diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index ae6de2653f56a887a2917c84be3e55616535e267..01b15bbea04f35ae7e9b73a9cf86eb5da8760bf3 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/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) {
diff --git a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
index 6a30568a937a07888ecc4bd7b106fbfde43e8a02..15fbc9e6587bbb7ce763ac7e7200e7bfbd206cf5 100644
--- a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
+++ b/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;
diff --git a/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js b/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
index 4715ed3b0fed6036022550d246f856fe9a689e75..116e8d8537e7e2190081c191c07ee9c6a2910d54 100644
--- a/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
+++ b/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);
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/POST_elementIds=329177&handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/POST_elementIds=329177&handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..c83f0983baeb47529744650af680789d24fa844e
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781.downloadModel/POST_elementIds=329177&handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser&token=MOCK_TOKEN_ID&
@@ -0,0 +1,63 @@
+<?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
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
index 0ab7ea8d342d85d8b1df2ed67da5d0511292b20a..b1e301093a37e90c7e003adfb607acfadd20ca73 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
@@ -6,14 +6,15 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -24,118 +25,160 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
public class SubModelCommand extends NewModelCommand {
-
- /**
- * Polygon that limits the area for the new model.
- *
- */
- private Path2D polygon;
-
- /**
- * Default constructor.
- *
- * @param model
- * original {@link NewModelCommand#model}
- * @param polygon
- * #polygon that limits the area for the new model
- */
- public SubModelCommand(Model model, Path2D polygon) {
- super(model);
- this.polygon = polygon;
- }
-
- @Override
- public Model execute() {
- CopyCommand copy = new CopyCommand(getModel());
- Model result = copy.execute();
-
- Set<Element> aliasNotToRemove = new HashSet<Element>();
-
- for (Element alias : result.getElements()) {
- if (polygon.intersects(alias.getBorder())) {
- aliasNotToRemove.add(alias);
- }
- }
- boolean added = false;
- do {
- Set<Element> iterativeAliasNotToRemove = new HashSet<>();
- for (Element alias : aliasNotToRemove) {
- Element parent = alias.getCompartment();
- if (parent != null) {
- if (!aliasNotToRemove.contains(parent)) {
- iterativeAliasNotToRemove.add(parent);
- }
- }
- if (alias instanceof Species) {
- parent = ((Species) alias).getComplex();
- if (parent != null) {
- if (!aliasNotToRemove.contains(parent)) {
- iterativeAliasNotToRemove.add(parent);
- }
- }
- }
- }
-
- added = iterativeAliasNotToRemove.size() != 0;
- aliasNotToRemove.addAll(iterativeAliasNotToRemove);
- } while (added);
-
- List<Element> aliasToRemove = new ArrayList<Element>();
- for (Element alias : result.getElements()) {
- if (!(polygon.intersects(alias.getBorder()))) {
- boolean remove = true;
- if (alias instanceof Species) {
- remove = ((Species) alias).getComplex() == null;
- }
- if (aliasNotToRemove.contains(alias)) {
- remove = false;
- }
- if (remove) {
- aliasToRemove.add(alias);
- if (alias instanceof Complex) {
- List<Species> aliases = ((Complex) alias).getAllChildren();
- aliasToRemove.addAll(aliases);
- }
- }
- }
-
- }
- for (Element alias : aliasToRemove) {
- result.removeElement(alias);
- }
-
- List<Reaction> reactionsToRemove = new ArrayList<Reaction>();
- for (Reaction reaction : result.getReactions()) {
- boolean remove = false;
- for (AbstractNode node : reaction.getNodes()) {
- if (node instanceof ReactionNode) {
- if (!result.getElements().contains(((ReactionNode) node).getElement())) {
- remove = true;
- break;
- }
- }
- }
- if (remove) {
- reactionsToRemove.add(reaction);
- }
- }
- for (Reaction reaction : reactionsToRemove) {
- result.removeReaction(reaction);
- }
-
- for (Layer layer : result.getLayers()) {
- List<LayerText> textToRemove = new ArrayList<LayerText>();
- for (LayerText text : layer.getTexts()) {
- if (!(polygon.intersects(text.getBorder()))) {
- textToRemove.add(text);
- }
- }
- for (LayerText text : textToRemove) {
- layer.removeLayerText(text);
- }
- }
-
- return result;
- }
+
+ Logger logger = Logger.getLogger(SubModelCommand.class);
+
+ /**
+ * Polygon that limits the area for the new model.
