Make antibody & condition visible.

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

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index b6fb4ebcf052cd6eaa9538b32909e7940f65510f..7584cfe94ed7ddd74f45320def558c4aab14152d 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -1,3 +1,4 @@
+import logging
 import urlparse
 from django.db import models
 from django.contrib.auth.models import User, UserManager
@@ -6,7 +7,9 @@ from django.db import connection
 from htsworkflow.frontend import settings
 from htsworkflow.frontend.reports.libinfopar import *
 
+
 # Create your models here.
+logger = logging.getLogger(__name__)
 
 class Antibody(models.Model):
     antigene = models.CharField(max_length=500, db_index=True)
@@ -17,8 +20,7 @@ class Antibody(models.Model):
         max_length=20,
         blank=True,
         null=True, 
-        db_index=True,
-        verbose_name = 'Short Name'
+        db_index=True
     )
     catalog = models.CharField(max_length=50, unique=True, db_index=True)
     antibodies = models.CharField(max_length=500, db_index=True)
@@ -36,8 +38,8 @@ class Cellline(models.Model):
     nickname = models.CharField(max_length=20,
         blank=True,
         null=True, 
-        db_index=True,
-        verbose_name = 'Short Name')
+        db_index=True)
+    
     notes = models.TextField(blank=True)
     def __unicode__(self):
         return unicode(self.cellline_name)
@@ -146,7 +148,7 @@ class Library(models.Model):
   # New field Aug/19/08
   # SQL to add column: alter table fctracker_library add column "replicate" smallint unsigned NULL;
   REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
-  replicate =  models.PositiveSmallIntegerField(choices=REPLICATE_NUM,default=1) 
+  replicate =  models.PositiveSmallIntegerField(choices=REPLICATE_NUM,blank=True,null=True) 
   experiment_type = models.ForeignKey(ExperimentType)
   library_type = models.ForeignKey(LibraryType, blank=True, null=True)
   creation_date = models.DateField(blank=True, null=True)
@@ -161,10 +163,13 @@ class Library(models.Model):
       ('1A', 'Ligation, then gel'),
       ('PCR', 'Ligation, then PCR'),
       ('1Ab', 'Ligation, PCR, then gel'),
-      ('1Aa', 'Ligation, gel, then PCR'),
+      ('1Ac', 'Ligation, gel, then 12x PCR'),
+      ('1Aa', 'Ligation, gel, then 18x PCR'),
       ('2A', 'Ligation, PCR, gel, PCR'),
       ('Done', 'Completed'),
     )
+  PROTOCOL_END_POINTS_DICT = dict(PROTOCOL_END_POINTS)
+  
   stopping_point = models.CharField(max_length=25, choices=PROTOCOL_END_POINTS, default='Done')
   amplified_from_sample = models.ForeignKey('self', blank=True, null=True, related_name='amplified_into_sample')  
   
@@ -177,17 +182,23 @@ class Library(models.Model):
   gel_cut_size = models.IntegerField(default=225, blank=True, null=True)
   insert_size = models.IntegerField(blank=True, null=True)
   notes = models.TextField(blank=True)
+
+  bioanalyzer_summary = models.TextField(blank=True,default="")
+  bioanalyzer_concentration = models.DecimalField(max_digits=5, 
+                                decimal_places=2, blank=True, null=True,
+                                help_text=u"(ng/\u00b5l)")
+  bioanalyzer_image_url = models.URLField(blank=True,default="")
   
   def __unicode__(self):
     return u'#%s: %s' % (self.id, self.library_name)
   
   class Meta:
-    verbose_name_plural = "libraries"
-    #ordering = ["-creation_date"] 
-    ordering = ["-id"]
+      verbose_name_plural = "libraries"
+      #ordering = ["-creation_date"] 
+      ordering = ["-id"]
   
   def antibody_name(self):
-    str ='<a target=_self href="/admin/samples/antibody/'+self.antibody.id.__str__()+'/" title="'+self.antibody.__str__()+'">'+self.antibody.nickname+'</a>' 
+    str ='<a target=_self href="/admin/samples/antibody/'+self.antibody.id.__str__()+'/" title="'+self.antibody.__str__()+'">'+self.antibody.label+'</a>' 
     return str
   antibody_name.allow_tags = True
 
@@ -211,6 +222,15 @@ class Library(models.Model):
     else:
         return False
 
+  def stopping_point_name(self):
+      end_points = Library.PROTOCOL_END_POINTS_DICT
+      name = end_points.get(self.stopping_point, None)
+      if name is None:
+          name = "Lookup Error"
+          logger.error("protocol stopping point in database didn't match names in library model")
+      return name
+      
+
   def libtags(self):
     affs = self.tags.all().order_by('tag_name')
     ar = []