mirror of
https://github.com/MillironX/nf-core_modules.git
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83 lines
3 KiB
Python
83 lines
3 KiB
Python
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#!/usr/bin/env python
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from rich import print
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from rich.table import Table
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import click
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import glob
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import os
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import yaml
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@click.command()
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@click.option(
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"--min_dups",
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default=5,
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show_default=True,
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help="Minimum number of duplicates to report",
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)
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@click.option(
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"--search_dir",
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default=f"{os.path.dirname(__file__)}/../tests/**/test.yml",
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show_default=True,
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help="Glob directory pattern used to find test YAML files",
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)
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def find_duplicate_md5s(min_dups, search_dir):
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"""
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Find duplicate file MD5 sums in test YAML files.
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"""
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md5_filenames = {}
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md5_output_fn_counts = {}
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module_counts = {}
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# Loop through all files in tests/ called test.yml
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for test_yml in glob.glob(search_dir, recursive=True):
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# Open file and parse YAML
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with open(test_yml, "r") as fh:
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test_config = yaml.safe_load(fh)
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# Loop through tests and check for duplicate md5s
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for test in test_config:
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for test_file in test.get("files", []):
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if "md5sum" in test_file:
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md5 = test_file["md5sum"]
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md5_filenames[md5] = md5_filenames.get(md5, []) + [
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os.path.basename(test_file.get("path"))
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]
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md5_output_fn_counts[md5] = md5_output_fn_counts.get(md5, 0) + 1
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# Log the module that this md5 was in
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modname = os.path.basename(os.path.dirname(test_yml))
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# If tool/subtool show the whole thing
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# Ugly code but trying to stat os-agnostic
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if os.path.basename(
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os.path.dirname(os.path.dirname(test_yml))
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) not in ["modules", "config", "subworkflows"]:
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modname = "{}/{}".format(
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os.path.basename(
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os.path.dirname(os.path.dirname(test_yml))
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),
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os.path.basename(os.path.dirname(test_yml)),
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)
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module_counts[md5] = module_counts.get(md5, []) + [modname]
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# Set up rich table
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table = Table(title="Duplicate MD5s", row_styles=["dim", ""])
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table.add_column("MD5", style="cyan", no_wrap=True)
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table.add_column("Count", style="magenta", justify="right")
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table.add_column("Num modules", style="blue", justify="right")
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table.add_column("Filenames", style="green")
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# Add rows - sort md5_output_fn_counts by value
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for md5 in sorted(md5_output_fn_counts, key=md5_output_fn_counts.get):
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if md5_output_fn_counts[md5] >= min_dups:
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table.add_row(
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md5,
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str(md5_output_fn_counts[md5]),
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str(len(set(module_counts[md5]))),
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", ".join(set(md5_filenames[md5])),
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)
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print(table)
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if __name__ == "__main__":
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find_duplicate_md5s()
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