Fix GenBank date format (#649)

vector-engineering · Jun 21, 2024 · 45a6c7c · 45a6c7c
1 parent d40d998
commit 45a6c7c
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Showing 6 changed files with 6 additions and 18 deletions.
diff --git a/workflow_flu_genbank_ingest/scripts/download_metadata.py b/workflow_flu_genbank_ingest/scripts/download_metadata.py
@@ -148,9 +148,7 @@ def main():
     )
     args = parser.parse_args()
 
-    # NCBI doesn't like an end date even close to today
-    # so set the maximum end date to today minus 14 days
-    max_date = (datetime.datetime.now() - datetime.timedelta(days=14)).isoformat()
+    max_date = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.00Z")
     if args.end_time > max_date:
         args.end_time = max_date
 

diff --git a/workflow_flu_genbank_ingest/scripts/download_sequences.py b/workflow_flu_genbank_ingest/scripts/download_sequences.py
@@ -56,9 +56,7 @@ def main():
     )
     args = parser.parse_args()
 
-    # NCBI doesn't like an end date even close to today
-    # so set the maximum end date to today minus 14 days
-    max_date = (datetime.datetime.now() - datetime.timedelta(days=14)).isoformat()
+    max_date = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.00Z")
     if args.end_time > max_date:
         args.end_time = max_date
 

diff --git a/workflow_rsv_genbank_ingest/scripts/download_metadata.py b/workflow_rsv_genbank_ingest/scripts/download_metadata.py
@@ -47,9 +47,7 @@ def main():
     )
     args = parser.parse_args()
 
-    # NCBI doesn't like an end date even close to today
-    # so set the maximum end date to today minus 14 days
-    max_date = (datetime.datetime.now() - datetime.timedelta(days=14)).isoformat()
+    max_date = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.00Z")
     if args.end_time > max_date:
         args.end_time = max_date
 

diff --git a/workflow_rsv_genbank_ingest/scripts/download_sequences.py b/workflow_rsv_genbank_ingest/scripts/download_sequences.py
@@ -56,9 +56,7 @@ def main():
     )
     args = parser.parse_args()
 
-    # NCBI doesn't like an end date even close to today
-    # so set the maximum end date to today minus 14 days
-    max_date = (datetime.datetime.now() - datetime.timedelta(days=14)).isoformat()
+    max_date = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.00Z")
     if args.end_time > max_date:
         args.end_time = max_date
 

diff --git a/workflow_sars2_genbank_ingest/scripts/download_metadata.py b/workflow_sars2_genbank_ingest/scripts/download_metadata.py
@@ -46,9 +46,7 @@ def main():
     )
     args = parser.parse_args()
 
-    # NCBI doesn't like an end date even close to today
-    # so set the maximum end date to today minus 14 days
-    max_date = (datetime.datetime.now() - datetime.timedelta(days=14)).isoformat()
+    max_date = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.00Z")
     if args.end_time > max_date:
         args.end_time = max_date
 

diff --git a/workflow_sars2_genbank_ingest/scripts/download_sequences.py b/workflow_sars2_genbank_ingest/scripts/download_sequences.py
@@ -56,9 +56,7 @@ def main():
     )
     args = parser.parse_args()
 
-    # NCBI doesn't like an end date even close to today
-    # so set the maximum end date to today minus 14 days
-    max_date = (datetime.datetime.now() - datetime.timedelta(days=14)).isoformat()
+    max_date = datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.00Z")
     if args.end_time > max_date:
         args.end_time = max_date