diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java index 98dcfa9c7778ac3ccf5ef4d4f264d8ba2861c452..f426805aebbb074372adb584168f929bc3cc8e2e 100644 --- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java +++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java @@ -2,9 +2,7 @@ package lcsb.mapviewer.cdplugin; import java.util.List; -import org.apache.logging.log4j.*; import org.apache.logging.log4j.core.LogEvent; - import org.junit.After; import org.junit.Before; import org.mockito.Mockito; @@ -13,7 +11,6 @@ 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; public class CdPluginFunctions { diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java index 529dcd0c59a95200fdc089c828ddb87b8d500ffc..0cfeba567763cb3c26503cff2ec90e461de6c456 100644 --- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java +++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java @@ -8,22 +8,18 @@ import javax.xml.bind.JAXBException; import org.apache.commons.io.IOUtils; import org.apache.commons.text.StringEscapeUtils; -import org.apache.logging.log4j.*; import org.apache.logging.log4j.core.LogEvent; - import org.sbgn.SbgnUtil; import org.sbgn.bindings.Sbgn; - import lcsb.mapviewer.common.MimeType; import lcsb.mapviewer.common.MinervaLoggerAppender; +import lcsb.mapviewer.converter.Converter; import lcsb.mapviewer.converter.ConverterException; import lcsb.mapviewer.converter.ConverterParams; -import lcsb.mapviewer.converter.Converter; import lcsb.mapviewer.converter.InvalidInputDataExecption; import lcsb.mapviewer.model.map.model.Model; - public class SbgnmlXmlConverter extends Converter { @Override @@ -77,6 +73,7 @@ public class SbgnmlXmlConverter extends Converter { throw new ConverterException(e); } } + @Override public String getCommonName() { return "SBGN-ML"; diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java index 4cd4aa512cd6c80c8946fe51d53632d959d63d73..84b9cdc5c0acefe8c90d331d0d5c1665a1cbff2e 100644 --- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java +++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java @@ -7,7 +7,6 @@ import static org.mockito.Mockito.times; import static org.mockito.Mockito.verify; import java.awt.Color; -import java.awt.Desktop; import java.awt.Graphics2D; import java.awt.Image; import java.awt.geom.GeneralPath; @@ -17,8 +16,6 @@ import java.awt.image.ImageObserver; import java.io.File; import java.nio.file.Files; -import javax.imageio.ImageIO; - import org.junit.After; import org.junit.AfterClass; import org.junit.Before; @@ -38,7 +35,7 @@ import lcsb.mapviewer.model.map.reaction.Reactant; import lcsb.mapviewer.model.map.reaction.Reaction; import lcsb.mapviewer.model.map.species.GenericProtein; -public class BioEntityConverterImplTest extends GraphicsTestFunctions{ +public class BioEntityConverterImplTest extends GraphicsTestFunctions { ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE); @@ -107,12 +104,9 @@ public class BioEntityConverterImplTest extends GraphicsTestFunctions{ BioEntityConverterImpl converter = new BioEntityConverterImpl(alias, false, colorExtractor); converter.draw(alias, graphics, new ConverterParams()); - - verify(graphics, times(1)).drawImage(any(Image.class), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), nullable(ImageObserver.class)); - } catch (Exception e) { throw e; } diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java index d70d97047fc9b51052aaf9cb68f3b0b8d4a6f543..7893741dbbfd3933e6955389b38ba5333f7508be 100644 --- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java +++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java @@ -12,7 +12,6 @@ import static org.mockito.Mockito.times; import static org.mockito.Mockito.verify; import java.awt.Color; -import java.awt.Desktop; import java.awt.Graphics2D; import java.awt.Image; import java.awt.geom.Point2D; @@ -23,9 +22,8 @@ import java.nio.file.Files; import java.util.ArrayList; import java.util.List; -import javax.imageio.ImageIO; - -import org.apache.logging.log4j.*; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.After; import org.junit.Before; import org.junit.Test; @@ -50,7 +48,7 @@ import lcsb.mapviewer.model.map.species.field.RegulatoryRegion; import lcsb.mapviewer.model.map.species.field.Residue; import lcsb.mapviewer.model.map.species.field.TranscriptionSite; -public class SpeciesConverterTest extends GraphicsTestFunctions{ +public class SpeciesConverterTest extends GraphicsTestFunctions { Logger logger = LogManager.getLogger(SpeciesConverterTest.class); ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE); diff --git a/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java index 9e862bbb58db6bb636593aec331e8a3f2043d7a9..b3e96a1a90e3322d70e91c6125c6f87b96a2895e 100644 --- a/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java +++ b/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java @@ -7,13 +7,11 @@ import static org.junit.Assert.fail; import java.util.Set; -import org.apache.logging.log4j.*; import org.junit.After; import org.junit.Before; import org.junit.Test; import org.w3c.dom.Node; - import lcsb.mapviewer.common.exception.InvalidXmlSchemaException; import lcsb.mapviewer.converter.ConverterTestFunctions; import lcsb.mapviewer.model.map.MiriamData; diff --git a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java index 544cc8e112f2816806c1be16584113a76699c972..4828f73ee3f45232fc919868e3dd8b75abd79e8c 100644 --- a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java +++ b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java @@ -2,32 +2,29 @@ package lcsb.mapviewer; import java.util.List; -import org.apache.logging.log4j.*; import org.apache.logging.log4j.core.LogEvent; - import org.junit.After; import org.junit.Before; - import lcsb.mapviewer.common.MinervaLoggerAppender; public class ModelTestFunctions { private MinervaLoggerAppender appender; - @Before - public final void _setUp() throws Exception { - MinervaLoggerAppender.unregisterLogEventStorage(appender); - appender = MinervaLoggerAppender.createAppender(); - } + @Before + public final void _setUp() throws Exception { + MinervaLoggerAppender.unregisterLogEventStorage(appender); + appender = MinervaLoggerAppender.createAppender(); + } - @After - public final void _tearDown() throws Exception { - MinervaLoggerAppender.unregisterLogEventStorage(appender); - } + @After + public final void _tearDown() throws Exception { + MinervaLoggerAppender.unregisterLogEventStorage(appender); + } - protected List<LogEvent> getWarnings() { - return appender.getWarnings(); - } + protected List<LogEvent> getWarnings() { + return appender.getWarnings(); + } } diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java index 9332296f1c30c0e7dfbdd2e71d0b6876eaf577b9..181c7cc548b40131397105dbabeb1fee3400f8a8 100644 --- a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java +++ b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java @@ -11,15 +11,13 @@ import java.util.List; import java.util.Set; import org.apache.commons.lang3.SerializationUtils; -import org.apache.logging.log4j.*; -import org.apache.logging.log4j.core.LogEvent; - +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.After; import org.junit.Before; import org.junit.Test; import lcsb.mapviewer.common.Configuration; - import lcsb.mapviewer.common.MinervaLoggerAppender; import lcsb.mapviewer.common.exception.InvalidArgumentException; import lcsb.mapviewer.model.cache.UploadedFileEntry; diff --git a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java index 4a547186bb102e552d954c6e91995ebebbee2e8c..d3c84726fc7950f909890ab0cc2d70ff09e71823 100644 --- a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java +++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java @@ -5,21 +5,19 @@ import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; import java.util.LinkedList; import java.util.List; import java.util.Queue; -import org.apache.logging.log4j.*; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.After; import org.junit.Before; import org.junit.Test; import org.mockito.Mockito; import lcsb.mapviewer.common.exception.InvalidArgumentException; -import lcsb.mapviewer.common.exception.NotImplementedException; -import lcsb.mapviewer.model.map.BioEntity; import lcsb.mapviewer.model.map.reaction.Reaction; import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction; import lcsb.mapviewer.model.map.species.Element; diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java index 7320d4af24a893e6228c88b007b2400d72cc8604..bb5e4a1bfe1d29b31369a3d32949bda688a4e214 100644 --- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java +++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java @@ -2,15 +2,14 @@ package lcsb.mapviewer.wikipathway; import java.io.ByteArrayInputStream; import java.io.File; -import java.io.FileInputStream; import java.io.InputStream; import java.io.PrintWriter; import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.List; -import java.util.Properties; -import org.apache.logging.log4j.*; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.logging.log4j.core.LogEvent; import org.apache.logging.log4j.core.LoggerContext; import org.pathvisio.core.model.ConverterException; @@ -20,7 +19,6 @@ import org.pathvisio.core.model.PathwayImporter; import org.pathvisio.desktop.PvDesktop; import org.pathvisio.desktop.plugin.Plugin; - import lcsb.mapviewer.common.MinervaLoggerAppender; import lcsb.mapviewer.converter.ConverterParams; import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser; diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java index c87b2789595983cf4f3386ea5af641f3f4412e86..789f997cf71fd886f7688fedb06f15821e99f1e5 100644 --- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java +++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java @@ -10,14 +10,15 @@ import java.io.IOException; import java.io.InputStream; import java.util.ArrayList; import java.util.Collection; -import java.util.LinkedHashSet; import java.util.LinkedHashMap; +import java.util.LinkedHashSet; import java.util.List; import java.util.Map; import java.util.Set; import org.apache.commons.io.IOUtils; -import org.apache.logging.log4j.*; +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.springframework.transaction.annotation.Transactional; @@ -33,9 +34,8 @@ import lcsb.mapviewer.commands.CopyCommand; import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand; import lcsb.mapviewer.commands.SubModelCommand; import lcsb.mapviewer.common.Configuration; -import lcsb.mapviewer.common.exception.InvalidArgumentException; -import lcsb.mapviewer.converter.ConverterException; import lcsb.mapviewer.converter.Converter; +import lcsb.mapviewer.converter.ConverterException; import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params; import lcsb.mapviewer.converter.graphics.DrawingException; import lcsb.mapviewer.converter.graphics.ImageGenerators; @@ -224,7 +224,8 @@ public class ModelRestImpl extends BaseRestImpl { Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token); ColorSchemaReader reader = new ColorSchemaReader(); - Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent(), overlay.getColorSchemaType()); + Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent(), + overlay.getColorSchemaType()); new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute(); } @@ -314,7 +315,8 @@ public class ModelRestImpl extends BaseRestImpl { if (overlay != null) { if (overlay.getInputData() != null) { ColorSchemaReader reader = new ColorSchemaReader(); - Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent(), overlay.getColorSchemaType()); + Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent(), + overlay.getColorSchemaType()); new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute(); } else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) { @@ -364,17 +366,9 @@ public class ModelRestImpl extends BaseRestImpl { ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user); - Params params = new Params(). - x(minX). - y(minY). - height((maxY - minY) / scale). - width((maxX - minX) / scale). - level(level - Configuration.MIN_ZOOM_LEVEL). - nested(false).// automatically set nested view as invalid - scale(scale). - colorExtractor(colorExtractor). - sbgn(topModel.getProject().isSbgnFormat()). - model(colorModel); + Params params = new Params().x(minX).y(minY).height((maxY - minY) / scale).width((maxX - minX) / scale) + .level(level - Configuration.MIN_ZOOM_LEVEL).nested(false).// automatically set nested view as invalid + scale(scale).colorExtractor(colorExtractor).sbgn(topModel.getProject().isSbgnFormat()).model(colorModel); if (overlay != null) { params.nested(overlay.isHierarchicalView()); } diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java index 5e4269de5bb75c90536d9db77584ad3eab0aad6b..73ba446fe789901742b1aebd38784dd7ef8d202e 100644 --- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java +++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java @@ -10,7 +10,8 @@ import java.util.List; import java.util.Map; import java.util.TreeMap; -import org.apache.logging.log4j.