+ *
+ */
+ private Path2D polygon;
+
+ private Set<Integer> elementIds;
+
+ private Set<Integer> reactionIds;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * original {@link NewModelCommand#model}
+ * @param polygon
+ * #polygon that limits the area for the new model
+ */
+ public SubModelCommand(Model model, Path2D polygon) {
+ this(model, polygon, new HashSet<>(), new HashSet<>());
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * original {@link NewModelCommand#model}
+ * @param polygon
+ * #polygon that limits the area for the new model
+ */
+ public SubModelCommand(Model model, Path2D polygon, Set<Integer> elementIds, Set<Integer> reactionIds) {
+ super(model);
+ this.polygon = polygon;
+ this.elementIds = elementIds;
+ this.reactionIds = reactionIds;
+ }
+
+ @Override
+ public Model execute() {
+ CopyCommand copy = new CopyCommand(getModel());
+ Model result = copy.execute();
+
+ Set<Element> inputElements = new HashSet<>();
+ if (elementIds.size() == 0) {
+ inputElements.addAll(result.getElements());
+ } else {
+ for (Element element : getModel().getElements()) {
+ if (elementIds.contains(element.getId())) {
+ inputElements.add(result.getElementByElementId(element.getElementId()));
+ }
+ }
+ }
+
+ Set<Element> aliasNotToRemove = new HashSet<>();
+
+ for (Element alias : result.getElements()) {
+ if (polygon.intersects(alias.getBorder())) {
+ aliasNotToRemove.add(alias);
+ }
+ }
+ aliasNotToRemove.retainAll(inputElements);
+
+ boolean added = false;
+ do {
+ Set<Element> iterativeAliasNotToRemove = new HashSet<>();
+ for (Element alias : aliasNotToRemove) {
+ Element parent = alias.getCompartment();
+ if (parent != null) {
+ if (!aliasNotToRemove.contains(parent)) {
+ iterativeAliasNotToRemove.add(parent);
+ }
+ }
+ if (alias instanceof Species) {
+ parent = ((Species) alias).getComplex();
+ if (parent != null) {
+ if (!aliasNotToRemove.contains(parent)) {
+ iterativeAliasNotToRemove.add(parent);
+ }
+ }
+ }
+ }
+
+ added = iterativeAliasNotToRemove.size() != 0;
+ aliasNotToRemove.addAll(iterativeAliasNotToRemove);
+ } while (added);
+
+ List<Element> aliasToRemove = new ArrayList<>();
+ for (Element element : result.getElements()) {
+ if (!(polygon.intersects(element.getBorder())) || !inputElements.contains(element)) {
+ boolean remove = true;
+ if (element instanceof Species) {
+ remove = ((Species) element).getComplex() == null;
+ }
+ if (aliasNotToRemove.contains(element)) {
+ remove = false;
+ }
+ if (remove) {
+ aliasToRemove.add(element);
+ if (element instanceof Complex) {
+ List<Species> aliases = ((Complex) element).getAllChildren();
+ aliasToRemove.addAll(aliases);
+ }
+ }
+ }
+
+ }
+ for (Element alias : aliasToRemove) {
+ result.removeElement(alias);
+ }
+
+ Set<String> reactionStringIds = new HashSet<>();
+ for (Reaction reaction : getModel().getReactions()) {
+ if (reactionIds.size() == 0 || reactionIds.contains(reaction.getId())) {
+ reactionStringIds.add(reaction.getElementId());
+ }
+ }
+
+ List<Reaction> reactionsToRemove = new ArrayList<>();
+ for (Reaction reaction : result.getReactions()) {
+ boolean remove = false;
+ if (!reactionStringIds.contains(reaction.getElementId())) {
+ remove = true;
+ } else {
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ if (!result.getElements().contains(node.getElement())) {
+ remove = true;
+ break;
+ }
+ }
+ }
+ if (remove) {
+ reactionsToRemove.add(reaction);
+ }
+ }
+ for (Reaction reaction : reactionsToRemove) {
+ result.removeReaction(reaction);
+ }
+
+ for (Layer layer : result.getLayers()) {
+ List<LayerText> textToRemove = new ArrayList<>();
+ for (LayerText text : layer.getTexts()) {
+ if (!(polygon.intersects(text.getBorder()))) {
+ textToRemove.add(text);
+ }
+ }
+ for (LayerText text : textToRemove) {
+ layer.removeLayerText(text);
+ }
+ }
+
+ return result;
+ }
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
index ccfb0bb1adb1959a048126a8de13f1522eabff26..d4e7f30e6ed84db9ffad7a6caa4a5ebdacddf562 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
@@ -2,167 +2,245 @@ package lcsb.mapviewer.commands;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
import java.awt.geom.Path2D;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
+import java.util.Arrays;
+import java.util.HashSet;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
public class SubModelCommandTest extends CommandTestFunctions {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetSubmodel1() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 0);
- polygon.lineTo(0, 100);
- polygon.lineTo(100, 100);
- polygon.lineTo(100, 0);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- assertEquals(2, copy.getElements().size());
- assertEquals(0, copy.getReactions().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodel2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(50, 50);
- polygon.lineTo(350, 50);
- polygon.lineTo(350, 200);
- polygon.lineTo(50, 200);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- assertEquals(9, copy.getElements().size());
- assertEquals(1, copy.getReactions().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodel3() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 200);
- polygon.lineTo(350, 200);
- polygon.lineTo(350, 400);
- polygon.lineTo(0, 400);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- double dx = 10;
- double dy = -10;
-
- new MoveCommand(copy, dx, dy).execute();
-
