--- a/data_manager/data_manager_semibin.py	Fri Oct 14 21:32:55 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-#!/usr/bin/env python
-#
-# Data manager for reference data for the MetaPhlAn Galaxy tools
-import argparse
-import json
-import subprocess
-from datetime import date
-from pathlib import Path
-
-
-# Utility functions for interacting with Galaxy JSON
-def read_input_json(json_fp):
-    """Read the JSON supplied from the data manager tool
-
-    Returns a tuple (param_dict,extra_files_path)
-
-    'param_dict' is an arbitrary dictionary of parameters
-    input into the tool; 'extra_files_path' is the path
-    to a directory where output files must be put for the
-    receiving data manager to pick them up.
-
-    NB the directory pointed to by 'extra_files_path'
-    doesn't exist initially, it is the job of the script
-    to create it if necessary.
-
-    """
-    with open(json_fp) as fh:
-        params = json.load(fh)
-    return (params['param_dict'],
-            Path(params['output_data'][0]['extra_files_path']))
-
-
-# Utility functions for creating data table dictionaries
-#
-# Example usage:
-# >>> d = create_data_tables_dict()
-# >>> add_data_table(d,'my_data')
-# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
-# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
-# >>> print(json.dumps(d))
-def create_data_tables_dict():
-    """Return a dictionary for storing data table information
-
-    Returns a dictionary that can be used with 'add_data_table'
-    and 'add_data_table_entry' to store information about a
-    data table. It can be converted to JSON to be sent back to
-    the data manager.
-
-    """
-    d = {
-        'data_tables': {}
-    }
-    return d
-
-
-def add_data_table(d, table):
-    """Add a data table to the data tables dictionary
-
-    Creates a placeholder for a data table called 'table'.
-
-    """
-    d['data_tables'][table] = []
-
-
-def add_data_table_entry(d, table, entry):
-    """Add an entry to a data table
-
-    Appends an entry to the data table 'table'. 'entry'
-    should be a dictionary where the keys are the names of
-    columns in the data table.
-
-    Raises an exception if the named data table doesn't
-    exist.
-
-    """
-    try:
-        d['data_tables'][table].append(entry)
-    except KeyError:
-        raise Exception("add_data_table_entry: no table '%s'" % table)
-
-
-def download_gtdb(data_tables, table_name, target_dp, test=False):
-    """Download GTDB
-
-    Creates references to the specified file(s) on the Galaxy
-    server in the appropriate data table (determined from the
-    file extension).
-
-    The 'data_tables' dictionary should have been created using
-    the 'create_data_tables_dict' and 'add_data_table' functions.
-
-    Arguments:
-      data_tables: a dictionary containing the data table info
-      table_name: name of the table
-      target_dp: directory to put copy or link to the data file
-
-    """
-    db_dp = target_dp
-    if not test:
-        cmd = "SemiBin download_GTDB --reference-db-data-dir %s" % (db_dp)
-        subprocess.check_call(cmd, shell=True)
-        dbkey = 'gtdb'
-        name = "GTDB reference genome generated by MMseqs2 used in SemiBin"
-    else:
-        dbkey = 'test'
-        name = "Test"
-        empty_fp = db_dp / Path("empty")
-        empty_fp.touch()
-    add_data_table_entry(
-        data_tables,
-        table_name,
-        dict(
-            dbkey=dbkey,
-            value='%s' % (date.today().strftime("%d%m%Y")),
-            name=name,
-            path=str(db_dp)))
-
-
-if __name__ == "__main__":
-    print("Starting...")
-
-    # Read command line
-    parser = argparse.ArgumentParser(description='Download reference genomes (GTDB)')
-    parser.add_argument('--json', help="Path to JSON file")
-    parser.add_argument('--test', action='store_true', help="Test")
-    args = parser.parse_args()
-    print("args   : %s" % args)
-
-    # Read the input JSON
-    json_fp = Path(args.json)
-    params, target_dp = read_input_json(json_fp)
-
-    # Make the target directory
-    print("Making %s" % target_dp)
-    target_dp.mkdir(parents=True, exist_ok=True)
-
-    # Set up data tables dictionary
-    data_tables = create_data_tables_dict()
-    add_data_table(data_tables, "gtdb")
-
-    # Fetch data from specified data sources
-    print("Download and build database")
-    download_gtdb(
-        data_tables,
-        "gtdb",
-        target_dp,
-        args.test)
-
-    # Write output JSON
-    print("Outputting JSON")
-    with open(json_fp, 'w') as fh:
-        json.dump(data_tables, fh, sort_keys=True)
-    print("Done.")