--- /dev/null
+from django.db import models
+from gaworkflow.frontend.fctracker.models import Library
+
+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) #Stanford is currenlty 25
+
+ 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,blank=False, null=False,default=2.5)
+ lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+ lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+
+ lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_3_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_4_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_5_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_6_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_7_cluster_estimate = models.IntegerField(blank=True, null=True)
+ lane_8_cluster_estimate = models.IntegerField(blank=True, null=True)
+
+ # lane_1_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_1_primer")
+ # lane_2_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_2_primer")
+ # lane_3_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_3_primer")
+ # lane_4_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_4_primer")
+ # lane_5_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_5_primer")
+ # lane_6_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_6_primer")
+ # lane_7_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_7_primer")
+ # lane_8_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_8_primer")
+
+ #Machine Names
+ CLUSTER_MAC = (
+ ('M304','M304'),
+ ('R349','R349'),
+ ('Tinkerbell','Tinkerbell'),
+ ('BitBit','BitBit'),
+ )
+
+ SEQ_MAC = (
+ ('EAS149','EAS149'),
+ ('EAS46','EAS46'),
+ ('EAS45','Paris'),
+ ('Britney','Britney'),
+ )
+
+ cluster_mac_id = models.CharField(max_length=50, choices=CLUSTER_MAC, default='BitBit')
+ seq_mac_id = models.CharField(max_length=50, choices=SEQ_MAC, verbose_name = 'Sequencer', default='Britney')
+
+ notes = models.TextField(blank=True)
+
+ def __str__(self):
+ #return '%s (%s)' % (self.flowcell_id, self.run_date)
+ return '%s' % (self.flowcell_id)
+
+
+ def Lanes(self):
+ 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)
+ Lanes.allow_tags = True
+
+ class Meta:
+ ordering = ["-run_date"]
+
+ class Admin:
+ save_on_top = True
+ date_hierarchy = "run_date"
+ save_on_top = True
+ 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']
+ list_display = ('flowcell_id','seq_mac_id','run_date', 'Lanes')
+ list_filter = ('seq_mac_id','cluster_mac_id')
+ fields = (
+ (None, {
+ 'fields': ('run_date', ('flowcell_id','cluster_mac_id','seq_mac_id'), ('read_length'),)
+ }),
+ ('Lanes:', {
+ ##'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'),)
+ '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'),)
+ }),
+ (None, {
+ 'fields' : ('notes',)
+ }),
+ )
+
+
+### -----------------------
+class DataRun(models.Model):
+ ConfTemplate = "CONFIG PARAMS WILL BE GENERATED BY THE PIPELINE SCRIPT.\nYOU'LL BE ABLE TO EDIT AFTER IF NEEDED."
+ run_folder = models.CharField(max_length=50,unique=True, db_index=True)
+ fcid = models.ForeignKey(FlowCell,verbose_name="Flowcell Id")
+ config_params = models.TextField(default=ConfTemplate)
+ run_start_time = models.DateTimeField(core=True)
+ RUN_STATUS_CHOICES = (
+ (0, 'Sequencer running'), ##Solexa Data Pipeline Not Yet Started'),
+ (1, 'Data Pipeline Started'),
+ (2, 'Data Pipeline Interrupted'),
+ (3, 'Data Pipeline Finished'),
+ (4, 'CollectReads Started'),
+ (5, 'CollectReads Finished'),
+ (6, 'QC Finished'),
+ (7, 'DONE'),
+ )
+ run_status = models.IntegerField(choices=RUN_STATUS_CHOICES, default=0)
+ run_note = models.TextField(blank=True)
+
+
+ def main_status(self):
+ return self.run_status
+
+ main_status.allow_tags = True
+
+ def Flowcell_Info(self):
+ str = '<b>'+self.fcid.__str__()+'</b>'
+ str += ' (c: '+self.fcid.cluster_mac_id+', s: '+self.fcid.seq_mac_id+')'
+ str += '<div style="margin-top:5px;">'
+ 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>'
+ str += '<div id="LanesOf'+self.fcid.__str__()+'" style="display:block;border:solid #cccccc 1px;width:350px">'
+ 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+')'
+ str += LanesList ## self.fcid.Lanes()
+ str += '</div>'
+ str += '<div><a title="open Flowcell record" href="/admin/exp_track/flowcell/'+self.fcid.id.__str__()+'/" target=_self>Edit Flowcell record</a></div>'
+ str += '</div>'
+ return str
+ Flowcell_Info.allow_tags = True
+
+ class Admin:
+ 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']
+
+ list_display = ('run_folder','Flowcell_Info','run_start_time','run_status','run_note')
+ list_filter = ('run_status','run_start_time')
projects / htsworkflow.git / blobdiff