def test_adding_repository(self):
rdf_writer = RDFWriter([self.doc])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.objects(subject=rdf_writer.hub_root,
predicate=ODMLNS.hasTerminology)
self.assertEqual(len(list(check)), 0)
check = rdf_writer.graph.objects(subject=URIRef(ODMLNS +
rdf_writer.docs[0].id),
predicate=ODMLNS.hasTerminology)
self.assertEqual(len(list(check)), 0)
url = "terminology_url"
self.doc.repository = url
rdf_writer = RDFWriter([self.doc])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subjects(predicate=RDF.type,
object=URIRef(url))
self.assertEqual(len(list(check)), 1)
check = rdf_writer.graph.objects(subject=rdf_writer.hub_root,
predicate=ODMLNS.hasTerminology)
self.assertEqual(len(list(check)), 1)
check = rdf_writer.graph.objects(subject=URIRef(ODMLNS +
rdf_writer.docs[0].id),
predicate=ODMLNS.hasTerminology)
self.assertEqual(len(list(check)), 1)
def test_convert_to_rdf(self):
rdf_writer = RDFWriter([self.doc, self.doc1])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subjects(predicate=RDF.type,
object=URIRef(ODMLNS.Document))
self.assertEqual(len(list(check)), 2)
def test_adding_repository(self):
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(
len(
list(
w.graph.objects(subject=w.hub_root,
predicate=odmlns.hasTerminology))), 0)
self.assertEqual(
len(
list(
w.graph.objects(subject=URIRef(odmlns + w.docs[0].id),
predicate=odmlns.hasTerminology))), 0)
url = "terminology_url"
self.doc.repository = url
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(
len(list(w.graph.subjects(predicate=RDF.type,
object=URIRef(url)))), 1)
self.assertEqual(
len(
list(
w.graph.objects(subject=w.hub_root,
predicate=odmlns.hasTerminology))), 1)
self.assertEqual(
len(
list(
w.graph.objects(subject=URIRef(odmlns + w.docs[0].id),
predicate=odmlns.hasTerminology))), 1)
def test_adding_doc_to_the_hub(self):
rdf_writer = RDFWriter([self.doc])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.objects(subject=rdf_writer.hub_root,
predicate=ODMLNS.hasDocument)
self.assertEqual(len(list(check)), 1)
def test_adding_repository(self):
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.objects(subject=w.hub_root, predicate=odmlns.hasTerminology))), 0)
self.assertEqual(len(list(w.g.objects(subject=URIRef(odmlns + w.docs[0].id), predicate=odmlns.hasTerminology))), 0)
url = "terminology_url"
self.doc.repository = url
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subjects(predicate=RDF.type, object=URIRef(url)))), 1)
self.assertEqual(len(list(w.g.objects(subject=w.hub_root, predicate=odmlns.hasTerminology))), 1)
self.assertEqual(len(list(w.g.objects(subject=URIRef(odmlns + w.docs[0].id), predicate=odmlns.hasTerminology))), 1)
def test_section_subclass(self):
p = os.path.join(dirname(dirname(abspath(__file__))), 'doc', 'section_subclasses.yaml')
with open(p, "r") as f:
subclass = yaml.load(f)
doc = odml.Document()
subclass_key = next(iter(subclass))
s = odml.Section("S", type=subclass_key)
doc.append(s)
w = RDFWriter(doc)
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subjects(predicate=RDF.type, object=URIRef(odmlns[subclass[subclass_key]])))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=RDF.type, object=URIRef(odmlns.Section)))), 0)
def test_adding_other_entities_properties(self):
doc = parse("""
s1[t1]
- p1
""")
version = "v1"
date = datetime.date(1979, 10, 12)
author = "nice person"
s_def = "comment"
s_ref = "reference"
p_unit = "u1"
p_name = "p1"
p_def = "p comment"
p_uncertainty = 13.0
p_dtype = "string"
p_value_origin = "value"
p_ref = "p_ref"
doc.version = version
doc.date = date
doc.author = author
doc.sections[0].definition = s_def
doc.sections[0].reference = s_ref
doc.sections[0].properties[0].name = p_name
doc.sections[0].properties[0].unit = p_unit
doc.sections[0].properties[0].definition = p_def
