Mercurial > repos > tduigou > retrorules

annotate query.py @ 4:815748762646 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5
author tduigou
date Thu, 02 Oct 2025 14:27:31 +0000
parents 95b4196b4ded
children
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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1 import argparse
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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2 import json
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
tduigou
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3 import logging
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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4 import sys
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95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
tduigou
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5 from typing import Dict, Tuple
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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7 import requests
6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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9 BASE_URL = "https://retrorules.org/api"
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6d20407d9a72 planemo upload for repository https://github.com/brsynth/galaxytools commit ccd77691de09b70e3048dca6be832dd93964c635-dirty
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12 def from_templates(
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13 smarts_str: str,
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14 template_ids_str: str,
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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15 reaction_ids_str: str,
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16 datasets_str: str,
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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17 chemical_domain_str: str,
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18 ec_number_str: str,
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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19 min_radius_int: int,
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20 valid_str: str,
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21 dedup_str: str,
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22 limit_int: int,
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23 offset_int: int,
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815748762646 planemo upload for repository https://github.com/brsynth/galaxytools commit d7030c1af6fe06a1d45af115756ee775721e39b5
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24 ) -> Tuple:
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25 url = f"{BASE_URL}/templates"
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26 params = []
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27 if smarts_str:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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28 params.append(("q", smarts_str))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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29 if template_ids_str:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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30 params.append(("template_ids", ",".join(template_ids_str)))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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31 if reaction_ids_str:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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32 params.append(("reaction_ids", ",".join(reaction_ids_str)))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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33 if datasets_str and datasets_str != "any":
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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34 params.append(("datasets", datasets_str))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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diff changeset
35 if chemical_domain_str and chemical_domain_str != "any":
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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36 params.append(("chemical_domain", chemical_domain_str))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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37 if ec_number_str:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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38 params.append(("ec", ec_number_str))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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39 if min_radius_int is not None:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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40 params.append(("min_radius", str(min_radius_int)))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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41 if valid_str and valid_str != "any":
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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42 params.append(("valid", valid_str))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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43 if dedup_str and dedup_str != "any":
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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44 params.append(("dedup", dedup_str))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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45 if limit_int:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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46 params.append(("limit", str(limit_int)))
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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47 if offset_int:
95b4196b4ded planemo upload for repository https://github.com/brsynth/galaxytools commit 5e85823d729e9e09adf66ccfb7c47701077dccff-dirty
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48 params.append(("offset", str(offset_int)))
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49 return url, params
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50
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51
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52 def from_templates_summary(template_id_str: str) -> Tuple:
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53 url = f"{BASE_URL}/templates/{template_id_str}/summary"
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54 params = {}
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55 return url, params
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56
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57
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58 def from_templates_sources(template_id_str: str) -> Tuple:
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59 url = f"{BASE_URL}/templates/{template_id_str}/sources"
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60 params = {}
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61 return url, params
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63
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64 def from_templates_count(
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65 smarts_str: str,
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66 template_ids_str: str,
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67 reaction_ids_str: str,
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68 datasets_str: str,
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69 chemical_domain_str: str,
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70 ec_number_str: str,
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71 min_radius_int: int,
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72 valid_str: str,
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73 dedup_str: str,
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74 ) -> Tuple:
3
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75 url = f"{BASE_URL}/templates_count"
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76 params = []
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77 if smarts_str:
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78 params.append(("q", smarts_str))
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79 if template_ids_str:
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80 params.append(("template_ids", ",".join(template_ids_str)))
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81 if reaction_ids_str:
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82 params.append(("reaction_ids", ",".join(reaction_ids_str)))
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83 if datasets_str and datasets_str != "any":
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84 params.append(("datasets", datasets_str))
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85 if chemical_domain_str and chemical_domain_str != "any":
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86 params.append(("chemical_domain", chemical_domain_str))
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87 if ec_number_str:
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88 params.append(("ec", ec_number_str))
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89 if min_radius_int is not None:
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90 params.append(("min_radius", str(min_radius_int)))
