
- * @param javaObject
+ * @param {DrugOptions|Drug} javaObject
  * @constructor
  */
 function Drug(javaObject) {
   TargettingStructure.call(this, javaObject);
   if (javaObject !== undefined) {
-    this.setBrandNames(javaObject.brandNames);
-    this.setReferences(javaObject.references);
-    this.setSynonyms(javaObject.synonyms);
-    this.setDescription(javaObject.description);
-    this.setBloodBrainBarrier(javaObject.bloodBrainBarrier);
+    if (javaObject instanceof Drug) {
+      this.setBrandNames(javaObject.getBrandNames());
+      this.setReferences(javaObject.getReferences());
+      this.setSynonyms(javaObject.getSynonyms());
+      this.setDescription(javaObject.getDescription());
+      this.setBloodBrainBarrier(javaObject.getBloodBrainBarrier());
+    } else {
+      this.setBrandNames(javaObject.brandNames);
+      this.setReferences(javaObject.references);
+      this.setSynonyms(javaObject.synonyms);
+      this.setDescription(javaObject.description);
+      this.setBloodBrainBarrier(javaObject.bloodBrainBarrier);
+    }
   }
 }
 

frontend-js/src/main/js/map/data/MiRna.js

@@ -2,9 +2,13 @@
 
 var TargettingStructure = require("./TargettingStructure");
 
+/**
+ * @typedef {TargettingStructureOptions} MiRnaOptions
+ */
+
 /**
  *
- * @param javaObject
+ * @param {MiRnaOptions|MiRna} javaObject
  * @constructor
  * @extends TargettingStructure
  */

frontend-js/src/main/js/map/data/Target.js

@@ -17,19 +17,26 @@ var logger = require('../../logger');
 
 /**
  *
- * @param {TargetOptions} javaObject
+ * @param {TargetOptions|Target} javaObject
  * @constructor
  */
 function Target(javaObject) {
-  this.setName(javaObject.name);
-  this.setTargetElements(javaObject.targetElements);
-  this.setTargetParticipants(javaObject.targetParticipants);
-  this.setReferences(javaObject.references);
+  if (javaObject instanceof Target) {
+    this.setName(javaObject.getName());
+    this.setTargetElements(javaObject.getTargetElements());
+    this.setTargetParticipants(javaObject.getTargetParticipants());
+    this.setReferences(javaObject.getReferences());
+  } else {
+    this.setName(javaObject.name);
+    this.setTargetElements(javaObject.targetElements);
+    this.setTargetParticipants(javaObject.targetParticipants);
+    this.setReferences(javaObject.references);
+  }
 }
 
 /**
  *
- * @param {IdentifiedElementInput[]} targetElements
+ * @param {IdentifiedElementInput[]|IdentifiedElement[]} targetElements
  */
 Target.prototype.setTargetElements = function (targetElements) {
   this._targetElements = [];
@@ -49,7 +56,7 @@ Target.prototype.getTargetElements = function () {
 
 /**
  *
- * @param {AnnotationOptions[]} targetParticipants
+ * @param {AnnotationOptions[]|Annotation[]} targetParticipants
  */
 Target.prototype.setTargetParticipants = function (targetParticipants) {
   this._targetParticipants = [];
@@ -100,7 +107,7 @@ Target.prototype.isVisible = function () {
 
 /**
  *
- * @param {AnnotationOptions[]} references
+ * @param {AnnotationOptions[]|Annotation[]} references
  */
 Target.prototype.setReferences = function (references) {
   this._references = [];

frontend-js/src/main/js/map/data/TargettingStructure.js

@@ -4,21 +4,32 @@
 
 var Target = require("./Target");
 
+// noinspection JSUnusedLocalSymbols
 var logger = require('../../logger');
 
+/**
+ * @typedef {Object} TargettingStructureOptions
+ * @property {string} name
+ * @property {number} id
+ * @property {TargetOptions[]} targets
+ */
+
 /**
  *
- * @param {Object} [javaObject]
- * @param {string} javaObject.name
- * @param {number} javaObject.id
- * @param {TargetOptions[]} javaObject.targets
+ * @param {TargettingStructureOptions|TargettingStructure} javaObject
  * @constructor
  */
 function TargettingStructure(javaObject) {
   if (javaObject !== undefined) {
-    this.setName(javaObject.name);
-    this.setId(javaObject.id);
-    this.setTargets(javaObject.targets);
+    if (javaObject instanceof TargettingStructure) {
+      this.setName(javaObject.getName());
+      this.setId(javaObject.getId());
+      this.setTargets(javaObject.getTargets());
+    } else {
+      this.setName(javaObject.name);
+      this.setId(javaObject.id);
+      this.setTargets(javaObject.targets);
+    }
   }
 }
 
