Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/mulled/mulled_build_files.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Build all composite mulled recipes discovered in TSV files. |
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2 |
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3 Use mulled-build-channel to build images for single recipes for a whole conda |
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4 channel. This script instead builds images for combinations of recipes. This |
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5 script can be given a single TSV file or a directory of TSV files to process. |
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6 |
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7 Examples: |
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8 |
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9 Build all recipes discovered in tsv files in a single directory. |
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10 |
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11 mulled-build-files build |
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12 |
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13 """ |
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14 |
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15 import collections |
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16 import glob |
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17 import os |
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18 import sys |
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19 |
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20 from ._cli import arg_parser |
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21 from .mulled_build import ( |
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22 add_build_arguments, |
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23 args_to_mull_targets_kwds, |
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24 BuildExistsException, |
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25 mull_targets, |
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26 target_str_to_targets, |
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27 ) |
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28 KNOWN_FIELDS = ["targets", "image_build", "name_override", "base_image"] |
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29 FALLBACK_LINE_TUPLE = collections.namedtuple("_Line", "targets image_build name_override base_image") |
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30 |
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31 |
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32 def main(argv=None): |
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33 """Main entry-point for the CLI tool.""" |
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34 parser = arg_parser(argv, globals()) |
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35 add_build_arguments(parser) |
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36 parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)') |
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37 parser.add_argument('files', metavar="FILES", default=".", |
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38 help="Path to directory (or single file) of TSV files describing composite recipes.") |
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39 args = parser.parse_args() |
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40 for target in generate_targets(args.files): |
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41 try: |
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42 ret = mull_targets( |
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43 target.targets, |
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44 image_build=target.image_build, |
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45 name_override=target.name_override, |
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46 base_image=target.base_image, |
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47 determine_base_image=False, |
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48 **args_to_mull_targets_kwds(args) |
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49 ) |
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50 except BuildExistsException: |
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51 continue |
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52 if ret > 0: |
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53 sys.exit(ret) |
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54 |
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55 |
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56 def generate_targets(target_source): |
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57 """Generate all targets from TSV files in specified file or directory.""" |
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58 target_source = os.path.abspath(target_source) |
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59 if os.path.isdir(target_source): |
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60 target_source_files = glob.glob(target_source + "/*.tsv") |
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61 else: |
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62 target_source_files = [target_source] |
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63 |
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64 for target_source_file in target_source_files: |
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65 # If no headers are defined we use the 4 default fields in the order |
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66 # that has been used in galaxy-tool-util / galaxy-lib < 20.01 |
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67 line_tuple = FALLBACK_LINE_TUPLE |
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68 with open(target_source_file) as f: |
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69 for line in f.readlines(): |
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70 if line: |
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71 line = line.strip() |
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72 if line.startswith('#'): |
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73 # headers can define a different column order |
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74 line_tuple = tuple_from_header(line) |
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75 else: |
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76 yield line_to_targets(line, line_tuple) |
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77 |
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78 |
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79 def tuple_from_header(header): |
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80 fields = header[1:].split('\t') |
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81 for field in fields: |
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82 assert field in KNOWN_FIELDS, f"'{field}' is not one of {KNOWN_FIELDS}" |
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83 # Make sure tuple contains all fields |
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84 for field in KNOWN_FIELDS: |
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85 if field not in fields: |
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86 fields.append(field) |
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87 return collections.namedtuple("_Line", "%s" % " ".join(fields)) |
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88 |
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89 |
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90 def line_to_targets(line_str, line_tuple): |
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91 """Parse a line so that some columns can remain unspecified.""" |
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92 line_parts = line_str.split("\t") |
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93 n_fields = len(line_tuple._fields) |
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94 targets_column = line_tuple._fields.index('targets') |
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95 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." |
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96 line_parts += [None] * (n_fields - len(line_parts)) |
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97 line_parts[targets_column] = target_str_to_targets(line_parts[targets_column]) |
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98 return line_tuple(*line_parts) |
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99 |
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100 |
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101 __all__ = ("main", ) |
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102 |
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103 |
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104 if __name__ == '__main__': |
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105 main() |