from django.conf import settings
from django.core.exceptions import ObjectDoesNotExist
from django.core import urlresolvers
+from django.utils import timezone
from django.db import models
from django.db.models.signals import post_init, pre_save
from htsworkflow.util.conversion import parse_flowcell_id
from htsworkflow.pipelines import runfolder
+import pytz
+
LOGGER = logging.getLogger(__name__)
default_pM = 5
try:
default_pM = int(settings.DEFAULT_PM)
-except ValueError, e:
+except AttributeError, e:
LOGGER.error("invalid value for frontend.default_pm")
# how many days to wait before trying to re-import a runfolder
def import_data_run(self, relative_pathname, run_xml_name, force=False):
"""Given a result directory import files"""
- now = datetime.datetime.now()
+ now = timezone.now()
run_dir = get_absolute_pathname(relative_pathname)
run_xml_path = os.path.join(run_dir, run_xml_name)
run.runfolder_name = run_xml_data.runfolder_name
run.cycle_start = run_xml_data.image_analysis.start
run.cycle_stop = run_xml_data.image_analysis.stop
- run.run_start_time = run_xml_data.image_analysis.date
+ naive_run_start_time = datetime.datetime.fromordinal(run_xml_data.image_analysis.date.toordinal())
+ run.run_start_time = pytz.timezone(settings.TIME_ZONE).localize(naive_run_start_time)
run.image_software = run_xml_data.image_analysis.software
run.image_version = run_xml_data.image_analysis.version
run.basecall_software = run_xml_data.bustard.software
run.basecall_version = run_xml_data.bustard.version
- run.alignment_software = run_xml_data.gerald.software
- run.alignment_version = run_xml_data.gerald.version
+ # we're frequently not running alignments
+ if run_xml_data.gerald:
+ run.alignment_software = run_xml_data.gerald.software
+ run.alignment_version = run_xml_data.gerald.version
- run.last_update_time = datetime.datetime.now()
+ run.last_update_time = timezone.now()
run.save()
run.update_result_files()
self.datafile_set.add(newfile)
- self.last_update_time = datetime.datetime.now()
+ self.last_update_time = timezone.now()
def lane_files(self):
lanes = {}
name = models.CharField(max_length=50)
mimetype = models.CharField(max_length=50, null=True, blank=True)
# regular expression from glob.fnmatch.translate
- regex = models.CharField(max_length=50, null=True, blank=True)
+ regex = models.TextField(null=True, blank=True)
def parse_filename(self, pathname):
"""Does filename match our pattern?