possibility to export part of the map as sbml/celldesigner/sbgnml model from plugin

frontend-js/src/main/js/ServerConnector.js

@@ -1937,6 +1937,20 @@ ServerConnector.getImageDownloadUrl = function (params) {
   });
 };
 
+/**
+ *
+ * @param {Object} params
+ * @param {string} [params.projectId]
+ * @param {number} params.modelId
+ * @param {string} [params.polygonString]
+ * @param {string} params.handlerClass
+ * @param {number} [params.backgroundOverlayId]
+ * @param {number} [params.zoomLevel]
+ * @param {number[]} [params.overlayIds]
+ * @param {number[]} [params.elementIds]
+ * @param {number[]} [params.reactionIds]
+ * @returns {Promise}
+ */
 ServerConnector.getModelDownloadUrl = function (params) {
   var self = this;
   var queryParams = {
@@ -1944,12 +1958,13 @@ ServerConnector.getModelDownloadUrl = function (params) {
     modelId: params.modelId
   };
   var filterParams = {
-    token: params.token,
     polygonString: params.polygonString,
     handlerClass: params.handlerClass,
     backgroundOverlayId: params.backgroundOverlayId,
     zoomLevel: params.zoomLevel,
-    overlayIds: this.idsToString(params.overlayIds)
+    overlayIds: this.idsToString(params.overlayIds),
+    elementIds: this.idsToString(params.elementIds),
+    reactionIds: this.idsToString(params.reactionIds)
   };
   return self.getProjectId(params.projectId).then(function (result) {
     queryParams.projectId = result;
@@ -1957,6 +1972,41 @@ ServerConnector.getModelDownloadUrl = function (params) {
   });
 };
 
+/**
+ *
+ * @param {Object} params
+ * @param {string} [params.projectId]
+ * @param {number} params.modelId
+ * @param {string} [params.polygonString]
+ * @param {string} params.handlerClass
+ * @param {number} [params.backgroundOverlayId]
+ * @param {number} [params.zoomLevel]
+ * @param {number[]} [params.overlayIds]
+ * @param {number[]} [params.elementIds]
+ * @param {number[]} [params.reactionIds]
+ * @returns {Promise}
+ */
+ServerConnector.getPartOfModelInExportFormat = function (params) {
+  var self = this;
+  var queryParams = {
+    projectId: params.projectId,
+    modelId: params.modelId
+  };
+  var filterParams = {
+    polygonString: params.polygonString,
+    handlerClass: params.handlerClass,
+    backgroundOverlayId: params.backgroundOverlayId,
+    zoomLevel: params.zoomLevel,
+    overlayIds: this.idsToString(params.overlayIds),
+    elementIds: this.idsToString(params.elementIds),
+    reactionIds: this.idsToString(params.reactionIds)
+  };
+  return self.getProjectId(params.projectId).then(function (result) {
+    queryParams.projectId = result;
+    return self.sendPostRequest(self.getModelPartUrl(queryParams), filterParams);
+  });
+};
+
 ServerConnector.getImageConverters = function () {
   var self = this;
   return self.getConfiguration().then(function (configuration) {

