import re
-from BeautifulSoup import BeautifulSoup
+from lxml.html import fromstring
try:
import json
except ImportError, e:
import simplejson as json
+import os
+import shutil
import sys
+import tempfile
+from urlparse import urljoin
+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.util.ethelp import validate_xhtml
+
+from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
LANE_SET = range(1,9)
-class ExperimentsTestCases(TestCase):
+NSMAP = {'libns':'http://jumpgate.caltech.edu/wiki/LibraryOntology#'}
+
+class ClusterStationTestCases(TestCase):
fixtures = ['test_flowcells.json']
+ def test_default(self):
+ c = models.ClusterStation.default()
+ self.assertEqual(c.id, 2)
+
+ c.isdefault = False
+ c.save()
+
+ total = models.ClusterStation.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 0)
+
+ other_default = models.ClusterStation.default()
+ self.assertEqual(other_default.id, 3)
+
+
+ def test_update_default(self):
+ old_default = models.ClusterStation.default()
+
+ c = models.ClusterStation.objects.get(pk=3)
+ c.isdefault = True
+ c.save()
+
+ new_default = models.ClusterStation.default()
+
+ self.assertNotEqual(old_default, new_default)
+ self.assertEqual(new_default, c)
+
+ total = models.ClusterStation.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 1)
+
+ def test_update_other(self):
+ old_default = models.ClusterStation.default()
+ total = models.ClusterStation.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 1)
+
+ c = models.ClusterStation.objects.get(pk=1)
+ c.name = "Primary Key 1"
+ c.save()
+
+ total = models.ClusterStation.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 1)
+
+ new_default = models.ClusterStation.default()
+ self.assertEqual(old_default, new_default)
+
+
+class SequencerTestCases(TestCase):
+ fixtures = ['test_flowcells.json']
+
+ def test_default(self):
+ # starting with no default
+ s = models.Sequencer.default()
+ self.assertEqual(s.id, 2)
+
+ total = models.Sequencer.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 1)
+
+ s.isdefault = False
+ s.save()
+
+ total = models.Sequencer.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 0)
+
+ other_default = models.Sequencer.default()
+ self.assertEqual(other_default.id, 7)
+
+ def test_update_default(self):
+ old_default = models.Sequencer.default()
+
+ s = models.Sequencer.objects.get(pk=1)
+ s.isdefault = True
+ s.save()
+
+ new_default = models.Sequencer.default()
+
+ self.assertNotEqual(old_default, new_default)
+ self.assertEqual(new_default, s)
+
+ total = models.Sequencer.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 1)
+
+
+ def test_update_other(self):
+ old_default = models.Sequencer.default()
+ total = models.Sequencer.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 1)
+
+ s = models.Sequencer.objects.get(pk=1)
+ s.name = "Primary Key 1"
+ s.save()
+
+ total = models.Sequencer.objects.filter(isdefault=True).count()
+ self.assertEqual(total, 1)
+
+ new_default = models.Sequencer.default()
+ self.assertEqual(old_default, new_default)
+
+
+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(fc_django.flowcell_id, fc_id)
- self.failUnlessEqual(fc_dict['sequencer'], fc_django.sequencer.name)
- self.failUnlessEqual(fc_dict['read_length'], fc_django.read_length)
- self.failUnlessEqual(fc_dict['notes'], fc_django.notes)
- self.failUnlessEqual(fc_dict['cluster_station'], fc_django.cluster_station.name)
+ self.assertEqual(fc_dict['flowcell_id'], fc_id)
+ self.assertEqual(fc_django.flowcell_id, fc_id)
+ self.assertEqual(fc_dict['sequencer'], fc_django.sequencer.name)
+ self.assertEqual(fc_dict['read_length'], fc_django.read_length)
+ self.assertEqual(fc_dict['notes'], fc_django.notes)
+ self.assertEqual(fc_dict['cluster_station'], fc_django.cluster_station.name)
for lane in fc_django.lane_set.all():
- lane_dict = fc_dict['lane_set'][lane.lane_number]
- self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
- self.failUnlessEqual(lane_dict['comment'], lane.comment)
- 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.id)
- self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
- self.failUnlessEqual(lane_dict['library_species'],
+ lane_contents = fc_dict['lane_set'][lane.lane_number]
+ lane_dict = multi_lane_to_dict(lane_contents)[lane.library_id]
+ self.assertEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
