class Antibody(models.Model):
antigene = models.CharField(max_length=500, db_index=True)
# New field Aug/20/08
- # SQL to add column:
+ # SQL to add column:
# alter table fctracker_antibody add column "nickname" varchar(20) NULL;
nickname = models.CharField(
max_length=20,
blank=True,
- null=True,
+ null=True,
db_index=True
)
catalog = models.CharField(max_length=50, blank=True, null=True)
cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
nickname = models.CharField(max_length=20,
blank=True,
- null=True,
+ null=True,
db_index=True)
-
+
notes = models.TextField(blank=True)
def __unicode__(self):
return unicode(self.cellline_name)
max_length=2000, unique=True, db_index=True)
nickname = models.CharField(max_length=20,
blank=True,
- null=True,
+ null=True,
db_index=True,
verbose_name = 'Short Name')
notes = models.TextField(blank=True)
class Meta:
ordering = ["condition_name"]
-
+
class ExperimentType(models.Model):
name = models.CharField(max_length=50, unique=True)
def __unicode__(self):
return unicode(self.name)
-class Tag(models.Model):
- tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)
- TAG_CONTEXT = (
- #('Antibody','Antibody'),
- #('Cellline', 'Cellline'),
- #('Condition', 'Condition'),
- ('Library', 'Library'),
- ('ANY','ANY'),
- )
- context = models.CharField(max_length=50,
- choices=TAG_CONTEXT, default='Library')
-
- def __unicode__(self):
- return u'%s' % (self.tag_name)
-
- class Meta:
- ordering = ["context","tag_name"]
-
+class Tag(models.Model):
+ tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)
+ TAG_CONTEXT = (
+ #('Antibody','Antibody'),
+ #('Cellline', 'Cellline'),
+ #('Condition', 'Condition'),
+ ('Library', 'Library'),
+ ('ANY','ANY'),
+ )
+ context = models.CharField(max_length=50,
+ choices=TAG_CONTEXT, default='Library')
+
+ def __unicode__(self):
+ return u'%s' % (self.tag_name)
+
+ class Meta:
+ ordering = ["context","tag_name"]
+
class Species(models.Model):
- scientific_name = models.CharField(max_length=256,
- unique=False,
+ scientific_name = models.CharField(max_length=256,
+ unique=False,
db_index=True
)
common_name = models.CharField(max_length=256, blank=True)
def __unicode__(self):
return u'%s (%s)' % (self.scientific_name, self.common_name)
-
+
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')
- contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Lab Name')
+ contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Lab Name')
email = models.EmailField(null=True,blank=True)
users = models.ManyToManyField('HTSUser', null=True, blank=True)
users.admin_order_field = "username"
-
+
def __unicode__(self):
str = unicode(self.name)
if self.contact is not None and len(self.contact) > 0:
- str += u' ('+self.contact+u')'
+ str += u' ('+self.contact+u')'
return str
def Users(self):
unique_together = (("name", "contact"),)
class LibraryType(models.Model):
- name = models.CharField(max_length=255, unique=True)
+ name = models.CharField(max_length=255, unique=True,
+ name="Adapter Type")
+ is_paired_end = models.BooleanField(default=True,
+ help_text="can you do a paired end run with this adapter")
+ can_multiplex = models.BooleanField(default=True,
+ help_text="Does this adapter provide multiplexing?")
