diff --git a/web/src/main/java/lcsb/mapviewer/bean/AbstractManagedBean.java b/web/src/main/java/lcsb/mapviewer/bean/AbstractManagedBean.java
deleted file mode 100644
index 8caa363dc146f987a72b0b54178b16376a29fc62..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/AbstractManagedBean.java
+++ /dev/null
@@ -1,547 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-import java.beans.PropertyVetoException;
-import java.beans.VetoableChangeListener;
-import java.beans.VetoableChangeSupport;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintStream;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.annotation.PostConstruct;
-import javax.faces.component.UIComponent;
-import javax.faces.context.ExternalContext;
-import javax.faces.context.FacesContext;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.bean.utils.IPrimefacesUtils;
-import lcsb.mapviewer.bean.utils.PrimefacesUtils;
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.events.Event;
-import lcsb.mapviewer.events.Listener;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Abstarct bean class containing basic functionality common for all beans
- * (property change listeners and vetoable property change listeners).
- *
- * @author Piotr Gawron
- *
- */
-public abstract class AbstractManagedBean implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Util class used to access information about current reqruest and general
- * information about P framework.
- */
- private transient IPrimefacesUtils primefacesUtils = new PrimefacesUtils();
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(AbstractManagedBean.class);
-
- /**
- * Set of verification listeners called when some property is changed. It's
- * marked transient because we don't want to store this in session. TODO it's
- * should be modified.
- */
- private final VetoableChangeSupport vchs = new VetoableChangeSupport(this);
-
- /**
- * Set of listeners called when some property is changed. It's marked
- * transient because we don't want to store this in session. TODO it's should
- * be modified.
- */
- private final PropertyChangeSupport pchs = new PropertyChangeSupport(this);
-
- /**
- * This map contains information about {@link Listener listeners} that should
- * be handled when {@link #callListeners(Event)} method is called. It's marked
- * transient because we don't want to store this in session. TODO it's should
- * be modified.
- */
- private transient Map<Class<? extends Event>, List<Listener<?>>> listeners = new HashMap<Class<? extends Event>, List<Listener<?>>>();
-
-
- /**
- * Default constructor. Adds generic log listener to property change
- * listeners.
- */
- public AbstractManagedBean() {
- // logger property listener
- PropertyChangeListener propertyChangeLogger = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: " + arg0.getOldValue() + " New: " + arg0.getNewValue());
- }
-
- };
- addPropertyChangeListener(propertyChangeLogger);
-
- }
-
- /**
- * Method run after creating all the beans. It's used for data initalization.
- */
- public abstract void init();
-
- /**
- * Initialize common data and call custom initializer of the bean.
- */
- @PostConstruct
- public void internalInit() {
- createSession();
- logger.debug("Initializing bean: " + this);
-
- // call init method for specific bean
- init();
- logger.debug("Bean: " + this + " initialized.");
- }
-
- /**
- * Creates http session if session hasn't been created yet.
- */
- public void createSession() {
- getPrimefacesUtils().createSession();
- }
-
- /**
- * Add property change listener that can VETO (cancel) the property change.
- *
- * @param listener
- * property listener
- */
- public final void addVetoablePropertyChangeListener(final VetoableChangeListener listener) {
- vchs.addVetoableChangeListener(listener);
- }
-
- /**
- * Removes property change l;istener that can VETO from the available
- * listeners.
- *
- * @param listener
- * listeren to be removed
- */
- public final void removeVetoablePropertyChangeListener(final VetoableChangeListener listener) {
- vchs.removeVetoableChangeListener(listener);
- }
-
- /**
- * Adds property change listener that is fired after property of a bean is
- * changed.
- *
- * @param listener
- * listener to be added
- */
- public final void addPropertyChangeListener(final PropertyChangeListener listener) {
- pchs.addPropertyChangeListener(listener);
- }
-
- /**
- * Removes property change listener from the list of all available listeners.
- *
- * @param listener
- * listener to be removed
- */
- public final void removePropertyChangeListener(final PropertyChangeListener listener) {
- pchs.removePropertyChangeListener(listener);
- }
-
- /**
- * Method that fires all vetoable property change listener for a given
- * property.
- *
- * @param propertyName
- * property that has changed
- * @param oldValue
- * old value of the property
- * @param newValue
- * new value of the property
- * @throws PropertyVetoException
- * if the change shouldn't be made this exception is thrown
- */
- protected final void fireVetoableChange(final String propertyName, final Object oldValue, final Object newValue) throws PropertyVetoException {
- vchs.fireVetoableChange(propertyName, oldValue, newValue);
- }
-
- /**
- * Method fires property change listener for a given property.
- *
- * @param propertyName
- * name of the property that has changed
- * @param oldValue
- * old value of the property
- * @param newValue
- * new value of the property
- */
- protected final void firePropertyChange(final String propertyName, final Object oldValue, final Object newValue) {
- if (oldValue != null || newValue != null) {
- pchs.firePropertyChange(propertyName, oldValue, newValue);
- }
- }
-
- /**
- * Returns list of all property change listeners for the bean (includes only
- * standard property change listeners, vetoable property change listeners are
- * excluded).
- *
- * @return list of property change listeners
- */
- protected final PropertyChangeListener[] getPropertyChangeListeners() {
- return pchs.getPropertyChangeListeners();
- }
-
- // TODO refactor these two methods to reduce copy-paste
-
- /**
- * Method sends to a client response with an attached file. The content of the
- * file is taken from the content param. Type defines MimeType of the content
- * (text file, xml, etc.) - this helps browser to properly handle response.
- *
- * @param content
- * - string with the file content
- * @param fileName
- * - name of the file that should popup in the client browser
- * @param type
- * - MIME type of the file
- * @throws IOException
- * exception thrown when there are some problems with sending file
- */
- protected final void sendFileAsResponse(String content, String fileName, MimeType type) throws IOException {
- // send the response to client
- FacesContext fc = FacesContext.getCurrentInstance();
- ExternalContext ec = fc.getExternalContext();
-
- ec.responseReset();
- ec.setResponseContentType(type.getTextRepresentation());
- ec.setResponseHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
- ec.addResponseHeader("Content-Type", type.getTextRepresentation());
-
- OutputStream output = ec.getResponseOutputStream();
- PrintStream printStream = new PrintStream(output);
- printStream.print(content);
-
- fc.responseComplete();
- }
-
- /**
- * Method sends to a client response with an attached file. Type defines
- * MimeType of the file content (text file, xml, etc.) - this helps browser to
- * properly handle response.
- *
- * @param file
- * - file which will be sent
- * @param fileName
- * - name of the file that should popup in the client browser
- * @param type
- * - MIME type of the file
- * @throws IOException
- * exception thrown when there are some problems with sending file
- */
- protected void sendFileAsResponse(File file, String fileName, MimeType type) throws IOException {
-
- // start sending
- FacesContext fc = FacesContext.getCurrentInstance();
- ExternalContext ec = fc.getExternalContext();
-
- ec.responseReset();
- ec.setResponseContentType(type.getTextRepresentation());
- ec.setResponseHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
-
- // attach file
- OutputStream output = ec.getResponseOutputStream();
- FileInputStream is = new FileInputStream(file);
- IOUtils.copy(is, output);
- fc.responseComplete();
-
- }
-
- /**
- * Clears whole data shared by this bean.
- */
- public abstract void clear();
-
- /**
- * Register new {@link Listener} in this bean.
- *
- * @param listener
- * listener that should be added
- */
- public void registerListener(Listener<?> listener) {
- List<Listener<?>> listenerList = getListeners().get(listener.getEventClass());
- if (listenerList == null) {
- listenerList = new ArrayList<Listener<?>>();
- listeners.put(listener.getEventClass(), listenerList);
- }
- listenerList.add(listener);
- }
-
- /**
- * This method will call all listeners associated with the specified
- * {@link Event}.
- *
- * @param event
- * {@link Event} for which listeners will be called
- */
- protected void callListeners(Event event) {
- List<Listener<?>> listenerList = getListeners().get(event.getClass());
- if (listenerList == null) {
- logger.warn("No listeners found for event: " + event);
- } else {
- for (Listener<?> listener : listenerList) {
- listener.handleEvent(event);
- }
- }
-
- }
-
- /**
- * Unregister {@link Listener} from this bean.
- *
- * @param listener
- * listener that should be removed
- */
- public void unregisterListener(Listener<?> listener) {
- List<Listener<?>> listenerList = listeners.get(listener.getEventClass());
- if (listenerList == null) {
- listenerList = new ArrayList<Listener<?>>();
- listeners.put(listener.getEventClass(), listenerList);
- }
- if (listenerList.contains(listener)) {
- listenerList.remove(listener);
- } else {
- throw new InvalidArgumentException("Listener " + listener + " wasn't registered.");
- }
-
- }
-
- /**
- * @param primefacesUtils
- * the primefacesUtils to set
- * @see #primefacesUtils
- */
- protected void setPrimefacesUtils(IPrimefacesUtils primefacesUtils) {
- this.primefacesUtils = primefacesUtils;
- }
-
- /**
- * Returns value of the parameter from http request call.
- *
- * @param name
- * name of the parameter
- * @return value of the request parameter
- */
- protected String getRequestParameter(String name) {
- return getPrimefacesUtils().getRequestParameter(name);
- }
-
- /**
- * Adds a parameter that will be stored in user session.
- *
- * @param key
- * name of the parameter
- * @param value
- * value of the parameter
- */
- protected void addSessionParam(String key, Object value) {
- getPrimefacesUtils().addSessionParam(key, value);
- }
-
- /**
- * Gets a value of the parameter stored in user session.
- *
- * @param key
- * name of the parameter
- * @return value of the user session parameter
- */
- protected Object getSessionParam(String key) {
- return getPrimefacesUtils().getSessionParam(key);
- }
-
- /**
- * @return the version of primefaces library
- */
- public String getPrimefacesVersion() {
- return getPrimefacesUtils().getVersion();
- }
-
- /**
- * Returns path on hard drive where the project is deplyed.
- *
- * @return path where the projest is running
- */
- public String getProjectDeployPath() {
- return getPrimefacesUtils().getPath();
- }
-
- /**
- * Sends an error message to the client.
- *
- * @param message
- * error message to be sent
- */
- protected void sendError(String message) {
- getPrimefacesUtils().error(message);
- }
-
- /**
- * Sends an error message to the client.
- *
- * @param message
- * error message to be sent
- * @param exception
- * exception which caused the error
- */
- protected void sendError(String message, Exception exception) {
- logger.error(message, exception);
- getPrimefacesUtils().error(message);
- }
-
- /**
- * Sends info message to the client.
- *
- * @param message
- * info message to be sent
- */
- protected void sendInfo(String message) {
- getPrimefacesUtils().info(message);
- }
-
- /**
- * Returns ip address of current client.
- *
- * @return IP addresss of the client
- */
- protected String getClientIpAddress() {
- return getPrimefacesUtils().getClientIpAddress();
- }
-
- /**
- * Returns a {@link UIComponent} corresponding to the client side component
- * with the identifier given in the parameter.
- *
- * @param id
- * identifier of a component
- * @return {@link UIComponent} corresponding to the client side component with
- * the identifier given in the parameter
- */
- protected UIComponent findComponent(String id) {
- return getPrimefacesUtils().findComponent(id);
- }
-
- /**
- * Returns bean identified by {@link Class}.
- *
- * @param clazz
- * class of the bean
- * @param <T>
- * class of the bean
- * @return bean identified by {@link Class}
- */
- public <T> T findBean(Class<T> clazz) {
- return getPrimefacesUtils().findBean(clazz);
- }
-
- /**
- * @return primefacesUtils.
- */
- public IPrimefacesUtils getPrimefacesUtils() {
- if (primefacesUtils == null) {
- primefacesUtils = new PrimefacesUtils();
- }
- return primefacesUtils;
- }
-
- /**
- * @return listeners.
- */
- public Map<Class<? extends Event>, List<Listener<?>>> getListeners() {
- if (listeners == null) {
- listeners = new HashMap<Class<? extends Event>, List<Listener<?>>>();
- }
- return listeners;
- }
-
- /**
- * @param listeners
- * general listeners.
- */
- public void setListeners(Map<Class<? extends Event>, List<Listener<?>>> listeners) {
- this.listeners = listeners;
- }
-
- /**
- * Executes javascript code on the client browser.
- *
- * @param javascript
- * javascript code
- */
- public void executeJavascript(String javascript) {
- getPrimefacesUtils().executeJavascript(javascript);
- }
-
- /**
- * Transform json string representing list of pairs with model and object id
- * (it can be list of alias ids or reaction ids) into a {@link List} of
- * {@link Pair pairs}.
- *
- * @param string
- * list containing pairs of identifiers
- * @return list of pairs with model and alias id: {@link Pair#left} contains
- * {@link Model#getId()} and {@link Pair#right} conatins
- * {@link lcsb.mapviewer.model.map.species.Element#id}.
- *
- */
- protected List<Pair<Integer, Integer>> deserializeJsonIds(String string) {
- List<Pair<Integer, Integer>> result = new ArrayList<>();
- @SuppressWarnings("unchecked")
- List<List<?>> list = new Gson().fromJson(string, List.class);
- for (List<?> list2 : list) {
- Integer left = null;
- Object leftObj = list2.get(0);
- if (leftObj instanceof Double) {
- left = ((Double) leftObj).intValue();
- } else if (leftObj instanceof String) {
- left = Integer.valueOf((String) leftObj);
- } else {
- throw new InvalidArgumentException("Don't know how to handle class: " + leftObj.getClass());
- }
-
- Integer right = null;
- Object rightObj = list2.get(1);
- if (rightObj instanceof Double) {
- right = ((Double) rightObj).intValue();
- } else if (rightObj instanceof String) {
- right = Integer.valueOf((String) rightObj);
- } else {
- throw new InvalidArgumentException("Don't know how to handle class: " + rightObj.getClass());
- }
-
- result.add(new Pair<Integer, Integer>(left, right));
- }
- return result;
- }
-
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/AbstractMarkerManagerBean.java b/web/src/main/java/lcsb/mapviewer/bean/AbstractMarkerManagerBean.java
deleted file mode 100644
index 2ec5a5d19c3b97f84650149c6cbc4b0756376154..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/AbstractMarkerManagerBean.java
+++ /dev/null
@@ -1,333 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.faces.event.ActionEvent;
-import javax.faces.event.AjaxBehaviorEvent;
-
-import org.apache.log4j.Logger;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.services.search.ElementIdentifierDetails;
-import lcsb.mapviewer.services.search.ISearchResultView;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
-
-/**
- * Abstract bean class containing interface to connect with google maps API on
- * the client side.
- *
- * @param <T>
- * type of search result returned by single query
- *
- * @author Piotr Gawron
- *
- */
-public abstract class AbstractMarkerManagerBean<T extends ISearchResultView> extends AbstractManagedBean {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(AbstractMarkerManagerBean.class);
-
- /**
- * Object with all results to be send to the client.
- */
- private List<T> results = new ArrayList<>();
-
- /**
- * List of elements that should be visualized on the map. Any element in
- * {@link #results} can be visualized at many places (or none at all) o the
- * map.
- */
- private List<ElementIdentifier> elementsOnMap = new ArrayList<>();
-
- /**
- * This field should be initialized by client side and contain name of the
- * javascript object that will accept callback with information about markers
- * on the map.
- */
- private String overlayCollection = "";
-
- /**
- * This method send the data to javascipt using javascipt class with the name
- * stored in drugOverlayCollection.
- */
- public final void refreshDataInJavascript() {
- refreshDataInJavascript(false);
- }
-
- /**
- * This method send the data to javascipt using javascipt class with the name
- * stored in drugOverlayCollection.
- *
- * @param autoZoom
- * determines if the map should auto zoom into the region containing
- * all elements.
- */
- public final void refreshDataInJavascript(final boolean autoZoom) {
- try {
- if ("".equals(overlayCollection)) {
- logger.warn(this.getClass().getSimpleName() + ": Cannot refresh data in JavaScript, because overlayCollection is not set");
- } else {
- String javascriptCode = "";
- List<String> ids = new ArrayList<>();
- for (ISearchResultView element : results) {
- ids.add(element.getUniqueId());
- }
- javascriptCode += "ServerConnector.setOverlayResultIds('" + overlayCollection + "'," + new Gson().toJson(ids) + ");";
- javascriptCode += "ServerConnector.updateOverlayCollection('" + overlayCollection + "'," + getGmapElementsInGson() + ", " + autoZoom + ");";
- executeJavascript(javascriptCode);
- }
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Sends detailed information to the broswer about specific element visualized
- * on the map in context of a search result (from {@link #results}) identified
- * by searchResultIdentifier ({@link ISearchResultView#getUniqueId()}).
- *
- * @param ei
- * element for which we send detailed data
- * @param searchResultIdentifier
- * identifier of {@link ISearchResultView} for which the details are
- * valid
- * @param dataToSend
- * data to be sent
- */
- private void sendDetailData(ElementIdentifier ei, String searchResultIdentifier, ElementIdentifierDetails dataToSend) {
- if ("".equals(overlayCollection)) {
- logger.warn(this.getClass().getSimpleName() + ": Cannot refresh data in JavaScript, because overlayCollection is not set");
- } else {
- Gson gsonParser = new Gson();
- String dataEncoded = "null";
- if (dataToSend != null) {
- dataEncoded = gsonParser.toJson(dataToSend);
- }
- String nameEncoded = gsonParser.toJson(overlayCollection);
- String resultResultIdEncoded = gsonParser.toJson(searchResultIdentifier);
- String elementIdEncoded = gsonParser.toJson(ei);
- String javascriptCode = "ServerConnector.updateOverviewElementDetailData(" + nameEncoded + "," + resultResultIdEncoded + "," + elementIdEncoded + ", "
- + dataEncoded + ");\n";
- executeJavascript(javascriptCode.toString());
- }
- }
-
- /**
- * This method register javascript class name for the callback.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public final void registerOverlayCollection(final ActionEvent actionEvent) {
- // get the request param with the overlay name
- overlayCollection = getRequestParameter("overlayName");
- }
-
- /**
- * Method called by client broswer to request detail information about
- * element.
- *
- * @param actionEvent
- * default {@link ActionEvent} object for jsf calls
- *
- * @see #sendDetailData(ElementIdentifier, String, ElementIdentifierDetails)
- */
- public final void requestDetailData(final ActionEvent actionEvent) {
- try {
- // get the request param with the overlay name
- String searchResultIdentifier = getRequestParameter("searchResultIdentifier");
- String objectIdentifier = getRequestParameter("objectIdentifier");
- String modelIdentifier = getRequestParameter("modelIdentifier");
- String type = getRequestParameter("type");
- ElementIdentifier ei = new ElementIdentifier(objectIdentifier, modelIdentifier, ElementIdentifierType.getTypeByJsName(type), null);
-
- T searchResult = null;
- for (T element : results) {
- if (element.getUniqueId().equals(searchResultIdentifier)) {
- searchResult = element;
- }
- }
- if (searchResult == null) {
- List<Pair<String, ElementIdentifierDetails>> results = getElementInformationForResult(ei);
- for (Pair<String, ElementIdentifierDetails> pair : results) {
- sendDetailData(ei, pair.getLeft(), pair.getRight());
- }
- sendDetailData(ei, "__FULL__", null);
-
- } else {
- sendDetailData(ei, searchResultIdentifier, getElementInformationForResult(ei, searchResult));
- }
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
-
- }
-
- /**
- * @param actionEvent
- * event from thefrom the client
- * @see #refreshDataInJavascript()
- */
- public final void refreshOverlayCollection(final AjaxBehaviorEvent actionEvent) {
- refreshOverlayCollection(new ActionEvent(actionEvent.getComponent()));
- }
-
- /**
- * @param actionEvent
- * event from thefrom the client
- * @see #refreshDataInJavascript()
- */
- public final void refreshOverlayCollection(final ActionEvent actionEvent) {
- refreshOverlayCollection();
- }
-
- /**
- * Refresh list of visible elements on the map (only map, the left panel is
- * untouched).
- */
- private void refreshOverlayCollection() {
- this.elementsOnMap.clear();
- for (T result : results) {
- this.elementsOnMap.addAll(getLightElementsForSearchResult(result));
- }
- refreshDataInJavascript();
- }
-
- /**
- * Returns {@link #elementsOnMap} in json format.
- *
- * @return {@link #elementsOnMap} in json format
- */
- private String getGmapElementsInGson() {
- return new Gson().toJson(elementsOnMap);
- }
-
- /**
- * Clears result in {@link #results} and {@link #elementsOnMap}.
- */
- protected void clearResults() {
- results.clear();
- elementsOnMap.clear();
- }
-
- /**
- * Adds result to the list of result that should be visualized on client side.
- *
- * @param result
- * result to add
- */
- protected void addResult(T result) {
- this.results.add(result);
- this.elementsOnMap.addAll(getLightElementsForSearchResult(result));
-
- }
-
- /**
- * Adds set of results to the list of result that should be visualized on
- * client side.
- *
- * @param results
- * collection of elements to add
- */
- protected void addResults(Collection<T> results) {
- for (T t : results) {
- addResult(t);
- }
- }
-
- /**
- * @return the results
- * @see #results
- */
- public List<T> getResults() {
- return results;
- }
-
- /**
- * This method split query string into list of queies that should be processed
- * by the bean.
- *
- * @param query
- * input query string
- * @param useFullName
- * treat query as a name (without splitting)
- * @return list of separate queries that could be obtained from input string
- */
- protected List<String> splitQuery(String query, boolean useFullName) {
- String tmpQuery = query.trim().toLowerCase();
-
- List<String> result = new ArrayList<>();
- String[] elements;
- if (query.contains(";")) {
- elements = tmpQuery.split(";");
- } else {
- elements = tmpQuery.split(",");
- }
-
- for (String string : elements) {
- result.add(string.trim());
- }
- if (!result.contains(tmpQuery) && useFullName) {
- result.add(tmpQuery);
- }
- return result;
- }
-
- /**
- * Returns list of {@link ElementIdentifier elements} that should be
- * visualized for single search result.
- *
- * @param result
- * object which we investigate
- * @return list of {@link ElementIdentifier elements} that should be
- * visualized for single search result
- */
- protected abstract List<ElementIdentifier> getLightElementsForSearchResult(T result);
-
- /**
- * Returns {@link ElementIdentifierDetails detailed information} about
- * {@link ElementIdentifier element} in context of search result.
- *
- * @param element
- * element for which we gather detailed information
- * @param result
- * {@link ISearchResultView} for which we want to have detailed
- * information
- * @return {@link ElementIdentifierDetails detailed information} about
- * {@link ElementIdentifier element} in context of search result,
- * <code>null</code> if such data doesn't exist
- */
- protected abstract ElementIdentifierDetails getElementInformationForResult(ElementIdentifier element, T result);
-
- /**
- * Returns {@link ElementIdentifierDetails detailed information} about
- * {@link ElementIdentifier element}.
- *
- * @param element
- * element for which we gather detailed information
- * @return list of {@link ElementIdentifierDetails detailed informations}
- * about {@link ElementIdentifier element}, or empty list if such data
- * doesn't exist, the information is a pair: identifier, data
- */
- protected abstract List<Pair<String, ElementIdentifierDetails>> getElementInformationForResult(ElementIdentifier element);
-
- /**
- * @return the elementsOnMap
- * @see #elementsOnMap
- */
- public List<ElementIdentifier> getElementsOnMap() {
- return elementsOnMap;
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java b/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
deleted file mode 100644
index 692c2af511d270b38661eeca476e730ec688d347..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
+++ /dev/null
@@ -1,510 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
-import java.beans.VetoableChangeListener;
-import java.io.File;
-import java.io.Serializable;
-import java.text.NumberFormat;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.commons.validator.routines.UrlValidator;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.FrameworkVersion;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.ConfigurationView;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * Bean used for managing configuration (configurable parameters of the system).
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "configurationMB")
-@ViewScoped
-public class ConfigurationBean extends AbstractManagedBean implements Serializable {
-
- /**
- * String representing {@link ConfigurationElementType#DEFAULT_MAP} system
- * property used by {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String DEFAULT_MODEL_PROPERTY = "DEFAULT_MODEL";
-
- /**
- * String representing {@link ConfigurationElementType#X_FRAME_DOMAIN} system
- * property used by {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String X_FRAME_PROPERTY = "X_FRAME";
-
- /**
- * String representing {@link #logoImg} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGO_IMG_PROPERTY = "LOGO_IMG";
-
- /**
- * String representing {@link #logoLink} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGO_LINK_PROPERTY = "LOGO_LINK";
-
- /**
- * String representing {@link #logoText} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGO_TEXT_PROPERTY = "LOGO_TEXT";
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ConfigurationBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of values for all possible configurable parameters.
- */
- private List<ConfigurationView> values = new ArrayList<>();
-
- /**
- * Release version of the framework.
- */
- private FrameworkVersion version;
-
- /**
- * Configrutaion params value.
- */
- private Map<ConfigurationElementType, String> valueMap = new HashMap<>();
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service used to access information about projects.
- *
- * @see IProjectService
- */
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
-
- @Override
- public final void init() {
- // listener that checks if the new default map exists in the system
- VetoableChangeListener selectedMapVetoChanged = new VetoableChangeListener() {
- @Override
- public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
- if ((DEFAULT_MODEL_PROPERTY).equals(arg0.getPropertyName())) {
- if (!projectService.projectExists((String) arg0.getNewValue())) {
- throw new PropertyVetoException("Project " + arg0.getNewValue() + " doesn't exist", arg0);
- } else {
- ProjectView view;
- try {
- view = projectService.getProjectViewByProjectId((String) arg0.getNewValue(),
- userBean.getAuthenticationToken());
- } catch (lcsb.mapviewer.services.SecurityException e) {
- throw new PropertyVetoException("You have no privilege to perform this operation", arg0);
- }
- if (!view.getStatus().equalsIgnoreCase("OK")) {
- throw new PropertyVetoException(
- "Project " + arg0.getNewValue() + " is invalid. Project status: " + view.getStatus(), arg0);
- }
- }
- }
- }
- };
- addVetoablePropertyChangeListener(selectedMapVetoChanged);
-
- PropertyChangeListener xFrameChanged = new PropertyChangeListener() {
-
- @Override
- public void propertyChange(PropertyChangeEvent arg0) {
- if ((X_FRAME_PROPERTY).equals(arg0.getPropertyName())) {
- Configuration.setxFrameDomain((String) arg0.getNewValue());
- }
- }
- };
- addPropertyChangeListener(xFrameChanged);
-
- // listener that checks if the new x-fram address is valid
- VetoableChangeListener xFrameVetoChanged = new VetoableChangeListener() {
- @Override
- public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
- if ((X_FRAME_PROPERTY).equals(arg0.getPropertyName())) {
- String domain = (String) arg0.getNewValue();
- if (!new UrlValidator().isValid(domain) && !(domain != null && domain.contains("localhost"))) {
- throw new PropertyVetoException("Invalid address: " + domain, arg0);
- }
- }
- }
- };
- addVetoablePropertyChangeListener(xFrameVetoChanged);
-
- version = configurationService.getSystemVersion(getProjectDeployPath());
-
- refreshValues(null);
-
- Configuration.setWebAppDir(new File(getPrimefacesUtils().getPath() + "../").getAbsolutePath() + "/");
- }
-
- /**
- * Refresh values from the database.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public final void refreshValues(final ActionEvent actionEvent) {
- values = configurationService.getAllValues();
- for (ConfigurationView view : values) {
- valueMap.put(view.getType(), view.getValue());
- }
- }
-
- /**
- * Save values to the database.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public final void saveValues(final ActionEvent actionEvent) {
- // first check if we have privileges
- if (getUserHasConfigurationView()) {
- setValues(values);
- configurationService.updateConfiguration(values);
- values = configurationService.getAllValues();
- }
- }
-
- /**
- * Checks if logged user can manage the configuration of the system.
- *
- * @return <code>true</code> if logged user can manage the configuration,
- * <code>false</code> otherwise
- */
- public final boolean getUserHasConfigurationView() {
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.CONFIGURATION_MANAGE);
- return result;
- }
-
- /**
- *
- * @return list of all configuration values
- * @see #values
- */
- public final List<ConfigurationView> getValues() {
- if (getUserHasConfigurationView()) {
- return values;
- } else {
- return new ArrayList<>();
- }
- }
-
- /**
- * Sets the new list of configurable parameters.
- *
- * @param values
- * list of configurable parameters with new values
- */
- public final void setValues(final List<ConfigurationView> values) {
- // when we set new values we should:
- // 1) check if they are correct (vchs listeners)
- // 2) notify apropriate listeners
-
- // for the naming convention of parameters take a look at {@link #vchs}
-
- // remember the old values from the system (!! not from the bean !!)
- List<ConfigurationView> old = configurationService.getAllValues();
- this.values = values;
- for (ConfigurationView el : values) {
- String newVal = el.getValue();
- String oldVal = null;
- for (ConfigurationView oldEl : old) {
- if (oldEl.getType().equals(el.getType())) {
- oldVal = oldEl.getValue();
- }
- }
- try {
- if (el.getType().equals(ConfigurationElementType.DEFAULT_MAP)) {
- fireVetoableChange(DEFAULT_MODEL_PROPERTY, oldVal, newVal);
- }
- } catch (PropertyVetoException e) { // if there was a veto then rollback
- // to system parameters
- this.values = old;
- logger.debug("Rollback because parameter " + el.getType().name() + " contains inproper value: " + newVal);
- sendError(e.getMessage());
- return;
- }
- }
- for (ConfigurationView el : values) {
- String newVal = el.getValue();
- String oldVal = null;
- for (ConfigurationView oldEl : old) {
- if (oldEl.getType().equals(el.getType())) {
- oldVal = oldEl.getValue();
- }
- }
- if (el.getType().equals(ConfigurationElementType.DEFAULT_MAP)) {
- firePropertyChange(DEFAULT_MODEL_PROPERTY, oldVal, newVal);
- } else if (el.getType().equals(ConfigurationElementType.X_FRAME_DOMAIN)) {
- firePropertyChange(X_FRAME_PROPERTY, oldVal, newVal);
- }
-
- }
- }
-
- @Override
- public void clear() {
- setValues(new ArrayList<ConfigurationView>());
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public FrameworkVersion getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(FrameworkVersion version) {
- this.version = version;
- }
-
- /**
- * Returns {@link ConfigurationElementType#GOOGLE_ANALYTICS_IDENTIFIER google
- * analytics identifier} used for tracking web-service usage.
- *
- * @return {@link ConfigurationElementType#GOOGLE_ANALYTICS_IDENTIFIER google
- * analytics identifier} used for tracking web-service usage
- */
- public String getGoogleAnalyticsIdentifier() {
- return valueMap.get(ConfigurationElementType.GOOGLE_ANALYTICS_IDENTIFIER);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LOGO_IMG logo image}.
- *
- * @return {@link ConfigurationElementType#LOGO_IMG logo image}
- */
- public String getLogoImg() {
- return valueMap.get(ConfigurationElementType.LOGO_IMG);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LOGO_LINK logo link}.
- *
- * @return {@link ConfigurationElementType#LOGO_LINK logo link}
- */
- public String getLogoLink() {
- return valueMap.get(ConfigurationElementType.LOGO_LINK);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LOGO_TEXT alt text for logo}.
- *
- * @return {@link ConfigurationElementType#LOGO_TEXT alt text for logo}
- */
- public String getLogoText() {
- return valueMap.get(ConfigurationElementType.LOGO_TEXT);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}
- */
- public String getLegendFile1() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_1);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}
- */
- public String getLegendFile2() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_2);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}
- */
- public String getLegendFile3() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_3);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}
- */
- public String getLegendFile4() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_4);
- }
-
- /**
- * Returns {@link ConfigurationElementType#USER_MANUAL_FILE user manual file}.
- *
- * @return {@link ConfigurationElementType#USER_MANUAL_FILE user manual file}
- */
- public String getUserManual() {
- return valueMap.get(ConfigurationElementType.USER_MANUAL_FILE);
- }
-
- /**
- * Returns {@link String} with estimated current memory usage (in MB).
- *
- * @return estimated current memory usage (in MB)
- */
- public String getMemoryUsage() {
- return NumberFormat.getInstance().format(configurationService.getMemoryUsage()) + " MB";
- }
-
- /**
- * Returns {@link String} with max memory available to JVM (in MB).
- *
- * @return max memory available to JVM (in MB)
- */
- public String getMaxMemory() {
- return NumberFormat.getInstance().format(configurationService.getMaxMemory()) + " MB";
- }
-
- /**
- * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with negative values.
- *
- * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with negative values
- */
- public String getMinColor() {
- return valueMap.get(ConfigurationElementType.MIN_COLOR_VAL);
- }
-
- /**
- * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with negative values.
