pluginanatomy - protege wiki

2/11/2016 PluginAnatomyProtegeWiki

http://protegewiki.stanford.edu/wiki/PluginAnatomy 1/11

FromProtegeWiki

Contents

1Introduction2Thevacuousplugininfiveminutes

2.1Build.xml2.2MANIFEST.MF2.3CompileandRun

3WritingViewandTabPlugins3.1AddingaViewPlugintothePlugin.xmlfile3.2LibrariesandtheBundleClasspath3.3TabPluginsandtheViewconfig.xmlFile

3.3.1Step1:Declaretheplugin3.3.2Step2:Layouttheviewsintheplugin3.3.3Step3:Saveaconfigurationfile3.3.4Step4:Testtheresults

4AddingMenuPlugins5UsingaReasoner6AdvancedTopics

6.1AddingNewPluginTypes6.1.1ThePluginConsumer6.1.2ThePluginLoader6.1.3ThePlugin6.1.4ThePluginInstance

6.2Frames,FrameSections,andRows6.2.1FrameListsandFrames6.2.2FrameSections6.2.3FrameSectionRows

7Glossary

Introduction

Thepurposeofthiswebpageistodescribesomeofthekeyingredientsofaplugin.Thepagewillbedirectedbythequickdevelopmentofapluginandcanindeedbeusedasaquickstartguide.InordertofocusattentiononthecorepluginconceptswewillusethelowestcommondenominatorofJavadevelopmenttoolsandthistutorialwillnotuseaJavaIDE.WewillassumethatthereaderhasanunderstandingofJavadevelopmentandknowshowtofollowalonginhisfavoriteIDE.Formoreinformationabouthowtoworkwithprotege4inanIDEIwilldirectthereadertothispage.ItispossibleforanexperienceddevelopertoskiptheantscriptssimplyfollowalonginanIDEbutwewouldstillrecommendabuildfileforthefinalversion.

Thesourcesforthefirstplugin(theexampletab)canbefoundhere(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/plugin/trunk/org.protege.editor.owl.examples.tab).Youcaneitherchecktheseoutfromsvnandusethisasaguideforreadingthetextorbuildthisprojectinaseriesofstepbystepstagesasdescribedbelow.Ifyoustartfromthecheckedoutversionthenyoucanbuildtheprojectbyfollowingthedirectionshere.

Thevacuousplugininfiveminutes

Icreateda(vacuous)pluginfromscratch,installeditandranitinjustunderfourminutes.ThereisalsoanewexpereimentalquickstartguideforstartinganewProtege5pluginwithmavenwhichwillprobablyevolveintothenewrecommendedstrategy.

Thesimplest(trivial)plugincanbebuiltfromsourcesinthefollowinglayout:

build.xmlMETAINFMANIFEST.MFlibresourcessrc

AswewillseeevenwithoutanyjavasourcesthisisasufficientbasisforbuildingapluginthatisrecognizedbyProtege4.Thereareonlytwofilesinthissourcetreethebuild.xmlfileandtheMANIFEST.MF.Thesefilescanbequicklyputtogetherfromtemplates.

Build.xml

Thetemplateforthebuild.xmlfilecanbedownloadedfromhere(http://smiprotege.stanford.edu/repos/protege/protege4/protegebase/trunk/etc/templatepluginbuild.xml).Onlytwothingsneedtobechangedinthisbuildfile.Theycanbefoundbysearchingforthestring"CHANGEME"inthefile.Thefirstthingtochangeisthenameoftheproject.Iwillcalltheprojecttheplugintutoiralproject:

Thenextsettingthatmustalmostalwaysbechangedisthenameoftheplugin.Inthiscase,thebuild.xmlalreadyhastherightnameforthepluginbutthisistheonlypluginforwhichthiswillbetrue:

Withtheseadjustmentsthebuild.xmlfileisready.

MANIFEST.MF

ThetemplatefortheMANIFEST.MFfilecanbedownloadedfromhere(http://smiprotege.stanford.edu/repos/protege/protege4/protegebase/trunk/etc/templatemanifest.mf).Onlyfivethingsneedtobechangedinthisfiletomakeituseableandtwoareoptional.Thesecanbefoundbysearchingforthestring"CHANGEME"inthefile.Thefirstchangeistosetthedisplaynamefortheplugin:

BundleName:TutorialPlugin

ThisisthenamethatisseenwhenProtege4startsupandinseveralpluginconfigurationscreens.Theseccondthingtochangeisthesymbolicnameoftheplugin.Theusualdefaultistousesthesamenameasthepluginnameinthebuild.xmlfile:

BundleSymbolicName:org.protege.editor.owl.examples.tab;singleton:=true

Notethe"singleton:=true"linethisisimportantsincemostProtege4pluginswillonlyworkiftheyareinstantiatedexactlyonce.Thenextthingstochangearethebundledescription,thevendorandthedocumentationurl:

BundleDescription:AsimplepluginforaplugindevelopmenttutorialBundleVendor:TheProtegeDevelopmentTeamBundleDocURL:www.perhaps.i.donthaveoneyet.com

Actuallythevendorandthedocurlareoptionalandcanbedeleted.TheMANIFEST.MFfileisnowready.



