Mercurial > repos > tduigou > retrorules

annotate query.py @ 2:58bbbff358d6 draft

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planemo upload for repository https://github.com/brsynth/galaxytools commit 469ebd8616b81810ead4633c278dc4c65ab8603b
author tduigou
date Mon, 15 Sep 2025 09:42:19 +0000
parents 6d20407d9a72
children 95b4196b4ded
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1 import argparse
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2 import json
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3 import logging
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4 import sys
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5 from typing import Dict, List
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7 import requests
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9 BASE_URL = "https://retrorules.org/api/v0.7"
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12 def from_ec_number(ec_number: str, min_diameter: int = None) -> List:
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13 url = f"{BASE_URL}/ecnumber"
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14 params = [("input", ec_number)]
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15 if min_diameter:
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16 params.append(("minDiameter", str(min_diameter)))
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17 return url, params
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20 def from_substrate(substrate: str, min_diameter: int = None) -> List:
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21 url = f"{BASE_URL}/substrate"
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22 params = [("input", substrate)]
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23 if min_diameter:
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24 params.append(("minDiameter", str(min_diameter)))
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25 return url, params
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28 def from_reaction_id(
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29 reaction_id: str, repository: str, min_diameter: int = None
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30 ) -> List:
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31 url = f"{BASE_URL}/reactionid"
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32 params = [("input", reaction_id)]
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33 params.append(("repo", repository))
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34 if min_diameter:
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35 params.append(("minDiameter", str(min_diameter)))
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36 return url, params
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39 def from_inchi(inchi: str, min_diameter: int = None) -> List:
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40 url = f"{BASE_URL}/inchi"
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41 params = [("input", inchi)]
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42 if min_diameter:
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43 params.append(("minDiameter", str(min_diameter)))
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44 return url, params
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47 def from_repository(repository: str, min_diameter: int = None) -> List:
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48 url = f"{BASE_URL}/repo"
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49 params = [("input", repository)]
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50 if min_diameter:
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51 params.append(("minDiameter", str(min_diameter)))
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52 return url, params
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55 def from_smarts_id(smarts_ids: List[str], min_diameter: int = None) -> List:
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56 url = f"{BASE_URL}/smartsid"
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57 params = [("input", smart_id) for smart_id in smarts_ids]
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58 if min_diameter:
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59 params.append(("minDiameter", str(min_diameter)))
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60 return url, params
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63 def query(url: str, params: Dict) -> Dict:
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64 response = requests.get(url, params=params)
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65 response.raise_for_status()
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66 return response.json()
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69 def write_json(path: str, data: Dict):
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70 with open(path, "w") as fd:
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71 json.dump(data, fd, indent=4)
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74 def main():
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75 parser = argparse.ArgumentParser(
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76 description="Query RetroRules API via command-line endpoints."
