def parse_datacite_dict(doc):
"""
:param doc: python dict containing datacite conform data to
be parsed.
"""
if not doc or "resource" not in doc:
msg = "Could not find root. "
msg += "Please escape any XML namespace using the '-n' command line option."
raise ParserException(msg)
datacite_root = doc["resource"]
if "identifier" not in datacite_root:
raise ParserException("Could not find identifier (DOI) node")
odml_doc = Document()
odml_doc.repository = "https://terminologies.g-node.org/v1.1/terminologies.xml"
odml_doc.date = date.today().isoformat()
root_sec = Section(name="DataCite", type="data_reference", parent=odml_doc)
supported_tags = setup_supported_tags()
for node_tag in datacite_root:
if node_tag in supported_tags:
helper = supported_tags[node_tag]
helper.func(helper, datacite_root[node_tag], root_sec)
else:
print("[Warning] Ignoring unsupported root node '%s'" % node_tag)
return odml_doc
def setUp(self):
"""
doc -- <section foo> -- <section subfoo>
\
-- <section bar> -- <section subbar>
"""
doc = Document("author")
foo = Section("foo", "footype")
doc.append(foo)
foo.append(Property("strprop", "somestring"))
foo.append(Property("txtprop", "some\ntext"))
subfoo = Section("subfoo", "footype")
foo.append(subfoo)
subfoo.append(Property("strprop", "somestring"))
subfoo.append(Property("txtprop", "some\ntext"))
bar = Section("bar", "bartype")
foo.append(bar)
bar.append(Property("strprop", "otherstring"))
bar.append(Property("txtprop", "other\ntext"))
subbar = Section("subbar", "bartype")
bar.append(subbar)
subbar.append(Property("strprop", "otherstring"))
subbar.append(Property("txtprop", "other\ntext"))
self.doc = doc
def setUp(self):
"""
doc -- <section sec_main> -- <section sub_main>
\
-- <section sec_branch> -- <section sub_branch>
"""
doc = Document("author")
sec_main = Section("sec_main", "maintype")
doc.append(sec_main)
sec_main.append(Property("strprop", "somestring"))
sec_main.append(Property("txtprop", "some\ntext"))
sub_main = Section("sub_main", "maintype")
sec_main.append(sub_main)
sub_main.append(Property("strprop", "somestring"))
sub_main.append(Property("txtprop", "some\ntext"))
sec_branch = Section("sec_branch", "branchtype")
sec_main.append(sec_branch)
sec_branch.append(Property("strprop", "otherstring"))
sec_branch.append(Property("txtprop", "other\ntext"))
sub_branch = Section("sub_branch", "branchtype")
sec_branch.append(sub_branch)
sub_branch.append(Property("strprop", "otherstring"))
sub_branch.append(Property("txtprop", "other\ntext"))
self.doc = doc
def test_parent(self):
s = Section("Section")
self.assertIsNone(s.parent)
s.parent = None
self.assertIsNone(s.parent)
s.parent = Document()
self.assertIsInstance(s.parent, BaseDocument)
self.assertIsInstance(s.parent._sections[0], BaseSection)
""" Test if child is removed from _sections of a parent after assigning
a new parent to the child """
p = s.parent
s.parent = Section("S")
self.assertEqual(len(p._sections), 0)
s = Section("section_doc", parent=Document())
self.assertIsInstance(s.parent, BaseDocument)
self.assertEqual(len(s.parent._sections), 1)
p = s.parent
s.parent = None
self.assertEqual(len(p._sections), 0)
self.assertEqual(s.parent, None)
s = Section("section_sec", parent=Section("S"))
self.assertIsInstance(s.parent, BaseSection)
self.assertEqual(len(s.parent._sections), 1)
p = s.parent
s.parent = None
self.assertEqual(len(p._sections), 0)
self.assertEqual(s.parent, None)
with self.assertRaises(ValueError):
Section("section_property", parent=Property("P"))
def setUp(self):
"""
doc -- <section foo> -- <section subfoo>
\
-- <section bar> -- <section subbar>
"""
doc = Document("author")
foo = Section("foo", "footype")
doc.append(foo)
foo.append(Property("strprop", "somestring"))
foo.append(Property("txtprop", "some\ntext"))
subfoo = Section("subfoo", "footype")
foo.append(subfoo)
subfoo.append(Property("strprop", "somestring"))
subfoo.append(Property("txtprop", "some\ntext"))
bar = Section("bar", "bartype")
foo.append(bar)
bar.append(Property("strprop", "otherstring"))
bar.append(Property("txtprop", "other\ntext"))
subbar = Section("subbar", "bartype")
bar.append(subbar)
subbar.append(Property("strprop", "otherstring"))
subbar.append(Property("txtprop", "other\ntext"))
self.doc = doc
def setUp(self):
"""
Set up local temporary terminology files in a temporary folder
"""
tmp_dir = create_test_dir(__file__)
tmp_name = os.path.basename(tmp_dir)
main_name = "%s_main.xml" % tmp_name
main_file_path = os.path.join(tmp_dir, main_name)
main_url = "file://%s" % pathname2url(main_file_path)
include_name = "%s_include.xml" % tmp_name
include_file_path = os.path.join(tmp_dir, include_name)
include_url = "file://%s" % pathname2url(include_file_path)
include_doc = Document()
_ = Section(name="include_sec", type="test", parent=include_doc)
save(include_doc, include_file_path)
main_doc = Document()
_ = Section(name="main_sec", type="test", include=include_url, parent=main_doc)
save(main_doc, main_file_path)
self.main_terminology_url = main_url
self.temp_dir_base = tmp_name
def test_create_section(self):
root = Document()
self.assertEqual(len(root.sections), 0)
name = "subsec"
sec_type = "subtype"
oid = "79b613eb-a256-46bf-84f6-207df465b8f7"
subsec = root.create_section(name, sec_type, oid)
self.assertEqual(len(root.sections), 1)
self.assertEqual(subsec.parent, root)
self.assertEqual(root.sections[name], subsec)
self.assertEqual(root.sections[name].type, sec_type)
self.assertEqual(root.sections[name].oid, oid)
name = "othersec"
subsec = root.create_section(name)
self.assertEqual(len(root.sections), 2)
self.assertEqual(subsec.parent, root)
self.assertEqual(root.sections[name], subsec)
self.assertEqual(root.sections[name].type, "n.s.")