- assertEquals(model.getElementByElementId("sa3").getCenterX(), copy.getElementByElementId("sa3").getCenterX() - dx, EPSILON);
- assertEquals(model.getElementByElementId("sa3").getCenterY(), copy.getElementByElementId("sa3").getCenterY() - dy, EPSILON);
-
- assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getX2(), copy.getReactionByReactionId("re3").getLines().get(0).getX2() - dx, EPSILON);
- assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getY2(), copy.getReactionByReactionId("re3").getLines().get(0).getY2() - dy, EPSILON);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodelWithoutCompartments() throws Exception {
- try {
- Model model = getModelForFile("testFiles/compartments.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 10);
- polygon.lineTo(10, 10);
- polygon.lineTo(10, 0);
- polygon.lineTo(0, 0);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- // we should cut off some of compartmets
- assertFalse(model.getLayers().iterator().next().getTexts().size() == copy.getLayers().iterator().next().getTexts().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodelWithoutCompartments2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/cutting_without_compartment.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 0);
- polygon.lineTo(0, 500);
- polygon.lineTo(300, 500);
- polygon.lineTo(300, 0);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-
- ModelComparator mc = new ModelComparator();
- assertEquals(0, mc.compare(copy, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetSubmodel1() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 100);
+ polygon.lineTo(100, 100);
+ polygon.lineTo(100, 0);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ assertEquals(2, copy.getElements().size());
+ assertEquals(0, copy.getReactions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodel2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(50, 50);
+ polygon.lineTo(350, 50);
+ polygon.lineTo(350, 200);
+ polygon.lineTo(50, 200);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ assertEquals(9, copy.getElements().size());
+ assertEquals(1, copy.getReactions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodel3() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 200);
+ polygon.lineTo(350, 200);
+ polygon.lineTo(350, 400);
+ polygon.lineTo(0, 400);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ double dx = 10;
+ double dy = -10;
+
+ new MoveCommand(copy, dx, dy).execute();
+
+ assertEquals(model.getElementByElementId("sa3").getCenterX(), copy.getElementByElementId("sa3").getCenterX() - dx,
+ EPSILON);
+ assertEquals(model.getElementByElementId("sa3").getCenterY(), copy.getElementByElementId("sa3").getCenterY() - dy,
+ EPSILON);
+
+ assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getX2(),
+ copy.getReactionByReactionId("re3").getLines().get(0).getX2() - dx, EPSILON);
+ assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getY2(),
+ copy.getReactionByReactionId("re3").getLines().get(0).getY2() - dy, EPSILON);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodelWithoutCompartments() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/compartments.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 10);
+ polygon.lineTo(10, 10);
+ polygon.lineTo(10, 0);
+ polygon.lineTo(0, 0);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ // we should cut off some of compartmets
+ assertFalse(model.getLayers().iterator().next().getTexts().size() == copy.getLayers().iterator().next().getTexts()
+ .size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodelWithoutCompartments2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/cutting_without_compartment.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 500);
+ polygon.lineTo(300, 500);
+ polygon.lineTo(300, 0);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+
+ ModelComparator mc = new ModelComparator();
+ assertEquals(0, mc.compare(copy, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodelWithElementIds() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 1000);
+ polygon.lineTo(1000, 1000);
+ polygon.lineTo(1000, 0);
+ polygon.closePath();
+ model.getElementByElementId("sa2").setId(-2);
+
+ Model copy = new SubModelCommand(model, polygon, new HashSet<>(Arrays.asList(-2)), new HashSet<>()).execute();
+
+ assertEquals(1, copy.getElements().size());
+ assertEquals(0, copy.getReactions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodelWithEmptyElementIds() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 1000);
+ polygon.lineTo(1000, 1000);
+ polygon.lineTo(1000, 0);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon, new HashSet<>(), new HashSet<>()).execute();
+
+ assertEquals(12, copy.getElements().size());
+ assertEquals(3, copy.getReactions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodelWithReactionIds() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 1000);
+ polygon.lineTo(1000, 1000);
+ polygon.lineTo(1000, 0);
+ polygon.closePath();
+ model.getReactions().iterator().next().setId(-2);
+
+ Model copy = new SubModelCommand(model, polygon, new HashSet<>(), new HashSet<>(Arrays.asList(-2))).execute();
+
+ assertEquals(1, copy.getReactions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index c2171f9fb93d19d327cf7e73f3fde0e92724ce88..974a5950987f032f73315b455f72e281681ed551 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -22,13 +22,8 @@ import org.springframework.web.bind.annotation.RestController;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.model.cache.FileEntry;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.services.SecurityException;
