def archive_samplesheet(run_id, original_samplesheet_path, samplesheet_csv_path, conf):
""" Archive samplesheet file in archive samplesheet directory.
Arguments:
run_id: The run id
original_samplesheet_path: samplesheet path in format xls if exists
samplesheet_csv_path: samplesheet path in format csv
conf: configuration dictionary
"""
# Add samplesheet to the archive of samplesheets
if (common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xls', conf) \
and original_samplesheet_path.endswith(".xls")) or \
(common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xlsx', conf) \
and original_samplesheet_path.endswith(".xlsx")):
cmd = 'cp ' + quote(original_samplesheet_path) + ' ' + quote(conf[TMP_PATH_KEY]) + \
' && cd ' + quote(conf[TMP_PATH_KEY]) + \
' && zip -q ' + quote(conf[BCL2FASTQ_SAMPLESHEETS_PATH_KEY] + '/' + \
conf[BCL2FASTQ_SAMPLESHEET_PREFIX_FILENAME_KEY] + 's.zip') + ' ' + \
quote(os.path.basename(samplesheet_csv_path)) + ' ' + quote(os.path.basename(original_samplesheet_path))
else:
cmd = 'cd ' + quote(conf[TMP_PATH_KEY]) + \
' && zip -q ' + quote(conf[BCL2FASTQ_SAMPLESHEETS_PATH_KEY] + '/' + \
conf[BCL2FASTQ_SAMPLESHEET_PREFIX_FILENAME_KEY] + 's.zip') + ' ' + \
quote(os.path.basename(samplesheet_csv_path))
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Error while archiving the samplesheet file for " + run_id,
'Error while archiving the samplesheet file.\nCommand line:\n' + cmd, conf)
return False
# Remove temporary samplesheet files
if common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xls', conf) or \
common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xlsx', conf):
file_to_remove = conf[TMP_PATH_KEY] + '/' + os.path.basename(original_samplesheet_path)
if os.path.exists(file_to_remove):
os.remove(file_to_remove)
return True
def aozan_main():
"""Aozan main method.
"""
# Define command line parser
parser = OptionParser(usage='usage: ' + Globals.APP_NAME_LOWER_CASE + '.sh [options] conf_file')
parser.add_option('-q', '--quiet', action='store_true', dest='quiet',
default=False, help='quiet')
parser.add_option('-v', '--version', action='store_true', dest='version', help='Aozan version')
parser.add_option('-e', '--exit-code', action='store_true', dest='exit_code',
help='Returns non zero exit code if a step fails')
parser.add_option('-c', '--conf', action='store_true', dest='conf',
help='Default Aozan configuration, loads before configuration file.')
# Parse command line arguments
(options, args) = parser.parse_args()
# Print Aozan current version
if options.version:
print Globals.WELCOME_MSG
sys.exit(0)
# Print default configuration option
if options.conf:
print common.print_default_configuration()
sys.exit(0)
# If no argument print usage
if len(args) < 1:
parser.print_help()
sys.exit(1)
# Create configuration object
conf = LinkedHashMap()
# Set the default value in the configuration object
common.set_default_conf(conf)
# Use default (US) locale
Locale.setDefault(Globals.DEFAULT_LOCALE)
# Check if OS is Linux
if not SystemUtils.isLinux():
sys.stderr.write('ERROR: Aozan can not be executed. Operating system is not Linux\n')
sys.exit(1)
# Check if configuration file exists
conf_file = args[0]
if not os.path.isfile(conf_file):
sys.stderr.write('ERROR: Aozan can not be executed. Configuration file is missing: ' + \
conf_file + '\n')
sys.exit(1)
# Load Aozan conf file
common.load_conf(conf, conf_file)
# End of Aozan if aozan is not enable
if common.is_conf_value_defined(AOZAN_ENABLE_KEY, 'false', conf):
sys.exit(0)
# Init logger
try:
Common.initLogger(conf[AOZAN_LOG_PATH_KEY], conf[AOZAN_LOG_LEVEL_KEY])
except AozanException, exp:
common.exception_msg(exp, conf)
def load_samplesheet(run_id, input_run_data_path, samplesheet_filename, conf):
""" Load the samplesheet.
