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__main__.py
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Thu, May 2, 15:18

__main__.py
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from .pipeline import Pipeline, ToolError, LoadError, check_singularity
from .eprint import EPrint
from .templates import template_pipeline
import colorama
import sys
import argparse
def __main():
"""Main method to be called when running directly.
Expects CLI arguments."""
colorama.init()
eprint = EPrint()
args = parse_args(sys.argv[1:])
if args.command == "template":
print(template_pipeline)
exit(0)
try:
check_singularity()
except ToolError as e:
eprint.red("Error when running `singularity`: {}".format(e.error))
eprint.yellow("Check your Singularity installation!")
sys.exit(1)
try:
try:
with open(args.pipeline) as f:
pipeline = Pipeline(f, imagefile=args.image, eprint_instance=eprint, dry_run=args.dry_run)
except IOError as e:
eprint.red("\nCannot open pipeline description {0}: {1}".format(args.pipeline, e.strerror))
raise LoadError()
except LoadError:
eprint.yellow("\nUnable to load pipeline description. Aborting.")
sys.exit(1)
try:
if args.command == "build":
pipeline.build(force=args.force)
elif args.command == "run":
pipeline.run()
elif args.command == "test":
pipeline.test(force=args.force, skip_run=args.skip_run)
elif args.command == "check":
pipeline.check()
else:
raise RuntimeError("Unknown command specified")
except RuntimeError as e:
eprint.red("ERROR: {}".format(e))
sys.exit(1)
def parse_args(args):
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="Pipeline, a wrapper around Singularity to build, run and test scientific pipelines."
)
parser.add_argument(
"command",
help="Command to execute",
choices=['build', 'run', 'test', 'check', 'template']
)
parser.add_argument(
"-p", "--pipeline",
default="pipeline.yaml",
help="Pipeline description file (default: '%(default)s')"
)
parser.add_argument(
"-i", "--image",
help="Singularity image file (default: as defined in pipeline description)"
)
parser.add_argument(
"-f", "--force",
action="store_true",
help="Force rebuilding the image or test data for validation (default: no)"
)
parser.add_argument(
"--no-bind",
action="store_true",
help="Omit runtime bind arguments (default: no). Useful in cases when user-supplied path binding is not allowed."
)
parser.add_argument(
"--skip-run",
action="store_true",
help="For testing, skip the run phase, only validating existing output (default: no)"
)
parser.add_argument(
"--dry-run",
action="store_true",
help="Output the intended command sequence without executing it (default: no)"
)
return parser.parse_args(args)
if __name__ == "__main__":
__main()

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