here's the exp_tack again; hopefully updated this time

diff --git a/gaworkflow/frontend/exp_track/__init__.py b/gaworkflow/frontend/exp_track/__init__.py
new file mode 100755 (executable)
index 0000000..e69de29

diff --git a/gaworkflow/frontend/exp_track/et_urls.py b/gaworkflow/frontend/exp_track/et_urls.py
new file mode 100755 (executable)
index 0000000..6acea12
--- /dev/null
+++ b/gaworkflow/frontend/exp_track/et_urls.py
@@ -0,0 +1,10 @@
+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
new file mode 100755 (executable)
index 0000000..8cd5d6d
--- /dev/null
+++ b/gaworkflow/frontend/exp_track/exptrack.py
@@ -0,0 +1,194 @@
+# 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
new file mode 100755 (executable)
index 0000000..2096148
--- /dev/null
+++ b/gaworkflow/frontend/exp_track/models.py
@@ -0,0 +1,144 @@
+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
new file mode 100755 (executable)
index 0000000..1d9aa8d
--- /dev/null
+++ b/gaworkflow/frontend/exp_track/views.py
@@ -0,0 +1,22 @@
+# 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})