--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_build_amrfinderplus.py	Thu Jan 05 14:28:07 2023 +0000
@@ -0,0 +1,257 @@
+import argparse
+import json
+import os
+import subprocess as sp
+from ftplib import FTP
+from io import BytesIO
+from pathlib import Path
+
+import pandas as pd
+
+
+class GetAmrFinderPlusDataManager:
+    """
+    Create the json file with database information for galaxy data manager
+    """
+
+    def __init__(self,
+                 amrfinderplus_database="amrfinderplus_database",
+                 db_name="amrfinderplus-db",
+                 amrfinderplus_version="latest",
+                 date_version=None):
+        self.data_table_name = amrfinderplus_database
+        self._db_name = db_name
+        self._amrfinderplus_version = amrfinderplus_version
+        self._amrfinderplus_date_version = date_version
+        self.data_table_entry = None
+        self.amrfinderplus_table_list = 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
+        return: The data table with database information
+        """
+        self.amrfinderplus_table_list = self.get_data_table_format()
+        amrfinderplus_value = f"amrfinderplus_V{self._amrfinderplus_version}" \
+                              f"_{self._amrfinderplus_date_version}"
+        amrfinderplus_name = f"V{self._amrfinderplus_version}" \
+                             f"-{self._amrfinderplus_date_version}"
+        data_info = dict(value=amrfinderplus_value,
+                         name=amrfinderplus_name,
+                         path=self._db_name)
+        self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
+        return self.amrfinderplus_table_list
+
+
+class DownloadAmrFinderPlusDatabase(GetAmrFinderPlusDataManager):
+    """
+    Download the amrfinderplus database from the ncbi.
+    Make the database available with hmm and indexed files
+    Build the data manager infos for galaxy
+    """
+
+    def __init__(self,
+                 output_dir=Path.cwd(),
+                 ncbi_url="ftp.ncbi.nlm.nih.gov",
+                 ftp_login="anonymous",
+                 ftp_password="anonymous",
+                 amrfinderplus_database="amrfinderplus_database",
+                 db_name="amrfinderplus-db",
+                 amrfinderplus_version="latest",
+                 json_file_path=None,
+                 date_version=None,
+                 amrfinderplus_db_path=None,
+                 test_mode=False):
+
+        super().__init__()
+        self.json_file_path = json_file_path
+        self._output_dir = output_dir
+        self._ncbi_ftp_url = ncbi_url
+        self._ncbi_database_path = "pathogen/Antimicrobial_resistance/AMRFinderPlus/database"
+        self._login = ftp_login
+        self._password = ftp_password
+        self._amrfinderplus_database = amrfinderplus_database
+        self._db_name = db_name
+        self._amrfinderplus_version = amrfinderplus_version
+        self._amrfinderplus_date_version = date_version
+        self.species_list = None
+        self.test_mode = test_mode
+        self.amrfinderplus_db_path = amrfinderplus_db_path
+
+    @staticmethod
+    def subprocess_cmd(command, *args):
+        """
+        Method to call external tools with any parameters
+        :param command: command name from the tool used (e.g. wget or makeblastdb)
+        :param args: free number of argument need for the command tool (e.g. -r, -P ...)
+        :return: launch the command line from the system
+        """
+        cmd = [command]
+        [cmd.append(i) for i in args]
+        proc = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
+        if proc.returncode != 0:
+            print(f'Error type {proc.returncode} with : \n {proc}')
+
+    def download_amrfinderplus_db(self):
+        """
+        Download the amrfinderplus database from the ncbi ftp server
+        """
+        self.amrfinderplus_db_path = f'{self._output_dir}/{self._db_name}'
+        os.makedirs(self.amrfinderplus_db_path)
+        if self._amrfinderplus_version == 'latest':
+            self.get_amrfinderplus_version()
+
+        amrfinderplus_ftp_path = f"ftp://{self._login}:" \
+                                 f"{self._password}@{self._ncbi_ftp_url}/" \
+                                 f"{self._ncbi_database_path}/" \
+                                 f"{self._amrfinderplus_version}/" \
+                                 f"{self._amrfinderplus_date_version}"
+        if self.test_mode is True:
+            file_list = ["AMR_DNA-Escherichia", "version.txt", "taxgroup.tab", "database_format_version.txt"]
+            output_option = "-O"
+            for file in file_list:
+                self.subprocess_cmd("wget",
+                                    "-nd",
+                                    "-np",
+                                    "-r",
+                                    f"{amrfinderplus_ftp_path}/{file}",
+                                    output_option,
