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comparison main_json.py @ 3:eb06af7c29a8 draft default tip

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 490623122691651ac91c33d75ea1898189be7512-dirty
author siwaa
date Thu, 15 Feb 2024 15:24:41 +0000
parents afc88ac8de69
children
comparison
equal deleted inserted replaced
2:afc88ac8de69 3:eb06af7c29a8
22 - '-datafolder' parameter : datafolder file path (optional, 22 - '-datafolder' parameter : datafolder file path (optional,
23 available only in some cases) 23 available only in some cases)
24 24
25 Outputs : 25 Outputs :
26 - output.json data file (jsonoutput_filepath) 26 - output.json data file (jsonoutput_filepath)
27
28 """ 27 """
29 28
30 MAIN_DEBUG=False # True for more information returned 29 MAIN_DEBUG=False # True for more information returned
31 30
32 import argparse 31 import argparse
47 if MAIN_DEBUG: r["sys.path"] = sys.path # debug 46 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
48 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug 47 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
49 48
50 data = dict() 49 data = dict()
51 json_response = 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")
52 55
53 try : 56 try :
54 parser = argparse.ArgumentParser() 57 parser = argparse.ArgumentParser()
55 parser.add_argument("-data", type=str, help="data json file path") 58 parser.add_argument("-data", type=str, help="data json file path")
56 parser.add_argument("-datafolder", type=str, help="datafolder file path") 59 parser.add_argument("-datafolder", type=str, help="datafolder file path")
79 r["warning"] = warn 82 r["warning"] = warn
80 data["action"] = 'help' 83 data["action"] = 'help'
81 84
82 r["data"] = data 85 r["data"] = data
83 86
84 # default configuration + maybe some modifications 87 # configuration
85 config = erecord_api.conf() # default (vle-2.0.0 version)
86 config.DB_add_vpz(vpz_id=1312, vpzname="wwdm.vpz", pkgname="wwdm")
87 if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug 88 if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug
88 89
89 r_init = erecord_api.init(config) 90 r_init = erecord_api.init(config)
90 if MAIN_DEBUG: r["init"] = r_init # debug 91 if MAIN_DEBUG: r["init"] = r_init # debug
91 92
97 response = erecord_api.error_case(data=data, msg=PM, e=e) 98 response = erecord_api.error_case(data=data, msg=PM, e=e)
98 json_response = json.loads(response) 99 json_response = json.loads(response)
99 100
100 r["response"] = json_response 101 r["response"] = json_response
101 102
102 # Restitution : json file 103 try :
103 jsonoutput_filepath = os.path.join(config.out_path, config.jsonoutput_filename) 104 # Restitution : json file
104 with open(jsonoutput_filepath, "w") as outfile: 105 jsonoutput_filepath = os.path.join(config.out_path,
105 json.dump(r, outfile) 106 config.jsonoutput_filename)
107 with open(jsonoutput_filepath, "w") as outfile:
108 json.dump(r, outfile)
106 109
110 except :
111 print(PM, " -- error when trying to open output json file --")
112