Commit 79e4b9f3 authored by Sascha Herzinger's avatar Sascha Herzinger
Browse files

formatted imports

parent 0d538d77
Pipeline #12060 passed with stage
in 11 minutes and 10 seconds
package lcsb.mapviewer.cdplugin.copypaste;
import org.apache.logging.log4j.*;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginReaction;
import jp.sbi.celldesigner.plugin.PluginSBase;
import jp.sbi.celldesigner.plugin.PluginSpecies;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import jp.sbi.celldesigner.plugin.*;
import lcsb.mapviewer.common.SystemClipboard;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
/**
* CD Plugin action responsible for translating annotation stored in notes to xml
......
package lcsb.mapviewer.cdplugin.copypaste;
import java.util.HashSet;
import java.util.Set;
import org.apache.logging.log4j.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.util.HashSet;
import java.util.Set;
/**
* This abstract class defines common function for {@link CopyAction} and
......
package lcsb.mapviewer.cdplugin.copypaste;
import java.awt.KeyEventDispatcher;
import java.awt.KeyboardFocusManager;
import java.awt.event.KeyEvent;
import org.apache.logging.log4j.*;
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
import jp.sbi.celldesigner.plugin.PluginSBase;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.awt.*;
import java.awt.event.KeyEvent;
/**
* This class represent a plugin to cell designer with copy past functionality
......
package lcsb.mapviewer.cdplugin.copypaste;
import java.awt.event.ActionEvent;
import org.apache.logging.log4j.*;
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.PluginAction;
import jp.sbi.celldesigner.plugin.PluginListOf;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.awt.event.ActionEvent;
/**
* This class represent action that copy species/reaction annotations and notes
......
package lcsb.mapviewer.cdplugin.copypaste;
import java.util.Set;
import org.apache.logging.log4j.*;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginReaction;
import jp.sbi.celldesigner.plugin.PluginSBase;
import jp.sbi.celldesigner.plugin.PluginSpecies;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import jp.sbi.celldesigner.plugin.*;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.SystemClipboard;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.MiriamData;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.util.Set;
/**
* CD Plugin action responsible for translating annotation stored in notes to
......
package lcsb.mapviewer.cdplugin.copypaste;
import java.awt.event.ActionEvent;
import org.apache.logging.log4j.*;
import jp.sbi.celldesigner.MainWindow;
import jp.sbi.celldesigner.plugin.PluginAction;
import jp.sbi.celldesigner.plugin.PluginListOf;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.awt.event.ActionEvent;
/**
* This class represent action that paste annotations and notes from clipboard
......
package lcsb.mapviewer.cdplugin.info;
import java.awt.Component;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.Toolkit;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import javax.swing.*;
import java.awt.*;
import java.util.ArrayList;
import java.util.List;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import org.apache.logging.log4j.*;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
/**
* This class represent a frame that visualize MIRIAM data and notes for a
* species. Only one instance of JFrame is stored in the class (only one window
......
package lcsb.mapviewer.cdplugin.info;
import java.awt.KeyEventDispatcher;
import java.awt.KeyboardFocusManager;
import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginSBase;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.List;
import javax.swing.Timer;
import org.apache.logging.log4j.*;
import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginSBase;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
/**
* This class represent a plugin to CellDesigner that add info text box with
* informations about species. Plugin run in pooling mode (there is no other way
......
package lcsb.mapviewer.cdplugin;
import lcsb.mapviewer.cdplugin.copypaste.AllCopyPasteTests;
import lcsb.mapviewer.cdplugin.info.AllInfoTests;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.cdplugin.copypaste.AllCopyPasteTests;
import lcsb.mapviewer.cdplugin.info.AllInfoTests;
@RunWith(Suite.class)
@SuiteClasses({AllCopyPasteTests.class,
AllInfoTests.class})
......
package lcsb.mapviewer.cdplugin;
import java.util.List;
import org.apache.logging.log4j.core.LogEvent;
import org.junit.*;
import org.mockito.Mockito;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginReaction;
import jp.sbi.celldesigner.plugin.PluginSpecies;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.common.UnitTestFailedWatcher;
import org.apache.logging.log4j.core.LogEvent;
import org.junit.After;
import org.junit.Before;
import org.junit.Rule;
import org.mockito.Mockito;
import java.util.List;
public class CdPluginFunctions {
......
