removing exp_track dir in order to redo a freash check in

diff --git a/gaworkflow/frontend/exp_track/__init__.py b/gaworkflow/frontend/exp_track/__init__.py
deleted file mode 100644 (file)
index e69de29..0000000

diff --git a/gaworkflow/frontend/exp_track/et_urls.py b/gaworkflow/frontend/exp_track/et_urls.py
deleted file mode 100644 (file)
index 6acea12..0000000
--- a/gaworkflow/frontend/exp_track/et_urls.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from django.conf.urls.defaults import *
-
-urlpatterns = patterns('',
-                                                                                                      
-    (r'^$', 'gaworkflow.frontend.exp_track.views.index'),
-    (r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.exp_track.views.detail'),
-    (r'^updStatus$', 'gaworkflow.frontend.exp_track.exptrack.updStatus'),
-    (r'^getConfile$', 'gaworkflow.frontend.exp_track.exptrack.getConfile'),
-    (r'^getLanesNames$', 'gaworkflow.frontend.exp_track.exptrack.getLaneLibs')   
-)

diff --git a/gaworkflow/frontend/exp_track/exptrack.py b/gaworkflow/frontend/exp_track/exptrack.py
deleted file mode 100644 (file)
index 8cd5d6d..0000000
--- a/gaworkflow/frontend/exp_track/exptrack.py
+++ /dev/null
@@ -1,194 +0,0 @@
-# some core functions of the exp tracker module
-from django.http import HttpResponse
-from datetime import datetime
-from string import *
-import re
-from gaworkflow.frontend import settings
-from gaworkflow.frontend.exp_track.models import FlowCell, DataRun
-from gaworkflow.frontend.fctracker.models import Library
-from django.core.exceptions import ObjectDoesNotExist
-from django.core.mail import send_mail, mail_admins
-
-def updStatus(request):
-    output=''
-    user = 'none'
-    pswd = ''
-    UpdatedStatus = 'unknown'
-    fcid = 'none'
-    runfolder = 'unknown'
-    ClIP = request.META['REMOTE_ADDR']
-    granted = False    
-
-    if request.has_key('user'):
-      user = request['user']
-
-    #Check access permission 
-    if (user == 'rami' and settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
-    if not granted: return HttpResponse("access denied.")
-
-
-    # ~~~~~~Parameters for the job ~~~~
-    if request.has_key('fcid'):
-      fcid = request['fcid']
-    else:
-      return HttpResponse('missing fcid')
-    
-    if request.has_key('runf'):
-      runfolder = request['runf']
-    else:
-      return HttpResponse('missing runf')
-
-    
-    if request.has_key('updst'):
-      UpdatedStatus = request['updst']
-    else:
-      return HttpResponse('missing status')
-    
-    # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
-
-    # Update Data Run status in DB
-    # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated 
-    try:
-      rec = DataRun.objects.get(run_folder=runfolder)
-      rec.run_status = UpdatedStatus
-
-      #if there's a message update that too
-      mytimestamp = datetime.now().__str__()
-      mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
-      if request.has_key('msg'):
-        rec.run_note += ", "+request['msg']+" ("+mytimestamp+")"
-      else :
-        if UpdatedStatus == '1':
-          rec.run_note = "Started ("+mytimestamp+")"
-
-      rec.save()
-      output = "Hello "+settings.ALLOWED_IPS[ClIP]+". Updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'"
-    except ObjectDoesNotExist:
-      output = "entry not found: "+fcid+", "+runfolder
-
-
-    #Notify researcher by email
-    # Doesn't work
-    #send_mail('Exp Tracker', 'Data Run Status '+output, 'rrauch@stanford.edu', ['rrrami@gmail.com'], fail_silently=False)
-    #mail_admins("test subject", "testing , testing", fail_silently=False)
-    # gives error: (49, "Can't assign requested address")
-    return HttpResponse(output)
-
-def generateConfile(fcid):
-    granted = False
-    ClIP = request.META['REMOTE_ADDR']
-    if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
-
-    if not granted: return HttpResponse("access denied.")
-
-    cnfgfile = 'READ_LENGTH 25\n'
-    cnfgfile += 'ANALYSIS eland\n'
-    cnfgfile += 'GENOME_FILE all_chr.fa\n'
-    cnfgfile += 'ELAND_MULTIPLE_INSTANCES 8\n'
-    genome_dir = 'GENOME_DIR /Volumes/Genomes/'
-    eland_genome = 'ELAND_GENOME /Volumes/Genomes/'
-    
-    try:                                                                                                                                              
-      rec = FlowCell.objects.get(flowcell_id=fcid)
-      
-      cnfgfile += '1:'+genome_dir+rec.lane_1_library.library_species.use_genome_build+'\n'
-      cnfgfile += '1:'+eland_genome+rec.lane_1_library.library_species.use_genome_build+'\n'
-
-      cnfgfile += '2:'+genome_dir+rec.lane_2_library.library_species.use_genome_build+'\n'
-      cnfgfile += '2:'+eland_genome+rec.lane_2_library.library_species.use_genome_build+'\n'
- 
-      cnfgfile += '3:'+genome_dir+rec.lane_3_library.library_species.use_genome_build+'\n'
-      cnfgfile += '3:'+eland_genome+rec.lane_3_library.library_species.use_genome_build+'\n'
