--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_semibin.py	Fri Oct 14 21:29:47 2022 +0000
@@ -0,0 +1,153 @@
+#!/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.")