bump owlapi versions to 3.5-SNAPSHOT

switch to com.github.ansell.owlapi as package to differentiate from upstream

add .gitignore

add slf4j-api dependency

add metainf-services dependency

add sesame dependencies

add commons-io test dependency to contract

avoid depending on junit and mockito in pom.xml by using dependencyManagement
switch the URL in the generated by message to this github fork
use maven properties file to fetch the current version

avoid synchronising static method for singleton creation
add log4j.properties files for tests
javadoc OWLRDFVocabulary so full URIs show up as tooltips in IDE
javadoc OWLRDFVocabulary.BUILT_IN_ANNOTATION_PROPERTY_IRIS
catch KRSS Error that can be thrown in ParsableOWLOntologyFactory
convert OWLOntologyManagerImpl to use ConcurrentMap and volatile variables

use concurrentmap in OWLOntologyManagerImpl for potential increased throughput internally as it is used everywhere in the api to track ontologies and their closures

make non-final variables in OWLOntologyManagerImpl volatile
convert OWLOntologyManagerImpl.autoGeneratedURICounter to use AtomicInteger
extend Namespaces enum with common prefixes

common prefixes are virtually never changed or assigned in any other way, without making them mandatory

also provide transformation to the OpenRDF Namespace class

add inUse boolean parameter to Namespaces to avoid legacy namespaces
IRI extensions to support org.openrdf.model.URI
OWLOntologyID extensions including support for org.openrdf.model.URI
add new helper constructor in SetOntologyID
add method of removing ontology from OWLOntologyManager using an OWLOntologyID

using this method ontologies can be easily removed even without pulling in the ontology, if the ontology is not in memory for instance
rework OWLObjectImpl.equals and OWLObjectImpl.hashCode

add note about OWLObjectImpl.hashCode being a source of errors in mutable objects and hashtables

includes an implementation of equals for OWLFacetRestriction that previously relied on the equals implementation in OWLObjectImpl that was broken by design, as it was only ever supposed to be a stub

fixed the bug for the future by ensuring that any class which overrides OWLObjectImpl overrides .equals and that they still have access to the stub equals implementation using super.owlObjectImplEquals(other) to avoid recoding it

fixed the hashcode implementation if objects are mutable, which they definitely are, as previously the hashcode on the first call to hashCode stayed even if the state changed, which would have caused very hard to find bugs

expand logic in OWLObjectImpl.equals and make owlObjectImplEquals non-abstract so it can be called from immediate subclasses

add calls to super.owlObjectImplEquals at the end of calls where previously there were calls to .equals at the start

should be more efficient this way as the most specific information, ie, the most specific interface is being checked straight after the null and this equals checks

fix bug in OWLObjectInverseOfImpl

remove some details from OWLFacetRestrictionImpl

remove another equality test that was added in the previous change that broke something
3516742 : consolidate RDF related classes into a single location
3521488 : switch to java.util.ServiceLoader for ParserFactory implementations

single location for OntologyFormat classes so they can be discovered

implement OntologyStorerFactoryRegistry and change references to formats

move TurtleOntologyFormat that was missed before

move default ontology format

add slf4j-api and logging configuration to api and apibinding so that during tests, service loading failures are displayed

add missing compile scope dependencies that aren't being passed through by owlapi-apibinding with runtime dependency scopes

update assembly plugin and add metaInf-services descriptor handler to merge services files in distribution

make dlsyntax a runtime dependency of owlapi-apibinding

constrain to only catch Error's that jump out of the KRSS parser

add test for OWLOntologyStorerFactoryRegistry

add note in AbstractServiceLoader to print the number of loaded services to the log

remove unnecessary circular reference between OWLOntologyFormat and PrefixOWLOntologyFormat

as... methods are actually simpler done as casts, as are instanceof calls

add specific getKey method to OWLOntologyFormat

fix tests

close output stream

reduce logging

fix hashcode in DefaultOntologyFormat

fix registry test tearDown

check if test ontology loaded properly by checking its axiom count

this has been failing tests with obscure errors due to relative comparisons that assume the ontology always loads properly

lower debugging level

allow cases with only annotations

remove explicit classloader from serviceloader call as it causes tests to fail in my openjdk-7 install

remove tests and references to the static instance

fix RDF/XML and OWLXML bug where OWLXML was being used to parse RDF/XML without error due to the lack of ordering for parsers in the SPI implementation

lower debug level

OWLManager changes

add new OWLManager method to enable use of custom ontology storer registries

extend ParsableOWLOntologyFactory to allow custom parser registries to be used

avoid NullPointerException and return Collections.emptyList() instead

implement OWLReasonerFactoryRegistry

make ontology storer factory registry test immune to changes in the SPI dependencies by clearing the registry before each run

move new OBOOntologyFormat direct dependencies into owlapi-api module

fix ConcurrentMap logic in AbstractServiceLoader

use OWLOntologyManagerFactoryRegistry instead of OWLManager

OWLOntologyManagerFactoryRegistry is a service provider interface front to track OWLManagerFactory instances using META-INF/services property files which can in turn provide OWLManager instances.

fix message

note in OWLReasonerFactoryRegistry that static instance is not mandatory

add compareTo for OWLOntologyFormat based on key string compareTo

make formats backwards compatible for instanceof, equals, and compareTo

work on compatibility so new interfaces are geared towards o.s.o.formats.*

move OWLManager from apibinding to impl to match its dependencies

move OWLFunctionalSyntaxFactory from apibinding to functional

uses service provider interface now, so the previous hard requirement on OWLManager is not present

api module now a runtime dependency for apibinding, as the tests are compiled using the runtime scope

remove metainf-services dependency in apibinding as OWLManager is gone

add SPI for concrete subclasses of OWLOntologyFormat along with Registry

Factory classes are needed as OWLOntologyFormat instances are allowed to be mutable, and all uses of OWLOntologyFormat so far is using "new XYZOntologyFormat()"

add RioRDFOntologyFormat and NTriplesOntologyFormat

migrate RDFXMLOntologyFormat and TurtleOntologyFormat so they are backwards compatible and can be used with the rio storer and parser in future

reform AbstractServiceLoader.get to explicitly use .equals instead of either .equals or .hashcode based on the implementation

add debug logging for service loading

add IRIs to OWLProfiles and a registry so they can be fetched based on their IRI

add accessor to go directly to a single reasoner instead of going through get() that will always return a collection
3536150 : fix bug with ontologyIRI and versionIRI loading ontology multiple times

before the patch, TypeOntologyHandler and TPVersionIRIHandler both overwrite existing values in the OWLOntologyID for the ontology

after the patch, TypeOntologyHandler and TPVersionIRIHandler both only set the values of ontologyIRI and versionIRI in the OWLOntologyID if they did not exist previously, so the first setting wins, instead of the current scenario where the last setting sometimes wins...

work on another case where the ontologyIRI in the ontologyID does not match the ontology document, and it is desirable to keep the ontologyIRI in the ontologyID instead of replacing it with the one in the document
3566810 : add RuntimeException hack to make getOntology consistent with createOntology

OWLOntologyManager containsVersion and getOntologyIDsByVersion
RIO-73 : ignore uncommon UTF8-BOM case