Merge pull request pwin#6 from pwin/v2.26

update fork from bitbucket repo

Author: pwin

.gitignore

@@ -0,0 +1,25 @@
+# These are some examples of commonly ignored file patterns.
+# You should customize this list as applicable to your project.
+# Learn more about .gitignore:
+#     https://www.atlassian.com/git/tutorials/saving-changes/gitignore
+
+# Compiled Python bytecode
+*.py[cod]
+__pycache__
+
+# Log files
+*.log
+
+*.old
+*.save
+*.bug
+*.egg-info
+build
+doc/doctrees/
+doc/html/
+
+# Generated by MacOS
+.DS_Store
+
+# Generated by Windows
+Thumbs.db

MANIFEST.in

@@ -20,6 +20,9 @@ include ./README.rst
 
 exclude .hg
 exclude .hg/*
+exclude .git
+exclude .git/*
+exclude .gitignore
 
 exclude doc/examples/contraindications.py
 

README.rst

@@ -10,8 +10,7 @@ Owlready2
    :alt: download stats
 
 
-# The source of this fork is at https://bitbucket.org/jibalamy/owlready2/src/master/
-
+         
 Owlready2 is a module for ontology-oriented programming in Python 3, including an optimized RDF quadstore.
 
 Owlready2 can:
@@ -431,6 +430,7 @@ version 2 - 0.20
 version 2 - 0.21
 ****************
 
+* Use Pellet 2.3.1 (same version as Protégé) instead of 2.4 (which has a bug in SWRL for many builtin predicates including equals and matches)
 * Much faster mangement of annotations on relations
 * Bugfixes:
   - Fix bug on blank node in RDFlib/SPARQL support
@@ -439,11 +439,77 @@ version 2 - 0.21
   - Fix 'no query solution' error in search()
   - Fix literal support in RDF lists, causing "TypeError: '<' not supported between instances of 'NoneType' and 'int'" when saving ontologies
   - Fix DifferentFrom SWRL builtin
+  - Fix string parsing in SWRL rules
+  - Fix string and boolean literal representation (str/repr) in SWRL rules
+  - Fix the inverse of subproperties having a symmetric superproperty
+
+version 2 - 0.22
+****************
+
+* Add support for disjoint unions (Class.disjoint_unions)
+* Add deepcopy support on class constructs, and automatically deep-copy constructs when needed (i.e. no more OwlReadySharedBlankNodeError)
+* Support the creation of blank nodes with RDFlib
+
+version 2 - 0.23
+****************
+
+* Add get_parents_of(), get_instances_of(), get_children_of() methods to ontology, for querying the hierarchical relations defined in a given ontology
+* Use Thing as default value for restrictions with number, instead of None
+* Add 'filter' parameter to save(), for filtering the entities saved (contributed by Javier de la Rosa)
+* Bugfixes:
+  - Fix value restriction with the false value 
+  - Fix blank node loading from different ontologies
+  - Fix constructs reused by several classes
+  - Fix 'Class.is_a = []' was not turning the list into an Owlready list
+  - Fix destroy_entity() - was not destroying the IRI of the entity
+  - Improve setup.py: ignore Cython if Cython installation fails
+
+version 2 - 0.24
+****************
+
+* Support intersection of searches (e.g. World.search(...) & World.search(...))
+* Add owlready2.reasoning.JAVA_MEMORY
+* Move development repository to Git
+* Bugfixes:
+  - Fix parsing of NTriples files that do not end with a new line
+  - Fix KeyError with Prop.python_name when several properties share the same name
+  - Fix get_ontology() calls in Python module imported by ontologies in a World that is not default_world
+  - Fix use of PyMedTermino2 in a World that is not default_world
+  - Fix World.as_rdflib_graph().get_context(onto) for ontology added after the creation of the RDFLIB graph
+  - Fix destroying SWRL rules
+  - Fix disjoint with non-atomic classes
+ 
+version 2 - 0.25
+****************
+
+* Allow the declaration of custom datatypes with declare_datatype()
+* Support the annotation of annotations (e.g. a comment on a comment)
+* search() now support the "subproperty_of" argument
+* search() now support the "bm25" argument (for full-text searches)
+* Bugfixes:
+  - Fix Concept.descendant_concepts() in PymedTermino2
+  - Update already loaded properties when new ontologies are loaded
+  - Now accept %xx quoted characters in file:// URL
+  - Improve error message on punned entities
+  - Property.get_relations() now considers inverse properties
+  - Fix "AttributeError: 'mappingproxy' object has no attribute 'pop'" error
+  - Fix Thing.instances()
 
