def _handler(dummy_signum, dummy_frame):
msg = "WARNING: Jacquard was interrupted before completing."
try:
logger.debug(msg)
finally:
print(msg, file=sys.stderr)
exit(1)
def _handler(dummy_signum, dummy_frame):
msg = "WARNING: Jacquard was interrupted before completing."
try:
logger.debug(msg)
finally:
print(msg, file=sys.stderr)
exit(1)
def test_initialize_logger_notVerbose(self):
tool = "foo"
args = Namespace(subparser_name=tool, log_file=None, verbose=None)
logger.initialize_logger(args)
logger.debug("bar")
output_lines = self.output.getvalue().rstrip().split("\n")
root_logger = logger.logging.getLogger()
self.assertEquals(["root: DEBUG: bar"], root_logger.handlers[0].buffer)
self.assertEquals(output_lines[0], "")
def _move_tmp_contents_to_original(args):
temp_dir = args.temp_working_dir
dest_dir = os.path.dirname(args.temp_working_dir)
logger.debug(
"Moving files from tmp directory [{}] to output "
"directory [{}]", temp_dir, dest_dir)
distutils.dir_util.copy_tree(temp_dir, dest_dir)
logger.debug("Output saved to [{}]", os.path.abspath(args.original_output))
logger.info("Output saved to [{}]", args.original_output)
_cleanup(temp_dir)
def execute(args, dummy_execution_context):
#for the moment, there is no good place to put the execution context
input_file = os.path.abspath(args.input)
output_file = os.path.abspath(args.output)
col_spec = None
if args.selected_columns_file:
col_spec = args.selected_columns_file
logger.debug("Expanding [{}] to [{}]",
input_file,
output_file)
logger.info("Expanding [{}] to [{}]",
args.input,
args.original_output)
vcf_reader = vcf.VcfReader(vcf.FileReader(input_file))
file_writer = vcf.FileWriter(output_file)
file_writer.open()
(columns, glossary_fields) = _get_actual_columns(vcf_reader, col_spec)
file_writer.write("#" + "\t".join(columns) + "\n")
line_count = 0
vcf_reader.open()
for vcf_record in vcf_reader.vcf_records():
row_dict = _create_row_dict(vcf_reader.split_column_header,
vcf_record)
new_line = []
for col in columns:
if col in row_dict:
new_line.append(row_dict[col])
else:
new_line.append(".")
file_writer.write("\t".join(new_line) + "\n")
line_count +=1
if line_count % 10000 == 0:
logger.info("Expanding: {} rows processed", line_count)
logger.info("Expand complete: {} rows processed", line_count)
file_writer.close()
glossary_writer = _get_glossary_writer(output_file)
glossary_writer.open()
_create_glossary(vcf_reader.metaheaders, glossary_fields, glossary_writer)
glossary_writer.close()
logger.info("Wrote glossary to [{}]",
os.path.basename(glossary_writer.output_filepath))
vcf_reader.close()
logger.debug("Wrote input [{}] to output [{}]", input_file, output_file)
def _move_tmp_contents_to_original(args):
temp_dir = args.temp_working_dir
dest_dir = os.path.dirname(args.temp_working_dir)
logger.debug("Moving files from tmp directory [{}] to output "
"directory [{}]",
temp_dir,
dest_dir)
distutils.dir_util.copy_tree(temp_dir, dest_dir)
logger.debug("Output saved to [{}]", os.path.abspath(args.original_output))
logger.info("Output saved to [{}]", args.original_output)
_cleanup(temp_dir)
def test_initialize_logger_notVerbose(self):
tool = "foo"
args = Namespace(subparser_name=tool,
log_file=None,
verbose=None)
logger.initialize_logger(args)
logger.debug("bar")
output_lines = self.output.getvalue().rstrip().split("\n")
root_logger = logger.logging.getLogger()
self.assertEquals(["root: DEBUG: bar"], root_logger.handlers[0].buffer)
self.assertEquals(output_lines[0], "")
def log_statistics(self):
cell_msg = "{}% ({}) cells were excluded because (--include_cells={})"
logger.info(cell_msg,
int(round(100 * self.cells_excluded / self.cell_count, 0)),
self.cells_excluded, self._args.include_cells)
row_msg = "{}% ({}) rows were excluded because (--include_rows={})"
logger.info(row_msg,
int(round(100 * self.rows_excluded / self.row_count, 0)),
