From 5e65fe5ca23e7db23cfcdc417cf73b98d2056c23 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 12 Mar 2018 13:26:01 +0100
Subject: [PATCH] script in frontend unt tests to refresh query cache for
 mocking server side

This sript refreshes all GET queries. Because of that some tests had to be modified. And api resposnes are reproducible now (sets results are changed to a "sorted" set, so with every query we should have the same response).
Second big change is that overlay iamages are stored differently (there are no overlays in submaps anymore)
---
 .../mapviewer/annotation/data/Target.java     |  409 +--
 .../annotation/services/ChEMBLParser.java     |   10 +-
 .../services/DrugbankHTMLParser.java          |    1 +
 .../services/ChemicalParserTest.java          |    4 +-
 frontend-js/package.json                      |    1 +
 frontend-js/scripts/refresh_mock_requests.js  |  210 ++
 frontend-js/src/main/js/Export.js             |    8 +-
 frontend-js/src/main/js/ServerConnector.js    |   77 +-
 .../src/main/js/gui/leftPanel/OverlayPanel.js |    4 +-
 .../src/main/js/map/AbstractCustomMap.js      |   13 +-
 frontend-js/src/main/js/map/CustomMap.js      |    2 +-
 .../src/main/js/map/data/LayoutData.js        |   15 +-
 frontend-js/src/main/js/map/data/MapModel.js  |    3 +-
 frontend-js/src/main/js/map/data/Project.js   |   11 +
 frontend-js/src/test/js/Admin-test.js         |    1 +
 .../src/test/js/ServerConnector-test.js       |   49 +-
 .../js/gui/admin/EditProjectDialog-test.js    |    4 +
 .../test/js/gui/admin/EditUserDialog-test.js  |    2 +
 .../test/js/gui/admin/UserAdminPanel-test.js  |    4 +
 .../js/gui/leftPanel/OverlayPanel-test.js     |    4 +-
 frontend-js/src/test/js/helper.js             |   11 +-
 .../src/test/js/map/AbstractCustomMap-test.js |   45 +-
 frontend-js/src/test/js/map/CustomMap-test.js |   24 +-
 .../src/test/js/map/data/LayoutData-test.js   |    5 +-
 .../src/test/js/map/data/MapModel-test.js     |    2 +-
 .../test/js/map/overlay/DrugDbOverlay-test.js |   22 +-
 .../js/map/overlay/SearchDbOverlay-test.js    |    4 +-
 .../js/map/window/AliasInfoWindow-test.js     |    7 +-
 frontend-js/src/test/js/mocha-config.js       |    1 +
 .../configuration/token=MOCK_TOKEN_ID&        |    2 +-
 .../apiCalls/doLogout/token=ADMIN_TOKEN_ID&   |    1 +
 .../apiCalls/doLogout/token=MOCK_TOKEN_ID&    |    2 +-
 .../versions/eboVir3/token=MOCK_TOKEN_ID&     |    1 -
 .../mesh/D000544/token=MOCK_TOKEN_ID&         |    2 +-
 .../mesh/D010300/token=MOCK_TOKEN_ID&         |    2 +-
 ....publicOverlay=true&token=ADMIN_TOKEN_ID&} |    0
 .../models/all/token=MOCK_TOKEN_ID&           |    2 +-
 .../publicOverlay=true&token=MOCK_TOKEN_ID&   |    1 +
 .../statistics/token=MOCK_TOKEN_ID&           |    2 +-
 .../token=MOCK_TOKEN_ID&                      |    2 +-
 ...elId&type=Compartment&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=345325&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=345330&token=MOCK_TOKEN_ID& |    2 +-
 ...=345330,345331,345337&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=345334&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=345337&token=MOCK_TOKEN_ID& |    2 +-
 .../id=345323,345332&token=MOCK_TOKEN_ID&     |    2 +-
 .../elements/id=345325&token=MOCK_TOKEN_ID&   |    2 +-
 .../models/all/token=MOCK_TOKEN_ID&           |    2 +-
 .../all/bioEntities/token=MOCK_TOKEN_ID&      |    2 +-
 .../overlays/18083/token=MOCK_TOKEN_ID&       |    2 +-
 .../publicOverlay=true&token=MOCK_TOKEN_ID&   |    1 +
 .../statistics/token=MOCK_TOKEN_ID&           |    2 +-
 .../token=MOCK_TOKEN_ID&                      |    2 +-
 .../query=NADH&token=MOCK_TOKEN_ID&           |    2 +-
 ...nds,modelId&id=436152&token=MOCK_TOKEN_ID& |    2 +-
 .../elements/id=436152&token=MOCK_TOKEN_ID&   |    2 +-
 .../models/all/token=MOCK_TOKEN_ID&           |    2 +-
 .../publicOverlay=true&token=MOCK_TOKEN_ID&   |    1 +
 .../drug_target_sample/token=MOCK_TOKEN_ID&   |    2 +-
 .../empty/models/all/token=MOCK_TOKEN_ID&     |    2 +-
 .../publicOverlay=true&token=MOCK_TOKEN_ID&   |    1 +
 .../projects/empty/token=MOCK_TOKEN_ID&       |    2 +-
 .../all/functions/7/token=MOCK_TOKEN_ID&      |    1 +
 .../all/parameters/7/token=MOCK_TOKEN_ID&     |    1 +
 .../token=MOCK_TOKEN_ID&                      | 2470 ++++++++++++++++-
 ...project.version=2.01&token=MOCK_TOKEN_ID&} |    0
 .../query=rotenone&token=MOCK_TOKEN_ID&       |    2 +-
 .../elements/3001/token=MOCK_TOKEN_ID&        |    1 -
 .../elements/329157/token=MOCK_TOKEN_ID&      |    1 +
 .../elements/329158/token=MOCK_TOKEN_ID&      |    1 -
 ...d,pinned,removed,type&token=MOCK_TOKEN_ID& |    2 +-
 ...d,pinned,removed,type&token=MOCK_TOKEN_ID& |    2 +-
 ...,modelId,removed,type&token=MOCK_TOKEN_ID& |    2 +-
 .../points/1.00,200.00/token=MOCK_TOKEN_ID&   |    2 +-
 .../comments/models/all/token=ADMIN_TOKEN_ID& |    2 +-
 .../comments/models/all/token=MOCK_TOKEN_ID&  |    2 +-
 .../query=NADH&token=MOCK_TOKEN_ID&           |    2 +-
 .../query=aspirin&token=MOCK_TOKEN_ID&        |    2 +-
 .../suggestedQueryList/token=MOCK_TOKEN_ID&   |    2 +-
 ...sortOrder=asc&start=0&token=MOCK_TOKEN_ID& |    2 +-
 ...query=hsa-miR-125a-3p&token=MOCK_TOKEN_ID& |    2 +-
 ...ics.PngImageGenerator&token=MOCK_TOKEN_ID& |  Bin 25 -> 15658 bytes
 ...CellDesignerXmlParser&token=MOCK_TOKEN_ID& | 2290 ++++++++++++++-
 ...el=5&model.id=15781&token=ADMIN_TOKEN_ID&} |    0
 ...184.79,365.76&count=1&token=MOCK_TOKEN_ID& |    2 +-
 ...oordinates=2.00,12.00&token=MOCK_TOKEN_ID& |    2 +-
 ...207.73,479.18&count=1&token=MOCK_TOKEN_ID& |    2 +-
 ...316.05,253.61&count=1&token=MOCK_TOKEN_ID& |    2 +-
 ...457.51,356.84&count=1&token=MOCK_TOKEN_ID& |    2 +-
 ...553.10,479.18&count=1&token=MOCK_TOKEN_ID& |    2 +-
 ...mple molecule,Unknown&token=MOCK_TOKEN_ID& |    2 +-
 ...mple molecule,Unknown&token=MOCK_TOKEN_ID& |    2 +-
 ...,329183,329184,329185&token=MOCK_TOKEN_ID& |    2 +-
 .../participantId=329167&token=MOCK_TOKEN_ID& |    2 +-
 ...tMatch=false&query=s1&token=MOCK_TOKEN_ID& |    2 +-
 ...ctMatch=true&query=s1&token=MOCK_TOKEN_ID& |    2 +-
 .../count=100&query=s1&token=MOCK_TOKEN_ID&   |    2 +-
 ...nds,modelId&id=329157&token=MOCK_TOKEN_ID& |    1 +
 ...nds,modelId&id=329159&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=329163&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=329167&token=MOCK_TOKEN_ID& |    2 +-
 ...elId&id=329168,329173&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=329170&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=329171&token=MOCK_TOKEN_ID& |    2 +-
 ...nds,modelId&id=329173&token=MOCK_TOKEN_ID& |    2 +-
 .../elements/id=329156&token=MOCK_TOKEN_ID&   |    2 +-
 ...,329183,329184,329185&token=MOCK_TOKEN_ID& |    2 +-
 ...,329183,329184,329185&token=MOCK_TOKEN_ID& |    2 +-
 ...,329162,329174,329180&token=MOCK_TOKEN_ID& |    2 +-
 .../elements/id=329157&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329158&token=MOCK_TOKEN_ID&   |    2 +-
 ...,329173,329175,329177&token=MOCK_TOKEN_ID& |    2 +-
 ...=329158,329165,329172&token=MOCK_TOKEN_ID& |    2 +-
 .../elements/id=329159&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329160&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329161&token=MOCK_TOKEN_ID&   |    2 +-
 .../id=329161,329165&token=MOCK_TOKEN_ID&     |    2 +-
 .../elements/id=329162&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329163&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329164&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329165&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329166&token=MOCK_TOKEN_ID&   |    2 +-
 .../id=329166,329171&token=MOCK_TOKEN_ID&     |    2 +-
 .../elements/id=329167&token=MOCK_TOKEN_ID&   |    2 +-
 .../id=329167,329168&token=MOCK_TOKEN_ID&     |    2 +-
 ...,329172,329173,329179&token=MOCK_TOKEN_ID& |    2 +-
 .../id=329167,329169&token=MOCK_TOKEN_ID&     |    2 +-
 .../id=329167,329172&token=MOCK_TOKEN_ID&     |    2 +-
 ...=329167,329173,329179&token=MOCK_TOKEN_ID& |    2 +-
 .../id=329167,329179&token=MOCK_TOKEN_ID&     |    2 +-
 .../elements/id=329168&token=MOCK_TOKEN_ID&   |    2 +-
 .../id=329168,329173&token=MOCK_TOKEN_ID&     |    2 +-
 .../id=329168,329177&token=MOCK_TOKEN_ID&     |    2 +-
 .../elements/id=329169&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329170&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329171&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329172&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329173&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329174&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329175&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329176&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329177&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329178&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329179&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329180&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329181&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329182&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329183&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329184&token=MOCK_TOKEN_ID&   |    2 +-
 .../elements/id=329185&token=MOCK_TOKEN_ID&   |    2 +-
 .../bioEntities/elements/token=MOCK_TOKEN_ID& |    2 +-
 .../reactions/id=153508&token=MOCK_TOKEN_ID&  |    2 +-
 .../reactions/id=153510&token=MOCK_TOKEN_ID&  |    2 +-
 .../reactions/id=153511&token=MOCK_TOKEN_ID&  |    2 +-
 .../reactions/id=153515&token=MOCK_TOKEN_ID&  |    2 +-
 .../reactions/id=153519&token=MOCK_TOKEN_ID&  |    2 +-
 .../reactions/id=153521&token=MOCK_TOKEN_ID&  |    2 +-
 .../reactions/token=MOCK_TOKEN_ID&            |    2 +-
 .../all/functions/5/token=MOCK_TOKEN_ID&      |    1 -
 .../all/parameters/7/token=MOCK_TOKEN_ID&     |    1 -
 ...sortOrder=asc&start=0&token=MOCK_TOKEN_ID& |    2 +-
 .../length=10&start=0&token=MOCK_TOKEN_ID&    |    2 +-
 .../sample/models/all/token=ADMIN_TOKEN_ID&   |    2 +-
 .../sample/models/all/token=MOCK_TOKEN_ID&    |    2 +-
 .../17296.downloadSource/token=MOCK_TOKEN_ID& |    1 -
 .../elements/329163/token=MOCK_TOKEN_ID&      |    2 +-
 .../elements/329163/token=MOCK_TOKEN_ID&      |    2 +-
 .../all/bioEntities/token=MOCK_TOKEN_ID&      |    2 +-
 .../18083.downloadSource/token=MOCK_TOKEN_ID& |    3 +
 ...&publicOverlay=false&token=ADMIN_TOKEN_ID& |    2 +-
 ...s&publicOverlay=false&token=MOCK_TOKEN_ID& |    2 +-
 .../publicOverlay=true&token=ADMIN_TOKEN_ID&  |    1 +
 .../publicOverlay=true&token=MOCK_TOKEN_ID&   |    1 +
 .../sample/overlays/token=ADMIN_TOKEN_ID&     |    1 +
 .../sample/overlays/token=MOCK_TOKEN_ID&      |    2 +-
 .../sample/statistics/token=MOCK_TOKEN_ID&    |    2 +-
 .../projects/sample/token=ADMIN_TOKEN_ID&     |    2 +-
 .../projects/sample/token=MOCK_TOKEN_ID&      |    2 +-
 .../apiCalls/projects/token=ADMIN_TOKEN_ID&   |    2 +-
 .../apiCalls/projects/token=MOCK_TOKEN_ID&    |    2 +-
 .../users/admin/token=ADMIN_TOKEN_ID&         |    2 +-
 .../users/anonymous/token=ADMIN_TOKEN_ID&     |    1 +
 .../users/anonymous/token=MOCK_TOKEN_ID&      |    2 +-
 .../apiCalls/users/token=ADMIN_TOKEN_ID&      |    2 +-
 .../apiCalls/users/token=MOCK_TOKEN_ID&       |    1 -
 .../lcsb/mapviewer/model/map/BioEntity.java   |   25 +
 .../mapviewer/model/map/layout/Layout.java    |   11 +-
 .../lcsb/mapviewer/model/map/model/Model.java |    9 +
 .../map/model/ModelSubmodelConnection.java    |  213 +-
 .../mapviewer/model/user/BasicPrivilege.java  |  287 +-
 .../java/lcsb/mapviewer/model/user/User.java  |   19 +
 .../modelutils/map/ElementUtils.java          |  417 ++-
 .../lcsb/mapviewer/api/BaseController.java    |    6 +-
 .../java/lcsb/mapviewer/api/BaseRestImpl.java |   49 +-
 .../ConfigurationController.java              |    4 +-
 .../configuration/ConfigurationRestImpl.java  |   33 +-
 .../mapviewer/api/files/FileRestImpl.java     |    4 +-
 .../lcsb/mapviewer/api/mesh/MeshRestImpl.java |    4 +-
 .../api/projects/ProjectMetaData.java         |    9 +
 .../api/projects/ProjectRestImpl.java         |   19 +-
 .../projects/chemicals/ChemicalRestImpl.java  |   25 +-
 .../projects/comments/CommentRestImpl.java    |    4 +-
 .../api/projects/drugs/DrugRestImpl.java      |   56 +-
 .../api/projects/mirnas/MiRnaRestImpl.java    |   27 +-
 .../api/projects/models/ModelMetaData.java    |   36 +-
 .../api/projects/models/ModelRestImpl.java    |    9 +-
 .../bioEntities/BioEntitiesRestImpl.java      |   52 +-
 .../elements/ElementsController.java          |    3 +-
 .../elements/ElementsRestImpl.java            |   28 +-
 .../reactions/ReactionsController.java        |    3 +-
 .../reactions/ReactionsRestImpl.java          |   19 +-
 .../models/functions/FunctionsRestImpl.java   |    6 +-
 .../models/parameters/ParametersRestImpl.java |   10 +-
 .../publications/PublicationsRestImpl.java    |   41 +-
 .../projects/models/units/UnitsRestImpl.java  |    8 +-
 .../projects/overlays/OverlayController.java  |    9 +-
 .../projects/overlays/OverlayRestImpl.java    |   75 +-
 .../mapviewer/api/users/UserController.java   |    6 +-
 .../mapviewer/api/users/UserRestImpl.java     |   37 +-
 .../lcsb/mapviewer/api/RestTestFunctions.java |    2 +-
 .../services/impl/LayoutService.java          |  185 +-
 .../services/impl/SearchService.java          | 1595 ++++++-----
 .../services/interfaces/ILayoutService.java   |   99 +-
 .../services/interfaces/ISearchService.java   |   13 +-
 .../services/search/ElementView.java          |  229 +-
 .../search/data/SearchElementResult.java      |   13 +-
 .../services/search/db/DbSearchCriteria.java  |  297 +-
 .../services/search/db/drug/DrugService.java  |   12 +-
 .../mapviewer/services/view/LayoutView.java   |  274 --
 .../services/view/LayoutViewFactory.java      |   89 -
 .../resources/applicationContext-service.xml  |    1 -
 .../services/impl/LayoutServiceTest.java      |   93 +-
 .../search/db/drug/DrugServiceTest.java       |   23 +-
 .../mapviewer/services/view/AllViewTests.java |    2 -
 .../services/view/LayoutViewFactoryTest.java  |  111 -
 .../services/view/LayoutViewTest.java         |   27 -
 237 files changed, 7512 insertions(+), 3112 deletions(-)
 create mode 100644 frontend-js/scripts/refresh_mock_requests.js
 create mode 100644 frontend-js/testFiles/apiCalls/doLogout/token=ADMIN_TOKEN_ID&
 delete mode 100644 frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID&
 rename frontend-js/testFiles/apiCalls/projects/all/overlays/14081/{PATCH_overlay.defaultOverlay=false&overlay.name=Pathways and compartments&overlay.publicOverlay=true&token=MOCK_TOKEN_ID& => PATCH_overlay.defaultOverlay=false&overlay.name=Pathways and compartments&overlay.publicOverlay=true&token=ADMIN_TOKEN_ID&} (100%)
 create mode 100644 frontend-js/testFiles/apiCalls/projects/complex_model_with_images/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/drug_target_sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/empty/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/functions/7/token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/parameters/7/token=MOCK_TOKEN_ID&
 rename frontend-js/testFiles/apiCalls/projects/sample/{PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.name=UNKNOWN DISEASE MAP&project.organism.resource=1570291&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID& => PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.name=UNKNOWN DISEASE MAP&project.organism.resource=9606&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID&} (100%)
 delete mode 100644 frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/bioEntities/elements/3001/token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/bioEntities/elements/329157/token=MOCK_TOKEN_ID&
 delete mode 100644 frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/bioEntities/elements/329158/token=MOCK_TOKEN_ID&
 rename frontend-js/testFiles/apiCalls/projects/sample/models/15781/{PATCH_model.id=15781&token=MOCK_TOKEN_ID& => PATCH_model.defaultCenterX=100&model.defaultCenterY=4&model.defaultZoomLevel=5&model.id=15781&token=ADMIN_TOKEN_ID&} (100%)
 create mode 100644 frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329157&token=MOCK_TOKEN_ID&
 delete mode 100644 frontend-js/testFiles/apiCalls/projects/sample/models/all/functions/5/token=MOCK_TOKEN_ID&
 delete mode 100644 frontend-js/testFiles/apiCalls/projects/sample/models/all/parameters/7/token=MOCK_TOKEN_ID&
 delete mode 100644 frontend-js/testFiles/apiCalls/projects/sample/overlays/17296.downloadSource/token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/sample/overlays/18083.downloadSource/token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=ADMIN_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID&
 create mode 100644 frontend-js/testFiles/apiCalls/users/anonymous/token=ADMIN_TOKEN_ID&
 delete mode 100644 frontend-js/testFiles/apiCalls/users/token=MOCK_TOKEN_ID&
 delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/LayoutView.java
 delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/LayoutViewFactory.java
 delete mode 100644 service/src/test/java/lcsb/mapviewer/services/view/LayoutViewFactoryTest.java
 delete mode 100644 service/src/test/java/lcsb/mapviewer/services/view/LayoutViewTest.java

diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
index ea406bd353..de8c9f6999 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
@@ -21,209 +21,210 @@ import lcsb.mapviewer.model.map.MiriamData;
  */
 public class Target implements Serializable {
 
-	/**
-	 * 
-	 */
-	private static final long				serialVersionUID = 1L;
-
-	/**
-	 * Default class logger.
-	 */
-	private static transient Logger	logger					 = Logger.getLogger(Target.class);
-
-	/**
-	 * Database from which target was received.
-	 */
-	private MiriamData							source;
-
-	/**
-	 * Name of the target.
-	 */
-	private String									name;
-
-	/**
-	 * Organism in which target is located.
-	 */
-	private MiriamData							organism;
-
-	/**
-	 * List of genes located in a target.
-	 */
-	private List<MiriamData>				genes						 = new ArrayList<>();
-
-	/**
-	 * List of references describing target.
-	 */
-	private List<MiriamData>				references			 = new ArrayList<>();
-
-	/**
-	 * Type of target.
-	 */
-	private TargetType							type;
-
-	/**
-	 * Default constructor.
-	 */
-	public Target() {
-
-	}
-
-	/**
-	 * Constructor that initializes target with some data.
-	 * 
-	 * @param source
-	 *          from where the information about target was retrieved
-	 * @param gene
-	 *          {@link MiriamData} that identifies gene
-	 * @param references
-	 *          list of references that support this target
-	 */
-	public Target(MiriamData source, MiriamData gene, Collection<MiriamData> references) {
-		this.source = source;
-		if (gene != null) {
-			addGene(gene);
-		}
-		addReferences(references);
-		if (genes.size() == 1) {
-			setType(TargetType.SINGLE_PROTEIN);
-		}
-	}
-
-	/**
-	 * @return the type
-	 * @see #type
-	 */
-	public TargetType getType() {
-		return type;
-	}
-
-	/**
-	 * @param type
-	 *          the type to set
-	 * @see #type
-	 */
-	public void setType(TargetType type) {
-		this.type = type;
-	}
-
-	/**
-	 * 
-	 * @return {@link #references} list
-	 */
-	@XmlElement(name = "pubmed")
-	public List<MiriamData> getReferences() {
-		return references;
-	}
-
-	/**
-	 * 
-	 * @param md
-	 *          new {@link #references} list
-	 */
-	public void addReference(MiriamData md) {
-		if (this.references.contains(md)) {
-			logger.warn("Target " + getName() + " already has MiriamData: " + md);
-		} else {
-			this.references.add(md);
-		}
-	}
-
-	/**
-	 * Adds gene to the gene list.
-	 * 
-	 * @param gene
-	 *          object to add
-	 */
-	public void addGene(MiriamData gene) {
-		if (gene == null) {
-			throw new InvalidArgumentException("Cannot add null element");
-		}
-		this.genes.add(gene);
-	}
-
-	/**
-	 * @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 organism
-	 * @see #organism
-	 */
-	public MiriamData getOrganism() {
-		return organism;
-	}
-
-	/**
-	 * @param organism
-	 *          the organism to set
-	 * @see #organism
-	 */
-	public void setOrganism(MiriamData organism) {
-		this.organism = organism;
-	}
-
-	/**
-	 * @return the geneCardId
-	 * @see #genes
-	 */
-	public List<MiriamData> getGenes() {
-		return genes;
-	}
-
-	/**
-	 * @param genes
-	 *          the genes to set
-	 * @see #genes
-	 */
-	public void setGenes(List<MiriamData> genes) {
-		this.genes = genes;
-	}
-
-	/**
-	 * @return the source
-	 * @see #source
-	 */
-	public MiriamData getSource() {
-		return source;
-	}
-
-	/**
-	 * @param source
-	 *          the source to set
-	 * @see #source
-	 */
-	public void setSource(MiriamData source) {
-		this.source = source;
-	}
-
-	/**
-	 * Adds set of references to the target.
-	 * 
-	 * @param references
-	 *          objects to add
-	 * 
-	 * @see #references
-	 */
-	public void addReferences(Collection<MiriamData> references) {
-		this.references.addAll(references);
-	}
-
-	@Override
-	public String toString() {
-		return "[" + this.getClass().getSimpleName() + "]: " + name + ", source: " + source + ", organism: " + organism + "; ";
-	}
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Default class logger.
+   */
+  private static transient Logger logger = Logger.getLogger(Target.class);
+
+  /**
+   * Database from which target was received.
+   */
+  private MiriamData source;
+
+  /**
+   * Name of the target.
+   */
+  private String name;
+
+  /**
+   * Organism in which target is located.
+   */
+  private MiriamData organism;
+
+  /**
+   * List of genes located in a target.
+   */
+  private List<MiriamData> genes = new ArrayList<>();
+
+  /**
+   * List of references describing target.
+   */
+  private List<MiriamData> references = new ArrayList<>();
+
+  /**
+   * Type of target.
+   */
+  private TargetType type;
+
+  /**
+   * Default constructor.
+   */
+  public Target() {
+
+  }
+
+  /**
+   * Constructor that initializes target with some data.
+   * 
+   * @param source
+   *          from where the information about target was retrieved
+   * @param gene
+   *          {@link MiriamData} that identifies gene
+   * @param references
+   *          list of references that support this target
+   */
+  public Target(MiriamData source, MiriamData gene, Collection<MiriamData> references) {
+    this.source = source;
+    if (gene != null) {
+      addGene(gene);
+    }
+    addReferences(references);
+    if (getGenes().size() == 1) {
+      setType(TargetType.SINGLE_PROTEIN);
+    }
+  }
+
+  /**
+   * @return the type
+   * @see #type
+   */
+  public TargetType getType() {
+    return type;
+  }
+
+  /**
+   * @param type
+   *          the type to set
+   * @see #type
+   */
+  public void setType(TargetType type) {
+    this.type = type;
+  }
+
+  /**
+   * 
+   * @return {@link #references} list
+   */
+  @XmlElement(name = "pubmed")
+  public List<MiriamData> getReferences() {
+    return references;
+  }
+
+  /**
+   * 
+   * @param md
+   *          new {@link #references} list
+   */
+  public void addReference(MiriamData md) {
+    if (this.references.contains(md)) {
+      logger.warn("Target " + getName() + " already has MiriamData: " + md);
+    } else {
+      this.references.add(md);
+    }
+  }
+
+  /**
+   * Adds gene to the gene list.
+   * 
+   * @param gene
+   *          object to add
+   */
+  public void addGene(MiriamData gene) {
+    if (gene == null) {
+      throw new InvalidArgumentException("Cannot add null element");
+    }
+    this.genes.add(gene);
+  }
+
+  /**
+   * @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 organism
+   * @see #organism
+   */
+  public MiriamData getOrganism() {
+    return organism;
+  }
+
+  /**
+   * @param organism
+   *          the organism to set
+   * @see #organism
+   */
+  public void setOrganism(MiriamData organism) {
+    this.organism = organism;
+  }
+
+  /**
+   * @return the geneCardId
+   * @see #genes
+   */
+  public List<MiriamData> getGenes() {
+    return genes;
+  }
+
+  /**
+   * @param genes
+   *          the genes to set
+   * @see #genes
+   */
+  public void setGenes(List<MiriamData> genes) {
+    this.genes = genes;
+  }
+
+  /**
+   * @return the source
+   * @see #source
+   */
+  public MiriamData getSource() {
+    return source;
+  }
+
+  /**
+   * @param source
+   *          the source to set
+   * @see #source
+   */
+  public void setSource(MiriamData source) {
+    this.source = source;
+  }
+
+  /**
+   * Adds set of references to the target.
+   * 
+   * @param references
+   *          objects to add
+   * 
+   * @see #references
+   */
+  public void addReferences(Collection<MiriamData> references) {
+    this.references.addAll(references);
+  }
+
+  @Override
+  public String toString() {
+    return "[" + this.getClass().getSimpleName() + "]: " + name + ", source: " + source + ", organism: " + organism
+        + "; ";
+  }
 
 }
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 76aa0b70e6..17ccdbbe7b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -243,19 +243,21 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
    * @return {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL} identifier
    *         that could be extracted from input data
    * @throws DrugSearchException
-   *           thrown when there is aproblem with annotations
+   *           thrown when there is a problem with annotations
    */
   private MiriamData targetComponentToMiriamData(Node targetComponent) throws DrugSearchException {
+    MiriamData result = null;
     Node uniprotAccessionId = getNode("accession", targetComponent.getChildNodes());
     if (uniprotAccessionId != null) {
       try {
-        return uniprotAnnotator.uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotAccessionId.getTextContent()));
+        result = uniprotAnnotator
+            .uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotAccessionId.getTextContent()));
+        result.setAnnotator(null);
       } catch (UniprotSearchException e) {
         throw new DrugSearchException(e);
       }
-    } else {
-      return null;
     }
+    return result;
   }
 
   /**
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index 5b7b563054..fb29370b70 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -380,6 +380,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
       MiriamData uniprotTarget = new MiriamData(MiriamType.UNIPROT, uniprotId);
       MiriamData hgncTarget = uniprotAnnotator.uniProtToHgnc(uniprotTarget);
       if (hgncTarget != null) {
+        hgncTarget.setAnnotator(null);
         result.addGene(hgncTarget);
       } else {
         result.addGene(uniprotTarget);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
index bc17b72cdf..d1ddba22fc 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -285,13 +285,12 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
   @Test
   public void testGetByTarget() throws Exception {
     try {
-      // Parkinson disease
       MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "TNF");
       List<MiriamData> targets = new ArrayList<>();
       targets.add(target);
       List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
       assertNotNull(list);
-      assertTrue(!list.isEmpty());
+      assertFalse(list.isEmpty());
 
     } catch (Exception e) {
       e.printStackTrace();
@@ -302,7 +301,6 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
   @Test
   public void testGetByInvalidTarget() throws Exception {
     try {
-      // Parkinson disease
       MiriamData target = new MiriamData(MiriamType.WIKIPEDIA, "TNF");
       List<MiriamData> targets = new ArrayList<>();
       targets.add(target);
diff --git a/frontend-js/package.json b/frontend-js/package.json
index b2a012041b..01223b0773 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -11,6 +11,7 @@
     "build": "npm run clean && npm run build:css && npm run build:js",
     "clean": "node scripts/clean.js",
     "deploy": "node scripts/deploy.js",
+    "refresh-mock-requests": "node scripts/refresh_mock_requests.js",
     "lint": "jshint src/.",
     "test": "istanbul cover node_modules/mocha/bin/_mocha -- --recursive src/test/js"
   },
diff --git a/frontend-js/scripts/refresh_mock_requests.js b/frontend-js/scripts/refresh_mock_requests.js
new file mode 100644
index 0000000000..ec9a61f66e
--- /dev/null
+++ b/frontend-js/scripts/refresh_mock_requests.js
@@ -0,0 +1,210 @@
+const testFolder = './testFiles/apiCalls';
+const apiBaseDir = 'http://localhost:8080/minerva/api/';
+const fs = require('fs');
+const path = require('path');
+const request = require('request');
+
+function listFiles(dir, filelist) {
+  var fs = fs || require('fs'),
+    files = fs.readdirSync(dir);
+  filelist = filelist || [];
+  files.forEach(function (file) {
+    if (fs.statSync(dir + '/' + file).isDirectory()) {
+      filelist = listFiles(dir + '/' + file, filelist);
+    }
+    else {
+      filelist.push(dir + "/" + file);
+    }
+  });
+  return filelist;
+}
+
+function extractUrl(file) {
+  var url = apiBaseDir + path.dirname(file);
+  url = url.replace(testFolder, "") + "/";
+  url = url.replace("/all/", "/*/");
+  //don't change "." character if it's part of a number
+  if (!/\.[0-9]+/.test(url)) {
+    url = url.replace(".", ":");
+  }
+  return url;
+}
+
+function extractLogin(file) {
+  var filename = file.replace(path.dirname(file), "").substr(1);
+  if (filename.endsWith("MOCK_TOKEN_ID&")) {
+    return "anonymous";
+  }
+  if (filename.endsWith("ADMIN_TOKEN_ID&")) {
+    return "admin";
+  }
+  return undefined;
+}
+
+function extractMethod(file) {
+  var filename = file.replace(path.dirname(file), "").substr(1);
+  var method = filename.split("=")[0];
+  var result;
+  if (method.indexOf("_") >= 0) {
+    result = method.split("_")[0];
+  } else {
+    result = "GET";
+  }
+  return result;
+}
+
+function setParam(params, key, value) {
+  if (key.indexOf(".") > 0) {
+    var topKey = key.split(".")[0];
+    if (params[topKey] === undefined) {
+      params[topKey] = {};
+    }
+    setParam(params[topKey], key.substr(topKey.length + 1), value)
+  } else {
+    if (value.indexOf("ALIAS.") >= 0) {
+      value = value.replace("ALIAS.", "ALIAS:")
+    }
+    if (value.indexOf("REACTION.") >= 0) {
+      value = value.replace("REACTION.", "REACTION:")
+    }
+    params[key] = value;
+  }
+}
+
+function extractParams(file) {
+  var filename = file.replace(path.dirname(file), "").substr(1);
+  var params = {};
+  var method = extractMethod(file);
+  if (filename.indexOf(method) === 0) {
+    filename = filename.substr(method.length + 1);
+  }
+  var tokens = filename.split("&");
+  for (var i = 0; i < tokens.length; i++) {
+    var token = tokens[i];
+    var key = token.split("=")[0];
+    var value = token.split("=")[1];
+
+    if (key !== "" && key !== "token") {
+      setParam(params, key, value)
+    }
+  }
+  return params;
+}
+
+function prepareQueries(filelist) {
+  var result = [];
+  for (var i = 0; i < filelist.length; i++) {
+    var file = filelist[i];
+    result.push({
+      file: file,
+      url: extractUrl(file),
+      method: extractMethod(file),
+      login: extractLogin(file),
+      params: extractParams(file)
+    })
+  }
+
+  return result;
+}
+
+function getAuthToken(login) {
+  var url = apiBaseDir + "doLogin?login=" + login;
+  if (login === "anonymous") {
+    url += "&password=";
+  } else if (login === "admin") {
+    url += "&password=admin";
+  }
+  return new Promise(function (resolve, reject) {
+    var params = {
+      method: "GET",
+      url: url
+    };
+    request(params, function (error, response, body) {
+      if (error) {
+        reject(new Error(error.message));
+      } else if (response.statusCode !== 200) {
+        reject(new Error(url + " rejected with status code: " + response.statusCode));
+      } else {
+        resolve(response.headers['set-cookie']);
+      }
+    });
+  }).then(function (value) {
+    return Promise.resolve(value[0]);
+  });
+
+
+}
+
+function executeQuery(query) {
+  var url = query.url + "?";
+  if (query.method === "GET") {
+    for (var key in query.params) {
+      if (query.params.hasOwnProperty(key)) {
+        url += key + "=" + query.params[key] + "&";
+      }
+    }
+  }
+  return getAuthToken(query.login).then(function (token) {
+    var params = {
+      method: query.method,
+      url: url,
+      headers: {'Cookie': token}
+    };
+
+    return new Promise(function (resolve, reject) {
+      request(params, function (error, response, body) {
+        if (error) {
+          reject(new Error(error.message));
+        } else if (response.statusCode !== 200) {
+          reject(new Error(url + " rejected with status code: " + response.statusCode));
+        } else {
+          // for some reason sometimes result is an object not a string
+          if (typeof body === 'string' || body instanceof String) {
+            resolve(body);
+          } else {
+            resolve(JSON.stringify(body));
+          }
+        }
+      });
+    });
+  }).then(function (content) {
+    var data = fs.readFileSync(query.file, 'utf8');
+    if (data !== content) {
+      console.log("Query response changed: " + url);
+      console.log("Query response changed: " + url);
+      fs.writeFileSync(query.file, content);
+
+      if (data.length < 1000 && content.length < 1000) {
+        console.log("\n\n");
+        console.log(data);
+        console.log(content);
+        console.log("\n\n");
+      }
+    }
+  });
+}
+
+function executeQueries(queries) {
+  var promises = [];
+  // for (var i = 0; i < 3; i++) {
+  for (var i = 0; i < queries.length; i++) {
+    var query = queries[i];
+    if (query.method !== "GET" || query.url.indexOf(":downloadModel") >= 0) {
+      console.log("Ignoring " + query.method + " query: " + query.url);
+    } else {
+      // console.log("Exec " + query.method + " query: " + query.url);
+      // console.log(query.params);
+      promises.push(executeQuery(query));
+    }
+  }
+  return Promise.all(promises);
+}
+
+
+var files = listFiles(testFolder);
+
+var queries = prepareQueries(files);
+return executeQueries(queries).catch(function (error) {
+  console.log(error);
+  process.exit(1);
+});
diff --git a/frontend-js/src/main/js/Export.js b/frontend-js/src/main/js/Export.js
index d2233fc56f..3c096991c0 100644
--- a/frontend-js/src/main/js/Export.js
+++ b/frontend-js/src/main/js/Export.js
@@ -47,19 +47,19 @@ Export.prototype._createGui = function() {
   new Header({
     element : headerDiv,
     customMap : null,
-    project : self.getProject(),
+    project : self.getProject()
   });
   self.getElement().appendChild(headerDiv);
 
   var panels = [ {
     name : "ELEMENTS",
-    panelClass : ElementExportPanel,
+    panelClass : ElementExportPanel
   }, {
     name : "NETWORK",
-    panelClass : NetworkExportPanel,
+    panelClass : NetworkExportPanel
   }, {
     name : "GRAPHICS",
-    panelClass : GraphicsExportPanel,
+    panelClass : GraphicsExportPanel
   } ];
 
   var tabDiv = Functions.createElement({
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 12033eba9e..55e847b974 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -760,45 +760,50 @@ ServerConnector.getProject = function (projectId) {
     projectId = result;
     queryParams.projectId = result;
     return self.sendGetRequest(self.getProjectUrl(queryParams, filterParams));
+  }).catch(function (error) {
+    return self.processNetworkError(error);
   }).then(function (content) {
-    var downloadedProject = new Project(content);
-    if (self._projectsById[projectId] !== undefined) {
-      self._projectsById[projectId].update(downloadedProject);
-    } else {
-      self._projectsById[projectId] = downloadedProject;
-    }
-    project = self._projectsById[projectId];
-    return self.getModels(projectId);
-  }).then(function (models) {
-    project.setModel(models[0]);
-    return self.getLoggedUser();
-  }).then(function (user) {
-    return self.getOverlays({
-      projectId: projectId,
-      creator: user.getLogin(),
-      publicOverlay: false
-    });
-  }).then(function (overlays) {
-    if (project.getModel() !== undefined) {
-      project.getModel().addLayouts(overlays);
+    if (content === null) {
+      return null;
     } else {
-      if (overlays.length > 0) {
-        logger.warn("Cannot add overlays to the project: " + project.getProjectId());
-      }
-    }
-    return project;
-  }).then(null, function (error) {
-    if ((error instanceof NetworkError)) {
-      switch (error.statusCode) {
-        case HttpStatus.NOT_FOUND:
-          return null;
-        case HttpStatus.FORBIDDEN:
-          return Promise.reject(new SecurityError("Access denied."));
-        default:
-          return Promise.reject(error);
+      var downloadedProject = new Project(content);
+      if (self._projectsById[projectId] !== undefined) {
+        self._projectsById[projectId].update(downloadedProject);
+      } else {
+        self._projectsById[projectId] = downloadedProject;
       }
-    } else {
-      return Promise.reject(error);
+      project = self._projectsById[projectId];
+      return self.getModels(projectId).then(function (models) {
+        project.setModel(models[0]);
+        return self.getOverlays({
+          projectId: projectId,
+          publicOverlay: true
+        });
+      }).then(function (overlays) {
+        if (project.getModel() !== undefined) {
+          project.getModel().addLayouts(overlays);
+        } else {
+          if (overlays.length > 0) {
+            logger.warn("Cannot add overlays to the project: " + project.getProjectId());
+          }
+        }
+        return self.getLoggedUser();
+      }).then(function (user) {
+        return self.getOverlays({
+          projectId: projectId,
+          creator: user.getLogin(),
+          publicOverlay: false
+        });
+      }).then(function (overlays) {
+        if (project.getModel() !== undefined) {
+          project.getModel().addLayouts(overlays);
+        } else {
+          if (overlays.length > 0) {
+            logger.warn("Cannot add overlays to the project: " + project.getProjectId());
+          }
+        }
+        return project;
+      });
     }
   });
 };
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index 0513d712d3..4faefd636b 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -374,6 +374,7 @@ OverlayPanel.prototype.refresh = function (showDefault) {
 
     var title = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE);
     var addButton = self.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
+    var tableElement = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
     if (user.getLogin() === "anonymous") {
       title.innerHTML = 'YOU ARE NOT LOGGED IN. PLEASE, <a href="#">LOG IN</a>'
         + 'TO UPLOAD AND VIEW CUSTOM OVERLAYS<br/><center><button>LOGIN</button></center>';
@@ -383,10 +384,11 @@ OverlayPanel.prototype.refresh = function (showDefault) {
       $(title).find("a")[0].onclick = openLoginDialog;
       $(title).find("button")[0].onclick = openLoginDialog;
       addButton.style.display = "none";
+      $(tableElement).hide();
     } else {
+      $(tableElement).show();
       title.innerHTML = self.getCustomOverlaysMessage();
       addButton.style.display = "block";
-      var tableElement = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
 
       table = $(tableElement).on('order.dt', function (e) {
         if ($(tableElement).dataTable().fnSettings().aaSorting[0][0] === 0) {
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index e64db0d71b..f48d578397 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -90,13 +90,14 @@ AbstractCustomMap.prototype.getMarkerSurfaceCollection = function () {
  *
  */
 AbstractCustomMap.prototype.setupLayouts = function () {
-  for (var i = 0; i < this.getLayouts().length; i++) {
-    var layout = this.getLayouts()[i];
-    var typeOptions = this.createTypeOptions(layout);
+  var overlays = this.getTopMap().getLayouts();
+  for (var i = 0; i < overlays.length; i++) {
+    var overlay = overlays[i];
+    var typeOptions = this.createTypeOptions(overlay);
     var mapType = new google.maps.ImageMapType(typeOptions);
-    this.getGoogleMap().mapTypes.set(layout.getId().toString(), mapType);
+    this.getGoogleMap().mapTypes.set(overlay.getId().toString(), mapType);
   }
-  this.getGoogleMap().setMapTypeId(this.getLayouts()[0].getId().toString());
+  this.getGoogleMap().setMapTypeId(overlays[0].getId().toString());
 };
 
