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 copy_layout(lims, process_id):
"""Copy placement layout from previous steps."""
process = Process(lims, id=process_id)
used_placements = []
# Get parent container layout
parent_container = None
for parent_process in process.parent_processes():
if parent_process:
for container in parent_process.output_containers():
if container.type != Containertype(lims, id='2'): # skip tubes
parent_container = container
if parent_container:
parent_placements = {}
for placement in parent_container.placements:
sample = parent_container.placements[placement].samples[0].name
parent_placements[sample] = placement
# Create new container and copy layout
new_container = Container.create(lims, type=parent_container.type)
placement_list = []
for artifact in process.analytes()[0]:
sample_name = artifact.samples[0].name
if sample_name in parent_placements:
placement = parent_placements[sample_name]
if placement not in used_placements:
placement_list.append([artifact, (new_container, placement)])
used_placements.append(placement)
process.step.placements.set_placement_list(placement_list)
process.step.placements.post()
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 submit_dx_samples():
form = SubmitDXSampleForm()
if form.validate_on_submit():
container_type = Containertype(lims, id='2') # Tube
workflow = Workflow(lims, id=app.config['LIMS_DX_SAMPLE_SUBMIT_WORKFLOW'])
for sample_name in form.parsed_samples:
# Get or create project
lims_projects = lims.get_projects(name=form.parsed_samples[sample_name]['project'])
if not lims_projects:
lims_project = Project.create(lims, name=form.parsed_samples[sample_name]['project'], researcher=form.researcher, udf={'Application': 'DX'})
else:
lims_project = lims_projects[0]
# Set sample udf data
udf_data = form.parsed_worklist[sample_name]
udf_data['Sample Type'] = form.parsed_samples[sample_name]['type']
udf_data['Dx Fragmentlengte (bp) Externe meting'] = form.pool_fragment_length.data
udf_data['Dx Conc. (ng/ul) Externe meting'] = form.pool_concentration.data
udf_data['Dx Exoomequivalent'] = form.parsed_samples[sample_name]['exome_count']
# Create sample
container = Container.create(lims, type=container_type, name=udf_data['Dx Fractienummer'])
sample = Sample.create(lims, container=container, position='1:1', project=lims_project, name=sample_name, udf=udf_data)
print sample.name, sample.artifact.name
# Add reagent label (barcode)
artifact = sample.artifact
artifact_xml_dom = minidom.parseString(artifact.xml())
for artifact_name_node in artifact_xml_dom.getElementsByTagName('name'):
parent = artifact_name_node.parentNode
reagent_label = artifact_xml_dom.createElement('reagent-label')
reagent_label.setAttribute('name', form.parsed_samples[sample_name]['barcode'])
parent.appendChild(reagent_label)
lims.put(artifact.uri, artifact_xml_dom.toxml(encoding='utf-8'))
lims.route_artifacts([sample.artifact], workflow_uri=workflow.uri)
return render_template('submit_dx_samples_done.html', title='Submit DX samples', project_name=lims_project.name, form=form)
return render_template('submit_dx_samples.html', title='Submit DX samples', form=form)
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 from_helix(lims, email_settings, input_file):
"""Upload samples from helix export file."""
project_name = 'Dx {filename}'.format(filename=input_file.name.rstrip('.csv').split('/')[-1])
helix_initials = project_name.split('_')[-1]
# Try lims connection
try:
lims.check_version()
except ConnectionError:
subject = "ERROR Lims Helix Upload: {0}".format(project_name)
message = "Can't connect to lims server, please contact a lims administrator."
send_email(email_settings['server'], email_settings['from'], email_settings['to_import_helix'], subject, message)
sys.exit(message)
# Get researcher using helix initials
for researcher in lims.get_researchers():
if researcher.fax == helix_initials: # Use FAX as intials field as the lims initials field can't be edited via the 5.0 web interface.
email_settings['to_import_helix'].append(researcher.email)
break
else: # No researcher found
subject = "ERROR Lims Helix Upload: {0}".format(project_name)
message = "Can't find researcher with initials: {0}.".format(helix_initials)
send_email(email_settings['server'], email_settings['from'], email_settings['to_import_helix'], subject, message)
sys.exit(message)
# Create project
if not lims.get_projects(name=project_name):
project = Project.create(lims, name=project_name, researcher=researcher, udf={'Application': 'DX'})
else:
subject = "ERROR Lims Helix Upload: {0}".format(project_name)
message = "Duplicate project / werklijst. Samples not loaded."
