def check_term(conn, term, predicates):
cur = conn.cursor()
html = gizmos.tree.build_tree(cur, "obi", term, predicate_ids=predicates)
# Create the DOM document element
parser = html5lib.HTMLParser(
tree=html5lib.treebuilders.getTreeBuilder("dom"))
dom = parser.parse(html)
# get the DOM tree
top = dom.documentElement
# Create the initial state (from pyRdfa)
actual = Graph()
options = Options(
output_default_graph=True,
output_processor_graph=True,
space_preserve=True,
transformers=[],
embedded_rdf=True,
vocab_expansion=False,
vocab_cache=True,
vocab_cache_report=False,
refresh_vocab_cache=False,
check_lite=False,
experimental_features=True,
)
state = ExecutionContext(
top,
actual,
base="http://purl.obolibrary.org/obo/",
options=options,
rdfa_version="1.1",
)
# Add the RDFa to the RDFLib graph (recursive)
parse_one_node(top, actual, None, state, [])
expected = Graph()
if predicates:
expected.parse(f"tests/resources/obi-tree-{term}-predicates.ttl",
format="turtle")
else:
expected.parse(f"tests/resources/obi-tree-{term}.ttl", format="turtle")
compare_graphs(actual, expected)
def _parse_1_1(node, graph, parent_object, incoming_state, parent_incomplete_triples) :
"""The (recursive) step of handling a single node. See the
U{RDFa syntax document<http://www.w3.org/TR/rdfa-syntax>} for further details.
This is the RDFa 1.1 (and higher) version.
@param node: the DOM node to handle
@param graph: the RDF graph
@type graph: RDFLib's Graph object instance
@param parent_object: the parent's object, as an RDFLib URIRef
@param incoming_state: the inherited state (namespaces, lang, etc)
@type incoming_state: L{state.ExecutionContext}
@param parent_incomplete_triples: list of hanging triples (the missing resource set to None) to be handled (or not)
by the current node.
@return: whether the caller has to complete it's parent's incomplete triples
@rtype: Boolean
"""
# Update the state. This means, for example, the possible local settings of
# namespaces and lang
state = None
state = ExecutionContext(node, graph, inherited_state=incoming_state)
#---------------------------------------------------------------------------------
# Handle the special case for embedded RDF, eg, in SVG1.2.
# This may add some triples to the target graph that does not originate from RDFa parsing
# If the function return TRUE, that means that an rdf:RDF has been found. No
# RDFa parsing should be done on that subtree, so we simply return...
if state.options.host_language in accept_embedded_rdf and node.nodeType == node.ELEMENT_NODE and handle_embeddedRDF(node, graph, state) :
return
#---------------------------------------------------------------------------------
# calling the host language specific massaging of the DOM
if state.options.host_language in host_dom_transforms and node.nodeType == node.ELEMENT_NODE :
for func in host_dom_transforms[state.options.host_language] : func(node, state)
#---------------------------------------------------------------------------------
# First, let us check whether there is anything to do at all. Ie,
# whether there is any relevant RDFa specific attribute on the element
#
if not has_one_of_attributes(node, "href", "resource", "about", "property", "rel", "rev", "typeof", "src", "vocab", "prefix") :
# nop, there is nothing to do here, just go down the tree and return...
for n in node.childNodes :
if n.nodeType == node.ELEMENT_NODE : parse_one_node(n, graph, parent_object, state, parent_incomplete_triples)
return
#-----------------------------------------------------------------
# The goal is to establish the subject and object for local processing
# The behaviour is slightly different depending on the presense or not
# of the @rel/@rev attributes
current_subject = None
current_object = None
typed_resource = None
if has_one_of_attributes(node, "rel", "rev") :
# in this case there is the notion of 'left' and 'right' of @rel/@rev
# in establishing the new Subject and the objectResource
# set first the subject
if node.hasAttribute("about") :
current_subject = state.getURI("about")
if node.hasAttribute("typeof") : typed_resource = current_subject
# get_URI may return None in case of an illegal CURIE, so
# we have to be careful here, not use only an 'else'
if current_subject == None :
current_subject = parent_object
else :
state.reset_list_mapping(origin = current_subject)
# set the object resource
current_object = state.getResource("resource", "href", "src")
if node.hasAttribute("typeof") and not node.hasAttribute("about") :
if current_object == None :
current_object = BNode()
typed_resource = current_object
if not node.hasAttribute("inlist") and current_object != None :
