Mercurial > repos > iuc > ncbi_eutils_egquery
comparison elink.py @ 3:d1789b4821fc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author | iuc |
---|---|
date | Wed, 23 Sep 2020 09:51:30 +0000 |
parents | 28f69754ddc5 |
children |
comparison
equal
deleted
inserted
replaced
2:08412cd072d0 | 3:d1789b4821fc |
---|---|
1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
2 from __future__ import print_function | |
3 | 2 |
4 import argparse | 3 import argparse |
5 import json | 4 import json |
5 import logging | |
6 import os | |
6 | 7 |
7 import eutils | 8 import eutils |
9 | |
10 | |
11 logging.basicConfig(level=logging.INFO) | |
8 | 12 |
9 | 13 |
10 if __name__ == '__main__': | 14 if __name__ == '__main__': |
11 parser = argparse.ArgumentParser(description='EFetch', epilog='') | 15 parser = argparse.ArgumentParser(description='EFetch', epilog='') |
12 parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)') | 16 parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)') |
13 parser.add_argument('dbfrom', help='Database containing input UIDs') | 17 parser.add_argument('dbfrom', help='Database containing input UIDs') |
14 parser.add_argument('cmd', choices=['neighbor', 'neighbor_score', | 18 parser.add_argument('cmd', choices=['neighbor', 'neighbor_score', |
15 'neighbor_history', 'acheck', 'ncheck', 'lcheck', | 19 'neighbor_history', 'acheck', 'ncheck', 'lcheck', |
16 'llinks', 'llinkslib', 'prlinks'], | 20 'llinks', 'llinkslib', 'prlinks'], |
17 help='ELink command mode') | 21 help='ELink command mode') |
18 # Only used in case of neighbor_history | 22 |
19 parser.add_argument('--history_out', type=argparse.FileType('w'), | 23 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)') |
20 help='Output history file', default='-') | |
21 | 24 |
22 parser.add_argument('--user_email', help="User email") | 25 parser.add_argument('--user_email', help="User email") |
23 parser.add_argument('--admin_email', help="Admin email") | 26 parser.add_argument('--admin_email', help="Admin email") |
27 | |
24 # ID Sources | 28 # ID Sources |
29 parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink') | |
30 parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink') | |
25 parser.add_argument('--id_list', help='list of ids') | 31 parser.add_argument('--id_list', help='list of ids') |
26 parser.add_argument('--id', help='Comma separated individual IDs') | 32 parser.add_argument('--id', help='Comma separated individual IDs') |
27 parser.add_argument('--history_file', help='Fetch results from previous query') | 33 parser.add_argument('--history_file', help='Fetch results from previous query') |
34 parser.add_argument('--history_xml', help='Fetch results from previous query') | |
35 | |
36 # Optional | |
37 parser.add_argument('--linkname', help='Restrict results to a specific link source') | |
38 parser.add_argument('--retmode', choices=['xml', 'json', 'uilist'], help='Output format') | |
28 | 39 |
29 # TODO: dates, linkname, term, holding | 40 # TODO: dates, linkname, term, holding |
30 # neighbor or neighbor_history and dbfrom is pubmed | 41 # neighbor or neighbor_history and dbfrom is pubmed |
31 # parser.add_argument('--datetype', help='Date type') | 42 # parser.add_argument('--datetype', help='Date type') |
32 # parser.add_argument('--reldate', help='In past N days') | 43 # parser.add_argument('--reldate', help='In past N days') |
35 | 46 |
36 # Output | 47 # Output |
37 args = parser.parse_args() | 48 args = parser.parse_args() |
38 | 49 |
39 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) | 50 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) |
40 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file) | |
41 | 51 |