-
-      cnfgfile += '4:'+genome_dir+rec.lane_4_library.library_species.use_genome_build+'\n'
-      cnfgfile += '4:'+eland_genome+rec.lane_4_library.library_species.use_genome_build+'\n'
-      
-      cnfgfile += '5:'+genome_dir+rec.lane_5_library.library_species.use_genome_build+'\n'
-      cnfgfile += '5:'+eland_genome+rec.lane_5_library.library_species.use_genome_build+'\n'
-
-      cnfgfile += '6:'+genome_dir+rec.lane_6_library.library_species.use_genome_build+'\n'
-      cnfgfile += '6:'+eland_genome+rec.lane_6_library.library_species.use_genome_build+'\n'
-
-      cnfgfile += '7:'+genome_dir+rec.lane_7_library.library_species.use_genome_build+'\n'
-      cnfgfile += '7:'+eland_genome+rec.lane_7_library.library_species.use_genome_build+'\n'
-
-      cnfgfile += '8:'+genome_dir+rec.lane_8_library.library_species.use_genome_build+'\n'
-      cnfgfile += '8:'+eland_genome+rec.lane_8_library.library_species.use_genome_build
-
-    except ObjectDoesNotExist:
-      cnfgfile = 'Entry not found for fcid  = '+fcid
-
-    return cnfgfile
-
-def getConfile(request):
-    granted = False
-    ClIP = request.META['REMOTE_ADDR']
-    if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
-
-    if not granted: return HttpResponse("access denied.")
-
-    fcid = 'none'
-    cnfgfile = ''
-    runfolder = 'unknown'
-    if request.has_key('fcid'):
-      fcid = request['fcid']
-      if request.has_key('runf'):
-        runfolder = request['runf']
-        try:
-          rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
-          cnfgfile = rec.config_params
-          #match_str = re.compile(r"READ_LENGTH.+$")
-          match_str = re.compile('^READ_LENGTH.+')
-          if not match_str.search(cnfgfile):
-            cnfgfile = generateConfile(fcid)
-            if match_str.search(cnfgfile):
-              rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
-              rec.config_params = cnfgfile
-              rec.save()
-            else:
-              cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile  
-            
-        except ObjectDoesNotExist:
-          cnfgfile = 'Entry not found for RunFolder = '+runfolder
-
-    return HttpResponse(cnfgfile)
-
-def getLaneLibs(request):
-    granted = False
-    ClIP = request.META['REMOTE_ADDR']
-    if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
-
-    if not granted: return HttpResponse("access denied.")
-
-    fcid = 'none'
-    outputfile = ''
-    if request.has_key('fcid'):
-      fcid = request['fcid']                                                                                                      
-      try:                                
-        rec = FlowCell.objects.get(flowcell_id=fcid)
-        #Ex: 071211
-        year = datetime.today().year.__str__()
-        year = replace(year,'20','')
-        month = datetime.today().month
-        if month < 10: month = "0"+month.__str__()
-        else: month = month.__str__() 
-        day = datetime.today().day
-        if day < 10: day = "0"+day.__str__()
-        else: day = day.__str__()
-        mydate = year+month+day
-        outputfile = '<?xml version="1.0" ?>'
-        outputfile += '\n<SolexaResult Date="'+mydate+'" Flowcell="'+fcid+'" Client="'+settings.ALLOWED_IPS[ClIP]+'">'
-        outputfile += '\n<Lane Index="1" Name="'+rec.lane_1_library.library_name+'" Library="'+rec.lane_1_library.library_id+'" Genome="'+rec.lane_1_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n<Lane Index="2" Name="'+rec.lane_2_library.library_name+'" Library="'+rec.lane_2_library.library_id+'" Genome="'+rec.lane_2_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n<Lane Index="3" Name="'+rec.lane_3_library.library_name+'" Library="'+rec.lane_3_library.library_id+'" Genome="'+rec.lane_3_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n<Lane Index="4" Name="'+rec.lane_4_library.library_name+'" Library="'+rec.lane_4_library.library_id+'" Genome="'+rec.lane_4_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n<Lane Index="5" Name="'+rec.lane_5_library.library_name+'" Library="'+rec.lane_5_library.library_id+'" Genome="'+rec.lane_5_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n<Lane Index="6" Name="'+rec.lane_6_library.library_name+'" Library="'+rec.lane_6_library.library_id+'" Genome="'+rec.lane_6_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n<Lane Index="7" Name="'+rec.lane_7_library.library_name+'" Library="'+rec.lane_7_library.library_id+'" Genome="'+rec.lane_7_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n<Lane Index="8" Name="'+rec.lane_8_library.library_name+'" Library="'+rec.lane_8_library.library_id+'" Genome="'+rec.lane_8_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
-        outputfile += '\n</SolexaResult>'
-      except ObjectDoesNotExist:
-        outputfile = 'Flowcell entry not found for: '+fcid
-    else: outputfile = 'Missing input: flowcell id'
-
-    return HttpResponse(outputfile)