# In this case the newly defined object is, in fact, the head of the list
# just reset the whole thing.
state.reset_list_mapping(origin = current_object)
elif node.hasAttribute("property") and not has_one_of_attributes(node, "content", "datatype") :
# this is the case when the property may take hold of @src and friends...
if node.hasAttribute("about") :
current_subject = state.getURI("about")
if node.hasAttribute("typeof") : typed_resource = current_subject
# get_URI_ref may return None in case of an illegal CURIE, so
# we have to be careful here, not use only an 'else'
if current_subject == None :
current_subject = parent_object
else :
state.reset_list_mapping(origin = current_subject)
if typed_resource == None and node.hasAttribute("typeof") :
typed_resource = state.getResource("resource", "href", "src")
if typed_resource == None :
typed_resource = BNode()
current_object = typed_resource
else :
current_object = current_subject
else :
# in this case all the various 'resource' setting attributes
# behave identically, though they also have their own priority
current_subject = state.getResource("about", "resource", "href", "src")
# get_URI_ref may return None in case of an illegal CURIE, so
# we have to be careful here, not use only an 'else'
if current_subject == None :
if node.hasAttribute("typeof") :
current_subject = BNode()
else :
current_subject = parent_object
else :
state.reset_list_mapping(origin = current_subject)
# in this case no non-literal triples will be generated, so the
# only role of the current_object Resource is to be transferred to
# the children node
current_object = current_subject
if node.hasAttribute("typeof") : typed_resource = current_subject
# ---------------------------------------------------------------------
## The possible typeof indicates a number of type statements on the typed resource
for defined_type in state.getURI("typeof") :
if typed_resource :
graph.add((typed_resource, ns_rdf["type"], defined_type))
# ---------------------------------------------------------------------
# In case of @rel/@rev, either triples or incomplete triples are generated
# the (possible) incomplete triples are collected, to be forwarded to the children
incomplete_triples = []
for prop in state.getURI("rel") :
if not isinstance(prop,BNode) :
if node.hasAttribute("inlist") :
if current_object != None :
state.add_to_list_mapping(prop, current_object)
else :
incomplete_triples.append((None, prop, None))
else :
theTriple = (current_subject, prop, current_object)
if current_object != None :
graph.add(theTriple)
else :
incomplete_triples.append(theTriple)
else :
state.options.add_warning(err_no_blank_node % "rel", warning_type=IncorrectBlankNodeUsage, node=node.nodeName)
for prop in state.getURI("rev") :
if not isinstance(prop,BNode) :
theTriple = (current_object,prop,current_subject)
if current_object != None :
graph.add(theTriple)
else :
incomplete_triples.append(theTriple)
else :
state.options.add_warning(err_no_blank_node % "rev", warning_type=IncorrectBlankNodeUsage, node=node.nodeName)
# ----------------------------------------------------------------------
# Generation of the literal values. The newSubject is the subject
# A particularity of property is that it stops the parsing down the DOM tree if an XML Literal is generated,
# because everything down there is part of the generated literal.
if node.hasAttribute("property") :
ProcessProperty(node, graph, current_subject, state, typed_resource).generate_1_1()
# ----------------------------------------------------------------------
# Setting the current object to a bnode is setting up a possible resource
# for the incomplete triples downwards
if current_object == None :
object_to_children = BNode()
else :
object_to_children = current_object
#-----------------------------------------------------------------------
# Here is the recursion step for all the children
for n in node.childNodes :
if n.nodeType == node.ELEMENT_NODE :
_parse_1_1(n, graph, object_to_children, state, incomplete_triples)
# ---------------------------------------------------------------------
# At this point, the parent's incomplete triples may be completed
for (s,p,o) in parent_incomplete_triples :
if s == None and o == None :
# This is an encoded version of a hanging rel for a collection:
incoming_state.add_to_list_mapping( p, current_subject )
else :
if s == None : s = current_subject
if o == None : o = current_subject
graph.add((s,p,o))
# Generate the lists, if any and if this is the level where a new list was originally created
if state.new_list and not state.list_empty() :
for prop in state.get_list_props() :
vals = state.get_list_value(prop)
heads = [ BNode() for r in vals ] + [ ns_rdf["nil"] ]
for i in xrange(0, len(vals)) :
graph.add( (heads[i], ns_rdf["first"], vals[i]) )
graph.add( (heads[i], ns_rdf["rest"], heads[i+1]) )
# Anchor the list
graph.add( (state.get_list_origin(), prop, heads[0]) )