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91 if valid_str and valid_str != "any":
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92 params.append(("valid", valid_str))
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93 if dedup_str and dedup_str != "any":
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94 params.append(("dedup", dedup_str))
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95 return url, params
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98 def from_templates_export(
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99 generation_token_str: str,
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100 smarts_str: str,
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101 template_ids_str: str,
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102 reaction_ids_str: str,
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103 datasets_str: str,
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104 chemical_domain_str: str,
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105 ec_number_str: str,
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106 min_radius_int: int,
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107 valid_str: str,
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108 dedup_str: str,
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109 ) -> Tuple:
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110 url = f"{BASE_URL}/templates_export"
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111 params = []
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112 if generation_token_str:
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113 params.append(("gen_token", generation_token_str))
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114 if smarts_str:
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115 params.append(("q", smarts_str))
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116 if template_ids_str:
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117 params.append(("template_ids", ",".join(template_ids_str)))
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118 if reaction_ids_str:
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119 params.append(("reaction_ids", ",".join(reaction_ids_str)))
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120 if datasets_str and datasets_str != "any":
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121 params.append(("datasets", datasets_str))
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122 if chemical_domain_str and chemical_domain_str != "any":
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123 params.append(("chemical_domain", chemical_domain_str))
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124 if ec_number_str:
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125 params.append(("ec", ec_number_str))
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126 if min_radius_int is not None:
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127 params.append(("min_radius", str(min_radius_int)))
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128 if valid_str and valid_str != "any":
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129 params.append(("valid", valid_str))
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130 if dedup_str and dedup_str != "any":
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131 params.append(("dedup", dedup_str))
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132 return url, params
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133
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134
3
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135 def query(url: str, params: Dict):
0
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136 response = requests.get(url, params=params)
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137 response.raise_for_status()
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138 return response
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139
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140
0
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141 def write_json(path: str, data: Dict):
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142 with open(path, "w") as fd:
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143 json.dump(data, fd, indent=4)
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144
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145
3
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146 def write_tab(path: str, data: str):
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147 with open(path, "w") as fd:
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148 fd.write(data)
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149
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150
0
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151 def main():
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152 parser = argparse.ArgumentParser(
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153 description="Query RetroRules API via command-line endpoints."
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154 )
2
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155 subparsers = parser.add_subparsers(dest="command")
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156
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157 # Subcommand: templates
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158 parser_tem = subparsers.add_parser("templates", help="From templates")
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159 parser_tem.add_argument("--input-smarts-str", help="Exact SMARTS")
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160 parser_tem.add_argument(
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161 "--input-template-ids-str",
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162 nargs="*",
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163 help="Space separated list of template IDs",
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164 )
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165 parser_tem.add_argument(
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166 "--input-reaction-ids-str",
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167 nargs="*",
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168 help="Space separated list of reaction IDs",
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169 )
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170 parser_tem.add_argument(
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171 "--input-datasets-str",
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172 default="any",
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173 choices=["any", "metanetx", "rhea", "uspto"],
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174 help="Select a specific database",
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175 )
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176 parser_tem.add_argument(
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177 "--input-chemical-domain-str",
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178 default="any",
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179 choices=["any", "biochem", "orgchem"],
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180 )
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181 parser_tem.add_argument(
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182 "--input-ec-number-str",
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183 help="EC number to filter templates",
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184 )
3
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185 parser_tem.add_argument(
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186 "--input-min-radius-int",
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187 type=int,
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188 help="Single radius of the template",
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189 )
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190 parser_tem.add_argument(
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191 "--input-valid-str",
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192 default="true",
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193 choices=["any", "true", "false"],
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194 help="By default only valid templates are returned",
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195 )
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196 parser_tem.add_argument(
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197 "--input-dedup-str",
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198 default="true",
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199 choices=["true", "false"],
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200 help="By default deduplicated templates are returned",
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201 )
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202 parser_tem.add_argument(
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203 "--input-limit-int",
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204 type=int,
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205 help="Limit number of returned templates",
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206 )
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207 parser_tem.add_argument(
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208 "--input-offset-int",