CompileandRun

Beforewecanstart,wemustsetthePROTEGE_HOMEenvironmentvariabletopointtoaProtege4distribution.ThispagehasdirectionsonhowtodothisindifferentoperatingsystemsbutfornowIwillassumethatweareonaunix(orosx)system.Inthatcase,thesystemvariablecanbesetwithasimplecommand

exportPROTEGE_HOME=/Users/tredmond/Desktop/Protege_4.1_beta

Thisvacuouspluginisnowreadytocompileandrun.AssumingthatthePROTEGE_HOMEenvironmentvariableissetcorrectly,thisplugincanbecompiledwiththesimplecommand

antinstall

Thefulltextofthebuildsessionisasfollows:

[[email protected]]$antinstallBuildfile:build.xml

init:[mkdir]Createddir:/private/tmp/org.protege.editor.owl.examples.tab/build[mkdir]Createddir:/private/tmp/org.protege.editor.owl.examples.tab/build/classes[mkdir]Createddir:/private/tmp/org.protege.editor.owl.examples.tab/build/classes/lib[mkdir]Createddir:/private/tmp/org.protege.editor.owl.examples.tab/build/lib

checkProtegeLibs:[echo]UsingProtegeHome=/Andromeda/Users/tredmond/dev/workspaces/protege4/owleditor/build/dist/equinoxtofindprotegejars

checkProtegeLibsAndReport:

buildlibs:[unjar]Expanding:/Andromeda/Users/tredmond/dev/workspaces/protege4/owleditor/build/dist/equinox/bundles/org.protege.common.jarinto/private/tmp/org.protege.editor.owl.examples.tab/build

compile:

build.manifest:[copy]Copying1fileto/private/tmp/org.protege.editor.owl.examples.tab/build

copy.resources:[mkdir]Createddir:/private/tmp/org.protege.editor.owl.examples.tab/build/classes/METAINF[copy]Copying1fileto/private/tmp/org.protege.editor.owl.examples.tab/build/classes/METAINF

jar:[jar]Buildingjar:/private/tmp/org.protege.editor.owl.examples.tab/build/org.protege.editor.owl.examples.tab.jar

install:[delete]Deletingdirectory/Andromeda/Users/tredmond/dev/workspaces/protege4/owleditor/build/dist/equinox/configuration/org.eclipse.core.runtime[delete]Deletingdirectory/Andromeda/Users/tredmond/dev/workspaces/protege4/owleditor/build/dist/equinox/configuration/org.eclipse.osgi[copy]Copying1fileto/Andromeda/Users/tredmond/dev/workspaces/protege4/owleditor/build/dist/equinox/plugins

BUILDSUCCESSFULTotaltime:2seconds[[email protected]]$

IfthePROTEGE_HOMEenvironmentvariableisnotsetcorrectlytheuserwillinsteadseethefollowing:

BUILDFAILED/private/tmp/org.protege.editor.owl.examples.tab/build.xml:74:missingprotegelibraries

Wecannowlookatwhatthebuildhasdonebyexploringtheprojectdirectorytree.

Weseethefollowingelements:

TheClassTreeis(approximately)aflattenedviewoftheplugin(thejarfile).Generallythislargelyconsistsofthe.classfilesthathavebeencompiledfromthejava.Butsincewehavenotwrittenanyjavayetthisisnotfound.Inaddition,thiswillcontainresourcesneededbythepluginandlibrariesthatthepluginneedsbutwhichcannotbefoundinotherProtegeplugins.TheGeneratedLibrarieswhichareextractedfromProtegeplugins.ThisisneededbecauseofadifferencebetweenhowJavaandOSGigetresourcesoutofJarfiles.OSGiallowsabundle(whichisaimplementedasajarfile)tocontainotherjarfiles.Ifthebundleclasspathisconfiguredcorrectly,OSGiwillloadclassesfromthosejarsinjars.ButJavadoesnothavethiscapability.SothebuildscriptextractsthejarfilesoutoftheOSGibundlesthatwillbeneededtocompilethebundle.NotethatthesejarfilesarenotcopiedtotheclasstreebecausetheProtege4/OSGienvironmentwillmaketheclassesandresourcesofthesejarfilesavailable.TheProtege4Pluginthisisthefinalartifactofthebuildprocess.Becausewehaverun"antinstall"ithasalsobeeninstalledintheProtegedistribution.

Ifthedeveloperisstillwithmethenheisnowreadytoruntheplugin.GototheProtegedistribution(theonepointedtobythePROTEGE_HOMEenvironmentvariable)andrunit.Weareparticularlyinterestedintheconsoleoutputbecausethisisgoingtobetheonlyindicationthatthispluginisrecognizedatall.Theconsoleoutputshouldlooklikethis:

StartingProtege4OWLEditor(Version4.1.111)Platform:Java:JVM1.5.0_16b06284Memory:207MLanguage:en,Country:USFramework:Eclipse(1.4.0)OS:MacOSX(10.5.6)Processor:ppcInstalledpluginPelletReasonerInstalledpluginDLQueryTabInstalledpluginOwlvizPluginInstalledpluginowleditorInstalledpluginTutorialPluginInstalledpluginTheOWLAPIInstalledpluginFactplusplusPlugin TutorialPluginPluginhasnoplugin.xmlresource

InthisoutputweseethattheTutorialPluginhasbeenrecognizedandinstalled.Inadditionthereisainformationalmessagethattheplugin.xmlfilehasnotbeenfound.ThisisalmostalwaysindicatesaproblembecausemostProtege4pluginsdependonaplugin.xmlresource.Wewilldescribehowtheplugin.xmlfileisgeneratedinthenextsections.



