diff env/lib/python3.9/site-packages/galaxy/tool_util/deps/mulled/mulled_build_files.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/deps/mulled/mulled_build_files.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,105 @@
+"""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.
+
+Examples:
+
+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 (
+    add_build_arguments,
+    args_to_mull_targets_kwds,
+    BuildExistsException,
+    mull_targets,
+    target_str_to_targets,
+)
+KNOWN_FIELDS = ["targets", "image_build", "name_override", "base_image"]
+FALLBACK_LINE_TUPLE = collections.namedtuple("_Line", "targets image_build name_override base_image")
+
+
+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(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", "%s" % " ".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()