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ontodev / robot

ROBOT is an OBO Tool
http://robot.obolibrary.org
BSD 3-Clause "New" or "Revised" License
260 stars 74 forks source link

Clean up Maven output #805

Closed jamesaoverton closed 3 years ago

jamesaoverton commented 3 years ago

The output of mvn is so noisy that it's hard to see any important messages. I'd like us to spend at least a few hours trying to clean that up, before we inevitably give up in despair.

beckyjackson commented 3 years ago

I tried to find a project-level setting for the Maven output, but it looks like it grabs the logging level from ${MAVEN_HOME}/conf/logging/simplelogger.properties. There are a couple of other tricks, but nothing that really is useful for us.

The best option I found is to run mvn test/mvn verify with the -q flag which displays error-level logging only. We can update our GH workflow to use this flag too. Thoughts?

jamesaoverton commented 3 years ago

It's good to know about the -q option, but it would be better to just reduce the noise at the source.

Even with -q our ROBOT unit tests are too noisy, and I think we should make them quieter.

I still think it's worth spending a couple of hours trying to revise our POMs and eliminate a chunk of the noise.

beckyjackson commented 3 years ago

A big part of the problem is we have A LOT of overlapping classes/resources. Upgrading the shade plugin version gives more details, but I worry this is going to be difficult to untangle:

