def test_identifiable(self):
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"biomaterial_id": {"identifiable" : "true"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertTrue(
template.lookup("donor_organism.biomaterial_id.identifiable"))
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"foo_bar": {"user_friendly" : "Foo bar"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertFalse(
template.lookup("donor_organism.foo_bar.identifiable"))
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"process_id": {"identifiable" : "true"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertTrue(
template.lookup("donor_organism.process_id.identifiable"))
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"protocol_id": {"identifiable" : "true"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertTrue(
template.lookup("donor_organism.protocol_id.identifiable"))
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"file_name": {"identifiable" : "true"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertTrue(
template.lookup("donor_organism.file_name.identifiable"))
def test_example(self):
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"foo_bar": {"example" : "Foo is a bar"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertEqual("Foo is a bar",
template.lookup("donor_organism.foo_bar.example"))
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"foo_bar": {"user_friendly" : "Foo bar"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertIsNone(template.lookup("donor_organism.foo_bar.example"))
def test_follows_item_refs(self):
data = '{"id" : "' + self.dummyProjectUri + '", "properties": { "foo_bar": {"type" : "array" , "items" : {"type" : "object", "id": "' + self.dummyDonorUri + '"}} } }'
template = schema_mock.get_template_for_json(data=data)
self.assertEqual(
"biomaterial",
template.lookup("project.foo_bar.schema.domain_entity"))
def test_get_key_for_label(self):
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"foo_bar": {"user_friendly" : "Foo bar"}} }'
template = schema_mock.get_template_for_json(data=data)
tabs = template.get_tabs_config()
self.assertEqual("donor_organism",
tabs.get_key_for_label("donor_organism"))
def test_no_schemas(self):
data = \
f'''{{
"id" : "{self.donorUri}",
"properties": {{
"foo_bar": {{
"user_friendly" : "Foo bar",
"description" : "this is a foo bar", "example" : "e.g. foo"
}}
}}
}}'''
file = "foo.xlsx"
spreadsheet_builder = SpreadsheetBuilder(file)
template = schema_mock.get_template_for_json(data=data)
spreadsheet_builder._build(template)
spreadsheet_builder.save_workbook()
reader = Reader("foo.xlsx")
sheet = reader["Donor organism"]
self.assertEqual("this is a foo bar",
sheet.cell(row=2, column=1).value)
self.assertEqual("FOO BAR", sheet.cell(row=1, column=1).value)
self.assertEqual("For example: e.g. foo",
sheet.cell(row=3, column=1).value.strip())
self.assertEqual("donor_organism.foo_bar",
sheet.cell(row=4, column=1).value)
# clean up
os.remove(file)
def test_get_key_for_label(self):
data = f'{{"id" : "{self.dummyDonorUri}"}}'
template = schema_mock.get_template_for_json(data=data)
tabs = template.get_tabs_config()
self.assertEqual("donor_organism",
tabs.get_key_for_label("Donor organism"))
self.assertEqual('donor_organism',
tabs.get_key_for_label('donor_organism'))
def test_get_tab_key(self):
# given:
project_data = f'{{"id":"{self.dummyProjectUri}"}}'
template = schema_mock.get_template_for_json(data=project_data)
# expect:
self.assertEqual('project', template.get_tab_key('project'))
self.assertEqual('project', template.get_tab_key('Project'))
def test_schema_lookup(self):
data = '{"id" : "' + self.dummyProjectUri + '", "properties": {"foo": "bar"} }'
template = schema_mock.get_template_for_json(data=data)
self.assertEqual("project",
template.lookup('project.schema.domain_entity'))
self.assertEqual("project", template.lookup('project.schema.module'))
self.assertEqual("type",
template.lookup('project.schema.high_level_entity'))