self.rows_excluded, self._args.include_rows)
for key, count in self.excluded_breakdown.items():
msg = "{} cells were excluded with [{}]"
logger.debug(msg, count, key)
def test_initialize_logger_verbose(self):
tool = "foo"
args = Namespace(subparser_name=tool, log_file=None, verbose=True)
logger.initialize_logger(args)
logger.debug("bar")
root_logger = logger.logging.getLogger()
current_time = datetime.now().strftime('%Y-%m-%d')
output_lines = self.output.getvalue().rstrip().split("\n")
self.assertRegexpMatches(output_lines[0],
"" + current_time + r".*\|DEBUG\|foo\|bar")
self.assertEquals(["root: DEBUG: bar"], root_logger.handlers[0].buffer)
self.assertRegexpMatches(output_lines[0],
r"" + current_time + "|DEBUG|foo|bar'")
def test_initialize_logger_verbose(self):
tool = "foo"
args = Namespace(subparser_name=tool,
log_file=None,
verbose=True)
logger.initialize_logger(args)
logger.debug("bar")
root_logger = logger.logging.getLogger()
current_time = datetime.now().strftime('%Y-%m-%d')
output_lines = self.output.getvalue().rstrip().split("\n")
self.assertRegexpMatches(output_lines[0], ""+current_time+r".*\|DEBUG\|foo\|bar")
self.assertEquals(["root: DEBUG: bar"], root_logger.handlers[0].buffer)
self.assertRegexpMatches(output_lines[0], r""+current_time+"|DEBUG|foo|bar'")
def execute(args, dummy_execution_context):
#for the moment, there is no good place to put the execution context
input_file = os.path.abspath(args.input)
output_file = os.path.abspath(args.output)
col_spec = None
if args.selected_columns_file:
col_spec = args.selected_columns_file
logger.debug("Expanding [{}] to [{}]", input_file, output_file)
logger.info("Expanding [{}] to [{}]", args.input, args.original_output)
vcf_reader = vcf.VcfReader(vcf.FileReader(input_file))
file_writer = vcf.FileWriter(output_file)
file_writer.open()
(columns, glossary_fields) = _get_actual_columns(vcf_reader, col_spec)
file_writer.write("#" + "\t".join(columns) + "\n")
line_count = 0
vcf_reader.open()
for vcf_record in vcf_reader.vcf_records():
row_dict = _create_row_dict(vcf_reader.split_column_header, vcf_record)
new_line = []
for col in columns:
if col in row_dict:
new_line.append(row_dict[col])
else:
new_line.append(".")
file_writer.write("\t".join(new_line) + "\n")
line_count += 1
if line_count % 10000 == 0:
logger.info("Expanding: {} rows processed", line_count)
logger.info("Expand complete: {} rows processed", line_count)
file_writer.close()
glossary_writer = _get_glossary_writer(output_file)
glossary_writer.open()
_create_glossary(vcf_reader.metaheaders, glossary_fields, glossary_writer)
glossary_writer.close()
logger.info("Wrote glossary to [{}]",
os.path.basename(glossary_writer.output_filepath))
vcf_reader.close()
logger.debug("Wrote input [{}] to output [{}]", input_file, output_file)
def log_statistics(self):
cell_msg = "{}% ({}) cells were excluded because (--include_cells={})"
logger.info(cell_msg,
int(round(100 * self.cells_excluded / self.cell_count, 0)),
self.cells_excluded,
self._args.include_cells)
row_msg = "{}% ({}) rows were excluded because (--include_rows={})"
logger.info(row_msg,
int(round(100 * self.rows_excluded / self.row_count, 0)),
self.rows_excluded,
self._args.include_rows)
for key, count in self.excluded_breakdown.items():
msg = "{} cells were excluded with [{}]"
logger.debug(msg, count, key)
def _get_unsorted_readers(vcf_readers):
unsorted_readers = []
for i, reader in enumerate(vcf_readers):
logger.info("Checking sort order of [{}] ({}/{})", reader.file_name,
i + 1, len(vcf_readers))
previous_record = None
reader.open()
for vcf_record in reader.vcf_records():
if previous_record and vcf_record < previous_record:
logger.debug(
"VCF file:chrom:pos [{}:{}:{}] is out of order".format(
reader.file_name, vcf_record.chrom, vcf_record.pos))
unsorted_readers.append(reader)
break
else:
previous_record = vcf_record
reader.close()
