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Commit 8a1d6600 authored by Piotr Gawron's avatar Piotr Gawron
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remove of unused feedback backend functionality 

additional small fixes on service layer (security errors were thrown too
often)
tests fixed
parent 6dba4a2a
Show whitespace changes
Inline Side-by-side
service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
View file @ 8a1d6600
......@@ -175,7 +175,7 @@ public class ModelService implements IModelService {
// lets copy model - it will access all elements...
new CopyCommand(model).execute();
for (ModelData m: model.getProject().getModels()) {
for (ModelData m : model.getProject().getModels()) {
new CopyCommand(m.getModel()).execute();
}
......@@ -188,10 +188,14 @@ public class ModelService implements IModelService {
}
}
}
if (!userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, model.getProject())) {
if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, model.getProject())) {
return model;
} else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
return model;
} else {
logger.debug(userService.getUserByToken(token).getLogin());
throw new SecurityException("User doesn't have access to project");
}
return model;
}
@Override
......
service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
View file @ 8a1d6600
......@@ -524,10 +524,13 @@ public class ProjectService implements IProjectService {
@Override
public ProjectView getProjectViewById(Integer id, AuthenticationToken token) throws UserAccessException {
Project project = projectDao.getById(id);
if (!userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
return projectViewFactory.create(project);
} else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
return projectViewFactory.create(project);
} else {
throw new UserAccessException("User cannot access project");
}
return projectViewFactory.create(project);
}
/**
......
web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
View file @ 8a1d6600
package lcsb.mapviewer.bean;
import java.awt.geom.Point2D;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
......@@ -11,29 +10,15 @@ import javax.faces.bean.ViewScoped;
import javax.faces.event.ActionEvent;
import org.apache.log4j.Logger;
import org.primefaces.model.map.LatLng;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.interfaces.ICommentService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.ElementIdentifierDetails;
import lcsb.mapviewer.services.search.comment.FullCommentView;
import lcsb.mapviewer.services.search.comment.FullCommentViewFactory;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
import lcsb.mapviewer.services.view.CommentView;
/**
......@@ -44,23 +29,7 @@ import lcsb.mapviewer.services.view.CommentView;
*/
@ManagedBean(name = "feedbackMB")
@ViewScoped
public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> implements Serializable {
/**
* How many elements to comment should be seen in drop down list on the client
* side.
*/
private static final int MAX_FEEDBACK_ELEMENTS_AMOUNT = 5;
/**
* What's the name of the general comment.
*/
private static final String GENERAL_POSITION = "<General>";
/**
* Feedback form on the client side.
*/
private static final String FEEDBACK_FORM_STRING = "feedbackForm";
public class FeedbackBean extends AbstractManagedBean implements Serializable {
/**
*
......@@ -72,56 +41,11 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
*/
private static Logger logger = Logger.getLogger(FeedbackBean.class);
/**
* Element to which we create comment.
*/
private String feedbackElement = GENERAL_POSITION;
/**
* List of possible elements to comment (names only).
*/
private List<String> feedbackElementStringList = new ArrayList<>();
/**
* Information if the comment should be visible.
*/
private boolean pinned = true;
/**
* Who put a comment.
*/
private String name = "";
/**
* Email of a person that comments.
*/
private String email = "";
/**
* Content of the comment.
*/
private String content = "";
/**
* List of comments available for current project.
*/
private List<CommentView> commentList = null;
/**
* Coordinates where comment should be placed.
*/
private Point2D lastCommentCoordinates = null;
/**
* List of possible elements to comment.
*/
private transient List<Object> feedbackElementList = new ArrayList<>();
/**
* Submodel that is currently commented.
*/
private transient Model commentedSubmodel = null;
/**
* Bean used for communication with the client side about the data related to
* users (including information about currently logged user).
......@@ -160,195 +84,6 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
@ManagedProperty(value = "#{UserService}")
private transient IUserService userService;
/**
* Method invoked by client to send a comment.
*
* @param actionEvent
* event from thefrom the client
*/
public void sendFeedback(final ActionEvent actionEvent) {
String feedbackName = getRequestParameter(FEEDBACK_FORM_STRING + ":feedbackName");
String feedbackEmail = getRequestParameter(FEEDBACK_FORM_STRING + ":feedbackEmail");
String feedbackContent = getRequestParameter(FEEDBACK_FORM_STRING + ":feedbackContent");
// find which object we are commenting on
Object tmp = null;
for (Object object : feedbackElementList) {
if (feedbackElement.equals(getDescription(object))) {
tmp = object;
}
}
// add a comment to db
commentService.addComment(feedbackName, feedbackEmail, feedbackContent, getCurrentTopModel(), lastCommentCoordinates, tmp, pinned, commentedSubmodel);
clearNameAndEmail();
content = "";
// refresh list of comments on the client side
refreshComments();
}
/**
* Set default values to {@link #name} and {@link #email}.
