This is a partial merge of the stanford branch with the caltech branch of

the web application, it doesn't work correctly yet, the libraries admin page
is broken, and lacks the ability to browe the 'made_for' column.

This is based on a merge that started a few month ago, but I hadn't finished
the merge, I'll need to check for more updates from their branch soon.

During the process I decided it would be a good idea to update to django 1.0
which is going to make things even more unstable, so I thought I should
check this work in progess in before continuing.

diff --git a/htsworkflow/frontend/analysis/an_urls.py b/htsworkflow/frontend/analysis/an_urls.py
deleted file mode 100644 (file)
index 57fa33e..0000000
--- a/htsworkflow/frontend/analysis/an_urls.py
+++ /dev/null
@@ -1,6 +0,0 @@
-from django.conf.urls.defaults import *
-
-urlpatterns = patterns('',                                               
-    (r'^updStatus$', 'htswfrontend.analys_track.main.updStatus'),
-    (r'^getProjects/$', 'htswfrontend.analys_track.main.getProjects'),
-)

diff --git a/htsworkflow/frontend/analysis/main.py b/htsworkflow/frontend/analysis/main.py
index 015a69c823503435c3eb2dfd98a3fbff1937edc2..511390b6d8bc9ae5fdc6ebd7a72afb98ce338287 100644 (file)
--- a/htsworkflow/frontend/analysis/main.py
+++ b/htsworkflow/frontend/analysis/main.py
@@ -3,8 +3,8 @@ from django.http import HttpResponse
 from datetime import datetime
 from string import *
 import re
-from htswfrontend import settings
-from htswfrontend.analys_track.models import Task, Project
+from htsworkflow.frontend import settings
+from htsworkflow.frontend.analysis.models import Task, Project
 from django.core.exceptions import ObjectDoesNotExist
 
 def updStatus(request):

diff --git a/htsworkflow/frontend/analysis/models.py b/htsworkflow/frontend/analysis/models.py
index 301be2721c891112438156042c6eee48b7782593..4b1c72d1d0b1faa9af538a622f0e69ab3dafc3be 100644 (file)
--- a/htsworkflow/frontend/analysis/models.py
+++ b/htsworkflow/frontend/analysis/models.py
@@ -1,6 +1,6 @@
 from django.db import models
 from datetime import datetime
-from htswfrontend.fctracker.models import Library 
+from htsworkflow.frontend.samples.models import Library 
 from string import *
 
 class Task(models.Model):
@@ -20,7 +20,7 @@ class Task(models.Model):
   ## 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())
+  submitted_on = models.DateTimeField(default=datetime.now())
   run_note = models.CharField(max_length=500,blank=True,null=True)
   
   def __str__(self):

diff --git a/htsworkflow/frontend/analysis/urls.py b/htsworkflow/frontend/analysis/urls.py
new file mode 100644 (file)
index 0000000..b1be3d2
--- /dev/null
+++ b/htsworkflow/frontend/analysis/urls.py
@@ -0,0 +1,6 @@
+from django.conf.urls.defaults import *
+
+urlpatterns = patterns('',
+    (r'^updStatus$', 'htsworkflow.frontend.analysis.main.updStatus'),
+    (r'^getProjects/$', 'htsworkflow.frontend.analysis.main.getProjects'),
+)

diff --git a/htsworkflow/frontend/eland_config/views.py b/htsworkflow/frontend/eland_config/views.py
index 25edea96fcaf893f4abdb8029c3ad171523daab0..d4be4ea2e082228e32ff8b7969d585fa1e7db0b8 100644 (file)
--- a/htsworkflow/frontend/eland_config/views.py
+++ b/htsworkflow/frontend/eland_config/views.py
@@ -4,7 +4,7 @@ from django.core.exceptions import ObjectDoesNotExist
 
 from htsworkflow.frontend.eland_config import forms
 from htsworkflow.frontend import settings
-from htsworkflow.frontend.fctracker import models
+from htsworkflow.frontend.samples import models
 