@RestController
@@ -120,50 +115,6 @@ public class ProjectController extends BaseController {
.body(file.getFileContent());
}
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadImage", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsImage(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
- ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
- DrawingException {
-
- FileEntry file = projectController.getModelAsImage(token, projectId, modelId, handlerClass, backgroundOverlayId,
- overlayIds, zoomLevel, polygonString);
- MediaType type = MediaType.APPLICATION_OCTET_STREAM;
- return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
- .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsModelFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
- ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
- ConverterException, InconsistentModelException {
-
- FileEntry file = projectController.getModelAsModelFile(token, projectId, modelId, handlerClass, backgroundOverlayId,
- overlayIds, zoomLevel, polygonString);
- MediaType type = MediaType.APPLICATION_OCTET_STREAM;
- return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
- .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
@RequestMapping(value = "/projects/{projectId}/logs/", method = { RequestMethod.GET }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getLogs(//
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 b0d4cee6b5a1daaa65835f322cb113bcb8e89719..528c189b5d01beacf58f447900357a3f34efa075 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
@@ -1,19 +1,12 @@
package lcsb.mapviewer.api.projects;
-import java.awt.Color;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileInputStream;
import java.io.IOException;
-import java.io.InputStream;
import java.io.Serializable;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.Comparator;
import java.util.HashSet;
import java.util.LinkedHashMap;
@@ -22,7 +15,6 @@ import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
-import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
@@ -34,21 +26,9 @@ import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.OperationNotAllowedException;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
-import lcsb.mapviewer.commands.ClearColorModelCommand;
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.ColorModelCommand;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
-import lcsb.mapviewer.commands.SubModelCommand;
-import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
@@ -58,7 +38,6 @@ import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.MapCanvasType;
import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.OverviewImage;
@@ -66,9 +45,6 @@ import lcsb.mapviewer.model.map.OverviewImageLink;
import lcsb.mapviewer.model.map.OverviewLink;
import lcsb.mapviewer.model.map.OverviewModelLink;
import lcsb.mapviewer.model.map.OverviewSearchLink;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -79,24 +55,12 @@ import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.utils.data.BuildInLayout;
@Transactional(value = "txManager")
public class ProjectRestImpl extends BaseRestImpl {
- /**
- * Constant defining size of the array returned by
- * {@link PathIterator#currentSegment(double[])} method. More information can be
- * found <a href=
- * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
- * >here</a>
- */
- private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
-
/**
* Default class logger.
*/
@@ -105,9 +69,6 @@ public class ProjectRestImpl extends BaseRestImpl {
@Autowired
private PublicationsRestImpl publicationsRestImpl;
- @Autowired
- private ILayoutService layoutService;
-
@Autowired
private IProjectService projectService;
@@ -240,224 +201,6 @@ public class ProjectRestImpl extends BaseRestImpl {
return project.getInputData();
}
- public FileEntry getModelAsImage(String token, String projectId, String modelId, String handlerClass,
- String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString) throws SecurityException,
- QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
- User user = getUserService().getUserByToken(token);
-
- Model topModel = getModelService().getLastModelByProjectId(projectId, token);
- if (topModel == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Model originalModel = topModel.getSubmodelById(modelId);
-
- if (originalModel == null) {
- throw new ObjectNotFoundException("Model with given id doesn't exist");
- }
-
- Layout overlay = null;
- if (!backgroundOverlayId.equals("")) {
- overlay = topModel.getLayoutByIdentifier(Integer.valueOf(backgroundOverlayId));
-
- if (overlay == null) {
- throw new ObjectNotFoundException("Unknown overlay in model. Layout.id=" + backgroundOverlayId);
- }
- } else {
- if (topModel.getLayouts().size() > 0) {
- overlay = topModel.getLayouts().get(0);
- }
- }
-
- Model colorModel = new CopyCommand(originalModel).execute();
- if (overlay != null) {
- if (overlay.getInputData() != null) {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
-
- new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute();
- } else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
- // this might not return true if we change CLEAN.title in future...
