Mercurial > repos > siwaa > erecord_file

annotate 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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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
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1 # -*- coding: UTF-8 -*-
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2 """
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3 main_file
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4
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5 Requests having as OUTput : 1 json data + maybe 1 more file (xls or zip)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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6
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7 Accepts actions (all) :
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8 'help'
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9 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
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10 'get_vpz_input' 'post_vpz_input'
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11 'get_vpz_output' 'post_vpz_output'
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12 'get_vpz_inout' 'post_vpz_inout'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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13 'get_vpz_experiment' 'post_vpz_experiment'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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14 'get_vpz_report_conditions' 'post_vpz_report_conditions'
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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15 'get_vpz_report' 'post_vpz_report'
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16
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17 Parameters (Inputs) :
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18 - '-action' parameter : action value (mandatory)
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19 - '-data' parameter : data (JSON format) (optional)
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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20 - '-datafolder' parameter : datafolder file path (optional,
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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21 available only in some cases)
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22 - '-experimentfile' parameter : experimentfile path (optional,
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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23 available only in some cases) :
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24
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25 If there is an action value into data, then this one is ignored.
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26
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27 Outputs :
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28 - output.json data file
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29 - 1 other file in following cases :
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30 - experiment.xls file
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31 if 'action' == get_vpz_experiment, post_vpz_experiment
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32 - conditions.xls file
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33 if 'action' == get_vpz_report_conditions,
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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34 post_vpz_report_conditions
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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35 - report.zip file
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36 if 'action' == get_vpz_report, post_vpz_report
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37 """
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38
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39 MAIN_DEBUG=False # True for more information returned
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40
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41 import argparse
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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42 import json
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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43 import erecord.api.erecord as erecord_api
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44 from erecord.api.cmn.views_mixins import ActionViewMixin
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45 import os
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46 import shutil
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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47 from erecord.api.cmn.utils.dir_and_file import create_dir_if_absent
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48 from erecord.api.cmn.configs.config import PROJECT_HOME
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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49 from erecord.api.cmn.configs.config import out_path
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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50
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51 PM = "[main_file.py]"
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52
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53 jsonoutput_filepath = os.path.join(out_path, "output.json") # tool.xml uses it
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54
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55 r = dict()
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56
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57 import sys
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58 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
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59 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
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60 if MAIN_DEBUG: r["out_path"] = out_path # debug
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61
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62 data = dict()
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63 json_response = dict()
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64
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65 create_dir_if_absent(PROJECT_HOME) # required
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66
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67 try :
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68 parser = argparse.ArgumentParser()
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69
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70 # -action
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71 available_action_list = ActionViewMixin.get_action_list()
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72 htext = "action value among : " + str(available_action_list)
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73 parser.add_argument("-action", default='help', help=htext,
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74 choices=available_action_list)
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75
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76 # -data
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77 parser.add_argument("-data", type=str, help="data json file path")
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78
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79 # -datafolder
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80 htext = "datafolder file path, available for action : "
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81 htext +="post_vpz_output, post_vpz_inout,"
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82 htext +="post_vpz_experiment, post_vpz_report"
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83 parser.add_argument("-datafolder", type=str, help=htext)
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84
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85 # -experimentfile
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86 htext = "experimentfile path, available for action : post_vpz_experiment"
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87 parser.add_argument("-experimentfile", type=str, help=htext)
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88
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89 args = parser.parse_args()
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90
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91 if (args.action is None) or (args.action == 'None') :
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92 warn = "NO action given => enforced to 'help'"
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93 r["warning"] = warn
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94 action = 'help' # enforced (default)
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95 else :
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96 action = args.action
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97
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98 if (args.data is None) or (args.data == 'None') :
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99 data = dict() # NO data (JSON format) given as argument
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100 else :
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101 jsoninput_filename = args.data
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102 inputfile = open(jsoninput_filename, 'r')
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103 data = json.load(inputfile) # get data
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104
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105 if (args.datafolder is None) or (args.datafolder == 'None') :
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106 pass # NO datafolder given
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107 else :
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108 data['datafolder'] = args.datafolder
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109
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110 if (args.experimentfile is None) or (args.experimentfile == 'None') :
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111 pass # NO experimentfile given
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112 else :
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113 data['experimentfile'] = args.experimentfile
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114
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115 data['action'] = action
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116
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117 r["data"] = data
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118 r_init = erecord_api.init()
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119 if MAIN_DEBUG: r["init"] = r_init # debug
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120 response = erecord_api.action(data)
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121 json_response = json.loads(response)
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122
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123 # Restitution : file (experiment.xls, conditions.xls, report.zip)
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124 if action in ['get_vpz_experiment', 'post_vpz_experiment',
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125 'get_vpz_report_conditions', 'post_vpz_report_conditions',
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126 'get_vpz_report', 'post_vpz_report']:
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127
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128 filename = json_response["outputfile_name"]
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129 outputfile_path = json_response["outputfile_path"]
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130 shutil.copyfile(src=outputfile_path,
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131 dst=os.path.join(out_path,filename)) # tool.xml uses them
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132
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133 if not MAIN_DEBUG: # some response information not kept
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134 for k in ('outputfile_name', 'outputfile_path', 'zip_file_path'):
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135 if k in json_response.keys():
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136 del(json_response[k])
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137
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138 except Exception as e :
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139
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140 response = erecord_api.error_case(data=data, msg=PM, e=e)
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141 json_response = json.loads(response)
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142
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143 r["response"] = json_response
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144
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145 # Restitution : json file
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146 with open(jsonoutput_filepath, "w") as outfile:
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147 json.dump(r, outfile)
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148