From 41656ba80c64e0278cb29f924f8c00adf3317902 Mon Sep 17 00:00:00 2001
From: Rami Rauch <rrauch@stanford.edu>
Date: Wed, 8 Jul 2009 22:44:45 +0000
Subject: [PATCH]

---
 .../htswfrontend/exp_track/exptrack.py        | 60 ++++++++++++++-----
 1 file changed, 44 insertions(+), 16 deletions(-)

diff --git a/htswfrontend/htswfrontend/exp_track/exptrack.py b/htswfrontend/htswfrontend/exp_track/exptrack.py
index 2105d45..62e6917 100755
--- a/htswfrontend/htswfrontend/exp_track/exptrack.py
+++ b/htswfrontend/htswfrontend/exp_track/exptrack.py
@@ -60,6 +60,7 @@ def updStatus(request):
       else :
         if UpdatedStatus == '1':
           rec.run_note = "Started ("+mytimestamp+")"
+          rec.run_start_time = datetime.now()
 
       rec.save()
       output = "Hello "+settings.ALLOWED_IPS[ClIP]+". Updated to:'"+DataRun.RUN_STATUS_CHOICES[int(UpdatedStatus)][1].__str__()+"'"
@@ -75,22 +76,18 @@ def updStatus(request):
     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_extended\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 = 'READ_LENGTH 36\n'  # 25
+      if rec.is_paired_end:
+        cnfgfile += 'ANALYSIS eland_pair\n'
+      else:
+        cnfgfile += 'ANALYSIS eland_extended\n'
+      cnfgfile += 'GENOME_FILE all_chr.fa\n'
+      cnfgfile += 'ELAND_MULTIPLE_INSTANCES 8\n'
+      genome_dir = 'GENOME_DIR /mnt/encodedisk6/genomes/' # /Volumes/Genomes/
+      eland_genome = 'ELAND_GENOME /mnt/encodedisk6/genomes/'  # /Volumes/Genomes/
+
       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'
 
@@ -120,7 +117,7 @@ def generateConfile(request,fcid):
 
     return cnfgfile
 
-def getConfile(request):
+def OLD_getConfile(request):
     granted = False
     ClIP = request.META['REMOTE_ADDR']
     if (settings.ALLOWED_IPS.has_key(ClIP)):  granted = True
@@ -137,7 +134,6 @@ def getConfile(request):
         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)
@@ -153,6 +149,38 @@ def getConfile(request):
 
     return HttpResponse(cnfgfile)
 
+
+def getConfParams(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'
+    paramstext = ''
+    
+    if request.has_key('fcid'):
+      fcid = request['fcid']
+      try:
+        rec = FlowCell.objects.get(flowcell_id=fcid)
+        paramstext =  'Lane:'+  rec.lane_1_library.library_id +':'+rec.lane_1_library.library_species.use_genome_build
+        paramstext += '\nLane:'+rec.lane_2_library.library_id +':'+rec.lane_2_library.library_species.use_genome_build
+        paramstext += '\nLane:'+rec.lane_3_library.library_id +':'+rec.lane_3_library.library_species.use_genome_build
+        paramstext += '\nLane:'+rec.lane_4_library.library_id +':'+rec.lane_4_library.library_species.use_genome_build
+        paramstext += '\nLane:'+rec.lane_5_library.library_id +':'+rec.lane_5_library.library_species.use_genome_build
+        paramstext += '\nLane:'+rec.lane_6_library.library_id +':'+rec.lane_6_library.library_species.use_genome_build
+        paramstext += '\nLane:'+rec.lane_7_library.library_id +':'+rec.lane_7_library.library_species.use_genome_build
+        paramstext += '\nLane:'+rec.lane_8_library.library_id +':'+rec.lane_8_library.library_species.use_genome_build
+        if rec.is_paired_end: paramstext += '\nIsPairedEnd::1'
+        else: paramstext += '\nIsPairedEnd::0'
+
+      except ObjectDoesNotExist:
+        paramstext = 'Flowcell entry not found for:  '+fcid
+    else: 
+      paramstext = 'missing input - flowcell id'
+
+    return HttpResponse(paramstext)
+
+
 def getLaneLibs(request):
     granted = False
     ClIP = request.META['REMOTE_ADDR']
-- 
2.30.2