- *
- * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with positive values
- */
- public String getMaxColor() {
- return valueMap.get(ConfigurationElementType.MAX_COLOR_VAL);
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
deleted file mode 100644
index 5cae8b626361a5b2b54c37eadd42394c59164a38..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
+++ /dev/null
@@ -1,1391 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.primefaces.model.DualListModel;
-import org.primefaces.model.menu.DefaultMenuItem;
-import org.primefaces.model.menu.DefaultMenuModel;
-import org.primefaces.model.menu.DefaultSubMenu;
-import org.primefaces.model.menu.MenuModel;
-
-import com.google.gson.Gson;
-import com.google.gson.reflect.TypeToken;
-
-import lcsb.mapviewer.bean.MapBean.ClientMapData;
-import lcsb.mapviewer.commands.ClearColorModelCommand;
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.ColorModelCommand;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.commands.SubModelCommand;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
-import lcsb.mapviewer.converter.graphics.SvgImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.services.interfaces.IExporterService;
-import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.utils.ColorSchemaReader;
-import lcsb.mapviewer.services.utils.data.BuildInLayout;
-import lcsb.mapviewer.services.utils.data.ExportColumn;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-import lcsb.mapviewer.services.view.PubmedAnnotatedElementsView;
-
-/**
- * Bean used to export data.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "exportMB")
-@ViewScoped
-public class ExportBean extends AbstractManagedBean {
-
- /**
- * Constant defining size of the array returned by
- * {@link PathIterator#currentSegment(double[])} method. More nformation 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.
- */
- private static Logger logger = Logger.getLogger(ExportBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of selected species (node) types to be exported.
- */
- private List<String> selectedSpeciesType = new ArrayList<>();
-
- /**
- * List of selected species (node) fields to be exported.
- */
- private List<String> selectedSpeciesColumn = new ArrayList<>();
-
- /**
- * List of selected species (node) types to be exported in export network
- * mode.
- */
- private List<String> selectedNetworkType = new ArrayList<>();
-
- /**
- * Network export file type.
- */
- private String selectedNetworkFileType = "";
-
- /**
- * List of species (nodes) types.
- */
- private List<String> speciesTypeList;
-
- /**
- * List of species (nodes) columns.
- */
- private List<String> speciesColumnList = new ArrayList<>();
-
- /**
- * List of file types for network export.
- */
- private List<String> networkFileTypeList = new ArrayList<>();
-
- /**
- * Part of the map (in polygon format) to be exported.
- */
- private String selectedPolygon = "";
-
- /**
- * On which model the export should be perfomerd.
- */
- private String selectedModelId = "";
-
- /**
- * Which layouts are visible in javascript.
- */
- private String visibleLayouts = "[]";
-
- /**
- * List of model names.
- */
- private List<String> models = new ArrayList<>();
-
- /**
- * List with information about available {@link AbstractImageGenerator}
- * classes. Left value defines name of the format, right the class that is
- * responsible to generate specific format.
- */
- private List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGenerators = new ArrayList<>();
-
- /**
- * Name of submodel to export.
- */
- private String selectedModelString;
-
- /**
- * List of {@link MiriamType} annotations to include in network export.
- */
- private DualListModel<Pair<MiriamType, String>> networkAvailableMiriam = new DualListModel<>();
-
- /**
- * List of components (compartments) to include in network export.
- */
- private DualListModel<String> networkIncludedComponent = new DualListModel<>();
-
- /**
- * List of components (compartments) to exclude in network export.
- */
- private DualListModel<String> networkExcludedComponent = new DualListModel<>();
-
- /**
- * List of {@link MiriamType} annotations to include in element export.
- */
- private DualListModel<Pair<MiriamType, String>> elementAvailableMiriam = new DualListModel<>();
-
- /**
- * List of components (compartments) to include in element export.
- */
- private DualListModel<String> elementIncludedComponent = new DualListModel<>();
-
- /**
- * List of components (compartments) to exclude in element export.
- */
- private DualListModel<String> elementExcludedComponent = new DualListModel<>();
-
- /**
- * Map between name of the node type and class.
- */
- private Map<String, Class<?>> speciesTypeMap = null;
-
- /**
- * Map between name of the column and column object.
- */
- private Map<String, ExportColumn> speciesColumnMap = new LinkedHashMap<>();
-
- /**
- * Map between name of the file type and file type.
- */
- private Map<String, ExportFileType> networkFileTypeMap = new LinkedHashMap<>();
-
- /**
- * List of publications for current model. If <code>null</code> then data is
- * not initialized (this list is lazy initialized, because it can be big).
- */
- private List<PubmedAnnotatedElementsView> pubmedModelSummary = null;
-
- /**
- * Class used to export images.
- */
- private transient ImageGenerators imageGenerator = null;
-
- /**
- * Right menu allowing user to export data from map. It's dynamically created
- * to handle all currently available formats. Menu is active when clicking on
- * some selected region on the map.
- */
- private transient MenuModel imageExportMenu;
-
- /**
- * Right menu allowing user to export data from map. It's dynamically created
- * to handle all currently available formats. Menu is active when clicking on
- * any place (except of selected region) on the map.
- */
- private transient MenuModel contextMenu;
-
- /**
- * Service that allows to export data of the map into other formats.
- */
- @ManagedProperty(value = "#{ExporterService}")
- private transient IExporterService exporterService;
-
- /**
- * Service that allows to access data abaout users.
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service that deal with {@link Layout layouts}.
- */
- @ManagedProperty(value = "#{LayoutService}")
- private transient ILayoutService layoutService;
-
- /**
- * Bean used for accessing information about currently browsed map.
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- /**
- * Bean managing currently logged user.
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Default constructor.
- */
- public ExportBean() {
- }
-
- /**
- * Fills lists with {@link MiriamType miriam types} and number of occurences
- * of this annotations in the parameter model.
- *
- * @param model
- * model from which annotations should be counted
- */
- private void fillAnnotationNumbers(Model model) {
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
-
- Map<MiriamType, Integer> annotations = new HashMap<>();
- for (MiriamType mt : MiriamType.values()) {
- annotations.put(mt, 0);
- }
- for (Model model2 : models) {
- for (Element alias : model2.getElements()) {
- for (MiriamData md : alias.getMiriamData()) {
- Integer amount = annotations.get(md.getDataType());
- amount += 1;
- annotations.put(md.getDataType(), amount);
- }
- }
- }
- List<Pair<MiriamType, String>> list = new ArrayList<>();
- for (MiriamType mt : MiriamType.values()) {
- list.add(new Pair<MiriamType, String>(mt, annotations.get(mt) + ""));
- }
- elementAvailableMiriam = new DualListModel<Pair<MiriamType, String>>(list, new ArrayList<>());
-
- annotations = new HashMap<>();
- for (MiriamType mt : MiriamType.values()) {
- annotations.put(mt, 0);
- }
- for (Model model2 : models) {
- for (Reaction reaction : model2.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- Integer amount = annotations.get(md.getDataType());
- amount += 1;
- annotations.put(md.getDataType(), amount);
- }
- }
- }
- list = new ArrayList<>();
- for (MiriamType mt : MiriamType.values()) {
- list.add(new Pair<MiriamType, String>(mt, annotations.get(mt) + ""));
- }
- networkAvailableMiriam = new DualListModel<Pair<MiriamType, String>>(list, new ArrayList<>());
-
- }
-
- /**
- * Method that exports elements.
- *
- * @throws IOException
- * thrown when there are some problems with sending file
- */
- public void downloadElements() throws IOException {
- Model model = getCurrentTopModel();
- if (model == null) {
- logger.warn("Unknown model. Skipping...");
- return;
- }
-
- List<Class<?>> speciesList = new ArrayList<Class<?>>();
- for (String string : selectedSpeciesType) {
- speciesList.add(getSpeciesTypeMap().get(string));
- }
-
- List<ExportColumn> speciesColumnList = new ArrayList<ExportColumn>();
- for (String string : selectedSpeciesColumn) {
- speciesColumnList.add(speciesColumnMap.get(string));
- }
-
- ExporterParameters params = new ExporterParameters().model(model).//
- included(elementIncludedComponent.getTarget()).//
- excluded(elementExcludedComponent.getTarget()).//
- column(speciesColumnList).//
- fileType(ExportFileType.TAB_SEPARATED).//
- type(speciesList);
-
- for (Pair<MiriamType, String> el : elementAvailableMiriam.getTarget()) {
- params.miriamType(el.getLeft());
- }
-
- // create a string with the repsonse
- String result = exporterService.getExportSpeciesString(params);
-
- // and send it as response
- sendFileAsResponse(result, "elements.txt", MimeType.TEXT);
- }
-
- /**
- * Method that exports network.
- *
- * @throws IOException
- * thrown when there are some problems with sending file
- */
- public void downloadNetwork() throws IOException {
- Model model = getCurrentTopModel();
-
- if (model == null) {
- logger.warn("Unknown model. Skipping...");
- return;
- }
-
- List<Class<?>> nodeTypes = new ArrayList<Class<?>>();
- for (String string : selectedNetworkType) {
- nodeTypes.add(getSpeciesTypeMap().get(string));
- }
-
- ExportFileType fileType = networkFileTypeMap.get(selectedNetworkFileType);
- ExporterParameters params = new ExporterParameters().model(model).//
- included(networkIncludedComponent.getTarget()).//
- excluded(networkExcludedComponent.getTarget()).//
- fileType(fileType).//
- type(nodeTypes).//
- column(ExportColumn.REACTION_ID).//
- column(ExportColumn.REACTION_TYPE);
-
- for (Pair<MiriamType, String> el : networkAvailableMiriam.getTarget()) {
- params.miriamType(el.getLeft());
- }
-
- // create a string with the repsonse
- String result = exporterService.getExportInteractionString(params);
-
- sendFileAsResponse(result, "network.txt", MimeType.TEXT);
- }
-
- /**
- * Methods that export model into svg format.
- *
- * @throws IOException
- * thrown when there are problems with intermediate file or the
- * output
- */
- public void downloadSvg() throws IOException {
- if (selectedModelString == null) {
- sendError("No model was selected");
- return;
- }
-
- Model model = getCurrentTopModel().getSubmodelByName(selectedModelString);
- if (selectedModelString.equals("null")) {
- model = getCurrentTopModel();
- }
-
- if (model == null) {
- sendError("Unknown model.");
- return;
- }
-
- // create svg file
- Params params = new Params().height(model.getHeight()).width(model.getWidth()).model(model).sbgn(getCurrentTopModel().getProject().isSbgnFormat());
- try {
- SvgImageGenerator sig = new SvgImageGenerator(params);
- File file = File.createTempFile("map", ".svg");
- sig.saveToFile(file.getAbsolutePath());
-
- sendFileAsResponse(file, "model.svg", MimeType.TEXT);
-
- // after finishing remove the file
- file.delete();
- } catch (Exception e) {
- logger.error(e, e);
- sendError("Internal server error. More information can be found in logs.");
- }
- }
-
- /**
- * Refresh list of submodel names.
- *
- * @param model
- * model for which list will be generated
- */
- private void fillSubmodelList(Model model) {
- models.clear();
- models.add(model.getName());
- for (Model m : model.getSubmodels()) {
- models.add(m.getName());
- }
- setSelectedModelString(model.getName());
- }
-
- /**
- * This method exports part of the model bounded by the polygon in
- * CellDesigner or SBGN-ML format.
- *
- * @param sbgnmlFormat
- * defines whether the model part is exported in CellDesigner or
- * SBGN-ML format
- * @throws IOException
- * thrown when there are some problems with sending file
- */
- public void downloadSelectedPart(boolean sbgnmlFormat) throws IOException {
- Model part = getSelectedPartOfSubmodel();
- if (part == null) {
- sendError("Unknown model.");
- return;
- }
-
- // export to CD format
- try {
- IConverter parser;
- if (sbgnmlFormat) {
- parser = new SbgnmlXmlConverter();
- } else {
- parser = new CellDesignerXmlParser();
- }
- InputStream is = parser.exportModelToInputStream(part);
- StringWriter strWriter = new StringWriter();
- IOUtils.copy(is, strWriter);
- String result = strWriter.toString();
-
- String fileExtension = parser.getFileExtension();
- MimeType mimeType = parser.getMimeType();
-
- sendFileAsResponse(result, "model.".concat(fileExtension), mimeType);
- } catch (InconsistentModelException e) {
- sendError(e.getMessage(), e);
- } catch (ConverterException e) {
- sendError("Internal server error.", e);
- }
-
- }
-
- /**
- * Returns part of the model that is currently selected on the client side.
- *
- * @return partial {@link Model} that is currently selected on the client side
- */
- public Model getSelectedPartOfSubmodel() {
- Model model = getCurrentTopModel().getSubmodelById(selectedModelId);
-
- if (model == null) {
- return null;
- }
-
- // transform polygon
- CoordinationConverter cc = new CoordinationConverter(model);
- Path2D polygon = cc.latLngToPolygon(selectedPolygon);
-
- // create model bounded by the polygon
- SubModelCommand subModelCommand = new SubModelCommand(model, polygon);
- Model part = subModelCommand.execute();
- return part;
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the selectedSpeciesType
- * @see #selectedSpeciesType
- */
- public List<String> getSelectedSpeciesType() {
- return selectedSpeciesType;
- }
-
- /**
- * @param selectedSpeciesType
- * the selectedSpeciesType to set
- * @see #selectedSpeciesType
- */
- public void setSelectedSpeciesType(List<String> selectedSpeciesType) {
- this.selectedSpeciesType = selectedSpeciesType;
- }
-
- /**
- * @return the selectedSpeciesColumn
- * @see #selectedSpeciesColumn
- */
- public List<String> getSelectedSpeciesColumn() {
- return selectedSpeciesColumn;
- }
-
- /**
- * @param selectedSpeciesColumn
- * the selectedSpeciesColumn to set
- * @see #selectedSpeciesColumn
- */
- public void setSelectedSpeciesColumn(List<String> selectedSpeciesColumn) {
- this.selectedSpeciesColumn = selectedSpeciesColumn;
- }
-
- /**
- * @return the selectedNetworkType
- * @see #selectedNetworkType
- */
- public List<String> getSelectedNetworkType() {
- return selectedNetworkType;
- }
-
- /**
- * @param selectedNetworkType
- * the selectedNetworkType to set
- * @see #selectedNetworkType
- */
- public void setSelectedNetworkType(List<String> selectedNetworkType) {
- this.selectedNetworkType = selectedNetworkType;
- }
-
- /**
- * @return the selectedNetworkFileType
- * @see #selectedNetworkFileType
- */
- public String getSelectedNetworkFileType() {
- return selectedNetworkFileType;
- }
-
- /**
- * @param selectedNetworkFileType
- * the selectedNetworkFileType to set
- * @see #selectedNetworkFileType
- */
- public void setSelectedNetworkFileType(String selectedNetworkFileType) {
- this.selectedNetworkFileType = selectedNetworkFileType;
- }
-
- /**
- * @return the speciesTypeList
- * @see #speciesTypeList
- */
- public List<String> getSpeciesTypeList() {
- if (speciesTypeList == null) {
- speciesTypeList = new ArrayList<>();
- for (String string : getSpeciesTypeMap().keySet()) {
- speciesTypeList.add(string);
- }
- }
- return speciesTypeList;
- }
-
- /**
- * @param speciesTypeList
- * the speciesTypeList to set
- * @see #speciesTypeList
- */
- public void setSpeciesTypeList(List<String> speciesTypeList) {
- this.speciesTypeList = speciesTypeList;
- }
-
- /**
- * @return the speciesColumnList
- * @see #speciesColumnList
- */
- public List<String> getSpeciesColumnList() {
- return speciesColumnList;
- }
-
- /**
- * @param speciesColumnList
- * the speciesColumnList to set
- * @see #speciesColumnList
- */
- public void setSpeciesColumnList(List<String> speciesColumnList) {
- this.speciesColumnList = speciesColumnList;
- }
-
- /**
- * @return the networkFileTypeList
- * @see #networkFileTypeList
- */
- public List<String> getNetworkFileTypeList() {
- return networkFileTypeList;
- }
-
- /**
- * @param networkFileTypeList
- * the networkFileTypeList to set
- * @see #networkFileTypeList
- */
- public void setNetworkFileTypeList(List<String> networkFileTypeList) {
- this.networkFileTypeList = networkFileTypeList;
- }
-
- /**
- * @return the selectedPolygon
- * @see #selectedPolygon
- */
- public String getSelectedPolygon() {
- return selectedPolygon;
- }
-
- /**
- * @param selectedPolygon
- * the selectedPolygon to set
- * @see #selectedPolygon
- */
- public void setSelectedPolygon(String selectedPolygon) {
- this.selectedPolygon = selectedPolygon;
- }
-
- /**
- * @return the exporter
- * @see #exporterService
- */
- public IExporterService getExporterService() {
- return exporterService;
- }
-
- /**
- * @param exporter
- * the exporter to set
- * @see #exporterService
- */
- public void setExporterService(IExporterService exporter) {
- this.exporterService = exporter;
- }
-
- /**
- * Creates list of components available for client.
- *
- * @param model
- * model used for components (compartments and pathways) generation
- */
- private void computeComponentMap(Model model) {
- if (model == null) {
- logger.warn("Unknown model. Skipping...");
- return;
- }
-
- Set<String> components = new HashSet<String>();
- for (Compartment alias : model.getCompartments()) {
- components.add(alias.getName());
- }
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- for (Compartment alias : submodel.getSubmodel().getModel().getCompartments()) {
- components.add(alias.getName());
- }
- }
- List<String> comp = new ArrayList<String>();
- comp.addAll(components);
- Collections.sort(comp);
-
- networkIncludedComponent = new DualListModel<String>(comp, new ArrayList<String>());
- networkExcludedComponent = new DualListModel<String>(comp, new ArrayList<String>());
- elementIncludedComponent = new DualListModel<String>(comp, new ArrayList<String>());
- elementExcludedComponent = new DualListModel<String>(comp, new ArrayList<String>());
- }
-
- /**
- * @return the selectedModelId
- * @see #selectedModelId
- */
- public String getSelectedModelId() {
- return selectedModelId;
- }
-
- /**
- * @param selectedModelId
- * the selectedModelId to set
- * @see #selectedModelId
- */
- public void setSelectedModelId(String selectedModelId) {
- this.selectedModelId = selectedModelId;
- }
-
- /**
- * @return the selectedModelString
- * @see #selectedModelString
- */
- public String getSelectedModelString() {
- return selectedModelString;
- }
-
- /**
- * @param selectedModelString
- * the selectedModelString to set
- * @see #selectedModelString
- */
- public void setSelectedModelString(String selectedModelString) {
- this.selectedModelString = selectedModelString;
- }
-
- /**
- * @return the models
- * @see #models
- */
- public List<String> getModels() {
- if (models.size() == 0) {
- Model model = getCurrentTopModel();
- computeComponentMap(model);
- fillSubmodelList(model);
- fillAnnotationNumbers(model);
- }
- return models;
- }
-
- /**
- * @param models
- * the models to set
- * @see #models
- */
- public void setModels(List<String> models) {
- this.models = models;
- }
-
- /**
- * @return the networkAvailableMiriam
- * @see #networkAvailableMiriam
- */
- public DualListModel<Pair<MiriamType, String>> getNetworkAvailableMiriam() {
- return networkAvailableMiriam;
- }
-
- /**
- * @param networkAvailableMiriam
- * the networkAvailableMiriam to set
- * @see #networkAvailableMiriam
- */
- public void setNetworkAvailableMiriam(DualListModel<Pair<MiriamType, String>> networkAvailableMiriam) {
- this.networkAvailableMiriam = networkAvailableMiriam;
- }
-
- /**
- * @return the elementAvailableMiriam
- * @see #elementAvailableMiriam
- */
- public DualListModel<Pair<MiriamType, String>> getElementAvailableMiriam() {
- return elementAvailableMiriam;
- }
-
- /**
- * @param elementAvailableMiriam
- * the elementAvailableMiriam to set
- * @see #elementAvailableMiriam
- */
- public void setElementAvailableMiriam(DualListModel<Pair<MiriamType, String>> elementAvailableMiriam) {
- this.elementAvailableMiriam = elementAvailableMiriam;
- }
-
- /**
- * @return the elementIncludedComponent
- * @see #elementIncludedComponent
- */
- public DualListModel<String> getElementIncludedComponent() {
- return elementIncludedComponent;
- }
-
- /**
- * @param elementIncludedComponent
- * the elementIncludedComponent to set
- * @see #elementIncludedComponent
- */
- public void setElementIncludedComponent(DualListModel<String> elementIncludedComponent) {
- this.elementIncludedComponent = elementIncludedComponent;
- }
-
- /**
- * @return the elementExcludedComponent
- * @see #elementExcludedComponent
- */
- public DualListModel<String> getElementExcludedComponent() {
- return elementExcludedComponent;
- }
-
- /**
- * @param elementExcludedComponent
- * the elementExcludedComponent to set
- * @see #elementExcludedComponent
- */
- public void setElementExcludedComponent(DualListModel<String> elementExcludedComponent) {
- this.elementExcludedComponent = elementExcludedComponent;
- }
-
- /**
- * @return the networkExcludedComponent
- * @see #networkExcludedComponent
- */
- public DualListModel<String> getNetworkExcludedComponent() {
- return networkExcludedComponent;
- }
-
- /**
- * @param networkExcludedComponent
- * the networkExcludedComponent to set
- * @see #networkExcludedComponent
- */
- public void setNetworkExcludedComponent(DualListModel<String> networkExcludedComponent) {
- this.networkExcludedComponent = networkExcludedComponent;
- }
-
- /**
- * @return the networkIncludedComponent
- * @see #networkIncludedComponent
- */
- public DualListModel<String> getNetworkIncludedComponent() {
- return networkIncludedComponent;
- }
-
- /**
- * @param networkIncludedComponent
- * the networkIncludedComponent to set
- * @see #networkIncludedComponent
- */
- public void setNetworkIncludedComponent(DualListModel<String> networkIncludedComponent) {
- this.networkIncludedComponent = networkIncludedComponent;
- }
-
- @Override
- public void init() {
-
- PropertyChangeListener modelPropertyChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (MapBean.CURRENT_MODEL_PROPERTY.equals(arg0.getPropertyName())) {
- computeComponentMap((Model) arg0.getNewValue());
- fillSubmodelList((Model) arg0.getNewValue());
- fillAnnotationNumbers((Model) arg0.getNewValue());
- }
- }
-
- };
- mapBean.addPropertyChangeListener(modelPropertyChangeListener);
-
- for (ExportColumn type : ExportColumn.values()) {
- if (type.getClazz().isAssignableFrom(Species.class)) {
- speciesColumnMap.put(type.getTitle(), type);
- speciesColumnList.add(type.getTitle());
- }
- }
-
- selectedNetworkFileType = ExportFileType.TAB_SEPARATED.getTitle();
- networkFileTypeMap.put(ExportFileType.TAB_SEPARATED.getTitle(), ExportFileType.TAB_SEPARATED);
- networkFileTypeList.add(ExportFileType.TAB_SEPARATED.getTitle());
-
- imageGenerator = new ImageGenerators();
- imageGenerators = imageGenerator.getAvailableImageGenerators();
-
- imageExportMenu = createImageSelectMenu();
-
- contextMenu = createContextMenu();
-
- // trigger event handler manually to initialize the data
- modelPropertyChangeListener
- .propertyChange(new PropertyChangeEvent(this, MapBean.CURRENT_MODEL_PROPERTY, mapBean.getCurrentTopModel(), mapBean.getCurrentTopModel()));
- }
-
- /**
- * Creates context menu that is active when clicking on some selected region
- * on the map.
- *
- * @return context menu that is active when clicking on some selected region
- * on the map
- */
- public MenuModel createImageSelectMenu() {
- MenuModel result = new DefaultMenuModel();
-
- DefaultMenuItem item = new DefaultMenuItem("Remove selection");
- item.setOnclick("customMap.removeSelection(); customMap.turnOnOffDrawing();");
- item.setStyleClass("addCommentContext");
- item.setAjax(false);
- item.setUrl("#");
- result.addElement(item);
-
- DefaultSubMenu exportModelSubmenu = new DefaultSubMenu("Export as model");
-
- item = new DefaultMenuItem("CellDesigner");
- item.setCommand("#{exportMB.downloadSelectedPart(false)}");
- item.setAjax(false);
- item.setStyleClass("addCommentContext");
- exportModelSubmenu.addElement(item);
-
- item = new DefaultMenuItem("SBGN-ML");
- item.setCommand("#{exportMB.downloadSelectedPart(true)}");
- item.setAjax(false);
- item.setStyleClass("addCommentContext");
- exportModelSubmenu.addElement(item);
- result.addElement(exportModelSubmenu);
-
- DefaultSubMenu exportImageSubmenu = new DefaultSubMenu("Export as image");
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGenerators) {
- item = new DefaultMenuItem(element.getLeft());
- item.setCommand("#{exportMB.downloadImage(\"" + element.getRight().getCanonicalName() + "\")}");
- item.setAjax(false);
- item.setStyleClass("addCommentContext");
- exportImageSubmenu.addElement(item);
- }
- result.addElement(exportImageSubmenu);
-
- return result;
- }
-
- /**
- * Creates context menu that is active when clicking on any place in the map
- * (except of some selected region).
- *
- * @return context menu that is active when clicking on any place in the map
- * (except of some selected region).
- */
- public MenuModel createContextMenu() {
- MenuModel result = new DefaultMenuModel();
-
- DefaultMenuItem addCommentItem = new DefaultMenuItem("Add comment");
- addCommentItem.setOncomplete("jsfCommentDialog.show();customMap.openCommentDialog();");
- addCommentItem.setStyleClass("addCommentContext");
- addCommentItem.setCommand("#{exportMB.nop()}");
- addCommentItem.setAjax(true);
- addCommentItem.setId("commentButton");
- result.addElement(addCommentItem);
-
- DefaultMenuItem item = new DefaultMenuItem("Select mode");
- item.setId("selectModeButton");
- item.setUrl("#");
- item.setOnclick("customMap.turnOnOffDrawing();");
- item.setAjax(false);
- item.setStyleClass("addCommentContext");
- result.addElement(item);
-
- DefaultSubMenu exportModelSubmenu = new DefaultSubMenu("Export as model");
-
- item = new DefaultMenuItem("CellDesigner");
- item.setCommand("#{exportMB.downloadSelectedPart(false)}");
- item.setAjax(false);
- item.setStyleClass("addCommentContext");
- exportModelSubmenu.addElement(item);
-
- item = new DefaultMenuItem("SBGN-ML");
- item.setCommand("#{exportMB.downloadSelectedPart(true)}");
- item.setAjax(false);
- item.setStyleClass("addCommentContext");
- exportModelSubmenu.addElement(item);
- result.addElement(exportModelSubmenu);
-
- DefaultSubMenu exportImageSubmenu = new DefaultSubMenu("Export as image");
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGenerators) {
- item = new DefaultMenuItem(element.getLeft());
- item.setCommand("#{exportMB.downloadImage(\"" + element.getRight().getCanonicalName() + "\")}");
- item.setAjax(false);
- item.setStyleClass("addCommentContext");
- exportImageSubmenu.addElement(item);
- }
- result.addElement(exportImageSubmenu);
-
- return result;
- }
-
- /**
- * @return the imageGenerators
- * @see #imageGenerators
- */
- public List<Pair<String, Class<? extends AbstractImageGenerator>>> getImageGenerators() {
- return imageGenerators;
- }
-
- /**
- * @param imageGenerators
- * the imageGenerators to set
- * @see #imageGenerators
- */
- public void setImageGenerators(List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGenerators) {
- this.imageGenerators = imageGenerators;
- }
-
- /**
- * @return the imageExportMenu
- * @see #imageExportMenu
- */
- public MenuModel getImageExportMenu() {
- return imageExportMenu;
- }
-
- /**
- * @param imageExportMenu
- * the imageExportMenu to set
- * @see #imageExportMenu
- */
- public void setImageExportMenu(MenuModel imageExportMenu) {
- this.imageExportMenu = imageExportMenu;
- }
-
- /**
- * @return the speciesTypeMap
- * @see #speciesTypeMap
- */
- protected Map<String, Class<?>> getSpeciesTypeMap() {
- if (speciesTypeMap == null) {
- speciesTypeMap = new LinkedHashMap<>();
- speciesTypeMap.put("Antisense RNA", AntisenseRna.class);
- speciesTypeMap.put("Complex", Complex.class);
- speciesTypeMap.put("Degraded", Degraded.class);
- speciesTypeMap.put("Drug", Drug.class);
- speciesTypeMap.put("Gene", Gene.class);
- speciesTypeMap.put("Ion", Ion.class);
- speciesTypeMap.put("Phenotype", Phenotype.class);
- speciesTypeMap.put("Protein", Protein.class);
- speciesTypeMap.put("RNA", Rna.class);
- speciesTypeMap.put("Molecule", SimpleMolecule.class);
- speciesTypeMap.put("Unknown", Unknown.class);
- speciesTypeMap.put("All", Species.class);
- }
- return speciesTypeMap;
- }
-
- /**
- * @param speciesTypeMap
- * the speciesTypeMap to set
- * @see #speciesTypeMap
- */
- protected void setSpeciesTypeMap(Map<String, Class<?>> speciesTypeMap) {
- this.speciesTypeMap = speciesTypeMap;
- }
-
- /**
- * @return the speciesColumnMap
- * @see #speciesColumnMap
- */
- protected Map<String, ExportColumn> getSpeciesColumnMap() {
- return speciesColumnMap;
- }
-
- /**
- * @param speciesColumnMap
- * the speciesColumnMap to set
- * @see #speciesColumnMap
- */
- protected void setSpeciesColumnMap(Map<String, ExportColumn> speciesColumnMap) {
- this.speciesColumnMap = speciesColumnMap;
- }
-
- /**
- * @return the networkFileTypeMap
- * @see #networkFileTypeMap
- */
- protected Map<String, ExportFileType> getNetworkFileTypeMap() {
- return networkFileTypeMap;
- }
-
- /**
- * @param networkFileTypeMap
- * the networkFileTypeMap to set
- * @see #networkFileTypeMap
- */
- protected void setNetworkFileTypeMap(Map<String, ExportFileType> networkFileTypeMap) {
- this.networkFileTypeMap = networkFileTypeMap;
- }
-
- /**
- * Downloads image that will be created by {@link AbstractImageGenerator}
- * implementation for which class name is given in the parameter.
- *
- * @param generatorClass
- * class name of {@link AbstractImageGenerator} to be used
- */
- public void downloadImage(String generatorClass) {
- try {
- Model originalModel = getCurrentTopModel().getSubmodelById(selectedModelId);
- ClientMapData clientData = mapBean.getMapDataByMapIdentifier(selectedModelId);
-
- if (originalModel == null) {
- sendError("Unknown model");
- return;
- }
-
- Layout layout = getCurrentTopModel().getLayoutByIdentifier(mapBean.getSelectedLayoutIdentifier());
- if (layout == null) {
- sendError("Unknown layout in model. Layout.id=" + mapBean.getSelectedLayoutIdentifier());
- return;
- }
-
- Model colorModel = new CopyCommand(originalModel).execute();
- if (layout.getInputData() != null) {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(layout.getInputData().getFileContent());
-
- new ColorModelCommand(colorModel, schemas, userService.getColorExtractorForUser(userBean.getLoggedUser())).execute();
- } else if (layout.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();
- }
- for (Element alias : colorModel.getElements()) {
- alias.setVisibilityLevel(0);
- }
-
- Integer level = Configuration.MIN_ZOOM_LEVEL;
- try {
- level = Integer.valueOf(clientData.getZoomLevel());
- } catch (NumberFormatException e) {
- logger.error("Problem with getting zoom level", e);
- }
-
- // transform polygon
- CoordinationConverter cc = new CoordinationConverter(colorModel);
- Path2D polygon = cc.latLngToPolygon(selectedPolygon);
-
- 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();
- }
- Double scale = Math.max(originalModel.getHeight(), originalModel.getWidth()) / (originalModel.getTileSize());
-
- for (int i = level; i > Configuration.MIN_ZOOM_LEVEL; i--) {
- scale /= 2;
- }
-
- ColorExtractor colorExtractor = userService.getColorExtractorForUser(userBean.getLoggedUser());
-
- Params params = new Params().//
- x(minX).//
- y(minY).//
- height((maxY - minY) / scale).//
- width((maxX - minX) / scale).//
- level(level).//
- nested(false).// automatically set nested view as invalid
- scale(scale).//
- minColor(colorExtractor.getMinColor()).//
- maxColor(colorExtractor.getMaxColor()).//
- sbgn(getCurrentTopModel().getProject().isSbgnFormat()).//
- model(colorModel);
- List<Integer> visibleLayoutIds = deserializeIdList(visibleLayouts);
- for (Integer integer : visibleLayoutIds) {
- Map<Object, ColorSchema> map = getLayoutService().getElementsForLayout(colorModel, integer, userBean.getAuthenticationToken());
- params.addVisibleLayout(map);
- }
-
- String extension = imageGenerator.getExtension(generatorClass);
- File file = File.createTempFile("map", "." + extension);
-
- MimeType type = imageGenerator.generate(generatorClass, params, file.getAbsolutePath());
- sendFileAsResponse(file, "model." + extension, type);
-
- // after finishing remove the file
- file.delete();
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
-
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
- /**
- * @return the pubmedModelSummary
- * @see #pubmedModelSummary
- */
- public List<PubmedAnnotatedElementsView> getPubmedModelSummary() {
- if (pubmedModelSummary == null) {
- pubmedModelSummary = exporterService.getPublicationModelSummary(getCurrentTopModel());
- }
- return pubmedModelSummary;
- }
-
- /**
- * @param pubmedModelSummary
- * the pubmedModelSummary to set
- * @see #pubmedModelSummary
- */
- public void setPubmedModelSummary(List<PubmedAnnotatedElementsView> pubmedModelSummary) {
- this.pubmedModelSummary = pubmedModelSummary;
- }
-
- /**
- * @return the visibleLayouts
- * @see #visibleLayouts
- */
- public String getVisibleLayouts() {
- return visibleLayouts;
- }
-
- /**
- * @param visibleLayouts
- * the visibleLayouts to set
- * @see #visibleLayouts
- */
- public void setVisibleLayouts(String visibleLayouts) {
- this.visibleLayouts = visibleLayouts;
- }
-
- /**
- * Deserialize list of integer identifiers encoded as an json array. Example
- * input string for two identifiers (123, 44) looks like:
- *
- * <pre>
- * "["123","44"]"
- * </pre>
- *
- * @param jsonString
- * list of identifiers as a json string array
- * @return list of integer identifiers
- */
- protected List<Integer> deserializeIdList(String jsonString) {
- return new Gson().fromJson(jsonString, new TypeToken<List<Integer>>() {
- }.getType());
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- /**
- * Returns currently browsed map.