[WARNING] httpclient-4.5.13.jar, httpclient-osgi-4.5.12.jar define 474 overlapping classes and resources: 
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpclient/pom.properties
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpclient/pom.xml
[WARNING]   - mozilla/public-suffix-list.txt
[WARNING]   - org.apache.http.auth.AUTH
[WARNING]   - org.apache.http.auth.AuthOption
[WARNING]   - org.apache.http.auth.AuthProtocolState
[WARNING]   - org.apache.http.auth.AuthScheme
[WARNING]   - org.apache.http.auth.AuthSchemeFactory
[WARNING]   - org.apache.http.auth.AuthSchemeProvider
[WARNING]   - org.apache.http.auth.AuthSchemeRegistry
[WARNING]   - 464 more...
[WARNING] httpcore-4.4.13.jar, httpcore-osgi-4.4.13.jar define 256 overlapping classes and resources: 
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpcore/pom.properties
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpcore/pom.xml
[WARNING]   - org.apache.http.ConnectionClosedException
[WARNING]   - org.apache.http.ConnectionReuseStrategy
[WARNING]   - org.apache.http.Consts
[WARNING]   - org.apache.http.ContentTooLongException
[WARNING]   - org.apache.http.ExceptionLogger
[WARNING]   - org.apache.http.ExceptionLogger$1
[WARNING]   - org.apache.http.ExceptionLogger$2
[WARNING]   - org.apache.http.FormattedHeader
[WARNING]   - 246 more...
[WARNING] httpclient-cache-4.5.13.jar, httpclient-osgi-4.5.12.jar define 85 overlapping classes and resources: 
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpclient-cache/pom.properties
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpclient-cache/pom.xml
[WARNING]   - org.apache.http.client.cache.CacheResponseStatus
[WARNING]   - org.apache.http.client.cache.HeaderConstants
[WARNING]   - org.apache.http.client.cache.HttpCacheContext
[WARNING]   - org.apache.http.client.cache.HttpCacheEntry
[WARNING]   - org.apache.http.client.cache.HttpCacheEntrySerializationException
[WARNING]   - org.apache.http.client.cache.HttpCacheEntrySerializer
[WARNING]   - org.apache.http.client.cache.HttpCacheInvalidator
[WARNING]   - org.apache.http.client.cache.HttpCacheStorage
[WARNING]   - 75 more...
[WARNING] bcpkix-jdk15on-1.68.jar, bcprov-jdk15on-1.68.jar, poi-5.0.0.jar, poi-ooxml-5.0.0.jar, poi-ooxml-lite-5.0.0.jar, xmlbeans-4.0.0.jar define 1 overlapping classes: 
[WARNING]   - META-INF.versions.9.module-info
[WARNING] commons-codec-1.15.jar, httpclient-osgi-4.5.12.jar define 226 overlapping classes and resources: 
[WARNING]   - META-INF/maven/commons-codec/commons-codec/pom.properties
[WARNING]   - META-INF/maven/commons-codec/commons-codec/pom.xml
[WARNING]   - org.apache.commons.codec.BinaryDecoder
[WARNING]   - org.apache.commons.codec.BinaryEncoder
[WARNING]   - org.apache.commons.codec.CharEncoding
[WARNING]   - org.apache.commons.codec.Charsets
[WARNING]   - org.apache.commons.codec.Decoder
[WARNING]   - org.apache.commons.codec.DecoderException
[WARNING]   - org.apache.commons.codec.Encoder
[WARNING]   - org.apache.commons.codec.EncoderException
[WARNING]   - 216 more...
[WARNING] elk-owl-implementation-0.4.3.jar, elk-owl-model-0.4.3.jar, elk-owlapi-0.4.3.jar, elk-reasoner-0.4.3.jar, elk-util-collections-0.4.3.jar, elk-util-common-0.4.3.jar, elk-util-concurrent-0.4.3.jar, elk-util-hashing-0.4.3.jar, elk-util-io-0.4.3.jar, elk-util-logging-0.4.3.jar, hamcrest-core-1.3.jar, xmlbeans-4.0.0.jar define 1 overlapping resource: 
[WARNING]   - LICENSE.txt
[WARNING] bcpkix-jdk15on-1.68.jar, bcprov-jdk15on-1.68.jar define 4 overlapping resources: 
[WARNING]   - META-INF/BC1024KE.DSA
[WARNING]   - META-INF/BC1024KE.SF
[WARNING]   - META-INF/BC2048KE.DSA
[WARNING]   - META-INF/BC2048KE.SF
[WARNING] woodstox-core-5.2.1.jar, woodstox-core-asl-4.1.4.jar define 203 overlapping classes: 
[WARNING]   - com.ctc.wstx.api.CommonConfig
[WARNING]   - com.ctc.wstx.api.EmptyElementHandler
[WARNING]   - com.ctc.wstx.api.EmptyElementHandler$HtmlEmptyElementHandler
[WARNING]   - com.ctc.wstx.api.EmptyElementHandler$SetEmptyElementHandler
[WARNING]   - com.ctc.wstx.api.InvalidCharHandler
[WARNING]   - com.ctc.wstx.api.InvalidCharHandler$FailingHandler
[WARNING]   - com.ctc.wstx.api.InvalidCharHandler$ReplacingHandler
[WARNING]   - com.ctc.wstx.api.ReaderConfig
[WARNING]   - com.ctc.wstx.api.ValidatorConfig
[WARNING]   - com.ctc.wstx.api.WriterConfig
[WARNING]   - 193 more...
[WARNING] jakarta.activation-api-1.2.1.jar, jakarta.xml.bind-api-2.3.2.jar define 2 overlapping resources: 
[WARNING]   - META-INF/LICENSE.md
[WARNING]   - META-INF/NOTICE.md
[WARNING] geronimo-activation_1.1_spec-1.1.jar, jakarta.activation-api-1.2.1.jar define 17 overlapping classes: 
[WARNING]   - javax.activation.ActivationDataFlavor
[WARNING]   - javax.activation.CommandInfo
[WARNING]   - javax.activation.CommandMap
[WARNING]   - javax.activation.CommandObject
[WARNING]   - javax.activation.DataContentHandler
[WARNING]   - javax.activation.DataContentHandlerFactory
[WARNING]   - javax.activation.DataHandler
[WARNING]   - javax.activation.DataSource
[WARNING]   - javax.activation.FileDataSource
[WARNING]   - javax.activation.FileTypeMap
[WARNING]   - 7 more...
[WARNING] batik-all-1.13.jar, batik-anim-1.13.jar define 399 overlapping classes and resources: 
[WARNING]   - org.apache.batik.anim.AbstractAnimation
[WARNING]   - org.apache.batik.anim.AnimationEngine
[WARNING]   - org.apache.batik.anim.AnimationEngine$AnimationInfo
[WARNING]   - org.apache.batik.anim.AnimationEngine$Listener
[WARNING]   - org.apache.batik.anim.AnimationEngine$Sandwich
[WARNING]   - org.apache.batik.anim.AnimationEngine$TargetInfo
[WARNING]   - org.apache.batik.anim.AnimationException
[WARNING]   - org.apache.batik.anim.ColorAnimation
[WARNING]   - org.apache.batik.anim.InterpolatingAnimation
[WARNING]   - org.apache.batik.anim.MotionAnimation
[WARNING]   - 389 more...
[WARNING] batik-all-1.13.jar, batik-awt-util-1.13.jar define 224 overlapping classes and resources: 
[WARNING]   - org.apache.batik.ext.awt.AreaOfInterestHintKey
[WARNING]   - org.apache.batik.ext.awt.AvoidTilingHintKey
[WARNING]   - org.apache.batik.ext.awt.BufferedImageHintKey
[WARNING]   - org.apache.batik.ext.awt.ColorSpaceHintKey
[WARNING]   - org.apache.batik.ext.awt.LinearGradientPaint
[WARNING]   - org.apache.batik.ext.awt.LinearGradientPaintContext
[WARNING]   - org.apache.batik.ext.awt.MultipleGradientPaint
[WARNING]   - org.apache.batik.ext.awt.MultipleGradientPaint$ColorSpaceEnum
[WARNING]   - org.apache.batik.ext.awt.MultipleGradientPaint$CycleMethodEnum
[WARNING]   - org.apache.batik.ext.awt.MultipleGradientPaintContext
[WARNING]   - 214 more...
