from django.db import models
-from datetime import datetime
-from gaworkflow.frontend.fctracker.models import Library
-from string import *
+from gaworkflow.frontend.fctracker.models import Library
-class Task(models.Model):
- task_name = models.CharField(max_length=50,unique=True, db_index=True)
- subject1 = models.ForeignKey(Library,related_name='sbj1_library',verbose_name="Subject")
- subject2 = models.ForeignKey(Library,related_name='sbj2_library',verbose_name="Subject 2 / Control",blank=True,null=True)
- CALCS = (
- ('QuEST', 'QuEST Peak Calling'),
- ('WingPeaks', 'Wing Peak Calling'),
- ('MACS', 'MACS Peak Calling'),
- ('qPCR', 'In Silico qPCR'),
- ('CompareLibs', 'Compare Libaraies'),
- ('ComparePeakCalls','Compare Peak Calls'),
- ('ProfileReads','Profile Reads')
+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'),
)
- apply_calc = models.CharField(max_length=50,choices=CALCS,verbose_name='Applied Calculation')
- ## userid = # logged in user
- task_status = models.CharField(max_length=500,blank=True,null=True,default='defined')
- results_location = models.CharField(max_length=2000,blank=True,null=True)
- submitted_on = models.DateTimeField(core=True,default=datetime.now())
- run_note = models.CharField(max_length=500,blank=True,null=True)
+ 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 on [%s]/[%s]' % (self.task_name,self.apply_calc,self.subject1,self.subject2)
+ #return '%s (%s)' % (self.flowcell_id, self.run_date)
+ return '%s' % (self.flowcell_id)
- def InProjects(self):
- return '...'
- ps = self.project_set.all()
- pstr = 'In '
- return pstr
- for p in ps:
- pstr += '%s, ' % (p.project_name)
- return pstr
+ 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:
- list_display = ('task_name','apply_calc','subject1','subject2','InProjects','submitted_on','task_status')
- list_filter = ('apply_calc',)
+ 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': (('task_name'),('apply_calc'),('subject1'),('subject2'))
- }),
- ('system fields', {
- 'classes': 'collapse',
- 'fields': (('submitted_on'),('task_status','run_note'))
- }),
- )
-
-
-class Project(models.Model):
- project_name = models.CharField(max_length=50,unique=True, db_index=True)
- tasks = models.ManyToManyField(Task,related_name='project_tasks',null=True)
- project_notes = models.CharField(max_length=500,blank=True,null=True)
-
- def __str__(self):
- return '%s' % (self.project_name)
+ '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',)
+ }),
+ )
- def ProjectTasks(self):
- ptasks = self.tasks.all().order_by('id')
- surl = 'http://m304-apple-server.stanford.edu/projects/'
- tstr = '<script>'
- tstr += 'function togView(eid){'
- tstr += 'f=document.getElementById(eid);'
- tstr += 'if(f.height==0){'
- tstr += 'f.height=600;'
- tstr += 'f.style.border=\'solid #cccccc 3px\';'
- tstr += '}else{'
- tstr += 'f.height=0;'
- tstr += 'f.style.border=\'none\';'
- tstr += '}'
- tstr += '}'
- tstr += '</script>'
- Style = ''
- if len(ptasks) > 8: Style = ' style="height:200px;overflow:auto" '
- tstr += '<div '+Style+'>'
- tstr += '<table><tr><th>Tasks</th><th>Job Status</th>'
- isregistered = False
- for t in ptasks:
- tstr += '<tr><td width=250>%s</td><td>%s</td></tr>' % (t.task_name,replace(t.task_status,'Complete','<span style="color:green;font-weight:bolder">Complete</span>'))
- if t.task_status != 'defined': isregistered = True
- tstr += '</table>'
- tstr += '</div>'
- tstr += '<div>'
- tstr += '<div align=center>'
- if isregistered:
- tstr += '<a onClick="togView(\'RFrame'+self.id.__str__()+'\');" href="'+surl+self.id.__str__()+'/" title="View Results Page" target="RFrame'+self.id.__str__()+'">VIEW PROJECT RESULTS</a>'
- tstr += '<a href="'+surl+self.id.__str__()+'/" title="View Results Page" target="_blank" style="margin-left:10px">(view in new window)</a>'
- else:
- tstr += 'REGISTERING ...'
-
- tstr += '</div>'
- tstr += '<iframe width="100%" height="0" frameborder="0" style="background-color:#ffffff" name="RFrame'+self.id.__str__()+'" id="RFrame'+self.id.__str__()+'"/></iframe>'
- tstr += '</div>'
- return tstr
-
- ProjectTasks.allow_tags = True
+### -----------------------
+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 ProjTitle(self):
- ptasks = self.tasks.all().order_by('id')
- tasks_counter = '<span style="color:#666666;font-size:85%">('+len(ptasks).__str__() + ' tasks)</span>'
- htmlstr = '%s<br/>%s' % (self.project_name,tasks_counter)
- return htmlstr
- ProjTitle.allow_tags = True
+ def main_status(self):
+ return self.run_status
- class Admin:
- list_display = ('ProjTitle','ProjectTasks')
- # list_filter = ('...',)
- fields = (
- (None, {
- 'fields': (('project_name'),('tasks'),('project_notes'))}),
- )
+ 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 / commitdiff