name = "subsubsec"
subsec = root.sections[0].create_section(name)
self.assertEqual(len(root.sections), 2)
self.assertEqual(subsec.parent, root.sections[0])
self.assertEqual(len(root.sections[0].sections), 1)
self.assertEqual(root.sections[0].sections[0].name, name)
def test_export_leaf(self):
doc = Document()
first = doc.create_section("first")
second = first.create_section("second")
third = first.create_section("third")
name = "prop1"
values = [1.3]
first.create_property(name, value=values)
name = "prop2"
values = ["words"]
first.create_property(name, value=values)
name = "prop3"
values = ["a", "b"]
second.create_property(name, value=values)
ex1 = first.export_leaf()
self.assertEqual(len(ex1.sections), 1)
self.assertEqual(len(ex1['first'].properties), 2)
self.assertEqual(len(ex1['first'].sections), 0)
ex2 = second.export_leaf()
self.assertEqual(len(ex2.sections), 1)
self.assertEqual(len(ex2['first'].properties), 2)
self.assertEqual(len(ex2['first'].sections), 1)
self.assertEqual(len(ex2['first']['second'].properties), 1)
ex3 = third.export_leaf()
self.assertEqual(len(ex3.sections), 1)
self.assertEqual(len(ex3['first'].properties), 2)
self.assertEqual(len(ex3['first'].sections), 1)
self.assertEqual(len(ex3['first']['third']), 0)
def test_create_section(self):
root = Document()
self.assertEqual(len(root.sections), 0)
name = "subsec"
type = "subtype"
oid = "79b613eb-a256-46bf-84f6-207df465b8f7"
subsec = root.create_section(name, type, oid)
self.assertEqual(len(root.sections), 1)
self.assertEqual(subsec.parent, root)
self.assertEqual(root.sections[name], subsec)
self.assertEqual(root.sections[name].type, type)
self.assertEqual(root.sections[name].oid, oid)
name = "othersec"
subsec = root.create_section(name)
self.assertEqual(len(root.sections), 2)
self.assertEqual(subsec.parent, root)
self.assertEqual(root.sections[name], subsec)
self.assertEqual(root.sections[name].type, "undefined")
name = "subsubsec"
subsec = root.sections[0].create_section(name)
self.assertEqual(len(root.sections), 2)
self.assertEqual(subsec.parent, root.sections[0])
self.assertEqual(len(root.sections[0].sections), 1)
self.assertEqual(root.sections[0].sections[0].name, name)
def test_read_write(self):
doc = Document("author")
sec = Section("name", "type")
doc.append(sec)
sec.append(Property("strprop", "somestring"))
sec.append(Property("txtprop", "some\ntext"))
sec.append(Property("intprop", 200))
sec.append(Property("floatprop", 2.00))
sec.append(Property("datetimeprop", dt.now()))
sec.append(Property("dateprop", dt.now().date()))
sec.append(Property("timeprop", dt.now().time()))
sec.append(Property("boolprop", True))
if sys.version_info < (3, 0):
str_doc = unicode(XMLWriter(doc))
else:
str_doc = str(XMLWriter(doc))
new_doc = XMLReader().fromString(str_doc)
new_sec = new_doc.sections[0]
p = new_sec.properties["strprop"]
assert (p.dtype == "string")
if sys.version_info < (3, 0):
assert (type(p.value[0]) == unicode)
else:
assert (type(p.value[0]) == str)
p = new_sec.properties["txtprop"]
assert (p.dtype == "text")
if sys.version_info < (3, 0):
assert (type(p.value[0]) == unicode)
else:
assert (type(p.value[0]) == str)
p = new_sec.properties["intprop"]
assert (p.dtype == "int")
assert (type(p.value[0]) == int)
p = new_sec.properties["floatprop"]
assert (p.dtype == "float")
assert (type(p.value[0]) == float)
p = new_sec.properties["datetimeprop"]
assert (p.dtype == "datetime")
assert (type(p.value[0]) == dt)
p = new_sec.properties["dateprop"]
assert (p.dtype == "date")
assert (type(p.value[0]) == date)
p = new_sec.properties["timeprop"]
assert (p.dtype == "time")
assert (type(p.value[0]) == time)
p = new_sec.properties["boolprop"]
assert (p.dtype == "boolean")
assert (type(p.value[0]) == bool)
def test_date(self):
datestring = "2000-01-02"