[WARNING] batik-all-1.13.jar, batik-bridge-1.13.jar define 402 overlapping classes and resources: 
[WARNING]   - org.apache.batik.bridge.AbstractGraphicsNodeBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGFilterPrimitiveElementBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGGradientElementBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGGradientElementBridge$SVGStopElementBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGGradientElementBridge$Stop
[WARNING]   - org.apache.batik.bridge.AbstractSVGLightingElementBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGLightingElementBridge$AbstractSVGLightElementBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGLightingElementBridge$SVGFeDistantLightElementBridge
[WARNING]   - org.apache.batik.bridge.AbstractSVGLightingElementBridge$SVGFePointLightElementBridge
[WARNING]   - 392 more...
[WARNING] batik-all-1.13.jar, batik-codec-1.13.jar define 46 overlapping class and resource: 
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.AbstractImageIORegistryEntry
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.AbstractImageIORegistryEntry$1
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIODebugUtil
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIOImageWriter
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIOJPEGImageWriter
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIOJPEGRegistryEntry
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIOPNGImageWriter
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIOPNGRegistryEntry
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIOTIFFImageWriter
[WARNING]   - org.apache.batik.ext.awt.image.codec.imageio.ImageIOTIFFRegistryEntry
[WARNING]   - 36 more...
[WARNING] batik-all-1.13.jar, batik-constants-1.13.jar define 1 overlapping classes: 
[WARNING]   - org.apache.batik.constants.XMLConstants
[WARNING] batik-all-1.13.jar, batik-css-1.13.jar define 240 overlapping classes and resources: 
[WARNING]   - org.apache.batik.css.dom.CSSOMComputedStyle
[WARNING]   - org.apache.batik.css.dom.CSSOMComputedStyle$ComputedCSSValue
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor$AbstractComponent
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor$AbstractModificationHandler
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor$BlueComponent
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor$ColorNumber
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor$FloatComponent
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor$GreenComponent
[WARNING]   - org.apache.batik.css.dom.CSSOMSVGColor$ModificationHandler
[WARNING]   - 230 more...
[WARNING] batik-all-1.13.jar, batik-dom-1.13.jar define 116 overlapping class and resource: 
[WARNING]   - org.apache.batik.dom.AbstractAttr
[WARNING]   - org.apache.batik.dom.AbstractAttr$AttrTypeInfo
[WARNING]   - org.apache.batik.dom.AbstractAttrNS
[WARNING]   - org.apache.batik.dom.AbstractCharacterData
[WARNING]   - org.apache.batik.dom.AbstractChildNode
[WARNING]   - org.apache.batik.dom.AbstractComment
[WARNING]   - org.apache.batik.dom.AbstractDOMImplementation
[WARNING]   - org.apache.batik.dom.AbstractDocument
[WARNING]   - org.apache.batik.dom.AbstractDocument$DocumentConfiguration
[WARNING]   - org.apache.batik.dom.AbstractDocument$DocumentConfiguration$ParameterNameList
[WARNING]   - 106 more...
[WARNING] batik-all-1.13.jar, batik-ext-1.13.jar define 7 overlapping classes: 
[WARNING]   - org.apache.batik.w3c.dom.ElementTraversal
[WARNING]   - org.apache.batik.w3c.dom.Location
[WARNING]   - org.apache.batik.w3c.dom.Window
[WARNING]   - org.apache.batik.w3c.dom.events.CustomEvent
[WARNING]   - org.apache.batik.w3c.dom.events.KeyboardEvent
[WARNING]   - org.apache.batik.w3c.dom.events.MutationNameEvent
[WARNING]   - org.apache.batik.w3c.dom.events.TextEvent
[WARNING] batik-all-1.13.jar, batik-extension-1.13.jar define 48 overlapping class and resource: 
[WARNING]   - org.apache.batik.extension.ExtensionElement
[WARNING]   - org.apache.batik.extension.GraphicsExtensionElement
[WARNING]   - org.apache.batik.extension.PrefixableStylableExtensionElement
[WARNING]   - org.apache.batik.extension.StylableExtensionElement
[WARNING]   - org.apache.batik.extension.svg.BatikBridgeExtension
[WARNING]   - org.apache.batik.extension.svg.BatikDomExtension
[WARNING]   - org.apache.batik.extension.svg.BatikDomExtension$BatikHistogramNormalizationElementFactory
[WARNING]   - org.apache.batik.extension.svg.BatikDomExtension$BatikRegularPolygonElementFactory
[WARNING]   - org.apache.batik.extension.svg.BatikDomExtension$BatikStarElementFactory
[WARNING]   - org.apache.batik.extension.svg.BatikDomExtension$ColorSwitchElementFactory
[WARNING]   - 38 more...
[WARNING] batik-all-1.13.jar, batik-gui-util-1.13.jar define 208 overlapping classes and resources: 
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$AddButtonAction
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$AddMediumDialog
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$AddMediumDialog$CancelButtonAction
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$AddMediumDialog$OKButtonAction
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$ClearButtonAction
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$Dialog
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$Dialog$CancelButtonAction
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$Dialog$OKButtonAction
[WARNING]   - org.apache.batik.util.gui.CSSMediaPanel$MediaListDataListener
[WARNING]   - 198 more...
[WARNING] batik-all-1.13.jar, batik-gvt-1.13.jar define 103 overlapping classes: 
[WARNING]   - org.apache.batik.gvt.AbstractGraphicsNode
[WARNING]   - org.apache.batik.gvt.CanvasGraphicsNode
[WARNING]   - org.apache.batik.gvt.CompositeGraphicsNode
[WARNING]   - org.apache.batik.gvt.CompositeGraphicsNode$1
[WARNING]   - org.apache.batik.gvt.CompositeGraphicsNode$Itr
[WARNING]   - org.apache.batik.gvt.CompositeGraphicsNode$ListItr
[WARNING]   - org.apache.batik.gvt.CompositeShapePainter
[WARNING]   - org.apache.batik.gvt.FillShapePainter
[WARNING]   - org.apache.batik.gvt.GVTTreeWalker
[WARNING]   - org.apache.batik.gvt.GraphicsNode
[WARNING]   - 93 more...
[WARNING] batik-all-1.13.jar, batik-i18n-1.13.jar define 4 overlapping classes: 
[WARNING]   - org.apache.batik.i18n.ExtendedLocalizable
[WARNING]   - org.apache.batik.i18n.LocaleGroup
[WARNING]   - org.apache.batik.i18n.Localizable
[WARNING]   - org.apache.batik.i18n.LocalizableSupport
[WARNING] batik-all-1.13.jar, batik-parser-1.13.jar define 57 overlapping classes and resources: 
[WARNING]   - org.apache.batik.parser.AWTPathProducer
[WARNING]   - org.apache.batik.parser.AWTPolygonProducer
