Merge discvr-23.11 to discvr-24.3

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

@@ -12,11 +12,13 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.ldk.LDKService;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineService;
+import org.labkey.api.pipeline.PipelineStatusFile;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
 import org.labkey.api.sequenceanalysis.RefNtSequenceModel;
@@ -34,6 +36,8 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -44,6 +48,7 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 /**
  * Created by bimber on 9/15/2014.
@@ -229,6 +234,60 @@ else if (!d.getFile().exists())
                     log.error("Unable to find file associated with analysis: " + m.getAnalysisId() + ", " + m.getAlignmentFile() + ", " + d.getFile().getPath() + " for container: " + (c == null ? m.getContainer() : c.getPath()));
                 }
             }
+
+            inspectForCoreFiles(m.getRunId(), log);
+        }
+    }
+
+    private void inspectForCoreFiles(Integer runId, Logger log)
+    {
+        if (runId == null)
+        {
+            return;
+        }
+
+        ExpRun run = ExperimentService.get().getExpRun(runId);
+        if (run == null)
+        {
+            log.info("Not ExpRun found for runId: " + runId);
+            return;
+        }
+        else if (run.getJobId() == null)
+        {
+            log.info("ExpRun lacks jobId: " + runId);
+            return;
+        }
+
+        PipelineStatusFile sf = PipelineService.get().getStatusFile(run.getJobId());
+        if (sf == null)
+        {
+            log.error("Unknown statusFile: " + run.getJobId() + ", for run: " + runId);
+            return;
+        }
+        else if (sf.getFilePath() == null)
+        {
+            log.error("StatusFile filepath is null: " + run.getJobId() + ", for run: " + runId);
+            return;
+        }
+
+        File root = new File(sf.getFilePath());
+        if (!root.exists())
+        {
+            log.error("Run fileroot does not exist: " + runId + " / " + root.getPath());
+            return;
+        }
+
+        try (Stream<Path> stream = Files.walk(root.toPath()))
+        {
+            List<Path> files = stream.filter(x -> x.getFileName().startsWith("core.")).toList();
+            if (!files.isEmpty())
+            {
+                files.forEach(x -> log.error("Found core file: " + x.toFile().getPath()));
+            }
+        }
+        catch (IOException e)
+        {
+            log.error("Error walking file root: " + run.getFilePathRootPath(), e);
         }
     }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SelectSamplesStep.java

@@ -3,6 +3,7 @@
 import htsjdk.samtools.util.Interval;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
@@ -41,7 +42,8 @@ public Provider()
         {
             super("SelectSamples", "Select Specific Samples", "GATK SelectVariants", "A VCF will be generated containing only the samples specified below.", Arrays.asList(
                 ToolParameterDescriptor.create(SAMPLE_INCLUDE, "Select Sample(s) Include", "Only variants of the selected type(s) will be included", "sequenceanalysis-trimmingtextarea", null, null),
-                ToolParameterDescriptor.create(SAMPLE_EXCLUDE, "Select Samples(s) To Exclude", "Variants of the selected type(s) will be excluded", "sequenceanalysis-trimmingtextarea", null, null)
+                ToolParameterDescriptor.create(SAMPLE_EXCLUDE, "Select Samples(s) To Exclude", "Variants of the selected type(s) will be excluded", "sequenceanalysis-trimmingtextarea", null, null),
+                ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--allow-nonoverlapping-command-line-samples"), "allowNnonoverlappingSamples", "Allow non-overlapping Samples", "Normally the job will fail is samples are selected that do not exist in the VCF.  If checked, this will be allowed.", "checkbox", null, null)
             ), PageFlowUtil.set("/sequenceanalysis/field/TrimmingTextArea.js"), "https://software.broadinstitute.org/gatk/");
         }
 
@@ -72,6 +74,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             });
         }
 
+        options.addAll(getClientCommandArgs());
+
         File outputVcf = new File(outputDirectory, SequenceTaskHelper.getUnzippedBaseName(inputVCF) + ".selectSamples.vcf.gz");
         getWrapper().execute(genome.getWorkingFastaFile(), inputVCF, outputVcf, options);
         if (!outputVcf.exists())

jbrowse/api-src/org/labkey/api/jbrowse/JBrowseService.java

@@ -48,6 +48,8 @@ static public void setInstance(JBrowseService instance)
 
     abstract public void registerLuceneIndexDetector(LuceneIndexDetector detector);
 