*/
private void clearNameAndEmail() {
if (getUserBean().getLoggedUser() != null) {
User user = getUserBean().getLoggedUser();
if (Configuration.ANONYMOUS_LOGIN.equals(user.getLogin())) {
name = "";
email = "";
} else {
name = user.getName() + " " + user.getSurname();
email = user.getEmail();
}
}
}
/**
* Method invoked by client to update list of elements to be commented based
* on coordinates in request params.
*
* @param actionEvent
* event from thefrom the client
*/
public void updateCommentList(final ActionEvent actionEvent) {
String latCoord = getRequestParameter("latCoord");
String lngCoord = getRequestParameter("lngCoord");
String modelIdentifier = getRequestParameter("submodelId");
LatLng latLng;
double lat = Double.parseDouble(latCoord);
double lng = Double.parseDouble(lngCoord);
latLng = new LatLng(lat, lng);
commentedSubmodel = getCurrentTopModel().getSubmodelById(modelIdentifier);
CoordinationConverter cc = new CoordinationConverter(commentedSubmodel);
lastCommentCoordinates = cc.toPoint(latLng);
feedbackElementList = searchService.getClosestElements(commentedSubmodel, lastCommentCoordinates, MAX_FEEDBACK_ELEMENTS_AMOUNT);
feedbackElementStringList = new ArrayList<String>();
feedbackElementStringList.add(GENERAL_POSITION);
for (Object object : feedbackElementList) {
String desc = getDescription(object);
feedbackElementStringList.add(desc);
}
}
/**
* Methods returns a list of elements that might be possible commented on
* based on the coordinates.
*
* @return list of closes elements (to the last coordinates of the mouse on
* the map) on the map that can be commoneted on
*/
public List<String> getFeedbackElementStringList() {
return feedbackElementStringList;
}
/**
* This method get a short description of the object to comment.
*
* @param object
* object for which we want a description
* @return short description of the object
*/
public String getDescription(final Object object) {
if (object instanceof Reaction) {
return "Reaction: " + ((Reaction) object).getIdReaction();
} else if (object instanceof Element) {
Element alias = (Element) object;
return alias.getStringType() + ": " + alias.getName();
} else {
throw new InvalidArgumentException("Unknown class type: " + object.getClass());
}
}
/**
* Sets list of elements for possible comment objects.
*
* @param feedbackElementStringList
* list of string representation of the elements to be commoneted on
*/
public void setFeedbackElementStringList(final List<String> feedbackElementStringList) {
this.feedbackElementStringList = feedbackElementStringList;
}
/**
* This method returns a description of the reactants for the selected
* reaction. TODO should be improved
*
* @return description of the reactants for the selected reaction
*/
public String getElementDescription1() {
// iterate over every potentail element to comment on
for (Object object : feedbackElementList) {
// check only reactions
if (object instanceof Reaction) {
Reaction reaction = (Reaction) object;
// with the same description as currently selected
if (feedbackElement.equals(getDescription(object))) {
String result = "Reactants: ";
for (Reactant reactant : reaction.getReactants()) {
result += reactant.getElement().getName() + ", ";
}
return result;
}
}
}
return "";
}
/**
* This method returns a description of the products for the selected
* reaction. TODO should be improved
*
* @return description of the products for the selected reaction
*/
public String getElementDescription3() {
// iterate over every potential element to comment on
for (Object object : feedbackElementList) {
// check only reactions
if (object instanceof Reaction) {
Reaction reaction = (Reaction) object;
// with the same description as currently selected object
if (feedbackElement.equals(getDescription(object))) {
String result = "Products: ";
for (Product product : reaction.getProducts()) {
result += product.getElement().getName() + ", ";
}
return result;
}
}
}
return "";
}
/**
* This method returns a description of the modifiers for the selected
* reaction. TODO should be improved
*
* @return description of the modifiers for the selected reaction
*/
public String getElementDescription2() {
// iterate over every potential element to comment on
for (Object object : feedbackElementList) {
// check only reactions
if (object instanceof Reaction) {
Reaction reaction = (Reaction) object;
// with the same description as currently selected object
if (feedbackElement.equals(getDescription(object))) {
String result = "Modifiers: ";
for (Modifier modifier : reaction.getModifiers()) {
result += modifier.getElement().getName() + ", ";
}
return result;
}
}
}
return "";
}
/**
* Method called to remove comment from the map.
