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minerva
core
Commits
9b9c33ed
Commit
9b9c33ed
authored
Sep 13, 2021
by
Piotr Gawron
Browse files
wildcard imports are prohibited now
parent
21fa9bed
Changes
874
Hide whitespace changes
Inline
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CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
View file @
9b9c33ed
...
...
@@ -3,7 +3,11 @@ package lcsb.mapviewer.cdplugin.copypaste;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
jp.sbi.celldesigner.plugin.*
;
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
lcsb.mapviewer.common.SystemClipboard
;
import
lcsb.mapviewer.common.exception.InvalidXmlSchemaException
;
...
...
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
View file @
9b9c33ed
...
...
@@ -9,7 +9,9 @@ import org.apache.logging.log4j.Logger;
import
lcsb.mapviewer.common.Pair
;
import
lcsb.mapviewer.common.exception.InvalidXmlSchemaException
;
import
lcsb.mapviewer.converter.annotation.XmlAnnotationParser
;
import
lcsb.mapviewer.model.map.*
;
import
lcsb.mapviewer.model.map.MiriamData
;
import
lcsb.mapviewer.model.map.MiriamRelationType
;
import
lcsb.mapviewer.model.map.MiriamType
;
/**
* This abstract class defines common function for {@link CopyAction} and
...
...
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
View file @
9b9c33ed
package
lcsb.mapviewer.cdplugin.copypaste
;
import
java.awt.*
;
import
java.awt.KeyEventDispatcher
;
import
java.awt.KeyboardFocusManager
;
import
java.awt.event.KeyEvent
;
import
org.apache.logging.log4j.LogManager
;
...
...
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
View file @
9b9c33ed
...
...
@@ -5,7 +5,11 @@ import java.util.Set;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
jp.sbi.celldesigner.plugin.*
;
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
lcsb.mapviewer.common.Pair
;
import
lcsb.mapviewer.common.SystemClipboard
;
import
lcsb.mapviewer.converter.annotation.XmlAnnotationParser
;
...
...
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java
View file @
9b9c33ed
package
lcsb.mapviewer.cdplugin.info
;
import
java.awt.*
;
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
java.util.ArrayList
;
import
java.util.List
;
import
javax.swing.*
;
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.LogManager
;
import
org.apache.logging.log4j.Logger
;
...
...
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
View file @
9b9c33ed
package
lcsb.mapviewer.cdplugin.info
;
import
java.awt.*
;
import
java.awt.event.*
;
import
java.awt.KeyEventDispatcher
;
import
java.awt.KeyboardFocusManager
;
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.
*
;
import
javax.swing.
Timer
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
jp.sbi.celldesigner.plugin.*
;
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
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java
View file @
9b9c33ed
...
...
@@ -3,10 +3,15 @@ package lcsb.mapviewer.cdplugin;
import
java.util.List
;
import
org.apache.logging.log4j.core.LogEvent
;
import
org.junit.*
;
import
org.junit.After
;
import
org.junit.Before
;
import
org.junit.Rule
;
import
org.mockito.Mockito
;
import
jp.sbi.celldesigner.plugin.*
;
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
;
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
View file @
9b9c33ed
package
lcsb.mapviewer.cdplugin.copypaste
;
import
static
org
.
junit
.
Assert
.*;
import
static
org
.
junit
.
Assert
.
assertEquals
;
import
static
org
.
junit
.
Assert
.
assertNotNull
;
import
static
org
.
junit
.
Assert
.
assertNull
;
import
java.util.Set
;
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
lcsb.mapviewer.model.map.MiriamData
;
import
lcsb.mapviewer.model.map.MiriamRelationType
;
import
lcsb.mapviewer.model.map.MiriamType
;
public
class
CopyPasteAbstractActionTest
extends
CdPluginFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
View file @
9b9c33ed
...
...
@@ -8,7 +8,10 @@ import static org.mockito.Mockito.times;
import
org.junit.Test
;
import
org.mockito.Mockito
;
import
jp.sbi.celldesigner.plugin.*
;
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
;
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java
View file @
9b9c33ed
...
...
@@ -2,7 +2,9 @@ package lcsb.mapviewer.cdplugin.info;
import
static
org
.
junit
.
Assert
.
assertEquals
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.Arrays
;
import
java.util.List
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java
View file @
9b9c33ed
package
lcsb.mapviewer.annotation.cache
;
import
java.io.*
;
import
java.net.*
;
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.*
;
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.*
;
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
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
View file @
9b9c33ed
package
lcsb.mapviewer.annotation.cache
;
import
java.util.*
;
import
java.util.concurrent.*
;
import
java.util.Calendar
;
import
java.util.Collection
;
import
java.util.LinkedList
;
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
javax.annotation.PostConstruct
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
View file @
9b9c33ed
package
lcsb.mapviewer.annotation.cache
;
import
java.io.*
;
import
java.net.*
;
import
java.util.concurrent.*
;
import
java.io.BufferedReader
;
import
java.io.DataOutputStream
;
import
java.io.FileNotFoundException
;
import
java.io.IOException
;
import
java.io.InputStreamReader
;
import
java.net.HttpURLConnection
;
import
java.net.MalformedURLException
;
import
java.net.URL
;
import
java.util.concurrent.Callable
;
import
java.util.concurrent.ExecutorService
;
import
java.util.concurrent.Executors
;
import
java.util.concurrent.Future
;
import
java.util.concurrent.TimeUnit
;
import
org.apache.commons.io.IOUtils
;
import
org.apache.logging.log4j.LogManager
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
View file @
9b9c33ed
...
