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comparison main_file.py @ 0:27e7e4d38e44 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
author siwaa
date Tue, 12 Dec 2023 17:33:05 +0000
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children 9e8f5f220917
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-1:000000000000 0:27e7e4d38e44
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
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 import os
46 import shutil
47 from erecord.api.cmn.utils.dir_and_file import create_dir_if_absent
48 from erecord.api.cmn.configs.config import PROJECT_HOME
49 from erecord.api.cmn.configs.config import out_path
50
51 PM = "[main_file.py]"
52
53 jsonoutput_filepath = os.path.join(out_path, "output.json") # tool.xml uses it
54
55 r = dict()
56
57 import sys
58 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
59 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
60 if MAIN_DEBUG: r["out_path"] = out_path # debug
61
62 data = dict()
63 json_response = dict()
64
65 create_dir_if_absent(PROJECT_HOME) # required
66
67 try :
68 parser = argparse.ArgumentParser()
69
70 # -action
71 available_action_list = ActionViewMixin.get_action_list()
72 htext = "action value among : " + str(available_action_list)
73 parser.add_argument("-action", default='help', help=htext,
74 choices=available_action_list)
75
76 # -data
77 parser.add_argument("-data", type=str, help="data json file path")
78
79 # -datafolder
80 htext = "datafolder file path, available for action : "
81 htext +="post_vpz_output, post_vpz_inout,"
82 htext +="post_vpz_experiment, post_vpz_report"
83 parser.add_argument("-datafolder", type=str, help=htext)
84
85 # -experimentfile
86 htext = "experimentfile path, available for action : post_vpz_experiment"
87 parser.add_argument("-experimentfile", type=str, help=htext)
88
89 args = parser.parse_args()
90
91 if (args.action is None) or (args.action == 'None') :
92 warn = "NO action given => enforced to 'help'"
93 r["warning"] = warn
94 action = 'help' # enforced (default)
95 else :
96 action = args.action
97
98 if (args.data is None) or (args.data == 'None') :
99 data = dict() # NO data (JSON format) given as argument
100 else :
101 jsoninput_filename = args.data
102 inputfile = open(jsoninput_filename, 'r')
103 data = json.load(inputfile) # get data
104
105 if (args.datafolder is None) or (args.datafolder == 'None') :
106 pass # NO datafolder given
107 else :
108 data['datafolder'] = args.datafolder
109
110 if (args.experimentfile is None) or (args.experimentfile == 'None') :
111 pass # NO experimentfile given
112 else :
113 data['experimentfile'] = args.experimentfile
114
115 data['action'] = action
116
117 r["data"] = data
118 r_init = erecord_api.init()
119 if MAIN_DEBUG: r["init"] = r_init # debug
120 response = erecord_api.action(data)
121 json_response = json.loads(response)
122
123 # Restitution : file (experiment.xls, conditions.xls, report.zip)
124 if action in ['get_vpz_experiment', 'post_vpz_experiment',
125 'get_vpz_report_conditions', 'post_vpz_report_conditions',
126 'get_vpz_report', 'post_vpz_report']:
127
128 filename = json_response["outputfile_name"]
129 outputfile_path = json_response["outputfile_path"]
130 shutil.copyfile(src=outputfile_path,
131 dst=os.path.join(out_path,filename)) # tool.xml uses them
132
133 if not MAIN_DEBUG: # some response information not kept
134 for k in ('outputfile_name', 'outputfile_path', 'zip_file_path'):
135 if k in json_response.keys():
136 del(json_response[k])
137
138 except Exception as e :
139
140 response = erecord_api.error_case(data=data, msg=PM, e=e)
141 json_response = json.loads(response)
142
143 r["response"] = json_response
144
145 # Restitution : json file
146 with open(jsonoutput_filepath, "w") as outfile:
147 json.dump(r, outfile)
148