ontologies commit
# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
# On branch cubrc
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#	modified:   pom.xml
#	new file:   src/main/java/alignment/karma/mapping/translation/D2rqMapping.java
#	new file:   src/main/java/alignment/karma/mapping/translation/KarmaTranslations.java
#	new file:   src/main/java/alignment/karma/mapping/translation/PersonMappingTranslations.java
#	new file:   src/main/java/alignment/karma/mapping/translation/TranslateMapping.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/LightWeightOntologyLoader.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/d2rq.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/karma.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/agent.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/amo.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/ao.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/artifact.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/bfo.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/bridge.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/cto.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/emo.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/ero.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/event.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/geo.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/graph.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/info.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/ito.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/meta.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/nlp.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/oboInOwl.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/purl.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/purl_ro.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/purl_rordf.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/quality.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/ro.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/snap.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/soa.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/span.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/spin.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/spin_rule.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/spin_sp.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/swrlb.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/time.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kdd/xo.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/kmdev.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/owl.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/personMappingOntology.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/r2rml.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/swrl.java
#	new file:   src/main/java/alignment/karma/mapping/translation/ontologies/xsd.java
#	new file:   src/main/java/alignment/karma/mapping/translation/query/KarmaMappingSparqlQuery.java
#	new file:   src/main/java/alignment/karma/mapping/translation/query/KarmaSparqlQueryVariable.java
#	modified:   src/main/java/edu/isi/karma/controller/command/alignment/GenerateR2RMLModelCommand.java
#	modified:   src/main/java/edu/isi/karma/modeling/alignment/GraphBuilder.java
#	new file:   src/main/java/resources/PersonMappingOntology.owl
#	new file:   src/main/java/resources/ontologies/15d338b7-8c06-43cf-b136-fb037a6a0324.owl
#	new file:   src/main/java/resources/ontologies/22-rdf-syntax-ns.rdf
#	new file:   src/main/java/resources/ontologies/AIRSAbductiveReasoningRules.owl
#	new file:   src/main/java/resources/ontologies/AIRSEmotionOntology.owl
#	new file:   src/main/java/resources/ontologies/AIRSGroundingOntology.owl
#	new file:   src/main/java/resources/ontologies/AIRSMetadataOntology.owl
#	new file:   src/main/java/resources/ontologies/AIRSMidLevelOntology.owl
#	new file:   src/main/java/resources/ontologies/AgentOntology.owl
#	new file:   src/main/java/resources/ontologies/AlgorithmicOntology.owl
#	new file:   src/main/java/resources/ontologies/ArtifactOntology.owl
#	new file:   src/main/java/resources/ontologies/COIndividuals_1.owl
#	new file:   src/main/java/resources/ontologies/CounterterrorismOntology.owl
#	new file:   src/main/java/resources/ontologies/DocumentModel_ILM.owl
#	new file:   src/main/java/resources/ontologies/EventOntology.owl
#	new file:   src/main/java/resources/ontologies/ExtendedRelationOntology.owl
#	new file:   src/main/java/resources/ontologies/GeopoliticalEntitiesAndCodes.owl
#	new file:   src/main/java/resources/ontologies/GeospatialOntology.owl
#	new file:   src/main/java/resources/ontologies/GraphOntology.owl
#	new file:   src/main/java/resources/ontologies/GroundingFramework.rdf
#	new file:   src/main/java/resources/ontologies/InformationEntityOntology.owl
#	new file:   src/main/java/resources/ontologies/InformationTechnologyOntology.owl
#	new file:   src/main/java/resources/ontologies/Interface4_rdf.owl
#	new file:   src/main/java/resources/ontologies/KDDOntology.rdf
#	new file:   src/main/java/resources/ontologies/LawEnforcementMode.owl
#	new file:   src/main/java/resources/ontologies/NLP_EventRelationTaxonomy.owl
#	new file:   src/main/java/resources/ontologies/QualityOntology.owl
#	new file:   src/main/java/resources/ontologies/TextRelationOntology.owl
#	new file:   src/main/java/resources/ontologies/TimeOntology.owl
#	new file:   src/main/java/resources/ontologies/al-Banshiri_Instances.owl
#	new file:   src/main/java/resources/ontologies/bfo-1.1.owl
#	new file:   src/main/java/resources/ontologies/d2rq.owl
#	new file:   src/main/java/resources/ontologies/dc-1.1.rdf
#	new file:   src/main/java/resources/ontologies/oboInOwl.owl
#	new file:   src/main/java/resources/ontologies/owl.rdf
#	new file:   src/main/java/resources/ontologies/rdf-schema.rdf
#	new file:   src/main/java/resources/ontologies/ro.owl
#	new file:   src/main/java/resources/ontologies/ro_bfo_bridge.owl
#	new file:   src/main/java/resources/ontologies/soa_ontology_3_1.owl
#	new file:   src/main/java/resources/ontologies/spin.rdf
#	new file:   src/main/java/resources/ontologies/spin_sp.rdf
#	new file:   src/main/java/resources/ontologies/swrl.owl
#	new file:   src/main/java/resources/ontologies/swrlb.owl
#	new file:   src/main/java/resources/ontologies/xo.owl
#	new file:   webkarma.iml
#
Merge remote-tracking branch 'origin/master' into cubrc

