Mercurial > repos > iuc > data_manager_pharokka

comparison data_manager/data_manager_fetch_pharokka_db.py @ 0:3b3daabcc63e draft

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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 07:51:13 +0000
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children bba8135dc024
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-1:000000000000 0:3b3daabcc63e
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()