 /**
@@ -179,7 +180,7 @@ AbstractCustomMap.prototype.createTypeOptions = function (param) {
       if (coord.y < 0 || coord.y >= maxTileYRange || coord.x < 0 || coord.x >= maxTileXRange) {
         return null;
       }
-      return "../map_images/" + param.getDirectory() + "/" + zoom + "/" + coord.x + "/" + coord.y + ".PNG";
+      return "../map_images/" + self.getProject().getDirectory() + "/" + param.getImagesDirectory(self.getId()) + "/" + zoom + "/" + coord.x + "/" + coord.y + ".PNG";
     },
     tileSize: new google.maps.Size(self.getTileSize(), self.getTileSize()),
     maxZoom: self.getMaxZoom(),
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 0aeb74b676..8210ae8252 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -239,7 +239,7 @@ CustomMap.prototype.openDataOverlay = function (param) {
         var submaps = self.getSubmaps();
         for (var i = 0; i < submaps.length; i++) {
           var submap = submaps[i];
-          submap.openDataOverlay(submap.getModel().getLayouts()[index].getId());
+          submap.openDataOverlay(identifier);
         }
         return Promise.resolve();
       }
diff --git a/frontend-js/src/main/js/map/data/LayoutData.js b/frontend-js/src/main/js/map/data/LayoutData.js
index ff680edb95..2ca0d9b61c 100644
--- a/frontend-js/src/main/js/map/data/LayoutData.js
+++ b/frontend-js/src/main/js/map/data/LayoutData.js
@@ -18,7 +18,7 @@ function LayoutData(layoutId, name) {
     var object = layoutId;
     this.setId(object.idObject);
     this.setName(object.name);
-    this.setDirectory(object.directory);
+    this.setImagesDirectory(object.images);
     this.setDescription(object.description);
     this.setCreator(object.creator);
     this.setContent(object.content);
@@ -112,12 +112,17 @@ LayoutData.prototype.setName = function (name) {
   this.name = name;
 };
 
-LayoutData.prototype.getDirectory = function () {
-  return this._directory;
+LayoutData.prototype.getImagesDirectory = function (modelId) {
+  for (var i = 0; i < this._imagesDirectory.length; i++) {
+    if (parseInt(this._imagesDirectory[i].modelId) === modelId) {
+      return this._imagesDirectory[i].path;
+    }
+  }
+  return null;
 };
 
-LayoutData.prototype.setDirectory = function (directory) {
-  this._directory = directory;
+LayoutData.prototype.setImagesDirectory = function (imagesDirectory) {
+  this._imagesDirectory = imagesDirectory;
 };
 
 LayoutData.prototype.updateAlias = function (layoutAlias) {
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index 84d207a521..13d25ed3b7 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -75,7 +75,6 @@ function MapModel(configuration) {
       this.setHeight(configuration.height);
       this.setMinZoom(configuration.minZoom);
       this.setMaxZoom(configuration.maxZoom);
-      this.addLayouts(configuration.layouts);
       this.addSubmodels(configuration.submodels);
       this.setCenterLatLng(configuration.centerLatLng);
       this.setTopLeftLatLng(configuration.topLeftLatLng);
@@ -631,7 +630,7 @@ MapModel.prototype.addLayout = function (layout) {
   if (object === undefined) {
     this._layoutsData[layoutData.getId()] = layoutData;
   } else {
-    logger.warn("Layout " + layoutData.getId() + " already exists in a model: " + this.getId());
+    throw new Error("Layout " + layoutData.getId() + " already exists in a model: " + this.getId());
   }
 };
 
diff --git a/frontend-js/src/main/js/map/data/Project.js b/frontend-js/src/main/js/map/data/Project.js
index 584f536720..457b8162ca 100644
--- a/frontend-js/src/main/js/map/data/Project.js
+++ b/frontend-js/src/main/js/map/data/Project.js
@@ -7,6 +7,7 @@ var ObjectWithListeners = require('../../ObjectWithListeners');
 var Annotation = require("./Annotation");
 var Model = require('./MapModel');
 
+// noinspection JSUnusedLocalSymbols
 var logger = require('../../logger');
 
 function Project(data) {
@@ -36,6 +37,7 @@ Project.prototype.loadFromData = function (data) {
   } else {
     self.setId(parseInt(data.idObject));
     self.setProjectId(data.projectId);
+    self.setDirectory(data.directory);
     self.setVersion(data.version);
     self.setName(data.name);
     self.setOverviewImages(data.overviewImageViews);
@@ -56,6 +58,7 @@ Project.prototype.update = function (data) {
   var self = this;
   self.setId(data.getId());
   self.setProjectId(data.getProjectId());
+  self.setDirectory(data.getDirectory());
   self.setVersion(data.getVersion());
   self.setName(data.getName());
   self.setOverviewImages(data.getOverviewImages());
@@ -107,6 +110,14 @@ Project.prototype.setProjectId = function (projectId) {
   this._projectId = projectId;
 };
 
+Project.prototype.getDirectory = function () {
+  return this._directory;
+};
+
+Project.prototype.setDirectory = function (directory) {
+  this._directory = directory;
+};
+
 Project.prototype.getVersion = function () {
   return this._version;
 };
diff --git a/frontend-js/src/test/js/Admin-test.js b/frontend-js/src/test/js/Admin-test.js
index 1de4186415..55e12a8e74 100644
--- a/frontend-js/src/test/js/Admin-test.js
+++ b/frontend-js/src/test/js/Admin-test.js
@@ -20,6 +20,7 @@ describe('Admin', function () {
   describe('logout', function () {
     it('default', function () {
       var admin = new Admin(helper.createCustomMapOptions());
+      helper.loginAsAdmin();
       var token = ServerConnector.getSessionData().getToken();
       return admin.init().then(function () {
         assert.ok(token === ServerConnector.getSessionData().getToken());
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index 868e4997c6..637a347c50 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -99,26 +99,28 @@ describe('ServerConnector', function () {
     });
   });
 
-  it('getReactions with empty list of ids', function () {
-    return ServerConnector.getReactions([]).then(function (result) {
-      assert.equal(result.length, 2);
-      var reaction = result[0];
-      assert.ok(reaction instanceof Reaction);
-      assert.equal(reaction.getId(), 153513);
-      assert.equal(reaction.getModelId(), 15781);
+  describe('getReactions', function () {
+    it('with empty list of ids', function () {
+      return ServerConnector.getReactions({ids: []}).then(function (result) {
+        assert.equal(result.length, 28);
+        var reaction = result[0];
+        assert.ok(reaction instanceof Reaction);
+        assert.equal(reaction.getId(), 153524);
+        assert.equal(reaction.getModelId(), 15781);
+      });
     });
-  });
-
-  it('getReactions without ids', function () {
-    return ServerConnector.getReactions([]).then(function (result) {
-      assert.equal(result.length, 2);
-      var reaction = result[0];
-      assert.ok(reaction instanceof Reaction);
-      assert.equal(reaction.getId(), 153513);
-      assert.equal(reaction.getModelId(), 15781);
+    it('without ids', function () {
+      return ServerConnector.getReactions([]).then(function (result) {
+        assert.equal(result.length, 28);
+        var reaction = result[0];
+        assert.ok(reaction instanceof Reaction);
+        assert.equal(reaction.getId(), 153524);
+        assert.equal(reaction.getModelId(), 15781);
+      });
     });
   });
 
+
   it('getElements with empty list of ids', function () {
     return ServerConnector.getAliases({}).then(function (result) {
       assert.equal(result.length, 30);
@@ -133,7 +135,7 @@ describe('ServerConnector', function () {
       assert.equal(result.length, 1);
       var layoutAlias = result[0];
       assert.ok(layoutAlias instanceof LayoutAlias);
-      assert.equal(-7602176, layoutAlias.getColor().value);
+      assert.equal(-7602176, layoutAlias.getColor().rgb);
       assert.equal(15781, layoutAlias.getModelId());
       assert.equal(329163, layoutAlias.getId());
     });
@@ -146,7 +148,7 @@ describe('ServerConnector', function () {
   });
 
   it('getOverlaySourceDownloadUrl', function () {
-    var id = 17296;
+    var id = 18083;
     return ServerConnector.getOverlaySourceDownloadUrl({
       overlayId: id
     }).then(function (url) {
@@ -320,13 +322,14 @@ describe('ServerConnector', function () {
 
   describe('getUsers', function () {
     it('default', function () {
+      helper.loginAsAdmin();
       return ServerConnector.getUsers().then(function (users) {
         assert.ok(users.length > 0);
       });
     });
     it('refresh', function () {
-      var user;
-      var users;
+      helper.loginAsAdmin();
+      var user, users;
       var modifiedName = "xxx name";
       return ServerConnector.getUsers().then(function (result) {
         users = result;
@@ -384,13 +387,15 @@ describe('ServerConnector', function () {
   });
 
   it('getSbmlFunction', function () {
-    return ServerConnector.getSbmlFunction({functionId: 5}).then(function (sbmlFunction) {
+    helper.setUrl("http://localhost:8080/?id=kinteics_test");
+    return ServerConnector.getSbmlFunction({functionId: 7}).then(function (sbmlFunction) {
       assert.equal("fun", sbmlFunction.getName());
-      assert.equal(5, sbmlFunction.getId());
+      assert.equal(7, sbmlFunction.getId());
     });
   });
 
   it('getSbmlParameter', function () {
+    helper.setUrl("http://localhost:8080/?id=kinteics_test");
     return ServerConnector.getSbmlParameter({parameterId: 7}).then(function (sbmlParameter) {
       assert.equal("local param", sbmlParameter.getName());
       assert.equal(7, sbmlParameter.getId());
diff --git a/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
index d5d1638bba..59a58a0520 100644
--- a/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
@@ -28,6 +28,7 @@ describe('EditProjectDialog', function () {
   });
 
   it('init', function () {
+    helper.loginAsAdmin();
     var dialog;
     var project;
     return ServerConnector.getProject().then(function (result) {
@@ -43,6 +44,7 @@ describe('EditProjectDialog', function () {
     });
   });
   it('saveOverlay', function () {
+    helper.loginAsAdmin();
     var dialog;
     var project;
     return ServerConnector.getProject().then(function (result) {
@@ -61,6 +63,7 @@ describe('EditProjectDialog', function () {
   });
 
   it('saveMap', function () {
+    helper.loginAsAdmin();
     var dialog;
     var project;
     return ServerConnector.getProject().then(function (result) {
@@ -79,6 +82,7 @@ describe('EditProjectDialog', function () {
   });
 
   it('saveUser', function () {
+    helper.loginAsAdmin();
     var dialog;
     var project;
     return ServerConnector.getProject().then(function (result) {
diff --git a/frontend-js/src/test/js/gui/admin/EditUserDialog-test.js b/frontend-js/src/test/js/gui/admin/EditUserDialog-test.js
index b4e2e2f832..b6061dcb0e 100644
--- a/frontend-js/src/test/js/gui/admin/EditUserDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/EditUserDialog-test.js
@@ -116,6 +116,7 @@ describe('EditUserDialog', function () {
   });
   describe('click privilege checkbox', function () {
     it('existing user', function () {
+      helper.loginAsAdmin();
       var dialog;
       var project;
       var user;
@@ -144,6 +145,7 @@ describe('EditUserDialog', function () {
   });
   describe('change privilege int value', function () {
     it('existing user', function () {
+      helper.loginAsAdmin();
       var dialog;
       var project;
       var user;
diff --git a/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js b/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js
index 28f5ad6e20..c7aebb1db4 100644
--- a/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js
+++ b/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js
@@ -13,6 +13,7 @@ describe('UsersAdminPanel', function () {
 
   describe('init', function () {
     it('default', function () {
+      helper.loginAsAdmin();
       var usersTab;
       var project;
       return ServerConnector.getProject().then(function (result) {
@@ -58,6 +59,7 @@ describe('UsersAdminPanel', function () {
   });
 
   it('refresh', function () {
+    helper.loginAsAdmin();
     var mapTab;
     var project;
     return ServerConnector.getProject().then(function (result) {
@@ -78,6 +80,7 @@ describe('UsersAdminPanel', function () {
   });
 
   it('showEditDialog', function () {
+    helper.loginAsAdmin();
     var mapTab;
     var project;
     return ServerConnector.getProject().then(function (result) {
@@ -97,6 +100,7 @@ describe('UsersAdminPanel', function () {
     });
   });
   it('onAddClicked', function () {
+    helper.loginAsAdmin();
     var mapTab;
     var project;
     return ServerConnector.getProject().then(function (result) {
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 b67812e01b..b96cafd5a1 100644
--- a/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
@@ -60,7 +60,7 @@ describe('OverlayPanel', function () {
   it('createRow', function () {
     var map = helper.createCustomMap();
 
-    var overlay = helper.createLayout();
+    var overlay = helper.createOverlay();
     overlay.setInputDataAvailable(true);
     overlay.setCreator("me");
     map.getModel().addLayout(overlay);
@@ -105,7 +105,7 @@ describe('OverlayPanel', function () {
   it('download', function () {
     var map = helper.createCustomMap();
 
-    var overlay = helper.createLayout();
+    var overlay = helper.createOverlay();
     overlay.setInputDataAvailable(true);
     map.getModel().addLayout(overlay);
 
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index 113d9e898b..2bac1b2696 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -320,16 +320,21 @@ Helper.prototype.createModel = function () {
     lng: 30
   });
 
-  var layout = this.createLayout();
+  var layout = this.createOverlay(result);
   result.addLayout(layout);
   return result;
 };
 
-Helper.prototype.createLayout = function () {
+Helper.prototype.createOverlay = function (model) {
+  var images = [];
+  if (model !== undefined) {
+    images.push({modelId: model.getId(), path: "xxx"});
+  }
   var id = this.idCounter++;
   return new LayoutData({
     idObject: id,
-    name: "testLayout" + id
+    name: "testLayout" + id,
+    images: images
   });
 };
 
diff --git a/frontend-js/src/test/js/map/AbstractCustomMap-test.js b/frontend-js/src/test/js/map/AbstractCustomMap-test.js
index 3e956487f8..27dcc3b958 100644
--- a/frontend-js/src/test/js/map/AbstractCustomMap-test.js
+++ b/frontend-js/src/test/js/map/AbstractCustomMap-test.js
@@ -46,6 +46,9 @@ describe('AbstractCustomMap', function () {
     var googleMap = helper.createGoogleMap();
 
     mockObject.setGoogleMap(googleMap);
+    mockObject.getTopMap = function () {
+      return mockObject
+    };
 
     mockObject.setupLayouts();
     assert.ok(mockObject.getGoogleMap().getMapTypeId().indexOf(layout.getId()) >= 0);
@@ -57,27 +60,39 @@ describe('AbstractCustomMap', function () {
 
   });
 
-  it("createTypeOptions", function () {
-    var layoutId = 40;
-    var layoutName = 'some layout name';
-    var layoutDirectory = 'dire45';
+  describe("createTypeOptions", function () {
+    it("default", function () {
+      var layoutId = 40;
+      var layoutName = 'some layout name';
+      var layoutDirectory = 'dire45';
 
-    var model = helper.createModel();
-    var layoutDataObj = {
-      idObject: layoutId,
-      name: layoutName,
-      directory: layoutDirectory
-    };
-    model.addLayout(layoutDataObj);
+      var model = helper.createModel();
+      var layoutDataObj = {
+        idObject: layoutId,
+        name: layoutName,
+        directory: layoutDirectory
+      };
+      model.addLayout(layoutDataObj);
 
-    var options = helper.createCustomMapOptions();
+      var options = helper.createCustomMapOptions();
 
-    var mockObject = new AbstractCustomMap(model, options);
+      var mockObject = new AbstractCustomMap(model, options);
 
-    var result = mockObject.createTypeOptions(layoutDataObj);
+      var result = mockObject.createTypeOptions(layoutDataObj);
 
-    assert.ok(result);
+      assert.ok(result);
 
+    });
+    it("getTileUrl", function () {
+      var coordinates = {x: 0, y: 0};
+      var map = helper.createCustomMap();
+
+      var typeOptions = map.createTypeOptions(map.getProject().getModel().getLayouts()[0]);
+      var url = typeOptions.getTileUrl(coordinates, 3);
+      assert.ok(url);
+      assert.ok(url.indexOf(coordinates.x) >= 0);
+      assert.ok(url.indexOf(coordinates.y) >= 0);
+    });
   });
 
   it("setMaxZoomLevel", function () {
diff --git a/frontend-js/src/test/js/map/CustomMap-test.js b/frontend-js/src/test/js/map/CustomMap-test.js
index 7e4600d0a0..d903043a02 100644
--- a/frontend-js/src/test/js/map/CustomMap-test.js
+++ b/frontend-js/src/test/js/map/CustomMap-test.js
@@ -105,7 +105,7 @@ describe('CustomMap', function () {
 
     it("with background overlay", function () {
       var map = helper.createCustomMap();
-      var layout = helper.createLayout();
+      var layout = helper.createOverlay();
       layout.setInitialized(true);
       layout.setInputDataAvailable(false);
       map.getModel().addLayout(layout);
@@ -118,12 +118,12 @@ describe('CustomMap', function () {
 
     it("with non background overlay", function () {
       var map = helper.createCustomMap();
-      var layout = helper.createLayout();
+      var layout = helper.createOverlay();
       layout.setInitialized(true);
       layout.setInputDataAvailable(true);
       map.getModel().addLayout(layout);
 
-      var emptyBackground = helper.createLayout();
+      var emptyBackground = helper.createOverlay();
       emptyBackground.setInputDataAvailable(false);
       emptyBackground.setName("Empty");
       map.getModel().addLayout(emptyBackground);
@@ -142,7 +142,7 @@ describe('CustomMap', function () {
       var reaction = helper.createReaction(map);
       map.getModel().addReaction(reaction);
 
-      var layout = helper.createLayout();
+      var layout = helper.createOverlay();
       layout.setInputDataAvailable(true);
       layout.setInitialized(true);
       var layoutAlias = helper.createLayoutAlias(alias);
@@ -213,7 +213,7 @@ describe('CustomMap', function () {
     it("with submap double opened", function () {
       var projectId = "complex_model_with_submaps";
       helper.setUrl("http://test/?id=" + projectId);
-      var customMap, filledSubmap ;
+      var customMap, filledSubmap;
       var filledSubmodelId = 16731;
       var overlayId = 18083;
 
@@ -229,7 +229,7 @@ describe('CustomMap', function () {
       }).then(function () {
         //after opening submap nothing should change
         assert.equal(1, filledSubmap.selectedLayoutOverlays[overlayId].length);
-      }).finally(function(){
+      }).finally(function () {
         return customMap.destroy();
       });
     });
@@ -238,7 +238,7 @@ describe('CustomMap', function () {
 
   it("removeSelectedLayout", function () {
     var map = helper.createCustomMap();
-    var layout = helper.createLayout();
+    var layout = helper.createOverlay();
     layout.setInitialized(true);
     layout.setInputDataAvailable(true);
     map.getModel().addLayout(layout);
@@ -254,7 +254,7 @@ describe('CustomMap', function () {
   describe("openInfoWindowForAlias", function () {
     it("default", function () {
       var map = helper.createCustomMap();
-      var layout = helper.createLayout();
+      var layout = helper.createOverlay();
       var alias = helper.createAlias();
       alias.setModelId(map.getId());
       var layoutAlias = helper.createLayoutAlias();
@@ -634,7 +634,7 @@ describe('CustomMap', function () {
     var alias = helper.createAlias();
     mockObject.getModel().addAlias(alias);
 
-    var layout = helper.createLayout();
+    var layout = helper.createOverlay();
     layout.setInputDataAvailable(true);
     layout.setInitialized(true);
     mockObject.getModel().addLayout(layout);
@@ -766,7 +766,7 @@ describe('CustomMap', function () {
     helper.createCommentDbOverlay(map);
 
     var alias = helper.createAlias(map);
-    alias.setId(329158);
+    alias.setId(329157);
     map.getModel().addAlias(alias);
 
     var ie = new IdentifiedElement(alias);
@@ -786,7 +786,7 @@ describe('CustomMap', function () {
     var commentOverlay = helper.createCommentDbOverlay(map);
 
     var alias = helper.createAlias(map);
-    alias.setId(329158);
+    alias.setId(329157);
     map.getModel().addAlias(alias);
 
     var ie = new IdentifiedElement(alias);
@@ -973,7 +973,7 @@ describe('CustomMap', function () {
 
     it("with session data overlays", function () {
       var project = helper.createProject();
-      var overlay1 = helper.createLayout();
+      var overlay1 = helper.createOverlay();
       overlay1.setInputDataAvailable(true);
       project.getModel().addLayout(overlay1);
 
diff --git a/frontend-js/src/test/js/map/data/LayoutData-test.js b/frontend-js/src/test/js/map/data/LayoutData-test.js
index 3932802d58..d9b1b1eb29 100644
--- a/frontend-js/src/test/js/map/data/LayoutData-test.js
+++ b/frontend-js/src/test/js/map/data/LayoutData-test.js
@@ -34,7 +34,7 @@ describe('LayoutData', function () {
         description: "test",
         status: "OK",
         progress: "0.00",
-        directory: "dir/subDir",
+        images: [{modelId: "15781", path: "subDir"}],
         creator: "admin ",
         inputDataAvailable: "true",
         idObject: 14852
@@ -42,7 +42,8 @@ describe('LayoutData', function () {
       var data = new LayoutData(obj);
       assert.ok(data);
       assert.equal(data.getInputDataAvailable(), true);
-      assert.equal(data.getDirectory(), "dir/subDir");
+      assert.equal(data.getImagesDirectory(15781), "subDir");
+      assert.equal(data.getImagesDirectory(15782), null);
     });
 
     it("from problematic json", function () {
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 77ae8c60ca..9cca529baa 100644
--- a/frontend-js/src/test/js/map/data/MapModel-test.js
+++ b/frontend-js/src/test/js/map/data/MapModel-test.js
@@ -27,7 +27,7 @@ describe('MapModel', function () {
 
   it("Get layout by id", function (done) {
     var model = helper.createModel();
-    var layout = helper.createLayout();
+    var layout = helper.createOverlay();
 
     model.getLayoutDataById(layout.getId()).then(function () {
       assert.ok(false, 'expected rejection');
diff --git a/frontend-js/src/test/js/map/overlay/DrugDbOverlay-test.js b/frontend-js/src/test/js/map/overlay/DrugDbOverlay-test.js
index 7f9b244057..0c0666f87f 100644
--- a/frontend-js/src/test/js/map/overlay/DrugDbOverlay-test.js
+++ b/frontend-js/src/test/js/map/overlay/DrugDbOverlay-test.js
@@ -43,17 +43,17 @@ describe('DrugDbOverlay', function () {
   });
 
   it("searchNamesByTarget", function () {
-    var map = helper.createCustomMap();
-    map.getModel().setId(15781);
-    var searchDb = helper.createDrugDbOverlay(map);
-
-    var target = new IdentifiedElement({
-      type: "ALIAS",
-      id: 329170,
-      modelId: 15781
-    });
-
-    return searchDb.searchNamesByTarget(target).then(function (drugNames) {
+    return ServerConnector.getProject().then(function (project) {
+      var map = helper.createCustomMap(project);
+      var searchDb = helper.createDrugDbOverlay(map);
+
+      var target = new IdentifiedElement({
+        type: "ALIAS",
+        id: 329170,
+        modelId: 15781
+      });
+      return searchDb.searchNamesByTarget(target);
+    }).then(function (drugNames) {
       assert.equal(drugNames.length, 1);
       assert.equal(drugNames[0], "NADH");
     });
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 0821e7e5bb..434a51968c 100644
--- a/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
+++ b/frontend-js/src/test/js/map/overlay/SearchDbOverlay-test.js
@@ -12,7 +12,7 @@ var assert = require('assert');
 var Promise = require('bluebird');
 
 describe('SearchDbOverlay', function () {
-  it("constructor 1", function () {
+  it("constructor", function () {
     var map = helper.createCustomMap();
     var oc = new SearchDbOverlay({
       map: map,
@@ -154,7 +154,7 @@ describe('SearchDbOverlay', function () {
         return searchDb.searchByCoordinates(searchParams);
       }).then(function (result) {
         // id of the parent
-        assert.equal(result[0].getId(), 329159);
+        assert.equal(result[0].getId(), 329158);
       });
 
     });
diff --git a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
index c7bda3c83f..cfa8310709 100644
--- a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
+++ b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
@@ -124,6 +124,7 @@ describe('AliasInfoWindow', function () {
     }).then(function (data) {
       var overlayDiv = aliasWindow.createOverlayInfoDiv(oc, data);
       assert.ok(functions.isDomElement(overlayDiv));
+      logger.debug(overlayDiv.innerHTML);
       assert.ok(overlayDiv.innerHTML.indexOf('NADH') >= 0);
 
     });
@@ -162,7 +163,7 @@ describe('AliasInfoWindow', function () {
       var oc = helper.createCommentDbOverlay(map);
 
       var alias = helper.createAlias();
-      alias.setId(3001);
+      alias.setId(329157);
       alias.setIsComplete(true);
       alias.setModelId(map.getId());
       map.getModel().addAlias(alias);
@@ -193,7 +194,7 @@ describe('AliasInfoWindow', function () {
       var oc = helper.createCommentDbOverlay(map);
 
       var alias = helper.createAlias(map);
-      alias.setId(3001);
+      alias.setId(329157);
       alias.setIsComplete(true);
 
       var aliasWindow = new AliasInfoWindow({
@@ -216,7 +217,7 @@ describe('AliasInfoWindow', function () {
     });
   });
 
-  it("createGeneticsDiv", function () {
+  xit("createGeneticsDiv", function () {
     var map;
     var overlay;
 
