def test_logger_from_conf(self):
with tempfile.TemporaryDirectory() as folder:
for logger_name, (mode, level, initialiser, streaming) in enumerate(
itertools.product(["a", "w"], ["WARNING", "INFO", "DEBUG"],
(LoggingConfiguration, MikadoConfiguration),
(False, True))):
with tempfile.NamedTemporaryFile(mode="wt", dir=folder, suffix=".log") as log:
if streaming is True:
name = None
else:
name = log.name
if initialiser == LoggingConfiguration:
conf = LoggingConfiguration()
conf.log = name
conf.log_level = level
else:
conf = MikadoConfiguration()
conf.log_settings.log = name
conf.log_settings.log_level = level
logger = create_logger_from_conf(conf, name="test_logger_from_conf" + str(logger_name), mode=mode)
self.assertTrue(os.path.exists(log.name) or streaming)
self.assertTrue(os.path.exists(log.name) != streaming) # Either we have created a streaming log or not
self.assertEqual(logging.getLevelName(logger.level), level, conf)
if streaming:
self.assertIsInstance(logger.handlers[0], logging.StreamHandler)
else:
self.assertIsInstance(logger.handlers[0], logging.FileHandler)
self.assertEqual(logger.handlers[0].mode, mode)
if streaming is False and os.path.exists(log.name):
os.remove(log.name)
def test_asn(self):
# Currently DISABLED because the ASN specifications requires the database to be where indicated by the
# relative path within the ASN. So for the time being this test is *not active*.
asns = [
os.path.join("blast", "asn", "blast.asn.gz"),
os.path.join("blast_parse_seqids", "asn", "blast.asn.gz")
]
for folder in ["sanitised", "uniprot"]:
conf = MikadoConfiguration()
targets = os.path.join(self.master, folder, "uniprot.fasta")
self.assertTrue(os.path.exists(targets))
for asn in asns:
asn = os.path.join(self.master, folder, asn)
self.assertTrue(os.path.exists(asn))
with tempfile.TemporaryDirectory() as out_folder:
conf.serialise.files.output_dir = out_folder
conf.serialise.files.blast_targets = [targets]
conf.serialise.files.transcripts = self.queries
conf.serialise.files.xml = [asn]
logger = create_default_logger(f"test_asn_{folder}")
out_db = os.path.join(out_folder, conf.db_settings.db)
conf.db_settings.db = out_db
self.run_loading(asn, out_db, logger, conf)
def setUp(self) -> None:
self.config = MikadoConfiguration()
self.ref = pkg_resources.resource_filename("Mikado.tests", "reference.gff3")
self.trinity = pkg_resources.resource_filename("Mikado.tests", "trinity.bed12")
self.pacbio = pkg_resources.resource_filename("Mikado.tests", "pacbio.bam")
self.files = {
"ref": {"filename": self.ref,
"label": "ref", "stranded": True, "score": 10, "exclude_redundant": False,
"strip_cds": False, "skip_split": True, "reference": True},
"pacbio": {"filename": self.pacbio,
"label": "pacbio", "stranded": True, "score": 5, "exclude_redundant": True,
"strip_cds": False, "skip_split": True, "reference": False},
"trinity": {"filename": self.trinity,
"label": "trinity", "stranded": False, "score": -1, "exclude_redundant": True,
"strip_cds": True, "skip_split": True, "reference": False},
}
def test_daa(self):
daa_base = os.path.join("diamond", "daa", "blast.daa")
for folder in ["sanitised", "uniprot"]:
targets = os.path.join(self.master, folder, "uniprot.fasta")
self.assertTrue(os.path.exists(targets))
daa = os.path.join(self.master, folder, daa_base)
self.assertTrue(os.path.exists(daa))
with tempfile.TemporaryDirectory() as out_folder:
conf = MikadoConfiguration()
out_db = os.path.join(out_folder, conf.db_settings.db)
conf.db_settings.db = out_db
conf.serialise.files.output_dir = out_folder
conf.serialise.files.blast_targets = [targets]
conf.serialise.files.transcripts = self.queries
conf.serialise.files.xml = [daa]
logger = create_default_logger(f"test_daa_{folder}")
self.assertTrue(tempfile.gettempdir() in out_db)
self.run_loading(daa, out_db, logger, conf)
def test_xml(self):
xml_base = os.path.join("xml", "blast.xml.gz")
for folder in ["sanitised", "uniprot"]:
for subfolder in ["blast", "blast_parse_seqids", "diamond"]:
targets = os.path.join(self.master, folder, "uniprot.fasta")
self.assertTrue(os.path.exists(targets))
xml = os.path.join(self.master, folder, subfolder, xml_base)
self.assertTrue(os.path.exists(xml))
with tempfile.TemporaryDirectory() as out_folder:
conf = MikadoConfiguration()
conf.serialise.files.output_dir = out_folder
out_db = os.path.join(out_folder, conf.db_settings.db)
conf.db_settings.db = out_db
conf.serialise.files.blast_targets = [targets]
conf.serialise.files.transcripts = self.queries
conf.serialise.files.xml = [xml]
logger = create_default_logger(
f"test_xml_{folder}_{subfolder}")
self.assertTrue(tempfile.gettempdir() in out_db)
self.run_loading(xml, out_db, logger, conf)
def test_tsv(self):
tsv_base = os.path.join("tsv", "blast.tsv.gz")
for folder in ["uniprot", "sanitised"]:
for subfolder in ["blast", "blast_parse_seqids", "diamond"]:
targets = os.path.join(self.master, folder, "uniprot.fasta")
self.assertTrue(os.path.exists(targets))
tsv = os.path.join(self.master, folder, subfolder, tsv_base)
self.assertTrue(os.path.exists(tsv))
with tempfile.TemporaryDirectory() as out_folder:
conf = MikadoConfiguration()
conf.serialise.files.output_dir = out_folder
conf.serialise.files.blast_targets = [targets]
conf.serialise.files.transcripts = self.queries
conf.serialise.files.xml = [tsv]
out_db = os.path.join(out_folder, conf.db_settings.db)
conf.db_settings.db = out_db
self.assertTrue(tempfile.gettempdir() in out_db)
logger = create_default_logger(
f"test_tsv_{folder}_{subfolder}", level="DEBUG")
self.run_loading(tsv, out_db, logger, conf)