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Auto-refactor lint cleanup #1205

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2 changes: 1 addition & 1 deletion src/org/labkey/panoramapremium/PanoramaPremiumController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ else if(isMolecule)
//skip selected precursors that are already excluded
selectedRowsKeys.forEach(id -> {
List<ExcludedPrecursor> prec = precursorsList.stream().filter(p -> p.getId() == id).toList();
ExcludedPrecursor precursor = prec.get(0);
ExcludedPrecursor precursor = prec.getFirst();
precursor.setIsPeptide(isPeptide);

if (isExcluding)
Expand Down
13 changes: 7 additions & 6 deletions src/org/labkey/targetedms/SkylineAuditLogManager.java
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Expand Up @@ -198,7 +198,7 @@ private int persistAuditLog(User user, AuditLogImportContext pContext, SkylineAu
ent.setDocumentGUID(pContext._documentGUID);
pContext._rootHash.update(ent.getEntryHash().getBytes(StandardCharsets.UTF_8));
// Insert at the beginning of the list so we can quickly iterate in reverse order for validation
entries.add(0, ent);
entries.addFirst(ent);
}
catch (XMLStreamException e)
{
Expand Down Expand Up @@ -247,7 +247,7 @@ private int persistAuditLog(User user, AuditLogImportContext pContext, SkylineAu
}

if (pContext._runId != null) //set the document version id on the chronologically last log entry.
entries.get(entries.size() - 1).setVersionId(pContext._runId);
entries.getLast().setVersionId(pContext._runId);

AuditLogTree treePointer = pContext._logTree;
int persistedEntriesCount = 0;
Expand Down Expand Up @@ -280,7 +280,7 @@ private int persistAuditLog(User user, AuditLogImportContext pContext, SkylineAu
}
}
if (persistedEntriesCount == 0) //if no entries were actually saved into the database we are uploading an earlier document version
entries.get(entries.size() - 1).insertRunAuditLogEntry(user, pContext._runId); //and still need to update the terminal entry with the versionId.
entries.getLast().insertRunAuditLogEntry(user, pContext._runId); //and still need to update the terminal entry with the versionId.

return entries.size();
}
Expand All @@ -304,7 +304,8 @@ private void verifyPostRequisites(AuditLogImportContext pContext, SkylineAuditLo
* Builds a tree of audit log entry tokens representing the document versioning tree
* @return the root node of the tree
*/
private AuditLogTree buildLogTree(@NotNull GUID pDocumentGUID) throws AuditLogException {
private AuditLogTree buildLogTree(@NotNull GUID pDocumentGUID)
{

TableInfo entryTbl = TargetedMSManager.getTableInfoSkylineAuditLogEntry();

Expand Down Expand Up @@ -440,7 +441,7 @@ private TargetedMSRun getNewRun(GUID pDocumentGUID, Container container)
run.setContainer(container);
run.setDocumentGUID(pDocumentGUID);
Table.insert(_user, TargetedMSManager.getTableInfoRuns(), run);
_logger.info(String.format("new run is inserted with id %d", run.getId()));
_logger.info("new run is inserted with id {}", run.getId());
return run;
}

Expand Down Expand Up @@ -564,7 +565,7 @@ public void addAVersionTest() throws IOException, AuditLogException

for(String fileName : testFileNames)
{
_logger.info("AuditLogFiles/" + fileName);
_logger.info("AuditLogFiles/{}", fileName);
runs.push(getNewRun(_docGUID));
tree = persistALogFile("AuditLogFiles/" + fileName, runs.peek());
}
Expand Down
2 changes: 1 addition & 1 deletion src/org/labkey/targetedms/SkylineBinaryDataHandler.java
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Expand Up @@ -50,7 +50,7 @@ public DataType getDataType()
}

@Override
public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context)
{
}

Expand Down
61 changes: 28 additions & 33 deletions src/org/labkey/targetedms/SkylineDocImporter.java
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Expand Up @@ -214,7 +214,7 @@ public TargetedMSRun importRun(RunInfo runInfo, PipelineJob job) throws IOExcept
// Skip if run was already fully imported
if (run.getStatusId() == SkylineDocImporter.STATUS_SUCCESS)
{
_log.info(_expData.getName() + " has already been imported so it does not need to be imported again");
_log.info("{} has already been imported so it does not need to be imported again", _expData.getName());
return run;
}