WritingViewandTabPlugins

ThepreviouspluginaddednofunctionalitytoProtege4.Wearenowgoingtodescribehowtoremedythissitutaion.SofarwehavenotmissedtheJavaIDEbutitisnowwhenwestartwritingabitofJavacodethattheJavaIDEwouldreallyshine.Buttoillustratethemainconcepts,wewillcontinuetoshowhowtobuildthepluginwithoutanydevelopmentenvironmentotherthanthatprovidedbythecoreJavatools.

AddingaViewPlugintothePlugin.xmlfile

Recallthatpreviouslywhenweranourplugin,Protege4complainedthattherewasnoplugin.xmlfile.Theplugin.xmlfilecontainsadeclarationofthewaysinwhichthepluginwillextendtheProtege4capabilitiesand(moreadvanced)thewaysinwhichtheplugincapabilitiescanbeextendedbyotherplugins.WewillstartbyaddingadeclarationthatthispluginwillimplementaProtegeView.

SofirstwewillgiveadefinitionofaProtegeview.ThepurposeofaProtegeviewistoprovideaviewofsomeaspectofanontology.IntheProtegeinterface,aProtegeviewiseasilyrecognized.Ithasaclearlydefinedborder.AtthetopofaProtegeviewisatitlebarandacollectionofbuttonsallowingtheuserto

splittheprotegeviewintotwocopiesofthesameviewoneabovetheother,splittheprotegeviewintotwocopiesofthesameviewonebesidetheother,floattheviewabovetheProtegeclientsothatitisvisibleinanycontext,closetheviewremovingitfromthetabthatcontainsit.

AnexampleofatypicalProtegeviewisshownbelow.

InordertodeclareourintentthatthispluginimplementaProtegeview,weaddthefollowingplugin.xmlfiletotherootoftheprojecttree:

Thisplugin.xmlfilestatesthatthispluginismakingasingleextensiontotheProtege4capabilities.Wewillcoverthemeaningofthepartsofthisextensiondeclarationlinebyline.Thefirstlinedefinestheidoftheextension.ThisparticularextensioniscalledtheExampleViewComponent.Theseconddecleration,

point="org.protege.editor.core.application.ViewComponent",

stateswhattheextensionistryingtodo.Thisextensionisattemptingtoimplementthefunctionalityrepresentedbytheextensionpointwiththename

org.protege.editor.core.application.ViewComponent.

ThelabeldeclarationtellsProtegewhattoputinthetitlebaroftheview.Theclassdeclarationindicateswhichclassimplementsthefunctionalityneededbythisview.Wewillgointotheimplementationofthatclassshortly.FinallythecategorydeclarationtellsProtegewhichmenuundertheViewmenushouldcontainthisview.

AverysimpleviewcanbewrittenbyextendingtheclassAbstractOWLViewComponentandimplementingthemethodsinitialiseOWLViewanddisposeOWLView.Averysimplesuchimplementationcanbefoundhere(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/plugin/trunk/org.protege.editor.owl.examples.tab/src/org/protege/editor/owl/examples/tab/ExampleViewComponent.java).Nowthisplugindependsonalibrarythatcanbefoundhere(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/plugin/trunk/org.protege.editor.owl.examples.tab/lib/examplelib.jar).Thislibraryshouldbedepositedinthelibdirectoryoftheproject.Thislibraryistrivialanditsonlypurposeistoshowhowtousealibraryinaplugin.Thedirectorytreeoftheprojectshouldnowlooklikethis:



Atthispointtheantinstalloperationwillcompile,buildandinstallthenewpluginwiththe"antinstall"command.Buttheinstalledpluginwon'truncorrectlyandwewillshowhowtofixthisbelow.

LibrariesandtheBundleClasspath

Afterweinstalltheplugin,wecanstartProtegetotrytousethe"ExampleViewComponent".IfyouclickontheViewmenuandthenselect"OntologyViews"youwillseethe"ExampleViewComponent"listedthere.HoweveronselectingthisviewandtryingtoplaceontheProtegescreen,thefollowingerrorwillarise:

Errorloggedjava.lang.NoClassDefFoundError:org/protege/owl/example/Metrics atjava.lang.Class.getDeclaredConstructors0(NativeMethod) atjava.lang.Class.privateGetDeclaredConstructors(Class.java:2357) atjava.lang.Class.getConstructor0(Class.java:2671) atjava.lang.Class.newInstance0(Class.java:321) atjava.lang.Class.newInstance(Class.java:303)...

Ifwelookattheplugincontentswiththe"jartf"commandthenwewillseethatthebuildfilecorrectlyputtheexamplelib.jarintotheplugin:

[[email protected]]$jartfbuild/org.protege.editor.owl.examples.tab.jarMETAINF/METAINF/MANIFEST.MFlib/org/org/protege/org/protege/owl/org/protege/owl/examples/org/protege/owl/examples/tab/lib/examplelib.jarorg/protege/owl/examples/tab/ExampleViewComponent.classplugin.xml[[email protected]]$

TheproblematthispointisintheMANIFEST.MFfile.TheBundleClasspathlineisasfollows:

BundleClassPath:.