diff --git a/frontend-js/src/test/js/mocha-config.js b/frontend-js/src/test/js/mocha-config.js
index 6c715e1587..2be1c6fc3d 100644
--- a/frontend-js/src/test/js/mocha-config.js
+++ b/frontend-js/src/test/js/mocha-config.js
@@ -156,6 +156,7 @@ afterEach(function () {
       this.test.error(new Error("Test didn't left clean document. Found: " + content));
     } else if ($._data(window, "events").resize) {
       logger.debug($._data(window, "events").resize);
+      $(window).off("resize");
       this.test.error(new Error("Test didn't left clean resize events handlers."));
     }
   }
diff --git a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
index 432c6e04dc..d4639b3c8f 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"},{"handler":"lcsb.mapviewer.converter.model.sbml.SbmlParser","extension":"xml","name":"SBML"}],"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":[],"annotators":[{"name":"BRENDA","description":"","className":"lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://www.brenda-enzymes.org"},{"name":"Biocompendium","description":"","className":"lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator","parametersDefinitions":[],"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":"CAZy","description":"","className":"lcsb.mapviewer.annotation.services.annotators.CazyAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://commonchemistry.org"},{"name":"Chebi","description":"","className":"lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Chemical"],"url":"http://www.ebi.ac.uk/chebi/"},{"name":"Uniprot","description":"","className":"lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator","parametersDefinitions":[],"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","description":"","className":"lcsb.mapviewer.annotation.services.annotators.GoAnnotator","parametersDefinitions":[],"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","description":"","className":"lcsb.mapviewer.annotation.services.annotators.HgncAnnotator","parametersDefinitions":[],"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":"KEGG","description":"Annotations extracted from KEGG ENZYME Database based on species EC numbers. Annotation include relevant publications and homologous genes for given EC numbers.","className":"lcsb.mapviewer.annotation.services.annotators.KeggAnnotator","parametersDefinitions":[{"name":"KEGG organism identifier","description":"Space-delimited list of organisms codes for which homologous genes (GENE section in the KEGG enzyme record) should be imported. Currently only ATH (Arabidopsis Thaliana) is supported.","type":"java.lang.String"}],"elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://www.genome.jp/kegg/"},{"name":"Protein Data Bank","description":"","className":"lcsb.mapviewer.annotation.services.annotators.PdbAnnotator","parametersDefinitions":[],"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 annotator","description":"","className":"lcsb.mapviewer.annotation.services.annotators.ReconAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Chemical","lcsb.mapviewer.model.map.reaction.Reaction"],"url":"http://humanmetabolism.org/"},{"name":"Entrez Gene","description":"","className":"lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"http://www.ncbi.nlm.nih.gov/gene"},{"name":"Ensembl","description":"","className":"lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"www.ensembl.org"},{"name":"STITCH","description":"","className":"lcsb.mapviewer.annotation.services.annotators.StitchAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.SimpleMolecule"],"url":"http://stitch.embl.de/"},{"name":"STRING","description":"","className":"lcsb.mapviewer.annotation.services.annotators.StringAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://string-db.org/"},{"name":"TAIR","description":"","className":"lcsb.mapviewer.annotation.services.annotators.TairAnnotator","parametersDefinitions":[],"elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://arabidopsis.org/index.jsp"}],"buildDate":"20/02/2018 13:27","reactionTypes":[{"name":"Catalysis","className":"lcsb.mapviewer.model.map.reaction.type.CatalysisReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown positive influence","className":"lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Generic Reaction","className":"lcsb.mapviewer.model.map.reaction.Reaction","parentClass":"lcsb.mapviewer.model.map.BioEntity"},{"name":"Known transition omitted","className":"lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced 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":"Unknown catalysis","className":"lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction","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":"Physical stimulation","className":"lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction","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":"Dissociation","className":"lcsb.mapviewer.model.map.reaction.type.DissociationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Inhibition","className":"lcsb.mapviewer.model.map.reaction.type.InhibitionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced physical stimulation","className":"lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Negative influence","className":"lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown inhibition","className":"lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Modulation","className":"lcsb.mapviewer.model.map.reaction.type.ModulationReaction","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":"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":"Trigger","className":"lcsb.mapviewer.model.map.reaction.type.TriggerReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"}],"version":"12.0.0","mapTypes":[{"name":"Downstream targets","id":"DOWNSTREAM_TARGETS"},{"name":"Pathway","id":"PATHWAY"},{"name":"Unknown","id":"UNKNOWN"}],"miriamTypes":{"CAZY":{"commonName":"CAZy","uris":["urn:miriam:cazy"],"homepage":"http://commonchemistry.org","registryIdentifier":"MIR:00000195"},"CHEMBL_TARGET":{"commonName":"ChEMBL target","uris":["urn:miriam:chembl.target"],"homepage":"https://www.ebi.ac.uk/chembldb/","registryIdentifier":"MIR:00000085"},"UNIPROT":{"commonName":"Uniprot","uris":["urn:miriam:uniprot"],"homepage":"http://www.uniprot.org/","registryIdentifier":"MIR:00000005"},"MI_R_BASE_MATURE_SEQUENCE":{"commonName":"miRBase Mature Sequence Database","uris":["urn:miriam:mirbase.mature"],"homepage":"http://www.mirbase.org/","registryIdentifier":"MIR:00000235"},"PFAM":{"commonName":"Protein Family Database","uris":["urn:miriam:pfam"],"homepage":"http://pfam.xfam.org//","registryIdentifier":"MIR:00000028"},"ENSEMBL_PLANTS":{"commonName":"Ensembl Plants","uris":["urn:miriam:ensembl.plant"],"homepage":"http://plants.ensembl.org/","registryIdentifier":"MIR:00000205"},"WIKIPEDIA":{"commonName":"Wikipedia 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diff --git a/frontend-js/testFiles/apiCalls/doLogout/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/doLogout/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000..48aa9beb26
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/doLogout/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{"status":"OK"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/doLogout/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/doLogout/token=MOCK_TOKEN_ID&
index 1a36cf5fc2..48aa9beb26 100644
--- a/frontend-js/testFiles/apiCalls/doLogout/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/doLogout/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"status":"ok"}
\ No newline at end of file
+{"status":"OK"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID&
deleted file mode 100644
index dcc51dce28..0000000000
--- a/frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID&
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/mesh/D000544/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/mesh/D000544/token=MOCK_TOKEN_ID&
index cde9de575d..92b88c2ad1 100644
--- a/frontend-js/testFiles/apiCalls/mesh/D000544/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/mesh/D000544/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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\ No newline at end of file
+{"description":"A degenerative disease of the BRAIN characterized by the insidious onset of DEMENTIA. Impairment of MEMORY, judgment, attention span, and problem solving skills are followed by severe APRAXIAS and a global loss of cognitive abilities. The condition primarily occurs after age 60, and is marked pathologically by severe cortical atrophy and the triad of SENILE PLAQUES; NEUROFIBRILLARY TANGLES; and NEUROPIL THREADS. (From Adams et al., Principles of Neurology, 6th ed, pp1049-57)","id":"D000544","name":"Alzheimer Disease","synonyms":["Presenile Alzheimer Dementia","Dementias, Alzheimer","Familial Alzheimer Disease (FAD)","Alzheimer Disease, Early Onset","Dementia, Primary Senile Degenerative","Alzheimer Syndrome","Acute Confusional Senile Dementia","Alzheimer Diseases, Familial (FAD)","Alzheimer Type Senile Dementia","Dementia, Alzheimer Type","Focal Onset Alzheimer's Disease","Early Onset Alzheimer Disease","Alzheimer Dementia","Late Onset Alzheimer Disease","Alzheimer Disease, Familial (FAD)","Primary Senile Degenerative Dementia","Alzheimer Sclerosis","Presenile Dementia","Dementia, Presenile","Alzheimer Dementias","Dementia, Alzheimer","Dementia, Senile","Senile Dementia","Dementia, Alzheimer-Type (ATD)","Alzheimer Type Dementia","Alzheimer's Disease, Focal Onset","Alzheimer Disease, Late Onset","Sclerosis, Alzheimer","Alzheimer-Type Dementia (ATD)","Alzheimer's Disease","Senile Dementia, Alzheimer Type","Senile Dementia, Acute Confusional","Familial Alzheimer Diseases (FAD)","Alzheimer Type Dementia (ATD)"]}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/mesh/D010300/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/mesh/D010300/token=MOCK_TOKEN_ID&
index bb1bc41aaf..689aa78129 100644
--- a/frontend-js/testFiles/apiCalls/mesh/D010300/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/mesh/D010300/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"synonyms":["Parkinson's Disease, Idiopathic","Primary Parkinsonism","Idiopathic Parkinson's Disease","Paralysis Agitans","Parkinsonism, Primary","Parkinson's Disease","Lewy Body Parkinson Disease","Parkinson's Disease, Lewy Body","Parkinson Disease, Idiopathic","Lewy Body Parkinson's Disease","Idiopathic Parkinson Disease"],"name":"Parkinson Disease","description":"A progressive, degenerative neurologic disease characterized by a TREMOR that is maximal at rest, retropulsion (i.e. a tendency to fall backwards), rigidity, stooped posture, slowness of voluntary movements, and a masklike facial expression. Pathologic features include loss of melanin containing neurons in the substantia nigra and other pigmented nuclei of the brainstem. LEWY BODIES are present in the substantia nigra and locus coeruleus but may also be found in a related condition (LEWY BODY DISEASE, DIFFUSE) characterized by dementia in combination with varying degrees of parkinsonism. (Adams et al., Principles of Neurology, 6th ed, p1059, pp1067-75)","id":"D010300"}
\ No newline at end of file
+{"description":"A progressive, degenerative neurologic disease characterized by a TREMOR that is maximal at rest, retropulsion (i.e. a tendency to fall backwards), rigidity, stooped posture, slowness of voluntary movements, and a masklike facial expression. Pathologic features include loss of melanin containing neurons in the substantia nigra and other pigmented nuclei of the brainstem. LEWY BODIES are present in the substantia nigra and locus coeruleus but may also be found in a related condition (LEWY BODY DISEASE, DIFFUSE) characterized by dementia in combination with varying degrees of parkinsonism. (Adams et al., Principles of Neurology, 6th ed, p1059, pp1067-75)","id":"D010300","name":"Parkinson Disease","synonyms":["Parkinson's Disease, Idiopathic","Primary Parkinsonism","Idiopathic Parkinson's Disease","Paralysis Agitans","Parkinsonism, Primary","Parkinson's Disease","Lewy Body Parkinson Disease","Parkinson's Disease, Lewy Body","Parkinson Disease, Idiopathic","Lewy Body Parkinson's Disease","Idiopathic Parkinson Disease"]}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/all/overlays/14081/PATCH_overlay.defaultOverlay=false&overlay.name=Pathways and compartments&overlay.publicOverlay=true&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/all/overlays/14081/PATCH_overlay.defaultOverlay=false&overlay.name=Pathways and compartments&overlay.publicOverlay=true&token=ADMIN_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/all/overlays/14081/PATCH_overlay.defaultOverlay=false&overlay.name=Pathways and compartments&overlay.publicOverlay=true&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/all/overlays/14081/PATCH_overlay.defaultOverlay=false&overlay.name=Pathways and compartments&overlay.publicOverlay=true&token=ADMIN_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/models/all/token=MOCK_TOKEN_ID&
index f71a795bea..4d494cbf39 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/models/all/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/models/all/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/overlays/publicOverlay=true&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..563f362405
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/statistics/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/statistics/token=MOCK_TOKEN_ID&
index 0e57e7d5d1..727fcd9ea3 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/statistics/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/statistics/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID&
index f3fd47b2f5..552552ec76 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities/elements/columns=id,bounds,modelId&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities/elements/columns=id,bounds,modelId&type=Compartment&token=MOCK_TOKEN_ID&
index 889f5e5170..f4b142eaf2 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities/elements/columns=id,bounds,modelId&type=Compartment&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities/elements/columns=id,bounds,modelId&type=Compartment&token=MOCK_TOKEN_ID&
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\ No newline at end of file
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345325&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345325&token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345325&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345325&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330&token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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\ No newline at end of file
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330,345331,345337&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330,345331,345337&token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330,345331,345337&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330,345331,345337&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345334&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345334&token=MOCK_TOKEN_ID&
index b30361a6e9..c595f56e00 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345334&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345334&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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\ No newline at end of file
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345337&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345337&token=MOCK_TOKEN_ID&
index 0845b7dc0f..bba8a61563 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345337&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345337&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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\ No newline at end of file
+[{"bounds":{"height":40.0,"width":80.0,"x":190.0,"y":44.0},"id":345337,"modelId":16731}]
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345323,345332&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345323,345332&token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345323,345332&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345323,345332&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345325&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/id=345325&token=MOCK_TOKEN_ID&
index 21687ff560..2eaedd7c2d 100644
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@@ -1 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/token=MOCK_TOKEN_ID&
index 19fa38ecdf..3ef88478ed 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/token=MOCK_TOKEN_ID&
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-[{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":20638,"tileSize":256,"width":600,"height":400,"minZoom":2,"maxZoom":4,"layouts":[{"idObject":19774,"modelId":20638,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"a2e4822a98337283e39f7b60acf85ec9/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":19775,"modelId":20638,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"a2e4822a98337283e39f7b60acf85ec9/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":19776,"modelId":20638,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"a2e4822a98337283e39f7b60acf85ec9/_empty0","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.17133464081945,"lng":-135.0},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":75.95934455387827,"lng":-90.0},"submodelType":"UNKNOWN"}]
\ No newline at end of file
+[{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":20638,"tileSize":256,"width":600,"height":400,"defaultCenterX":null,"defaultCenterY":null,"defaultZoomLevel":null,"minZoom":2,"maxZoom":4,"submodels":[],"centerLatLng":{"lat":79.17133464081945,"lng":-135.0},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":75.95934455387827,"lng":-90.0},"submodelType":"UNKNOWN"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/empty/overlays/publicOverlay=true&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/empty/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..9b8de965d1
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/empty/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"defaultOverlay":false,"description":null,"idObject":19774,"images":[{"modelId":20638,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID&
index 3eb029a6a4..552fdf86e0 100644
--- a/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"version":"0","disease":null,"organism":null,"idObject":19187,"status":"Ok","progress":100.0,"name":"UNKNOWN DISEASE MAP","projectId":"empty","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
+{"version":"piotr.gawron@uni.lu","disease":null,"organism":null,"idObject":19187,"status":"Ok","directory":"a2e4822a98337283e39f7b60acf85ec9","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"empty","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/functions/7/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/functions/7/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..f56a11451c
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/functions/7/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"arguments":["x","y"],"definition":"<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n<lambda>\n<bvar>\n<ci> x </ci>\n</bvar>\n<bvar>\n<ci> y </ci>\n</bvar>\n<apply>\n<plus/>\n<ci> x </ci>\n<ci> y </ci>\n<cn type=\"integer\"> 2 </cn>\n</apply>\n</lambda>\n\n</math>","functionId":"fun","id":7,"mathMlPresentation":"\n<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n<mrow>\n<mo>λ</mo>\n<mrow>\n<mo>(</mo>\n<mi> x </mi>\n<mo>,</mo>\n<mi> y </mi>\n<mo>,</mo>\n<mrow>\n<mi> x </mi>\n<mo>+</mo>\n<mi> y </mi>\n<mo>+</mo>\n<mn> 2 </mn>\n</mrow>\n<mo>)</mo>\n</mrow>\n</mrow>\n\n</math>\n","name":"fun"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/parameters/7/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/parameters/7/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..121179ef72
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/parameters/7/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"global":false,"id":7,"name":"local param","parameterId":"local_param","unitsId":24,"value":5.0}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample.downloadSource/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample.downloadSource/token=MOCK_TOKEN_ID&
index 6489f980dd..9bd01a8dbc 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample.downloadSource/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample.downloadSource/token=MOCK_TOKEN_ID&
@@ -1 +1,2469 @@
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+Name: Carney complex, multiple neoplasia and lentiginosis
+Description: RecName: Full=Sodium/calcium exchanger 1; AltName: Full=Na(+)/Ca(2+)-exchange protein 1; Flags: Precursor;
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+Synonyms: CNC, NCX1
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+Symbol: CNC
+Name: Carney complex, multiple neoplasia and lentiginosis
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+Previous Symbols:
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+<body>notes for reaction
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+<rdf:li rdf:resource="urn:miriam:pubmed:123"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00041" species="s15">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa14</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00042" species="s16">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa15</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re22" id="re22" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s16" alias="sa15"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s15" alias="sa14"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00049" species="s16">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa15</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00050" species="s15">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa14</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re23" id="re23" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>DISSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s12" alias="csa1"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s8" alias="sa8"/>
+<celldesigner:baseProduct species="s7" alias="sa7"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="2" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="2" num1="1" num2="2" tShapeIndex="2">0.18282782549923482,-0.02987100654295849 0.35006352924185036,-0.10231438664656078 0.3085675700621304,0.07830364386236799 0.08461516922978274,0.12492176357975968 0.29646415360973166,-0.03506343865856057 1.558752596681942,-2.118127685609399</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00043" species="s12">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>csa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00044" species="s8">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa8</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00045" species="s7">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa7</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re24" id="re24" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s4" alias="sa4"/>
+<celldesigner:baseReactant species="s12" alias="csa1"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s9" alias="sa9"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="2" num1="0" num2="3" tShapeIndex="2">0.4041225406185376,0.1671832431277971 0.5704248266570819,0.08721453185432626 0.35094316257607705,-3.1667282618214054E-4 0.6454315665797781,0.2748705762795411 0.5207541327645231,-0.156262363889701 -0.4844017975381516,2.3675726722098025</celldesigner:editPoints>
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+</annotation>
+<listOfReactants>
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+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00055" species="s12">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>csa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00056" species="s9">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa9</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re26" id="re26" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s22" alias="sa22">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s22" alias="sa23">
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+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s20" alias="sa24" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="S"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Curve"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s21" alias="sa25" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="S"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Curve"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="1">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.47954866008462904,-0.37000470145745523 0.9297602256699617,-0.5236483309825986</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00061" species="s22">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa22</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00062" species="s20">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa24</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00063" species="s22">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa23</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00064" species="s21">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa25</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re27" id="re27" reversible="false">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>asd
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s23" alias="sa26">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s23" alias="sa27">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s24" alias="sa28" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="S"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Curve"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s25" alias="sa29" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="S"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Curve"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>-0.2598501687659524,-1.4924508108998107 0.1811739606709441,-1.5643296326517722</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00065" species="s23">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa26</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00066" species="s24">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa28</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00067" species="s23">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa27</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00068" species="s25">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa29</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re885" id="re28" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s4532" alias="sa35">
+<celldesigner:linkAnchor position="SSE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2612" alias="sa30">
+<celldesigner:linkAnchor position="NNE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s815" alias="sa34" targetLineIndex="-1,0">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+<celldesigner:reactantLink reactant="s817" alias="sa33" targetLineIndex="-1,0">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s841" alias="sa31" targetLineIndex="-1,1">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="horizontal"/>
+<celldesigner:lineDirection index="1" value="vertical"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.6252698493415991,-0.5048003480862278</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+<celldesigner:listOfModification>
+<celldesigner:modification type="CATALYSIS" modifiers="s2611" aliases="sa32" targetLineIndex="-1,2">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+</celldesigner:listOfModification>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re885">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_631.3"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00046" species="s4532">
+<annotation>
+<celldesigner:extension>
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+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00047" species="s815">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa34</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00051" species="s817">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa33</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00052" species="s2612">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa30</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00053" species="s841">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa31</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<listOfModifiers>
+<modifierSpeciesReference metaid="CDMT00057" species="s2611">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa32</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+</listOfModifiers>
+</reaction>
+<reaction metaid="re886" id="re29" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s2612" alias="sa30">
+<celldesigner:linkAnchor position="NNW"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s4532" alias="sa35">
+<celldesigner:linkAnchor position="SSW"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+<celldesigner:listOfModification>
+<celldesigner:modification type="CATALYSIS" modifiers="s2611" aliases="sa32" targetLineIndex="-1,3">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+</celldesigner:listOfModification>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re886">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_1493.4"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00058" species="s2612">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa30</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00059" species="s4532">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa35</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<listOfModifiers>
+<modifierSpeciesReference metaid="CDMT00060" species="s2611">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa32</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+</listOfModifiers>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.name=UNKNOWN DISEASE MAP&project.organism.resource=1570291&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.name=UNKNOWN DISEASE MAP&project.organism.resource=9606&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID&
similarity index 100%
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\ No newline at end of file
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&
index 9eecb4345a..853cb049c9 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,pinned,removed,type&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,removed,type&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,removed,type&token=MOCK_TOKEN_ID&
index 41b5f0f752..b238bf3249 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,removed,type&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/columns=elementId,icon,id,modelId,removed,type&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"elementId":"Point2D.Double[241.01, 372.35]","modelId":15781,"icon":"icons/comment.png","id":4506,"type":"POINT","removed":false},{"elementId":"Point2D.Double[643.96, 144.09]","modelId":15781,"icon":"icons/comment.png","id":4507,"type":"POINT","removed":false}]
\ No newline at end of file
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/points/1.00,200.00/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/points/1.00,200.00/token=MOCK_TOKEN_ID&
index 16684fbe71..524f4fda8b 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/points/1.00,200.00/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/points/1.00,200.00/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/token=ADMIN_TOKEN_ID&
index 69c32f9cf8..1d4e26fd81 100644
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/all/token=MOCK_TOKEN_ID&
index 15846794a5..3adae03ca4 100644
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/drugs.search/query=NADH&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/drugs.search/query=NADH&token=MOCK_TOKEN_ID&
index 106995c7e4..db00a18e27 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/drugs.search/query=NADH&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/drugs.search/query=NADH&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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\ No newline at end of file
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/drugs.search/query=aspirin&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/drugs.search/query=aspirin&token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/sample/drugs.search/query=aspirin&token=MOCK_TOKEN_ID&
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@@ -1 +1 @@
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\ No newline at end of file
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID&
index 6489f980dd..0252df8ac6 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID&
@@ -1 +1,2289 @@
-{"info":"dummy resposne"}
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<notes></notes><listOfUnitDefinitions>
+</listOfUnitDefinitions>
+<listOfFunctionDefinitions>
+</listOfFunctionDefinitions>
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="1305" sizeY="473"/>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s_id_sa13" name="s14"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>SemanticZoomLevelVisibility: 2
+
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</body></html></celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s_id_csa1</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_sa13</celldesigner:proteinReference>
+<celldesigner:name>s14</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+</celldesigner:listOfIncludedSpecies>
+<celldesigner:listOfCompartmentAliases>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:complexSpeciesAlias id="csa1" species="s_id_csa1" >
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="271.0" y="207.0" w="101.0" h="164.0" />
+<celldesigner:font size="12.0"/><celldesigner:view state="usual"/>
+<celldesigner:usualView><celldesigner:innerPosition x="271.0" y="207.0"/><celldesigner:boxSize width="101.0" height="164.0"/><celldesigner:singleLine width="2.0"/><celldesigner:paint color="FFF7F7F7" scheme="Color"/></celldesigner:usualView>
+<celldesigner:briefView><celldesigner:innerPosition x="271.0" y="207.0"/><celldesigner:boxSize width="101.0" height="164.0"/><celldesigner:singleLine width="101.0"/><celldesigner:paint color="FFF7F7F7" scheme="Color"/></celldesigner:briefView>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa11" species="s_id_sa11" >
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="105.0" y="203.5" w="70.0" h="25.0" />
+<celldesigner:font size="12.0"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView><celldesigner:innerPosition x="105.0" y="203.5"/><celldesigner:boxSize width="70.0" height="25.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="7FCCCCCC" scheme="Color"/></celldesigner:usualView>
+<celldesigner:briefView><celldesigner:innerPosition x="105.0" y="203.5"/><celldesigner:boxSize width="70.0" height="25.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="7FCCCCCC" scheme="Color"/></celldesigner:briefView>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa6" species="s_id_sa6" >
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="101.0" y="129.5" w="90.0" h="25.0" />
+<celldesigner:font size="12.0"/>
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+RefSeq_ID: NP_001106272.1, NP_001106271.1, NP_001106273.1, NP_001239553.1, NP_066920.1
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+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference species="s_id_sa23">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa22</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference species="s_id_sa24">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa24</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="s_id_sa23">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa23</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference species="s_id_sa25">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa25</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re4" id="re4" name="" reversible="false" >
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType><celldesigner:baseReactants>
+<celldesigner:baseReactant species="s_id_sa5" alias="sa5" >
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s_id_sa6" alias="sa6" >
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:listOfModification>
+</celldesigner:listOfModification>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference species="s_id_sa5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="s_id_sa6">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa6</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re27" id="re27" name="" reversible="false" >
+<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>asd</body></html></notes><annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType><celldesigner:baseReactants>
+<celldesigner:baseReactant species="s_id_sa27" alias="sa26" >
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s_id_sa27" alias="sa27" >
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s_id_sa28" alias="sa28" >
+<celldesigner:linkAnchor position="S"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:reactantLink></celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s_id_sa29" alias="sa29" >
+<celldesigner:linkAnchor position="S"/>
+<celldesigner:connectScheme connectPolicy="direct" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection  index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:productLink></celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints >-0.2598501687659524,-1.4924508108998107 0.18117396067094418,-1.564329632651772</celldesigner:editPoints>
+<celldesigner:listOfModification>
+</celldesigner:listOfModification>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference species="s_id_sa27">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa26</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference species="s_id_sa28">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa28</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="s_id_sa27">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa27</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference species="s_id_sa29">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa29</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re13" id="re13" name="" reversible="false" >
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType><celldesigner:baseReactants>
+<celldesigner:baseReactant species="s_id_sa2" alias="sa2" >
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s_id_sa3" alias="sa3" >
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:listOfModification>
+</celldesigner:listOfModification>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference species="s_id_sa2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="s_id_sa3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re19" id="re19" name="" reversible="false" >
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType><celldesigner:baseReactants>
+<celldesigner:baseReactant species="s_id_sa7" alias="sa7" >
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s_id_sa8" alias="sa8" >
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:listOfModification>
+</celldesigner:listOfModification>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference species="s_id_sa7">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa7</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="s_id_sa8">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa8</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re15" id="re15" name="" reversible="false" >
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType><celldesigner:baseReactants>
+<celldesigner:baseReactant species="s_id_sa4" alias="sa4" >
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s_id_sa9" alias="sa9" >
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:listOfModification>
+</celldesigner:listOfModification>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference species="s_id_sa4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="s_id_sa9">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa9</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+<reaction metaid="re17" id="re17" name="" reversible="false" >
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType><celldesigner:baseReactants>
+<celldesigner:baseReactant species="s_id_sa8" alias="sa8" >
+<celldesigner:linkAnchor position="SSE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s_id_sa12" alias="sa12" >
+<celldesigner:linkAnchor position="NNW"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0" >
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:listOfModification>
+</celldesigner:listOfModification>
+<celldesigner:line width="1.0" color="FF000000" type="Straight" />
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference species="s_id_sa8">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa8</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference species="s_id_sa12">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa12</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model></sbml>
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.id=15781&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.defaultCenterX=100&model.defaultCenterY=4&model.defaultZoomLevel=5&model.id=15781&token=ADMIN_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.id=15781&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.defaultCenterX=100&model.defaultCenterY=4&model.defaultZoomLevel=5&model.id=15781&token=ADMIN_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=1&token=MOCK_TOKEN_ID&
index 3ab3e25631..118e4d80c0 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=1&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=1&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"modelId":15781,"id":329171,"type":"ALIAS"}]
\ No newline at end of file
+[{"id":329171,"modelId":15781,"type":"ALIAS"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=2.00,12.00&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=2.00,12.00&token=MOCK_TOKEN_ID&
index 74af28b2d6..3765ea2243 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=2.00,12.00&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=2.00,12.00&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"modelId":15781,"id":329173,"type":"ALIAS"},{"modelId":15781,"id":153511,"type":"REACTION"},{"modelId":15781,"id":153510,"type":"REACTION"},{"modelId":15781,"id":329168,"type":"ALIAS"},{"modelId":15781,"id":153519,"type":"REACTION"}]
\ No newline at end of file
+[{"id":329173,"modelId":15781,"type":"ALIAS"},{"id":153511,"modelId":15781,"type":"REACTION"},{"id":153510,"modelId":15781,"type":"REACTION"},{"id":329168,"modelId":15781,"type":"ALIAS"},{"id":153519,"modelId":15781,"type":"REACTION"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=1&token=MOCK_TOKEN_ID&
index 3ab3e25631..118e4d80c0 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=1&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=1&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"modelId":15781,"id":329171,"type":"ALIAS"}]
\ No newline at end of file
+[{"id":329171,"modelId":15781,"type":"ALIAS"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=1&token=MOCK_TOKEN_ID&
index 4b516e9d53..e3ea48b0bf 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=1&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=1&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"modelId":15781,"id":329159,"type":"ALIAS"}]
\ No newline at end of file
+[{"id":329159,"modelId":15781,"type":"ALIAS"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=457.51,356.84&count=1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=457.51,356.84&count=1&token=MOCK_TOKEN_ID&
index 8916c4e02e..ab72e0f5a4 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=457.51,356.84&count=1&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=457.51,356.84&count=1&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"modelId":15781,"id":153521,"type":"REACTION"}]
\ No newline at end of file
+[{"id":153521,"modelId":15781,"type":"REACTION"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=1&token=MOCK_TOKEN_ID&
index 8916c4e02e..ab72e0f5a4 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=1&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=1&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"modelId":15781,"id":153521,"type":"REACTION"}]
\ No newline at end of file
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities.search/count=100&query=s1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities.search/count=100&query=s1&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329167&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329167&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329168,329173&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329168,329173&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329170&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329170&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329171&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329171&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329173&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329173&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329156&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329156&token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&sortColumn=pubmedId&sortOrder=asc&start=0&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&sortColumn=pubmedId&sortOrder=asc&start=0&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"totalSize":1,"data":[{"elements":[{"modelId":15781,"id":153508,"type":"REACTION"}],"publication":{"resource":"123","link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":860355,"type":"PUBMED","article":{"title":"The importance of an innervated and intact antrum and pylorus in preventing postoperative duodenogastric reflux and gastritis.","authors":["Keighley MR"," Asquith P"," Edwards JA"," Alexander-Williams J."],"journal":"The British journal of surgery","year":1975,"link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":"123","citationCount":12,"stringAuthors":"Keighley MR,  Asquith P,  Edwards JA,  Alexander-Williams J."}}}],"start":0,"length":1}
\ No newline at end of file
+{"data":[{"elements":[{"id":153508,"modelId":15781,"type":"REACTION"}],"publication":{"annotatorClassName":"","article":{"title":"The importance of an innervated and intact antrum and pylorus in preventing postoperative duodenogastric reflux and gastritis.","authors":["Keighley MR"," Asquith P"," Edwards JA"," Alexander-Williams J."],"journal":"The British journal of surgery","year":1975,"link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":"123","citationCount":14,"stringAuthors":"Keighley MR,  Asquith P,  Edwards JA,  Alexander-Williams J."},"descriptionByType":"","descriptionByTypeRelation":"","id":860355,"link":"http://www.ncbi.nlm.nih.gov/pubmed/123","resource":"123","type":"PUBMED"}}],"filteredSize":1,"length":1,"start":0,"totalSize":1}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&start=0&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&start=0&token=MOCK_TOKEN_ID&
index c4097f530a..228f650c5a 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&start=0&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/all/publications/length=10&start=0&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"totalSize":1,"data":[{"elements":[{"modelId":15781,"id":153508,"type":"REACTION"}],"publication":{"resource":"123","link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":860355,"type":"PUBMED","article":{"title":"The importance of an innervated and intact antrum and pylorus in preventing postoperative duodenogastric reflux and gastritis.","authors":["Keighley MR"," Asquith P"," Edwards JA"," Alexander-Williams J."],"journal":"The British journal of surgery","year":1975,"link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":"123","citationCount":12,"stringAuthors":"Keighley MR,  Asquith P,  Edwards JA,  Alexander-Williams J."}}}],"start":0,"length":1}
\ No newline at end of file
+{"data":[{"elements":[{"id":153508,"modelId":15781,"type":"REACTION"}],"publication":{"annotatorClassName":"","article":{"title":"The importance of an innervated and intact antrum and pylorus in preventing postoperative duodenogastric reflux and gastritis.","authors":["Keighley MR"," Asquith P"," Edwards JA"," Alexander-Williams J."],"journal":"The British journal of surgery","year":1975,"link":"http://www.ncbi.nlm.nih.gov/pubmed/123","id":"123","citationCount":14,"stringAuthors":"Keighley MR,  Asquith P,  Edwards JA,  Alexander-Williams J."},"descriptionByType":"","descriptionByTypeRelation":"","id":860355,"link":"http://www.ncbi.nlm.nih.gov/pubmed/123","resource":"123","type":"PUBMED"}}],"filteredSize":1,"length":1,"start":0,"totalSize":1}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=ADMIN_TOKEN_ID&
index ffb8ec95f2..b8a5f9e85d 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=ADMIN_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=ADMIN_TOKEN_ID&
@@ -1 +1 @@
-[{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":15781,"tileSize":256,"width":1305,"height":473,"minZoom":2,"maxZoom":5,"layouts":[{"idObject":14081,"modelId":15781,"name":"Pathways and compartments","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":14082,"modelId":15781,"name":"Network","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":14083,"modelId":15781,"name":"Empty","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false"},{"idObject":18076,"modelId":15781,"name":"C:\\fakepath\\test.txt","description":"xxx","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18076","creator":"","inputDataAvailable":"true"},{"idObject":18077,"modelId":15781,"name":"xxx","description":"yyy","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18077","creator":"","inputDataAvailable":"true"}],"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0},"submodelType":"UNKNOWN"}]
\ No newline at end of file
+[{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":15781,"tileSize":256,"width":1305,"height":473,"defaultCenterX":100.0,"defaultCenterY":4.0,"defaultZoomLevel":5,"minZoom":2,"maxZoom":5,"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0},"submodelType":"UNKNOWN"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=MOCK_TOKEN_ID&
index ffb8ec95f2..b8a5f9e85d 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":15781,"tileSize":256,"width":1305,"height":473,"minZoom":2,"maxZoom":5,"layouts":[{"idObject":14081,"modelId":15781,"name":"Pathways and compartments","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":14082,"modelId":15781,"name":"Network","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":14083,"modelId":15781,"name":"Empty","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false"},{"idObject":18076,"modelId":15781,"name":"C:\\fakepath\\test.txt","description":"xxx","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18076","creator":"","inputDataAvailable":"true"},{"idObject":18077,"modelId":15781,"name":"xxx","description":"yyy","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18077","creator":"","inputDataAvailable":"true"}],"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0},"submodelType":"UNKNOWN"}]
\ No newline at end of file
+[{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":15781,"tileSize":256,"width":1305,"height":473,"defaultCenterX":100.0,"defaultCenterY":4.0,"defaultZoomLevel":5,"minZoom":2,"maxZoom":5,"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0},"submodelType":"UNKNOWN"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/17296.downloadSource/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/17296.downloadSource/token=MOCK_TOKEN_ID&
deleted file mode 100644
index 6489f980dd..0000000000
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/17296.downloadSource/token=MOCK_TOKEN_ID&
+++ /dev/null
@@ -1 +0,0 @@
-{"info":"dummy resposne"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/18076/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18076/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
index 3824a9b13d..3171849a1b 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/18076/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18076/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"type":"ALIAS","overlayContent":{"type":"GENERIC","geneVariations":[],"value":1.0,"modelId":15781,"idObject":"329163"}}
\ No newline at end of file
+{"overlayContent":{"modelId":15781,"idObject":"329163","value":1.0,"color":null,"description":null,"type":"GENERIC","geneVariations":[],"uniqueId":"329163"},"type":"ALIAS"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
index 2d295d704f..827cfdbf7a 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/15781/bioEntities/elements/329163/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"type":"ALIAS","overlayContent":{"description":"upstream","type":"GENETIC_VARIANT","geneVariations":[{"position":100,"originalDna":"AC","modifiedDna":"A","contig":"chr1","referenceGenomeType":"UCSC","referenceGenomeVersion":"eboVir3","references":[]}],"color":{"value":-7602176,"falpha":0.0},"modelId":15781,"idObject":"329163"}}
\ No newline at end of file
+{"overlayContent":{"modelId":15781,"idObject":"329163","value":null,"color":{"alpha":255,"rgb":-7602176},"description":"upstream","type":"GENETIC_VARIANT","geneVariations":[{"position":100,"originalDna":"AC","modifiedDna":"A","contig":"chr1","allelFrequency":null,"variantIdentifier":null,"referenceGenomeType":"UCSC","referenceGenomeVersion":"eboVir3","references":[]}],"uniqueId":"329163"},"type":"ALIAS"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/all/bioEntities/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/all/bioEntities/token=MOCK_TOKEN_ID&
index 97e6ce8412..5d022530f6 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/all/bioEntities/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18077/models/all/bioEntities/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"type":"ALIAS","overlayContent":{"color":{"value":-7602176,"falpha":0.0},"modelId":15781,"idObject":"329163"}}]
\ No newline at end of file
+[{"overlayContent":{"modelId":15781,"idObject":"329163","value":null,"color":{"alpha":255,"rgb":-7602176},"uniqueId":"329163"},"type":"ALIAS"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/18083.downloadSource/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18083.downloadSource/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..b96e577ee7
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/18083.downloadSource/token=MOCK_TOKEN_ID&
@@ -0,0 +1,3 @@
+name	value
+s1	1
+
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=admin&publicOverlay=false&token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=admin&publicOverlay=false&token=ADMIN_TOKEN_ID&
index 3929d3d472..22a16bb51d 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=admin&publicOverlay=false&token=ADMIN_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=admin&publicOverlay=false&token=ADMIN_TOKEN_ID&
@@ -1 +1 @@
-[{"idObject":26107,"modelId":15781,"name":"s1","description":"","status":"OK","publicOverlay":false,"defaultOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.26107","creator":"admin","inputDataAvailable":"true"},{"idObject":26108,"modelId":15781,"name":"s2","description":"","status":"OK","publicOverlay":false,"defaultOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.26108","creator":"admin","inputDataAvailable":"true"}]
\ No newline at end of file
+[{"creator":"admin","defaultOverlay":false,"description":"","idObject":26107,"images":[{"modelId":15781,"path":".26107"}],"inputDataAvailable":true,"name":"s1","publicOverlay":false},{"creator":"admin","defaultOverlay":false,"description":"","idObject":26108,"images":[{"modelId":15781,"path":".26108"}],"inputDataAvailable":true,"name":"s2","publicOverlay":false}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=anonymous&publicOverlay=false&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=anonymous&publicOverlay=false&token=MOCK_TOKEN_ID&
index 7fde3a9b9d..0637a088a0 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=anonymous&publicOverlay=false&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/creator=anonymous&publicOverlay=false&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"modelId":15781,"name":"test","description":"test","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/sample0.0235076236865853214852","creator":"admin ","inputDataAvailable":"true","idObject":14852},{"modelId":15781,"name":"react","description":"","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/sample0.757974388121998714853","creator":"admin ","inputDataAvailable":"true","idObject":14853}]
\ No newline at end of file
+[]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000..490c516171
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","publicOverlay":true}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..490c516171
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","publicOverlay":true}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000..f96087ce10
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","publicOverlay":true},{"creator":"admin","defaultOverlay":false,"description":"","idObject":26107,"images":[{"modelId":15781,"path":".26107"}],"inputDataAvailable":true,"name":"s1","publicOverlay":false},{"creator":"admin","defaultOverlay":false,"description":"","idObject":26108,"images":[{"modelId":15781,"path":".26108"}],"inputDataAvailable":true,"name":"s2","publicOverlay":false}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID&
index f19c8c7dd8..490c516171 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"idObject":14081,"modelId":15781,"name":"Pathways and compartments","description":"","status":"Not available","publicOverlay":true,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":14082,"modelId":15781,"name":"Network","description":"","status":"Not available","publicOverlay":true,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":14083,"modelId":15781,"name":"Empty","description":"","status":"Not available","publicOverlay":true,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false"},{"idObject":18076,"modelId":15781,"name":"C:\\fakepath\\test.txt","description":"xxx","status":"OK","publicOverlay":true,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18076","creator":"","inputDataAvailable":"true"},{"idObject":18077,"modelId":15781,"name":"xxx","description":"yyy","status":"OK","publicOverlay":true,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18077","creator":"","inputDataAvailable":"true"},{"idObject":18095,"modelId":15781,"name":"a test","description":"test2 casadsadasdqqq","status":"OK","publicOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18095","creator":"admin","inputDataAvailable":"true"},{"idObject":20660,"modelId":15781,"name":"","description":"","status":"OK","publicOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.20660","creator":"admin","inputDataAvailable":"true"}]
\ No newline at end of file
+[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","publicOverlay":true}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID&
index e486585b45..acf3b43f01 100644
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index 276e2108f4..d8ea0d7d04 100644
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ewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.BioEntity":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.species.GenericProtein":{"require-at-least-one":true,"annotation-list":["HGNC","HGNC_SYMBOL"]},"lcsb.mapviewer.model.map.reaction.type.TransportReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.species.IonChannelProtein":{"require-at-least-one":true,"annotation-list":["HGNC","HGNC_SYMBOL"]},"lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.species.Phenotype":{"require-at-least-one":true,"annotation-list":[]},"lcsb.mapviewer.model.map.species.Drug":{"require-at-least-one":true,"annotation-list":[]},"lcsb.mapviewer.model.map.species.Element":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.reaction.type.DissociationReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.compartment.SquareCompartment":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.species.Ion":{"require-at-least-one":true,"annotation-list":["CHEBI","PUBCHEM_SUBSTANCE","PUBCHEM"]},"lcsb.mapviewer.model.map.reaction.Reaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.compartment.RightSquareCompartment":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.reaction.type.TranslationReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.species.AntisenseRna":{"require-at-least-one":true,"annotation-list":[]},"lcsb.mapviewer.model.map.species.Complex":{"require-at-least-one":true,"annotation-list":[]},"lcsb.mapviewer.model.map.species.Unknown":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.reaction.type.TruncationReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.species.TruncatedProtein":{"require-at-least-one":true,"annotation-list":["HGNC","HGNC_SYMBOL"]},"lcsb.mapviewer.model.map.compartment.Compartment":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.compartment.TopSquareCompartment":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.species.Species":{"require-at-least-one":false,"annotation-list":[]},"lcsb.mapviewer.model.map.species.Rna":{"require-at-least-one":true,"annotation-list":["HGNC","HGNC_SYMBOL"]},"lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]},"lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction":{"require-at-least-one":true,"annotation-list":["PUBMED"]}},"element-valid-annotations":{"lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.Chemical":["KEGG_COMPOUND","PUBMED","CHEBI","HMDB","PUBCHEM_SUBSTANCE","PUBCHEM"],"lcsb.mapviewer.model.map.species.Degraded":["PUBMED"],"lcsb.mapviewer.model.map.compartment.PathwayCompartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.species.SimpleMolecule":["KEGG_COMPOUND","PUBMED","CHEBI","HMDB","PUBCHEM_SUBSTANCE","PUBCHEM"],"lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.ReceptorProtein":["HGNC","KEGG_GENES","REFSEQ","INTERPRO","MGD","PUBMED","CHEMBL_TARGET","UNIPROT_ISOFORM","ENTREZ","HGNC_SYMBOL","ENSEMBL","PANTHER","EC","UNIPROT"],"lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.Gene":["HGNC","KEGG_GENES","ENTREZ","REFSEQ","MGD","PUBMED","HGNC_SYMBOL","ENSEMBL","PANTHER","UNIPROT"],"lcsb.mapviewer.model.map.compartment.OvalCompartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.Protein":["HGNC","KEGG_GENES","REFSEQ","INTERPRO","MGD","PUBMED","CHEMBL_TARGET","UNIPROT_ISOFORM","ENTREZ","HGNC_SYMBOL","ENSEMBL","PANTHER","EC","UNIPROT"],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.BioEntity":["PUBMED"],"lcsb.mapviewer.model.map.species.GenericProtein":["HGNC","KEGG_GENES","REFSEQ","INTERPRO","MGD","PUBMED","CHEMBL_TARGET","UNIPROT_ISOFORM","ENTREZ","HGNC_SYMBOL","ENSEMBL","PANTHER","EC","UNIPROT"],"lcsb.mapviewer.model.map.reaction.type.TransportReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.IonChannelProtein":["HGNC","KEGG_GENES","REFSEQ","INTERPRO","MGD","PUBMED","CHEMBL_TARGET","UNIPROT_ISOFORM","ENTREZ","HGNC_SYMBOL","ENSEMBL","PANTHER","EC","UNIPROT"],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.Phenotype":["MESH_2012","PUBMED","OMIM","GO"],"lcsb.mapviewer.model.map.species.Drug":["CHEMBL_COMPOUND","DRUGBANK","PUBMED","CHEBI","HMDB"],"lcsb.mapviewer.model.map.species.Element":["PUBMED"],"lcsb.mapviewer.model.map.reaction.type.DissociationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.compartment.SquareCompartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.species.Ion":["KEGG_COMPOUND","PUBMED","CHEBI","HMDB","PUBCHEM_SUBSTANCE","PUBCHEM"],"lcsb.mapviewer.model.map.reaction.Reaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.compartment.RightSquareCompartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.reaction.type.TranslationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.AntisenseRna":["PUBMED"],"lcsb.mapviewer.model.map.species.Complex":["INTERPRO","MESH_2012","PUBMED","EC","CHEMBL_TARGET","GO"],"lcsb.mapviewer.model.map.species.Unknown":["PUBMED"],"lcsb.mapviewer.model.map.reaction.type.TruncationReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.species.TruncatedProtein":["HGNC","KEGG_GENES","REFSEQ","INTERPRO","MGD","PUBMED","CHEMBL_TARGET","UNIPROT_ISOFORM","ENTREZ","HGNC_SYMBOL","ENSEMBL","PANTHER","EC","UNIPROT"],"lcsb.mapviewer.model.map.compartment.Compartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.compartment.TopSquareCompartment":["MESH_2012","PUBMED","GO"],"lcsb.mapviewer.model.map.species.Species":["PUBMED"],"lcsb.mapviewer.model.map.species.Rna":["HGNC","KEGG_GENES","ENTREZ","REFSEQ","MGD","PUBMED","HGNC_SYMBOL","ENSEMBL","PANTHER","UNIPROT"],"lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"],"lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction":["KEGG_REACTION","PUBMED","COG","KEGG_PATHWAY","REACTOME"]},"element-annotators":{"lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction":[],"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment":["Gene 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\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index 4f9d07386c..a54150fd8b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -2,9 +2,12 @@ package lcsb.mapviewer.model.map;
 
 import java.io.Serializable;
 import java.util.Collection;
+import java.util.Comparator;
 import java.util.List;
 
+import lcsb.mapviewer.common.comparator.IntegerComparator;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
 
 /**
  * Interface that describes bio entity on the map (like Protein or Reaction).
@@ -13,6 +16,28 @@ import lcsb.mapviewer.model.map.model.Model;
  * 
  */
 public interface BioEntity extends Serializable {
+  Comparator<? super BioEntity> ID_COMPARATOR = new Comparator<BioEntity>() {
+
+    @Override
+    public int compare(BioEntity o1, BioEntity o2) {
+      Integer id1 = null;
+      Integer id2 = null;
+      if (o1 != null) {
+        id1 = o1.getId();
+        if (o1 instanceof Reaction) {
+          id1 *= -1;
+        }
+      }
+      if (o2 != null) {
+        id2 = o2.getId();
+        if (o2 instanceof Reaction) {
+          id2 *= -1;
+        }
+      }
+      return new IntegerComparator().compare(id1, id2);
+    }
+  };
+
   /**
    * Returns list of {@link MiriamData annotations} for the object.
    *
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
index acb3b4612a..0597502175 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
@@ -1,6 +1,7 @@
 package lcsb.mapviewer.model.map.layout;
 
 import java.io.Serializable;
+import java.util.Comparator;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -38,6 +39,14 @@ public class Layout implements Serializable {
    */
   private static final long serialVersionUID = 1L;
 