package lcsb.mapviewer.cdplugin.copypaste;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import org.apache.logging.log4j.*;
import org.junit.Test;
import org.mockito.Mockito;
import jp.sbi.celldesigner.plugin.PluginListOf;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import lcsb.mapviewer.common.SystemClipboard;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Test;
import org.mockito.Mockito;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
public class CopyActionTest extends CdPluginFunctions {
Logger logger = LogManager.getLogger(CopyActionTest.class);
......
package lcsb.mapviewer.cdplugin.copypaste;
import static org.junit.Assert.*;
import java.util.Set;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.*;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.*;
import java.util.Set;
import static org.junit.Assert.*;
public class CopyPasteAbstractActionTest extends CdPluginFunctions {
Logger logger = LogManager.getLogger(CopyPasteAbstractActionTest.class);
......
package lcsb.mapviewer.cdplugin.copypaste;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.mockito.Mockito.when;
import java.awt.event.KeyEvent;
import org.junit.Test;
import org.mockito.Mockito;
import jp.sbi.celldesigner.plugin.PluginListOf;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import lcsb.mapviewer.common.SystemClipboard;
import org.junit.Test;
import org.mockito.Mockito;
import java.awt.event.KeyEvent;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.mockito.Mockito.when;
public class CopyPastePluginTest extends CdPluginFunctions {
......
package lcsb.mapviewer.cdplugin.copypaste;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.atLeast;
import static org.mockito.Mockito.times;
import org.junit.Test;
import org.mockito.Mockito;
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginReaction;
import jp.sbi.celldesigner.plugin.PluginSpecies;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import lcsb.mapviewer.common.SystemClipboard;
import org.junit.Test;
import org.mockito.Mockito;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.atLeast;
import static org.mockito.Mockito.times;
public class PasteActionTest extends CdPluginFunctions {
......
package lcsb.mapviewer.cdplugin.info;
import static org.junit.Assert.assertEquals;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.logging.log4j.*;
import org.junit.Test;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import static org.junit.Assert.assertEquals;
public class InfoFrameTest extends CdPluginFunctions {
Logger logger = LogManager.getLogger(InfoFrameTest.class);
......
package lcsb.mapviewer.cdplugin.info;
import static org.junit.Assert.assertEquals;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Test;
import java.util.Arrays;
import java.util.List;
import org.apache.logging.log4j.*;
import org.junit.Test;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import static org.junit.Assert.assertEquals;
public class InfoPluginTest extends CdPluginFunctions {
......
package lcsb.mapviewer.annotation.cache;
import java.util.HashMap;
import java.util.Map;
import org.apache.logging.log4j.*;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.cache.CacheType;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.springframework.stereotype.Service;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.cache.CacheType;
import java.util.HashMap;
import java.util.Map;
/**
* Implementation of cache that stores everything in application memory. Data is
......
package lcsb.mapviewer.annotation.cache;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.net.HttpURLConnection;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.util.Calendar;
import java.util.List;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.ScheduledThreadPoolExecutor;
import java.util.concurrent.ThreadFactory;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.output.CountingOutputStream;
import org.apache.commons.net.ftp.FTP;
import org.apache.commons.net.ftp.FTPClient;
import org.apache.commons.net.ftp.FTPFile;
import org.apache.commons.net.ftp.FTPReply;
import org.apache.logging.log4j.*;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.exception.InvalidStateException;
......@@ -38,8 +8,27 @@ import lcsb.mapviewer.model.user.ConfigurationElementType;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.ConfigurationDao;
import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.output.CountingOutputStream;
import org.apache.commons.net.ftp.FTP;
import org.apache.commons.net.ftp.FTPClient;
import org.apache.commons.net.ftp.FTPFile;
import org.apache.commons.net.ftp.FTPReply;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.util.Calendar;
import java.util.List;
import java.util.concurrent.*;
/**
* Interface for accessing and storing big files. They are stored in local file
* system.
......
package lcsb.mapviewer.annotation.cache;
import java.io.IOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
import java.io.IOException;
/**
* Interface used for retrieving data that are no longer valid in the cache
......
package lcsb.mapviewer.annotation.cache;
import org.apache.logging.log4j.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.cache.CacheType;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.cache.CacheType;
/**
* Cache used by the application. It contains two sub-classes responsible for
* application level cache (for single run of the application) and database
......
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