+import urlparse
from django.db import models
-from django.contrib.auth.models import User
+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 *
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 = (
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)
+ users = models.ManyToManyField('HTSUser', null=True, blank=True)
+ users.admin_order_field = "username"
def __unicode__(self):
str = unicode(self.name)
- if len(self.contact) != 0:
+ if self.contact is not None and len(self.contact) > 0:
str += u' ('+self.contact+u')'
return str
+ def Users(self):
+ users = self.users.all().order_by('username')
+ return ", ".join([unicode(a) for a in users ])
+
class Meta:
ordering = ["name","contact"]
unique_together = (("name", "contact"),)
+class LibraryType(models.Model):
+ name = models.CharField(max_length=255, unique=True)
+
+ def __unicode__(self):
+ return unicode(self.name)
+
+
class Library(models.Model):
-
- library_id = models.CharField(max_length=30, primary_key=True, db_index=True)
+ id = models.CharField(max_length=10, primary_key=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()
+ # 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")
+ 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)
# 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)
-
- EXPERIMENT_TYPES = (
- ('INPUT_RXLCh','INPUT_RXLCh'),
- ('ChIP-seq', 'ChIP-seq'),
- ('Sheared', 'Sheared'),
- ('RNA-seq', 'RNA-seq'),
- ('Methyl-seq', 'Methyl-seq'),
- ('DIP-seq', 'DIP-seq'),
- )
- experiment_type = models.CharField(max_length=50, choices=EXPERIMENT_TYPES,
- default='RNA-seq')
-
+ 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.ForeignKey(User)
+ 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 = (
('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("Undiluted concentration (ng/ul)", max_digits=5, decimal_places=2, default=0, blank=True, null=True)
- successful_pM = models.DecimalField(max_digits=5, decimal_places=2, 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)
ten_nM_dilution = models.BooleanField()
avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
notes = models.TextField(blank=True)
def __unicode__(self):
- return u'#%s: %s' % (self.library_id, self.library_name)
+ return u'#%s: %s' % (self.id, self.library_name)
class Meta:
verbose_name_plural = "libraries"
- ordering = ["-creation_date"] #["-library_id"]
+ #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>'
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')
return u'%s' % ( ", ".join(ar))
def DataRun(self):
- str ='<a target=_self href="/admin/experiments/datarun/?q='+self.library_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
def aligned_m_reads(self):
- return getLibReads(self.library_id)
+ return getLibReads(self.id)
def aligned_reads(self):
- res = getLibReads(self.library_id)
+ res = getLibReads(self.id)
# Check data sanity
if res[2] != "OK":
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)])
+
+
+
+
+
+class HTSUser(User):
+ """
+ Provide some site-specific customization for the django user class
+ """
+ #objects = UserManager()
+ class Meta:
+ ordering = ['first_name', 'last_name', 'username']
+
+ def admin_url(self):
+ return '/admin/%s/%s/%d' % (self._meta.app_label, self._meta.module_name, 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
+ """
+ u = HTSUser.objects.filter(pk=instance.id)
+ if len(u) == 0:
+ 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