from django.db import models
from django.contrib.auth.models import User
from htsworkflow.frontend import settings
+from htsworkflow.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)
verbose_name_plural = "antibodies"
ordering = ["antigene"]
class Admin:
- list_display = ('antigene','antibodies','catalog','source','biology','notes')
+ list_display = ('antigene','nickname','antibodies','catalog','source','biology','notes')
list_filter = ('antibodies','source')
fields = (
(None, {
- 'fields': (('antigene','antibodies'),('catalog','source'),('biology'),('notes'))
+ 'fields': (('antigene','nickname','antibodies'),('catalog','source'),('biology'),('notes'))
}),
)
}),
)
-class Lab(models.Model):
-
- name = models.CharField(max_length=100, blank=False, unique=True)
+class Affiliation(models.Model):
+ name = models.CharField(max_length=256, db_index=True, core=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):
- return self.name
-
- class Admin:
- pass
+ str = self.name
+ if self.contact != '':
+ str += ' ('+self.contact+')'
+ return str
-class UserProfile(models.Model):
-
- # This allows you to use user.get_profile() to get this object
- user = models.ForeignKey(User, unique=True)
-
- lab = models.ForeignKey(Lab)
- #email = models.CharField(max_length=50, blank=True, null=True)
-
- def __str__(self):
- return '%s (%s lab)' % (self.user, self.lab)
-
class Meta:
- #verbose_name_plural = "people"
- #ordering = ["lab"]
- pass
-
- class Admin:
- #fields = (
- # (None, {
- # 'fields': (('email', 'lab'), ('email'))
- # }),
- #)
- pass
+ ordering = ["name","contact"]
+ unique_together = (("name", "contact"),)
+ class Admin:
+ list_display = ('name','contact','email')
+ fields = (
+ (None, {
+ 'fields': (('name','contact','email'))
+ }),
+ )
class Library(models.Model):
cell_line = models.ForeignKey(Cellline,core=True)
condition = models.ForeignKey(Condition,core=True)
antibody = models.ForeignKey(Antibody,blank=True,null=True,core=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'),
class Meta:
verbose_name_plural = "libraries"
- ordering = ["-library_id"]
-
+ ordering = ["-creation_date"] #["-library_id"]
+
+ def antibody_name(self):
+ return self.antibody.nickname
+
+ def org(self):
+ return self.library_species.common_name
+
+ def affiliation(self):
+ affs = self.affiliations.all().order_by('name')
+ tstr = ''
+ ar = []
+ for t in affs:
+ ar.append(t.__str__())
+ return '%s' % (", ".join(ar))
+
+
+ def aligned_reads(self):
+ res = getLibReads(self.library_id)
+ 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:
+ bgcolor = '#ff3300' # Red
+ rc_thr = [10000000,5000000,3000000]
+ if self.experiment_type == 'RNA-seq':
+ rc_thr = [20000000,10000000,6000000]
+
+ if res[1] > rc_thr[0]:
+ bgcolor = '#66ff66' # Green
+ else:
+ if res[1] > rc_thr[1]:
+ bgcolor ='#00ccff' # Blue
+ else:
+ 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 += '</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_name', 'library_id']
- list_display = ('library_id', 'library_name', 'made_for', 'creation_date', 'stopping_point')
+ ##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_links = ('library_id', 'library_name')
- list_filter = ('stopping_point', 'library_species', 'made_for', 'made_by', 'experiment_type')
+
+ list_filter = ('experiment_type','affiliations','library_species','made_for', 'made_by','replicate')
fields = (
(None, {
- 'fields': (('library_id', 'library_name'), ('library_species', 'experiment_type'),)
+ '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',)
}),
- ('Run Information:', {
- 'fields' : (('ten_nM_dilution','successful_pM'),)
- }),
- )
-
-class FlowCell(models.Model):
-
- flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
- run_date = models.DateTimeField(core=True)
- advanced_run = models.BooleanField(default=False)
- read_length = models.IntegerField(default=32)
-
-
- FLOWCELL_STATUSES = (
- ('No', 'Not run'),
- ('F', 'Failed'),
- ('Del', 'Data deleted'),
- ('A', 'Data available'),
- ('In', 'In progress'),
- )
- flowcell_status = models.CharField(max_length=10, choices=FLOWCELL_STATUSES)
-
- lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
- lane_2_library = models.ForeignKey(Library, related_name="lane_2_library")
- lane_3_library = models.ForeignKey(Library, related_name="lane_3_library")
