def test_with_errors(self):
try:
with TemporaryDirectory() as tmpdir:
with path.changed_directory(tmpdir):
raise ValueError("die mid-context")
except ValueError as err:
assert "die mid-context" in str(err)
finally:
assert os.getcwd() == self.original_dir
def prepare_data(_logging_only: bool = False) -> List[str]:
""" Rebuild any dynamically buildable data """
flavours = ["bacteria", "fungi", "plants"]
with path.changed_directory(path.get_full_path(__file__, "css")):
built_files = [os.path.abspath("%s.css" % flavour) for flavour in flavours]
if path.is_outdated(built_files, glob.glob("*.scss")):
logging.info("CSS files out of date, rebuilding")
for flavour in flavours:
target = "%s.css" % flavour
assert os.path.exists(flavour + ".scss"), flavour
result = scss.Compiler(output_style="expanded").compile(flavour + ".scss")
assert result
with open(target, "w") as out:
out.write(result)
return []
def run_on_record(record: Record, results: Optional[SMCOGTreeResults],
options: ConfigType) -> SMCOGTreeResults:
""" Generates phylogeny trees of the classifications made by SMCOGs
"""
if results and isinstance(results, SMCOGTreeResults):
return results
# create the smcogs output directory if required
relative_output_dir = os.path.relpath(
os.path.join(options.output_dir, "smcogs"), os.getcwd())
smcogs_dir = os.path.abspath(relative_output_dir)
if not os.path.exists(smcogs_dir):
os.mkdir(smcogs_dir)
nrpspks_genes = record.get_nrps_pks_cds_features()
with path.changed_directory(smcogs_dir):
trees = generate_trees(smcogs_dir,
record.get_cds_features_within_regions(),
nrpspks_genes)
return SMCOGTreeResults(record.id, relative_output_dir, trees)
def get_git_version(
fallback_filename: Optional[str] = GIT_VERSION_FALLBACK_FILENAME
) -> str:
"""Get the sha1 of the current git version"""
git_version = ""
try:
with changed_directory(os.path.dirname(__file__)):
version_cmd = execute(['git', 'rev-parse', '--short', 'HEAD'])
status_cmd = execute(['git', 'status', '--porcelain'])
if version_cmd.successful() and status_cmd.successful():
git_version = version_cmd.stdout.strip()
changes = status_cmd.stdout.splitlines()
if changes:
git_version += "(changed)"
except OSError:
pass
if git_version == "" and fallback_filename:
if locate_file(fallback_filename, silent=True):
with open(fallback_filename, 'rt') as handle:
git_version = handle.read().strip()
return git_version
def write_clusterblast_output(options: ConfigType,
record: Record,
cluster_result: RegionResult,
proteins: Dict[str, Protein],
searchtype: str = "clusterblast") -> None:
""" Writes a text form of clusterblast results to file.
Arguments:
options: the antismash config
record: the record that the results came from
cluster_result: the RegionResult object to write information about
proteins: a dict mapping protein name to Protein
searchtype: the name of the module of which to write results for
Returns:
None
"""
assert isinstance(proteins, dict)
region_number = cluster_result.region.get_region_number()
filename = "%s_c%d.txt" % (record.id, region_number)
with changed_directory(_get_output_dir(options, searchtype)):
_write_output(filename, record, cluster_result, proteins)
def test_functions(self):
with TemporaryDirectory() as tmpdir:
assert os.getcwd() != tmpdir
with path.changed_directory(tmpdir):
assert os.getcwd() == tmpdir
assert os.getcwd() == self.original_dir