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209 type=int,
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210 help="Offset the list of returned templates",
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211 )
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212 parser_tem.add_argument(
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213 "--output-data-json",
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214 required=True,
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215 help="Path to output JSON file",
0
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216 )
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217
3
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218 # Subcommand: templates-summary
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219 parser_tem_sum = subparsers.add_parser("templates-summary", help="From templates-summary")
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220 parser_tem_sum.add_argument("--input-template-id-str", required=True, help="Template ID")
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221 parser_tem_sum.add_argument(
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222 "--output-data-json",
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223 required=True,
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224 help="Path to output JSON file",
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225 )
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226
3
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227 # Subcommand: templates-sources
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228 parser_tem_sou = subparsers.add_parser("templates-sources", help="From templates-sources")
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229 parser_tem_sou.add_argument("--input-template-id-str", required=True, help="Template ID")
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230 parser_tem_sou.add_argument(
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231 "--output-data-json",
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232 required=True,
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233 help="Path to output JSON file",
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234 )
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235
3
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236 # Subcommand: templates-count
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237 parser_cou = subparsers.add_parser("templates-count", help="From templates-count")
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238 parser_cou.add_argument("--input-smarts-str", help="Exact SMARTS")
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239 parser_cou.add_argument(
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240 "--input-template-ids-str",
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241 nargs="*",
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242 help="Space separated list of template IDs",
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243 )
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244 parser_cou.add_argument(
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245 "--input-reaction-ids-str",
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246 nargs="*",
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247 help="Space separated list of reaction IDs",
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248 )
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249 parser_cou.add_argument(
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250 "--input-datasets-str",
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251 default="any",
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252 choices=["any", "metanetx", "rhea", "uspto"],
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253 help="Select a specific database",
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254 )
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255 parser_cou.add_argument(
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256 "--input-chemical-domain-str",
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257 default="any",
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258 choices=["any", "biochem", "orgchem"],
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259 )
3
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260 parser_cou.add_argument(
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261 "--input-ec-number-str",
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262 help="EC number to filter templates",
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263 )
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264 parser_cou.add_argument(
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265 "--input-min-radius-int",
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266 type=int,
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267 help="Single radius of the template",
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268 )
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269 parser_cou.add_argument(
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270 "--input-valid-str",
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271 default="true",
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272 choices=["any", "true", "false"],
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273 help="By default only valid templates are returned",
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274 )
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275 parser_cou.add_argument(
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276 "--input-dedup-str",
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277 default="true",
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278 choices=["true", "false"],
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279 help="By default deduplicated templates are returned",
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280 )
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281 parser_cou.add_argument(
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282 "--output-data-json",
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283 required=True,
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284 help="Path to output JSON file",
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285 )
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286
3
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287 # Subcommand: templates-export
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288 parser_exp = subparsers.add_parser("templates-export", help="From templates-export")
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289 parser_exp.add_argument(
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290 "--input-generation-token-str",
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291 help="Generation token from RetroRules web interface",
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292 )
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293 parser_exp.add_argument("--input-smarts-str", help="Exact SMARTS")
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294 parser_exp.add_argument(
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295 "--input-template-ids-str",
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296 nargs="*",
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297 help="Space separated list of template IDs",
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298 )
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299 parser_exp.add_argument(
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300 "--input-reaction-ids-str",
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301 nargs="*",
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302 help="Space separated list of reaction IDs",
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303 )
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304 parser_exp.add_argument(
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305 "--input-datasets-str",
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306 default="any",
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307 choices=["any", "metanetx", "rhea", "uspto"],
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308 help="Select a specific database",
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309 )
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310 parser_exp.add_argument(
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311 "--input-chemical-domain-str",
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312 default="any",
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313 choices=["any", "biochem", "orgchem"],
0
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314 )
3
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315 parser_exp.add_argument(
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316 "--input-ec-number-str",
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317 help="EC number to filter templates",
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318 )
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319 parser_exp.add_argument(
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320 "--input-min-radius-int",
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321 type=int,
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322 help="Single radius of the template",