*; +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.springframework.transaction.annotation.Transactional; @@ -21,7 +22,6 @@ import lcsb.mapviewer.api.ObjectNotFoundException; import lcsb.mapviewer.api.QueryException; import lcsb.mapviewer.common.Configuration; import lcsb.mapviewer.common.Pair; -import lcsb.mapviewer.common.exception.InvalidArgumentException; import lcsb.mapviewer.common.geometry.ColorParser; import lcsb.mapviewer.model.Project; import lcsb.mapviewer.model.cache.FileEntry; diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java index 22c24c69a69780d64df5f468a6881d2303670347..1c1b38f637cff1f62662c6220dbd5dacd5e31fc3 100644 --- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java +++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java @@ -1,26 +1,20 @@ package lcsb.mapviewer.api.projects.drugs; import static org.junit.Assert.assertNotNull; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.ArgumentMatchers.anyString; import java.util.List; import java.util.Map; -import org.apache.logging.log4j.*; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.After; import org.junit.AfterClass; import org.junit.Before; import org.junit.Test; -import org.mockito.Mockito; import org.springframework.beans.factory.annotation.Autowired; import lcsb.mapviewer.api.RestTestFunctions; -import lcsb.mapviewer.common.exception.InvalidStateException; import lcsb.mapviewer.model.map.model.Model; -import lcsb.mapviewer.services.SecurityException; -import lcsb.mapviewer.services.interfaces.IModelService; -import lcsb.mapviewer.services.interfaces.IProjectService; public class DrugRestImplTest extends RestTestFunctions { Logger logger = LogManager.getLogger(DrugRestImplTest.class); diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java index f9ac4d836c3b0c2c78698e5591aab9d889c09b9a..17fad52ec4708266de79ce5214edf3d6fdd3adb4 100644 --- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java +++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java @@ -1,16 +1,14 @@ package lcsb.mapviewer.web.bean.utils; import java.io.File; -import java.io.FileInputStream; import java.io.IOException; -import java.io.InputStream; -import java.util.Properties; import javax.annotation.PostConstruct; import javax.faces.context.FacesContext; import javax.servlet.ServletContext; -import org.apache.logging.log4j.*; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.logging.log4j.core.LoggerContext; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; diff --git a/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java b/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java index 8e85c08bc3c6ca3e96167b45f859da1eafc6c91a..1f2fcba2fca238cf02ba87b394d5b815a01fbdda 100644 --- a/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java +++ b/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java @@ -1,10 +1,8 @@ package lcsb.mapviewer.web.config; -import java.io.InputStream; import java.net.URL; import java.util.Arrays; import java.util.HashSet; -import java.util.Properties; import javax.servlet.FilterRegistration; import javax.servlet.ServletContext; @@ -12,7 +10,8 @@ import javax.servlet.ServletRegistration; import javax.servlet.SessionCookieConfig; import javax.servlet.SessionTrackingMode; -import org.apache.logging.log4j.*; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.logging.log4j.core.LoggerContext; import org.primefaces.webapp.filter.FileUploadFilter; import org.springframework.security.web.session.HttpSessionEventPublisher; @@ -72,8 +71,8 @@ public class WebAppInitializer implements WebApplicationInitializer { dispatcherContext.setParent(rootContext); dispatcherContext.register(SpringWebConfig.class); - ServletRegistration.Dynamic dispatcher = - container.addServlet("dispatcher", new DispatcherServlet(dispatcherContext)); + ServletRegistration.Dynamic dispatcher = container.addServlet("dispatcher", + new DispatcherServlet(dispatcherContext)); dispatcher.setLoadOnStartup(1); dispatcher.addMapping("/api/*"); @@ -100,7 +99,6 @@ public class WebAppInitializer implements WebApplicationInitializer { FilterRegistration.Dynamic apiFilterReg = container.addFilter("apiFilter", apiFilter); apiFilterReg.addMappingForUrlPatterns(null, true, "/api/*"); - /* * =============== COOKIE SETTINGS =============== */