Added a fix for collection date format

EBI-Metagenomics · Jul 23, 2024 · da4ca1c · da4ca1c
1 parent e0f5bcd
commit da4ca1c
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/genomeuploader/genome_upload.py b/genomeuploader/genome_upload.py
@@ -506,7 +506,10 @@ def combine_ENA_info(genomeInfo, ENADict):
         else:
             run = genomeInfo[g]["accessions"][0]
             genomeInfo[g]["sequencingMethod"] = ENADict[run]["instrumentModel"]
-            genomeInfo[g]["collectionDate"] = ENADict[run]["collectionDate"]
+            if ENADict[run]["collectionDate"].lower() == "not applicable":
+                genomeInfo[g]["collectionDate"] = "not provided"
+            else:
+                genomeInfo[g]["collectionDate"] = ENADict[run]["collectionDate"]
             genomeInfo[g]["study"] = ENADict[run]["study"]
             genomeInfo[g]["description"] = ENADict[run]["projectDescription"]
             genomeInfo[g]["sample_accessions"] = ENADict[run]["sampleAccession"]
@@ -517,7 +520,6 @@ def combine_ENA_info(genomeInfo, ENADict):
         genomeInfo[g]["accessions"] = ','.join(genomeInfo[g]["accessions"])
 
 
-
 def getAccessions(accessionsFile):
     accessionDict = {}
     with open(accessionsFile, 'r') as f: