Hi Neil,
No. I do not have things working with a MySQL database yet.
Thank you for your suggestion to double-check renaming of the JDBC driver to driver.jar.
Yes. I have followed the directions provided and have placed the properly named driver.jar file into the Protege install root folder. (I followed that instruction the first time as stated in the documentation) I am still getting the same error.
Below is a tree listing of the directory where I have placed the JDBC driver.
I believe this is as per following the instructions. driver.jar is right at the top of the command output.
As I mentioned before, the driver testing I have done with DbSchema tells me the driver is good.
I have been experimenting with different MySQL database versions and JDBC drivers.
A few questions:
- As stated in the forum MySQL 5.5, 5.6, and 5.7 is supported. Is there a specific version recommended? For example,
mysql-5.7.36-linux-glibc2.12-x86_64.tar.gz should be good?
- And JDBC driver
mysql-connector-java-8.0.27.tar.gz should be good?
I am thinking maybe I have a bad combination of MySQL supported version and JDBC supported version on linux? could you provide the specific link to the supported linux mysql and JDBC drivers that have been proven to work from your experience?
Thank you.
Code: Select all
~/Protege_3.5$ tree
.
|-- driver.jar
|-- examples
|-- collaborativeNewspaper
|-- annotation_collaborativeNewspaper.pprj
|-- annotation_collaborativeNewspaper.rdf
|-- annotation_collaborativeNewspaper.rdfs
|-- collaborativeNewspaper.pins
|-- collaborativeNewspaper.pont
|__ collaborativeNewspaper.pprj
|-- collaborativePizza
|-- annotation_collaborativePizza.owl.pprj
|-- annotation_collaborativePizza.owl.rdf
|-- annotation_collaborativePizza.owl.rdfs
|-- collaborativePizza.owl
|__ collaborativePizza.owl.pprj
|-- newspaper
|-- newspaper.pins
|-- newspaper.pont
|__ newspaper.pprj
|-- pizza
|-- pizza.owl
|__ pizza.owl.pprj
|-- rdf
|-- MotorVehicle.pprj
|-- MotorVehicle.rdf
|__ MotorVehicle.rdfs
|-- server
|-- sqwrl
|-- SQWRLCollectionExamples.owl
|-- SQWRLCollectionExamples.pprj
|-- SQWRLCoreExamples.owl
|__ SQWRLCoreExamples.pprj
|__ wines
|-- wines.pins
|-- wines.pont
|__ wines.pprj
|-- lax.jar
|-- licensing.txt
|-- log4j.xml
|-- logging.properties
|-- logs
|-- protege_10.log
|-- protege_11.log
|-- protege_11.log.lck
|-- protege_12.log
|-- protege_13.log
|-- protege_14.log
|-- protege_15.log
|-- protege_16.log
|-- protege_17.log
|-- protege_17.log.lck
|-- protege_18.log
|__ protege_19.log
|-- looks.jar
|-- plugins
|-- ca.uvic.cs.chisel.jambalaya
|-- bsf.jar
|-- doc
|-- gradient.gif
|-- jambalaya_about.html
|-- jambalaya_docs.html
|-- quick_views.png
|__ shrimplogo.png
|-- gxl.jar
|-- jambalaya.jar
|-- js.jar
|-- layouts.jar
|-- libsea.jar
|-- license.html
|-- piccolo.jar
|-- piccolox.jar
|-- plugin.properties
|__ treemap.jar
|-- com.enterprise_architecture.essential.integration.widgets
|-- about_integration_tab.html
|-- bsf-all-3.0.jar
|-- COPYING.txt
|-- essentialAMLogo.jpg
|-- essentialProjectLogo.jpg
|-- help_integration_tab.html
|-- integration_engine.jar
|-- integration_icon_16px.png
|-- integration_tab.jar
|-- integration_tab.properties
|-- integration_tab.properties.EN
|-- js.jar
|-- jython.jar
|-- plugin.properties
|-- protege_banners_2017_integration.png
|-- readme.txt
|-- saxon9.jar
|-- script_job.jar
|-- xml-apis.jar
|__ xsltc.jar
|-- com.enterprise_architecture.essential.snapshot
|-- about_snapshot_tab.html
|-- COPYING.txt
|-- essentialAMLogo.jpg
|-- essentialProjectLogo.jpg
|-- essential-snapshot-tab-1.5.jar
|-- help_snapshot_tab.html
|-- plugin.properties
|-- protege_banners_2017_snapshot.png
|-- snapshot_icon_16px.png
|-- snapshot_icon.png
|-- snapshottab.properties
|__ snapshottab.properties.EN
|-- com.enterprise_architecture.essential.update
|-- about_update_tab.html
|-- activation.jar
|-- bsf-all-3.0.jar
|-- commons-io-1.4.jar
|-- compile_update_pack.sh
|-- COPYING.txt
|-- essentialAMLogo.jpg
|-- essentialProjectLogo.jpg
|-- essential-update-tab-3.0.jar
|-- examplepack.xml
|-- help_update_tab.html
|-- jaxb-api.jar
|-- jaxb-impl.jar
|-- js.jar
|-- jsr173_1.0_api.jar
|-- jython.jar
|-- plugin.properties
|-- plugin.properties.EN
|-- protege_banners_2017_update.png
|-- script_job.jar
|-- update_icon_16px.png
|-- updatepack.xsd
|-- updatetab.properties
|-- updatetab.properties.EN
|__ xml-apis.jar
|-- com.enterprise_architecture.essential.widgets
|-- about_easreport_tab.html
|-- auto_layout.png
|-- autoText_specification.png
|-- commons-codec-1.14.jar
|-- commons-codec-1.3
|__ LICENSE.txt
|-- commons-logging-1.1
|-- LICENSE.txt
|__ NOTICE.txt
|-- commons-logging-1.2.jar
|-- COPYING.txt
|-- essentialAMLogo.jpg
|-- essentialProjectLogo.jpg
|-- essentialreportxml.xsd
|-- essential-widgets-4.2.1.jar
|-- essential-xml-4.2.jar
|-- help_easreport_tab.html
|-- history.xml
|-- httpclient-4.5.10.jar
|-- httpcomponents-client-4.0
|-- LICENSE.txt
|__ NOTICE.txt
|-- httpcomponents-core-4.0.1
|-- LICENSE.txt
|__ NOTICE.txt
|-- httpcore-4.4.13.jar
|-- httpmime-4.5.10.jar
|-- JGoLayout.jar
|-- plugin.properties
|-- protege_banners_2017_viewer.png
|-- readme.txt
|-- reporttab.properties
|-- reporttab.properties.EN
|__ viewer_icon_16px.png
|-- dfki.protege.ontoviz
|-- build.xml
|-- grappa1_2.jar
|-- ontoviz-tab.jar
|-- protege.properties
|__ readme.txt
|-- edu.stanford.bmir.protegex.bp.ref
|-- about_bp_import.html
|-- about_bp_ref.html
|-- bioportalReference.jar
|-- bioportal-services-lib.jar
|-- glazedlists_java15-1.9.0.jar
|-- plugin.properties
|-- xpp3_min-1.1.4c.jar
|__ xstream-1.3.1.jar
|-- edu.stanford.smi.protege.collab
|-- about_protege_collab.html
|-- jcalendar.jar
|-- plugin.properties
|__ protege-collab.jar
|-- edu.stanford.smi.protege.script
|-- about_script_console.html
|-- antlr-2.7.6.jar
|-- asm-2.2.jar
|-- asm-analysis-2.2.jar
|-- asm-tree-2.2.jar
|-- asm-util-2.2.jar
|-- bsf.jar
|-- bsfperl.jar
|-- bsh.jar
|-- doap.rdf
|-- groovy-1.5.6.jar
|-- jarVersions.txt
|-- jruby.jar
|-- jython.jar
|-- plugin.properties
|-- ProtegeScript.jar
|__ readme
|-- edu.stanford.smi.protege.stringsearch
|-- doc
|__ about_string_search_tab.html
|-- plugin.properties
|-- readme
|__ string-search-tab.jar
|-- edu.stanford.smi.protegex.changeanalysis
|-- ca.uvic.cs.chisel.cajun.jar
|-- change-analysis.jar
|-- jcalendar-1.3.3.jar
|-- jcommon-1.0.16.jar
|-- jfreechart-1.0.13.jar
|-- layouts.jar
|-- org.eclipse.draw2d_3.2.100.v20070522.jar
|-- piccolo.jar
|-- piccolox.jar
|__ plugin.properties
|-- edu.stanford.smi.protegex.changes
|-- change-management.jar
|-- doc
|__ ChangesDoc.doc
|-- icu4j.jar
|-- plugin.properties
|__ projects
|-- changes.pprj
|-- changes.rdf
|__ changes.rdfs
|-- edu.stanford.smi.protegex.chatPlugin
|-- chat.jar
|__ plugin.properties
|-- edu.stanford.smi.protegex.datamaster
|-- about-datamaster.html
|-- datamaster.jar
|-- mysql-connector-COPYING
|-- mysql-connector-java-5.1.6-bin.jar
|-- mysql-connector-README.txt
|__ plugin.properties
|-- edu.stanford.smi.protegex.ezpal
|-- doc
|-- template.pins
|-- template.pont
|__ template.pprj
|-- ezpal-tab.jar
|-- plugin.properties
|__ readme
|-- edu.stanford.smi.protegex.facets_tab
|__ facet-constraints-tab.jar
|-- edu.stanford.smi.protegex.instance_tree
|__ instance-tree.jar
|-- edu.stanford.smi.protegex.metaanalysis
|-- meta-analysis.jar
|__ plugin.properties
|-- edu.stanford.smi.protegex.owl
|-- abox.owl
|-- absolute.owl
|-- antlr-2.7.5.jar
|-- antlr-runtime-3.3.jar
|-- arq-extra.jar
|-- arq.jar
|-- assert.owl
|-- axis.jar
|-- commons-discovery-0.4.jar
|-- commons-lang-2.0.jar
|-- commons-logging-1.1.1.jar
|-- concurrent.jar
|-- ddm.owl
|-- doap.rdf
|-- drools-compiler-5.4.0-SNAPSHOT.jar
|-- drools-core-5.4.0-SNAPSHOT.jar
|-- edtftpj-1.5.2.jar
|-- ekitspell.jar
|-- forms.owl
|-- icu4j_3.4.4.jar
|-- implicit-imports.repository
|-- iri.jar
|-- jcalendar.jar
|-- jdom.jar
|-- jena-dig.jar
|-- jena.jar
|-- jep-2.4.0.jar
|-- json.jar
|-- junit.jar
|-- kazuki.jar
|-- knowledge-api-5.4.0-SNAPSHOT.jar
|-- knowledge-internal-api-5.4.0-SNAPSHOT.jar
|-- log4j-1.2.12.jar
|-- mvel2-2.1.0.drools8.jar
|-- org.eclipse.jdt.core_3.7.0.v_B61.jar
|-- orphanNodesAlg.jar
|-- owl-portability.jar
|-- owl-portability-p3.jar
|-- OWLProfiles.owl
|-- OWLProfiles.pprj
|-- owlsyntax.jar
|-- plugin.properties
|-- protegeForms.owl
|-- protege.owl
|-- protege-owl.jar
|-- protege-system.forms
|-- query.owl
|-- rdfb.owl
|-- slf4j-api-1.5.8.jar
|-- slf4j-log4j12-1.5.8.jar
|-- sqwrl.owl
|-- ss.owl
|-- stax-api-1.0.1.jar
|-- swingx-1.0.jar
|-- swrla.owl
|-- swrl-api.jar
|-- swrla.pprj
|-- swrlb.owl
|-- swrl-drools-bridge.jar
|-- swrli.owl
|-- swrl-jess-bridge.jar
|-- swrlm.owl
|-- swrl.owl
|-- swrl-tab-p3.jar
|-- SWRLXML.owl
|-- swrlx.owl
|-- tbox.owl
|-- temporal.owl
|-- versions.txt
|-- wstx-asl-3.2.9.jar
|-- xercesImpl.jar
|-- xml-apis.jar
|__ xsp.owl
|-- edu.stanford.smi.protegex.owl.inference.pellet
|-- aterm-java-1.6.jar
|-- commons-lang-2.2.jar
|-- owlapi-apibinding.jar
|-- owlapi-api.jar
|-- owlapi-change.jar
|-- owlapi-debugging.jar
|-- owlapi-dig1_1.jar
|-- owlapi-functionalparser.jar
|-- owlapi-functionalrenderer.jar
|-- owlapi-impl.jar
|-- owlapi-krssparser.jar
|-- owlapi-metrics.jar
|-- owlapi-oboparser.jar
|-- owlapi-owlxmlparser.jar
|-- owlapi-owlxmlrenderer.jar
|-- owlapi-rdfapi.jar
|-- owlapi-rdfxmlparser.jar
|-- owlapi-rdfxmlrenderer.jar
|-- owlapi-util.jar
|-- pellet.jar
|-- plugin.properties
|-- protege-pellet.jar
|-- relaxngDatatype.jar
|-- versions.txt
|__ xsdlib.jar
|-- edu.stanford.smi.protegex.pal_tabs
|-- about_pal_tabs.html
|-- antlr.jar
|-- examples
|-- DatesAndTimes
|-- DatesAndTimes.pins
|-- DatesAndTimes.pont
|__ DatesAndTimes.pprj
|-- pal_query
|-- pal_query.pins
|-- pal_query.pont
|__ pal_query.pprj
|__ Worldhistory
|-- DatesAndTimes.pins
|-- DatesAndTimes.pont
|-- DatesAndTimes.pprj
|-- Worldhistory.pins
|-- Worldhistory.pont
|__ Worldhistory.pprj
|-- pal.jar
|__ plugin.properties
|-- edu.stanford.smi.protegex.prompt
|-- about_prompt.html
|-- doc
|-- activate_prompt.htm
|-- compare_mode.htm
|-- configure_prompt.htm
|-- conflicts_tab.htm
|-- create_op_dialog.htm
|-- creating.htm
|-- edit_dialog.htm
|-- edit_operation.htm
|-- extract_mode.htm
|-- images
|-- Add.gif
|-- BackReferences.gif
|-- choosename.gif
|-- chooserole.gif
|-- compare_mode.gif
|-- config1.gif
|-- config3.gif
|-- configure1.gif
|-- conflict_tab.gif
|-- Create.gif
|-- create_op_dialog.gif
|-- creati1.gif
|-- creati2.gif
|-- creati3.gif
|-- creati4.gif
|-- creating_op_tab.gif
|-- Delete.gif
|-- dummy_conflict.gif
|-- dummy.gif
|-- edit_dialog.gif
|-- enable1.gif
|-- enable2.gif
|-- Find.gif
|-- header_line.gif
|-- includ1.gif
|-- includ2.gif
|-- initia4.gif
|-- initial1gif.gif
|-- initial_menu.gif
|-- initial_open.gif
|-- instal1.gif
|-- Load.gif
|-- Local.gif
|-- Mapped.gif
|-- prompt_configure_box.gif
|-- prompt_init.gif
|-- prompt_uninit.gif
|-- Remove.gif
|-- result_window.gif
|-- select_class.gif
|-- serving_nerd.gif
|-- source1.gif
|-- source_bases.gif
|-- Source.gif
|-- suggest_tab.gif
|-- Up.gif
|-- View.gif
|-- view_sources2.gif
|__ warning.gif
|-- image_table.htm
|-- index.html
|-- initialize_prompt.htm
|-- install_prompt.htm
|-- merge_mode.htm
|-- move_frames_mode.htm
|-- new_operations.htm
|-- operations.htm
|-- overview.htm
|-- perform_operation.htm
|-- prompt_configure_box.htm
|-- prompt_menu.htm
|-- prompt_tab.htm
|-- remove_operation.htm
|-- remove_suffix.htm
|-- resolve_conflict.htm
|-- result_window.htm
|-- set_up_prompt.htm
|-- source_bases.htm
|-- suggestions.htm
|__ view_source_bases.htm
|-- jacl.jar
|-- jython.jar
|-- plugin.properties
|-- plugins
|-- ca.uvic.cs.cogz
|-- cajun.jar
|-- cogz.jar
|-- docs
|-- install.txt
|__ release_notes.txt
|-- gnujaxp.jar
|-- itext-1.4.3.jar
|-- jcommon-1.0.5.jar
|-- jfreechart-1.0.2-experimental.jar
|-- jfreechart-1.0.2.jar
|-- layouts.jar
|-- org.eclipse.draw2d_3.2.100.v20070522.jar
|-- org.eclipse.emf.common_2.4.0.v200806091234.jar
|-- org.eclipse.emf.ecore_2.4.0.v200806091234.jar
|-- org.eclipse.emf.ecore.xmi_2.4.0.v200806091234.jar
|-- org.eclipse.eodm_0.9.1.v200710090302.jar
|-- org.eclipse.eodm.doc_0.9.1.v200710090302.jar
|-- org.eclipse.eodm.editor_0.8.0.v200710090352.jar
|-- org.eclipse.eodm.owl_0.9.1.v200710090302.jar
|-- org.eclipse.eodm.rdf_0.9.1.v200710090302.jar
|-- piccolo.jar
|-- piccolox.jar
|-- pqviz.common.jar
|__ reportstyle.css
|-- edu.stanford.smi.protegex.promptx.foam
|-- align.jar
|-- commons-logging.jar
|-- config
|-- alignmentParametersComplete.txt
|-- alignmentParametersSimple.txt
|-- file_properties_local.xml
|-- manifest.txt
|-- rules.obj
|-- stopwords.txt
|__ tree.obj
|-- foam.jar
|-- googleapi.jar
|-- jwnl.jar
|-- kaon2.jar
|-- weka.jar
|__ xercesImpl.jar
|-- edu.stanford.smi.protegex.promptx.mappingDomainPSM
|__ mappingDomainPSM.jar
|-- edu.stanford.smi.protegex.promptx.simpleMappingStorage
|__ simpleMappingStorage.jar
|-- edu.stanford.smi.protegex.promptx.synonyms
|__ synonyms.jar
|__ edu.stanford.smi.protegex.promptx.umls
|-- kss-api-5.0.jar
|-- PromptUMLSPlugin.properties
|__ umls.jar
|-- prompt.jar
|-- tcljava.jar
|__ vkbc.jar
|-- edu.stanford.smi.protegex.query.lucene
|-- lucene-core.jar
|-- luceneQueryPlugin.jar
|-- phonetix.jar
|-- plugin.properties
|-- versions.txt
|__ xstream.jar
|-- edu.stanford.smi.protegex.rdf_backend
|-- about_rdf_backend.html
|-- plugin.properties
|-- rdf-api.jar
|-- rdf-backend.jar
|-- readme
|__ xerces.jar
|-- edu.stanford.smi.protegex.standard_extensions
|-- html_export
|-- footer.html
|-- header.html
|-- HTMLExportConfigurations.xml
|-- htmlexport.css
|-- htmlexport.properties
