from django.db import models
-from gaworkflow.frontend.fctracker.models import Library
+from datetime import datetime
+from gaworkflow.frontend.fctracker.models import Library
+from string import *
-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'),
+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')
)
+ 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)' % (self.flowcell_id, self.run_date)
- return '%s' % (self.flowcell_id)
+ return '"%s" - %s on [%s]/[%s]' % (self.task_name,self.apply_calc,self.subject1,self.subject2)
+ 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:
- 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')
+ list_display = ('task_name','apply_calc','subject1','subject2','InProjects','submitted_on','task_status')
+ list_filter = ('apply_calc',)
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',)
- }),
- )
+ '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)
+ 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
-### -----------------------
-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'),
- )
- run_status = models.IntegerField(choices=RUN_STATUS_CHOICES, default=0)
- run_note = models.TextField(blank=True)
-
- def Flowcell_Info(self):
- str = '<b>'+self.fcid.__str__()+'</b>'
- 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 Lanes</a>'
- str += '<div id="LanesOf'+self.fcid.__str__()+'" style="display:none;border:solid #cccccc 1px;width:300px">'
- 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/>'
- str += LanesList ## self.fcid.Lanes()
- str += '<br/><a title="open Flowcell record" href="/admin/exp_track/flowcell/'+self.fcid.id.__str__()+'/" target=_self>Edit Flowcell record</a>'
- str += '</div></div>'
- return str
- Flowcell_Info.allow_tags = 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 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']
+ 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
- list_display = ('run_folder','Flowcell_Info','run_start_time','run_status','run_note')
- list_filter = ('run_status','run_start_time')
+ ProjTitle.allow_tags = True
+
+ class Admin:
+ list_display = ('ProjTitle','ProjectTasks')
+ # list_filter = ('...',)
+ fields = (
+ (None, {
+ 'fields': (('project_name'),('tasks'),('project_notes'))}),
+ )
projects / htsworkflow.git / commitdiff