1 from django.db import models
2 from django.contrib.auth.models import User
3 from htsworkflow.frontend import settings
4 from htsworkflow.frontend.reports.libinfopar import *
6 # Create your models here.
8 class Antibody(models.Model):
9 antigene = models.CharField(max_length=500, db_index=True)
12 # alter table fctracker_antibody add column "nickname" varchar(20) NULL;
13 nickname = models.CharField(
18 verbose_name = 'Short Name'
20 catalog = models.CharField(max_length=50, unique=True, db_index=True)
21 antibodies = models.CharField(max_length=500, db_index=True)
22 source = models.CharField(max_length=500, blank=True, db_index=True)
23 biology = models.TextField(blank=True)
24 notes = models.TextField(blank=True)
25 def __unicode__(self):
26 return u'%s - %s (%s)' % (self.antigene, self.antibodies, self.catalog)
28 verbose_name_plural = "antibodies"
29 ordering = ["antigene"]
31 class Cellline(models.Model):
32 cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
33 nickname = models.CharField(max_length=20,
37 verbose_name = 'Short Name')
38 notes = models.TextField(blank=True)
39 def __unicode__(self):
40 return unicode(self.cellline_name)
43 ordering = ["cellline_name"]
45 class Condition(models.Model):
46 condition_name = models.CharField(
47 max_length=2000, unique=True, db_index=True)
48 nickname = models.CharField(max_length=20,
52 verbose_name = 'Short Name')
53 notes = models.TextField(blank=True)
55 def __unicode__(self):
56 return unicode(self.condition_name)
59 ordering = ["condition_name"]
61 class Tag(models.Model):
62 tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)
64 #('Antibody','Antibody'),
65 #('Cellline', 'Cellline'),
66 #('Condition', 'Condition'),
67 ('Library', 'Library'),
70 context = models.CharField(max_length=50,
71 choices=TAG_CONTEXT, default='Library')
73 def __unicode__(self):
74 return u'%s' % (self.tag_name)
77 ordering = ["context","tag_name"]
79 class Species(models.Model):
80 scientific_name = models.CharField(max_length=256,
84 common_name = models.CharField(max_length=256, blank=True)
85 #use_genome_build = models.CharField(max_length=100, blank=False, null=False)
87 def __unicode__(self):
88 return u'%s (%s)' % (self.scientific_name, self.common_name)
91 verbose_name_plural = "species"
92 ordering = ["scientific_name"]
94 class Affiliation(models.Model):
95 name = models.CharField(max_length=256, db_index=True, verbose_name='Group Name')
96 contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Contact Name')
97 email = models.EmailField(null=True,blank=True)
99 def __unicode__(self):
100 str = unicode(self.name)
101 if len(self.contact) != 0:
102 str += u' ('+self.contact+u')'
106 ordering = ["name","contact"]
107 unique_together = (("name", "contact"),)
109 class Library(models.Model):
110 id = models.AutoField(primary_key=True)
111 library_id = models.CharField(max_length=30, db_index=True)
112 library_name = models.CharField(max_length=100, unique=True)
113 library_species = models.ForeignKey(Species)
114 cell_line = models.ForeignKey(Cellline)
115 condition = models.ForeignKey(Condition)
116 antibody = models.ForeignKey(Antibody,blank=True,null=True)
117 # New field Aug/25/08. SQL: alter table fctracker_library add column "lib_affiliation" varchar(256) NULL;
118 affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True)
119 # new field Nov/14/08
120 tags = models.ManyToManyField(Tag,related_name='library_tags',blank=True,null=True)
121 # New field Aug/19/08
122 # SQL to add column: alter table fctracker_library add column "replicate" smallint unsigned NULL;
123 REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
124 replicate = models.PositiveSmallIntegerField(choices=REPLICATE_NUM,default=1)
127 ('INPUT_RXLCh','INPUT_RXLCh'),
128 ('ChIP-seq', 'ChIP-seq'),
129 ('Sheared', 'Sheared'),
130 ('RNA-seq', 'RNA-seq'),
131 ('Methyl-seq', 'Methyl-seq'),
132 ('DIP-seq', 'DIP-seq'),
134 experiment_type = models.CharField(max_length=50, choices=EXPERIMENT_TYPES,
137 creation_date = models.DateField(blank=True, null=True)
138 made_for = models.CharField(max_length=50, blank=True,
139 verbose_name='ChIP/DNA/RNA Made By')
140 made_by = models.CharField(max_length=50, blank=True, default="Lorian")
142 PROTOCOL_END_POINTS = (
144 ('Sample', 'Raw sample'),
145 ('Progress', 'In progress'),
146 ('1A', 'Ligation, then gel'),
147 ('PCR', 'Ligation, then PCR'),
148 ('1Ab', 'Ligation, PCR, then gel'),
149 ('1Aa', 'Ligation, gel, then PCR'),
150 ('2A', 'Ligation, PCR, gel, PCR'),
151 ('Done', 'Completed'),
153 stopping_point = models.CharField(max_length=25, choices=PROTOCOL_END_POINTS, default='Done')
154 amplified_from_sample = models.ForeignKey('self', blank=True, null=True)
156 undiluted_concentration = models.DecimalField("Concentration",
157 max_digits=5, decimal_places=2, default=0, blank=True, null=True,
158 help_text="Undiluted concentration (ng/ul)")
159 successful_pM = models.DecimalField(max_digits=5, decimal_places=2, blank=True, null=True)
160 ten_nM_dilution = models.BooleanField()
161 avg_lib_size = models.IntegerField(default=225, blank=True, null=True)
162 notes = models.TextField(blank=True)
164 def __unicode__(self):
165 return u'#%s: %s' % (self.library_id, self.library_name)
168 verbose_name_plural = "libraries"
169 ordering = ["-creation_date"] #["-library_id"]
171 def antibody_name(self):
172 str ='<a target=_self href="/admin/samples/antibody/'+self.antibody.id.__str__()+'/" title="'+self.antibody.__str__()+'">'+self.antibody.nickname+'</a>'
174 antibody_name.allow_tags = True
177 return self.library_species.common_name
179 def affiliation(self):
180 affs = self.affiliations.all().order_by('name')
184 ar.append(t.__unicode__())
185 return '%s' % (", ".join(ar))
188 affs = self.tags.all().order_by('tag_name')
191 ar.append(t.__unicode__())
192 return u'%s' % ( ", ".join(ar))
195 str ='<a target=_self href="/admin/experiments/datarun/?q='+self.library_id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
197 DataRun.allow_tags = True
199 def aligned_m_reads(self):
200 return getLibReads(self.library_id)
202 def aligned_reads(self):
203 res = getLibReads(self.library_id)
207 return u'<div style="border:solid red 2px">'+res[2]+'</div>'
209 rc = "%1.2f" % (res[1]/1000000.0)
210 # 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
212 bgcolor = '#ff3300' # Red
213 rc_thr = [10000000,5000000,3000000]
214 if self.experiment_type == 'RNA-seq':
215 rc_thr = [20000000,10000000,6000000]
217 if res[1] > rc_thr[0]:
218 bgcolor = '#66ff66' # Green
220 if res[1] > rc_thr[1]:
221 bgcolor ='#00ccff' # Blue
223 if res[1] > rc_thr[2]:
224 bgcolor ='#ffcc33' # Orange
225 tstr = '<div style="background-color:'+bgcolor+';color:black">'
226 tstr += res[0].__unicode__()+' Lanes, '+rc+' M Reads'
228 else: tstr = 'not processed yet'
230 aligned_reads.allow_tags = True