htsworkflow/frontend/experiments/models.py

   1 from django.db import models
   2 from htsworkflow.frontend.samples.models import *
   3 from django.core.exceptions import ObjectDoesNotExist
   4
   5 class FlowCell(models.Model):
   6
   7   flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
   8   run_date = models.DateTimeField()
   9   advanced_run = models.BooleanField(default=False)
  10   read_length = models.IntegerField(default=32) #Stanford is currenlty 25
  11
  12   lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
  13   lane_2_library = models.ForeignKey(Library, related_name="lane_2_library")
  14   lane_3_library = models.ForeignKey(Library, related_name="lane_3_library")
  15   lane_4_library = models.ForeignKey(Library, related_name="lane_4_library")
  16   lane_5_library = models.ForeignKey(Library, related_name="lane_5_library")
  17   lane_6_library = models.ForeignKey(Library, related_name="lane_6_library")
  18   lane_7_library = models.ForeignKey(Library, related_name="lane_7_library")
  19   lane_8_library = models.ForeignKey(Library, related_name="lane_8_library")
  20
  21   lane_1_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  22   lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  23   lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  24   lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  25   lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  26   lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  27   lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  28   lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
  29
  30   lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
  31   lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)
  32   lane_3_cluster_estimate = models.IntegerField(blank=True, null=True)
  33   lane_4_cluster_estimate = models.IntegerField(blank=True, null=True)
  34   lane_5_cluster_estimate = models.IntegerField(blank=True, null=True)
  35   lane_6_cluster_estimate = models.IntegerField(blank=True, null=True)
  36   lane_7_cluster_estimate = models.IntegerField(blank=True, null=True)
  37   lane_8_cluster_estimate = models.IntegerField(blank=True, null=True)
  38
  39   # lane_1_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_1_primer")
  40   # lane_2_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_2_primer")
  41   # lane_3_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_3_primer")
  42   # lane_4_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_4_primer")
  43   # lane_5_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_5_primer")
  44   # lane_6_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_6_primer")
  45   # lane_7_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_7_primer")
  46   # lane_8_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_8_primer")
  47
  48   #Machine Names
  49   CLUSTER_MAC = (
  50       ('M304','Cardinal'),
  51       ('R349','R349'),
  52       ('Tinkerbell','Tinkerbell'),
  53       ('BitBit','BitBit'),
  54     )
  55
  56   SEQ_MAC = (
  57       ('EAS149','Stanford'),
  58       ('EAS46','EAS46'),
  59       ('EAS45','Paris'),
  60       ('Britney','Britney'),
  61     )
  62
  63   cluster_mac_id = models.CharField(max_length=50, choices=CLUSTER_MAC, default='BitBit')
  64   seq_mac_id = models.CharField(max_length=50, choices=SEQ_MAC, verbose_name = 'Sequencer', default='Britney')
  65
  66   notes = models.TextField(blank=True)
  67
  68   def __unicode__(self):
  69       return unicode(self.flowcell_id)
  70
  71   def Create_LOG(self):
  72     str = ''
  73     str +='<a target=_balnk href="/experiments/'+self.flowcell_id+'" title="Create XLS like sheet for this Flowcell ..." ">Create LOG</a>'
  74     try:
  75       t = DataRun.objects.get(fcid=self.id)
  76       str +='<br/><a target=_self href="/admin/experiments/datarun/?q='+self.flowcell_id+'" title="Check Data Runs ..." ">DataRun ..</a>'
  77     except ObjectDoesNotExist:
  78       str += '<br/><span style="color:red">not sequenced</span>'
  79     return str
  80   Create_LOG.allow_tags = True
  81
  82   def Lanes(self):
  83     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)
  84   Lanes.allow_tags = True
  85
  86   class Meta:
  87     ordering = ["-run_date"]
  88
  89
  90 ### -----------------------
  91 class DataRun(models.Model):
  92   ConfTemplate = "CONFIG PARAMS WILL BE GENERATED BY THE PIPELINE SCRIPT.\nYOU'LL BE ABLE TO EDIT AFTER IF NEEDED."
  93   run_folder = models.CharField(max_length=50,unique=True, db_index=True)
  94   fcid = models.ForeignKey(FlowCell,verbose_name="Flowcell Id")
  95   config_params = models.TextField(default=ConfTemplate)
  96   run_start_time = models.DateTimeField()
  97   RUN_STATUS_CHOICES = (
  98       (0, 'Sequencer running'), ##Solexa Data Pipeline Not Yet Started'),
  99       (1, 'Data Pipeline Started'),
 100       (2, 'Data Pipeline Interrupted'),
 101       (3, 'Data Pipeline Finished'),
 102       (4, 'CollectReads Started'),
 103       (5, 'CollectReads Finished'),
 104       (6, 'QC Finished'),
 105       (7, 'DONE'),
 106     )
 107   run_status = models.IntegerField(choices=RUN_STATUS_CHOICES, default=0)
 108   run_note = models.TextField(blank=True)
 109
 110
 111   def main_status(self):
 112     str = '<div'
 113     if self.run_status >= 5:
 114       str += ' style="color:green">'
 115       str += '<b>'+self.RUN_STATUS_CHOICES[self.run_status][1]+'</b>'
 116       str += '<br/><br/>' #<span style="color:red;font-size:80%;">New!</span>'
 117       str +='<br/><a target=_balnk href="'+settings.TASKS_PROJS_SERVER+'/Flowcells/'+self.fcid.flowcell_id+'/'+self.fcid.flowcell_id+'_QC_Summary.html" title="View QC Summaries of this run ..." ">View QC Page</a>'
 118     else:
 119       str += '>'+self.RUN_STATUS_CHOICES[self.run_status][1]
 120
 121     str += '</div>'
 122     return str
 123   main_status.allow_tags = True
 124
 125   main_status.allow_tags = True
 126
 127   def Flowcell_Info(self):
 128     str = '<b>'+self.fcid.__str__()+'</b>'
 129     str += '  (c: '+self.fcid.cluster_mac_id+',  s: '+self.fcid.seq_mac_id+')'
 130     str += '<div style="margin-top:5px;">'
 131     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/hide lanes</a>'
 132     str += '<div id="LanesOf'+self.fcid.__str__()+'" style="display:block;border:solid #cccccc 1px;width:350px">'
 133     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+')'
 134     str += LanesList ## self.fcid.Lanes()
 135     str += '</div>'
 136     str += '<div><a title="open Flowcell record" href="/admin/exp_track/flowcell/'+self.fcid.id.__str__()+'/" target=_self>Edit Flowcell record</a>'
 137     #str += '<span style="color:red;font-size:80%;margin-left:15px;margin-right:3px">New!</span>'
 138     str +='<a style="margin-left:15px;" target=_balnk href="/exp_track/'+self.fcid.flowcell_id+'" title="View XLS like sheet for this Flowcell LOG ..." ">GA LOG Page</a>'
 139     str += '</div>'
 140     str += '</div>'
 141     return str
 142   Flowcell_Info.allow_tags = True