return unsorted_readers
def _get_unsorted_readers(vcf_readers):
unsorted_readers = []
for i, reader in enumerate(vcf_readers):
logger.info("Checking sort order of [{}] ({}/{})",
reader.file_name,
i+1,
len(vcf_readers)
)
previous_record = None
reader.open()
for vcf_record in reader.vcf_records():
if previous_record and vcf_record < previous_record:
logger.debug("VCF file:chrom:pos [{}:{}:{}] is out of order"
.format(reader.file_name,
vcf_record.chrom,
vcf_record.pos))
unsorted_readers.append(reader)
break
else:
previous_record = vcf_record
reader.close()
return unsorted_readers
def _cleanup(temp_working_dir):
if temp_working_dir and os.path.exists(temp_working_dir):
logger.debug("Cleaning up tmp directory")
shutil.rmtree(temp_working_dir)
def _dispatch(modules, arguments):
try:
command, args = _parse_command_line_args(modules, arguments)
execution_context = _get_execution_context(arguments)
logger.initialize_logger(args)
logger.debug("Jacquard run begins")
logger.debug("cwd|{}", os.getcwd())
logger.debug("command|{}", " ".join(arguments))
command_validator.preflight(command, args)
logger.info("Jacquard begins (v{})", __version__)
logger.info("Saving log to [{}]",
os.path.basename(logger.log_filename))
logger.debug("Writing output to tmp directory [{}]",
args.temp_working_dir)
command.execute(args, execution_context)
_move_tmp_contents_to_original(args)
if logger.WARNING_OCCURRED:
logger.info("Done. (See warnings above)")
else:
logger.info("Done")
except utils.UsageError as usage_error:
message = "Jacquard usage problem: {}".format(str(usage_error))
logger.debug(message)
print(message, file=sys.stderr)
try:
print("See 'jacquard {} --help'.".format(args.subparser_name),
file=sys.stderr)
except NameError: #could not determine the command
print("See 'jacquard --help'.", file=sys.stderr)
sys.exit(1)
except Exception as exception: #pylint: disable=broad-except
logger.error(str(exception))
logger.error("Jacquard encountered an unanticipated problem. "
"Please review log file and contact your sysadmin "
"or Jacquard support for assistance.")
logger.debug(traceback.format_exc())
sys.exit(1)
finally:
try:
_cleanup(args.temp_working_dir)
except Exception: #pylint: disable=broad-except
pass #we tried
def _cleanup(temp_working_dir):
if temp_working_dir and os.path.exists(temp_working_dir):
logger.debug("Cleaning up tmp directory")
shutil.rmtree(temp_working_dir)
def _dispatch(modules, arguments):
try:
command, args = _parse_command_line_args(modules, arguments)
execution_context = _get_execution_context(arguments)
logger.initialize_logger(args)
logger.debug("Jacquard run begins")
logger.debug("cwd|{}", os.getcwd())
logger.debug("command|{}", " ".join(arguments))
command_validator.preflight(command, args)
logger.info("Jacquard begins (v{})", __version__)
logger.info("Saving log to [{}]",
os.path.basename(logger.log_filename))
logger.debug("Writing output to tmp directory [{}]",
args.temp_working_dir)
command.execute(args, execution_context)
_move_tmp_contents_to_original(args)
if logger.WARNING_OCCURRED:
logger.info("Done. (See warnings above)")
else:
logger.info("Done")
except utils.UsageError as usage_error:
message = "Jacquard usage problem: {}".format(str(usage_error))
logger.debug(message)
print(message, file=sys.stderr)
try:
print("See 'jacquard {} --help'.".format(args.subparser_name),
file=sys.stderr)
except NameError: #could not determine the command
print("See 'jacquard --help'.", file=sys.stderr)
sys.exit(1)
except Exception as exception: #pylint: disable=broad-except
logger.error(str(exception))
logger.error("Jacquard encountered an unanticipated problem. "
"Please review log file and contact your sysadmin "
"or Jacquard support for assistance.")
logger.debug(traceback.format_exc())
sys.exit(1)
finally:
try:
_cleanup(args.temp_working_dir)
except Exception: #pylint: disable=broad-except
pass #we tried
