From cb94ded3ea7d28a81ab41fc88ffd291bc0f8c079 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Fri, 13 Nov 2020 22:29:10 +0100
Subject: generation of dates a little more robust

---
 scripts/create_sra_metadata/create_sra_metadata.py              | 2 +-
 scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index 77cdf0d..85d4e9e 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -200,7 +200,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
                         if VALUE_text_list[1].isalpha():
                             date_to_write = parse(VALUE_text).strftime('%Y-%m-%d')
                     elif len(VALUE_text_list) == 2:
-                        date_to_write = VALUE_text + '-15'
+                        date_to_write = parse(VALUE_text).strftime('%Y-%m') + '-15'
                     else:
                         if int(VALUE_text) < 2020:
                             date_to_write = "{}-12-15".format(VALUE_text)
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index 8fbacd1..1352027 100755
--- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -358,7 +358,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                             else:
                                 info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
                         elif len(GBQualifier_value_text.split('-')) == 2:
-                            date_to_write += '-15'
+                            date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m') + '-15'
 
                             if 'additional_collection_information' in info_for_yaml_dict['sample']:
                                 info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
-- 
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