Expand Down Expand Up @@ -249,9 +249,9 @@ public TargetedMSRun importRun(RunInfo runInfo, PipelineJob job) throws IOExcept
saveRunDocumentSize(run);

updateRunStatus(IMPORT_STARTED);
_log.info("Starting to import Skyline document from " + run.getFileName());
_log.info("Starting to import Skyline document from {}", run.getFileName());
importSkylineDoc(run, inputFile.toNioPathForRead().toFile());
_log.info("Completed import of Skyline document from " + run.getFileName());
_log.info("Completed import of Skyline document from {}", run.getFileName());

updateRunStatus(IMPORT_SUCCEEDED, STATUS_SUCCESS);

Expand Down Expand Up @@ -401,17 +401,14 @@ private void importSkylineDoc(TargetedMSRun run, File f) throws XMLStreamExcepti
modInfo, libraryNameIdMap, pepGroup, parser, peptides, smallMolecules, parser.getTransitionSettings());
if (++peptideGroupCount % 100 == 0)
{
_log.info("Imported " + peptideGroupCount + " peptide groups.");
_log.info("Imported {} peptide groups.", peptideGroupCount);
}
}

if (!_shouldSaveTransitionChromInfos)
{
TargetedMSModule targetedMSModule = ModuleLoader.getInstance().getModule(TargetedMSModule.class);
_log.info("None of the " + parser.getTransitionChromInfoCount() + " TransitionChromInfos in the file " +
"were imported because they exceed the limit of " +
targetedMSModule.MAX_TRANSITION_CHROM_INFOS_PROPERTY.getEffectiveValue(_container) + " and there are more than " +
targetedMSModule.MAX_PRECURSORS_PROPERTY.getEffectiveValue(_container) + " precursors");
_log.info("None of the {} TransitionChromInfos in the file were imported because they exceed the limit of {} and there are more than {} precursors", parser.getTransitionChromInfoCount(), targetedMSModule.MAX_TRANSITION_CHROM_INFOS_PROPERTY.getEffectiveValue(_container), targetedMSModule.MAX_PRECURSORS_PROPERTY.getEffectiveValue(_container));
}

// Done parsing document
Expand Down Expand Up @@ -546,7 +543,7 @@ private void calculateSampleFileIRTStats(TargetedMSRun run, ReplicateInfo replic
return;
}

_log.info("Calculating iRT correlations for " + replicateInfo.skylineIdSampleFileIdMap.size() + " sample(s)");
_log.info("Calculating iRT correlations for {} sample(s)", replicateInfo.skylineIdSampleFileIdMap.size());

// Get the iRT scale to which we are comparing each sample
SimpleFilter iRTFilter = new SimpleFilter(FieldKey.fromParts("iRTScaleId"), run.getiRTscaleId());
Expand Down Expand Up @@ -600,7 +597,7 @@ private void calculateSampleFileIRTStats(TargetedMSRun run, ReplicateInfo replic
updatedCount++;
}
}
_log.info("Finished calculating iRT correlations for all samples. " + updatedCount + " had a regression line calculated.");
_log.info("Finished calculating iRT correlations for all samples. {} had a regression line calculated.", updatedCount);

}

Expand Down Expand Up @@ -691,9 +688,9 @@ private void deleteOldSampleFiles(ReplicateInfo replicateInfo)
return;
}

_log.info(String.format("Updating previously imported data for %d old sample files.", total));
_log.info("Updating previously imported data for {} old sample files.", total);
_log.debug("Found data for the following old sample files in the QC folder:");
replicateInfo.oldSamplesToDelete.keySet().forEach(key -> _log.debug(String.format(" %s", key)));
replicateInfo.oldSamplesToDelete.keySet().forEach(key -> _log.debug(" {}", key));

List<Long> existingSamples = new LongArrayList(total);
replicateInfo.oldSamplesToDelete.forEach((key, value) -> value.forEach(existingSample -> existingSamples.add(existingSample.getId())));
Expand All @@ -709,7 +706,7 @@ private void deleteOldSampleFiles(ReplicateInfo replicateInfo)
}
catch (URISyntaxException e)
{
_log.error("Unable to delete file " + srcFile + ". May be an invalid path. This file is no longer needed on the server.");
_log.error("Unable to delete file {}. May be an invalid path. This file is no longer needed on the server.", srcFile);
}
}
}
Expand Down Expand Up @@ -819,7 +816,7 @@ private void insertDigestSettings(PeptideSettings pepSettings)
}
else
{
enzyme = existingEnzymes.get(0);
enzyme = existingEnzymes.getFirst();
}

