diff esummary.py @ 3:d1789b4821fc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"

--- a/esummary.py	Wed Mar 11 04:02:33 2020 -0400
+++ b/esummary.py	Wed Sep 23 09:51:30 2020 +0000
@@ -1,32 +1,106 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
 import argparse
+import json
+import logging
+import os
 
 import eutils
 
 
+logging.basicConfig(level=logging.INFO)
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='ESummary', epilog='')
     parser.add_argument('db', help='Database to use')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+
+    parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
+
+    # ID source
+    parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink')
+    parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink')
     parser.add_argument('--id_list', help='list of ids')
     parser.add_argument('--id', help='Comma separated individual IDs')
-    parser.add_argument('--history_file', help='Filter existing history')
-    parser.add_argument('--user_email', help="User email")
-    parser.add_argument('--admin_email', help="Admin email")
+    parser.add_argument('--history_file', help='Fetch results from previous query')
+    parser.add_argument('--history_xml', help='Fetch results from previous query')
+
+    # Output
+    parser.add_argument('--retmode', help='Retmode')
+    parser.add_argument('--retstart', type=int, default=0, help='Retstart - Starting rec number (0)')
+    parser.add_argument('--retmax', type=int, default=20, help='Retmax - max number of recs returned (20, max 100000')
+
     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 = {
         'db': args.db,
     }
 
-    if args.history_file is not None:
-        payload.update(c.get_history())
+    for attr in ('retmode', 'retmax', 'retstart'):
+        if getattr(args, attr, None) is not None:
+            payload[attr] = getattr(args, attr)
+
+    results = []
+    qkeys = []
+    if args.history_file is not None or args.history_xml is not None:
+        payload['retmode'] = args.retmode
+        if args.history_file is not None:
+            input_histories = c.get_histories()
+        else:
+            input_histories = c.extract_histories_from_xml_file(args.history_xml)
+
+        for hist in input_histories:
+            qkeys += [hist['query_key']]
+            tmp_payload = payload
+            tmp_payload.update(hist)
+            results += [c.summary(**tmp_payload)]
     else:
+        # There is no uilist retmode
+        if args.retmode == "uilist":
+            payload['retmode'] = 'xml'
+        else:
+            payload['retmode'] = args.retmode
+        merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
         payload['id'] = ','.join(merged_ids)
+        qkeys += [1]
+        results += [c.summary(**payload)]
+
+    # There could be multiple sets of results if a history was supplied
+    if args.history_file is not None or args.history_xml is not None:
+        # Multiple result sets can be returned
+        # Create a directory for the output files
+        current_directory = os.getcwd()
+        final_directory = os.path.join(current_directory, r'downloads')
+        if not os.path.exists(final_directory):
+            os.makedirs(final_directory)
 
-    print(c.summary(**payload))
+        logging.info("Writing files:")
+        count = 0
+        if args.retmode == 'json':
+            for result in results:
+                qkey = qkeys[count]
+                count += 1
+                file_path = os.path.join('downloads', '%s-querykey%s.json' % (args.db, qkey))
+                logging.info('%s-link%s.json' % (args.db, count))
+                with open(file_path, 'w') as handle:
+                    json_data = c.jsonstring2jsondata(result)
+                    handle.write(json.dumps(json_data, indent=4))
+        else:
+            for result in results:
+                qkey = qkeys[count]
+                count += 1
+                file_path = os.path.join('downloads', '%s-querykey%s.xml' % (args.db, qkey))
+                logging.info('%s-link%s.xml' % (args.db, count))
+                with open(file_path, 'w') as handle:
+                    handle.write(result)
+    else:
+        # When rettype is uilist, convert to text format (which elink does not do)
+        if args.retmode == 'json':
+            json_data = c.jsonstring2jsondata(results[0])
+            print(json.dumps(json_data, indent=4))
+        else:
+            print(results[0])