From 2eab71a70b8630649303a9319e1baf9fa06f8ab4 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Fri, 10 Jul 2020 15:39:02 +0200
Subject: metadata with missing host_species are not created

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

(limited to 'scripts')

diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index 10ac85b..a31bd36 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -242,6 +242,11 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
         not_created_accession_list.append([accession, 'technology not found'])
         continue
 
+    if 'host_species' not in info_for_yaml_dict['host']:
+        #print(accession, ' - technology not found')
+        not_created_accession_list.append([accession, 'missing host species'])
+        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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