gaworkflow/frontend/exp_track/models.py

   1 from django.db import models
   2 from gaworkflow.frontend.fctracker.models import Library
   3
   4 class FlowCell(models.Model):
   5
   6   flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
   7   run_date = models.DateTimeField(core=True)
   8   advanced_run = models.BooleanField(default=False)
   9   read_length = models.IntegerField(default=32) #Stanford is currenlty 25
  10
  11   lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
  12   lane_2_library = models.ForeignKey(Library, related_name="lane_2_library")
  13   lane_3_library = models.ForeignKey(Library, related_name="lane_3_library")
  14   lane_4_library = models.ForeignKey(Library, related_name="lane_4_library")
  15   lane_5_library = models.ForeignKey(Library, related_name="lane_5_library")
  16   lane_6_library = models.ForeignKey(Library, related_name="lane_6_library")
  17   lane_7_library = models.ForeignKey(Library, related_name="lane_7_library")
  18   lane_8_library = models.ForeignKey(Library, related_name="lane_8_library")
  19
  20   lane_1_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  21   lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  22   lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  23   lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  24   lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  25   lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  26   lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  27   lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  28
  29   lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
  30   lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)
  31   lane_3_cluster_estimate = models.IntegerField(blank=True, null=True)
  32   lane_4_cluster_estimate = models.IntegerField(blank=True, null=True)
  33   lane_5_cluster_estimate = models.IntegerField(blank=True, null=True)
  34   lane_6_cluster_estimate = models.IntegerField(blank=True, null=True)
  35   lane_7_cluster_estimate = models.IntegerField(blank=True, null=True)
  36   lane_8_cluster_estimate = models.IntegerField(blank=True, null=True)
  37
  38   # lane_1_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_1_primer")
  39   # lane_2_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_2_primer")
  40   # lane_3_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_3_primer")
  41   # lane_4_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_4_primer")
  42   # lane_5_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_5_primer")
  43   # lane_6_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_6_primer")
  44   # lane_7_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_7_primer")
  45   # lane_8_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_8_primer")
  46
  47   #Machine Names
  48   CLUSTER_MAC = (
  49       ('M304','M304'),
  50       ('R349','R349'),
  51       ('Tinkerbell','Tinkerbell'),
  52       ('BitBit','BitBit'),
  53     )
  54
  55   SEQ_MAC = (
  56       ('EAS149','EAS149'),
  57       ('EAS46','EAS46'),
  58       ('EAS45','Paris'),
  59       ('Britney','Britney'),
  60     )
  61
  62   cluster_mac_id = models.CharField(max_length=50, choices=CLUSTER_MAC, default='BitBit')
  63   seq_mac_id = models.CharField(max_length=50, choices=SEQ_MAC, verbose_name = 'Sequencer', default='Britney')
  64
  65   notes = models.TextField(blank=True)
  66
  67   def __str__(self):
  68     #return '%s (%s)' % (self.flowcell_id, self.run_date)
  69     return '%s' % (self.flowcell_id)
  70
  71
  72   def Lanes(self):
  73     return '<div><span style="margin-right:10px">1)%s</span><span style="margin-right:10px">2)%s</span><span style="margin-right:10px">3)%s</span><span style="margin-right:10px">4)%s</span><span style="margin-right:10px">5)%s</span><span style="margin-right:10px">6)%s</span><span style="margin-right:10px">7)%s</span><span style="margin-right:10px">8)%s</span></div>' % (self.lane_1_library,self.lane_2_library,self.lane_3_library,self.lane_4_library,self.lane_5_library,self.lane_6_library,self.lane_7_library,self.lane_8_library)
  74   Lanes.allow_tags = True
  75
  76   class Meta:
  77     ordering = ["-run_date"]
  78
  79   class Admin:
  80     save_on_top = True
  81     date_hierarchy = "run_date"
  82     save_on_top = True
  83     search_fields = ['flowcell_id','seq_mac_id','cluster_mac_id','=lane_1_library__library_id','=lane_2_library__library_id','=lane_3_library__library_id','=lane_4_library__library_id','=lane_5_library__library_id','=lane_6_library__library_id','=lane_7_library__library_id','=lane_8_library__library_id']
  84     list_display = ('flowcell_id','seq_mac_id','run_date', 'Lanes')
  85     list_filter = ('seq_mac_id','cluster_mac_id')
  86     fields = (
  87         (None, {
  88             'fields': ('run_date', ('flowcell_id','cluster_mac_id','seq_mac_id'), ('read_length'),)
  89         }),
  90         ('Lanes:', {
  91             ##'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate', 'lane_1_primer'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate', 'lane_2_primer'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate', 'lane_3_primer'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate', 'lane_4_primer'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate', 'lane_5_primer'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate', 'lane_6_primer'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate', 'lane_7_primer'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate', 'lane_8_primer'),)
  92            'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)
  93         }),
  94         (None, {
  95             'fields' : ('notes',)
  96         }),
  97     )
  98
  99
 100 ### -----------------------
 101 class DataRun(models.Model):
