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Merge pull request #286 from nf-core/dev
Dev -> Master for v1.12.0 release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,152 @@ | ||
| #!/usr/bin/env python | ||
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| ## This script is used to generate scan *.nf.test files for function/process/workflow name and return as a JSON list | ||
| # It is functionally similar to nf-test list but fills a gap until feature https://github.com/askimed/nf-test/issues/196 is added | ||
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| import argparse | ||
| import json | ||
| import logging | ||
| import re | ||
|
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| from itertools import chain | ||
| from pathlib import Path | ||
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| def parse_args() -> argparse.Namespace: | ||
| """ | ||
| Parse command line arguments and return an ArgumentParser object. | ||
| Returns: | ||
| argparse.ArgumentParser: The ArgumentParser object with the parsed arguments. | ||
| """ | ||
| parser = argparse.ArgumentParser( | ||
| description="Scan *.nf.test files for function/process/workflow name and return as a JSON list" | ||
| ) | ||
| parser.add_argument( | ||
| "-p", | ||
| "--paths", | ||
| nargs="+", | ||
| default=["."], | ||
| help="List of directories or files to scan", | ||
| ) | ||
| parser.add_argument( | ||
| "-l", | ||
| "--log-level", | ||
| choices=["DEBUG", "INFO", "WARNING", "ERROR"], | ||
| default="INFO", | ||
| help="Logging level", | ||
| ) | ||
| parser.add_argument( | ||
| "-t", | ||
| "--types", | ||
| nargs="+", | ||
| choices=["function", "process", "workflow", "pipeline"], | ||
| default=["function", "process", "workflow", "pipeline"], | ||
| help="Types of tests to include.", | ||
| ) | ||
| return parser.parse_args() | ||
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| def find_files(paths: list[str]) -> list[Path]: | ||
| """ | ||
| Find all files matching pattern *.nf.test recursively from a list of paths. | ||
| Args: | ||
| paths (list): List of directories or files to scan. | ||
| Returns: | ||
| list: List of files matching the pattern *.nf.test. | ||
| """ | ||
| # this is a bit clunky | ||
| result = [] | ||
| for path in paths: | ||
| path_obj = Path(path) | ||
| # If Path is the exact nf-test file add to list: | ||
| if path_obj.match("*.nf.test"): | ||
| result.append(path_obj) | ||
| # Else recursively search for nf-test files: | ||
| else: | ||
| for file in path_obj.rglob("*.nf.test"): | ||
| result.append(file) | ||
| return result | ||
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| def process_files(files: list[Path]) -> list[str]: | ||
| """ | ||
| Process the files and return lines that begin with 'workflow', 'process', or 'function' and have a single string afterwards. | ||
| Args: | ||
| files (list): List of files to process. | ||
| Returns: | ||
| list: List of lines that match the criteria. | ||
| """ | ||
| result = [] | ||
| for file in files: | ||
| with open(file, "r") as f: | ||
| is_pipeline_test = True | ||
| lines = f.readlines() | ||
| for line in lines: | ||
| line = line.strip() | ||
| if line.startswith(("workflow", "process", "function")): | ||
| words = line.split() | ||
| if len(words) == 2 and re.match(r'^".*"$', words[1]): | ||
| result.append(line) | ||
| is_pipeline_test = False | ||
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| # If no results included workflow, process or function | ||
| # Add a dummy result to fill the 'pipeline' category | ||
| if is_pipeline_test: | ||
| result.append("pipeline 'PIPELINE'") | ||
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| return result | ||
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| def generate( | ||
| lines: list[str], types: list[str] = ["function", "process", "workflow", "pipeline"] | ||
| ) -> dict[str, list[str]]: | ||
| """ | ||
| Generate a dictionary of function, process and workflow lists from the lines. | ||
| Args: | ||
| lines (list): List of lines to process. | ||
| types (list): List of types to include. | ||
| Returns: | ||
| dict: Dictionary with function, process and workflow lists. | ||
| """ | ||
| result: dict[str, list[str]] = { | ||
| "function": [], | ||
| "process": [], | ||
| "workflow": [], | ||
| "pipeline": [], | ||
| } | ||
| for line in lines: | ||
| words = line.split() | ||
| if len(words) == 2: | ||
| keyword = words[0] | ||
| name = words[1].strip("'\"") # Strip both single and double quotes | ||
| if keyword in types: | ||
| result[keyword].append(name) | ||
| return result | ||
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| if __name__ == "__main__": | ||
|
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| # Utility stuff | ||
| args = parse_args() | ||
| logging.basicConfig(level=args.log_level) | ||
|
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| # Parse nf-test files for targets of tests | ||
| files = find_files(args.paths) | ||
| lines = process_files(files) | ||
| result = generate(lines) | ||
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| # Get only relevant results (specified by -t) | ||
| # Unique using a set | ||
| target_results = list( | ||
| {item for sublist in map(result.get, args.types) for item in sublist} | ||
| ) | ||
|
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| # Print to stdout | ||
| print(json.dumps(target_results)) |
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