Mercurial > repos > iuc > data_manager_pharokka
comparison data_manager/data_manager_fetch_pharokka_db.py @ 0:97f310b8e308 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
author | iuc |
---|---|
date | Thu, 20 Apr 2023 07:51:43 +0000 |
parents | |
children | 50caca83e7c9 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:97f310b8e308 |
---|---|
1 #!/usr/bin/env python | |
2 | |
3 import argparse | |
4 import json | |
5 import os | |
6 import subprocess | |
7 import sys | |
8 from datetime import datetime | |
9 | |
10 | |
11 def main(): | |
12 # Parse Command Line | |
13 parser = argparse.ArgumentParser(description="Create data manager JSON.") | |
14 parser.add_argument("--out", dest="output", action="store", help="JSON filename") | |
15 parser.add_argument("--version", dest="version", action="store", help="Version of the DB") | |
16 parser.add_argument( | |
17 "--test", | |
18 action="store_true", | |
19 help="option to test the script with an lighted database", | |
20 ) | |
21 | |
22 args = parser.parse_args() | |
23 | |
24 # the output file of a DM is a json containing args that can be used by the DM | |
25 # most tools mainly use these args to find the extra_files_path for the DM, which can be used | |
26 # to store the DB data | |
27 with open(args.output) as fh: | |
28 params = json.load(fh) | |
29 | |
30 workdir = params["output_data"][0]["extra_files_path"] | |
31 os.mkdir(workdir) | |
32 | |
33 time = datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") | |
34 db_value = "db_from_{0}".format(time) | |
35 db_path = os.path.join(workdir, db_value) | |
36 | |
37 # create DB | |
38 if args.test: # the test only checks that the pharokka download script is available and copies the test DB | |
39 | |
40 # check if install_databases.py is there | |
41 command_args = ["install_databases.py", "-h"] | |
42 proc = subprocess.Popen(args=command_args, shell=False) | |
43 return_code = proc.wait() | |
44 if return_code: | |
45 print("Error downloading Pharokka database.", file=sys.stderr) | |
46 sys.exit(return_code) | |
47 | |
48 # copy the test DB | |
49 test_db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "subset_pharokka_db") | |
50 command_args = ["cp", "-r", test_db_path, db_path] | |
51 else: | |
52 command_args = ["install_databases.py", "-o", db_path] | |
53 | |
54 proc = subprocess.Popen(args=command_args, shell=False) | |
55 return_code = proc.wait() | |
56 if return_code: | |
57 print("Error downloading Pharokka database.", file=sys.stderr) | |
58 sys.exit(return_code) | |
59 | |
60 # Update Data Manager JSON and write to file | |
61 data_manager_entry = { | |
62 "data_tables": { | |
63 "pharokka_db": { | |
64 "value": db_value, | |
65 "dbkey": db_value, | |
66 "version": args.version, | |
67 "name": f"Pharokka DB version {args.version} downloaded at {datetime.now()}", | |
68 "path": db_path, | |
69 } | |
70 } | |
71 } | |
72 | |
73 with open(os.path.join(args.output), "w+") as fh: | |
74 json.dump(data_manager_entry, fh, sort_keys=True) | |
75 | |
76 | |
77 if __name__ == "__main__": | |
78 main() |