diff --git a/frontend-js/.idea/dictionaries/piotr_gawron.xml b/frontend-js/.idea/dictionaries/piotr_gawron.xml
deleted file mode 100644
index 6a8c909a47f60a556bc261805af778533e72b7eb..0000000000000000000000000000000000000000
--- a/frontend-js/.idea/dictionaries/piotr_gawron.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<component name="ProjectDictionaryState">
- <dictionary name="piotr.gawron">
- <words>
- <w>mailto</w>
- </words>
- </dictionary>
-</component>
\ No newline at end of file
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
new file mode 100644
index 0000000000000000000000000000000000000000..5a2467eaa76ab190321650e56fd53c285b1001bb
--- /dev/null
+++ b/frontend-js/src/main/js/map/data/UserPreferences.js
@@ -0,0 +1,62 @@
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+function UserPreferences(javaObject) {
+ if (javaObject !== undefined) {
+ this.setProjectUpload(javaObject["project-upload"]);
+ this.setElementAnnotators(javaObject["element-annotators"]);
+ this.setElementRequiredAnnotations(javaObject["element-required-annotations"]);
+ this.setElementValidAnnotations(javaObject["element-valid-annotations"]);
+ } else {
+ this._projectUpload = {};
+ this._elementAnnotators = {};
+ this._elementRequiredAnnotations = {};
+ this._elementValidAnnotations = {};
+ }
+}
+
+UserPreferences.prototype.setProjectUpload = function (projectUpload) {
+ this._projectUpload = {
+ autoResize: projectUpload["auto-resize"],
+ validateMiriam: projectUpload["validate-miriam"],
+ annotateModel: projectUpload["annotate-model"],
+ cacheData: projectUpload["cache-data"],
+ semanticZooming: projectUpload["semantic-zooming"],
+ sbgn: projectUpload["sbgn"]
+ };
+};
+UserPreferences.prototype.getProjectUpload = function () {
+ return this._projectUpload;
+};
+UserPreferences.prototype.setElementAnnotators = function (elementAnnotators) {
+ this._elementAnnotators = elementAnnotators;
+};
+UserPreferences.prototype.getElementAnnotators = function (className) {
+ return this._elementAnnotators[className];
+};
+UserPreferences.prototype.setElementRequiredAnnotations = function (elementRequiredAnnotations) {
+ this._elementRequiredAnnotations = {};
+ for (var key in elementRequiredAnnotations) {
+ if (elementRequiredAnnotations.hasOwnProperty(key)) {
+ var data = elementRequiredAnnotations[key];
+ this._elementRequiredAnnotations[key] = {
+ requiredAtLeastOnce: data["require-at-least-one"],
+ list: data["annotation-list"]
+ };
+ }
+ }
+};
+UserPreferences.prototype.getElementRequiredAnnotations = function (className) {
+ return this._elementRequiredAnnotations[className];
+};
+UserPreferences.prototype.setElementValidAnnotations = function (elementValidAnnotations) {
+ this._elementValidAnnotations = elementValidAnnotations;
+};
+UserPreferences.prototype.getElementValidAnnotations = function (className) {
+ return this._elementValidAnnotations[className];
+};
+
+module.exports = UserPreferences;
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index f0233456579a476d169c47b1958127da75e44650..47c121d93f8026b52257cb4b97ac9a328c31376c 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -25,6 +25,7 @@ var SearchDbOverlay = require("../../main/js/map/overlay/SearchDbOverlay");
var User = require("../../main/js/map/data/User");
var Cookies = require('js-cookie');
+var fs = require('fs');
var GuiConnector = require('../../main/js/GuiConnector');
@@ -37,10 +38,10 @@ function Helper(configuration) {
this.EPSILON = Helper.EPSILON;
}
-Helper.prototype.setConfiguration = function (configuration) {
+Helper.prototype.setConfiguration = function(configuration) {
this._configuration = configuration;
};
-Helper.prototype.getConfiguration = function () {
+Helper.prototype.getConfiguration = function() {
return this._configuration;
};
@@ -143,7 +144,7 @@ Helper.prototype.createComment = function (element) {
return result;
};
-Helper.prototype.createProject = function() {
+Helper.prototype.createProject = function () {
var result = new Project();
result.setProjectId("testId");
result.setId(this.idCounter++);
@@ -151,17 +152,17 @@ Helper.prototype.createProject = function() {
return result;
};
-Helper.prototype.createUser = function() {
+Helper.prototype.createUser = function () {
var result = new User({
- login : "test_login",
- id : this.idCounter++,
