htswfrontend/htswfrontend/htsw_reports/libinfopar.py

   1 from htswfrontend import settings
   2 from django.http import HttpResponse
   3 from datetime import datetime
   4 from string import *
   5 import re
   6 from xml.sax import make_parser
   7 from xml.sax.handler import ContentHandler
   8 import urllib
   9 import urllib2
  10 import os
  11
  12 '''
  13 Example library node from LibraryInfo.xml:
  14 <Library Name="SL14">
  15 <Track Flowcell="FC10135" Lane="4" Filename="071005_FC10135_s4_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2438679" Complexity="4.51989e-06"/>
  16 <Track Flowcell="FC11977" Lane="6" Filename="070928_FC11977_s6_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2007880" Complexity="0"/>
  17 <Track Flowcell="FC13593" Lane="5" Filename="071002_FC13593_s5_FoxP2_polyclonal_pfsk1_SL14.align_25.hg18.txt" Count=" 2533720" Complexity="1.97771e-06"/>
  18 </Library>
  19 '''
  20 class LibInfoHandler(ContentHandler):
  21   def __init__ (self, searchTerm):
  22     self.searchTerm= searchTerm
  23     self.currlibid = ''
  24     self.LanesCount, self.ReadsCount = 0, 0
  25     self.Msg = 'OK'
  26
  27   def startElement(self, name, attrs):
  28     try:
  29       if name == 'Library':
  30         self.currlibid = attrs.get('Name',"")
  31       elif name == 'Track' and self.searchTerm == self.currlibid:
  32         self.LanesCount += len(attrs.get('Lane',""))
  33         self.ReadsCount += int(attrs.get('Count',""))
  34     except:
  35       self.Msg = 'failed parsing xml file'
  36     return
  37
  38   #def characters (self, ch):
  39     # return ..
  40
  41   #def endElement(self, name):
  42     # return ..
  43
  44 class LibInfoHandlerByFlowCell(ContentHandler):
  45   def __init__ (self, searchTerm):
  46     self.searchTerm = searchTerm
  47     self.LanesCount, self.ReadsCount, self.LaneReadsCount = 0, 0, [0,0,0,0,0,0,0,0]
  48     self.Msg = 'OK'
  49
  50   def startElement(self, name, attrs):
  51     try:
  52       if name == 'Track' and attrs.get('Flowcell',"") == self.searchTerm:
  53         self.LanesCount += len(attrs.get('Lane',""))
  54         self.ReadsCount += int(attrs.get('Count',""))
  55         # this loop is to separate between multiple lanes in one Lane attrbute of a Track tag
  56         for l in attrs.get('Lane',""): self.LaneReadsCount[int(l)-1] += int(attrs.get('Count',""))
  57     except:
  58       self.Msg = 'failed parsing xml file'
  59     return
  60
  61
  62 ## TO DO: Change this to read the LibraryInfo.xml only ONCE per ReoprtRequest (do it in the models.py). + Read it directly from the analysis_server
  63
  64 def getLibReads(search_term,search_by):
  65   searchTerm= search_term
  66   parser = make_parser()
  67
  68   if search_by == 'ByLib':
  69     curHandler = LibInfoHandler(searchTerm)
  70   elif search_by == 'ByFC':
  71     curHandler = LibInfoHandlerByFlowCell(searchTerm)
  72
  73   parser.setContentHandler(curHandler)
  74
  75   folder_loc = '/htsworkflow/htswfrontend/htswfrontend'  # DEV
  76   #folder_loc = '/Library/WebServer/gaworkflow/gaworkflow/frontend'  # PROD
  77   parser.parse(open(folder_loc+'/htsw_reports/LibInfo/LibraryInfo.xml'))
  78   arRes = []
  79   arRes.append(curHandler.LanesCount)
  80   arRes.append(curHandler.ReadsCount)
  81
  82   if search_by == 'ByFC':  arRes.append(curHandler.LaneReadsCount)
  83
  84   arRes.append(curHandler.Msg)
  85
  86   return arRes
  87
  88 def getWebPage(url,params):
  89   pdata = urllib.urlencode(params)
  90   req = urllib2.Request(url,pdata)
  91   wpage = urllib2.urlopen(req)
  92   restext = wpage.read()
  93   wpage.close()
  94   return restext
  95
  96 def refreshLibInfoFile(request):
  97  varStatus = 'getting conf file from exp trac server'
  98  url = settings.TASKS_PROJS_SERVER+'/LibraryInfo.xml'
  99  params = {}
 100  readw = getWebPage(url,params)
 101  # make sure file content starts as xml
 102  match_str = re.compile('^<\?xml.+')
 103  if match_str.search(readw): ##tempstr):
 104    # Rename current file with timestamp
 105    year = datetime.today().year.__str__()
 106    year = replace(year,'20','')
 107    month = datetime.today().month
 108    if month < 10: month = "0"+month.__str__()
 109    else: month = month.__str__()
 110    day = datetime.today().day
 111    if day < 10: day = "0"+day.__str__()
 112    else: day = day.__str__()
 113    mydate = year+month+day
 114    folder_loc = '/htsworkflow/htswfrontend/htswfrontend'  # DEV
 115    #folder_loc = '/Library/WebServer/gaworkflow/gaworkflow/frontend'  # PROD
 116    folder = folder_loc+'/htsw_reports/LibInfo/'
 117    os.rename(folder+'LibraryInfo.xml',folder+mydate+'_LibraryInfo.xml')
 118    # create file in curret folder
 119    file_path = os.path.join(folder,'LibraryInfo.xml')
 120    f = open(file_path, 'w')
 121    f.write(readw)
 122    f.close()
 123    varStatus = 'OK. LibraryInfo.xml refreshed at Web server.'
 124  else:
 125    varStatus = 'Failed reading valid LibraryInfo.xml server reply:\n'+readw
 126  return HttpResponse(varStatus)