-
- // if it's clean then remove coloring
- new ClearColorModelCommand(colorModel).execute();
- } else if (overlay.isHierarchicalView()) {
- new SetFixedHierarchyLevelCommand(colorModel, overlay.getHierarchyViewLevel()).execute();
- }
- }
-
- Integer level = Configuration.MIN_ZOOM_LEVEL;
- if (!zoomLevel.equals("")) {
- level = Integer.valueOf(zoomLevel);
- }
-
- Path2D polygon = stringToPolygon(polygonString, colorModel);
-
- Double minX = originalModel.getWidth();
- Double minY = originalModel.getHeight();
- Double maxX = 0.0;
- Double maxY = 0.0;
-
- PathIterator pathIter = polygon.getPathIterator(null);
- while (!pathIter.isDone()) {
- final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
- if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
- minX = Math.min(minX, segment[0]);
- maxX = Math.max(maxX, segment[0]);
- minY = Math.min(minY, segment[1]);
- maxY = Math.max(maxY, segment[1]);
- }
- pathIter.next();
- }
-
- maxX = Math.min(originalModel.getWidth(), maxX);
- maxY = Math.min(originalModel.getHeight(), maxY);
- minX = Math.max(0.0, minX);
- minY = Math.max(0.0, minY);
-
- Double scale = Math.max(originalModel.getHeight(), originalModel.getWidth()) / (originalModel.getTileSize());
-
- for (int i = level; i > Configuration.MIN_ZOOM_LEVEL; i--) {
- scale /= 2;
- }
-
- ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user);
-
- Params params = new Params().//
- x(minX).//
- y(minY).//
- height((maxY - minY) / scale).//
- width((maxX - minX) / scale).//
- level(level - Configuration.MIN_ZOOM_LEVEL).//
- nested(false).// automatically set nested view as invalid
- scale(scale).//
- colorExtractor(colorExtractor).//
- sbgn(topModel.getProject().isSbgnFormat()).//
- model(colorModel);
- if (overlay != null) {
- params.nested(overlay.isHierarchicalView());
- }
- List<Integer> visibleLayoutIds = deserializeIdList(overlayIds);
- for (Integer integer : visibleLayoutIds) {
- Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, token);
- params.addVisibleLayout(map);
- }
-
- ImageGenerators imageGenerator = new ImageGenerators();
- String extension = imageGenerator.getExtension(handlerClass);
- File file = File.createTempFile("map", "." + extension);
-
- imageGenerator.generate(handlerClass, params, file.getAbsolutePath());
-
- UploadedFileEntry entry = new UploadedFileEntry();
- entry.setOriginalFileName("map." + extension);
- entry.setFileContent(IOUtils.toByteArray(new FileInputStream(file)));
- entry.setLength(entry.getFileContent().length);
- file.delete();
- return entry;
-
- }
-
- private Path2D stringToPolygon(String polygonString, Model colorModel) {
- String[] stringPointArray = polygonString.split(";");
-
- List<Point2D> points = new ArrayList<>();
- for (String string : stringPointArray) {
- if (!string.trim().equals("")) {
- double x = Double.valueOf(string.split(",")[0]);
- double y = Double.valueOf(string.split(",")[1]);
- points.add(new Point2D.Double(x, y));
- }
- }
-
- if (points.size() <= 2) {
- points.clear();
- points.add(new Point2D.Double(0, 0));
- points.add(new Point2D.Double(colorModel.getWidth(), 0));
- points.add(new Point2D.Double(colorModel.getWidth(), colorModel.getHeight()));
- points.add(new Point2D.Double(0, colorModel.getHeight()));
- }
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(points.get(0).getX(), points.get(0).getY());
- for (int i = 1; i < points.size(); i++) {
- Point2D point = points.get(i);
- polygon.lineTo(point.getX(), point.getY());
- }
- polygon.closePath();
- return polygon;
- }
-
- private List<Integer> deserializeIdList(String overlayIds) {
- List<Integer> result = new ArrayList<>();
- String[] tmp = overlayIds.split(",");
- for (String string : tmp) {
- if (!string.equals("")) {
- result.add(Integer.valueOf(string));
- }
- }
- return result;
- }
-
- public FileEntry getModelAsModelFile(String token, String projectId, String modelId, String handlerClass,
- String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString)
- throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
- ConverterException, InconsistentModelException {
- User user = getUserService().getUserByToken(token);
- Model topModel = getModelService().getLastModelByProjectId(projectId, token);
- if (topModel == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Model originalModel = topModel.getSubmodelById(modelId);
-
- if (originalModel == null) {
- throw new ObjectNotFoundException("Model with given id doesn't exist");
- }
-
- Path2D polygon = stringToPolygon(polygonString, originalModel);
-
- // create model bounded by the polygon
- SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon);
- Model part = subModelCommand.execute();
-
- // Get list of overlay ids
- String[] overlayIdsList;
- if (overlayIds == null || overlayIds.trim().isEmpty()) {
- overlayIdsList = new String[0];
- } else {
- overlayIdsList = overlayIds.split(",");
- }
- // Remove all colors
- if (overlayIdsList.length > 0) {
-
- for (Element element : part.getElements()) {
- element.setColor(Color.WHITE);
- }
- }
- // Color with overlays
- for (String overlayId : overlayIdsList) {
- Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token);
-
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
-
- new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
- }
-
- IConverter parser = getModelParser(handlerClass);
- InputStream is = parser.exportModelToInputStream(part);
-
- String fileExtension = parser.getFileExtension();
-
- UploadedFileEntry entry = new UploadedFileEntry();
- entry.setOriginalFileName("model." + fileExtension);
- entry.setFileContent(IOUtils.toByteArray(is));
- entry.setLength(entry.getFileContent().length);
- return entry;
-
- }
-
public Map<String, Object> getStatistics(String projectId, String token)
throws SecurityException, ObjectNotFoundException {
Map<String, Object> result = new TreeMap<>();
@@ -740,7 +483,8 @@ public class ProjectRestImpl extends BaseRestImpl {
