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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 (

KNOWN_FIELDS = ["targets", "image_build", "name_override", "base_image"]
FALLBACK_LINE_TUPLE = collections.namedtuple("FALLBACK_LINE_TUPLE", "targets image_build name_override base_image")

[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 target in generate_targets(args.files): try: ret = mull_targets( target.targets, image_build=target.image_build, name_override=target.name_override, base_image=target.base_image, determine_base_image=False, **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(f"{target_source}/*.tsv") else: target_source_files = [target_source] for target_source_file in target_source_files: # If no headers are defined we use the 4 default fields in the order # that has been used in galaxy-tool-util / galaxy-lib < 20.01 line_tuple = FALLBACK_LINE_TUPLE with open(target_source_file) as f: for line in f.readlines(): if line: line = line.strip() if line.startswith("#"): # headers can define a different column order line_tuple = tuple_from_header(line) else: yield line_to_targets(line, line_tuple) def tuple_from_header(header): fields = header[1:].split("\t") for field in fields: assert field in KNOWN_FIELDS, f"'{field}' is not one of {KNOWN_FIELDS}" # Make sure tuple contains all fields for field in KNOWN_FIELDS: if field not in fields: fields.append(field) return collections.namedtuple("_Line", f"{' '.join(fields)}") def line_to_targets(line_str, line_tuple): """Parse a line so that some columns can remain unspecified.""" line_parts = line_str.split("\t") n_fields = len(line_tuple._fields) targets_column = line_tuple._fields.index("targets") assert ( len(line_parts) <= n_fields ), f"Too many fields in line [{line_str}], expect at most {n_fields} - targets, image build number, and name override." line_parts += [None] * (n_fields - len(line_parts)) line_parts[targets_column] = target_str_to_targets(line_parts[targets_column]) return line_tuple(*line_parts) __all__ = ("main",) if __name__ == "__main__": main()