Merge pull request #224 from LabKey/fb_merge_23.3_to_develop

bbimber · web-flow · commit 5347a9b004d0 · 2023-05-05T12:38:48.000-07:00
Merge discvr-23.3 to develop
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/AlignmentMetricsHandler.java b/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");
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java b/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());
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UnmappedSequenceBasedGenotypeHandler.java b/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");
                     }
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java b/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;
diff --git a/blast/src/org/labkey/blast/model/BlastJob.java b/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;

Original file line number	Diff line number	Diff line change
`@@ -83,7 +83,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`83`	`83`	`RecordedAction action = new RecordedAction(getName());`
`84`	`84`	`action.setStartTime(new Date());`
`85`	`85`
`86`		`- Integer windowSize = params.has("windowSize") && params.get("windowSize") != null ? Integer.valueOf(params.getInt("windowSize")) : null;`
	`86`	`+ Integer windowSize = params.has("windowSize") && !params.isNull("windowSize") ? Integer.valueOf(params.getInt("windowSize")) : null;`
`87`	`87`	`if (windowSize == null)`
`88`	`88`	`{`
`89`	`89`	`job.error("No window size provided, aborting");`
Original file line number	Diff line number	Diff line change
`@@ -202,7 +202,7 @@ else if (genomeIds.isEmpty())`
`202`	`202`	`throw new PipelineJobException("No genome ID found for inputs");`
`203`	`203`	`}`
`204`	`204`
`205`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.forceSitesFile") != null)`
	`205`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.forceSitesFile"))`
`206`	`206`	`{`
`207`	`207`	`int dataId = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.forceSitesFile");`
`208`	`208`	`ExpData data = ExperimentService.get().getExpData(dataId);`
`@@ -215,7 +215,7 @@ else if (genomeIds.isEmpty())`
`215`	`215`	`ctx.getSequenceSupport().cacheExpData(data);`
`216`	`216`	`}`
`217`	`217`
`218`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.exclude_intervals") != null)`
	`218`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.exclude_intervals"))`
`219`	`219`	`{`
`220`	`220`	`int dataId = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.exclude_intervals");`
`221`	`221`	`ExpData data = ExperimentService.get().getExpData(dataId);`
`@@ -306,7 +306,7 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport`
`306`	`306`
`307`	`307`	`private String getBasename(JobContext ctx)`
`308`	`308`	`{`
`309`		`- String basename = ctx.getParams().get("variantCalling.GenotypeGVCFs.fileBaseName") != null ? ctx.getParams().getString("variantCalling.GenotypeGVCFs.fileBaseName") : "CombinedGenotypes";`
	`309`	`+ String basename = !ctx.getParams().isNull("variantCalling.GenotypeGVCFs.fileBaseName") ? ctx.getParams().getString("variantCalling.GenotypeGVCFs.fileBaseName") : "CombinedGenotypes";`
`310`	`310`	`basename = basename.replaceAll(".vcf.gz$", "");`
`311`	`311`	`basename = basename.replaceAll(".vcf$", "");`
`312`	`312`
`@@ -363,7 +363,7 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa`
`363`	`363`	`}`
`364`	`364`
`365`	`365`	`File forceCallSitesFile = null;`
`366`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.forceSitesFile") != null)`
	`366`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.forceSitesFile"))`
`367`	`367`	`{`
`368`	`368`	`forceCallSitesFile = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("variantCalling.GenotypeGVCFs.forceSitesFile"));`
`369`	`369`	`if (!forceCallSitesFile.exists())`
`@@ -375,7 +375,7 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa`
`375`	`375`	`}`
`376`	`376`
`377`	`377`	`int maxSamplesPerWorkspace = 500;`
`378`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.maxSamplesPerWorkspace") != null)`