Toincludetheexamplelib.jarinthejarfile,theBundleClasspathlinemustbemodifiedtoincludethislibrary:

BundleClassPath:.,lib/examplelib.jar

Notethatusingacolonorasemicoloninsteadofthecommadoesnotwork.Alsoentering./lib/examplib.jardoesnotworkeither.Thisistheosgimechanismformakingthislibraryavailabletothisplugin.NotethatsincetheMANIFEST.MFfiledoesnothaveanExportPackagedeclaration,theseclasseswillonlybevisiblewithinthepluginandwillnotbeexportedtoanyotherpluginintheProtege4environmeht.ThisispartofthepluginisolationprovidedbyOSGithatallowsdifferentpluginstousedifferentlibrarieswithoutconflicts.

NowthepluginworkscorrectlyandIcaninstalltheviewintotheActiveOntologyTab:

.

TabPluginsandtheViewconfig.xmlFile

TheothermostcommonplugintypeistheProtegetab.InordertomakeaProtegetab,thedeveloperneedstogenerateanduseaviewconfig.xmlfilefortheproject.Inthissectionwewillshowhowtodothis.ItturnsoutthatatabcanusuallybeputtogetherwithoutwritinganyJavacode.Thestepsforwritingatabpluginare

1.addadeclarationofthetabpluginintheplugin.xmlfile.2.startProtegeandgraphicallyconfigurethetabinquestion.3.savetheconfigurationandincludeitwiththesourcefilesforthetab.4.testbyrestartingProtegeandrunningthetabwiththedefaultconfiguration.

Thesestepsaredescribedinmoredetailbelow.

Step1:Declaretheplugin

Thefirstthingthatthatneedstobedoneistodeclarethetabintheplugin.xmlfile.



AnimportantlineintheabovedeclarationofthetabisthedefaultViewConfigFileName.Thisnamesaresourcethattheprotegepluginwilllookfortocreatethedefaultlayoutofthetab.

Step2:Layouttheviewsintheplugin

Wecannowcompilethispluginandinstallitasbefore.NowwhenwerunProtege4,wewillseeanewtabcalledthe"ExampleTab"inthetabsmenu(Window>Tabs).Enablethistab.SincewehavenotyetcreatedtheviewconfigexampleTab.xmlfile,youwillseethatthetabisempty.

Nowinstallandlayoutsomeviewsintothistab.InmycaseImadetheviewslooklikethis:

Step3:Saveaconfigurationfile

NowintheWindowmenuselect"ExportCurrentTab"andsavethefileas

viewconfigexampleTab.xml

intheprojectdirectory.InmycasetheviewconfigexampleTabfilelookedlikethis:

NowbeforewecompletethisProtegesession,gototheWindowmenuandclick"Resetselectedtabtodefaultstate".Youwillseethatthetabisnowemptyagain.NowexitProtege.

Thedirectorytreeoftheprojectshouldnowlooklikethis:



Step4:Testtheresults

Installthepluginagain.NotethatthebuildscriptautomaticallyfoundtheviewconfigexampleTab.xmlfileandputitintotheplugin:

[[email protected]]$jartfbuild/org.protege.editor.owl.examples.tab.jarMETAINF/METAINF/MANIFEST.MFlib/org/org/protege/org/protege/owl/org/protege/owl/examples/org/protege/owl/examples/tab/lib/examplelib.jarorg/protege/owl/examples/tab/ExampleViewComponent.classplugin.xmlviewconfigexampleTab.xml[[email protected]]$

RunProtegeandgototheExampleTab.Itisempty?Thereasonforthisisthatthetabhasbeencustomizedtohavenothinginitfromthelastsession.Clickonthetabsmenuandclickon"Resetselectedtabtodefaultstate".Nowyouwillseetheviewsthatweconfiguredinthetabbefore.Thisisnowthedefaultstateforthetabanditwillbewhatotherusersseewhentheyusethispluginforthefirsttime.

AddingMenuPlugins

Ihavecreatedasmallmenuprojecthere(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/org.protege.example.menu/trunk)thatshowshowtocreateseveraldifferentmenutypes.Laterwewillusethisprojectastheexamplethatdrivesthiswikipage.

AddinganewmenutoProtege4.1isveryeasy.Thetwothingsthatthedeveloperneedstoaccomplisharetowritethecodeforthemenuactionandtoaddanentrytotheplugin.xml.Iwilltakearealworldexampletoillustratetheprocess.Inthisexample,IamwritingapluginthatcausesProtegetodisplayanontologythatisstoredinadatabaseformat.IwanttoputthisinthefilemenuofProtege4.1justunderotheritemssuchas"New","Open","OpenRecent"and"OpenfromURL".

Towritethecodeforthemenuplugin,thedevelopermerelyneedstoextendProtegeOWLAction.Thethreemethodsthatthedeveloperneedstowriteareinitialise,disposeandactionPerformed.Ithinkthatthemeaningofthesethreemethodsisprettyclearandthiscanbeaveryeasytask.