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323 )
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324 parser_exp.add_argument(
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325 "--input-valid-str",
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326 default="true",
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327 choices=["any", "true", "false"],
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328 help="By default only valid templates are returned",
0
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329 )
3
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330 parser_exp.add_argument(
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331 "--input-dedup-str",
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332 default="true",
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333 choices=["true", "false"],
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334 help="By default deduplicated templates are returned",
0
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335 )
3
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336 parser_exp.add_argument(
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337 "--output-data-json",
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338 help="Path to output JSON file",
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339 )
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340 parser_exp.add_argument(
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341 "--output-data-csv",
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342 help="Path to output CSV file",
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343 )
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344 parser_exp.add_argument(
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345 "--output-data-tsv",
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346 help="Path to output TSV file",
0
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347 )
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348
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349 logging.info("Query RetroRules - start")
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350 args = parser.parse_args()
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351
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352 try:
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353 logging.info("Build arguments")
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354 url, params = "", {}
3
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355 if args.command == "templates":
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356 url, params = from_templates(
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357 smarts_str=args.input_smarts_str,
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358 template_ids_str=args.input_template_ids_str,
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359 reaction_ids_str=args.input_reaction_ids_str,
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360 datasets_str=args.input_datasets_str,
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361 chemical_domain_str=args.input_chemical_domain_str,
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362 ec_number_str=args.input_ec_number_str,
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363 min_radius_int=args.input_min_radius_int,
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364 valid_str=args.input_valid_str,
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365 dedup_str=args.input_dedup_str,
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366 limit_int=args.input_limit_int,
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367 offset_int=args.input_offset_int,
0
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diff changeset
368 )
3
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369 elif args.command == "templates-summary":
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370 url, _ = from_templates_summary(
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371 template_id_str=args.input_template_id_str,
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372 )
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373 elif args.command == "templates-sources":
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374 url, _ = from_templates_sources(
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375 template_id_str=args.input_template_id_str,
0
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376 )
3
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377 elif args.command == "templates-count":
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378 url, params = from_templates_count(
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379 smarts_str=args.input_smarts_str,
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380 template_ids_str=args.input_template_ids_str,
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381 reaction_ids_str=args.input_reaction_ids_str,
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382 datasets_str=args.input_datasets_str,
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383 chemical_domain_str=args.input_chemical_domain_str,
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384 ec_number_str=args.input_ec_number_str,
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385 min_radius_int=args.input_min_radius_int,
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386 valid_str=args.input_valid_str,
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387 dedup_str=args.input_dedup_str,
0
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388 )
3
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389 elif args.command == "templates-export":
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390 url, params = from_templates_export(
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391 generation_token_str=args.input_generation_token_str,
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392 smarts_str=args.input_smarts_str,
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393 template_ids_str=args.input_template_ids_str,
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394 reaction_ids_str=args.input_reaction_ids_str,
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395 datasets_str=args.input_datasets_str,
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396 chemical_domain_str=args.input_chemical_domain_str,
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397 ec_number_str=args.input_ec_number_str,
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398 min_radius_int=args.input_min_radius_int,
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diff changeset
399 valid_str=args.input_valid_str,
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400 dedup_str=args.input_dedup_str,
0
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401 )
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402 else:
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403 parser.print_help()
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404 sys.exit(1)
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405
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406 logging.info("Query API")
3
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407 response = query(url=url, params=params)
0
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408
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409 logging.info("Write data")
3
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410 if "output_data_json" in vars(args) and args.output_data_json:
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411 write_json(path=args.output_data_json, data=response.json())
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412 if "output_data_csv" in vars(args) and args.output_data_csv:
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413 write_tab(path=args.output_data_csv, data=response.text)
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414 if "output_data_tsv" in vars(args) and args.output_data_tsv:
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415 write_tab(path=args.output_data_tsv, data=response.text)
0
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416 except requests.HTTPError as e:
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417 logging.error(f"HTTP error: {e.response.status_code} - {e.response.text}")
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418 sys.exit(1)
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419 except Exception as e:
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420 logging.error(f"Error: {e}")
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421 sys.exit(1)
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422
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423 logging.info("Query RetroRules - end")
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424
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425
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426 if __name__ == "__main__":
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427 logging.basicConfig(
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428 level=logging.INFO,
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429 format="%(asctime)s - %(levelname)s - %(message)s",
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430 datefmt="%d-%m-%Y %H:%M",
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431 )
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432 main()