From 9b1457763c08028179b0987d385d1fe879062b64 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Tue, 7 Jul 2020 22:07:35 +0200
Subject: if the technology is not found, the YAML file is not created; managed
 longer species strings

---
 scripts/create_sra_metadata/create_sra_metadata.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'scripts/create_sra_metadata')

diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index 470980e..ef0d119 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -197,7 +197,6 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
         if INSTRUMENT_MODEL in term_to_uri_dict:
             info_for_yaml_dict['technology']['sample_sequencing_technology'] = [term_to_uri_dict[INSTRUMENT_MODEL]]
         else:
-            info_for_yaml_dict['technology']['additional_technology_information'] = INSTRUMENT_MODEL
             missing_value_list.append('\t'.join([accession, 'sample_sequencing_technology', INSTRUMENT_MODEL]))
     #else:
     #    print(accession, 'Missing INSTRUMENT_MODEL', info_for_yaml_dict)
@@ -237,6 +236,10 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
         info_for_yaml_dict['sample']['collection_date'] = '1970-01-01'
         info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing"
 
+    if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
+        print(accession, ' - technology not found')
+        continue
+
     with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw:
         json.dump(info_for_yaml_dict, fw, indent=2)
     
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