def test_register_run(self):
out = io.StringIO()
register_run(self.run_args, self.db, out)
# Check that accession number is printed
self.assertEqual(out.getvalue(), "Registered run 1 in the database\n")
# Check that attributes are saved in the database
self.assertEqual(self.db.query_run_file(1), "abc")
def test_unregister_samples(self):
register_run(self.run_args, self.db)
out = io.StringIO()
sample_file = temp_sample_file(self.samples)
args = ["1", sample_file.name]
register_sample_annotations(args, True, self.db, out)
unregister_samples(["1"], self.db)
self.assertEqual(self.db._query_nonstandard_annotations(1), {})
self.assertEqual(self.db.query_sample_accessions(1), [])
def test_unregister_samples(self):
register_run(self.run_args, self.db)
out = io.StringIO()
sample_file = temp_sample_file(self.samples)
args = ["1", sample_file.name]
register_sample_annotations(args, True, self.db, out)
unregister_samples(["1"], self.db)
self.assertEqual(self.db._query_nonstandard_annotations(1), {})
self.assertEqual(self.db.query_sample_accessions(1), [])
def test_rgister_run(self):
out = io.StringIO()
register_run(self.run_args, self.db, out)
# Check that accession number is printed
self.assertEqual(out.getvalue(), "Registered run 1 in the database\n")
# Check that attributes are saved in the database
self.assertEqual(self.db._query_run(1),
(u'2008-09-21', u'Illumina-MiSeq', u'Nextera XT', 1,
u'abc', u'mdsnfa adsf'))
def test_rgister_run(self):
out = io.StringIO()
register_run(self.run_args, self.db, out)
# Check that accession number is printed
self.assertEqual(
out.getvalue(),
"Registered run 1 in the database\n"
)
# Check that attributes are saved in the database
self.assertEqual(self.db._query_run(1), (
u'2008-09-21', u'Illumina-MiSeq', u'Nextera XT', 1,
u'abc', u'mdsnfa adsf'))
def test_register_samples(self):
register_run(self.run_args, self.db)
out = io.StringIO()
sample_file = temp_sample_file(self.samples)
args = ["1", sample_file.name]
register_sample_annotations(args, True, self.db, out)
# Check that accession number is assigned
obs_accessions = self.db.query_barcoded_sample_accessions(
1, [("abc123", "GGGCCT")])
self.assertEqual(obs_accessions, [1])
# Check that annotations are saved to the database
self.assertEqual(
self.db.query_sample_annotations(1),
{"SampleType": "Oral swab", "bb": "cd e29"})
def test_register_samples(self):
register_run(self.run_args, self.db)
out = io.StringIO()
sample_file = temp_sample_file(self.samples)
args = ["1", sample_file.name]
register_sample_annotations(args, True, self.db, out)
# Check that accession number is assigned
obs_accessions = self.db.query_barcoded_sample_accessions(
1, [("abc123", "GGGCCT")])
self.assertEqual(obs_accessions, [1])
# Check that annotations are saved to the database
self.assertEqual(self.db.query_sample_annotations(1), {
"SampleType": "Oral swab",
"bb": "cd e29"
})
def test_register_annotations(self):
register_run(self.run_args, self.db)
sample_file = temp_sample_file(self.samples)
args = ["1", sample_file.name]
register_sample_annotations(args, True, self.db)
# Update SampleType, add fg
new_annotations = {"SampleType": "Feces", "fg": "hi5 34"}
modified_samples = [x.copy() for x in self.samples]
modified_samples[0].update(new_annotations)
# Remove bb
del modified_samples[0]["bb"]
sample_file = temp_sample_file(modified_samples)
args = ["1", sample_file.name]
register_sample_annotations(args, False, self.db)
self.assertEqual(self.db.query_sample_annotations(1), new_annotations)
def test_register_annotations(self):
register_run(self.run_args, self.db)
sample_file = temp_sample_file(self.samples)
args = [ "1", sample_file.name]
register_sample_annotations(args, True, self.db)
# Update SampleType, add fg
new_annotations = {"SampleType": "Feces", "fg": "hi5 34"}
modified_samples = [x.copy() for x in self.samples]
modified_samples[0].update(new_annotations)
# Remove bb
del modified_samples[0]["bb"]
sample_file = temp_sample_file(modified_samples)
args = ["1", sample_file.name]
register_sample_annotations(args, False, self.db)
self.assertEqual(
self.db.query_sample_annotations(1), new_annotations)
