def test_set_placements_list(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)
c1 = Container(uri='http://testgenologics.com:4040/containers/c1', 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, (c1, '3:1')], [a2, (c1, '4:1')]]
s.set_placement_list(new_placements)
assert elements_equal(s.root, ElementTree.fromstring(self.modloc_step_placements_xml))
def __get__(self, instance, cls):
from genologics.entities import Container
instance.get()
node = instance.root.find(self.tag)
if node is None:
return (None, None)
uri = node.find('container').attrib['uri']
return Container(instance.lims, uri=uri), node.find('value').text
def save_containers(self, container_details: ObjectifiedElement):
"""Save a batch of containers."""
container_uri = f"{self.get_uri()}/containers/batch/create"
results = self.save_xml(container_uri, container_details)
container_map = {}
for link in results.findall("link"):
lims_container = Container(self, uri=link.attrib["uri"])
container_map[lims_container.name] = lims_container
return container_map
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 test_create_entity(self):
with patch('genologics.lims.requests.post',
return_value=Mock(content=self.sample_creation, status_code=201)) as patch_post:
l = 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" limsid="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))
def get(self):
limsl = lims.Lims(BASEURI, USERNAME, PASSWORD)
#qPCR queues
queues = {}
queues['MiSeq'] = Queue(limsl, id='1002')
queues['NovaSeq'] = Queue(limsl, id='1666')
queues['LibraryValidation'] = Queue(limsl, id='41')
methods = queues.keys()
pools = {}
for method in methods:
pools[method] = {}
if queues[method].artifacts:
tree = ET.fromstring(queues[method].xml())
if tree.find('next-page') is not None:
flag = True
next_page_uri = tree.find('next-page').attrib['uri']
while flag:
next_page = ET.fromstring(
Queue(limsl, uri=next_page_uri).xml())
for elem in next_page.findall('artifacts'):
tree.insert(0, elem)
if next_page.find('next-page') is not None:
next_page_uri = next_page.find(
'next-page').attrib['uri']
else:
flag = False
for artifact in tree.iter('artifact'):
queue_time = artifact.find('queue-time').text
container = Container(limsl,
uri=artifact.find('location').find(
'container').attrib['uri']).name
art = Artifact(limsl, uri=artifact.attrib['uri'])
value = artifact.find('location').find('value').text
library_type = ''
runmode = ''
if not 'lambda DNA' in art.name:
library_type = art.samples[0].project.udf[
"Library construction method"]
try:
runmode = art.samples[0].project.udf[
'Sequencing platform']
except KeyError:
runmode = 'NA'
if container in pools[method]:
pools[method][container]['samples'].append({
'name':
art.name,
'well':
value,
'queue_time':
queue_time
})
if library_type and library_type not in pools[method][
container]['library_types']:
pools[method][container]['library_types'].append(
library_type)
if runmode and runmode not in pools[method][container][
'runmodes']:
pools[method][container]['runmodes'].append(
runmode)
else:
pools[method][container] = {
'samples': [{
'name': art.name,
'well': value,
'queue_time': queue_time
}],
'library_types': [library_type],
'runmodes': [runmode]
}
self.set_header("Content-type", "application/json")
self.write(json.dumps(pools))
def get(self):
limsl = lims.Lims(BASEURI, USERNAME, PASSWORD)
#sequencing queues are currently taken as the following
#Miseq- Step 7: Denature, Dilute and load sample
#Novaseq Step 11: Load to flow cell
queues = {}
queues['MiSeq'] = Queue(limsl, id='55')
queues['NovaSeq'] = Queue(limsl, id='1662')
methods = queues.keys()
pools = {}
for method in methods:
pools[method] = {}
if queues[method].artifacts:
tree = ET.fromstring(queues[method].xml())
for artifact in tree.iter('artifact'):
queue_time = artifact.find('queue-time').text
container = Container(limsl,
uri=artifact.find('location').find(
'container').attrib['uri']).name
attr_name = Artifact(limsl,
uri=artifact.attrib['uri']).name
value = artifact.find('location').find('value').text
proj_and_samples = {}
conc_qpcr = ''
is_rerun = False
art = Artifact(limsl, uri=artifact.attrib['uri'])
if method is 'MiSeq':
#FinishedLibrary
if 'Concentration' in dict(art.udf.items()).keys():
conc_qpcr = art.udf['Concentration']
#InhouseLibrary
elif 'Pool Conc. (nM)' in dict(art.udf.items()).keys():
conc_qpcr = str(art.udf['Pool Conc. (nM)'])
else:
pass
is_rerun = art.udf["Rerun"]
elif method is 'NovaSeq':
if 'Concentration' in dict(art.udf.items()).keys():
conc_qpcr = art.udf["Concentration"]
if 'Rerun' in dict(art.udf.items()).keys():
is_rerun = art.udf["Rerun"]
else:
new_art = art.parent_process.input_output_maps[0][
0]
# The loop iterates 4 times as the values were found within the first 4 preceding
# parent processes(through trial and error). If the values are not found within 4 iterations, they can be looked up
# manually in LIMS. The loop is structured so as its not very clear in the genologics API which of the parent processes
# will contain the values in post process and 4 seemed to get everything for the data at hand.
i = 0
while i < 4:
if 'Concentration' in dict(
new_art['post-process-uri'].udf.items(
)).keys():
conc_qpcr = new_art[
'post-process-uri'].udf[
"Concentration"]
if 'Rerun' in dict(
new_art['post-process-uri'].udf.
