Allow arbitrarily long regexes in experiment.FileType table

[htsworkflow.git] / htsworkflow / frontend / experiments / models.py

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index e3771cbde31be4f654fd44dc5b043ed847144257..6c952db1bb431b9f136600e3ec5849f25ebcf78a 100644 (file)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -9,6 +9,7 @@ import uuid
 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
 
@@ -16,6 +17,8 @@ from htsworkflow.frontend.samples.models import Library
 from htsworkflow.util.conversion import parse_flowcell_id
 from htsworkflow.pipelines import runfolder
 
+import pytz
+
 LOGGER = logging.getLogger(__name__)
 default_pM = 5
 try:
@@ -219,7 +222,7 @@ class FlowCell(models.Model):
 
     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)
 
@@ -243,7 +246,8 @@ class FlowCell(models.Model):
             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
@@ -253,7 +257,7 @@ class FlowCell(models.Model):
                 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()
@@ -356,7 +360,7 @@ class DataRun(models.Model):
 
                     self.datafile_set.add(newfile)
 
-        self.last_update_time = datetime.datetime.now()
+        self.last_update_time = timezone.now()
 
     def lane_files(self):
         lanes = {}
@@ -391,7 +395,7 @@ class FileType(models.Model):
     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?