 import os
 import glob

diff --git a/htsworkflow/frontend/experiments/et_urls.py b/htsworkflow/frontend/experiments/et_urls.py
deleted file mode 100755 (executable)
index 7ad709d..0000000
--- a/htsworkflow/frontend/experiments/et_urls.py
+++ /dev/null
@@ -1,12 +0,0 @@
-from django.conf.urls.defaults import *
-
-urlpatterns = patterns('',
-                                                                                                      
-    (r'^$', 'htswfrontend.exp_track.views.index'),
-    (r'^liblist$', 'htswfrontend.exp_track.views.test_Libs'),
-    #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.exp_track.views.detail'),
-    (r'^(?P<fcid>.+)/$', 'htswfrontend.exp_track.views.makeFCSheet'),
-    (r'^updStatus$', 'htswfrontend.exp_track.exptrack.updStatus'),
-    (r'^getConfile$', 'htswfrontend.exp_track.exptrack.getConfile'),
-    (r'^getLanesNames$', 'htswfrontend.exp_track.exptrack.getLaneLibs')   
-)

diff --git a/htsworkflow/frontend/experiments/experiments.py b/htsworkflow/frontend/experiments/experiments.py
new file mode 100755 (executable)
index 0000000..d11cda7
--- /dev/null
+++ b/htsworkflow/frontend/experiments/experiments.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 htsworkflow.frontend import settings
+from htsworkflow.frontend.experiments.models import FlowCell, DataRun
+from htsworkflow.frontend.samples.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(request,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. IP: "+ClIP)
+
+    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(request,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/htsworkflow/frontend/experiments/exptrack.py b/htsworkflow/frontend/experiments/exptrack.py
deleted file mode 100755 (executable)
index 6486b5c..0000000
--- a/htsworkflow/frontend/experiments/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 htswfrontend import settings
-from htswfrontend.exp_track.models import FlowCell, DataRun
-from htswfrontend.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(request,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. IP: "+ClIP)
-
-    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(request,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/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 08397e6f9267e2717b1dd72907819d9c52bb944e..4e7e696797a1f6afb6a93a18ee315dff2d46d868 100755 (executable)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -1,9 +1,9 @@
 from django.db import models
-from htswfrontend.fctracker.models import *
+from htsworkflow.frontend.samples.models import *
 
 class FlowCell(models.Model):
   
-  flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
+  flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
   run_date = models.DateTimeField(core=True)
   advanced_run = models.BooleanField(default=False)
   read_length = models.IntegerField(default=32) #Stanford is currenlty 25

diff --git a/htsworkflow/frontend/experiments/urls.py b/htsworkflow/frontend/experiments/urls.py
new file mode 100755 (executable)
index 0000000..62ade81
--- /dev/null
+++ b/htsworkflow/frontend/experiments/urls.py
@@ -0,0 +1,12 @@
+from django.conf.urls.defaults import *
+
+urlpatterns = patterns('',
+                                                                                                      
+    (r'^$', 'htsworkflow.frontend.experiments.views.index'),
+    (r'^liblist$', 'htsworkflow.frontend.experiments.views.test_Libs'),
+    #(r'^(?P<run_folder>.+)/$', 'gaworkflow.frontend.experiments.views.detail'),
+    (r'^(?P<fcid>.+)/$', 'htsworkflow.frontend.experiments.views.makeFCSheet'),
+    (r'^updStatus$', 'htsworkflow.frontend.experiments.experiments.updStatus'),
+    (r'^getConfile$', 'htsworkflow.frontend.experiments.experiments.getConfile'),
+    (r'^getLanesNames$', 'htsworkflow.frontend.experiments.experiments.getLaneLibs')   
+)

diff --git a/htsworkflow/frontend/experiments/views.py b/htsworkflow/frontend/experiments/views.py
index 38880166cd00fe644624c4d382608f288ec74a9d..11d09cfe23a8ce068d324bb7ef4bab48fe34987b 100755 (executable)
--- a/htsworkflow/frontend/experiments/views.py
+++ b/htsworkflow/frontend/experiments/views.py
@@ -3,7 +3,7 @@
 #shortcut to the above modules
 from django.shortcuts import render_to_response, get_object_or_404
 #from htswfrontend.fctracker.models import *
-from htswfrontend.exp_track.models import *
+from htsworkflow.frontend.experiments.models import *
 from django.http import HttpResponse
 from django.core.exceptions import ObjectDoesNotExist
 

diff --git a/htsworkflow/frontend/reports/ht_urls.py b/htsworkflow/frontend/reports/ht_urls.py
deleted file mode 100644 (file)
index 39871b8..0000000
--- a/htsworkflow/frontend/reports/ht_urls.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from django.conf.urls.defaults import *
-
-urlpatterns = patterns('',                                               
-    (r'^updLibInfo$', 'htswfrontend.htsw_reports.libinfopar.refreshLibInfoFile'),
-)

