Explicitly set default min and max dates when missing - sometimes con…

…fig.get can return None values??

workflow_flu_genbank_ingest/Snakefile

@@ -17,7 +17,11 @@ data_folder = os.path.join("..", config["data_folder"])
 static_data_folder = os.path.join("..", config["static_data_folder"])
 
 min_date = pd.to_datetime(config.get('min_date', '2019-12-01'))
+if min_date is None:
+    min_date = '2019-12-01'
 max_date = pd.to_datetime(datetime.date.today().isoformat())
+if max_date is None:
+    max_date = datetime.date.today().isoformat()
 
 chunks = [d for d in pd.period_range(start=min_date, end=max_date, freq=config.get('dl_chunk_period', 'W'))]
 DL_CHUNKS = [i for i in range(len(chunks))]

workflow_rsv_genbank_ingest/Snakefile

@@ -17,7 +17,11 @@ data_folder = os.path.join("..", config["data_folder"])
 static_data_folder = os.path.join("..", config["static_data_folder"])
 
 min_date = pd.to_datetime(config.get('min_date', '2019-12-01'))
+if min_date is None:
+    min_date = '2019-12-01'
 max_date = pd.to_datetime(datetime.date.today().isoformat())
+if max_date is None:
+    max_date = datetime.date.today().isoformat()
 
 chunks = [d for d in pd.period_range(start=min_date, end=max_date, freq=config.get('dl_chunk_period', 'W'))]
 DL_CHUNKS = [i for i in range(len(chunks))]

workflow_sars2_genbank_ingest/Snakefile

@@ -32,7 +32,11 @@ rule all:
         metadata = os.path.join(data_folder, "metadata.csv")
 
 min_date = pd.to_datetime(config.get('min_date', '2019-12-01'))
+if min_date is None:
+    min_date = '2019-12-01'
 max_date = pd.to_datetime(config.get('end_date_cutoff', datetime.date.today().isoformat()))
+if max_date is None:
+    max_date = datetime.date.today().isoformat()
 
 chunks = [d for d in pd.period_range(start=min_date, end=max_date, freq=config.get('dl_chunk_period', 'W'))]
 DL_CHUNKS = [i for i in range(len(chunks))]