+import types
+import logging
+import urlparse
from django.db import models
-from django.contrib.auth.models import User
-from htsworkflow.frontend import settings
-#from htsworkflow.reports.libinfopar import *
+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.reports.libinfopar import *
-# Create your models here.
+logger = logging.getLogger(__name__)
class Antibody(models.Model):
- antigene = models.CharField(max_length=500, db_index=True)
- # New field Aug/20/08
- # SQL to add column: alter table fctracker_antibody add column "nickname" varchar(20) NULL;
- nickname = models.CharField(max_length=20,blank=True,null=True, db_index=True,verbose_name = 'Short Name')
- catalog = models.CharField(max_length=50, unique=True, db_index=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)
- def __str__(self):
- return '%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
- class Meta:
- verbose_name_plural = "antibodies"
- ordering = ["antigene"]
- class Admin:
- list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
- list_filter = ('antibodies','source')
- fields = (
- (None, {
- 'fields': (('antigene','nickname','antibodies'),('catalog','source'),('biology'),('notes'))
- }),
- )
+ antigene = models.CharField(max_length=500, db_index=True)
+ # New field Aug/20/08
+ # SQL to add column:
+ # alter table fctracker_antibody add column "nickname" varchar(20) NULL;
+ nickname = models.CharField(
+ max_length=20,
+ blank=True,
+ null=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, 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' % (self.antigene, self.antibodies)
+ class Meta:
+ verbose_name_plural = "antibodies"
+ ordering = ["antigene"]
class Cellline(models.Model):
- cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s' % (self.cellline_name)
+ cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
+ nickname = models.CharField(max_length=20,
+ blank=True,
+ null=True,
+ db_index=True)
- class Meta:
- ordering = ["cellline_name"]
+ notes = models.TextField(blank=True)
+ def __unicode__(self):
+ return unicode(self.cellline_name)
- class Admin:
- fields = (
- (None, {
- 'fields': (('cellline_name'),('notes'),)
- }),
- )
+ class Meta:
+ ordering = ["cellline_name"]
class Condition(models.Model):
- condition_name = models.CharField(max_length=2000, unique=True, db_index=True)
- notes = models.TextField(blank=True)
- def __str__(self):
- return '%s' % (self.condition_name)
+ condition_name = models.CharField(
+ max_length=2000, unique=True, db_index=True)
+ nickname = models.CharField(max_length=20,
+ blank=True,
+ null=True,
+ db_index=True,
+ verbose_name = 'Short Name')
+ notes = models.TextField(blank=True)
- class Meta:
- ordering = ["condition_name"]
+ def __unicode__(self):
+ return unicode(self.condition_name)
- class Admin:
- fields = (
- (None, {
- 'fields': (('condition_name'),('notes'),)
- }),
- )
+ 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 Species(models.Model):
-
- scientific_name = models.CharField(max_length=256, unique=False, db_index=True)
+ scientific_name = models.CharField(max_length=256,
+ unique=False,
+ db_index=True
+ )
common_name = models.CharField(max_length=256, blank=True)
- use_genome_build = models.CharField(max_length=100, blank=False, null=False)
+ #use_genome_build = models.CharField(max_length=100, blank=False, null=False)
+
+ def __unicode__(self):
+ return u'%s (%s)' % (self.scientific_name, self.common_name)
- def __str__(self):
- return '%s (%s)|%s' % (self.scientific_name, self.common_name, self.use_genome_build)
-
class Meta:
verbose_name_plural = "species"
ordering = ["scientific_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('scientific_name', 'common_name'), ('use_genome_build'))
- }),
- )
+
+ @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='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 __str__(self):
- str = self.name
- if self.contact != '':
- str += ' ('+self.contact+')'
+ 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')'
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 Admin:
- list_display = ('name','contact','email')
- fields = (
- (None, {
- 'fields': (('name','contact','email'))
- }),
- )
+class LibraryType(models.Model):
+ name = models.CharField(max_length=255, unique=True,
+ verbose_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)
+
+ 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=6, null=False)
+ sequence = models.CharField(max_length=12, blank=True, null=True)
+
+ class Meta:
+ verbose_name_plural = "multiplex indicies"
+ unique_together = ('adapter_type', 'multiplex_id')
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)
+ hidden = models.BooleanField(default=False)
+ 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,filter_interface=models.HORIZONTAL)
- # 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)
-