+    abstract public void cacheDefaultQuery(User u, String sessionId, String trackId);
+
     public interface LuceneIndexDetector
     {
         SequenceOutputFile findMatchingLuceneIndex(SequenceOutputFile vcfFile, List<String> infoFieldsToIndex, User u, @Nullable Logger log) throws PipelineJobException;

jbrowse/src/org/labkey/jbrowse/JBrowseController.java

@@ -1035,5 +1035,15 @@ public void setIncludeDefaultFields(boolean includeDefaultFields)
             this.includeDefaultFields = includeDefaultFields;
         }
     }
+
+    @RequiresPermission(ReadPermission.class)
+    public static class GetLuceneCacheInfoAction extends ReadOnlyApiAction<Object>
+    {
+        @Override
+        public ApiResponse execute(Object form, BindException errors)
+        {
+            return new ApiSimpleResponse("cacheInfo", JBrowseLuceneSearch.reportCacheInfo());
+        }
+    }
 }
 

jbrowse/src/org/labkey/jbrowse/JBrowseFieldUtils.java

@@ -132,12 +132,14 @@ public static Map<String, JBrowseFieldDescriptor> getGenotypeDependentFields(@Nu
                         else
                         {
                             ret.put(VARIABLE_SAMPLES, new JBrowseFieldDescriptor(VARIABLE_SAMPLES, "All samples with this variant", true, true, VCFHeaderLineType.Character, 7).multiValued(true).label("Samples With Variant"));
+                            ret.put(HOMOZYGOUS_VAR, new JBrowseFieldDescriptor(HOMOZYGOUS_VAR, "Samples that are homozygous for the variant allele", false, true, VCFHeaderLineType.Character, 8).multiValued(true).label("Samples Homozygous for Variant"));
                             ret.put(N_HET, new JBrowseFieldDescriptor(N_HET, "The number of samples with this allele that are heterozygous", false, true, VCFHeaderLineType.Integer, 9).label("# Heterozygotes"));
                             ret.put(N_HOMVAR, new JBrowseFieldDescriptor(N_HOMVAR, "The number of samples with this allele that are homozygous", false, true, VCFHeaderLineType.Integer, 9).label("# Homozygous Variant"));
                             ret.put(N_CALLED, new JBrowseFieldDescriptor(N_CALLED, "The number of samples with called genotypes at this position", false, true, VCFHeaderLineType.Integer, 9).label("# Genotypes Called"));
                             ret.put(FRACTION_HET, new JBrowseFieldDescriptor(FRACTION_HET, "The fraction of samples with this allele that are heterozygous", false, true, VCFHeaderLineType.Float, 9).label("Fraction Heterozygotes"));
 
                             ret.get(VARIABLE_SAMPLES).allowableValues(header.getSampleNamesInOrder());
+                            ret.get(HOMOZYGOUS_VAR).allowableValues(header.getSampleNamesInOrder());
                         }
                     }
                 }

jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java

@@ -1,6 +1,7 @@
 package org.labkey.jbrowse;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
 import org.apache.lucene.analysis.Analyzer;
 import org.apache.lucene.analysis.standard.StandardAnalyzer;
 import org.apache.lucene.document.Document;
@@ -15,16 +16,22 @@
 import org.apache.lucene.search.BooleanClause;
 import org.apache.lucene.search.BooleanQuery;
 import org.apache.lucene.search.IndexSearcher;
+import org.apache.lucene.search.LRUQueryCache;
 import org.apache.lucene.search.MatchAllDocsQuery;
 import org.apache.lucene.search.Query;
+import org.apache.lucene.search.QueryCache;
+import org.apache.lucene.search.QueryCachingPolicy;
 import org.apache.lucene.search.Sort;
 import org.apache.lucene.search.SortField;
 import org.apache.lucene.search.TopFieldDocs;
+import org.apache.lucene.search.UsageTrackingQueryCachingPolicy;
 import org.apache.lucene.store.Directory;
 import org.apache.lucene.store.FSDirectory;
-import org.apache.lucene.util.NumericUtils;
 import org.jetbrains.annotations.Nullable;
+import org.json.JSONArray;
 import org.json.JSONObject;
+import org.labkey.api.cache.Cache;
+import org.labkey.api.cache.CacheManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.jbrowse.AbstractJBrowseFieldCustomizer;
@@ -33,6 +40,7 @@
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.security.User;
 import org.labkey.api.settings.AppProps;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.jbrowse.model.JBrowseSession;
 import org.labkey.jbrowse.model.JsonFile;
 