doc = Document(date=datestring)
self.assertIsInstance(doc.date, datetime.date)
self.assertEqual(
doc.date,
datetime.datetime.strptime(datestring, FORMAT_DATE).date())
doc.date = None
self.assertIsNone(doc.date)
doc.date = datestring
self.assertIsInstance(doc.date, datetime.date)
self.assertEqual(
doc.date,
datetime.datetime.strptime(datestring, FORMAT_DATE).date())
doc.date = []
self.assertIsNone(doc.date)
doc.date = {}
self.assertIsNone(doc.date)
doc.date = ()
self.assertIsNone(doc.date)
doc.date = ""
self.assertIsNone(doc.date)
with self.assertRaises(ValueError):
doc.date = "some format"
def test_get_terminology_equivalent(self):
repo_file = os.path.join(RES_DIR, self.local_repo_file)
local_url = "file://%s" % pathname2url(repo_file)
doc = Document(repository=local_url)
teq = doc.get_terminology_equivalent()
self.assertIsInstance(teq, BaseDocument)
self.assertEqual(len(teq), 1)
self.assertEqual(teq.sections[0].name, "Repository test")
doc.repository = None
self.assertIsNone(doc.get_terminology_equivalent())
def test_id(self):
doc = Document()
self.assertIsNotNone(doc.id)
doc = Document("D", oid="79b613eb-a256-46bf-84f6-207df465b8f7")
self.assertEqual(doc.id, "79b613eb-a256-46bf-84f6-207df465b8f7")
doc = Document("D", oid="id")
self.assertNotEqual(doc.id, "id")
# Make sure id cannot be reset programmatically.
with self.assertRaises(AttributeError):
doc.id = "someId"
def test_date(self):
datestring = "2000-01-02"
doc = Document(date=datestring)
self.assertIsInstance(doc.date, datetime.date)
self.assertEqual(doc.date,
datetime.datetime.strptime(datestring, FORMAT_DATE).date())
doc.date = None
self.assertIsNone(doc.date)
doc.date = datestring
self.assertIsInstance(doc.date, datetime.date)
self.assertEqual(doc.date,
datetime.datetime.strptime(datestring, FORMAT_DATE).date())
doc.date = []
self.assertIsNone(doc.date)
doc.date = {}
self.assertIsNone(doc.date)
doc.date = ()
self.assertIsNone(doc.date)
doc.date = ""
self.assertIsNone(doc.date)
with self.assertRaises(ValueError):
doc.date = "some format"
def test_doc(self):
"""
Test if a document and its attributes get converted correctly from rdf to odml.
"""
doc = Document()
doc.author = "D. N. Adams"
doc.version = 42
doc.date = datetime.date(1979, 10, 12)
rdf_writer = RDFWriter(doc).get_rdf_str()
rdf_reader = RDFReader().from_string(rdf_writer, "turtle")
self.assertEqual(rdf_reader[0].author, "D. N. Adams")
self.assertEqual(rdf_reader[0].version, "42")
self.assertEqual(rdf_reader[0].date, datetime.date(1979, 10, 12))
def test_get_terminology_equivalent(self):
dir_path = os.path.dirname(os.path.realpath(__file__))
repo_file = os.path.join(dir_path, "resources",
"local_repository_file_v1.1.xml")
local_url = "file://%s" % pathname2url(repo_file)
doc = Document(repository=local_url)
teq = doc.get_terminology_equivalent()
self.assertIsInstance(teq, BaseDocument)
self.assertEqual(len(teq), 1)
self.assertEqual(teq.sections[0].name, "Repository test")
doc.repository = None
self.assertIsNone(doc.get_terminology_equivalent())
def test_get_terminology_equivalent(self):
dir_path = os.path.dirname(os.path.realpath(__file__))
repo_file = os.path.join(dir_path, "resources",
"local_repository_file_v1.1.xml")
local_url = "file://%s" % pathname2url(repo_file)
doc = Document(repository=local_url)
teq = doc.get_terminology_equivalent()
self.assertIsInstance(teq, BaseDocument)
self.assertEqual(len(teq), 1)
self.assertEqual(teq.sections[0].name, "Repository test")
doc.repository = None
self.assertIsNone(doc.get_terminology_equivalent())
def test_read_write(self):
doc = Document("author")
sec = Section("name", "type")
doc.append(sec)
sec.append(Property("strprop", "somestring"))
sec.append(Property("txtprop", "some\ntext"))
sec.append(Property("intprop", 200))
sec.append(Property("floatprop", 2.00))