+  public static final Comparator<Layout> ID_COMPARATOR = new Comparator<Layout>() {
+
+    @Override
+    public int compare(Layout o1, Layout o2) {
+      return o1.getId() - o2.getId();
+    }
+  };
+
   /**
    * Default class logger.
    */
@@ -111,7 +120,7 @@ public class Layout implements Serializable {
    */
   @Cascade({ CascadeType.ALL })
   @OneToMany(fetch = FetchType.LAZY, mappedBy = "parentLayout", orphanRemoval = true)
-  private Set<Layout> layouts = new HashSet<Layout>();
+  private Set<Layout> layouts = new HashSet<>();
 
   /**
    * If the layout is connected to a submap then this object determine layout of
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 1fd990051d..c489420b26 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
@@ -2,6 +2,7 @@ package lcsb.mapviewer.model.map.model;
 
 import java.util.Calendar;
 import java.util.Collection;
+import java.util.Comparator;
 import java.util.List;
 import java.util.Set;
 
@@ -33,6 +34,14 @@ import lcsb.mapviewer.model.map.species.Species;
  */
 public interface Model {
 
+  Comparator<? super Model> ID_COMPARATOR = new Comparator<Model>() {
+
+    @Override
+    public int compare(Model o1, Model o2) {
+      return o1.getId() - o2.getId();
+    }
+  };
+
   /**
    * Adds element to the model.
    * 
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java
index 6a332da81c..db3674b9e1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java
@@ -1,5 +1,7 @@
 package lcsb.mapviewer.model.map.model;
 
+import java.util.Comparator;
+
 import javax.persistence.DiscriminatorValue;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
@@ -18,106 +20,113 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
 @DiscriminatorValue("MODEL_SUBMODEL_LINK")
 public class ModelSubmodelConnection extends SubmodelConnection {
 
-	/**
-	 * 
-	 */
-	private static final long	serialVersionUID = 1L;
-
-	/**
-	 * Super (parent) model.
-	 */
-	@ManyToOne(fetch = FetchType.LAZY)
-	private ModelData					parentModel;
-
-	/**
-	 * Default constructor.
-	 */
-	public ModelSubmodelConnection() {
-
-	}
-
-	/**
-	 * Default constructor that initialize some fields.
-	 * 
-	 * @param submodel
-	 *          {@link SubmodelConnection#submodel}
-	 * @param type
-	 *          {@link SubmodelConnection#type}
-	 */
-	public ModelSubmodelConnection(ModelData submodel, SubmodelType type) {
-		super(submodel, type);
-	}
-
-	/**
-	 * Default constructor that initialize some fields.
-	 * 
-	 * @param model
-	 *          {@link SubmodelConnection#submodel}
-	 * @param type
-	 *          {@link SubmodelConnection#type}
-	 */
-	public ModelSubmodelConnection(Model model, SubmodelType type) {
-		super(model.getModelData(), type);
-	}
-
-	/**
-	 * Constructor that creates copy of the {@link ModelSubmodelConnection}
-	 * object.
-	 * 
-	 * @param original
-	 *          original object from which copy is prepared
-	 */
-	public ModelSubmodelConnection(ModelSubmodelConnection original) {
-		super(original);
-		this.setParentModel(original.getParentModel());
-	}
-
-	/**
-	 * Default constructor that initialize some fields.
-	 * 
-	 * @param submodel
-	 *          {@link SubmodelConnection#submodel}
-	 * @param type
-	 *          {@link SubmodelConnection#type}
-	 * @param name
-	 *          {@link SubmodelConnection#name}
-	 */
-	public ModelSubmodelConnection(Model submodel, SubmodelType type, String name) {
-		super(submodel, type, name);
-	}
-
-	/**
-	 * @return the parentModel
-	 * @see #parentModel
-	 */
-	public ModelData getParentModel() {
-		return parentModel;
-	}
-
-	/**
-	 * @param parentModel
-	 *          the parentModel to set
-	 * @see #parentModel
-	 */
-	public void setParentModel(ModelData parentModel) {
-		this.parentModel = parentModel;
-	}
-
-	/**
-	 * @param model
-	 *          the parent model to set
-	 * @see #parentModel
-	 */
-	public void setParentModel(Model model) {
-		setParentModel(model.getModelData());
-	}
-
-	@Override
-	public ModelSubmodelConnection copy() {
-		if (this.getClass() == ModelSubmodelConnection.class) {
-			return new ModelSubmodelConnection(this);
-		} else {
-			throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
-		}
-	}
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  public static final Comparator<? super ModelSubmodelConnection> ID_COMPARATOR = new Comparator<ModelSubmodelConnection>() {
+
+    @Override
+    public int compare(ModelSubmodelConnection o1, ModelSubmodelConnection o2) {
+      return o1.getId() - o2.getId();
+    }
+  };
+
+  /**
+   * Super (parent) model.
+   */
+  @ManyToOne(fetch = FetchType.LAZY)
+  private ModelData parentModel;
+
+  /**
+   * Default constructor.
+   */
+  public ModelSubmodelConnection() {
+
+  }
+
+  /**
+   * Default constructor that initialize some fields.
+   * 
+   * @param submodel
+   *          {@link SubmodelConnection#submodel}
+   * @param type
+   *          {@link SubmodelConnection#type}
+   */
+  public ModelSubmodelConnection(ModelData submodel, SubmodelType type) {
+    super(submodel, type);
+  }
+
+  /**
+   * Default constructor that initialize some fields.
+   * 
+   * @param model
+   *          {@link SubmodelConnection#submodel}
+   * @param type
+   *          {@link SubmodelConnection#type}
+   */
+  public ModelSubmodelConnection(Model model, SubmodelType type) {
+    super(model.getModelData(), type);
+  }
+
+  /**
+   * Constructor that creates copy of the {@link ModelSubmodelConnection} object.
+   * 
+   * @param original
+   *          original object from which copy is prepared
+   */
+  public ModelSubmodelConnection(ModelSubmodelConnection original) {
+    super(original);
+    this.setParentModel(original.getParentModel());
+  }
+
+  /**
+   * Default constructor that initialize some fields.
+   * 
+   * @param submodel
+   *          {@link SubmodelConnection#submodel}
+   * @param type
+   *          {@link SubmodelConnection#type}
+   * @param name
+   *          {@link SubmodelConnection#name}
+   */
+  public ModelSubmodelConnection(Model submodel, SubmodelType type, String name) {
+    super(submodel, type, name);
+  }
+
+  /**
+   * @return the parentModel
+   * @see #parentModel
+   */
+  public ModelData getParentModel() {
+    return parentModel;
+  }
+
+  /**
+   * @param parentModel
+   *          the parentModel to set
+   * @see #parentModel
+   */
+  public void setParentModel(ModelData parentModel) {
+    this.parentModel = parentModel;
+  }
+
+  /**
+   * @param model
+   *          the parent model to set
+   * @see #parentModel
+   */
+  public void setParentModel(Model model) {
+    setParentModel(model.getModelData());
+  }
+
+  @Override
+  public ModelSubmodelConnection copy() {
+    if (this.getClass() == ModelSubmodelConnection.class) {
+      return new ModelSubmodelConnection(this);
+    } else {
+      throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+    }
+  }
 }
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java b/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java
index 8a11ebcfe7..7da82d48c5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java
@@ -1,6 +1,7 @@
 package lcsb.mapviewer.model.user;
 
 import java.io.Serializable;
+import java.util.Comparator;
 
 import javax.persistence.Column;
 import javax.persistence.DiscriminatorColumn;
@@ -18,8 +19,10 @@ import javax.persistence.InheritanceType;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
 /**
- * Class that defines user privilege. Privilege has an access level (typicaly 0,
+ * Class that defines user privilege. Privilege has an access level (typically 0,
  * 1 value), type of the privilege and user reference.
  * 
  * @author Piotr Gawron
@@ -32,141 +35,149 @@ import javax.persistence.Table;
 @DiscriminatorValue("BASIC_PRIVILEGE")
 public class BasicPrivilege 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 int								id;
-
-	/**
-	 * Which user this privilege concerns.
-	 */
-	@ManyToOne(fetch = FetchType.LAZY)
-	private User							user;
-
-	/**
-	 * Type of the privilege.
-	 */
-	@Enumerated(EnumType.STRING)
-	private PrivilegeType			type;
-
-	/**
-	 * Access level of the privilege. By default 0 means that user doesn't have
-	 * privilege and value greater than 0 means that user has privilege. It's
-	 * possible to implement different behaviour for different level values.
-	 */
-	private int								level;
-
-	/**
-	 * Constructor that initialize the privilege with given data.
-	 * 
-	 * @param level
-	 *          level on which the privilege is set
-	 * @param type
-	 *          type of the privilege
-	 * @param user
-	 *          user for which this privilege is set
-	 */
-	public BasicPrivilege(int level, PrivilegeType type, User user) {
-		this.level = level;
-		this.type = type;
-		this.user = user;
-	}
-
-	/**
-	 * Default constructor.
-	 */
-	public BasicPrivilege() {
-	}
-
-	/**
-	 * Checks if the privilege is with the same type as privilege given in the
-	 * parameter.
-	 * 
-	 * @param privilege
-	 *          other privilege to compare
-	 * @return <code>true</code> if privilege is of the same type as an argument,
-	 *         <code>false</code> otherwise
-	 */
-	public boolean equalsPrivilege(BasicPrivilege privilege) {
-		if (privilege == null) {
-			return false;
-		}
-		return type.equals(privilege.getType());
-	}
-
-	/**
-	 * @return the id
-	 * @see #id
-	 */
-	public int getId() {
-		return id;
-	}
-
-	/**
-	 * @param id
-	 *          the id to set
-	 * @see #id
-	 */
-	public void setId(int id) {
-		this.id = id;
-	}
-
-	/**
-	 * @return the user
-	 * @see #user
-	 */
-	public User getUser() {
-		return user;
-	}
-
-	/**
-	 * @param user
-	 *          the user to set
-	 * @see #user
-	 */
-	public void setUser(User user) {
-		this.user = user;
-	}
-
-	/**
-	 * @return the type
-	 * @see #type
-	 */
-	public PrivilegeType getType() {
-		return type;
-	}
-
-	/**
-	 * @param type
-	 *          the type to set
-	 * @see #type
-	 */
-	public void setType(PrivilegeType type) {
-		this.type = type;
-	}
-
-	/**
-	 * @return the level
-	 * @see #level
-	 */
-	public int getLevel() {
-		return level;
-	}
-
-	/**
-	 * @param level
-	 *          the level to set
-	 * @see #level
-	 */
-	public void setLevel(int level) {
-		this.level = level;
-	}
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  public static final Comparator<? super BasicPrivilege> ID_COMPARATOR = new Comparator<BasicPrivilege>() {
+
+    @Override
+    public int compare(BasicPrivilege o1, BasicPrivilege o2) {
+      return new IntegerComparator().compare(o1.getId(), o2.getId());
+    }
+  };
+
+  /**
+   * Unique identifier in the database.
+   */
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  @Column(name = "idDb", unique = true, nullable = false)
+  private int id;
+
+  /**
+   * Which user this privilege concerns.
+   */
+  @ManyToOne(fetch = FetchType.LAZY)
+  private User user;
+
+  /**
+   * Type of the privilege.
+   */
+  @Enumerated(EnumType.STRING)
+  private PrivilegeType type;
+
+  /**
+   * Access level of the privilege. By default 0 means that user doesn't have
+   * privilege and value greater than 0 means that user has privilege. It's
+   * possible to implement different behaviour for different level values.
+   */
+  private int level;
+
+  /**
+   * Constructor that initialize the privilege with given data.
+   * 
+   * @param level
+   *          level on which the privilege is set
+   * @param type
+   *          type of the privilege
+   * @param user
+   *          user for which this privilege is set
+   */
+  public BasicPrivilege(int level, PrivilegeType type, User user) {
+    this.level = level;
+    this.type = type;
+    this.user = user;
+  }
+
+  /**
+   * Default constructor.
+   */
+  public BasicPrivilege() {
+  }
+
+  /**
+   * Checks if the privilege is with the same type as privilege given in the
+   * parameter.
+   * 
+   * @param privilege
+   *          other privilege to compare
+   * @return <code>true</code> if privilege is of the same type as an argument,
+   *         <code>false</code> otherwise
+   */
+  public boolean equalsPrivilege(BasicPrivilege privilege) {
+    if (privilege == null) {
+      return false;
+    }
+    return type.equals(privilege.getType());
+  }
+
+  /**
+   * @return the id
+   * @see #id
+   */
+  public int getId() {
+    return id;
+  }
+
+  /**
+   * @param id
+   *          the id to set
+   * @see #id
+   */
+  public void setId(int id) {
+    this.id = id;
+  }
+
+  /**
+   * @return the user
+   * @see #user
+   */
+  public User getUser() {
+    return user;
+  }
+
+  /**
+   * @param user
+   *          the user to set
+   * @see #user
+   */
+  public void setUser(User user) {
+    this.user = user;
+  }
+
+  /**
+   * @return the type
+   * @see #type
+   */
+  public PrivilegeType getType() {
+    return type;
+  }
+
+  /**
+   * @param type
+   *          the type to set
+   * @see #type
+   */
+  public void setType(PrivilegeType type) {
+    this.type = type;
+  }
+
+  /**
+   * @return the level
+   * @see #level
+   */
+  public int getLevel() {
+    return level;
+  }
+
+  /**
+   * @param level
+   *          the level to set
+   * @see #level
+   */
+  public void setLevel(int level) {
+    this.level = level;
+  }
 }
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 f9634def04..744af47751 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.model.user;
 
 import java.awt.Color;
 import java.io.Serializable;
+import java.util.Comparator;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -17,6 +18,8 @@ import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
 import javax.persistence.Table;
 
+import lcsb.mapviewer.common.comparator.StringComparator;
+
 /**
  * Class representing user.
  * 
@@ -32,6 +35,22 @@ public class User implements Serializable {
    */
   private static final long serialVersionUID = 1L;
 
+  public static final Comparator<? super User> LOGIN_COMPARATOR = new Comparator<User>() {
+
+    @Override
+    public int compare(User o1, User o2) {
+      String login1 = null;
+      String login2 = null;
+      if (o1 != null) {
+        login1 = o1.getLogin();
+      }
+      if (o2 != null) {
+        login2 = o2.getLogin();
+      }
+      return new StringComparator().compare(login1, login2);
+    }
+  };
+
   /**
    * Unique identifier in the database.
    */
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 5b6b011b97..aff8c626bc 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -2,8 +2,8 @@ package lcsb.mapviewer.modelutils.map;
 
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.HashSet;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -24,238 +24,237 @@ import lcsb.mapviewer.model.map.species.Element;
  */
 public final class ElementUtils {
 
-	/**
-	 * This object contains inheritance tree for {@link BioEntity}
-	 * interface.
-	 */
-	private static ClassTreeNode													annotatedObjectTree	= null;
+  /**
+   * This object contains inheritance tree for {@link BioEntity} interface.
+   */
+  private static ClassTreeNode annotatedObjectTree = null;
 
-	/**
-	 * Map between class names (used as user input) and implementation of
-	 * {@link Element} class.
-	 */
-	private static Map<String, Class<? extends Element>>	elementClasses			= null;
+  /**
+   * Map between class names (used as user input) and implementation of
+   * {@link Element} class.
+   */
+  private static Map<String, Class<? extends Element>> elementClasses = null;
 
-	/**
-	 * Map between class names (used as user input) and implementation of
-	 * {@link Reaction} class.
-	 */
-	private static Map<String, Class<? extends Reaction>>	reactionClasses			= null;
+  /**
+   * Map between class names (used as user input) and implementation of
+   * {@link Reaction} class.
+   */
+  private static Map<String, Class<? extends Reaction>> reactionClasses = null;
 
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private final Logger																	logger							= Logger.getLogger(ElementUtils.class);
+  /**
+   * Default class logger.
+   */
+  @SuppressWarnings("unused")
+  private final Logger logger = Logger.getLogger(ElementUtils.class);
 
-	/**
-	 * This method return tag that identifies {@link BioEntity}. This tag
-	 * should be used in warning messages.
-	 * 
-	 * @param element
-	 *          tag for this element is created
-	 * @return tag that identifies element
-	 */
-	public String getElementTag(BioEntity element) {
-		return getElementTag(element, null);
-	}
+  /**
+   * This method return tag that identifies {@link BioEntity}. This tag should be
+   * used in warning messages.
+   * 
+   * @param element
+   *          tag for this element is created
+   * @return tag that identifies element
+   */
+  public String getElementTag(BioEntity element) {
+    return getElementTag(element, null);
+  }
 
-	/**
-	 * This method return tag that identifies {@link BioEntity}. This tag
-	 * should be used in warning messages.
-	 * 
-	 * @param element
-	 *          tag for this element is created
-	 * @param annotator
-	 *          this object identifies class that will produce warning. it can be
-	 *          null (in such situation it will be skipped in the tag)
-	 * @return tag that identifies element
-	 */
-	public String getElementTag(BioEntity element, Object annotator) {
-		String id = null;
-		if (element instanceof Element) {
-			id = ((Element) element).getElementId();
-		} else if (element instanceof Reaction) {
-			id = ((Reaction) element).getIdReaction();
-		} else {
-			throw new NotImplementedException("Unknown class: " + element.getClass());
-		}
-		if (annotator != null) {
-			return "[" + annotator.getClass().getSimpleName() + "]\t[" + element.getClass().getSimpleName() + " " + id + "]\t";
-		} else {
-			return "[" + element.getClass().getSimpleName() + " " + id + "]\t";
-		}
-	}
+  /**
+   * This method return tag that identifies {@link BioEntity}. This tag should be
+   * used in warning messages.
+   * 
+   * @param element
+   *          tag for this element is created
+   * @param annotator
+   *          this object identifies class that will produce warning. it can be
+   *          null (in such situation it will be skipped in the tag)
+   * @return tag that identifies element
+   */
+  public String getElementTag(BioEntity element, Object annotator) {
+    String id = null;
+    if (element instanceof Element) {
+      id = ((Element) element).getElementId();
+    } else if (element instanceof Reaction) {
+      id = ((Reaction) element).getIdReaction();
+    } else {
+      throw new NotImplementedException("Unknown class: " + element.getClass());
+    }
+    if (annotator != null) {
+      return "[" + annotator.getClass().getSimpleName() + "]\t[" + element.getClass().getSimpleName() + " " + id
+          + "]\t";
+    } else {
+      return "[" + element.getClass().getSimpleName() + " " + id + "]\t";
+    }
+  }
 
-	/**
-	 * Returns {@link #annotatedObjectTree}.
-	 * 
-	 * @return {@link #annotatedObjectTree}
-	 */
-	public ClassTreeNode getAnnotatedElementClassTree() {
-		if (annotatedObjectTree == null) {
-			Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
-			Set<Class<? extends BioEntity>> classes = reflections.getSubTypesOf(BioEntity.class);
+  /**
+   * Returns {@link #annotatedObjectTree}.
+   * 
+   * @return {@link #annotatedObjectTree}
+   */
+  public ClassTreeNode getAnnotatedElementClassTree() {
+    if (annotatedObjectTree == null) {
+      Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
+      Set<Class<? extends BioEntity>> classes = reflections.getSubTypesOf(BioEntity.class);
 
-			annotatedObjectTree = new ClassTreeNode(BioEntity.class);
-			annotatedObjectTree.setData(false);
+      annotatedObjectTree = new ClassTreeNode(BioEntity.class);
+      annotatedObjectTree.setData(false);
 
-			Map<Class<?>, ClassTreeNode> map = new HashMap<Class<?>, ClassTreeNode>();
-			map.put(Object.class, annotatedObjectTree);
-			for (Class<? extends BioEntity> class1 : classes) {
-				if (map.get(class1) == null) {
-					ClassTreeNode node = new ClassTreeNode(class1);
-					// set information if the class annotation should be required
-					for (RequireAnnotationMap val : RequireAnnotationMap.values()) {
-						if (val.getClazz().equals(class1)) {
-							node.setData(true);
-						}
-					}
-					map.put(class1, node);
-				}
-			}
-			for (Class<? extends BioEntity> class1 : classes) {
-				ClassTreeNode parent = map.get(class1.getSuperclass());
-				ClassTreeNode child = map.get(class1);
-				parent.getChildren().add(child);
-				child.setParent(parent);
-			}
+      Map<Class<?>, ClassTreeNode> map = new LinkedHashMap<Class<?>, ClassTreeNode>();
+      map.put(Object.class, annotatedObjectTree);
+      for (Class<? extends BioEntity> class1 : classes) {
+        if (map.get(class1) == null) {
+          ClassTreeNode node = new ClassTreeNode(class1);
+          // set information if the class annotation should be required
+          for (RequireAnnotationMap val : RequireAnnotationMap.values()) {
+            if (val.getClazz().equals(class1)) {
+              node.setData(true);
+            }
+          }
+          map.put(class1, node);
+        }
+      }
+      for (Class<? extends BioEntity> class1 : classes) {
+        ClassTreeNode parent = map.get(class1.getSuperclass());
+        ClassTreeNode child = map.get(class1);
+        parent.getChildren().add(child);
+        child.setParent(parent);
+      }
 
-			// set information if the class annotation should be required for children
-			// classes (if not explicitly set in child then inherit it from parent)
-			for (Class<? extends BioEntity> class1 : classes) {
-				ClassTreeNode child = map.get(class1);
-				Boolean value = (Boolean) child.getData();
-				if (value == null) {
-					ClassTreeNode parent = map.get(class1.getSuperclass());
-					while (parent.getData() == null) {
-						parent = parent.getParent();
-					}
-					child.setData(parent.getData());
-				}
-			}
-			for (ClassTreeNode node : map.values()) {
-				Collections.sort(node.getChildren(), new ClassTreeNodeNameComparator());
-			}
+      // set information if the class annotation should be required for children
+      // classes (if not explicitly set in child then inherit it from parent)
+      for (Class<? extends BioEntity> class1 : classes) {
+        ClassTreeNode child = map.get(class1);
+        Boolean value = (Boolean) child.getData();
+        if (value == null) {
+          ClassTreeNode parent = map.get(class1.getSuperclass());
+          while (parent.getData() == null) {
+            parent = parent.getParent();
+          }
+          child.setData(parent.getData());
+        }
+      }
+      for (ClassTreeNode node : map.values()) {
+        Collections.sort(node.getChildren(), new ClassTreeNodeNameComparator());
+      }
 
-		}
-		return annotatedObjectTree;
-	}
+    }
+    return annotatedObjectTree;
+  }
 
-	/**
-	 * Returns list of classes that extends {@link Element} class, but don't have
-	 * children (leaves in the hierarchy tree).
-	 * 
-	 * @return list of classes that extends {@link Element} class, but don't have
-	 *         children (leaves in the hierarchy tree)
-	 */
-	public List<Class<? extends Element>> getAvailableElementSubclasses() {
-		List<Class<? extends Element>> result = new ArrayList<Class<? extends Element>>();
-		if (elementClasses == null) {
-			refreshClasses();
-		}
-		result.addAll(elementClasses.values());
-		Collections.sort(result, new ClassNameComparator());
-		return result;
-	}
+  /**
+   * Returns list of classes that extends {@link Element} class, but don't have
+   * children (leaves in the hierarchy tree).
+   * 
+   * @return list of classes that extends {@link Element} class, but don't have
+   *         children (leaves in the hierarchy tree)
+   */
+  public List<Class<? extends Element>> getAvailableElementSubclasses() {
+    List<Class<? extends Element>> result = new ArrayList<Class<? extends Element>>();
+    if (elementClasses == null) {
+      refreshClasses();
+    }
+    result.addAll(elementClasses.values());
+    Collections.sort(result, new ClassNameComparator());
+    return result;
+  }
 
-	/**
-	 * Refresh list of known implementation of {@link Element} class.
-	 */
-	protected void refreshClasses() {
-		List<Class<? extends Element>> tmp = new ArrayList<>();
+  /**
+   * Refresh list of known implementation of {@link Element} class.
+   */
+  protected void refreshClasses() {
+    List<Class<? extends Element>> tmp = new ArrayList<>();
 
-		Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
-		elementClasses = new HashMap<String, Class<? extends Element>>();
-		Set<Class<? extends Element>> classes = reflections.getSubTypesOf(Element.class);
+    Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
+    elementClasses = new LinkedHashMap<String, Class<? extends Element>>();
+    Set<Class<? extends Element>> classes = reflections.getSubTypesOf(Element.class);
 
-		Set<Class<?>> toRemove = new HashSet<Class<?>>();
+    Set<Class<?>> toRemove = new HashSet<Class<?>>();
 
-		for (Class<? extends Element> class1 : classes) {
-			toRemove.add(class1.getSuperclass());
-			tmp.add(class1);
-		}
-		for (Class<?> clazz : toRemove) {
-			tmp.remove(clazz);
-		}
-		for (Class<? extends Element> class1 : tmp) {
-			elementClasses.put(class1.getSimpleName(), class1);
-		}
+    for (Class<? extends Element> class1 : classes) {
+      toRemove.add(class1.getSuperclass());
+      tmp.add(class1);
+    }
+    for (Class<?> clazz : toRemove) {
+      tmp.remove(clazz);
+    }
+    for (Class<? extends Element> class1 : tmp) {
+      elementClasses.put(class1.getSimpleName(), class1);
+    }
 
-		List<Class<? extends Reaction>> rTmp = new ArrayList<Class<? extends Reaction>>();
+    List<Class<? extends Reaction>> rTmp = new ArrayList<Class<? extends Reaction>>();
 
-		reflections = new Reflections("lcsb.mapviewer.model.map.reaction.type");
-		reactionClasses = new HashMap<String, Class<? extends Reaction>>();
+    reflections = new Reflections("lcsb.mapviewer.model.map.reaction.type");
+    reactionClasses = new LinkedHashMap<String, Class<? extends Reaction>>();
 
-		Set<Class<? extends Reaction>> rClasses = reflections.getSubTypesOf(Reaction.class);
+    Set<Class<? extends Reaction>> rClasses = reflections.getSubTypesOf(Reaction.class);
 
-		toRemove = new HashSet<Class<?>>();
+    toRemove = new HashSet<Class<?>>();
 
-		for (Class<? extends Reaction> class1 : rClasses) {
-			if (!(class1.isAnonymousClass() || class1.isMemberClass())) {
-				toRemove.add(class1.getSuperclass());
-				rTmp.add(class1);
-			}
-		}
-		for (Class<?> clazz : toRemove) {
-			rTmp.remove(clazz);
-		}
-		for (Class<? extends Reaction> class1 : rTmp) {
-			reactionClasses.put(class1.getSimpleName().replaceAll("Reaction", ""), class1);
-		}
+    for (Class<? extends Reaction> class1 : rClasses) {
+      if (!(class1.isAnonymousClass() || class1.isMemberClass())) {
+        toRemove.add(class1.getSuperclass());
+        rTmp.add(class1);
+      }
+    }
+    for (Class<?> clazz : toRemove) {
+      rTmp.remove(clazz);
+    }
+    for (Class<? extends Reaction> class1 : rTmp) {
+      reactionClasses.put(class1.getSimpleName().replaceAll("Reaction", ""), class1);
+    }
 
-	}
+  }
 
-	/**
-	 * Returns a {@link Class} that extends {@link BioEntity} for a given
-	 * name.
-	 * 
-	 * @param name
-	 *          name of the class
-	 * @return {@link Class} that extends {@link BioEntity} for a given name
-	 */
-	public Class<?> getClassByName(String name) {
-		if (elementClasses == null) {
-			refreshClasses();
-		}
-		Class<?> result = elementClasses.get(name);
-		if (result == null) {
-			result = reactionClasses.get(name);
-		}
-		return result;
-	}
+  /**
+   * Returns a {@link Class} that extends {@link BioEntity} for a given name.
+   * 
+   * @param name
+   *          name of the class
+   * @return {@link Class} that extends {@link BioEntity} for a given name
+   */
+  public Class<?> getClassByName(String name) {
+    if (elementClasses == null) {
+      refreshClasses();
+    }
+    Class<?> result = elementClasses.get(name);
+    if (result == null) {
+      result = reactionClasses.get(name);
+    }
+    return result;
+  }
 
-	/**
-	 * Return list of {@link Reaction} classes that are available in the system.
-	 * 
-	 * @return list of {@link Reaction} classes that are available in the system
-	 */
-	public List<Class<? extends Reaction>> getAvailableReactionSubclasses() {
-		List<Class<? extends Reaction>> result = new ArrayList<Class<? extends Reaction>>();
-		if (reactionClasses == null) {
-			refreshClasses();
-		}
-		result.addAll(reactionClasses.values());
-		Collections.sort(result, new ClassNameComparator());
-		return result;
-	}
+  /**
+   * Return list of {@link Reaction} classes that are available in the system.
+   * 
+   * @return list of {@link Reaction} classes that are available in the system
+   */
+  public List<Class<? extends Reaction>> getAvailableReactionSubclasses() {
+    List<Class<? extends Reaction>> result = new ArrayList<Class<? extends Reaction>>();
+    if (reactionClasses == null) {
+      refreshClasses();
+    }
+    result.addAll(reactionClasses.values());
+    Collections.sort(result, new ClassNameComparator());
+    return result;
+  }
 
-	/**
-	 * @param elementClasses
-	 *          the elementClasses to set
-	 * @see #elementClasses
-	 */
-	protected static void setElementClasses(Map<String, Class<? extends Element>> elementClasses) {
-		ElementUtils.elementClasses = elementClasses;
-	}
+  /**
+   * @param elementClasses
+   *          the elementClasses to set
+   * @see #elementClasses
+   */
+  protected static void setElementClasses(Map<String, Class<? extends Element>> elementClasses) {
+    ElementUtils.elementClasses = elementClasses;
+  }
 
-	/**
-	 * @param reactionClasses
-	 *          the reactionClasses to set
-	 * @see #reactionClasses
-	 */
-	protected static void setReactionClasses(Map<String, Class<? extends Reaction>> reactionClasses) {
-		ElementUtils.reactionClasses = reactionClasses;
-	}
+  /**
+   * @param reactionClasses
+   *          the reactionClasses to set
+   * @see #reactionClasses
+   */
+  protected static void setReactionClasses(Map<String, Class<? extends Reaction>> reactionClasses) {
+    ElementUtils.reactionClasses = reactionClasses;
+  }
 
 }
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
index 90a1431e51..8ebc1d5730 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
@@ -3,7 +3,7 @@ package lcsb.mapviewer.api;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.Map;
 
 import org.apache.log4j.Logger;
@@ -57,7 +57,7 @@ public abstract class BaseController {
 
   public Map<String, Object> parseBody(String body) throws IOException, JsonParseException, JsonMappingException {
     if (body == null || body.isEmpty()) {
-      return new HashMap<>();
+      return new TreeMap<>();
     }
     ObjectNode result = mapper.readValue(body, ObjectNode.class);
     return mapper.convertValue(result, Map.class);
@@ -68,7 +68,7 @@ public abstract class BaseController {
   }
 
   protected Map<String, String> parsePostBody(String body) {
-    Map<String, String> result = new HashMap<>();
+    Map<String, String> result = new TreeMap<>();
     String[] parameters = body.split("&");
     for (String string : parameters) {
       int position = string.indexOf("=");
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 54e58c6f1d..f7120613d4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -7,9 +7,9 @@ import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
 
 import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerConfigurationException;
@@ -31,6 +31,7 @@ import lcsb.mapviewer.annotation.services.MiriamConnector;
 import lcsb.mapviewer.annotation.services.PubmedParser;
 import lcsb.mapviewer.annotation.services.PubmedSearchException;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -81,12 +82,12 @@ public abstract class BaseRestImpl {
   private Transformer mathMlTransformer;
 
   protected Map<String, Object> okStatus() {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     return result;
   }
 
-  protected Map<String, Object> createMinifiedSearchResult(Object object) {
-    Map<String, Object> result = new HashMap<>();
+  protected Map<String, Object> createMinifiedSearchResult(BioEntity object) {
+    Map<String, Object> result = new TreeMap<>();
     if (object instanceof Element) {
       result.put("type", ElementIdentifierType.ALIAS);
       Element element = (Element) object;
@@ -106,7 +107,7 @@ public abstract class BaseRestImpl {
 
   protected Map<String, Object> createAnnotation(MiriamData annotation) {
     if (annotation != null && annotation.getDataType() != null) {
-      Map<String, Object> result = new HashMap<>();
+      Map<String, Object> result = new TreeMap<>();
       if (annotation.getDataType().getUris().size() > 0) {
         try {
           result.put("link", miriamConnector.getUrlString(annotation));
@@ -154,7 +155,7 @@ public abstract class BaseRestImpl {
   };
 
   protected Map<String, Object> createAnnotation(AnnotationView annotation) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     if (annotation != null && annotation.getType() != null) {
       MiriamType type = MiriamType.getTypeByCommonName(annotation.getType());
       result.put("link", annotation.getLink());
@@ -174,7 +175,7 @@ public abstract class BaseRestImpl {
   }
 
   protected Map<String, Object> createAnnotation(Article article) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     if (article != null) {
       MiriamType type = MiriamType.PUBMED;
       result.put("link", miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, article.getId())));
@@ -201,8 +202,12 @@ public abstract class BaseRestImpl {
     return result;
   }
 
-  protected List<Model> getModels(String projectId, String modelId, String token) throws SecurityException {
+  protected List<Model> getModels(String projectId, String modelId, String token)
+      throws SecurityException, ObjectNotFoundException {
     Model model = modelService.getLastModelByProjectId(projectId, token);
+    if (model == null) {
+      throw new ObjectNotFoundException("Project with given id doesn't exist");
+    }
     List<Model> models = new ArrayList<>();
 
     if (!modelId.equals("*")) {
@@ -213,6 +218,7 @@ public abstract class BaseRestImpl {
       models.addAll(model.getSubmodels());
       models.add(model);
     }
+    models.sort(Model.ID_COMPARATOR);
     return models;
   }
 
@@ -269,6 +275,11 @@ public abstract class BaseRestImpl {
         if (targetedObjects2 != null) {
           size2 = targetedObjects2.size();
         }
+        if (size1 == size2) {
+          String name1 = (String) o1.get("name");
+          String name2 = (String) o2.get("name");
+          return new StringComparator().compare(name1, name2);
+        }
         return -size1.compareTo(size2);
       }
     });
@@ -276,22 +287,24 @@ public abstract class BaseRestImpl {
   }
 
   protected Map<String, Object> prepareTarget(Target target, List<Model> models) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("name", target.getName());
     result.put("references", createAnnotations(target.getReferences()));
     result.put("targetParticipants", createAnnotations(target.getGenes()));
 
     List<Map<String, Object>> targetedObjects = new ArrayList<>();
+    List<BioEntity> bioEntities = new ArrayList<>();
     for (Model model : models) {
-      for (BioEntity object : model.getBioEntities()) {
-        if (elementMatcher.elementMatch(target, object)) {
-          Map<String, Object> elementMapping = new HashMap<>();
-
-          elementMapping.put("id", object.getId());
-          elementMapping.put("type", getType(object));
-          elementMapping.put("modelId", model.getId());
-          targetedObjects.add(elementMapping);
-        }
+      bioEntities.addAll(model.getBioEntities());
+    }
+    bioEntities.sort(BioEntity.ID_COMPARATOR);
+    for (BioEntity bioEntity : bioEntities) {
+      if (elementMatcher.elementMatch(target, bioEntity)) {
+        Map<String, Object> elementMapping = new TreeMap<>();
+        elementMapping.put("id", bioEntity.getId());
+        elementMapping.put("type", getType(bioEntity));
+        elementMapping.put("modelId", bioEntity.getModel().getId());
+        targetedObjects.add(elementMapping);
       }
     }
 
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
index 274113cab0..9a4b359533 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
@@ -1,9 +1,9 @@
 package lcsb.mapviewer.api.configuration;
 
 import java.io.IOException;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
 
 import javax.servlet.ServletContext;
 
@@ -43,7 +43,7 @@ public class ConfigurationController extends BaseController {
       MediaType.APPLICATION_JSON_VALUE })
   public Map<String, Object> getConfiguration(@CookieValue(value = Configuration.AUTH_TOKEN) String token)
       throws SecurityException {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("options", configurationController.getAllValues(token));
     result.put("imageFormats", configurationController.getImageFormats(token));
     result.put("modelFormats", configurationController.getModelFormats(token));
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index fcdc73a49a..5329f03f22 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -2,13 +2,14 @@ package lcsb.mapviewer.api.configuration;
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.Arrays;
 import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.Queue;
 import java.util.Set;
+import java.util.TreeMap;
 