public Map<String, Object> removeProject(String token, String projectId, String path)
throws SecurityException, QueryException {
Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (getConfigurationService().getConfigurationValue(ConfigurationElementType.DEFAULT_MAP).equals(project.getProjectId())) {
+ if (getConfigurationService().getConfigurationValue(ConfigurationElementType.DEFAULT_MAP)
+ .equals(project.getProjectId())) {
throw new OperationNotAllowedException("You cannot remove default map");
}
getProjectService().removeProject(project, path, true, token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
index aa9b1dbe903dcf34c32f13e835d5ec62cb9d3841..c72604753660d2bfb4462e08e3271b41e277a4a7 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
@@ -6,11 +6,13 @@ import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.CookieValue;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import com.fasterxml.jackson.core.JsonParseException;
@@ -19,7 +21,13 @@ import com.fasterxml.jackson.databind.JsonMappingException;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.cache.FileEntry;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.services.SecurityException;
@RestController
@@ -63,4 +71,50 @@ public class ModelController extends BaseController {
return modelController.updateModel(projectId, modelId, data, token);
}
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadImage", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getModelAsImage(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "handlerClass") String handlerClass, //
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
+ ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ DrawingException {
+
+ FileEntry file = modelController.getModelAsImage(token, projectId, modelId, handlerClass, backgroundOverlayId,
+ overlayIds, zoomLevel, polygonString);
+ MediaType type = MediaType.APPLICATION_OCTET_STREAM;
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = { RequestMethod.GET,
+ RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getModelAsModelFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "handlerClass") String handlerClass, //
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString, //
+ @RequestParam(value = "elementIds", defaultValue = "") String elementIds, //
+ @RequestParam(value = "reactionIds", defaultValue = "") String reactionIds //
+ ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ ConverterException, InconsistentModelException {
+
+ FileEntry file = modelController.getModelAsModelFile(token, projectId, modelId, handlerClass, backgroundOverlayId,
+ overlayIds, zoomLevel, polygonString, elementIds, reactionIds);
+ MediaType type = MediaType.APPLICATION_OCTET_STREAM;
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
}
\ No newline at end of file
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 5e3659dbc1a4d3ece5da1918825bc07267448108..bf5adaf6922b73d6f059e71c5b02f80309e6466d 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
@@ -1,29 +1,76 @@
package lcsb.mapviewer.api.projects.models;
+import java.awt.Color;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.commons.io.IOUtils;
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.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.commands.ClearColorModelCommand;
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.commands.ColorModelCommand;
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
+import lcsb.mapviewer.commands.SubModelCommand;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.FileEntry;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+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.SubmodelType;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.utils.ColorSchemaReader;
+import lcsb.mapviewer.services.utils.data.BuildInLayout;
@Transactional(value = "txManager")
public class ModelRestImpl extends BaseRestImpl {
+ /**
+ * Constant defining size of the array returned by
+ * {@link PathIterator#currentSegment(double[])} method. More information can be
+ * found <a href=
+ * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
+ * >here</a>
+ */
+ private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
+
+ @Autowired
+ private ILayoutService layoutService;
+
/**
* Default class logger.
*/
@@ -132,7 +179,6 @@ public class ModelRestImpl extends BaseRestImpl {
} else {
throw new InvalidArgumentException();
}
-
}
private Double parseDouble(Object value) throws QueryException {
@@ -156,4 +202,249 @@ public class ModelRestImpl extends BaseRestImpl {
throw new QueryException("Don't know how to change " + value.getClass() + " into Double");
}
}
+
+ public FileEntry getModelAsModelFile(String token, String projectId, String modelId, String handlerClass,
+ String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString, String elementIds,
+ String reactionIds) throws SecurityException, QueryException, IOException, InvalidColorSchemaException,
+ CommandExecutionException, ConverterException, InconsistentModelException {
+ User user = getUserService().getUserByToken(token);
+ Model originalModel = getModelByModelId(token, projectId, modelId);
+
+ Path2D polygon = stringToPolygon(polygonString, originalModel);
+
+ Set<Integer> elementIdsList = stringListToIntegerSet(elementIds);
+ Set<Integer> reactionIdsList = stringListToIntegerSet(reactionIds);
+
+ // create model bounded by the polygon
+ SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon, elementIdsList, reactionIdsList);
+ Model part = subModelCommand.execute();
+
+ // Get list of overlay ids
+ String[] overlayIdsList = stringListToArray(overlayIds);
+ // Remove all colors
+ if (overlayIdsList.length > 0) {
+ for (Element element : part.getElements()) {
+ element.setColor(Color.WHITE);
+ }
+ }
+ // Color with overlays
+ for (String overlayId : overlayIdsList) {
+ Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token);
+
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+
