def route_to_workflow(lims, process_id, workflow):
"""Route artifacts to a workflow."""
process = Process(lims, id=process_id)
# Get all artifacts with workflow status == completed.
artifacts_completed = [
action_artifact['artifact']
for action_artifact in process.step.actions.get_next_actions()
if action_artifact['action'] == 'complete'
]
if workflow == 'post_bioinf':
# Remove research artifacts
route_artifacts = [
artifact for artifact in artifacts_completed
if artifact.samples[0].udf['Dx Stoftest code'] !=
config.research_stoftest_code
]
lims.route_artifacts(route_artifacts,
workflow_uri=Workflow(
lims, id=config.post_bioinf_workflow).uri)
elif workflow == 'sequencing':
lims.route_artifacts(artifacts_completed,
workflow_uri=Workflow(
lims, id=config.sequencing_workflow).uri)
def _get_current_WF(self):
art = self.process.all_inputs()[0]
art_XML = api.GET(APIURI + 'artifacts/' + art.id)
art_dom = parseString( art_XML )
WF_node = art_dom.getElementsByTagName('workflow-stage')[-1]
wf_id = WF_node.getAttribute('uri').split('/stages/')[0].split('/')[-1]
try:
return Workflow(lims,id = wf_id)
except:
sys.exit('Could not get the current Work Flow. Contact lims developer.')
def unpooling(lims, process_id):
"""Unpool samples after sequencing."""
process = Process(lims, id=process_id)
pool_artifact = process.all_inputs()[0]
pool_artifact_parent_process = pool_artifact.parent_process
pool_artifact_demux = lims.get(pool_artifact.uri + '/demux')
run_id = pool_artifact.name # Assume run id is set as pool name using placement/artifact/set_runid_name
sample_artifacts = [] # sample artifacts before pooling
sample_projects = {}
for artifact in pool_artifact_parent_process.result_files():
if (artifact.name == 'SampleSheet csv'
or artifact.name == 'Sample Sheet') and artifact.files:
file_id = artifact.files[0].id
sample_sheet = lims.get_file_contents(id=file_id)
project_index = None
sample_index = None
for line in sample_sheet.split('\n'):
data = line.rstrip().split(',')
if 'Sample_Project' in data and 'Sample_ID' in data:
project_index = data.index('Sample_Project')
sample_index = data.index('Sample_ID')
elif project_index and len(data) >= project_index:
sample_projects[data[sample_index]] = data[project_index]
for node in pool_artifact_demux.getiterator('artifact'):
if node.find('samples'):
if len(node.find('samples').findall('sample')) == 1:
sample_artifact = Artifact(lims, uri=node.attrib['uri'])
sample = sample_artifact.samples[0] # 1 sample per artifact.
# Get sample sequencing run and project from samplesheet
sample_artifact.udf['Dx Sequencing Run ID'] = run_id
if 'Sample Type' in sample.udf and 'library' in sample.udf[
'Sample Type']: # Use sample.name for external (clarity_portal) samples
sample_artifact.udf[
'Dx Sequencing Run Project'] = sample_projects[
sample.name]
else: # Use sample_artifact.name for Dx samples (upload via Helix)
sample_artifact.udf[
'Dx Sequencing Run Project'] = sample_projects[
sample_artifact.name]
sample_artifact.put()
if sample_artifact.samples[
0].project and sample_artifact.samples[0].project.udf[
'Application'] == 'DX': # Only move DX production samples to post sequencing workflow
sample_artifacts.append(sample_artifact)
lims.route_artifacts(sample_artifacts,
workflow_uri=Workflow(
lims, id=config.post_sequencing_workflow).uri)
def get_current_WF(self):
# This should be done in a better way...
# pick any art from the current wf:
art = self.input_arts[0]
art_XML = api.GET(APIURI + 'artifacts/' + art.id)
art_dom = parseString(art_XML)
# look for the last "workflow-stage" node, since that's
# where we currently are
WF_node = art_dom.getElementsByTagName('workflow-stage')[-1]
wf_id = WF_node.getAttribute('uri').split('/stages/')[0].split('/')[-1]
self.current_WF = Workflow(lims, id=wf_id)
if not self.current_WF:
sys.exit(
'Could not get the current Work Flow. Contact lims developer.')
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 stoftestcode_to_workflow(lims, stoftestcode):
"""Return workflow based on helix stoftestcode."""
if stoftestcode in config.stoftestcode_workflow:
return Workflow(lims, id=config.stoftestcode_workflow[stoftestcode])
else:
return None
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)
import config
# Setup lims connection
baseuri = 'https://usf-lims.umcutrecht.nl'
username = '******'
password = '******'
lims = Lims(baseuri, username, password)
old_queue = Queue(
lims, id=''
) # Example: Dx Sample registratie zuivering v1.0 = 1142 (same as step id)
old_stage = Stage(
lims, uri=''
) # Example: Dx Sample registratie zuivering v1.0 = https://usf-lims.umcutrecht.nl/api/v2/configuration/workflows/751/stages/2119
new_workflow = Workflow(lims, id='') # Example: Dx Exoom KAPA v1.6 = 901
skip_artifacts = [''] # Add samples that should not be moved to new workflow
artifacts = []
print '# Old queue:', len(old_queue.artifacts)
for artifact in old_queue.artifacts:
if artifact.name not in skip_artifacts:
print 'Move:', artifact.name
artifacts.append(artifact)
else:
print 'Keep:', artifact.name
print '# Move to new workflow:', len(artifacts)
# Move things to new workflow, uncomment to enable.