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..d350d59b6131c28a72bc47bb2f8ba281a0018a74 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 +71,48 @@ 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 }, 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 = modelController.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());
+ }
+
}
\ 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..f735bb5937aa81e1c578ebfb0d15a1142caa8d6e 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 +1,77 @@
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.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.
*/
@@ -156,4 +204,225 @@ 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)
+ 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 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/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..75e4f09a45a7bffdb355311eaf3b0e8891a6f6e1 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
@@ -1,6 +1,8 @@
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;
@@ -14,8 +16,13 @@ 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 +100,80 @@ 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", "", "", "", "", "");
+ 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");
+ } 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");
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
}