Mercurial > repos > frogs > data_manager_frogs

annotate data_manager/FROGS_data_manager.py @ 0:7403d6c4f510 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
author frogs
date Mon, 23 Aug 2021 10:21:10 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
1 #!/usr/bin/env python3
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
2 # -*- coding: utf-8 -*-
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
3 #
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
4 # Copyright (C) 2021 INRA
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
5 #
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
6 # This program is free software: you can redistribute it and/or modify
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
7 # it under the terms of the GNU General Public License as published by
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
8 # the Free Software Foundation, either version 3 of the License, or
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
9 # (at your option) any later version.
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
10 #
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
11 # This program is distributed in the hope that it will be useful,
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
14 # GNU General Public License for more details.
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
15 #
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
16 # You should have received a copy of the GNU General Public License
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
18 #
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
19
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
20 __author__ = 'David Christiany Migale Jouy en Josas / Maria Bernard - Sigenae Jouy en Josas'
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
21 __copyright__ = 'Copyright (C) 2020 INRAE'
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
22 __license__ = 'GNU General Public License'
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
23 __version__ = '3.2.3'
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
24 __email__ = 'frogs-support@inrae.fr'
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
25 __status__ = 'prod'
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
26
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
27 # import json
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
28 import argparse
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
29 import os
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
30 # import sys
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
31 import tarfile
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
32 import time
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
33 import urllib
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
34
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
35 from galaxy.util.json import from_json_string, to_json_string
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
36
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
37 import requests
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
38
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
39 # GALAXY_database=~/galaxy/galaxy-20.09/database
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
40 # FROGS_data_manager.py --database=frogs_db_data --all_dbs=false \
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
41 # --date=0 --amplicons=16S --bases=SILVA --filters=Pintail100 \
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
42 # --only_last_versions=true \
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
43 # --tool_data=/home/maria/galaxy/galaxy-20.09/tool-data \
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
44 # --output $GALAXY_database/objects/e/7/7/dataset_e7766c39-8f36-450c-adf5-3e4ee8d5c562.dat
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
45
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
46
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
47 def get_args():
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
48 parser = argparse.ArgumentParser()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
49 parser.add_argument("-d", "--database")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
50 parser.add_argument("--all_dbs")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
51 parser.add_argument("--date")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
52 parser.add_argument("--amplicons")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
53 parser.add_argument("--bases")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
54 parser.add_argument("--filters")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
55 parser.add_argument("--only_last_versions")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
56 parser.add_argument("--tool_data")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
57 parser.add_argument("-o", "--output")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
58 args = parser.parse_args()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
59
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
60 return args
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
61
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
62
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
63 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table):
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
64 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
65 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
66 data_manager_dict['data_tables'][data_table].append(data_table_entry)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
67 return data_manager_dict
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
68
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
69
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
70 def keep_only_last_version(db_index):
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
71 db_dict = dict()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
72 for line in db_index:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
73 db_type = "_".join(line[1:4]) if line[3] != "" else "_".join(line[1:3])
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
74 if db_type not in db_dict:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
75 db_dict[db_type] = line
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
76 return list(db_dict.values())
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
77
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
78
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
79 def frogs_sources(data_manager_dict, target_directory):
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
80
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
81 # variables
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
82 amplicons_list = []
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
83 bases_list = []
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
84 filters_list = []
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
85 if args.all_dbs == "false":
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
86 amplicons_list = [amplicon.lower().strip() for amplicon in args.amplicons.split(",") if amplicon != ""]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
87 bases_list = [base.lower().strip() for base in args.bases.split(",") if base != ""]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
88 filters_list = [filter.lower().strip() for filter in args.filters.split(",") if filter != ""]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
89 bottom_date = int(args.date)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
90 tool_data_path = args.tool_data
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
91
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
92 # get frogs database index
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
93 frogs_db_index_link = "http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv"
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
94 with requests.Session() as s:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
95 download = s.get(frogs_db_index_link)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
96 decoded_content = download.content.decode('utf-8')
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
97 db_index = decoded_content.splitlines()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
98 db_index = [line.split("\t") for line in db_index[1:]]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
99 db_index = [[line[0], line[1].lower(), line[2].lower(), line[3].lower()] + line[4:] for line in db_index]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
100
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
101 # filter databases
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
102 if args.all_dbs == "false":