send_email(email_settings['server'], email_settings['from'], email_settings['to_import_helix'], subject, message)
sys.exit(message)
container_type = Containertype(lims, id='2') # Tube
# match header and udf fields
udf_column = {
'Dx Onderzoeknummer': {'column': 'Onderzoeknummer'},
'Dx Fractienummer': {'column': 'Fractienummer'},
'Dx Monsternummer': {'column': 'Monsternummer'},
'Dx Concentratie (ng/ul)': {'column': 'Concentratie (ng/ul)'},
'Dx Materiaal type': {'column': 'Materiaal'},
'Dx Foetus': {'column': 'Foetus'},
'Dx Foetus ID': {'column': 'Foet_id'},
'Dx Foetus geslacht': {'column': 'Foetus_geslacht'},
'Dx Overleden': {'column': 'Overleden'},
'Dx Opslaglocatie': {'column': 'Opslagpositie'},
'Dx Spoed': {'column': 'Spoed'},
'Dx NICU Spoed': {'column': 'NICU Spoed'},
'Dx Persoons ID': {'column': 'Persoons_id'},
'Dx Werklijstnummer': {'column': 'Werklijstnummer'},
'Dx Familienummer': {'column': 'Familienummer'},
'Dx Geslacht': {'column': 'Geslacht'},
'Dx Geboortejaar': {'column': 'Geboortejaar'},
'Dx Meet ID': {'column': 'Stof_meet_id'},
'Dx Stoftest code': {'column': 'Stoftestcode'},
'Dx Stoftest omschrijving': {'column': 'Stoftestomschrijving'},
'Dx Onderzoeksindicatie': {'column': 'Onderzoeksindicatie'},
'Dx Onderzoeksreden': {'column': 'Onderzoeksreden'},
'Dx Protocolcode': {'column': 'Protocolcode'},
'Dx Protocolomschrijving': {'column': 'Protocolomschrijving'},
'Dx Einddatum': {'column': 'Einddatum'},
'Dx Gerelateerde onderzoeken': {'column': 'Gerelateerde onderzoeken'},
}
header = input_file.readline().rstrip().split(',') # expect header on first line
for udf in udf_column:
udf_column[udf]['index'] = header.index(udf_column[udf]['column'])
# Setup email
subject = "Lims Helix Upload: {0}".format(project_name)
message = "Project: {0}\n\nSamples:\n".format(project_name)
# Parse samples
for line in input_file:
data = line.rstrip().strip('"').split('","')
udf_data = {'Sample Type': 'DNA isolated', 'Dx Import warning': ''} # required lims input
for udf in udf_column:
# Transform specific udf
if udf in ['Dx Overleden', 'Dx Spoed', 'Dx NICU Spoed']:
udf_data[udf] = clarity_epp.upload.utils.char_to_bool(data[udf_column[udf]['index']])
elif udf in ['Dx Geslacht', 'Dx Foetus geslacht']:
udf_data[udf] = clarity_epp.upload.utils.transform_sex(data[udf_column[udf]['index']])
elif udf == 'Dx Foetus':
udf_data[udf] = bool(data[udf_column[udf]['index']].strip())
elif udf == 'Dx Concentratie (ng/ul)':
udf_data[udf] = data[udf_column[udf]['index']].replace(',', '.')
