class CoreDbTests(unittest.TestCase):
def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run = (
u"2015-10-11", u"HiSeq", u"Nextera XT", 1,
u"run_file.fastq", u"Bob's run",
)
self.run_acc = self.db.register_run(*self.run)
self.sample_bcs = [
("Sample1", "ABC"),
("Sample2", "DEF"),
("My.Sample3", "GHI"),
]
self.single_sample = self.sample_bcs[0]
self.annotations = {
"SampleType": "Oral swab",
"SubjectID": "Subj23",
"study_group": "Healthy",
"study_day": "1",
}
def test_register_run(self):
self.assertEqual(self.run_acc, 1)
self.assertTrue(self.db.query_run_exists(self.run_acc))
obs_run = self.db._query_run(self.run_acc)
self.assertEqual(self.run, obs_run)
# Registering the run twice should raise an error
self.assertRaises(ValueError, self.db.register_run, *self.run)
def test_query_run_exists(self):
self.assertTrue(self.db.query_run_exists(1))
def test_register_samples(self):
# Here, accessions given by database cursor. In other tests,
# we double-check that we can actually find the samples in a
# query
registered_accessions = self.db.register_samples(
1, self.sample_bcs)
self.assertEqual(registered_accessions, [1, 2, 3])
# Registering the samples again should raise an error
self.assertRaises(
ValueError, self.db.register_samples, 1, self.sample_bcs)
def test_query_barcoded_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(
self.db.query_barcoded_sample_accessions(1, self.sample_bcs),
[1, 2, 3])
def test_query_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(
self.db.query_sample_accessions(1), [1, 2, 3])
def test_remove_samples(self):
self.db.register_samples(1, self.sample_bcs)
self.db.remove_samples([1, 2, 3])
self.assertEqual(self.db.query_sample_accessions(1), [])
def test_register_and_remove_annotations(self):
sample_accessions = self.db.register_samples(1, self.sample_bcs)
for acc in sample_accessions:
ann = [(acc, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.db.remove_annotations(sample_accessions)
for acc in sample_accessions:
self.assertEqual(
self.db.query_sample_annotations(acc), {})
def test_register_and_query_annotations(self):
self.db.register_samples(1, [("Sample1", "GGCCTT")])
ann = [(1, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.assertEqual(
self.db.query_sample_annotations(1), self.annotations)
def test_collect_standard_annotations(self):
a = [
(1, "SampleType", "a"),
(1, "HostSpecies", "b"),
(2, "SubjectID", "c"),
]
obs = CoreDb._collect_standard_annotations(a)
self.assertEqual(obs, {1: ["a", None, "b"], 2: [None, "c", None]})
class CoreDbTests(unittest.TestCase):
def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run = (
u"2015-10-11",
u"HiSeq",
u"Nextera XT",
1,
u"run_file.fastq",
u"Bob's run",
)
self.run_acc = self.db.register_run(*self.run)
self.sample_bcs = [
("Sample1", "ABC"),
("Sample2", "DEF"),
("My.Sample3", "GHI"),
]
self.single_sample = self.sample_bcs[0]
self.annotations = {
"SampleType": "Oral swab",
"SubjectID": "Subj23",
"study_group": "Healthy",
"study_day": "1",
}
def test_register_run(self):
self.assertEqual(self.run_acc, 1)
self.assertTrue(self.db.query_run_exists(self.run_acc))
obs_run = self.db._query_run(self.run_acc)
self.assertEqual(self.run, obs_run)
# Registering the run twice should raise an error
self.assertRaises(ValueError, self.db.register_run, *self.run)
def test_query_run_exists(self):
self.assertTrue(self.db.query_run_exists(1))
def test_register_samples(self):
# Here, accessions given by database cursor. In other tests,
# we double-check that we can actually find the samples in a
# query
registered_accessions = self.db.register_samples(1, self.sample_bcs)
self.assertEqual(registered_accessions, [1, 2, 3])
# Registering the samples again should raise an error
self.assertRaises(ValueError, self.db.register_samples, 1,
self.sample_bcs)
def test_query_barcoded_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(
self.db.query_barcoded_sample_accessions(1, self.sample_bcs),
[1, 2, 3])
def test_query_sample_accessions(self):
self.db.register_samples(1, self.sample_bcs)
self.assertEqual(self.db.query_sample_accessions(1), [1, 2, 3])
def test_remove_samples(self):
self.db.register_samples(1, self.sample_bcs)
self.db.remove_samples([1, 2, 3])
self.assertEqual(self.db.query_sample_accessions(1), [])
def test_register_and_remove_annotations(self):
sample_accessions = self.db.register_samples(1, self.sample_bcs)
for acc in sample_accessions:
ann = [(acc, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.db.remove_annotations(sample_accessions)
for acc in sample_accessions:
self.assertEqual(self.db.query_sample_annotations(acc), {})
def test_register_and_query_annotations(self):
self.db.register_samples(1, [("Sample1", "GGCCTT")])
ann = [(1, k, v) for k, v in self.annotations.items()]
self.db.register_annotations(ann)
self.assertEqual(self.db.query_sample_annotations(1), self.annotations)
def test_collect_standard_annotations(self):
a = [
