diff esearch.py @ 0:9d18e6815994 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/esearch.py	Thu Jul 07 02:39:52 2016 -0400
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+import json
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='ESearch', epilog='')
+    parser.add_argument('db', help='Database to use')
+    parser.add_argument('term', help='Query')
+    parser.add_argument('--history_file', help='Filter existing history')
+    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')
+    # History
+    parser.add_argument('--history_out', type=argparse.FileType('w'),
+                        help='Output history file')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+
+    payload = {
+        'db': args.db,
+        'term': args.term,
+        'retstart': 0,
+        'retmax': 20,
+        # hmmm @ retmax
+    }
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    if args.history_out is not None:
+        payload['usehistory'] = 'y'
+
+    for attr in ('datetype', 'reldate', 'mindate', 'maxdate'):
+        if getattr(args, attr, None) is not None:
+            payload[attr] = getattr(args, attr)
+
+    results = c.search(**payload)
+
+    if args.history_out is not None:
+        history = c.extract_history(results)
+        args.history_out.write(json.dumps(history, indent=4))
+
+    print results