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