(1, "SampleType", "a"),
(1, "HostSpecies", "b"),
(2, "SubjectID", "c"),
]
obs = CoreDb._collect_standard_annotations(a)
self.assertEqual(obs, {1: ["a", None, "b"], 2: [None, "c", None]})
class RegisterScriptTests(unittest.TestCase):
def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run_args = [
"abc",
"--lane", "1",
"--date", "2008-09-21",
"--type", "Illumina-MiSeq",
"--comment", "mdsnfa adsf",
]
self.samples = [{
"SampleID": "abc123",
"BarcodeSequence": "GGGCCT",
"SampleType": "Oral swab",
"bb": "cd e29",
}]
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_illumina_file(self):
tmp_dir = tempfile.mkdtemp()
fastq_dir = (
"Miseq/160511_M03543_0047_000000000-APE6Y/Data/Intensities/"
"BaseCalls")
fastq_name = "Undetermined_S0_L001_R1_001.fastq.gz"
os.makedirs(os.path.join(tmp_dir, fastq_dir))
relative_fp = os.path.join(fastq_dir, fastq_name)
absolute_fp = os.path.join(tmp_dir, relative_fp)
f = gzip.GzipFile(absolute_fp, "w")
f.write("@M03543:21:C8LJ2ANXX:1:2209:1084:2044 1:N:0:NNNNNNNN+NNNNNNNN")
f.close()
out = io.StringIO()
original_cwd = os.getcwd()
os.chdir(tmp_dir)
try:
register_illumina_file(
[relative_fp, "abcd efg"], self.db, out)
finally:
os.chdir(original_cwd)
shutil.rmtree(tmp_dir)
self.assertEqual(self.db._query_run(1), (
u'2016-05-11', u'Illumina-MiSeq', u'Nextera XT', 1,
unicode(relative_fp), u'abcd efg'))
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_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_register_sample_types(self):
f = tempfile.NamedTemporaryFile("wt")
f.write(SAMPLE_TYPES_TSV)
f.seek(0)
register_sample_types([f.name], self.db)
self.assertEqual(
self.db.query_standard_sample_types(),
SAMPLE_TYPES_VALS)
# Add a new sample type and re-register
new_line = "Extra type 1 Just to test"
f2 = tempfile.NamedTemporaryFile("wt")
f2.write(SAMPLE_TYPES_TSV + new_line)
f2.seek(0)
register_sample_types([f2.name], self.db)
self.assertEqual(
self.db.query_standard_sample_types(),
SAMPLE_TYPES_VALS + [("Extra type", 1, "Just to test")])
def test_register_host_species(self):
f = tempfile.NamedTemporaryFile("wt")
f.write(HOST_SPECIES_TSV)
f.seek(0)
register_host_species([f.name], self.db)
self.assertEqual(
self.db.query_standard_host_species(),
HOST_SPECIES_VALS)
# Add a new species to the file and re-register
new_line = "Hippo Test 1243"
f2 = tempfile.NamedTemporaryFile("wt")
f2.write(HOST_SPECIES_TSV + new_line)
f2.seek(0)
register_host_species([f2.name], self.db)
self.assertEqual(
self.db.query_standard_host_species(),
HOST_SPECIES_VALS + [("Hippo", "Test", 1243)])
class RegisterScriptTests(unittest.TestCase):
def setUp(self):
self.db = CoreDb(":memory:")
self.db.create_tables()
self.run_args = [
"abc",
"--lane",
"1",
"--date",
"2008-09-21",
"--type",
"Illumina-MiSeq",
"--comment",
"mdsnfa adsf",
]
self.samples = [{
"SampleID": "abc123",
"BarcodeSequence": "GGGCCT",
"SampleType": "Oral swab",
"bb": "cd e29",
}]
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_illumina_file(self):
tmp_dir = tempfile.mkdtemp()
fastq_dir = (
"Miseq/160511_M03543_0047_000000000-APE6Y/Data/Intensities/"
"BaseCalls")
fastq_name = "Undetermined_S0_L001_R1_001.fastq.gz"
os.makedirs(os.path.join(tmp_dir, fastq_dir))
relative_fp = os.path.join(fastq_dir, fastq_name)
absolute_fp = os.path.join(tmp_dir, relative_fp)
f = gzip.GzipFile(absolute_fp, "w")
f.write(
"@M03543:21:C8LJ2ANXX:1:2209:1084:2044 1:N:0:NNNNNNNN+NNNNNNNN")
f.close()
out = io.StringIO()
original_cwd = os.getcwd()
os.chdir(tmp_dir)
try:
register_illumina_file([relative_fp, "abcd efg"], self.db, out)
finally:
os.chdir(original_cwd)
shutil.rmtree(tmp_dir)
self.assertEqual(self.db._query_run(1),
(u'2016-05-11', u'Illumina-MiSeq', u'Nextera XT', 1,
unicode(relative_fp), u'abcd efg'))
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_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_register_sample_types(self):
f = tempfile.NamedTemporaryFile("wt")
f.write(SAMPLE_TYPES_TSV)
f.seek(0)
register_sample_types([f.name], self.db)
self.assertEqual(self.db.query_standard_sample_types(),
SAMPLE_TYPES_VALS)
# Add a new sample type and re-register
new_line = "Extra type 1 Just to test"
f2 = tempfile.NamedTemporaryFile("wt")
f2.write(SAMPLE_TYPES_TSV + new_line)
f2.seek(0)
register_sample_types([f2.name], self.db)
self.assertEqual(
self.db.query_standard_sample_types(),
SAMPLE_TYPES_VALS + [("Extra type", 1, "Just to test")])
def test_register_host_species(self):
f = tempfile.NamedTemporaryFile("wt")
f.write(HOST_SPECIES_TSV)
f.seek(0)
register_host_species([f.name], self.db)
self.assertEqual(self.db.query_standard_host_species(),
HOST_SPECIES_VALS)
# Add a new species to the file and re-register
new_line = "Hippo Test 1243"
f2 = tempfile.NamedTemporaryFile("wt")
f2.write(HOST_SPECIES_TSV + new_line)
f2.seek(0)
register_host_species([f2.name], self.db)
self.assertEqual(self.db.query_standard_host_species(),
HOST_SPECIES_VALS + [("Hippo", "Test", 1243)])