+                                    f"{self.amrfinderplus_db_path}/{file}")
+        else:
+            output_option = "-P"
+            self.subprocess_cmd("wget",
+                                "-nd",
+                                "-np",
+                                "-r",
+                                amrfinderplus_ftp_path,
+                                output_option,
+                                self.amrfinderplus_db_path)
+
+    def make_hmm_profile(self):
+        """
+        Make the hmm profile using the AMR.LIB file previously download
+        """
+        hmm_file = Path(f"{self.amrfinderplus_db_path}/AMR.LIB")
+        if Path.exists(hmm_file) and self.test_mode is False:
+            self.subprocess_cmd("hmmpress", "-f", hmm_file)
+        else:
+            print("hmm_file file is missing to make hmm profiles")
+
+    def extract_filelist_makeblast(self):
+        """
+        Extract le list of species which have file in the database
+        return: a filtered species list of available species in the database
+        """
+        taxa_group_path = Path(f"{self.amrfinderplus_db_path}/taxgroup.tab")
+        if Path.exists(taxa_group_path):
+            taxa_table = pd.read_table(taxa_group_path)
+            taxa_table.columns = ["taxgroup", "gpipe_taxgroup", "number_of_nucl_ref_genes"]
+            taxa_df = taxa_table[taxa_table.number_of_nucl_ref_genes > 0].filter(items=["taxgroup"], axis=1)
+            if self.test_mode is True:
+                taxa_df = taxa_df[taxa_df.taxgroup == "Escherichia"].taxgroup
+            else:
+                taxa_df = taxa_df.taxgroup
+            self.species_list = list(taxa_df)
+        else:
+            print("taxgroup.tab file is missing to list available species")
+
+    def make_blastdb(self):
+        """
+        Index fasta file for blast
+        """
+        self.extract_filelist_makeblast()
+        nucl_file_db_list = [f'{self.amrfinderplus_db_path}/AMR_DNA-{specie}' for specie in self.species_list]
+        amr_dna = f'{self.amrfinderplus_db_path}/AMR_CDS'
+        amr_prot = f'{self.amrfinderplus_db_path}/AMRProt'
+        os.chdir(self.amrfinderplus_db_path)
+        if Path(amr_dna).exists():
+            nucl_file_db_list.append(amr_dna)
+        else:
+            print("No file AMR_CDS detected for indexing")
+        if Path(amr_prot).exists():
+            self.subprocess_cmd("makeblastdb", "-in", amr_prot, "-dbtype", "prot")
+        else:
+            print("No file AMRProt detected for indexing")
+        [self.subprocess_cmd("makeblastdb", "-in", file, "-dbtype", "nucl") for file in nucl_file_db_list]
+
+    def get_amrfinderplus_version(self, version_file="version.txt",
+                                  database_version_file="database_format_version.txt"):
+        """
+        Check the version when latest if provided and update the number
+        param version_file: name of the file containing version information
+        param database_version_file: name of the file containing date version information
+        """
+        ftp = FTP(self._ncbi_ftp_url)
+        ftp.login(self._login, self._password)
+        ftp.cwd(f"{self._ncbi_database_path}/{self._amrfinderplus_version}")
+        db_version = BytesIO()
+        db_date_version = BytesIO()
+        ftp.retrbinary(f'RETR {version_file}', db_version.write)
+        ftp.retrbinary(f'RETR {database_version_file}', db_date_version.write)
+        self._amrfinderplus_date_version = db_version.getvalue().decode("utf-8").splitlines()[0]
+        self._amrfinderplus_version = '.'.join(
+            db_date_version.getvalue().decode("utf-8").splitlines()[0].split(".")[:2])
+
+    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("--db_version", default="latest",
+                            help="select the major version of the database (e.g. 3.10, 3.8), default is latest")
+    arg_parser.add_argument("--db_date",
+                            help="select the date into the database version (e.g. 2022-10-11.2)")
+    arg_parser.add_argument("--test", action='store_true',
+                            help="option to test the script with an lighted database")
+    return arg_parser.parse_args()
+
+
+def main():
+    all_args = parse_arguments()
+    amrfinderplus_download = DownloadAmrFinderPlusDatabase(amrfinderplus_version=all_args.db_version,
+                                                           date_version=all_args.db_date,
+                                                           json_file_path=all_args.data_manager_json,
+                                                           test_mode=all_args.test)
+    amrfinderplus_download.read_json_input_file()
+    amrfinderplus_download.download_amrfinderplus_db()
+    amrfinderplus_download.make_hmm_profile()
+    amrfinderplus_download.make_blastdb()
+    amrfinderplus_download.write_json_infos()
+
+
+if __name__ == '__main__':
+    main()