htsworkflow/pipelines/test/test_retrive_config.py

   1 import os
   2 import re
   3
   4 try:
   5     import json
   6 except ImportError, e:
   7     import simplejson as json
   8
   9 from django.test import TestCase
  10
  11 from htsworkflow.frontend.auth import apidata
  12 from htsworkflow.pipelines.retrieve_config import format_gerald_config, getCombinedOptions
  13
  14 class RetrieveTestCases(TestCase):
  15     fixtures = ['test_flowcells.json']
  16
  17     def setUp(self):
  18         pass
  19
  20     def test_format_gerald(self):
  21         flowcell_request = self.client.get('/experiments/config/FC12150/json', apidata)
  22         self.failUnlessEqual(flowcell_request.status_code, 200)
  23
  24         print dir(flowcell_request)
  25         flowcell_info = json.loads(flowcell_request.content)
  26
  27         options = getCombinedOptions(['-f','FC12150','-g',os.getcwd()])
  28         genome_map = {u'Homo sapiens': '/tmp/hg18' }
  29
  30         config = format_gerald_config(options, flowcell_info, genome_map)
  31         config_lines = config.split('\n')
  32         lane3 = [ line for line in config_lines if re.search('Lane3', line) ]
  33         self.failUnlessEqual(len(lane3), 1)
  34         self.failUnlessEqual(lane3[0], '# Lane3: SL039 | Paired ends 99 GM12892')
  35         human = [ line for line in config_lines if re.search('hg18', line) ]
  36         self.failUnlessEqual(len(human), 1)
  37         self.failUnlessEqual(human[0], '345678:ELAND_GENOME /tmp/hg18')
  38         # we changed the api to force unknown genomes to be sequencing
  39         sequencing = [ line for line in config_lines if re.search('sequence_pair', line) ]
  40         self.failUnlessEqual(len(sequencing), 2)
  41
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