- *
- * @return currently browsed map
- */
- private Model getCurrentTopModel() {
- return mapBean.getCurrentTopModel();
- }
-
- /**
- * @return the contextMenu
- * @see #contextMenu
- */
- public MenuModel getContextMenu() {
- return contextMenu;
- }
-
- /**
- * @param contextMenu
- * the contextMenu to set
- * @see #contextMenu
- */
- public void setContextMenu(MenuModel contextMenu) {
- this.contextMenu = contextMenu;
- }
-
- /**
- * Method that does nothing (workaround for menu buttons).
- */
- public void nop() {
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
deleted file mode 100644
index 6aaba2b3815fa466a1fb8f8b45306f91f5530307..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
+++ /dev/null
@@ -1,300 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.Model;
-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.view.CommentView;
-
-/**
- * Bean used for managing comments.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "feedbackMB")
-@ViewScoped
-public class FeedbackBean extends AbstractManagedBean implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(FeedbackBean.class);
-
- /**
- * List of comments available for current project.
- */
- private List<CommentView> commentList = null;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for communication with the client side about the map currently
- * visualized.
- *
- * @see MapBean
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- /**
- * Service that manages comments.
- */
- @ManagedProperty(value = "#{CommentService}")
- private transient ICommentService commentService;
-
- /**
- * Service that allows to query the database to find elements in the model.
- */
- @ManagedProperty(value = "#{SearchService}")
- private transient ISearchService searchService;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Method called to remove comment from the map.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void removeComment(final ActionEvent actionEvent) {
- try {
- logger.debug("Remove comment");
- if (getUserHasCommentPrivilege()) {
- String commentId = getRequestParameter("missingConnectionForm:commentId");
- String reason = getRequestParameter("missingConnectionForm:removeCommentContent");
- commentService.deleteComment(userBean.getLoggedUser(), commentId, reason);
- } else {
- logger.error("Somebody try to hack the system: " + userBean.getLogin(), new Exception());
- }
- } catch (InvalidArgumentException e) {
- logger.error(e.getMessage(), e);
- }
- refreshCommentList();
- }
-
-
- /**
- * Method called to remove comment from the map.
- *
- * @param comment
- * comment to be removed
- */
- public void removeComment(CommentView comment) {
- try {
- logger.debug("Remove comment");
- if (getUserHasCommentPrivilege()) {
- String commentId = comment.getIdObject() + "";
- commentService.deleteComment(userBean.getLoggedUser(), commentId, "");
- } else {
- sendError("You don't have privilege to remove comment");
- }
- } catch (InvalidArgumentException e) {
- sendError("Internal server error", e);
- }
- refreshCommentList();
- }
-
- /**
- * Returns true if user can manage current comments.
- *
- * @return <code>true</code> if user has privilege to manage the comments,
- * <code>false</code> otherwise
- */
- public boolean getUserHasCommentPrivilege() {
- Project project = getCurrentProject();
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
- return result;
- }
-
- /**
- * This method refresh the list of comments for the current model and put it.
- * on the list
- */
- public void refreshCommentList() {
- try {
- if (getCurrentTopModel() == null) {
- logger.warn("Unknown map");
- return;
- }
- if (!getUserHasCommentPrivilege()) {
- commentList = new ArrayList<>();
- logger.warn("User has not privilages");
- return;
- } else {
- commentList = commentService.getCommentsByMap(getCurrentTopModel(), userBean.getAuthenticationToken());
- }
- } catch (Exception e) {
- sendError("Internal server error. More info in logs.", e);
- }
- }
-
- @Override
- public void clear() {
- setCommentList(new ArrayList<>());
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the commentService
- * @see #commentService
- */
- public ICommentService getCommentService() {
- return commentService;
- }
-
- /**
- * @param commentService
- * the commentService to set
- * @see #commentService
- */
- public void setCommentService(ICommentService commentService) {
- this.commentService = commentService;
- }
-
- /**
- * @return the searchService
- * @see #searchService
- */
- public ISearchService getSearchService() {
- return searchService;
- }
-
- /**
- * @param searchService
- * the searchService to set
- * @see #searchService
- */
- public void setSearchService(ISearchService searchService) {
- this.searchService = searchService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the commentList
- * @see #commentList
- */
- public List<CommentView> getCommentList() {
- if (commentList == null) {
- refreshCommentList();
- }
- return commentList;
- }
-
- /**
- * @param commentList
- * the commentList to set
- * @see #commentList
- */
- public void setCommentList(List<CommentView> commentList) {
- this.commentList = commentList;
- }
-
- /**
- * Returns currently browsed map.
- *
- * @return currently browsed map
- */
- private Model getCurrentTopModel() {
- return mapBean.getCurrentTopModel();
- }
-
- /**
- * Returns identifier of browsed map (if such map wasn't setup it will be
- * default identifier).
- *
- * @return identifier of browsed map
- */
- private Project getCurrentProject() {
- return getCurrentTopModel().getProject();
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
- @Override
- public void init() {
- clear();
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java b/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
deleted file mode 100644
index 278b5f362fc4403159aaeba007b62b53ea736b26..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
+++ /dev/null
@@ -1,222 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.io.Serializable;
-import java.nio.charset.StandardCharsets;
-import java.util.Map;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.RequestScoped;
-import javax.faces.context.FacesContext;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.LayoutView;
-
-/**
- * Bean used for galaxy connector.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "galaxyMB")
-@RequestScoped
-public class GalaxyBean extends AbstractManagedBean implements Serializable {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(GalaxyBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Status of the processed request.
- */
- private String status = null;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service used for managing layouts.
- */
- @ManagedProperty(value = "#{LayoutService}")
- private transient ILayoutService layoutService;
-
- @Override
- public void clear() {
- status = null;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public String getStatus() {
- if (status == null) {
- try {
- Map<String, String> requestParams = FacesContext.getCurrentInstance().getExternalContext()
- .getRequestParameterMap();
- String identifier = requestParams.get("identifier");
- String schema = requestParams.get("expression_value");
- String login = requestParams.get("login");
- String password = requestParams.get("password");
- String modelName = requestParams.get("model");
-
- String token = userService.login(login, password);
- Model model = (Model) modelService.getLastModelByProjectId(modelName, token);
- User user = null;
- if (token != null) {
- user = userService.getUserByToken(token);
- }
- LayoutView layout = layoutService.getLayoutByName(model, identifier);
- if (identifier == null) {
- status = "ERROR. Identifier cannot be null";
- } else if (schema == null) {
- status = "ERROR. Expression values schema cannot be null";
- } else if (user == null) {
- status = "ERROR. Invalid credentials.";
- } else if (modelName == null) {
- status = "ERROR. Model cannot be null.";
- } else if (model == null) {
- status = "ERROR. " + modelName + " model doesn't exist.";
- } else if (layout != null) {
- status = "ERROR. Layout with given identifier (\"" + identifier + "\") already exists.";
- } else {
- createLayout(identifier, schema, model, user);
- }
- if (!status.equals("OK")) {
- logger.warn("Problem in galaxy connector: " + status);
- }
- } catch (Exception e) {
- logger.error(e, e);
- status = "INTERNAL SERVER ERROR";
- }
- } else {
- logger.debug("Status already set...");
- }
- return status;
- }
-
- /**
- * Creates layout from coloring data.
- *
- * @param identifier
- * identifier of layout
- * @param schema
- * coloring schema (in string format)
- * @param model
- * model for which we create layout
- * @param user
- * user who will own the layout
- */
- protected void createLayout(String identifier, String schema, Model model, User user) {
- String directory = getProjectDeployPath() + "../map_images/" + model.getProject().getDirectory() + "/"
- + model.getProject().getProjectId() + Math.random();
-
- InputStream stream = new ByteArrayInputStream(schema.getBytes(StandardCharsets.UTF_8));
- // the following call will execute asynchronically
- try {
- CreateLayoutParams params = new CreateLayoutParams().name(identifier).//
- directory(directory).//
- model(model).//
- colorInputStream(stream).//
- user(user).//
- async(true);
- layoutService.createLayout(params);
- status = "OK";
-
- } catch (InvalidColorSchemaException e) {
- status = "Problem with input file: " + e.getMessage();
- } catch (Exception e) {
- logger.error(e, e);
- status = "Internal server error. More details can be found in log file.";
- }
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- public void setStatus(String status) {
- this.status = status;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- @Override
- public void init() {
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java b/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
deleted file mode 100644
index 89300005b0100ec6299c0e1aa6142cbbfa376fc5..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
+++ /dev/null
@@ -1,814 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.Serializable;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.log4j.Logger;
-import org.primefaces.event.FileUploadEvent;
-import org.primefaces.model.UploadedFile;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
-import lcsb.mapviewer.events.Listener;
-import lcsb.mapviewer.events.ObjectAddedEvent;
-import lcsb.mapviewer.events.ObjectRemovedEvent;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
-import lcsb.mapviewer.services.search.layout.FullLayoutAliasViewFactory;
-import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
-import lcsb.mapviewer.services.search.layout.LightLayoutAliasViewFactory;
-import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
-import lcsb.mapviewer.services.search.layout.LightLayoutReactionViewFactory;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-import lcsb.mapviewer.services.view.LayoutView;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * Bean used to managing different layouts on current map.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "layoutMB")
-@ViewScoped
-public class LayoutBean extends AbstractManagedBean implements Serializable {
-
- /**
- * String representing {@link #layoutFile} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LAYOUT_FILE_PROPERTY = "LAYOUT_FILE";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(LayoutBean.class);
-
- /**
- * List of custom layouts available for current user.
- */
- private List<LayoutView> customLayouts = null;
-
- /**
- * List of general layouts.
- */
- private List<LayoutView> generalLayouts = null;
-
- /**
- * Layout selected by user for editing.
- */
- private LayoutView selectedLayout = null;
-
- /**
- * Name of currently edited/created layout.
- */
- private String layoutName = "";
-
- /**
- * Description of currently edited/created layout.
- */
- private String layoutDescription = "";
-
- /**
- * Type of uploaded layout.
- */
- private ColorSchemaType layoutType = ColorSchemaType.GENERIC;
-
- /**
- * Bool information if any error during parsing layout occurred.
- */
- private boolean errorOccurred = false;
-
- /**
- * This param should identifie layout currently visualized. However this is not
- * handled properly yet.
- */
- private LayoutView visualizedLayout = new LayoutView();
-
- /**
- * File uploaded by user.
- */
- private transient File layoutFile = null;
-
- /**
- * Service used for managing layouts.
- */
- @ManagedProperty(value = "#{LayoutService}")
- private transient ILayoutService layoutService;
-
- /**
- * Service used for accessing information about maps.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for communication with the client side about the map currently
- * visualized.
- *
- * @see MapBean
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- @Override
- public void init() {
- refreshCustomLayouts(null);
-
- PropertyChangeListener uploadedFilePropertyChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LAYOUT_FILE_PROPERTY.equals(arg0.getPropertyName())) {
- try {
- File file = (File) arg0.getNewValue();
- ZipEntryFileFactory zife = new ZipEntryFileFactory();
- LayoutZipEntryFile zif = zife.createLayoutZipEntryFile(layoutName, new FileInputStream(file));
- layoutName = zif.getName();
- layoutDescription = zif.getDescription();
- String typeStr = zif.getHeaderParameter(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
- if (typeStr != null) {
- try {
- layoutType = ColorSchemaType.valueOf(typeStr);
- } catch (IllegalArgumentException e) {
- layoutType = ColorSchemaType.GENERIC;
- sendError("Invalid type of overview: " + typeStr);
- }
- }
- } catch (Exception e) {
- sendError("Internal server error.", e);
- }
- }
- }
- };
- addPropertyChangeListener(uploadedFilePropertyChangeListener);
-
- // after object was added, refresh custom layouts list
- this.registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- logger.debug("Refreshing layouts after add: ");
- Model model = getCurrentTopModel();
- LayoutView layout = (LayoutView) event.getObject();
- if (model != null && model.getId().equals(layout.getModelId())) {
- logger.debug("OK");
- refreshCustomLayouts(null);
- mapBean.updateModelView();
- } else {
- logger.debug("NOT OK");
- }
- }
- });
-
- // after object was removed, refresh custom layouts list
- this.registerListener(new Listener<ObjectRemovedEvent>(ObjectRemovedEvent.class) {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectRemovedEvent event) {
- Model model = getCurrentTopModel();
- LayoutView layout = (LayoutView) event.getObject();
- if (model != null && model.getId().equals(layout.getModelId())) {
- refreshCustomLayouts(null);
- mapBean.updateModelView();
- }
- }
- });
- }
-
- /**
- * Check if logged user has privilege to add new layout for current map.
- *
- * @return true if logged user has privilege to add new layout for current map
- */
- public boolean getUserHasAddLayoutPrivilege() {
- User user = userBean.getLoggedUser();
- Model model = getCurrentTopModel();
- if (model == null) {
- return false;
- }
- return layoutService.userCanAddLayout(model, user);
- }
-
- /**
- * Check if user can remove actually selected layout.
- *
- * @return <i>true</i> if user can remove actually selected layout,<br/>
- * <i>false</i> otherwise
- */
- public boolean getUserHasRemoveLayoutPrivilege() {
- User user = userBean.getLoggedUser();
- return layoutService.userCanRemoveLayout(selectedLayout, user);
- }
-
- /**
- * Refresh list of custom layouts.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void refreshCustomLayouts(final ActionEvent actionEvent) {
- User user = userBean.getLoggedUser();
- Model model = getCurrentTopModel();
- customLayouts = layoutService.getCustomLayouts(model, user, true, user);
- generalLayouts = layoutService.getGeneralLayouts(model);
- }
-
- /**
- * This method handle upload of a file.
- *
- * @param event
- * event send by the client with a file reference
- */
- public void handleFileUpload(final FileUploadEvent event) {
- try {
- logger.debug(event.getFile().getFileName() + " is uploaded.");
- UploadedFile uploadedFile = event.getFile();
- String filename = FilenameUtils.getBaseName(uploadedFile.getFileName());
- String extension = FilenameUtils.getExtension(uploadedFile.getFileName());
- File file = File.createTempFile(filename + "-layout-", "." + extension);
- file.delete();
- InputStream input = uploadedFile.getInputstream();
- Files.copy(input, file.toPath());
- input.close();
- this.setLayoutFile(file);
- } catch (Exception e) {
- sendError("Problem with uploading...", e);
- }
- }
-
- /**
- * Adds public layout to the project selected in the parameter.
- *
- * @param project
- * where the new layout should be added
- * @throws SecurityException
- */
- public void addAnonymousLayout(ProjectView project) throws SecurityException {
- errorOccurred = false;
- Model model = modelService.getLastModelByProjectId(project.getProjectId(), userBean.getAuthenticationToken());
- addLayout(model, null);
- }
-
- /**
- * This method adds new layout to the model given in parameter.
- *
- *
- * @param model
- * where the new layout should be added
- * @param user
- * who should be the owenr of new layout (if <code>null</code> the
- * layout will be available to everybody)
- */
- private void addLayout(Model model, User user) {
- if (model == null) {
- errorOccurred = true;
- sendError("Unknown model.");
- return;
- }
- try {
- String directory = getProjectDeployPath() + "../map_images/" + model.getProject().getDirectory() + "/"
- + model.getProject().getProjectId() + Math.random();
-
- // the following call will execute asynchronically
- CreateLayoutParams params = new CreateLayoutParams().name(layoutName).//
- directory(directory).//
- model(model).//
- description(layoutDescription).//
- colorInputStream(new FileInputStream(layoutFile)).//
- layoutFileName(layoutFile.getName()).//
- user(user).//
- colorSchemaType(layoutType).//
- async(true);
- LayoutView view = layoutService.createLayout(params);
- layoutName = "";
- layoutFile = null;
-
- ObjectAddedEvent event = new ObjectAddedEvent(view);
- super.callListeners(event);
-
- sendInfo("File processed successfully. Generating layout.");
- } catch (IOException e) {
- errorOccurred = true;
- logger.error("Problem with uploading layout", e);
- sendError(e.getMessage());
- } catch (InvalidColorSchemaException e) {
- errorOccurred = true;
- logger.error("Problem with uploading layout", e);
- sendError(e.getMessage());
- } catch (Exception e) {
- logger.error("Problem with uploading layout", e);
- sendError("Unknown problem with uploaded file...");
- }
- }
-
- /**
- * This method adds a new custom layout to currently selected map.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void addLayout(final ActionEvent actionEvent) {
- errorOccurred = false;
- User user = userBean.getLoggedUser();
- Model model = getCurrentTopModel();
-
- if (!getUserHasAddLayoutPrivilege()) {
- errorOccurred = true;
- sendError("You cannot add new layout");
- return;
- }
- addLayout(model, user);
- }
-
- /**
- * Removes layout selected by the client.
- *
- * @param actionEvent
- * action event from client side
- */
- public void removeLayout(final ActionEvent actionEvent) {
- removeLayout(selectedLayout);
- }
-
- /**
- * Removes layout given in the parameter.
- *
- * @param layout
- * layout that should be removed
- */
- public void removeLayout(LayoutView layout) {
- errorOccurred = false;
- try {
- User user = userBean.getLoggedUser();
- if (!layoutService.userCanRemoveLayout(layout, user)) {
- errorOccurred = true;
- sendError("You cannot remove this layout");
- return;
- }
- layoutService.removeLayout(layout, getProjectDeployPath());
-
- ObjectRemovedEvent event = new ObjectRemovedEvent(layout);
- super.callListeners(event);
- } catch (Exception e) {
- errorOccurred = true;
- sendError("Problem with removing layout", e);
- }
- }
-
- /**
- * Updates selectedLayout in the service layer.
- *
- * @param actionEvent
- * action event from client side
- */
- public void updateLayout(final ActionEvent actionEvent) {
- errorOccurred = false;
- if (!getUserHasRemoveLayoutPrivilege()) {
- errorOccurred = true;
- sendError("You cannot update this layout");
- return;
- }
- try {
- layoutService.updateLayout(selectedLayout);
- refreshCustomLayouts(actionEvent);
- } catch (Exception e) {
- errorOccurred = true;
- sendError("Problem with updating layout", e);
- }
- }
-
- /**
- * Updates layout in the service layer.
- *
- * @param layout
- * layout for update
- */
- public void updateLayout(final LayoutView layout) {
- errorOccurred = false;
- User user = userBean.getLoggedUser();
- if (!layoutService.userCanRemoveLayout(layout, user)) {
- errorOccurred = true;
- sendError("You cannot update this layout");
- return;
- }
- try {
- layoutService.updateLayout(layout);
- refreshCustomLayouts(null);
- } catch (Exception e) {
- errorOccurred = true;
- sendError("Problem with updating layout", e);
- }
- }
-
- /**
- * Returns the number of layouts that can be uploaded by the user.
- *
- * @return number of layouts that can still be uploaded by the user
- */
- public int getAvailableCustomLayoutNumber() {
- User user = userBean.getLoggedUser();
- return (int) layoutService.getAvailableCustomLayoutsNumber(user);
- }
-
- @Override
- public void clear() {
- setCustomLayouts(null);
- setSelectedLayout(null);
- setLayoutFile(null);
- setLayoutName(null);
- setErrorOccurred(false);
- setLayoutType(ColorSchemaType.GENERIC);
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
- /**
- * @return the selectedLayout
- * @see #selectedLayout
- */
- public LayoutView getSelectedLayout() {
- return selectedLayout;
- }
-
- /**
- * @param selectedLayout
- * the selectedLayout to set
- * @see #selectedLayout
- */
- public void setSelectedLayout(LayoutView selectedLayout) {
- this.selectedLayout = selectedLayout;
- }
-
- /**
- * @return the customLayouts
- * @see #customLayouts
- */
- public List<LayoutView> getCustomLayouts() {
- return customLayouts;
- }
-
- /**
- * @param customLayouts
- * the customLayouts to set
- * @see #customLayouts
- */
- public void setCustomLayouts(List<LayoutView> customLayouts) {
- this.customLayouts = customLayouts;
- }
-
- /**
- * @return the layoutFile
- * @see #layoutFile
- */
- public File getLayoutFile() {
- return layoutFile;
- }
-
- /**
- * @param layoutFile
- * the layoutFile to set
- * @see #layoutFile
- */
- public void setLayoutFile(File layoutFile) {
- File oldFile = this.layoutFile;
- this.layoutFile = layoutFile;
- firePropertyChange(LAYOUT_FILE_PROPERTY, oldFile, layoutFile);
- }
-
- /**
- * @return the layoutName
- * @see #layoutName
- */
- public String getLayoutName() {
- return layoutName;
- }
-
- /**
- * @param layoutName
- * the layoutName to set
- * @see #layoutName
- */
- public void setLayoutName(String layoutName) {
- this.layoutName = layoutName;
- }
-
- /**
- * @return the errorOccurred
- * @see #errorOccurred
- */
- public boolean isErrorOccurred() {
- return errorOccurred;
- }
-
- /**
- * @param errorOccurred
- * the errorOccurred to set
- * @see #errorOccurred
- */
- public void setErrorOccurred(boolean errorOccurred) {
- this.errorOccurred = errorOccurred;
- }
-
- /**
- * @return the visualizedLayout
- * @see #visualizedLayout
- */
- public LayoutView getVisualizedLayout() {
- return visualizedLayout;
- }
-
- /**
- * @param visualizedLayout
- * the visualizedLayout to set
- * @see #visualizedLayout
- */
- public void setVisualizedLayout(LayoutView visualizedLayout) {
- this.visualizedLayout = visualizedLayout;
- }
-
- /**
- * Updates information in {@link #visualizedLayout} object.
- *
- * @param actionEvent
- * action event from client side
- */
- public void getVisualizedLayoutDetails(final ActionEvent actionEvent) {
- if (visualizedLayout.getName() != null && !visualizedLayout.getName().trim().equals("")) {
- visualizedLayout = layoutService.getLayoutByName(getCurrentTopModel(), visualizedLayout.getName());
- if (visualizedLayout == null) {
- visualizedLayout = new LayoutView();
- } else {
- // we have new element to vizualize
- ObjectAddedEvent event = new ObjectAddedEvent(visualizedLayout);
- super.callListeners(event);
- }
- }
- }
-
- /**
- * @return the generalLayouts
- * @see #generalLayouts
- */
- public List<LayoutView> getGeneralLayouts() {
- return generalLayouts;
- }
-
- /**
- * @param generalLayouts
- * the generalLayouts to set
- * @see #generalLayouts
- */
- public void setGeneralLayouts(List<LayoutView> generalLayouts) {
- this.generalLayouts = generalLayouts;
- }
-
- /**
- * Method that allows to donlwoad input data for given layout.
- *
- * @param layout
- * layout for which input data will be downloaded
- *
- * @throws IOException
- * thrown when there are some problems with sending file
- * @throws SecurityException
- */
- public void downloadInputData(LayoutView layout) throws IOException, SecurityException {
- // get input data from database
- byte[] data = layoutService.getInputDataForLayout(layout, userBean.getAuthenticationToken());
- String string = new String(data, StandardCharsets.UTF_8);
-
- sendFileAsResponse(string, "layout_" + layout.getIdObject() + ".txt", MimeType.TEXT);
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the layoutDescription
- * @see #layoutDescription
- */
- public String getLayoutDescription() {
- return layoutDescription;
- }
-
- /**
- * @param layoutDescription
- * the layoutDescription to set
- * @see #layoutDescription
- */
- public void setLayoutDescription(String layoutDescription) {
- this.layoutDescription = layoutDescription;
- }
-
- /**
- * This method sends list of aliases that should be visualized in a
- * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser.
- *
- * @throws IOException
- * thrown when there is a problem with accessing information about
- * layout
- */
- public void retreiveActiveAliasesForLayout() throws IOException {
- int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
- String string = "[]";
- try {
- List<LightLayoutAliasView> list = layoutService.getAliasesForLayout(getCurrentTopModel(), layoutId,
- userBean.getAuthenticationToken());
- LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
- string = factory.createGson(list);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- executeJavascript("ServerConnector.addAliasesForLayout('" + layoutId + "','" + string + "');");
- }
-
- /**
- * This method sends full information about aliases that are visualized in a
- * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser and identified
- * by list of identifiers.
- *
- * @throws IOException
- * thrown when there is a problem with accessing information about
- * layout
- */
- public void retreiveFullAliasesForLayout() {
- int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
- String string = "[]";
- try {
- List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
- List<FullLayoutAliasView> list = layoutService.getFullAliasesForLayoutByIds(getCurrentTopModel(), identifiers,
- layoutId, userBean.getAuthenticationToken());
- string = new FullLayoutAliasViewFactory().createGson(list);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- executeJavascript("ServerConnector.updateAliasesForLayout('" + layoutId + "','" + string + "');");
- }
-
- /**
- * This method sends list of reactions that should be visualized in a
- * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser.
- *
- * @throws IOException
- * thrown when there is a problem with accessing information about
- * layout
- */
- public void retreiveActiveReactionsForLayout() throws IOException {
- int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
- String string = "[]";
- try {
- List<LightLayoutReactionView> list = layoutService.getReactionsForLayout(getCurrentTopModel(), layoutId,
- userBean.getAuthenticationToken());
- LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
- string = factory.createGson(list);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- executeJavascript("ServerConnector.addReactionsForLayout('" + layoutId + "','" + string + "');");
- }
-
- /**
- * @return the layoutType
- * @see #layoutType
- */
- public ColorSchemaType getLayoutType() {
- return layoutType;
- }
-
- /**
- * @param layoutType
- * the layoutType to set
- * @see #layoutType
- */
- public void setLayoutType(ColorSchemaType layoutType) {
- this.layoutType = layoutType;
- }
-
- /**
- * Returns list of available layout types.
- *
- * @return list of available layout types
- */
- public ColorSchemaType[] getColorSchemaTypes() {
- return ColorSchemaType.values();
- }
-
- /**
- * Returns currently browsed map.
- *
- * @return currently browsed map
- */
- private Model getCurrentTopModel() {
- return mapBean.getCurrentTopModel();
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java b/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
deleted file mode 100644
index bf2709f766b291eef1fb78ad4c7170f014474a41..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
+++ /dev/null
@@ -1,1037 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.awt.geom.Point2D;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
-import java.beans.VetoableChangeListener;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.component.UIComponent;
-import javax.faces.event.ActionEvent;
-
-import org.apache.log4j.Logger;
-import org.primefaces.component.dialog.Dialog;
-import org.primefaces.context.RequestContext;
-import org.primefaces.model.map.LatLng;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.data.FullAliasView;
-import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
-import lcsb.mapviewer.services.search.data.LightAliasView;
-import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
-import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.search.data.LightReactionViewFactory;
-import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-import lcsb.mapviewer.services.view.ModelView;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * This bean is responsible for providing general data about current map and
- * receiving general information from client javascript.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "mapMB")
-@ViewScoped
-public class MapBean extends AbstractManagedBean implements Serializable {
-
- /**
- * String representing {@link #currentMapId} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String CURRENT_MODEL_ID_PROPERTY = "CURRENT_MODEL_ID";
-
- /**
- * String representing {@link #currentMap} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String CURRENT_MODEL_PROPERTY = "CURRENT_MODEL";
-
- /**
- * Name of the session field that store {@link ClientMapData#centerCoordinateY y
- * coordinate} of the browsable model (this will is used when page is
- * refreshed).
- */
- public static final String Y_COORD_SESSION_PARAM = "Y_COORD";
-
- /**
- * Name of the session field that store {@link ClientMapData#centerCoordinateX x
- * coordinate} of the browsable model (this will is used when page is
- * refreshed).
- */
- public static final String X_COORD_SESSION_PARAM = "X_COORD";
-
- /**
- * Name of the session field that store {@link ClientMapData#zoomLevel zoom
- * level} of the browsable model (this will is used when page is refreshed).
- */
- public static final String ZOOM_LEVEL_SESSION_PARAM = "LEVEL";
-
- /**
- * Name of the session field that store {@link ClientMapData#selectedLayout
- * selected layout} of the browsable model (this will is used when page is
- * refreshed).
- */
- public static final String SELECTED_LAYOUT_SESSION_PARAM = "SELECTED_LAYOUT";
-
- /**
- * Default organism by which results should be filtered (homo sapiens by
- * default).
- */
-
- private static final MiriamData DEFAULT_ORGANISM = TaxonomyBackend.HUMAN_TAXONOMY;
-
- /**
- * Object representing currently visualized project.
- */
- private ProjectView currentProjectView = null;
-
- /**
- * Name of the current project.
- */
- private String currentMapId = null;
-
- /**
- * Map currently browsed.
- */
- private transient Model currentMap = null;
-
- /**
- * This class store information about browsing single map/submap.
- *
- * @author Piotr Gawron
- *
- */
- public class ClientMapData implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Configuration of the map used by the javascript frontend.
- */
- private ModelView mapConfig = null;
-
- /**
- * Converter of coordinates dedicated to the map (every map must have a
- * different converter, because the size and number of layers in the maps are
- * different).
- */
- private CoordinationConverter cConverter;
-
- /**
- * Type of the model (used only in case of submodels).
- */
- private String type = "";
-
- /**
- * X coordinate of map center.
- */
- private String centerCoordinateX = "";
-
- /**
- * Y coordinate of map center.
- */
- private String centerCoordinateY = "";
-
- /**
- * Level at which map is browsed.
- */
- private String zoomLevel = "" + Configuration.MIN_ZOOM_LEVEL;
-
- /**
- * Layout currently visualized.