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -102,7 +103,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
         .getAvailableImageGenerators();
 
     for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGeneratorList) {
-      Map<String, Object> row = new HashMap<>();
+      Map<String, Object> row = new TreeMap<>();
       row.put("name", element.getLeft());
       row.put("handler", element.getRight().getCanonicalName());
       row.put("extension", imageGenerators.getExtension(element.getRight()));
@@ -118,7 +119,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
     List<Map<String, Object>> result = new ArrayList<>();
 
     for (IConverter converter : converters) {
-      Map<String, Object> row = new HashMap<>();
+      Map<String, Object> row = new TreeMap<>();
       row.put("name", converter.getCommonName());
       row.put("handler", converter.getClass().getCanonicalName());
       row.put("extension", converter.getFileExtension());
@@ -131,7 +132,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
     verifyToken(token);
     List<Map<String, Object>> result = new ArrayList<>();
     for (ColorSchemaType type : ColorSchemaType.values()) {
-      Map<String, Object> map = new HashMap<>();
+      Map<String, Object> map = new TreeMap<>();
       map.put("name", type.name());
       result.add(map);
     }
@@ -156,7 +157,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
         queue.add(child);
       }
       if (elementClass.isAssignableFrom(clazz.getClazz())) {
-        Map<String, String> row = new HashMap<>();
+        Map<String, String> row = new TreeMap<>();
         row.put("className", clazz.getClazz().getName());
         row.put("name", clazz.getCommonName());
         if (clazz.getParent() == null) {
@@ -177,7 +178,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   }
 
   public Map<String, Object> getMiriamTypes(String id) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (MiriamType type : MiriamType.values()) {
       result.put(type.name(), createMiriamTypeResponse(type));
     }
@@ -185,7 +186,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> createMiriamTypeResponse(MiriamType type) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("commonName", type.getCommonName());
     result.put("homepage", type.getDbHomepage());
     result.put("registryIdentifier", type.getRegistryIdentifier());
@@ -195,7 +196,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   }
 
   public Object getModificationStateTypes(String token) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (ModificationState type : ModificationState.values()) {
       result.put(type.name(), createModificationStateResponse(type));
     }
@@ -203,14 +204,14 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> createModificationStateResponse(ModificationState type) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("commonName", type.getFullName());
     result.put("abbreviation", type.getAbbreviation());
     return result;
   }
 
   public Map<String, Object> getPrivilegeTypes(String id) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (PrivilegeType type : PrivilegeType.values()) {
       result.put(type.name(), createPrivilegeTypeResponse(type));
     }
@@ -218,7 +219,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> createPrivilegeTypeResponse(PrivilegeType type) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("commonName", type.getCommonName());
     if (type.getPrivilegeObjectType() != null) {
       result.put("objectType", type.getPrivilegeObjectType().getSimpleName());
@@ -242,7 +243,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareAnnotator(ElementAnnotator annotator) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("className", annotator.getClass().getName());
     result.put("name", annotator.getCommonName());
     result.put("description", annotator.getDescription());
@@ -255,7 +256,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   public List<Map<String, Object>> getMapTypes(String token) {
     List<Map<String, Object>> result = new ArrayList<>();
     for (SubmodelType type : SubmodelType.values()) {
-      Map<String, Object> row = new HashMap<>();
+      Map<String, Object> row = new TreeMap<>();
       row.put("id", type.name());
       row.put("name", type.getCommonName());
       result.add(row);
@@ -280,9 +281,11 @@ public class ConfigurationRestImpl extends BaseRestImpl {
     List<Map<String, Object>> result = new ArrayList<>();
     if (folder.exists()) {
       File[] listOfFiles = folder.listFiles();
+      Arrays.sort(listOfFiles);
+
       for (int i = 0; i < listOfFiles.length; i++) {
         if (listOfFiles[i].isFile()) {
-          Map<String, Object> row = new HashMap<>();
+          Map<String, Object> row = new TreeMap<>();
           row.put("url", "resources/js/plugins/" + listOfFiles[i].getName());
           row.put("load-on-start", false);
           result.add(row);
@@ -296,7 +299,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
   public List<Map<String, Object>> getUnitTypes(String token) {
     List<Map<String, Object>> result = new ArrayList<>();
     for (SbmlUnitType type : SbmlUnitType.values()) {
-      Map<String, Object> row = new HashMap<>();
+      Map<String, Object> row = new TreeMap<>();
       row.put("id", type.name());
       row.put("name", type.getCommonName());
       result.add(row);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
index bb2ecfeae8..d2ab017ef8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
@@ -1,6 +1,6 @@
 package lcsb.mapviewer.api.files;
 
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.Map;
 
 import org.apache.commons.lang3.ArrayUtils;
@@ -63,7 +63,7 @@ public class FileRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> serializeEntry(UploadedFileEntry fileEntry) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("id", fileEntry.getId());
     result.put("filename", fileEntry.getOriginalFileName());
     result.put("length", fileEntry.getLength());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java
index 52ecc08744..e3f8eb6da2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java
@@ -1,6 +1,6 @@
 package lcsb.mapviewer.api.mesh;
 
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.Map;
 
 import org.apache.log4j.Logger;
@@ -33,7 +33,7 @@ public class MeshRestImpl extends BaseRestImpl {
     if (mesh == null) {
       throw new ObjectNotFoundException("Object not found: " + id);
     }
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("name", mesh.getName());
     result.put("id", mesh.getMeSHId());
     result.put("description", mesh.getDescription());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
index 3a03cb2743..9f209f5307 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
@@ -32,6 +32,7 @@ public class ProjectMetaData implements Serializable {
 
   private Integer idObject;
   private String status;
+  private String directory;
   private Double progress;
   private String notifyEmail;
   private Boolean warnings;
@@ -265,4 +266,12 @@ public class ProjectMetaData implements Serializable {
   public void setErrors(Boolean errors) {
     this.errors = errors;
   }
+
+  public String getDirectory() {
+    return directory;
+  }
+
+  public void setDirectory(String directory) {
+    this.directory = directory;
+  }
 }
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 69fb7e38da..173549cf1e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -13,7 +13,7 @@ import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -146,6 +146,7 @@ public class ProjectRestImpl extends BaseRestImpl {
       }
     }
     result.setWarnings(project.getWarnings().size() > 0);
+    result.setDirectory(project.getDirectory());
     result.setErrors(project.getErrors() != null && !project.getErrors().isEmpty());
     if (set.size() > 0) {
       result.setTopOverviewImage(factory.create(set.iterator().next()));
@@ -361,19 +362,13 @@ public class ProjectRestImpl extends BaseRestImpl {
 
   public Map<String, Object> getStatistics(String projectId, String token)
       throws SecurityException, ObjectNotFoundException {
-    Map<String, Object> result = new HashMap<>();
-    Model model = getModelService().getLastModelByProjectId(projectId, token);
-    if (model == null) {
-      throw new ObjectNotFoundException("Project with given id doesn't exist");
-    }
+    Map<String, Object> result = new TreeMap<>();
 
-    Map<MiriamType, Integer> elementAnnotations = new HashMap<>();
+    Map<MiriamType, Integer> elementAnnotations = new TreeMap<>();
     for (MiriamType mt : MiriamType.values()) {
       elementAnnotations.put(mt, 0);
     }
-    Set<Model> models = new HashSet<>();
-    models.add(model);
-    models.addAll(model.getSubmodels());
+    List<Model> models = super.getModels(projectId, "*", token);
 
     for (Model model2 : models) {
       for (Element alias : model2.getElements()) {
@@ -386,7 +381,7 @@ public class ProjectRestImpl extends BaseRestImpl {
     }
     result.put("elementAnnotations", elementAnnotations);
 
-    Map<MiriamType, Integer> reactionAnnotations = new HashMap<>();
+    Map<MiriamType, Integer> reactionAnnotations = new TreeMap<>();
     for (MiriamType mt : MiriamType.values()) {
       reactionAnnotations.put(mt, 0);
     }
@@ -705,7 +700,7 @@ public class ProjectRestImpl extends BaseRestImpl {
       index++;
     }
 
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("data", resultList);
     result.put("totalSize", logEntries.size());
     result.put("filteredSize", filteredList.size());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index 2c8427aaa9..0c014d44a3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -1,7 +1,7 @@
 package lcsb.mapviewer.api.projects.chemicals;
 
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -66,24 +66,17 @@ public class ChemicalRestImpl extends BaseRestImpl {
       organism = TaxonomyBackend.HUMAN_TAXONOMY;
     }
     Chemical chemical = chemicalService.getByName(query,
-        new DbSearchCriteria().model(model).organisms(organism).colorSet(0).disease(project.getDisease()));
+        new DbSearchCriteria().project(project).organisms(organism).colorSet(0).disease(project.getDisease()));
     if (chemical != null) {
-      List<Model> models = getModels(model);
+      List<Model> models = getModels(projectId, "*", token);
       result.add(prepareChemical(chemical, columnSet, models));
     }
 
     return result;
   }
 
-  private List<Model> getModels(Model model) {
-    List<Model> models = new ArrayList<>();
-    models.add(model);
-    models.addAll(model.getSubmodels());
-    return models;
-  }
-
   protected Map<String, Object> prepareChemical(Chemical chemical, Set<String> columnsSet, List<Model> models) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
 
     String description = "Mesh term not available";
     List<String> synonyms = new ArrayList<>();
@@ -178,11 +171,13 @@ public class ChemicalRestImpl extends BaseRestImpl {
       throw new QueryException("Project doesn't have disease associated to it");
     }
 
+    List<Model> models = getModels(projectId, "*", token);
+    Element element = null;
+
     Integer dbId = Integer.valueOf(targetId);
     List<Element> targets = new ArrayList<>();
     if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
-      Element element = model.getElementByDbId(dbId);
-      for (Model m : model.getSubmodels()) {
+      for (Model m : models) {
         if (element == null) {
           element = m.getElementByDbId(dbId);
         }
@@ -202,12 +197,10 @@ public class ChemicalRestImpl extends BaseRestImpl {
     Set<String> columnSet = createChemicalColumnSet(columns);
 
     List<Chemical> chemicals = chemicalService.getForTargets(targets,
-        new DbSearchCriteria().model(model).organisms(organism).disease(project.getDisease()));
+        new DbSearchCriteria().project(project).organisms(organism).disease(project.getDisease()));
 
     List<Map<String, Object>> result = new ArrayList<>();
 
-    List<Model> models = getModels(model);
-
     for (Chemical chemical : chemicals) {
       result.add(prepareChemical(chemical, columnSet, models));
     }
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
index 4b777b9bc7..8f7673f1b5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.api.projects.comments;
 
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -107,7 +107,7 @@ public class CommentRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> preparedComment(Comment comment, Set<String> columnsSet, boolean admin) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (String string : columnsSet) {
       String column = string.toLowerCase();
       Object value = null;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index af6ef3756f..873f061078 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -1,7 +1,7 @@
 package lcsb.mapviewer.api.projects.drugs;
 
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -61,22 +61,15 @@ public class DrugRestImpl extends BaseRestImpl {
     if (organism == null) {
       organism = TaxonomyBackend.HUMAN_TAXONOMY;
     }
-    Drug drug = drugService.getByName(query, new DbSearchCriteria().model(model).organisms(organism).colorSet(0));
+    Drug drug = drugService.getByName(query, new DbSearchCriteria().project(project).organisms(organism).colorSet(0));
     if (drug != null) {
-      List<Model> models = getModels(model);
+      List<Model> models = getModels(projectId, "*", token);
       result.add(prepareDrug(drug, columnSet, models));
     }
 
     return result;
   }
 
-  private List<Model> getModels(Model model) {
-    List<Model> models = new ArrayList<>();
-    models.add(model);
-    models.addAll(model.getSubmodels());
-    return models;
-  }
-
   /**
    * @return the userService
    * @see #userService
@@ -112,7 +105,7 @@ public class DrugRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareDrug(Drug drug, Set<String> columnsSet, List<Model> models) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (String string : columnsSet) {
       String column = string.toLowerCase();
       Object value = null;
@@ -184,22 +177,10 @@ public class DrugRestImpl extends BaseRestImpl {
     }
     Project project = model.getProject();
 
+    List<Model> models = getModels(projectId, "*", token);
+
     Integer dbId = Integer.valueOf(targetId);
-    List<Element> targets = new ArrayList<>();
-    if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
-      Element element = model.getElementByDbId(dbId);
-      for (Model m : model.getSubmodels()) {
-        if (element == null) {
-          element = m.getElementByDbId(dbId);
-        }
-      }
-      if (element == null) {
-        throw new QueryException("Invalid element identifier for given project");
-      }
-      targets.add(element);
-    } else {
-      throw new QueryException("Targeting for the type not implemented");
-    }
+    List<Element> targets = getTargets(targetType, models, dbId);
     MiriamData organism = project.getOrganism();
     if (organism == null) {
       organism = TaxonomyBackend.HUMAN_TAXONOMY;
@@ -207,12 +188,10 @@ public class DrugRestImpl extends BaseRestImpl {
 
     Set<String> columnSet = createDrugColumnSet(columns);
 
-    List<Drug> drugs = drugService.getForTargets(targets, new DbSearchCriteria().model(model).organisms(organism));
+    List<Drug> drugs = drugService.getForTargets(targets, new DbSearchCriteria().project(project).organisms(organism));
 
     List<Map<String, Object>> result = new ArrayList<>();
 
-    List<Model> models = getModels(model);
-
     for (Drug drug : drugs) {
       result.add(prepareDrug(drug, columnSet, models));
     }
@@ -220,6 +199,25 @@ public class DrugRestImpl extends BaseRestImpl {
     return result;
   }
 
+  private List<Element> getTargets(String targetType, List<Model> models, Integer dbId) throws QueryException {
+    List<Element> targets = new ArrayList<>();
+    if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
+      Element element = null;
+      for (Model m : models) {
+        if (element == null) {
+          element = m.getElementByDbId(dbId);
+        }
+      }
+      if (element == null) {
+        throw new QueryException("Invalid element identifier for given project");
+      }
+      targets.add(element);
+    } else {
+      throw new QueryException("Targeting for the type not implemented");
+    }
+    return targets;
+  }
+
   public List<String> getSuggestedQueryList(String projectId, String token)
       throws SecurityException, DrugSearchException {
     Project project = getProjectService().getProjectByProjectId(projectId, token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
index a292ef60b5..eafa62324c 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
@@ -1,11 +1,11 @@
 package lcsb.mapviewer.api.projects.mirnas;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -57,24 +57,18 @@ public class MiRnaRestImpl extends BaseRestImpl {
     if (organism == null) {
       organism = TaxonomyBackend.HUMAN_TAXONOMY;
     }
-    MiRNA miRna = miRnaService.getByName(query, new DbSearchCriteria().model(model).organisms(organism).colorSet(0));
+    MiRNA miRna = miRnaService.getByName(query,
+        new DbSearchCriteria().project(project).organisms(organism).colorSet(0));
     if (miRna != null) {
-      List<Model> models = getModels(model);
+      List<Model> models = getModels(projectId, "*", token);
       result.add(prepareMiRna(miRna, columnSet, models));
     }
 
     return result;
   }
 
-  private List<Model> getModels(Model model) {
-    List<Model> models = new ArrayList<>();
-    models.add(model);
-    models.addAll(model.getSubmodels());
-    return models;
-  }
-
   private Map<String, Object> prepareMiRna(MiRNA miRna, Set<String> columnsSet, List<Model> models) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (String string : columnsSet) {
       String column = string.toLowerCase();
       Object value = null;
@@ -131,11 +125,13 @@ public class MiRnaRestImpl extends BaseRestImpl {
     }
     Project project = model.getProject();
 
+    List<Model> models = getModels(projectId, "*", token);
+
     Integer dbId = Integer.valueOf(targetId);
     List<Element> targets = new ArrayList<>();
     if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
-      Element element = model.getElementByDbId(dbId);
-      for (Model m : model.getSubmodels()) {
+      Element element = null;
+      for (Model m : models) {
         if (element == null) {
           element = m.getElementByDbId(dbId);
         }
@@ -154,12 +150,11 @@ public class MiRnaRestImpl extends BaseRestImpl {
 
     Set<String> columnSet = createMiRnaColumnSet(columns);
 
-    List<MiRNA> miRnas = miRnaService.getForTargets(targets, new DbSearchCriteria().model(model).organisms(organism));
+    List<MiRNA> miRnas = miRnaService.getForTargets(targets,
+        new DbSearchCriteria().project(project).organisms(organism));
 
     List<Map<String, Object>> result = new ArrayList<>();
 
-    List<Model> models = getModels(model);
-
     for (MiRNA miRna : miRnas) {
       result.add(prepareMiRna(miRna, columnSet, models));
     }
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 e7effa77c3..c8f7f601e0 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
@@ -8,14 +8,11 @@ import java.util.List;
 import org.primefaces.model.map.LatLng;
 
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.layout.Layout;
 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;
-import lcsb.mapviewer.services.view.LayoutView;
-import lcsb.mapviewer.services.view.LayoutViewFactory;
 
 public class ModelMetaData implements Serializable {
 
@@ -49,7 +46,7 @@ public class ModelMetaData implements Serializable {
   private Double defaultCenterX;
 
   private Double defaultCenterY;
-  
+
   private Integer defaultZoomLevel;
 
   /**
@@ -62,8 +59,6 @@ public class ModelMetaData implements Serializable {
    */
   private Integer maxZoom;
 
-  private List<LayoutView> layouts = new ArrayList<>();
-
   /**
    * List of submodels in the model.
    */
@@ -115,19 +110,15 @@ public class ModelMetaData implements Serializable {
     this.setDefaultZoomLevel(model.getDefaultZoomLevel());
 
     List<ModelMetaData> submodels = new ArrayList<>();
-    for (ModelSubmodelConnection connection : model.getSubmodels()) {
+    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);
     }
-    LayoutViewFactory factory = new LayoutViewFactory();
-    for (Layout layout : model.getLayouts()) {
-      if (layout.isPublicLayout()) {
-        layouts.add(factory.create(layout));
-      }
-    }
     this.setSubmodels(submodels);
-
   }
 
   protected ModelMetaData() {
@@ -320,23 +311,6 @@ public class ModelMetaData implements Serializable {
     this.submodels = submodels;
   }
 
-  /**
-   * @return the layouts
-   * @see #layouts
-   */
-  public List<LayoutView> getLayouts() {
-    return layouts;
-  }
-
-  /**
-   * @param layouts
-   *          the layouts to set
-   * @see #layouts
-   */
-  public void setLayouts(List<LayoutView> layouts) {
-    this.layouts = layouts;
-  }
-
   /**
    * @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 b39b48d148..b59b1e7903 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
@@ -6,7 +6,6 @@ import java.util.Map;
 import java.util.Set;
 
 import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.BaseRestImpl;
@@ -18,14 +17,10 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelData;
 import lcsb.mapviewer.model.user.PrivilegeType;
 import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
 
 @Transactional(value = "txManager")
 public class ModelRestImpl extends BaseRestImpl {
 
-  @Autowired
-  private ILayoutService layoutService;
-
   /**
    * Default class logger.
    */
@@ -53,9 +48,6 @@ public class ModelRestImpl extends BaseRestImpl {
       List<ModelMetaData> metaDataToProcess = new ArrayList<>();
       metaDataToProcess.add(result);
       metaDataToProcess.addAll(result.getSubmodels());
-      for (ModelMetaData submodelData : metaDataToProcess) {
-        submodelData.setLayouts(layoutService.getGeneralLayouts(model.getSubmodelById(submodelData.getIdObject())));
-      }
       return result;
     }
   }
@@ -68,6 +60,7 @@ public class ModelRestImpl extends BaseRestImpl {
       List<Model> models = new ArrayList<>();
       models.add(model);
       models.addAll(model.getSubmodels());
+      models.sort(Model.ID_COMPARATOR);
       for (Model model2 : models) {
         result.add(getModel(project.getProjectId(), model2.getId() + "", token));
       }
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
index 9e79f1a7f4..8555e11437 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
@@ -27,66 +27,26 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
   @SuppressWarnings("unused")
   private Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
 
-  @Autowired
-  private IUserService userService;
-
-  @Autowired
-  private IModelService modelService;
-
   @Autowired
   private ISearchService searchService;
 
-  /**
-   * @return the userService
-   * @see #userService
-   */
-  public IUserService getUserService() {
-    return userService;
-  }
-
-  /**
-   * @param userService
-   *          the userService to set
-   * @see #userService
-   */
-  public void setUserService(IUserService userService) {
-    this.userService = userService;
-  }
-
   public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token,
       Point2D coordinates, Integer count, String perfectMatch) throws UserAccessException, SecurityException {
     List<Map<String, Object>> resultMap = new ArrayList<>();
 
-    Model model = modelService.getLastModelByProjectId(projectId, token);
+    Model model = getModelService().getLastModelByProjectId(projectId, token);
 
     Model submodel = model.getSubmodelById(modelId);
 
     List<BioEntity> elements = searchService.getClosestElements(submodel, coordinates, count,
         perfectMatch.equalsIgnoreCase("true"));
-    for (Object object : elements) {
+    for (BioEntity object : elements) {
       Map<String, Object> result = createMinifiedSearchResult(object);
       resultMap.add(result);
     }
     return resultMap;
   }
 
-  /**
-   * @return the modelService
-   * @see #modelService
-   */
-  public IModelService getModelService() {
-    return modelService;
-  }
-
-  /**
-   * @param modelService
-   *          the modelService to set
-   * @see #modelService
-   */
-  public void setModelService(IModelService modelService) {
-    this.modelService = modelService;
-  }
-
   /**
    * @return the searchService
    * @see #searchService
@@ -108,12 +68,12 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
       Integer maxElements, String perfectMatch) throws SecurityException {
     List<Map<String, Object>> resultMap = new ArrayList<>();
 
-    Model model = modelService.getLastModelByProjectId(projectId, token);
+    Model model = getModelService().getLastModelByProjectId(projectId, token);
 
     Integer limit = Integer.valueOf(maxElements);
     boolean match = perfectMatch.equals("true");
-    List<Object> elements = searchService.searchByQuery(model, query, limit, match);
-    for (Object object : elements) {
+    List<BioEntity> elements = searchService.searchByQuery(model, query, limit, match);
+    for (BioEntity object : elements) {
       Map<String, Object> result = createMinifiedSearchResult(object);
       resultMap.add(result);
     }
@@ -121,7 +81,7 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
   }
 
   public String[] getSuggestedQueryList(String projectId, String token) throws SecurityException {
-    Model model = modelService.getLastModelByProjectId(projectId, token);
+    Model model = getModelService().getLastModelByProjectId(projectId, token);
     return searchService.getSuggestedQueryList(model);
   }
 
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
index d7bdf46683..8a45c60fa2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
@@ -13,6 +13,7 @@ import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 
 import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.services.SecurityException;
 
@@ -32,7 +33,7 @@ public class ElementsController extends BaseController {
 			@RequestParam(value = "includedCompartmentIds", defaultValue = "") String includedCompartmentIds, //
 			@RequestParam(value = "excludedCompartmentIds", defaultValue = "") String excludedCompartmentIds, //
 			@CookieValue(value = Configuration.AUTH_TOKEN) String token//
-	) throws SecurityException {
+	) throws SecurityException, QueryException {
 		return projectController.getElements(projectId, id, columns, modelId, token, type, includedCompartmentIds, excludedCompartmentIds);
 	}
 
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index d2ba60ddee..34a94e8266 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -1,17 +1,19 @@
 package lcsb.mapviewer.api.projects.models.bioEntities.elements;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.species.AntisenseRna;
@@ -23,7 +25,6 @@ import lcsb.mapviewer.model.map.species.field.ElementModification;
 import lcsb.mapviewer.model.map.species.field.Structure;
 import lcsb.mapviewer.model.map.species.field.UniprotRecord;
 import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
 import lcsb.mapviewer.services.view.OverviewImageViewFactory;
 
 @Transactional(value = "txManager")
@@ -40,7 +41,7 @@ public class ElementsRestImpl extends BaseRestImpl {
 
   public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId,
       String token, String type, String includedCompartmentIds, String excludedCompartmentIds)
-      throws UserAccessException, SecurityException {
+      throws QueryException, SecurityException {
     Set<Integer> ids = new HashSet<>();
     if (!id.equals("")) {
       for (String str : id.split(",")) {
@@ -59,20 +60,25 @@ public class ElementsRestImpl extends BaseRestImpl {
     Set<Compartment> excludedCompartments = getCompartments(excludedCompartmentIds, models);
     Set<String> columnsSet = createElementColumnSet(columns);
 
-    List<Map<String, Object>> result = new ArrayList<>();
+    List<Element> elements = new ArrayList<>();
 
     for (Model model2 : models) {
       for (Element element : model2.getElements()) {
         if (ids.size() == 0 || ids.contains(element.getId())) {
           if (types.size() == 0 || types.contains(element.getStringType().toLowerCase())) {
             if (matchIncludedExcludedCompartments(element, includedCompartments, excludedCompartments)) {
-              result.add(preparedElement(element, columnsSet));
+              elements.add(element);
             }
           }
         }
       }
     }
+    elements.sort(BioEntity.ID_COMPARATOR);
+    List<Map<String, Object>> result = new ArrayList<>();
+    for (Element element : elements) {
+      result.add(preparedElement(element, columnsSet));
 
+    }
     return result;
   }
 
@@ -125,7 +131,7 @@ public class ElementsRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> preparedElement(Element element, Set<String> columnsSet) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (String string : columnsSet) {
       String column = string.toLowerCase();
       Object value = null;
@@ -200,10 +206,10 @@ public class ElementsRestImpl extends BaseRestImpl {
   }
 
   protected Map<String, Object> getOthersForElement(Element element) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     List<Map<String, Object>> modifications = new ArrayList<>();
     String structuralState = null;
-    Map<String, Object> structures = new HashMap<>();
+    Map<String, Object> structures = new TreeMap<>();
     if (element instanceof Protein) {
       Protein protein = ((Protein) element);
       modifications = getModifications(protein.getModificationResidues());
@@ -231,7 +237,7 @@ public class ElementsRestImpl extends BaseRestImpl {
     List<Map<String, Object>> result = new ArrayList<>();
     for (ElementModification region : elements) {
       if (region.getState() != null) {
-        Map<String, Object> row = new HashMap<>();
+        Map<String, Object> row = new TreeMap<>();
         row.put("name", region.getName());
         String state = region.getState().name();
         row.put("state", state);
@@ -242,7 +248,7 @@ public class ElementsRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> getStructures(Set<UniprotRecord> uniprots) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (UniprotRecord uniprotRec : uniprots) {
       Set<Object> structs = new HashSet<>();
       for (Structure struct : uniprotRec.getStructures()) {
@@ -254,7 +260,7 @@ public class ElementsRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> createBounds(Double x, Double y, Double width, Double height) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("x", x);
     result.put("y", y);
     result.put("width", width);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
index ed788baecf..b53c678caf 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
@@ -13,6 +13,7 @@ import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 
 import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.services.SecurityException;
 
@@ -30,7 +31,7 @@ public class ReactionsController extends BaseController {
 			@RequestParam(value = "columns", defaultValue = "") String columns, //
 			@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
 			@RequestParam(value = "participantId", defaultValue = "") String participantId//
-	) throws SecurityException {
+	) throws SecurityException,QueryException {
 		return reactionController.getReactions(projectId, id, columns, modelId, token, participantId);
 	}
 
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
index dc0c052216..c9d63f5459 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -2,11 +2,11 @@ package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 
 import javax.xml.transform.TransformerException;
 
@@ -16,7 +16,9 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
 import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
 import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
@@ -65,7 +67,7 @@ public class ReactionsRestImpl extends BaseRestImpl {
   }
 
   public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String modelId,
-      String token, String participantElementId) throws UserAccessException, SecurityException {
+      String token, String participantElementId) throws UserAccessException, SecurityException, QueryException {
     Set<Integer> ids = new HashSet<>();
     if (!id.equals("")) {
       for (String str : id.split(",")) {
@@ -84,18 +86,23 @@ public class ReactionsRestImpl extends BaseRestImpl {
     }
     Set<String> columnsSet = createReactionColumnSet(columns);
 
-    List<Map<String, Object>> result = new ArrayList<>();
+    List<Reaction> elements = new ArrayList<>();
 
     for (Model model2 : models) {
       for (Reaction reaction : model2.getReactions()) {
         if (ids.size() == 0 || ids.contains(reaction.getId())) {
           if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
-            result.add(preparedReaction(reaction, columnsSet));
+            elements.add(reaction);
           }
         }
       }
     }
+    elements.sort(BioEntity.ID_COMPARATOR);
+    List<Map<String, Object>> result = new ArrayList<>();
+    for (Reaction element : elements) {
+      result.add(preparedReaction(element, columnsSet));
 
+    }
     return result;
   }
 
@@ -109,7 +116,7 @@ public class ReactionsRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (String string : columnsSet) {
       String column = string.toLowerCase();
       Object value = null;
@@ -165,7 +172,7 @@ public class ReactionsRestImpl extends BaseRestImpl {
     if (kinetics == null) {
       return null;
     }
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("definition", kinetics.getDefinition());
     try {
       result.put("mathMlPresentation", super.mathMLToPresentationML(kinetics.getDefinition()));
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
index aa0214b288..356823ab67 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.api.projects.models.functions;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.List;
 import java.util.Map;
 
@@ -43,7 +43,7 @@ public class FunctionsRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> functionToMap(SbmlFunction function) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("id", function.getId());
     result.put("functionId", function.getFunctionId());
     result.put("name", function.getName());
@@ -57,7 +57,7 @@ public class FunctionsRestImpl extends BaseRestImpl {
     return result;
   }
 
-  public List<Map<String, Object>> getFunctions(String projectId, String modelId, String token) throws SecurityException {
+  public List<Map<String, Object>> getFunctions(String projectId, String modelId, String token) throws SecurityException, QueryException {
     List<Map<String, Object>> result = new ArrayList<>();
     List<Model> models = getModels(projectId, modelId, token);
     for (Model model : models) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java
index c76f1bed4e..5cf7ba05c9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java
@@ -1,7 +1,7 @@
 package lcsb.mapviewer.api.projects.models.parameters;
 
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -41,7 +41,7 @@ public class ParametersRestImpl extends BaseRestImpl {
   }
 
   private Set<SbmlParameter> getParametersFromProject(String projectId, String modelId, String token)
-      throws SecurityException {
+      throws SecurityException, ObjectNotFoundException {
     List<Model> models = getModels(projectId, modelId, token);
     Set<SbmlParameter> parameters = new HashSet<>();
 
@@ -57,7 +57,7 @@ public class ParametersRestImpl extends BaseRestImpl {
   }
 
   private Set<SbmlParameter> getGlobalParametersFromProject(String projectId, String modelId, String token)
-      throws SecurityException {
+      throws SecurityException, ObjectNotFoundException {
     List<Model> models = getModels(projectId, modelId, token);
     Set<SbmlParameter> parameters = new HashSet<>();
 
@@ -68,7 +68,7 @@ public class ParametersRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> parameterToMap(SbmlParameter parameter, boolean global) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("id", parameter.getId());
     result.put("parameterId", parameter.getParameterId());
     result.put("name", parameter.getName());
@@ -83,7 +83,7 @@ public class ParametersRestImpl extends BaseRestImpl {
   }
 
   public List<Map<String, Object>> getParameters(String projectId, String modelId, String token)
-      throws SecurityException {
+      throws SecurityException, QueryException {
     List<Map<String, Object>> result = new ArrayList<>();
     Set<SbmlParameter> globalParameters = getGlobalParametersFromProject(projectId, modelId, token);
     Set<SbmlParameter> parameters = getParametersFromProject(projectId, modelId, token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index f303d013d5..343de635ee 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.api.projects.models.publications;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -26,8 +25,6 @@ import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.interfaces.ISearchService;
 import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@@ -51,32 +48,24 @@ public class PublicationsRestImpl extends BaseRestImpl {
 
   public SortedMap<MiriamData, List<BioEntity>> getPublications(Collection<Model> models) {
     SortedMap<MiriamData, List<BioEntity>> publications = new TreeMap<>();
+
+    List<BioEntity> bioEntities = new ArrayList<>();
     for (Model modelData : models) {
-      for (Element element : modelData.getElements()) {
-        for (MiriamData md : element.getMiriamData()) {
-          if (md.getDataType().equals(MiriamType.PUBMED)) {
-            List<BioEntity> list = publications.get(md);
-            if (list == null) {
-              list = new ArrayList<>();
-              publications.put(md, list);
-            }
-            list.add(element);
+      bioEntities.addAll(modelData.getBioEntities());
+    }
+    bioEntities.sort(BioEntity.ID_COMPARATOR);
+    for (BioEntity bioEntity : bioEntities) {
+      for (MiriamData md : bioEntity.getMiriamData()) {
+        if (md.getDataType().equals(MiriamType.PUBMED)) {
+          List<BioEntity> list = publications.get(md);
+          if (list == null) {
+            list = new ArrayList<>();
+            publications.put(md, list);
           }
+          list.add(bioEntity);
         }
       }
-      for (Reaction reaction : modelData.getReactions()) {
-        for (MiriamData md : reaction.getMiriamData()) {
-          if (md.getDataType().equals(MiriamType.PUBMED)) {
-            List<BioEntity> list = publications.get(md);
-            if (list == null) {
-              list = new ArrayList<>();
-              publications.put(md, list);
-            }
-            list.add(reaction);
-          }
-        }
 
-      }
     }
     return publications;
   }
@@ -164,7 +153,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
           elements.add(createMinifiedSearchResult(object));
         }
 
-        Map<String, Object> row = new HashMap<>();
+        Map<String, Object> row = new TreeMap<>();
         row.put("elements", elements);
         row.put("publication", createAnnotation(entry.getKey()));
         resultList.add(row);
@@ -172,7 +161,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
       index++;
     }
 
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("data", resultList);
     result.put("totalSize", publications.size());
     result.put("filteredSize", filteredList.size());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
index 887b551fbe..9ceda914f5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
@@ -1,7 +1,7 @@
 package lcsb.mapviewer.api.projects.models.units;
 
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.List;
 import java.util.Map;
 
@@ -40,7 +40,7 @@ public class UnitsRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> unitToMap(SbmlUnit unit) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("id", unit.getId());
     result.put("unitId", unit.getUnitId());
     result.put("name", unit.getName());
@@ -53,7 +53,7 @@ public class UnitsRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> factorToMap(SbmlUnitTypeFactor factor) {
-    Map<String, Object> result =  new HashMap<>();
+    Map<String, Object> result =  new TreeMap<>();
     result.put("id", factor.getId());
     result.put("exponent", factor.getExponent());
     result.put("multiplier", factor.getMultiplier());
@@ -62,7 +62,7 @@ public class UnitsRestImpl extends BaseRestImpl {
     return result;
   }
 
-  public List<Map<String, Object>> getUnits(String projectId, String modelId, String token) throws SecurityException {
+  public List<Map<String, Object>> getUnits(String projectId, String modelId, String token) throws SecurityException, ObjectNotFoundException {
     List<Map<String, Object>> result = new ArrayList<>();
     List<Model> models = getModels(projectId, modelId, token);
     for (Model model : models) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
index 409f066fa6..c82b512905 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
@@ -24,7 +24,6 @@ import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.model.cache.FileEntry;
 import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.view.LayoutView;
 
 @RestController
 public class OverlayController extends BaseController {
@@ -40,7 +39,7 @@ public class OverlayController extends BaseController {
 
   @RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.GET }, produces = {
       MediaType.APPLICATION_JSON_VALUE })
-  public List<LayoutView> getOverlayList(//
+  public List<Map<String, Object>> getOverlayList(//
       @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
       @PathVariable(value = "projectId") String projectId, //
       @RequestParam(value = "creator", defaultValue = "") String creator, //
@@ -51,7 +50,7 @@ public class OverlayController extends BaseController {
 
   @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/", method = { RequestMethod.GET }, produces = {
       MediaType.APPLICATION_JSON_VALUE })
-  public LayoutView getOverlayById(//
+  public Map<String, Object> getOverlayById(//
       @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
       @PathVariable(value = "projectId") String projectId, //
       @PathVariable(value = "overlayId") String overlayId//
@@ -99,7 +98,7 @@ public class OverlayController extends BaseController {
 
   @RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.POST }, produces = {
       MediaType.APPLICATION_JSON_VALUE })
-  public LayoutView addOverlay(//
+  public Map<String, Object> addOverlay(//
       @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
       @PathVariable(value = "projectId") String projectId, //
       @RequestParam(value = "name") String name, //
@@ -124,7 +123,7 @@ public class OverlayController extends BaseController {
 
   @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.PATCH }, produces = {
       MediaType.APPLICATION_JSON_VALUE })
-  public LayoutView updateOverlay(//
+  public Map<String, Object> updateOverlay(//
       @RequestBody String body, //
       @PathVariable(value = "projectId") String projectId, //
       @PathVariable(value = "overlayId") String overlayId, //
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index 4bc6766e04..6e1fe9f0ee 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -5,9 +5,9 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
 
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -35,7 +35,6 @@ import lcsb.mapviewer.services.search.layout.FullLayoutReactionView;
 import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
 import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
 import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-import lcsb.mapviewer.services.view.LayoutView;
 
 @Transactional(value = "txManager")
 public class OverlayRestImpl extends BaseRestImpl {
@@ -55,8 +54,8 @@ public class OverlayRestImpl extends BaseRestImpl {
   @Autowired
   private LayoutDao layoutDao;
 
-  public List<LayoutView> getOverlayList(String token, String projectId, String creatorLogin, String publicOverlay)
-      throws SecurityException, QueryException {
+  public List<Map<String, Object>> getOverlayList(String token, String projectId, String creatorLogin,
+      String publicOverlay) throws SecurityException, QueryException {
     Model model = getModelService().getLastModelByProjectId(projectId, token);
     if (model == null) {
       return new ArrayList<>();
@@ -72,7 +71,43 @@ public class OverlayRestImpl extends BaseRestImpl {
     if (publicOverlay != null && !publicOverlay.isEmpty()) {
       publicData = publicOverlay.equalsIgnoreCase("true");
     }
-    return layoutService.getCustomLayouts(model, token, publicData, creator);
+    return overlaysToMap(layoutService.getCustomLayouts(model, token, publicData, creator));
+  }
+
+  private List<Map<String, Object>> overlaysToMap(List<Layout> overlays) {
+    overlays.sort(Layout.ID_COMPARATOR);
+    List<Map<String, Object>> result = new ArrayList<>();
+    for (Layout overlay : overlays) {
+      result.add(overlayToMap(overlay));
+    }
+    return result;
+  }
+
+  private Map<String, Object> overlayToMap(Layout overlay) {
+
+    Map<String, Object> result = new TreeMap<>();
+    result.put("idObject", overlay.getId());
+    result.put("name", overlay.getTitle());
+    result.put("description", overlay.getDescription());
+    result.put("publicOverlay", overlay.isPublicLayout());
+    result.put("defaultOverlay", overlay.isDefaultOverlay());
+    List<Map<String, Object>> images = new ArrayList<>();
+    List<Layout> childLayouts = new ArrayList<>();
+    childLayouts.add(overlay);
+    childLayouts.addAll(overlay.getLayouts());
+    childLayouts.sort(Layout.ID_COMPARATOR);
+    for (Layout child : childLayouts) {
+      Map<String, Object> image = new TreeMap<>();
+      image.put("path", child.getDirectory());
+      image.put("modelId", child.getModel().getId());
+      images.add(image);
+    }
+    result.put("images", images);
+    if (overlay.getCreator() != null) {
+      result.put("creator", overlay.getCreator().getLogin());
+    }
+    result.put("inputDataAvailable", overlay.getInputData() != null);
+    return result;
   }
 
   /**
@@ -101,16 +136,18 @@ public class OverlayRestImpl extends BaseRestImpl {
       throw new QueryException("Project with given id doesn't exist");
     }
     List<LightLayoutAliasView> speciesList = layoutService.getAliasesForLayout(model, overlayId, token);
+    speciesList.sort(LightLayoutAliasView.ID_COMPARATOR);
     for (LightLayoutAliasView lightLayoutAliasView : speciesList) {
-      Map<String, Object> element = new HashMap<>();
+      Map<String, Object> element = new TreeMap<>();
       element.put("type", ElementIdentifierType.ALIAS);
       element.put("overlayContent", lightLayoutAliasView);
       result.add(element);
     }
 
     List<LightLayoutReactionView> reactions = layoutService.getReactionsForLayout(model, overlayId, token);
+    speciesList.sort(LightLayoutReactionView.ID_COMPARATOR);
     for (LightLayoutReactionView lightReactionView : reactions) {
-      Map<String, Object> element = new HashMap<>();
+      Map<String, Object> element = new TreeMap<>();
       element.put("type", ElementIdentifierType.REACTION);
       element.put("overlayContent", lightReactionView);
       result.add(element);
@@ -118,13 +155,13 @@ public class OverlayRestImpl extends BaseRestImpl {
     return result;
   }
 