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77 )
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78 subparsers = parser.add_subparsers(dest="command")
0
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80 # Subcommand: EC number
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81 parser_ecn = subparsers.add_parser("ec-number", help="From EC number")
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82 parser_ecn.add_argument(
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83 "--input-ec-number-str", required=True, help="EC number such as 1.1.1.1"
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84 )
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85 parser_ecn.add_argument("--input-min-diameter-int", type=int, help="Min diameter")
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86 parser_ecn.add_argument(
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87 "--output-data-json", required=True, help="Output results, JSON format"
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88 )
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89
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90 # Subcommand: Substrate
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91 parser_sub = subparsers.add_parser("substrate", help="From substrate")
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92 parser_sub.add_argument(
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93 "--input-substrate-str", required=True, help="Substrate label"
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94 )
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95 parser_sub.add_argument("--input-min-diameter-int", type=int, help="Min diameter")
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96 parser_sub.add_argument(
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97 "--output-data-json", required=True, help="Output results, JSON format"
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98 )
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100 # Subcommand: Reaction ID
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101 parser_rea = subparsers.add_parser("reaction-id", help="From Reaction ID")
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102 parser_rea.add_argument(
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103 "--input-reaction-id-str", required=True, help="Reaction ID"
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104 )
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105 parser_rea.add_argument("--input-repository-str", required=True, help="Repository")
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106 parser_rea.add_argument("--input-min-diameter-int", type=int, help="Min diameter")
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107 parser_rea.add_argument(
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108 "--output-data-json", required=True, help="Output results, JSON format"
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109 )
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110
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111 # Subcommand: InChI
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112 parser_inc = subparsers.add_parser("inchi", help="From InChI")
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113 parser_inc.add_argument("--input-inchi-str", required=True, help="InChI")
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114 parser_inc.add_argument("--input-min-diameter-int", type=int, help="Min diameter")
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115 parser_inc.add_argument(
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116 "--output-data-json", required=True, help="Output results, JSON format"
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117 )
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118
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119 # Subcommand: Repository
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120 parser_rep = subparsers.add_parser("repository", help="From Repository")
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121 parser_rep.add_argument("--input-repository-str", required=True, help="InChI")
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122 parser_rep.add_argument("--input-min-diameter-int", type=int, help="Min diameter")
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123 parser_rep.add_argument(
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124 "--output-data-json", required=True, help="Output results, JSON format"
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125 )
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126
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127 # Subcommand: Smarts ID
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128 parser_sma = subparsers.add_parser("smarts-id", help="From Smarts ID")
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129 parser_sma.add_argument(
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130 "--input-smarts-id-str", nargs="+", required=True, help="Smarts ID"
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131 )
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132 parser_sma.add_argument("--input-min-diameter-int", type=int, help="Min diameter")
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133 parser_sma.add_argument(
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134 "--output-data-json", required=True, help="Output results, JSON format"
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135 )
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136
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137 logging.info("Query RetroRules - start")
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138 args = parser.parse_args()
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139
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140 try:
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141 logging.info("Build arguments")
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142 url, params = "", {}
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143 if args.command == "ec-number":
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144 url, params = from_ec_number(
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145 ec_number=args.input_ec_number_str,
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146 min_diameter=args.input_min_diameter_int,
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147 )
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148 elif args.command == "substrate":
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149 url, params = from_substrate(
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150 substrate=args.input_substrate_str,
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151 min_diameter=args.input_min_diameter_int,
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152 )
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153 elif args.command == "reaction-id":
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154 url, params = from_reaction_id(
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155 reaction_id=args.input_reaction_id_str,
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156 repository=args.input_repository_str,
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157 min_diameter=args.input_min_diameter_int,
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158 )
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159 elif args.command == "inchi":
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160 url, params = from_inchi(
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161 inchi=args.input_inchi_str,
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162 min_diameter=args.input_min_diameter_int,
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163 )
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164 elif args.command == "repository":
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165 url, params = from_repository(
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166 repository=args.input_repository_str,
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167 min_diameter=args.input_min_diameter_int,
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168 )
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169 elif args.command == "smarts-id":
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170 url, params = from_smarts_id(
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171 smarts_ids=args.input_smarts_id_str,
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172 min_diameter=args.input_min_diameter_int,
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173 )
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174 else:
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175 parser.print_help()
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176 sys.exit(1)
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177
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178 logging.info("Query API")
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179 data = query(url=url, params=params)
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180
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181 logging.info("Write data")
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182 write_json(path=args.output_data_json, data=data)
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183 except requests.HTTPError as e:
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184 logging.error(f"HTTP error: {e.response.status_code} - {e.response.text}")
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185 sys.exit(1)
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186 except Exception as e:
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187 logging.error(f"Error: {e}")
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188 sys.exit(1)
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189
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190 logging.info("Query RetroRules - end")
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191
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192
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193 if __name__ == "__main__":
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194 logging.basicConfig(
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195 level=logging.INFO,
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196 format="%(asctime)s - %(levelname)s - %(message)s",
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197 datefmt="%d-%m-%Y %H:%M",
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198 )
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199 main()