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

@@ -137,6 +137,38 @@ function createProjectData(options) {
         }
       });
     },
+    /**
+     * Export part of the map that includes bioEntities into a known format.
+     *
+     * @param {Object} param
+     * @param {string} param.handlerClass format defined in {Configuration#getModelConverters}
+     * @param {number} param.modelId id of the model
+     * @param {Array} param.bioEntities
+     * @returns {Promise}
+     */
+    exportToMapFormat: function (param) {
+      var exportParams = {
+        projectId: map.getProject().getProjectId(),
+        modelId: param.modelId,
+        handlerClass: param.handlerClass,
+        elementIds: [],
+        reactionIds: []
+      };
+      for (var i = 0; i < param.bioEntities.length; i++) {
+        var ie = new IdentifiedElement(param.bioEntities[i]);
+        if (ie.getType() === "ALIAS") {
+          exportParams.elementIds.push(ie.getId());
+        } else if (ie.getType() === "REACTION") {
+          exportParams.reactionIds.push(ie.getId());
+        } else {
+          return Promise.reject(new Error("Unsupported bioentity type: " + ie.getType()));
+        }
+        if (ie.getModelId() !== param.modelId) {
+          return Promise.reject(new Error("Export of bioEntities from few maps is not supported. ModelId: " + param.modelId + "; element modelId: " + ie.getModelId()));
+        }
+      }
+      return options.map.getServerConnector().getPartOfModelInExportFormat(exportParams);
+    },
     getAllBioEntities: function () {
       var models = map.getProject().getModels();
       var result = [];
@@ -312,7 +344,7 @@ function createWrapperFunctionForDialogGuiUpdate(param) {
  * @param {CustomMap} options.map
  * @param {Plugin} options.plugin
  * @param {string} options.pluginId
- * @returns {{getVisibleDataOverlays: function(): (Promise<DataOverlay[]>|*), addListener: addListener, removeListener: removeListener, removeAllListeners: function(): Array, getHighlightedBioEntities: function(*=): *, showBioEntity: function(*=): *, hideBioEntity: function(*=): Promise<T>, setCenter: function(*): PromiseLike, getCenter: function(*): Point, getBounds: function(*): Bounds, fitBounds: function(*): void, setZoom: function(*): *, getZoom: function(*): number, openMap: function(*): PromiseLike}}
+ * @returns {{getVisibleDataOverlays: (function(): (Promise<DataOverlay[]>|*)), addListener: addListener, removeListener: removeListener, removeAllListeners: (function(): Array), getHighlightedBioEntities: (function(*=): Promise<Array | never>), showBioEntity: (function(*=): *), hideBioEntity: (function(*=): Promise<any | never>), setCenter: (function(*): PromiseLike), getCenter: (function(*): Point), getBounds: (function(*): Bounds), fitBounds: (function(*): void), setZoom: (function(*): *), getZoom: (function(*): number), openMap: (function(*): PromiseLike)}}
  */
 function createProjectMap(options) {
   var map = options.map;
@@ -569,7 +601,7 @@ function createProjectMap(options) {
  * @param {CustomMap} options.map
  * @param {Plugin} options.plugin
  * @param {string} options.pluginId
- * @returns {{data: {getBioEntityById: function(*=): Promise<any>, getAllBioEntities: function(): *, getReactionsWithElement: function(*=): *, getProjectId: function(): string, getName: function(): string, getVersion: function(): string, getDisease: getDisease, getOrganism: getOrganism, getModels: function(): *[]}, map: {getVisibleDataOverlays: function(): (Promise<DataOverlay[]>|*), addListener: addListener, removeListener: removeListener, removeAllListeners: function(): Array, getHighlightedBioEntities: function(*=): *, showBioEntity: function(*=): *, hideBioEntity: function(*=): Promise<T>, setCenter: function(*): PromiseLike, getCenter: function(*): Point, getBounds: function(*): Bounds, fitBounds: function(*): void, setZoom: function(*): *, getZoom: function(*): number, openMap: function(*): PromiseLike}}}