Nowthedeveloperneedstoaddanentrytotheplugin.xml(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/org.protege.example.menu/trunk/plugin.xml)file.Inmycasetheentrylookslikethis:

The"id"attributeofloadDatabaseissimplyashortidentifierforthepluginthatisnotseenbytheuser.The"point"attributeindicatesthatthepluginbeingdeclaredhereisamenuplugin.The

lineindicatestheclassthatimplementstheactionthatthismenuperformsandthe

lineindicatesthatthemenuistobeusedinthecontextoftheowleditor.Theonlyotherlineinthisplugin.xml(http://smiprotege/repos/protege/protege4/incubator/v3/org.protege.owlapi.bridge/trunk/plugin.xml)thatisabitmysteriousisthelinethatsays:

Thepurposeofthislineistoindicateexactlywherethemenushouldbeplaced.Thefirstpartofthevalue,

org.protege.editor.core.application.menu.FileMenu

indicatesthattheparentofmy"LoadDatabaseOntology"menuisthefilemenu.Thestringismakingareferencetothefilemenudeclaration

fromtheplugin.xml(http://smiprotege/repos/protege/protege4/plugins/org.protege.editor.core.application/trunk/plugin.xml)filefortheorg.protege.editor.core.applicationplugin.Thefirstpartofthestring


is

org.protege.editor.core.application

whichistheidentifieroftheplugindeclaringthemenuand"menu.FileMenu"istheidofthepluginfromtheplugin.xmlfile.

ButnowIneedtoexplainthemeaningoftheSlotAAZportionofthepathinmyoriginalmenudeclaration:

TheSlotAAZstringindicatesexactlywherethe"LoadDatabaseOntology"shouldappearintheFilemenu.Thisstring(SlotAAZ)isparsedasagroup(SlotAA)andanindex(Z).FirstthegroupandtheindexareusedtosortthechildrenoftheFilemenu.Thechildrenaresortedfirstbygroupbutwhentwochildrenhavethesamegrouptheyarethensortedbygroupindex.Inadditiontothis,childrenwiththesamegrouparegroupedtogetherinthemenu.



Inparticular,ifItrackdownthedeclarationsofthe"New","Open","OpenRecent"and"OpenfromURL"menusIfindthattheyallhaveagroupidentifierofSlotAA.Thisiswhytheyappearinthefilemenutogetherfollowedbyaseparatorbar.ByspecifyingthatmymenushouldhaveagroupofSlotAA,IamtellingProtegethatIwantmymenutobegroupedwiththesemenus.BygivingmymenuanindexofZIamtellingProtegethatIwantmymenutogoattheendofthelist.

ThealgorithmusedbyProtegetodeterminethelocationoftheplugincanbeobservedbyturningonloggingforthemenubuilder.Thiscaneasilybedonebyeditingthelog4j.xmlintheProtegeinstallationdirectory.Firstmodifythesectionthatsays

tosay

Thisallowstheconsoletoshowdebugmessages.Thenaddthelines

ThiswillcauseProtegetogeneratesomewhatverboselogstotheconsole(theselogsalsoshowupinalogfilein${homedirectory}/.Protege/logs/protege###.log).Therelevantlinesformymenupluginareasfollows.First

Parsed:[Menu:LoadDatabaseOntology]parentId=org.protege.editor.core.application.menu.FileMenu

indicatesthatProtegewasabletoparsethepathformymenupluginanddeterminethattheidoftheparentis


thegroupisSlotAAandthegroupindexisZ.Nextweseetheline

[Menu:File]parentof[Menu:LoadDatabaseOntology]

whichindicatesthatProtegewassuccessfullyabletofindadeclaredmenuwiththerightidtobetheparentofmymenu.ThislinealsoindicatesthatProtegesuccessfullydecipheredthegroup(SlotAA)andtheindex(Z).Finallytherearethelines:

Adding[Menu:File]tomenubarGivingFilethechild[Menu:New...]GivingFilethechild[Menu:Open...]GivingFilethechild[Menu:Openrecent]GivingFilethechild[Menu:OpenfromURL...]GivingFilethechild[Menu:LoadDatabaseOntology]GivingFilethechild[Menu:Save]GivingFilethechild[Menu:Saveas...]GivingFilethechild[Menu:Gatherontologies...]GivingFilethechild[Menu:Exportinferredaxiomsasontology...]GivingFilethechild[Menu:Ontologylibraries...]GivingFilethechild[Menu:Loadedontologysources...]GivingFilethechild[Menu:Checkforplugins...]GivingFilethechild[Menu:Close]

thatindicatethattheFilemenuwassuccessfullypopulated.

UsingaReasoner

Usuallywhenapluginwantstouseareasoner,thepluginshouldusethereasonerthatisinitializedandusedbyProtege.ThisreasonercouldbetheFaCT++,HermiT,Pelletorotherreasonersandisselectedandinitializedattheusersrequest.Toexplainhowthisworkswewillexplainhowthefollowing(nottoouseful)codefromamenupluginworks.

