def setUp(self):
et = ElementTree.fromstring(
'''<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<test-entry>
<pooled-inputs>
<pool output-uri="{uri}/out1" name="pool1">
<input uri="{uri}/in1"/>
<input uri="{uri}/in2"/>
</pool>
<pool output-uri="{uri}/out2" name="pool2">
<input uri="{uri}/in3"/>
<input uri="{uri}/in4"/>
</pool>
</pooled-inputs>
</test-entry>'''.format(uri='http://testgenologics.com:4040'))
self.lims = Lims('http://testgenologics.com:4040',
username='******',
password='******')
self.instance1 = Mock(root=et, lims=self.lims)
self.dict1 = XmlPooledInputDict(self.instance1)
self.out1 = Artifact(self.lims,
uri='http://testgenologics.com:4040/out1')
self.in1 = Artifact(self.lims,
uri='http://testgenologics.com:4040/in1')
self.in2 = Artifact(self.lims,
uri='http://testgenologics.com:4040/in2')
def setUp(self):
et = ElementTree.fromstring(
"""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<test-entry>
<artifact uri="http://testgenologics.com:4040/api/v2/artifacts/a1"></artifact>
<artifact uri="http://testgenologics.com:4040/api/v2/artifacts/a2"></artifact>
<other>thing</other>
</test-entry>
""")
self.lims = Lims('http://testgenologics.com:4040',
username='******',
password='******')
self.a1 = Artifact(self.lims, id='a1')
self.a2 = Artifact(self.lims, id='a2')
self.instance1 = Mock(root=et, lims=self.lims)
et = ElementTree.fromstring(
"""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<test-entry>
<nesting>
<artifact uri="http://testgenologics.com:4040/api/v2/artifacts/a1"></artifact>
<artifact uri="http://testgenologics.com:4040/api/v2/artifacts/a2"></artifact>
</nesting>
</test-entry>
""")
self.instance2 = Mock(root=et, lims=self.lims)
def test_set_list(self):
el = EntityList(self.instance1, 'artifact', Artifact)
assert len(el) == 2
assert len(el.instance.root.findall('artifact')) == 2
a3 = Artifact(self.lims, id='a3')
a4 = Artifact(self.lims, id='a4')
el[0:2] = [a3, a4]
assert len(el) == 2
assert el[0] == a3
assert el[1] == a4
def test___add__(self):
el1 = EntityList(self.instance1, 'artifact', Artifact)
assert len(el1) == 2
assert len(el1.instance.root.findall('artifact')) == 2
el2 = [Artifact(self.lims, id='a3'), Artifact(self.lims, id='a4')]
el3 = el1 + el2
assert len(el3) == 4
assert el3[:2] == el1
assert el3[2:] == el2
def _parse_element(self, element, **kwargs):
from pyclarity_lims.entities import Artifact
dict.__setitem__(
self,
element.attrib.get('name'),
(
Artifact(self.instance.lims, uri=element.attrib.get('output-uri')),
tuple(Artifact(self.instance.lims, uri=sub.attrib.get('uri')) for sub in element.findall('input'))
)
)
def test__iadd__(self):
el1 = EntityList(self.instance1, 'artifact', Artifact)
id1 = id(el1)
assert len(el1) == 2
assert len(el1.instance.root.findall('artifact')) == 2
el2 = [Artifact(self.lims, id='a3'), Artifact(self.lims, id='a4')]
el1 += el2
id2 = id(el1)
assert id1 == id2 # still the same object
assert len(el1) == 4
assert el1[2:] == el2
def test_get_placements_list(self):
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)):
a1 = Artifact(uri='http://testgenologics.com:4040/artifacts/a1',
lims=self.lims)
a2 = Artifact(uri='http://testgenologics.com:4040/artifacts/a2',
lims=self.lims)
c1 = Container(uri='http://testgenologics.com:4040/containers/c1',
lims=self.lims)
expected_placements = [(a1, (c1, '1:1')), (a2, (c1, '2:1'))]
assert s.get_placement_list() == expected_placements