sec.append(Property("datetimeprop", dt.now()))
sec.append(Property("dateprop", dt.now().date()))
sec.append(Property("timeprop", dt.now().time()))
sec.append(Property("boolprop", True))
str_doc = unicode(XMLWriter(doc))
new_doc = XMLReader().fromString(str_doc)
new_sec = new_doc.sections[0]
v = new_sec.properties["strprop"].value
assert (v.dtype == "string")
assert (type(v.data) == unicode)
v = new_sec.properties["txtprop"].value
assert (v.dtype == "text")
assert (type(v.data) == unicode)
v = new_sec.properties["intprop"].value
assert (v.dtype == "int")
assert (type(v.data) == int)
v = new_sec.properties["floatprop"].value
assert (v.dtype == "float")
assert (type(v.data) == float)
v = new_sec.properties["datetimeprop"].value
assert (v.dtype == "datetime")
assert (type(v.data) == dt)
v = new_sec.properties["dateprop"].value
assert (v.dtype == "date")
assert (type(v.data) == date)
v = new_sec.properties["timeprop"].value
assert (v.dtype == "time")
assert (type(v.data) == time)
v = new_sec.properties["boolprop"].value
assert (v.dtype == "boolean")
assert (type(v.data) == bool)
def test_read_write(self):
doc = Document("author")
sec = Section("name", "type")
doc.append(sec)
sec.append(Property("strprop", "somestring"))
sec.append(Property("txtprop", "some\ntext"))
sec.append(Property("intprop", 200))
sec.append(Property("floatprop", 2.00))
sec.append(Property("datetimeprop", dt.now()))
sec.append(Property("dateprop", dt.now().date()))
sec.append(Property("timeprop", dt.now().time()))
sec.append(Property("boolprop", True))
str_doc = unicode(XMLWriter(doc))
new_doc = XMLReader().fromString(str_doc)
new_sec = new_doc.sections[0]
v = new_sec.properties["strprop"].value
assert(v.dtype == "string")
assert(type(v.data) == unicode)
v = new_sec.properties["txtprop"].value
assert(v.dtype == "text")
assert(type(v.data) == unicode)
v = new_sec.properties["intprop"].value
assert(v.dtype == "int")
assert(type(v.data) == int)
v = new_sec.properties["floatprop"].value
assert(v.dtype == "float")
assert(type(v.data) == float)
v = new_sec.properties["datetimeprop"].value
assert(v.dtype == "datetime")
assert(type(v.data) == dt)
v = new_sec.properties["dateprop"].value
assert(v.dtype == "date")
assert(type(v.data) == date)
v = new_sec.properties["timeprop"].value
assert(v.dtype == "time")
assert(type(v.data) == time)
v = new_sec.properties["boolprop"].value
assert(v.dtype == "boolean")
assert(type(v.data) == bool)
def setUp(self):
doc = Document()
sec = Section(name="sec1", type="test", parent=doc)
Section(name="sec2", type="test", parent=sec)
Property(name="prop1", values=[1.3], parent=sec)
self.doc = doc
def test_sections_cardinality(self):
"""
Tests the basic assignment rules for Section sections cardinality
on init and re-assignment but does not test sections assignment or
the actual cardinality validation.
"""
doc = Document()
# -- Test set cardinality on Section init
# Test empty init
sec_card_none = Section(name="sec_cardinality_none", type="test", parent=doc)
self.assertIsNone(sec_card_none.sec_cardinality)
# Test single int max init
sec_card_max = Section(name="sec_cardinality_max", sec_cardinality=10, parent=doc)
self.assertEqual(sec_card_max.sec_cardinality, (None, 10))
# Test tuple init
sec_card_min = Section(name="sec_cardinality_min", sec_cardinality=(2, None), parent=doc)
self.assertEqual(sec_card_min.sec_cardinality, (2, None))
# -- Test Section properties cardinality re-assignment
sec = Section(name="sec", sec_cardinality=(None, 10), parent=doc)
self.assertEqual(sec.sec_cardinality, (None, 10))
# Use general method to reduce redundancy
self._test_cardinality_re_assignment(sec, 'sec_cardinality')
def test_property(self):
"""
Test if a property and its attributes get converted correctly from rdf to odml.