+ self.assertEqual(lane_dict['comment'], lane.comment)
+ self.assertEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
+ self.assertEqual(lane_dict['lane_number'], lane.lane_number)
+ self.assertEqual(lane_dict['library_name'], lane.library.library_name)
+ self.assertEqual(lane_dict['library_id'], lane.library.id)
+ self.assertAlmostEqual(float(lane_dict['pM']), float(lane.pM))
+ self.assertEqual(lane_dict['library_species'],
lane.library.library_species.scientific_name)
-
+
response = self.client.get('/experiments/config/%s/json' % (fc_id,), apidata)
# strptime isoformat string = '%Y-%m-%dT%H:%M:%S'
fc_json = json.loads(response.content)
- self.failUnlessEqual(fc_json['flowcell_id'], fc_id)
- self.failUnlessEqual(fc_json['sequencer'], fc_django.sequencer.name)
- self.failUnlessEqual(fc_json['read_length'], fc_django.read_length)
- self.failUnlessEqual(fc_json['notes'], fc_django.notes)
- self.failUnlessEqual(fc_json['cluster_station'], fc_django.cluster_station.name)
+ self.assertEqual(fc_json['flowcell_id'], fc_id)
+ self.assertEqual(fc_json['sequencer'], fc_django.sequencer.name)
+ self.assertEqual(fc_json['read_length'], fc_django.read_length)
+ self.assertEqual(fc_json['notes'], fc_django.notes)
+ self.assertEqual(fc_json['cluster_station'], fc_django.cluster_station.name)
for lane in fc_django.lane_set.all():
- lane_dict = fc_json['lane_set'][unicode(lane.lane_number)]
- self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
- self.failUnlessEqual(lane_dict['comment'], lane.comment)
- 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.id)
- self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
- self.failUnlessEqual(lane_dict['library_species'],
+ lane_contents = fc_json['lane_set'][unicode(lane.lane_number)]
+ lane_dict = multi_lane_to_dict(lane_contents)[lane.library_id]
+
+ self.assertEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
+ self.assertEqual(lane_dict['comment'], lane.comment)
+ self.assertEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
+ self.assertEqual(lane_dict['lane_number'], lane.lane_number)
+ self.assertEqual(lane_dict['library_name'], lane.library.library_name)
+ self.assertEqual(lane_dict['library_id'], lane.library.id)
+ self.assertAlmostEqual(float(lane_dict['pM']), float(lane.pM))
+ self.assertEqual(lane_dict['library_species'],
lane.library.library_species.scientific_name)
def test_invalid_flowcell(self):
Make sure we get a 404 if we request an invalid flowcell ID
"""
response = self.client.get('/experiments/config/nottheone/json', apidata)
- self.failUnlessEqual(response.status_code, 404)
+ self.assertEqual(response.status_code, 404)
def test_no_key(self):
"""
Require logging in to retrieve meta data
"""
- response = self.client.get(u'/experiments/config/303TUAAXX/json')
- self.failUnlessEqual(response.status_code, 403)
+ response = self.client.get(u'/experiments/config/FC12150/json')
+ self.assertEqual(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)
- self.failUnlessEqual(response.status_code, 200)
+ response = self.client.get('/experiments/config/FC12150/json', apidata)
+ self.assertEqual(response.status_code, 200)
flowcell = json.loads(response.content)
- self.failUnlessEqual(flowcell['lane_set']['3']['library_id'], 'SL039')
+ lane_contents = flowcell['lane_set']['3']
+ lane_library = lane_contents[0]
+ self.assertEqual(lane_library['library_id'], 'SL039')
response = self.client.get('/samples/library/SL039/json', apidata)
- self.failUnlessEqual(response.status_code, 200)
+ self.assertEqual(response.status_code, 200)
library_sl039 = json.loads(response.content)
- self.failUnlessEqual(library_sl039['library_id'], 'SL039')
+ self.assertEqual(library_sl039['library_id'], 'SL039')
def test_raw_id_field(self):
"""
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)
+
+ tree = fromstring(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(':')
+ xpath_expression = '//input[@id="id_lane_set-%d-library"]'
+ input_field = tree.xpath(xpath_expression % (i,))[0]
+ library_field = input_field.find('../strong')
+ library_id, library_name = library_field.text.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)
+ self.assertEqual(library_id, expected_ids[i])
+ self.assertEqual(input_field.attrib['value'], library_id)
+
+ def test_library_to_flowcell_link(self):
+ """
+ Make sure the library page includes links to the flowcell pages.
