Allow cellline and conditition to be blank [ticket:115] [ticket:105]

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

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index 9301d4f3eb788d5c1d3d63d493a671059dea38e3..7f90f2521010c92434084f7afd60e4d055eb466b 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -99,8 +99,8 @@ class Species(models.Model):
     ordering = ["scientific_name"]
   
 class Affiliation(models.Model):
-  name = models.CharField(max_length=256, db_index=True, verbose_name='Group Name')
-  contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Contact Name')  
+  name = models.CharField(max_length=256, db_index=True, verbose_name='Name')
+  contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Lab Name')  
   email = models.EmailField(null=True,blank=True)
   
   def __unicode__(self):
@@ -115,11 +115,13 @@ class Affiliation(models.Model):
 
 class Library(models.Model):
   id = models.AutoField(primary_key=True)
-  library_id = models.CharField(max_length=30, db_index=True)
+  library_id = models.CharField(max_length=30, db_index=True, unique=True)
   library_name = models.CharField(max_length=100, unique=True)
   library_species = models.ForeignKey(Species)
-  cell_line = models.ForeignKey(Cellline)
-  condition = models.ForeignKey(Condition)
+  # new field 2008 Mar 5, alter table samples_library add column "hidden" NOT NULL default 0;
+  hidden = models.BooleanField()
+  cell_line = models.ForeignKey(Cellline, blank=True, null=True)
+  condition = models.ForeignKey(Condition, blank=True, null=True)
   antibody = models.ForeignKey(Antibody,blank=True,null=True)
   # New field Aug/25/08. SQL: alter table fctracker_library add column "lib_affiliation" varchar(256)  NULL;
   affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True)
@@ -147,10 +149,10 @@ class Library(models.Model):
       ('Done', 'Completed'),
     )
   stopping_point = models.CharField(max_length=25, choices=PROTOCOL_END_POINTS, default='Done')
-  amplified_from_sample = models.ForeignKey('self', blank=True, null=True)  
+  amplified_from_sample = models.ForeignKey('self', blank=True, null=True, related_name='amplified_into_sample')  
   
   undiluted_concentration = models.DecimalField("Concentration", 
-      max_digits=5, decimal_places=2, default=0, blank=True, null=True,
+      max_digits=5, decimal_places=2, blank=True, null=True,
       help_text=u"Undiluted concentration (ng/\u00b5l)") 
       # note \u00b5 is the micro symbol in unicode
   successful_pM = models.DecimalField(max_digits=9, decimal_places=1, blank=True, null=True)
@@ -163,7 +165,8 @@ class Library(models.Model):
   
   class Meta:
     verbose_name_plural = "libraries"
-    ordering = ["-creation_date"] #["-library_id"]
+    #ordering = ["-creation_date"] 
+    ordering = ["-library_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>' 
@@ -180,6 +183,15 @@ class Library(models.Model):
     for t in affs:
         ar.append(t.__unicode__())
     return '%s' % (", ".join(ar))
+    
+  def is_archived(self):
+    """
+    returns True if archived else False
+    """
+    if self.longtermstorage_set.count() > 0:
+        return True
+    else:
+        return False
 
   def libtags(self):
     affs = self.tags.all().order_by('tag_name')
@@ -228,6 +240,10 @@ class Library(models.Model):
 
   def public(self):
     SITE_ROOT = '/'
-    summary_url = urlparse.urljoin(SITE_ROOT, 'library/%s' % (self.library_id))
+    summary_url = self.get_absolute_url()
     return '<a href="%s">S</a>' % (summary_url,)
   public.allow_tags = True
+
+  @models.permalink
+  def get_absolute_url(self):
+    return ('htsworkflow.frontend.samples.views.library_to_flowcells', [str(self.library_id)])