- lane_4_library = models.ForeignKey(Library, related_name="lane_4_library")
- lane_5_library = models.ForeignKey(Library, related_name="lane_5_library")
- lane_6_library = models.ForeignKey(Library, related_name="lane_6_library")
- lane_7_library = models.ForeignKey(Library, related_name="lane_7_library")
- lane_8_library = models.ForeignKey(Library, related_name="lane_8_library")
-
- lane_1_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
- lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
- lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
- lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
- lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
- lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
- lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
- lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2, default=4)
-
- lane_1_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
- lane_2_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
- lane_3_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
- lane_4_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
- lane_5_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
- lane_6_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
- lane_7_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
- lane_8_cluster_estimate = models.CharField(max_length=25, blank=True, null=True)
-
- kit_1000148 = models.IntegerField(blank=True, null=True)
- kit_1000147 = models.IntegerField(blank=True, null=True)
- kit_1000183 = models.IntegerField(blank=True, null=True)
- kit_1001625 = models.IntegerField(blank=True, null=True)
-
- cluster_station_id = models.CharField(max_length=50, blank=True, null=True)
- sequencer_id = models.CharField(max_length=50, blank=True, null=True)
-
- notes = models.TextField(blank=True)
-
- def __str__(self):
- return '%s (%s)' % (self.flowcell_id, self.run_date)
-
- class Meta:
- ordering = ["-run_date"]
-
- class Admin:
- date_hierarchy = "run_date"
- save_as = True
- save_on_top = True
- search_fields = ['flowcell_id', 'lane_1_library__library_id', 'lane_1_library__library_name', 'lane_2_library__library_id', 'lane_2_library__library_name', 'lane_3_library__library_id', 'lane_3_library__library_name', 'lane_4_library__library_id', 'lane_4_library__library_name', 'lane_5_library__library_id', 'lane_5_library__library_name', 'lane_6_library__library_id', 'lane_6_library__library_name', 'lane_7_library__library_id', 'lane_7_library__library_name', 'lane_8_library__library_id', 'lane_8_library__library_name']
- list_display = ('run_date', 'flowcell_status', 'flowcell_id', 'lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library')
- list_display_links = ('run_date', 'flowcell_id', 'lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library')
- fields = (
- (None, {
- 'fields': ('run_date', ('flowcell_id', 'flowcell_status'), ('read_length', 'advanced_run'),)
- }),
- ('Lanes:', {
- 'fields' : (('lane_1_library', 'lane_1_pM'), ('lane_2_library', 'lane_2_pM'), ('lane_3_library', 'lane_3_pM'), ('lane_4_library', 'lane_4_pM'), ('lane_5_library', 'lane_5_pM'), ('lane_6_library', 'lane_6_pM'), ('lane_7_library', 'lane_7_pM'), ('lane_8_library', 'lane_8_pM'),)
+ ('Library/Project Affiliation:', {
+ 'fields' : (('affiliations'),)
}),
- (None, {
- 'fields' : ('notes',)
- }),
- ('Kits & Machines:', {
- 'classes': 'collapse',
- 'fields' : (('kit_1000148', 'kit_1000147', 'kit_1000183', 'kit_1001625'), ('cluster_station_id', 'sequencer_id'),)
- }),
- ('Cluster Estimates:', {
- 'classes': 'collapse',
- 'fields' : (('lane_1_cluster_estimate', 'lane_2_cluster_estimate'), ('lane_3_cluster_estimate', 'lane_4_cluster_estimate'), ('lane_5_cluster_estimate', 'lane_6_cluster_estimate'), ('lane_7_cluster_estimate', 'lane_8_cluster_estimate',),)
- }),
- )
+ )
-# Did not finish implementing, removing to avoid further confusion.
-#class ElandResult(models.Model):
-#
-# class Admin: pass
-#
-# flow_cell = models.ForeignKey(FlowCell)
-# config_file = models.FileField(upload_to=settings.UPLOADTO_CONFIG_FILE)
-# eland_result_pack = models.FileField(upload_to=settings.UPLOADTO_ELAND_RESULT_PACKS)
-# bed_file_pack = models.FileField(upload_to=settings.UPLOADTO_BED_PACKS)
-#
-# notes = models.TextField(blank=True)
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