from django.db import models
from django.contrib.auth.models import User
from htsworkflow.frontend import settings
-#from htsworkflow.reports.libinfopar import *
+from htsworkflow.frontend.reports.libinfopar import *
# Create your models here.
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,
+ 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 __unicode__(self):
+ return u'%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
+ 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)
-
- class Meta:
- ordering = ["cellline_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('cellline_name'),('notes'),)
- }),
- )
+ 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,
+ verbose_name = 'Short Name')
+ notes = models.TextField(blank=True)
+ def __unicode__(self):
+ return unicode(self.cellline_name)
+
+ 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)
-
- class Meta:
- ordering = ["condition_name"]
-
- class Admin:
- fields = (
- (None, {
- 'fields': (('condition_name'),('notes'),)
- }),
- )
-
+ 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)
+
+ def __unicode__(self):
+ return unicode(self.condition_name)
+
+ class Meta:
+ ordering = ["condition_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 __str__(self):
- return '%s (%s)|%s' % (self.scientific_name, self.common_name, self.use_genome_build)
+ def __unicode__(self):
+ return u'%s (%s)' % (self.scientific_name, self.common_name)
class Meta:
verbose_name_plural = "species"
ordering = ["scientific_name"]
- class Admin:
- fields = (
- (None, {
- 'fields': (('scientific_name', 'common_name'), ('use_genome_build'))
- }),
- )
-
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')
email = models.EmailField(null=True,blank=True)
- def __str__(self):
- str = self.name
- if self.contact != '':
- str += ' ('+self.contact+')'
+ def __unicode__(self):
+ str = unicode(self.name)
+ if len(self.contact) != 0:
+ str += u' ('+self.contact+u')'
return str
class Meta:
ordering = ["name","contact"]
unique_together = (("name", "contact"),)
- class Admin:
- list_display = ('name','contact','email')
- fields = (
- (None, {
- 'fields': (('name','contact','email'))
- }),
- )
-
class Library(models.Model):
library_id = models.CharField(max_length=30, primary_key=True, db_index=True)
condition = models.ForeignKey(Condition)
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)
+ 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;
REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
default='RNA-seq')
creation_date = models.DateField(blank=True, null=True)
- made_for = models.ForeignKey(User, edit_inline=models.TABULAR)
+ made_for = models.ForeignKey(User)
made_by = models.CharField(max_length=50, blank=True, default="Lorian")
PROTOCOL_END_POINTS = (
avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
notes = models.TextField(blank=True)
- def __str__(self):
- return '#%s: %s' % (self.library_id, self.library_name)
+ def __unicode__(self):
+ return u'#%s: %s' % (self.library_id, self.library_name)
class Meta:
verbose_name_plural = "libraries"
ordering = ["-creation_date"] #["-library_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.nickname+'</a>'
+ return str
+ antibody_name.allow_tags = True
- def org(self):
+ def organism(self):
return self.library_species.common_name
def affiliation(self):
tstr = ''
ar = []
for t in affs:
- ar.append(t.__str__())
+ ar.append(t.__unicode__())
return '%s' % (", ".join(ar))
+ 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.library_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)
def aligned_reads(self):
res = getLibReads(self.library_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[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'
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'),)
- }),
- )
-
projects / htsworkflow.git / blobdiff