+ That work with flowcell IDs that have parenthetical comments.
+ """
+ self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
+ response = self.client.get('/library/11070/')
+ self.assertEqual(response.status_code, 200)
+ status = validate_xhtml(response.content)
+ if status is not None: self.assertTrue(status)
+
+ tree = fromstring(response.content)
+ flowcell_spans = tree.xpath('//span[@property="libns:flowcell_id"]',
+ namespaces=NSMAP)
+ self.assertEqual(flowcell_spans[0].text, '30012AAXX (failed)')
+ failed_fc_span = flowcell_spans[0]
+ failed_fc_a = failed_fc_span.getparent()
+ # make sure some of our RDF made it.
+ self.assertEqual(failed_fc_a.get('typeof'), 'libns:IlluminaFlowcell')
+ self.assertEqual(failed_fc_a.get('href'), '/flowcell/30012AAXX/')
+ fc_response = self.client.get(failed_fc_a.get('href'))
+ self.assertEqual(fc_response.status_code, 200)
+ status = validate_xhtml(response.content)
+ if status is not None: self.assertTrue(status)
+
+ fc_lane_response = self.client.get('/flowcell/30012AAXX/8/')
+ self.assertEqual(fc_lane_response.status_code, 200)
+ status = validate_xhtml(response.content)
+ if status is not None: self.assertTrue(status)
+
+
+ def test_pooled_multiplex_id(self):
+ fc_dict = experiments.flowcell_information('42JU1AAXX')
+ lane_contents = fc_dict['lane_set'][3]
+ self.assertEqual(len(lane_contents), 2)
+ lane_dict = multi_lane_to_dict(lane_contents)
+
+ self.assertEqual(lane_dict['12044']['index_sequence'],
+ {u'1': u'ATCACG',
+ u'2': u'CGATGT',
+ u'3': u'TTAGGC'})
+ self.assertEqual(lane_dict['11045']['index_sequence'],
+ {u'1': u'ATCACG'})
+
+
+
+ def test_lanes_for(self):
+ """
+ Check the code that packs the django objects into simple types.
+ """
+ user = 'test'
+ lanes = experiments.lanes_for(user)
+ self.assertEqual(len(lanes), 5)
+
+ response = self.client.get('/experiments/lanes_for/%s/json' % (user,), apidata)
+ lanes_json = json.loads(response.content)
+ self.assertEqual(len(lanes), len(lanes_json))
+ for i in range(len(lanes)):
+ self.assertEqual(lanes[i]['comment'], lanes_json[i]['comment'])
+ self.assertEqual(lanes[i]['lane_number'], lanes_json[i]['lane_number'])
+ self.assertEqual(lanes[i]['flowcell'], lanes_json[i]['flowcell'])
+ self.assertEqual(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.assertEqual(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.assertRaises(ObjectDoesNotExist, experiments.lanes_for, user)
+
+ response = self.client.get('/experiments/lanes_for/%s/json' % (user,), apidata)
+ self.assertEqual(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.assertEqual(fc.get_raw_data_directory(), raw_dir)
+
+ fc.flowcell_id = flowcell_id + " (failed)"
+ self.assertEqual(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.assertEqual(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.assertEqual(srf4.file_type, srf_file_type)
+ self.assertEqual(srf4.library_id, '11060')
+ self.assertEqual(srf4.data_run.flowcell.flowcell_id, 'FC12150')
+ self.assertEqual(
+ srf4.data_run.flowcell.lane_set.get(lane_number=4).library_id,
+ '11060')
+ self.assertEqual(
+ srf4.pathname,
+ os.path.join(settings.RESULT_HOME_DIR, srf4.relative_pathname))
+
+ lane_files = run.lane_files()
+ self.assertEqual(lane_files[4]['srf'], srf4)
+
+ runxml= result_dict['FC12150/C1-37/run_FC12150_2007-09-27.xml']
+ self.assertEqual(runxml.file_type, runxml_file_type)
+ self.assertEqual(runxml.library_id, None)
+
+ import1 = len(models.DataRun.objects.filter(result_dir='FC12150/C1-37'))
+ # what happens if we import twice?