-  public LayoutView getOverlayById(String token, String projectId, String overlayId)
+  public Map<String, Object> getOverlayById(String token, String projectId, String overlayId)
       throws SecurityException, QueryException {
     Model model = getModelService().getLastModelByProjectId(projectId, token);
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    return layoutService.getLayoutById(Integer.valueOf(overlayId), token);
+    return overlayToMap(layoutService.getLayoutById(Integer.valueOf(overlayId), token));
   }
 
   public FileEntry getOverlaySource(String token, String projectId, String overlayId)
@@ -135,7 +172,7 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
     try {
       Integer id = Integer.valueOf(overlayId);
-      Layout layout = layoutService.getLayoutDataById(id, token);
+      Layout layout = layoutService.getLayoutById(id, token);
       if (layout == null) {
         throw new QueryException("Invalid overlay id");
       }
@@ -147,14 +184,14 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
   }
 
-  public LayoutView updateOverlay(String token, String projectId, String overlayId, Map<String, Object> overlayData)
-      throws QueryException, SecurityException {
+  public Map<String, Object> updateOverlay(String token, String projectId, String overlayId,
+      Map<String, Object> overlayData) throws QueryException, SecurityException {
     if (overlayData == null) {
       throw new QueryException("overlay field cannot be undefined");
     }
     try {
       Integer id = Integer.valueOf(overlayId);
-      Layout layout = layoutService.getLayoutDataById(id, token);
+      Layout layout = layoutService.getLayoutById(id, token);
       if (layout == null) {
         throw new ObjectNotFoundException("overlay doesn't exist");
       }
@@ -184,7 +221,7 @@ public class OverlayRestImpl extends BaseRestImpl {
         }
       }
       layoutDao.update(layout);
-      return layoutService.getLayoutById(Integer.valueOf(overlayId), token);
+      return getOverlayById(token, layout.getModel().getProject().getProjectId(), overlayId);
     } catch (NumberFormatException e) {
       throw new ObjectNotFoundException("overlay doesn't exist");
     }
@@ -206,7 +243,7 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
     try {
       Integer id = Integer.valueOf(overlayId);
-      LayoutView layout = layoutService.getLayoutById(id, token);
+      Layout layout = layoutService.getLayoutById(id, token);
       if (layout == null) {
         throw new ObjectNotFoundException("Overlay doesn't exist");
       }
@@ -238,7 +275,7 @@ public class OverlayRestImpl extends BaseRestImpl {
     this.layoutDao = layoutDao;
   }
 
-  public LayoutView addOverlay(String token, String projectId, String name, String description, String content,
+  public Map<String, Object> addOverlay(String token, String projectId, String name, String description, String content,
       String fileId, String filename, String type) throws SecurityException, QueryException, IOException {
     User user = getUserService().getUserByToken(token);
     if (Configuration.ANONYMOUS_LOGIN.equals(user.getLogin())) {
@@ -280,10 +317,10 @@ public class OverlayRestImpl extends BaseRestImpl {
         }
       }
 
-      LayoutView layout = layoutService.createLayout(new CreateLayoutParams().async(false).colorInputStream(stream)
+      Layout layout = layoutService.createLayout(new CreateLayoutParams().async(false).colorInputStream(stream)
           .description(description).layoutFileName(filename).model(model).name(name).user(user)
           .colorSchemaType(colorSchemaType).directory("."));
-      return layoutService.getLayoutById(Integer.valueOf(layout.getIdObject()), token);
+      return getOverlayById(token, projectId, layout.getId() + "");
     } catch (InvalidColorSchemaException e) {
       throw new QueryException(e.getMessage(), e);
     }
@@ -298,7 +335,7 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
     Model model = topModel.getSubmodelById(modelId);
 
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     if (ElementIdentifierType.ALIAS.getJsName().equals(elementType)) {
       FullLayoutAliasView layoutAliasView = layoutService.getFullAliasForLayout(model, elementId, overlayId, token);
       result.put("type", ElementIdentifierType.ALIAS);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index 33ee71a1b5..c5a5d4731c 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -1,7 +1,7 @@
 package lcsb.mapviewer.api.users;
 
 import java.io.IOException;
-import java.util.HashMap;
+import java.util.TreeMap;
 import java.util.List;
 import java.util.Map;
 
@@ -71,7 +71,7 @@ public class UserController extends BaseController {
 
       userService.login(login, password, request.getSession().getId());
 
-      Map<String, Object> result = new HashMap<>();
+      Map<String, Object> result = new TreeMap<>();
 
       result.put("info", "Login successful. TOKEN returned as a cookie");
       return result;
@@ -135,7 +135,7 @@ public class UserController extends BaseController {
       new SecurityContextLogoutHandler().logout(request, response, auth);
     }
 
-    Map<String, String> result = new HashMap<>();
+    Map<String, String> result = new TreeMap<>();
     result.put("status", "OK");
 
     final Boolean useSecureCookie = false;
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 5044560529..fdd195ebda 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
@@ -1,11 +1,11 @@
 package lcsb.mapviewer.api.users;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -90,7 +90,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareUse(User user, Set<String> columnsSet, boolean admin) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (String string : columnsSet) {
       String column = string.toLowerCase();
       Object value = null;
@@ -127,7 +127,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> preparePreferences(User user) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     UserAnnotationSchema schema = getProjectService().prepareUserAnnotationSchema(user);
     result.put("project-upload", prepareProjectUploadPreferences(schema));
     result.put("element-annotators", prepareElementAnnotators(schema.getClassAnnotators()));
@@ -145,12 +145,12 @@ public class UserRestImpl extends BaseRestImpl {
    * @return
    */
   private Map<String, Object> prepareAnnotatorsParams(List<UserAnnotatorsParam> annotatorsParams) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (UserAnnotatorsParam param : annotatorsParams) {
       String className = param.getAnnotatorClassName().getName();
       Map<String, String> annotatorParams = (Map<String, String>) result.get(className);
       if (annotatorParams == null) {
-        annotatorParams = new HashMap<>();
+        annotatorParams = new TreeMap<>();
         result.put(className, annotatorParams);
       }
       annotatorParams.put(param.getParamName(), param.getParamValue());
@@ -159,7 +159,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (UserClassValidAnnotations userClassAnnotators : classValidAnnotators) {
       result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getValidMiriamTypes()));
     }
@@ -202,9 +202,9 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareRequiredAnnotations(List<UserClassRequiredAnnotations> classRequiredAnnotators) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (UserClassRequiredAnnotations requiredAnnotations : classRequiredAnnotators) {
-      Map<String, Object> row = new HashMap<>();
+      Map<String, Object> row = new TreeMap<>();
       row.put("require-at-least-one", requiredAnnotations.getRequireAtLeastOneAnnotation());
       List<String> miriamTypes = new ArrayList<>();
 
@@ -251,7 +251,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareElementAnnotators(List<UserClassAnnotators> classAnnotators) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     for (UserClassAnnotators userClassAnnotators : classAnnotators) {
       result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getAnnotators()));
     }
@@ -277,7 +277,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareProjectUploadPreferences(UserAnnotationSchema schema) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("validate-miriam", schema.getValidateMiriamTypes());
     result.put("annotate-model", schema.getAnnotateModel());
     result.put("cache-data", schema.getCacheData());
@@ -290,7 +290,10 @@ public class UserRestImpl extends BaseRestImpl {
   private List<Map<String, Object>> preparePrivileges(User user) {
     List<Map<String, Object>> result = new ArrayList<>();
     Set<PrivilegeType> definedDefaultProjectPrivilegeTypes = new HashSet<>();
-    for (BasicPrivilege privilege : user.getPrivileges()) {
+    List<BasicPrivilege> privileges = new ArrayList<>();
+    privileges.addAll(user.getPrivileges());
+    privileges.sort(BasicPrivilege.ID_COMPARATOR);
+    for (BasicPrivilege privilege : privileges) {
       if (privilege instanceof ObjectPrivilege) {
         if (Project.class.equals(privilege.getType().getPrivilegeObjectType())
             && ((ObjectPrivilege) privilege).getIdObject() == null) {
@@ -307,7 +310,7 @@ public class UserRestImpl extends BaseRestImpl {
         result.add(prepareDefaultObjectPrivilege(privilegeType));
       }
     }
-    Map<String, Object> customLayouts = new HashMap<>();
+    Map<String, Object> customLayouts = new TreeMap<>();
     customLayouts.put("type", "CUSTOM_LAYOUTS_AVAILABLE");
     customLayouts.put("value", layoutService.getAvailableCustomLayoutsNumber(user));
     result.add(customLayouts);
@@ -315,7 +318,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareDefaultObjectPrivilege(PrivilegeType privilegeType) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("type", privilegeType);
     ConfigurationView value = configurationService.getValue(privilegeType);
     if (value == null) {
@@ -332,7 +335,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareObjectPrivilege(ObjectPrivilege privilege) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     result.put("type", privilege.getType());
     result.put("value", privilege.getLevel());
     result.put("objectId", privilege.getIdObject());
@@ -340,7 +343,7 @@ public class UserRestImpl extends BaseRestImpl {
   }
 
   private Map<String, Object> prepareBasicPrivilege(BasicPrivilege privilege) {
-    Map<String, Object> result = new HashMap<>();
+    Map<String, Object> result = new TreeMap<>();
     if (privilege.getClass().equals(BasicPrivilege.class)) {
       result.put("type", privilege.getType());
       result.put("value", privilege.getLevel());
@@ -374,7 +377,9 @@ public class UserRestImpl extends BaseRestImpl {
     Set<String> columnSet = createUserColumnSet(columns);
 
     List<Map<String, Object>> result = new ArrayList<>();
-    for (User user : getUserService().getUsers(token)) {
+    List<User> users = getUserService().getUsers(token);
+    users.sort(User.LOGIN_COMPARATOR);
+    for (User user : users) {
       result.add(prepareUse(user, columnSet, isAdmin));
     }
     return result;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index 37c0ec0204..48dd19fd01 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -169,7 +169,7 @@ public abstract class RestTestFunctions {
     return doc;
   }
 
-  private static Map<String, Model> models = new HashMap<String, Model>();
+  private static Map<String, Model> models = new HashMap<>();
 
   protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
     Model result = null;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index e868eb6e7e..5a82534e0b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -6,10 +6,8 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 import javax.annotation.PostConstruct;
 import javax.mail.MessagingException;
@@ -68,8 +66,6 @@ import lcsb.mapviewer.services.search.layout.LightLayoutReactionViewFactory;
 import lcsb.mapviewer.services.utils.ColorSchemaReader;
 import lcsb.mapviewer.services.utils.EmailSender;
 import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
-import lcsb.mapviewer.services.view.LayoutView;
-import lcsb.mapviewer.services.view.LayoutViewFactory;
 
 /**
  * Implementation of the layout service.
@@ -91,12 +87,6 @@ public class LayoutService implements ILayoutService {
   @Autowired
   private LayoutDao layoutDao;
 
-  /**
-   * Factory object used for creation of {@link LayoutView} elements.
-   */
-  @Autowired
-  private LayoutViewFactory layoutViewFactory;
-
   /**
    * Service that manages and gives access to user information.
    */
@@ -118,7 +108,7 @@ public class LayoutService implements ILayoutService {
   private IConfigurationService configurationService;
 
   /**
-   * Utils that help to manage the sessions in custom multithreaded
+   * Utility class that helps to manage the sessions in custom multi-threaded
    * implementation.
    */
   @Autowired
@@ -156,10 +146,9 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public boolean userCanRemoveLayout(LayoutView layout, User user) {
-    Layout originalLayout = layoutDao.getById(layout.getIdObject());
-    User creator = originalLayout.getCreator();
-    Project project = originalLayout.getModel().getProject();
+  public boolean userCanRemoveLayout(Layout layout, User user) {
+    User creator = layout.getCreator();
+    Project project = layout.getModel().getProject();
     if (creator == null) {
       return userService.userHasPrivilege(user, PrivilegeType.LAYOUT_MANAGEMENT, project);
     } else {
@@ -168,21 +157,6 @@ public class LayoutService implements ILayoutService {
     }
   }
 
-  @Override
-  public List<LayoutView> getCustomLayouts(Model model, User user, Boolean publicOverlay, User creator) {
-    // TODO remove publicOverlay and creator params
-    List<LayoutView> result = new ArrayList<>();
-    if (model == null || user == null) {
-      return result;
-    }
-    List<Layout> layouts = layoutDao.getLayoutsByModel(model, user, false);
-    for (Layout layout : layouts) {
-      result.add(layoutViewFactory.create(layout));
-    }
-    Collections.sort(result, LayoutView.ID_COMPARATOR);
-    return result;
-  }
-
   private boolean userCanViewOverlay(Layout overlay, User user) {
     if (overlay.isPublicLayout()) {
       return true;
@@ -201,28 +175,11 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public List<LayoutView> getGeneralLayouts(Model model) {
-    List<LayoutView> result = new ArrayList<LayoutView>();
-    if (model == null) {
-      return result;
-    }
-    List<Layout> layouts = layoutDao.getLayoutsByModel(model);
-    for (Layout layout : layouts) {
-      if (layout.isPublicLayout()) {
-        result.add(layoutViewFactory.create(layout));
-      }
-    }
-    Collections.sort(result, LayoutView.ID_COMPARATOR);
-    return result;
-  }
-
-  @Override
-  public void removeLayout(LayoutView layout, final String homeDir) throws IOException {
+  public void removeLayout(Layout layout, final String homeDir) throws IOException {
     final String dir;
-    final Layout dbLayout = layoutDao.getById(layout.getIdObject());
     if (homeDir != null) {
-      if (dbLayout.getModel().getProject().getDirectory() != null) {
-        dir = homeDir + "/../map_images/" + dbLayout.getModel().getProject().getDirectory() + "/";
+      if (layout.getModel().getProject().getDirectory() != null) {
+        dir = homeDir + "/../map_images/" + layout.getModel().getProject().getDirectory() + "/";
       } else {
         dir = homeDir + "/../map_images/";
       }
@@ -230,22 +187,22 @@ public class LayoutService implements ILayoutService {
       dir = null;
     }
 
-    String projectId = dbLayout.getModel().getProject().getProjectId();
+    String projectId = layout.getModel().getProject().getProjectId();
     String email = null;
-    User user = dbLayout.getCreator();
+    User user = layout.getCreator();
     if (user != null) {
       email = user.getEmail();
     }
 
-    dbLayout.getModel().removeLayout(dbLayout);
-    layoutDao.delete(dbLayout);
+    layout.getModel().removeLayout(layout);
+    layoutDao.delete(layout);
 
-    LogParams params = new LogParams().object(dbLayout).type(LogType.LAYOUT_REMOVED);
+    LogParams params = new LogParams().object(layout).type(LogType.LAYOUT_REMOVED);
     logService.log(params);
 
     if (email != null) {
       try {
-        sendSuccesfullRemoveEmail(projectId, layout.getName(), email);
+        sendSuccesfullRemoveEmail(projectId, layout.getTitle(), email);
       } catch (MessagingException e) {
         logger.error(e);
       }
@@ -255,7 +212,7 @@ public class LayoutService implements ILayoutService {
       public void run() {
         MapGenerator generator = new MapGenerator();
         try {
-          generator.removeLayout(dbLayout, dir);
+          generator.removeLayout(layout, dir);
         } catch (IOException e) {
           logger.error(e);
         }
@@ -266,26 +223,14 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public void updateLayout(LayoutView layout) {
-    Layout dbLayout = layoutDao.getById(layout.getIdObject());
-    dbLayout.setTitle(layout.getName());
-    dbLayout.setDescription(layout.getDescription());
-    if (layout.getCreator().isEmpty()) {
-      dbLayout.setCreator(null);
-      dbLayout.setPublicLayout(true);
-    } else {
-      User user = userService.getUserByLogin(layout.getCreator());
-      dbLayout.setCreator(user);
-      dbLayout.setPublicLayout(false);
-    }
-
-    layoutDao.update(dbLayout);
+  public void updateLayout(Layout layout) {
+    layoutDao.update(layout);
   }
 
   @Override
-  public void addViewPrivilegeToLayout(LayoutView layout, User user) {
+  public void addViewPrivilegeToLayout(Layout layout, User user) {
     ObjectPrivilege privilege = new ObjectPrivilege();
-    privilege.setIdObject(layout.getIdObject());
+    privilege.setIdObject(layout.getId());
     privilege.setLevel(1);
     privilege.setType(PrivilegeType.LAYOUT_VIEW);
     privilege.setUser(user);
@@ -293,9 +238,9 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public void dropViewPrivilegeFromLayout(LayoutView layout, User user) {
+  public void dropViewPrivilegeFromLayout(Layout layout, User user) {
     ObjectPrivilege privilege = new ObjectPrivilege();
-    privilege.setIdObject(layout.getIdObject());
+    privilege.setIdObject(layout.getId());
     privilege.setLevel(0);
     privilege.setType(PrivilegeType.LAYOUT_VIEW);
     privilege.setUser(user);
@@ -303,7 +248,7 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public LayoutView createLayoutWithImages(final CreateLayoutParams params)
+  public Layout createLayoutWithImages(final CreateLayoutParams params)
       throws IOException, InvalidColorSchemaException, CommandExecutionException {
     ColorSchemaReader reader = new ColorSchemaReader();
     final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
@@ -456,11 +401,11 @@ public class LayoutService implements ILayoutService {
     } else {
       computations.run();
     }
-    return layoutViewFactory.create(topLayout);
+    return topLayout;
   }
 
   @Override
-  public LayoutView createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
+  public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
     ColorSchemaReader reader = new ColorSchemaReader();
     final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
         TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
@@ -557,7 +502,7 @@ public class LayoutService implements ILayoutService {
     logService.log(logParams);
 
     computations.start();
-    return layoutViewFactory.create(topLayout);
+    return topLayout;
   }
 
   /**
@@ -611,19 +556,6 @@ public class LayoutService implements ILayoutService {
     this.userService = userService;
   }
 
-  @Override
-  public LayoutView getLayoutByName(Model model, String name) {
-    if (model == null) {
-      return null;
-    }
-    Layout layout = layoutDao.getLayoutByName(model, name);
-    if (layout != null) {
-      return layoutViewFactory.create(layout);
-    } else {
-      return null;
-    }
-  }
-
   /**
    * Sends notification email that layout was removed.
    *
@@ -891,11 +823,6 @@ public class LayoutService implements ILayoutService {
     return sb.toString();
   }
 
-  @Override
-  public byte[] getInputDataForLayout(LayoutView layoutView, String token) throws SecurityException {
-    return getInputDataForLayout(layoutView.getIdObject(), token);
-  }
-
   /**
    * Returns byte array containing data from original input file that was used to
    * generate the layout.
@@ -908,7 +835,7 @@ public class LayoutService implements ILayoutService {
    * @throws SecurityException
    */
   private byte[] getInputDataForLayout(int layoutId, String token) throws SecurityException {
-    Layout layout = getLayoutDataById(layoutId, token);
+    Layout layout = getLayoutById(layoutId, token);
     if (layout == null) {
       return null;
     } else {
@@ -986,41 +913,6 @@ public class LayoutService implements ILayoutService {
     }
   }
 
-  @Override
-  public List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers,
-      int layoutId, String token) throws SecurityException {
-    try {
-      Set<Integer> ids = new HashSet<>();
-      for (Pair<Integer, Integer> pair : identifiers) {
-        ids.add(pair.getRight());
-      }
-
-      ColorSchemaReader reader = new ColorSchemaReader();
-      Collection<ColorSchema> schemas;
-      schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
-      // colors here are not important
-      ColorModelCommand command = new ColorModelCommand(model, schemas,
-          new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
-      FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
-      List<FullLayoutAliasView> result = new ArrayList<>();
-
-      // TODO poor performance, improve it
-      for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
-        if (entry.getKey() instanceof Element) {
-          Element alias = (Element) entry.getKey();
-          if (ids.contains(alias.getId())) {
-            result.add(factory.create(new Pair<Element, ColorSchema>(alias, entry.getValue())));
-          }
-        }
-      }
-      return result;
-    } catch (InvalidColorSchemaException e) {
-      throw new InvalidStateException(e);
-    } catch (IOException e) {
-      throw new InvalidStateException(e);
-    }
-  }
-
   @Override
   public EmailSender getEmailSender() {
     return emailSender;
@@ -1032,22 +924,25 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public List<LayoutView> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator)
+  public List<Layout> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator)
       throws SecurityException {
-    return this.getCustomLayouts(model, userService.getUserByToken(token), publicOverlay, creator);
-  }
-
-  @Override
-  public LayoutView getLayoutById(int overlayId, String token) throws SecurityException {
-    Layout layout = getLayoutDataById(overlayId, token);
-    if (layout == null) {
-      return null;
+    User user = userService.getUserByToken(token);
+    List<Layout> result = new ArrayList<>();
+    if (model == null || user == null) {
+      return result;
+    }
+    List<Layout> overlays = layoutDao.getLayoutsByModel(model, creator, publicOverlay);
+    for (Layout overlay : overlays) {
+      if (userCanViewOverlay(overlay, user)) {
+        result.add(overlay);
+      }
     }
-    return layoutViewFactory.create(layout);
+    Collections.sort(result, Layout.ID_COMPARATOR);
+    return result;
   }
 
   @Override
-  public Layout getLayoutDataById(int overlayId, String token) throws SecurityException {
+  public Layout getLayoutById(int overlayId, String token) throws SecurityException {
     Layout layout = layoutDao.getById(overlayId);
     if (layout == null) {
       return null;
@@ -1116,7 +1011,7 @@ public class LayoutService implements ILayoutService {
   }
 
   @Override
-  public boolean userCanRemoveLayout(LayoutView layout, String authenticationToken) throws SecurityException {
+  public boolean userCanRemoveLayout(Layout layout, String authenticationToken) throws SecurityException {
     User user = userService.getUserByToken(authenticationToken);
     return userCanRemoveLayout(layout, user);
   }
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index 34186d37bb..fcaba2c69f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -44,9 +44,6 @@ import lcsb.mapviewer.model.map.statistics.SearchType;
 import lcsb.mapviewer.persist.dao.map.ModelDao;
 import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
 import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.overlay.IconManager;
-import lcsb.mapviewer.services.overlay.IconType;
-import lcsb.mapviewer.services.search.IHeavyView;
 import lcsb.mapviewer.services.search.data.FullAliasView;
 import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
 import lcsb.mapviewer.services.search.data.FullReactionView;
@@ -65,811 +62,791 @@ import lcsb.mapviewer.services.utils.SearchIndexer;
 @Transactional(value = "txManager")
 public class SearchService implements ISearchService {
 