Conflicts:
	src/main/java/alignment/karma/mapping/translation/D2rqMapping.java
	src/main/java/alignment/karma/mapping/translation/PersonMappingTranslations.java
	src/main/java/alignment/karma/mapping/translation/ontologies/BadOntology.java
Merge branch 'cubrc' into cubrc-updated-dependencies

Conflicts:
	pom.xml
	webkarma.iml
updated dependency versions
everything but semantictypeutil moved
added dbtype as a top level class
moved of everything to appropriate modules

note that although this compiles, it will not run as required reflection functionality is not yet implemented
this is a working build of the modularized code
reflection added, seems to be working
fixed gitignore
fixed gitignore
updated pom files to use dependency management and proper versions of internal dependencies
moved some files around, moved python to the cleaning project. fixed offline generation
Merge branch 'origin/development'

Conflicts:
	.gitignore
	README.md
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Interpretor.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Partition.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgSynthesis.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Program.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature1.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature4.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/RecordDistiller.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Test.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Ruler.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Tokenizer.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/Tools.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/CntFeature.java
	karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordFeatureSet.java
	karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationOutput.java
	karma-commands/commands-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/alignment/GenerateR2RMLModelCommand.java
	karma-commands/commands-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/ApplyHistoryFromR2RMLModelCommand.java
	karma-commands/commands-alignment-openrdf/src/main/java/edu/isi/karma/kr2rml/WorksheetModelWriter.java
	karma-commands/commands-alignment/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner.java
	karma-commands/commands-alignment/src/main/java/edu/isi/karma/modeling/alignment/learner/SteinerNodes.java
	karma-commands/commands-alignment/src/main/java/edu/isi/karma/modeling/research/Approach1.java
	karma-commands/commands-alignment/src/main/java/edu/isi/karma/modeling/research/Approach2.java
	karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/InvokeCleaningServiceCommand.java
	karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/InvokeCleaningServiceCommandFactory.java
	karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/SubmitCleaningCommandFactory.java
	karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/DatabaseTableImport.java
	karma-commands/commands-import/import-xml/src/main/java/edu/isi/karma/imp/json/XMLImport.java
	karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/SubmitEditPythonTransformationCommand.java
	karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/SubmitPythonTransformationCommand.java
	karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/InvokeServiceCommand.java
	karma-common/src/main/java/edu/isi/karma/controller/command/CommandPreferences.java
	karma-common/src/main/java/edu/isi/karma/controller/history/CommandHistory.java
	karma-common/src/main/java/edu/isi/karma/imp/csv/CSVFileImport.java
	karma-common/src/main/java/edu/isi/karma/imp/json/JsonImport.java
	karma-common/src/main/java/edu/isi/karma/kr2rml/KR2RMLMapping.java
	karma-common/src/main/java/edu/isi/karma/kr2rml/KR2RMLMappingGenerator.java
	karma-common/src/main/java/edu/isi/karma/kr2rml/KR2RMLWorksheetRDFGenerator.java
	karma-common/src/main/java/edu/isi/karma/kr2rml/TemplateTermSet.java
	karma-common/src/main/java/edu/isi/karma/kr2rml/TemplateTermSetBuilder.java
	karma-common/src/main/java/edu/isi/karma/kr2rml/WorksheetR2RMLJenaModelParser.java
	karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilder.java
	karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphUtil.java
	karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphVizUtil.java
	karma-common/src/main/java/edu/isi/karma/modeling/alignment/SemanticModel.java
	karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraph.java
	karma-common/src/main/java/edu/isi/karma/rep/metadata/WorksheetProperties.java
	karma-common/src/main/java/edu/isi/karma/util/Preferences.java
	karma-common/src/main/java/edu/isi/karma/view/ViewPreferences.java
	karma-common/src/main/java/edu/isi/karma/webserver/ExecutionController.java
	karma-web/src/main/config/modeling.properties
	karma-web/src/main/webapp/index.jsp
	karma-web/src/main/webapp/publish/CSV/crystal-bridges-records_Sheet1
	karma-web/src/main/webapp/web-karma_1.html
	karma-web/src/main/webapp/web-karma_2.html
	pom.xml
resolved merge conflicts/artifacts
removed non-existent pom entry from parent pom
removed unneeded module dependencies, moved some files to the appropriate place
removed a bit of duplicate code
removed all unused imports
removed some commented out code that addressed issues with larger ontologies but removed funcionality