42 payload = { | 52 payload = { |
43 'dbfrom': args.dbfrom, | 53 'dbfrom': args.dbfrom, |
44 'cmd': args.cmd, | 54 'cmd': args.cmd, |
45 } | 55 } |
46 if args.history_file is not None: | |
47 payload.update(c.get_history()) | |
48 else: | |
49 payload['id'] = ','.join(merged_ids) | |
50 | 56 |
51 # DB can be 'none' in a few cases. | 57 # DB can be 'none' in a few cases. |
52 if args.db != "none": | 58 if args.db != "none": |
53 payload['db'] = args.db | 59 payload['db'] = args.db |
54 | 60 |
55 results = c.link(**payload) | 61 if args.linkname is not None: |
62 payload['linkname'] = args.linkname | |
56 | 63 |
57 if args.cmd == "neighbor_history": | 64 results = [] |
58 history = c.extract_history(results) | 65 qkeys = [] |
59 args.history_out.write(json.dumps(history, indent=4)) | 66 if args.history_file is not None or args.history_xml is not None: |
67 payload['retmode'] = args.retmode | |
68 if args.history_file is not None: | |
69 input_histories = c.get_histories() | |
70 else: | |
71 input_histories = c.extract_histories_from_xml_file(args.history_xml) | |
72 for hist in input_histories: | |
73 qkeys += [hist['query_key']] | |
74 tmp_payload = payload | |
75 tmp_payload.update(hist) | |
76 results += [c.link(**tmp_payload)] | |
77 else: | |
78 # There is no uilist retmode | |
79 if args.retmode == "uilist": | |
80 payload['retmode'] = 'xml' | |
81 else: | |
82 payload['retmode'] = args.retmode | |
83 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json) | |
84 payload['id'] = ','.join(merged_ids) | |
85 qkeys += [1] | |
86 results += [c.link(**payload)] | |
60 | 87 |
61 print(results) | 88 # There could be multiple sets of results if a history was supplied |
89 if args.history_file is not None or args.history_xml is not None: | |
90 # Multiple result sets can be returned | |
91 # Create a directory for the output files | |
92 current_directory = os.getcwd() | |
93 final_directory = os.path.join(current_directory, r'downloads') | |
94 if not os.path.exists(final_directory): | |
95 os.makedirs(final_directory) | |
96 | |
97 logging.info("Writing files:") | |
98 # When rettype is uilist, convert to text format (which elink does not do) | |
99 count = 0 | |
100 if args.retmode == 'uilist': | |
101 for result in results: | |
102 qkey = qkeys[count] | |
103 count += 1 | |
104 ids = c.xmlstring2UIlist(result) | |
105 file_path = os.path.join('downloads', '%s-querykey%s.tabular' % (args.db, qkey)) | |
106 logging.info('%s.tabular' % (args.db)) | |
107 with open(file_path, 'w') as handle: | |
108 for id in ids: | |
109 handle.write(id) | |
110 handle.write(os.linesep) | |
111 elif args.retmode == 'json': | |
112 for result in results: | |
113 qkey = qkeys[count] | |
114 count += 1 | |
115 file_path = os.path.join('downloads', '%s-querykey%s.json' % (args.db, qkey)) | |
116 logging.info('%s-link%s.json' % (args.db, count)) | |
117 with open(file_path, 'w') as handle: | |
118 json_data = c.jsonstring2jsondata(result) | |
119 handle.write(json.dumps(json_data, indent=4)) | |
120 else: | |
121 for result in results: | |
122 qkey = qkeys[count] | |
123 count += 1 | |
124 file_path = os.path.join('downloads', '%s-querykey%s.xml' % (args.db, qkey)) | |
125 logging.info('%s-link%s.xml' % (args.db, count)) | |
126 with open(file_path, 'w') as handle: | |
127 handle.write(result) | |
128 else: | |
129 # When rettype is uilist, convert to text format (which elink does not do) | |
130 if args.retmode == 'uilist': | |
131 ids = c.xmlstring2UIlist(results[0]) | |
132 for id in ids: | |
133 print(id) | |
134 elif args.retmode == 'json': | |
135 json_data = c.jsonstring2jsondata(results[0]) | |
136 print(json.dumps(json_data, indent=4)) | |
137 else: | |
138 print(results[0]) |