"""
doc = Document()
sec1 = Section(name="sec1", type="test", parent=doc)
prop2 = Property(name="numbers",
definition="any number",
dtype="float",
parent=sec1,
values=[1, 3.4, 67.8, -12],
unit="meter",
uncertainty=0.8,
value_origin="force",
reference="Experiment 1")
rdf_writer = RDFWriter(doc).get_rdf_str()
rdf_reader = RDFReader().from_string(rdf_writer, "turtle")
prop = rdf_reader[0].sections[0].properties["numbers"]
self.assertEqual(prop.name, "numbers")
self.assertEqual(prop.dtype, "float")
self.assertEqual(prop.id, prop2.id)
self.assertEqual(prop.parent, rdf_reader[0].sections[0])
self.assertEqual(len(prop.values), 4)
self.assertEqual(prop.values, [1, 3.4, 67.8, -12])
self.assertEqual(prop.definition, "any number")
self.assertEqual(prop.unit, "meter")
self.assertEqual(prop.uncertainty, "0.8")
self.assertEqual(prop.value_origin, "force")
self.assertEqual(prop.reference, "Experiment 1")
def test_reorder(self):
# Test reorder of document sections
doc = Document()
sec_one = Section(name="sec_one", parent=doc)
sec_two = Section(name="sec_two", parent=doc)
sec_three = Section(name="sec_three", parent=doc)
self.assertEqual(doc.sections[0].name, sec_one.name)
self.assertEqual(doc.sections[2].name, sec_three.name)
sec_three.reorder(0)
self.assertEqual(doc.sections[0].name, sec_three.name)
self.assertEqual(doc.sections[2].name, sec_two.name)
# Test reorder of document sections
sec = Section(name="main")
sec_one = Section(name="sec_one", parent=sec)
sec_two = Section(name="sec_two", parent=sec)
sec_three = Section(name="sec_three", parent=sec)
self.assertEqual(sec.sections[0].name, sec_one.name)
self.assertEqual(sec.sections[2].name, sec_three.name)
sec_three.reorder(0)
self.assertEqual(sec.sections[0].name, sec_three.name)
self.assertEqual(sec.sections[2].name, sec_two.name)
# Test Exception on unconnected section
with self.assertRaises(ValueError):
sec.reorder(0)
def test_contains(self):
sec = Section(name="root")
subsec = Section(name="subsec", type="test")
prop = Property(name="prop")
# Test not contains on empty child-lists.
self.assertIsNone(sec.contains(subsec))
self.assertIsNone(sec.contains(prop))
# Test contains of Section and Property
subsec.parent = sec
simisec = Section(name="subsec", type="test")
self.assertEqual(sec.contains(simisec).name, subsec.name)
prop.parent = sec
simiprop = Property(name="prop")
self.assertEqual(sec.contains(simiprop).name, prop.name)
# Test not contains on mismatching Section name/type and Property name
self.assertIsNone(sec.contains(Section(name="subsec", type="typetest")))
self.assertIsNone(sec.contains(Section(name="typesec", type="test")))
self.assertIsNone(sec.contains(Property(name="prop_two")))
# Test fail on non-Section/Property objects
with self.assertRaises(ValueError):
sec.contains(Document())
with self.assertRaises(ValueError):
sec.contains("some info")
def test_simple_attributes(self):
author = "HPL"
version = "4.8.15"
doc = Document(author=author, version=version)
self.assertEqual(doc.author, author)
self.assertEqual(doc.version, version)
doc.author = ""
doc.version = ""
self.assertIsNone(doc.author)
self.assertIsNone(doc.version)
doc.author = author
doc.version = version
self.assertEqual(doc.author, author)
self.assertEqual(doc.version, version)
def test_get_path(self):
doc = Document()
sec = Section(name="parent", parent=doc)
# Check root path for a detached Property.
prop = Property(name="prop")
self.assertEqual("/", prop.get_path())
# Check absolute path of Property in a Document.
prop.parent = sec
self.assertEqual("/%s:%s" % (sec.name, prop.name), prop.get_path())
def test_read_write(self):
doc = Document("author")
sec = Section("name", "type", parent=doc)
sec.append(Property("strprop", "somestring"))
sec.append(Property("txtprop", "some\ntext"))
sec.append(Property("intprop", 200))
sec.append(Property("floatprop", 2.00))
sec.append(Property("datetimeprop", dt.now()))
sec.append(Property("dateprop", dt.now().date()))
sec.append(Property("timeprop", dt.now().time()))
sec.append(Property("boolprop", True))
str_doc = str(XMLWriter(doc))
new_doc = XMLReader().from_string(str_doc)
new_sec = new_doc.sections[0]
prop = new_sec.properties["strprop"]
self.assertEqual(prop.dtype, "string")
self.assertIsInstance(prop.values[0], str)
prop = new_sec.properties["txtprop"]
self.assertEqual(prop.dtype, "text")
self.assertIsInstance(prop.values[0], str)
prop = new_sec.properties["intprop"]
self.assertEqual(prop.dtype, "int")
self.assertIsInstance(prop.values[0], int)
prop = new_sec.properties["floatprop"]
self.assertEqual(prop.dtype, "float")
self.assertIsInstance(prop.values[0], float)
prop = new_sec.properties["datetimeprop"]
self.assertEqual(prop.dtype, "datetime")
self.assertIsInstance(prop.values[0], dt)
prop = new_sec.properties["dateprop"]
self.assertEqual(prop.dtype, "date")
self.assertIsInstance(prop.values[0], date)
prop = new_sec.properties["timeprop"]
self.assertEqual(prop.dtype, "time")
self.assertIsInstance(prop.values[0], time)
prop = new_sec.properties["boolprop"]
self.assertEqual(prop.dtype, "boolean")
self.assertIsInstance(prop.values[0], bool)
def test_id(self):
doc = Document()
self.assertIsNotNone(doc.id)
doc = Document("D", oid="79b613eb-a256-46bf-84f6-207df465b8f7")
self.assertEqual(doc.id, "79b613eb-a256-46bf-84f6-207df465b8f7")
doc = Document("D", oid="id")
self.assertNotEqual(doc.id, "id")
# Make sure id cannot be reset programmatically.
with self.assertRaises(AttributeError):
doc.id = "someId"
def test_new_id(self):
doc = Document()
