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Merged
labkey-adam merged 2 commits into from
Oct 12, 2026
Merged

Cache improvements #1293

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2b31f6f
Cache improvements
labkey-adam Oct 10, 2026
bdab801
Require key class at cache construction time
labkey-adam Oct 10, 2026
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13 changes: 7 additions & 6 deletions src/org/labkey/targetedms/parser/AbstractChromInfo.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
import org.labkey.api.data.Container;
import org.labkey.api.exp.api.ExpData;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.util.Tuple3;
import org.labkey.api.util.UnexpectedException;
import org.labkey.targetedms.PanoramaBadDataException;
import org.labkey.targetedms.TargetedMSRun;
Expand Down Expand Up @@ -56,10 +55,12 @@ public abstract class AbstractChromInfo extends ChromInfo<PrecursorChromInfoAnno

private static final Logger LOG = LogManager.getLogger(AbstractChromInfo.class);

private static final BlockingCache<Tuple3<Path, Long, Integer>, CachedBytes> ON_DEMAND_CHROM_CACHE = new BlockingCache<>(CacheManager.getCache(100, CacheManager.HOUR, "SKYD chromatogram cache"), (key, argument) -> {
Path path = key.first;
long offset = key.second;
int length = key.third;
private record ChromKey(Path path, long offset, int length) {}

private static final BlockingCache<ChromKey, CachedBytes> ON_DEMAND_CHROM_CACHE = new BlockingCache<>(CacheManager.getCache(ChromKey.class, 100, CacheManager.HOUR, "SKYD chromatogram cache"), (key, argument) -> {
Path path = key.path();
long offset = key.offset();
int length = key.length();

long startTime = System.currentTimeMillis();
LOG.debug("Loading chromatogram from {}, offset {}, length {}", path, offset, length);
Expand Down Expand Up @@ -242,7 +243,7 @@ private CompressedBytesAndStatus getCompressedBytesAndStatus(TargetedMSRun run)
else
{
LOG.debug("Attempting to fetch chromatogram bytes (possibly cached) from {} for {}", skydPath, this);
CachedBytes diskBytes = ON_DEMAND_CHROM_CACHE.get(new Tuple3<>(skydPath, _chromatogramOffset, _chromatogramLength));
CachedBytes diskBytes = ON_DEMAND_CHROM_CACHE.get(new ChromKey(skydPath, _chromatogramOffset, _chromatogramLength));
if (diskBytes == null)
{
status = Chromatogram.SourceStatus.skydMissing;
Expand Down
8 changes: 4 additions & 4 deletions src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java
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Expand Up @@ -47,7 +47,7 @@
import java.util.List;
import java.util.zip.DataFormatException;

import static org.labkey.targetedms.parser.speclib.LibSpectrum.*;
import static org.labkey.targetedms.parser.speclib.LibSpectrum.SpectrumKey;

/**
* User: vsharma
Expand Down Expand Up @@ -172,14 +172,14 @@ private static String getLibCacheKey(@NotNull Container container, String pathSt
};

private static final BlockingCache<String, String> _libCache =
new BlockingCache<>(CacheManager.getStringKeyCache(LIBCACHE_LIMIT, LIBCACHE_LIFETIME,
new BlockingCache<>(CacheManager.getCache(String.class, LIBCACHE_LIMIT, LIBCACHE_LIFETIME,
"SpeclibCache"), _libCacheLoader)
{
@Override
public void remove(@NotNull String key)
public boolean remove(@NotNull String key)
{
deleteTempFile(key);
super.remove(key);
return super.remove(key);
}

@Override
Expand Down
4 changes: 2 additions & 2 deletions src/org/labkey/targetedms/query/ModificationManager.java
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Expand Up @@ -46,8 +46,8 @@
public class ModificationManager
{
private static final int CACHE_SIZE = 10; // Cache results for up to 10 runs.
private static final Cache<String, Map<Long, Set<Pair<Integer, Integer>>>> PEPTIDE_STR_MOD_INDEXES = CacheManager.getCache(CACHE_SIZE, CacheManager.DAY, "Peptide structural modification indexes");
private static final Cache<String, Map<Pair<Long,Long>, Set<Integer>>> PEPTIDE_ISOTOPE_MOD_INDEXES = CacheManager.getCache(CACHE_SIZE, CacheManager.DAY, "Peptide isotope modification indexes");
private static final Cache<String, Map<Long, Set<Pair<Integer, Integer>>>> PEPTIDE_STR_MOD_INDEXES = CacheManager.getCache(String.class, CACHE_SIZE, CacheManager.DAY, "Peptide structural modification indexes");
private static final Cache<String, Map<Pair<Long,Long>, Set<Integer>>> PEPTIDE_ISOTOPE_MOD_INDEXES = CacheManager.getCache(String.class, CACHE_SIZE, CacheManager.DAY, "Peptide isotope modification indexes");

private ModificationManager() {}

Expand Down
2 changes: 1 addition & 1 deletion src/org/labkey/targetedms/query/PeptideManager.java
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Expand Up @@ -35,7 +35,7 @@
public class PeptideManager
{
private static final int CACHE_SIZE = 10;
private static final Cache<String, Set<Long>> PEPTIDE_IDS_WITH_SPECTRA = CacheManager.getCache(CACHE_SIZE, CacheManager.DAY, "Peptide IDs with library spectra");
private static final Cache<String, Set<Long>> PEPTIDE_IDS_WITH_SPECTRA = CacheManager.getCache(String.class, CACHE_SIZE, CacheManager.DAY, "Peptide IDs with library spectra");

private PeptideManager() {}

Expand Down
4 changes: 2 additions & 2 deletions src/org/labkey/targetedms/query/PrecursorManager.java
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Expand Up @@ -58,8 +58,8 @@
public class PrecursorManager
{
private static final int CACHE_SIZE = 10; // Cache results for up to 10 runs.
private static final Cache<String, Set<Long>> PRECURSOR_IDS_WITH_CHROMATOGRAMS = CacheManager.getCache(CACHE_SIZE, CacheManager.DAY, "Precursors having chromatograms");
private static final Cache<String, Set<Long>> PRECURSOR_IDS_WITH_SPECTRA = CacheManager.getCache(CACHE_SIZE, CacheManager.DAY, "Precursors having library spectra");
private static final Cache<String, Set<Long>> PRECURSOR_IDS_WITH_CHROMATOGRAMS = CacheManager.getCache(String.class, CACHE_SIZE, CacheManager.DAY, "Precursors having chromatograms");
private static final Cache<String, Set<Long>> PRECURSOR_IDS_WITH_SPECTRA = CacheManager.getCache(String.class, CACHE_SIZE, CacheManager.DAY, "Precursors having library spectra");

private PrecursorManager() {}

Expand Down
2 changes: 1 addition & 1 deletion src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java
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Expand Up @@ -122,7 +122,7 @@ private static boolean isLargeSpectrumLibrary(Path libPath)
}

private static final BlockingCache<PrecursorKey, List<PeptideIdRtInfo>> _peptideIdRtsCache =
CacheManager.getBlockingCache(CACHE_SIZE, CacheManager.DAY, "TargetedMS peptide ID retention times",
CacheManager.getBlockingCache(PrecursorKey.class, CACHE_SIZE, CacheManager.DAY, "TargetedMS peptide ID retention times",
(precursor, argument) -> {
if (!(argument instanceof Container))
{
Expand Down
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