default_pM = 5
try:
default_pM = int(settings.DEFAULT_PM)
-except ValueError, e:
+except ValueError as e:
LOGGER.error("invalid value for frontend.default_pm")
# how many days to wait before trying to re-import a runfolder
ordering = ["-isdefault", "name"]
def __unicode__(self):
- return unicode(self.name)
+ return str(self.name)
@classmethod
def default(cls):
ordering = ["-isdefault", "-active", "name"]
def __unicode__(self):
- name = [unicode(self.name)]
+ name = [str(self.name)]
if self.instrument_name is not None:
- name.append("(%s)" % (unicode(self.instrument_name),))
+ name.append("(%s)" % (str(self.instrument_name),))
return " ".join(name)
@models.permalink
notes = models.TextField(blank=True)
def __unicode__(self):
- return unicode(self.flowcell_id)
+ return str(self.flowcell_id)
def Lanes(self):
html = ['<table>']
"""Convert our boolean 'is paired' flag to a name
"""
if self.paired_end:
- return u"Paired"
+ return "Paired"
else:
- return u"Single"
+ return "Single"
@models.permalink
def get_absolute_url(self):
result_home_dir = os.path.join(settings.RESULT_HOME_DIR, '')
run_xml_re = re.compile(glob.fnmatch.translate('run*.xml'))
- dataruns = dict([(x.result_dir, x) for x in self.datarun_set.all()])
-
result_dirs = []
for dirpath, dirnames, filenames in os.walk(result_root):
for filename in filenames:
if run_xml_re.match(filename):
# we have a run directory
relative_pathname = get_relative_pathname(dirpath)
- cached_run = dataruns.get(relative_pathname, None)
- now = datetime.datetime.now()
- if (cached_run is None):
- self.import_data_run(relative_pathname, filename)
- elif (now - cached_run.last_update_time).days > \
- RESCAN_DELAY:
- self.import_data_run(relative_pathname,
- filename, cached_run)
-
- def import_data_run(self, relative_pathname, run_xml_name, run=None):
+ self.import_data_run(relative_pathname, filename)
+
+ def import_data_run(self, relative_pathname, run_xml_name, force=False):
"""Given a result directory import files"""
+ now = datetime.datetime.now()
run_dir = get_absolute_pathname(relative_pathname)
run_xml_path = os.path.join(run_dir, run_xml_name)
- run_xml_data = runfolder.load_pipeline_run_xml(run_xml_path)
- LOGGER.debug("Importing run from %s" % (relative_pathname,))
- if run is None:
+ runs = DataRun.objects.filter(result_dir = relative_pathname)
+ if len(runs) == 0:
run = DataRun()
+ created = True
+ elif len(runs) > 1:
+ raise RuntimeError("Too many data runs for %s" % (
+ relative_pathname,))
+ else:
+ run = runs[0]
+ created = False
+
+ if created or force or (now-run.last_update_time).days > RESCAN_DELAY:
+ LOGGER.debug("Importing run from %s" % (relative_pathname,))
+ run_xml_data = runfolder.load_pipeline_run_xml(run_xml_path)
run.flowcell = self
run.status = RUN_STATUS_REVERSE_MAP['DONE']
run.result_dir = relative_pathname
run.alignment_software = run_xml_data.gerald.software
run.alignment_version = run_xml_data.gerald.version
- run.last_update_time = datetime.datetime.now()
- run.save()
+ run.last_update_time = datetime.datetime.now()
+ run.save()
- run.update_result_files()
+ run.update_result_files()
# FIXME: should we automatically update dataruns?
[str(self.id)])
def __unicode__(self):
- return self.flowcell.flowcell_id + ':' + unicode(self.lane_number)
+ return self.flowcell.flowcell_id + ':' + str(self.lane_number)
class DataRun(models.Model):