+ * @returns {{data: {getBioEntityById: (function(*=): Promise<any>), getAllBioEntities: (function(): *), getReactionsWithElement: (function(*=): *), getProjectId: (function(): string), getName: (function(): string), getVersion: (function(): string), getDisease: getDisease, getOrganism: getOrganism, getModels: (function(): *[])}, map: {getVisibleDataOverlays: (function(): (Promise<DataOverlay[]>|*)), addListener: addListener, removeListener: removeListener, removeAllListeners: (function(): Array), getHighlightedBioEntities: (function(*=): Promise<Array|never>), showBioEntity: (function(*=): *), hideBioEntity: (function(*=): Promise<any|never>), setCenter: (function(*): PromiseLike), getCenter: (function(*): Point), getBounds: (function(*): Bounds), fitBounds: (function(*): void), setZoom: (function(*): *), getZoom: (function(*): number), openMap: (function(*): PromiseLike)}}}
  */
 function createProject(options) {
   return {
@@ -635,17 +667,16 @@ function createPluginData(options) {
  * @param {HTMLElement} options.element
  * @param {Configuration} options.configuration
  * @param {ServerConnector} options.serverConnector
- * @returns {{pluginId: string|string, element: *, project: {data: {getBioEntityById: function(*=): Promise<any>, getAllBioEntities: function(): *, getReactionsWithElement: function(*=): *, getProjectId: function(): string, getName: function(): string, getVersion: function(): string, getDisease: getDisease, getOrganism: getOrganism, getModels: function(): *[]}, map: {getVisibleDataOverlays: function(): (Promise<DataOverlay[]>|*), addListener: addListener, removeListener: removeListener, removeAllListeners: function(): Array, getHighlightedBioEntities: function(*=): *, showBioEntity: function(*=): *, hideBioEntity: function(*=): Promise<T>, setCenter: function(*): PromiseLike, getCenter: function(*): Point, getBounds: function(*): Bounds, fitBounds: function(*): void, setZoom: function(*): *, getZoom: function(*): number, openMap: function(*): PromiseLike}}, configuration: {options: ConfigurationOption[], overlayTypes: string[], imageConverters: ImageConverter[], modelConverters: ModelConverter[], elementTypes: BioEntityType[], reactionTypes: BioEntityType[], miriamTypes: MiriamType[], mapTypes: MapType[], modificationStateTypes: ModificationStateType[], privilegeTypes: PrivilegeType[], annotators: Annotator[]}, pluginData: {setGlobalParam: function(*=, *=): *, getGlobalParam: function(*=): *, setUserParam: function(*=, *=): *, getUserParam: function(*=): *}}}
+ * @returns {{pluginId: (string|string), element: HTMLElement, project: {data: {getBioEntityById: (function(*=): Promise<any>), getAllBioEntities: (function(): *), getReactionsWithElement: (function(*=): *), getProjectId: (function(): string), getName: (function(): string), getVersion: (function(): string), getDisease: getDisease, getOrganism: getOrganism, getModels: (function(): *[])}, map: {getVisibleDataOverlays: (function(): (Promise<DataOverlay[]>|*)), addListener: addListener, removeListener: removeListener, removeAllListeners: (function(): Array), getHighlightedBioEntities: (function(*=): Promise<Array|never>), showBioEntity: (function(*=): *), hideBioEntity: (function(*=): Promise<any|never>), setCenter: (function(*): PromiseLike), getCenter: (function(*): Point), getBounds: (function(*): Bounds), fitBounds: (function(*): void), setZoom: (function(*): *), getZoom: (function(*): number), openMap: (function(*): PromiseLike)}}, configuration: {options: ConfigurationOption[], overlayTypes: string[], imageConverters: ImageConverter[], modelConverters: ModelConverter[], elementTypes: BioEntityType[], reactionTypes: BioEntityType[], miriamTypes: MiriamType[], mapTypes: MapType[], modificationStateTypes: ModificationStateType[], privilegeTypes: PrivilegeType[], annotators: Annotator[]}, pluginData: {setGlobalParam: (function(*=, *=): *), getGlobalParam: (function(*=): *), setUserParam: (function(*=, *=): *), getUserParam: (function(*=): *)}}}
  * @constructor
  */
 function MinervaPluginProxy(options) {
-  return {
-    pluginId: options.pluginId,
-    element: options.element,
-    project: createProject(options),
-    configuration: createConfiguration(options),
-    pluginData: createPluginData(options)
-  };
+  this.pluginId = options.pluginId;
+  this.element = options.element;
+  this.project = createProject(options);
+  this.configuration = createConfiguration(options);
+  this.pluginData = createPluginData(options);
+
 }
 
