Bugfix LoFreq variant import

Author: bbimber

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.325-12.326.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column codon type VARCHAR(4000);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.325-12.326.sql

@@ -0,0 +1 @@
+ALTER TABLE sequenceanalysis.aa_snps_by_codon ALTER column codon VARCHAR(4000);

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -179,7 +179,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 12.325;
+        return 12.326;
     }
 
     @Override

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java

@@ -243,11 +243,17 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i
             return;
         }
 
-        JSONArray aaSubstitutions = sample.getJSONArray("aaSubstitutions");
+        ViralSnpUtil.deleteExistingValues(job, analysisId, SequenceAnalysisSchema.TABLE_AA_SNP_BY_CODON, null);
+
+        if (!sample.containsKey("aaSubstitutions"))
+        {
+            job.getLogger().info("JSON does not contain aaSubstitutions, skipping");
+            return;
+        }
 
+        JSONArray aaSubstitutions = sample.getJSONArray("aaSubstitutions");
         Map<Integer, List<VariantContext>> consensusMap = ViralSnpUtil.readVcfToMap(consensusVCF);
 
-        ViralSnpUtil.deleteExistingValues(job, analysisId, SequenceAnalysisSchema.TABLE_AA_SNP_BY_CODON, null);
         TableInfo aaTable = SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_AA_SNP_BY_CODON);
 
         //This is SARS-CoV-2 specific, so this is a safe assumption