Arguments:
run id: The run id
input_run_data_path: The input run data path
samplesheet_filename: samplesheet filename
conf: configuration dictionary
Return:
a Samplesheet object and the original path of the samplesheet
"""
run_info_path = input_run_data_path + '/RunInfo.xml'
if not os.path.isfile(run_info_path):
error("no RunInfo.xml file found for run " + run_id,
"No RunInfo.xml file found for run " + run_id + ': ' + run_info_path + '.\n', conf)
return None, None
run_info = RunInfo.parse(run_info_path)
flow_cell_id = run_info.getFlowCell()
common.log("INFO", "Flowcell id: " + flow_cell_id, conf)
common.log("INFO", "Samplesheet format: " + str(conf[BCL2FASTQ_SAMPLESHEET_FORMAT_KEY]), conf)
try:
if common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xls', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'xls',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'csv', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'csv',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xlsx', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'xlsx',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'command', conf):
action_error_msg = 'Error while creating Bcl2fastq CSV samplesheet file'
if not common.is_conf_key_exists(BCL2FASTQ_SAMPLESHEET_GENERATOR_COMMAND_KEY, conf):
error(action_error_msg + ' for run ' + run_id, action_error_msg + ' the command is empty.', conf)
return None, None
input_samplesheet_generated_path = conf[TMP_PATH_KEY] + '/' + samplesheet_filename + 'generated.csv'
cmd = conf[
BCL2FASTQ_SAMPLESHEET_GENERATOR_COMMAND_KEY] + ' ' + run_id + ' ' + quote(input_samplesheet_generated_path)
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error(action_error_msg + ' for run ' + run_id,
action_error_msg + '.\nCommand line:\n' + cmd, conf)
if not os.path.exists(input_samplesheet_generated_path):
error(action_error_msg + ' for run ' + run_id,
action_error_msg + ', the external command did not create Bcl2fastq CSV file:\n' + cmd, conf)
return None, None
# Load CSV samplesheet file
samplesheet = SampleSheetCSVReader(input_samplesheet_generated_path).read()
# Remove generated samplesheet
os.unlink(input_samplesheet_generated_path)
return samplesheet, None
else:
error('Error while creating Bcl2fastq CSV samplesheet file for run ' + run_id,
'No method to get Bcl2fastq samplesheet file has been defined. Please, set the ' +
'"bcl2fastq.samplesheet.format" property.\n',
conf)
return None, None
except AozanException, exp:
print StringUtils.stackTraceToString(exp)
error("Error reading samplesheet: " + samplesheet_filename, exp.getMessage(), conf)
return None, None
try:
# Initialize the QC object
qc = QC(Settings(conf), input_run_data_path, fastq_input_dir, qc_output_dir, conf[TMP_PATH_KEY], run_id)
# Compute the report
report = qc.computeReport()
except AozanException, exp:
error("Error while computing QC report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
except Throwable, exp:
error("Error while computing QC report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
# Remove QC data if not demand
if common.is_conf_value_defined(QC_REPORT_SAVE_RAW_DATA_KEY, 'false', conf):
try:
os.remove(qc_output_dir + '/data-' + run_id + '.txt')
# qc.writeRawData(report, qc_output_dir + '/data-' + run_id + '.txt')
except AozanException, exp:
error("Error while removing QC raw data for run " + run_id + ".", exp.getMessage(), conf)
return False
# Write the XML report
if common.is_conf_value_equals_true(QC_REPORT_SAVE_REPORT_DATA_KEY, conf):
try:
qc.writeXMLReport(report, qc_output_dir + '/' + run_id + '.xml')
except AozanException, exp:
error("Error while computing QC XML report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
except Throwable, exp:
