def test_correct_index_location_metazoa(self):
""" Tests that the files returned actually exist.
Tests the Metazoa division instead of the main division.
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="ensembl_division",
value="EnsemblMetazoa")
key_value_pair.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="organism_name",
value="Octopus bimaculoides")
key_value_pair.save()
surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]
for file in files:
urllib.request.urlopen(file.source_url)
# Make sure the organism object got created by making sure
# this doesn't raise an exception.
Organism.objects.get(name="OCTOPUS_BIMACULOIDES")
def test_correct_index_location(self):
""" Tests that the files returned actually exist.
Uses an organism in the main division.
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="ensembl_division",
value="Ensembl")
key_value_pair.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="organism_name",
value="Danio rerio")
key_value_pair.save()
surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]
# Make sure the organism object got created by making sure
# this doesn't raise an exception.
Organism.objects.get(name="DANIO_RERIO")
for file in files:
urllib.request.urlopen(file.source_url)
def test_single_plant(self):
""" Tests that the files returned actually exist.
Tests the Metazoa division instead of the main division.
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="ensembl_division",
value="EnsemblPlants")
key_value_pair.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="organism_name",
value="Arabidopsis thaliana")
key_value_pair.save()
surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]
for file in files:
urllib.request.urlopen(file.source_url)
# Make sure the organism object got created by making sure
# this doesn't raise an exception.
Organism.objects.get(name="ARABIDOPSIS_THALIANA")
def test_correct_index_location_protist(self):
""" Tests that the files returned actually exist.
Tests the Metazoa division instead of the main division.
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="ensembl_division",
value="EnsemblProtists")
key_value_pair.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="organism_name",
value="Leishmania major")
key_value_pair.save()
surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]
for file in files:
urllib.request.urlopen(file.source_url)
def test_correct_index_location(self):
""" Tests that the files returned actually exist.
Uses an organism in the main division.
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()
self.survey_job = survey_job
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="ensembl_division",
value="Ensembl")
key_value_pair.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="organism_name",
value="Danio rerio")
key_value_pair.save()
surveyor = TranscriptomeIndexSurveyor(self.survey_job)
files = surveyor.discover_species()[0]
for file in files:
urllib.request.urlopen(file.source_url)