- name : "some name",
- surname : "surname",
+ login: "test_login",
+ id: this.idCounter++,
+ name: "some name",
+ surname: "surname",
});
return result;
};
-Helper.prototype.createAlias = function(map) {
+Helper.prototype.createAlias = function (map) {
var mapId;
if (map === undefined) {
mapId = this.idCounter++;
@@ -169,15 +170,15 @@ Helper.prototype.createAlias = function(map) {
mapId = map.getId();
}
var result = new Alias({
- idObject : this.idCounter++,
- name : "Test element",
- type : "RNA",
- modelId : mapId,
- bounds : {
- x : 10.0,
- y : 20.0,
- width : 30.0,
- height : 40.0,
+ idObject: this.idCounter++,
+ name: "Test element",
+ type: "RNA",
+ modelId: mapId,
+ bounds: {
+ x: 10.0,
+ y: 20.0,
+ width: 30.0,
+ height: 40.0,
},
references: [],
});
@@ -198,10 +199,10 @@ Helper.prototype.createLayoutAlias = function (alias) {
modelId = this.idCounter++;
}
var result = new LayoutAlias({
- idObject : id,
- value : 0.2,
- color : {
- a : 23
+ idObject: id,
+ value: 0.2,
+ color: {
+ a: 23
},
modelId: modelId,
geneVariations: [{}]
@@ -386,6 +387,18 @@ Helper.prototype.setUrl = function (url) {
GuiConnector.init();
};
+Helper.prototype.readFile = function (filename) {
+ return new Promise(function (resolve, reject) {
+ fs.readFile(filename, 'utf8', function (err, content) {
+ if (err) {
+ reject(err);
+ } else {
+ resolve(content);
+ }
+ });
+ });
+};
+
Helper.EPSILON = 1e-6;
module.exports = Helper;
diff --git a/frontend-js/src/test/js/map/data/UserPreferences-test.js b/frontend-js/src/test/js/map/data/UserPreferences-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..2f9c8e86e455206c03fe93135dbd7ce5cfea3fdd
--- /dev/null
+++ b/frontend-js/src/test/js/map/data/UserPreferences-test.js
@@ -0,0 +1,30 @@
+"use strict";
+
+require("../../mocha-config")
+/* exported logger */
+
+var UserPreferences = require('../../../../main/js/map/data/UserPreferences');
+
+var logger = require('../../logger');
+
+var chai = require('chai');
+var assert = chai.assert;
+
+var fs = require('fs');
+var Promise = require('fs');
+
+describe('UserPreferences', function () {
+ it("constructor", function () {
+ return helper.readFile("testFiles/preferences.json").then(function (content) {
+ var object = new UserPreferences(JSON.parse(content));
+ assert.ok(object);
+ assert.notOk(object.getProjectUpload().autoResize);
+ assert.ok(object.getProjectUpload().cacheData);
+
+ assert.ok(object.getElementAnnotators("lcsb.mapviewer.model.map.species.Protein").length > 0);
+ assert.ok(object.getElementValidAnnotations("lcsb.mapviewer.model.map.species.Protein").length > 0);
+ assert.ok(object.getElementRequiredAnnotations("lcsb.mapviewer.model.map.species.Protein").requiredAtLeastOnce);
+ assert.ok(object.getElementRequiredAnnotations("lcsb.mapviewer.model.map.species.Protein").list.length > 0);
+ })
+ });
+});
diff --git a/frontend-js/testFiles/preferences.json b/frontend-js/testFiles/preferences.json
new file mode 100644
index 0000000000000000000000000000000000000000..5f017aff41908460c352cd9f128b38771241ae54
--- /dev/null
+++ b/frontend-js/testFiles/preferences.json
@@ -0,0 +1,753 @@
+{
+ "element-required-annotations": {
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Chemical": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "CHEBI",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Degraded": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.PathwayCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.SimpleMolecule": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "CHEBI",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.ReceptorProtein": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Gene": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.OvalCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Protein": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "HGNC",
+ "HGNC_SYMBOL"
+ ]
+ },
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "PUBMED"
+ ]
+ },
+ "lcsb.mapviewer.model.map.BioEntity": {
+ "require-at-least-one": true,
+ "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": true,
+ "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": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Ion": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ "CHEBI",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE"