[WARNING]   - org.apache.batik.parser.AWTPolylineProducer
[WARNING]   - org.apache.batik.parser.AWTTransformProducer
[WARNING]   - org.apache.batik.parser.AbstractParser
[WARNING]   - org.apache.batik.parser.AbstractScanner
[WARNING]   - org.apache.batik.parser.AngleHandler
[WARNING]   - org.apache.batik.parser.AngleParser
[WARNING]   - org.apache.batik.parser.ClockHandler
[WARNING]   - org.apache.batik.parser.ClockParser
[WARNING]   - 47 more...
[WARNING] batik-all-1.13.jar, batik-rasterizer-1.13.jar, batik-svgrasterizer-1.13.jar define 1 overlapping resource: 
[WARNING]   - org/apache/batik/apps/rasterizer/resources/rasterizer.policy
[WARNING] batik-all-1.13.jar, batik-script-1.13.jar define 15 overlapping classes and resources: 
[WARNING]   - META-INF/imports/script.txt
[WARNING]   - org.apache.batik.script.ImportInfo
[WARNING]   - org.apache.batik.script.Interpreter
[WARNING]   - org.apache.batik.script.InterpreterException
[WARNING]   - org.apache.batik.script.InterpreterFactory
[WARNING]   - org.apache.batik.script.InterpreterPool
[WARNING]   - org.apache.batik.script.ScriptEventWrapper
[WARNING]   - org.apache.batik.script.jpython.JPythonInterpreter
[WARNING]   - org.apache.batik.script.jpython.JPythonInterpreterFactory
[WARNING]   - org.apache.batik.script.rhino.BatikSecurityController
[WARNING]   - 5 more...
[WARNING] batik-all-1.13.jar, batik-slideshow-1.13.jar define 4 overlapping classes: 
[WARNING]   - org.apache.batik.apps.slideshow.Main
[WARNING]   - org.apache.batik.apps.slideshow.Main$1
[WARNING]   - org.apache.batik.apps.slideshow.Main$RenderThread
[WARNING]   - org.apache.batik.apps.slideshow.Main$TransitionThread
[WARNING] batik-all-1.13.jar, batik-svg-dom-1.13.jar define 119 overlapping classes and resources: 
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGItem
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGList
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGMatrix
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGNormPathSegList
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGNormPathSegList$NormalizedPathSegListBuilder
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGNormPathSegList$SVGPathSegGenericItem
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGNumber
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGNumberList
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGNumberList$NumberListBuilder
[WARNING]   - org.apache.batik.dom.svg.AbstractSVGPathSegList
[WARNING]   - 109 more...
[WARNING] batik-all-1.13.jar, batik-svgbrowser-1.13.jar define 299 overlapping classes and resources: 
[WARNING]   - org.apache.batik.apps.svgbrowser.AboutDialog
[WARNING]   - org.apache.batik.apps.svgbrowser.AboutDialog$1
[WARNING]   - org.apache.batik.apps.svgbrowser.AboutDialog$2
[WARNING]   - org.apache.batik.apps.svgbrowser.AbstractCompoundCommand
[WARNING]   - org.apache.batik.apps.svgbrowser.AbstractUndoableCommand
[WARNING]   - org.apache.batik.apps.svgbrowser.Application
[WARNING]   - org.apache.batik.apps.svgbrowser.DOMDocumentTree
[WARNING]   - org.apache.batik.apps.svgbrowser.DOMDocumentTree$DOMDocumentTreeAdapter
[WARNING]   - org.apache.batik.apps.svgbrowser.DOMDocumentTree$DOMDocumentTreeEvent
[WARNING]   - org.apache.batik.apps.svgbrowser.DOMDocumentTree$DOMDocumentTreeListener
[WARNING]   - 289 more...
[WARNING] batik-all-1.13.jar, batik-svggen-1.13.jar define 158 overlapping class and resource: 
[WARNING]   - org.apache.batik.svggen.AbstractImageHandlerEncoder
[WARNING]   - org.apache.batik.svggen.AbstractSVGConverter
[WARNING]   - org.apache.batik.svggen.AbstractSVGFilterConverter
[WARNING]   - org.apache.batik.svggen.CachedImageHandler
[WARNING]   - org.apache.batik.svggen.CachedImageHandlerBase64Encoder
[WARNING]   - org.apache.batik.svggen.CachedImageHandlerJPEGEncoder
[WARNING]   - org.apache.batik.svggen.CachedImageHandlerPNGEncoder
[WARNING]   - org.apache.batik.svggen.ClipKey
[WARNING]   - org.apache.batik.svggen.DOMGroupManager
[WARNING]   - org.apache.batik.svggen.DOMTreeManager
[WARNING]   - 148 more...
[WARNING] batik-all-1.13.jar, batik-svgpp-1.13.jar define 11 overlapping class and resource: 
[WARNING]   - org.apache.batik.apps.svgpp.Main
[WARNING]   - org.apache.batik.apps.svgpp.Main$DocWidthHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$DoctypeHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$NewlineHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$NoFormatHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$OptionHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$PublicIdHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$SystemIdHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$TabWidthHandler
[WARNING]   - org.apache.batik.apps.svgpp.Main$XMLDeclHandler
[WARNING]   - 1 more...
[WARNING] batik-all-1.13.jar, batik-svgrasterizer-1.13.jar define 46 overlapping classes and resources: 
[WARNING]   - org.apache.batik.apps.rasterizer.DefaultSVGConverterController
[WARNING]   - org.apache.batik.apps.rasterizer.DestinationType
[WARNING]   - org.apache.batik.apps.rasterizer.Main
[WARNING]   - org.apache.batik.apps.rasterizer.Main$1
[WARNING]   - org.apache.batik.apps.rasterizer.Main$10
[WARNING]   - org.apache.batik.apps.rasterizer.Main$11
[WARNING]   - org.apache.batik.apps.rasterizer.Main$12
[WARNING]   - org.apache.batik.apps.rasterizer.Main$13
[WARNING]   - org.apache.batik.apps.rasterizer.Main$14
[WARNING]   - org.apache.batik.apps.rasterizer.Main$15
[WARNING]   - 36 more...
[WARNING] batik-all-1.13.jar, batik-swing-1.13.jar define 168 overlapping classes and resources: 
[WARNING]   - org.apache.batik.swing.JSVGCanvas
[WARNING]   - org.apache.batik.swing.JSVGCanvas$1
[WARNING]   - org.apache.batik.swing.JSVGCanvas$2
[WARNING]   - org.apache.batik.swing.JSVGCanvas$3
[WARNING]   - org.apache.batik.swing.JSVGCanvas$4
[WARNING]   - org.apache.batik.swing.JSVGCanvas$5
[WARNING]   - org.apache.batik.swing.JSVGCanvas$6
[WARNING]   - org.apache.batik.swing.JSVGCanvas$AffineAction
[WARNING]   - org.apache.batik.swing.JSVGCanvas$CanvasSVGListener
[WARNING]   - org.apache.batik.swing.JSVGCanvas$CanvasUserAgent
[WARNING]   - 158 more...
[WARNING] batik-all-1.13.jar, batik-transcoder-1.13.jar define 61 overlapping class and resource: 
[WARNING]   - org.apache.batik.transcoder.AbstractTranscoder
[WARNING]   - org.apache.batik.transcoder.DefaultErrorHandler
[WARNING]   - org.apache.batik.transcoder.ErrorHandler
[WARNING]   - org.apache.batik.transcoder.SVGAbstractTranscoder
[WARNING]   - org.apache.batik.transcoder.SVGAbstractTranscoder$SVGAbstractTranscoderUserAgent
