import re
+from BeautifulSoup import BeautifulSoup
try:
import json
except ImportError, e:
import simplejson as json
+import os
+import shutil
import sys
+import tempfile
+from django.conf import settings
from django.core import mail
+from django.core.exceptions import ObjectDoesNotExist
from django.test import TestCase
from htsworkflow.frontend.experiments import models
from htsworkflow.frontend.experiments import experiments
from htsworkflow.frontend.auth import apidata
+from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
+
+LANE_SET = range(1,9)
+
class ExperimentsTestCases(TestCase):
fixtures = ['test_flowcells.json']
def setUp(self):
- pass
+ self.tempdir = tempfile.mkdtemp(prefix='htsw-test-experiments-')
+ settings.RESULT_HOME_DIR = self.tempdir
+
+ self.fc1_id = 'FC12150'
+ self.fc1_root = os.path.join(self.tempdir, self.fc1_id)
+ os.mkdir(self.fc1_root)
+ self.fc1_dir = os.path.join(self.fc1_root, 'C1-37')
+ os.mkdir(self.fc1_dir)
+ runxml = 'run_FC12150_2007-09-27.xml'
+ shutil.copy(os.path.join(TESTDATA_DIR, runxml),
+ os.path.join(self.fc1_dir, runxml))
+ for i in range(1,9):
+ shutil.copy(
+ os.path.join(TESTDATA_DIR,
+ 'woldlab_070829_USI-EAS44_0017_FC11055_1.srf'),
+ os.path.join(self.fc1_dir,
+ 'woldlab_070829_SERIAL_FC12150_%d.srf' %(i,))
+ )
+
+ self.fc2_dir = os.path.join(self.tempdir, '42JTNAAXX')
+ os.mkdir(self.fc2_dir)
+ os.mkdir(os.path.join(self.fc2_dir, 'C1-25'))
+ os.mkdir(os.path.join(self.fc2_dir, 'C1-37'))
+ os.mkdir(os.path.join(self.fc2_dir, 'C1-37', 'Plots'))
+
+ def tearDown(self):
+ shutil.rmtree(self.tempdir)
def test_flowcell_information(self):
"""
Check the code that packs the django objects into simple types.
"""
- for fc_id in [u'303TUAAXX', u"42JTNAAXX", "42JU1AAXX"]:
+ for fc_id in [u'FC12150', u"42JTNAAXX", "42JU1AAXX"]:
fc_dict = experiments.flowcell_information(fc_id)
fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
self.failUnlessEqual(fc_dict['flowcell_id'], fc_id)
self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
- self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
- self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
+ self.failUnlessEqual(lane_dict['library_id'], lane.library.id)
+ self.failUnlessAlmostEqual(float(lane_dict['pM']), float(lane.pM))
self.failUnlessEqual(lane_dict['library_species'],
lane.library.library_species.scientific_name)
self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
- self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
- self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
+ self.failUnlessEqual(lane_dict['library_id'], lane.library.id)
+ self.failUnlessAlmostEqual(float(lane_dict['pM']), float(lane.pM))
self.failUnlessEqual(lane_dict['library_species'],
lane.library.library_species.scientific_name)
"""
Require logging in to retrieve meta data
"""
- response = self.client.get(u'/experiments/config/303TUAAXX/json')
+ response = self.client.get(u'/experiments/config/FC12150/json')
self.failUnlessEqual(response.status_code, 403)
def test_library_id(self):
"""
Library IDs should be flexible, so make sure we can retrive a non-numeric ID
"""
- response = self.client.get('/experiments/config/303TUAAXX/json', apidata)
+ response = self.client.get('/experiments/config/FC12150/json', apidata)
self.failUnlessEqual(response.status_code, 200)
flowcell = json.loads(response.content)
self.failUnlessEqual(library_sl039['library_id'], 'SL039')
+ def test_raw_id_field(self):
+ """
+ Test ticket:147
+
+ Library's have IDs, libraries also have primary keys,
+ we eventually had enough libraries that the drop down combo box was too
+ hard to filter through, unfortnately we want a field that uses our library
+ id and not the internal primary key, and raw_id_field uses primary keys.
+
+ This tests to make sure that the value entered in the raw library id field matches
+ the library id looked up.
