Mercurial > repos > tduigou > retrorules

comparison 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
comparison
equal deleted inserted replaced
3:95b4196b4ded 4:815748762646
15 reaction_ids_str: str, 15 reaction_ids_str: str,
16 datasets_str: str, 16 datasets_str: str,
17 chemical_domain_str: str, 17 chemical_domain_str: str,
18 ec_number_str: str, 18 ec_number_str: str,
19 min_radius_int: int, 19 min_radius_int: int,
20 valid_str: str, 20 valid_str: str,
21 dedup_str: str, 21 dedup_str: str,
22 limit_int: int, 22 limit_int: int,
23 offset_int: int, 23 offset_int: int,
24 ) -> Tuple: 24 ) -> Tuple:
25 url = f"{BASE_URL}/templates" 25 url = f"{BASE_URL}/templates"
26 params = [] 26 params = []
27 if smarts_str: 27 if smarts_str:
28 params.append(("q", smarts_str)) 28 params.append(("q", smarts_str))
29 if template_ids_str: 29 if template_ids_str:
46 params.append(("limit", str(limit_int))) 46 params.append(("limit", str(limit_int)))
47 if offset_int: 47 if offset_int:
48 params.append(("offset", str(offset_int))) 48 params.append(("offset", str(offset_int)))
49 return url, params 49 return url, params
50 50
51
51 def from_templates_summary(template_id_str: str) -> Tuple: 52 def from_templates_summary(template_id_str: str) -> Tuple:
52 url = f"{BASE_URL}/templates/{template_id_str}/summary" 53 url = f"{BASE_URL}/templates/{template_id_str}/summary"
53 params = {} 54 params = {}
54 return url, params 55 return url, params
55 56
57
56 def from_templates_sources(template_id_str: str) -> Tuple: 58 def from_templates_sources(template_id_str: str) -> Tuple:
57 url = f"{BASE_URL}/templates/{template_id_str}/sources" 59 url = f"{BASE_URL}/templates/{template_id_str}/sources"
58 params = {} 60 params = {}
59 return url, params 61 return url, params
62
60 63
61 def from_templates_count( 64 def from_templates_count(
62 smarts_str: str, 65 smarts_str: str,
63 template_ids_str: str, 66 template_ids_str: str,
64 reaction_ids_str: str, 67 reaction_ids_str: str,
65 datasets_str: str, 68 datasets_str: str,
66 chemical_domain_str: str, 69 chemical_domain_str: str,
67 ec_number_str: str, 70 ec_number_str: str,
68 min_radius_int: int, 71 min_radius_int: int,
69 valid_str: str, 72 valid_str: str,
70 dedup_str: str, 73 dedup_str: str,
71 ) -> Tuple: 74 ) -> Tuple:
72 url = f"{BASE_URL}/templates_count" 75 url = f"{BASE_URL}/templates_count"
73 params = [] 76 params = []
74 if smarts_str: 77 if smarts_str:
75 params.append(("q", smarts_str)) 78 params.append(("q", smarts_str))
76 if template_ids_str: 79 if template_ids_str:
89 params.append(("valid", valid_str)) 92 params.append(("valid", valid_str))
90 if dedup_str and dedup_str != "any": 93 if dedup_str and dedup_str != "any":
91 params.append(("dedup", dedup_str)) 94 params.append(("dedup", dedup_str))
92 return url, params 95 return url, params
93 96
97
94 def from_templates_export( 98 def from_templates_export(
95 generation_token_str: str, 99 generation_token_str: str,
96 smarts_str: str, 100 smarts_str: str,
97 template_ids_str: str, 101 template_ids_str: str,
98 reaction_ids_str: str, 102 reaction_ids_str: str,
99 datasets_str: str, 103 datasets_str: str,
100 chemical_domain_str: str, 104 chemical_domain_str: str,
101 ec_number_str: str, 105 ec_number_str: str,
102 min_radius_int: int, 106 min_radius_int: int,
103 valid_str: str, 107 valid_str: str,
104 dedup_str: str, 108 dedup_str: str,
105 ) -> Tuple: 109 ) -> Tuple:
106 url = f"{BASE_URL}/templates_export" 110 url = f"{BASE_URL}/templates_export"
107 params = [] 111 params = []
108 if generation_token_str: 112 if generation_token_str:
109 params.append(("gen_token", generation_token_str)) 113 params.append(("gen_token", generation_token_str))
110 if smarts_str: 114 if smarts_str:
125 params.append(("valid", valid_str)) 129 params.append(("valid", valid_str))
126 if dedup_str and dedup_str != "any": 130 if dedup_str and dedup_str != "any":
127 params.append(("dedup", dedup_str)) 131 params.append(("dedup", dedup_str))
128 return url, params 132 return url, params
129 133
134
130 def query(url: str, params: Dict): 135 def query(url: str, params: Dict):
131 response = requests.get(url, params=params) 136 response = requests.get(url, params=params)
132 response.raise_for_status() 137 response.raise_for_status()
133 return response 138 return response
134 139
140
135 def write_json(path: str, data: Dict): 141 def write_json(path: str, data: Dict):
136 with open(path, "w") as fd: 142 with open(path, "w") as fd:
137 json.dump(data, fd, indent=4) 143 json.dump(data, fd, indent=4)
138 144
145
139 def write_tab(path: str, data: str): 146 def write_tab(path: str, data: str):
140 with open(path, "w") as fd: 147 with open(path, "w") as fd:
141 fd.write(data) 148 fd.write(data)
149
142 150
143 def main(): 151 def main():
144 parser = argparse.ArgumentParser( 152 parser = argparse.ArgumentParser(
145 description="Query RetroRules API via command-line endpoints." 153 description="Query RetroRules API via command-line endpoints."
146 ) 154 )
213 parser_tem_sum.add_argument( 221 parser_tem_sum.add_argument(
214 "--output-data-json", 222 "--output-data-json",
215 required=True, 223 required=True,
216 help="Path to output JSON file", 224 help="Path to output JSON file",
217 ) 225 )
218 226
219 # Subcommand: templates-sources 227 # Subcommand: templates-sources
220 parser_tem_sou = subparsers.add_parser("templates-sources", help="From templates-sources") 228 parser_tem_sou = subparsers.add_parser("templates-sources", help="From templates-sources")
221 parser_tem_sou.add_argument("--input-template-id-str", required=True, help="Template ID") 229 parser_tem_sou.add_argument("--input-template-id-str", required=True, help="Template ID")
222 parser_tem_sou.add_argument( 230 parser_tem_sou.add_argument(
223 "--output-data-json", 231 "--output-data-json",