Prevent failures when:

optional biosample/sra columns are empty
bs-description is not present

.gitignore

@@ -19,3 +19,5 @@ docker-compose-*.yaml
 
 # ignore folders
 **/.Rproj.user
+**/test_data/*
+**/gisaid_cli/*

tools.py

@@ -14,6 +14,7 @@
 from datetime import datetime, timedelta
 from cerberus import Validator
 import re
+import shutil
 
 from config.seqsender.seqsender_schema import schema as seqsender_schema
 from settings import SCHEMA_EXCLUSIONS, BIOSAMPLE_REGEX, SRA_REGEX, GISAID_REGEX, GENBANK_REGEX, GENBANK_REGEX_CMT, GENBANK_REGEX_SRC
@@ -132,6 +133,17 @@ def parse_hold_date(config_dict: Dict[str, Any]):
 def get_metadata(database: List[str], organism: str, metadata_file: str, config_dict: Dict[str, Any], skip_validation: bool = False) -> pd.DataFrame:
 	# Read in metadata file
 	metadata = file_handler.load_csv(metadata_file)
+	# Adding some default handling for bs-description here - it's not mandatory for biosample submission, but is required in the workflow
+	if 'bs-description' not in metadata.columns:
+	# Create 'bs-description' by joining 'organism', 'bs-host', and 'bs-host_disease' columns
+		metadata['bs-description'] = metadata[['organism', 'bs-host', 'bs-host_disease']].apply(
+		lambda row: ' '.join(row.dropna().astype(str)), axis=1
+	)
+	# If there are empty biosample or sra columns in the metadata sheet, assume they are unused optional columns and drop them before pandera attempts to validate
+	columns_to_drop = [col for col in metadata.columns if (col.startswith('bs-') or col.startswith('sra-')) and metadata[col].replace('', pd.NA).apply(lambda x: x.strip() if isinstance(x, str) else x).isna().all()]
+	metadata = metadata.drop(columns=columns_to_drop)
+	shutil.copy(metadata_file, metadata_file + ".bak")
+	file_handler.save_csv(metadata, metadata_file)
 	# Update seqsender base schema to include needed checks
 	if "BioSample" in database or "SRA" in database:
 		seqsender_schema.update_columns({"bioproject":{"checks":Check.str_matches(r"^(?!\s*$).+"),"nullable":False,"required":True}})