- */
- private String selectedLayout = "";
-
- /**
- * @return the mapConfig
- * @see #mapConfig
- */
- public ModelView getMapConfig() {
- return mapConfig;
- }
-
- /**
- * @param mapConfig
- * the mapConfig to set
- * @see #mapConfig
- */
- public void setMapConfig(ModelView mapConfig) {
- this.mapConfig = mapConfig;
- // set information about location and zooming (if it's set in the session)
- if (getSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setZoomLevel((String) getSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject()));
- // when we refresh map and have defined coordinates then tell the client
- // side that it shouldn't fit it into the bounds
- mapConfig.setFitMapBounds(false);
- } else {
- setZoomLevel("");
- }
- if (getSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setCenterCoordinateX((String) getSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject()));
- // when we refresh map and have defined coordinates then tell the client
- // side that it shouldn't fit it into the bounds
- mapConfig.setFitMapBounds(false);
- } else {
- setCenterCoordinateX("");
- }
- if (getSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setCenterCoordinateY((String) getSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject()));
- } else {
- setCenterCoordinateY("");
- }
- setSelectedLayout("");
- if (getSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setSelectedLayout((String) getSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject()));
- } else {
- if (mapConfig.getLayouts().size() > 0) {
- setSelectedLayout("cv" + mapConfig.getLayouts().get(0).getIdObject());
- } else {
- logger.warn("No layouts for model: " + mapConfig.getIdObject());
-
- }
- }
- }
-
- /**
- * @return the cConverter
- * @see #cConverter
- */
- public CoordinationConverter getcConverter() {
- return cConverter;
- }
-
- /**
- * @param cConverter
- * the cConverter to set
- * @see #cConverter
- */
- public void setcConverter(CoordinationConverter cConverter) {
- this.cConverter = cConverter;
- }
-
- /**
- * @return the centerCoordinateX
- * @see #centerCoordinateX
- */
- public String getCenterCoordinateX() {
- return centerCoordinateX;
- }
-
- /**
- * @param centerCoordinateX
- * the centerCoordinateX to set
- * @see #centerCoordinateX
- */
- public void setCenterCoordinateX(String centerCoordinateX) {
- if (centerCoordinateX != null && !centerCoordinateX.isEmpty()) {
- addSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject(), centerCoordinateX);
- }
- this.centerCoordinateX = centerCoordinateX;
- }
-
- /**
- * @return the centerCoordinateY
- * @see #centerCoordinateY
- */
- public String getCenterCoordinateY() {
- return centerCoordinateY;
- }
-
- /**
- * @param centerCoordinateY
- * the centerCoordinateY to set
- * @see #centerCoordinateY
- */
- public void setCenterCoordinateY(String centerCoordinateY) {
- if (centerCoordinateY != null && !centerCoordinateY.isEmpty()) {
- addSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject(), centerCoordinateY);
- }
- this.centerCoordinateY = centerCoordinateY;
- }
-
- /**
- * @return the zoomLevel
- * @see #zoomLevel
- */
- public String getZoomLevel() {
- return zoomLevel;
- }
-
- /**
- * @param zoomLevel
- * the zoomLevel to set
- * @see #zoomLevel
- */
- public void setZoomLevel(String zoomLevel) {
- if (zoomLevel != null && !zoomLevel.isEmpty()) {
- addSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject(), zoomLevel);
- }
- this.zoomLevel = zoomLevel;
- }
-
- /**
- * @return the selectedLayout
- * @see #selectedLayout
- */
- public String getSelectedLayout() {
- return selectedLayout;
- }
-
- /**
- * @param selectedLayout
- * the selectedLayout to set
- * @see #selectedLayout
- */
- public void setSelectedLayout(String selectedLayout) {
- if (selectedLayout != null && !selectedLayout.isEmpty()) {
- addSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject(), selectedLayout);
- }
- this.selectedLayout = selectedLayout;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- }
-
- /**
- * Top map of currently browsed model.
- */
- private ClientMapData topModelMapData = null;
-
- /**
- * List of all model/submodels that are browsed in the current window.
- */
- private List<ClientMapData> mapDataList = new ArrayList<>();
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService confService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Factory used to create {@link FullAliasView} elements.
- */
- @ManagedProperty(value = "#{FullAliasViewFactory}")
- private transient FullAliasViewFactory fullAliasViewFactory;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(MapBean.class);
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- @Override
- public void init() {
- // when model is changed we have to change few parameters as well
- PropertyChangeListener modelChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (CURRENT_MODEL_PROPERTY.equals(arg0.getPropertyName())) {
- updateModelView();
- }
- }
-
- };
- addPropertyChangeListener(modelChanged);
-
- // when we change id we should propagate the change to model
- PropertyChangeListener mapIdChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (CURRENT_MODEL_ID_PROPERTY.equals(arg0.getPropertyName())) {
- try {
- setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getNewValue(),
- userBean.getAuthenticationToken()));
- setCurrentProjectView(getProjectService().getProjectViewByProjectId(currentMap.getProject().getProjectId(),
- userBean.getAuthenticationToken()));
- } catch (Exception e) {
- try {
- setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getOldValue(),
- userBean.getAuthenticationToken()));
- } catch (SecurityException e1) {
- logger.error(e1, e1);
- }
- logger.error(e, e);
- }
- }
- }
-
- };
- addPropertyChangeListener(mapIdChangeListener);
-
- // when we change id we should propagate the change to model
- VetoableChangeListener vetoMapIdChangeListener = new VetoableChangeListener() {
- @Override
- public void vetoableChange(PropertyChangeEvent arg0) throws PropertyVetoException {
- if (!getProjectService().projectExists((String) arg0.getNewValue())) {
- throw new PropertyVetoException("Project with id \"" + arg0.getNewValue() + "\" doesn't exist.", arg0);
- }
- }
-
- };
- addVetoablePropertyChangeListener(vetoMapIdChangeListener);
-
- // set id from request parameters (id is the url GET parameter)
- setCurrentMapId(getRequestParameter("id"));
-
- }
-
- /**
- * Refresh information about models.
- */
- protected void updateModelView() {
-
- Model model = getCurrentTopModel();
- // configuration
- ModelView topView = modelService.getModelView(model, userBean.getLoggedUser());
-
- mapDataList = new ArrayList<>();
-
- ClientMapData cmd = new ClientMapData();
- cmd.setMapConfig(topView);
- cmd.setType("N/A");
- // coordinates converter
- cmd.setcConverter(new CoordinationConverter(model));
-
- mapDataList.add(cmd);
- topModelMapData = cmd;
-
- for (ModelView view : topView.getSubmodels()) {
- cmd = new ClientMapData();
- cmd.setMapConfig(view);
- // coordinates converter
- cmd.setcConverter(new CoordinationConverter(model.getSubmodelById(view.getIdObject())));
- cmd.setType(model.getSubmodelConnectionById(view.getIdObject()).getType().getCommonName());
- mapDataList.add(cmd);
- }
- }
-
- /**
- * This method center map in the client using coordinates from client.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void centerMap(final ActionEvent actionEvent) {
- createSubmodelDialog(actionEvent);
-
- // we have plain coordinates (not lat lng)
- String xCoord = getRequestParameter("xCoord");
- String yCoord = getRequestParameter("yCoord");
- String modelIdentifier = getRequestParameter("submodelId");
- if (modelIdentifier == null) {
- sendError("submodelId param wasn't set");
- return;
- }
- Integer modelId = Integer.valueOf(modelIdentifier);
-
- ClientMapData selectedMapData = null;
- for (ClientMapData mapData : getMapDataList()) {
- if (mapData.getMapConfig().getIdObject().equals(modelId)) {
- selectedMapData = mapData;
- }
- }
- if (selectedMapData == null) {
- sendError("Cannot find map with the identifier: " + modelId);
- return;
- }
-
- LatLng latLng;
- if (xCoord != null && yCoord != null) {
- double x = Double.parseDouble(xCoord);
- double y = Double.parseDouble(yCoord);
- latLng = selectedMapData.getcConverter().toLatLng(new Point2D.Double(x, y));
- } else {
- String latCoord = getRequestParameter("latCoord");
- String lngCoord = getRequestParameter("lngCoord");
- double lat = Double.parseDouble(latCoord);
- double lng = Double.parseDouble(lngCoord);
- latLng = new LatLng(lat, lng);
- }
- centerMapInJavascript(latLng, selectedMapData);
- }
-
- /**
- * Method responsible for centering map in client using coordinates given as a
- * parameter.
- *
- * @param mapData
- * defines which map we want to center. If the value is not set then
- * default one is selected
- *
- * @param latLng
- * - coordinates
- */
- private void centerMapInJavascript(final LatLng latLng, ClientMapData mapData) {
- double lat = latLng.getLat();
- double lng = latLng.getLng();
- logger.debug("Center map in js (" + lat + "," + lng + ")");
- executeJavascript("customMap.setCenter(" + mapData.getMapConfig().getIdObject() + ", new google.maps.LatLng(" + lat
- + "," + lng + "));");
- }
-
- /**
- * Check if user can see the map.
- *
- * @return <i>true</i> if user can see the map,<br/>
- * <i> false otherwise</i>
- */
- public boolean getUserHasViewPrivilege() {
- Project project = getCurrentProject();
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project);
- if (!result) {
- logger.debug("User doesn't have privilege");
- }
- return result;
- }
-
- /**
- * This is artifitial method called by the client side to pass some parameters
- * to the bean:
- * <ul>
- * <li>{@link #centerCoordinateX},</li>
- * <li>{@link #centerCoordinateY},</li>
- * <li>{@link #selectedLayout},</li>
- * <li>{@link #zoomLevel}.</li>
- * </ul>
- */
- public void actualizeParams() {
-
- }
-
- /**
- * Returns the index of layout that is currently visualized.
- *
- * @return index of layout that is currently visualized.
- */
- public Integer getSelectedLayoutIdentifier() {
- if (topModelMapData.getSelectedLayout() == null) {
- return null;
- } else {
- String str = topModelMapData.getSelectedLayout().replaceAll("[^0-9]", "");
- Integer id = null;
- try {
- id = Integer.parseInt(str);
- } catch (NumberFormatException e) {
- logger.warn("Problem with layout identifier: " + topModelMapData.getSelectedLayout());
- }
- return id;
- }
- }
-
- /**
- * Returns level on which the map is currently browsed. It's not equal to the
- * zoom level, becuse zoom level is shifted by
- * {@link lcsb.mapviewer.common.Configuration.MIN_ZOOM_LEVEL} value.
- *
- * @param mapData
- * defines on which map we are looking for zoom level. If the value is
- * not set then default one is selected
- * @return level on which the map is currently browsed
- */
- public Integer getLevel(ClientMapData mapData) {
- String zoomLevel = mapData.getZoomLevel();
- if (zoomLevel == null) {
- return null;
- }
- Integer res = null;
- try {
- res = Integer.valueOf(zoomLevel) - Configuration.MIN_ZOOM_LEVEL;
- } catch (NumberFormatException e) {
- logger.warn("Problem with zoomLevel: " + zoomLevel);
- }
- return res;
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the mapDataList
- * @see #mapDataList
- */
- public List<ClientMapData> getMapDataList() {
- return mapDataList;
- }
-
- /**
- * Creates dialog on client side for submodel.
- *
- * @param actionEvent
- * event from the client
- */
- public void createSubmodelDialog(final ActionEvent actionEvent) {
- try {
- String dialogGroup = "_gmapForm:submodelDialogGroup";
- String idParamName = "submodelId";
- String dialogIdPrefix = "submodelDialog";
-
- UIComponent panelGroup = findComponent(dialogGroup);
- if (panelGroup == null) {
- sendError("Cannot find " + dialogGroup + " component.");
- return;
- }
- String id = getRequestParameter(idParamName);
- if (id == null) {
- sendError(idParamName + " request param cannot be null.");
- return;
- }
- if (id.equals(getCurrentTopModel().getId() + "")) {
- logger.debug("TopModel doesn't require window");
- return;
- }
- id = dialogIdPrefix + id;
- for (UIComponent child : panelGroup.getChildren()) {
- if (child instanceof Dialog) {
- if (child.getId().equals(id)) {
- logger.debug("Dialog " + id + " found");
- return;
- }
- }
- }
- for (ModelSubmodelConnection model : getCurrentTopModel().getSubmodelConnections()) {
- Integer modelId = model.getSubmodel().getId();
- id = dialogIdPrefix + modelId;
- Dialog dialog = new Dialog();
- dialog.setId(id);
- dialog.setWidgetVar(id);
- dialog.setHeader("Submodel: " + model.getSubmodel().getName());
- dialog.setMinimizable(true);
- panelGroup.getChildren().add(dialog);
- }
-
- RequestContext requestContext = RequestContext.getCurrentInstance();
- requestContext.update(dialogGroup);
-
- } catch (Exception e) {
- logger.error(e, e);
- sendError(e.getMessage());
- }
- }
-
- /**
- * Returns map configuration in Gson format.
- *
- * @return map configuration in Gson format
- */
- public String getGsonConfiguration() {
- return new Gson().toJson(getMapDataList().get(0).getMapConfig());
- }
-
- /**
- * @return the topModelMapData
- * @see #topModelMapData
- */
- public ClientMapData getTopModelMapData() {
- if (topModelMapData == null) {
- updateModelView();
- }
- return topModelMapData;
- }
-
- /**
- * @param topModelMapData
- * the topModelMapData to set
- * @see #topModelMapData
- */
- public void setTopModelMapData(ClientMapData topModelMapData) {
- this.topModelMapData = topModelMapData;
- }
-
- /**
- * Returns {@link ClientMapData} for (sub)model identified by identifier.
- *
- * @param identifier
- * identifier of the model
- * @return {@link ClientMapData}
- */
- public ClientMapData getMapDataByMapIdentifier(String identifier) {
- Integer id = Integer.parseInt(identifier);
- return getMapDataByMapIdentifier(id);
- }
-
- /**
- * Returns {@link ClientMapData} for (sub)model identified by identifier.
- *
- * @param identifier
- * identifier of the model
- * @return {@link ClientMapData}
- */
- public ClientMapData getMapDataByMapIdentifier(Integer identifier) {
- // in case we haven't initialized mapdata we need to do it here (it's a
- // workaround...)
- if (getMapDataList().size() == 0) {
- updateModelView();
- }
- for (ClientMapData md : getMapDataList()) {
- if (md.getMapConfig().getIdObject().equals(identifier)) {
- return md;
- }
- }
- return null;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * Sets zoom level for submodel. Parameters are passed using http request
- * mechainsm/
- */
- public void setModelZoomLevel() {
- String mapId = getRequestParameter("mapId");
- String zoomLevel = getRequestParameter("zoomLevel");
-
- Integer id = Integer.valueOf(mapId);
-
- for (ClientMapData cmd : getMapDataList()) {
- if (cmd.getMapConfig().getIdObject().equals(id)) {
- cmd.setZoomLevel(zoomLevel);
- return;
- }
- }
- sendError("Cannot find model with id: " + id);
-
- }
-
- /**
- * Sends list of aliases (with given identifiers) to the browser. Identifiers
- * are passed as a json string in request parameter <i>ids</i>. Each identifier
- * is a pair containing information about {@link Model#getId() model id} and
- * {@link lcsb.mapviewer.model.map.species.Element#id alias id}. Data is very
- * light - contains only information about the location on the model.
- *
- */
- public void retreiveLightAliases() {
- List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
- List<LightAliasView> list = modelService.getLightAliasesByIds(getCurrentTopModel(), identifiers);
- LightAliasViewFactory factory = new LightAliasViewFactory();
- String string = factory.createGson(list);
- executeJavascript("ServerConnector.addAliases(" + string + ");");
- }
-
- /**
- * Sends list of reactions (with given identifiers) to the browser. Identifiers
- * are passed as a json string in request parameter <i>ids</i>. Each identifier
- * is a pair containing information about {@link Model#getId() model id} and
- * {@link lcsb.mapviewer.model.map.reaction.Reaction#id reaction id}.
- *
- */
- public void retreiveLightReactions() {
- List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
- List<LightReactionView> list = modelService.getLightReactionsByIds(getCurrentTopModel(), identifiers);
- LightReactionViewFactory factory = new LightReactionViewFactory();
- String string = factory.createGson(list);
- executeJavascript("ServerConnector.addReactions('" + string + "');");
- }
-
- /**
- * @return the fullAliasViewFactory
- * @see #fullAliasViewFactory
- */
- public FullAliasViewFactory getFullAliasViewFactory() {
- if (fullAliasViewFactory == null) {
- fullAliasViewFactory = findBean(FullAliasViewFactory.class);
- }
- return fullAliasViewFactory;
- }
-
- /**
- * @param fullAliasViewFactory
- * the fullAliasViewFactory to set
- * @see #fullAliasViewFactory
- */
- public void setFullAliasViewFactory(FullAliasViewFactory fullAliasViewFactory) {
- this.fullAliasViewFactory = fullAliasViewFactory;
- }
-
- /**
- * @return the currentMapId
- * @see #currentMapId
- */
- public final String getCurrentMapId() {
- // if user didn't provide id then use default one
- if (currentMapId == null) {
- String tmp = confService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
- if (tmp == null) {
- logger.warn("Cannot find default map in the system.");
- }
- setCurrentMapId(tmp);
- }
- return currentMapId;
- }
-
- /**
- * @param currentMapId
- * the currentMapId to set
- * @see #currentMapId
- */
- public final void setCurrentMapId(String currentMapId) {
- try {
- fireVetoableChange(CURRENT_MODEL_ID_PROPERTY, this.currentMapId, currentMapId);
- String oldValue = this.currentMapId;
- this.currentMapId = currentMapId;
- firePropertyChange(CURRENT_MODEL_ID_PROPERTY, oldValue, currentMapId);
- } catch (PropertyVetoException e) {
- logger.warn("Cannot change property: " + CURRENT_MODEL_ID_PROPERTY + ". Form: \"" + this.currentMapId
- + "\" into: \"" + currentMapId + "\"");
- }
- }
-
- /**
- * Return {@link #currentMap currently browsed map}.
- *
- * @return currently browsed map
- */
- protected final Model getCurrentTopModel() {
- if (currentMap == null) {
- try {
- setCurrentTopModel(
- this.getModelService().getLastModelByProjectId(getCurrentMapId(), userBean.getAuthenticationToken()));
- } catch (SecurityException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
- return currentMap;
- }
-
- /**
- * @return the currentProject
- * @see #currentProject
- */
- public Project getCurrentProject() {
- return getCurrentTopModel().getProject();
- }
-
- /**
- * @param topModel
- * the topModel to set
- * @see #currentMap
- */
- private void setCurrentTopModel(Model topModel) {
- Model oldValue = this.currentMap;
- this.currentMap = topModel;
- firePropertyChange(CURRENT_MODEL_PROPERTY, oldValue, topModel);
- }
-
- /**
- * @return the currentProjectView
- * @see #currentProjectView
- */
- public ProjectView getCurrentProjectView() {
- return currentProjectView;
- }
-
- /**
- * @param currentProjectView
- * the currentProjectView to set
- * @see #currentProjectView
- */
- public void setCurrentProjectView(ProjectView currentProjectView) {
- this.currentProjectView = currentProjectView;
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- /**
- * @return the confService
- * @see #confService
- */
- public IConfigurationService getConfService() {
- return confService;
- }
-
- /**
- * @param confService
- * the confService to set
- * @see #confService
- */
- public void setConfService(IConfigurationService confService) {
- this.confService = confService;
- }
-
- /**
- * Returns organism associated with currently viewed project. If organism is not
- * set then {@link #DEFAULT_ORGANISM} is returned.
- *
- * @return organism associated with currently viewed project
- */
- public MiriamData getOrganism() {
- MiriamData organism = getCurrentProject().getOrganism();
- if (organism == null || organism.getResource().isEmpty()) {
- organism = DEFAULT_ORGANISM;
- }
- return organism;
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MiriamBean.java b/web/src/main/java/lcsb/mapviewer/bean/MiriamBean.java
deleted file mode 100644
index 40783c58b4eb7a81fb7289d3c1e982b239550146..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/MiriamBean.java
+++ /dev/null
@@ -1,284 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.services.interfaces.IMiriamService;
-
-import org.apache.log4j.Logger;
-
-/**
- * Bean used to redirect client to proper external site from miriam data uri.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "miriamMB")
-@ViewScoped
-public class MiriamBean extends AbstractManagedBean implements Serializable {
-
- /**
- * String representing {@link #type} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String TYPE_PROPERTY = "TYPE";
-
- /**
- * String representing {@link #resource} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String RESOURCE_PROPERTY = "RESOURCE";
-
- /**
- * String representing {@link #linkDescription} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LINK_DESCRIPTION_PROPERTY = "LINK_DESCRIPTION";
-
- /**
- * String representing {@link #redirectLink} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String REDIRECTION_LINK_PROPERTY = "REDIRECTION_LINK";
-
- /**
- * String representing {@link #message} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String MESSAGE_PROPERTY = "MESSAGE";
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(MiriamBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Type of the resource.
- */
- private String type = "";
-
- /**
- * Resource identrifier.
- */
- private String resource = "";
-
- /**
- * Link where user should be redirected.
- */
- private String redirectLink = null;
-
- /**
- * Description of the link.
- */
- private String linkDescription = "";
-
- /**
- * Message to the client (OK/ERROR).
- */
- private String message = "";
-
- /**
- * Service accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
- * registry</a>.
- */
- @ManagedProperty(value = "#{MiriamService}")
- private transient IMiriamService miriamService;
-
- /**
- * List of all supported miriamTypes.
- */
- private List<MiriamType> miriamTypes = new ArrayList<MiriamType>();
-
- @Override
- public void init() {
- // when type or resource id changes we have to update redirect link
- PropertyChangeListener selectedModelChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (TYPE_PROPERTY.equals(arg0.getPropertyName()) || RESOURCE_PROPERTY.equals(arg0.getPropertyName())) {
- if (type != null && resource != null) {
- try {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, miriamService.getTypeForUri(type), resource);
- setRedirectLink(miriamService.getUrlForMiriamData(md));
- if (redirectLink == null || redirectLink.trim().equals("")) {
- setMessage("Invalid miriam data: " + type + ":" + resource);
- setLinkDescription("");
- } else {
- setMessage("You should be redirected in 5 seconds. If the page does not reload you can use direct ");
- setLinkDescription("link");
- }
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- setRedirectLink(null);
- setLinkDescription("");
- setMessage("Internal server error");
- }
- } else {
- setRedirectLink(null);
- setLinkDescription("");
- setMessage("Invalid miriam data: " + type + ":" + resource);
- }
- }
- }
- };
- addPropertyChangeListener(selectedModelChanged);
-
- for (MiriamType type : MiriamType.values()) {
- miriamTypes.add(type);
- }
- }
-
- /**
- *
- * @return {@link #linkDescription}
- */
- public String getLinkDescription() {
- return linkDescription;
- }
-
- /**
- * Sets {@link #linkDescription}. Property change listeners will be thrown
- * after value change.
- *
- * @param linkDescription
- * new {@link #linkDescription}
- */
- public void setLinkDescription(final String linkDescription) {
- String oldValue = this.linkDescription;
- this.linkDescription = linkDescription;
- firePropertyChange(LINK_DESCRIPTION_PROPERTY, oldValue, linkDescription);
- }
-
- /**
- *
- * @return {@link #type}
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets {@link #type}. Property change listeners will be thrown after value
- * change.
- *
- * @param type
- * new {@link #type}
- */
- public void setType(final String type) {
- String oldValue = this.type;
- this.type = type;
- firePropertyChange(TYPE_PROPERTY, oldValue, type);
- }
-
- /**
- *
- * @return {@link #resource}
- */
- public String getResource() {
- return resource;
- }
-
- /**
- * Sets {@link #resource}. Property change listeners will be thrown after
- * value change.
- *
- * @param resource
- * new {@link #resource}
- */
- public void setResource(final String resource) {
- String oldValue = this.resource;
- this.resource = resource;
- firePropertyChange(RESOURCE_PROPERTY, oldValue, resource);
- }
-
- /**
- *
- * @return {@link #message}
- */
- public String getMessage() {
- return message;
- }
-
- /**
- * Sets {@link #message}. Property change listeners will be thrown after value
- * change.
- *
- * @param message
- * new {@link #message}
- */
- public void setMessage(final String message) {
- String oldValue = this.message;
- this.message = message;
- firePropertyChange(MESSAGE_PROPERTY, oldValue, message);
- }
-
- /**
- *
- * @return {@link #redirectLink}
- */
- public String getRedirectLink() {
- return redirectLink;
- }
-
- /**
- * Sets {@link #redirectLink}. Property change listeners will be thrown after
- * value change.
- *
- * @param redirectLink
- * new {@link #redirectLink}
- */
- public void setRedirectLink(final String redirectLink) {
- String oldValue = this.redirectLink;
- this.redirectLink = redirectLink;
- firePropertyChange(REDIRECTION_LINK_PROPERTY, oldValue, redirectLink);
- }
-
- @Override
- public void clear() {
- setType("");
- setResource("");
- setRedirectLink(null);
- setLinkDescription("");
- setMessage("");
- }
-
- /**
- * @return the miriamService
- * @see #miriamService
- */
- public IMiriamService getMiriamService() {
- return miriamService;
- }
-
- /**
- * @param miriamService
- * the miriamService to set
- * @see #miriamService
- */
- public void setMiriamService(IMiriamService miriamService) {
- this.miriamService = miriamService;
- }
-
- /**
- * @return the miriamTypes
- * @see #miriamTypes
- */
- public List<MiriamType> getMiriamTypes() {
- return miriamTypes;
- }
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MissingConnectionBean.java b/web/src/main/java/lcsb/mapviewer/bean/MissingConnectionBean.java
deleted file mode 100644
index 482e9cf4606a4d9427cf763446bf5d534195d71d..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/MissingConnectionBean.java
+++ /dev/null
@@ -1,228 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.graph.DataMiningType;
-import lcsb.mapviewer.services.interfaces.IDataMiningService;
-import lcsb.mapviewer.services.search.ElementIdentifierDetails;
-import lcsb.mapviewer.services.search.ISearchResultView;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.view.DataMiningSetView;
-
-/**
- * This bean is responsible for providing information about suggested
- * connections between nodes (for now genes only) that doesn't exist on the map.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "missingConnectionMB")
-@ViewScoped
-public class MissingConnectionBean extends AbstractMarkerManagerBean<ISearchResultView> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(MissingConnectionBean.class);
-
- /**
- * Gene name for which we want to find suggested connections.
- */
- private String geneName = "";
-
- /**
- * List of all {@link DataMiningType}.
- */
- private List<DataMiningType> dataMiningTypes = new ArrayList<DataMiningType>();
-
- /**
- * Bean used for communication with the client side about the map currently
- * visualized.
- *
- * @see MapBean
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- /**
- * Service that manages data mining information.
- */
- @ManagedProperty(value = "#{DataMiningService}")
- private transient IDataMiningService dataMiningService;
-
- /**
- * This method is looking for suggested connections for the specified gene.
- * name
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void search(final ActionEvent actionEvent) {
- logger.error("Not Implemented");
- // if (getCurrentTopModel() == null) {
- // logger.warn("Unknown model. Skipping...");
- // return;
- // }
- //
- // clearResults();
- // // find species that probably shoud be connected with the geneName
- // Collection<Element> connections =
- // dataMiningService.getSpeciesWithMissingConnectionsByGeneName(getCurrentTopModel(),
- // geneName);
- //
- // List<SpeciesAlias> aliases = new ArrayList<SpeciesAlias>();
- // for (Element element : connections) {
- // if (element instanceof Species) {
- // Species species = (Species) element;
- //
- // List<SpeciesAlias> tmp =
- // getCurrentTopModel().getAliasesBySpeciesId(species.getIdSpecies());
- // aliases.addAll(tmp);
- //
- // } else {
- // logger.warn("Unknown class type: " + element.getClass());
- // }
- // ConverterParams params = mapBean.getOverlayConverter().new
- // ConverterParams()
- // .model(getCurrentTopModel()).icon(IconManager.getInstance().getEmpyIcon()).border(true).addObjects(aliases);
- // addResults(mapBean.getOverlayConverter().objectsToSearchResults(params));
- // }
- // // and send it to the client
- // refreshOverlayCollection();
- }
-
- @Override
- public void clear() {
- setGeneName("");
- clearResults();
- refreshDataInJavascript();
- }
-
- /**
- * @return the geneName
- * @see #geneName
- */
- public String getGeneName() {
- return geneName;
- }
-
- /**
- * @param geneName
- * the geneName to set
- * @see #geneName
- */
- public void setGeneName(String geneName) {
- this.geneName = geneName;
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
- /**
- * @return the dataMiningService
- * @see #dataMiningService
- */
- public IDataMiningService getDataMiningService() {
- return dataMiningService;
- }
-
- /**
- * @param dataMiningService
- * the dataMiningService to set
- * @see #dataMiningService
- */
- public void setDataMiningService(IDataMiningService dataMiningService) {
- this.dataMiningService = dataMiningService;
- }
-
- @Override
- public void init() {
- for (DataMiningType type : DataMiningType.values()) {
- dataMiningTypes.add(type);
- }
- }
-
- /**
- * @return the dataMiningTypes
- * @see #dataMiningTypes
- */
- public List<DataMiningType> getDataMiningTypes() {
- return dataMiningTypes;
- }
-
- /**
- * @param dataMiningTypes
- * the dataMiningTypes to set
- * @see #dataMiningTypes
- */
- public void setDataMiningTypes(List<DataMiningType> dataMiningTypes) {
- this.dataMiningTypes = dataMiningTypes;
- }
-
- /**
- * Method that allows to donlwoad input data for given data mining set.
- *
- * @param dms
- * data minig set for which input data will be downloaded
- *
- * @throws IOException
- * thrown when there are some problems with sending file
- */
- public void downloadInputData(DataMiningSetView dms) throws IOException {
- // get input data from database
- byte[] data = dataMiningService.getInputDataForLayout(dms);
- String string = new String(data, StandardCharsets.UTF_8);
-
- sendFileAsResponse(string, "data_mining_" + dms.getIdObject() + ".txt", MimeType.TEXT);
- }
-
- @Override
- protected List<ElementIdentifier> getLightElementsForSearchResult(ISearchResultView result) {
- logger.error("Not implemented");
- return new ArrayList<>();
- }
-
- @Override
- protected ElementIdentifierDetails getElementInformationForResult(ElementIdentifier element, ISearchResultView result) {
- throw new NotImplementedException();
- }
-
- @Override
- protected List<Pair<String, ElementIdentifierDetails>> getElementInformationForResult(ElementIdentifier element) {
- throw new NotImplementedException();
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
deleted file mode 100644
index 6a6c30a73b45ce4dc5f82c14421deb226c664252..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
+++ /dev/null
@@ -1,1523 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
-import java.beans.VetoableChangeListener;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.Serializable;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-import org.primefaces.event.FileUploadEvent;
-import org.primefaces.event.TransferEvent;
-import org.primefaces.model.DualListModel;
-import org.primefaces.model.TreeNode;
-import org.primefaces.model.UploadedFile;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.zip.DataMiningZipEntryFile;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.InputFileType;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
-import lcsb.mapviewer.events.Listener;
-import lcsb.mapviewer.events.ObjectAddedEvent;
-import lcsb.mapviewer.events.ObjectModifiedEvent;
-import lcsb.mapviewer.events.ObjectRemovedEvent;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.graph.DataMiningType;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
-import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.view.LayoutView;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * This bean is responsible for managing projects. It allows to
- * create/modify/remove project.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "projectMB")
-@ViewScoped
-public class ProjectBean extends AbstractManagedBean implements Serializable {
-
- /**
- * String representing {@link #selectedProject} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String SELECTED_PROJECT_PROPERTY = "SELECTED_PROJECT";
-
- /**
- * String representing {@link #mapFile} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String MAP_FILE_PROPERTY = "MAP_FILE";
-
- /**
- * String representing {@link #newMapAutoResize} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String AUTO_RESIZE_MAP_PROPERTY = "AUTO_RESIZE_MAP";
-
- /**
- * String representing {@link #newProjectId} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String PROJECT_ID_PROPERTY = "PROJECT_ID";
-
- /**
- * String representing {@link #newMapVersion} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String MAP_VERSION_PROPERTY = "MAP_VERSION";
-
- /**
- * String representing {@link #selectedAnnotatorTreeNodeData} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY = "SELECTED_ANNOTATOR_TREE_NODE_DATA";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ProjectBean.class);
-
- /**
- * List of projects visible on client side. It's lazy loaded.
- */
- private List<ProjectView> projects = null;
-
- /**
- * Project selected for editing (or new project to create).
- */
- private ProjectView selectedProject;
-
- /**
- * Identifier of the project.
- */
- private String newProjectId = "auto_name";
-
- /**
- * Name of the project.
- */
- private String newProjectName = "UNKNOWN DISEASE MAP";
-
- /**
- * Disease of the project.
- */
- private String newProjectDisease;
-
- /**
- * Organism of the project.
- */
- private String newProjectOrganism;
-
- /**
- * Version of the project.
- */
- private String newMapVersion = "0";
-
- /**
- * Should we annotate model automatically.
- */
- private String annotateModel = "false";
-
- /**
- * Should we cache data from external resources connected to this map.
- */
- private String cacheModel = "false";
-
- /**
- * Should the maunal annotations of the model be verified.
- */
- private String verifyAnnotationsModel = "false";
-
- /**
- * Should we resize the model (to normalize margins).
- */
- private String newMapAutoResize = "true";
-
- /**
- * Is the uploaded model a complex multi-files project or not.
- */
- private String complexModel = "false";
-
- /**
- * Is the {@link lcsb.mapviewer.services.utils.data.BuildInLayout#NORMAL}
- * default layout when generating new project.
- */
- private String networkLayoutAsDefault = "false";
-
- /**
- * List of zip entries corresponding to model (and submodels) in the complex
- * project thas is to be uploaded.
- */
- private List<ModelZipEntryFile> modelZipEntries = new ArrayList<ModelZipEntryFile>();
-
- /**
- * List of zip entries corresponding to data mining files in the complex
- * project.
