+import logging
import urlparse
from django.db import models
from django.contrib.auth.models import User, UserManager
+from django.core import urlresolvers
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)
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)
+ catalog = models.CharField(max_length=50, blank=True, null=True)
antibodies = models.CharField(max_length=500, db_index=True)
- source = models.CharField(max_length=500, blank=True, db_index=True)
- biology = models.TextField(blank=True)
- notes = models.TextField(blank=True)
+ source = models.CharField(max_length=500, blank=True, null=True, db_index=True)
+ biology = models.TextField(blank=True, null=True)
+ notes = models.TextField(blank=True, null=True)
def __unicode__(self):
- return u'%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
+ return u'%s - %s' % (self.antigene, self.antibodies)
class Meta:
verbose_name_plural = "antibodies"
ordering = ["antigene"]
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)
class Meta:
ordering = ["condition_name"]
+
class ExperimentType(models.Model):
name = models.CharField(max_length=50, unique=True)
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')
def __unicode__(self):
return unicode(self.name)
+
class Library(models.Model):
id = models.CharField(max_length=10, primary_key=True)
library_name = models.CharField(max_length=100, unique=True)
library_species = models.ForeignKey(Species)
- # new field 2008 Mar 5, alter table samples_library add column "hidden" NOT NULL default 0;
hidden = models.BooleanField()
- # new field 2009 Oct 6, alter table samples_library add column "account_number" varchar(100) NULL
account_number = models.CharField(max_length=100, null=True, blank=True)
- cell_line = models.ForeignKey(Cellline, blank=True, null=True, verbose_name="Background")
+ cell_line = models.ForeignKey(Cellline, blank=True, null=True,
+ verbose_name="Background")
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)
- # new field Nov/14/08
- tags = models.ManyToManyField(Tag,related_name='library_tags',blank=True,null=True)
- # New field Aug/19/08
- # SQL to add column: alter table fctracker_library add column "replicate" smallint unsigned NULL;
+ affiliations = models.ManyToManyField(
+ Affiliation,related_name='library_affiliations',null=True)
+ tags = models.ManyToManyField(Tag,related_name='library_tags',
+ blank=True,null=True)
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)
made_for = models.CharField(max_length=50, blank=True,
- verbose_name='ChIP/DNA/RNA Made By')
+ verbose_name='ChIP/DNA/RNA Made By')
made_by = models.CharField(max_length=50, blank=True, default="Lorian")
PROTOCOL_END_POINTS = (
('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'),
)
- 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')
+ 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',
+ related_name='amplified_into_sample',
+ blank=True, null=True)
undiluted_concentration = models.DecimalField("Concentration",
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)
+ successful_pM = models.DecimalField(max_digits=9,
+ decimal_places=1, blank=True, null=True)
ten_nM_dilution = models.BooleanField()
- avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
+ 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
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 = []
else: tstr = 'not processed yet'
return tstr
aligned_reads.allow_tags = True
-
+
def public(self):
SITE_ROOT = '/'
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.id)])
+ def get_admin_url(self):
+ return urlresolvers.reverse('admin:samples_library_change',
+ args=(self.id,))
+
class HTSUser(User):
"""
Provide some site-specific customization for the django user class
projects / htsworkflow.git / blobdiff