--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/plasmidfinder_fetch_database.py	Tue Feb 14 14:25:43 2023 +0000
@@ -0,0 +1,212 @@
+import argparse
+import json
+import os
+import tarfile
+from datetime import datetime
+from pathlib import Path
+
+import requests
+
+
+class GetPlasmidfinderDataManager:
+    """
+    Create the json file with database information for galaxy data manager
+    """
+
+    def __init__(self,
+                 plasmidfinder_database="plasmidfinder_database",
+                 db_name="plasmidfinder-db",
+                 plasmidfinder_version="latest"):
+        self.data_table_name = plasmidfinder_database
+        self._db_name = db_name
+        self._plasmidfinder_version = plasmidfinder_version
+        self._plasmidfinder_date_version = None
+        self.data_table_entry = None
+        self.plasmidfinder_table_list = None
+        self._commit_number = None
+
+    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):
+        """
+        Create the empty data table format and add all the information into
+        Commit number is added if latest is required instead of version number
+        return: The data table with database information
+        """
+        self.plasmidfinder_table_list = self.get_data_table_format()
+        if self._plasmidfinder_version == "latest":
+            version_value = self._commit_number
+        else:
+            version_value = self._plasmidfinder_version
+        plasmidfinder_value = f"plasmidfinder_{self._commit_number}" \
+                              f"_{self._plasmidfinder_date_version}"
+        plasmidfinder_name = f"{version_value}" \
+                             f"_{self._plasmidfinder_date_version}"
+        data_info = dict(value=plasmidfinder_value,
+                         name=plasmidfinder_name,
+                         date=self._plasmidfinder_date_version,
+                         path=self._db_name)
+        self.plasmidfinder_table_list["data_tables"][self.data_table_name] = [data_info]
+        return self.plasmidfinder_table_list
+
+
+class DownloadPlasmidfinderDatabase(GetPlasmidfinderDataManager):
+    """
+    Download the plasmidfinder database from the bitbucket repository.
+    Build the data manager info for galaxy
+    """
+
+    def __init__(self,
+                 output_dir=Path.cwd(),
+                 plasmidfinder_url="https://bitbucket.org/genomicepidemiology/plasmidfinder_db/get/",
+                 db_name="plasmidfinder-db",
+                 db_tmp="tmp_database",
+                 plasmidfinder_version="latest",
+                 json_file_path=None,
+                 date_version=datetime.now().strftime("%Y-%m-%d")):
+
+        super().__init__()
+        self.json_file_path = json_file_path
+        self._output_dir = output_dir
+        self._plasmidfinder_url = plasmidfinder_url
+        self._temporary_folder = db_tmp
+        self._db_name = db_name
+        self._db_name_tar = f'{db_name}.gz'
+        self._plasmidfinder_version = plasmidfinder_version
+        self._plasmidfinder_date_version = date_version
+        self._commit_number = None
+
+    def extract_db_commit(self, request_header, title_name="content-disposition"):
+        """
+        Extract the commit if to add the information as identifier of the download
+        @request_header: a request object obtained from requests.get()
+        @title_name: the tag to search in the header of the requests object
+        return: the value of the commit
+        """
+        db_info = request_header.headers[title_name]
+        commit_number = db_info.split("-")[2].split(".")[0]
+        return commit_number
+
+    def untar_files(self, file_path: Path, extracted_path_output: Path):
+        """
+        untar the download archive
+        @file_path: input path of the tar.gz file
+        @extracted_path_output: output path of the extract folder
+        return: the path of the output
+        """
+        try:
+            with file_path.open('rb') as fh_in, \
+                    tarfile.open(fileobj=fh_in, mode='r:gz') as tar_file:
+                tar_file.extractall(path=extracted_path_output)
+                print(f'Untar the database in {extracted_path_output}')
+                return extracted_path_output
+        except OSError:
+            os.sys.exit(f'ERROR: Could not extract {file_path}')
+
+    def choose_db_version(self):
+        """
+        Update the url link depending on the version choosen by user.
+        This method could be upgraded simply by adding the new versions
+        """
+        if self._plasmidfinder_version == "latest":
+            self._plasmidfinder_url = f"{self._plasmidfinder_url}master.gz"
+        elif self._plasmidfinder_version == "2.1":
+            self._plasmidfinder_url = f"{self._plasmidfinder_url}1307168.gz"
+
+    def download_database(self):
+        """
+        Download the plasmidfinder database using requests lib
+        Make the directory and temporary directory for download
+        Untar the download files
+        """
+        self._output_dir = Path(self._output_dir)
+        self.choose_db_version()
+        try:
+            request_info = requests.get(self._plasmidfinder_url)
+            request_info.raise_for_status()
+            self._commit_number = self.extract_db_commit(request_info)
+            output_tar_path = self._output_dir.joinpath(self._temporary_folder)
+            output_tar_path_file = output_tar_path.joinpath(self._db_name_tar)
+            output_path = self._output_dir.joinpath(self._db_name)
+            os.makedirs(output_tar_path)
+            os.makedirs(output_path)
+            with open(output_tar_path_file, 'wb') as output_dir:
+                output_dir.write(request_info.content)
+            untar_output = self.untar_files(file_path=output_tar_path_file, extracted_path_output=output_tar_path.joinpath(self._db_name))
+
+            self.moove_download_files(older_path=untar_output, new_path=output_path)
+        except requests.exceptions.HTTPError as http_error:
+            print(f"Requests Error: {http_error}")
+            print(f"Fail to import Plasmidfinder database from {self._plasmidfinder_url}")
+
+    def moove_download_files(self, older_path, new_path, expression_search="*fsa"):
+        """
+        Clean downloaded data by mooving fasta files in the final folder
+        @older_path: previous path where the files are located
+        @new_path: final path where files will be mooved
+        @expression_search: keep only file with this expression
+        """
+        fasta_files = Path(older_path).rglob(expression_search)
+        file_list_paths = [file for file in fasta_files if file.is_file()]
+        [self.keep_filename(pathname=path, output_path=new_path) for path in file_list_paths]
+
+    def keep_filename(self, pathname, output_path):
+        """
+        Moove files
+        @pathname: previous path
+        @output_path: final path
+        """
+        Path.replace(pathname, output_path.joinpath(pathname.name))
+
+    def read_json_input_file(self):
+        """
+        Import the json file
+        """
+        with open(self.json_file_path) as fh:
+            params = json.load(fh)
+        target_dir = params['output_data'][0]['extra_files_path']
+        os.makedirs(target_dir)
+        self._output_dir = target_dir
+
+    def write_json_infos(self):
+        """
+        Write in the imported json file
+        """
+        with open(self.json_file_path, 'w') as fh:
+            json.dump(self.get_data_manager(), fh, sort_keys=True)
+
+
+def parse_arguments():
+    """
+    List of arguments provided by the user
+    return: parsed arguments
+    """
+    # parse options and arguments
+    arg_parser = argparse.ArgumentParser()
+    arg_parser.add_argument("data_manager_json",
+                            help="json file from galaxy")
+    arg_parser.add_argument("-v", "--db_version",
+                            help="version of the plasmidfinder (latest or 2.1)")
+    return arg_parser.parse_args()
+
+
+def main():
+    all_args = parse_arguments()
+    plasmidfinder_download = DownloadPlasmidfinderDatabase(json_file_path=all_args.data_manager_json, plasmidfinder_version=all_args.db_version)
+    plasmidfinder_download.read_json_input_file()
+    plasmidfinder_download.download_database()
+    plasmidfinder_download.write_json_infos()
+
+
+if __name__ == '__main__':
+    main()