items()).keys():
is_rerun = new_art[
'post-process-uri'].udf["Rerun"]
break
else:
new_art = new_art[
'parent-process'].input_output_maps[0][
0]
i = i + 1
for sample in art.samples:
project = sample.project.id
if project in pools[method]:
if container in pools[method][project]['plates']:
pools[method][project]['plates'][container][
'samples'].append(sample.name)
else:
pools[method][project]['plates'][container] = {
'samples': [sample.name],
'well': value,
'queue_time': queue_time,
'conc_pool_qpcr': conc_qpcr,
'is_rerun': is_rerun
}
else:
setup = sample.project.udf['Sequencing setup']
lanes = sample.project.udf[
'Sequence units ordered (lanes)']
librarytype = sample.project.udf[
'Library construction method']
runmode = sample.project.udf['Sequencing platform']
final_loading_conc = 'TBD'
if method is 'NovaSeq':
try:
final_loading_conc = Artifact(
limsl, uri=artifact.attrib['uri']
).udf['Final Loading Concentration (pM)']
except KeyError:
pass
pools[method][project] = {
'name': sample.project.name,
'setup': setup,
'lanes': lanes,
'runmode': runmode,
'final_loading_conc': final_loading_conc,
'librarytype': librarytype,
'plates': {
container: {
'samples': [sample.name],
'well': value,
'queue_time': queue_time,
'conc_pool_qpcr': conc_qpcr,
'is_rerun': is_rerun
}
}
}
self.set_header("Content-type", "application/json")
self.write(json.dumps(pools))
def get(self):
limsl = lims.Lims(BASEURI, USERNAME, PASSWORD)
#qPCR queues
queues = {}
queues['MiSeq'] = Queue(limsl, id='1002')
queues['NovaSeq'] = Queue(limsl, id='1666')
queues['LibraryValidation'] = Queue(limsl, id='41')
methods = queues.keys()
pools = {}
qpcr_control_names = [
'AM7852', 'E.Coli genDNA', 'Endogenous Positive Control',
'Exogenous Positive Control', 'Human Brain Reference RNA',
'lambda DNA', 'mQ Negative Control', 'NA10860', 'NA11992',
'NA11993', 'NA12878', 'NA12891', 'NA12892',
'No Amplification Control', 'No Reverse Transcriptase Control',
'No Template Control', 'PhiX v3', 'Universal Human Reference RNA',
'lambda DNA (qPCR)'
]
for method in methods:
pools[method] = {}
if queues[method].artifacts:
tree = ET.fromstring(queues[method].xml())
if tree.find('next-page') is not None:
flag = True
next_page_uri = tree.find('next-page').attrib['uri']
while flag:
next_page = ET.fromstring(
Queue(limsl, uri=next_page_uri).xml())
for elem in next_page.findall('artifacts'):
tree.insert(0, elem)
if next_page.find('next-page') is not None:
next_page_uri = next_page.find(
'next-page').attrib['uri']
else:
flag = False
for artifact in tree.iter('artifact'):
queue_time = artifact.find('queue-time').text
container = Container(limsl,
uri=artifact.find('location').find(
'container').attrib['uri']).name
art = Artifact(limsl, uri=artifact.attrib['uri'])
value = artifact.find('location').find('value').text
library_type = ''
runmode = ''
#skip if the Artifact is a control
if art.name in qpcr_control_names:
continue
library_type = art.samples[0].project.udf.get(
"Library construction method", 'NA')
try:
runmode = art.samples[0].project.udf[
'Sequencing platform']
except KeyError:
runmode = 'NA'
if container in pools[method]:
pools[method][container]['samples'].append({
'name':
art.name,
'well':
value,
'queue_time':
queue_time
})
if library_type and library_type not in pools[method][
container]['library_types']:
pools[method][container]['library_types'].append(
library_type)
if runmode and runmode not in pools[method][container][
'runmodes']:
pools[method][container]['runmodes'].append(
runmode)
else:
pools[method][container] = {
'samples': [{
'name': art.name,
'well': value,
'queue_time': queue_time
}],
'library_types': [library_type],
'runmodes': [runmode]
}
self.set_header("Content-type", "application/json")
self.write(json.dumps(pools))
def main(args):
lims = Lims(BASEURI, USERNAME, PASSWORD)
cont = Container(lims, id=args.flowcell)
cont.name = cont.id
cont.put()