diff elink.py @ 3:c09fcbe4b16a draft

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

--- a/elink.py	Wed Mar 11 04:03:36 2020 -0400
+++ b/elink.py	Wed Sep 23 09:48:53 2020 +0000
@@ -1,12 +1,16 @@
 #!/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='EFetch', epilog='')
     parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
@@ -15,16 +19,23 @@
                                         '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('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
 
     parser.add_argument('--user_email', help="User email")
     parser.add_argument('--admin_email', help="Admin email")
+
     # ID Sources
+    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='Fetch results from previous query')
+    parser.add_argument('--history_xml', help='Fetch results from previous query')
+
+    # Optional
+    parser.add_argument('--linkname', help='Restrict results to a specific link source')
+    parser.add_argument('--retmode', choices=['xml', 'json', 'uilist'], help='Output format')
 
     # TODO: dates, linkname, term, holding
     # neighbor or neighbor_history and dbfrom is pubmed
@@ -37,25 +48,91 @@
     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.linkname is not None:
+        payload['linkname'] = args.linkname
+
+    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.link(**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.link(**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)
 
-    if args.cmd == "neighbor_history":
-        history = c.extract_history(results)
-        args.history_out.write(json.dumps(history, indent=4))
-
-    print(results)
+        logging.info("Writing files:")
+        # When rettype is uilist, convert to text format (which elink does not do)
+        count = 0
+        if args.retmode == 'uilist':
+            for result in results:
+                qkey = qkeys[count]
+                count += 1
+                ids = c.xmlstring2UIlist(result)
+                file_path = os.path.join('downloads', '%s-querykey%s.tabular' % (args.db, qkey))
+                logging.info('%s.tabular' % (args.db))
+                with open(file_path, 'w') as handle:
+                    for id in ids:
+                        handle.write(id)
+                        handle.write(os.linesep)
+        elif 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 == 'uilist':
+            ids = c.xmlstring2UIlist(results[0])
+            for id in ids:
+                print(id)
+        elif args.retmode == 'json':
+            json_data = c.jsonstring2jsondata(results[0])
+            print(json.dumps(json_data, indent=4))
+        else:
+            print(results[0])