doc.sections[0].properties[0].uncertainty = p_uncertainty
doc.sections[0].properties[0].dtype = p_dtype
doc.sections[0].properties[0].value_origin = p_value_origin
doc.sections[0].properties[0].reference = p_ref
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasDocVersion, object=Literal(version)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasDate, object=Literal(date, datatype=XSD.date)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasAuthor, object=Literal(author)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasName, object=Literal("s1")))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasType, object=Literal("t1")))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasDefinition, object=Literal(s_def)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasReference, object=Literal(s_ref)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasName, object=Literal(p_name)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasUnit, object=Literal(p_unit)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasDefinition, object=Literal(p_def)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasUncertainty, object=Literal(p_uncertainty)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasDtype, object=Literal(p_dtype)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasValueOrigin, object=Literal(p_value_origin)))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=odmlns.hasReference, object=Literal(p_ref)))), 1)
def test_mandatory_attrs_section(self):
"""
Test if ParserError is thrown if mandatory attributes are missing for section.
"""
rdf_writer = RDFWriter([self.doc])
rdf_writer.convert_to_rdf()
for rdf_sec in rdf_writer.graph.subjects(predicate=ODMLNS.hasName,
object=Literal("sec1")):
rdf_writer.graph.remove((rdf_sec, ODMLNS.hasName, Literal("sec1")))
new_graph = rdf_writer.graph.serialize(format="turtle").decode("utf-8")
with self.assertRaises(ParserException):
RDFReader().from_string(new_graph, "turtle")
def test_section_subclass(self):
file_path = os.path.join(odml.__path__[0], 'resources',
'section_subclasses.yaml')
with open(file_path, "r") as subclass_file:
subclass = yaml.safe_load(subclass_file)
doc = odml.Document()
subclass_key = next(iter(subclass))
sec = odml.Section("S", type=subclass_key)
doc.append(sec)
rdf_writer = RDFWriter(doc)
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subjects(predicate=RDF.type,
object=URIRef(
ODMLNS[subclass[subclass_key]]))
self.assertEqual(len(list(check)), 1)
check = rdf_writer.graph.subjects(predicate=RDF.type,
object=URIRef(ODMLNS.Section))
self.assertEqual(len(list(check)), 0)
def test_adding_values(self):
doc = parse("""
s1[t1]
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=RDF.li))), 0)
self.assertEqual(len(list(
w.g.subject_objects(predicate=URIRef("%s_1" % str(RDF))))), 0)
doc = parse("""
s1[t1]
- p1
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subjects(predicate=RDF.li,
object=Literal("val")))), 0)
self.assertEqual(len(list(w.g.subjects(predicate=URIRef("%s_1" % str(RDF)),
object=Literal("val")))), 1)
doc.sections[0].properties[0].append("val2")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=RDF.li))), 0)
self.assertEqual(len(list(w.g.subjects(predicate=RDF.li, object=Literal("val")))), 0)
self.assertEqual(len(list(w.g.subjects(predicate=RDF.li, object=Literal("val2")))), 0)
self.assertEqual(len(list(w.g.subjects(predicate=URIRef("%s_1" % str(RDF)),
object=Literal("val")))), 1)
self.assertEqual(len(list(w.g.subjects(predicate=URIRef("%s_2" % str(RDF)),
object=Literal("val2")))), 1)
doc = parse("""
s1[t1]
- p1
s2[t2]
- p1
- p2
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subjects(predicate=RDF.li, object=Literal("val")))), 0)
self.assertEqual(len(list(w.g.subjects(predicate=URIRef("%s_1" % str(RDF)),