-	private SemanticZoomLevelMatcher							zoomLevelMatcher					 = new SemanticZoomLevelMatcher();
-
-	/**
-	 * Prefix used in search by name interface to limit results only to species.
-	 */
-	public static final String										SPECIES_SEARCH_PREFIX			 = "species";
-
-	/**
-	 * Prefix used in search by name interface to limit results only to reactions.
-	 */
-	public static final String										REACTION_SEARCH_PREFIX		 = "reaction";
-
-	/**
-	 * Prefix used in search by name interface to limit results only to
-	 * {@link Element}.
-	 */
-	private static final String										ELEMENT_SEARCH_PREFIX			 = "element";
-
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private static Logger													logger										 = Logger.getLogger(SearchService.class.getName());
-
-	/**
-	 * Data access object for models.
-	 */
-	@Autowired
-	private ModelDao															modelDao;
-
-	/**
-	 * Service used for managing search history.
-	 */
-	@Autowired
-	private ISearchHistoryService									searchHistoryService;
-
-	/**
-	 * Factory object used to create {@link FullAliasView} objects.
-	 */
-	@Autowired
-	private FullAliasViewFactory									fullAliasViewFactory;
-
-	/**
-	 * Factory object used to create {@link FullReactionView} objects.
-	 */
-	@Autowired
-	private FullReactionViewFactory								fullReactionViewFactory;
-
-	/**
-	 * Object used for indexing elements on the map.
-	 */
-	private SearchIndexer													searchIndexer							 = new SearchIndexer();
-
-	/**
-	 * This object maps class of elements on the map into short string prefixes
-	 * used in the search query. For instance elements of the {@link Complex}
-	 * class could be searched with the prefix "complex" (example query:
-	 * "complex:alpha subcomplex").
-	 */
-	private Map<Class<? extends Element>, String>	speciesSearchPrefix				 = new HashMap<>();
-
-	/**
-	 * This object maps short string prefixes into class of elements on the map
-	 * that will be searched. For instance prefix "complex" might refer to
-	 * {@link Complex} class and and example query would look like:
-	 * "complex:alpha subcomplex".
-	 */
-	private Map<String, Class<? extends Element>>	speciesSearchReversePrefix = new HashMap<>();
-
-	/**
-	 * Default constructor that set list of prefixes used in the search queries.
-	 */
-	public SearchService() {
-		addSearchPrefix("complex", Complex.class);
-		addSearchPrefix("degrded", Degraded.class);
-		addSearchPrefix("drug", Drug.class);
-		addSearchPrefix("gene", Gene.class);
-		addSearchPrefix("ion", Ion.class);
-		addSearchPrefix("phenotype", Phenotype.class);
-		addSearchPrefix("protein", Protein.class);
-		addSearchPrefix("rna", Rna.class);
-		addSearchPrefix("molecule", SimpleMolecule.class);
-		addSearchPrefix("unknown", Unknown.class);
-	}
-
-	/**
-	 * Adds search prefix for an element class.
-	 * 
-	 * @param prefix
-	 *          string prefix used in search queries
-	 * @param clazz
-	 *          class for which this prefix stands
-	 */
-	private void addSearchPrefix(String prefix, Class<? extends Element> clazz) {
-		speciesSearchPrefix.put(clazz, prefix);
-		speciesSearchReversePrefix.put(prefix, clazz);
-	}
-
-	/**
-	 * Private class that defines internal search result element. Contains
-	 * reference to original result and match score of the result.
-	 * 
-	 * @author Piotr Gawron
-	 * 
-	 */
-	private class SearchResult implements Comparable<SearchResult> {
-		/**
-		 * Reference to the original object.
-		 */
-		private Object obj;
-
-		/**
-		 * Score of the result.
-		 */
-		private double score;
-
-		@Override
-		public int compareTo(SearchResult o) {
-			if (score == o.getScore()) {
-				return 0;
-			} else if (score < o.getScore()) {
-				return 1;
-			} else {
-				return -1;
-			}
-		}
-
-		/**
-		 * @return the obj
-		 */
-		public Object getObj() {
-			return obj;
-		}
-
-		/**
-		 * @param obj
-		 *          the obj to set
-		 */
-		public void setObj(Object obj) {
-			this.obj = obj;
-		}
-
-		/**
-		 * @return the score
-		 */
-		public double getScore() {
-			return score;
-		}
-
-		/**
-		 * @param score
-		 *          the score to set
-		 */
-		public void setScore(double score) {
-			this.score = score;
-		}
-	};
-
-	/**
-	 * Return the list of elements that match the query (sorted by match score)
-	 * limited to the element of class defined by type.
-	 * 
-	 * @param model
-	 *          model where the search is performed
-	 * @param query
-	 *          query string
-	 * @param limit
-	 *          maximum number of elements that can be returned by the search
-	 *          engine
-	 * @param perfectMatch
-	 *          should only perfect match be allowed
-	 * @param type
-	 *          class type of the elements that limits the results
-	 * @return list of object found for the query string sorted by the score value
-	 */
-	protected List<IHeavyView> searchByIndexedQuery(Model model, String query, int limit, Boolean perfectMatch, Class<? extends Element> type) {
-		List<IHeavyView> result = new ArrayList<>();
-		if (query.startsWith(REACTION_SEARCH_PREFIX)) {
-			return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
-		} else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
-			result.add(fullAliasViewFactory.create(model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""))));
-		} else if (query.startsWith(ELEMENT_SEARCH_PREFIX)) {
-			return getElementById(model, query.replaceFirst(ELEMENT_SEARCH_PREFIX, "").toLowerCase());
-		} else {
-			Set<Element> aliases = model.getElements();
-
-			List<SearchResult> sortedResults = new ArrayList<SearchService.SearchResult>();
-			for (Element alias : aliases) {
-				if (type.isAssignableFrom(alias.getClass())) {
-					List<SearchIndex> indexes = alias.getSearchIndexes();
-					if (indexes.size() == 0) {
-						indexes = searchIndexer.createIndexForAlias(alias);
-						alias.setSearchIndexes(indexes);
-					}
-					for (SearchIndex searchIndex : indexes) {
-						double score = searchIndexer.match(query, searchIndex);
-						if (perfectMatch != null && perfectMatch) {
-							if (query.equals(searchIndex.getValue())) {
-								SearchResult sResult = new SearchResult();
-								sResult.setObj(alias);
-								sResult.setScore(1);
-								sortedResults.add(sResult);
-								break;
-							}
-						} else if (score > 0 || (query.equals("") && type != Element.class)) {
-							SearchResult sResult = new SearchResult();
-							sResult.setObj(alias);
-							sResult.setScore(score);
-							if (score == 0) {
-								sResult.setScore(alias.getId());
-							}
-							sortedResults.add(sResult);
-							break;
-						}
-					}
-				}
-				if (result.size() >= limit) {
-					break;
-
-				}
-			}
-			Collections.sort(sortedResults);
-			for (SearchResult searchResult : sortedResults) {
-				if (searchResult.getObj() instanceof Reaction) {
-					result.add(fullReactionViewFactory.create((Reaction) searchResult.getObj()));
-				} else if (searchResult.getObj() instanceof Element) {
-					result.add(fullAliasViewFactory.create((Element) searchResult.getObj()));
-				} else {
-					throw new InvalidStateException("Unknown class type: " + searchResult.getObj().getClass());
-				}
-				if (result.size() >= limit) {
-					break;
-				}
-			}
-		}
-		return result;
-	}
-
-	/**
-	 * Returns list with the reaction with a given id. If reaction with such id
-	 * doesn't exist then empty list is returned.
-	 * 
-	 * @param model
-	 *          where the search is performed
-	 * @param reactionId
-	 *          id of the reaction
-	 * @return list that contains reaction with given id (or empty list if such
-	 *         reaction doesn't exist)
-	 */
-	private List<IHeavyView> getReactionById(Model model, String reactionId) {
-		Set<Reaction> reactions = model.getReactions();
-		for (Reaction reaction : reactions) {
-			if (searchIndexer.getQueryStringForIndex(reaction.getIdReaction().toLowerCase(), new ArrayList<>()).equals(reactionId)) {
-				return reactionToResultList(reaction);
-			}
-			if (Integer.toString(reaction.getId()).equals(reactionId)) {
-				return reactionToResultList(reaction);
-			}
-		}
-		return new ArrayList<>();
-	}
-
-	/**
-	 * Returns list with the element with a given id. If element with such id
-	 * doesn't exist then empty list is returned.
-	 * 
-	 * @param topModel
-	 *          where the search is performed
-	 * @param elementId
-	 *          id of the element
-	 * @return list that contains element with given id (or empty list if such
-	 *         element doesn't exist)
-	 */
-	private List<IHeavyView> getElementById(Model topModel, String elementId) {
-		List<IHeavyView> result = new ArrayList<>();
-
-		Set<Model> models = new HashSet<>();
-		models.add(topModel);
-		models.addAll(topModel.getSubmodels());
-		for (Model model : models) {
-			for (Element element : model.getElements()) {
-				if (searchIndexer.getQueryStringForIndex(element.getElementId().toLowerCase(), new ArrayList<>()).equals(elementId)) {
-					result.add(fullAliasViewFactory.create(element));
-				} else if (Integer.toString(element.getId()).equals(elementId)) {
-					result.add(fullAliasViewFactory.create(element));
-				}
-			}
-		}
-		return result;
-	}
-
-	/**
-	 * Transform {@link Reaction} into set of result entries.
-	 * 
-	 * @param reaction
-	 *          reaction to be transformed
-	 * @return set of result entries for all element of the {@link Reaction}
-	 */
-	private List<IHeavyView> reactionToResultList(Reaction reaction) {
-		List<IHeavyView> result = new ArrayList<>();
-		result.add(fullReactionViewFactory.create(reaction));
-		for (ReactionNode node : reaction.getReactionNodes()) {
-			result.add(fullAliasViewFactory.create(node.getElement()));
-		}
-		return result;
-	}
-
-	@Override
-	public SearchElementResult searchByCoordinates(CoordinatesSearchParams params) {
-		SearchElementResult result = new SearchElementResult("");
-		boolean nested = params.isNested();
-
-		List<Object> results = new ArrayList<Object>();
-
-		Set<Element> aliases = params.getModel().getElements();
-		Point2D point = new Point2D.Double(params.getX(), params.getY());
-		for (Element alias : aliases) {
-			if (alias instanceof Species) {
-				if (alias.contains(point)) {
-					if (isVisible(alias, params)) {
-						results.add(alias);
-					}
-				}
-			}
-		}
-		double dist = params.getDistance();
-		if (results.size() == 0) {
-			Reaction r = null;
-			Set<Reaction> reactions = params.getModel().getReactions();
-			for (Reaction reaction : reactions) {
-				double newDist = reaction.getDistanceFromPoint(point);
-				if (newDist < dist) {
-					if (isVisible(reaction, params)) {
-						r = reaction;
-						dist = reaction.getDistanceFromPoint(point);
-					}
-				}
-			}
-			if (r != null) {
-				result.addAll(reactionToResultList(r));
-				return result;
-			} else if (nested) {
-				for (Element alias : aliases) {
-					if (alias instanceof Compartment) {
-						if (alias.contains(point)) {
-							if (isVisible(alias, params)) {
-								results.add(alias);
-							}
-						}
-					}
-				}
-			}
-		}
-
-		if (results.size() > 1) {
-			Element alias = (Element) results.get(0);
-			for (Object obj : results) {
-				if (((Element) (obj)).getSize() < alias.getSize()) {
-					alias = (Element) obj;
-				}
-			}
-			results.clear();
-			results.add(alias);
-		}
-		if (results.size() == 0) {
-			return result;
-		} else {
-			Object obj = results.get(0);
-			if (obj instanceof Element) {
-				result.add(fullAliasViewFactory.create((Element) obj));
-				return result;
-			} else if (obj instanceof Reaction) {
-				result.addAll(reactionToResultList((Reaction) obj));
-				return result;
-			} else {
-				throw new InvalidStateException("Unknown class type: " + obj.getClass());
-			}
-		}
-	}
-
-	/**
-	 * Check if reaction is visible for the user. Reaction is visible when at
-	 * least one node of the reaction is visible.
-	 * 
-	 * @param reaction
-	 *          which reaction is tested
-	 * @param params
-	 *          params that determines the client search environment (zoom level,
-	 *          type of the layout)
-	 * @return <code>true</code> if reaction is visible for the user,
-	 *         <code>false</code> otherwise
-	 */
-	private boolean isVisible(Reaction reaction, CoordinatesSearchParams params) {
-		if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
-			return true;
-		}
-		if (!params.isNested()) {
-			return true;
-		}
-		for (ReactionNode node : reaction.getReactionNodes()) {
-			if (isVisible(node.getElement(), params)) {
-				return true;
-			}
-		}
-		return false;
-	}
-
-	/**
-	 * Checks if alias is visible for the user. Alias is invisible when the search
-	 * is performed on the hierarchical layout and the alias is hidden by the
-	 * complex or compartment.
-	 * 
-	 * @param alias
-	 *          alias to be checked for visibility
-	 * @param params
-	 *          that determines the client search environment (zoom level, type of
-	 *          the layout)
-	 * @return <code>true</code> if alias is visible for the user,
-	 *         <code>false</code> otherwise
-	 */
-	private boolean isVisible(Element alias, CoordinatesSearchParams params) {
-		if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
-			return true;
-		}
-		return (!params.isNested()) || zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel());
-	}
-
-	@Override
-	public SearchElementResult searchByQuery(Model model, String query, int limit, Boolean perfectMatch, String ipAddress) {
-		query = query.toLowerCase();
-		SearchElementResult result = new SearchElementResult(query);
-		if (query == null) {
-			throw new InvalidArgumentException("Invalid query: null");
-		}
-
-		MiriamData mt = getMiriamTypeForQuery(query);
-		if (mt != null) {
-			result.addAll(searchByMiriam(model, mt, limit));
-		} else {
-			String indexQuery = searchIndexer.getQueryStringForIndex(query, speciesSearchReversePrefix.keySet());
-			Class<? extends Element> type = searchIndexer.getTypeForQuery(query, speciesSearchReversePrefix);
-
-			List<IHeavyView> partResult = searchByIndexedQuery(model, indexQuery, limit, perfectMatch, type);
-
-			for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
-				partResult.addAll(searchByIndexedQuery(connection.getSubmodel().getModel(), indexQuery, limit - partResult.size(), perfectMatch, type));
-				if (partResult.size() >= limit) {
-					break;
-				}
-			}
-
-			result.addAll(partResult);
-		}
-		if (model.getProject() != null && ipAddress != null) {
-			searchHistoryService.addQuery(query, SearchType.GENERAL, ipAddress, model.getProject().getProjectId());
-		}
-		return result;
-	}
-
-	/**
-	 * Returns elements that are annotated with the given miriam data.
-	 * 
-	 * @param topModel
-	 *          model where elements are looked for
-	 * @param md
-	 *          miriam annotation to identifiy interesting elements
-	 * @param limit
-	 *          max number of elements to find
-	 * @return elements that are annotated with the given miriam data
-	 */
-	private List<IHeavyView> searchByMiriam(Model topModel, MiriamData md, int limit) {
-		List<IHeavyView> result = new ArrayList<>();
-		Set<Model> models = new HashSet<>();
-		models.add(topModel);
-		models.addAll(topModel.getSubmodels());
-		for (Model model : models) {
-			for (BioEntity obj : model.getElementsByAnnotation(md)) {
-				if (result.size() >= limit) {
-					break;
-				}
-				if (obj instanceof Element) {
-					result.add(fullAliasViewFactory.create((Element) obj));
-				} else if (obj instanceof Reaction) {
-					result.addAll(reactionToResultList((Reaction) obj));
-				} else {
-					throw new InvalidClassException("Unknown class: " + obj.getClass());
-				}
-			}
-		}
-		return result;
-	}
-
-	/**
-	 * Tries to transform query into {@link MiriamData}.
-	 * 
-	 * @param string
-	 *          query to transform
-	 * @return {@link MiriamData} that described query or null if query cannot be
-	 *         converted
-	 */
-	protected MiriamData getMiriamTypeForQuery(String string) {
-		for (MiriamType mt : MiriamType.values()) {
-			if (string.startsWith(mt.toString().toLowerCase() + ":")) {
-				return new MiriamData(mt, string.substring(mt.toString().length() + 1));
-			}
-		}
-		return null;
-	}
-
-	@Override
-	public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
-		List<BioEntity> result = new ArrayList<>();
-
-		// probably this could be improved algorithmitically, right now all objects
-		// are sorted by distance, and numberOfElements closest are chosen as a list
-		// of results
-		List<DistanceToObject> tmpList = new ArrayList<>();
-		for (Reaction reaction : model.getReactions()) {
-			tmpList.add(new DistanceToObject(reaction, point));
-		}
-		for (Element alias : model.getElements()) {
-			if (alias instanceof Species) {
-				tmpList.add(new DistanceToObject(alias, point));
-			}
-		}
-		Collections.sort(tmpList);
-		int size = Math.min(tmpList.size(), numberOfElements);
-		for (int i = 0; i < size; i++) {
-			if (!perfectHit) {
-				result.add(tmpList.get(i).getReference());
-			} else if (tmpList.get(i).getDistance() < Configuration.EPSILON) {
-				result.add(tmpList.get(i).getReference());
-			}
-		}
-		return result;
-	}
-
-	/**
-	 * This class represents distance between object and some point. It's designed
-	 * to help sort objects by their distance to some point. It It contains two
-	 * fields: object reference and distance.
-	 * 
-	 * @author Piotr Gawron
-	 * 
-	 */
-	private class DistanceToObject implements Comparable<DistanceToObject> {
-		/**
-		 * Reference to the object.
-		 */
-		private BioEntity	reference;
-
-		/**
-		 * Distance between the object and some point.
-		 */
-		private double		distance;
-
-		/**
-		 * Size of the object.
-		 */
-		private double		size;
-
-		/**
-		 * Constructor for reaction objects.
-		 * 
-		 * @param reaction
-		 *          reaction reference to store
-		 * @param point
-		 *          point from which the distance will be computed
-		 */
-		DistanceToObject(Reaction reaction, Point2D point) {
-			reference = reaction;
-			distance = reaction.getDistanceFromPoint(point);
-			size = 0;
-		}
-
-		/**
-		 * Constructor for alias objects.
-		 * 
-		 * @param alias
-		 *          alias reference to store
-		 * @param point
-		 *          point from which the distance will be computed
-		 */
-		DistanceToObject(Element alias, Point2D point) {
-			reference = alias;
-			distance = alias.getDistanceFromPoint(point);
-			size = alias.getSize();
-
-		}
-
-		@Override
-		public int compareTo(DistanceToObject arg0) {
-			if (arg0.getDistance() < getDistance()) {
-				return 1;
-			} else if (arg0.getDistance() > getDistance()) {
-				return -1;
-			} else {
-				if (arg0.getSize() < getSize()) {
-					return 1;
-				} else if (arg0.getSize() > getSize()) {
-					return -1;
-				} else {
-					return 0;
-				}
-			}
-		}
-
-		/**
-		 * @return the reference
-		 * @see #reference
-		 */
-		public BioEntity getReference() {
-			return reference;
-		}
-
-		/**
-		 * @return the distance
-		 * @see #distance
-		 */
-		public double getDistance() {
-			return distance;
-		}
-
-		/**
-		 * @return the size
-		 * @see #size
-		 */
-		public double getSize() {
-			return size;
-		}
-	}
-
-	/**
-	 * Object containing autocomplete lists for models. For every model the map
-	 * between String and List is stored. The key in this map is incomplete typed
-	 * word, and value list contains suggestions that should appear for this word.
-	 */
-	private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<Model, Map<String, List<String>>>();
-
-	@Override
-	public List<String> getAutocompleteList(Model model, String query) {
-		Map<String, List<String>> autoCompleteMap = autoCompleteLists.get(model);
-		if (autoCompleteMap == null) {
-			autoCompleteMap = createAutocompleteMap(model);
-			autoCompleteLists.put(model, autoCompleteMap);
-		}
-		List<String> result = autoCompleteMap.get(query.toLowerCase().trim());
-		if (result == null) {
-			result = new ArrayList<String>();
-		}
-		return result;
-	}
-
-	/**
-	 * Creates autocomplete map for a model. The key in this map is incomplete
-	 * typed word, and value list contains suggestions that should appear for this
-	 * word.
-	 * 
-	 * @param model
-	 *          model for which the autocomplete map is created
-	 * @return autocomplete map for a model. The key in this map is incomplete
-	 *         typed word, and value list contains suggestions that should appear
-	 *         for this word.
-	 */
-	private Map<String, List<String>> createAutocompleteMap(Model model) {
-		Map<String, List<String>> result = new HashMap<String, List<String>>();
-
-		String[] sortedPossibilites = getSuggestedQueryList(model);
-		for (int i = 0; i < sortedPossibilites.length; i++) {
-			String mainString = sortedPossibilites[i];
-			for (int j = 0; j < mainString.length(); j++) {
-				String substring = mainString.substring(0, j + 1);
-				if (result.get(substring) != null) {
-					continue;
-				}
-
-				List<String> list = new ArrayList<String>();
-				for (int k = 0; k < Configuration.getAutocompleteSize(); k++) {
-					if (k + i >= sortedPossibilites.length) {
-						break;
-					} else if (sortedPossibilites[k + i].startsWith(substring)) {
-						list.add(sortedPossibilites[k + i]);
-					}
-				}
-
-				// by default, the selection in autocomplete is set on the first
-				// element, so if the first element is not equals to the query then add
-				// the element
-				if (!list.get(0).equalsIgnoreCase(substring)) {
-					list.add(0, substring);
-				}
-
-				result.put(substring, list);
-			}
-		}
-		return result;
-	}
-
-	@Override
-	public String[] getSuggestedQueryList(Model model) {
-		Set<String> possibilities = new HashSet<String>();
-		for (Element alias : model.getElements()) {
-			if (alias instanceof Species) {
-				possibilities.addAll(getSearchPossibilitiesForAlias(alias));
-			}
-		}
-		for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
-			for (Element alias : connection.getSubmodel().getModel().getElements()) {
-				if (alias instanceof Species) {
-					possibilities.addAll(getSearchPossibilitiesForAlias(alias));
-				}
-			}
-		}
-		String[] sortedPossibilites = new String[possibilities.size()];
-		int index = 0;
-		for (String string : possibilities) {
-			sortedPossibilites[index++] = string;
-		}
-		Arrays.sort(sortedPossibilites);
-		return sortedPossibilites;
-	}
-
-	/**
-	 * Returns the list of all human readable search possibilities for alias.
-	 * 
-	 * @param element
-	 *          object for which we look for a list of searchable strings
-	 * @return the list of all human readable search possibilities for alias
-	 */
-	private List<String> getSearchPossibilitiesForAlias(Element element) {
-		List<String> result = new ArrayList<String>();
-		result.add(element.getName().trim().toLowerCase().replace(",", ""));
-		for (String string : element.getSynonyms()) {
-			result.add(string.trim().toLowerCase().replace(",", ""));
-		}
-		for (String string : element.getFormerSymbols()) {
-			result.add(string.trim().toLowerCase().replace(",", ""));
-		}
-		String name = element.getFullName();
-		if (name != null) {
-			result.add(name.trim().toLowerCase().replace(",", ""));
-		}
-		return result;
-	}
-
-	/**
-	 * @return the modelDao
-	 */
-	public ModelDao getModelDao() {
-		return modelDao;
-	}
-
-	/**
-	 * @param modelDao
-	 *          the modelDao to set
-	 */
-	public void setModelDao(ModelDao modelDao) {
-		this.modelDao = modelDao;
-	}
-
-	/**
-	 * @return the searchHistoryService
-	 */
-	public ISearchHistoryService getSearchHistoryService() {
-		return searchHistoryService;
-	}
-
-	/**
-	 * @param searchHistoryService
-	 *          the searchHistoryService to set
-	 */
-	public void setSearchHistoryService(ISearchHistoryService searchHistoryService) {
-		this.searchHistoryService = searchHistoryService;
-	}
-
-	@Override
-	public void assignIcons(SearchElementResult results, int iconSet) {
-		int iconId = 0;
-		for (IHeavyView result : results.getElements()) {
-			if (result instanceof FullAliasView) {
-				((FullAliasView) result).setIcon(IconManager.getInstance().getIconForIndex(iconId++, IconType.SEARCH, iconSet));
-			} else if (result instanceof FullReactionView) {
-				continue;
-			} else {
-				throw new InvalidArgumentException("Unknown element of the result list: " + result.getClass());
-			}
-		}
-	}
-
-	@Override
-	public List<Object> searchByQuery(Model model, String query, int limit, Boolean perfectMatch) {
-		SearchElementResult resultElement = searchByQuery(model, query, limit, perfectMatch, null);
-		List<Object> result = new ArrayList<>();
-		for (IHeavyView view : resultElement.getElements()) {
-			if (view instanceof FullAliasView) {
-				FullAliasView elementView = (FullAliasView) view;
-				Element element = model.getSubmodelById(elementView.getModelId()).getElementByDbId(Integer.valueOf(elementView.getIdObject()));
-				result.add(element);
-			} else if (view instanceof FullReactionView) {
-				FullReactionView reactionView = (FullReactionView) view;
-				Reaction element = model.getSubmodelById(reactionView.getModelId()).getReactionByDbId(Integer.valueOf(reactionView.getIdObject()));
-				result.add(element);
-			}
-		}
-		return result;
-	}
+  private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
+  /**
+   * Prefix used in search by name interface to limit results only to species.
+   */
+  public static final String SPECIES_SEARCH_PREFIX = "species";
+
+  /**
+   * Prefix used in search by name interface to limit results only to reactions.
+   */
+  public static final String REACTION_SEARCH_PREFIX = "reaction";
+
+  /**
+   * Prefix used in search by name interface to limit results only to
+   * {@link Element}.
+   */
+  private static final String ELEMENT_SEARCH_PREFIX = "element";
+
+  /**
+   * Default class logger.
+   */
+  @SuppressWarnings("unused")
+  private static Logger logger = Logger.getLogger(SearchService.class.getName());
+
+  /**
+   * Data access object for models.
+   */
+  @Autowired
+  private ModelDao modelDao;
+
+  /**
+   * Service used for managing search history.
+   */
+  @Autowired
+  private ISearchHistoryService searchHistoryService;
+
+  /**
+   * Factory object used to create {@link FullAliasView} objects.
+   */
+  @Autowired
+  private FullAliasViewFactory fullAliasViewFactory;
+
+  /**
+   * Factory object used to create {@link FullReactionView} objects.
+   */
+  @Autowired
+  private FullReactionViewFactory fullReactionViewFactory;
+
+  /**
+   * Object used for indexing elements on the map.
+   */
+  private SearchIndexer searchIndexer = new SearchIndexer();
+
+  /**
+   * This object maps class of elements on the map into short string prefixes used
+   * in the search query. For instance elements of the {@link Complex} class could
+   * be searched with the prefix "complex" (example query: "complex:alpha
+   * subcomplex").
+   */
+  private Map<Class<? extends Element>, String> speciesSearchPrefix = new HashMap<>();
+
+  /**
+   * This object maps short string prefixes into class of elements on the map that
+   * will be searched. For instance prefix "complex" might refer to
+   * {@link Complex} class and and example query would look like: "complex:alpha
+   * subcomplex".
+   */
+  private Map<String, Class<? extends Element>> speciesSearchReversePrefix = new HashMap<>();
+
+  /**
+   * Default constructor that set list of prefixes used in the search queries.
+   */
+  public SearchService() {
+    addSearchPrefix("complex", Complex.class);
+    addSearchPrefix("degrded", Degraded.class);
+    addSearchPrefix("drug", Drug.class);
+    addSearchPrefix("gene", Gene.class);
+    addSearchPrefix("ion", Ion.class);
+    addSearchPrefix("phenotype", Phenotype.class);
+    addSearchPrefix("protein", Protein.class);
+    addSearchPrefix("rna", Rna.class);
+    addSearchPrefix("molecule", SimpleMolecule.class);
+    addSearchPrefix("unknown", Unknown.class);
+  }
+
+  /**
+   * Adds search prefix for an element class.
+   * 
+   * @param prefix
+   *          string prefix used in search queries
+   * @param clazz
+   *          class for which this prefix stands
+   */
+  private void addSearchPrefix(String prefix, Class<? extends Element> clazz) {
+    speciesSearchPrefix.put(clazz, prefix);
+    speciesSearchReversePrefix.put(prefix, clazz);
+  }
+
+  /**
+   * Private class that defines internal search result element. Contains reference
+   * to original result and match score of the result.
+   * 
+   * @author Piotr Gawron
+   * 
+   */
+  private class SearchResult implements Comparable<SearchResult> {
+    /**
+     * Reference to the original object.
+     */
+    private BioEntity obj;
+
+    /**
+     * Score of the result.
+     */
+    private double score;
+
+    @Override
+    public int compareTo(SearchResult o) {
+      if (score == o.getScore()) {
+        return obj.getId() - o.getObj().getId();
+      } else if (score < o.getScore()) {
+        return 1;
+      } else {
+        return -1;
+      }
+    }
+
+    /**
+     * @return the obj
+     */
+    public BioEntity getObj() {
+      return obj;
+    }
+
+    /**
+     * @param obj
+     *          the obj to set
+     */
+    public void setObj(BioEntity obj) {
+      this.obj = obj;
+    }
+
+    /**
+     * @return the score
+     */
+    public double getScore() {
+      return score;
+    }
+
+    /**
+     * @param score
+     *          the score to set
+     */
+    public void setScore(double score) {
+      this.score = score;
+    }
+  };
+
+  /**
+   * Return the list of elements that match the query (sorted by match score)
+   * limited to the element of class defined by type.
+   * 
+   * @param model
+   *          model where the search is performed
+   * @param query
+   *          query string
+   * @param limit
+   *          maximum number of elements that can be returned by the search engine
+   * @param perfectMatch
+   *          should only perfect match be allowed
+   * @param type
+   *          class type of the elements that limits the results
+   * @return list of object found for the query string sorted by the score value
+   */
+  protected List<BioEntity> searchByIndexedQuery(Model model, String query, int limit, Boolean perfectMatch,
+      Class<? extends Element> type) {
+    List<BioEntity> result = new ArrayList<>();
+    if (query.startsWith(REACTION_SEARCH_PREFIX)) {
+      return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
+    } else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
+      result.add(model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, "")));
+    } else if (query.startsWith(ELEMENT_SEARCH_PREFIX)) {
+      return getElementById(model, query.replaceFirst(ELEMENT_SEARCH_PREFIX, "").toLowerCase());
+    } else {
+      Set<Element> aliases = model.getElements();
+
+      List<SearchResult> sortedResults = new ArrayList<>();
+      for (Element alias : aliases) {
+        if (type.isAssignableFrom(alias.getClass())) {
+          List<SearchIndex> indexes = alias.getSearchIndexes();
+          if (indexes.size() == 0) {
+            indexes = searchIndexer.createIndexForAlias(alias);
+            alias.setSearchIndexes(indexes);
+          }
+          for (SearchIndex searchIndex : indexes) {
+            double score = searchIndexer.match(query, searchIndex);
+            if (perfectMatch != null && perfectMatch) {
+              if (query.equals(searchIndex.getValue())) {
+                SearchResult sResult = new SearchResult();
+                sResult.setObj(alias);
+                sResult.setScore(1);
+                sortedResults.add(sResult);
+                break;
+              }
+            } else if (score > 0 || (query.equals("") && type != Element.class)) {
+              SearchResult sResult = new SearchResult();
+              sResult.setObj(alias);
+              sResult.setScore(score);
+              if (score == 0) {
+                sResult.setScore(alias.getId());
+              }
+              sortedResults.add(sResult);
+              break;
+            }
+          }
+        }
+        if (result.size() >= limit) {
+          break;
+
+        }
+      }
+      Collections.sort(sortedResults);
+      for (SearchResult searchResult : sortedResults) {
+        if (searchResult.getObj() instanceof Reaction) {
+          result.add(searchResult.getObj());
+        } else if (searchResult.getObj() instanceof Element) {
+          result.add(searchResult.getObj());
+        } else {
+          throw new InvalidStateException("Unknown class type: " + searchResult.getObj().getClass());
+        }
+        if (result.size() >= limit) {
+          break;
+        }
+      }
+    }
+    return result;
+  }
+
+  /**
+   * Returns list with the reaction with a given id. If reaction with such id
+   * doesn't exist then empty list is returned.
+   * 
+   * @param model
+   *          where the search is performed
+   * @param reactionId
+   *          id of the reaction
+   * @return list that contains reaction with given id (or empty list if such
+   *         reaction doesn't exist)
+   */
+  private List<BioEntity> getReactionById(Model model, String reactionId) {
+    Set<Reaction> reactions = model.getReactions();
+    for (Reaction reaction : reactions) {
+      if (searchIndexer.getQueryStringForIndex(reaction.getIdReaction().toLowerCase(), new ArrayList<>())
+          .equals(reactionId)) {
+        return reactionToResultList(reaction);
+      }
+      if (Integer.toString(reaction.getId()).equals(reactionId)) {
+        return reactionToResultList(reaction);
+      }
+    }
+    return new ArrayList<>();
+  }
+
+  /**
+   * Returns list with the element with a given id. If element with such id
+   * doesn't exist then empty list is returned.
+   * 
+   * @param topModel
+   *          where the search is performed
+   * @param elementId
+   *          id of the element
+   * @return list that contains element with given id (or empty list if such
+   *         element doesn't exist)
+   */
+  private List<BioEntity> getElementById(Model topModel, String elementId) {
+    List<BioEntity> result = new ArrayList<>();
+
+    Set<Model> models = new HashSet<>();
+    models.add(topModel);
+    models.addAll(topModel.getSubmodels());
+    for (Model model : models) {
+      for (Element element : model.getElements()) {
+        if (searchIndexer.getQueryStringForIndex(element.getElementId().toLowerCase(), new ArrayList<>())
+            .equals(elementId)) {
+          result.add(element);
+        } else if (Integer.toString(element.getId()).equals(elementId)) {
+          result.add(element);
+        }
+      }
+    }
+    return result;
+  }
+
+  /**
+   * Transform {@link Reaction} into set of result entries.
+   * 
+   * @param reaction
+   *          reaction to be transformed
+   * @return set of result entries for all element of the {@link Reaction}
+   */
+  private List<BioEntity> reactionToResultList(Reaction reaction) {
+    List<BioEntity> result = new ArrayList<>();
+    result.add(reaction);
+    for (ReactionNode node : reaction.getReactionNodes()) {
+      result.add(node.getElement());
+    }
+    return result;
+  }
+
+  @Override
+  public SearchElementResult searchByCoordinates(CoordinatesSearchParams params) {
+    SearchElementResult result = new SearchElementResult("");
+    boolean nested = params.isNested();
+
+    List<Object> results = new ArrayList<Object>();
+
+    Set<Element> aliases = params.getModel().getElements();
+    Point2D point = new Point2D.Double(params.getX(), params.getY());
+    for (Element alias : aliases) {
+      if (alias instanceof Species) {
+        if (alias.contains(point)) {
+          if (isVisible(alias, params)) {
+            results.add(alias);
+          }
+        }
+      }
+    }
+    double dist = params.getDistance();
+    if (results.size() == 0) {
+      Reaction r = null;
+      Set<Reaction> reactions = params.getModel().getReactions();
+      for (Reaction reaction : reactions) {
+        double newDist = reaction.getDistanceFromPoint(point);
+        if (newDist < dist) {
+          if (isVisible(reaction, params)) {
+            r = reaction;
+            dist = reaction.getDistanceFromPoint(point);
+          }
+        }
+      }
+      if (r != null) {
+        result.addAll(reactionToResultList(r));
+        return result;
+      } else if (nested) {
+        for (Element alias : aliases) {
+          if (alias instanceof Compartment) {
+            if (alias.contains(point)) {
+              if (isVisible(alias, params)) {
+                results.add(alias);
+              }
+            }
+          }
+        }
+      }
+    }
+
+    if (results.size() > 1) {
+      Element alias = (Element) results.get(0);
+      for (Object obj : results) {
+        if (((Element) (obj)).getSize() < alias.getSize()) {
+          alias = (Element) obj;
+        }
+      }
+      results.clear();
+      results.add(alias);
+    }
+    if (results.size() == 0) {
+      return result;
+    } else {
+      Object obj = results.get(0);
+      if (obj instanceof Element) {
+        result.add((BioEntity) obj);
+        return result;
+      } else if (obj instanceof Reaction) {
+        result.addAll(reactionToResultList((Reaction) obj));
+        return result;
+      } else {
+        throw new InvalidStateException("Unknown class type: " + obj.getClass());
+      }
+    }
+  }
+
+  /**
+   * Check if reaction is visible for the user. Reaction is visible when at least
+   * one node of the reaction is visible.
+   * 
+   * @param reaction
+   *          which reaction is tested
+   * @param params
+   *          params that determines the client search environment (zoom level,
+   *          type of the layout)
+   * @return <code>true</code> if reaction is visible for the user,
+   *         <code>false</code> otherwise
+   */
+  private boolean isVisible(Reaction reaction, CoordinatesSearchParams params) {
+    if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
+      return true;
+    }
+    if (!params.isNested()) {
+      return true;
+    }
+    for (ReactionNode node : reaction.getReactionNodes()) {
+      if (isVisible(node.getElement(), params)) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Checks if alias is visible for the user. Alias is invisible when the search
+   * is performed on the hierarchical layout and the alias is hidden by the
+   * complex or compartment.
+   * 
+   * @param alias
+   *          alias to be checked for visibility
+   * @param params
+   *          that determines the client search environment (zoom level, type of
+   *          the layout)
+   * @return <code>true</code> if alias is visible for the user,
+   *         <code>false</code> otherwise
+   */
+  private boolean isVisible(Element alias, CoordinatesSearchParams params) {
+    if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
+      return true;
+    }
+    return (!params.isNested()) || zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel());
+  }
+
+  @Override
+  public SearchElementResult searchByQuery(Model model, String query, int limit, Boolean perfectMatch,
+      String ipAddress) {
+    query = query.toLowerCase();
+    SearchElementResult result = new SearchElementResult(query);
+    if (query == null) {
+      throw new InvalidArgumentException("Invalid query: null");
+    }
+
+    MiriamData mt = getMiriamTypeForQuery(query);
+    if (mt != null) {
+      result.addAll(searchByMiriam(model, mt, limit));
+    } else {
+      String indexQuery = searchIndexer.getQueryStringForIndex(query, speciesSearchReversePrefix.keySet());
+      Class<? extends Element> type = searchIndexer.getTypeForQuery(query, speciesSearchReversePrefix);
+
+      List<BioEntity> partResult = searchByIndexedQuery(model, indexQuery, limit, perfectMatch, type);
+
+      for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+        partResult.addAll(searchByIndexedQuery(connection.getSubmodel().getModel(), indexQuery,
+            limit - partResult.size(), perfectMatch, type));
+        if (partResult.size() >= limit) {
+          break;
+        }
+      }
+
+      result.addAll(partResult);
+    }
+    if (model.getProject() != null && ipAddress != null) {
+      searchHistoryService.addQuery(query, SearchType.GENERAL, ipAddress, model.getProject().getProjectId());
+    }
+    return result;
+  }
+
+  /**
+   * Returns elements that are annotated with the given miriam data.
+   * 
+   * @param topModel
+   *          model where elements are looked for
+   * @param md
+   *          miriam annotation to identify interesting elements
+   * @param limit
+   *          max number of elements to find
+   * @return elements that are annotated with the given miriam data
+   */
+  private List<BioEntity> searchByMiriam(Model topModel, MiriamData md, int limit) {
+    List<BioEntity> result = new ArrayList<>();
+    Set<Model> models = new HashSet<>();
+    models.add(topModel);
+    models.addAll(topModel.getSubmodels());
+    List<BioEntity> elements = new ArrayList<>();
+    for (Model model : models) {
+      elements.addAll(model.getElementsByAnnotation(md));
+    }
+    elements.sort(BioEntity.ID_COMPARATOR);
+    for (BioEntity obj : elements) {
+      if (result.size() >= limit) {
+        break;
+      }
+      if (obj instanceof Element) {
+        result.add((Element) obj);
+      } else if (obj instanceof Reaction) {
+        result.addAll(reactionToResultList((Reaction) obj));
+      } else {
+        throw new InvalidClassException("Unknown class: " + obj.getClass());
+      }
+    }
+    return result;
+  }
+
+  /**
+   * Tries to transform query into {@link MiriamData}.
+   * 
+   * @param string
+   *          query to transform
+   * @return {@link MiriamData} that described query or null if query cannot be
+   *         converted
+   */
+  protected MiriamData getMiriamTypeForQuery(String string) {
+    for (MiriamType mt : MiriamType.values()) {
+      if (string.startsWith(mt.toString().toLowerCase() + ":")) {
+        return new MiriamData(mt, string.substring(mt.toString().length() + 1));
+      }
+    }
+    return null;
+  }
+
+  @Override
+  public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
+    List<BioEntity> result = new ArrayList<>();
+
+    // probably this could be improved algorithmitically, right now all objects
+    // are sorted by distance, and numberOfElements closest are chosen as a list
+    // of results
+    List<DistanceToObject> tmpList = new ArrayList<>();
+    for (Reaction reaction : model.getReactions()) {
+      tmpList.add(new DistanceToObject(reaction, point));
+    }
+    for (Element alias : model.getElements()) {
+      if (alias instanceof Species) {
+        tmpList.add(new DistanceToObject(alias, point));
+      }
+    }
+    Collections.sort(tmpList);
+    int size = Math.min(tmpList.size(), numberOfElements);
+    for (int i = 0; i < size; i++) {
+      if (!perfectHit) {
+        result.add(tmpList.get(i).getReference());
+      } else if (tmpList.get(i).getDistance() < Configuration.EPSILON) {
+        result.add(tmpList.get(i).getReference());
+      }
+    }
+    return result;
+  }
+
+  /**
+   * This class represents distance between object and some point. It's designed
+   * to help sort objects by their distance to some point. It It contains two
+   * fields: object reference and distance.
+   * 
+   * @author Piotr Gawron
+   * 
+   */
+  private class DistanceToObject implements Comparable<DistanceToObject> {
+    /**
+     * Reference to the object.
+     */
+    private BioEntity reference;
+
+    /**
+     * Distance between the object and some point.
+     */
+    private double distance;
+
+    /**
+     * Size of the object.
+     */
+    private double size;
+
+    /**
+     * Constructor for reaction objects.
+     * 
+     * @param reaction
+     *          reaction reference to store
+     * @param point
+     *          point from which the distance will be computed
+     */
+    DistanceToObject(Reaction reaction, Point2D point) {
+      reference = reaction;
+      distance = reaction.getDistanceFromPoint(point);
+      size = 0;
+    }
+
+    /**
+     * Constructor for alias objects.
+     * 
+     * @param alias
+     *          alias reference to store
+     * @param point
+     *          point from which the distance will be computed
+     */
+    DistanceToObject(Element alias, Point2D point) {
+      reference = alias;
+      distance = alias.getDistanceFromPoint(point);
+      size = alias.getSize();
+
+    }
+
+    @Override
+    public int compareTo(DistanceToObject arg0) {
+      if (arg0.getDistance() < getDistance()) {
+        return 1;
+      } else if (arg0.getDistance() > getDistance()) {
+        return -1;
+      } else {
+        if (arg0.getSize() < getSize()) {
+          return 1;
+        } else if (arg0.getSize() > getSize()) {
+          return -1;
+        } else {
+          return 0;
+        }
+      }
+    }
+
+    /**
+     * @return the reference
+     * @see #reference
+     */
+    public BioEntity getReference() {
+      return reference;
+    }
+
+    /**
+     * @return the distance
+     * @see #distance
+     */
+    public double getDistance() {
+      return distance;
+    }
+
+    /**
+     * @return the size
+     * @see #size
+     */
+    public double getSize() {
+      return size;
+    }
+  }
+
+  /**
+   * Object containing autocomplete lists for models. For every model the map
+   * between String and List is stored. The key in this map is incomplete typed
+   * word, and value list contains suggestions that should appear for this word.
+   */
+  private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<Model, Map<String, List<String>>>();
+
+  @Override
+  public List<String> getAutocompleteList(Model model, String query) {
+    Map<String, List<String>> autoCompleteMap = autoCompleteLists.get(model);
+    if (autoCompleteMap == null) {
+      autoCompleteMap = createAutocompleteMap(model);
+      autoCompleteLists.put(model, autoCompleteMap);
+    }
+    List<String> result = autoCompleteMap.get(query.toLowerCase().trim());
+    if (result == null) {
+      result = new ArrayList<String>();
+    }
+    return result;
+  }
+
+  /**
+   * Creates autocomplete map for a model. The key in this map is incomplete typed
+   * word, and value list contains suggestions that should appear for this word.
+   * 
+   * @param model
+   *          model for which the autocomplete map is created
+   * @return autocomplete map for a model. The key in this map is incomplete typed
+   *         word, and value list contains suggestions that should appear for this
+   *         word.
+   */
+  private Map<String, List<String>> createAutocompleteMap(Model model) {
+    Map<String, List<String>> result = new HashMap<String, List<String>>();
+
+    String[] sortedPossibilites = getSuggestedQueryList(model);
+    for (int i = 0; i < sortedPossibilites.length; i++) {
+      String mainString = sortedPossibilites[i];
+      for (int j = 0; j < mainString.length(); j++) {
+        String substring = mainString.substring(0, j + 1);
+        if (result.get(substring) != null) {
+          continue;
+        }
+
+        List<String> list = new ArrayList<String>();
+        for (int k = 0; k < Configuration.getAutocompleteSize(); k++) {
+          if (k + i >= sortedPossibilites.length) {
+            break;
+          } else if (sortedPossibilites[k + i].startsWith(substring)) {
+            list.add(sortedPossibilites[k + i]);
+          }
+        }
+
+        // by default, the selection in autocomplete is set on the first
+        // element, so if the first element is not equals to the query then add
+        // the element
+        if (!list.get(0).equalsIgnoreCase(substring)) {
+          list.add(0, substring);
+        }
+
+        result.put(substring, list);
+      }
+    }
+    return result;
+  }
+
+  @Override
+  public String[] getSuggestedQueryList(Model model) {
+    Set<String> possibilities = new HashSet<String>();
+    for (Element alias : model.getElements()) {
+      if (alias instanceof Species) {
+        possibilities.addAll(getSearchPossibilitiesForAlias(alias));
+      }
+    }
+    for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+      for (Element alias : connection.getSubmodel().getModel().getElements()) {
+        if (alias instanceof Species) {
+          possibilities.addAll(getSearchPossibilitiesForAlias(alias));
+        }
+      }
+    }
+    String[] sortedPossibilites = new String[possibilities.size()];
+    int index = 0;
+    for (String string : possibilities) {
+      sortedPossibilites[index++] = string;
+    }
+    Arrays.sort(sortedPossibilites);
+    return sortedPossibilites;
+  }
+
+  /**
+   * Returns the list of all human readable search possibilities for alias.
+   * 
+   * @param element
+   *          object for which we look for a list of searchable strings
+   * @return the list of all human readable search possibilities for alias
+   */
+  private List<String> getSearchPossibilitiesForAlias(Element element) {
+    List<String> result = new ArrayList<String>();
+    result.add(element.getName().trim().toLowerCase().replace(",", ""));
+    for (String string : element.getSynonyms()) {
+      result.add(string.trim().toLowerCase().replace(",", ""));
+    }
+    for (String string : element.getFormerSymbols()) {
+      result.add(string.trim().toLowerCase().replace(",", ""));
+    }
+    String name = element.getFullName();
+    if (name != null) {
+      result.add(name.trim().toLowerCase().replace(",", ""));
+    }
+    return result;
+  }
+
+  /**
+   * @return the modelDao
+   */
+  public ModelDao getModelDao() {
+    return modelDao;
+  }
+
+  /**
+   * @param modelDao
+   *          the modelDao to set
+   */
+  public void setModelDao(ModelDao modelDao) {
+    this.modelDao = modelDao;
+  }
+
+  /**
+   * @return the searchHistoryService
+   */
+  public ISearchHistoryService getSearchHistoryService() {
+    return searchHistoryService;
+  }
+
+  /**
+   * @param searchHistoryService
+   *          the searchHistoryService to set
+   */
+  public void setSearchHistoryService(ISearchHistoryService searchHistoryService) {
+    this.searchHistoryService = searchHistoryService;
+  }
+
+  @Override
+  public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch) {
+    SearchElementResult resultElement = searchByQuery(model, query, limit, perfectMatch, null);
+    return resultElement.getElements();
+  }
 
 }
\ No newline at end of file
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
index 4b2c24e810..8ee8ed38a7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -8,7 +8,6 @@ import java.util.List;
 import java.util.Map;
 
 import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.model.map.layout.ColorSchema;
 import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
 import lcsb.mapviewer.model.map.layout.Layout;
@@ -21,7 +20,6 @@ import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
 import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
 import lcsb.mapviewer.services.utils.EmailSender;
 import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-import lcsb.mapviewer.services.view.LayoutView;
 
 /**
  * Service that manages layouts of the map.
@@ -308,27 +306,7 @@ public interface ILayoutService {
    * @return <code>true</code> if user can remove layout, <code>false</code>
    *         otherwise
    */
-  boolean userCanRemoveLayout(LayoutView layout, User user);
-
-  /**
-   * Returns list of custom layouts.
-   * 
-   * @param model
-   *          model where the layouts lay on
-   * @param user
-   *          user who asks for the layouts
-   * @return list of custom layouts
-   */
-  List<LayoutView> getCustomLayouts(Model model, User user, Boolean publicOverlay, User creator);
-
-  /**
-   * Returns list of general publicly available layouts.
-   * 
-   * @param model
-   *          model where the layouts lay on
-   * @return list of custom layouts
-   */
-  List<LayoutView> getGeneralLayouts(Model model);
+  boolean userCanRemoveLayout(Layout layout, User user);
 
   /**
    * Removes layout from the system.
@@ -340,7 +318,7 @@ public interface ILayoutService {
    * @throws IOException
    *           thrown when there are problems with removing layout files
    */
-  void removeLayout(LayoutView layout, String homeDir) throws IOException;
+  void removeLayout(Layout layout, String homeDir) throws IOException;
 
   /**
    * Updates data about the layout.
@@ -348,7 +326,7 @@ public interface ILayoutService {
    * @param layout
    *          layout to update
    */
-  void updateLayout(LayoutView layout);
+  void updateLayout(Layout layout);
 
   /**
    * Adds view privilege to the layout for the user.
@@ -358,7 +336,7 @@ public interface ILayoutService {
    * @param user
    *          who should own the privilege
    */
-  void addViewPrivilegeToLayout(LayoutView layout, User user);
+  void addViewPrivilegeToLayout(Layout layout, User user);
 
   /**
    * Removes view privilege to the layout from the user.
@@ -368,7 +346,7 @@ public interface ILayoutService {
    * @param user
    *          who shouldn't have the privilege
    */
-  void dropViewPrivilegeFromLayout(LayoutView layout, User user);
+  void dropViewPrivilegeFromLayout(Layout layout, User user);
 
   /**
    * Create layout based on the data in the parameter.
@@ -382,7 +360,7 @@ public interface ILayoutService {
    *           if the coloring source is invalid
    * @throws CommandExecutionException
    */
-  LayoutView createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException;
+  Layout createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException;
 
   /**
    * Create layout based on the data in the parameter. Layout will contain set of
@@ -398,7 +376,7 @@ public interface ILayoutService {
    * @throws InvalidColorSchemaException
    *           if the coloring source is invalid
    */
-  LayoutView createLayoutWithImages(CreateLayoutParams params)
+  Layout createLayoutWithImages(CreateLayoutParams params)
       throws IOException, CommandExecutionException, InvalidColorSchemaException;
 
   /**
@@ -411,29 +389,6 @@ public interface ILayoutService {
    */
   long getAvailableCustomLayoutsNumber(User user);
 
-  /**
-   * Returns layout identified by name and model.
-   * 
-   * @param model
-   *          model where the layouts lay on
-   * @param name
-   *          name of the layout
-   * @return layout
-   */
-  LayoutView getLayoutByName(Model model, String name);
-
-  /**
-   * Returns byte array containing data from original input file that was used to
-   * generate the layout.
-   * 
-   * @param layout
-   *          layout for which we want to retrieve original file data
-   * @return original data file for given layout, if such file is not stored in
-   *         database (compatibility reasons) then null is returned
-   * @throws SecurityException
-   */
-  byte[] getInputDataForLayout(LayoutView layout, String token) throws SecurityException;
-
   /**
    * Returns a list of {@link LightLayoutAliasView aliases} that are visualized in
    * a {@link lcsb.mapviewer.model.map.layout.Layout}.
@@ -469,7 +424,7 @@ public interface ILayoutService {
    * parameter.
    * 
    * @param model
-   *          model where data is lcoated
+   *          model where data is located
    * @param layoutId
    *          identifier of the layout
    * @return a list of {@link LightLayoutReactionView reactions} that are
@@ -478,27 +433,6 @@ public interface ILayoutService {
    */
   Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, String token) throws SecurityException;
 
-  /**
-   * Returns a list of {@link FullLayoutAliasView aliases} that are visualized in
-   * a {@link lcsb.mapviewer.model.map.layout.Layout} and have given identifiers.
-   * 
-   * @param model
-   *          model where data is located
-   * @param layoutId
-   *          identifier of the layout
-   * @param identifiers
-   *          list of alias identifiers in a given submodel. Every {@link Pair}
-   *          contains information about {@link Model#getId() model identifier}
-   *          (in {@link Pair#left}) and
-   *          {@link lcsb.mapviewer.model.map.species.Element#getId() alias
-   *          identifier} (in {@link Pair#right}).
-   * @return a list of {@link LightLayoutAliasView aliases} that are visualized in
-   *         a {@link lcsb.mapviewer.model.map.layout.Layout}
-   * @throws SecurityException
-   */
-  List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers,
-      int layoutId, String token) throws SecurityException;
-
   FullLayoutAliasView getFullAliasForLayout(Model model, Integer id, int layoutId, String token)
       throws SecurityException;
 
@@ -520,13 +454,20 @@ public interface ILayoutService {
    */
   void setEmailSender(EmailSender emailSender);
 
-  List<LayoutView> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator)
+  /**
+   * Returns list of custom layouts.
+   * 
+   * @param model
+   *          model where the layouts lay on
+   * @param user
+   *          user who asks for the layouts
+   * @return list of custom layouts
+   */
+  List<Layout> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator)
       throws SecurityException;
 
-  LayoutView getLayoutById(int overlayId, String token) throws SecurityException;
-
-  Layout getLayoutDataById(int overlayId, String authenticationToken) throws SecurityException;
+  Layout getLayoutById(int overlayId, String token) throws SecurityException;
 
-  boolean userCanRemoveLayout(LayoutView layout, String authenticationToken) throws SecurityException;
+  boolean userCanRemoveLayout(Layout layout, String authenticationToken) throws SecurityException;
 
