Mercurial > repos > siwaa > erecord_json

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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
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
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1 # -*- coding: UTF-8 -*-
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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2 """
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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3 main_json
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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5 Requests having only 1 json data as OUTput
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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7 Accepts actions :
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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8 'get_vpz_input' 'post_vpz_input'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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9 'get_vpz_output' 'post_vpz_output'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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10 'get_vpz_inout' 'post_vpz_inout'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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11 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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12 'help'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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14 Refused actions :
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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15 'get_vpz_experiment' 'post_vpz_experiment'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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16 'get_vpz_report_conditions' 'post_vpz_report_conditions'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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17 'get_vpz_report' 'post_vpz_report'
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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19 Parameters (Inputs) :
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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20 - '-data' parameter : data (JSON format) (optional)
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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21 A required action value must be included into data.
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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22 - '-datafolder' parameter : datafolder file path (optional,
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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23 available only in some cases)
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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25 Outputs :
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26 - output.json data file (jsonoutput_filepath)
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27 """
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29 MAIN_DEBUG=False # True for more information returned
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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31 import argparse
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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32 import json
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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33 import erecord.api.erecord as erecord_api
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34
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35 import os
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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37 PM = "[main_json.py]"
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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39 UNACCEPTED_ACTIONS_LIST = ['get_vpz_experiment', 'post_vpz_experiment',
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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40 'get_vpz_report_conditions', 'post_vpz_report_conditions',
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41 'get_vpz_report', 'post_vpz_report']
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43 r = dict()
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45 import sys
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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46 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
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47 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
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48
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49 data = dict()
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50 json_response = dict()
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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51
3
eb06af7c29a8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 490623122691651ac91c33d75ea1898189be7512-dirty
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52 # default configuration + maybe some modifications
eb06af7c29a8 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 490623122691651ac91c33d75ea1898189be7512-dirty
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53 config = erecord_api.conf() # default (vle-2.0.0 version)
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54 config.DB_add_vpz(vpz_id=1312, vpzname="wwdm.vpz", pkgname="wwdm")
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55
0
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56 try :
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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57 parser = argparse.ArgumentParser()
8a0659f23df7 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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58 parser.add_argument("-data", type=str, help="data json file path")
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59 parser.add_argument("-datafolder", type=str, help="datafolder file path")
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60
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61 args = parser.parse_args()
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63 if (args.data is None) or (args.data == 'None') :
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64 warn = "NO data (JSON format) given => action enforced to 'help'"
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65 r["warning"] = warn
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66 data = {'action':'help'} # enforced (default)
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67 else:
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68 jsoninput_filename = args.data
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69 inputfile = open(jsoninput_filename, 'r')
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70 data = json.load(inputfile) # get data
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71
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72 if (args.datafolder is None) or (args.datafolder == 'None') :
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73 pass # NO datafolder given
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74 else :
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75 data['datafolder'] = args.datafolder
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76
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77 # Pre-filtering : Unaccepted actions => enforced to 'help' action
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78 if "action" in data.keys() :
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79 a = data["action"]
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80 if a in UNACCEPTED_ACTIONS_LIST :
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81 warn = "Unaccepted action '"+a+"' => action enforced to 'help'"
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82 r["warning"] = warn
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83 data["action"] = 'help'
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84
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85 r["data"] = data
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86
3
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87 # configuration
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88 if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug
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89
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90 r_init = erecord_api.init(config)
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91 if MAIN_DEBUG: r["init"] = r_init # debug
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92
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93 response = erecord_api.action(config, data)
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94 json_response = json.loads(response)
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95
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96 except Exception as e :
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97
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98 response = erecord_api.error_case(data=data, msg=PM, e=e)
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99 json_response = json.loads(response)
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100
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101 r["response"] = json_response
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102
3
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103 try :
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104 # Restitution : json file
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105 jsonoutput_filepath = os.path.join(config.out_path,
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106 config.jsonoutput_filename)
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107 with open(jsonoutput_filepath, "w") as outfile:
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108 json.dump(r, outfile)
0
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109
3
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110 except :
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111 print(PM, " -- error when trying to open output json file --")
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112