Mercurial > repos > siwaa > erecord_file

annotate main_file.py @ 3:aa5c088856c8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
author siwaa
date Thu, 15 Feb 2024 15:24:53 +0000
parents 9e8f5f220917
children 4c45f7b92955
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
1 # -*- coding: UTF-8 -*-
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
2 """
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
3 main_file
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
4
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
5 Requests having as OUTput : 1 json data + maybe 1 more file (xls or zip)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
6
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
7 Accepts actions (all) :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
8 'help'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
9 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
10 'get_vpz_input' 'post_vpz_input'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
11 'get_vpz_output' 'post_vpz_output'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
12 'get_vpz_inout' 'post_vpz_inout'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
13 'get_vpz_experiment' 'post_vpz_experiment'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
14 'get_vpz_report_conditions' 'post_vpz_report_conditions'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
15 'get_vpz_report' 'post_vpz_report'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
16
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
17 Parameters (Inputs) :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
18 - '-action' parameter : action value (mandatory)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
19 - '-data' parameter : data (JSON format) (optional)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
20 - '-datafolder' parameter : datafolder file path (optional,
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
21 available only in some cases)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
22 - '-experimentfile' parameter : experimentfile path (optional,
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
23 available only in some cases) :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
24
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
25 If there is an action value into data, then this one is ignored.
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
26
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
27 Outputs :
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
28 - output.json data file (jsonoutput_filepath)
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
29 - 1 other file in following cases :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
30 - experiment.xls file
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
31 if 'action' == get_vpz_experiment, post_vpz_experiment
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
32 - conditions.xls file
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
33 if 'action' == get_vpz_report_conditions,
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
34 post_vpz_report_conditions
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
35 - report.zip file
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
36 if 'action' == get_vpz_report, post_vpz_report
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
37 """
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
38
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
39 MAIN_DEBUG=False # True for more information returned
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
40
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
41 import argparse
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
42 import json
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
43 import erecord.api.erecord as erecord_api
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
44 from erecord.api.cmn.views_mixins import ActionViewMixin
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
45 from erecord.api.cmn.utils.errors import build_error_content
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
46
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
47 import os
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
48 import shutil
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
49
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
50 PM = "[main_file.py]"
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
51
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
52 r = dict()
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
53
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
54 import sys
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
55 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
56 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
57
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
58 data = dict()
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
59 json_response = dict()
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
60
3
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
61 # default configuration + maybe some modifications
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
62 config = erecord_api.conf() # default (vle-2.0.0 version)
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
63 config.DB_add_vpz(vpz_id=1312, vpzname="wwdm.vpz", pkgname="wwdm")
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
64
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
65 try :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
66 parser = argparse.ArgumentParser()
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
67
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
68 # -action
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
69 available_action_list = ActionViewMixin.get_action_list()
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
70 htext = "action value among : " + str(available_action_list)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
71 parser.add_argument("-action", default='help', help=htext,
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
72 choices=available_action_list)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
73
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
74 # -data
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
75 parser.add_argument("-data", type=str, help="data json file path")
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
76
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
77 # -datafolder
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
78 htext = "datafolder file path, available for action : "
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
79 htext +="post_vpz_output, post_vpz_inout,"
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
80 htext +="post_vpz_experiment, post_vpz_report"
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
81 parser.add_argument("-datafolder", type=str, help=htext)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
82
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
83 # -experimentfile
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
84 htext = "experimentfile path, available for action : post_vpz_experiment"
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
85 parser.add_argument("-experimentfile", type=str, help=htext)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
86
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
87 args = parser.parse_args()
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
88
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
89 if (args.action is None) or (args.action == 'None') :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
90 warn = "NO action given => enforced to 'help'"
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
91 r["warning"] = warn
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
92 action = 'help' # enforced (default)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
93 else :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
94 action = args.action
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
95
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
96 if (args.data is None) or (args.data == 'None') :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
97 data = dict() # NO data (JSON format) given as argument
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
98 else :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
99 jsoninput_filename = args.data
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
100 inputfile = open(jsoninput_filename, 'r')
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
101 data = json.load(inputfile) # get data
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
102
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
103 if (args.datafolder is None) or (args.datafolder == 'None') :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
104 pass # NO datafolder given
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
105 else :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
106 data['datafolder'] = args.datafolder
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
107
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
108 if (args.experimentfile is None) or (args.experimentfile == 'None') :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
109 pass # NO experimentfile given
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
110 else :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
111 data['experimentfile'] = args.experimentfile
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
112
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
113 data['action'] = action
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
114
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
115 r["data"] = data
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
116
3
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
117 # configuration
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
118 if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
119
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
120 r_init = erecord_api.init(config)
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
121 if MAIN_DEBUG: r["init"] = r_init # debug
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
122
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
123 response = erecord_api.action(config, data)
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
124 json_response = json.loads(response)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
125
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
126 # Restitution : file (experiment.xls, conditions.xls, report.zip)
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
127 # Note :
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
128 # tool.xml command "touch" the file (in case of failed to be copied here)
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
129 # for it to exist (even if empty) => able to be found
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
130 if action in ['get_vpz_experiment', 'post_vpz_experiment',
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
131 'get_vpz_report_conditions', 'post_vpz_report_conditions',
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
132 'get_vpz_report', 'post_vpz_report']:
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
133 try:
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
134 filename = json_response["outputfile_name"]
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
135 outputfile_path = json_response["outputfile_path"]
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
136 shutil.copyfile(src=outputfile_path,
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
137 dst=os.path.join(config.out_path,filename))
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
138 # tool.xml uses them
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
139
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
140 if not MAIN_DEBUG: # some response information not kept
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
141 for k in ('outputfile_name', 'outputfile_path', 'zip_file_path'):
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
142 if k in json_response.keys(): del(json_response[k])
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
143
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
144 except Exception as e :
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
145
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
146 msg = PM+"[second file "
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
147 if "outputfile_name" in json_response.keys() :
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
148 msg = "('"+ json_response["outputfile_name"] + "')"
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
149 msg = " restitution]"
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
150 cnt = build_error_content(exception=e, errormsg=msg)
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
siwaa
parents: 0
diff changeset
151 json_response["error PLUS"] = str(cnt)
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
152
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
153 except Exception as e :
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
154
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
155 response = erecord_api.error_case(data=data, msg=PM, e=e)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
156 json_response = json.loads(response)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
157
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
158 r["response"] = json_response
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
159
3
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
160 try :
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
161 # Restitution : json file
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
162 jsonoutput_filepath = os.path.join(config.out_path,
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
163 config.jsonoutput_filename)
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
164 with open(jsonoutput_filepath, "w") as outfile:
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
165 json.dump(r, outfile)
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
166 except :
aa5c088856c8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
siwaa
parents: 2
diff changeset
167 print(PM, " -- error when trying to open output json file --")
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
parents:
diff changeset
168