+ new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
+ }
+
+ IConverter parser = getModelParser(handlerClass);
+ InputStream is = parser.exportModelToInputStream(part);
+
+ String fileExtension = parser.getFileExtension();
+
+ UploadedFileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName("model." + fileExtension);
+ entry.setFileContent(IOUtils.toByteArray(is));
+ entry.setLength(entry.getFileContent().length);
+ return entry;
+
+ }
+
+ protected Set<Integer> stringListToIntegerSet(String elementIds) {
+ Set<Integer> result = new HashSet<>();
+ if (elementIds != null) {
+ String[] stringIds = elementIds.split(",");
+ for (String string : stringIds) {
+ if (!string.trim().isEmpty()) {
+ result.add(Integer.valueOf(string));
+ }
+ }
+ }
+ return result;
+ }
+
+ private Model getModelByModelId(String token, String projectId, String modelId)
+ throws SecurityException, ObjectNotFoundException {
+ Model topModel = getModelService().getLastModelByProjectId(projectId, token);
+ if (topModel == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Model originalModel = topModel.getSubmodelById(modelId);
+
+ if (originalModel == null) {
+ throw new ObjectNotFoundException("Model with given id doesn't exist");
+ }
+ return originalModel;
+ }
+
+ private String[] stringListToArray(String overlayIds) {
+ String[] overlayIdsList;
+ if (overlayIds == null || overlayIds.trim().isEmpty()) {
+ overlayIdsList = new String[0];
+ } else {
+ overlayIdsList = overlayIds.split(",");
+ }
+ return overlayIdsList;
+ }
+
+ public FileEntry getModelAsImage(String token, String projectId, String modelId, String handlerClass,
+ String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString) throws SecurityException,
+ QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
+ User user = getUserService().getUserByToken(token);
+
+ Model topModel = getModelService().getLastModelByProjectId(projectId, token);
+ if (topModel == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Model originalModel = topModel.getSubmodelById(modelId);
+
+ if (originalModel == null) {
+ throw new ObjectNotFoundException("Model with given id doesn't exist");
+ }
+
+ Layout overlay = null;
+ if (!backgroundOverlayId.equals("")) {
+ overlay = topModel.getLayoutByIdentifier(Integer.valueOf(backgroundOverlayId));
+
+ if (overlay == null) {
+ throw new ObjectNotFoundException("Unknown overlay in model. Layout.id=" + backgroundOverlayId);
+ }
+ } else {
+ if (topModel.getLayouts().size() > 0) {
+ overlay = topModel.getLayouts().get(0);
+ }
+ }
+
+ Model colorModel = new CopyCommand(originalModel).execute();
+ if (overlay != null) {
+ if (overlay.getInputData() != null) {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+
+ new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute();
+ } else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
+ // this might not return true if we change CLEAN.title in future...
+
+ // if it's clean then remove coloring
+ new ClearColorModelCommand(colorModel).execute();
+ } else if (overlay.isHierarchicalView()) {
+ new SetFixedHierarchyLevelCommand(colorModel, overlay.getHierarchyViewLevel()).execute();
+ }
+ }
+
+ Integer level = Configuration.MIN_ZOOM_LEVEL;
+ if (!zoomLevel.equals("")) {
+ level = Integer.valueOf(zoomLevel);
+ }
+
+ Path2D polygon = stringToPolygon(polygonString, colorModel);
+
+ Double minX = originalModel.getWidth();
+ Double minY = originalModel.getHeight();
+ Double maxX = 0.0;
+ Double maxY = 0.0;
+
+ PathIterator pathIter = polygon.getPathIterator(null);
+ while (!pathIter.isDone()) {
+ final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
+ if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
+ minX = Math.min(minX, segment[0]);
+ maxX = Math.max(maxX, segment[0]);
+ minY = Math.min(minY, segment[1]);
+ maxY = Math.max(maxY, segment[1]);
+ }
+ pathIter.next();
+ }
+
+ maxX = Math.min(originalModel.getWidth(), maxX);
+ maxY = Math.min(originalModel.getHeight(), maxY);
+ minX = Math.max(0.0, minX);
+ minY = Math.max(0.0, minY);
+
+ Double scale = Math.max(originalModel.getHeight(), originalModel.getWidth()) / (originalModel.getTileSize());
+
+ for (int i = level; i > Configuration.MIN_ZOOM_LEVEL; i--) {
+ scale /= 2;
+ }
+
+ ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user);
+
+ Params params = new Params().//
+ x(minX).//
+ y(minY).//
+ height((maxY - minY) / scale).//
+ width((maxX - minX) / scale).//
+ level(level - Configuration.MIN_ZOOM_LEVEL).//
+ nested(false).// automatically set nested view as invalid
+ scale(scale).//
+ colorExtractor(colorExtractor).//
+ sbgn(topModel.getProject().isSbgnFormat()).//
+ model(colorModel);
+ if (overlay != null) {
+ params.nested(overlay.isHierarchicalView());
+ }
+ List<Integer> visibleLayoutIds = deserializeIdList(overlayIds);
+ for (Integer integer : visibleLayoutIds) {
+ Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, token);
+ params.addVisibleLayout(map);
+ }
+
+ ImageGenerators imageGenerator = new ImageGenerators();
+ String extension = imageGenerator.getExtension(handlerClass);
+ File file = File.createTempFile("map", "." + extension);
+
+ imageGenerator.generate(handlerClass, params, file.getAbsolutePath());
+
+ UploadedFileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName("map." + extension);
+ entry.setFileContent(IOUtils.toByteArray(new FileInputStream(file)));
+ entry.setLength(entry.getFileContent().length);
+ file.delete();
+ return entry;
+
+ }
+
+ private Path2D stringToPolygon(String polygonString, Model colorModel) {
+ String[] stringPointArray = polygonString.split(";");
+
+ List<Point2D> points = new ArrayList<>();
+ for (String string : stringPointArray) {
+ if (!string.trim().equals("")) {
+ double x = Double.valueOf(string.split(",")[0]);
+ double y = Double.valueOf(string.split(",")[1]);
+ points.add(new Point2D.Double(x, y));
+ }
+ }
+
+ if (points.size() <= 2) {
+ points.clear();
