diff elink.py @ 0:32ac58827a97 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elink.py	Thu Jul 07 02:40:06 2016 -0400
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+import argparse
+import json
+
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='EFetch', epilog='')
+    parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
+    parser.add_argument('dbfrom', help='Database containing input UIDs')
+    parser.add_argument('cmd', choices=['neighbor', 'neighbor_score',
+                                        'neighbor_history', 'acheck', 'ncheck', 'lcheck',
+                                        'llinks', 'llinkslib', 'prlinks'],
+                        help='ELink command mode')
+    # Only used in case of neighbor_history
+    parser.add_argument('--history_out', type=argparse.FileType('w'),
+                        help='Output history file', default='-')
+
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    # ID Sources
+    parser.add_argument('--id_list', help='list of ids')
+    parser.add_argument('--id', help='Comma separated individual IDs')
+    parser.add_argument('--history_file', help='Fetch results from previous query')
+
+    # TODO: dates, linkname, term, holding
+    # neighbor or neighbor_history and dbfrom is pubmed
+    # parser.add_argument('--datetype', help='Date type')
+    # parser.add_argument('--reldate', help='In past N days')
+    # parser.add_argument('--mindate', help='Minimum date')
+    # parser.add_argument('--maxdate', help='maximum date')
+
+    # Output
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+    merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
+
+    payload = {
+        'dbfrom': args.dbfrom,
+        'cmd': args.cmd,
+    }
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    else:
+        payload['id'] = ','.join(merged_ids)
+
+    # DB can be 'none' in a few cases.
+    if args.db != "none":
+        payload['db'] = args.db
+
+    results = c.link(**payload)
+
+    if args.cmd == "neighbor_history":
+        history = c.extract_history(results)
+        args.history_out.write(json.dumps(history, indent=4))
+
+    print results