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comparison main_json.py @ 0:8a0659f23df7 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
author siwaa
date Tue, 12 Dec 2023 17:37:35 +0000
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children afc88ac8de69
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-1:000000000000 0:8a0659f23df7
1 # -*- coding: UTF-8 -*-
2 """
3 main_json
4
5 Requests having only 1 json data as OUTput
6
7 Accepts actions :
8 'get_vpz_input' 'post_vpz_input'
9 'get_vpz_output' 'post_vpz_output'
10 'get_vpz_inout' 'post_vpz_inout'
11 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
12 'help'
13
14 Refused actions :
15 'get_vpz_experiment' 'post_vpz_experiment'
16 'get_vpz_report_conditions' 'post_vpz_report_conditions'
17 'get_vpz_report' 'post_vpz_report'
18
19 Parameters (Inputs) :
20 - '-data' parameter : data (JSON format) (optional)
21 A required action value must be included into data.
22 - '-datafolder' parameter : datafolder file path (optional,
23 available only in some cases)
24
25 Outputs :
26 - output.json data file
27 """
28
29 MAIN_DEBUG=False # True for more information returned
30
31 import argparse
32 import json
33 import erecord.api.erecord as erecord_api
34 import os
35 from erecord.api.cmn.utils.dir_and_file import create_dir_if_absent
36 from erecord.api.cmn.configs.config import PROJECT_HOME
37 from erecord.api.cmn.configs.config import out_path
38
39 PM = "[main_json.py]"
40
41 UNACCEPTED_ACTIONS_LIST = ['get_vpz_experiment', 'post_vpz_experiment',
42 'get_vpz_report_conditions', 'post_vpz_report_conditions',
43 'get_vpz_report', 'post_vpz_report']
44
45 jsonoutput_filepath = os.path.join(out_path, "output.json") # tool.xml uses it
46
47 r = dict()
48
49 import sys
50 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
51 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
52 if MAIN_DEBUG: r["out_path"] = out_path # debug
53
54 data = dict()
55 json_response = dict()
56
57 create_dir_if_absent(PROJECT_HOME) # required
58
59 try :
60 parser = argparse.ArgumentParser()
61 parser.add_argument("-data", type=str, help="data json file path")
62 parser.add_argument("-datafolder", type=str, help="datafolder file path")
63
64 args = parser.parse_args()
65
66 if (args.data is None) or (args.data == 'None') :
67 warn = "NO data (JSON format) given => action enforced to 'help'"
68 r["warning"] = warn
69 data = {'action':'help'} # enforced (default)
70 else:
71 jsoninput_filename = args.data
72 inputfile = open(jsoninput_filename, 'r')
73 data = json.load(inputfile) # get data
74
75 if (args.datafolder is None) or (args.datafolder == 'None') :
76 pass # NO datafolder given
77 else :
78 data['datafolder'] = args.datafolder
79
80 # Pre-filtering : Unaccepted actions => enforced to 'help' action
81 if "action" in data.keys() :
82 a = data["action"]
83 if a in UNACCEPTED_ACTIONS_LIST :
84 warn = "Unaccepted action '"+a+"' => action enforced to 'help'"
85 r["warning"] = warn
86 data["action"] = 'help'
87
88 r["data"] = data
89 r_init = erecord_api.init()
90 if MAIN_DEBUG: r["init"] = r_init # debug
91 response = erecord_api.action(data)
92 json_response = json.loads(response)
93
94 except Exception as e :
95
96 response = erecord_api.error_case(data=data, msg=PM, e=e)
97 json_response = json.loads(response)
98
99 r["response"] = json_response
100
101 # Restitution : json file
102 with open(jsonoutput_filepath, "w") as outfile:
103 json.dump(r, outfile)
104