- */
- private List<DataMiningZipEntryFile> dataMiningZipEntries = new ArrayList<DataMiningZipEntryFile>();
-
- /**
- * List of zip entries corresponding to layout files in the complex project.
- */
- private List<LayoutZipEntryFile> layoutZipEntries = new ArrayList<LayoutZipEntryFile>();
-
- /**
- * Should the map be displayed in SBGN format.
- */
- private String sbgnFormat = "false";
-
- private String semanticOverlay = "false";
-
- /**
- * List of zip entries corresponding to
- * {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} files in the
- * complex project.
- */
- private List<ImageZipEntryFile> imageZipEntries = new ArrayList<ImageZipEntryFile>();
-
- /**
- * Uploaded file with the data in CellDesigner format.
- */
- private File mapFile = null;
-
- /**
- * Service used to access information about projects.
- *
- * @see IProjectService
- */
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for communication with the client side about the data related to
- * layouts.
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{layoutMB}")
- private transient LayoutBean layoutBean;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Tree with information about classes that can be annotated and which
- * annotators should be used for these classes.
- */
- private TreeNode annotatorsTree;
-
- /**
- * Element of {@link #annotatorsTree} that is currently edited.
- */
- private AnnotatedObjectTreeRow selectedAnnotatorTreeNodeData;
-
- /**
- * List of annotators for {@link #selectedAnnotatorTreeNodeData} that is
- * currently edited.
- */
- private DualListModel<String> annotators = new DualListModel<String>();
-
- /**
- * List of valid {@link MiriamType} for {@link #selectedAnnotatorTreeNodeData}
- * that is currently edited.
- */
- private DualListModel<MiriamType> validMiriam = new DualListModel<MiriamType>();
-
- /**
- * List of required {@link MiriamType} for
- * {@link #selectedAnnotatorTreeNodeData} that is currently edited.
- */
- private DualListModel<MiriamType> requiredMiriam = new DualListModel<MiriamType>();
-
- /**
- * List of all {@link DataMiningType}.
- */
- private List<DataMiningType> dataMiningTypes = new ArrayList<DataMiningType>();
-
- /**
- * Listener used to verify the modification of the project.
- */
- private transient VetoableChangeListener selectedProjectVetoChanged;
-
- {
- selectedProjectVetoChanged = new VetoableChangeListener() {
- @Override
- public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
- try {
- if (SELECTED_PROJECT_PROPERTY.equals(arg0.getPropertyName())) {
-
- ProjectView oldVal = (ProjectView) arg0.getOldValue();
- ProjectView newVal = (ProjectView) arg0.getNewValue();
-
- // if we change to null then it's ok
- if (newVal == null) {
- return;
- }
-
- ProjectView fromDb = projectService.getProjectViewByProjectId(newVal.getProjectId(),
- userBean.getAuthenticationToken());
- String defaultMap = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
-
- // check if we change the name properly
- if (oldVal != null && oldVal.getIdObject() != null && oldVal.getIdObject().equals(newVal.getIdObject())) {
- if (oldVal.getProjectId().equals(newVal.getProjectId())) {
- // name hasn't changed
- return;
- } else if (oldVal.getProjectId().equals(defaultMap)) {
- // we try to change the name of default map
- throw new PropertyVetoException("Cannot change the name of default project.", arg0);
- } else if (fromDb == null || fromDb.getIdObject() == null) {
- // there is no project with the new name
- return;
- } else if (fromDb.getIdObject().equals(newVal.getIdObject())) {
- // project with the same id is the same project
- return;
- } else {
- throw new PropertyVetoException(
- "Cannot change the name of project. Project with this name already exists.", arg0);
- }
-
- }
-
- if (fromDb != null && fromDb.getIdObject() != null) {
- if (fromDb.getIdObject().equals(newVal.getIdObject())) {
- return;
- } else {
- throw new PropertyVetoException("Project with this name already exists.", arg0);
- }
- }
-
- }
- } catch (Exception e) {
- throw new PropertyVetoException("Unexpected problem: " + e.getMessage(), arg0);
- }
- }
- };
- }
-
- @Override
- public void init() {
-
- addVetoablePropertyChangeListener(selectedProjectVetoChanged);
-
- // uploaded file chagnge listener
- PropertyChangeListener mapFileChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (MAP_FILE_PROPERTY.equals(arg0.getPropertyName())) {
- File file = (File) arg0.getNewValue();
- clearZipEntriesData();
- complexModel = "false";
- if (file != null) {
- if (file.getName().toLowerCase().endsWith("zip")) {
- // when zip file is uploaded preprocess it to retrieve entries in
- // zip file
- ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
- complexModel = "true";
- try {
- ZipFile zipFile = new ZipFile(file);
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- ZipEntryFile zef = zefFactory.createZipEntryFile(entry, zipFile);
- if (zef != null) {
- // assign zip entries to proper lists
- if (zef instanceof ModelZipEntryFile) {
- modelZipEntries.add((ModelZipEntryFile) zef);
- } else if (zef instanceof ImageZipEntryFile) {
- imageZipEntries.add((ImageZipEntryFile) zef);
- } else if (zef instanceof LayoutZipEntryFile) {
- layoutZipEntries.add((LayoutZipEntryFile) zef);
- } else if (zef instanceof DataMiningZipEntryFile) {
- dataMiningZipEntries.add((DataMiningZipEntryFile) zef);
- } else {
- logger.warn("Unknown class type: " + zef.getClass());
- sendError("Internal server error");
- }
- }
- }
- zipFile.close();
- } catch (IOException e) {
- logger.error(e, e);
- }
- }
- }
- String name = FilenameUtils.getName(file.getName()).replaceAll(" ", "_");
- if (name.indexOf("-cd-") > 0) {
- name = name.substring(0, name.indexOf("-cd-"));
- }
- setNewProjectId(name);
- }
- }
-
- };
- addPropertyChangeListener(mapFileChangeListener);
-
- annotatorsTree = projectService.createClassAnnotatorTree(userBean.getLoggedUser());
-
- // this listener will be called when user start to edit list of
- // ElementAnnotator for a given class type
- PropertyChangeListener selectedAnnotatorTreeNodeChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY.equals(arg0.getPropertyName())) {
- AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) arg0.getNewValue();
- annotators = new DualListModel<String>(data.getValidAnnotators(), data.getUsedAnnotators());
- validMiriam = new DualListModel<MiriamType>(data.getMissingValidAnnotations(), data.getValidAnnotations());
- requiredMiriam = new DualListModel<MiriamType>(data.getMissingRequiredAnnotations(),
- data.getRequiredAnnotations());
- }
- }
-
- };
-
- addPropertyChangeListener(selectedAnnotatorTreeNodeChangeListener);
-
- Listener<ObjectAddedEvent> layoutAddedListener = new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- boolean projectFound = false;
- LayoutView layout = (LayoutView) event.getObject();
-
- for (ProjectView project : getProjects()) {
- if (project.getModelId() != null && project.getModelId().equals(layout.getModelId())) {
- projectFound = true;
- project.addLayout(layout);
- }
- }
-
- if (!projectFound) {
- logger.warn("After adding layout cannot find project for the layout. LayoutId: " + layout.getIdObject()
- + "; ModelId: " + layout.getModelId());
- }
- }
- };
- layoutBean.registerListener(layoutAddedListener);
-
- layoutBean.registerListener(createLayoutRemovedListener());
-
- setSelectedAnnotatorTreeNodeData((AnnotatedObjectTreeRow) annotatorsTree.getData());
-
- for (DataMiningType dm : DataMiningType.values()) {
- dataMiningTypes.add(dm);
- }
-
- // when new project is added refresh list of projects
- registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- refreshProjectList(null);
- }
- });
-
- customizeUserParameters();
-
- }
-
- /**
- * Sets default values for some checkboxes specific for a user. (The values are
- * stored in databsae)
- */
- public void customizeUserParameters() {
- if (userBean.getLoggedUser() != null) {
- User user = userBean.getLoggedUser();
- if (user.getAnnotationSchema() != null) {
- setSbgnFormat(user.getAnnotationSchema().getSbgnFormat());
- setNetworkLayoutAsDefault(user.getAnnotationSchema().getNetworkLayoutAsDefault());
- }
- }
- }
-
- /**
- * Sets {@link #networkLayoutAsDefault}.
- *
- * @param value
- * new value
- */
- private void setNetworkLayoutAsDefault(Boolean value) {
- if (value) {
- setNetworkLayoutAsDefault("true");
- } else {
- setNetworkLayoutAsDefault("false");
- }
- }
-
- /**
- * Sets {@link #sbgnFormat}.
- *
- * @param value
- * new value
- */
- private void setSbgnFormat(boolean value) {
- if (value) {
- setSbgnFormat("true");
- } else {
- setSbgnFormat("false");
- }
- }
-
- /**
- * Creates listener that should be called when layout is removed.
- *
- * @return listener that should be called when layout is removed
- */
- public Listener<ObjectRemovedEvent> createLayoutRemovedListener() {
- return new Listener<ObjectRemovedEvent>(ObjectRemovedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectRemovedEvent event) {
- boolean projectFound = false;
- LayoutView layout = (LayoutView) event.getObject();
- for (ProjectView project : getProjects()) {
- if (project.getModelId().equals(layout.getModelId())) {
- projectFound = true;
- LayoutView layoutToRemove = null;
- for (LayoutView oldLayout : project.getLayouts()) {
- if (oldLayout.getIdObject().equals(layout.getIdObject())) {
- layoutToRemove = oldLayout;
- }
- }
- if (layoutToRemove == null) {
- logger.warn("After removing layout from db cannot find layout in the project to remove. LayoutId: "
- + layout.getIdObject() + "; ModelId: " + layout.getModelId());
- } else {
- project.getLayouts().remove(layoutToRemove);
- }
- }
- }
-
- if (!projectFound) {
- logger.warn("After removing layout cannot find project for the layout. LayoutId: " + layout.getIdObject()
- + "; ModelId: " + layout.getModelId());
- }
- }
- };
- }
-
- /**
- * Refresh list of projects.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void refreshProjectList(final ActionEvent actionEvent) {
- if (projects == null) {
- logger.warn("Strange behaviour: refreshing project list withouth accessing...");
- projects = new ArrayList<>();
- }
- projects.clear();
- List<ProjectView> localProjectList;
- try {
- localProjectList = projectService.getAllProjectViews(userBean.getAuthenticationToken());
- for (ProjectView projectRow : localProjectList) {
- projects.add(projectRow);
- }
- Collections.sort(projects);
- } catch (SecurityException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- /**
- * This method handle upload of a file.
- *
- * @param event
- * event send by the client with a file reference
- */
- public void handleFileUpload(final FileUploadEvent event) {
- try {
- logger.debug(event.getFile().getFileName() + " is uploaded.");
- UploadedFile uploadedFile = event.getFile();
- String filename = FilenameUtils.getBaseName(uploadedFile.getFileName());
- String extension = FilenameUtils.getExtension(uploadedFile.getFileName());
- File file = File.createTempFile(filename + "-cd-", "." + extension);
- file.delete();
- InputStream input = uploadedFile.getInputstream();
- Files.copy(input, file.toPath());
- input.close();
-
- this.setMapFile(file);
- } catch (Exception e) {
- sendError("Problem with uploading...", e);
- }
- }
-
- /**
- * Generates project based on the information provided by the client.
- *
- * @param file
- * file with the model in CellDesigner format
- * @throws SecurityException
- */
- protected void generateProject(final File file) throws SecurityException {
- // if project with this name already exists then add random suffix
- String projectId = getNewProjectId();
- if (projectService.projectExists(getNewProjectId())) {
- sendError("Project with identifier: \"" + getNewProjectId() + "\" already exists.");
- return;
- }
-
- // get proper paths:
- // to directory with images
- String imagePath = getProjectDeployPath() + "/../map_images/" + md5(projectId) + "/";
- String version = getNewMapVersion();
-
- boolean autoResize = newMapAutoResize.equalsIgnoreCase("true");
-
- CreateProjectParams params = new CreateProjectParams();
-
- params.complex("true".equalsIgnoreCase(complexModel));
- params.projectId(projectId);
- params.projectName(newProjectName);
- params.projectDisease(newProjectDisease);
- params.projectOrganism(newProjectOrganism);
- params.version(version);
- params.projectFile(file);
- params.autoResize(autoResize);
- params.images(true);
- params.async(true);
- params.notifyEmail(userBean.getLoggedUser().getEmail());
- params.projectDir(imagePath);
- params.annotatorsMap(annotatorsTree);
- params.addUser(userBean.getLogin(), null);
- params.annotations("true".equalsIgnoreCase(annotateModel));
- params.analyzeAnnotations("true".equalsIgnoreCase(verifyAnnotationsModel));
- params.cacheModel("true".equalsIgnoreCase(cacheModel));
- params.validAnnotations(annotatorsTree);
- params.requiredAnnotations(annotatorsTree);
- params.authenticationToken(userBean.getAuthenticationToken());
- for (ZipEntryFile submodel : getZipEntries()) {
- params.addZipEntry(submodel);
- }
- params.sbgnFormat("true".equalsIgnoreCase(sbgnFormat));
- params.semanticZoom("true".equalsIgnoreCase(semanticOverlay));
- params.networkLayoutAsDefault("true".equalsIgnoreCase(networkLayoutAsDefault));
- projectService.createProject(params);
- projectService.updateClassAnnotatorTreeForUser(userBean.getLoggedUser(), annotatorsTree,
- sbgnFormat.equalsIgnoreCase("true"), networkLayoutAsDefault.equalsIgnoreCase("true"));
-
- ObjectAddedEvent event = new ObjectAddedEvent(
- projectService.getProjectByProjectId(projectId, userBean.getAuthenticationToken()));
- callListeners(event);
- }
-
- /**
- * Returns list of all zip entries in the currently processed file.
- *
- * @return list of all zip entries in the currently processed file
- */
- private Collection<ZipEntryFile> getZipEntries() {
- List<ZipEntryFile> result = new ArrayList<ZipEntryFile>();
- result.addAll(modelZipEntries);
- result.addAll(imageZipEntries);
- result.addAll(layoutZipEntries);
- result.addAll(dataMiningZipEntries);
- return result;
- }
-
- /**
- * Method that computes md5 hash for a given {@link String}.
- *
- * @param data
- * input string
- * @return md5 hash for input string
- */
- private String md5(String data) {
- try {
- MessageDigest md = MessageDigest.getInstance("MD5");
- byte[] mdbytes = md.digest(data.getBytes());
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mdbytes.length; i++) {
- // CHECKSTYLE:OFF
- // this magic formula transforms int into hex value
- sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
- // CHECKSTYLE:ON
- }
- return sb.toString();
- } catch (NoSuchAlgorithmException e) {
- logger.fatal("Problem with instance of MD5 encoder", e);
- }
-
- return null;
- }
-
- /**
- * Returns project currently selected and edited by the client side.
- *
- * @return project view currently selected and edited by the client side
- */
- public ProjectView getSelectedProject() {
- if (selectedProject == null) {
- selectedProject = projectService.createEmpty();
- }
- return selectedProject;
- }
-
- /**
- * Set new currently selected and edited project.
- *
- * @param selectedProject
- * view of the new currently selected and edited project
- */
- public void setSelectedProject(final ProjectView selectedProject) {
- ProjectView oldValue = this.selectedProject;
- this.selectedProject = selectedProject;
- try {
- fireVetoableChange(SELECTED_PROJECT_PROPERTY, oldValue, selectedProject);
- firePropertyChange(SELECTED_PROJECT_PROPERTY, oldValue, selectedProject);
- logger.debug("Selected project was set to: " + this.selectedProject.getProjectId());
- } catch (PropertyVetoException e) {
- this.selectedProject = oldValue;
- sendError(e.getMessage(), e);
- }
- }
-
- /**
- * Method which update a project.
- *
- * @param actionEvent
- * event from thefrom the client
- * @throws SecurityException
- */
- public void updateSelectedProject(final ActionEvent actionEvent) throws SecurityException {
-
- // first we need small trick (maybe this should be improved)
-
- ProjectView newProject = selectedProject;
- // get old version of the project from db
- ProjectView oldProject = projectService.getProjectViewById(newProject.getIdObject(),
- userBean.getAuthenticationToken());
-
- // set old version
- setSelectedProject(oldProject);
- // now, change to the new one (property change listener will ensure that
- // everything is fine)
- setSelectedProject(newProject);
-
- // if everything is ok then update in db
- if (selectedProject != null) {
- projectService.updateProject(selectedProject);
- } else {
- logger.warn("Problem during updating project...");
- }
- refreshProjectList(actionEvent);
-
- callListeners(new ObjectModifiedEvent(newProject));
- }
-
- /**
- * Removes project selected by client.
- *
- * @param actionEvent
- * client side action
- */
- public void removeSelectedProject(final ActionEvent actionEvent) {
- try {
- logger.debug("Removing project: " + selectedProject);
- String defaultMap = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
- String projectId = selectedProject.getProjectId();
-
- // find out what is the name of the project in db
- ProjectView project = projectService.getProjectViewById(selectedProject.getIdObject(),
- userBean.getAuthenticationToken());
- if (project != null) {
- projectId = project.getProjectId();
- }
-
- logger.debug("Removing project: " + projectId);
-
- // if the project name is a default one then don't remove it
- if (defaultMap.equals(projectId)) {
- sendError("Cannot remove default map. To remove this map change the default map in configuration tab first.");
- } else {
- projectService.removeProject(selectedProject, getProjectDeployPath(), true, userBean.getAuthenticationToken());
- callListeners(new ObjectRemovedEvent(selectedProject));
- refreshProjectList(actionEvent);
- }
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Checks if user can manage projects.
- *
- * @return <code>true</code> if user can amange projects, <code>false</code>
- * otherwise
- */
- public boolean getUserHasManagePrivileges() {
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.PROJECT_MANAGEMENT);
- return result;
- }
-
- /**
- * Checks if user can add project.
- *
- * @return <code>true</code> if user can add projects, <code>false</code>
- * otherwise
- */
- public boolean getUserHasAddMapPrivileges() {
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.ADD_MAP);
- return result;
- }
-
- /**
- * Gets project identifier for newly created project.
- *
- * @return name of the new project
- */
- public String getNewProjectId() {
- return newProjectId;
- }
-
- /**
- * Sets project identifier for the newly created project.
- *
- * @param newProjectId
- * new name for the new project
- */
- public void setNewProjectId(final String newProjectId) {
- String oldValue = this.newProjectId;
- this.newProjectId = newProjectId;
- firePropertyChange(PROJECT_ID_PROPERTY, oldValue, newProjectId);
- }
-
- /**
- * @return {@link #newMapVersion}
- */
- public String getNewMapVersion() {
- return newMapVersion;
- }
-
- /**
- * Sets new value for {@link #newMapVersion}. Property change listeners will be
- * thrown for "newMapVersion" property.
- *
- * @param newMapVersion
- * {@link #newMapVersion}
- */
- public void setNewMapVersion(final String newMapVersion) {
- String oldValue = this.newMapVersion;
- this.newMapVersion = newMapVersion;
- firePropertyChange(MAP_VERSION_PROPERTY, oldValue, newMapVersion);
- }
-
- /**
- *
- * @return {@link #mapFile}
- */
- public File getMapFile() {
- return mapFile;
- }
-
- /**
- * Sets new value for {@link #mapFile}. Property change listeners will be thrown
- * for "mapFile" property.
- *
- * @param mapFile
- * {@link #mapFile}
- */
- public void setMapFile(final File mapFile) {
- File oldValue = this.mapFile;
- this.mapFile = mapFile;
- firePropertyChange(MAP_FILE_PROPERTY, oldValue, mapFile);
- }
-
- /**
- * Method that creates a project.
- */
- public void createProject() {
- try {
- if (getMapFile() == null) {
- sendError("File cannot be null");
- } else {
- generateProject(getMapFile());
- }
- } catch (Exception e) {
- sendError("Internal server error.", e);
- }
- }
-
- /**
- *
- * @return {@link #newMapAutoResize}
- */
- public String getNewMapAutoResize() {
- return newMapAutoResize;
- }
-
- /**
- * Sets new value for {@link #newMapAutoResize}. Property change listeners will
- * be thrown for "newMapAutoResize" property.
- *
- * @param newMapAutoResize
- * {@link #newMapAutoResize}
- */
- public void setNewMapAutoResize(final String newMapAutoResize) {
- String oldValue = this.newMapAutoResize;
- this.newMapAutoResize = newMapAutoResize;
- firePropertyChange(AUTO_RESIZE_MAP_PROPERTY, oldValue, newMapAutoResize);
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- /**
- * @return the projects
- * @see #projects
- */
- public List<ProjectView> getProjects() {
- if (projects == null) {
- projects = new ArrayList<>();
- refreshProjectList(null);
- }
- return projects;
- }
-
- /**
- * @param projects
- * the projects to set
- * @see #projects
- */
- public void setProjects(List<ProjectView> projects) {
- this.projects = projects;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the annotateModel
- * @see #annotateModel
- */
- public String getAnnotateModel() {
- return annotateModel;
- }
-
- /**
- * @param annotateModel
- * the annotateModel to set
- * @see #annotateModel
- */
- public void setAnnotateModel(String annotateModel) {
- this.annotateModel = annotateModel;
- }
-
- /**
- * @return the cacheModel
- * @see #cacheModel
- */
- public String getCacheModel() {
- return cacheModel;
- }
-
- /**
- * @param cacheModel
- * the cacheModel to set
- * @see #cacheModel
- */
- public void setCacheModel(String cacheModel) {
- this.cacheModel = cacheModel;
- }
-
- /**
- * @return the verifyAnnotationsModel
- * @see #verifyAnnotationsModel
- */
- public String getVerifyAnnotationsModel() {
- return verifyAnnotationsModel;
- }
-
- /**
- * @param verifyAnnotationsModel
- * the verifyAnnotationsModel to set
- * @see #verifyAnnotationsModel
- */
- public void setVerifyAnnotationsModel(String verifyAnnotationsModel) {
- this.verifyAnnotationsModel = verifyAnnotationsModel;
- }
-
- /**
- * Method that exports selected project warnings.
- *
- * @throws IOException
- * thrown when there are some problems with sending file
- */
- public void downloadWarnings() throws IOException {
- // and send it as response
- sendFileAsResponse(StringUtils.join(selectedProject.getWarnings(), "\n"), "warnings.txt", MimeType.TEXT);
- }
-
- /**
- * @return the complexModel
- * @see #complexModel
- */
- public String getComplexModel() {
- return complexModel;
- }
-
- /**
- * @param complexModel
- * the complexModel to set
- * @see #complexModel
- */
- public void setComplexModel(String complexModel) {
- this.complexModel = complexModel;
- }
-
- /**
- * Returns list of all available submodel types.
- *
- * @return list of all available submodel types
- */
- public SubmodelType[] getSubmodelTypes() {
- return SubmodelType.values();
- }
-
- /**
- * Returns list of all possible {@link InputFileType}.
- *
- * @return array with all possible values of {@link InputFileType} enum
- */
- public InputFileType[] getFileTypes() {
- return InputFileType.values();
- }
-
- /**
- * @return the annotatorsTree
- * @see #annotatorsTree
- */
- public TreeNode getAnnotatorsTree() {
- return annotatorsTree;
- }
-
- /**
- * @param annotatorsTree
- * the annotatorsTree to set
- * @see #annotatorsTree
- */
- public void setAnnotatorsTree(TreeNode annotatorsTree) {
- this.annotatorsTree = annotatorsTree;
- }
-
- /**
- * @return the annotators
- * @see #annotators
- */
- public DualListModel<String> getAnnotators() {
- return annotators;
- }
-
- /**
- * @param annotators
- * the annotators to set
- * @see #annotators
- */
- public void setAnnotators(DualListModel<String> annotators) {
- this.annotators = annotators;
- }
-
- /**
- * @return the selectedAnnotatorTreeNodeData
- * @see #selectedAnnotatorTreeNodeData
- */
- public AnnotatedObjectTreeRow getSelectedAnnotatorTreeNodeData() {
- return selectedAnnotatorTreeNodeData;
- }
-
- /**
- * @param selectedAnnotatorTreeNodeData
- * the selectedAnnotatorTreeNodeData to set
- * @see #selectedAnnotatorTreeNodeData
- */
- public void setSelectedAnnotatorTreeNodeData(AnnotatedObjectTreeRow selectedAnnotatorTreeNodeData) {
- AnnotatedObjectTreeRow oldValue = this.selectedAnnotatorTreeNodeData;
- this.selectedAnnotatorTreeNodeData = selectedAnnotatorTreeNodeData;
-
- firePropertyChange(SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY, oldValue, selectedAnnotatorTreeNodeData);
- }
-
- /**
- * Method called when list of annotators in {@link #annotators} changed.
- *
- * @param event
- * primefaces event
- */
- public void onTransfer(TransferEvent event) {
- updateAnnotatorTreeNodeData();
- }
-
- /**
- * This method updates data in {@link #selectedAnnotatorTreeNodeData}.
- */
- private void updateAnnotatorTreeNodeData() {
- this.selectedAnnotatorTreeNodeData.setValidAnnotators(annotators.getSource());
- this.selectedAnnotatorTreeNodeData.setUsedAnnotators(annotators.getTarget());
- this.selectedAnnotatorTreeNodeData.setMissingValidAnnotations(validMiriam.getSource());
- this.selectedAnnotatorTreeNodeData.setValidAnnotations(validMiriam.getTarget());
- this.selectedAnnotatorTreeNodeData.setMissingRequiredAnnotations(requiredMiriam.getSource());
- this.selectedAnnotatorTreeNodeData.setRequiredAnnotations(requiredMiriam.getTarget());
- }
-
- /**
- * Method called when list of annotators in {@link #annotators} changed order.
- */
- public void onReorder() {
- updateAnnotatorTreeNodeData();
- }
-
- /**
- * @return the validMiriam
- * @see #validMiriam
- */
- public DualListModel<MiriamType> getValidMiriam() {
- return validMiriam;
- }
-
- /**
- * @param validMiriam
- * the validMiriam to set
- * @see #validMiriam
- */
- public void setValidMiriam(DualListModel<MiriamType> validMiriam) {
- this.validMiriam = validMiriam;
- }
-
- /**
- * @return the requiredMiriam
- * @see #requiredMiriam
- */
- public DualListModel<MiriamType> getRequiredMiriam() {
- return requiredMiriam;
- }
-
- /**
- * @param requiredMiriam
- * the requiredMiriam to set
- * @see #requiredMiriam
- */
- public void setRequiredMiriam(DualListModel<MiriamType> requiredMiriam) {
- this.requiredMiriam = requiredMiriam;
- }
-
- /**
- * @return the dataMiningTypes
- * @see #dataMiningTypes
- */
- public List<DataMiningType> getDataMiningTypes() {
- return dataMiningTypes;
- }
-
- /**
- * @param dataMiningTypes
- * the dataMiningTypes to set
- * @see #dataMiningTypes
- */
- public void setDataMiningTypes(List<DataMiningType> dataMiningTypes) {
- this.dataMiningTypes = dataMiningTypes;
- }
-
- /**
- * @return the layoutBean
- * @see #layoutBean
- */
- public LayoutBean getLayoutBean() {
- return layoutBean;
- }
-
- /**
- * @param layoutBean
- * the layoutBean to set
- * @see #layoutBean
- */
- public void setLayoutBean(LayoutBean layoutBean) {
- this.layoutBean = layoutBean;
- }
-
- /**
- * Clears list with information about zip entries in currently processed zip
- * file.
- */
- private void clearZipEntriesData() {
- dataMiningZipEntries.clear();
- imageZipEntries.clear();
- layoutZipEntries.clear();
- modelZipEntries.clear();
-
- }
-
- /**
- * @return the dataMiningZipEntries
- * @see #dataMiningZipEntries
- */
- public List<DataMiningZipEntryFile> getDataMiningZipEntries() {
- return dataMiningZipEntries;
- }
-
- /**
- * @param dataMiningZipEntries
- * the dataMiningZipEntries to set
- * @see #dataMiningZipEntries
- */
- public void setDataMiningZipEntries(List<DataMiningZipEntryFile> dataMiningZipEntries) {
- this.dataMiningZipEntries = dataMiningZipEntries;
- }
-
- /**
- * @return the modelZipEntries
- * @see #modelZipEntries
- */
- public List<ModelZipEntryFile> getModelZipEntries() {
- return modelZipEntries;
- }
-
- /**
- * @param modelZipEntries
- * the modelZipEntries to set
- * @see #modelZipEntries
- */
- public void setModelZipEntries(List<ModelZipEntryFile> modelZipEntries) {
- this.modelZipEntries = modelZipEntries;
- }
-
- /**
- * @return the layoutZipEntries
- * @see #layoutZipEntries
- */
- public List<LayoutZipEntryFile> getLayoutZipEntries() {
- return layoutZipEntries;
- }
-
- /**
- * @param layoutZipEntries
- * the layoutZipEntries to set
- * @see #layoutZipEntries
- */
- public void setLayoutZipEntries(List<LayoutZipEntryFile> layoutZipEntries) {
- this.layoutZipEntries = layoutZipEntries;
- }
-
- /**
- * @return the imageZipEntries
- * @see #imageZipEntries
- */
- public List<ImageZipEntryFile> getImageZipEntries() {
- return imageZipEntries;
- }
-
- /**
- * @param imageZipEntries
- * the imageZipEntries to set
- * @see #imageZipEntries
- */
- public void setImageZipEntries(List<ImageZipEntryFile> imageZipEntries) {
- this.imageZipEntries = imageZipEntries;
- }
-
- /**
- * @return the newProjectName
- * @see #newProjectName
- */
- public String getNewProjectName() {
- return newProjectName;
- }
-
- /**
- * @param newProjectName
- * the newProjectName to set
- * @see #newProjectName
- */
- public void setNewProjectName(String newProjectName) {
- this.newProjectName = newProjectName;
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public String getSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- * @see #sbgnFormat
- */
- public void setSbgnFormat(String sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- }
-
- /**
- * @return the networkLayoutAsDefault
- * @see #networkLayoutAsDefault
- */
- public String getNetworkLayoutAsDefault() {
- return networkLayoutAsDefault;
- }
-
- /**
- * @param networkLayoutAsDefault
- * the networkLayoutAsDefault to set
- * @see #networkLayoutAsDefault
- */
- public void setNetworkLayoutAsDefault(String networkLayoutAsDefault) {
- this.networkLayoutAsDefault = networkLayoutAsDefault;
- }
-
- /**
- * @return new project disease.
- */
- public String getNewProjectDisease() {
- return newProjectDisease;
- }
-
- /**
- * @param newProjectDisease
- * sets the disease
- */
- public void setNewProjectDisease(String newProjectDisease) {
- this.newProjectDisease = newProjectDisease;
- }
-
- /**
- * Method that trigger download of a file in jsf. The file is the source file
- * used to create project given in the parameter.
- *
- * @param projectView
- * view of the {@link Project} for which we are looking for an original
- * source file
- * @throws IOException
- * thrown when there is a problem with sending file
- * @throws SecurityException
- */
- public void downloadInputData(ProjectView projectView) throws IOException, SecurityException {
- // get input data from database
- byte[] data = projectService.getInputDataForProject(projectView);
- Project project = projectService.getProjectByProjectId(projectView.getProjectId(),
- userBean.getAuthenticationToken());
- String string = new String(data, StandardCharsets.UTF_8);
-
- String fileName = project.getInputData().getOriginalFileName();
- MimeType respMimeType = null;
- if (fileName.endsWith("xml")) {
- respMimeType = MimeType.XML;
- } else if (fileName.endsWith("zip")) {
- respMimeType = MimeType.ZIP;
- } else if (fileName.endsWith("sbgn")) {
- respMimeType = MimeType.XML;
- } else {
- logger.warn("Cannot determine mime type of file: " + fileName);
- respMimeType = MimeType.TEXT;
- }
- sendFileAsResponse(string, fileName, respMimeType);
- }
-
- /**
- * @return the newProjectOrganism
- * @see #newProjectOrganism
- */
- public String getNewProjectOrganism() {
- return newProjectOrganism;
- }
-
- /**
- * @param newProjectOrganism
- * the newProjectOrganism to set
- * @see #newProjectOrganism
- */
- public void setNewProjectOrganism(String newProjectOrganism) {
- this.newProjectOrganism = newProjectOrganism;
- }
-
- /**
- * @return the semanticOverlay
- * @see #semanticOverlay
- */
- public String getSemanticOverlay() {
- return semanticOverlay;
- }
-
- /**
- * @param semanticOverlay
- * the semanticOverlay to set
- * @see #semanticOverlay
- */
- public void setSemanticOverlay(String semanticOverlay) {
- this.semanticOverlay = semanticOverlay;
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ReferenceGenomeBean.java b/web/src/main/java/lcsb/mapviewer/bean/ReferenceGenomeBean.java
deleted file mode 100644
index ded4cc6c881eaee65e2f36590eb0218c5dd75ed9..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/ReferenceGenomeBean.java
+++ /dev/null
@@ -1,738 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
-import java.beans.VetoableChangeListener;
-import java.io.IOException;
-import java.io.Serializable;
-import java.net.URISyntaxException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.log4j.Logger;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
-import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
-import lcsb.mapviewer.services.view.ReferenceGenomeView;
-
-/**
- * This bean is responsible for managing reference genome and related data.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "referenceGenomeMB")
-@ViewScoped
-public class ReferenceGenomeBean extends AbstractManagedBean implements Serializable {
-
- /**
- * String representing {@link #selectedReferenceGenomeType} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String REFERENCE_GENOME_TYPE_PROPERTY = "TYPE";
-
- /**
- * String representing {@link #selectedOrganism} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String SELECTED_ORGANISM_PROPERTY = "ORGANISM";
-
- /**
- * String representing {@link #selectedVersion} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- protected static final String SELECTED_VERSION_PROPERTY = "VERSION";
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReferenceGenomeBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Selected reference genome type used during uploading reference genome.