publicvoidactionPerformed(ActionEvente){OWLClasslastSelectedClass=getOWLWorkspace().getOWLSelectionModel().getLastSelectedClass();if(lastSelectedClass!=null){OWLReasonerManagerreasonerManager=getOWLModelManager().getOWLReasonerManager();ReasonerUtilities.warnUserIfReasonerIsNotConfigured(getOWLWorkspace(),reasonerManager);if(reasonerManager.getReasonerStatus()==ReasonerStatus.INITIALIZED){OWLReasonerreasoner=reasonerManager.getCurrentReasoner();SetsubClasses=reasoner.getSubClasses(lastSelectedClass,true).getFlattened();if(!subClasses.isEmpty()){LOGGER.info("Inferredsubclassesof"+getOWLModelManager().getRendering(lastSelectedClass)+"are:");for(OWLClasssubClass:subClasses){LOGGER.info("\t"+getOWLModelManager().getRendering(subClass));}}else{LOGGER.info(getOWLModelManager().getRendering(lastSelectedClass)+"hasnoinferredsubclasses.");}}}}

Thiscodecreatesanactionthatwheninvokedwillprintsomemessagesaboutinferredsubclassestothelog.ThefirstthingtonoticeisthattheOWLReasonerManageristhecentralclassforaccessingtheProtegereasoneranditcanbeobtainedfromtheOWLModelManager.Thisclasscanbeusedtodeterminethestatusofthereasoner,getthecurrentProtegereasonerorgetareasonerfactoryforcreatingnewinstancesofaProtegereasoner.

Oncethereasonermanagerisobtainedcodeaboveinformstheuserifthereasonerisnotinitializedorisininconsistentstate.ThiswarninghasbeenincludedasastandardProtegeutilitysothattheuserwillgetaconsistentmessagewhenthereasonerisnotreadyforinference.ThisistheapproachtakenbytheDLQuerypluginforinstancebecauseitdoesnotmakesensetousetheDLQuerypluginifthereasonerisnotinitialized.Howeveranalternativeapproachistoquietlycheckthestatusofthereasonerandonlyusethereasonerifitisinagoodenoughstate.ThisisthestrategytakenbythecodethatdisplaysinferencessuchastheinferredsuperclassesandtheconsistencyofclassesandpropertiesastheusernavigatesthroughtheProtegeinterface.

ThenextthingthathappensisthatthecodechecksthestatusofthecurrentreasonerwiththecallreasonerManager.getReasonerStatus().ThiscallreturnsaReasonerStatusenumerationwhichcurrentlycantakeonthefollowingvalues:

NO_REASONER_FACTORY_CHOSEN:theuserhasnotyetselectedatypeofreasoner.REASONER_NOT_INITIALIZED:theuserhasselectedwhattypeofreasonerhewantsbuthasnotinitializedityet.INITIALIZATION_IN_PROGRESS:thereasonerisintheprocessofbeinginitialized.Pluginsshouldnotseethisstate.INITIALIZED:thereasonerisreadyforuse.INCONSISTENT:thereasonerwasinitializedbuttheontologyisinconsistent.Inthisstate,reasonersarenotusable.OUT_OF_SYNC:thereasonerisreadybutitisnotuptodatewiththelatestchangesintheontology.Thereasonerisusableinthisstatebutitmayproducemisleadingresults.Itcanbebroughtuptodatewithareasoner.flush()call.



FinallythecodeaboveobtainstheProtegereasoner(whichimplementstheOWLapiOWLReasonerinterface)andusesOWLapicallstoobtaininformation.

Insomecasestheabovestrategyisnotsufficient.Forexample,theexplanationpluginsneedtocreatetheirownreasonersandsotheyneedareasonerfactory.Inthiscasetheplugincanmakethecall:

reasonerManager.getCurrentReasonerFactory().getReasonerFactory()

toobtainthereasonerfactory(aninstanceoftheOWLapiinterfaceOWLReasonerFactory).

AdvancedTopics

AddingNewPluginTypes

WorkinProgress

OneoftheadvantagesofusingtheOSGi/Eclipseframeworkisthatitnaturallyallowsdeveloperstodefinetheirownplugintypes.Forexample,theSWRLtab,beingwrittenbyMartinO'Connor,delegatestheworkofexecutingtheSWRLrulestoaruleengineplugin.ItisanticipatedthattherewillbetworuleenginepluginsthatarearecompatiblewiththeSWRLtab.OneofthesepluginswillbebasedontheJessruleengineandtheotherpluginwillbebasedontheDROOLSruleengine.

WewillillustratehowthisisdonewithtwoProtegebundles.Thesourcesforthesebundlescanbefound

http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer

and

http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/producer

Bothbundlescanbequicklyinstalledthroughtheincludedantscripts.

Theconsumerbundlebehavesasfollows.ItaddsamenuitemtoarunningProtegeenvironment.Thismenuisfoundatthebottomoftheeditmenu.Whentheuserclicksonthismenuitem,theconsumerbundleperformsthefollowingactions:

1.itlooksforallcustom_extension_pointpluginsintherunningProtegeenvironment,2.itinstantiateseachpluginfoundandfinally3.itcallsthedoSomething()methodonthatplugininstance.

Thisbehaviorisprovidedthroughtheinteractionoffourcomponents:

theconsumercodethatisresponsibleforloopingthroughasetofpluginsandinvokingthem.thepluginloaderthatisresponsibleforcalculatingandreturningasetofpluginsthatmatchaspecifiction.thepluginthatisajavaencodingofdataencodedinplugin.xmlfilesprovidedbythebundles.theplugininstancethatisaninstantiationofapluginthatdoestheactualworkoftheplugin.