 module.exports = MinervaPluginProxy;

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

@@ -181,10 +181,10 @@ describe('MinervaPluginProxy', function () {
 
   describe("getBioEntityById", function () {
     it("for alias", function () {
-      var map, proxy;
+      var map;
       return ServerConnector.getProject().then(function (project) {
         map = helper.createCustomMap(project);
-        proxy = createProxy(map);
+        var proxy = createProxy(map);
         return proxy.project.data.getBioEntityById({
           id: 329177,
           modelId: 15781,
@@ -198,10 +198,10 @@ describe('MinervaPluginProxy', function () {
     });
 
     it("for reaction", function () {
-      var map, proxy;
+      var map;
       return ServerConnector.getProject().then(function (project) {
         map = helper.createCustomMap(project);
-        proxy = createProxy(map);
+        var proxy = createProxy(map);
         return proxy.project.data.getBioEntityById({
           id: 153508,
           modelId: 15781,
@@ -216,6 +216,26 @@ describe('MinervaPluginProxy', function () {
     });
   });
 
+  describe("exportToMapFormat", function () {
+    it("for alias", function () {
+      var map;
+      return ServerConnector.getProject().then(function (project) {
+        map = helper.createCustomMap(project);
+        var proxy = createProxy(map);
+        return proxy.project.data.exportToMapFormat({
+          modelId: 15781,
+          bioEntities: [{id: 329177, modelId: 15781, type: "ALIAS"}],
+          handlerClass: helper.getConfiguration().getModelConverters()[0].handler
+        });
+      }).then(function (result) {
+        assert.ok(result);
+      }).then(function () {
+        map.destroy();
+      });
+    });
+
+  });
+
   describe("showElement", function () {
     it("alias", function () {
       var elementToShow = {
@@ -238,7 +258,8 @@ describe('MinervaPluginProxy', function () {
           color: "#FF0000"
         }
       };
-      var map, proxy;
+      var map;
+      var proxy;
       return ServerConnector.getProject().then(function (project) {
         map = helper.createCustomMap(project);
         proxy = createProxy(map);

frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/POST_elementIds=329177&handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID&

+<?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">
+<listOfUnitDefinitions>
+</listOfUnitDefinitions>
+<listOfFunctionDefinitions>
+</listOfFunctionDefinitions>
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="1305" sizeY="473"/>
+<celldesigner:listOfIncludedSpecies>
+</celldesigner:listOfIncludedSpecies>
+<celldesigner:listOfCompartmentAliases>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases>
+</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa10" species="s_id_sa10" >
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="0.0" y="186.0" w="80.0" h="30.0" />
+<celldesigner:font size="12.0"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView><celldesigner:innerPosition x="0.0" y="186.0"/><celldesigner:boxSize width="80.0" height="30.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFFF00FF" scheme="Color"/></celldesigner:usualView>
+<celldesigner:briefView><celldesigner:innerPosition x="0.0" y="186.0"/><celldesigner:boxSize width="80.0" height="30.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFFF00FF" scheme="Color"/></celldesigner:briefView>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfProteins></celldesigner:listOfProteins>
+<celldesigner:listOfGenes></celldesigner:listOfGenes>
+<celldesigner:listOfRNAs></celldesigner:listOfRNAs>
+<celldesigner:listOfAntisenseRNAs></celldesigner:listOfAntisenseRNAs>
+<celldesigner:listOfLayers></celldesigner:listOfLayers>
+</celldesigner:extension>
+</annotation>
+<listOfCompartments>
+<compartment metaid="default" id="default" name="" size="1" units="volume" >
+<annotation>
+<celldesigner:extension>
+<celldesigner:name></celldesigner:name>
+</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>
+<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>
+</body></html></notes>
+</compartment>
+</listOfCompartments>
+<listOfSpecies><species  name="s10" id="s_id_sa10" metaid="s_id_sa10" initialAmount="0.0" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>DRUG</celldesigner:class>
+<celldesigner:name>s10</celldesigner:name>
+</celldesigner:speciesIdentity>
+</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>
+</species>
+</listOfSpecies>
+<listOfReactions>
+</listOfReactions>
+<notes></notes></model></sbml>
\ No newline at end of file