def archive_demux_stat(run_id, fastq_output_dir, reports_data_path, basecall_stats_file,
basecall_stats_prefix, samplesheet_csv_path, conf):
""" Archive demultplexing statistics results file.
Arguments:
run_id: The run id
fastq_output_dir: fastq directory to save result on demultiplexing
reports_data_path: directory to save archives
basecall_stats_file: file to archive
basecall_stats_prefix: prefix file to archive
samplesheet_csv_path: samplesheet in csv
conf: configuration dictionary
"""
archive_run_dirname = basecall_stats_prefix + run_id
archive_run_dir = reports_data_path + '/' + archive_run_dirname
archive_run_tar_file = reports_data_path + '/' + basecall_stats_file
# With bcl2fastq 2
cmd_list = []
cmd_list.extend(['cd', quote(fastq_output_dir), '&&'])
cmd_list.extend(['mkdir', quote(archive_run_dir), '&&'])
cmd_list.extend(['cp', '-r', 'Reports', 'Stats', 'InterOp', quote(samplesheet_csv_path), quote(archive_run_dir), '&&'])
cmd_list.extend(['tar cjf', quote(archive_run_tar_file), '-C', quote(reports_data_path), quote(archive_run_dirname)])
cmd = " ".join(cmd_list)
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Error while saving the basecall stats files for " + run_id,
'Error while saving the basecall stats files.\nCommand line:\n' + cmd, conf)
return False
# Set read only basecall stats archives files
common.chmod(archive_run_tar_file, conf)
return True
def create_run_summary_reports(run_id, conf):
""" Copy main files and directory from hiseq run directory to save in report run data directory.
Save data in two distinct directory on hiseq and on report, and tar.bz2 version
Arguments:
run_id: the run id
conf: configuration dictionary
"""
hiseq_data_path = hiseq_run.find_hiseq_run_path(run_id, conf)
tmp_base_path = conf[TMP_PATH_KEY]
reports_data_base_path = conf[REPORTS_DATA_PATH_KEY]
source_path = hiseq_data_path + '/' + run_id
reports_data_path = common.get_report_run_data_path(run_id, conf)
report_prefix = 'report_'
hiseq_log_prefix = 'hiseq_log_'
report_archive_file = report_prefix + run_id + '.tar.bz2'
hiseq_log_archive_file = hiseq_log_prefix + run_id + '.tar.bz2'
# Save quality control data
tmp_path = tmp_base_path + '/' + run_id
# Check if reports_data_path exists
if not os.path.exists(reports_data_base_path):
error("Failed to create report archive: Report directory does not exist",
"Failed to create report archive: Report directory does not exist: " + reports_data_base_path, conf)
return False
# Check if temporary directory exists
if not os.path.exists(tmp_base_path):
error("Failed to create report archive: Temporary directory does not exist",
"Failed to create report archive: Temporary directory does not exist: " + tmp_base_path, conf)
return False
# Check if reports archive exists
if os.path.exists(reports_data_path + '/' + report_archive_file):
error("Failed to create report archive: Report archive already exists for run " + run_id,
"Failed to create report archive: Report archive already exists for run " + run_id + " : " + report_archive_file, conf)
return False
# Check if hiseq log archive exists
if os.path.exists(reports_data_path + '/' + hiseq_log_archive_file):
error("Failed to create report archive: Hiseq log archive already exists for run " + run_id,
"Failed to create report archive: Hiseq log archive already exists for run " + run_id + " : " + hiseq_log_archive_file, conf)
return False
# Create if not exist archive directory for the run
if not os.path.exists(reports_data_path):
os.mkdir(reports_data_path)
# Create run tmp directory
if os.path.exists(tmp_path):
error("Failed to create report archive: Temporary run data directory already exists for run " + run_id,
"Failed to create report archive: Temporary run data directory already exists for run " + run_id + " : " + hiseq_log_archive_file, conf)
else:
os.mkdir(tmp_path)
# Define set file to copy in report archive, check if exists (depend on parameters Illumina)
files = ['InterOp', 'RunInfo.xml', 'runParameters.xml', 'RunParameters.xml']
files_to_copy = list_existing_files(source_path, files)
if len(files_to_copy) == 0:
