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Source code for galaxy.tool_util.deps.mulled.mulled_build_files

"""Build all composite mulled recipes discovered in TSV files.

Use mulled-build-channel to build images for single recipes for a whole conda
channel. This script instead builds images for combinations of recipes. This
script can be given a single TSV file or a directory of TSV files to process.


Build all recipes discovered in tsv files in a single directory.

    mulled-build-files build


import collections
import glob
import os
import sys

from ._cli import arg_parser
from .mulled_build import (

[docs]def main(argv=None): """Main entry-point for the CLI tool.""" parser = arg_parser(argv, globals()) add_build_arguments(parser) parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)') parser.add_argument('files', metavar="FILES", default=".", help="Path to directory (or single file) of TSV files describing composite recipes.") args = parser.parse_args() for (targets, image_build, name_override) in generate_targets(args.files): try: ret = mull_targets( targets, image_build=image_build, name_override=name_override, **args_to_mull_targets_kwds(args) ) except BuildExistsException: continue if ret > 0: sys.exit(ret)
def generate_targets(target_source): """Generate all targets from TSV files in specified file or directory.""" target_source = os.path.abspath(target_source) if os.path.isdir(target_source): target_source_files = glob.glob(target_source + "/*.tsv") else: target_source_files = [target_source] for target_source_file in target_source_files: with open(target_source_file, "r") as f: for line in f.readlines(): if line: line = line.strip() if not line or line.startswith("#"): continue yield line_to_targets(line) def line_to_targets(line_str): line = _parse_line(line_str) return (target_str_to_targets(line.targets), line.image_build, line.name_override) _Line = collections.namedtuple("_Line", ["targets", "image_build", "name_override"]) def _parse_line(line_str): line_parts = line_str.split("\t") assert len(line_parts) < 3, "Too many fields in line [%s], expect at most 3 - targets, image build number, and name override." % line_str line_parts += [None] * (3 - len(line_parts)) return _Line(*line_parts) __all__ = ("main", ) if __name__ == '__main__': main()