diff --git a/htsworkflow/frontend/reports/models.py b/htsworkflow/frontend/reports/models.py
index 8554688d90dbef2d38f1e6d0e4a9803909d526be..ddcdc535d488a04b05359ee5c43ff5320a7a2d31 100644 (file)
--- a/htsworkflow/frontend/reports/models.py
+++ b/htsworkflow/frontend/reports/models.py
@@ -2,11 +2,11 @@ from django.db import models
 from django.db.models import Q
 from django.core.exceptions import ObjectDoesNotExist
 from datetime import datetime
-from htswfrontend.fctracker.models import * 
-from htswfrontend.analys_track.models import *
-from htswfrontend.exp_track.models import *
+from htsworkflow.frontend.samples.models import * 
+from htsworkflow.frontend.analysis.models import *
+from htsworkflow.frontend.experiments.models import *
 from string import *
-from htswfrontend.htsw_reports.utils import *
+from htsworkflow.frontend.reports.utils import *
 import re
 ##from p1 import LibInfo
 from libinfopar import *
@@ -218,8 +218,8 @@ class ProgressReport(models.Model):
     return 'coming up ..'
 
   QPCR = models.CharField(max_length=500,blank=True,null=True)    
-  submitted_to_DCC = models.DateTimeField(core=True,blank=True,null=True)
-  submitted_to_NCBI = models.DateTimeField(core=True,blank=True,null=True)
+  submitted_to_DCC = models.DateTimeField(blank=True,null=True)
+  submitted_to_NCBI = models.DateTimeField(blank=True,null=True)
   note_about_DCC =  models.TextField(blank=True)
   note_about_NCBI = models.TextField(blank=True)
   

diff --git a/htsworkflow/frontend/reports/urls.py b/htsworkflow/frontend/reports/urls.py
new file mode 100644 (file)
index 0000000..9b0acf9
--- /dev/null
+++ b/htsworkflow/frontend/reports/urls.py
@@ -0,0 +1,5 @@
+from django.conf.urls.defaults import *
+
+urlpatterns = patterns('',                                               
+    (r'^updLibInfo$', 'htsworkflow.reports.libinfopar.refreshLibInfoFile'),
+)

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index c4e1e3ce97475acf280edb5e640bef3f368aa129..b393028c62cf038d03739c98ebdfd62aee7929c9 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -1,7 +1,7 @@
 from django.db import models
 from django.contrib.auth.models import User
 from htsworkflow.frontend import settings
-from htsworkflow.reports.libinfopar import *
+#from htsworkflow.reports.libinfopar import *
 
 # Create your models here.
 
@@ -63,7 +63,7 @@ class Condition(models.Model):
 
 class Species(models.Model):
   
-  scientific_name = models.CharField(max_length=256, unique=False, db_index=True, core=True)
+  scientific_name = models.CharField(max_length=256, unique=False, db_index=True)
   common_name = models.CharField(max_length=256, blank=True)
   use_genome_build = models.CharField(max_length=100, blank=False, null=False)
 
@@ -82,7 +82,7 @@ class Species(models.Model):
       )
 
 class Affiliation(models.Model):
-  name = models.CharField(max_length=256, db_index=True, core=True,verbose_name='Group Name')
+  name = models.CharField(max_length=256, db_index=True, verbose_name='Group Name')
   contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Contact Name')  
   email = models.EmailField(null=True,blank=True)
   
@@ -106,12 +106,12 @@ class Affiliation(models.Model):
 
 class Library(models.Model):
   
-  library_id = models.CharField(max_length=30, primary_key=True, db_index=True, core=True)
-  library_name = models.CharField(max_length=100, unique=True, core=True)
-  library_species = models.ForeignKey(Species, core=True)
-  cell_line = models.ForeignKey(Cellline,core=True)
-  condition = models.ForeignKey(Condition,core=True)
-  antibody = models.ForeignKey(Antibody,blank=True,null=True,core=True)
+  library_id = models.CharField(max_length=30, primary_key=True, db_index=True)
+  library_name = models.CharField(max_length=100, unique=True)
+  library_species = models.ForeignKey(Species)
+  cell_line = models.ForeignKey(Cellline)
+  condition = models.ForeignKey(Condition)
+  antibody = models.ForeignKey(Antibody,blank=True,null=True)
   # New field Aug/25/08. SQL: alter table fctracker_library add column "lib_affiliation" varchar(256)  NULL;
   affiliations = models.ManyToManyField(Affiliation,related_name='library_affiliations',null=True,filter_interface=models.HORIZONTAL)
   # New field Aug/19/08
@@ -131,7 +131,7 @@ class Library(models.Model):
                                      default='RNA-seq')
   
   creation_date = models.DateField(blank=True, null=True)
-  made_for = models.ForeignKey(User)
+  made_for = models.ForeignKey(User, edit_inline=models.TABULAR)
   made_by = models.CharField(max_length=50, blank=True, default="Lorian")
   
