def test_append(self):
el = XmlAttributeList(self.instance1,
tag='test-tag',
nesting=['test-tags'])
el.append({'attrib1': 'value21'})
elements_equal(
el.instance.root.find('test-tags').findall('test-tag')[-1],
ElementTree.fromstring('''<test-tag attrib1="value21" />'''))
def test_append(self):
rl = XmlReagentLabelList(self.instance1)
rl.append('another label')
assert rl == ['label name', 'another label']
elements_equal(
rl.instance.root.findall('reagent-label')[1],
ElementTree.fromstring(
'''<reagent-label name="another label"/>'''))
def test_insert(self):
el = XmlAttributeList(self.instance1,
tag='test-tag',
nesting=['test-tags'])
el.insert(1, {'attrib1': 'value21'})
elements_equal(
el.instance.root.find('test-tags').findall('test-tag')[1],
ElementTree.fromstring('''<test-tag attrib1="value21" />'''))
elements_equal(
el.instance.root.find('test-tags').findall('test-tag')[2],
ElementTree.fromstring(
'''<test-tag attrib1="value11" attrib2="value12" attrib3="value13" />'''
))
def test_advance(self):
with patch('requests.Session.get',
return_value=Mock(content=self.step_xml, status_code=200)):
with patch('pyclarity_lims.lims.requests.post',
return_value=Mock(content=self.step_xml,
status_code=201)) as patch_post:
s = Step(self.lims, id='s1')
s.advance()
assert elements_equal(
ElementTree.fromstring(
patch_post.call_args_list[0][1]['data']),
ElementTree.fromstring(self.step_xml))
def test_set_placements_list_fail(self):
a1 = Artifact(uri='http://testgenologics.com:4040/artifacts/a1',
lims=self.lims)
a2 = Artifact(uri='http://testgenologics.com:4040/artifacts/a2',
lims=self.lims)
c2 = Container(uri='http://testgenologics.com:4040/containers/c2',
lims=self.lims)
s = StepPlacements(uri=self.lims.get_uri('steps', 's1', 'placements'),
lims=self.lims)
with patch('requests.Session.get',
return_value=Mock(content=self.original_step_placements_xml,
status_code=200)):
new_placements = [(a1, (c2, '1:1')), (a2, (c2, '1:1'))]
s.placement_list = new_placements
assert elements_equal(
s.root,
ElementTree.fromstring(self.modcont_step_placements_xml))
def test_create(self):
inputs = [
Mock(spec=Artifact,
lims=self.lims,
uri='http://testgenologics.com:4040/api/v2/artifacts/a1'),
Mock(spec=Artifact,
lims=self.lims,
uri='http://testgenologics.com:4040/api/v2/artifacts/a2')
]
protocol_step = NamedMock(
spec=ProtocolStep,
real_name='My fancy step',
uri=
'http://testgenologics.com:4040/api/v2/configuration//protocols/p1/steps/p1s1',
permitted_containers=['Tube'])
with patch('pyclarity_lims.lims.requests.post',
return_value=Mock(content=self.step_xml,
status_code=201)) as patch_post:
Step.create(self.lims,
protocol_step=protocol_step,
inputs=inputs,
replicates=[1, 2])
data = '''<?xml version='1.0' encoding='utf-8'?>
<stp:step-creation xmlns:stp="http://genologics.com/ri/step">
<configuration uri="http://testgenologics.com:4040/api/v2/configuration//protocols/p1/steps/p1s1">
My fancy step
</configuration>
<container-type>Tube</container-type>
<inputs>
<input uri="http://testgenologics.com:4040/api/v2/artifacts/a1" replicates="1"/>
<input uri="http://testgenologics.com:4040/api/v2/artifacts/a2" replicates="2"/>
</inputs>
</stp:step-creation>
'''
assert elements_equal(
ElementTree.fromstring(
patch_post.call_args_list[0][1]['data']),
ElementTree.fromstring(data))
def test_create_entity(self):
with patch('pyclarity_lims.lims.requests.post',
return_value=Mock(content=self.sample_creation,
status_code=201)) as patch_post:
Sample.create(
self.lims,
project=Project(self.lims, uri='project'),
container=Container(self.lims, uri='container'),
position='1:1',
name='s1',
)
data = '''<?xml version=\'1.0\' encoding=\'utf-8\'?>
<smp:samplecreation xmlns:smp="http://genologics.com/ri/sample">
<name>s1</name>
<project uri="project" />
<location>
<container uri="container" />
<value>1:1</value>
</location>
</smp:samplecreation>'''
assert elements_equal(
ElementTree.fromstring(
patch_post.call_args_list[0][1]['data']),
ElementTree.fromstring(data))