+ """
+ expected_ids = [u'10981',u'11016',u'SL039',u'11060',
+ u'11061',u'11062',u'11063',u'11064']
+ self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
+ response = self.client.get('/admin/experiments/flowcell/153/')
+ soup = BeautifulSoup(response.content)
+ for i in range(0,8):
+ input_field = soup.find(id='id_lane_set-%d-library' % (i,))
+ library_field = input_field.findNext('strong')
+ library_id, library_name = library_field.string.split(':')
+ # strip leading '#' sign from name
+ library_id = library_id[1:]
+ self.failUnlessEqual(library_id, expected_ids[i])
+ self.failUnlessEqual(input_field['value'], library_id)
+
+ def test_lanes_for(self):
+ """
+ Check the code that packs the django objects into simple types.
+ """
+ user = 'test'
+ lanes = experiments.lanes_for(user)
+ self.failUnlessEqual(len(lanes), 5)
+
+ response = self.client.get('/experiments/lanes_for/%s/json' % (user,), apidata)
+ lanes_json = json.loads(response.content)
+ self.failUnlessEqual(len(lanes), len(lanes_json))
+ for i in range(len(lanes)):
+ self.failUnlessEqual(lanes[i]['comment'], lanes_json[i]['comment'])
+ self.failUnlessEqual(lanes[i]['lane_number'], lanes_json[i]['lane_number'])
+ self.failUnlessEqual(lanes[i]['flowcell'], lanes_json[i]['flowcell'])
+ self.failUnlessEqual(lanes[i]['run_date'], lanes_json[i]['run_date'])
+
+ def test_lanes_for_no_lanes(self):
+ """
+ Do we get something meaningful back when the user isn't attached to anything?
+ """
+ user = 'supertest'
+ lanes = experiments.lanes_for(user)
+ self.failUnlessEqual(len(lanes), 0)
+
+ response = self.client.get('/experiments/lanes_for/%s/json' % (user,), apidata)
+ lanes_json = json.loads(response.content)
+
+ def test_lanes_for_no_user(self):
+ """
+ Do we get something meaningful back when its the wrong user
+ """
+ user = 'not a real user'
+ self.failUnlessRaises(ObjectDoesNotExist, experiments.lanes_for, user)
+
+ response = self.client.get('/experiments/lanes_for/%s/json' % (user,), apidata)
+ self.failUnlessEqual(response.status_code, 404)
+
+
+ def test_raw_data_dir(self):
+ """Raw data path generator check"""
+ flowcell_id = self.fc1_id
+ raw_dir = os.path.join(settings.RESULT_HOME_DIR, flowcell_id)
+
+ fc = models.FlowCell.objects.get(flowcell_id=flowcell_id)
+ self.failUnlessEqual(fc.get_raw_data_directory(), raw_dir)
+
+ fc.flowcell_id = flowcell_id + " (failed)"
+ self.failUnlessEqual(fc.get_raw_data_directory(), raw_dir)
+
+
+ def test_data_run_import(self):
+ srf_file_type = models.FileType.objects.get(name='SRF')
+ runxml_file_type = models.FileType.objects.get(name='run_xml')
+ flowcell_id = self.fc1_id
+ flowcell = models.FlowCell.objects.get(flowcell_id=flowcell_id)
+ flowcell.update_data_runs()
+ self.failUnlessEqual(len(flowcell.datarun_set.all()), 1)
+
+ run = flowcell.datarun_set.all()[0]
+ result_files = run.datafile_set.all()
+ result_dict = dict(((rf.relative_pathname, rf) for rf in result_files))
+
+ srf4 = result_dict['FC12150/C1-37/woldlab_070829_SERIAL_FC12150_4.srf']
+ self.failUnlessEqual(srf4.file_type, srf_file_type)
+ self.failUnlessEqual(srf4.library_id, '11060')
+ self.failUnlessEqual(srf4.data_run.flowcell.flowcell_id, 'FC12150')
+ self.failUnlessEqual(
+ srf4.data_run.flowcell.lane_set.get(lane_number=4).library_id,
+ '11060')
+ self.failUnlessEqual(
+ srf4.pathname,
+ os.path.join(settings.RESULT_HOME_DIR, srf4.relative_pathname))
+
+ lane_files = run.lane_files()
+ self.failUnlessEqual(lane_files[4]['srf'], srf4)
+
+ runxml= result_dict['FC12150/C1-37/run_FC12150_2007-09-27.xml']
+ self.failUnlessEqual(runxml.file_type, runxml_file_type)
+ self.failUnlessEqual(runxml.library_id, None)
+
+
+ def test_read_result_file(self):
+ """make sure we can return a result file
+ """
+ flowcell_id = self.fc1_id