- */
- private ReferenceGenomeType selectedReferenceGenomeType = null;
-
- /**
- * Selected organism used during uploading reference genome.
- */
- private MiriamData selectedOrganism = null;
-
- /**
- * Selected version of reference genome used during uploading reference
- * genome.
- */
- private String selectedVersion = null;
-
- /**
- * Url of uploaded genome.
- */
- private String selectedUrl = null;
-
- /**
- * List of currently available genome types.
- */
- private List<ReferenceGenomeType> genomeTypes = new ArrayList<>();
-
- /**
- * List of available organism for currenntly selected genome type.
- */
- private List<MiriamData> availableOrganisms = new ArrayList<>();
-
- /**
- * List of available genome version for selected organism and genome type.
- */
- private List<String> availableVersions = new ArrayList<>();
-
- /**
- * List of all downloaded genomes.
- */
- private List<ReferenceGenome> downloadedGenomes = new ArrayList<>();
-
- /**
- * Mapping between organism taxonomy id and name.
- */
- private Map<MiriamData, String> organismName = new HashMap<>();
-
- /**
- * {@link ReferenceGenome} that is currently edited.
- */
- private ReferenceGenome editedReferenceGenome = null;
-
- /**
- * Name of gene mapping that is going to be added.
- */
- private String selectedReferenceGenomeGeneMappingName = null;
-
- /**
- * Url to the gene mapping that is going to be added.
- */
- private String selectedReferenceGenomeGeneMappingUrl = null;
-
- /**
- * Service that manages reference genomes.
- */
- @ManagedProperty(value = "#{ReferenceGenomeService}")
- private transient IReferenceGenomeService referenceGenomeService;
-
- /**
- * Object that allows to access information about taxonomy.
- */
- @ManagedProperty(value = "#{TaxonomyBackend }")
- private transient TaxonomyBackend taxonomyBackend;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for communication with the client side about the map currently
- * visualized.
- *
- * @see MapBean
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- @Override
- public void init() {
- PropertyChangeListener selectedReferenceGenomeTypePropertyChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (REFERENCE_GENOME_TYPE_PROPERTY.equals(arg0.getPropertyName())) {
- try {
- setAvailableOrganisms(referenceGenomeService.getOrganismsByReferenceGenomeType((ReferenceGenomeType) arg0.getNewValue()));
- if (availableOrganisms.size() > 0) {
- setSelectedOrganism(availableOrganisms.get(0));
- }
- } catch (ReferenceGenomeConnectorException e) {
- sendError("Problem with accessing information about available organisms", e);
- } catch (Exception e) {
- sendError("Internal Server Error", e);
- }
- }
- }
- };
- addPropertyChangeListener(selectedReferenceGenomeTypePropertyChangeListener);
-
- PropertyChangeListener selectedOrganismPropertyChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (SELECTED_ORGANISM_PROPERTY.equals(arg0.getPropertyName())) {
- try {
- setAvailableVersions(referenceGenomeService.getAvailableGenomeVersions(selectedReferenceGenomeType, (MiriamData) arg0.getNewValue()));
- if (getAvailableVersions().size() > 0) {
- setSelectedVersion(availableVersions.get(0));
- }
- } catch (ReferenceGenomeConnectorException e) {
- sendError("Problem with accessing information about available organism versions", e);
- } catch (Exception e) {
- sendError("Internal Server Error", e);
- }
- }
- }
- };
- addPropertyChangeListener(selectedOrganismPropertyChangeListener);
-
- VetoableChangeListener selectedOrganismVetoablePropertyChangeListener = new VetoableChangeListener() {
- @Override
- public void vetoableChange(PropertyChangeEvent evt) throws PropertyVetoException {
- if (SELECTED_ORGANISM_PROPERTY.equals(evt.getPropertyName())) {
- if (!getAvailableOrganisms().contains(evt.getNewValue())) {
- throw new PropertyVetoException("Cannot change organism to: " + evt.getNewValue() + ". Organism is not available in current organisms list.", evt);
- }
- }
-
- }
- };
- addVetoablePropertyChangeListener(selectedOrganismVetoablePropertyChangeListener);
-
- PropertyChangeListener selectedVersionPropertyChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (SELECTED_VERSION_PROPERTY.equals(arg0.getPropertyName())) {
- setSelectedUrl(referenceGenomeService.getUrlForGenomeVersion(selectedReferenceGenomeType, selectedOrganism, (String) arg0.getNewValue()));
- }
- }
- };
- addPropertyChangeListener(selectedVersionPropertyChangeListener);
-
- VetoableChangeListener selectedVersionVetoablePropertyChangeListener = new VetoableChangeListener() {
- @Override
- public void vetoableChange(PropertyChangeEvent evt) throws PropertyVetoException {
- if (SELECTED_VERSION_PROPERTY.equals(evt.getPropertyName())) {
- if (!getAvailableVersions().contains(evt.getNewValue())) {
- throw new PropertyVetoException(
- "Cannot change organism version to to: " + evt.getNewValue() + ". Version is not available in current organisms list.", evt);
- }
- }
- }
- };
- addVetoablePropertyChangeListener(selectedVersionVetoablePropertyChangeListener);
-
- for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
- genomeTypes.add(type);
- }
-
- setSelectedReferenceGenomeType(ReferenceGenomeType.UCSC);
-
- refreshDownloadedGenomes();
- }
-
- @Override
- public void clear() {
- }
-
- /**
- * @return the selectedReferenceGenomeType
- * @see #selectedReferenceGenomeType
- */
- public ReferenceGenomeType getSelectedReferenceGenomeType() {
- return selectedReferenceGenomeType;
- }
-
- /**
- * @param selectedReferenceGenomeType
- * the selectedReferenceGenomeType to set
- * @see #selectedReferenceGenomeType
- */
- public void setSelectedReferenceGenomeType(ReferenceGenomeType selectedReferenceGenomeType) {
- ReferenceGenomeType oldValue = this.selectedReferenceGenomeType;
- this.selectedReferenceGenomeType = selectedReferenceGenomeType;
- firePropertyChange(REFERENCE_GENOME_TYPE_PROPERTY, oldValue, selectedReferenceGenomeType);
- }
-
- /**
- * @return the selectedOrganism
- * @see #selectedOrganism
- */
- public MiriamData getSelectedOrganism() {
- return selectedOrganism;
- }
-
- /**
- * @param selectedOrganism
- * the selectedOrganism to set
- * @see #selectedOrganism
- */
- public void setSelectedOrganism(MiriamData selectedOrganism) {
- MiriamData oldValue = this.selectedOrganism;
-
- try {
- fireVetoableChange(SELECTED_ORGANISM_PROPERTY, oldValue, selectedOrganism);
- this.selectedOrganism = selectedOrganism;
- firePropertyChange(SELECTED_ORGANISM_PROPERTY, oldValue, selectedOrganism);
- } catch (PropertyVetoException e) {
- }
- }
-
- /**
- * @return the selectedVersion
- * @see #selectedVersion
- */
- public String getSelectedVersion() {
- return selectedVersion;
- }
-
- /**
- * @param selectedVersion
- * the selectedVersion to set
- * @see #selectedVersion
- */
- public void setSelectedVersion(String selectedVersion) {
- String oldValue = this.selectedVersion;
- try {
- fireVetoableChange(SELECTED_VERSION_PROPERTY, oldValue, selectedVersion);
- this.selectedVersion = selectedVersion;
- firePropertyChange(SELECTED_VERSION_PROPERTY, oldValue, selectedVersion);
- } catch (PropertyVetoException e) {
- }
-
- }
-
- /**
- * @return the selectedUrl
- * @see #selectedUrl
- */
- public String getSelectedUrl() {
- return selectedUrl;
- }
-
- /**
- * @param selectedUrl
- * the selectedUrl to set
- * @see #selectedUrl
- */
- public void setSelectedUrl(String selectedUrl) {
- this.selectedUrl = selectedUrl;
- }
-
- /**
- * @return the genomeTypes
- * @see #genomeTypes
- */
- public List<ReferenceGenomeType> getGenomeTypes() {
- return genomeTypes;
- }
-
- /**
- * @param genomeTypes
- * the genomeTypes to set
- * @see #genomeTypes
- */
- public void setGenomeTypes(List<ReferenceGenomeType> genomeTypes) {
- this.genomeTypes = genomeTypes;
- }
-
- /**
- * @return the referenceGenomeService
- * @see #referenceGenomeService
- */
- public IReferenceGenomeService getReferenceGenomeService() {
- return referenceGenomeService;
- }
-
- /**
- * @param referenceGenomeService
- * the referenceGenomeService to set
- * @see #referenceGenomeService
- */
- public void setReferenceGenomeService(IReferenceGenomeService referenceGenomeService) {
- this.referenceGenomeService = referenceGenomeService;
- }
-
- /**
- * @return the availableOrganisms
- * @see #availableOrganisms
- */
- public List<MiriamData> getAvailableOrganisms() {
- return availableOrganisms;
- }
-
- /**
- * @param availableOrganisms
- * the availableOrganisms to set
- * @see #availableOrganisms
- */
- public void setAvailableOrganisms(List<MiriamData> availableOrganisms) {
- logger.debug("set available org");
- this.availableOrganisms = availableOrganisms;
- }
-
- /**
- * @return the availableVersions
- * @see #availableVersions
- */
- public List<String> getAvailableVersions() {
- return availableVersions;
- }
-
- /**
- * @param availableVersions
- * the availableVersions to set
- * @see #availableVersions
- */
- public void setAvailableVersions(List<String> availableVersions) {
- this.availableVersions = availableVersions;
- }
-
- /**
- * @return the downloadedGenomes
- * @see #downloadedGenomes
- */
- public List<ReferenceGenome> getDownloadedGenomes() {
- return downloadedGenomes;
- }
-
- /**
- * @param downloadedGenomes
- * the downloadedGenomes to set
- * @see #downloadedGenomes
- */
- public void setDownloadedGenomes(List<ReferenceGenome> downloadedGenomes) {
- this.downloadedGenomes = downloadedGenomes;
- }
-
- /**
- * Downloads genome and adds it to the project (download will be processed
- * asynchronously).
- */
- public void downloadGenome() {
- try {
- referenceGenomeService.addReferenceGenome(selectedReferenceGenomeType, selectedOrganism, selectedVersion, selectedUrl);
- } catch (IOException e) {
- sendError("Problem with downloading file...", e);
- } catch (URISyntaxException e) {
- sendError("Provided url is invalid: " + selectedUrl, e);
- } catch (ReferenceGenomeExistsException e) {
- sendError(e.getMessage(), e);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Downloads genome mapping and adds it to the project (download will be
- * processed asynchronously).
- */
- public void downloadGenomeGeneMapping() {
- try {
- referenceGenomeService
- .addReferenceGenomeGeneMapping(editedReferenceGenome, selectedReferenceGenomeGeneMappingName, selectedReferenceGenomeGeneMappingUrl);
- } catch (IOException e) {
- sendError("Problem with downloading file...", e);
- } catch (URISyntaxException e) {
- sendError("Provided url is invalid: " + selectedUrl, e);
- } catch (ReferenceGenomeConnectorException e) {
- sendError(e.getMessage(), e);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Refresh list of downloaded genomes.
- */
- public void refreshDownloadedGenomes() {
- setDownloadedGenomes(referenceGenomeService.getDownloadedGenomes());
- if (editedReferenceGenome != null) {
- for (ReferenceGenome genome : downloadedGenomes) {
- if (genome.getId() == editedReferenceGenome.getId()) {
- setEditedReferenceGenome(genome);
- }
- }
- }
- }
-
- /**
- * Gets name of organism by {@link MiriamType#TAXONOMY} id.
- *
- * @param md
- * identifier of the organism
- * @return name of organism
- */
- public String getOrganismName(MiriamData md) {
- if (md == null) {
- return null;
- } else {
- if (organismName.containsKey(md)) {
- return organismName.get(md);
- }
- try {
- String result = taxonomyBackend.getNameForTaxonomy(md);
- organismName.put(md, result);
- return result;
- } catch (TaxonomySearchException e) {
- sendError("Problem with accesing taxonomy database", e);
- return null;
- }
- }
- }
-
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- public TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
- /**
- * @return the editedReferenceGenome
- * @see #editedReferenceGenome
- */
- public ReferenceGenome getEditedReferenceGenome() {
- return editedReferenceGenome;
- }
-
- /**
- * @param editedReferenceGenome
- * the editedReferenceGenome to set
- * @see #editedReferenceGenome
- */
- public void setEditedReferenceGenome(ReferenceGenome editedReferenceGenome) {
- this.editedReferenceGenome = editedReferenceGenome;
- }
-
- /**
- * @return the selectedReferenceGenomeGeneMappingName
- * @see #selectedReferenceGenomeGeneMappingName
- */
- public String getSelectedReferenceGenomeGeneMappingName() {
- return selectedReferenceGenomeGeneMappingName;
- }
-
- /**
- * @param selectedReferenceGenomeGeneMappingName
- * the selectedReferenceGenomeGeneMappingName to set
- * @see #selectedReferenceGenomeGeneMappingName
- */
- public void setSelectedReferenceGenomeGeneMappingName(String selectedReferenceGenomeGeneMappingName) {
- this.selectedReferenceGenomeGeneMappingName = selectedReferenceGenomeGeneMappingName;
- }
-
- /**
- * @return the selectedReferenceGenomeGeneMappingUrl
- * @see #selectedReferenceGenomeGeneMappingUrl
- */
- public String getSelectedReferenceGenomeGeneMappingUrl() {
- return selectedReferenceGenomeGeneMappingUrl;
- }
-
- /**
- * @param selectedReferenceGenomeGeneMappingUrl
- * the selectedReferenceGenomeGeneMappingUrl to set
- * @see #selectedReferenceGenomeGeneMappingUrl
- */
- public void setSelectedReferenceGenomeGeneMappingUrl(String selectedReferenceGenomeGeneMappingUrl) {
- this.selectedReferenceGenomeGeneMappingUrl = selectedReferenceGenomeGeneMappingUrl;
- }
-
- /**
- * Checks if currently logged user has privilege for managing genomes.
- *
- * @return <code>true</code> if user has access to manage privileges
- */
- public boolean getUserHasManageGenomesPrivilege() {
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.MANAGE_GENOMES);
- return result;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * Adds genome mapping to genome.
- *
- * @param genome
- * genome to which genome mapping will be added
- */
- public void addGeneMapping(ReferenceGenome genome) {
- try {
- referenceGenomeService.addReferenceGenomeGeneMapping(genome, selectedReferenceGenomeGeneMappingName, selectedReferenceGenomeGeneMappingUrl);
- refreshDownloadedGenomes();
- } catch (IOException e) {
- sendError("Problem with downloading file...", e);
- } catch (URISyntaxException e) {
- sendError("Provided url is invalid: " + selectedUrl, e);
- } catch (ReferenceGenomeConnectorException e) {
- sendError(e.getMessage(), e);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Removes genome mapping from the system.
- *
- * @param genomeMapping
- * genome mapping to be removed
- */
- public void removeGeneMapping(ReferenceGenomeGeneMapping genomeMapping) {
- try {
- referenceGenomeService.removeReferenceGenomeGeneMapping(genomeMapping);
- refreshDownloadedGenomes();
- } catch (IOException e) {
- sendError("Problem with removing file...", e);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Removes genome from the system.
- *
- * @param genome
- * genome to be removed
- */
- public void removeGenome(ReferenceGenome genome) {
- try {
- referenceGenomeService.removeGenome(genome);
- refreshDownloadedGenomes();
- } catch (IOException e) {
- sendError("Problem with removing file...", e);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Sends information about genome to javacsript code.
- *
- * @param actionEvent
- * JSF event
- */
- public final void requestJavasciptGenomeDetails(final ActionEvent actionEvent) {
- try {
- // get the request params
- String type = getRequestParameter("type");
- String version = getRequestParameter("version");
-
- String organismId = getRequestParameter("organismId");
- MiriamData organism = null;
- if (organismId != null && !organismId.isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, organismId);
- } else {
- organism = mapBean.getCurrentProject().getOrganism();
- }
- ReferenceGenomeView result = null;
- if (organism == null) {
- logger.warn("Organism not defined");
- } else {
- try {
- ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
- result = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version);
- } catch (IllegalArgumentException e) {
- logger.warn("Cannot find type: " + type);
- }
- }
- String json = "null";
- if (result != null) {
- json = new Gson().toJson(result);
- }
- String javascriptCode = "ServerConnector.updateReferenceGenomeData('" + organismId + "','" + type + "','" + version + "'," + json + ");\n";
- executeJavascript(javascriptCode.toString());
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
-
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/SearchBean.java b/web/src/main/java/lcsb/mapviewer/bean/SearchBean.java
deleted file mode 100644
index 012985286262fda410348e98d18e6a380fbb9a79..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/SearchBean.java
+++ /dev/null
@@ -1,589 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.log4j.Logger;
-import org.primefaces.event.SelectEvent;
-import org.primefaces.model.map.LatLng;
-
-import lcsb.mapviewer.bean.MapBean.ClientMapData;
-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.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IDataMiningService;
-import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.interfaces.ISearchService.CoordinatesSearchParams;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.ElementIdentifierDetails;
-import lcsb.mapviewer.services.search.IHeavyView;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
-import lcsb.mapviewer.services.search.data.FullAliasView;
-import lcsb.mapviewer.services.search.data.FullReactionView;
-import lcsb.mapviewer.services.search.data.SearchElementResult;
-import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-
-/**
- * Bean used for searching elements in the current map.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "searchMB")
-@ViewScoped
-public class SearchBean extends AbstractMarkerManagerBean<SearchElementResult> implements Serializable {
-
- /**
- * Name of the session field that store last query.
- */
- public static final String STRING_SEARCH_SESSION_PARAM = "SEARCH_QUERY";
-
- /**
- * Name of the session field that store coordinates of last click.
- */
- public static final String COORDINATE_SEARCH_SESSION_PARAM = "SEARCH_COORD";
-
- /**
- * Name of the session field that store model identifier where the last click
- * was performed.
- */
- public static final String COORDINATE_SEARCH_MODEL_ID_SESSION_PARAM = "SEARCH_COORD_MODEL_ID";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(SearchBean.class);
-
- /**
- * Should search by name be perfectly matched.
- */
- private String perfectMatchParam = "";
-
- /**
- * This parameter define the maximum distance between reaction and coordinates
- * that is acceptable in search.
- */
- private double searchDistance = 0;
-
- /**
- * Maximum number of search results.
- */
- private Integer maxNumberOfResults;
-
- /**
- * Bean used for communication with the client side about the map currently
- * visualized.
- *
- * @see MapBean
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for managing data mining information.
- */
- @ManagedProperty(value = "#{missingConnectionMB}")
- private transient MissingConnectionBean missingConnectionBean;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service that allows to query the database to find elements in the model.
- */
- @ManagedProperty(value = "#{SearchService}")
- private transient ISearchService searchService;
-
- /**
- * Service that manages data mining information.
- */
- @ManagedProperty(value = "#{DataMiningService}")
- private transient IDataMiningService dataMiningService;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- @Override
- public void init() {
- // set the default max distance
- String dist = configurationService.getConfigurationValue(ConfigurationElementType.SEARCH_DISTANCE);
- try {
- setSearchDistance(Double.valueOf(dist));
- } catch (NumberFormatException e) {
- logger.error("Problem with distance param: " + dist, e);
- }
-
- // set the max number of results
- String results = configurationService.getConfigurationValue(ConfigurationElementType.SEARCH_RESULT_NUMBER);
- try {
- setMaxNumberOfResults(Integer.valueOf(results));
- } catch (NumberFormatException e) {
- logger.error("Problem with max number of search results: " + results, e);
- }
-
- // if by chance we already opened this model in pur session then restore
- // search results
- try {
- refreshSearch();
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Method called when client selects element from autocomplete in search field
- * (call search method).
- *
- * @param event
- * select event send by the client
- */
- public void autocompleteHandleSelect(final SelectEvent event) {
- String searchText = getRequestParameter("tabView:mainForm:searchText_input");
- search(searchText);
- }
-
- /**
- * This method search the model with a string query.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void search(final ActionEvent actionEvent) {
- String searchText = getRequestParameter("tabView:mainForm:searchText_input");
- search(searchText);
- }
-
- /**
- * Look for elements using query given in the parameter.
- *
- * @param query
- * search query
- */
- protected void search(String query) {
- addSessionParam(STRING_SEARCH_SESSION_PARAM + getCurrentMapId(), query);
- addSessionParam(COORDINATE_SEARCH_SESSION_PARAM + getCurrentMapId(), null);
-
- String ipAddress = getClientIpAddress();
- logger.debug("Search: " + query);
-
- // clear results
- clearResults();
-
- boolean perfectMatch = perfectMatchParam.equalsIgnoreCase("true");
-
- try {
-
- // clear suggested connections (it should be refactorized to listeners)
- missingConnectionBean.setGeneName(null);
- missingConnectionBean.search(null);
-
- // find all matching objects
- int set = 0;
- for (String string : splitQuery(query, false)) {
- SearchElementResult result = searchService.searchByQuery(getCurrentTopModel(), string, maxNumberOfResults, perfectMatch, ipAddress);
- searchService.assignIcons(result, set++);
- super.addResult(result);
- }
-
- // send markers to client
- refreshDataInJavascript(true);
-
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * This method is invoked by client when map is clicked.
- *
- * @param actionEvent
- * event data
- */
- public void mapClicked(final ActionEvent actionEvent) {
- String modelIdentifier = getRequestParameter("submodelId");
- String latCoord = getRequestParameter("latCoord");
- String lngCoord = getRequestParameter("lngCoord");
- logger.debug("Submap clicked (id=" + modelIdentifier + ")");
- Integer id = null;
- try {
- id = Integer.valueOf(modelIdentifier);
- } catch (NumberFormatException e) {
- sendError("Model identifier is invalid: " + modelIdentifier);
- return;
- }
- Model model = getCurrentTopModel().getSubmodelById(id);
- if (model == null) {
- sendError("SubModel with id: " + modelIdentifier + " doesn't exist.");
- return;
- }
- LatLng latLng = null;
- if (latCoord != null && lngCoord != null) {
- try {
- double lat = Double.parseDouble(latCoord);
- double lng = Double.parseDouble(lngCoord);
- latLng = new LatLng(lat, lng);
- } catch (NumberFormatException e) {
- sendError("Invalid latLng coordinates: " + latCoord + "," + lngCoord);
- return;
- }
- } else {
- sendError("Invalid latLng coordinates: " + latCoord + "," + lngCoord);
- return;
- }
- CoordinationConverter converter = mapBean.getMapDataByMapIdentifier(modelIdentifier).getcConverter();
-
- addSessionParam(STRING_SEARCH_SESSION_PARAM + getCurrentMapId(), null);
- Point2D coord = converter.toPoint(latLng);
- addSessionParam(COORDINATE_SEARCH_SESSION_PARAM + getCurrentMapId(), coord);
- addSessionParam(COORDINATE_SEARCH_MODEL_ID_SESSION_PARAM + getCurrentMapId(), model.getId());
- searchByCoordinates(coord, model);
- }
-
- /**
- * Find something on the map close to coordinates.
- *
- * @param coordinates
- * point where we are looking for something
- * @param model
- * map on which we search for an element
- */
- private void searchByCoordinates(final Point2D coordinates, Model model) {
- try {
- ClientMapData mapData = mapBean.getMapDataByMapIdentifier(model.getId());
- // clear results
- clearResults();
-
- // clear suggested connections (it should be refactorized to listeners)
- missingConnectionBean.setGeneName(null);
- missingConnectionBean.search(null);
-
- // compute the distance on the map (it depends a little on the zoomLevel)
- double distance = mapData.getcConverter().scale(searchDistance, mapData.getZoomLevel());
-
- // set search params
- CoordinatesSearchParams searchParams = new CoordinatesSearchParams();
- searchParams.model(model);
- searchParams.point(coordinates);
- searchParams.distance(distance);
- searchParams.layoutIdentifier(mapBean.getSelectedLayoutIdentifier());
- searchParams.level(mapBean.getLevel(mapData));
-
- // find objects on the map
- SearchElementResult result = searchService.searchByCoordinates(searchParams);
- searchService.assignIcons(result, 0);
- addResult(result);
-
- // send markers to the map
- refreshDataInJavascript(false);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Refresh search result using data stored in the session as search input (for
- * instance when the webpage is refreshed).
- */
- private void refreshSearch() {
- String query = (String) getSessionParam(STRING_SEARCH_SESSION_PARAM + getCurrentMapId());
- if (query != null) {
- search(query);
- } else {
- Point2D coord = (Point2D) getSessionParam(COORDINATE_SEARCH_SESSION_PARAM + getCurrentMapId());
- Integer modelId = (Integer) getSessionParam(COORDINATE_SEARCH_MODEL_ID_SESSION_PARAM + getCurrentMapId());
- Model model = getCurrentTopModel().getSubmodelById(modelId);
- if (coord != null && model != null) {
- searchByCoordinates(coord, model);
- }
- }
- }
-
- /**
- * Returns list of autocomple strings for the string query.
- *
- * @param query
- * query for which autocomplete is returned
- * @return list of autocomple strings
- */
- public List<String> autocomplete(final String query) {
- return searchService.getAutocompleteList(getCurrentTopModel(), query);
- }
-
- @Override
- public void clear() {
- setPerfectMatchParam("false");
- addSessionParam(STRING_SEARCH_SESSION_PARAM + getCurrentMapId(), null);
- addSessionParam(COORDINATE_SEARCH_SESSION_PARAM + getCurrentMapId(), null);
- addSessionParam(COORDINATE_SEARCH_MODEL_ID_SESSION_PARAM + getCurrentMapId(), null);
- clearResults();
- refreshDataInJavascript();
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- if (mapBean == null) {
- mapBean = findBean(MapBean.class);
- }
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
- /**
- * @return the dataMiningService
- * @see #dataMiningService
- */
- public IDataMiningService getDataMiningService() {
- return dataMiningService;
- }
-
- /**
- * @param dataMiningService
- * the dataMiningService to set
- * @see #dataMiningService
- */
- public void setDataMiningService(IDataMiningService dataMiningService) {
- this.dataMiningService = dataMiningService;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the searchService
- * @see #searchService
- */
- public ISearchService getSearchService() {
- return searchService;
- }
-
- /**
- * @param searchService
- * the searchService to set
- * @see #searchService
- */
- public void setSearchService(ISearchService searchService) {
- this.searchService = searchService;
- }
-
- /**
- * @return the perfectMatchParam
- * @see #perfectMatchParam
- */
- public String getPerfectMatchParam() {
- return perfectMatchParam;
- }
-
- /**
- * @param perfectMatchParam
- * the perfectMatchParam to set
- * @see #perfectMatchParam
- */
- public void setPerfectMatchParam(String perfectMatchParam) {
- this.perfectMatchParam = perfectMatchParam;
- }
-
- /**
- * @return the searchDistance
- * @see #searchDistance
- */
- public double getSearchDistance() {
- return searchDistance;
- }
-
- /**
- * @param searchDistance
- * the searchDistance to set
- * @see #searchDistance
- */
- public void setSearchDistance(double searchDistance) {
- this.searchDistance = searchDistance;
- }
-
- /**
- * @return the missingConnectionBean
- * @see #missingConnectionBean
- */
- public MissingConnectionBean getMissingConnectionBean() {
- return missingConnectionBean;
- }
-
- /**
- * @param missingConnectionBean
- * the missingConnectionBean to set
- * @see #missingConnectionBean
- */
- public void setMissingConnectionBean(MissingConnectionBean missingConnectionBean) {
- this.missingConnectionBean = missingConnectionBean;
- }
-
- /**
- * @return the maxNumberOfResults
- * @see #maxNumberOfResults
- */
- public Integer getMaxNumberOfResults() {
- return maxNumberOfResults;
- }
-
- /**
- * @param maxNumberOfResults
- * the maxNumberOfResults to set
- * @see #maxNumberOfResults
- */
- public void setMaxNumberOfResults(Integer maxNumberOfResults) {
- this.maxNumberOfResults = maxNumberOfResults;
- }
-
- @Override
- protected List<ElementIdentifier> getLightElementsForSearchResult(SearchElementResult searchResult) {
- SearchElementResult searchElementResult = (SearchElementResult) searchResult;
- List<ElementIdentifier> result = new ArrayList<>();
- for (IHeavyView element : searchElementResult.getElements()) {
- if (element instanceof FullAliasView) {
- FullAliasView alias = (FullAliasView) element;
- result.add(new ElementIdentifier(alias.getUniqueId(), alias.getModelId(), ElementIdentifierType.ALIAS, alias.getIcon()));
- } else if (element instanceof FullReactionView) {
- FullReactionView reaction = (FullReactionView) element;
- result.add(new ElementIdentifier(reaction.getUniqueId(), reaction.getModelId(), ElementIdentifierType.REACTION, null));
- } else {
- throw new InvalidArgumentException("ISearchResultView conatins invalid object: " + element.getClass());
- }
- }
- return result;
- }
-
- @Override
- protected ElementIdentifierDetails getElementInformationForResult(ElementIdentifier element, SearchElementResult result) {
- throw new NotImplementedException();
- }
-
- @Override
- protected List<Pair<String, ElementIdentifierDetails>> getElementInformationForResult(ElementIdentifier element) {
- throw new NotImplementedException();
- }
-
- /**
- * Returns currently browsed map.
- *
- * @return currently browsed map
- */
- private Model getCurrentTopModel() {
- return getMapBean().getCurrentTopModel();
- }
-
- /**
- * Returns identifier of browsed map (if such map wasn't setup it will be
- * default identifier).
- *
- * @return identifier of browsed map
- */
- private String getCurrentMapId() {
- return mapBean.getCurrentMapId();
- }
-
- /**
- * Returns curently browsed project.
- *
- * @return curently browsed project
- */
- private Project getCurrentProject() {
- return getCurrentTopModel().getProject();
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/StatusBean.java b/web/src/main/java/lcsb/mapviewer/bean/StatusBean.java
deleted file mode 100644
index 87a74b5ebae0058d58b223e358b6f64809d469c6..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/StatusBean.java
+++ /dev/null
@@ -1,116 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.services.interfaces.IExternalServicesService;
-
-import org.apache.log4j.Logger;
-
-/**
- * Bean used for checking the status of different services used by the system.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "statusMB")
-@ViewScoped
-public class StatusBean extends AbstractManagedBean implements Serializable {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(StatusBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of statuses of modules that use external resources.
- */
- private transient List<ExternalServiceStatus> statuses = new ArrayList<ExternalServiceStatus>();
-
- /**
- * Service used for getting the statuses of modules that used external
- * resources.
