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command_line_doc_generator.py
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command_line_doc_generator.py
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#!/usr/bin/env python3
import argparse
import json
from pathlib import Path
import re
import subprocess
def rstlink2mdlink(rst_string):
pattern = re.compile(r"(?P<text_before>.*)`(?P<text_link>.+)<(?P<text_url>.+)>`_(?P<text_after>.*)")
if not pattern.match(rst_string):
return rst_string
link = pattern.match(rst_string).groupdict()
return f"{link['text_before']+'['+link['text_link'].strip()+']('+link['text_url']+')'+link['text_after']}"
def get_enum_extensions(enum_list):
pattern = re.compile(r".*\.(?P<extension>\w+).*")
return ", ".join(pattern.match(enum_string).groupdict()['extension'].upper() for enum_string in enum_list)
def get_file_content(file_path):
return Path(file_path).read_text()
def main():
parser = argparse.ArgumentParser(description="Creates config_biobb.json and config_biobb.yml files.",
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
epilog="Examples: \nconfigs_generator.py -i path/to/testconffile/conf.yml -o path/to/outputdir")
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--json_schemas_folder', '-j', required=True,
help='json_schemas folder in biobb_example/biobb_example')
required_args.add_argument('--config_folder', '-c', required=True,
help='config folder in biobb_example/biobb_example')
required_args.add_argument('--biobb_name', '-b', required=True,
help='biobb_name')
required_args.add_argument('--output', '-o', required=True, help='Output md file')
args = parser.parse_args()
biobb_name = args.biobb_name
biobb_title = f"BioBB {biobb_name.split('_')[1].upper()}"
config_url = f"https://github.com/bioexcel/{biobb_name}/blob/master/{biobb_name}/test/data/config/"
config_path = args.config_folder
with open(args.output, 'w') as out:
# Write document title
out.write(f"# {biobb_title} Command Line Help\n")
out.write(f"Generic usage:\n")
out.write(f"```python\n")
out.write(f"biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>\n")
out.write(f"```\n")
out.write(f"-----------------\n")
out.write(f"\n")
for json_file_path in Path(args.json_schemas_folder).glob('*.json'):
block_name = json_file_path.stem
if block_name == biobb_name:
continue
with open(json_file_path) as json_file:
json_dict = json.load(json_file)
block_description = rstlink2mdlink(json_dict['title'])
block_help = " " + "\n ".join(subprocess.getoutput(f'{block_name} -h').split('\n'))
out.write(f"\n")
out.write(f"## {block_name.capitalize()}\n")
out.write(f"{block_description}\n")
out.write(f"### Get help\n")
out.write(f"Command:\n")
out.write(f"```python\n")
out.write(f"{block_name} -h\n")
out.write(f"```\n")
out.write(f"{block_help}\n")
out.write(f"### I / O Arguments\n")
out.write(f"Syntax: input_argument (datatype) : Definition\n")
out.write(f"\n")
out.write(f"Config input / output arguments for this building block:\n")
command_line_list = []
for argument, argument_dict in json_dict['properties'].items():
if argument != 'properties':
out.write(f"* **{argument}** (*{argument_dict['type']}*): {argument_dict['description']}. File type: {argument_dict['filetype']}. [Sample file]({argument_dict['sample']}). Accepted formats: {get_enum_extensions(argument_dict['enum'])}\n")
if argument_dict['sample']:
sample_file = argument_dict['sample'].split('/')[-1]
else:
sample_file = f"{argument_dict['filetype']}.{get_enum_extensions(argument_dict['enum']).split(',')[0].lower()}"
command_line_list.append(f"--{argument} {sample_file}")
out.write(f"### Config\n")
out.write(f"Syntax: input_parameter (datatype) - (default_value) Definition\n")
out.write(f"\n")
out.write(f"Config parameters for this building block:\n")
for argument, argument_dict in json_dict['properties']['properties']['properties'].items():
out.write(f"* **{argument}** (*{argument_dict['type']}*): ({argument_dict['default']}) {rstlink2mdlink(argument_dict['description'])}.\n")
for extension in ['yml', 'json']:
if extension == 'yml':
out.write(f"### YAML\n")
else:
out.write(f"### {extension.upper()}\n")
config_file_name = 'config_'+block_name+'.'+extension
command_line_str = " ".join(['--config', config_file_name] + command_line_list)
out.write(f"#### [Common config file]({config_url+config_file_name})\n")
out.write(f"```python\n")
out.write(f"{get_file_content(str(Path(config_path).joinpath(config_file_name)))}\n")
out.write(f"```\n")
docker_file_name = 'config_'+block_name+'_docker.'+extension
if Path(config_path).joinpath(docker_file_name).exists():
out.write(f"#### [Docker config file]({config_url+docker_file_name})\n")
out.write(f"```python\n")
out.write(f"{get_file_content(str(Path(config_path).joinpath(docker_file_name)))}\n")
out.write(f"```\n")
singularity_file_name = 'config_' + block_name + '_singularity.'+extension
if Path(config_path).joinpath(singularity_file_name).exists():
out.write(f"#### [Singularity config file]({config_url+singularity_file_name})\n")
out.write(f"```python\n")
out.write(f"{get_file_content(str(Path(config_path).joinpath(singularity_file_name)))}\n")
out.write(f"```\n")
out.write(f"#### Command line\n")
out.write(f"```python\n")
out.write(f"{block_name} {command_line_str}\n")
out.write(f"```\n")
if __name__ == '__main__':
main()