Merge branch 'add-condition'

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

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index 0a65651abb02a54c4bb397ec93a12a058d73d20f..e49d23b16e98cde532377ae7ab08d24bfb7bb7f1 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -1,12 +1,14 @@
+import logging
 import urlparse
 from django.db import models
 from django.contrib.auth.models import User, UserManager
 from django.db.models.signals import pre_save, post_save
 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 +19,7 @@ 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 +37,8 @@ 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)
@@ -99,6 +100,10 @@ class Species(models.Model):
   class Meta:
     verbose_name_plural = "species"
     ordering = ["scientific_name"]
+
+  @models.permalink
+  def get_absolute_url(self):
+    return ('htsworkflow.frontend.samples.views.species', [str(self.id)])
   
 class Affiliation(models.Model):
   name = models.CharField(max_length=256, db_index=True, verbose_name='Name')
@@ -146,7 +151,7 @@ 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 +166,13 @@ 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')  
   
@@ -188,12 +196,12 @@ class Library(models.Model):
     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
 
@@ -217,6 +225,15 @@ 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 = []
@@ -271,9 +288,6 @@ class Library(models.Model):
   @models.permalink
   def get_absolute_url(self):
     return ('htsworkflow.frontend.samples.views.library_to_flowcells', [str(self.id)])
-    
-  
-    
 
 
 class HTSUser(User):