- 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')
-
+ affiliations = models.ManyToManyField(
+ Affiliation,related_name='library_affiliations',null=True)
+ tags = models.ManyToManyField(Tag,related_name='library_tags',
+ blank=True,null=True)
+ REPLICATE_NUM = [(x,x) for x in range(1,7)]
+ replicate = models.PositiveSmallIntegerField(choices=REPLICATE_NUM,
+ blank=True,null=True)
+ experiment_type = models.ForeignKey(ExperimentType)
+ 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.ForeignKey(User, edit_inline=models.TABULAR)
+ 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'),
('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)
-
- 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)
- ten_nM_dilution = models.BooleanField()
- avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
+ 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)
+ ten_nM_dilution = models.BooleanField(default=False)
+ gel_cut_size = models.IntegerField(default=225, blank=True, null=True)
+ insert_size = models.IntegerField(blank=True, null=True)
notes = models.TextField(blank=True)
-
- def __str__(self):
- return '#%s: %s' % (self.library_id, self.library_name)
-
+
+ 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"] #["-library_id"]
-
+ verbose_name_plural = "libraries"
+ #ordering = ["-creation_date"]
+ ordering = ["-id"]
+
def antibody_name(self):
- return self.antibody.nickname
+ 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 org(self):
+ 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_expressions = self.multiplex_id.split(',')
+ for multiplex_term in multiplex_expressions:
+ pairs = multiplex_term.split('-')
+ if len(pairs) == 1:
+ key = pairs[0]
+ seq = self._lookup_index(pairs[0])
+ elif len(pairs) == 2:
+ key = pairs[0] + '-' + pairs[1]
+ seq0 = self._lookup_index(pairs[0])
+ seq1 = self._lookup_index(pairs[1])
+ if seq0 is None or seq1 is None:
+ seq = None
+ else:
+ seq = seq0 + '-' + seq1
+ else:
+ raise RuntimeError("Too many - seperated sequences")
+ if seq is None:
+ seq = 'Err: index not found'
+ sequences[key] = seq
+ return sequences
+
+ def _lookup_index(self, multiplex_id):
+ try:
+ multiplex = MultiplexIndex.objects.get(
+ adapter_type = self.library_type.id,
+ multiplex_id = multiplex_id)
+ return multiplex.sequence
+ except MultiplexIndex.DoesNotExist, e:
+ return None
+
+ def index_sequence_text(self, seperator=' '):
+ """Return formatted multiplex index sequences"""
+ sequences = self.index_sequences()
+ if sequences is None:
+ return ""
+ if type(sequences) in types.StringTypes:
+ return 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 = ''
ar = []
for t in affs:
- ar.append(t.__str__())
+ 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 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 = []
+ for t in affs:
+ ar.append(t.__unicode__())
+ 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>'
+ return str
+ DataRun.allow_tags = True
+
+ def aligned_m_reads(self):
+ return getLibReads(self.id)
def aligned_reads(self):
- res = getLibReads(self.library_id)
+ res = getLibReads(self.id)
+
+ # Check data sanity
+ if res[2] != "OK":
+ return u'<div style="border:solid red 2px">'+res[2]+'</div>'
+
rc = "%1.2f" % (res[1]/1000000.0)
# Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
if res[0] > 0:
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].__str__()+' Lanes, '+rc+' M Reads'
+ 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
- class Admin:
- date_hierarchy = "creation_date"
- save_as = True
- save_on_top = True
- ##search_fields = ['library_id','library_name','affiliations__name','affiliations__contact','made_by','made_for','antibody__antigene','antibody__catalog','antibody__antibodies','antibody__source','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
- search_fields = ['library_id','library_name','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
- #list_display = ('affiliation','library_id','aligned_reads','library_name','experiment_type','org','replicate','antibody_name','cell_line','made_by','creation_date')
- list_display = ('library_id','library_name','experiment_type','replicate','antibody_name','made_by','creation_date')
- #list_display_links = ('library_id', 'library_name')
-
- list_filter = ('experiment_type','affiliations','library_species', 'made_by','replicate')
- fields = (
- (None, {
- 'fields': (('replicate','library_id','library_name'),('library_species'),('experiment_type'),('cell_line','condition','antibody'),)
- }),
- ('Creation Information:', {
- 'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('undiluted_concentration', 'library_size'), 'notes',)
- }),
- ('Library/Project Affiliation:', {
- 'fields' : (('affiliations'),)
- }),
- )
+ 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
+ """
+ #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