old_id = doc.id
# Test assign new generated id.
doc.new_id()
self.assertNotEqual(old_id, doc.id)
# Test assign new custom id.
old_id = doc.id
doc.new_id("79b613eb-a256-46bf-84f6-207df465b8f7")
self.assertNotEqual(old_id, doc.id)
self.assertEqual("79b613eb-a256-46bf-84f6-207df465b8f7", doc.id)
# Test invalid custom id exception.
with self.assertRaises(ValueError):
doc.new_id("crash and burn")
def test_export_leaf(self):
doc = Document()
sec_a_name = "first"
sec_b_name = "second"
first = doc.create_section(sec_a_name)
second = first.create_section(sec_b_name)
_ = first.create_section("third")
prop_aa = first.create_property("prop1", value=[1.3])
_ = first.create_property("prop5", value=["abc"])
prop_ba = second.create_property("prop2", value=["words"])
_ = second.create_property("prop3", value=["a", "b"])
_ = second.create_property("prop4", value=[3])
export_doc = prop_aa.export_leaf()
self.assertEqual(len(export_doc[sec_a_name].properties), 2)
self.assertEqual(len(export_doc[sec_a_name].sections), 0)
export_doc = prop_ba.export_leaf()
self.assertEqual(len(export_doc.sections), 1)
self.assertEqual(len(export_doc[sec_a_name].properties), 2)
self.assertEqual(len(export_doc[sec_a_name].sections), 1)
self.assertEqual(len(export_doc[sec_a_name][sec_b_name].properties), 3)
def test_append(self):
main = Section(name="main")
self.assertListEqual(main.sections, [])
self.assertListEqual(main.properties, [])
# Test append Section
sec = Section(name="sec1")
main.append(sec)
self.assertEqual(len(main.sections), 1)
self.assertEqual(sec.parent, main)
# Test fail on Section list or tuple append
with self.assertRaises(ValueError):
main.append([Section(name="sec2"), Section(name="sec3")])
with self.assertRaises(ValueError):
main.append((Section(name="sec2"), Section(name="sec3")))
self.assertEqual(len(main.sections), 1)
# Test append Property
prop = Property(name="prop")
main.append(prop)
self.assertEqual(len(main.properties), 1)
self.assertEqual(prop.parent, main)
# Test fail on Property list or tuple append
with self.assertRaises(ValueError):
main.append([Property(name="prop2"), Property(name="prop3")])
with self.assertRaises(ValueError):
main.append((Property(name="prop2"), Property(name="prop3")))
self.assertEqual(len(main.properties), 1)
# Test fail on unsupported value
with self.assertRaises(ValueError):
main.append(Document())
with self.assertRaises(ValueError):
main.append("Section")
# Test fail on same name entities
with self.assertRaises(KeyError):
main.append(Section(name="sec1"))
self.assertEqual(len(main.sections), 1)
with self.assertRaises(KeyError):
main.append(Property(name="prop"))
self.assertEqual(len(main.properties), 1)
def test_new_id(self):
doc = Document()
old_id = doc.id
# Test assign new generated id.
doc.new_id()
self.assertNotEqual(old_id, doc.id)
# Test assign new custom id.
old_id = doc.id
doc.new_id("79b613eb-a256-46bf-84f6-207df465b8f7")
self.assertNotEqual(old_id, doc.id)
self.assertEqual("79b613eb-a256-46bf-84f6-207df465b8f7", doc.id)
# Test invalid custom id exception.
with self.assertRaises(ValueError):
doc.new_id("crash and burn")
def test_path(self):
sec = Section(name="center")
self.assertEqual(sec.get_path(), "/")
subsec = Section(name="leaf", parent=sec)
self.assertEqual(subsec.get_path(), "/leaf")
doc = Document()
sec.parent = doc
self.assertEqual(sec.get_path(), "/center")
self.assertEqual(subsec.get_path(), "/center/leaf")
top = Section(name="top", parent=doc)
sec.parent = top
self.assertEqual(sec.get_path(), "/top/center")
self.assertEqual(subsec.get_path(), "/top/center/leaf")
subsec.parent = None
self.assertEqual(subsec.get_path(), "/")
def test_name(self):
# Test id is used when name is not provided
s = Section()
self.assertIsNotNone(s.name)
self.assertEqual(s.name, s.id)
# Test name is properly set on init
name = "rumpelstilzchen"
s = Section(name)
self.assertEqual(s.name, name)
name = "rumpelstilzchen"
s = Section(name=name)
self.assertEqual(s.name, name)
# Test name can be properly set on single and connected Sections
sec = Section()
