Merge discvr-23.3 to develop

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/AlignmentMetricsHandler.java

@@ -83,7 +83,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             RecordedAction action = new RecordedAction(getName());
             action.setStartTime(new Date());
 
-            Integer windowSize = params.has("windowSize") && params.get("windowSize") != null ? Integer.valueOf(params.getInt("windowSize")) : null;
+            Integer windowSize = params.has("windowSize") && !params.isNull("windowSize") ? Integer.valueOf(params.getInt("windowSize")) : null;
             if (windowSize == null)
             {
                 job.error("No window size provided, aborting");

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java

@@ -202,7 +202,7 @@ else if (genomeIds.isEmpty())
                 throw new PipelineJobException("No genome ID found for inputs");
             }
 
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.forceSitesFile") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.forceSitesFile"))
             {
                 int dataId = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.forceSitesFile");
                 ExpData data = ExperimentService.get().getExpData(dataId);
@@ -215,7 +215,7 @@ else if (genomeIds.isEmpty())
                 ctx.getSequenceSupport().cacheExpData(data);
             }
 
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.exclude_intervals") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.exclude_intervals"))
             {
                 int dataId = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.exclude_intervals");
                 ExpData data = ExperimentService.get().getExpData(dataId);
@@ -306,7 +306,7 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport
 
         private String getBasename(JobContext ctx)
         {
-            String basename = ctx.getParams().get("variantCalling.GenotypeGVCFs.fileBaseName") != null ? ctx.getParams().getString("variantCalling.GenotypeGVCFs.fileBaseName") : "CombinedGenotypes";
+            String basename = !ctx.getParams().isNull("variantCalling.GenotypeGVCFs.fileBaseName") ? ctx.getParams().getString("variantCalling.GenotypeGVCFs.fileBaseName") : "CombinedGenotypes";
             basename = basename.replaceAll(".vcf.gz$", "");
             basename = basename.replaceAll(".vcf$", "");
 
@@ -363,7 +363,7 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
             }
 
             File forceCallSitesFile = null;
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.forceSitesFile") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.forceSitesFile"))
             {
                 forceCallSitesFile = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("variantCalling.GenotypeGVCFs.forceSitesFile"));
                 if (!forceCallSitesFile.exists())
@@ -375,7 +375,7 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
             }
 
             int maxSamplesPerWorkspace = 500;
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.maxSamplesPerWorkspace") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.maxSamplesPerWorkspace"))
             {
                 maxSamplesPerWorkspace = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.maxSamplesPerWorkspace");
             }
@@ -629,7 +629,7 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
 
             GenotypeGVCFsWrapper wrapper = new GenotypeGVCFsWrapper(job.getLogger());
             List<String> toolParams = new ArrayList<>();
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.stand_call_conf") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.stand_call_conf"))
             {
                 toolParams.add("-stand-call-conf");
                 toolParams.add(ctx.getParams().get("variantCalling.GenotypeGVCFs.stand_call_conf").toString());
@@ -642,13 +642,13 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
             toolParams.add("-AX");
             toolParams.add("ExcessHet");
 
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.maxGenotypeCount") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.maxGenotypeCount"))
             {
                 toolParams.add("-max-genotype-count");
                 toolParams.add(String.valueOf(ctx.getParams().get("variantCalling.GenotypeGVCFs.maxGenotypeCount")));
             }
 
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.exclude_intervals") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.exclude_intervals"))
             {
                 toolParams.add("-XL");
                 int dataId = Integer.parseInt(ctx.getParams().get("variantCalling.GenotypeGVCFs.exclude_intervals").toString());
@@ -663,7 +663,7 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
                 toolParams.add(bed.getPath());
             }
 
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs.max_alternate_alleles") != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.max_alternate_alleles"))
             {
                 toolParams.add("--max-alternate-alleles");
                 toolParams.add(ctx.getParams().get("variantCalling.GenotypeGVCFs.max_alternate_alleles").toString());

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UnmappedSequenceBasedGenotypeHandler.java

@@ -232,7 +232,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     }
 
                     int minAlignmentLength = 0;
-                    if (params.get("minAlignmentLength") != null)
+                    if (!params.isNull("minAlignmentLength"))
                     {
                         minAlignmentLength = params.getInt("minAlignmentLength");
                     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java

@@ -257,7 +257,7 @@ public Map<String, String> getParameters()
 
         for (String key : json.keySet())
         {
-            ret.put(key, json.opt(key) == null ? null : String.valueOf(json.get(key)));
+            ret.put(key, json.isNull(key) ? null : String.valueOf(json.get(key)));
         }
 
         return ret;

blast/src/org/labkey/blast/model/BlastJob.java

@@ -112,7 +112,8 @@ public void setParams(String params)
         }
         catch (JSONException e)
         {
-            _log.error("Unable to parse BlastJob config for: " + _objectid + " in container: " + ContainerManager.getForId(_container).getPath() + ", was: " + _params);
+            String containerPath = getContainer() == null || ContainerManager.getForId(getContainer()) == null ? "<MISSING: " + getContainer() + ">" : ContainerManager.getForId(getContainer()).getPath();
+            _log.error("Unable to parse BlastJob config for: " + _objectid + " in container: " + containerPath + ", was: " + _params);
         }
     }
 
@@ -249,7 +250,7 @@ public File getOutputDir()
             throw new UnsupportedOperationException("this can only be called from the webserver");
         }
 
-        Container c = ContainerManager.getForId(_container);
+        Container c = ContainerManager.getForId(getContainer());
         if (c == null)
         {
             return null;