	`378`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.maxSamplesPerWorkspace"))`
`379`	`379`	`{`
`380`	`380`	`maxSamplesPerWorkspace = ctx.getParams().getInt("variantCalling.GenotypeGVCFs.maxSamplesPerWorkspace");`
`381`	`381`	`}`
`@@ -629,7 +629,7 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge`
`629`	`629`
`630`	`630`	`GenotypeGVCFsWrapper wrapper = new GenotypeGVCFsWrapper(job.getLogger());`
`631`	`631`	`List<String> toolParams = new ArrayList<>();`
`632`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.stand_call_conf") != null)`
	`632`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.stand_call_conf"))`
`633`	`633`	`{`
`634`	`634`	`toolParams.add("-stand-call-conf");`
`635`	`635`	`toolParams.add(ctx.getParams().get("variantCalling.GenotypeGVCFs.stand_call_conf").toString());`
`@@ -642,13 +642,13 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge`
`642`	`642`	`toolParams.add("-AX");`
`643`	`643`	`toolParams.add("ExcessHet");`
`644`	`644`
`645`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.maxGenotypeCount") != null)`
	`645`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.maxGenotypeCount"))`
`646`	`646`	`{`
`647`	`647`	`toolParams.add("-max-genotype-count");`
`648`	`648`	`toolParams.add(String.valueOf(ctx.getParams().get("variantCalling.GenotypeGVCFs.maxGenotypeCount")));`
`649`	`649`	`}`
`650`	`650`
`651`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.exclude_intervals") != null)`
	`651`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.exclude_intervals"))`
`652`	`652`	`{`
`653`	`653`	`toolParams.add("-XL");`
`654`	`654`	`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`
`663`	`663`	`toolParams.add(bed.getPath());`
`664`	`664`	`}`
`665`	`665`
`666`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs.max_alternate_alleles") != null)`
	`666`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.max_alternate_alleles"))`
`667`	`667`	`{`
`668`	`668`	`toolParams.add("--max-alternate-alleles");`
`669`	`669`	`toolParams.add(ctx.getParams().get("variantCalling.GenotypeGVCFs.max_alternate_alleles").toString());`
Original file line number	Diff line number	Diff line change
`@@ -232,7 +232,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`232`	`232`	`}`
`233`	`233`
`234`	`234`	`int minAlignmentLength = 0;`
`235`		`- if (params.get("minAlignmentLength") != null)`
	`235`	`+ if (!params.isNull("minAlignmentLength"))`
`236`	`236`	`{`
`237`	`237`	`minAlignmentLength = params.getInt("minAlignmentLength");`
`238`	`238`	`}`
Original file line number	Diff line number	Diff line change
`@@ -257,7 +257,7 @@ public Map<String, String> getParameters()`
`257`	`257`
`258`	`258`	`for (String key : json.keySet())`
`259`	`259`	`{`
`260`		`- ret.put(key, json.opt(key) == null ? null : String.valueOf(json.get(key)));`
	`260`	`+ ret.put(key, json.isNull(key) ? null : String.valueOf(json.get(key)));`
`261`	`261`	`}`
`262`	`262`
`263`	`263`	`return ret;`
Original file line number	Diff line number	Diff line change
`@@ -112,7 +112,8 @@ public void setParams(String params)`
`112`	`112`	`}`
`113`	`113`	`catch (JSONException e)`
`114`	`114`	`{`
`115`		`- _log.error("Unable to parse BlastJob config for: " + _objectid + " in container: " + ContainerManager.getForId(_container).getPath() + ", was: " + _params);`
	`115`	`+ String containerPath = getContainer() == null \|\| ContainerManager.getForId(getContainer()) == null ? "<MISSING: " + getContainer() + ">" : ContainerManager.getForId(getContainer()).getPath();`
	`116`	`+ _log.error("Unable to parse BlastJob config for: " + _objectid + " in container: " + containerPath + ", was: " + _params);`
`116`	`117`	`}`
`117`	`118`	`}`
`118`	`119`
`@@ -249,7 +250,7 @@ public File getOutputDir()`
`249`	`250`	`throw new UnsupportedOperationException("this can only be called from the webserver");`
`250`	`251`	`}`
`251`	`252`
`252`		`- Container c = ContainerManager.getForId(_container);`
	`253`	`+ Container c = ContainerManager.getForId(getContainer());`
`253`	`254`	`if (c == null)`
`254`	`255`	`{`
`255`	`256`	`return null;`