def _parse_element(self, element, lims, **kwargs):
from pyclarity_lims.entities import Artifact, Container
input_art = Artifact(lims, uri=element.attrib['uri'])
loc = element.find('location')
location = (None, None)
if loc:
location = (
Container(lims, uri=loc.find('container').attrib['uri']),
loc.find('value').text
)
qt = element.find('queue-time')
queue_date = None
if qt is not None:
h, s, t = qt.text.rpartition(':')
qt = h + t
microsec = ''
if '.' in qt:
microsec = '.%f'
date_format = '%Y-%m-%dT%H:%M:%S' + microsec
try:
queue_date = datetime.datetime.strptime(qt, date_format + '%z')
except ValueError:
# support for python 2.7 ignore time zone
# use python 3 for timezone support
if '+' in qt:
qt = qt.split('+')[0]
else:
qt_array = qt.split('-')
qt = qt_array[0] + "-" + qt_array[1] + "-" + qt_array[2]
queue_date = datetime.datetime.strptime(qt, date_format)
list.append(self, (input_art, queue_date, location))
def test_parse(self):
action = XmlAction(self.instance1, tag='next-action')
assert action['action'] == 'nextstep'
assert action['step'] == ProtocolStep(
self.lims, uri='http://testgenologics.com:4040/prt/1/stp/1')
assert action['artifact'] == Artifact(
self.lims, uri='http://testgenologics.com:4040/arts/a1')
def get_queue_art(self, art_id, pos, microsec, time_delta):
if version_info[0] == 2:
return (Artifact(self.lims, id=art_id),
datetime.datetime(2011, 12, 25, 1, 10,
10, microsec), (Container(self.lims,
id='c1'), pos))
else:
return (Artifact(self.lims, id=art_id),
datetime.datetime(2011,
12,
25,
1,
10,
10,
microsec,
tzinfo=datetime.timezone(time_delta)),
(Container(self.lims, id='c1'), pos))
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_append(self):
el = EntityList(self.instance1, 'artifact', Artifact)
assert len(el) == 2
assert len(el.instance.root.findall('artifact')) == 2
a3 = Artifact(self.lims, id='a3')
el.append(a3)
assert len(el) == 3
assert el[2] == a3
assert len(el._elems) == 3
assert len(el.instance.root.findall('artifact')) == 3
def _parse_element(self, element, lims, **kwargs):
from pyclarity_lims.entities import Artifact, Container
input = Artifact(lims, uri=element.attrib['uri'])
loc = element.find('location')
location = (None, None)
if loc:
location = (
Container(lims, uri=loc.find('container').attrib['uri']),
loc.find('value').text
)
list.append(self, (input, location))
def _parse_element(self, element, **kwargs):
from pyclarity_lims.entities import Artifact, ProtocolStep
for k, v in element.attrib.items():
if k == 'artifact-uri':
k = 'artifact'
v = Artifact(self.instance.lims, uri=v)
elif k in ('step-uri', 'rework-step-uri'):
k = k[:-(len('-uri'))]
v = ProtocolStep(self.instance.lims, uri=v)
dict.__setitem__(self, k, v)
def test_set(self):
el = EntityList(self.instance1, 'artifact', Artifact)
assert len(el) == 2
assert len(el.instance.root.findall('artifact')) == 2
a3 = Artifact(self.lims, id='a3')
el[1] = a3
assert len(el) == 2
assert el[1] == a3
assert len(el._elems) == 2
assert el.instance.root.findall('artifact')[1].attrib[
'uri'] == 'http://testgenologics.com:4040/api/v2/artifacts/a3'
def test___setitem__(self):
assert len(
self.dict1.rootnode(self.dict1.instance).findall('placement')) == 1
art2 = Artifact(lims=self.lims, id='a2')
self.dict1['A:1'] = art2
assert len(
self.dict1.rootnode(self.dict1.instance).findall('placement')) == 1
self.dict1['A:2'] = art2
assert len(