@@ -26,7 +37,7 @@ function TargettingStructure(javaObject) {
  *
  * @param {string} name
  */
-TargettingStructure.prototype.setName = function(name) {
+TargettingStructure.prototype.setName = function (name) {
   this._name = name;
 };
 
@@ -34,7 +45,7 @@ TargettingStructure.prototype.setName = function(name) {
  *
  * @returns {string}
  */
-TargettingStructure.prototype.getName = function() {
+TargettingStructure.prototype.getName = function () {
   return this._name;
 };
 
@@ -42,7 +53,7 @@ TargettingStructure.prototype.getName = function() {
  *
  * @param {number} id
  */
-TargettingStructure.prototype.setId = function(id) {
+TargettingStructure.prototype.setId = function (id) {
   this._id = id;
 };
 
@@ -50,15 +61,15 @@ TargettingStructure.prototype.setId = function(id) {
  *
  * @returns {number}
  */
-TargettingStructure.prototype.getId = function() {
+TargettingStructure.prototype.getId = function () {
   return this._id;
 };
 
 /**
  *
- * @param {TargetOptions[]} targets
+ * @param {TargetOptions[]|Target[]} targets
  */
-TargettingStructure.prototype.setTargets = function(targets) {
+TargettingStructure.prototype.setTargets = function (targets) {
   this._targets = [];
   for (var i = 0; i < targets.length; i++) {
     this._targets.push(new Target(targets[i]));
@@ -69,7 +80,7 @@ TargettingStructure.prototype.setTargets = function(targets) {
  *
  * @returns {Target[]}
  */
-TargettingStructure.prototype.getTargets = function() {
+TargettingStructure.prototype.getTargets = function () {
   return this._targets;
 };
 
@@ -78,11 +89,11 @@ TargettingStructure.prototype.getTargets = function() {
  * @param {IdentifiedElement[]} targetIdentifiedElement
  * @returns {Target[]}
  */
-TargettingStructure.prototype.getTargetsForIdentifiedElement = function(targetIdentifiedElement) {
+TargettingStructure.prototype.getTargetsForIdentifiedElement = function (targetIdentifiedElement) {
   var result = [];
-  this.getTargets().forEach(function(target) {
+  this.getTargets().forEach(function (target) {
     var targetOk = false;
-    target.getTargetElements().forEach(function(identifiedElement){
+    target.getTargetElements().forEach(function (identifiedElement) {
       if (targetIdentifiedElement.equals(identifiedElement)) {
         targetOk = true;
       }

frontend-js/src/main/js/plugin/MinervaPluginProxy.js

 "use strict";
 
 var Annotation = require('../map/data/Annotation');
+var Chemical = require('../map/data/Chemical');
+var Drug = require('../map/data/Drug');
 var IdentifiedElement = require('../map/data/IdentifiedElement');
+var MiRna = require('../map/data/MiRna');
 var UserDbOverlay = require('../map/overlay/UserDbOverlay');
+var SearchDbOverlay = require('../map/overlay/SearchDbOverlay');
 var Configuration = require('../Configuration');
 
 var Bounds = require('../map/canvas/Bounds');
@@ -37,6 +41,7 @@ var Promise = require("bluebird");
  * @property {function(): *} getDisease
  * @property {function(): *} getOrganism
  * @property {function(): *[]} getModels
+ * @property {function(): *[]} getOverviewImages
  * @property {function(): DataOverlay[]} getDataOverlays
  */
 
@@ -46,18 +51,22 @@ var Promise = require("bluebird");
  * @property {function(): (Promise<DataOverlay[]>|*)} getVisibleDataOverlays
  * @property {function(number|DataOverlay): (Promise<DataOverlay[]>|*)} showDataOverlay
  * @property {function(number|DataOverlay): (Promise<DataOverlay[]>|*)} hideDataOverlay
+ * @property {function({id: number}): void} showOverviewImage
+ * @property {function(): void} hideOverviewImage
  * @property {function(*)} addListener
  * @property {function(*)} removeListener
  * @property {function(): Array} removeAllListeners
  * @property {(function(*=): Promise<Array|never>)} getHighlightedBioEntities
  * @property {(function(*=): Promise<any|never>)} hideBioEntity
- * @property {(function(*): PromiseLike)} setCenter
+ * @property {(function({modelId: number, x: number, y: number}): Promise|PromiseLike)} setCenter
  * @property {(function(*): Point)} getCenter
  * @property {(function(*): Bounds)} getBounds
  * @property {(function(*): void)} fitBounds
- * @property {(function(*): *)} setZoom
+ * @property {(function({modelId: number, zoom: number}): Promise|PromiseLike)} setZoom
  * @property {(function(*): number)} getZoom
  * @property {(function(*): PromiseLike)} openMap
+ * @property {function({dbOverlayName: string, [query]:string, [perfect]: boolean, [fitBounds]:boolean, [coordinates]:Point}): Promise|PromiseLike} triggerSearch
+ * @property {function(): Promise|PromiseLike} clear
  */
 
