import shutil
import sys
import tempfile
+from urlparse import urljoin
from django.conf import settings
from django.core import mail
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
u'11061',u'11062',u'11063',u'11064']
self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
response = self.client.get('/admin/experiments/flowcell/153/')
+
tree = fromstring(response.content)
for i in range(0,8):
xpath_expression = '//input[@id="id_lane_set-%d-library"]'
"""
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)
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('rel'), 'libns:flowcell')
+ 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')
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
response = self.client.get('/experiments/started/153/', {'send':'1','bcc':'on'})
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.assertTrue(len(m.body) > 0)
+ self.assertEqual(m.bcc, bcc)
def test_email_navigation(self):
"""
"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)
- divs = tree.xpath('//div[@rel="libns:sequenced_by"]',
- namespaces=NSMAP)
- self.assertEqual(len(divs), 1)
- self.assertEqual(divs[0].attrib['rel'], 'libns:sequenced_by')
- self.assertEqual(divs[0].attrib['resource'], '/sequencer/2')
-
- name = divs[0].xpath('./span[@property="libns:sequencer_name"]')
+ 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 = divs[0].xpath(
+ instrument = seq[0].xpath(
'./span[@property="libns:sequencer_instrument"]')
self.assertEqual(len(instrument), 1)
self.assertEqual(instrument[0].text, 'ILLUMINA-EC5D15')
- model = divs[0].xpath(
+ 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