Improve logic in mGAPReleaseGenerator around VCF indexes

Author: bbimber

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java

@@ -50,6 +50,7 @@
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler;
+import org.labkey.api.sequenceanalysis.pipeline.HasJobParams;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
@@ -280,17 +281,27 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
                 throw new PipelineJobException("Some ids are missing demographics data: " + StringUtils.join(ids, ","));
             }
 
-            // NOTE: this is a bit of a cludge
-            Integer luceneIndexId = ctx.getParams().optInt("luceneIndex");
-            if (luceneIndexId == null)
+            getAndValidateLuceneIndex(ctx.getJob(), ctx.getParams());
+        }
+
+        private SequenceOutputFile getAndValidateLuceneIndex(PipelineJob job, JSONObject params) throws PipelineJobException
+        {
+            Integer luceneIndexId = params.optInt("luceneIndex");
+            if (luceneIndexId == null || luceneIndexId == 0)
             {
                 throw new PipelineJobException("Missing luceneIndex ID");
             }
 
-            ExpData d = ExperimentService.get().getExpData(luceneIndexId);
+            SequenceOutputFile so = SequenceOutputFile.getForId(luceneIndexId);
+            if (so == null)
+            {
+                throw new PipelineJobException("Unable to find lucene index output file for: " + luceneIndexId);
+            }
+
+            ExpData d = so.getExpData();
             if (d == null)
             {
-                throw new PipelineJobException("Unable to find lucene index file for: " + luceneIndexId);
+                throw new PipelineJobException("Unable to find lucene index expdata for: " + luceneIndexId);
             }
 
             if (d.getFile() == null || !d.getFile().exists())
@@ -301,7 +312,7 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
             File fieldList = new File(d.getFile().getParentFile(), "fieldList.txt");
             if (!fieldList.exists())
             {
-                throw new PipelineJobException("Lucene index missing fieldList.txt: " + luceneIndexId);
+                throw new PipelineJobException("Lucene index missing fieldList.txt: " + fieldList.getPath());
             }
 
             List<String> fields = new ArrayList<>();
@@ -322,10 +333,18 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
                 throw new PipelineJobException(e);
             }
 
-            if (!IndexVariantsForMgapStep.getInfoFieldsToIndex(ctx.getJob().getContainer(), ctx.getJob().getUser()).equals(fields))
+            List<String> expectedFields = IndexVariantsForMgapStep.getInfoFieldsToIndex(job.getContainer(), job.getUser());
+            if (!expectedFields.equals(fields))
             {
+                job.getLogger().warn("Expected fields:");
+                job.getLogger().warn(StringUtils.join(expectedFields, ";"));
+                job.getLogger().warn("Found:");
+                job.getLogger().warn(StringUtils.join(fields, ";"));
+
                 throw new PipelineJobException("The fields in the lucene index do not match the expected fields: " + luceneIndexId);
             }
+
+            return so;
         }
 
         private File getTrackListFile(File outputDir)
@@ -432,7 +451,12 @@ else if (so.getCategory().endsWith("Release Track"))
                     throw new PipelineJobException("Unable to find novel sites VCF for release: " + release);
                 }
 
-                SequenceOutputFile luceneIndex = JBrowseService.get().findMatchingLuceneIndex(so, IndexVariantsForMgapStep.getInfoFieldsToIndex(job.getContainer(), job.getUser()), job.getUser(), job.getLogger());
+                if (!(job instanceof HasJobParams hjp))
+                {
+                    throw new PipelineJobException("Expected PipelineJob to implement HasJobParams");
+                }
+
+                SequenceOutputFile luceneIndex = getAndValidateLuceneIndex(job, hjp.getParameterJson());
                 if (luceneIndex == null)
                 {
                     throw new PipelineJobException("Unable to lucene index matching the input VCF: " + so.getFile().getPath());