+ flowcell.import_data_run('FC12150/C1-37',
+ 'run_FC12150_2007-09-27.xml')
+ self.assertEqual(
+ len(models.DataRun.objects.filter(result_dir='FC12150/C1-37')),
+ import1)
+
+ 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.assertEqual(response.status_code, 200)
+ mimetype = f.file_type.mimetype
+ if mimetype is None:
+ mimetype = 'application/octet-stream'
+
+ self.assertEqual(mimetype, response['content-type'])
+
+ def test_flowcell_rdf(self):
+ import RDF
+ from htsworkflow.util.rdfhelp import get_model, \
+ fromTypedNode, \
+ load_string_into_model, \
+ rdfNS, \
+ libraryOntology, \
+ dump_model
+
+ model = get_model()
+
+ expected = {'1': ['11034'],
+ '2': ['11036'],
+ '3': ['12044','11045'],
+ '4': ['11047','13044'],
+ '5': ['11055'],
+ '6': ['11067'],
+ '7': ['11069'],
+ '8': ['11070']}
+ url = '/flowcell/42JU1AAXX/'
+ response = self.client.get(url)
+ self.assertEqual(response.status_code, 200)
+ status = validate_xhtml(response.content)
+ if status is not None: self.assertTrue(status)
+
+ ns = urljoin('http://localhost', url)
+ load_string_into_model(model, 'rdfa', response.content, ns=ns)
+ body = """prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+ prefix libns: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
+
+ select ?flowcell ?flowcell_id ?lane_id ?library_id
+ where {
+ ?flowcell a libns:IlluminaFlowcell ;
+ libns:flowcell_id ?flowcell_id ;
+ libns:has_lane ?lane .
+ ?lane libns:lane_number ?lane_id ;
+ libns:library ?library .
+ ?library libns:library_id ?library_id .
+ }"""
+ query = RDF.SPARQLQuery(body)
+ count = 0
+ for r in query.execute(model):
+ count += 1
+ self.assertEqual(fromTypedNode(r['flowcell_id']), u'42JU1AAXX')
+ lane_id = fromTypedNode(r['lane_id'])
+ library_id = fromTypedNode(r['library_id'])
+ self.assertTrue(library_id in expected[lane_id])
+ self.assertEqual(count, 10)
+
+
+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.assertEqual(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.assertEqual(ft['file_type'],
+ file_type_objects.get(name=typename))
+ self.assertEqual(ft.get('lane', None), lane)
+ self.assertEqual(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.assertEqual(result['file_type'],
+ file_type_objects.get(name=typename))
+ self.assertEqual(result.get('lane',None), lane)
+ self.assertEqual(result.get('end', None), end)
class TestEmailNotify(TestCase):
fixtures = ['test_flowcells.json']
def test_started_email_not_logged_in(self):
response = self.client.get('/experiments/started/153/')
- self.failUnlessEqual(response.status_code, 302)
+ self.assertEqual(response.status_code, 302)
def test_started_email_logged_in_user(self):
self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
response = self.client.get('/experiments/started/153/')
- self.failUnlessEqual(response.status_code, 302)
-
+ self.assertEqual(response.status_code, 302)
+
def test_started_email_logged_in_staff(self):
- self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
+ self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
response = self.client.get('/experiments/started/153/')
- self.failUnlessEqual(response.status_code, 200)
+ self.assertEqual(response.status_code, 200)
def test_started_email_send(self):
- self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
+ self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
response = self.client.get('/experiments/started/153/')
- self.failUnlessEqual(response.status_code, 200)
-
- self.failUnless('pk1@example.com' in response.content)
- self.failUnless('Lane #8 : (11064) Paired ends 104' in response.content)
+ self.assertEqual(response.status_code, 200)
+
+ self.assertTrue('pk1@example.com' in response.content)
+ self.assertTrue('Lane #8 : (11064) Paired ends 104' in response.content)
response = self.client.get('/experiments/started/153/', {'send':'1','bcc':'on'})
- self.failUnlessEqual(response.status_code, 200)
- self.failUnlessEqual(len(mail.outbox), 4)
+ self.assertEqual(response.status_code, 200)
+ self.assertEqual(len(mail.outbox), 4)
+ bcc = set(settings.NOTIFICATION_BCC).intersect(set(settings.MANAGERS))
for m in mail.outbox:
- self.failUnless(len(m.body) > 0)
+ self.assertTrue(len(m.body) > 0)
+ self.assertEqual(m.bcc, bcc)
def test_email_navigation(self):
"""
Can we navigate between the flowcell and email forms properly?