 }
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
index 08d53f7a87..f1369c3088 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
@@ -283,7 +283,7 @@ public interface ISearchService {
 	 */
 	SearchElementResult searchByQuery(Model model, String query, int limit, Boolean perfectMatch, String ipAddress);
 
-	List<Object> searchByQuery(Model model, String query, int limit, Boolean perfectMatch);
+	List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch);
 
 	/**
 	 * Returns the closest elements to the coordinates on the model.
@@ -309,17 +309,6 @@ public interface ISearchService {
 	 */
 	List<String> getAutocompleteList(Model model, String query);
 
-	/**
-	 * Assign icons to elements in {@link SearchElementResult search result}.
-	 * 
-	 * @param results
-	 *          search result to be modified
-	 * @param iconSet
-	 *          icon set to be used
-	 * @see lcsb.mapviewer.services.overlay.IconManager
-	 */
-	void assignIcons(SearchElementResult results, int iconSet);
-
 	String[] getSuggestedQueryList(Model model);
 
 }
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/ElementView.java b/service/src/main/java/lcsb/mapviewer/services/search/ElementView.java
index d721fbce28..515a8ec1e1 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementView.java
@@ -1,9 +1,10 @@
 package lcsb.mapviewer.services.search;
 
 import java.io.Serializable;
+import java.util.Comparator;
 
 /**
- * Abstract view of objects. Contains only identificator of element. Subclasses
+ * Abstract view of objects. Contains only identifier of element. Subclasses
  * contain additional (partial) information that should be send to the client
  * side.
  * 
@@ -12,114 +13,122 @@ import java.io.Serializable;
  */
 public abstract class ElementView implements Serializable {
 
-	/**
-	 * 
-	 */
-	private static final long	serialVersionUID = 1L;
-
-	/**
-	 * Identifier of the {@link lcsb.mapviewer.model.map.model.Model} where Alias
-	 * is located.
-	 */
-	private Integer						modelId;
-
-	/**
-	 * Database identifier of the object that we pass to the bean layer.
-	 */
-	private String						idObject;
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param identifier
-	 *          unique identifier of the object ({@link #idObject})
-	 * @param modelId
-	 *          identifier of the model ({@link #modelId})
-	 * 
-	 */
-	protected ElementView(String identifier, Integer modelId) {
-		this.idObject = identifier;
-		this.modelId = modelId;
-	}
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param identifier
-	 *          unique identifier of the object ({@link #idObject})
-	 * @param modelId
-	 *          identifier of the model ({@link #modelId})
-	 * 
-	 */
-	protected ElementView(Integer identifier, Integer modelId) {
-		this.idObject = identifier + "";
-		this.modelId = modelId;
-	}
-
-	/**
-	 * Constructor that should be used only for (de)serialization.
-	 */
-	protected ElementView() {
-	}
-
-	/**
-	 * @return the modelId
-	 * @see #modelId
-	 */
-	public Integer getModelId() {
-		return modelId;
-	}
-
-	/**
-	 * @param modelId
-	 *          the modelId to set
-	 * @see #modelId
-	 */
-	public void setModelId(Integer modelId) {
-		this.modelId = modelId;
-	}
-
-	/**
-	 * @return the idObject
-	 * @see #idObject
-	 */
-	public String getIdObject() {
-		return idObject;
-	}
-
-	/**
-	 * @param idObject
-	 *          the idObject to set
-	 * @see #idObject
-	 */
-	public void setIdObject(String idObject) {
-		this.idObject = idObject;
-	}
-
-	/**
-	 * @param idObject
-	 *          the idObject to set
-	 * @see #idObject
-	 */
-	public void setIdObject(Integer idObject) {
-		this.idObject = idObject + "";
-	}
-
-	/**
-	 * @return the uniqueId
-	 * @see #uniqueId
-	 */
-	public String getUniqueId() {
-		return idObject;
-	}
-
-	/**
-	 * @param uniqueId
-	 *          the uniqueId to set
-	 * @see #uniqueId
-	 */
-	public void setUniqueId(String uniqueId) {
-		this.idObject = uniqueId;
-	}
+  public static final Comparator<? super ElementView> ID_COMPARATOR = new Comparator<ElementView>() {
+
+    @Override
+    public int compare(ElementView o1, ElementView o2) {
+      return o1.getIdObject().compareTo(o2.getIdObject());
+    }
+  };
+
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Identifier of the {@link lcsb.mapviewer.model.map.model.Model} where Alias is
+   * located.
+   */
+  private Integer modelId;
+
+  /**
+   * Database identifier of the object that we pass to the bean layer.
+   */
+  private String idObject;
+
+  /**
+   * Default constructor.
+   * 
+   * @param identifier
+   *          unique identifier of the object ({@link #idObject})
+   * @param modelId
+   *          identifier of the model ({@link #modelId})
+   * 
+   */
+  protected ElementView(String identifier, Integer modelId) {
+    this.idObject = identifier;
+    this.modelId = modelId;
+  }
+
+  /**
+   * Default constructor.
+   * 
+   * @param identifier
+   *          unique identifier of the object ({@link #idObject})
+   * @param modelId
+   *          identifier of the model ({@link #modelId})
+   * 
+   */
+  protected ElementView(Integer identifier, Integer modelId) {
+    this.idObject = identifier + "";
+    this.modelId = modelId;
+  }
+
+  /**
+   * Constructor that should be used only for (de)serialization.
+   */
+  protected ElementView() {
+  }
+
+  /**
+   * @return the modelId
+   * @see #modelId
+   */
+  public Integer getModelId() {
+    return modelId;
+  }
+
+  /**
+   * @param modelId
+   *          the modelId to set
+   * @see #modelId
+   */
+  public void setModelId(Integer modelId) {
+    this.modelId = modelId;
+  }
+
+  /**
+   * @return the idObject
+   * @see #idObject
+   */
+  public String getIdObject() {
+    return idObject;
+  }
+
+  /**
+   * @param idObject
+   *          the idObject to set
+   * @see #idObject
+   */
+  public void setIdObject(String idObject) {
+    this.idObject = idObject;
+  }
+
+  /**
+   * @param idObject
+   *          the idObject to set
+   * @see #idObject
+   */
+  public void setIdObject(Integer idObject) {
+    this.idObject = idObject + "";
+  }
+
+  /**
+   * @return the uniqueId
+   * @see #uniqueId
+   */
+  public String getUniqueId() {
+    return idObject;
+  }
+
+  /**
+   * @param uniqueId
+   *          the uniqueId to set
+   * @see #uniqueId
+   */
+  public void setUniqueId(String uniqueId) {
+    this.idObject = uniqueId;
+  }
 
 }
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/SearchElementResult.java b/service/src/main/java/lcsb/mapviewer/services/search/data/SearchElementResult.java
index 02d0129b08..ef8a63c135 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/SearchElementResult.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/SearchElementResult.java
@@ -4,6 +4,7 @@ import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.services.search.IHeavyView;
 import lcsb.mapviewer.services.search.ISearchResultView;
 
@@ -28,7 +29,7 @@ public class SearchElementResult implements Serializable, ISearchResultView {
 	/**
 	 * List of elements found as a results of the search operation.
 	 */
-	private List<IHeavyView>	elements				 = new ArrayList<>();
+	private List<BioEntity>	elements				 = new ArrayList<>();
 
 	/**
 	 * Default constructor.
@@ -73,7 +74,7 @@ public class SearchElementResult implements Serializable, ISearchResultView {
 	 * @return the elements
 	 * @see #elements
 	 */
-	public List<IHeavyView> getElements() {
+	public List<BioEntity> getElements() {
 		return elements;
 	}
 
@@ -82,7 +83,7 @@ public class SearchElementResult implements Serializable, ISearchResultView {
 	 *          the elements to set
 	 * @see #elements
 	 */
-	public void setElements(List<IHeavyView> elements) {
+	public void setElements(List<BioEntity> elements) {
 		this.elements = elements;
 	}
 
@@ -92,7 +93,7 @@ public class SearchElementResult implements Serializable, ISearchResultView {
 	 * @param results
 	 *          elements to add
 	 */
-	public void addAll(List<IHeavyView> results) {
+	public void addAll(List<BioEntity> results) {
 		elements.addAll(results);
 	}
 
@@ -102,7 +103,7 @@ public class SearchElementResult implements Serializable, ISearchResultView {
 	 * @param result
 	 *          element to add
 	 */
-	public void add(FullAliasView result) {
+	public void add(BioEntity result) {
 		elements.add(result);
 	}
 
@@ -122,7 +123,7 @@ public class SearchElementResult implements Serializable, ISearchResultView {
 	 *          index of the element to return
 	 * @return i-th element in this search result
 	 */
-	public IHeavyView get(int i) {
+	public BioEntity get(int i) {
 		return elements.get(i);
 	}
 
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchCriteria.java b/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchCriteria.java
index 99305b7331..286401ef4b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchCriteria.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchCriteria.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.services.search.db;
 import java.util.ArrayList;
 import java.util.List;
 
+import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.model.Model;
 
@@ -16,152 +17,152 @@ import lcsb.mapviewer.model.map.model.Model;
  */
 public class DbSearchCriteria {
 
-	/**
-	 * Ip address of the client that requested this search.
-	 */
-	private String					 ipAddress;
-
-	/**
-	 * Id of disease to which results should be contextualized.
-	 * 
-	 */
-	private MiriamData			 disease;
-
-	/**
-	 * Model where client is looking for the results.
-	 */
-	private Model						 model;
-
-	/**
-	 * List of organisms used for filtering results. If the list is null or empty
-	 * then filtering shouldn't be applied. Organisms must be represented as
-	 * {@link lcsb.mapviewer.model.map.MiriamType#TAXONOMY} MiriamData objects.
-	 * 
-	 */
-	private List<MiriamData> organisms = new ArrayList<>();
-
-	/**
-	 * Which set of icons should be used for representing results.
-	 * 
-	 */
-	private int							 colorSet	 = 0;
-
-	/**
-	 * @return the ipAddress
-	 * @see #ipAddress
-	 */
-	public String getIpAddress() {
-		return ipAddress;
-	}
-
-	/**
-	 * @param ipAddress
-	 *          the ipAddress to set
-	 * @see #ipAddress
-	 * @return this object after changes
-	 */
-	public DbSearchCriteria ipAddress(String ipAddress) {
-		this.ipAddress = ipAddress;
-		return this;
-	}
-
-	/**
-	 * @return the model
-	 * @see #model
-	 */
-	public Model getModel() {
-		return model;
-	}
-
-	/**
-	 * @param model
-	 *          the model to set
-	 * @see #model
-	 * @return this object after changes
-	 */
-	public DbSearchCriteria model(Model model) {
-		this.model = model;
-		return this;
-	}
-
-	/**
-	 * @return the organisms
-	 * @see #organisms
-	 */
-	public List<MiriamData> getOrganisms() {
-		return organisms;
-	}
-
-	/**
-	 * @param organisms
-	 *          the organisms to add
-	 * @see #organisms
-	 * @return this object after changes
-	 */
-	public DbSearchCriteria organisms(List<MiriamData> organisms) {
-		this.organisms.addAll(organisms);
-		return this;
-	}
-
-	/**
-	 * @return the colorSet
-	 * @see #colorSet
-	 */
-	public int getColorSet() {
-		return colorSet;
-	}
-
-	/**
-	 * @param colorSet
-	 *          the colorSet to set
-	 * @see #colorSet
-	 * @return this object after changes
-	 */
-	public DbSearchCriteria colorSet(int colorSet) {
-		this.colorSet = colorSet;
-		return this;
-	}
-
-	/**
-	 * @param organism
-	 *          the organism to add
-	 * @see #organisms
-	 * @return this object after changes
-	 */
-	public DbSearchCriteria organisms(MiriamData organism) {
-		this.organisms.add(organism);
-		return this;
-	}
-
-	/**
-	 * @param organisms
-	 *          the organisms to add
-	 * @see #organisms
-	 * @return this object after changes
-	 */
-	public DbSearchCriteria organisms(MiriamData[] organisms) {
-		for (MiriamData miriamData : organisms) {
-			this.organisms.add(miriamData);
-		}
-		return this;
-	}
-
-	/**
-	 * @return the disease
-	 * @see #disease
-	 */
-	public MiriamData getDisease() {
-		return disease;
-	}
-
-	/**
-	 * @param disease
-	 *          the disease to set
-	 * @see #disease
-	 * @return this object after changes
-	 */
-	public DbSearchCriteria disease(MiriamData disease) {
-		this.disease = disease;
-		return this;
-	}
+  /**
+   * Ip address of the client that requested this search.
+   */
+  private String ipAddress;
+
+  /**
+   * Id of disease to which results should be contextualized.
+   * 
+   */
+  private MiriamData disease;
+
+  /**
+   * Project where client is looking for the results.
+   */
+  private Project project;
+
+  /**
+   * List of organisms used for filtering results. If the list is null or empty
+   * then filtering shouldn't be applied. Organisms must be represented as
+   * {@link lcsb.mapviewer.model.map.MiriamType#TAXONOMY} MiriamData objects.
+   * 
+   */
+  private List<MiriamData> organisms = new ArrayList<>();
+
+  /**
+   * Which set of icons should be used for representing results.
+   * 
+   */
+  private int colorSet = 0;
+
+  /**
+   * @return the ipAddress
+   * @see #ipAddress
+   */
+  public String getIpAddress() {
+    return ipAddress;
+  }
+
+  /**
+   * @param ipAddress
+   *          the ipAddress to set
+   * @see #ipAddress
+   * @return this object after changes
+   */
+  public DbSearchCriteria ipAddress(String ipAddress) {
+    this.ipAddress = ipAddress;
+    return this;
+  }
+
+  /**
+   * @return the project
+   * @see #model
+   */
+  public Project getProject() {
+    return project;
+  }
+
+  /**
+   * @param project
+   *          the project to set
+   * @see #project
+   * @return this object after changes
+   */
+  public DbSearchCriteria project(Project project) {
+    this.project = project;
+    return this;
+  }
+
+  /**
+   * @return the organisms
+   * @see #organisms
+   */
+  public List<MiriamData> getOrganisms() {
+    return organisms;
+  }
+
+  /**
+   * @param organisms
+   *          the organisms to add
+   * @see #organisms
+   * @return this object after changes
+   */
+  public DbSearchCriteria organisms(List<MiriamData> organisms) {
+    this.organisms.addAll(organisms);
+    return this;
+  }
+
+  /**
+   * @return the colorSet
+   * @see #colorSet
+   */
+  public int getColorSet() {
+    return colorSet;
+  }
+
+  /**
+   * @param colorSet
+   *          the colorSet to set
+   * @see #colorSet
+   * @return this object after changes
+   */
+  public DbSearchCriteria colorSet(int colorSet) {
+    this.colorSet = colorSet;
+    return this;
+  }
+
+  /**
+   * @param organism
+   *          the organism to add
+   * @see #organisms
+   * @return this object after changes
+   */
+  public DbSearchCriteria organisms(MiriamData organism) {
+    this.organisms.add(organism);
+    return this;
+  }
+
+  /**
+   * @param organisms
+   *          the organisms to add
+   * @see #organisms
+   * @return this object after changes
+   */
+  public DbSearchCriteria organisms(MiriamData[] organisms) {
+    for (MiriamData miriamData : organisms) {
+      this.organisms.add(miriamData);
+    }
+    return this;
+  }
+
+  /**
+   * @return the disease
+   * @see #disease
+   */
+  public MiriamData getDisease() {
+    return disease;
+  }
+
+  /**
+   * @param disease
+   *          the disease to set
+   * @see #disease
+   * @return this object after changes
+   */
+  public DbSearchCriteria disease(MiriamData disease) {
+    this.disease = disease;
+    return this;
+  }
 }
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index c3217f0a99..96c39d550e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -211,14 +211,12 @@ public class DrugService extends DbSearchService implements IDrugService {
     } catch (DrugSearchException e) {
       logger.error("Problem with accessing ChEMBL parser", e);
     }
-    if (searchCriteria.getIpAddress() != null && searchCriteria.getModel() != null) {
+    if (searchCriteria.getIpAddress() != null && searchCriteria.getProject() != null) {
       searchHistoryService.addQuery(name, SearchType.GENERAL, searchCriteria.getIpAddress(),
-          searchCriteria.getModel().getProject().getProjectId());
+          searchCriteria.getProject().getProjectId());
     }
 
     return drug;
-    // return drugViewFactory.create(drug, searchCriteria.getModel(),
-    // searchCriteria.getColorSet());
   }
 
   @Override
@@ -362,13 +360,13 @@ public class DrugService extends DbSearchService implements IDrugService {
   @Override
   public List<String> getSuggestedQueryList(Project project, MiriamData organism) throws DrugSearchException {
     Set<String> resultSet = new HashSet<>();
-    for (String string: drugBankParser.getSuggestedQueryList(project, organism)) {
+    for (String string : drugBankParser.getSuggestedQueryList(project, organism)) {
       resultSet.add(string.toLowerCase());
     }
-    for (String string: chEMBLParser.getSuggestedQueryList(project, organism)) {
+    for (String string : chEMBLParser.getSuggestedQueryList(project, organism)) {
       resultSet.add(string.toLowerCase());
     }
-    
+
     List<String> result = new ArrayList<>();
     result.addAll(resultSet);
     Collections.sort(result);
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/LayoutView.java b/service/src/main/java/lcsb/mapviewer/services/view/LayoutView.java
deleted file mode 100644
index 67a7bf92a7..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/LayoutView.java
+++ /dev/null
@@ -1,274 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-import java.util.Comparator;
-
-import lcsb.mapviewer.model.map.layout.Layout;
-
-/**
- * This class is a client view that represents {@link Layout} class.
- * 
- * @author Piotr Gawron
- * 
- */
-public class LayoutView extends AbstractView<Layout> implements Serializable {
-  /**
-   * 
-   */
-  private static final long serialVersionUID = 1L;
-
-  /**
-   * Comparator for {@link LayoutView} that use database identifier as a key for
-   * comparison.
-   */
-  public static final Comparator<LayoutView> ID_COMPARATOR = new Comparator<LayoutView>() {
-
-    @Override
-    public int compare(LayoutView arg0, LayoutView arg1) {
-      if (arg0 == null) {
-        return -1;
-      } else if (arg1 == null) {
-        return 1;
-      } else if (arg0.getIdObject() == null) {
-        return -1;
-      } else if (arg1.getIdObject() == null) {
-        return 1;
-      } else {
-        return arg0.getIdObject() - arg1.getIdObject();
-      }
-    }
-
-  };
-
-  /**
-   * Database identifier of the model to which layout belongs to.
-   */
-  private Integer modelId;
-
-  /**
-   * Name of the layout.
-   */
-  private String name;
-
-  /**
-   * Short description of the layout.
-   */
-  private String description;
-
-  /**
-   * Status of processing the layout.
-   * {@link lcsb.mapviewer.db.model.map.layout.LayoutStatus LayoutStatus} defines
-   * possible values.
-   */
-  private String status;
-
-  /**
-   * Should the data overlay be accessible by everybody.
-   */
-  private Boolean publicOverlay;
-
-  /**
-   * Should the data overlay be shown on start.
-   */
-  private Boolean defaultOverlay;
-
-  /**
-   * Processing progress (value between 0..100).
-   */
-  private String progress;
-
-  /**
-   * Where the files generated for this layout are stored.
-   */
-  private String directory;
-
-  /**
-   * Who created the layout.
-   */
-  private String creator;
-
-  /**
-   * "true" if input file from which layout was created is available, "false"
-   * otherwise.
-   */
-  private String inputDataAvailable;
-
-  /**
-   * Default constructor.
-   */
-  public LayoutView() {
-    super(null);
-  }
-
-  /**
-   * Constructor that creates view from the original layout.
-   * 
-   * @param layout
-   *          original layout
-   */
-  protected LayoutView(Layout layout) {
-    super(layout);
-  }
-
-  /**
-   * @return the modelId
-   * @see #modelId
-   */
-  public Integer getModelId() {
-    return modelId;
-  }
-
-  /**
-   * @param modelId
-   *          the modelId to set
-   * @see #modelId
-   */
-  public void setModelId(Integer modelId) {
-    this.modelId = modelId;
-  }
-
-  /**
-   * @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 description
-   * @see #description
-   */
-  public String getDescription() {
-    return description;
-  }
-
-  /**
-   * @param description
-   *          the description to set
-   * @see #description
-   */
-  public void setDescription(String description) {
-    this.description = description;
-  }
-
-  /**
-   * @return the status
-   * @see #status
-   */
-  public String getStatus() {
-    return status;
-  }
-
-  /**
-   * @param status
-   *          the status to set
-   * @see #status
-   */
-  public void setStatus(String status) {
-    this.status = status;
-  }
-
-  /**
-   * @return the progress
-   * @see #progress
-   */
-  public String getProgress() {
-    return progress;
-  }
-
-  /**
-   * @param progress
-   *          the progress to set
-   * @see #progress
-   */
-  public void setProgress(String progress) {
-    this.progress = progress;
-  }
-
-  /**
-   * @return the directory
-   * @see #directory
-   */
-  public String getDirectory() {
-    return directory;
-  }
-
-  /**
-   * @param directory
-   *          the directory to set
-   * @see #directory
-   */
-  public void setDirectory(String directory) {
-    this.directory = directory;
-  }
-
-  /**
-   * @return the creator
-   * @see #creator
-   */
-  public String getCreator() {
-    return creator;
-  }
-
-  /**
-   * @param creator
-   *          the creator to set
-   * @see #creator
-   */
-  public void setCreator(String creator) {
-    this.creator = creator;
-  }
-
-  /**
-   * @return the inputDataAvailable
-   * @see #inputDataAvailable
-   */
-  public String getInputDataAvailable() {
-    return inputDataAvailable;
-  }
-
-  /**
-   * @param inputDataAvailable
-   *          the inputDataAvailable to set
-   * @see #inputDataAvailable
-   */
-  public void setInputDataAvailable(String inputDataAvailable) {
-    this.inputDataAvailable = inputDataAvailable;
-  }
-
-  /**
-   * @return the publicOverlay
-   * @see #publicOverlay
-   */
-  public Boolean getPublicOverlay() {
-    return publicOverlay;
-  }
-
-  /**
-   * @param publicOverlay
-   *          the publicOverlay to set
-   * @see #publicOverlay
-   */
-  public void setPublicOverlay(Boolean publicOverlay) {
-    this.publicOverlay = publicOverlay;
-  }
-
-  public Boolean getDefaultOverlay() {
-    return defaultOverlay;
-  }
-
-  public void setDefaultOverlay(Boolean defaultOverlay) {
-    this.defaultOverlay = defaultOverlay;
-  }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/LayoutViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/LayoutViewFactory.java
deleted file mode 100644
index 912f7066cb..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/LayoutViewFactory.java
+++ /dev/null
@@ -1,89 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import org.apache.log4j.Logger;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.Layout;
-
-/**
- * Factory class for {@link LayoutView} class.
- * 
- * @author Piotr Gawron
- * 
- */
-public class LayoutViewFactory extends AbstractViewFactory<Layout, LayoutView> {
-  /**
-   * Default class logger.
-   */
-  @SuppressWarnings("unused")
-  private static Logger logger = Logger.getLogger(LayoutViewFactory.class);
-
-  @Override
-  public LayoutView create(Layout layout) {
-    LayoutView result = new LayoutView(layout);
-    if (layout == null) {
-      return result;
-    }
-    if (layout.getModel() != null) {
-      result.setModelId(layout.getModel().getId());
-    }
-    result.setName(layout.getTitle());
-    Project project = getProjectForLayout(layout);
-    if (project != null && project.getDirectory() != null) {
-      result.setDirectory(project.getDirectory() + "/" + layout.getDirectory());
-    } else {
-      result.setDirectory(layout.getDirectory());
-    }
-    if (layout.getCreator() != null) {
-      result.setCreator(layout.getCreator().getLogin());
-    } else {
-      result.setCreator("");
-    }
-    result.setStatus(layout.getStatus().getCommonName());
-    result.setPublicOverlay(layout.isPublicLayout());
-    result.setDefaultOverlay(layout.isDefaultOverlay());
-    result.setProgress(String.format("%1$,.2f", layout.getProgress()));
-
-    result.setDescription(layout.getDescription());
-    if (layout.getInputData() != null) {
-      result.setInputDataAvailable("true");
-    } else {
-      result.setInputDataAvailable("false");
-    }
-    return result;
-  }
-
-  /**
-   * Returns projects associated with model. It might be tricky, because some
-   * layouts are connected to models that are not directly attached to project
-   * (they are attached by parent or grand-parent).
-   * 
-   * @param layout
-   *          layout for which project will be returned
-   * @return {@link Project} to which {@link Layout layout} belongs to
-   */
-  protected Project getProjectForLayout(Layout layout) {
-    if (layout.getModel() != null) {
-      if (layout.getModel().getProject() != null) {
-        return layout.getModel().getProject();
-      }
-    }
-    if (layout.getParentLayout() != null) {
-      return getProjectForLayout(layout.getParentLayout());
-    }
-    return null;
-  }
-
-  @Override
-  public String createGson(LayoutView object) {
-    return new Gson().toJson(object);
-  }
-
-  @Override
-  public Layout viewToObject(LayoutView view) {
-    throw new NotImplementedException();
-  }
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index 8e9ec634b7..d62ebc6cf3 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -50,7 +50,6 @@
 	<bean id="AnnotationViewFactory" class="lcsb.mapviewer.services.view.AnnotationViewFactory"/>
 	<bean id="ConfigurationViewFactory" class="lcsb.mapviewer.services.view.ConfigurationViewFactory"/>
 	<bean id="DataMiningViewFactory" class="lcsb.mapviewer.services.view.DataMiningViewFactory"/>
-	<bean id="LayoutViewFactory" class="lcsb.mapviewer.services.view.LayoutViewFactory"/>
 	<bean id="OverviewImageViewFactory" class="lcsb.mapviewer.services.view.OverviewImageViewFactory"/>
 	<bean id="OverviewLinkViewFactory" class="lcsb.mapviewer.services.view.OverviewLinkViewFactory"/>
 	<bean id="ReferenceGenomeViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeViewFactory"/>
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index 3e3cc18f68..ddb9936f61 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -39,7 +39,6 @@ import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
 import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
 import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
 import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.view.LayoutView;
 
 public class LayoutServiceTest extends ServiceTestFunctions {
   Logger logger = Logger.getLogger(LayoutServiceTest.class);
@@ -60,6 +59,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
 
   // assume that we have admin account with all the privileges
   String adminToken;
+  String token;
 
   @Before
   public void setUp() throws Exception {
@@ -99,6 +99,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
 
     originalSender = layoutService.getEmailSender();
     layoutService.setEmailSender(Mockito.mock(EmailSender.class));
+    token = userService.login(user.getLogin(), "passwd");
   }
 
   @After
@@ -131,7 +132,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           model(model).//
           colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
           user(user);
-      LayoutView row = layoutService.createLayout(params);
+      Layout row = layoutService.createLayout(params);
 
       assertFalse(layoutService.userCanAddLayout(model, user));
 
@@ -166,7 +167,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           model(model).//
           colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
           user(user);
-      LayoutView row = layoutService.createLayout(params);
+      Layout row = layoutService.createLayout(params);
 
       assertEquals(0, layoutService.getAvailableCustomLayoutsNumber(user));
 
@@ -190,7 +191,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
   @Test
   public void testGetCustomLayouts() throws Exception {
     try {
-      List<LayoutView> layouts = layoutService.getCustomLayouts(model, user, false, user);
+      List<Layout> layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertNotNull(layouts);
       assertEquals(0, layouts.size());
 
@@ -201,15 +202,16 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           model(model).//
           colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
           user(user);
-      LayoutView row = layoutService.createLayout(params);
+      Layout row = layoutService.createLayout(params);
 
       assertNotNull(row);
-      assertNotNull(row.getIdObject());
+      assertTrue(row.getId() > 0);
 
-      layouts = layoutService.getCustomLayouts(model, user, false, user);
+      layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertEquals(1, layouts.size());
 
-      layouts = layoutService.getCustomLayouts(model, user2, false, user2);
+      String token2 = userService.login(user2.getLogin(), "passwd");
+      layouts = layoutService.getCustomLayouts(model, token2, false, user2);
       assertEquals(0, layouts.size());
 
       layoutService.removeLayout(row, null);
@@ -220,36 +222,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
     }
   }
 
-  @Test
-  public void testGetLayoutByName() throws Exception {
-    try {
-      String name = "testName";
-      LayoutView layout = layoutService.getLayoutByName(model, name);
-      assertNull(layout);
-      userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
-
-      CreateLayoutParams params = new CreateLayoutParams().name(name).//
-          directory("testDir").//
-          model(model).//
-          colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
-          user(user);
-      LayoutView row = layoutService.createLayout(params);
-
-      layout = layoutService.getLayoutByName(model, name);
-      assertNotNull(layout);
-
-      layoutService.removeLayout(row, null);
-
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
   @Test
   public void testUpdateLayout() throws Exception {
     try {
-      List<LayoutView> layouts = layoutService.getCustomLayouts(model, user, false, user);
+      List<Layout> layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertNotNull(layouts);
       assertEquals(0, layouts.size());
 
@@ -260,19 +236,19 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           model(model).//
           colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
           user(user);
-      LayoutView row = layoutService.createLayout(params);
+      Layout row = layoutService.createLayout(params);
 
-      layouts = layoutService.getCustomLayouts(model, user, false, user);
+      layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertEquals(1, layouts.size());
-      assertEquals("Test", layouts.get(0).getName());
+      assertEquals("Test", layouts.get(0).getTitle());
 
-      row.setName("New name");
+      row.setTitle("New name");
 
       layoutService.updateLayout(row);
 
-      layouts = layoutService.getCustomLayouts(model, user, false, user);
+      layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertEquals(1, layouts.size());
-      assertEquals("New name", layouts.get(0).getName());
+      assertEquals("New name", layouts.get(0).getTitle());
 
       layoutService.removeLayout(row, null);
 
@@ -285,7 +261,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
   @Test(timeout = 15000)
   public void testCreateAsyncLayout() throws Exception {
     try {
-      List<LayoutView> layouts = layoutService.getCustomLayouts(model, user, false, user);
+      List<Layout> layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertNotNull(layouts);
       assertEquals(0, layouts.size());
 
@@ -298,27 +274,27 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           async(true);
 
       long logCounter = logDao.getCount();
-      LayoutView row = layoutService.createLayout(params);
+      Layout row = layoutService.createLayout(params);
 
       assertNotNull(row);
-      assertNotNull(row.getIdObject());
+      assertTrue(row.getId() > 0);
 
-      Layout layoutDb = layoutDao.getById(row.getIdObject());
+      Layout layoutDb = layoutDao.getById(row.getId());
       do {
         Thread.sleep(200);
         layoutDao.refresh(layoutDb);
       } while (layoutDb.getStatus() != LayoutStatus.OK);
 
-      layouts = layoutService.getCustomLayouts(model, user, false, user);
+      layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertEquals(1, layouts.size());
 
       long logCounter2 = logDao.getCount();
       assertTrue("Log didn't appeard after creating layout", logCounter < logCounter2);
 
-      LayoutView layout = layouts.get(0);
+      Layout layout = layouts.get(0);
       logger.debug(layout.getStatus() + ", " + layout.getProgress());
 
-      assertFalse("Layout images weren't generated...", layout.getStatus().equalsIgnoreCase("Not available"));
+      assertFalse("Layout images weren't generated...", layout.getStatus().equals(LayoutStatus.NA));
 
       logCounter = logDao.getCount();
       layoutService.removeLayout(layout, null);
@@ -361,7 +337,6 @@ public class LayoutServiceTest extends ServiceTestFunctions {
 
       layoutService.createLayout(params);
 
-      String token = userService.login(user.getLogin(), "passwd");
       Project pr2 = projectService.getProjectByProjectId(localProject.getProjectId(), token);
 
       Model fromDbModel = pr2.getModels().iterator().next().getModel();
@@ -387,7 +362,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
   @Test
   public void testInputDataInLayout() throws Exception {
     try {
-      List<LayoutView> layouts = layoutService.getCustomLayouts(model, user, false, user);
+      List<Layout> layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertNotNull(layouts);
       assertEquals(0, layouts.size());
 
@@ -399,14 +374,12 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           user(user).//
           async(false);
 
-      LayoutView row = layoutService.createLayout(params);
-
-      String token = userService.login(user.getLogin(), "passwd");
+      Layout row = layoutService.createLayout(params);
 
       assertNotNull(row);
-      assertNotNull(row.getIdObject());
-      assertTrue("true".equalsIgnoreCase(row.getInputDataAvailable()));
-      byte[] inputData = layoutService.getInputDataForLayout(row, token);
+      assertTrue(row.getId() > 0);
+      assertNotNull(row.getInputData());
+      byte[] inputData = row.getInputData().getFileContent();
       assertNotNull(inputData);
       byte[] originalData = IOUtils.toByteArray(new FileInputStream("testFiles/enricoData/ge001.txt"));
       assertEquals(new String(originalData, StandardCharsets.UTF_8), new String(inputData, StandardCharsets.UTF_8));
@@ -422,7 +395,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
   @Test
   public void testGetLayoutAliases() throws Exception {
     try {
-      List<LayoutView> layouts = layoutService.getCustomLayouts(model, user, false, user);
+      List<Layout> layouts = layoutService.getCustomLayouts(model, token, false, user);
       assertNotNull(layouts);
       assertEquals(0, layouts.size());
 
@@ -437,15 +410,15 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           user(user).//
           async(false);
 
-      LayoutView row = layoutService.createLayout(params);
+      Layout row = layoutService.createLayout(params);
 
       String token = userService.login(user.getLogin(), "passwd");
 
-      List<LightLayoutAliasView> result = layoutService.getAliasesForLayout(model, row.getIdObject(), token);
+      List<LightLayoutAliasView> result = layoutService.getAliasesForLayout(model, row.getId(), token);
 
       assertTrue(result.size() > 0);
 
-      List<LightLayoutReactionView> result2 = layoutService.getReactionsForLayout(model, row.getIdObject(), token);
+      List<LightLayoutReactionView> result2 = layoutService.getReactionsForLayout(model, row.getId(), token);
 
       assertEquals(1, result2.size());
 
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java
index fb7154befa..71b032ec51 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java
@@ -15,6 +15,7 @@ import org.apache.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.data.Drug;
 import lcsb.mapviewer.annotation.data.Target;
@@ -27,12 +28,16 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
 import lcsb.mapviewer.services.ServiceTestFunctions;
 import lcsb.mapviewer.services.search.db.DbSearchCriteria;
 
 public class DrugServiceTest extends ServiceTestFunctions {
   Logger logger = Logger.getLogger(DrugServiceTest.class);
 
+  @Autowired
+  ElementDao elementDao;
+
   @Before
   public void setUp() throws Exception {
   }
@@ -60,7 +65,7 @@ public class DrugServiceTest extends ServiceTestFunctions {
       Project project = new Project();
       project.setProjectId("TesT");
       project.addModel(model);
-      Drug drug = drugService.getByName("Diazoxide", new DbSearchCriteria().model(model).ipAddress("ip"));
+      Drug drug = drugService.getByName("Diazoxide", new DbSearchCriteria().project(project).ipAddress("ip"));
       assertNotNull(drug);
       assertNotNull(drug.getName());
       assertFalse(drug.getName().trim().equals(""));
@@ -132,6 +137,22 @@ public class DrugServiceTest extends ServiceTestFunctions {
     }
   }
 
+  @Test
+  public void testAnnotationsInDrug() throws Exception {
+    try {
+      Drug test = drugService.getByName("Selegiline", new DbSearchCriteria().organisms(TaxonomyBackend.HUMAN_TAXONOMY));
+      assertNotNull(test);
+      for (Target target : test.getTargets()) {
+        for (MiriamData md : target.getGenes()) {
+          assertNull(md.getAnnotator());
+        }
+      }
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testDornaseAplha() throws Exception {
     try {
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
index 07a5323d15..2d904ce118 100644
--- a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
@@ -13,8 +13,6 @@ import org.junit.runners.Suite.SuiteClasses;
     DataMiningViewFactoryTest.class, //
     DataMiningViewTest.class, //
     FrameworkVersionViewTest.class, //
-    LayoutViewFactoryTest.class, //
-    LayoutViewTest.class, //
     OverviewImageViewFactoryTest.class, //
     OverviewImageViewTest.class, //
     OverviewLinkViewFactoryTest.class, //
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/LayoutViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/view/LayoutViewFactoryTest.java
deleted file mode 100644
index 5d808c639b..0000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/LayoutViewFactoryTest.java
+++ /dev/null
@@ -1,111 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-public class LayoutViewFactoryTest extends ServiceTestFunctions {
-
-	@Autowired
-	LayoutViewFactory	layoutViewFactory;
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testCreateEmpty() throws Exception {
-		try {
-			Object object = layoutViewFactory.create(null);
-			assertNotNull(object);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCreateGson() throws Exception {
-		try {
-			LayoutView object = layoutViewFactory.create(null);
-			assertNotNull(layoutViewFactory.createGson(object));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetProject() throws Exception {
-		try {
-			Layout layout = new Layout();
-			Project project = layoutViewFactory.getProjectForLayout(layout);
-			assertNull(project);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetProject2() throws Exception {
-		try {
-			Project project = new Project();
-			project.setProjectId("TES_T1_23");
-			Layout layout = new Layout();
-			Model md = new ModelFullIndexed(null);
-			md.setProject(project);
-			layout.setModel(md);
-			Project project2 = layoutViewFactory.getProjectForLayout(layout);
-			assertEquals(project, project2);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetProject3() throws Exception {
-		try {
-			Project project = new Project();
-			project.setProjectId("TES_T1_23");
-			Layout toplayout = new Layout();
-			Layout layout = new Layout();
-			Model md = new ModelFullIndexed(null);
-			md.setProject(project);
-
-			Model submodel = new ModelFullIndexed(null);
-
-			ModelSubmodelConnection msc = new ModelSubmodelConnection();
-			msc.setParentModel(md);
-			msc.setSubmodel(submodel);
-
-			md.addSubmodelConnection(msc);
-
-			layout.setModel(submodel);
-			toplayout.addLayout(layout);
-			toplayout.setModel(md);
-			Project project2 = layoutViewFactory.getProjectForLayout(layout);
-			assertEquals(project, project2);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/LayoutViewTest.java b/service/src/test/java/lcsb/mapviewer/services/view/LayoutViewTest.java
deleted file mode 100644
index fd819fbf1e..0000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/LayoutViewTest.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class LayoutViewTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testSerialization() {
-		try {
-			SerializationUtils.serialize(new LayoutView());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-}
-- 
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