elif udf in ['Dx Monsternummer', 'Dx Fractienummer']:
udf_data[udf] = clarity_epp.upload.utils.transform_sample_name(data[udf_column[udf]['index']])
elif udf == 'Dx Gerelateerde onderzoeken':
udf_data[udf] = data[udf_column[udf]['index']].replace(',', ';')
elif udf == 'Dx Einddatum':
date = datetime.strptime(data[udf_column[udf]['index']], '%d-%m-%Y') # Helix format (14-01-2021)
udf_data[udf] = date.strftime('%Y-%m-%d') # LIMS format (2021-01-14)
else:
udf_data[udf] = data[udf_column[udf]['index']]
sample_name = udf_data['Dx Monsternummer']
# Set 'Dx Handmatig' udf
if udf_data['Dx Foetus'] or udf_data['Dx Overleden'] or udf_data['Dx Materiaal type'] not in ['BL', 'BLHEP', 'BM', 'BMEDTA']:
udf_data['Dx Handmatig'] = True
else:
udf_data['Dx Handmatig'] = False
# Set 'Dx Familie status' udf
if udf_data['Dx Onderzoeksreden'] == 'Bevestiging diagnose':
udf_data['Dx Familie status'] = 'Kind'
elif udf_data['Dx Onderzoeksreden'] == 'Prenataal onderzoek':
udf_data['Dx Familie status'] = 'Kind'
elif udf_data['Dx Onderzoeksreden'] == 'Eerstegraads-verwantenond':
udf_data['Dx Familie status'] = 'Kind'
elif udf_data['Dx Onderzoeksreden'] == 'Partneronderzoek':
udf_data['Dx Familie status'] = 'Kind'
elif udf_data['Dx Onderzoeksreden'] == 'Informativiteitstest':
udf_data['Dx Familie status'] = 'Ouder'
else:
udf_data['Dx Import warning'] = ';'.join(['Onbekende onderzoeksreden, familie status niet ingevuld.', udf_data['Dx Import warning']])
# Set 'Dx Geslacht' and 'Dx Geboortejaar' with 'Foetus' information if 'Dx Foetus == True'
if udf_data['Dx Foetus']:
udf_data['Dx Geslacht'] = udf_data['Dx Foetus geslacht']
udf_data['Dx Geboortejaar'] = ''
# Set 'Dx Geslacht = Onbekend' if 'Dx Onderzoeksindicatie == DSD00'
if udf_data['Dx Onderzoeksindicatie'] == 'DSD00' and udf_data['Dx Familie status'] == 'Kind':
udf_data['Dx Geslacht'] = 'Onbekend'
# Check 'Dx Familienummer' and correct
if '/' in udf_data['Dx Familienummer']:
udf_data['Dx Import warning'] = ';'.join([
'Meerdere familienummers, laatste wordt gebruikt. ({0})'.format(udf_data['Dx Familienummer']),
udf_data['Dx Import warning']
])
udf_data['Dx Familienummer'] = udf_data['Dx Familienummer'].split('/')[-1].strip(' ')
sample_list = lims.get_samples(name=sample_name)
if sample_list:
sample = sample_list[0]
if udf_data['Dx Protocolomschrijving'] in sample.udf['Dx Protocolomschrijving']:
message += "{0}\tERROR: Duplicate sample and Protocolomschrijving code: {1}.\n".format(sample_name, udf_data['Dx Protocolomschrijving'])
else:
# Update existing sample if new Protocolomschrijving and thus workflow.
# Append udf fields
append_udf = [
'Dx Onderzoeknummer', 'Dx Onderzoeksindicatie', 'Dx Onderzoeksreden', 'Dx Werklijstnummer', 'Dx Protocolcode', 'Dx Protocolomschrijving',
'Dx Meet ID', 'Dx Stoftest code', 'Dx Stoftest omschrijving'
]
for udf in append_udf:
sample.udf[udf] = ';'.join([udf_data[udf], str(sample.udf[udf])])
# Update udf fields
update_udf = ['Dx Overleden', 'Dx Spoed', 'Dx NICU Spoed', 'Dx Handmatig', 'Dx Opslaglocatie', 'Dx Import warning']
for udf in update_udf:
sample.udf[udf] = udf_data[udf]
# Add to new workflow
workflow = clarity_epp.upload.utils.stoftestcode_to_workflow(lims, udf_data['Dx Stoftest code'])
if workflow:
sample.put()
lims.route_artifacts([sample.artifact], workflow_uri=workflow.uri)
message += "{0}\tUpdated and added to workflow: {1}.\n".format(sample.name, workflow.name)
else:
message += "{0}\tERROR: Stoftest code {1} is not linked to a workflow.\n".format(sample.name, udf_data['Dx Stoftest code'])
else:
# Check other samples from patient
sample_list = lims.get_samples(udf={'Dx Persoons ID': udf_data['Dx Persoons ID']})
for sample in sample_list:
if sample.udf['Dx Protocolomschrijving'] == udf_data['Dx Protocolomschrijving'] and sample.udf['Dx Foetus'] == udf_data['Dx Foetus']:
udf_data['Dx Import warning'] = ';'.join(['Onderzoek reeds uitgevoerd.', udf_data['Dx Import warning']])