ThePluginConsumer

ThePluginconsumeressentiallyusesthepluginloader(describedbelow)toloopthroughaseriesofpluginsandinstantiateandinvokethem.ThecodethatdoesthisworkcanbefoundintheMyPluginConsumer(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer/src/org/protege/example/extension/point/MyPluginConsumer.java)classandlookslikethefollowing:

publicvoidactionPerformed(ActionEvente){MyPluginLoaderloader=newMyPluginLoader(getOWLModelManager());for(MyPluginplugin:loader.getPlugins()){try{MyPluginInstancei=plugin.newInstance();i.doSomething();}catch(Exceptionex){ProtegeApplication.getErrorLog().logError(ex);}}}

Thisisatypicalexampleofhowapluginconsumerwillwork.Itusesapluginloadertofindasetofpluginsthataretheninstantiated(plugin.newInstance())andtheninvoked(i.doSomething()).Forthemostpart,thepluginconsumerdoesnothavetoworrytoomuchaboutthedetailsoftheProtegeplugininfrastructure.ThelogicofthePluginconsumerisdefinedbythetaskathand.

ThePluginLoader

Thepluginloader(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer/src/org/protege/example/extension/point/MyPluginLoader.java)isresponsibleforsearchingforpluginsofthecustom_extension_pointtype.ThepluginloaderextendstheAbstractPluginLoaderclasswhichhandlesmostofthelogicofcreatingandfindingplugins.Minimally,allthedeveloperneedstodotoimplementthepluginloaderistoimplementaconstructorandacreateinstancemethod.Theconstructorlookslikethis:

publicMyPluginLoader(OWLModelManagerowlModelManager){super(MyPlugin.CONSUMER_ID,MyPlugin.ID);this.owlModelManager=owlModelManager;}

andthisistypical.ThesignificanceofthetwoargumentstothesuperconstructorwillbeexplainedwhenIdescribethePluginimplementation.Essentiallytheydefinewhichtypeofpluginisbeingsearchedforbythisloader.Inaddition,theconstructorforthispluginloadertakesanowlModelManagerargumentsothathecanpassthisargumenttotheconstructorfortheplugins.ThecreateInstancemethodthenisresponsibleforconstructingtheplugin:

protectedMyPlugincreateInstance(IExtensionextension){returnnewMyPlugin(owlModelManager,extension);}

InadditionthereisagetExtensionMatchermethodthatcanbeusedtorestrictthesetofpluginsthatarereturnedbythispluginloader.GenerallyitisnotnecessarytoimplementthegetExtensionMatcherinterface.

ThePlugin

Essentiallytheplugin(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer/src/org/protege/example/extension/point/MyPlugin.java)isaPOJOrepresentingadeclarationofaplugininaplugin.xmlfile.Tounderstandthisweneedtolookatthetwodeclarationsintwoseparateplugin.xmlfiles.Thefirstdeclarationisfoundinthebundlefortheconsumerplugin.Thisdeclarationrepresentsarequestforaparticulartypeofservice.Inourcasethedeclaration(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer/plugin.xml)lookslikethis:



Thisdeclarationdefines

theidentifieroftheplugintype,custom_extension_point,whichisthenamebywhichplugindevelopersrefertothisplugintype,ThisstringcorrespondstotheMyPlugin.IDthatwepassedtotheAbstractPluginLoaderconstructorabove.Notethatitispossiblefordifferentbundlestodeclareanextensionpointtheuserfriendlynameoftheplugintypeandapointertothexmlschemafortheplugintype.

Ibelievethatthelastitem,theschema(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer/schema/custom_extension_point.exsd),isnotmandatorybutitisextremelyusefulfordevelopersanditiscreatednaturallywhenpluginsaredevelopedusingtheeclipseIDE.

Thepluginproducerprovidedadeclaration(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/producer/plugin.xml)forhisextensionthatmatchestheextensionpointdeclarationabove.Inourexampletheextensiondeclarationlookslikethis:

Thepluginclass,MyPlugin(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer/src/org/protege/example/extension/point/MyPlugin.java),extendstheAbstractProtegePluginclass.TheAbstractProtegePluginclassprovidesmanyutilitiesthatmakeiteasytowritethepluginclass.Inparticular,togetthe"type"fieldtheMyPluginclassprovidesanaccessor:

/***getsthedeclaredtypefieldfortheplugin*/publicStringgetType(){returngetPluginProperty(TYPE_PARAM,"nulltype");}

Inaddition,theAbstractProtegePluginclassdoesthetrickyaspectsofinstantiatingthepluginleavingonlythetaskofinitializingtheinstantiatedplugintotheMyPluginclass:

/***Createsaninstanceoftheplugin.Itisexpectedthat*thisinstancewillbe"setup",buttheinstance's*initialisemethodwillnothavebeencalledintheinstantiation*process.*/publicMyPluginInstancenewInstance()throwsClassNotFoundException,IllegalAccessException,InstantiationException{ MyPluginInstancempi=super.newInstance();mpi.setup(modelManager,getType());returnmpi;}

ThePluginInstance

Theplugininstanceclass(http://smiprotege.stanford.edu/repos/protege/protege4/misc/examples/custom.extension/trunk/consumer/src/org/protege/example/extension/point/api/MyPluginInstance.java)isresponsibleforperformingwhatevertaskitisthatthepluginissupposedtoperform.InourcasetheplugininstancewillimplementthedoSomething()method.ThisclassmustimplementtheProtegePluginInstanceinterfacethoughitisnotclearthatthisisreallyneededanymore.TheProtegePluginInstanceinterfacehasonlyonemethod,initialise(),butmanyplugins,suchastheoneinthisexample,havetheirowninitailizationmethodsthatarecalledbythePluginLoader.

