Mercurial > repos > siwaa > erecord_file

annotate main_file.py @ 2:9e8f5f220917 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
author siwaa
date Thu, 15 Feb 2024 14:44:47 +0000
parents 27e7e4d38e44
children aa5c088856c8
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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
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1 # -*- coding: UTF-8 -*-
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2 """
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3 main_file
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5 Requests having as OUTput : 1 json data + maybe 1 more file (xls or zip)
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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'
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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10 'get_vpz_input' 'post_vpz_input'
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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11 'get_vpz_output' 'post_vpz_output'
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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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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17 Parameters (Inputs) :
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18 - '-action' parameter : action value (mandatory)
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19 - '-data' parameter : data (JSON format) (optional)
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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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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 (jsonoutput_filepath)
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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
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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
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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
2
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45 from erecord.api.cmn.utils.errors import build_error_content
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46
0
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47 import os
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48 import shutil
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49
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50 PM = "[main_file.py]"
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51
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52 r = dict()
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53
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54 import sys
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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55 if MAIN_DEBUG: r["sys.path"] = sys.path # debug
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56 if MAIN_DEBUG: r["sys.argv"] = sys.argv # debug
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57
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58 data = dict()
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59 json_response = dict()
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60
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61 try :
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62 parser = argparse.ArgumentParser()
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63
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64 # -action
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65 available_action_list = ActionViewMixin.get_action_list()
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66 htext = "action value among : " + str(available_action_list)
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67 parser.add_argument("-action", default='help', help=htext,
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68 choices=available_action_list)
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69
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70 # -data
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71 parser.add_argument("-data", type=str, help="data json file path")
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72
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73 # -datafolder
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74 htext = "datafolder file path, available for action : "
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75 htext +="post_vpz_output, post_vpz_inout,"
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76 htext +="post_vpz_experiment, post_vpz_report"
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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77 parser.add_argument("-datafolder", type=str, help=htext)
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78
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79 # -experimentfile
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80 htext = "experimentfile path, available for action : post_vpz_experiment"
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81 parser.add_argument("-experimentfile", type=str, help=htext)
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82
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83 args = parser.parse_args()
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84
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85 if (args.action is None) or (args.action == 'None') :
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86 warn = "NO action given => enforced to 'help'"
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87 r["warning"] = warn
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88 action = 'help' # enforced (default)
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89 else :
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90 action = args.action
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91
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92 if (args.data is None) or (args.data == 'None') :
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93 data = dict() # NO data (JSON format) given as argument
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94 else :
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95 jsoninput_filename = args.data
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96 inputfile = open(jsoninput_filename, 'r')
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97 data = json.load(inputfile) # get data
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98
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99 if (args.datafolder is None) or (args.datafolder == 'None') :
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100 pass # NO datafolder given
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101 else :
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102 data['datafolder'] = args.datafolder
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103
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104 if (args.experimentfile is None) or (args.experimentfile == 'None') :
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105 pass # NO experimentfile given
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106 else :
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107 data['experimentfile'] = args.experimentfile
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108
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109 data['action'] = action
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110
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111 r["data"] = data
2
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112
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113 # default configuration + maybe some modifications
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114 config = erecord_api.conf() # default (vle-2.0.0 version)
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115 config.DB_add_vpz(vpz_id=1312, vpzname="wwdm.vpz", pkgname="wwdm")
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116 if MAIN_DEBUG: r["config"] = config.get_as_dict() # debug
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117
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118 r_init = erecord_api.init(config)
0
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119 if MAIN_DEBUG: r["init"] = r_init # debug
2
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120
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121 response = erecord_api.action(config, data)
0
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122 json_response = json.loads(response)
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123
2
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124 # Restitution : file (experiment.xls, conditions.xls, report.zip)
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125 # Note :
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126 # tool.xml command "touch" the file (in case of failed to be copied here)
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127 # for it to exist (even if empty) => able to be found
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128 if action in ['get_vpz_experiment', 'post_vpz_experiment',
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129 'get_vpz_report_conditions', 'post_vpz_report_conditions',
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130 'get_vpz_report', 'post_vpz_report']:
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131 try:
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132 filename = json_response["outputfile_name"]
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133 outputfile_path = json_response["outputfile_path"]
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134 shutil.copyfile(src=outputfile_path,
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135 dst=os.path.join(config.out_path,filename))
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136 # tool.xml uses them
0
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137
2
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138 if not MAIN_DEBUG: # some response information not kept
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139 for k in ('outputfile_name', 'outputfile_path', 'zip_file_path'):
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140 if k in json_response.keys(): del(json_response[k])
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141
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142 except Exception as e :
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143
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144 msg = PM+"[second file "
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145 if "outputfile_name" in json_response.keys() :
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146 msg = "('"+ json_response["outputfile_name"] + "')"
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147 msg = " restitution]"
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148 cnt = build_error_content(exception=e, errormsg=msg)
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149 json_response["error PLUS"] = str(cnt)
0
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150
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151 except Exception as e :
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152
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153 response = erecord_api.error_case(data=data, msg=PM, e=e)
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154 json_response = json.loads(response)
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156 r["response"] = json_response
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157
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158 # Restitution : json file
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159 jsonoutput_filepath = os.path.join(config.out_path, config.jsonoutput_filename)
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160 with open(jsonoutput_filepath, "w") as outfile:
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161 json.dump(r, outfile)
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162