Mercurial > repos > siwaa > erecord_json

annotate main_json.py @ 0:8a0659f23df7 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
author siwaa
date Tue, 12 Dec 2023 17:37:35 +0000
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children afc88ac8de69
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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
siwaa
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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
siwaa
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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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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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6
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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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 :
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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26 - output.json data file
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 """
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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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
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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34 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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35 from erecord.api.cmn.utils.dir_and_file import create_dir_if_absent
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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36 from erecord.api.cmn.configs.config import PROJECT_HOME
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 from erecord.api.cmn.configs.config import out_path
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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38
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39 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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41 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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42 'get_vpz_report_conditions', 'post_vpz_report_conditions',
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43 '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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45 jsonoutput_filepath = os.path.join(out_path, "output.json") # tool.xml uses it
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47 r = 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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48
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49 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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50 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
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 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
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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52 if MAIN_DEBUG: r["out_path"] = out_path # debug
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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53
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54 data = 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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55 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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56
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57 create_dir_if_absent(PROJECT_HOME) # required
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
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59 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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60 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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61 parser.add_argument("-data", type=str, help="data json file path")
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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62 parser.add_argument("-datafolder", type=str, help="datafolder file path")
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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63
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64 args = parser.parse_args()
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65
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66 if (args.data is None) or (args.data == 'None') :
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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67 warn = "NO data (JSON format) given => action enforced to '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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68 r["warning"] = warn
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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69 data = {'action':'help'} # enforced (default)
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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70 else:
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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71 jsoninput_filename = args.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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72 inputfile = open(jsoninput_filename, 'r')
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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73 data = json.load(inputfile) # get 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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74
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75 if (args.datafolder is None) or (args.datafolder == 'None') :
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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76 pass # NO datafolder given
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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77 else :
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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78 data['datafolder'] = args.datafolder
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79
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80 # Pre-filtering : Unaccepted actions => enforced to 'help' action
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81 if "action" in data.keys() :
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82 a = data["action"]
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83 if a in UNACCEPTED_ACTIONS_LIST :
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84 warn = "Unaccepted action '"+a+"' => action enforced to 'help'"
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85 r["warning"] = warn
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86 data["action"] = 'help'
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87
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88 r["data"] = data
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89 r_init = erecord_api.init()
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90 if MAIN_DEBUG: r["init"] = r_init # debug
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91 response = erecord_api.action(data)
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92 json_response = json.loads(response)
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93
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94 except Exception as e :
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95
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96 response = erecord_api.error_case(data=data, msg=PM, e=e)
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97 json_response = json.loads(response)
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98
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99 r["response"] = json_response
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100
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101 # Restitution : json file
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102 with open(jsonoutput_filepath, "w") as outfile:
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103 json.dump(r, outfile)
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104