[WARNING]   - org.apache.batik.transcoder.ToSVGAbstractTranscoder
[WARNING]   - org.apache.batik.transcoder.Transcoder
[WARNING]   - org.apache.batik.transcoder.TranscoderException
[WARNING]   - org.apache.batik.transcoder.TranscoderInput
[WARNING]   - org.apache.batik.transcoder.TranscoderOutput
[WARNING]   - 51 more...
[WARNING] batik-all-1.13.jar, batik-util-1.13.jar define 83 overlapping classes and resources: 
[WARNING]   - org.apache.batik.Version
[WARNING]   - org.apache.batik.util.AbstractParsedURLProtocolHandler
[WARNING]   - org.apache.batik.util.ApplicationSecurityEnforcer
[WARNING]   - org.apache.batik.util.Base64DecodeStream
[WARNING]   - org.apache.batik.util.Base64EncoderStream
[WARNING]   - org.apache.batik.util.BatikSecurityManager
[WARNING]   - org.apache.batik.util.CSSConstants
[WARNING]   - org.apache.batik.util.ClassFileUtilities
[WARNING]   - org.apache.batik.util.ClassFileUtilities$ClassFile
[WARNING]   - org.apache.batik.util.ClassFileUtilities$Jar
[WARNING]   - 73 more...
[WARNING] batik-all-1.13.jar, batik-ttf2svg-1.13.jar define 1 overlapping classes: 
[WARNING]   - org.apache.batik.apps.ttf2svg.Main
[WARNING] batik-all-1.13.jar, batik-xml-1.13.jar define 7 overlapping class and resource: 
[WARNING]   - org.apache.batik.xml.LexicalUnits
[WARNING]   - org.apache.batik.xml.XMLCharacters
[WARNING]   - org.apache.batik.xml.XMLException
[WARNING]   - org.apache.batik.xml.XMLScanner
[WARNING]   - org.apache.batik.xml.XMLStreamNormalizingReader
[WARNING]   - org.apache.batik.xml.XMLUtilities
[WARNING]   - org/apache/batik/xml/scanner/resources/Messages.properties
[WARNING] xml-apis-1.4.01.jar, xml-apis-ext-1.3.04.jar define 5 overlapping resources: 
[WARNING]   - license/LICENSE
[WARNING]   - license/LICENSE.dom-documentation.txt
[WARNING]   - license/LICENSE.dom-software.txt
[WARNING]   - license/NOTICE
[WARNING]   - license/README.dom.txt
[WARNING] geronimo-stax-api_1.0_spec-1.0.1.jar, xml-apis-1.4.01.jar define 33 overlapping classes: 
[WARNING]   - javax.xml.stream.EventFilter
[WARNING]   - javax.xml.stream.FactoryConfigurationError
[WARNING]   - javax.xml.stream.Location
[WARNING]   - javax.xml.stream.StreamFilter
[WARNING]   - javax.xml.stream.XMLEventFactory
[WARNING]   - javax.xml.stream.XMLEventReader
[WARNING]   - javax.xml.stream.XMLEventWriter
[WARNING]   - javax.xml.stream.XMLInputFactory
[WARNING]   - javax.xml.stream.XMLOutputFactory
[WARNING]   - javax.xml.stream.XMLReporter
[WARNING]   - 23 more...
[WARNING] jaxen-1.1.4.jar, xml-apis-1.4.01.jar define 1 overlapping classes: 
[WARNING]   - org.w3c.dom.UserDataHandler
[WARNING] fluent-hc-4.5.12.jar, httpclient-osgi-4.5.12.jar define 16 overlapping classes and resources: 
[WARNING]   - META-INF/maven/org.apache.httpcomponents/fluent-hc/pom.properties
[WARNING]   - META-INF/maven/org.apache.httpcomponents/fluent-hc/pom.xml
[WARNING]   - org.apache.http.client.fluent.Async
[WARNING]   - org.apache.http.client.fluent.Async$ExecRunnable
[WARNING]   - org.apache.http.client.fluent.Content
[WARNING]   - org.apache.http.client.fluent.ContentResponseHandler
[WARNING]   - org.apache.http.client.fluent.Executor
[WARNING]   - org.apache.http.client.fluent.Form
[WARNING]   - org.apache.http.client.fluent.HttpHeader
[WARNING]   - org.apache.http.client.fluent.InternalByteArrayEntity
[WARNING]   - 6 more...
[WARNING] httpclient-osgi-4.5.12.jar, httpmime-4.5.12.jar define 26 overlapping classes and resources: 
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpmime/pom.properties
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpmime/pom.xml
[WARNING]   - org.apache.http.entity.mime.AbstractMultipartForm
[WARNING]   - org.apache.http.entity.mime.FormBodyPart
[WARNING]   - org.apache.http.entity.mime.FormBodyPartBuilder
[WARNING]   - org.apache.http.entity.mime.Header
[WARNING]   - org.apache.http.entity.mime.HttpBrowserCompatibleMultipart
[WARNING]   - org.apache.http.entity.mime.HttpMultipart
[WARNING]   - org.apache.http.entity.mime.HttpMultipart$1
[WARNING]   - org.apache.http.entity.mime.HttpMultipartMode
[WARNING]   - 16 more...
[WARNING] httpcore-nio-4.4.13.jar, httpcore-osgi-4.4.13.jar define 245 overlapping classes and resources: 
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpcore-nio/pom.properties
[WARNING]   - META-INF/maven/org.apache.httpcomponents/httpcore-nio/pom.xml
[WARNING]   - org.apache.http.impl.nio.DefaultClientIOEventDispatch
[WARNING]   - org.apache.http.impl.nio.DefaultHttpClientIODispatch
[WARNING]   - org.apache.http.impl.nio.DefaultHttpServerIODispatch
[WARNING]   - org.apache.http.impl.nio.DefaultNHttpClientConnection
[WARNING]   - org.apache.http.impl.nio.DefaultNHttpClientConnectionFactory
[WARNING]   - org.apache.http.impl.nio.DefaultNHttpServerConnection
[WARNING]   - org.apache.http.impl.nio.DefaultNHttpServerConnectionFactory
[WARNING]   - org.apache.http.impl.nio.DefaultServerIOEventDispatch
[WARNING]   - 235 more...
[WARNING] java-ipv6-0.17.jar, scala-library-2.12.12.jar define 2 overlapping resources: 
[WARNING]   - LICENSE
[WARNING]   - NOTICE
[WARNING] annotations-3.0.1.jar, jsr305-3.0.1.jar define 37 overlapping classes and resources: 
[WARNING]   - META-INF/maven/com.google.code.findbugs/jsr305/pom.properties
[WARNING]   - META-INF/maven/com.google.code.findbugs/jsr305/pom.xml
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.CheckForSigned
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.Detainted
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - javax.annotation.MatchesPattern$Checker
[WARNING]   - javax.annotation.Nonnegative
[WARNING]   - javax.annotation.Nonnegative$Checker
[WARNING]   - 27 more...
[WARNING] explanation-workbench-3.0.0.jar, jfact-4.0.4.jar, org.semanticweb.hermit-1.3.8.413.jar define 1 overlapping resource: 
[WARNING]   - plugin.xml
[WARNING] owlapi-api-4.5.6.jar, owlapi-distribution-4.5.6.jar define 770 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-api/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-api/pom.xml
[WARNING]   - org.semanticweb.owlapi.OWLAPIConfigProvider
[WARNING]   - org.semanticweb.owlapi.annotations.HasPriority
[WARNING]   - org.semanticweb.owlapi.change.AbstractCompositeOntologyChange
[WARNING]   - org.semanticweb.owlapi.change.AddAxiomData
[WARNING]   - org.semanticweb.owlapi.change.AddClassExpressionClosureAxiom
[WARNING]   - org.semanticweb.owlapi.change.AddClassExpressionClosureAxiom$FillerCollector
[WARNING]   - org.semanticweb.owlapi.change.AddImportData
[WARNING]   - org.semanticweb.owlapi.change.AddOntologyAnnotationData
[WARNING]   - 760 more...