"""
- self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
+ 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.assertEqual(response.status_code, 200)
+ self.assertTrue(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))
-
+ self.assertTrue(re.search('<a href="/admin/experiments/flowcell/153/">[^<]+</a>', response.content))
+
+def multi_lane_to_dict(lane):
+ """Convert a list of lane entries into a dictionary indexed by library ID
+ """
+ return dict( ((x['library_id'],x) for x in lane) )
+
+class TestSequencer(TestCase):
+ fixtures = ['test_flowcells.json',
+ ]
+
+ def test_name_generation(self):
+ seq = models.Sequencer()
+ seq.name = "Seq1"
+ seq.instrument_name = "HWI-SEQ1"
+ seq.model = "Imaginary 5000"
+
+ self.assertEqual(unicode(seq), "Seq1 (HWI-SEQ1)")
+
+ def test_lookup(self):
+ fc = models.FlowCell.objects.get(pk=153)
+ self.assertEqual(fc.sequencer.model,
+ "Illumina Genome Analyzer IIx")
+ self.assertEqual(fc.sequencer.instrument_name,
+ "ILLUMINA-EC5D15")
+ # well actually we let the browser tack on the host name
+ url = fc.get_absolute_url()
+ self.assertEqual(url, '/flowcell/FC12150/')
+
+ def test_rdf(self):
+ response = self.client.get('/flowcell/FC12150/', apidata)
+ tree = fromstring(response.content)
+ seq_by = tree.xpath('//div[@rel="libns:sequenced_by"]',
+ namespaces=NSMAP)
+ self.assertEqual(len(seq_by), 1)
+ self.assertEqual(seq_by[0].attrib['rel'], 'libns:sequenced_by')
+ seq = seq_by[0].getchildren()
+ self.assertEqual(len(seq), 1)
+ self.assertEqual(seq[0].attrib['about'], '/sequencer/2')
+ self.assertEqual(seq[0].attrib['typeof'], 'libns:Sequencer')
+
+ name = seq[0].xpath('./span[@property="libns:sequencer_name"]')
+ self.assertEqual(len(name), 1)
+ self.assertEqual(name[0].text, 'Tardigrade')
+ instrument = seq[0].xpath(
+ './span[@property="libns:sequencer_instrument"]')
+ self.assertEqual(len(instrument), 1)
+ self.assertEqual(instrument[0].text, 'ILLUMINA-EC5D15')
+ model = seq[0].xpath(
+ './span[@property="libns:sequencer_model"]')
+ self.assertEqual(len(model), 1)
+ self.assertEqual(model[0].text, 'Illumina Genome Analyzer IIx')
+
+ def test_flowcell_with_rdf_validation(self):
+ from htsworkflow.util.rdfhelp import add_default_schemas, \
+ dump_model, \
+ get_model, \
+ load_string_into_model
+ from htsworkflow.util.rdfinfer import Infer
+
+ model = get_model()
+ add_default_schemas(model)
+ inference = Infer(model)
+
+ url ='/flowcell/FC12150/'
+ response = self.client.get(url)
+ self.assertEqual(response.status_code, 200)
+ status = validate_xhtml(response.content)
+ if status is not None: self.assertTrue(status)
+
+ load_string_into_model(model, 'rdfa', response.content)
+
+ errmsgs = list(inference.run_validation())
+ self.assertEqual(len(errmsgs), 2)
+ for errmsg in errmsgs:
+ self.assertEqual(errmsg, 'Missing type for: http://localhost/')
+
+ def test_lane_with_rdf_validation(self):
+ from htsworkflow.util.rdfhelp import add_default_schemas, \
+ dump_model, \
+ get_model, \
+ load_string_into_model
+ from htsworkflow.util.rdfinfer import Infer
+
+ model = get_model()
+ add_default_schemas(model)
+ inference = Infer(model)
+
+ url = '/lane/1193'
+ response = self.client.get(url)
+ self.assertEqual(response.status_code, 200)
+ status = validate_xhtml(response.content)
+ if status is not None: self.assertTrue(status)
+
+ load_string_into_model(model, 'rdfa', response.content)
+
+ errmsgs = list(inference.run_validation())
+ self.assertEqual(len(errmsgs), 2)
+ for errmsg in errmsgs:
+ self.assertEqual(errmsg, 'Missing type for: http://localhost/')
projects / htsworkflow.git / blobdiff