#!/usr/bin/env python
"""Module containing the Drugbank class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
from biobb_io.api.common import check_output_path, check_mandatory_property, download_drugbank, write_sdf
[docs]class Drugbank(BiobbObject):
"""
| biobb_io Drugbank
| This class is a wrapper for the `Drugbank <https://www.drugbank.ca/>`_ REST API.
| Download a single component in SDF format from the `Drugbank <https://www.drugbank.ca/>`_ REST API.
Args:
output_sdf_path (str): Path to the output SDF component file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_drugbank.sdf>`_. Accepted formats: sdf (edam:format_3814).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **drugbank_id** (*str*) - (None) Drugbank component id.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_io.api.drugbank import drugbank
prop = {
'drugbank_id': 'DB00530'
}
drugbank(output_sdf_path='/path/to/newComponent.sdf',
properties=prop)
Info:
* wrapped_software:
* name: Drugbank
* license: Creative Commons
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, output_sdf_path,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"out": {"output_sdf_path": output_sdf_path}
}
# Properties specific for BB
self.drugbank_id = properties.get('drugbank_id', None)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.output_sdf_path = check_output_path(self.io_dict["out"]["output_sdf_path"], "output_sdf_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Drugbank <api.drugbank.Drugbank>` api.drugbank.Drugbank object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
check_mandatory_property(self.drugbank_id, 'drugbank_id', self.out_log, self.__class__.__name__)
self.drugbank_id = self.drugbank_id.strip().lower()
url = "https://www.drugbank.ca/structures/small_molecule_drugs/%s.sdf?type=3d"
# Downloading SDF file
sdf_string = download_drugbank(self.drugbank_id, url, self.out_log, self.global_log)
write_sdf(sdf_string, self.output_sdf_path, self.out_log, self.global_log)
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def drugbank(output_sdf_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`Drugbank <api.drugbank.Drugbank>` class and
execute the :meth:`launch() <api.drugbank.Drugbank.launch>` method."""
return Drugbank(output_sdf_path=output_sdf_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Download a component in SDF format from the Drugbank (https://www.drugbank.ca/).", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('-o', '--output_sdf_path', required=True, help="Path to the output SDF component file. Accepted formats: sdf.")
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
drugbank(output_sdf_path=args.output_sdf_path,
properties=properties)
if __name__ == '__main__':
main()