self.dict1.rootnode(self.dict1.instance).findall('placement')) == 2
assert self.dict1['A:2'] == art2
def test_workflow_stages_and_statuses(self):
a = Artifact(uri=self.lims.get_uri('artifacts', 'a1'), lims=self.lims)
expected_wf_stage = [
(Stage(self.lims,
uri=url + '/api/v2/configuration/workflows/1/stages/2'),
'QUEUED', 'Test workflow s2'),
(Stage(self.lims,
uri=url + '/api/v2/configuration/workflows/1/stages/1'),
'COMPLETE', 'Test workflow s1')
]
with patch('requests.Session.get',
return_value=Mock(content=self.root_artifact_xml,
status_code=200)):
assert a.workflow_stages_and_statuses == expected_wf_stage
def setUp(self):
et = ElementTree.fromstring(
"""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<test-entry xmlns:udf="http://genologics.com/ri/userdefined">
<placement uri="http://testgenologics.com:4040/api/v2/artifacts/a1" limsid="a1">
<value>A:1</value>
</placement>
<other>thing</other>
</test-entry>""")
self.lims = Lims('http://testgenologics.com:4040',
username='******',
password='******')
self.instance1 = Mock(root=et, lims=self.lims)
self.dict1 = PlacementDictionary(self.instance1)
self.art1 = Artifact(lims=self.lims, id='a1')
def _get_dict(self, lims, node):
from pyclarity_lims.entities import Artifact, Process
if node is None:
return None
result = dict()
for key in ['limsid', 'output-type', 'output-generation-type']:
try:
result[key] = node.attrib[key]
except KeyError:
pass
for uri in ['uri', 'post-process-uri']:
try:
result[uri] = Artifact(lims, uri=node.attrib[uri])
except KeyError:
pass
node = node.find('parent-process')
if node is not None:
result['parent-process'] = Process(lims, node.attrib['uri'])
return result
def test_next_actions(self):
s = StepActions(uri=self.lims.get_uri('steps', 'step_id', 'actions'),
lims=self.lims)
with patch('requests.Session.get',
return_value=Mock(
content=self.step_actions_no_escalation_xml,
status_code=200)):
step1 = Step(self.lims,
uri='http://testgenologics.com:4040/steps/s1')
step2 = Step(self.lims,
uri='http://testgenologics.com:4040/steps/s2')
artifact = Artifact(
self.lims, uri='http://testgenologics.com:4040/artifacts/a1')
expected_next_actions = [{
'artifact': artifact,
'action': 'requeue',
'step': step1,
'rework-step': step2
}]
assert s.next_actions == expected_next_actions
def test_escalation(self):
s = StepActions(uri=self.lims.get_uri('steps', 'step_id', 'actions'),
lims=self.lims)
with patch('requests.Session.get',
return_value=Mock(content=self.step_actions_xml,
status_code=200)):
with patch('requests.post',
return_value=Mock(content=self.dummy_xml,
status_code=200)):
r = Researcher(
uri='http://testgenologics.com:4040/researchers/r1',
lims=self.lims)
a = Artifact(uri='http://testgenologics.com:4040/artifacts/r1',
lims=self.lims)
expected_escalation = {
'status': 'Reviewed',
'author': r,
'artifacts': [a],
'request': 'no comments',
'answer': 'no comments',
'reviewer': r
}
assert s.escalation == expected_escalation
def test_input_artifact_list(self):
a = Artifact(uri=self.lims.get_uri('artifacts', 'a1'), lims=self.lims)
with patch('requests.Session.get',
return_value=Mock(content=self.root_artifact_xml,
status_code=200)):
assert a.input_artifact_list() == []
def _parse_element(self, element, **kwargs):
from pyclarity_lims.entities import Artifact
key = element.find('value').text
dict.__setitem__(self, key, Artifact(self.instance.lims, uri=element.attrib['uri']))