From 9f31ac441e69d4e07bf93235cfa0459a077fb00c Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 6 Jun 2020 16:12:44 +0200
Subject: fixed collection-date management using a parser

---
 scripts/from_genbank_to_fasta_and_yaml.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index fc09615..9c8e9b9 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -8,8 +8,8 @@ import json
 import os
 import requests
 
-from dateutil import parser
 from datetime import date
+from dateutil.parser import parse
 
 num_ids_for_request = 100
 
@@ -312,7 +312,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                         GBQualifier_value_text_list = GBQualifier_value_text.split('-')
 
                         if GBQualifier_value_text_list[1].isalpha():
-                            date_to_write = GBQualifier_value_text_list[1] + '-' + GBQualifier_value_text_list[0] + '-' + GBQualifier_value_text_list[2]
+                            date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
 
                     info_for_yaml_dict['sample']['collection_date'] = date_to_write
                 elif GBQualifier_name_text in ['lat_lon', 'country']:
-- 
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