def bpreport(self):
if not self._check_pargs(["project"]):
return
if not self.pargs.statusdb_project_name:
self.pargs.statusdb_project_name = self.pargs.project
kw = vars(self.pargs)
basedir = os.path.abspath(os.path.join(self.app.controller._meta.root_path, self.app.controller._meta.path_id))
flist = find_samples(basedir, **vars(self.pargs))
if not len(flist) > 0:
self.log.info("No samples/sample configuration files found")
return
if self.pargs.no_statusdb:
sample_name_map = None
else:
p_con = ProjectSummaryConnection(dbname=self.app.config.get("db", "projects"), **vars(self.app.pargs))
s_con = SampleRunMetricsConnection(dbname=self.app.config.get("db", "samples"), **vars(self.app.pargs))
try:
sample_name_map = get_scilife_to_customer_name(self.pargs.statusdb_project_name, p_con, s_con, get_barcode_seq=True)
except ValueError as e:
self.log.warn(str(e))
self.log.warn("No such project {} defined in statusdb; try using option --statusdb_project_name".format(self.app.pargs.project))
sample_name_map = None
kw.update(project_name=self.pargs.project, flist=flist, basedir=basedir, sample_name_map=sample_name_map)
out_data = best_practice_note(**kw)
self.log.info("Wrote report to directory {}; use Makefile to generate pdf report".format(basedir))
self.app._output_data['stdout'].write(out_data['stdout'].getvalue())
self.app._output_data['stderr'].write(out_data['stderr'].getvalue())
self.app._output_data['debug'].write(out_data['debug'].getvalue())
def bpreport(self):
if not self._check_pargs(["project"]):
return
kw = vars(self.pargs)
basedir = os.path.abspath(
os.path.join(self.app.controller._meta.root_path,
self.app.controller._meta.path_id))
flist = find_samples(basedir, **vars(self.pargs))
if not len(flist) > 0:
self.log.info("No samples/sample configuration files found")
return
if self.pargs.no_statusdb:
sample_name_map = None
else:
if not self._check_pargs(["statusdb_project_name"]):
return
p_con = ProjectSummaryConnection(dbname=self.app.config.get(
"db", "projects"),
**vars(self.app.pargs))
s_con = SampleRunMetricsConnection(dbname=self.app.config.get(
"db", "samples"),
**vars(self.app.pargs))
sample_name_map = get_scilife_to_customer_name(
self.pargs.statusdb_project_name, p_con, s_con)
kw.update(project_name=self.pargs.project,
flist=flist,
basedir=basedir,
sample_name_map=sample_name_map)
out_data = best_practice_note(**kw)
self.log.info(
"Wrote report to directory {}; use Makefile to generate pdf report"
.format(basedir))
self.app._output_data['stdout'].write(out_data['stdout'].getvalue())
self.app._output_data['stderr'].write(out_data['stderr'].getvalue())
self.app._output_data['debug'].write(out_data['debug'].getvalue())