user preferences are processed on client side

frontend-js/.idea/dictionaries/piotr_gawron.xml

-<component name="ProjectDictionaryState">
-  <dictionary name="piotr.gawron">
-    <words>
-      <w>mailto</w>
-    </words>
-  </dictionary>
-</component>
\ No newline at end of file

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

+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+function UserPreferences(javaObject) {
+  if (javaObject !== undefined) {
+    this.setProjectUpload(javaObject["project-upload"]);
+    this.setElementAnnotators(javaObject["element-annotators"]);
+    this.setElementRequiredAnnotations(javaObject["element-required-annotations"]);
+    this.setElementValidAnnotations(javaObject["element-valid-annotations"]);
+  } else {
+    this._projectUpload = {};
+    this._elementAnnotators = {};
+    this._elementRequiredAnnotations = {};
+    this._elementValidAnnotations = {};
+  }
+}
+
+UserPreferences.prototype.setProjectUpload = function (projectUpload) {
+  this._projectUpload = {
+    autoResize: projectUpload["auto-resize"],
+    validateMiriam: projectUpload["validate-miriam"],
+    annotateModel: projectUpload["annotate-model"],
+    cacheData: projectUpload["cache-data"],
+    semanticZooming: projectUpload["semantic-zooming"],
+    sbgn: projectUpload["sbgn"]
+  };
+};
+UserPreferences.prototype.getProjectUpload = function () {
+  return this._projectUpload;
+};
+UserPreferences.prototype.setElementAnnotators = function (elementAnnotators) {
+  this._elementAnnotators = elementAnnotators;
+};
+UserPreferences.prototype.getElementAnnotators = function (className) {
+  return this._elementAnnotators[className];
+};
+UserPreferences.prototype.setElementRequiredAnnotations = function (elementRequiredAnnotations) {
+  this._elementRequiredAnnotations = {};
+  for (var key in elementRequiredAnnotations) {
+    if (elementRequiredAnnotations.hasOwnProperty(key)) {
+      var data = elementRequiredAnnotations[key];
+      this._elementRequiredAnnotations[key] = {
+        requiredAtLeastOnce: data["require-at-least-one"],
+        list: data["annotation-list"]
+      };
+    }
+  }
+};
+UserPreferences.prototype.getElementRequiredAnnotations = function (className) {
+  return this._elementRequiredAnnotations[className];
+};
+UserPreferences.prototype.setElementValidAnnotations = function (elementValidAnnotations) {
+  this._elementValidAnnotations = elementValidAnnotations;
+};
+UserPreferences.prototype.getElementValidAnnotations = function (className) {
+  return this._elementValidAnnotations[className];
+};
+
+module.exports = UserPreferences;

frontend-js/src/test/js/helper.js

@@ -25,6 +25,7 @@ var SearchDbOverlay = require("../../main/js/map/overlay/SearchDbOverlay");
 var User = require("../../main/js/map/data/User");
 
 var Cookies = require('js-cookie');
+var fs = require('fs');
 
 var GuiConnector = require('../../main/js/GuiConnector');
 
@@ -37,10 +38,10 @@ function Helper(configuration) {
   this.EPSILON = Helper.EPSILON;
 }
 
-Helper.prototype.setConfiguration = function (configuration) {
+Helper.prototype.setConfiguration = function(configuration) {
   this._configuration = configuration;
 };
-Helper.prototype.getConfiguration = function () {
+Helper.prototype.getConfiguration = function() {
   return this._configuration;
 };
 
@@ -143,7 +144,7 @@ Helper.prototype.createComment = function (element) {
   return result;
 };
 
-Helper.prototype.createProject = function() {
+Helper.prototype.createProject = function () {
   var result = new Project();
   result.setProjectId("testId");
   result.setId(this.idCounter++);
@@ -151,17 +152,17 @@ Helper.prototype.createProject = function() {
   return result;
 };
 
-Helper.prototype.createUser = function() {
+Helper.prototype.createUser = function () {
   var result = new User({
-    login : "test_login",
-    id : this.idCounter++,
-    name : "some name",
-    surname : "surname",
+    login: "test_login",
+    id: this.idCounter++,
+    name: "some name",
+    surname: "surname",
   });
   return result;
 };
 
