Mercurial > repos > siwaa > erecord_text

comparison main_text.py @ 0:5edb952b394e draft default tip

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_text commit c9272a57d834895bf21c987be7d7416532cfa23f-dirty
author siwaa
date Tue, 27 Feb 2024 07:58:55 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5edb952b394e
1 # -*- coding: UTF-8 -*-
2 """
3 main_text
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 (string 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 (jsonoutput_filepath)
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
35 import os
36
37 PM = "[main_text.py]"
38
39 UNACCEPTED_ACTIONS_LIST = ['get_vpz_experiment', 'post_vpz_experiment',
40 'get_vpz_report_conditions', 'post_vpz_report_conditions',
41 'get_vpz_report', 'post_vpz_report']
42
43 r = dict()
44
45 import sys
46 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
47 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
48
49 data = dict()
50 json_response = dict()
51
52 # default configuration + maybe some modifications
53 config = erecord_api.conf() # default (vle-2.0.0 version)
54 config.DB_add_vpz(vpz_id=1312, vpzname="wwdm.vpz", pkgname="wwdm")
55
56 try :
57 parser = argparse.ArgumentParser()
58 parser.add_argument("-data", type=str, help="data in string format")
59 parser.add_argument("-datafolder", type=str, help="datafolder file path")
60
61 args = parser.parse_args()
62
63 if (args.data is None) or (args.data == 'None') :
64 warn = "NO data (string format) given => action enforced to 'help'"
65 r["warning"] = warn
66 data = {'action':'help'} # enforced (default)
67 else:
68 #jsoninput_filename = args.data
69 #inputfile = open(jsoninput_filename, 'r')
70 #data = json.load(inputfile) # get data
71
72 # examples
73 # {"action":"pkg_list"}
74 # {"action": "post_vpz_output", "pkgname": "wwdm", "vpzname": "wwdm.vpz", "style": "compactlist", "plan":"linear", "restype" : "matrix", "cond_wwdm.A": [0.0063, 0.0065, 0.0067], "cond_wwdm.B": 0.00201, "duration":6.0, "outselect": "view"}
75
76 jsoninput_text = args.data
77 try :
78
79 # restore sanitized text
80 MAPPING = {'>': '__gt__', '<': '__lt__', "'": '__sq__', '"': '__dq__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__', '@': '__at__', '\n': '__cn__', '\r': '__cr__', '\t': '__tc__', '#': '__pd__'}
81 for key, value in MAPPING.items():
82 jsoninput_text = jsoninput_text.replace(value, key)
83
84 data = json.loads(jsoninput_text) # get data
85 except:
86 warn = "Failed to get json data from string '" +jsoninput_text+ "'"
87 warn = warn + " => action enforced to 'help'"
88 r["warning"] = warn
89 data = {'action':'help'} # enforced (default)
90
91 if (args.datafolder is None) or (args.datafolder == 'None') :
92 pass # NO datafolder given
93 else :
94 data['datafolder'] = args.datafolder
95
96 # Pre-filtering : Unaccepted actions => enforced to 'help' action
97 if "action" in data.keys() :
98 a = data["action"]
99 if a in UNACCEPTED_ACTIONS_LIST :
100 warn = "Unaccepted action '"+a+"' => action enforced to 'help'"
101 r["warning"] = warn
102 data["action"] = 'help'
103
104 r["data"] = data
105
106 # configuration
107 if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug
108
109 r_init = erecord_api.init(config)
110 if MAIN_DEBUG: r["init"] = r_init # debug
111
112 response = erecord_api.action(config, data)
113 json_response = json.loads(response)
114
115 except Exception as e :
116
117 response = erecord_api.error_case(data=data, msg=PM, e=e)
118 json_response = json.loads(response)
119
120 r["response"] = json_response
121
122 try :
123 # Restitution : json file
124 jsonoutput_filepath = os.path.join(config.out_path,
125 config.jsonoutput_filename)
126 with open(jsonoutput_filepath, "w") as outfile:
127 json.dump(r, outfile)
128
129 except :
130 print(PM, " -- error when trying to open output json file --")
131