diff --git a/gaworkflow/frontend/exp_track/models.py b/gaworkflow/frontend/exp_track/models.py
deleted file mode 100644 (file)
index 2096148..0000000
--- a/gaworkflow/frontend/exp_track/models.py
+++ /dev/null
@@ -1,144 +0,0 @@
-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')

diff --git a/gaworkflow/frontend/exp_track/views.py b/gaworkflow/frontend/exp_track/views.py
deleted file mode 100644 (file)
index 1d9aa8d..0000000
--- a/gaworkflow/frontend/exp_track/views.py
+++ /dev/null
@@ -1,22 +0,0 @@
-# Create your views here.
-#from django.template import Context, loader
-#shortcut to the above modules
-from django.shortcuts import render_to_response, get_object_or_404
-from gaworkflow.frontend.exp_track.models import DataRun
-from django.http import HttpResponse
-
-def index(request):
-    all_runs = DataRun.objects.all().order_by('-run_start_time')
-    #t = loader.get_template('exptrack/index.html')
-    #c = Context({
-    #    'data_run_list': all_runs,
-    #})
-    #return HttpResponse(t.render(c)) 
-    # shortcut to the above module usage
-    return render_to_response('exptrack/index.html',{'data_run_list': all_runs}) 
-    
-def detail(request, run_folder):
-    html_str = '<h2>Exp Track Details Page</h2>'
-    html_str += 'Run Folder: '+run_folder
-    r = get_object_or_404(DataRun,run_folder=run_folder)
-    return render_to_response('exptrack/detail.html',{'run_f': r})