- */
- @ManagedProperty(value = "#{ExternalServicesService}")
- private transient IExternalServicesService externalServicesService;
-
- /**
- * Refresh statuses.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void refreshStatuses(final ActionEvent actionEvent) {
- try {
- statuses = externalServicesService.getExternalServiceStatuses();
- // if the status list is empty then add default list of services to check
- if (statuses.size() == 0) {
- externalServicesService.registerDefaultServices();
- statuses = externalServicesService.getExternalServiceStatuses();
- if (statuses.size() == 0) {
- sendError("List of know services is empty");
- }
- }
- } catch (Exception e) {
- logger.error(e);
- sendError("Internal server error. More info in logs.");
- }
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the externalServicesService
- * @see #externalServicesService
- */
- public IExternalServicesService getExternalServicesService() {
- return externalServicesService;
- }
-
- /**
- * @param externalServicesService
- * the externalServicesService to set
- * @see #externalServicesService
- */
- public void setExternalServicesService(IExternalServicesService externalServicesService) {
- this.externalServicesService = externalServicesService;
- }
-
- /**
- * @return the statuses
- * @see #statuses
- */
- public List<ExternalServiceStatus> getStatuses() {
- return statuses;
- }
-
- /**
- * @param statuses
- * the statuses to set
- * @see #statuses
- */
- public void setStatuses(List<ExternalServiceStatus> statuses) {
- this.statuses = statuses;
- }
-
- @Override
- public void init() {
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/UserBean.java b/web/src/main/java/lcsb/mapviewer/bean/UserBean.java
deleted file mode 100644
index ad57da482f7c29d33617020b9ad8c47d93131ad0..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/UserBean.java
+++ /dev/null
@@ -1,605 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.IOException;
-import java.util.Map;
-
-import javax.faces.application.FacesMessage;
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.SessionScoped;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.ExternalContext;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.validator.ValidatorException;
-import javax.servlet.RequestDispatcher;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-
-import org.apache.log4j.Logger;
-import org.primefaces.context.RequestContext;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.events.ObjectModifiedEvent;
-import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.ILogService;
-import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.UserView;
-
-/**
- * Bean used for managing logged user data.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "userMB")
-@SessionScoped
-public class UserBean extends AbstractManagedBean {
-
- /**
- * String representing {@link #login} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGIN_PROPERTY = "LOGIN";
-
- /**
- * String representing {@link #password} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String PASSWORD_PROPERTY = "PASSWORD";
-
- /**
- * String representing {@link #loggedUser} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGGED_USER_PROPERTY = "USER";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UserBean.class);
-
- /**
- * Login of currently logged user.
- */
- private String login = "";
-
- private String authenticationToken;
-
- /**
- * Password of currently logged user.
- */
- private String password = "";
-
- /**
- * Email address that should be used when requesting an account.
- */
- private String requestAccountEmail = "";
-
- /**
- * Currently logged user. The user is transient because it contains information
- * from db and to serialize it properly we should provide apropriate converter.
- */
- private User loggedUser = null;
-
- /**
- * Object to use to edit user's profile.
- */
- private UserView editUser = null;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service used to access logs.
- *
- * @see ILogService
- */
- @ManagedProperty(value = "#{LogService}")
- private transient ILogService logService;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Default constructor.
- */
- public UserBean() {
- super();
- // we have to clear default list of property change listeners (we don't
- // want
- // to put passwords in the log file ;-))
- for (PropertyChangeListener listener : getPropertyChangeListeners()) {
- removePropertyChangeListener(listener);
- }
-
- // and now add custom logger property listener
- PropertyChangeListener propertyChangeLogger = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (PASSWORD_PROPERTY.equals(arg0.getPropertyName())) {
- logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: *** New: ***");
- } else {
- logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: " + arg0.getOldValue() + " New: "
- + arg0.getNewValue());
- }
- }
-
- };
- addPropertyChangeListener(propertyChangeLogger);
- }
-
- @Override
- public void init() {
- PropertyChangeListener loginPasswordChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LOGIN_PROPERTY.equals(arg0.getPropertyName()) || PASSWORD_PROPERTY.equals(arg0.getPropertyName())) {
- authenticationToken = getUserService().login(login, password);
- if (authenticationToken != null) {
- setLoggedUser(getUserService().getUserByLogin(login));
- } else {
- authenticationToken = getUserService().login(Configuration.ANONYMOUS_LOGIN, "");
- setLoggedUser(getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN));
- }
- }
- }
- };
- addPropertyChangeListener(loginPasswordChanged);
-
- PropertyChangeListener loggedUserChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LOGGED_USER_PROPERTY.equals(arg0.getPropertyName())) {
- getLogService().setLoggedUser(getLoggedUser());
- }
- }
- };
- addPropertyChangeListener(loggedUserChanged);
-
- PropertyChangeListener logServiceLoggedUserChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LOGGED_USER_PROPERTY.equals(arg0.getPropertyName())) {
- if (!getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN).equals(arg0.getOldValue())) {
- LogParams params = new LogParams().type(LogType.USER_LOGOUT).object(arg0.getOldValue());
- getLogService().log(params);
- }
-
- if (!getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN).equals(arg0.getNewValue())) {
- LogParams params = new LogParams().type(LogType.USER_LOGIN).object(arg0.getNewValue());
- getLogService().log(params);
- }
- }
- }
- };
- addPropertyChangeListener(logServiceLoggedUserChanged);
-
- setLoggedUser(getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN));
- setRequestAccountEmail(
- getConfigurationService().getConfigurationValue(ConfigurationElementType.REQUEST_ACCOUNT_EMAIL));
-
- }
-
- /**
- *
- * @return {@link #login}
- */
- public String getLogin() {
- return login;
- }
-
- /**
- * Sets new login value. Property change listeners for "login" property will be
- * thrown after setting this value.
- *
- * @param login
- * new {@link #login} value
- */
- public void setLogin(final String login) {
- String oldLogin = this.login;
- this.login = login;
- firePropertyChange(LOGIN_PROPERTY, oldLogin, login);
- }
-
- /**
- * Perform spring login operation.
- *
- * @throws IOException
- * thrown when underlaying layer throws this exception
- * @throws ServletException
- * thrown when underlaying layer will throw this exception
- */
- public void doLogin() throws IOException, ServletException {
- doLogin(null);
- }
-
- /**
- * Perform spring login operation.
- *
- * @param id
- * name of the map which should be used after authentication
- *
- * @throws IOException
- * thrown when underlaying layer throws this exception
- * @throws ServletException
- * thrown when underlaying layer will throw this exception
- */
- public void doLogin(String id) throws IOException, ServletException {
- FacesContext context = FacesContext.getCurrentInstance();
- ExternalContext externalContext = context.getExternalContext();
-
- ServletRequest request = (ServletRequest) externalContext.getRequest();
- Map<?, ?> map = request.getParameterMap();
- for (Object obj : map.keySet()) {
- try {
- String[] arr = (String[]) map.get(obj);
- if (obj.equals("username")) {
- setLogin(arr[0]);
- }
- if (obj.equals("password")) {
- setPassword(arr[0]);
- }
- } catch (ClassCastException e) {
- logger.error("WTF", e);
- }
- }
-
- // now perform spring authentication
- String requestDispatcher = Configuration.SPRING_SECURITY_ACTION;
- logger.debug(id);
- if (id != null) {
- requestDispatcher += "?id=" + id;
- }
- logger.debug(requestDispatcher);
-
- RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest())
- .getRequestDispatcher(requestDispatcher);
-
- dispatcher.forward((ServletRequest) externalContext.getRequest(), (ServletResponse) externalContext.getResponse());
-
- context.responseComplete();
- }
-
- /**
- * Performs spring login as anonymous.
- *
- * @throws IOException
- * thrown when underlaying layer throws this exception
- * @throws ServletException
- * thrown when underlaying layer will throw this exception
- */
- public void anonymousLogin() throws IOException, ServletException {
- setLogin(Configuration.ANONYMOUS_LOGIN);
- setPassword("");
- FacesContext context = FacesContext.getCurrentInstance();
- ExternalContext externalContext = context.getExternalContext();
- ServletRequest request = (ServletRequest) externalContext.getRequest();
- Map<?, ?> map = request.getParameterMap();
- for (Object obj : map.keySet()) {
- try {
- String[] arr = (String[]) map.get(obj);
- if (obj.equals("username")) {
- arr[0] = Configuration.ANONYMOUS_LOGIN;
- }
- if (obj.equals("password")) {
- arr[0] = "";
- }
- } catch (ClassCastException e) {
- logger.error("WTF", e);
- }
- }
-
- RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest())
- .getRequestDispatcher(Configuration.SPRING_SECURITY_ACTION);
-
- dispatcher.forward((ServletRequest) externalContext.getRequest(), (ServletResponse) externalContext.getResponse());
-
- context.responseComplete();
- }
-
- /**
- * Perform spring logout operation.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void doLogout(final ActionEvent actionEvent) {
- try {
- FacesContext context = FacesContext.getCurrentInstance();
- ExternalContext externalContext = context.getExternalContext();
-
- RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest())
- .getRequestDispatcher(Configuration.SPRING_SECURITY_LOGOUT);
-
- dispatcher.forward((ServletRequest) externalContext.getRequest(),
- (ServletResponse) externalContext.getResponse());
-
- context.responseComplete();
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
-
- }
- }
-
- /**
- *
- * @return {@link #password}
- */
- public String getPassword() {
- return password;
- }
-
- /**
- * Sets new password value. Property change listeners for "password" property
- * will be thrown after setting this value.
- *
- * @param password
- * new {@link #password} value
- */
- public void setPassword(final String password) {
- String oldPassword = this.password;
- this.password = password;
- firePropertyChange(PASSWORD_PROPERTY, oldPassword, password);
- }
-
- /**
- *
- * @return {@link #loggedUser}
- */
- public User getLoggedUser() {
- if (loggedUser == null) {
- loggedUser = getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN);
- }
- return loggedUser;
- // return userService.getUserById(loggedUser.getIdObject());
- }
-
- /**
- * Sets new loggedUser value. Property change listeners for "loggedUser"
- * property will be thrown after setting this value.
- *
- * @param user
- * new {@link #loggedUser} value
- */
- public void setLoggedUser(final User user) {
- User oldUser = this.loggedUser;
- // loggedUser = getUserService().getUserView(user);
- loggedUser = user;
- firePropertyChange(LOGGED_USER_PROPERTY, oldUser, loggedUser);
- }
-
- /**
- * Check if user has privileges to manage the users.
- *
- * @return <i>true</i> if user has privileges to manage the users,<br/>
- * <i>false</i> otherwise
- */
- public boolean getUserHasManagePrivileges() {
- User user = getLoggedUser();
- if (user == null) {
- return false;
- }
- boolean result = getUserService().userHasPrivilege(user, PrivilegeType.USER_MANAGEMENT);
- return result;
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- if (userService == null) {
- userService = findBean(IUserService.class);
- }
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- if (configurationService == null) {
- configurationService = findBean(IConfigurationService.class);
- }
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the requestAccountEmail
- * @see #requestAccountEmail
- */
- public String getRequestAccountEmail() {
- return requestAccountEmail;
- }
-
- /**
- * @param requestAccountEmail
- * the requestAccountEmail to set
- * @see #requestAccountEmail
- */
- public void setRequestAccountEmail(String requestAccountEmail) {
- this.requestAccountEmail = requestAccountEmail;
- }
-
- /**
- * @return the logService
- * @see #logService
- */
- public ILogService getLogService() {
- if (logService == null) {
- logService = findBean(ILogService.class);
- }
- return logService;
- }
-
- /**
- * @param logService
- * the logService to set
- * @see #logService
- */
- public void setLogService(ILogService logService) {
- this.logService = logService;
- }
-
- /**
- * Refresh edit user.
- */
- public void refreshEditUser() {
- if (!loggedUser.getLogin().equals(Configuration.ANONYMOUS_LOGIN)) {
- this.setEditUser(getUserService().getUserRow(loggedUser));
- RequestContext.getCurrentInstance().reset(":tabView:userForm2:panel");
- }
- }
-
- /**
- * @param ctx
- * context
- * @param component
- * ui component
- * @param value
- * the new value
- * @throws ValidatorException
- * if validation fails
- */
- public void checkOldPassword(FacesContext ctx, UIComponent component, Object value) throws ValidatorException {
- UIInput passwordComp = (UIInput) component.getAttributes().get("passwordComp");
- if (passwordComp != null) {
- String password = null;
- password = (String) passwordComp.getValue();
- if (password != null && !password.isEmpty()) {
- String oldPassword = (String) value;
- if (oldPassword == null || oldPassword.isEmpty()
- || !this.getUserService().encodePassword(oldPassword).equals(editUser.getCryptedPassword())) {
- ((UIInput) component).setValid(false);
- FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR,
- "Typed old password does not match stored one.", null);
- throw new ValidatorException(message);
- }
- }
- }
- }
-
- /**
- * @param ctx
- * context
- * @param component
- * ui component
- * @param value
- * the new value
- * @throws ValidatorException
- * if validation fails
- */
- public void checkNewPassword(FacesContext ctx, UIComponent component, Object value) throws ValidatorException {
- UIInput passwordComp = (UIInput) component.getAttributes().get("passwordComp");
- if (passwordComp != null) {
- String password = null;
- password = (String) passwordComp.getValue();
- if (password != null && !password.isEmpty()) {
- String oldPassword = (String) value;
- if (oldPassword == null || oldPassword.isEmpty()
- || !this.getUserService().encodePassword(oldPassword).equals(editUser.getCryptedPassword())) {
- ((UIInput) component).setValid(false);
- FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR,
- "Typed old password does not match stored one.", null);
- throw new ValidatorException(message);
- }
- }
- }
- }
-
- /**
- * Update selected user.
- */
- public void updateUser() {
- getUserService().updateUser(editUser);
- setLoggedUser(getUserService().getUserByLogin(login));
- ObjectModifiedEvent event = new ObjectModifiedEvent(editUser);
- callListeners(event);
- }
-
- /**
- * @return editable instance of the object.
- */
- public UserView getEditUser() {
- return editUser;
- }
-
- /**
- * @param editUser
- * instance to be edited.
- */
- public void setEditUser(UserView editUser) {
- this.editUser = editUser;
- }
-
- /**
- * @return the authenticationToken
- * @see #authenticationToken
- */
- public String getAuthenticationToken() {
- if (authenticationToken == null) {
- authenticationToken = getUserService().login(Configuration.ANONYMOUS_LOGIN, "");
- }
- return authenticationToken;
- }
-
- /**
- * @param authenticationToken
- * the authenticationToken to set
- * @see #authenticationToken
- */
- public void setAuthenticationToken(String authenticationToken) {
- this.authenticationToken = authenticationToken;
- }
-
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/UsersBean.java b/web/src/main/java/lcsb/mapviewer/bean/UsersBean.java
deleted file mode 100644
index 286acd8d7107b8e0baef21134c5fe71f37280a03..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/UsersBean.java
+++ /dev/null
@@ -1,390 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.events.Listener;
-import lcsb.mapviewer.events.ObjectAddedEvent;
-import lcsb.mapviewer.events.ObjectModifiedEvent;
-import lcsb.mapviewer.events.ObjectRemovedEvent;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.UserView;
-import lcsb.mapviewer.services.view.UserView.UserProjectPrivilegeView;
-
-import org.apache.log4j.Logger;
-
-/**
- * Bean used for managing users.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "usersMB")
-@ViewScoped
-public class UsersBean extends AbstractManagedBean implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UsersBean.class);
-
- /**
- * List of all users to be managed in the client.
- */
- private List<UserView> userList = new ArrayList<UserView>();
-
- /**
- * List of all available {@link PrivilegeType} for any {@link Project}.
- */
- private List<PrivilegeType> projectPrivilegeTypes = new ArrayList<PrivilegeType>();
-
- /**
- * User selected for updating/removing in the client.
- */
- private UserView selectedUser;
-
- /**
- * Privilege for the map selected on the manage page.
- */
- private UserProjectPrivilegeView projectPrivilege;
-
- /**
- * Bean used for communication with the client side about the data related to
- * currently logged user.
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean resposnisble for managing projects.
- *
- * @see ProjectBean
- */
- @ManagedProperty(value = "#{projectMB}")
- private transient ProjectBean projectBean;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- @Override
- public void init() {
- setSelectedUser(userService.createEmptyUserRow());
- setProjectPrivilege(selectedUser.new UserProjectPrivilegeView());
-
- for (PrivilegeType pt : PrivilegeType.values()) {
- if (pt.getPrivilegeObjectType() != null && pt.getPrivilegeObjectType().equals(Project.class)) {
- projectPrivilegeTypes.add(pt);
- }
- }
- Collections.sort(projectPrivilegeTypes, new Comparator<PrivilegeType>() {
- @Override
- public int compare(PrivilegeType o1, PrivilegeType o2) {
- return o1.getCommonName().compareTo(o2.getCommonName());
- }
- });
-
- // after user was modified, refresh user list
- this.registerListener(new Listener<ObjectModifiedEvent>(ObjectModifiedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectModifiedEvent event) {
- refreshUserList(null);
- }
- });
-
- // after user was added, refresh user list
- this.registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- refreshUserList(null);
- }
- });
-
- // after user was removed, refresh user list
- this.registerListener(new Listener<ObjectRemovedEvent>(ObjectRemovedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectRemovedEvent event) {
- refreshUserList(null);
- }
- });
-
- // after project is added refresh information about users (to include
- // privileges for new project)
- projectBean.registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- refreshUserList(null);
- }
- });
-
- refreshUserList(null);
- }
-
- /**
- * Refresh list of users.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void refreshUserList(final ActionEvent actionEvent) {
- try {
- userList.clear();
- List<UserView> localUserList = userService.getAllUserRows();
- userList.addAll(localUserList);
- Collections.sort(userList);
- } catch (Exception e) {
- logger.error(e);
- sendError("Internal server error. More info in logs.");
- }
- }
-
- /**
- *
- * @return {@link #selectedUser}
- */
- public UserView getSelectedUser() {
- return selectedUser;
- }
-
- /**
- * Sets new selectedUser value. Property change listeners for "selectedUser"
- * property will be thrown after setting this value.
- *
- * @param selectedUser
- * new {@link #selectedUser} value
- */
- public void setSelectedUser(final UserView selectedUser) {
- this.selectedUser = selectedUser;
- this.selectedUser.getPdm().setRowIndex(-1);
- this.projectPrivilege = null;
- }
-
- /**
- * Update selected user.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void updateSelectedUser(final ActionEvent actionEvent) {
- userService.updateUser(this.selectedUser);
- ObjectModifiedEvent event = new ObjectModifiedEvent(this.selectedUser);
- callListeners(event);
- }
-
- /**
- * Update users.
- *
- * @param users
- * users to update
- */
- public void updateUsers(Collection<UserView> users) {
- userService.updateUsers(users);
- ObjectModifiedEvent event = new ObjectModifiedEvent(users);
- callListeners(event);
- }
-
- /**
- * Remove selected user.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void removeSelectedUser(final ActionEvent actionEvent) {
- if (Configuration.ANONYMOUS_LOGIN.equals(this.selectedUser.getLogin())) {
- sendError("Cannot remove guest account");
- return;
- }
- userService.deleteUser(this.selectedUser);
- ObjectRemovedEvent event = new ObjectRemovedEvent(this.selectedUser);
- callListeners(event);
- }
-
- /**
- * Creates new empty user view and set it for editing.
- *
- * @param actionEvent
- * clients side action event
- */
- public void prepareEmptyUser(final ActionEvent actionEvent) {
- this.selectedUser = userService.createEmptyUserRow();
- }
-
- /**
- * Adds new user (stored in {@link #selectedUser} field) to the database.
- *
- * @param actionEvent
- * client side action event
- */
- public void addSelectedUser(final ActionEvent actionEvent) {
- userService.addUser(this.selectedUser);
- ObjectAddedEvent event = new ObjectAddedEvent(this.selectedUser);
- callListeners(event);
- }
-
- /**
- * Check if user has privileges to manage the users.
- *
- * @return <i>true</i> if user has privileges to manage the users,<br/>
- * <i>false</i> otherwise
- */
- public boolean getUserHasManagePrivileges() {
- User user = userBean.getLoggedUser();
- if (user == null) {
- return false;
- }
- boolean result = userService.userHasPrivilege(user, PrivilegeType.USER_MANAGEMENT);
- return result;
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the userList
- * @see #userList
- */
- public List<UserView> getUserList() {
- return userList;
- }
-
- /**
- * @param userList
- * the userList to set
- * @see #userList
- */
- public void setUserList(List<UserView> userList) {
- this.userList = userList;
- }
-
- /**
- * @return the projectPrivilege
- * @see #projectPrivilege
- */
- public UserProjectPrivilegeView getProjectPrivilege() {
- return projectPrivilege;
- }
-
- /**
- * @param projectPrivilege
- * the projectPrivilege to set
- * @see #projectPrivilege
- */
- public void setProjectPrivilege(UserProjectPrivilegeView projectPrivilege) {
- this.projectPrivilege = projectPrivilege;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the projectPrivilegeTypes
- * @see #projectPrivilegeTypes
- */
- public List<PrivilegeType> getProjectPrivilegeTypes() {
- return projectPrivilegeTypes;
- }
-
- /**
- * @param projectPrivilegeTypes
- * the projectPrivilegeTypes to set
- * @see #projectPrivilegeTypes
- */
- public void setProjectPrivilegeTypes(List<PrivilegeType> projectPrivilegeTypes) {
- this.projectPrivilegeTypes = projectPrivilegeTypes;
- }
-
- /**
- * @return the projectBean
- * @see #projectBean
- */
- public ProjectBean getProjectBean() {
- return projectBean;
- }
-
- /**
- * @param projectBean
- * the projectBean to set
- * @see #projectBean
- */
- public void setProjectBean(ProjectBean projectBean) {
- this.projectBean = projectBean;
- }
-}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/package-info.java b/web/src/main/java/lcsb/mapviewer/bean/package-info.java
deleted file mode 100644
index 0936e7b1e30ba9204d6ff1ff5b9b434b915dd7fe..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/bean/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * Provides beans to communicate with client side.
- */
-package lcsb.mapviewer.bean;
-
diff --git a/web/src/main/webapp/WEB-INF/components/admin/footer.xhtml b/web/src/main/webapp/WEB-INF/components/admin/footer.xhtml
deleted file mode 100644
index 3d995f9d3243b6d61d0c19ba0d25c9e2f6ea0ca5..0000000000000000000000000000000000000000
--- a/web/src/main/webapp/WEB-INF/components/admin/footer.xhtml
+++ /dev/null
@@ -1,22 +0,0 @@
-<html xmlns="http://www.w3.org/1999/xhtml"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:ui="http://java.sun.com/jsf/facelets"
- xmlns:p="http://primefaces.org/ui">
-
-
-<div id="footerTable">
-<table width="100%" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td align="left"><a href="#{configurationMB.logoLink}" title="#{configurationMB.logoText}" target="_blank">
- <h:graphicImage library="images" name="#{configurationMB.logoImg}" width="80" height="80" border="0" alt="#{configurationMB.logoText}"/>
- </a></td>
- <td align="center" class="footerText">MiNERVA version #{configurationMB.version.version};<br/> build #{configurationMB.version.time};<br/>git: #{configurationMB.version.gitVersion}</td>
- <td align="right"><a href="http://wwwen.uni.lu/lcsb/" title="LCSB - Luxembourg Centre for Systems Biomedicine" target="_blank">
- <h:graphicImage library="images" name="lcsb.png" width="80" height="80" border="0" alt="LCSB - Luxembourg Centre for Systems Biomedicine"/>
- </a></td>
- </tr>
-</table>
-</div>
-</html>
-
diff --git a/web/src/main/webapp/WEB-INF/components/admin/statistics.xhtml b/web/src/main/webapp/WEB-INF/components/admin/statistics.xhtml
deleted file mode 100644
index 4a4c3a1c9480d7e439a6a8958e5fa2f960617332..0000000000000000000000000000000000000000
--- a/web/src/main/webapp/WEB-INF/components/admin/statistics.xhtml
+++ /dev/null
@@ -1,28 +0,0 @@
-<html xmlns="http://www.w3.org/1999/xhtml"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:ui="http://java.sun.com/jsf/facelets"
- xmlns:p="http://primefaces.org/ui">
-
-<!-- This component contains short code used for Google Analytics statistics. -->
-
-<script type="text/javascript">
- var googleAnalyticsId = "#{configurationMB.googleAnalyticsIdentifier}";
-
-
- //enable statistics only when there is identifier defined
- if (googleAnalyticsId != "") {
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', googleAnalyticsId]);
- _gaq.push(['_trackPageview']);
-
- (function() {
- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
- })();
- }
-</script>
-
-
-</html>
diff --git a/web/src/main/webapp/WEB-INF/web.xml b/web/src/main/webapp/WEB-INF/web.xml
index 9753c6e538f5d961575b59e3c5bed7823d2aba2c..e5bdde9887143378115fb88f8aa02e458522cba8 100644
--- a/web/src/main/webapp/WEB-INF/web.xml
+++ b/web/src/main/webapp/WEB-INF/web.xml
@@ -187,6 +187,7 @@
<tracking-mode>COOKIE</tracking-mode>
<cookie-config>
<name>MINERVA_AUTH_TOKEN</name><!-- default is jsessionid -->
+ <http-only>false</http-only>
</cookie-config>
</session-config>
<filter>
diff --git a/web/src/test/java/lcsb/mapviewer/AllWebTests.java b/web/src/test/java/lcsb/mapviewer/AllWebTests.java
index c394dd619eb3f3fa9c10ec0ff7695787e7accc97..22334086463ca6538d7fb73e60a5d2f26b868e5b 100644
--- a/web/src/test/java/lcsb/mapviewer/AllWebTests.java
+++ b/web/src/test/java/lcsb/mapviewer/AllWebTests.java
@@ -4,12 +4,10 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
-import lcsb.mapviewer.bean.AllBeanTests;
import lcsb.mapviewer.validator.AllValidatorTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllBeanTests.class, //
- AllValidatorTests.class,//
+@SuiteClasses({ AllValidatorTests.class,//
})
public class AllWebTests {
diff --git a/web/src/test/java/lcsb/mapviewer/bean/AbstractManagedBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/AbstractManagedBeanTest.java
deleted file mode 100644
index 48b0cf4118c75e2f37da185a05f18776b994ac9e..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/AbstractManagedBeanTest.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.mutable.MutableInt;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.events.Event;
-import lcsb.mapviewer.events.Listener;
-
-public class AbstractManagedBeanTest {
- Logger logger = Logger.getLogger(AbstractManagedBeanTest.class);
-
- class AbstractManagedBeanMock extends AbstractManagedBean {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- public void clear() {
- }
-
- public void callMockEvent(String data) {
- callListeners(new EventMock(data));
- }
-
- @Override
- public void init() {
- // TODO Auto-generated method stub
-
- }
-
- };
-
- class EventMock extends Event {
- String data = "";
-
- public EventMock(String d) {
- data = d;
- }
- }
-
- AbstractManagedBeanMock mockBean;
-
- @Before
- public void setUp() throws Exception {
- mockBean = new AbstractManagedBeanMock();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testListeners() throws Exception {
- final MutableInt called = new MutableInt(0);
- try {
- Listener<EventMock> listener = new Listener<EventMock>(EventMock.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(EventMock event) {
- called.add(1);
- }
- };
-
- mockBean.registerListener(listener);
- assertEquals(new MutableInt(0), called);
- mockBean.callMockEvent("hi");
- assertEquals(new MutableInt(1), called);
- mockBean.callMockEvent("hi2");
- assertEquals(new MutableInt(2), called);
- mockBean.unregisterListener(listener);
- mockBean.callMockEvent("hi3");
- assertEquals(new MutableInt(2), called);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveListeners() throws Exception {
- final MutableInt called = new MutableInt(0);
- try {
- Listener<EventMock> listener = new Listener<EventMock>(EventMock.class) {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(EventMock event) {
- called.add(1);
- }
- };
-
- try {
- mockBean.unregisterListener(listener);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/AllBeanTests.java b/web/src/test/java/lcsb/mapviewer/bean/AllBeanTests.java
deleted file mode 100644
index f63c521e6347238527d6ace674a9a233cb49da7b..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/AllBeanTests.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ //
- AbstractManagedBeanTest.class, //
- ConfigurationBeanTest.class, //
- ExportBeanTest.class, //
- FeedbackBeanTest.class, //
- GalaxyBeanTest.class, //
- LayoutBeanTest.class, //
- MapBeanTest.class, //
- MiriamBeanTest.class, //
- MissingConnectionBeanTest.class, //
- ProjectBeanTest.class, //
- SearchBeanTest.class, //
- UserBeanTest.class, //
- UsersBeanTest.class,//
-})
-public class AllBeanTests {
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
deleted file mode 100644
index 6e2f4dad0de63c7cdce591b54be5210b80d3919a..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.view.ConfigurationViewFactory;
-
-public class ConfigurationBeanTest extends WebTestFunctions {
-
- ConfigurationBean cBean;
- UserBean uBean;
- String oldValue;
- User user2;
-
- @Autowired
- ConfigurationViewFactory configurationViewFactory;
-
- @Before
- public void setUp() throws Exception {
- dbUtils.setAutoFlush(true);
- cBean = getConfigurationBean();
-
- uBean = getUserBean();
-
- user2 = new User();
- userService.addUser(user2);
- userService.setUserPrivilege(user2, PrivilegeType.CONFIGURATION_MANAGE, 1);
- userService.setUserPrivilege(user2, PrivilegeType.ADD_MAP, 1);
- uBean.setLoggedUser(user2);
-
- oldValue = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
-
- }
-
- @After
- public void tearDown() throws Exception {
- userService.deleteUser(user2);
- uBean.setLoggedUser(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN));
- configurationService.setConfigurationValue(ConfigurationElementType.DEFAULT_MAP, oldValue);
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(cBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/CustomPrimefacesUtils.java b/web/src/test/java/lcsb/mapviewer/bean/CustomPrimefacesUtils.java
deleted file mode 100644
index 251761a3c183ecb90ef54946c19483527d9688bf..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/CustomPrimefacesUtils.java
+++ /dev/null
@@ -1,141 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.faces.component.UIComponent;
-
-import lcsb.mapviewer.bean.utils.IPrimefacesUtils;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-import org.apache.log4j.Logger;
-
-public class CustomPrimefacesUtils implements IPrimefacesUtils {
- Logger logger = Logger.getLogger(CustomPrimefacesUtils.class);
-
- private String path = "tmp/";
- private String ip = "127.0.0.1";
- private String version = "unknown";
-
- private Map<String, String> requestParams = new HashMap<>();
- private Map<String, Object> callbackObjects = new HashMap<>();
-
- private Map<String, Object> sessionParams = new HashMap<>();
-
- private List<String> errors = new ArrayList<>();
- private List<String> infos = new ArrayList<>();
-
- @Override
- public String getRequestParameter(String name) {
- return requestParams.get(name);
- }
-
- @Override
- public String getPath() {
- return path;
- }
-
- @Override
- public String getClientIpAddress() {
- return ip;
- }
-
- @Override
- public void error(String message) {
- errors.add(message);
- logger.debug("PF ERROR message: " + message, new Exception());
- }
-
- @Override
- public void info(String message) {
- infos.add(message);
- logger.debug("PF Info message: " + message);
- }
-
- @Override
- public String getVersion() {
- return version;
- }
-
- @Override
- public UIComponent findComponent(String id) {
- throw new NotImplementedException();
- }
-
- @Override
- public void addCallbackParam(String key, Object value) {
- callbackObjects.put(key, value);
- }
-
- /**
- * @return the errors
- * @see #errors
- */
- public List<String> getErrors() {
- return errors;
- }
-
- /**
- * @param errors
- * the errors to set
- * @see #errors
- */
- public void setErrors(List<String> errors) {
- this.errors = errors;
- }
-
- /**
- * @return the infos
- * @see #infos
- */
- public List<String> getInfos() {
- return infos;
- }
-
- /**
- * @param infos
- * the infos to set
- * @see #infos
- */
- public void setInfos(List<String> infos) {
- this.infos = infos;
- }
-
- public Object getCallbackParam(String key) {
- return callbackObjects.get(key);
- }
-
- @Override
- public Map<String, String> getRequestParameterMap() {
- return requestParams;
- }
-
- @Override
- public void addSessionParam(String key, Object value) {
- sessionParams.put(key, value);
-
- }
-
- @Override
- public Object getSessionParam(String key) {
- return sessionParams.get(key);
- }
-
- @Override
- public void createSession() {
-
- }
-
- @Override
- public <T> T findBean(Class<T> clazz) {
- throw new NotImplementedException();
- }
-
- @Override
- public void executeJavascript(String javascript) {
- logger.debug("Executing Javascript:\n\n-------------\n\n" + javascript + "\n\n-------------\n\n");
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/ExportBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/ExportBeanTest.java
deleted file mode 100644
index db4028633373275dfce531d2a0f4214f70e132a1..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/ExportBeanTest.java
+++ /dev/null
@@ -1,256 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.primefaces.model.DualListModel;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.utils.data.ExportColumn;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-
-public class ExportBeanTest extends WebTestFunctions {
- static Logger logger = Logger.getLogger(ExportBeanTest.class);
-
- private ExportBean exportBean;
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- exportBean = getExportBean();
-
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetSpeciesTypeMap() {
- try {