...
@@ -2,7 +2,10 @@ package lcsb.mapviewer.annotation.cache;
import
java.io.StringWriter
;
import
javax.xml.bind.*
;
import
javax.xml.bind.JAXBContext
;
import
javax.xml.bind.JAXBException
;
import
javax.xml.bind.Marshaller
;
import
javax.xml.bind.Unmarshaller
;
import
org.apache.commons.lang3.SerializationException
;
import
org.apache.logging.log4j.LogManager
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java
View file @
9b9c33ed
...
...
@@ -9,7 +9,9 @@ import javax.xml.bind.annotation.XmlRootElement;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
uk.ac.ebi.chebi.webapps.chebiWS.model.*
;
import
uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem
;
import
uk.ac.ebi.chebi.webapps.chebiWS.model.Entity
;
import
uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem
;
/**
* This class represents <a href="http://www.ebi.ac.uk/chebi/">chebi</a> object.
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
View file @
9b9c33ed
...
...
@@ -5,7 +5,6 @@ import java.util.ArrayList;
import
java.util.Collection
;
import
java.util.Comparator
;
import
java.util.List
;
import
java.util.Set
;
import
javax.xml.bind.annotation.XmlRootElement
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java
View file @
9b9c33ed
package
lcsb.mapviewer.annotation.data
;
import
java.io.Serializable
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.List
;
import
java.util.Set
;
import
javax.xml.bind.annotation.XmlRootElement
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
View file @
9b9c33ed
...
...
@@ -2,18 +2,31 @@ package lcsb.mapviewer.annotation.services;
import
java.io.IOException
;
import
java.net.URLEncoder
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.Collection
;
import
java.util.HashSet
;
import
java.util.List
;
import
java.util.Set
;
import
org.apache.commons.lang3.SerializationException
;
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
org.w3c.dom.*
;
import
lcsb.mapviewer.annotation.cache.*
;
import
lcsb.mapviewer.annotation.data.*
;
import
lcsb.mapviewer.annotation.services.annotators.*
;
import
org.w3c.dom.Document
;
import
org.w3c.dom.Node
;
import
org.w3c.dom.NodeList
;
import
lcsb.mapviewer.annotation.cache.GeneralCacheInterface
;
import
lcsb.mapviewer.annotation.cache.SourceNotAvailable
;
import
lcsb.mapviewer.annotation.cache.WebPageDownloader
;
import
lcsb.mapviewer.annotation.data.Drug
;
import
lcsb.mapviewer.annotation.data.Target
;
import
lcsb.mapviewer.annotation.data.TargetType
;
import
lcsb.mapviewer.annotation.services.annotators.AnnotatorException
;
import
lcsb.mapviewer.annotation.services.annotators.HgncAnnotator
;
import
lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator
;
import
lcsb.mapviewer.annotation.services.annotators.UniprotSearchException
;
import
lcsb.mapviewer.common.XmlParser
;
import
lcsb.mapviewer.common.exception.InvalidArgumentException
;
import
lcsb.mapviewer.common.exception.InvalidXmlSchemaException
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
View file @
9b9c33ed
package
lcsb.mapviewer.annotation.services
;
import
java.io.IOException
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.Collection
;
import
java.util.Collections
;
import
java.util.HashSet
;
import
java.util.List
;
import
java.util.Set
;
import
org.apache.commons.lang3.StringUtils
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
lcsb.mapviewer.annotation.cache.*
;
import
lcsb.mapviewer.annotation.cache.CachableInterface
;
import
lcsb.mapviewer.annotation.cache.SourceNotAvailable
;
import
lcsb.mapviewer.annotation.cache.XmlSerializer
;
import
lcsb.mapviewer.annotation.data.Drug
;
import
lcsb.mapviewer.annotation.services.annotators.AnnotatorException
;
import
lcsb.mapviewer.annotation.services.annotators.HgncAnnotator
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
View file @
9b9c33ed
package
lcsb.mapviewer.annotation.services
;
import
java.io.IOException
;
import
java.util.*
;
import
java.util.ArrayList
;
import
java.util.HashMap
;
import
java.util.HashSet
;
import
java.util.List
;
import
java.util.Map
;
import
java.util.Set
;
import
org.apache.commons.lang3.SerializationException
;
import
org.apache.http.HttpStatus
;
...
...
@@ -12,7 +17,11 @@ import org.w3c.dom.Node;
import
com.google.gson.Gson
;
import
lcsb.mapviewer.annotation.cache.*
;
import
lcsb.mapviewer.annotation.cache.CachableInterface
;
import
lcsb.mapviewer.annotation.cache.GeneralCacheInterface
;
import
lcsb.mapviewer.annotation.cache.SourceNotAvailable
;
import
lcsb.mapviewer.annotation.cache.WebPageDownloader
;
import
lcsb.mapviewer.annotation.cache.XmlSerializer
;
import
lcsb.mapviewer.annotation.data.MeSH
;
import
lcsb.mapviewer.annotation.services.annotators.AnnotatorException
;
import
lcsb.mapviewer.common.exception.InvalidArgumentException
;
...
...
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