# -------------------------------------------------------------------
# This should be it...
# -------------------------------------------------------------------
return
def _parse_1_1(node, graph, parent_object, incoming_state,
parent_incomplete_triples):
"""The (recursive) step of handling a single node. See the
U{RDFa syntax document<http://www.w3.org/TR/rdfa-syntax>} for further details.
This is the RDFa 1.1 (and higher) version.
@param node: the DOM node to handle
@param graph: the RDF graph
@type graph: RDFLib's Graph object instance
@param parent_object: the parent's object, as an RDFLib URIRef
@param incoming_state: the inherited state (namespaces, lang, etc)
@type incoming_state: L{state.ExecutionContext}
@param parent_incomplete_triples: list of hanging triples (the missing resource set to None) to be handled (or not)
by the current node.
@return: whether the caller has to complete it's parent's incomplete triples
@rtype: Boolean
"""
# Update the state. This means, for example, the possible local settings of
# namespaces and lang
state = None
state = ExecutionContext(node, graph, inherited_state=incoming_state)
#---------------------------------------------------------------------------------
# Handle the special case for embedded RDF, eg, in SVG1.2.
# This may add some triples to the target graph that does not originate from RDFa parsing
# If the function return TRUE, that means that an rdf:RDF has been found. No
# RDFa parsing should be done on that subtree, so we simply return...
if state.options.host_language in accept_embedded_rdf and node.nodeType == node.ELEMENT_NODE and handle_embeddedRDF(
node, graph, state):
return
#---------------------------------------------------------------------------------
# calling the host language specific massaging of the DOM
if state.options.host_language in host_dom_transforms and node.nodeType == node.ELEMENT_NODE:
for func in host_dom_transforms[state.options.host_language]:
func(node, state)
#---------------------------------------------------------------------------------
# First, let us check whether there is anything to do at all. Ie,
# whether there is any relevant RDFa specific attribute on the element
#
if not has_one_of_attributes(node, "href", "resource", "about", "property",
"rel", "rev", "typeof", "src", "vocab",
"prefix"):
# nop, there is nothing to do here, just go down the tree and return...
for n in node.childNodes:
if n.nodeType == node.ELEMENT_NODE:
parse_one_node(n, graph, parent_object, state,
parent_incomplete_triples)
return
#-----------------------------------------------------------------
# The goal is to establish the subject and object for local processing
# The behaviour is slightly different depending on the presense or not
# of the @rel/@rev attributes
current_subject = None
current_object = None
typed_resource = None
if has_one_of_attributes(node, "rel", "rev"):
# in this case there is the notion of 'left' and 'right' of @rel/@rev
# in establishing the new Subject and the objectResource
# set first the subject
if node.hasAttribute("about"):
current_subject = state.getURI("about")
if node.hasAttribute("typeof"): typed_resource = current_subject
# get_URI may return None in case of an illegal CURIE, so
# we have to be careful here, not use only an 'else'
if current_subject == None:
current_subject = parent_object
else:
state.reset_list_mapping(origin=current_subject)
# set the object resource
current_object = state.getResource("resource", "href", "src")
if node.hasAttribute("typeof") and not node.hasAttribute("about"):
if current_object == None:
current_object = BNode()
typed_resource = current_object
if not node.hasAttribute("inlist") and current_object != None:
# In this case the newly defined object is, in fact, the head of the list
# just reset the whole thing.
state.reset_list_mapping(origin=current_object)
elif node.hasAttribute("property") and not has_one_of_attributes(
node, "content", "datatype"):