[WARNING] owlapi-apibinding-4.5.6.jar, owlapi-distribution-4.5.6.jar define 5 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-apibinding/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-apibinding/pom.xml
[WARNING]   - org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory
[WARNING]   - org.semanticweb.owlapi.apibinding.OWLManager
[WARNING]   - org.semanticweb.owlapi.apibinding.OWLManager$InjectorConstants
[WARNING] owlapi-compatibility-4.5.6.jar, owlapi-distribution-4.5.6.jar define 85 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-compatibility/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-compatibility/pom.xml
[WARNING]   - de.uulm.ecs.ai.owlapi.krssparser.KRSS2OntologyFormat
[WARNING]   - org.coode.owl.krssparser.KRSSOntologyFormat
[WARNING]   - org.coode.owlapi.latex.LatexAxiomsListOntologyFormat
[WARNING]   - org.coode.owlapi.latex.LatexOntologyFormat
[WARNING]   - org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntax
[WARNING]   - org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxClassExpressionParser
[WARNING]   - org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxClassFrameParser
[WARNING]   - org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser
[WARNING]   - 75 more...
[WARNING] owlapi-distribution-4.5.6.jar, owlapi-fixers-4.5.6.jar define 97 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-fixers/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-fixers/pom.xml
[WARNING]   - org.semanticweb.owlapitools.builders.BaseAnnotationPropertyBuilder
[WARNING]   - org.semanticweb.owlapitools.builders.BaseBuilder
[WARNING]   - org.semanticweb.owlapitools.builders.BaseDataBuilder
[WARNING]   - org.semanticweb.owlapitools.builders.BaseDataPropertyBuilder
[WARNING]   - org.semanticweb.owlapitools.builders.BaseDomainBuilder
[WARNING]   - org.semanticweb.owlapitools.builders.BaseEntityBuilder
[WARNING]   - org.semanticweb.owlapitools.builders.BaseObjectBuilder
[WARNING]   - org.semanticweb.owlapitools.builders.BaseObjectPropertyBuilder
[WARNING]   - 87 more...
[WARNING] owlapi-distribution-4.5.6.jar, owlapi-impl-4.5.6.jar define 219 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-impl/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-impl/pom.xml
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.DefaultNode
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.DefaultNodeSet
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.NodeFactory
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.OWLClassNode
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.OWLClassNodeSet
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.OWLDataPropertyNode
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.OWLDataPropertyNodeSet
[WARNING]   - org.semanticweb.owlapi.reasoner.impl.OWLDatatypeNode
[WARNING]   - 209 more...
[WARNING] owlapi-distribution-4.5.6.jar, owlapi-oboformat-4.5.6.jar define 71 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-oboformat/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-oboformat/pom.xml
[WARNING]   - org.obolibrary.macro.AbstractMacroExpansionVisitor
[WARNING]   - org.obolibrary.macro.MacroExpansionGCIVisitor
[WARNING]   - org.obolibrary.macro.MacroExpansionGCIVisitor$MacroExpansions
[WARNING]   - org.obolibrary.macro.MacroExpansionGCIVisitor$MacroExpansions$GCIVisitor
[WARNING]   - org.obolibrary.macro.MacroExpansionVisitor
[WARNING]   - org.obolibrary.macro.MacroExpansionVisitor$MacroExpansions
[WARNING]   - org.obolibrary.macro.MacroExpansionVisitor$Visitor
[WARNING]   - org.obolibrary.macro.ManchesterSyntaxTool
[WARNING]   - 61 more...
[WARNING] owlapi-distribution-4.5.6.jar, owlapi-parsers-4.5.6.jar define 604 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-parsers/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-parsers/pom.xml
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParser
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParserFactory
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParser
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParser$JJCalls
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParser$LookaheadSuccess
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParserConstants
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParserTokenManager
[WARNING]   - org.semanticweb.owlapi.dlsyntax.parser.JavaCharStream
[WARNING]   - 594 more...
[WARNING] owlapi-distribution-4.5.6.jar, owlapi-rio-4.5.6.jar define 75 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-rio/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-rio/pom.xml
[WARNING]   - org.semanticweb.owlapi.formats.AbstractRioRDFDocumentFormatFactory
[WARNING]   - org.semanticweb.owlapi.formats.BinaryRDFDocumentFormat
[WARNING]   - org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory
[WARNING]   - org.semanticweb.owlapi.formats.N3DocumentFormat
[WARNING]   - org.semanticweb.owlapi.formats.N3DocumentFormatFactory
[WARNING]   - org.semanticweb.owlapi.formats.NQuadsDocumentFormat
[WARNING]   - org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory
[WARNING]   - org.semanticweb.owlapi.formats.NTriplesDocumentFormat
[WARNING]   - 65 more...
[WARNING] owlapi-distribution-4.5.6.jar, owlapi-tools-4.5.6.jar define 85 overlapping classes and resources: 
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-tools/pom.properties
[WARNING]   - META-INF/maven/net.sourceforge.owlapi/owlapi-tools/pom.xml
[WARNING]   - com.clarkparsia.owlapi.explanation.AxiomConverter
[WARNING]   - com.clarkparsia.owlapi.explanation.BlackBoxExplanation
[WARNING]   - com.clarkparsia.owlapi.explanation.BlackBoxExplanation$1
[WARNING]   - com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator
[WARNING]   - com.clarkparsia.owlapi.explanation.ExplanationGenerator
[WARNING]   - com.clarkparsia.owlapi.explanation.HSTExplanationGenerator
[WARNING]   - com.clarkparsia.owlapi.explanation.HSTExplanationGenerator$1
[WARNING]   - com.clarkparsia.owlapi.explanation.MultipleExplanationGenerator
[WARNING]   - 75 more...
[WARNING] commons-logging-1.1.3.jar, jcl-over-slf4j-1.7.22.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING] geronimo-activation_1.1_spec-1.1.jar, geronimo-javamail_1.4_spec-1.7.1.jar define 2 overlapping classes: 
[WARNING]   - org.apache.geronimo.osgi.locator.Activator
[WARNING]   - org.apache.geronimo.osgi.locator.ProviderLocator
[WARNING] axiom-dom-1.2.14.jar, axiom-impl-1.2.14.jar define 3 overlapping resources: 
[WARNING]   - META-INF/axiom.xml
[WARNING]   - META-INF/maven/org.apache.ws.commons.axiom/axiom-common-impl/pom.properties
[WARNING]   - META-INF/maven/org.apache.ws.commons.axiom/axiom-common-impl/pom.xml
balhoff commented 3 years ago