|__ images
|-- class.abstract.gif
|-- class.gif
|-- class.metaclass.abstract.gif
|-- class.metaclass.gif
|-- facet.gif
|-- instance.gif
|-- ProtegeLogo.gif
|-- slot.gif
|-- slot.inherited.gif
|-- slot.inherited.overridden.gif
|__ slot.overridden.gif
|-- JGo.jar
|-- JGoLayout.jar
|-- plugin.properties
|-- standard-extensions.jar
|__ standard_extensions_text.properties
|-- edu.stanford.smi.protegex.xml_tab
|-- about_xml_tab.html
|-- plugin.properties
|__ xml-tab.jar
|-- org.protege.owl.axiome
|-- axiome.jar
|-- collections-generic-4.01.jar
|-- colt-1.2.0.jar
|-- concurrent-1.3.4.jar
|-- jung-3d-2.0.jar
|-- jung-3d-demos-2.0.jar
|-- jung-algorithms-2.0.jar
|-- jung-api-2.0.jar
|-- jung-api-2.0-tests.jar
|-- jung-graph-impl-2.0.jar
|-- jung-io-2.0.jar
|-- jung-jai-2.0.jar
|-- jung-jai-samples-2.0.jar
|-- jung-samples-2.0.jar
|-- jung-visualization-2.0.jar
|-- plugin.properties
|-- stax-api-1.0.1.jar
|-- swingx-1.0.jar
|__ wstx-asl-3.2.6.jar
|-- org.protege.owl.mappingmaster
|-- jaxen-1.1.3.jar
|-- jdom.jar
|-- jxl.jar
|-- MappingMaster.jar
|-- plugin.properties
|-- ssm.owl
|-- stax-api-1.0.1.jar
|__ xml-apis.jar
|-- se.liu.ida.JessTab
|-- JessTab17.jar
|__ plugin.properties
|-- uk.ac.iam.soton.akt.tgviztab
|-- plugin.properties
|-- TG_v1.4.1.jar
|__ TGVizTab-v1.4-b2.jar
|-- uk.ac.man.cs.mig.coode.debugger
|-- OWLDebugger.jar
|__ plugin.properties
|-- uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
|-- jakarta-oro-2.0.8.jar
|-- ManchesterOWLSyntaxEditor.jar
|__ plugin.properties
|-- uk.ac.man.cs.mig.coode.owldoc
|-- AbstractSyntax.jar
|-- languages
|-- Labels-cn.xml
|-- Labels-es.xml
|__ Labels-fi.xml
|-- OWLDoc.jar
|__ plugin.properties
|-- uk.ac.man.cs.mig.coode.owlindividualstab
|-- OWLDLIndividualsTab.jar
|__ plugin.properties
|-- uk.ac.man.cs.mig.coode.owlviz
|-- batik-awt-util.jar
|-- batik-dom.jar
|-- batik-extension.jar
|-- batik-ext.jar
|-- batik-svg-dom.jar
|-- batik-svggen.jar
|-- batik-util.jar
|-- batik-xml.jar
|-- OWLViz.jar
|__ plugin.properties
|-- uk.ac.man.cs.mig.coode.protege.wizard
|-- BasicWizardsLibrary.jar
|__ plugin.properties
|__ uk.ac.man.cs.mig.coode.protege.wizard.owl
|-- meta.owl
|-- OWLWizards.jar
|__ plugin.properties
|-- Protege
|-- Protege.ico
|-- protege.jar
|-- Protege.lax
|-- protege.properties
|-- protege_text.properties
|-- readme.txt
|-- regid.2013-04.edu.stanford.protege_c4292884-1f07-11b2-bffa-ec480a7e09a1.swidtag
|-- run_protege_server.sh
|-- run_protege.sh
|-- shutdown_protege_server.sh
|-- unicode_panel.jar
|__ Uninstall_Protege 3.5
|-- InstallScript.iap_xml
|-- installvariables.properties
|-- Logs
|__ Protege_3.5_Install_03_30_2022_18_16_47.log
|-- uninstaller.jar
|-- Uninstall Protege 3.5
|__ Uninstall Protege 3.5.lax