   PROTOCOL_END_POINTS = (
@@ -207,13 +207,14 @@ class Library(models.Model):
     save_on_top = True
     ##search_fields = ['library_id','library_name','affiliations__name','affiliations__contact','made_by','made_for','antibody__antigene','antibody__catalog','antibody__antibodies','antibody__source','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
     search_fields = ['library_id','library_name','cell_line__cellline_name','library_species__scientific_name','library_species__common_name','library_species__use_genome_build']
-    list_display = ('affiliation','library_id','aligned_reads','library_name','experiment_type','org','replicate','antibody_name','cell_line','made_by','creation_date')
-    list_display_links = ('library_id', 'library_name')
+    #list_display = ('affiliation','library_id','aligned_reads','library_name','experiment_type','org','replicate','antibody_name','cell_line','made_by','creation_date')
+    list_display = ('library_id','library_name','experiment_type','replicate','antibody_name','made_by','creation_date')
+    #list_display_links = ('library_id', 'library_name')
 
-    list_filter = ('experiment_type','affiliations','library_species','made_for', 'made_by','replicate')
+    list_filter = ('experiment_type','affiliations','library_species', 'made_by','replicate')
     fields = (
         (None, {
-            'fields': (('replicate','library_id','library_name'),('library_species'),('experiment_type'),('cell_line','condition','antibody'),)
+        'fields': (('replicate','library_id','library_name'),('library_species'),('experiment_type'),('cell_line','condition','antibody'),)
         }),
         ('Creation Information:', {
             'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('undiluted_concentration', 'library_size'), 'notes',)

diff --git a/htsworkflow/frontend/settings.py b/htsworkflow/frontend/settings.py
index ec400418a4e4fcecaba21dd07014d1fc5e6d18ba..32272242a3548c5b943754f902e1241ccef2f737 100644 (file)
--- a/htsworkflow/frontend/settings.py
+++ b/htsworkflow/frontend/settings.py
@@ -143,11 +143,11 @@ INSTALLED_APPS = (
     'django.contrib.sessions',
     'django.contrib.sites',
     'htsworkflow.frontend.eland_config',
-    'htsworkflow.frontend.fctracker',
+    'htsworkflow.frontend.samples',
     # modules from htsworkflow branch
-    #'htswfrontend.exp_track',
-    #'htswfrontend.analys_track', 
-    #'htswfrontend.htsw_reports',
+    'htsworkflow.frontend.experiments',
+    'htsworkflow.frontend.analysis', 
+    'htsworkflow.frontend.reports',
     'django.contrib.databrowse',
 )
 

diff --git a/htsworkflow/frontend/urls.py b/htsworkflow/frontend/urls.py
index e06d92d65059819074b9cb5f3f4d0ae0b859b008..51bf8c41bab1cec970e7d735de87ae4a35610391 100644 (file)
--- a/htsworkflow/frontend/urls.py
+++ b/htsworkflow/frontend/urls.py
@@ -2,9 +2,9 @@ from django.conf.urls.defaults import *
 
 # Databrowser:
 from django.contrib import databrowse
-from fctracker.models import Library, FlowCell
+from htsworkflow.frontend.samples.models import Library
 databrowse.site.register(Library)
-databrowse.site.register(FlowCell)
+#databrowse.site.register(FlowCell)
 
 urlpatterns = patterns('',
     # Base:
@@ -12,9 +12,12 @@ urlpatterns = patterns('',
     # Admin:
      (r'^admin/', include('django.contrib.admin.urls')),
     # ExpTrack:
-     (r'^experiments/', include('htswfrontend.experiments.et_urls')),
+     (r'^experiments/', include('htsworkflow.frontend.experiments.urls')),
     # AnalysTrack:
-     (r'^analysis/', include('htswfrontend.analysis.an_urls')),
+     (r'^analysis/', include('htsworkflow.frontend.analysis.urls')),
     # Report Views:
     # (r'^reports/', include('gaworkflow.frontend....urls')),
+    
+    # databrowser
+    (r'^databrowse/(.*)', databrowse.site.root)
 )