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/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
index d350d59b6131c28a72bc47bb2f8ba281a0018a74..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
@@ -93,8 +93,8 @@ public class ModelController extends BaseController {
.body(file.getFileContent());
}
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ @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, //
@@ -103,12 +103,14 @@ public class ModelController extends BaseController {
@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 = "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);
+ 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())
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 f735bb5937aa81e1c578ebfb0d15a1142caa8d6e..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
@@ -10,6 +10,7 @@ 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;
@@ -58,8 +59,6 @@ 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
@@ -180,7 +179,6 @@ public class ModelRestImpl extends BaseRestImpl {
} else {
throw new InvalidArgumentException();
}
-
}
private Double parseDouble(Object value) throws QueryException {
@@ -206,37 +204,25 @@ public class ModelRestImpl extends BaseRestImpl {
}
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 {
+ 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 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");
- }
+ 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);
+ SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon, elementIdsList, reactionIdsList);
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(",");
- }
+ String[] overlayIdsList = stringListToArray(overlayIds);
// Remove all colors
if (overlayIdsList.length > 0) {
-
for (Element element : part.getElements()) {
element.setColor(Color.WHITE);
}
@@ -264,6 +250,43 @@ public class ModelRestImpl extends BaseRestImpl {
}
+ 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,
@@ -424,5 +447,4 @@ public class ModelRestImpl extends BaseRestImpl {
return result;
}
-
}
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 75e4f09a45a7bffdb355311eaf3b0e8891a6f6e1..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
@@ -9,6 +9,7 @@ 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;
@@ -117,8 +118,8 @@ public class ModelRestImplTest extends RestTestFunctions {
public void testGetModelAsImage() throws Exception {
try {
ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
- FileEntry result = modelRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(),
- "", "", "", "");
+ FileEntry result = modelRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(), "",
+ "", "", "");
assertNotNull(result);
} catch (Exception e) {
e.printStackTrace();
@@ -141,7 +142,7 @@ public class ModelRestImplTest extends RestTestFunctions {
public void testGetModelAsFileModel() throws Exception {
try {
ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
- modelRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "");
+ modelRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "", null, null);
fail("Exception expected");
} catch (QueryException e) {
} catch (Exception e) {
@@ -155,7 +156,7 @@ public class ModelRestImplTest extends RestTestFunctions {
try {
ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
modelRest.getModelAsModelFile(token, "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "", "", "",
- "0,0;90,0;90,90;90,0");
+ "0,0;90,0;90,90;90,0", null, null);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -166,7 +167,7 @@ public class ModelRestImplTest extends RestTestFunctions {
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");
+ modelRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0", null, null);
fail("Exception expected");
} catch (QueryException e) {
} catch (Exception e) {
@@ -175,5 +176,26 @@ public class ModelRestImplTest extends RestTestFunctions {
}
}
-
+ @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;
+ }
+ }
}