-Helper.prototype.createAlias = function(map) {
+Helper.prototype.createAlias = function (map) {
   var mapId;
   if (map === undefined) {
     mapId = this.idCounter++;
@@ -169,15 +170,15 @@ Helper.prototype.createAlias = function(map) {
     mapId = map.getId();
   }
   var result = new Alias({
-    idObject : this.idCounter++,
-    name : "Test element",
-    type : "RNA",
-    modelId : mapId,
-    bounds : {
-      x : 10.0,
-      y : 20.0,
-      width : 30.0,
-      height : 40.0,
+    idObject: this.idCounter++,
+    name: "Test element",
+    type: "RNA",
+    modelId: mapId,
+    bounds: {
+      x: 10.0,
+      y: 20.0,
+      width: 30.0,
+      height: 40.0,
     },
     references: [],
   });
@@ -198,10 +199,10 @@ Helper.prototype.createLayoutAlias = function (alias) {
     modelId = this.idCounter++;
   }
   var result = new LayoutAlias({
-    idObject : id,
-    value : 0.2,
-    color : {
-      a : 23
+    idObject: id,
+    value: 0.2,
+    color: {
+      a: 23
     },
     modelId: modelId,
     geneVariations: [{}]
@@ -386,6 +387,18 @@ Helper.prototype.setUrl = function (url) {
   GuiConnector.init();
 };
 
+Helper.prototype.readFile = function (filename) {
+  return new Promise(function (resolve, reject) {
+    fs.readFile(filename, 'utf8', function (err, content) {
+      if (err) {
+        reject(err);
+      } else {
+        resolve(content);
+      }
+    });
+  });
+};
+
 Helper.EPSILON = 1e-6;
 
 module.exports = Helper;

frontend-js/src/test/js/map/data/UserPreferences-test.js

+"use strict";
+
+require("../../mocha-config")
+/* exported logger */
+
+var UserPreferences = require('../../../../main/js/map/data/UserPreferences');
+
+var logger = require('../../logger');
+
+var chai = require('chai');
+var assert = chai.assert;
+
+var fs = require('fs');
+var Promise = require('fs');
+
+describe('UserPreferences', function () {
+  it("constructor", function () {
+    return helper.readFile("testFiles/preferences.json").then(function (content) {
+      var object = new UserPreferences(JSON.parse(content));
+      assert.ok(object);
+      assert.notOk(object.getProjectUpload().autoResize);
+      assert.ok(object.getProjectUpload().cacheData);
+
+      assert.ok(object.getElementAnnotators("lcsb.mapviewer.model.map.species.Protein").length > 0);
+      assert.ok(object.getElementValidAnnotations("lcsb.mapviewer.model.map.species.Protein").length > 0);
+      assert.ok(object.getElementRequiredAnnotations("lcsb.mapviewer.model.map.species.Protein").requiredAtLeastOnce);
+      assert.ok(object.getElementRequiredAnnotations("lcsb.mapviewer.model.map.species.Protein").list.length > 0);
+    })
+  });
+});

persist/src/db/11.1.0/fix_db_20170829.sql

@@ -4,3 +4,10 @@ alter table user_annotation_schema_table add column autoresizemap boolean defaul
 alter table user_annotation_schema_table add column cachedata boolean default true;
 alter table user_annotation_schema_table add column semanticzooming boolean default false;
 alter table class_required_annotation_table RENAME column requireatlestoneannotation to requireatleastoneannotation;
+
+-- rename config annotation class name
+update class_annotator_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+update class_required_annotation_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+update class_valid_annotation_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+
+

rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java

@@ -128,7 +128,7 @@ public class UserRestImpl extends BaseRestImpl {
 	private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
 		Map<String, Object> result = new HashMap<>();
 		for (UserClassValidAnnotations userClassAnnotators : classValidAnnotators) {
-			result.put(userClassAnnotators.getClassName(), userClassAnnotators.getValidMiriamTypes());
+			result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getValidMiriamTypes()));
 		}
 		return result;
 	}
@@ -158,7 +158,12 @@ public class UserRestImpl extends BaseRestImpl {
 		for (UserClassRequiredAnnotations requiredAnnotations : classRequiredAnnotators) {
 			Map<String, Object> row = new HashMap<>();
 			row.put("require-at-least-one", requiredAnnotations.getRequireAtLeastOneAnnotation());
-			row.put("annotation-list", requiredAnnotations.getRequiredMiriamTypes());
+			List<String> miriamTypes = new ArrayList<>();
+
+			for (MiriamType mt : requiredAnnotations.getRequiredMiriamTypes()) {
+				miriamTypes.add(mt.name());
+			}
+			row.put("annotation-list", miriamTypes);
 			result.put(requiredAnnotations.getClassName(), row);
 		}
 		return result;
@@ -200,7 +205,7 @@ public class UserRestImpl extends BaseRestImpl {
 	private Map<String, Object> prepareElementAnnotators(List<UserClassAnnotators> classAnnotators) {
 		Map<String, Object> result = new HashMap<>();
 		for (UserClassAnnotators userClassAnnotators : classAnnotators) {
-			result.put(userClassAnnotators.getClassName(), userClassAnnotators.getAnnotators());
+			result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getAnnotators()));
 		}
 		return result;
 	}