object=Literal("val")))), 3)
def test_section_subclass(self):
p = os.path.join(odml.__path__[0], 'resources',
'section_subclasses.yaml')
with open(p, "r") as f:
subclass = yaml.load(f)
doc = odml.Document()
subclass_key = next(iter(subclass))
s = odml.Section("S", type=subclass_key)
doc.append(s)
w = RDFWriter(doc)
w.convert_to_rdf()
self.assertEqual(
len(
list(
w.graph.subjects(predicate=RDF.type,
object=URIRef(
odmlns[subclass[subclass_key]])))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=RDF.type,
object=URIRef(odmlns.Section)))), 0)
def test_adding_sections(self):
doc = odml.Document()
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=odmlns.hasSection))), 0)
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=odmlns.hasSection))), 9)
w = RDFWriter([self.doc, self.doc1])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=odmlns.hasSection))), 18)
def test_adding_sections(self):
doc = odml.Document()
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(
len(list(w.g.subject_objects(predicate=odmlns.hasSection))), 0)
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(
len(list(w.g.subject_objects(predicate=odmlns.hasSection))), 9)
w = RDFWriter([self.doc, self.doc1])
w.convert_to_rdf()
self.assertEqual(
len(list(w.g.subject_objects(predicate=odmlns.hasSection))), 18)
def test_adding_properties(self):
doc = parse("""
s1[t1]
- s11[t1]
s2[t2]
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=odmlns.hasProperty))), 0)
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=odmlns.hasProperty))), 12)
w = RDFWriter([self.doc, self.doc1])
w.convert_to_rdf()
self.assertEqual(len(list(w.g.subject_objects(predicate=odmlns.hasProperty))), 24)
def test_adding_sections(self):
doc = odml.Document()
rdf_writer = RDFWriter([doc])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subject_objects(predicate=ODMLNS.hasSection)
self.assertEqual(len(list(check)), 0)
rdf_writer = RDFWriter([self.doc])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subject_objects(predicate=ODMLNS.hasSection)
self.assertEqual(len(list(check)), 9)
rdf_writer = RDFWriter([self.doc, self.doc1])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subject_objects(predicate=ODMLNS.hasSection)
self.assertEqual(len(list(check)), 18)
def test_adding_properties(self):
doc = parse("""
s1[t1]
- s11[t1]
s2[t2]
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(
len(list(w.g.subject_objects(predicate=odmlns.hasProperty))), 0)
w = RDFWriter([self.doc])
w.convert_to_rdf()
self.assertEqual(
len(list(w.g.subject_objects(predicate=odmlns.hasProperty))), 12)
w = RDFWriter([self.doc, self.doc1])
w.convert_to_rdf()
self.assertEqual(
len(list(w.g.subject_objects(predicate=odmlns.hasProperty))), 24)
def test_adding_properties(self):
doc = parse("""
s1[t1]
- s11[t1]
s2[t2]
""")
rdf_writer = RDFWriter([doc])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subject_objects(predicate=ODMLNS.hasProperty)
self.assertEqual(len(list(check)), 0)
rdf_writer = RDFWriter([self.doc])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subject_objects(predicate=ODMLNS.hasProperty)
self.assertEqual(len(list(check)), 12)
rdf_writer = RDFWriter([self.doc, self.doc1])
rdf_writer.convert_to_rdf()
check = rdf_writer.graph.subject_objects(predicate=ODMLNS.hasProperty)
self.assertEqual(len(list(check)), 24)
def test_convert_to_rdf(self):
w = RDFWriter([self.doc, self.doc1])
w.convert_to_rdf()
doc_subjects = w.g.subjects(predicate=RDF.type, object=URIRef(odmlns.Document))
self.assertEqual(len(list(doc_subjects)), 2)
def test_adding_doc_to_the_hub(self):
w = RDFWriter([self.doc])
w.convert_to_rdf()
hub_hasDocument = w.graph.objects(subject=w.hub_root,
predicate=odmlns.hasDocument)
self.assertEqual(len(list(hub_hasDocument)), 1)
def test_convert_to_rdf(self):