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
103 # filter by amplicons
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
104 if len(amplicons_list) != 0:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
105 db_index = [line for line in db_index if any([amplicon in amplicons_list for amplicon in line[1].split(',')])]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
106 # filter by base
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
107 if len(bases_list) != 0:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
108 db_index = [line for line in db_index if line[2] in bases_list]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
109 # filter by filters
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
110 if len(filters_list) != 0:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
111 db_index = [line for line in db_index if line[3] in filters_list]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
112 # filter by date
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
113 if bottom_date != 0:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
114 db_index = [line for line in db_index if int(line[0]) >= bottom_date]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
115 if args.only_last_versions == "true":
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
116 # keep only last version
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
117 db_index = keep_only_last_version(db_index)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
118
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
119 # get frogs dbs
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
120 os.chdir(target_directory)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
121 dir_name = "frogs_db_" + time.strftime("%Y%m%d")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
122 os.mkdir(dir_name)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
123 dbs = set([])
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
124 for line in db_index:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
125 value = line[5]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
126 name = value.replace("_", " ") if "_" not in line[4] else value.replace(line[4], "").replace("_", " ") + line[4]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
127 link = line[6]
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
128 name_dir = "".join([line[6].replace(".tar.gz", "").split("/")[-1]])
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
129 file_path = tool_data_path + "/frogs_db/" + name_dir
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
130 if not os.path.exists(file_path): # if the file is not already in frogs_db directory
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
131
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
132 # download frogs db
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
133 dl_file = urllib.request.URLopener()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
134 dl_file.retrieve(link, "tmp.tar.gz")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
135
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
136 # unzip frogs db
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
137 with tarfile.open("tmp.tar.gz") as tar:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
138 tar.extractall(dir_name)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
139 tar.close()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
140 os.remove('tmp.tar.gz')
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
141
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
142 # get fasta file path
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
143 tmp = set(os.listdir(dir_name))
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
144 new_db = dir_name + "/" + "".join(tmp.difference(dbs))
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
145 files = os.listdir(new_db)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
146 fasta = "".join([file for file in files if file.endswith('.fasta')])
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
147 path = new_db + '/' + fasta
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
148 dbs = os.listdir(dir_name)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
149 # release = value + "_" + time.strftime("%Y-%m-%d")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
150 # date = time.strftime("%Y%m%d")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
151 path = os.path.join(target_directory, path)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
152
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
153 data_table_entry = dict(name=name, value=value, path=path)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
154 _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_db")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
155
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
156 # def HVL_sources(data_manager_dict,target_directory):
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
157 # HVL_dir = "http://genoweb.toulouse.inra.fr/frogs_databanks/HVL/ITS/UNITE_s_7.1_20112016"
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
158 # os.chdir(target_directory)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
159 # for link in [HVL_dir + "/Unite_s_7.1_20112016_ITS1.fasta",HVL_dir + "/Unite_s_7.1_20112016_ITS2.fasta"]:
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
160 # file_name=link.split("/")[-1].replace('.fasta',"_"+time.strftime("%Y-%m-%d")+".fasta")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
161 # dl_file = urllib.URLopener()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
162 # dl_file.retrieve(link,file_name)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
163
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
164 # #get fasta file path
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
165 # path = os.path.join(target_directory,file_name)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
166 # if link.endswith('ITS1.fasta'):
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
167 # name = "UNITE 7.1 ITS1 " + time.strftime("%Y-%m-%d")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
168 # elif link.endswith('ITS2.fasta'):
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
169 # name = "UNITE 7.1 ITS2 " + time.strftime("%Y-%m-%d")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
170 # value=file_name.replace('.fasta','')
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
171
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
172 # data_table_entry = dict(name = name, value = value, path=path)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
173 # _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_HVL_db")
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
174
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
175
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
176 def main():
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
177
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
178 # get args from command line
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
179 global args
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
180 args = get_args()
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
181
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
182 # Extract json file params
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
183 data_manager_dict = {}
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
184 filename = args.output
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
185 params = from_json_string(open(filename).read())
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
186 target_directory = params['output_data'][0]['extra_files_path']
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
187 os.mkdir(target_directory)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
188
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
189 # if args.database=="frogs_db_data":
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
190 frogs_sources(data_manager_dict, target_directory)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
191 # elif args.database=="HVL_db_data":
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
192 # HVL_sources(data_manager_dict,target_directory)
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
193
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
194 # save info to json file
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
195 open(filename, 'wt').write(to_json_string(data_manager_dict))
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
196
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
197
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
198 if __name__ == "__main__":
7403d6c4f510 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304"
frogs
parents:
diff changeset
199 main()