def test_2_make_note(self):
"""Make a note subset by example flowcell and project"""
s_con = SampleRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
fc_con = FlowcellRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
p_con = ProjectSummaryConnection(username=self.user, password=self.pw, url=self.url)
paragraphs = sample_note_paragraphs()
headers = sample_note_headers()
samples = s_con.get_samples(self.examples["flowcell"], self.examples["project"])
project = p_con.get_entry(self.examples["project"])
samples = p_con.map_srm_to_name(self.examples["project"], fc_id=self.examples["flowcell"], use_bc_map=True)
for k,v in samples.items():
s_param = parameters
s = s_con.get_entry(k)
s_param.update({key:s[srm_to_parameter[key]] for key in srm_to_parameter.keys()})
fc = "{}_{}".format(s["date"], s["flowcell"])
s_param["phix_error_rate"] = fc_con.get_phix_error_rate(str(fc), s["lane"])
s_param['avg_quality_score'] = s_con.calc_avg_qv(s["name"])
s_param['rounded_read_count'] = round(float(s_param['rounded_read_count'])/1e6,1) if s_param['rounded_read_count'] else None
s_param['customer_name'] = project['samples'][v["sample"]].get('customer_name', None)
if project:
s_param['ordered_amount'] = p_con.get_ordered_amount(self.examples["project"])
s_param['customer_reference'] = s_param.get('customer_reference', project['customer_reference'])
s_param['uppnex_project_id'] = s_param.get('uppnex_project_id', project['uppnex_id'])
s_param['success'] = sequencing_success(s_param, cutoffs)
s_param.update({k:"N/A" for k in s_param.keys() if s_param[k] is None})
make_note("{}.pdf".format(s["barcode_name"]), headers, paragraphs, **s_param)
def test_4_srm_map(self):
"""Test getting a sample mapping from srm to project samples"""
p_con = ProjectSummaryConnection(username=self.user,
password=self.pw,
url=self.url)
samples = p_con.map_srm_to_name(self.examples["project"],
fc_id=self.examples["flowcell"],
use_ps_map=False,
check_consistency=True)
print samples
def test_4_srm_map(self):
"""Test getting a sample mapping from srm to project samples"""
p_con = ProjectSummaryConnection(username=self.user, password=self.pw, url=self.url)
samples = p_con.map_srm_to_name(self.examples["project"], fc_id=self.examples["flowcell"], use_ps_map=False, check_consistency=True)
print samples