w = RDFWriter([self.doc, self.doc1])
w.convert_to_rdf()
doc_subjects = w.graph.subjects(predicate=RDF.type,
object=URIRef(odmlns.Document))
self.assertEqual(len(list(doc_subjects)), 2)
def test_adding_other_entities_properties(self):
doc = parse("""
s1[t1]
- p1
""")
version = "v1"
date = datetime.date(1979, 10, 12)
author = "nice person"
s_def = "comment"
s_ref = "reference"
p_unit = "u1"
p_name = "p1"
p_def = "p comment"
p_uncertainty = 13.0
p_dtype = "string"
p_value_origin = "value"
p_ref = "p_ref"
doc.version = version
doc.date = date
doc.author = author
doc.sections[0].definition = s_def
doc.sections[0].reference = s_ref
doc.sections[0].properties[0].name = p_name
doc.sections[0].properties[0].unit = p_unit
doc.sections[0].properties[0].definition = p_def
doc.sections[0].properties[0].uncertainty = p_uncertainty
doc.sections[0].properties[0].dtype = p_dtype
doc.sections[0].properties[0].value_origin = p_value_origin
doc.sections[0].properties[0].reference = p_ref
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasDocVersion,
object=Literal(version)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasDate,
object=Literal(date,
datatype=XSD.date)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasAuthor,
object=Literal(author)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasName,
object=Literal("s1")))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasType,
object=Literal("t1")))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasDefinition,
object=Literal(s_def)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasReference,
object=Literal(s_ref)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasName,
object=Literal(p_name)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasUnit,
object=Literal(p_unit)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasDefinition,
object=Literal(p_def)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasUncertainty,
object=Literal(p_uncertainty)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasDtype,
object=Literal(p_dtype)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasValueOrigin,
object=Literal(p_value_origin)))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=odmlns.hasReference,
object=Literal(p_ref)))), 1)
def test_adding_values(self):
doc = parse("""
s1[t1]
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.graph.subject_objects(predicate=RDF.li))),
0)
self.assertEqual(
len(
list(
w.graph.subject_objects(predicate=URIRef("%s_1" %
str(RDF))))), 0)
doc = parse("""
s1[t1]
- p1
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(
len(list(w.graph.subjects(predicate=RDF.li,
object=Literal("val")))), 0)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=URIRef("%s_1" % str(RDF)),
object=Literal("val")))), 1)
doc.sections[0].properties[0].append("val2")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(len(list(w.graph.subject_objects(predicate=RDF.li))),
0)
self.assertEqual(
len(list(w.graph.subjects(predicate=RDF.li,
object=Literal("val")))), 0)
self.assertEqual(
len(
list(w.graph.subjects(predicate=RDF.li,
object=Literal("val2")))), 0)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=URIRef("%s_1" % str(RDF)),
object=Literal("val")))), 1)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=URIRef("%s_2" % str(RDF)),
object=Literal("val2")))), 1)
doc = parse("""
s1[t1]
- p1
s2[t2]
- p1
- p2
""")
w = RDFWriter([doc])
w.convert_to_rdf()
self.assertEqual(
len(list(w.graph.subjects(predicate=RDF.li,
object=Literal("val")))), 0)
self.assertEqual(
len(
list(
w.graph.subjects(predicate=URIRef("%s_1" % str(RDF)),
object=Literal("val")))), 3)
def test_adding_doc_to_the_hub(self):
w = RDFWriter([self.doc])
w.convert_to_rdf()
hub_hasDocument = w.g.objects(subject=w.hub_root, predicate=odmlns.hasDocument)
self.assertEqual(len(list(hub_hasDocument)), 1)