Mercurial > repos > siwaa > erecord_json
view main_json.py @ 0:8a0659f23df7 draft
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_json commit 88beb443a737b4c4d42bb0011a26a0acf535c366
author | siwaa |
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date | Tue, 12 Dec 2023 17:37:35 +0000 |
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children | afc88ac8de69 |
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# -*- coding: UTF-8 -*- """ main_json Requests having only 1 json data as OUTput Accepts actions : 'get_vpz_input' 'post_vpz_input' 'get_vpz_output' 'post_vpz_output' 'get_vpz_inout' 'post_vpz_inout' 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list' 'help' Refused actions : 'get_vpz_experiment' 'post_vpz_experiment' 'get_vpz_report_conditions' 'post_vpz_report_conditions' 'get_vpz_report' 'post_vpz_report' Parameters (Inputs) : - '-data' parameter : data (JSON format) (optional) A required action value must be included into data. - '-datafolder' parameter : datafolder file path (optional, available only in some cases) Outputs : - output.json data file """ MAIN_DEBUG=False # True for more information returned import argparse import json import erecord.api.erecord as erecord_api import os from erecord.api.cmn.utils.dir_and_file import create_dir_if_absent from erecord.api.cmn.configs.config import PROJECT_HOME from erecord.api.cmn.configs.config import out_path PM = "[main_json.py]" UNACCEPTED_ACTIONS_LIST = ['get_vpz_experiment', 'post_vpz_experiment', 'get_vpz_report_conditions', 'post_vpz_report_conditions', 'get_vpz_report', 'post_vpz_report'] jsonoutput_filepath = os.path.join(out_path, "output.json") # tool.xml uses it r = dict() import sys if MAIN_DEBUG: r["sys.path"] = sys.path # debug if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug if MAIN_DEBUG: r["out_path"] = out_path # debug data = dict() json_response = dict() create_dir_if_absent(PROJECT_HOME) # required try : parser = argparse.ArgumentParser() parser.add_argument("-data", type=str, help="data json file path") parser.add_argument("-datafolder", type=str, help="datafolder file path") args = parser.parse_args() if (args.data is None) or (args.data == 'None') : warn = "NO data (JSON format) given => action enforced to 'help'" r["warning"] = warn data = {'action':'help'} # enforced (default) else: jsoninput_filename = args.data inputfile = open(jsoninput_filename, 'r') data = json.load(inputfile) # get data if (args.datafolder is None) or (args.datafolder == 'None') : pass # NO datafolder given else : data['datafolder'] = args.datafolder # Pre-filtering : Unaccepted actions => enforced to 'help' action if "action" in data.keys() : a = data["action"] if a in UNACCEPTED_ACTIONS_LIST : warn = "Unaccepted action '"+a+"' => action enforced to 'help'" r["warning"] = warn data["action"] = 'help' r["data"] = data r_init = erecord_api.init() if MAIN_DEBUG: r["init"] = r_init # debug response = erecord_api.action(data) json_response = json.loads(response) except Exception as e : response = erecord_api.error_case(data=data, msg=PM, e=e) json_response = json.loads(response) r["response"] = json_response # Restitution : json file with open(jsonoutput_filepath, "w") as outfile: json.dump(r, outfile)