 102   ConfTemplate = "CONFIG PARAMS WILL BE GENERATED BY THE PIPELINE SCRIPT.\nYOU'LL BE ABLE TO EDIT AFTER IF NEEDED."
 103   run_folder = models.CharField(max_length=50,unique=True, db_index=True)
 104   fcid = models.ForeignKey(FlowCell,verbose_name="Flowcell Id")
 105   config_params = models.TextField(default=ConfTemplate)
 106   run_start_time = models.DateTimeField(core=True)
 107   RUN_STATUS_CHOICES = (
 108       (0, 'Sequencer running'), ##Solexa Data Pipeline Not Yet Started'),
 109       (1, 'Data Pipeline Started'),
 110       (2, 'Data Pipeline Interrupted'),
 111       (3, 'Data Pipeline Finished'),
 112       (4, 'CollectReads Started'),
 113       (5, 'CollectReads Finished'),
 114     )
 115   run_status = models.IntegerField(choices=RUN_STATUS_CHOICES, default=0)
 116   run_note = models.TextField(blank=True)
 117
 118   def Flowcell_Info(self):
 119     str = '<b>'+self.fcid.__str__()+'</b>'
 120     str += '<div style="margin-top:5px;">'
 121     str +='<a title="View Lane List here ..."  onClick="el = document.getElementById(\'LanesOf'+self.fcid.__str__()+'\');if(el) (el.style.display==\'none\'?el.style.display=\'block\':el.style.display=\'none\')" style="cursor:pointer;color: #5b80b2;">View Lanes</a>'
 122     str += '<div id="LanesOf'+self.fcid.__str__()+'" style="display:none;border:solid #cccccc 1px;width:300px">'
 123     LanesList = '1: '+self.fcid.lane_1_library.__str__()+' ('+self.fcid.lane_1_library.library_species.use_genome_build+')<br/>2: '+self.fcid.lane_2_library.__str__()+' ('+self.fcid.lane_2_library.library_species.use_genome_build+')<br/>3: '+self.fcid.lane_3_library.__str__()+' ('+self.fcid.lane_3_library.library_species.use_genome_build+')<br/>4: '+self.fcid.lane_4_library.__str__()+' ('+self.fcid.lane_4_library.library_species.use_genome_build+')<br/>5: '+self.fcid.lane_5_library.__str__()+' ('+self.fcid.lane_5_library.library_species.use_genome_build+')<br/>6: '+self.fcid.lane_6_library.__str__()+' ('+self.fcid.lane_6_library.library_species.use_genome_build+')<br/>7: '+self.fcid.lane_7_library.__str__()+' ('+self.fcid.lane_7_library.library_species.use_genome_build+')<br/>8: '+self.fcid.lane_8_library.__str__()+' ('+self.fcid.lane_8_library.library_species.use_genome_build+')<br/>'
 124     str += LanesList ## self.fcid.Lanes()
 125     str += '<br/><a title="open Flowcell record" href="/admin/exp_track/flowcell/'+self.fcid.id.__str__()+'/" target=_self>Edit Flowcell record</a>'
 126     str += '</div></div>'
 127     return str
 128   Flowcell_Info.allow_tags = True
 129
 130   class Admin:
 131     search_fields = ['run_folder','run_note','config_params','=fcid__lane_1_library__library_id','=fcid__lane_2_library__library_id','=fcid__lane_3_library__library_id','=fcid__lane_4_library__library_id','=fcid__lane_5_library__library_id','=fcid__lane_6_library__library_id','=fcid__lane_7_library__library_id','=fcid__lane_8_library__library_id']
 132
 133     list_display = ('run_folder','Flowcell_Info','run_start_time','run_status','run_note')
 134     list_filter = ('run_status','run_start_time')