I've long felt like something was not right with owlapi-distribution and its OWL API dependencies. It seems like it bundles all the OWL API classes together but also depends on the individual modules, e.g., owlapi-distribution-4.5.6.jar, owlapi-parsers-4.5.6.jar define 604 overlapping classes and resources.

jamesaoverton commented 3 years ago

@balhoff do you think it would make sense for ROBOT to depend on the distinct OWLAPI package instead of owlapi-distribution?

balhoff commented 3 years ago

I use owlapi-distribution in all my projects, but I always see these duplication warnings. Maybe we can bother @ignazio1977 for his advice?

beckyjackson commented 3 years ago

I went ahead and included the distinct packages instead of owlapi-distribution, based on what is listed in sources, and I ran into a bunch of "cannot find symbol" errors, for example:

[ERROR] /Users/tauber/github/robot/robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java:[562,25] cannot find symbol
[ERROR]   symbol:   method isIRI()
[ERROR]   location: interface org.semanticweb.owlapi.model.OWLAnnotationValue
[ERROR] /Users/tauber/github/robot/robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java:[729,22] cannot find symbol
[ERROR]   symbol:   method isAnonymous()
[ERROR]   location: variable f of type org.semanticweb.owlapi.model.OWLDataRange

Any ideas why this might happen?

beckyjackson commented 3 years ago

I'd like to add that these methods should be in owlapi-api, which is included in the dependencies... so it seems strange that these no longer work.