*
......@@ -368,7 +103,7 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
} catch (InvalidArgumentException e) {
logger.error(e.getMessage(), e);
}
refreshComments();
refreshCommentList();
}
/**
......@@ -409,25 +144,6 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
@Override
public void clear() {
setCommentList(new ArrayList<>());
clearResults();
refreshDataInJavascript();
}
/**
* @return the feedbackElement
* @see #feedbackElement
*/
public String getFeedbackElement() {
return feedbackElement;
}
/**
* @param feedbackElement
* the feedbackElement to set
* @see #feedbackElement
*/
public void setFeedbackElement(String feedbackElement) {
this.feedbackElement = feedbackElement;
}
/**
......@@ -498,74 +214,6 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
this.userService = userService;
}
/**
* @return the pinned
* @see #pinned
*/
public boolean isPinned() {
return pinned;
}
/**
* @param pinned
* the pinned to set
* @see #pinned
*/
public void setPinned(boolean pinned) {
this.pinned = pinned;
}
/**
* @return the name
* @see #name
*/
public String getName() {
return name;
}
/**
* @param name
* the name to set
* @see #name
*/
public void setName(String name) {
this.name = name;
}
/**
* @return the email
* @see #email
*/
public String getEmail() {
return email;
}
/**
* @param email
* the email to set
* @see #email
*/
public void setEmail(String email) {
this.email = email;
}
/**
* @return the content
* @see #content
*/
public String getContent() {
return content;
}
/**
* @param content
* the content to set
* @see #content
*/
public void setContent(String content) {
this.content = content;
}
/**
* @return the commentList
* @see #commentList
......@@ -586,42 +234,6 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
this.commentList = commentList;
}
@Override
public void init() {
clearNameAndEmail();
}
/**
* Refresh list of comments to be visualized.
*/
protected void refreshComments() {
clearResults();
for (FullCommentView marker : commentService.getCommentMarkers(getCurrentTopModel())) {
addResult(marker);
}
refreshDataInJavascript();
}
@Override
protected List<ElementIdentifier> getLightElementsForSearchResult(FullCommentView view) {
return new FullCommentViewFactory().searchResultToElementIdentifier(view, getCurrentTopModel());
}
@Override
protected ElementIdentifierDetails getElementInformationForResult(ElementIdentifier element, FullCommentView result) {
throw new NotImplementedException();
}
@Override
protected List<Pair<String, ElementIdentifierDetails>> getElementInformationForResult(ElementIdentifier element) {
List<Pair<String, ElementIdentifierDetails>> result = new ArrayList<>();
int counter = 0;
for (ElementIdentifierDetails detail : commentService.getElementInformationForResult(element, getCurrentTopModel())) {
result.add(new Pair<String, ElementIdentifierDetails>("" + (counter++), detail));
}
return result;
}
/**
* Returns currently browsed map.
*
......@@ -658,4 +270,9 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
this.mapBean = mapBean;
}
@Override
public void init() {
clear();
}
}
web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
View file @ 8a1d6600
......@@ -740,7 +740,7 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
logger.debug("Selected project was set to: " + this.selectedProject.getProjectId());
} catch (PropertyVetoException e) {
this.selectedProject = oldValue;
sendError(e.getMessage());
sendError(e.getMessage(), e);
}
}
......
web/src/test/java/lcsb/mapviewer/bean/DrugBeanTest.java
View file @ 8a1d6600
......@@ -12,7 +12,6 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
......@@ -20,7 +19,6 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.search.ElementIdentifierDetails;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
import lcsb.mapviewer.services.view.AuthenticationToken;
public class DrugBeanTest extends WebTestFunctions {
......@@ -39,15 +37,15 @@ public class DrugBeanTest extends WebTestFunctions {
// commit at the end of the test case
dbUtils.createSessionForCurrentThread();
Project p = projectService.getProjectByProjectId(projectId,token);
Project p = projectService.getProjectByProjectId(projectId, adminToken);
if (p != null) {
projectService.removeProject(p, null, false, token);
projectService.removeProject(p, null, false, adminToken);
}
}
@After
public void tearDown() throws Exception {
Project p = projectService.getProjectByProjectId(projectId, token);
Project p = projectService.getProjectByProjectId(projectId, adminToken);
if (p != null) {
projectService.removeProject(p, null, false, adminToken);
}
......@@ -86,10 +84,13 @@ public class DrugBeanTest extends WebTestFunctions {
projectDao.refresh(project);
model = project.getModels().iterator().next().getModel();
getUserBean().setAuthenticationToken(adminToken);
// set current map
getMapBean().setCurrentMapId(project.getProjectId());
List<Pair<String, ElementIdentifierDetails>> result = drugBean.getElementInformationForResult(new ElementIdentifier(model.getElementByElementId("sa2"), ""));
List<Pair<String, ElementIdentifierDetails>> result = drugBean
.getElementInformationForResult(new ElementIdentifier(model.getElementByElementId("sa2"), ""));
assertTrue(result.size() > 0);
......
web/src/test/java/lcsb/mapviewer/bean/LayoutBeanTest.java
View file @ 8a1d6600
......@@ -14,6 +14,7 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.Project;
......@@ -23,6 +24,7 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.user.BasicPrivilege;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.LayoutDao;
import lcsb.mapviewer.services.view.ProjectView;
......@@ -56,7 +58,7 @@ public class LayoutBeanTest extends WebTestFunctions {
createUser();
Project p = projectService.getProjectByProjectId(projectId, token);
Project p = projectService.getProjectByProjectId(projectId, adminToken);
if (p != null) {
projectService.removeProject(p, null, false, adminToken);
}
......@@ -67,7 +69,7 @@ public class LayoutBeanTest extends WebTestFunctions {
public void tearDown() throws Exception {
userDao.delete(user);