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_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)