@@ -51,20 +59,24 @@
 import java.util.StringTokenizer;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 
 import static org.labkey.jbrowse.JBrowseFieldUtils.VARIABLE_SAMPLES;
 import static org.labkey.jbrowse.JBrowseFieldUtils.getSession;
 import static org.labkey.jbrowse.JBrowseFieldUtils.getTrack;
 
 public class JBrowseLuceneSearch
 {
+    private static final Logger _log = LogHelper.getLogger(JBrowseLuceneSearch.class, "Logger related to JBrowse/Lucene indexing and queries");
     private final JBrowseSession _session;
     private final JsonFile _jsonFile;
     private final User _user;
     private final String[] specialStartPatterns = {"*:* -", "+", "-"};
     private static final String ALL_DOCS = "all";
     private static final String GENOMIC_POSITION = "genomicPosition";
+    private static final int maxCachedQueries = 1000;
+    private static final long maxRamBytesUsed = 250 * 1024 * 1024L;
+
+    private static final Cache<String, LRUQueryCache> _cache = CacheManager.getStringKeyCache(1000, CacheManager.UNLIMITED, "JBrowseLuceneSearchCache");
 
     private JBrowseLuceneSearch(final JBrowseSession session, final JsonFile jsonFile, User u)
     {
@@ -85,6 +97,17 @@ public static JBrowseLuceneSearch create(String sessionId, String trackId, User
         return new JBrowseLuceneSearch(session, getTrack(session, trackId, u), u);
     }
 
+    private static synchronized QueryCache getCacheForSession(String trackObjectId) {
+        LRUQueryCache qc = _cache.get(trackObjectId);
+        if (qc == null)
+        {
+            qc = new LRUQueryCache(maxCachedQueries, maxRamBytesUsed);
+            _cache.put(trackObjectId, qc);
+        }
+
+        return qc;
+    }
+
     private String templateReplace(final String searchString) {
         String result = searchString;
         Pattern pattern = Pattern.compile("~(.*?)~");
@@ -148,6 +171,8 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
         )
         {
             IndexSearcher indexSearcher = new IndexSearcher(indexReader);
+            indexSearcher.setQueryCache(getCacheForSession(_jsonFile.getObjectId()));
+            indexSearcher.setQueryCachingPolicy(new ForceMatchAllDocsCachingPolicy());
 
             List<String> stringQueryParserFields = new ArrayList<>();
             Map<String, SortField.Type> numericQueryParserFields = new HashMap<>();
@@ -245,7 +270,7 @@ else if (numericQueryParserFields.containsKey(fieldName))
                     throw new IllegalArgumentException("Could not find type for sort field: " + sortField);
                 }
 
-                sort = new Sort(new SortField(sortField, fieldType, sortReverse));
+                sort = new Sort(new SortField(sortField + "_sort", fieldType, sortReverse));
             }
 
             // Get chunks of size {pageSize}. Default to 1 chunk -- add to the offset to get more.
@@ -263,7 +288,7 @@ else if (numericQueryParserFields.containsKey(fieldName))
             for (int i = pageSize * offset; i < Math.min(pageSize * (offset + 1), topDocs.scoreDocs.length); i++)
             {
                 JSONObject elem = new JSONObject();
-                Document doc = indexSearcher.doc(topDocs.scoreDocs[i].doc);
+                Document doc = indexSearcher.storedFields().document(topDocs.scoreDocs[i].doc);
 
