def to_json(self):
ret = {
'project_id': self.project_id,
'open_date': format_date(self.open_date),
'close_date': format_date(self.close_date),
'project_status': self.status,
'researcher_name': self.researcher_name,
'nb_quoted_samples': self.nb_quoted_samples,
'udfs': self.udfs
}
return ret
def to_json(self):
return {
'created_date': format_date(self.created_date),
'cst_date': format_date(self.cst_date),
'run_id': self.udfs.get('RunID'),
'run_status': self.udfs.get('Run Status'),
'sample_ids': sorted(list(self.samples)),
'project_ids': sorted(list(self.projects)),
'lanes': list(self.lanes.values()),
'instrument_id': self.udfs.get('InstrumentID'),
'nb_reads': self.udfs.get('Read'),
'nb_cycles': self.udfs.get('Cycle')
}
def to_json(self):
return {
'sample_id': self.sample_name,
'project_id': self.project_name,
'statuses': self.all_statuses(),
'current_status': self.status,
'started_date': format_date(self.started_date),
'finished_date': format_date(self.finished_date),
'library_type': self.library_type,
'species': self.species,
'required_yield': self.required_yield,
'required_coverage': self.coverage
}
def to_json(self):
sample_per_status, status = self.samples_per_status()
ret = {
'project_id': self.project_id,
'nb_samples': len(self.samples),
'library_type': self.library_types,
'required_yield': self.required_yield,
'required_coverage': self.coverage,
'species': self.species,
'open_date': format_date(self.open_date),
'close_date': format_date(self.close_date),
'project_status': self.status,
'researcher_name': self.researcher_name,
'nb_quoted_samples': self.nb_quoted_samples,
'finished_date': format_date(self.finished_date),
'started_date': format_date(self.started_date),
'status': status
}
ret.update(sample_per_status)
return ret
def to_flatten_json(self):
most_recent_step = sorted(self.specific_steps.values(), key=lambda p: p.date_run, reverse=True)[0]
data = []
for artifact in most_recent_step.artifacts.values():
element = {
'id': self.id,
'step_link': cfg['lims_url'] + '/clarity/work-complete/' + str(most_recent_step.id),
'step_run': len(self.specific_steps),
'date_completed': format_date(most_recent_step.date_run),
'protocol': status_cfg.protocol_names.get(self.type, self.type),
'project': artifact.project_id,
}
element.update(artifact.to_json())
data.append(element)
return data
def to_json(self):
most_recent_step = sorted(self.specific_steps.values(), key=lambda p: p.date_run, reverse=True)[0]
projects = set()
data = {
'id': self.id,
'step_link': cfg['lims_url'] + '/clarity/work-complete/' + str(most_recent_step.id),
'step_run': len(self.specific_steps),
'date_completed': format_date(most_recent_step.date_run),
'samples': [],
'protocol': status_cfg.protocol_names.get(self.type, self.type),
'nsamples': len(most_recent_step.artifacts)
}
passing_samples = 0
for k, v in sorted(most_recent_step.artifacts.items()):
projects.add(v.project_id)
data['samples'].append(v.to_json())
if v.qc_flag == 'PASSED':
passing_samples += 1
data['pc_qc_flag_pass'] = (passing_samples / len(most_recent_step.artifacts)) * 100
data['project_ids'] = sorted(projects)
return data