# Add sample to workflow
workflow = clarity_epp.upload.utils.stoftestcode_to_workflow(lims, udf_data['Dx Stoftest code'])
if workflow:
container = Container.create(lims, type=container_type, name=udf_data['Dx Fractienummer'])
sample = Sample.create(lims, container=container, position='1:1', project=project, name=sample_name, udf=udf_data)
lims.route_artifacts([sample.artifact], workflow_uri=workflow.uri)
message += "{0}\tCreated and added to workflow: {1}.\n".format(sample.name, workflow.name)
else:
message += "{0}\tERROR: Stoftest code {1} is not linked to a workflow.\n".format(sample_name, udf_data['Dx Stoftest code'])
# Send final email
send_email(email_settings['server'], email_settings['from'], email_settings['to_import_helix'], subject, message)
def submit_samples():
form = SubmitSampleForm()
if form.validate_on_submit():
# Create lims project
lims_project = Project.create(
lims,
name=app.config['LIMS_INDICATIONS'][form.indicationcode.data]['project_name_prefix'],
researcher=form.researcher,
udf={'Application': form.indicationcode.data}
)
lims_project.name = '{0}_{1}'.format(lims_project.name, lims_project.id)
lims_project.put()
# Save attachment
attachment = form.attachment.data
if attachment:
temp_dir = mkdtemp()
attachment_path = path.join(temp_dir, secure_filename(attachment.filename))
attachment.save(attachment_path)
print attachment_path
lims.upload_new_file(lims_project, attachment_path)
rmtree(temp_dir)
# Create Samples
lims_container_type = Containertype(lims, id='2') # Tube
sample_artifacts = []
for sample in form.parsed_samples:
lims_container = Container.create(lims, type=lims_container_type, name=sample['name'])
sample_udf_data = {
'Sample Type': 'DNA library',
'Dx Fragmentlengte (bp) Externe meting': form.pool_fragment_length.data,
'Dx Conc. (ng/ul) Externe meting': form.pool_concentration.data,
'Dx Exoomequivalent': sample['exome_count'],
}
lims_sample = Sample.create(lims, container=lims_container, position='1:1', project=lims_project, name=sample['name'], udf=sample_udf_data)
print lims_sample.name, lims_sample.artifact.name
artifact = lims_sample.artifact
sample_artifacts.append(artifact)
# Add reagent label (barcode)
artifact_xml_dom = minidom.parseString(artifact.xml())
for artifact_name_node in artifact_xml_dom.getElementsByTagName('name'):
parent = artifact_name_node.parentNode
reagent_label = artifact_xml_dom.createElement('reagent-label')
reagent_label.setAttribute('name', sample['barcode'])
parent.appendChild(reagent_label)
lims.put(artifact.uri, artifact_xml_dom.toxml(encoding='utf-8'))
# Route artifacts to workflow
workflow = Workflow(lims, id=app.config['LIMS_INDICATIONS'][form.indicationcode.data]['workflow_id'])
lims.route_artifacts(sample_artifacts, workflow_uri=workflow.uri)
# Send email
subject = "Clarity Portal Sample Upload - {0}".format(lims_project.name)
message = "Gebruikersnaam\t{0}\n".format(form.username.data)
message += "Indicatie code\t{0}\n".format(form.indicationcode.data)
message += "Lims Project naam\t{0}\n".format(lims_project.name)
message += "Pool - Fragment lengte\t{0}\n".format(form.pool_fragment_length.data)
message += "Pool - Concentratie\t{0}\n".format(form.pool_concentration.data)
message += "Pool - Exoom equivalenten\t{0}\n\n".format(form.sum_exome_count)
message += "Sample naam\tBarcode\tExome equivalenten\tSample type\n"
for sample in form.parsed_samples:
message += "{0}\t{1}\t{2}\t{3}\n".format(sample['name'], sample['barcode'], sample['exome_count'], sample['type'])
send_email(app.config['EMAIL_FROM'], app.config['LIMS_INDICATIONS'][form.indicationcode.data]['email_to'], subject, message)
return render_template('submit_samples_done.html', title='Submit samples', project_name=lims_project.name, form=form)
return render_template('submit_samples.html', title='Submit samples', form=form)
def main(args):
lims = Lims(BASEURI, USERNAME, PASSWORD)
cont = Container(lims, id=args.flowcell)
cont.name = cont.id
cont.put()