--- a/data_manager/data_manager_amrfinderplus.py	Mon Nov 14 13:40:22 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-import argparse
-import json
-import os
-import re
-import subprocess as sp
-
-from datetime import datetime
-from pathlib import Path
-
-
-class GetDataManager:
-
-    def __init__(self):
-        self.data_table_name = "amrfinderplus_database"
-        self._db_name = "amrfinderplus-db"
-        self._db_path = Path().absolute()
-        self._today = datetime.now().strftime("%Y-%m-%d_%H:%M")
-
-    def get_data_table_format(self):
-        """
-        Skeleton of a data_table format
-        return: a data table formatted for json output
-        """
-        self.data_table_entry = {
-            "data_tables": {
-                self.data_table_name: {}
-            }
-        }
-        return self.data_table_entry
-
-    def get_data_manager(self, amrfinderplus_version):
-        self.amrfinderplus_table_list = self.get_data_table_format()
-
-        data_info = dict(value=self._today,
-                         name=amrfinderplus_version,
-                         path=self._db_name)
-        self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
-        return self.amrfinderplus_table_list
-
-    def update_amrfinderplus_db(self):
-        amrfinderplus_db_path = Path(self._db_path).joinpath(self._db_name)
-        cmd = [
-            'amrfinder_update',
-            '--database', str(amrfinderplus_db_path),
-            '--force_update'
-        ]
-        print(cmd)
-        proc = sp.run(
-            cmd,
-            stdout=sp.PIPE,
-            stderr=sp.PIPE,
-            universal_newlines=True
-        )
-        if (proc.returncode != 0):
-            print(
-                f"ERROR: AMRFinderPlus failed! command: 'amrfinder_update --force_update --database {amrfinderplus_db_path}', error code: {proc.returncode}")
-        else:
-            return amrfinderplus_db_path
-
-    def get_amrfinderplus_version(self, amrfinderplus_path):
-        version_file = Path(f'{amrfinderplus_path}/latest/version.txt')
-        with open(version_file, "r") as version:
-            version_value = version.read()
-        version_value = re.sub("\n", "", version_value)
-        return version_value
-
-    def parse_arguments(self):
-        # parse options and arguments
-        arg_parser = argparse.ArgumentParser()
-        arg_parser.add_argument("data_manager_json")
-        arg_parser.add_argument("-t", "--test", action='store_true',
-                                help="option to test the script with an lighted database")
-        return arg_parser.parse_args()
-
-    def read_json_input_file(self, json_file_path):
-        with open(json_file_path) as fh:
-            params = json.load(fh)
-        target_dir = params['output_data'][0]['extra_files_path']
-        os.makedirs(target_dir)
-        return Path(target_dir)
-
-    def write_json_infos(self, json_file_path, data_manager_infos):
-        with open(json_file_path, 'w') as fh:
-            json.dump(data_manager_infos, fh, sort_keys=True)
-
-
-def main():
-    # init the class
-    amrfinderplus_download = GetDataManager()
-    # import the arguments
-    all_args = amrfinderplus_download.parse_arguments()
-    # read the json input from galaxy to define the db path
-    path_to_download = amrfinderplus_download.read_json_input_file(json_file_path=all_args.data_manager_json)
-    # change the path to th json information
-    amrfinderplus_download._db_path = path_to_download
-    # download the last amrfinderplus database
-    amrfinder_output = amrfinderplus_download.update_amrfinderplus_db()
-    # extract the version number of the database
-    amrfinder_version = amrfinderplus_download.get_amrfinderplus_version(amrfinder_output)
-    # make a dic with database information
-    amrfinderplus_json_output = amrfinderplus_download.get_data_manager(amrfinder_version)
-    amrfinderplus_download.write_json_infos(json_file_path=all_args.data_manager_json,
-                                            data_manager_infos=amrfinderplus_json_output)
-
-
-if __name__ == '__main__':
-    main()