def __unicode__(self):
- return unicode(self.name)
+ return unicode(self.name)
+
+ class Meta:
+ ordering = ["-id"]
+
+class MultiplexIndex(models.Model):
+ """Map adapter types to the multiplex sequence"""
+ adapter_type = models.ForeignKey(LibraryType)
+ multiplex_id = models.CharField(max_length=3, null=False)
+ sequence = models.CharField(max_length=12, blank=True, null=True)
+
+ class Meta:
+ unique_together = ('adapter_type', 'multiplex_id')
class Library(models.Model):
id = models.CharField(max_length=10, primary_key=True)
blank=True,null=True)
REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
replicate = models.PositiveSmallIntegerField(choices=REPLICATE_NUM,
- blank=True,null=True)
+ blank=True,null=True)
experiment_type = models.ForeignKey(ExperimentType)
- library_type = models.ForeignKey(LibraryType, blank=True, null=True)
+ library_type = models.ForeignKey(LibraryType, blank=True, null=True,
+ verbose_name="Adapter Type")
+ multiplex_id = models.CharField(max_length=128,
+ blank=True, null=True,
+ verbose_name="Index ID")
creation_date = models.DateField(blank=True, null=True)
- made_for = models.CharField(max_length=50, blank=True,
+ made_for = models.CharField(max_length=50, blank=True,
verbose_name='ChIP/DNA/RNA Made By')
made_by = models.CharField(max_length=50, blank=True, default="Lorian")
-
+
PROTOCOL_END_POINTS = (
('?', 'Unknown'),
('Sample', 'Raw sample'),
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",
+
+ undiluted_concentration = models.DecimalField("Concentration",
max_digits=5, decimal_places=2, blank=True, null=True,
- help_text=u"Undiluted concentration (ng/\u00b5l)")
+ 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)
notes = models.TextField(blank=True)
bioanalyzer_summary = models.TextField(blank=True,default="")
- bioanalyzer_concentration = models.DecimalField(max_digits=5,
+ 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 = ["-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.label+'</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
def organism(self):
return self.library_species.common_name
+ def index_sequences(self):
+ """Return a dictionary of multiplex index id to sequence
+ Return None if the library can't multiplex,
+
+ """
+ if self.library_type is None:
+ return None
+ if not self.library_type.can_multiplex:
+ return None
+ if self.multiplex_id is None or len(self.multiplex_id) == 0:
+ return 'Err: id empty'
+ sequences = {}
+ multiplex_ids = self.multiplex_id.split(',')
+ for multiplex_id in multiplex_ids:
+ try:
+ multiplex = MultiplexIndex.objects.get(
+ adapter_type = self.library_type.id,
+ multiplex_id = multiplex_id)
+ sequences[multiplex_id] = multiplex.sequence
+ except MultiplexIndex.DoesNotExist, e:
+ sequences[multiplex_id] = 'Err: index not found'
+ return sequences
+
+ def index_sequence_text(self, seperator=' '):
+ """Return formatted multiplex index sequences"""
+ sequences = self.index_sequences()
+ multiplex_ids = sequences.keys()
+ multiplex_ids.sort()
+ return seperator.join(( "%s:%s" %(i,sequences[i]) for i in multiplex_ids))
+ index_sequence_text.short_description = "Index"
+
+
def affiliation(self):
affs = self.affiliations.all().order_by('name')
tstr = ''
for t in affs:
ar.append(t.__unicode__())
return '%s' % (", ".join(ar))
-
+
def is_archived(self):
"""
returns True if archived else False
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')
return u'%s' % ( ", ".join(ar))
def DataRun(self):
- str ='<a target=_self href="/admin/experiments/datarun/?q='+self.id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
+ str ='<a target=_self href="/admin/experiments/datarun/?q='+self.id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
return str
DataRun.allow_tags = True
if res[1] > rc_thr[1]:
bgcolor ='#00ccff' # Blue
else:
- if res[1] > rc_thr[2]:
+ if res[1] > rc_thr[2]:
bgcolor ='#ffcc33' # Orange
tstr = '<div style="background-color:'+bgcolor+';color:black">'
tstr += res[0].__unicode__()+' Lanes, '+rc+' M Reads'
tstr += '</div>'
- else: tstr = 'not processed yet'
+ 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 __unicode__(self):
#return unicode(self.username) + u" (" + unicode(self.get_full_name()) + u")"
return unicode(self.get_full_name()) + u' (' + unicode(self.username) + ')'
-
+
def HTSUserInsertID(sender, instance, **kwargs):
"""
Force addition of HTSUsers when someone just modifies the auth_user object
cursor = connection.cursor()
cursor.execute('INSERT INTO samples_htsuser (user_ptr_id) VALUES (%s);' % (instance.id,))
cursor.close()
-
+
post_save.connect(HTSUserInsertID, sender=User)
projects / htsworkflow.git / blobdiff