I wanted to replace owlapi-distribution, because even when I exclude certain modules from it, there are still overlapping classes, so there will always be warnings... 😞

ignazio1977 commented 3 years ago

Looks like a version conflict, I think in your new configuration some jars have changed their loading order and now you're picking some old ones and some new ones, while before it would be just one jar overriding all others.

Owlapi-distribution is not much more than one package in place of owlapi-apibinding and it's dependencies, so I would try using that first - possibly checking for parsers jars, they should be included but I'm unsure.

I'll take a look at the source of those errors, they should have been taken care of by the shading plugin.

On Wed, 10 Mar 2021, 14:50 Becky Jackson, notifications@github.com wrote:

I'd like to add that these methods should be in owlapi-api, which is included in the dependencies... so it seems strange that these no longer work.

I wanted to replace owlapi-distribution, because even when I exclude certain modules from it, there are still overlapping classes, so there will always be warnings... 😞

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ontodev/robot/issues/805#issuecomment-795538358, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAT2AJPP4Z236CRWDHTOTMLTC52KTANCNFSM4WVUDEFQ .

ignazio1977 commented 3 years ago

I see three OWLAPI versions pulled in, one directly in your main pom and two indirectly from HermiT and JFact dependencies. Those two need excluding, I'd think - the reasoners themselves should work with whichever OWLAPI versions you give them, bar bugs, however it would be worthy to update to the latest HermiT. I've got a couple of minor improvements about to be released with it as well, so maybe a few weeks from now?

ignazio1977 commented 3 years ago

This patch removes conflicting dependencies (at least the ones I could spot) and I get a successful build out of it.

I could spot a few warnings for overlapping classes in the maven logs but it seemed to be far fewer.

diff --git a/pom.xml b/pom.xml
index bd49177..6a8800d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -164,7 +164,7 @@
     </dependency>
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
-      <artifactId>owlapi-distribution</artifactId>
+      <artifactId>owlapi-apibinding</artifactId>
       <version>4.5.6</version>
     </dependency>
     <dependency>
@@ -190,11 +190,23 @@
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>org.semanticweb.hermit</artifactId>
       <version>1.3.8.413</version>
+      <exclusions>
+        <exclusion>
+          <groupId>net.sourceforge.owlapi</groupId>
+          <artifactId>owlapi-distribution</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>jfact</artifactId>
       <version>4.0.4</version>
+      <exclusions>
+        <exclusion>
+          <groupId>net.sourceforge.owlapi</groupId>
+          <artifactId>owlapi-distribution</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
   </dependencies>

diff --git a/robot-core/pom.xml b/robot-core/pom.xml
index 0b06b7a..c7d5818 100644
--- a/robot-core/pom.xml
+++ b/robot-core/pom.xml
@@ -98,11 +98,23 @@
       <groupId>org.geneontology</groupId>
       <artifactId>expression-materializing-reasoner</artifactId>
       <version>0.1.3</version>
+      <exclusions>
+        <exclusion>
+          <groupId>net.sourceforge.owlapi</groupId>
+          <artifactId>owlapi-distribution</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>org.geneontology</groupId>
       <artifactId>obographs</artifactId>
       <version>0.0.8</version>
+      <exclusions>
+        <exclusion>
+          <groupId>net.sourceforge.owlapi</groupId>
+          <artifactId>owlapi-distribution</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
@@ -152,6 +164,12 @@
       <groupId>org.geneontology</groupId>
       <artifactId>owl-diff_2.12</artifactId>
       <version>1.1.1</version>
+      <exclusions>
+        <exclusion>
+          <groupId>net.sourceforge.owlapi</groupId>
+          <artifactId>owlapi-distribution</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
   </dependencies>
 </project>
beckyjackson commented 3 years ago

Thanks for your help @ignazio1977 - I applied those changes to the poms just from master, but I'm actually not able to get a successful build:

[ERROR] /Users/tauber/github/robot/robot-core/src/main/java/org/obolibrary/robot/QueryOperation.java:[134,54] incompatible types: org.obolibrary.robot.QueryOperation.JenaTriplesHandler cannot be converted to org.eclipse.rdf4j.rio.RDFHandler
[ERROR] /Users/tauber/github/robot/robot-core/src/main/java/org/obolibrary/robot/metrics/OntologyMetrics.java:[1010,31] cannot find symbol
  symbol:   class Construct
  location: class org.semanticweb.owlapi.util.DLExpressivityChecker

I even tried including owlapi-api and got the same message. I'm only able to build successfully by including owlapi-distribution. I'm not sure why you're able to get a successful build, and I cannot - maybe it's different Java versions?

beckyjackson commented 3 years ago

Never mind, I was able to get rid of the error by including the following in both pom.xml and robot-core/pom.xml (which I thought just pom.xml would work, but it doesn't seem to like that)

<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-api</artifactId>
  <version>4.5.6</version>
</dependency>
<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-apibinding</artifactId>
  <version>4.5.6</version>
</dependency>
<dependency>
  <groupId>net.sourceforge.owlapi</groupId>
  <artifactId>owlapi-rio</artifactId>
  <version>4.5.6</version>
</dependency>

I also just needed to exclude owlapi-distribution from the Whelk dependency, and it's looking a lot better now. Thanks again for your help!