Add pages to show information about a particular flowcell.

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

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index a32d0bdb9ee76d1c924a42bf9d41fbd28222228b..10599e2174c0330cd2e16908bdf602179ac6f943 100755 (executable)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -1,8 +1,11 @@
+import logging
+
+from django.core.exceptions import ObjectDoesNotExist
+from django.core import urlresolvers
 from django.db import models
+
 from htsworkflow.frontend.samples.models import *
 from htsworkflow.frontend.settings import options
-from django.core.exceptions import ObjectDoesNotExist
-import logging
 
 class ClusterStation(models.Model):
   name = models.CharField(max_length=50, unique=True)
@@ -22,9 +25,6 @@ try:
 except ValueError,e:
   logging.error("invalid value for frontend.default_pm")
 
-
-  
-
 class FlowCell(models.Model):
   
   flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
@@ -32,6 +32,7 @@ class FlowCell(models.Model):
   advanced_run = models.BooleanField(default=False)
   paired_end = models.BooleanField(default=False)
   read_length = models.IntegerField(default=32) #Stanford is currenlty 25
+  control_lane = models.IntegerField(choices=[(1,1),(2,2),(3,3),(4,4),(5,5),(6,6),(7,7),(8,8),(0,'All Lanes')], null=True)
 
   cluster_station = models.ForeignKey(ClusterStation, default=3)
   sequencer = models.ForeignKey(Sequencer, default=1)
@@ -73,7 +74,26 @@ class FlowCell(models.Model):
 
   class Meta:
     ordering = ["-run_date"]
-  
+
+  def get_admin_url(self):
+    # that's the django way... except it didn't work
+    #return urlresolvers.reverse('admin_experiments_FlowCell_change', args=(self.id,))
+    return '/admin/experiments/flowcell/%s/' % (self.id,)
+
+  def flowcell_type(self):
+    """
+    Convert our boolean 'is paired' flag to a name
+    """
+    if self.paired_end:
+      return u"Paired"
+    else:
+      return u"Single"
+
+  @models.permalink
+  def get_absolute_url(self):
+      return ('htsworkflow.frontend.experiments.views.flowcell_detail',
+              [str(self.flowcell_id)])
+    
 ### -----------------------
 class DataRun(models.Model):
   ConfTemplate = "CONFIG PARAMS WILL BE GENERATED BY THE PIPELINE SCRIPT.\nYOU'LL BE ABLE TO EDIT AFTER IF NEEDED."
@@ -128,11 +148,22 @@ class DataRun(models.Model):
     return str
   Flowcell_Info.allow_tags = True
 
+LANE_STATUS_CODES = [(0, 'Failed'),
+                    (1, 'Marginal'),
+                    (2, 'Good'),]
+LANE_STATUS_MAP = dict((int(k),v) for k,v in LANE_STATUS_CODES )
+LANE_STATUS_MAP[None] = "Unknown"
 
 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)])
   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)
+  cluster_estimate = models.IntegerField(blank=True, null=True)                                       
+  status = models.IntegerField(choices=LANE_STATUS_CODES, null=True, blank=True) 
   comment = models.TextField(null=True, blank=True)
+
+  @models.permalink
+  def get_absolute_url(self):
+       return ('htsworkflow.frontend.experiments.views.flowcell_lane_detail',
+               [str(self.flowcell.flowcell_id), str(self.lane_number)])