self.assertNotEqual(sec.name, "sec")
sec.name = "sec"
self.assertEqual(sec.name, "sec")
subsec_a = Section(parent=sec)
self.assertNotEqual(subsec_a.name, "subsec_a")
subsec_a.name = "subsec_a"
self.assertEqual(subsec_a.name, "subsec_a")
# Test subsection name can be changed with siblings
subsec_b = Section(name="subsec_b", parent=sec)
self.assertEqual(subsec_b.name, "subsec_b")
subsec_b.name = "subsec"
self.assertEqual(subsec_b.name, "subsec")
# Test subsection name set will fail on existing sibling with same name
with self.assertRaises(KeyError):
subsec_b.name = "subsec_a"
self.assertEqual(subsec_b.name, "subsec")
# Test section name set will fail on existing same name document sibling
doc = Document()
sec_a = Section(name="a", parent=doc)
sec_b = Section(name="b", parent=doc)
with self.assertRaises(KeyError):
sec_b.name = "a"
def test_parent(self):
p = Property("property_section", parent=Section("S"))
self.assertIsInstance(p.parent, BaseSection)
self.assertEqual(len(p.parent._props), 1)
""" Test if child is removed from _props of a parent after assigning
a new parent to the child """
prop_parent = p.parent
p.parent = Section("S1")
self.assertEqual(len(prop_parent._props), 0)
self.assertIsInstance(p.parent, BaseSection)
self.assertIsInstance(p.parent._props[0], BaseProperty)
prop_parent = p.parent
p.parent = None
self.assertIsNone(p.parent)
self.assertEqual(len(prop_parent._props), 0)
with self.assertRaises(ValueError):
Property("property_prop", parent=Property("P"))
with self.assertRaises(ValueError):
Property("property_doc", parent=Document())
def test_set_values_cardinality(self):
doc = Document()
sec = Section(name="sec", type="sec_type", parent=doc)
prop = Property(name="prop", val_cardinality=1, parent=sec)
# Test Property values cardinality min assignment
prop.set_values_cardinality(1)
self.assertEqual(prop.val_cardinality, (1, None))
# Test Property values cardinality keyword min assignment
prop.set_values_cardinality(min_val=2)
self.assertEqual(prop.val_cardinality, (2, None))
# Test Property values cardinality max assignment
prop.set_values_cardinality(None, 1)
self.assertEqual(prop.val_cardinality, (None, 1))
# Test Property values cardinality keyword max assignment
prop.set_values_cardinality(max_val=2)
self.assertEqual(prop.val_cardinality, (None, 2))
# Test Property values cardinality min max assignment
prop.set_values_cardinality(1, 2)
self.assertEqual(prop.val_cardinality, (1, 2))
# Test Property values cardinality keyword min max assignment
prop.set_values_cardinality(min_val=2, max_val=5)
self.assertEqual(prop.val_cardinality, (2, 5))
# Test Property values cardinality empty reset
prop.set_values_cardinality()
self.assertIsNone(prop.val_cardinality)
# Test Property values cardinality keyword empty reset
prop.set_values_cardinality(1)
self.assertIsNotNone(prop.val_cardinality)
prop.set_values_cardinality(min_val=None, max_val=None)
self.assertIsNone(prop.val_cardinality)
def test_simple_attributes(self):
author = "HPL"
version = "4.8.15"
doc = Document(author=author, version=version)
self.assertEqual(doc.author, author)
self.assertEqual(doc.version, version)
doc.author = ""
doc.version = ""
self.assertIsNone(doc.author)
self.assertIsNone(doc.version)
doc.author = author
doc.version = version
self.assertEqual(doc.author, author)
self.assertEqual(doc.version, version)
def test_section(self):
"""
Test if a section and its attributes get converted correctly from rdf to odml.
"""
doc = Document()
sec1 = Section(name="sec1",
type="test",
parent=doc,
definition="Interesting stuff.",
reference="The Journal")
Section(name="sec2", type="test", parent=sec1)
rdf_writer = RDFWriter(doc).get_rdf_str()
rdf_reader = RDFReader().from_string(rdf_writer, "turtle")
self.assertEqual(rdf_reader[0].sections[0].name, "sec1")
self.assertEqual(rdf_reader[0].sections[0].type, "test")
self.assertEqual(rdf_reader[0].sections[0].id, sec1.id)
self.assertEqual(rdf_reader[0].sections[0].definition,
"Interesting stuff.")
