diff --git a/genomeuploader/genome_upload.py b/genomeuploader/genome_upload.py index 2416c53..8f9cb60 100755 --- a/genomeuploader/genome_upload.py +++ b/genomeuploader/genome_upload.py @@ -429,7 +429,8 @@ def extract_ENA_info(genomeInfo, uploadDir, webin, password): country = "not provided" collectionDate = sampleInfo["collection_date"].lower() - if not collectionDate or collectionDate == "missing" or collectionDate == "not applicable": + if not collectionDate or collectionDate == "missing" or collectionDate in \ + ["not applicable", "not available"]: collectionDate = "not provided" tempDict[runAccession] = { @@ -482,7 +483,7 @@ def combine_ENA_info(genomeInfo, ENADict): collectionDate = collectionList[0] if multipleElementSet(collectionList): collectionDate = "not provided" - if collectionDate.lower() == "not applicable": + if collectionDate.lower() in ["not applicable", "not available"]: collectionDate = "not provided" genomeInfo[g]["collectionDate"] = collectionDate @@ -514,7 +515,7 @@ def combine_ENA_info(genomeInfo, ENADict): else: run = genomeInfo[g]["accessions"][0] genomeInfo[g]["sequencingMethod"] = ENADict[run]["instrumentModel"] - if ENADict[run]["collectionDate"].lower() == "not applicable": + if ENADict[run]["collectionDate"].lower() in ["not applicable", "not available"]: genomeInfo[g]["collectionDate"] = "not provided" else: genomeInfo[g]["collectionDate"] = ENADict[run]["collectionDate"]