--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py	Tue May 24 11:46:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +0,0 @@
-#!/usr/bin/env python
-# Errol Strain, estrain@gmail.com
-# Database downloads for NCBI AMRFinderPlus
-
-import sys
-import os
-import tempfile
-import shutil
-import json
-import re
-import argparse
-from ftplib import FTP
-
-
-def download_from_ncbi(output_directory):
-    NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
-    FILENAME = 'version.txt' 
-    NCBI_DOWNLOAD_PATH = '/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/'
-    
-    email = 'anonymous@example.com'
-
-    cwd = os.getcwd() 
-    os.chdir(output_directory)
-
-    ftp = FTP( NCBI_FTP_SERVER )
-    ftp.login( 'anonymous', email)
-    ftp.cwd(NCBI_DOWNLOAD_PATH)
-    
-    #exclude the allele counts folder
-    files = ftp.nlst()
-    files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files)
-
-    for f in files:
-      ftp.retrbinary("RETR " + f, open(f, 'wb').write)
-
-    files = ftp.nlst()
-    files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files)
-    pointmuts = filter(lambda x: re.search(r'^((?!tab|(?:invokername=tab)).)*$', x), files)
-    pointmuts = filter(lambda x: re.search(r'AMR_DNA-', x), pointmuts)
-
-
-    # Make blast databases
-    blastcmd = "makeblastdb -in AMRProt -dbtype prot -logfile /dev/null"
-    os.system(blastcmd)
-    blastcmd = "makeblastdb -in AMR_CDS -dbtype nucl -logfile /dev/null"
-    os.system(blastcmd)
-
-    for f in pointmuts:
-      blastcmd = "makeblastdb -in " + f +" -dbtype nucl -logfile /dev/null"
-      os.system(blastcmd)
-
-    # Make HMM indexes
-    hmmcmd="hmmpress -f AMR.LIB > /dev/null 2> /dev/null"
-    os.system(hmmcmd)
- 
-    # Read in version
-    with open("version.txt") as f:
-      version = f.readline().rstrip()
-
-    ftp.quit()
-    
-    os.chdir(cwd)    
-    
-    return version 
-
-def print_json (version,argspath,argsname,argsout):
-
-    data_table_entry = {
-      'data_tables' : {
-        'amrfinderplus': [
-          {
-            "value":version,
-            "name":argsname,
-            "path":argspath,
-          }
-        ]
-      }
-    }
-
-    with open(argsout, 'w') as fh:
-      json.dump(data_table_entry, fh, indent=2, sort_keys=True)
-        
-def main():
-   
-    parser = argparse.ArgumentParser(description='Download NCBI amrFinderPlus Databases')
-    parser.add_argument('--name', type=str, required=True, nargs=1, help='Database name')
-    parser.add_argument('--out', type=str, required=True, nargs=1, help='output file')
-
-    args = parser.parse_args()
-
-    with open(args.out[0]) as fh:
-        params = json.load(fh)
-
-    output_directory = params['output_data'][0]['extra_files_path']
-    os.mkdir(output_directory)
-    data_manager_dict = {}
-
-    #Fetch the files and build blast databases
-    version=download_from_ncbi(output_directory)    
-
-    tablename = "AMRFinderPlus Database " + version
-
-    #shutil.copytree("amrdb",args.path[0])
-    print_json(version,output_directory,tablename,args.out[0])
-
-if __name__ == "__main__": main()

--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml	Tue May 24 11:46:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<tool id="data_manager_amrfinderplus" name="AMRFinderPlus Data Manger" tool_type="manage_data" version="0.0.3" profile="20.01">
-    <requirements>
-        <requirement type="package">blast</requirement>
-        <requirement type="package">hmmer</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        python $__tool_directory__/data_manager_amrfinderplus.py --name $amrdbname --out ${output_file};
-    ]]></command>
-    <inputs>
-      <param name="amrdbname" type="text" value="latest" label="Release Version - Note: only latest release is supported"/>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="data_manager_json"/>
-    </outputs>
-    <tests>
-        <test>
-        </test>
-    </tests>
-    <help>
-    </help>
-    <citations>
-     Refer to https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ for latest database version number.
-    </citations>
-</tool>

--- a/data_manager_amrfinderplus/data_manager_conf.xml	Tue May 24 11:46:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<data_managers>
-    <data_manager tool_file="data_manager/data_manager_amrfinderplus.xml" id="data_manager_amrfinderplus">
-      <data_table name="amrfinderplus">
-        <output>
-          <column name="value" />
-          <column name="name" />
-          <column name="path" output_ref="output_file" >
-            <move type="directory" relativize_symlinks="True">
-              <src>${path}</src>
-              <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">amrfinderplus/${value}</target>
-            </move>
-            <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/amrfinderplus/${value}</value_translation>
-            <value_translation type="function">abspath</value_translation>
-          </column>
-        </output>
-      </data_table>
-    </data_manager>
-</data_managers>

--- a/data_manager_amrfinderplus/test-data/amrfinder_databases.loc	Tue May 24 11:46:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# this is a tab separated file describing the location of amrfinder databases
-#
-# the columns are:
-# value name path
-#
-# for example
-# 2021-04-14 May22DB /tmp/tool-data/amrfinderdatabases/May22DB

--- a/data_manager_amrfinderplus/tool-data/amrfinder_databases.loc	Tue May 24 11:46:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# this is a tab separated file describing the location of amrfinder databases
-#
-# the columns are:
-# value name path
-#
-# for example
-# 2021-04-14 May22DB /tmp/tool-data/amrfinderdatabases/May22DB

--- a/data_manager_amrfinderplus/tool_data_table_conf.xml.sample	Tue May 24 11:46:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="amrfinderplus" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/amrfinderplus.loc" />
-    </table>
-</tables>

--- a/data_manager_amrfinderplus/tool_data_table_conf.xml.test	Tue May 24 11:46:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="amrfinderplus" comment_char="#" allow_duplicate_entries="False">
-        <columns>value,name, path</columns>
-        <file path="${__HERE__}/test-data/amrfinderplus.loc" />
-    </table>
-</tables>