def sample_status_per_plate(session):
"""This function queries the lims database for sample information and aggregate at the plate name level"""
match = json.loads(request.args.get('match', '{}'))
project_name = match.get('project_id')
all_plates = defaultdict(Container)
sample_to_container = {}
for result in get_sample_info(session, project_name, udfs=['Prep Workflow', 'Species']):
(pjct_name, sample_name, container, wellx, welly, udf_name, udf_value) = result
all_plates[container].name = container
all_plates[container].project_id = pjct_name
if udf_name == 'Prep Workflow':
all_plates[container].samples[sanitize_user_id(sample_name)].planned_library = udf_value
if udf_name == 'Species':
all_plates[container].samples[sanitize_user_id(sample_name)].species = udf_value
sample_to_container[sample_name] = container
for result in get_samples_and_processes(
session,
project_name,
workstatus='COMPLETE',
list_process=list(status_cfg.step_completed_to_status) \
+ list(status_cfg.additional_step_completed) \
+ list(status_cfg.library_type_step_completed)
):
(pjct_name, sample_name, process_name, process_status, date_run) = result
container = sample_to_container.get(sample_name)
all_plates[container].samples[sanitize_user_id(sample_name)].add_completed_process(process_name, date_run)
for result in non_QC_queues(session, project_name, list_process=status_cfg.step_queued_to_status):
pjct_name, sample_name, process_name, queued_date = result
container = sample_to_container.get(sample_name)
all_plates[container].samples[sanitize_user_id(sample_name)].add_queue_location(process_name, queued_date)
return [p.to_json() for p in all_plates.values()]
def sample_status_per_project(session):
"""This function queries the lims database for sample information and aggregate at the project name level"""
match = json.loads(request.args.get('match', '{}'))
project_name = match.get('project_id')
all_projects = defaultdict(Project)
for project_info in get_project_info(session, project_name, udfs=['Number of Quoted Samples']):
pjct_name, open_date, firstname, lastname, udf_name , nb_quoted_samples = project_info
all_projects[pjct_name].name = pjct_name
all_projects[pjct_name].open_date = open_date.isoformat() + 'Z'
all_projects[pjct_name].researcher_name = '%s %s' % (firstname, lastname)
all_projects[pjct_name].nb_quoted_samples = nb_quoted_samples
for result in get_samples_and_processes(
session,
project_name,
workstatus='COMPLETE',
list_process=list(status_cfg.step_completed_to_status) \
+ list(status_cfg.additional_step_completed) \
+ list(status_cfg.library_type_step_completed)
):
(pjct_name, sample_name, process_name, process_status, date_run) = result
all_projects[pjct_name].samples[sanitize_user_id(sample_name)].add_completed_process(process_name, date_run)
for result in non_QC_queues(session, project_name, list_process=status_cfg.step_queued_to_status):
pjct_name, sample_name, process_name, queued_date = result
all_projects[pjct_name].samples[sanitize_user_id(sample_name)].add_queue_location(process_name, queued_date)
for result in get_sample_info(session, project_name, udfs=['Prep Workflow', 'Species']):
(pjct_name, sample_name, container, wellx, welly, udf_name, udf_value) = result
if udf_name == 'Prep Workflow':
all_projects[pjct_name].samples[sanitize_user_id(sample_name)].planned_library = udf_value
if udf_name == 'Species':
all_projects[pjct_name].samples[sanitize_user_id(sample_name)].species = udf_value
return [p.to_json() for p in all_projects.values()]
def _create_samples_info(session, match):
"""Query the LIMS database for sample information and create SampleInfo objects"""
all_samples = defaultdict(data_models.SampleInfo)
project_id = match.get('project_id')
project_status = match.get('project_status', 'open')
sample_id = match.get('sample_id')
time_since = match.get('createddate')
for result in queries.get_sample_info(session,
project_id,
sample_id,
time_since=time_since,
udfs='all',
project_status=project_status):
(pjct_name, sample_name, container, wellx, welly, udf_name,
udf_value) = result
s = all_samples[sanitize_user_id(sample_name)]
s.sample_name = sanitize_user_id(sample_name)
s.project_name = pjct_name
s.plate_name = container
s.original_name = sample_name
s.udfs[udf_name] = udf_value
return all_samples.values()
def _create_samples(session, match):
"""Query the LIMS database for sample information and create Sample objects"""
all_samples = defaultdict(data_models.Sample)
project_id = match.get('project_id')
project_status = match.get('project_status', 'open')
sample_id = match.get('sample_id')
sample_time_since = match.get('createddate')
process_limit_date = match.get('process_limit_date')
detailed = request.args.get('detailed') in ['true', 'True', True]
if detailed:
list_process_complete = None
list_process_queued = None
else:
list_process_complete = list(status_cfg.step_completed_to_status) \
+ list(status_cfg.additional_step_completed) \
+ list(status_cfg.library_type_step_completed) \
+ status_cfg.started_steps
list_process_queued = status_cfg.step_queued_to_status
udfs_to_fields = {
'Prep Workflow': 'planned_library',
'Species': 'species',
'Required Yield (Gb)': 'required_yield',
'Coverage (X)': 'coverage'
}
for result in queries.get_sample_info(session,
project_id,
sample_id,
project_status=project_status,
time_since=sample_time_since,
udfs=list(udfs_to_fields)):
(pjct_name, sample_name, container, wellx, welly, udf_name,
udf_value) = result
s = all_samples[sanitize_user_id(sample_name)]
s.sample_name = sanitize_user_id(sample_name)
s.project_name = pjct_name
s.plate_name = container
s.original_name = sample_name
if udf_name in udfs_to_fields:
setattr(all_samples[sanitize_user_id(sample_name)],
udfs_to_fields[udf_name], udf_value)
for result in queries.get_samples_and_processes(
session,
project_id,
sample_id,
project_status=project_status,
workstatus='COMPLETE',
list_process=list_process_complete,
time_since=sample_time_since,
process_limit_date=process_limit_date):
(pjct_name, sample_name, process_name, process_status, date_run,
process_id) = result
all_samples[sanitize_user_id(sample_name)].add_completed_process(
process_name, date_run, process_id)
for result in queries.get_sample_in_queues_or_progress(
session,
project_id,
sample_id,
list_process=list_process_queued,
time_since=sample_time_since,
project_status=project_status,
process_limit_date=process_limit_date):
pjct_name, sample_name, process_name, queued_date, queue_id, process_id, process_date = result
if not process_id:
all_samples[sanitize_user_id(sample_name)].add_queue_location(
process_name, queued_date, queue_id)
else:
all_samples[sanitize_user_id(sample_name)].add_inprogress(
process_name, process_date, process_id)
return all_samples.values()
def test_sanitize_user_id():
assert clarity.sanitize_user_id(
'this?that$other another:more') == 'this_that_other_another_more'
