annotate epost.py @ 10:0ccb2855dd55 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 851b88d92fa7740880a5edf407f629bf3f7f7bf0
author iuc
date Fri, 04 Oct 2024 14:35:17 +0000
parents c09fcbe4b16a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
1 #!/usr/bin/env python
1
0fc65a60436f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 0
diff changeset
2
0
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
3 import argparse
1
0fc65a60436f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 0
diff changeset
4
0
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
5 import eutils
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
6
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
7
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
8 if __name__ == '__main__':
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
9 parser = argparse.ArgumentParser(description='EPost', epilog='')
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
10 parser.add_argument('db', help='Database to use')
3
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
11 parser.add_argument('--user_email', help="User email")
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
12 parser.add_argument('--admin_email', help="Admin email")
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
13
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
14 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
15
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
16 # ID source
0
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
17 parser.add_argument('--id_list', help='list of ids')
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
18 parser.add_argument('--id', help='Comma separated individual IDs')
3
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
19 parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink')
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
20 parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink')
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
21
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
22 # Target history
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
23 parser.add_argument('--history_xml', help='Post to new QueryKey in an existing WebEnv (XML)')
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
24 parser.add_argument('--history_file', help='Post to new QueryKey in an existing WebEnv (JSON)')
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
25 parser.add_argument('--webenv', help='Post to new WebEnv (History ID)')
0
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
26
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
27 args = parser.parse_args()
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
28
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
29 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
30
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
31 payload = {}
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
32 if args.history_file is not None:
3
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
33 hist = c.get_history()
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
34 payload['WebEnv'] = hist['WebEnv']
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
35 elif args.history_xml is not None:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
36 hist = c.extract_history_from_xml_file(args.history_xml)
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
37 payload['WebEnv'] = hist['WebEnv']
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
38 elif args.webenv is not None:
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
39 payload['WebEnv'] = args.webenv
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
40
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
41 merged_ids = c.parse_ids(args.id_list, args.id, None, args.id_xml, args.id_json)
c09fcbe4b16a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents: 1
diff changeset
42 payload['id'] = ','.join(merged_ids)
0
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
43
1
0fc65a60436f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 0
diff changeset
44 print(c.post(args.db, **payload))