Auto-create missing FASTA dictionary on track import

Author: bbimber

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

@@ -60,6 +60,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenomeManager;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
+import org.labkey.api.sequenceanalysis.run.CreateSequenceDictionaryWrapper;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.Job;
 import org.labkey.api.util.JobRunner;
@@ -230,15 +231,13 @@ private int addTrackForLibrary(File file, String trackName, String trackDescript
         }
 
         SAMSequenceDictionary dict = null;
-        if (genome.getSequenceDictionary().exists())
+        if (!genome.getSequenceDictionary().exists())
         {
-            dict = SAMSequenceDictionaryExtractor.extractDictionary(genome.getSequenceDictionary().toPath());
-        }
-        else
-        {
-            getJob().getLogger().warn("genome dictionary not found, will not be able to import some kinds of tracks");
+            SequencePipelineService.get().ensureSequenceDictionaryExists(genome.getWorkingFastaFile(), getJob().getLogger(), false);
         }
 
+        dict = SAMSequenceDictionaryExtractor.extractDictionary(genome.getSequenceDictionary().toPath());
+
         if (SequenceUtil.FILETYPE.bed.getFileType().isType(file))
         {
             validateAndTransformTsv(file, outputFile, nameTranslationMap, knownChrs, 0, 1, 2, -1, dict, action);