def test_add_dry_run_option_with_argparse(self):
"""add_dry_run_option enables '--dry-run' with ArgumentParser
"""
p = ArgumentParser()
add_dry_run_option(p)
args = p.parse_args(['--dry-run'])
self.assertTrue(args.dry_run)
def add_archive_command(cmdparser):
"""Create a parser for the 'archive' command
"""
p = cmdparser.add_command('archive',help="Copy analyses to 'archive' area",
usage="%prog archive [OPTIONS] [ANALYSIS_DIR]",
version="%prog "+__version__,
description="Copy sequencing analysis data directory "
"ANALYSIS_DIR to 'archive' destination.")
p.add_option('--archive_dir',action='store',
dest='archive_dir',default=None,
help="specify top-level archive directory to copy data under. "
"ARCHIVE_DIR can be a local directory, or a remote location in the "
"form '[[user@]host:]directory'. Overrides the default settings.")
p.add_option('--platform',action='store',
dest='platform',default=None,
help="specify the platform e.g. 'hiseq', 'miseq' etc (overrides "
"automatically determined platform, if any). Use 'other' for cases "
"where the platform is unknown.")
p.add_option('--year',action='store',
dest='year',default=None,
help="specify the year e.g. '2014' (default is the current year)")
default_group = __settings.archive.group
p.add_option('--group',action='store',dest='group',default=default_group,
help="specify the name of group for the archived files NB only works "
"when the archive is a local directory (default: %s)" % default_group)
default_chmod = __settings.archive.chmod
p.add_option('--chmod',action='store',dest='chmod',default=default_chmod,
help="specify chmod operations for the archived files (default: "
"%s)" % default_chmod)
p.add_option('--force',action='store_true',dest='force',default=False,
help="perform archiving operation even if key metadata items are "
"not set")
add_dry_run_option(p)
add_debug_option(p)
def test_add_dry_run_option(self):
"""add_dry_run_option enables '--dry-run'
"""
# Skip the test if optparse not available
if not OPTPARSE_AVAILABLE:
raise unittest.SkipTest("'optparse' not available")
p = OptionParser()
add_dry_run_option(p)
options, args = p.parse_args(['--dry-run'])
self.assertTrue(options.dry_run)
def add_merge_fastq_dirs_command(cmdparser):
"""Create a parser for the 'merge_fastq_dirs' command
"""
p = cmdparser.add_command('merge_fastq_dirs',help="Combine bcl-to-fastq runs",
usage="%prog merge_fastq_dirs [OPTIONS] [ANALYSIS_DIR]",
description="Automatically merge fastq directories from "
"multiple bcl-to-fastq runs within ANALYSIS_DIR. Use this "
"command if 'make_fastqs' step was run multiple times to "
"process subsets of lanes.")
p.add_option('--primary-unaligned-dir',action='store',
dest='unaligned_dir',default='bcl2fastq',
help="merge fastqs from additional bcl-to-fastq directories into "
"UNALIGNED_DIR. Original data will be moved out of the way first. "
"Defaults to 'bcl2fastq'.")
add_dry_run_option(p)
add_debug_option(p)
# Add info command
p.add_command('info',help="Get information about ANALYSIS_DIR",
usage="%prog info [OPTIONS] ANALYSIS_DIR",
description="Report information on processed Illumina "
"sequence data in ANALYSIS_DIR.")
add_debug_option(p.parser_for('info'))
# Add copy command
p.add_command('copy',help="Copy fastqs from ANALYSIS_DIR",
usage="%prog copy [OPTIONS] ANALYSIS_DIR DEST_DIR",
description="Copy fastqs from ANALYSIS_DIR to DEST_DIR.")
p.parser_for('copy').add_option('--projects',action='store',dest='projects',default=None,
help="Restrict copying to projects matching the "
"supplied pattern")
p.parser_for('copy').add_option('--fastq-dir',action='store',dest='fastq_dir',default=None,
help="Only copy fastqs from the specified FASTQ_DIR")
add_dry_run_option(p.parser_for('copy'))
add_debug_option(p.parser_for('copy'))
# Process the command line
cmd,options,args = p.parse_args()
if len(args) < 1:
p.error("Need to supply a directory to examine")
if options.debug:
logging.getLogger().setLevel(logging.DEBUG)
# Acquire data for putative analysis directory
dirn = os.path.abspath(args[0])
print "Examining %s" % dirn
analysis_dir = utils.AnalysisDir(dirn)
if not (analysis_dir.n_projects and analysis_dir.n_sequencing_data):
logging.warning("Not an analysis directory")
sys.exit()
# Deal with commands