Django 1.1 doesn't support validators so remove it for the time

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

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 4e060f9330229ed5125313ffadc5f2a7e2ff4121..36f6abdb2c9b3d299444941a645080dec182bbe5 100755 (executable)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -13,14 +13,15 @@ from django.db import models
 from django.db.models.signals import post_init
 
 from htsworkflow.frontend.samples.models import Library
-from htsworkflow.frontend.samples.results import parse_flowcell_id
+from htsworkflow.util.conversion import parse_flowcell_id
 from htsworkflow.pipelines import runfolder
 
+logger = logging.getLogger(__name__)
 default_pM = 5
 try:
   default_pM = int(settings.DEFAULT_PM)
 except ValueError,e:
-  logging.error("invalid value for frontend.default_pm")
+  logger.error("invalid value for frontend.default_pm")
 
 RUN_STATUS_CHOICES = (
     (0, 'Sequencer running'), ##Solexa Data Pipeline Not Yet Started'),
@@ -101,8 +102,9 @@ class FlowCell(models.Model):
 
   @models.permalink
   def get_absolute_url(self):
+      flowcell_id, status = parse_flowcell_id(self.flowcell_id)
       return ('htsworkflow.frontend.experiments.views.flowcell_detail',
-              [str(self.flowcell_id)])
+              [str(flowcell_id)])
     
   def get_raw_data_directory(self):
       """Return location of where the raw data is stored"""
@@ -114,7 +116,7 @@ class FlowCell(models.Model):
       result_root = self.get_raw_data_directory()
       if result_root is None:
           return
-  
+
       result_home_dir = os.path.join(settings.RESULT_HOME_DIR,'')
       run_xml_re = re.compile(glob.fnmatch.translate('run*.xml'))
       
@@ -144,10 +146,12 @@ class FlowCell(models.Model):
       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
+
       run.last_update_time = datetime.datetime.now()
       run.save()
 
       run.update_result_files()
+
       
 # FIXME: should we automatically update dataruns?
 #        Or should we expect someone to call update_data_runs?
@@ -168,9 +172,15 @@ LANE_STATUS_CODES = [(0, 'Failed'),
 LANE_STATUS_MAP = dict((int(k),v) for k,v in LANE_STATUS_CODES )
 LANE_STATUS_MAP[None] = "Unknown"
 
+def is_valid_lane(value):
+    if value >= 1 and value <= 8:
+        return True
+    else:
+          return False
+
 class Lane(models.Model):
   flowcell = models.ForeignKey(FlowCell)
-  lane_number = models.IntegerField(choices=[(1,1),(2,2),(3,3),(4,4),(5,5),(6,6),(7,7),(8,8)])
+  lane_number = models.IntegerField() 
   library = models.ForeignKey(Library)
   pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
   cluster_estimate = models.IntegerField(blank=True, null=True)                                       
@@ -180,9 +190,11 @@ class Lane(models.Model):
   @models.permalink
   def get_absolute_url(self):
        return ('htsworkflow.frontend.experiments.views.flowcell_lane_detail',
-               [str(self.flowcell.flowcell_id), str(self.lane_number)])
+               [str(self.id)])
+
+  def __unicode__(self):
+      return self.flowcell.flowcell_id + ':' + unicode(self.lane_number)
 
-                        
 ### -----------------------
 class DataRun(models.Model):
     flowcell = models.ForeignKey(FlowCell,verbose_name="Flowcell Id")
@@ -198,7 +210,7 @@ class DataRun(models.Model):
 
     def update_result_files(self):
         abs_result_dir = get_absolute_pathname(self.result_dir)
-        
+
         for dirname, dirnames, filenames in os.walk(abs_result_dir):
             for filename in filenames:
                 pathname = os.path.join(dirname, filename)
@@ -288,12 +300,15 @@ class FileType(models.Model):
         #return u"<FileType: %s>" % (self.name,)
         return self.name
 
+def str_uuid():
+    """Helper function to set default UUID in DataFile"""
+    return str(uuid.uuid1())
 
 class DataFile(models.Model):
     """Store map from random ID to filename"""
-    random_key = models.CharField(max_length=16,
+    random_key = models.CharField(max_length=64,
                                   db_index=True,
-                                  default=uuid.uuid1)
+                                  default=str_uuid)
     data_run = models.ForeignKey(DataRun, db_index=True)
     library = models.ForeignKey(Library, db_index=True, null=True, blank=True)
     file_type = models.ForeignKey(FileType)