mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
4e5406c221
* Add helper script to find duplicate test YAML md5s * Count how many modules the duplicates affect
82 lines
3 KiB
Python
82 lines
3 KiB
Python
#!/usr/bin/env python
|
|
|
|
from rich import print
|
|
from rich.table import Table
|
|
import click
|
|
import glob
|
|
import os
|
|
import yaml
|
|
|
|
|
|
@click.command()
|
|
@click.option(
|
|
"--min_dups",
|
|
default=5,
|
|
show_default=True,
|
|
help="Minimum number of duplicates to report",
|
|
)
|
|
@click.option(
|
|
"--search_dir",
|
|
default=f"{os.path.dirname(__file__)}/../tests/**/test.yml",
|
|
show_default=True,
|
|
help="Glob directory pattern used to find test YAML files",
|
|
)
|
|
def find_duplicate_md5s(min_dups, search_dir):
|
|
"""
|
|
Find duplicate file MD5 sums in test YAML files.
|
|
"""
|
|
md5_filenames = {}
|
|
md5_output_fn_counts = {}
|
|
module_counts = {}
|
|
|
|
# Loop through all files in tests/ called test.yml
|
|
for test_yml in glob.glob(search_dir, recursive=True):
|
|
# Open file and parse YAML
|
|
with open(test_yml, "r") as fh:
|
|
test_config = yaml.safe_load(fh)
|
|
# Loop through tests and check for duplicate md5s
|
|
for test in test_config:
|
|
for test_file in test.get("files", []):
|
|
if "md5sum" in test_file:
|
|
md5 = test_file["md5sum"]
|
|
md5_filenames[md5] = md5_filenames.get(md5, []) + [
|
|
os.path.basename(test_file.get("path"))
|
|
]
|
|
md5_output_fn_counts[md5] = md5_output_fn_counts.get(md5, 0) + 1
|
|
# Log the module that this md5 was in
|
|
modname = os.path.basename(os.path.dirname(test_yml))
|
|
# If tool/subtool show the whole thing
|
|
# Ugly code but trying to stat os-agnostic
|
|
if os.path.basename(
|
|
os.path.dirname(os.path.dirname(test_yml))
|
|
) not in ["modules", "config", "subworkflows"]:
|
|
modname = "{}/{}".format(
|
|
os.path.basename(
|
|
os.path.dirname(os.path.dirname(test_yml))
|
|
),
|
|
os.path.basename(os.path.dirname(test_yml)),
|
|
)
|
|
module_counts[md5] = module_counts.get(md5, []) + [modname]
|
|
|
|
# Set up rich table
|
|
table = Table(title="Duplicate MD5s", row_styles=["dim", ""])
|
|
table.add_column("MD5", style="cyan", no_wrap=True)
|
|
table.add_column("Count", style="magenta", justify="right")
|
|
table.add_column("Num modules", style="blue", justify="right")
|
|
table.add_column("Filenames", style="green")
|
|
|
|
# Add rows - sort md5_output_fn_counts by value
|
|
for md5 in sorted(md5_output_fn_counts, key=md5_output_fn_counts.get):
|
|
if md5_output_fn_counts[md5] >= min_dups:
|
|
table.add_row(
|
|
md5,
|
|
str(md5_output_fn_counts[md5]),
|
|
str(len(set(module_counts[md5]))),
|
|
", ".join(set(md5_filenames[md5])),
|
|
)
|
|
|
|
print(table)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
find_duplicate_md5s()
|