common.log("WARNING",
"Archive " + hiseq_log_archive_file + " not created: none file exists " + str(files) +
' in ' + source_path, conf)
else:
cmd = 'cd ' + quote(source_path) + ' && ' + \
'cp -rp ' + files_to_copy + ' ' + quote(tmp_path) + ' && ' + \
'cd ' + quote(tmp_base_path) + ' && ' + \
'mv ' + quote(run_id) + ' ' + quote(hiseq_log_prefix + run_id) + ' && ' + \
'tar cjf ' + quote(reports_data_path + '/' + hiseq_log_archive_file) + ' ' + quote(hiseq_log_prefix + run_id) + ' && ' +\
'rm -rf ' + quote(tmp_path)
# + ' && rm -rf ' + hiseq_log_prefix + run_id
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Failed to create report archive: Error while saving Illumina quality control for run " + run_id,
"Failed to create report archive: Error saving Illumina quality control.\nCommand line:\n" + cmd, conf)
return False
# Save html reports
if os.path.exists(tmp_path):
cmd = 'rm -rf ' + quote(tmp_path)
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Failed to create report archive: Error while removing existing temporary directory",
"Failed to create report archive: Error while removing existing temporary directory.\nCommand line:\n" + cmd, conf)
return False
os.mkdir(tmp_path)
# Define set file to copy in report archive, check if exists (depend on parameters Illumina)
if common.get_rta_major_version(run_id, conf) == 1:
files = ['./Data/Status_Files', './Data/reports', './Data/Status.htm', './First_Base_Report.htm']
else:
files = ['./Config', './Recipe', './RTALogs', './RTAConfiguration.xml', './RunCompletionStatus.xml']
files_to_copy = list_existing_files(source_path, files)
if len(files_to_copy) == 0:
common.log("WARNING", "Archive " + report_archive_file + " not created: none file exists " + str(
files) + ' in ' + source_path, conf)
else:
cmd = 'cd ' + quote(source_path) + ' && ' + \
'cp -rp ' + files_to_copy + ' ' + quote(tmp_path) + ' && ' + \
'cd ' + quote(tmp_base_path) + ' && ' + \
'mv ' + quote(run_id) + ' ' + quote(report_prefix + run_id) + ' && ' + \
'tar cjf ' + quote(reports_data_path + '/' + report_archive_file) + ' ' + quote(report_prefix + run_id) + ' && ' + \
'mv ' + quote(report_prefix + run_id) + ' ' + quote(reports_data_path)
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Failed to create report archive: Error while saving Illumina HTML reports for run " + run_id,
"Failed to create report archive: Error saving Illumina HTML reports.\nCommand line:\n" + cmd, conf)
return False
# Create index.hml file
common.create_html_index_file(conf, run_id, [HISEQ_STEP_KEY])
# Set read only the report directory
common.chmod_files_in_dir(reports_data_path + '/' + report_prefix, None, conf)
# Set read only archives files
common.chmod(reports_data_path + '/' + report_archive_file, conf)
common.chmod(reports_data_path + '/' + hiseq_log_archive_file, conf)
return True
# Check if the report has been generated
if not os.path.exists(html_report_file):
error("Error while computing QC report for run " + run_id + ".", "No HTML report generated", conf)
return False
# Archive the reports
cmd = 'cd ' + quote(reports_data_path) + ' && ' + \
'tar cjf qc_' + run_id + '.tar.bz2 qc_' + run_id
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Error while saving the QC archive file for " + run_id,
'Error while saving the QC archive file.\nCommand line:\n' + cmd, conf)
return False
# Set read only basecall stats archives files
common.chmod(reports_data_path + '/qc_' + run_id + '.tar.bz2', conf)
# Check if the report has been generated
if not os.path.exists(html_report_file):
error("Error while computing QC report for run " + run_id + ".", "No HTML report generated", conf)
return False
# The output directory must be read only
if not common.chmod_files_in_dir(qc_output_dir, None, conf):
error("Error while setting the output QC directory to read only for run " + run_id,
'Error while setting the output QC directory to read only.\nCommand line:\n' + cmd, conf)
return False
# Create index.hml file
sessions = [Settings.HISEQ_STEP_KEY, Settings.DEMUX_STEP_KEY, Settings.QC_STEP_KEY]
common.create_html_index_file(conf, run_id, sessions)