+version 2 - 0.26
+****************
+
+* Module owlready2.dl_render allows rendering entities to Description Logics (contributed by Simon Bin)
+* Bugfixes:
+  - Adjustment in the comparison of strings  from SameAs and DiferrentFrom,  allowing equal comparison regardless of the case-sensitive (contributed by Thiago Feijó)
+  - Fix transitive equivalent_to relations between classes and OWL constructs
+  - Fix AnnotationProperty[entity] where entity is a predefined OWL entity (e.g. comment or Thing)
+  - Fix entity.AnnotationProperty where entity is a predefined OWL entity (e.g. comment or Thing)
+
+
 Links
 -----
 
-Owlready2 on BitBucket (development repository): https://bitbucket.org/jibalamy/owlready2
+Owlready2 on BitBucket (Git development repository): https://bitbucket.org/jibalamy/owlready2
 
 Owlready2 on PyPI (Python Package Index, stable release): https://pypi.python.org/pypi/Owlready2
 

TODO.rst

@@ -4,7 +4,6 @@ Owlready2 TODO list
 * Add support for property chain in entity.property.indirect()
 * Add functions/methods for copying entities from an ontology to another
 * Obtain individual property value inferred by HermiT
-* Add rule support
 
 * Support additional file formats:
   * OWL/XML write

__init__.py

@@ -17,7 +17,7 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-VERSION = "0.20"
+VERSION = "0.25"
 
 JAVA_EXE = "java"
 
@@ -61,7 +61,7 @@
 owlready2.namespace.IndividualValueList     = IndividualValueList
 owlready2.entity.Thing              = Thing
 owlready2.entity.Nothing            = Nothing
-owlready2.entity.ClassConstruct     = ClassConstruct
+owlready2.entity.Construct          = Construct
 owlready2.entity.And                = And
 owlready2.entity.Or                 = Or
 owlready2.entity.Not                = Not
@@ -82,20 +82,20 @@
 owlready2.disjoint.Or = Or
 owlready2.prop.Restriction             = Restriction
 owlready2.prop.ConstrainedDatatype     = ConstrainedDatatype
-owlready2.prop.ClassConstruct          = ClassConstruct
+owlready2.prop.Construct               = Construct
 owlready2.prop.AnnotationProperty      = AnnotationProperty
 owlready2.prop.Thing                   = Thing
-#owlready2.prop.ValueList               = ValueList
+owlready2.prop.PropertyChain           = PropertyChain
 owlready2.prop._check_superclasses     = True
 
 owlready2.prop.ThingClass              = ThingClass
 owlready2.prop.And                     = And
 owlready2.prop.Or                      = Or
 owlready2.prop.OneOf                   = OneOf
-owlready2.annotation.ClassConstruct    = ClassConstruct
+owlready2.annotation.Construct         = Construct
 
 owlready2.individual._keep_most_specific = _keep_most_specific
-owlready2.individual.ClassConstruct      = ClassConstruct
+owlready2.individual.Construct           = Construct
 owlready2.individual.TransitiveProperty  = TransitiveProperty
 owlready2.individual.SymmetricProperty   = SymmetricProperty
 owlready2.individual.ReflexiveProperty   = ReflexiveProperty
@@ -104,6 +104,9 @@
 owlready2.class_construct.Thing       = Thing
 owlready2.class_construct.ThingClass  = ThingClass
 owlready2.class_construct.EntityClass = EntityClass
+
+#owlready2.reasoning.Construct = Construct
+
 del owlready2
 
 from owlready2.rule            import *

annotation.py

@@ -52,25 +52,34 @@
 #         return bnode
 
 class _AnnotList(CallbackListWithLanguage):
-  __slots__ = ["_property", "_target", "_target_d", "_annot"]
-  def __init__(self, l, source, property, target, target_d, annot):
+  __slots__ = ["namespace", "_property", "_target", "_target_d", "_annot", "_od_2_bnode"]
+  def __init__(self, l, source, property, target, target_d, annot, namespace, od_2_bnode):
     list.__init__(self, l)
-    self._obj      = source
-    self._property = property
-    self._target   = target
-    self._target_d = target_d
-    self._annot    = annot
+    self.namespace   = namespace
+    self._obj        = source
+    self._property   = property
+    self._target     = target
+    self._target_d   = target_d
+    self._annot      = annot
+    self._od_2_bnode = od_2_bnode
 
   def _callback(self, obj, old):
     old = set(old)
     new = set(self)
 
+    if isinstance(obj, _AnnotList): # Annotate an annotation
+      storid = obj._od_2_bnode[self._target, self._target_d]
+    else:
+      storid = obj.storid
+    
     # Add before, in order to avoid destroying the axiom and then recreating, if all annotations are modified
     for added in new - old:
-      x = obj.namespace.ontology._add_annotation_axiom(obj.storid, self._property, self._target, self._target_d, self._annot, *obj.namespace.ontology._to_rdf(added))
+      o, d = obj.namespace.ontology._to_rdf(added)
+      bnode = obj.namespace.ontology._add_annotation_axiom(storid, self._property, self._target, self._target_d, self._annot, o, d)
+      self._od_2_bnode[o, d] = bnode
 
     for removed in old - new:
-      obj.namespace.ontology._del_annotation_axiom    (obj.storid, self._property, self._target, self._target_d, self._annot, *obj.namespace.ontology._to_rdf(removed))
+      obj.namespace.ontology._del_annotation_axiom(storid, self._property, self._target, self._target_d, self._annot, *obj.namespace.ontology._to_rdf(removed))
 
 
 class AnnotationPropertyClass(PropertyClass):
@@ -80,34 +89,43 @@ class AnnotationPropertyClass(PropertyClass):
   def __getitem__(Annot, entity):
     if isinstance(entity, tuple):
       source, property, target = entity
-      if hasattr(source,   "storid"):
-        world = source.namespace.world # if Annot is in owl_world (e.g. comment), use the world of the source
-        source_orig = source
-        source      = source.storid
+      
+      if   hasattr(source, "storid"):
+        namespace = source.namespace # if Annot is in owl_world (e.g. comment), use the namespace of the source
+      elif isinstance(source, _AnnotList):
+        namespace = source._obj.namespace
       else:
-        world = self.namespace.world
+        namespace = Annot.namespace
+        
       if hasattr(property, "storid"): property = property.storid
-      target, target_d = world._to_rdf(target)
+      target, target_d = namespace.world._to_rdf(target)
+      
+      if   hasattr(source, "storid"):
+        source_orig = source
+        source      = source.storid
+      elif isinstance(source, _AnnotList):
+        source_orig = source
+        source      = source._od_2_bnode[target, target_d]
+        
       l = []
-      for bnode in world._get_annotation_axioms(source, property, target, target_d):
-        for o, d in world._get_triples_sp_od(bnode, Annot.storid):
-          l.append(world._to_python(o, d))
+      
+      od_2_bnode = {}
+      for bnode in namespace.world._get_annotation_axioms(source, property, target, target_d):
+        for o, d in namespace.world._get_triples_sp_od(bnode, Annot.storid):
+          l.append(namespace.world._to_python(o, d))
+          od_2_bnode[o, d] = bnode
 
-      return _AnnotList(l, source_orig, property, target, target_d, Annot.storid)
+      return _AnnotList(l, source_orig, property, target, target_d, Annot.storid, namespace, od_2_bnode)
 
     else:
-      if Annot is entity.namespace.world._props.get(Annot._python_name) and not isinstance(entity, ClassConstruct): # use cached value
+      if Annot is entity.namespace.world._props.get(Annot._python_name) and not isinstance(entity, Construct): # use cached value
         r = getattr(entity, Annot._python_name)
         if isinstance(r, list): return r # May not be a list if hacked (e.g. Concept.terminology)
       return Annot._get_values_for_individual(entity)
-      
+    
   def __setitem__(Annot, index, values):
     if not isinstance(values, list): values = [values]
-    
-    if isinstance(index, tuple):
-      Annot[index].reinit(values)
-    else:
-      return setattr(index, Annot.python_name, values)
+    Annot[index].reinit(values)
 
   def __call__(Prop, type, c, *args):
     raise ValueError("Cannot create a property value restriction on an annotation property!")

base.py

@@ -114,7 +114,7 @@ def _universal_abbrev(iri):
 _universal_abbrev("http://www.w3.org/2002/07/owl#FunctionalProperty")
 _universal_abbrev("http://www.w3.org/2002/07/owl#InverseFunctionalProperty")
 
-SPECIAL_ATTRS      = { "namespace",  "name", "_name", "iri", "_iri", "storid", "is_a", "equivalent_to", "_equivalent_to", "disjoint_with", "_disjoint_with", "defined_class", "__class__", "__qualname__", "__module__", "__doc__", "__bases__" }
+SPECIAL_ATTRS      = { "namespace",  "name", "_name", "iri", "_iri", "storid", "is_a", "equivalent_to", "_equivalent_to", "disjoint_with", "_disjoint_with", "defined_class", "_disjoint_unions", "__class__", "__qualname__", "__module__", "__doc__", "__bases__" }
 SPECIAL_PROP_ATTRS = { "namespace",  "name", "_name", "python_name", "_python_name", "_domain", "_property_chain", "_inverse_property", "inverse_property", "inverse", "_range", "iri", "_iri", "storid", "is_a", "equivalent_to", "_equivalent_to", "disjoint_with", "_disjoint_with", "__class__", "__qualname__", "__module__", "__doc__", "__bases__" }
 
 
@@ -183,6 +183,21 @@ def set_datatype_iri(datatype, iri):
   _universal_datatype_2_abbrev         [datatype] =  _universal_iri_2_abbrev[iri]
   _universal_datatype_2_abbrev_unparser[datatype] = (_universal_iri_2_abbrev[iri], unparser)
 
+  
+def declare_datatype(datatype, iri, parser, unparser):
+  storid = _universal_abbrev(iri)
+  from owlready2 import WORLDS
+  for world in WORLDS:
+    world.graph.execute("INSERT INTO resources VALUES (?,?)", (storid, iri))
+    if world.graph._abbreviate_d:
+      world.graph._abbreviate_d  [iri]    = storid
+      world.graph._unabbreviate_d[storid] = iri
+      
+  _universal_datatype_2_abbrev         [datatype] =  storid
+  _universal_datatype_2_abbrev_unparser[datatype] = (storid, unparser)
+  _universal_abbrev_2_datatype         [storid]   =  datatype
+  _universal_abbrev_2_datatype_parser  [storid]   = (datatype, parser)
+  return storid
 
 owl_alldisjointproperties = _universal_abbrev("http://www.w3.org/2002/07/owl#AllDisjointProperties")
 owl_equivalentproperty    = _universal_abbrev("http://www.w3.org/2002/07/owl#equivalentProperty")
@@ -255,6 +270,13 @@ def set_datatype_iri(datatype, iri):
 owl_bottomobjectproperty     = _universal_abbrev("http://www.w3.org/2002/07/owl#bottomObjectProperty")
 owl_bottomdataproperty       = _universal_abbrev("http://www.w3.org/2002/07/owl#bottomDataProperty")
 
+owl_disjointunion            = _universal_abbrev("http://www.w3.org/2002/07/owl#disjointUnionOf")
+
+#owlready_direct_is_a         = _universal_abbrev("http://www.lesfleursdunormal.fr/static/_downloads/owlready_ontology.owl#direct_is_a")
+#owlready_is_a_construct         = _universal_abbrev("http://www.lesfleursdunormal.fr/static/_downloads/owlready_ontology.owl#is_a_construct")
+#owlready_context_is_a        = _universal_abbrev("http://www.lesfleursdunormal.fr/static/_downloads/owlready_ontology.owl#context_is_a")
+owlready_concrete            = _universal_abbrev("http://www.lesfleursdunormal.fr/static/_downloads/owlready_ontology.owl#concrete")
+
 issubclass_python = issubclass