+ flowcell = models.FlowCell.objects.get(flowcell_id=flowcell_id)
+ flowcell.update_data_runs()
+
+ #self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
+
+ result_files = flowcell.datarun_set.all()[0].datafile_set.all()
+ for f in result_files:
+ url = '/experiments/file/%s' % ( f.random_key,)
+ response = self.client.get(url)
+ self.failUnlessEqual(response.status_code, 200)
+ mimetype = f.file_type.mimetype
+ if mimetype is None:
+ mimetype = 'application/octet-stream'
+
+ self.failUnlessEqual(mimetype, response['content-type'])
+
+class TestFileType(TestCase):
+ def test_file_type_unicode(self):
+ file_type_objects = models.FileType.objects
+ name = 'QSEQ tarfile'
+ file_type_object = file_type_objects.get(name=name)
+ self.failUnlessEqual(u"<FileType: QSEQ tarfile>",
+ unicode(file_type_object))
+
+class TestFileType(TestCase):
+ def test_find_file_type(self):
+ file_type_objects = models.FileType.objects
+ cases = [('woldlab_090921_HWUSI-EAS627_0009_42FC3AAXX_l7_r1.tar.bz2',
+ 'QSEQ tarfile', 7, 1),
+ ('woldlab_091005_HWUSI-EAS627_0010_42JT2AAXX_1.srf',
+ 'SRF', 1, None),
+ ('s_1_eland_extended.txt.bz2','ELAND Extended', 1, None),
+ ('s_7_eland_multi.txt.bz2', 'ELAND Multi', 7, None),
+ ('s_3_eland_result.txt.bz2','ELAND Result', 3, None),
+ ('s_1_export.txt.bz2','ELAND Export', 1, None),
+ ('s_1_percent_call.png', 'IVC Percent Call', 1, None),
+ ('s_2_percent_base.png', 'IVC Percent Base', 2, None),
+ ('s_3_percent_all.png', 'IVC Percent All', 3, None),
+ ('s_4_call.png', 'IVC Call', 4, None),
+ ('s_5_all.png', 'IVC All', 5, None),
+ ('Summary.htm', 'Summary.htm', None, None),
+ ('run_42JT2AAXX_2009-10-07.xml', 'run_xml', None, None),
+ ]
+ for filename, typename, lane, end in cases:
+ ft = models.find_file_type_metadata_from_filename(filename)
+ self.failUnlessEqual(ft['file_type'],
+ file_type_objects.get(name=typename))
+ self.failUnlessEqual(ft.get('lane', None), lane)
+ self.failUnlessEqual(ft.get('end', None), end)
+
+ def test_assign_file_type_complex_path(self):
+ file_type_objects = models.FileType.objects
+ cases = [('/a/b/c/woldlab_090921_HWUSI-EAS627_0009_42FC3AAXX_l7_r1.tar.bz2',
+ 'QSEQ tarfile', 7, 1),
+ ('foo/woldlab_091005_HWUSI-EAS627_0010_42JT2AAXX_1.srf',
+ 'SRF', 1, None),
+ ('../s_1_eland_extended.txt.bz2','ELAND Extended', 1, None),
+ ('/bleem/s_7_eland_multi.txt.bz2', 'ELAND Multi', 7, None),
+ ('/qwer/s_3_eland_result.txt.bz2','ELAND Result', 3, None),
+ ('/ty///1/s_1_export.txt.bz2','ELAND Export', 1, None),
+ ('/help/s_1_percent_call.png', 'IVC Percent Call', 1, None),
+ ('/bored/s_2_percent_base.png', 'IVC Percent Base', 2, None),
+ ('/example1/s_3_percent_all.png', 'IVC Percent All', 3, None),
+ ('amonkey/s_4_call.png', 'IVC Call', 4, None),
+ ('fishie/s_5_all.png', 'IVC All', 5, None),
+ ('/random/Summary.htm', 'Summary.htm', None, None),
+ ('/notrandom/run_42JT2AAXX_2009-10-07.xml', 'run_xml', None, None),
+ ]
+ for filename, typename, lane, end in cases:
+ result = models.find_file_type_metadata_from_filename(filename)
+ self.failUnlessEqual(result['file_type'],
+ file_type_objects.get(name=typename))
+ self.failUnlessEqual(result.get('lane',None), lane)
+ self.failUnlessEqual(result.get('end', None), end)
+
class TestEmailNotify(TestCase):
fixtures = ['test_flowcells.json']
self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
response = self.client.get('/experiments/started/153/')
self.failUnlessEqual(response.status_code, 200)
- self.failUnless(re.search('Flowcell 303TUAAXX', response.content))
+ self.failUnless(re.search('Flowcell FC12150', response.content))
# require that navigation back to the admin page exists
self.failUnless(re.search('<a href="/admin/experiments/flowcell/153/">[^<]+</a>', response.content))
+
projects / htsworkflow.git / blobdiff