diff efetch.py @ 3:d1789b4821fc draft

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

--- a/efetch.py	Wed Mar 11 04:02:33 2020 -0400
+++ b/efetch.py	Wed Sep 23 09:51:30 2020 +0000
@@ -1,36 +1,111 @@
 #!/usr/bin/env python
+
 import argparse
+import glob
+import json
+import logging
+import os
+
 
 import eutils
 
 
+logging.basicConfig(level=logging.INFO)
+
+
+def handleEfetchException(e, db, payload):
+    logging.error('No results returned. This could either be due to no records matching the supplied IDs for the query database or it could be an error due to invalid parameters.  The reported exception was "%s".\n\nPayload used for the efetch query to database "%s"\n\n%s', e, db, json.dumps(payload, indent=4))
+
+    # Create a file in the downloads folder so that the user can access run information
+    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('The following files were downloaded:')
+    print(os.listdir(final_directory))
+
+    file_path = os.path.join('downloads', 'no_results.txt')
+    with open(file_path, 'w') as handle:
+        handle.write('No results')
+
+
+def localFetch(db, gformat, newname, **payload):
+    problem = None
+    try:
+        c.fetch(db, **payload)
+
+        for chunk, file in enumerate(glob.glob('downloads/EFetch *')):
+            os.rename(file, '%s%s.%s' % (newname, chunk + 1, gformat))
+
+    except Exception as e:
+        problem = e
+        handleEfetchException(e, db, payload)
+    else:
+        print('The following files were downloaded:')
+        print(os.listdir('downloads'))
+
+    return problem
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='EFetch', 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_json', help='list of ids in a json file as returned by esearch or elink')
+    parser.add_argument('--id_xml', help='list of ids in an xml 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_file', help='Fetch results from previous query (JSON)')
+    parser.add_argument('--history_xml', help='Fetch results from previous query (XML)')
 
     # Output
     parser.add_argument('--retmode', help='Retmode')
     parser.add_argument('--rettype', help='Rettype')
+    parser.add_argument('--galaxy_format', help='Galaxy format')
     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 = {}
-    if args.history_file is not None:
-        payload.update(c.get_history())
-    else:
-        payload['id'] = ','.join(merged_ids)
-
     for attr in ('retmode', 'rettype'):
         if getattr(args, attr, None) is not None:
             payload[attr] = getattr(args, attr)
 
-    c.fetch(args.db, ftype=args.retmode, **payload)
+    if args.history_file is not None or args.history_xml is not None:
+        if args.history_file is not None:
+            input_histories = c.get_histories()
+        else:
+            input_histories = c.extract_histories_from_xml_file(args.history_xml)
+
+        problem = None
+        for hist in input_histories:
+            qkey = hist['query_key']
+            tmp_payload = payload
+            tmp_payload.update(hist)
+            newname = 'downloads/EFetch-%s-%s-querykey%s-chunk' % (args.rettype, args.retmode, qkey)
+            problem = localFetch(args.db, args.galaxy_format, newname, **tmp_payload)
+
+            if os.path.exists('downloads'):
+                os.rename('downloads', 'downloads-qkey%s' % (qkey))
+
+        if not os.path.exists('downloads'):
+            os.makedirs('downloads')
+
+        for relpath in glob.glob('downloads-qkey*/*'):
+            file = os.path.basename(relpath)
+            os.rename(relpath, 'downloads/%s' % (file))
+
+        if problem is not None:
+            raise(problem)
+
+    else:
+        merged_ids = c.parse_ids(args.id_list, args.id, args.history_file, args.id_xml, args.id_json)
+        payload['id'] = ','.join(merged_ids)
+        newname = 'downloads/EFetch-%s-%s-chunk' % (args.rettype, args.retmode)
+        localFetch(args.db, args.galaxy_format, newname, **payload)