+ points.add(new Point2D.Double(0, 0));
+ points.add(new Point2D.Double(colorModel.getWidth(), 0));
+ points.add(new Point2D.Double(colorModel.getWidth(), colorModel.getHeight()));
+ points.add(new Point2D.Double(0, colorModel.getHeight()));
+ }
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(points.get(0).getX(), points.get(0).getY());
+ for (int i = 1; i < points.size(); i++) {
+ Point2D point = points.get(i);
+ polygon.lineTo(point.getX(), point.getY());
+ }
+ polygon.closePath();
+ return polygon;
+ }
+
+ private List<Integer> deserializeIdList(String overlayIds) {
+ List<Integer> result = new ArrayList<>();
+ String[] tmp = overlayIds.split(",");
+ for (String string : tmp) {
+ if (!string.equals("")) {
+ result.add(Integer.valueOf(string));
+ }
+ }
+ return result;
+ }
+
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
index 047dc151eb97251d2100ffab99867fed5b30afa5..195a8d73a56c803e0253ebcd57f1a73c9e012b71 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
@@ -187,9 +187,13 @@ public class ConvertRestImplTest extends RestTestFunctions {
String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
ByteArrayOutputStream result1 = convertRestImpl.converToImage(token, "SBML", "svg", result);
- FileOutputStream outputStream = new FileOutputStream("testFiles/convert/glycolysis2.svg");
+ File output = new File("testFiles/convert/glycolysis2.svg");
+
+ FileOutputStream outputStream = new FileOutputStream(output);
outputStream.write(result1.toByteArray());
outputStream.close();
+ assertTrue(output.exists());
+ output.delete();
} catch (Exception e) {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index 79afcc01ea2719718cb3cd963afb71ac545c066d..60688c8ccacebe8141366abac7056c762baf23ea 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -4,9 +4,8 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.times;
import java.util.ArrayList;
@@ -28,17 +27,12 @@ import org.springframework.util.MultiValueMap;
import com.google.gson.Gson;
import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.persist.dao.ProjectDao;
@@ -71,32 +65,6 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void tearDown() throws Exception {
}
- @Test
- public void testGetModelAsImageForInvalidConverter() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token, "sample", "0", "", "", "", "", "");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsImage() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- FileEntry result = projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(),
- "", "", "", "");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testGetModelDataDependencies() throws Exception {
try {
@@ -117,55 +85,6 @@ public class ProjectRestImplTest extends RestTestFunctions {
projectRest.getProject("unknown_model_id", token);
}
- @Test
- public void testGetModelAsImage2() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "");
- fail("Exception expected");
- } catch (QueryException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel2() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token, "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "", "", "",
- "0,0;90,0;90,90;90,0");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel3() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0");
- fail("Exception expected");
- } catch (QueryException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testGetProject() throws Exception {
try {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
index d3435cc35db0867789a427c34393ba3d98e1d809..80fe6f15bc32b675e78678324bae8452893aef32 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
@@ -1,12 +1,15 @@
package lcsb.mapviewer.api.projects.models;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.ArgumentMatchers.refEq;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import org.junit.After;
import org.junit.Before;
@@ -14,8 +17,13 @@ import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
+import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IProjectService;
@@ -93,4 +101,101 @@ public class ModelRestImplTest extends RestTestFunctions {
return _modelRestImpl;
}
+ @Test
+ public void testGetModelAsImageForInvalidConverter() throws Exception {
+ try {
+ ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
+ modelRest.getModelAsImage(token, "sample", "0", "", "", "", "", "");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsImage() throws Exception {
+ try {
+ ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
+ FileEntry result = modelRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(), "",
+ "", "", "");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsImage2() throws Exception {
+ try {
+ ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
+ modelRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel() throws Exception {
+ try {
+ ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
+ modelRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "", null, null);
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel2() throws Exception {
+ try {
+ ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
+ modelRest.getModelAsModelFile(token, "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "", "", "",
+ "0,0;90,0;90,90;90,0", null, null);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel3() throws Exception {
+ try {
+ ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
+ modelRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0", null, null);
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEmptyStringListToIntegerList() throws Exception {
+ try {
+ Set<Integer> ids = _modelRestImpl.stringListToIntegerSet("");
+ assertNotNull(ids);
+ assertEquals(0, ids.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testStringListToIntegerArray() throws Exception {
+ try {
+ Set<Integer> ids = _modelRestImpl.stringListToIntegerSet("12,3");
+ assertNotNull(ids);
+ assertEquals(2, ids.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}