# this is the case when the property may take hold of @src and friends...
if node.hasAttribute("about"):
current_subject = state.getURI("about")
if node.hasAttribute("typeof"): typed_resource = current_subject
# get_URI_ref may return None in case of an illegal CURIE, so
# we have to be careful here, not use only an 'else'
if current_subject == None:
current_subject = parent_object
else:
state.reset_list_mapping(origin=current_subject)
if typed_resource == None and node.hasAttribute("typeof"):
typed_resource = state.getResource("resource", "href", "src")
if typed_resource == None:
typed_resource = BNode()
current_object = typed_resource
else:
current_object = current_subject
else:
# in this case all the various 'resource' setting attributes
# behave identically, though they also have their own priority
current_subject = state.getResource("about", "resource", "href", "src")
# get_URI_ref may return None in case of an illegal CURIE, so
# we have to be careful here, not use only an 'else'
if current_subject == None:
if node.hasAttribute("typeof"):
current_subject = BNode()
else:
current_subject = parent_object
else:
state.reset_list_mapping(origin=current_subject)
# in this case no non-literal triples will be generated, so the
# only role of the current_object Resource is to be transferred to
# the children node
current_object = current_subject
if node.hasAttribute("typeof"): typed_resource = current_subject
# ---------------------------------------------------------------------
## The possible typeof indicates a number of type statements on the typed resource
for defined_type in state.getURI("typeof"):
if typed_resource:
graph.add((typed_resource, ns_rdf["type"], defined_type))
# ---------------------------------------------------------------------
# In case of @rel/@rev, either triples or incomplete triples are generated
# the (possible) incomplete triples are collected, to be forwarded to the children
incomplete_triples = []
for prop in state.getURI("rel"):
if not isinstance(prop, BNode):
if node.hasAttribute("inlist"):
if current_object != None:
state.add_to_list_mapping(prop, current_object)
else:
incomplete_triples.append((None, prop, None))
else:
theTriple = (current_subject, prop, current_object)
if current_object != None:
graph.add(theTriple)
else:
incomplete_triples.append(theTriple)
else:
state.options.add_warning(err_no_blank_node % "rel",
warning_type=IncorrectBlankNodeUsage,
node=node.nodeName)
for prop in state.getURI("rev"):
if not isinstance(prop, BNode):
theTriple = (current_object, prop, current_subject)
if current_object != None:
graph.add(theTriple)
else:
incomplete_triples.append(theTriple)
else:
state.options.add_warning(err_no_blank_node % "rev",
warning_type=IncorrectBlankNodeUsage,
node=node.nodeName)
# ----------------------------------------------------------------------
# Generation of the literal values. The newSubject is the subject
# A particularity of property is that it stops the parsing down the DOM tree if an XML Literal is generated,
# because everything down there is part of the generated literal.
if node.hasAttribute("property"):
ProcessProperty(node, graph, current_subject, state,
typed_resource).generate_1_1()
# ----------------------------------------------------------------------
# Setting the current object to a bnode is setting up a possible resource
# for the incomplete triples downwards
if current_object == None:
object_to_children = BNode()
else:
object_to_children = current_object
#-----------------------------------------------------------------------
# Here is the recursion step for all the children
for n in node.childNodes:
if n.nodeType == node.ELEMENT_NODE:
_parse_1_1(n, graph, object_to_children, state, incomplete_triples)
# ---------------------------------------------------------------------
# At this point, the parent's incomplete triples may be completed
for (s, p, o) in parent_incomplete_triples:
if s == None and o == None:
# This is an encoded version of a hanging rel for a collection:
incoming_state.add_to_list_mapping(p, current_subject)
else:
if s == None: s = current_subject
if o == None: o = current_subject
graph.add((s, p, o))
# Generate the lists, if any and if this is the level where a new list was originally created
if state.new_list and not state.list_empty():
for prop in state.get_list_props():
vals = state.get_list_value(prop)
heads = [BNode() for r in vals] + [ns_rdf["nil"]]
for i in xrange(0, len(vals)):
graph.add((heads[i], ns_rdf["first"], vals[i]))
graph.add((heads[i], ns_rdf["rest"], heads[i + 1]))
# Anchor the list
graph.add((state.get_list_origin(), prop, heads[0]))
# -------------------------------------------------------------------
# This should be it...
# -------------------------------------------------------------------
return