self.assertEqual(rdf_reader[0].sections[0].reference, "The Journal")
self.assertEqual(rdf_reader[0].sections[0].parent, rdf_reader[0])
self.assertEqual(len(rdf_reader[0].sections[0].sections), 1)
def test_comparison(self):
doc_auth = "author"
doc_ver = "ver1.0"
doc_a = Document(author=doc_auth, version=doc_ver)
doc_b = Document(author=doc_auth, version=doc_ver)
self.assertEqual(doc_a, doc_b)
doc_b.author = "someone else"
self.assertNotEqual(doc_a, doc_b)
doc_b.author = doc_auth
# Test section equality with subsections
# Test equality with subsection of different entities
# with same content and same children order
sec_type = "sec type"
sec_def = "an odml test section"
sec_ref = "from over there"
subsec_aa = Section(name="subsecA", type=sec_type,
definition=sec_def, reference=sec_ref)
subsec_ab = Section(name="subsecB", type=sec_type,
definition=sec_def, reference=sec_ref)
subsec_ba = Section(name="subsecA", type=sec_type,
definition=sec_def, reference=sec_ref)
subsec_bb = Section(name="subsecB", type=sec_type,
definition=sec_def, reference=sec_ref)
doc_a.extend([subsec_aa, subsec_ab])
doc_b.extend([subsec_ba, subsec_bb])
self.assertEqual(doc_a, doc_b)
self.assertEqual(doc_a.sections, doc_b.sections)
doc_b.sections[0].name = "newSubsecA"
self.assertNotEqual(doc_a, doc_b)
self.assertNotEqual(doc_a.sections, doc_b.sections)
doc_b.sections[0].name = "subsecA"
# Test inequality with different number of children
doc_b.remove(doc_b.sections[1])
self.assertNotEqual(doc_a, doc_b)
self.assertNotEqual(doc_a.sections, doc_b.sections)
# Test equality with subsection of different entities
# with same content and different children order
doc_b.remove(doc_b.sections[0])
doc_b.extend([subsec_bb, subsec_ba])
self.assertEqual(doc_a, doc_b)
self.assertEqual(doc_a.sections, doc_b.sections)
doc_b.sections[0].name = "newSubsecB"
self.assertNotEqual(doc_a, doc_b)
self.assertNotEqual(doc_a.sections, doc_b.sections)
doc_b.sections[0].name = "subsecB"
# Test section equality with properties
# Test equality with properties of different entities
# with same content and same children order
prop_aa = Property(name="propA", definition="propDef")
prop_ab = Property(name="propB", definition="propDef")
prop_ba = Property(name="propA", definition="propDef")
prop_bb = Property(name="propB", definition="propDef")
doc_a.sections["subsecA"].extend([prop_aa, prop_ab])
doc_b.sections["subsecA"].extend([prop_ba, prop_bb])
self.assertEqual(doc_a, doc_b)
doc_b.sections["subsecA"].properties[0].name = "newPropA"
self.assertNotEqual(doc_a, doc_b)
doc_b.sections["subsecA"].properties[0].name = "propA"
# Test inequality with different number of children
doc_b.sections["subsecA"].remove(doc_b.sections["subsecA"].properties[1])
self.assertNotEqual(doc_a, doc_b)
# Test equality with properties of different entities
# with same content and different children order
doc_b.sections["subsecA"].remove(doc_b.sections["subsecA"].properties[0])
doc_b.sections["subsecA"].extend([prop_bb, prop_ba])
self.assertEqual(doc_a, doc_b)
doc_b.sections["subsecA"].properties[0].name = "newPropB"
self.assertNotEqual(doc_a, doc_b)
def test_insert(self):
doc = Document()
sec_one = Section(name="sec_one", parent=doc)
sec_two = Section(name="sec_two", parent=doc)
subsec = Section(name="sec_three")
self.assertNotEqual(doc.sections[1].name, subsec.name)
doc.insert(1, subsec)
self.assertEqual(len(doc.sections), 3)
self.assertEqual(doc.sections[1].name, subsec.name)
self.assertEqual(doc.sections[0].name, sec_one.name)
self.assertEqual(doc.sections[2].name, sec_two.name)
self.assertEqual(subsec.parent, doc)
# Test invalid object
with self.assertRaises(ValueError):
doc.insert(1, Document())
with self.assertRaises(ValueError):
doc.insert(1, Property(name="prop_one"))
with self.assertRaises(ValueError):
doc.insert(1, "some info")
self.assertEqual(len(doc), 3)
# Test same name entries
with self.assertRaises(ValueError):
doc.insert(0, subsec)
self.assertEqual(len(doc), 3)
def test_append(self):
doc = Document()
self.assertListEqual(doc.sections, [])
# Test append Section
sec = Section(name="sec_one")
doc.append(sec)
self.assertEqual(len(doc.sections), 1)
self.assertEqual(sec.parent, doc)
# Test fail on Section list or tuple append
with self.assertRaises(ValueError):
doc.append([Section(name="sec_two"), Section(name="sec_three")])
with self.assertRaises(ValueError):
doc.append((Section(name="sec_two"), Section(name="sec_three")))
self.assertEqual(len(doc.sections), 1)
# Test fail on unsupported value
with self.assertRaises(ValueError):
doc.append(Document())
with self.assertRaises(ValueError):
doc.append("Section")
with self.assertRaises(ValueError):
doc.append(Property(name="prop"))
# Test fail on same name entities
with self.assertRaises(KeyError):
doc.append(Section(name="sec_one"))
self.assertEqual(len(doc.sections), 1)
def test_extend(self):
doc = Document()
self.assertListEqual(doc.sections, [])
# Test extend with Section list
doc.extend([Section(name="sec_one"), Section(name="sec_two")])
self.assertEqual(len(doc), 2)
self.assertEqual(len(doc.sections), 2)
self.assertEqual(doc.sections[0].name, "sec_one")
# Test fail on non iterable
with self.assertRaises(TypeError):
doc.extend(1)
self.assertEqual(len(doc.sections), 2)
# Test fail on non Section entry
with self.assertRaises(ValueError):
doc.extend([Document()])
with self.assertRaises(ValueError):
doc.extend([Property(name="prop")])
with self.assertRaises(ValueError):
doc.extend([5])
self.assertEqual(len(doc.sections), 2)
# Test fail on same name entities
with self.assertRaises(KeyError):
doc.extend([Section(name="sec_three"), Section(name="sec_one")])
self.assertEqual(len(doc.sections), 2)