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comparison main_file__OriginalNOK.py @ 4:4c45f7b92955 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 882e24ac5dbef67295dd4466908b7eea02e34697-dirty
author siwaa
date Thu, 15 Feb 2024 17:12:58 +0000
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3:aa5c088856c8 4:4c45f7b92955
1 # -*- coding: UTF-8 -*-
2 """
3 main_file
4
5 Requests having as OUTput : 1 json data + maybe 1 more file (xls or zip)
6
7 Accepts actions (all) :
8 'help'
9 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
10 'get_vpz_input' 'post_vpz_input'
11 'get_vpz_output' 'post_vpz_output'
12 'get_vpz_inout' 'post_vpz_inout'
13 'get_vpz_experiment' 'post_vpz_experiment'
14 'get_vpz_report_conditions' 'post_vpz_report_conditions'
15 'get_vpz_report' 'post_vpz_report'
16
17 Parameters (Inputs) :
18 - '-action' parameter : action value (mandatory)
19 - '-data' parameter : data (JSON format) (optional)
20 - '-datafolder' parameter : datafolder file path (optional,
21 available only in some cases)
22 - '-experimentfile' parameter : experimentfile path (optional,
23 available only in some cases) :
24
25 If there is an action value into data, then this one is ignored.
26
27 Outputs :
28 - output.json data file (jsonoutput_filepath)
29 - 1 other file in following cases :
30 - experiment.xls file
31 if 'action' == get_vpz_experiment, post_vpz_experiment
32 - conditions.xls file
33 if 'action' == get_vpz_report_conditions,
34 post_vpz_report_conditions
35 - report.zip file
36 if 'action' == get_vpz_report, post_vpz_report
37 """
38
39 MAIN_DEBUG=False # True for more information returned
40
41 import argparse
42 import json
43 import erecord.api.erecord as erecord_api
44 from erecord.api.cmn.views_mixins import ActionViewMixin
45 from erecord.api.cmn.utils.errors import build_error_content
46
47 import os
48 import shutil
49
50 PM = "[main_file.py]"
51
52 r = dict()
53
54 import sys
55 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
56 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
57
58 data = dict()
59 json_response = dict()
60
61 # default configuration + maybe some modifications
62 config = erecord_api.conf() # default (vle-2.0.0 version)
63 config.DB_add_vpz(vpz_id=1312, vpzname="wwdm.vpz", pkgname="wwdm")
64
65 try :
66 parser = argparse.ArgumentParser()
67
68 # -action
69 available_action_list = ActionViewMixin.get_action_list()
70 htext = "action value among : " + str(available_action_list)
71 parser.add_argument("-action", default='help', help=htext,
72 choices=available_action_list)
73
74 # -data
75 parser.add_argument("-data", type=str, help="data json file path")
76
77 # -datafolder
78 htext = "datafolder file path, available for action : "
79 htext +="post_vpz_output, post_vpz_inout,"
80 htext +="post_vpz_experiment, post_vpz_report"
81 parser.add_argument("-datafolder", type=str, help=htext)
82
83 # -experimentfile
84 htext = "experimentfile path, available for action : post_vpz_experiment"
85 parser.add_argument("-experimentfile", type=str, help=htext)
86
87 args = parser.parse_args()
88
89 if (args.action is None) or (args.action == 'None') :
90 warn = "NO action given => enforced to 'help'"
91 r["warning"] = warn
92 action = 'help' # enforced (default)
93 else :
94 action = args.action
95
96 if (args.data is None) or (args.data == 'None') :
97 data = dict() # NO data (JSON format) given as argument
98 else :
99 jsoninput_filename = args.data
100 inputfile = open(jsoninput_filename, 'r')
101 data = json.load(inputfile) # get data
102
103 if (args.datafolder is None) or (args.datafolder == 'None') :
104 pass # NO datafolder given
105 else :
106 data['datafolder'] = args.datafolder
107
108 if (args.experimentfile is None) or (args.experimentfile == 'None') :
109 pass # NO experimentfile given
110 else :
111 data['experimentfile'] = args.experimentfile
112
113 data['action'] = action
114
115 r["data"] = data
116
117 # configuration
118 if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug
119
120 r_init = erecord_api.init(config)
121 if MAIN_DEBUG: r["init"] = r_init # debug
122
123 response = erecord_api.action(config, data)
124 json_response = json.loads(response)
125
126 # Restitution : file (experiment.xls, conditions.xls, report.zip)
127 # Note :
128 # tool.xml command "touch" the file (in case of failed to be copied here)
129 # for it to exist (even if empty) => able to be found
130 if action in ['get_vpz_experiment', 'post_vpz_experiment',
131 'get_vpz_report_conditions', 'post_vpz_report_conditions',
132 'get_vpz_report', 'post_vpz_report']:
133 try:
134 filename = json_response["outputfile_name"]
135 outputfile_path = json_response["outputfile_path"]
136 shutil.copyfile(src=outputfile_path,
137 dst=os.path.join(config.out_path,filename))
138 # tool.xml uses them
139
140 if not MAIN_DEBUG: # some response information not kept
141 for k in ('outputfile_name', 'outputfile_path', 'zip_file_path'):
142 if k in json_response.keys(): del(json_response[k])
143
144 except Exception as e :
145
146 msg = PM+"[second file "
147 if "outputfile_name" in json_response.keys() :
148 msg = "('"+ json_response["outputfile_name"] + "')"
149 msg = " restitution]"
150 cnt = build_error_content(exception=e, errormsg=msg)
151 json_response["error PLUS"] = str(cnt)
152
153 except Exception as e :
154
155 response = erecord_api.error_case(data=data, msg=PM, e=e)
156 json_response = json.loads(response)
157
158 r["response"] = json_response
159
160 try :
161 # Restitution : json file
162 jsonoutput_filepath = os.path.join(config.out_path,
163 config.jsonoutput_filename)
164 with open(jsonoutput_filepath, "w") as outfile:
165 json.dump(r, outfile)
166 except :
167 print(PM, " -- error when trying to open output json file --")
168