htsworkflow/frontend/reports/libinfopar.py

   1 from django.conf 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.request, urllib.parse, urllib.error
   9 import urllib.request, urllib.error, urllib.parse
  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
  22   def __init__ (self, searchTerm):
  23     self.searchTerm= searchTerm
  24     self.currlibid = ''
  25     self.LanesCount, self.ReadsCount = 0, 0
  26     self.Msg = 'OK'
  27
  28   def startElement(self, name, attrs):
  29     try:
  30       if name == 'Library':
  31         self.currlibid = attrs.get('Name',"")
  32       elif name == 'Track' and self.searchTerm == self.currlibid:
  33         self.LanesCount += len(attrs.get('Lane',""))
  34         self.ReadsCount += int(attrs.get('Count',""))
  35       #else:
  36       #  self.Msg += ' | name = '+name+', currlibid = '+ self.currlibid
  37     except:
  38       self.Msg = 'failed parsing xml file'
  39     return
  40
  41   #def characters (self, ch):
  42     # return ..
  43
  44   #def endElement(self, name):
  45     # return ..
  46
  47
  48 ## 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
  49
  50 def getLibReads(libid):
  51   searchTerm= libid
  52   parser = make_parser()
  53   curHandler = LibInfoHandler(searchTerm)
  54   parser.setContentHandler(curHandler)
  55   reports_dir = os.path.split(__file__)[0]
  56   library_info = os.path.join(reports_dir, 'LibraryInfo.xml')
  57   parser.parse(open(library_info))
  58   arRes = []
  59   arRes.append(curHandler.LanesCount)
  60   arRes.append(curHandler.ReadsCount)
  61   arRes.append(curHandler.Msg)
  62
  63   return arRes
  64
  65 def getWebPage(url,params):
  66   pdata = urllib.parse.urlencode(params)
  67   req = urllib.request.Request(url,pdata)
  68   wpage = urllib.request.urlopen(req)
  69   restext = wpage.read()
  70   wpage.close()
  71   return restext
  72
  73 def refreshLibInfoFile(request):
  74  varStatus = 'getting conf file from exp trac server'
  75  url = settings.TASKS_PROJS_SERVER+'/LibraryInfo.xml'
  76  params = {}
  77  readw = getWebPage(url,params)
  78  # make sure file content starts as xml
  79  match_str = re.compile('^<\?xml.+')
  80  if match_str.search(readw): ##tempstr):
  81    # Rename current file with timestamp
  82    year = datetime.today().year.__str__()
  83    year = replace(year,'20','')
  84    month = datetime.today().month
  85    if month < 10: month = "0"+month.__str__()
  86    else: month = month.__str__()
  87    day = datetime.today().day
  88    if day < 10: day = "0"+day.__str__()
  89    else: day = day.__str__()
  90    mydate = year+month+day
  91    folder_loc = '/htsworkflow/htswfrontend/htswfrontend'  # DEV
  92    #folder_loc = '/Library/WebServer/gaworkflow/gaworkflow/frontend'  # PROD
  93    folder = folder_loc+'/htsw_reports/LibInfo/'
  94    os.rename(folder+'LibraryInfo.xml',folder+mydate+'_LibraryInfo.xml')
  95    # create file in curret folder
  96    file_path = os.path.join(folder,'LibraryInfo.xml')
  97    f = open(file_path, 'w')
  98    f.write(readw)
  99    f.close()
 100    varStatus = 'OK. LibraryInfo.xml refreshed at Web server.'
 101  else:
 102    varStatus = 'Failed reading valid LibraryInfo.xml server reply:\n'+readw
 103  return HttpResponse(varStatus)