From: Unknown Author Date: Fri, 8 Aug 2008 23:29:32 +0000 (+0000) Subject: some code cleaning X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=4d33210b4a03537dc6d1184cf30dbb262bd98704 some code cleaning --- diff --git a/gaworkflow/frontend/exp_track/models.py b/gaworkflow/frontend/exp_track/models.py index baf40c1..be0bb9c 100644 --- a/gaworkflow/frontend/exp_track/models.py +++ b/gaworkflow/frontend/exp_track/models.py @@ -1,134 +1,115 @@ 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 '
1)%s2)%s3)%s4)%s5)%s6)%s7)%s8)%s
' % (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 = '' + Style = '' + if len(ptasks) > 8: Style = ' style="height:200px;overflow:auto" ' + tstr += '
' + tstr += '' + isregistered = False + for t in ptasks: + tstr += '' % (t.task_name,replace(t.task_status,'Complete','Complete')) + 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 = ''+self.fcid.__str__()+'' - str += '
' - str +='View Lanes' - str += '
' - return str - Flowcell_Info.allow_tags = True + tstr += '
TasksJob Status
%s%s
' + tstr += '
' + tstr += '
' + tstr += '
' + if isregistered: + tstr += 'VIEW PROJECT RESULTS' + tstr += '(view in new window)' + else: + tstr += 'REGISTERING ...' + + tstr += '
' + tstr += '' + tstr += '
' + 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 = '('+len(ptasks).__str__() + ' tasks)' + htmlstr = '%s
%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'))}), + )