def test_lookup_key_in_tab(self):
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"foo_bar": {"user_friendly" : "Foo bar"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertEqual(
"donor_organism.foo_bar",
template.get_key_for_label("Foo bar", "Donor organism"))
with self.assertRaises(UnknownKeyException):
template.get_key_for_label("Bar foo", "Donor organism")
def test_retrieveable(self):
data = '{"id" : "' + self.dummyDonorUri + '", "properties": {"foo_bar": {"format" : "date-time"}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertTrue(
template.lookup("donor_organism.uuid.external_reference"))
self.assertTrue(template.lookup("donor_organism.uuid.identifiable"))
self.assertFalse(
template.lookup("donor_organism.foo_bar.external_reference"))
self.assertFalse(
template.lookup("donor_organism.foo_bar.identifiable"))
with self.assertRaises(UnknownKeyException):
self.assertTrue(
template.lookup("donor_organism.format.uuid.retrievable"))
def test_get_tab_key_not_found(self):
# given:
donor_organism_data = f'{{"id": "{self.dummyDonorUri}"}}'
template = schema_mock.get_template_for_json(data=donor_organism_data)
# when:
exception_raised = None
try:
template.get_tab_key('does not exist')
except UnknownKeyException as exception:
exception_raised = exception
# then:
self.assertIsNotNone(exception_raised)
def test_get_tab_key_case_insensitive(self):
# given:
donor_organism_data = f'{{"id": "{self.dummyDonorUri}"}}'
template = schema_mock.get_template_for_json(data=donor_organism_data)
# and:
self.assertEqual('donor_organism',
template.get_tab_key('donor_organism'))
self.assertEqual('donor_organism',
template.get_tab_key('Donor organism'))
self.assertEqual('donor_organism',
template.get_tab_key('donOr orGanisM'))
self.assertEqual('donor_organism',
template.get_tab_key('DONOR ORGANISM'))
# and:
self.assertEqual('donor_organism',
template.get_tab_key('donor_organism'))
self.assertEqual('donor_organism',
template.get_tab_key('DONOR_ORGANISM'))
def test_referenced_property(self):
dir_path = os.path.dirname(os.path.realpath(__file__))
biomaterial_core_path = os.path.realpath(os.sep + os.sep + dir_path +
os.sep +
"biomaterial_core.json")
data = '{"id" : "' + self.dummyDonorUri + '", "properties": { "biomaterial_core" : {"user_friendly": "foo", "description" : "foo bar" , "$ref" : "file:' + biomaterial_core_path + '"}}}'
template = schema_mock.get_template_for_json(data=data)
self.assertEqual(
"foo",
template.lookup("donor_organism.biomaterial_core.user_friendly"))
self.assertEqual(
"foo bar",
template.lookup("donor_organism.biomaterial_core.description"))
self.assertEqual(
"biomaterial id",
template.lookup(
"donor_organism.biomaterial_core.biomaterial_id.user_friendly")
)
self.assertEqual(
"a biomaterial id",
template.lookup(
"donor_organism.biomaterial_core.biomaterial_id.description"))
def test_has_type_list(self):
data = '{"id" : "' + self.dummyDonorUri + '", "properties": { "foo_bar": {"type" : "array" , "items" : {"type": "string"}} } }'
template = schema_mock.get_template_for_json(data=data)
self.assertEqual("string",
template.lookup("donor_organism.foo_bar.value_type"))
self.assertTrue(template.lookup("donor_organism.foo_bar.multivalue"))
def test_required_fields(self):
data = '{"id" : "' + self.dummyDonorUri + '", "required": ["foo_bar"], "properties": { "foo_bar": {"user_friendly" : "Foo bar"}, "bar_foo" : {}} }'
template = schema_mock.get_template_for_json(data=data)
self.assertTrue(template.lookup("donor_organism.foo_bar.required"))
self.assertFalse(template.lookup("donor_organism.bar_foo.required"))
def test_unknown_key_exception(self):
data = '{"id" : "' + self.dummyProjectUri + '", "properties": {"foo": "bar"} }'
template = schema_mock.get_template_for_json(data=data)
with self.assertRaises(UnknownKeyException):
template.lookup('foo')
def test_no_root_schema(self):
data = '{"properties": {"foo": "bar"} }'
with self.assertRaises(RootSchemaException):
schema_mock.get_template_for_json(data=data)