                 for (IndexableField field : doc.getFields()) {
                     String fieldName = field.name();
@@ -345,4 +370,70 @@ public boolean isAvailable(Container c, User u)
             return true;
         }
     }
+
+    public static class ForceMatchAllDocsCachingPolicy implements QueryCachingPolicy {
+        private final UsageTrackingQueryCachingPolicy defaultPolicy = new UsageTrackingQueryCachingPolicy();
+
+        @Override
+        public boolean shouldCache(Query query) throws IOException {
+            if (query instanceof BooleanQuery bq) {
+                for (BooleanClause clause : bq) {
+                    if (clause.getQuery() instanceof MatchAllDocsQuery) {
+                        return true;
+                    }
+                }
+            }
+
+            return defaultPolicy.shouldCache(query);
+        }
+
+        @Override
+        public void onUse(Query query) {
+            defaultPolicy.onUse(query);
+        }
+    }
+
+    public static JSONArray reportCacheInfo()
+    {
+        JSONArray cacheInfo = new JSONArray();
+        for (String sessionId : _cache.getKeys())
+        {
+            LRUQueryCache qc = _cache.get(sessionId);
+            JSONObject info = new JSONObject();
+            info.put("cacheSize", qc.getCacheSize());
+            info.put("cacheCount", qc.getCacheCount());
+            info.put("hitCount", qc.getHitCount());
+            info.put("missCount", qc.getMissCount());
+            info.put("evictionCount", qc.getEvictionCount());
+            info.put("totalCount", qc.getTotalCount());
+            cacheInfo.put(info);
+        }
+
+        return cacheInfo;
+    }
+
+    public void cacheDefaultQuery()
+    {
+        try
+        {
+            JBrowseLuceneSearch.clearCache(_jsonFile.getObjectId());
+            doSearch(_user, ALL_DOCS, 100, 0, GENOMIC_POSITION, false);
+        }
+        catch (ParseException | IOException e)
+        {
+            _log.error("Unable to cache default query for: " + _jsonFile.getObjectId(), e);
+        }
+    }
+
+    public static void clearCache(@Nullable String jbrowseTrackId)
+    {
+        if (jbrowseTrackId == null)
+        {
+            _cache.clear();
+        }
+        else
+        {
+            _cache.remove(jbrowseTrackId);
+        }
+    }
 }

jbrowse/src/org/labkey/jbrowse/JBrowseServiceImpl.java

@@ -312,6 +312,13 @@ public void registerLuceneIndexDetector(LuceneIndexDetector detector)
         _detectors.add(detector);
     }
 
+    @Override
+    public void cacheDefaultQuery(User u, String sessionId, String trackId)
+    {
+        JBrowseLuceneSearch luceneSearch = JBrowseLuceneSearch.create(sessionId, trackId, u);
+        luceneSearch.cacheDefaultQuery();
+    }
+
     public static final class DefaultLuceneIndexDetector implements LuceneIndexDetector
     {
         @Override

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -51,9 +51,9 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
 import org.labkey.api.view.UnauthorizedException;
+import org.labkey.jbrowse.JBrowseLuceneSearch;
 import org.labkey.jbrowse.JBrowseManager;
 import org.labkey.jbrowse.JBrowseSchema;
-import org.labkey.jbrowse.pipeline.IndexVariantsStep;
 import org.labkey.jbrowse.pipeline.JBrowseLucenePipelineJob;
 import org.labkey.sequenceanalysis.run.util.TabixRunner;
 
@@ -964,6 +964,8 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool
             }
             else if (existingLuceneDir != null && existingLuceneDir.exists())
             {
+                JBrowseLuceneSearch.clearCache(getObjectId());
+
                 // Note: this could exist, but be an empty folder:
                 if (luceneDir.exists())
                 {
@@ -1004,7 +1006,7 @@ else if (sizeInGb > 50)
                     try
                     {
                         PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainerObj());
-                        PipelineService.get().queueJob(new JBrowseLucenePipelineJob(getContainerObj(), null, root, vcf, luceneDir, getInfoFieldsToIndex(), allowLenientLuceneProcessing()));
+                        PipelineService.get().queueJob(new JBrowseLucenePipelineJob(getContainerObj(), null, root, getObjectId(), vcf, luceneDir, getInfoFieldsToIndex(), allowLenientLuceneProcessing()));
                     }
                     catch (PipelineValidationException e)
                     {
@@ -1030,6 +1032,7 @@ else if (sizeInGb > 50)
                 if (forceReprocess || !doesLuceneIndexExist())
                 {
                     JBrowseLucenePipelineJob.prepareLuceneIndex(targetFile, luceneDir, log, getInfoFieldsToIndex(), allowLenientLuceneProcessing());
+                    JBrowseLuceneSearch.clearCache(getObjectId());
                 }
                 else
                 {