+ ]
+ },
+ "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": true,
+ "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": true,
+ "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": true,
+ "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": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.compartment.TopSquareCompartment": {
+ "require-at-least-one": true,
+ "annotation-list": [
+ ]
+ },
+ "lcsb.mapviewer.model.map.species.Species": {
+ "require-at-least-one": true,
+ "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_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Chemical": [
+ "CHEBI",
+ "HMDB",
+ "KEGG_COMPOUND",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Degraded": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.compartment.PathwayCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.SimpleMolecule": [
+ "CHEBI",
+ "HMDB",
+ "KEGG_COMPOUND",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.ReceptorProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Gene": [
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT"
+ ],
+ "lcsb.mapviewer.model.map.compartment.OvalCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Protein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.BioEntity": [
+ ],
+ "lcsb.mapviewer.model.map.species.GenericProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TransportReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.IonChannelProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.Phenotype": [
+ "GO",
+ "MESH_2012",
+ "OMIM",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Drug": [
+ "CHEBI",
+ "CHEMBL_COMPOUND",
+ "DRUGBANK",
+ "HMDB",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Element": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.DissociationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.SquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Ion": [
+ "CHEBI",
+ "HMDB",
+ "KEGG_COMPOUND",
+ "PUBCHEM",
+ "PUBCHEM_SUBSTANCE",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.Reaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.RightSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranslationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.AntisenseRna": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Complex": [
+ "CHEMBL_TARGET",
+ "EC",
+ "GO",
+ "INTERPRO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Unknown": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TruncationReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.compartment.LeftSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.species.TruncatedProtein": [
+ "CHEMBL_TARGET",
+ "EC",
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "INTERPRO",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT",
+ "UNIPROT_ISOFORM"
+ ],
+ "lcsb.mapviewer.model.map.compartment.Compartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.compartment.TopSquareCompartment": [
+ "GO",
+ "MESH_2012",
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Species": [
+ "PUBMED"
+ ],
+ "lcsb.mapviewer.model.map.species.Rna": [
+ "ENSEMBL",
+ "ENTREZ",
+ "HGNC",
+ "HGNC_SYMBOL",
+ "KEGG_GENES",
+ "MGD",
+ "PANTHER",
+ "PUBMED",
+ "REFSEQ",
+ "UNIPROT"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction": [
+ "KEGG_PATHWAY",
+ "KEGG_REACTION",
+ "PUBMED",
+ "REACTOME"
+ ]
+ },
+ "element-annotators": {
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.BottomSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Chemical": [
+ "Chebi"
+ ],
+ "lcsb.mapviewer.model.map.species.Degraded": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.PathwayCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.SimpleMolecule": [
+ "Chebi"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.ReceptorProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Gene": [
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.compartment.OvalCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Protein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.BioEntity": [
+ ],
+ "lcsb.mapviewer.model.map.species.GenericProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TransportReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.IonChannelProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.Phenotype": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Drug": [
+ ],
+ "lcsb.mapviewer.model.map.species.Element": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.DissociationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.SquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Ion": [
+ "Chebi"
+ ],
+ "lcsb.mapviewer.model.map.reaction.Reaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.RightSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TranslationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.AntisenseRna": [
+ ],
+ "lcsb.mapviewer.model.map.species.Complex": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Unknown": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.TruncationReaction": [
+ ],
+ "lcsb.mapviewer.model.map.compartment.LeftSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction": [
+ ],
+ "lcsb.mapviewer.model.map.species.TruncatedProtein": [
+ "Biocompendium",
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.compartment.Compartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.compartment.TopSquareCompartment": [
+ "Gene Ontology"
+ ],
+ "lcsb.mapviewer.model.map.species.Species": [
+ ],
+ "lcsb.mapviewer.model.map.species.Rna": [
+ "HGNC"
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction": [
+ ],
+ "lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction": [
+ ]
+ },
+ "project-upload": {
+ "auto-resize": false,
+ "sbgn": false,
+ "cache-data": true,
+ "semantic-zooming": false,
+ "annotate-model": false,
+ "validate-miriam": false
+ }
+}
\ No newline at end of file
diff --git a/persist/src/db/11.1.0/fix_db_20170829.sql b/persist/src/db/11.1.0/fix_db_20170829.sql
index c5d18a2ac2cca017e749cd449d76970d507c4047..43eead655e216bcbb59e7ed06b9e8befea12e27b 100644
--- a/persist/src/db/11.1.0/fix_db_20170829.sql
+++ b/persist/src/db/11.1.0/fix_db_20170829.sql
@@ -4,3 +4,10 @@ alter table user_annotation_schema_table add column autoresizemap boolean defaul
alter table user_annotation_schema_table add column cachedata boolean default true;
alter table user_annotation_schema_table add column semanticzooming boolean default false;
alter table class_required_annotation_table RENAME column requireatlestoneannotation to requireatleastoneannotation;
+
+-- rename config annotation class name
+update class_annotator_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+update class_required_annotation_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+update class_valid_annotation_table set classname ='lcsb.mapviewer.model.map.BioEntity' where classname ='lcsb.mapviewer.model.map.AnnotatedObject';
+
+
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 0ed3cd9889fe6e0510dbe6773e1e5e8146a50b03..b3dbe1354330db2b53e19797776072ead5ffca71 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
@@ -128,7 +128,7 @@ public class UserRestImpl extends BaseRestImpl {
private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
Map<String, Object> result = new HashMap<>();
for (UserClassValidAnnotations userClassAnnotators : classValidAnnotators) {
- result.put(userClassAnnotators.getClassName(), userClassAnnotators.getValidMiriamTypes());
+ result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getValidMiriamTypes()));
}
return result;
}
@@ -158,7 +158,12 @@ public class UserRestImpl extends BaseRestImpl {
for (UserClassRequiredAnnotations requiredAnnotations : classRequiredAnnotators) {
Map<String, Object> row = new HashMap<>();
row.put("require-at-least-one", requiredAnnotations.getRequireAtLeastOneAnnotation());
- row.put("annotation-list", requiredAnnotations.getRequiredMiriamTypes());
+ List<String> miriamTypes = new ArrayList<>();
+
+ for (MiriamType mt : requiredAnnotations.getRequiredMiriamTypes()) {
+ miriamTypes.add(mt.name());
+ }
+ row.put("annotation-list", miriamTypes);
result.put(requiredAnnotations.getClassName(), row);
}
return result;
@@ -200,7 +205,7 @@ public class UserRestImpl extends BaseRestImpl {
private Map<String, Object> prepareElementAnnotators(List<UserClassAnnotators> classAnnotators) {
Map<String, Object> result = new HashMap<>();
for (UserClassAnnotators userClassAnnotators : classAnnotators) {
- result.put(userClassAnnotators.getClassName(), userClassAnnotators.getAnnotators());
+ result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getAnnotators()));
}
return result;
}