 
@@ -95,10 +104,20 @@ function getFullElements(customMap, identifiedElements) {
     identifiedElements,
     function (item) {
       if (item.length === undefined) {
-        return customMap.getSubmapById(item.getModelId()).getModel().getByIdentifiedElement(item, true).then(
-          function (fullElement) {
-            result.push(fullElement);
-          });
+        if (item instanceof IdentifiedElement) {
+          return customMap.getSubmapById(item.getModelId()).getModel().getByIdentifiedElement(item, true).then(
+            function (fullElement) {
+              result.push(fullElement);
+            });
+        } else if (item instanceof Drug) {
+          result.push(new Drug(item));
+        } else if (item instanceof Chemical) {
+          result.push(new Chemical(item));
+        } else if (item instanceof MiRna) {
+          result.push(new MiRna(item));
+        } else {
+          return Promise.reject(new Error("Unknown object type: " + item.constructor.name));
+        }
       } else {
         return getFullElements(customMap, item).then(function (resultRow) {
           result.push(resultRow);
@@ -284,6 +303,19 @@ function createProjectData(options) {
         });
       }
       return result;
+    },
+    getOverviewImages: function () {
+      var result = [];
+      for (var i = 0; i < map.getProject().getOverviewImages().length; i++) {
+        var image = map.getProject().getOverviewImages()[i];
+        result.push({
+          id: image.idObject,
+          filename: image.filename,
+          width: image.width,
+          height: image.height
+        });
+      }
+      return result;
     }
   };
 }
@@ -401,6 +433,44 @@ function createProjectMap(options) {
   var listenersData = [];
 
   return {
+    /**
+     *
+     * @param {Object} params
+     * @param {string} params.dbOverlayName
+     * @param {string} [params.query]
+     * @param {boolean} [params.perfect]
+     * @param {boolean} [params.fitBounds]
+     * @param {Point} [params.coordinates]
+     * @param {number} [params.modelId]
+     * @param {number} [params.zoom]
+     *
+     *
+     * @return {Promise|PromiseLike}
+     */
+    triggerSearch: function (params) {
+      var dbOverlay = getOverlayByName(map, params.dbOverlayName);
+      if (params.query !== undefined) {
+        return dbOverlay.searchByQuery(params.query, params.perfect, params.fitBounds);
+      } else if (dbOverlay instanceof SearchDbOverlay) {
+        return dbOverlay.searchByCoordinates({
+          coordinates: params.coordinates,
+          modelId: params.modelId,
+          fitBounds: params.fitBounds,
+          zoom: params.zoom
+        });
+      } else {
+        return Promise.reject(new Error("Don't know how to handle your query"));
+      }
+    },
+    /**
+     *
+     * @return {PromiseLike|Promise}
+     */
+    clear: function () {
+      map.getServerConnector().getSessionData(map.getProject()).setShowComments(false);
+      return Promise.all([map.clearDbOverlays(), map.refreshComments()]);
+    },
+
     getVisibleDataOverlays: function () {
       return map.getVisibleDataOverlays();
     },
@@ -420,6 +490,21 @@ function createProjectMap(options) {
     hideDataOverlay: function (param) {
       return map.hideDataOverlay(param);
     },
+    /**
+     *
+     * @param {Object} param
+     * @param {number} param.id
+     */
+    showOverviewImage: function (param) {
+      map.getOverviewDialog().showOverview(param.id);
+    },
+    /**
+     *
+     */
+    hideOverviewImage: function () {
+      map.getOverviewDialog().close();
+    },
+
     /**
      *
      * @param {Object} param
@@ -608,6 +693,15 @@ function createProjectMap(options) {
         return map.getOverlayByName(pluginId).removeSurface(surfaceElements);
       });
     },
+
+    /**
+     *
+     * @param {Object} params
+     * @param {number} params.modelId
+     * @param {number} params.x
+     * @param {number} params.y
+     * @return {Promise|PromiseLike}
+     */
     setCenter: function (params) {
       var submap = map.getSubmapById(params.modelId);
       if (submap === null) {
@@ -638,6 +732,14 @@ function createProjectMap(options) {