- Map<String, Class<?>> types = exportBean.getSpeciesTypeMap();
- assertNotNull(types);
- assertTrue(types.keySet().size() > 10);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSpeciesTypeList() {
- try {
- List<String> types = exportBean.getSpeciesTypeList();
- assertNotNull(types);
- assertTrue(types.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSpeciesColumnList() {
- try {
- List<String> types = exportBean.getSpeciesColumnList();
- assertNotNull(types);
- assertTrue(types.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNetworkFileTypeList() {
- try {
- List<String> types = exportBean.getNetworkFileTypeList();
- assertNotNull(types);
- assertTrue(types.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModels() {
- try {
- List<String> types = exportBean.getModels();
- assertNotNull(types);
- assertTrue(types.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetImageGenerators() {
- try {
- List<?> types = exportBean.getImageGenerators();
- assertNotNull(types);
- assertTrue(types.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetImageExportMenu() {
- try {
- Object obj = exportBean.getImageExportMenu();
- assertNotNull(obj);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNetworkAvailableMiriam() throws Exception {
- Project project = null;
- try {
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- Model model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
- model.setTileSize(256);
- project.addModel(model);
- modelDao.add(model);
-
- getMapBean().setCurrentMapId(projectId);
- DualListModel<Pair<MiriamType, String>> obj = exportBean.getNetworkAvailableMiriam();
- assertNotNull(obj);
- assertTrue(obj.getSource().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- if (project != null) {
- projectService.removeProject(project, null, false, adminToken);
- }
-
- }
- }
-
- @Test
- public void testGetElementAvailableMiriam() throws Exception {
- Project project = null;
- try {
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- Model model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
- model.setTileSize(256);
- project.addModel(model);
- modelDao.add(model);
-
- getMapBean().setCurrentMapId(projectId);
- DualListModel<Pair<MiriamType, String>> obj = exportBean.getElementAvailableMiriam();
- assertNotNull(obj);
- assertTrue(obj.getSource().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- if (project != null) {
- projectService.removeProject(project, null, false, adminToken);
- }
-
- }
- }
-
- @Test
- public void testGetComponentList() {
- try {
- DualListModel<String> obj = exportBean.getNetworkExcludedComponent();
- assertNotNull(obj);
- obj = exportBean.getNetworkIncludedComponent();
- assertNotNull(obj);
- obj = exportBean.getElementExcludedComponent();
- assertNotNull(obj);
- obj = exportBean.getElementIncludedComponent();
- assertNotNull(obj);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSpeciesColumnMap() {
- try {
- Map<String, ExportColumn> types = exportBean.getSpeciesColumnMap();
- assertNotNull(types);
- assertTrue(types.keySet().size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNetworkFileTypeMap() {
- try {
- Map<String, ExportFileType> types = exportBean.getNetworkFileTypeMap();
- assertNotNull(types);
- assertTrue(types.keySet().size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(exportBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDesearializationIdList() {
- try {
- List<Integer> list = exportBean.deserializeIdList("[\"123\",\"346\"]");
- assertNotNull(list);
- assertEquals(2, list.size());
- assertEquals((Integer) 123, list.get(0));
- assertEquals((Integer) 346, list.get(1));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/FeedbackBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/FeedbackBeanTest.java
deleted file mode 100644
index e4bee4e7561ff82c9ea5953344071ce66f75dc84..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/FeedbackBeanTest.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class FeedbackBeanTest extends WebTestFunctions {
-
- FeedbackBean feedbackBean;
-
- @Before
- public void setUp() throws Exception {
- feedbackBean = getFeedbackBean();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(feedbackBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
deleted file mode 100644
index 21b132558e623e4bf1a8e8468fa9fdb3ad4aeee9..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.SecurityException;
-
-public class GalaxyBeanTest extends WebTestFunctions {
-
- GalaxyBean galaxyBean;
-
- @Before
- public void setUp() throws Exception {
- galaxyBean = new GalaxyBean();
- galaxyBean.setLayoutService(layoutService);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- @Ignore
- public void test() throws SecurityException {
- galaxyBean.createLayout("CC75308E16F6AA9C", "NAME\tVALUE\nSNCA\t1\nPINK1\t-1\n",
- (Model) modelService.getLastModelByProjectId("pdmap", adminToken), userService.getUserByLogin("galaxy"));
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(galaxyBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/LayoutBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/LayoutBeanTest.java
deleted file mode 100644
index d6295ff11d0abc3dbb42f1a13ede34cbee078f7b..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/LayoutBeanTest.java
+++ /dev/null
@@ -1,230 +0,0 @@
-package lcsb.mapviewer.bean;
-
-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 java.io.File;
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-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;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.LayoutStatus;
-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;
-
-public class LayoutBeanTest extends WebTestFunctions {
- Logger logger = Logger.getLogger(LayoutBeanTest.class);
-
- LayoutBean layoutBean;
-
- UserBean userBean;
-
- ProjectBean projectBean;
-
- MapBean mapBean;
-
- @Autowired
- LayoutDao layoutDao;
-
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- // we use custom threads because in layoutservice there is commit somewhere
- // called, and because of that hibernate session injected by spring cannot
- // commit at the end of the test case
- dbUtils.createSessionForCurrentThread();
-
- userBean = getUserBean();
- layoutBean = getLayoutBean();
- projectBean = getProjectBean();
- mapBean = getMapBean();
-
- createUser();
-
- Project p = projectService.getProjectByProjectId(projectId, adminToken);
- if (p != null) {
- projectService.removeProject(p, null, false, adminToken);
- }
-
- }
-
- @After
- public void tearDown() throws Exception {
- userDao.delete(user);
-
- Project p = projectService.getProjectByProjectId(projectId, adminToken);
- if (p != null) {
- projectService.removeProject(p, null, false, adminToken);
- }
-
- // close session
- dbUtils.closeSessionForCurrentThread();
-
- }
-
- @Ignore
- @Test(timeout = 15000)
- public void testAddLayout() throws Exception {
- Project project = new Project();
- try {
- dbUtils.setAutoFlush(true);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename("testFiles/sample.xml"));
- model.setTileSize(256);
-
- project.setProjectId(projectId);
- project.addModel(model);
-
- projectDao.add(project);
- projectDao.flush();
- projectDao.commit();
- projectDao.refresh(project);
- model = project.getModels().iterator().next().getModel();
-
- projectBean.refreshProjectList(null);
-
- layoutBean.setLayoutFile(new File("testFiles/layout.txt"));
-
- // set current map
- getUserBean().setAuthenticationToken(adminToken);
- mapBean.setCurrentMapId(project.getProjectId());
- getMapBean().setCurrentMapId(project.getProjectId());
-
- User guest = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
- // add user a privilege for viewing layouts
- BasicPrivilege privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, guest);
- userService.setUserPrivilege(guest, privilege);
- userDao.flush();
-
- // generate new layout
- layoutBean.addAnonymousLayout(projectService.getProjectViewById(project.getId(), token));
-
- // wait until layout is generated
- Integer id = modelDao.getById(model.getId()).getLayouts().get(0).getId();
- Layout l = layoutDao.getById(id);
- do {
- Thread.sleep(200);
- layoutDao.refresh(l);
- logger.debug(l.getStatus());
- } while (l.getStatus().equals(LayoutStatus.NA) || l.getStatus().equals(LayoutStatus.GENERATING));
-
- ProjectView projectView = projectBean.getProjects().get(projectBean.getProjects().size() - 1);
-
- assertEquals(1, projectView.getLayouts().size());
- assertTrue(projectView.getLayouts().get(0).getCreator().isEmpty());
-
- assertEquals(0, layoutBean.getCustomLayouts().size());
- assertEquals(1, layoutBean.getGeneralLayouts().size());
- assertEquals(1, mapBean.getTopModelMapData().getMapConfig().getLayouts().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Ignore
- @Test(timeout = 15000)
- public void testAddLayoutForUser() throws Exception {
- Project project = new Project();
- try {
- dbUtils.setAutoFlush(true);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename("testFiles/sample.xml"));
- model.setTileSize(256);
-
- project.setProjectId(projectId);
- project.addModel(model);
-
- projectDao.add(project);
- projectDao.flush();
- projectDao.commit();
-
- projectBean.refreshProjectList(null);
-
- getUserBean().setAuthenticationToken(adminToken);
- getMapBean().setCurrentMapId(projectId);
- layoutBean.setLayoutFile(new File("testFiles/layout.txt"));
-
- // set current map
- mapBean.setCurrentMapId(project.getProjectId());
- getMapBean().setCurrentMapId(project.getProjectId());
-
- // add user a privilege for adding layouts
- userBean.setLoggedUser(user);
- BasicPrivilege privilege = new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user);
- userService.setUserPrivilege(user, privilege);
-
- // add user a privilege for viewing layouts
- privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user);
- userService.setUserPrivilege(user, privilege);
- userDao.flush();
- userDao.commit();
-
- layoutBean.addLayout(null);
-
- // wait until layout is generated
- Integer id = Integer.valueOf(layoutService.getCustomLayouts(model, user, true, user).get(0).getIdObject());
- Layout l = layoutDao.getById(id);
- do {
- Thread.sleep(200);
- layoutDao.refresh(l);
- } while (l.getStatus().equals(LayoutStatus.NA) || l.getStatus().equals(LayoutStatus.GENERATING));
-
- ProjectView projectView = null;
- for (ProjectView view : projectBean.getProjects()) {
- if (view.getIdObject().equals(project.getId())) {
- projectView = view;
- }
- }
-
- assertNotNull(projectView);
- // check if layout appears on project list
- assertEquals(1, projectView.getLayouts().size());
- assertFalse(projectView.getLayouts().get(0).getCreator().isEmpty());
-
- // check if layout appears on layout list in current model (mapBean)
-
- assertEquals(1, layoutBean.getCustomLayouts().size());
- assertEquals(0, layoutBean.getGeneralLayouts().size());
- assertEquals(1, mapBean.getTopModelMapData().getMapConfig().getCustomLayouts().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test(timeout = 5000)
- public void testSearialization() {
- try {
- SerializationUtils.serialize(layoutBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/MapBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/MapBeanTest.java
deleted file mode 100644
index c2685289b27ee6c78c7feee9256a7bf62e9750e4..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/MapBeanTest.java
+++ /dev/null
@@ -1,102 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-
-import java.io.Serializable;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-
-public class MapBeanTest extends WebTestFunctions {
-
- MapBean bean;
- UserBean userBean;
- ProjectBean projectBean;
-
- Project project;
-
- @Before
- public void setUp() throws Exception {
- projectBean = getProjectBean();
-
- userBean = getUserBean();
- user = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
- userBean.setLoggedUser(user);
-
- bean = getMapBean();
-
- bean.setCurrentMapId(configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP));
-
- project = new Project();
- project.setProjectId("Some_id");
- projectDao.add(project);
-
- Model model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
- project.addModel(model);
- modelDao.add(model);
-
- userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
- }
-
- @After
- public void tearDown() throws Exception {
- projectDao.delete(project);
- }
-
- @Test
- public void testVetoSelectedMap() {
- String oldVal = bean.getCurrentMapId();
- bean.setCurrentMapId("test bla bl");
- assertEquals(oldVal, bean.getCurrentMapId());
- }
-
- @Test
- @Ignore("Not valid anymore")
- public void testVetoSelectedMap2() {
- String oldVal = bean.getCurrentMapId();
- bean.setCurrentMapId(project.getProjectId());
- assertFalse(oldVal.equals(bean.getCurrentMapId()));
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(bean);
- SerializationUtils.serialize(bean.getTopModelMapData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDeserializationOfIds() {
- try {
- String str = "[[863,\"58998\"],[863,\"59000\"],[863,\"59001\"],[863,\"59003\"],[863,\"59006\"],[863,\"59008\"],[863,\"59010\"],[863,\"59011\"]]";
- List<Pair<Integer, Integer>> list = bean.deserializeJsonIds(str);
- assertEquals(8, list.size());
- assertEquals((Integer) 863, list.get(0).getLeft());
- assertEquals((Integer) 58998, list.get(0).getRight());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/MiriamBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/MiriamBeanTest.java
deleted file mode 100644
index 94e9728587e94f6b6bfbbf0b06481495da116b8e..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/MiriamBeanTest.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MiriamBeanTest extends WebTestFunctions {
- MiriamBean miriamBean;
-
- @Before
- public void setUp() throws Exception {
- miriamBean = getMiriamBean();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(miriamBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/MissingConnectionBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/MissingConnectionBeanTest.java
deleted file mode 100644
index 66ed01892862d689757e9668ea6f1d3190f183e0..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/MissingConnectionBeanTest.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MissingConnectionBeanTest extends WebTestFunctions {
- MissingConnectionBean missingConnectionBean;
-
- @Before
- public void setUp() throws Exception {
- missingConnectionBean = getMissingConnectionBean();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(missingConnectionBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/ProjectBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/ProjectBeanTest.java
deleted file mode 100644
index a958e652b7f813edd0818bc301af495432aca200..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/ProjectBeanTest.java
+++ /dev/null
@@ -1,194 +0,0 @@
-package lcsb.mapviewer.bean;
-
-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 java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.primefaces.event.FileUploadEvent;
-import org.primefaces.model.UploadedFile;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectStatus;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.services.view.ProjectView;
-import lcsb.mapviewer.services.view.ProjectViewFactory;
-
-public class ProjectBeanTest extends WebTestFunctions {
- Logger logger = Logger.getLogger(ProjectBeanTest.class);
-
- ProjectBean projectBean;
- UserBean userBean;
-
- String defaultMap;
-
- String projectId = "Some_id";
-
- @Autowired
- ProjectViewFactory projectViewFactory;
-
- @Before
- public void setUp() throws Exception {
- dbUtils.setAutoFlush(true);
-
- // we use custom threads because in layoutservice there is commit somewhere
- // called, and because of that hibernate session injected by spring cannot
- // commit at the end of the test case
- dbUtils.createSessionForCurrentThread();
-
- defaultMap = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
-
- projectBean = getProjectBean();
- userBean = getUserBean();
- }
-
- @After
- public void tearDown() throws Exception {
- configurationService.setConfigurationValue(ConfigurationElementType.DEFAULT_MAP, defaultMap);
-
- Project p = projectService.getProjectByProjectId(projectId, adminToken);
- if (p != null) {
- projectService.removeProject(p, null, false, adminToken);
- }
- // close session
- dbUtils.closeSessionForCurrentThread();
-
- // close session
- dbUtils.closeSessionForCurrentThread();
- }
-
- @Test
- public void testOnRemoveCheck() throws Exception {
- try {
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- projectDao.commit();
-
- configurationService.setConfigurationValue(ConfigurationElementType.DEFAULT_MAP, projectId);
-
- ProjectView row = projectService.getProjectViewByProjectId(projectId, adminToken);
-
- getUserBean().setAuthenticationToken(adminToken);
- projectBean.setSelectedProject(row);
- projectBean.removeSelectedProject(null);
-
- assertNotNull(projectService.getProjectViewByProjectId(projectId, adminToken));
-
- configurationService.setConfigurationValue(ConfigurationElementType.DEFAULT_MAP, "test bla");
-
- projectBean.removeSelectedProject(null);
-
- ProjectView pv = projectService.getProjectViewByProjectId(projectId, adminToken);
- if (pv != null && pv.getIdObject() != null) {
- assertEquals(ProjectStatus.REMOVING.toString(), pv.getStatus());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testOnChangeCheck() throws Exception {
- try {
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- configurationService.setConfigurationValue(ConfigurationElementType.DEFAULT_MAP, projectId);
-
- ProjectView row = projectService.getProjectViewByProjectId(projectId, adminToken);
-
- userBean.setAuthenticationToken(adminToken);
- projectBean.setSelectedProject(row);
-
- ProjectView row2 = new ProjectView(row);
-
- row2.setProjectId("shdfsjkfhsd");
-
- // this set should be rollback (we cannot change the name of default
- // project)
- projectBean.setSelectedProject(row2);
-
- assertEquals(row, projectBean.getSelectedProject());
-
- row2 = projectViewFactory.create(null);
- row2.setProjectId(projectId);
-
- // this set should be rollback (we cannot create a new project with the
- // name that already exists in a system)
- projectBean.setSelectedProject(row2);
-
- assertEquals(row, projectBean.getSelectedProject());
-
- row2.setProjectId(projectId + "haha");
-
- // this set shouldn't be rollback
- projectBean.setSelectedProject(row2);
-
- assertEquals(row2, projectBean.getSelectedProject());
-
- projectDao.delete(project);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testOnUploadCheck() throws Exception {
- try {
- File file = new File("testFiles/complex_model.zip");
- InputStream inputStream = new FileInputStream(file);
- FileUploadEvent event = Mockito.mock(FileUploadEvent.class);
- UploadedFile uploadedFile = Mockito.mock(UploadedFile.class);
- Mockito.when(uploadedFile.getFileName()).thenReturn(file.getName());
- Mockito.when(uploadedFile.getContentType()).thenReturn("application/octet-stream");
- Mockito.when(uploadedFile.getInputstream()).thenReturn(inputStream);
- Mockito.when(event.getFile()).thenReturn(uploadedFile);
-
- projectBean.handleFileUpload(event);
- assertNotNull(projectBean.getMapFile());
- assertTrue(projectBean.getComplexModel().equalsIgnoreCase("true"));
- assertEquals(5, projectBean.getModelZipEntries().size());
- ZipEntryFile zef = projectBean.getModelZipEntries().get(0);
- assertTrue(zef instanceof ModelZipEntryFile);
- assertFalse(((ModelZipEntryFile) zef).getName().contains("xml"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- *
- * @throws Exception
- */
- @Test
- public void testSearialization() throws Exception {
- try {
- SerializationUtils.serialize(projectBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/ReferenceGenomeBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/ReferenceGenomeBeanTest.java
deleted file mode 100644
index 3a5bebbae9883e768cae02d2c36d484f9911b549..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/ReferenceGenomeBeanTest.java
+++ /dev/null
@@ -1,55 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.persist.DbUtils;
-
-public class ReferenceGenomeBeanTest extends WebTestFunctions {
- Logger logger = Logger.getLogger(ReferenceGenomeBeanTest.class);
-
- ReferenceGenomeBean referenceGenomeBean;
-
- @Autowired
- DbUtils dbUtils;
-
- @Before
- public void setUp() throws Exception {
- referenceGenomeBean = super.getReferenceGenomeBean();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSetOrganism() {
- try {
- referenceGenomeBean.setSelectedOrganism(TaxonomyBackend.HUMAN_TAXONOMY);
- assertNotNull(referenceGenomeBean.getSelectedUrl());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetPrivilege() {
- try {
- Boolean result = referenceGenomeBean.getUserHasManageGenomesPrivilege();
- assertNotNull(result);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/SearchBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/SearchBeanTest.java
deleted file mode 100644
index 7e77496e30603c2cad13084dfeedf0c47ed51159..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/SearchBeanTest.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SearchBeanTest extends WebTestFunctions {
-
- SearchBean searchBean;
-
- @Before
- public void setUp() throws Exception {
- searchBean = getSearchBean();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(searchBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/UserBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/UserBeanTest.java
deleted file mode 100644
index cecf9f8facf6f145a4e2be75cacaeb0eed1c82ed..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/UserBeanTest.java
+++ /dev/null
@@ -1,84 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import static org.junit.Assert.assertFalse;
-
-import java.io.ByteArrayOutputStream;
-import java.io.ObjectOutputStream;
-import java.io.Serializable;
-
-import lcsb.mapviewer.model.user.User;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class UserBeanTest extends WebTestFunctions {
- static Logger logger = Logger.getLogger(UserBeanTest.class);
-
- UserBean bean;
-
- @Before
- public void setUp() throws Exception {
- bean = new UserBean();
- bean.setUserService(userService);
- bean.setConfigurationService(configurationService);
- bean.setLogService(logService);
- bean.init();
- createUser();
- }
-
- @After
- public void tearDown() throws Exception {
- userService.deleteUser(user);
- }
-
- @Test
- public void test() {
-
- bean.setLoggedUser(user);
- User user = bean.getLoggedUser();
- bean.setLogin("Test");
- User user2 = bean.getLoggedUser();
-
- assertFalse(user.equals(user2));
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() throws Exception {
- try {
-
- SerializationUtils.serialize(bean);
-
- ByteArrayOutputStream byteOutputStream = new ByteArrayOutputStream();
- ObjectOutputStream objectOutputStream = new ObjectOutputStream(byteOutputStream);
- objectOutputStream.writeObject(bean);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearialization2() throws Exception {
- try {
- ByteArrayOutputStream byteOutputStream = new ByteArrayOutputStream();
- ObjectOutputStream objectOutputStream = new ObjectOutputStream(byteOutputStream);
- objectOutputStream.writeObject(bean);
- objectOutputStream.flush();
- objectOutputStream.close();
-
- logger.debug(byteOutputStream.toByteArray().length);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/UsersBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/UsersBeanTest.java
deleted file mode 100644
index 56f548d896bb1bca9877b5ca6514eb42f70028ab..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/UsersBeanTest.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.Serializable;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class UsersBeanTest extends WebTestFunctions {
- UsersBean usersBean;
-
- @Before
- public void setUp() throws Exception {
- usersBean = getUsersBean();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(usersBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java b/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
deleted file mode 100644
index af6b07728d1bdf9579c96fd73c5bb37ed04109a4..0000000000000000000000000000000000000000
--- a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
+++ /dev/null
@@ -1,718 +0,0 @@
-package lcsb.mapviewer.bean;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.annotation.services.ChEMBLParser;
-import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.ConfigurationDao;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
-import lcsb.mapviewer.persist.dao.graphics.PolylineDao;
-import lcsb.mapviewer.persist.dao.log.LogDao;
-import lcsb.mapviewer.persist.dao.map.CommentDao;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.persist.dao.map.ReactionDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
-import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
-import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.interfaces.ICommentService;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IDataMiningService;
-import lcsb.mapviewer.services.interfaces.IExporterService;
-import lcsb.mapviewer.services.interfaces.IExternalServicesService;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.ILogService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
-import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
-import lcsb.mapviewer.services.search.db.drug.IDrugService;
-import lcsb.mapviewer.services.view.ModelViewFactory;
-
-@Transactional(value = "txManager")
-@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/applicationContext-annotation.xml", //
- "/applicationContext-service.xml", //
- "/dataSource.xml", //
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class WebTestFunctions {
- private Logger logger = Logger.getLogger(WebTestFunctions.class);
-
- @Autowired
- protected ChEMBLParser chemblParser;
-
- @Autowired
- protected DrugbankHTMLParser drugBankHTMLParser;
-
- @Autowired
- protected ModelAnnotator modelAnnotator;
-
- @Autowired
- protected BiocompendiumAnnotator restService;
-
- public double EPSILON = 1e-6;
-
- @Autowired
- protected IConfigurationService configurationService;
-
- @Autowired
- protected IModelService modelService;
-
- @Autowired
- protected IExternalServicesService externalServicesService;
-
- @Autowired
- protected ILayoutService layoutService;
-
- @Autowired
- protected ILogService logService;
-
- @Autowired
- protected IExporterService exportService;
-
- @Autowired
- protected LogDao logDao;
-
- @Autowired
- protected SearchHistoryDao searchHistoryDao;
-
- @Autowired
- protected PasswordEncoder passwordEncoder;
-
- @Autowired
- protected IUserService userService;
-
- @Autowired
- protected ConfigurationDao configurationDao;
-
- @Autowired
- protected IDataMiningService dataMiningService;
-
- @Autowired
- protected ISearchService searchService;
-
- @Autowired
- protected IDrugService drugService;
-
- @Autowired
- protected IChemicalService chemicalService;
-
- @Autowired
- protected IProjectService projectService;
-
- @Autowired
- protected ProjectDao projectDao;
-
- @Autowired
- protected CacheQueryDao cacheQueryDao;
-
- @Autowired
- protected PolylineDao polylineDao;
-
- @Autowired
- protected ModelDao modelDao;
-
- @Autowired
- protected ICommentService commentService;
-
- @Autowired
- protected UserDao userDao;
-
- @Autowired
- protected PrivilegeDao privilegeDao;
-
- @Autowired
- protected CommentDao commentDao;
-
- @Autowired
- protected DbUtils dbUtils;
-
- @Autowired
- protected ReactionDao reactionDao;
-
- @Autowired
- protected ElementDao aliasDao;
-
- @Autowired
- protected ModelViewFactory modelViewFactory;
-
- @Autowired
- protected IReferenceGenomeService referenceGenomeService;
-
- protected User user;
-
- private ConfigurationBean configurationBean;
- private LayoutBean layoutBean;
- private MapBean mapBean;
- private ProjectBean projectBean;
- private UserBean userBean;
-
- private ExportBean exportBean;
-
- private FeedbackBean feedbackBean;
- private MiriamBean miriamBean;
- private MissingConnectionBean missingConnectionBean;
- private SearchBean searchBean;
- private UsersBean usersBean;
-
- private ReferenceGenomeBean referenceGenomeBean;
-
- protected CustomPrimefacesUtils primefacesUtils = new CustomPrimefacesUtils();
-
- String token;
-
- String adminToken;
-
- @Before
- public void generalSetUp() {
- dbUtils.setAutoFlush(false);
- createConfigurationBean();
- createLayoutBean();
- createMapBean();
- createProjectBean();
- createUserBean();
- createExportBean();
- createFeedbackBean();
- createMiriamBean();
- createMissingConnectionBean();
- createSearchBean();
- createUsersBean();
- createReferenceGenomeBean();
-
- configurationBean.internalInit();
- layoutBean.internalInit();
- mapBean.internalInit();
- projectBean.internalInit();
- userBean.internalInit();
-
- exportBean.internalInit();
-
- feedbackBean.internalInit();
- miriamBean.internalInit();
- missingConnectionBean.internalInit();
- searchBean.internalInit();
- usersBean.internalInit();
-
- referenceGenomeBean.internalInit();
-
- token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
-
- // assume that we have admin account with all the privileges
- adminToken = userService.login("admin", "admin");
-
- }
-
- @After
- public void generatTearDown() throws IOException {
- File f = new File("map_images");
- if (f.exists()) {
- logger.info("Removing output test directory: " + f.getAbsolutePath());
- FileUtils.deleteDirectory(f);
- }
-
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- /**
- * This method remove model with all connections from db (used only when the db
- * must be handled manually)
- *
- * @param id
- */
- protected void removeModelById(int id) {
- modelDao.delete(modelDao.getById(id));
- }
-
- protected void createUser() {
- user = userDao.getUserByLogin("john.doe");
- if (user == null) {
- user = new User();
- user.setName("John");
- user.setSurname("Doe");
- user.setEmail("john.doe@uni.lu");
- user.setLogin("john.doe");
- user.setCryptedPassword(passwordEncoder.encode("passwd"));
- userDao.add(user);
- }
- }
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- }
- Model result = WebTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- WebTestFunctions.models.put(fileName, result);
- }
- return result;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-
- protected UserBean getUserBean() {
- if (userBean == null) {
- createUserBean();
- }
- return userBean;
- }
-
- protected LayoutBean getLayoutBean() {
- if (layoutBean == null) {
- createLayoutBean();
- }
- return layoutBean;
- }
-
- private void createUserBean() {
- if (userBean != null) {
- return;
- }
- userBean = new UserBean();
- userBean.setPrimefacesUtils(primefacesUtils);
-
- userBean.setUserService(userService);
- userBean.setConfigurationService(configurationService);
- userBean.setLogService(logService);
-
- }
-
- private void createLayoutBean() {
- if (layoutBean != null) {
- return;
- }
- layoutBean = new LayoutBean();
- layoutBean.setPrimefacesUtils(primefacesUtils);
-
- layoutBean.setLayoutService(layoutService);
- layoutBean.setModelService(modelService);
- layoutBean.setUserBean(getUserBean());
- layoutBean.setMapBean(getMapBean());
-
- }
-
- protected MapBean getMapBean() {
- if (mapBean == null) {
- createMapBean();
- }
- return mapBean;
- }
-
- private void createMapBean() {
- if (mapBean != null) {
- return;
- }
- mapBean = new MapBean();
- mapBean.setPrimefacesUtils(primefacesUtils);
-
- mapBean.setConfService(configurationService);
- mapBean.setModelService(modelService);
- mapBean.setProjectService(projectService);
- mapBean.setConfigurationService(configurationService);
- mapBean.setModelService(modelService);
- mapBean.setUserService(userService);
- mapBean.setUserBean(getUserBean());
- }
-
- protected ProjectBean getProjectBean() {
- if (projectBean == null) {
- createProjectBean();
- }
- return projectBean;
- }
-
- private void createProjectBean() {
- if (projectBean != null) {
- return;
- }
- projectBean = new ProjectBean();
- projectBean.setPrimefacesUtils(primefacesUtils);
-
- projectBean.setConfigurationService(configurationService);
- projectBean.setModelService(modelService);
- projectBean.setProjectService(projectService);
- projectBean.setUserService(userService);
-
- projectBean.setLayoutBean(getLayoutBean());
- projectBean.setUserBean(getUserBean());
- }
-
- protected ExportBean getExportBean() {
- if (exportBean == null) {
- createExportBean();
- }
- return exportBean;
- }
-
- private void createExportBean() {
- if (exportBean != null) {
- return;
- }
- exportBean = new ExportBean();
- exportBean.setPrimefacesUtils(primefacesUtils);
-
- exportBean.setExporterService(exportService);
- exportBean.setMapBean(getMapBean());
- }
-
- protected ConfigurationBean getConfigurationBean() {
- if (configurationBean == null) {
- createConfigurationBean();
- }
- return configurationBean;
- }
-
- private void createConfigurationBean() {
- if (configurationBean != null) {
- return;
- }
- configurationBean = new ConfigurationBean();
- configurationBean.setPrimefacesUtils(primefacesUtils);
-
- configurationBean.setConfigurationService(configurationService);
- configurationBean.setUserService(userService);
- configurationBean.setProjectService(projectService);
-
- configurationBean.setUserBean(getUserBean());
- }
-
- protected FeedbackBean getFeedbackBean() {
- if (feedbackBean == null) {
- createFeedbackBean();
- }
- return feedbackBean;
- }
-
- protected MiriamBean getMiriamBean() {
- if (miriamBean == null) {
- createMiriamBean();
- }
- return miriamBean;
- }
-
- protected MissingConnectionBean getMissingConnectionBean() {
- if (missingConnectionBean == null) {
- createMissingConnectionBean();
- }
- return missingConnectionBean;
- }
-
- protected SearchBean getSearchBean() {
- if (searchBean == null) {
- createSearchBean();
- }
- return searchBean;
- }
-
- protected UsersBean getUsersBean() {
- if (usersBean == null) {
- createUsersBean();
- }
- return usersBean;
- }
-
- private void createFeedbackBean() {
- if (feedbackBean != null) {
- return;
- }
- feedbackBean = new FeedbackBean();
- feedbackBean.setPrimefacesUtils(primefacesUtils);
-
- feedbackBean.setCommentService(commentService);
- feedbackBean.setUserService(userService);
- feedbackBean.setUserBean(userBean);
-
- feedbackBean.setUserBean(getUserBean());
- feedbackBean.setMapBean(getMapBean());
-
- }
-
- private void createMiriamBean() {
- if (miriamBean != null) {
- return;
- }
- miriamBean = new MiriamBean();
- miriamBean.setPrimefacesUtils(primefacesUtils);
-
- }
-
- private void createMissingConnectionBean() {
- if (missingConnectionBean != null) {
- return;
- }
- missingConnectionBean = new MissingConnectionBean();
- missingConnectionBean.setPrimefacesUtils(primefacesUtils);
- }
-
- private void createSearchBean() {
- if (searchBean != null) {
- return;
- }
- searchBean = new SearchBean();
- searchBean.setPrimefacesUtils(primefacesUtils);
-
- searchBean.setConfigurationService(configurationService);
- searchBean.setUserService(userService);
-
- searchBean.setUserBean(getUserBean());
- searchBean.setMapBean(getMapBean());
- }
-
- private void createUsersBean() {
- if (usersBean != null) {
- return;
- }
- usersBean = new UsersBean();
- usersBean.setPrimefacesUtils(primefacesUtils);
-
- usersBean.setUserService(userService);
-
- usersBean.setUserBean(getUserBean());
- usersBean.setProjectBean(getProjectBean());
- }
-
- public ReferenceGenomeBean getReferenceGenomeBean() {
- if (referenceGenomeBean == null) {
- createReferenceGenomeBean();
- }
- return referenceGenomeBean;
- }
-
- private void createReferenceGenomeBean() {
- if (referenceGenomeBean != null) {
- return;
- }
- referenceGenomeBean = new ReferenceGenomeBean();
- referenceGenomeBean.setPrimefacesUtils(primefacesUtils);
-
- referenceGenomeBean.setReferenceGenomeService(referenceGenomeService);
- referenceGenomeBean.setUserBean(getUserBean());
- referenceGenomeBean.setUserService(userService);
- referenceGenomeBean.setMapBean(getMapBean());
-
- }
-
-}