Frames,FrameSections,andRows

InProgress

ItisnotclearthatthisneedstobeherebutthisisanextremelycentralProtegeconcept.IngeneralplugindeveloperswillnotneedtobuildcustomFramelistsandcansimplyusethetoplevelOWLFrameListconcepts.

MostofthediscussionwillfocusonasmallerandsmallersectionofthethefollowingProtege4.1screen.ThisdiagramshowsthestandardProtege4.1classestabasitdisplayssomeinformationabouttheselectedclasswhichistheCountryclassinthepizzaontology.



FrameListsandFrames

ThediagrambelowshowsaFrameListshowingadescriptionoftheCountryclass.TheOWLFrameLististheswingobjectthatisresponsiblefordisplayingsomeobjectcalledtherootobjectfortheOWLFrameList.Inthiscase,therootobjectforthisframelististheCountryOWLclass.FrequentlytherootobjectoftheforaframelistisanOWLentitybutthisisnotrequired.TheconstructorfortheOWLFrameListobjecttakesanOWLFrameobjectwhichmanagesthecontentmodeloftheOWLFrameList.TheassociatedOWLFrameobjectalsohasarootobjectandinthiscasetherootobjectistheCountryclass.

Whileitmaynotbevisuallyimmediatelyapparent,theinformationbeingdisplayedisactuallyarenditionofalistofaxioms.Thusforinstance,theclassexpressionrepresentedinthesectionunderneathEquivalentClassesrepresentstheaxiom

CountrySubClassOfDomainConceptand{America,England,France,Germany,Italy}.

SimilarlythefirstindividualdisplayedunderMembersrepresentstheaxiom

AmericaTypeCountry.

ThefactthatthesearenotdisplayedsimplyastheassociatedaxiomsisankeypartofthepurposeoftheOWLFrameList.ThetaskoftheOWLFrameListbelowistodescribetheCountryclass.ForauseritmakessensethatintheMemberssectionofthatOWLFrameListhewouldseealistoftheindividualsinthatclass.Itwouldmakelesssensetotheuserifasetofaxiomswasdisplayedthere.

FrameSections

OWLFramesaregroupedintoaseriesofsectionseachofwhichshowsaparticulartypeofaxioms.Inthediagrambelowwehaveaframesectionthatisrenderingalistofclassassertionaxioms.



FrameSectionRows

Glossary

TherearesometermsthatcomeupnaturallyinthediscussionofProtege4plugindevelopmentthatrequireabitofexplanation.TheProtege4pluginmechanismhasthreelayersandthetermsusedtodescribepluginsisslightlydifferentateachoftheselayers:

ExtensionPointistheeclipsetermforwhatProtegefolkoftencallaplugin.OSGi(http://www.osgi.org/Main/HomePage)isthebottomlayeroftheProtegepluginarchitecture.ItisapowerfulindustrystandardframeworkwhichprovidesmodularityandservicesbeyondthatprovidedbytheJavaspecifications.InOSGi,thetermOSGibundleisusedtorepresentaselfcontainedunitofcodethatcanbeintroducedintotheOSGiframeworkandwhichwillimportandexportclassesandresourcesinacontrolledway.AnOSGiBundleiscollectionofsoftwaregroupedintoasinglejarfile.WhenthissoftwarerunsintheOSGienvironment,itrunsinaprotectedspacewhereitcandefineexactlywhatjavaclassesfromthesurroundingenvironmentareneededandwhatjavaclassesareincompatiblewithitsoperation.Bundleshavenames,versionnumbers,developercontactinformationandactivationentrypoints.APluginisadeclaredservicethatimplementssomefunctionalityofusetotheProtegeplatform.TheProtegePluginmechanismisbasedontheEclipsepluginmechanismwherepluginsaredeclaredinafilecalledplugin.xml.TheEclipseRichClientPlatform(http://wiki.eclipse.org/index.php/Rich_Client_Platform)isanenvironmentbuiltontopofOSGiwhichprovidesadditionalfeaturestoeasethebuildingofa"Rich"client.Protege4onlyusessomeofthefeaturesofthisrichclientplatform.Inparticular,Protege4doesnotuseSWTandmanyofthegraphicalrelatedcapabilities.ButProtege4doesusethedeclarativeplugincapabilitiesprovidedbyeclipse.ItisherethatsomeofthepoweroftheOSGiplatformbecomesmanifest,becausewehavebeenabletouseonlythosebundlesfromtheeclipseRichClientplatformthatweneed.Inthissetting,OSGibundlescreatedaccordingtocertainconventionsbecomeEclipsePlugins.TheProtege4PluginlayerprovidessomeadditionalconveniencemethodsovertheEclipsePluginframework.CertaineclipsepluginsthatextendProtege4capabilitiesarecalledProtege4plugins.

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ThispagewaslastmodifiedonSeptember1,2013,at06:34.

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