PeptideSettings.EnzymeDigestionSettings digestSettings = pepSettings.getEnzymeDigestionSettings();
Expand Down Expand Up @@ -988,9 +985,9 @@ private void handleReplicateExclusions(Replicate replicate, ReplicateAnnotation
// If there is an ignore_in_QC annotation and we already have existing exclusions, don't insert but compare and
// give a warning if there is a mismatch.
if (!shouldExcludeFromAnnot)
_log.warn("Replicate " + replicate.getName() + " has an ignore_in_QC=false annotation but there are existing exclusions that were added within Panorama or from a previous import.");
_log.warn("Replicate {} has an ignore_in_QC=false annotation but there are existing exclusions that were added within Panorama or from a previous import.", replicate.getName());
else if (!hasExistingExcludeAllMetrics)
_log.warn("Replicate " + replicate.getName() + " has an ignore_in_QC=true annotation but there are existing metric specific exclusions that were added within Panorama.");
_log.warn("Replicate {} has an ignore_in_QC=true annotation but there are existing metric specific exclusions that were added within Panorama.", replicate.getName());
}
}
}
Expand Down Expand Up @@ -1074,7 +1071,7 @@ else if (SkylineFileUtils.EXT_SKY_LOG.equalsIgnoreCase(ext))
newScale = true;
else
{
iRTScaleId = scaleIds.get(0);
iRTScaleId = scaleIds.getFirst();
SimpleFilter iRTFilter = new SimpleFilter(FieldKey.fromParts("iRTScaleId"), iRTScaleId);
List<IrtPeptide> existingScale = new TableSelector(TargetedMSManager.getTableInfoiRTPeptide(), iRTFilter, null).getArrayList(IrtPeptide.class);

Expand Down Expand Up @@ -1123,7 +1120,7 @@ private ArrayList<IrtPeptide> normalizeIrtImportAndReweighValues(List<IrtPeptide
IRegressionFunction regressionLine = IrtRegressionCalculator.calcRegressionLine(new RetentionTimeProviderImpl(importScale), new ArrayList<>(existingStandards.values()), new ArrayList<>(existingLibrary.values()), _log);

if (regressionLine == null)
throw new PipelineJobException(makeIrtStandardsErrorMsg(existingScale.get(0).getiRTScaleId(), new ArrayList<>(existingStandards.values()), importScale));
throw new PipelineJobException(makeIrtStandardsErrorMsg(existingScale.getFirst().getiRTScaleId(), new ArrayList<>(existingStandards.values()), importScale));

applyIrtRegressionLine(regressionLine, importScale);

Expand Down Expand Up @@ -1284,7 +1281,7 @@ else if(!pepGroup.isDecoy())
}

// CONSIDER: If there is already an identical entry in the PeptideGroup table re-use it.
_log.info("Inserting " + pepGroup.getLabel());
_log.info("Inserting {}", pepGroup.getLabel());
pepGroup = Table.insert(_user, TargetedMSManager.getTableInfoPeptideGroup(), pepGroup);

for (Protein protein : pepGroup.getProteins())
Expand Down Expand Up @@ -1332,7 +1329,7 @@ else if(!pepGroup.isDecoy())
peptideCount++;
if (peptideCount % 50 == 0)
{
_log.debug(String.format("Inserted %d peptides", peptideCount));
_log.debug("Inserted {} peptides", peptideCount);
}
}
case MOLECULE -> {
Expand All @@ -1346,7 +1343,7 @@ else if(!pepGroup.isDecoy())
moleculeCount++;
if (moleculeCount % 50 == 0)
{
_log.debug(String.format("Inserted %d molecules", moleculeCount));
_log.debug("Inserted {} molecules", moleculeCount);
}
}
}
Expand All @@ -1356,11 +1353,11 @@ else if(!pepGroup.isDecoy())
}
if(peptideCount > 0)
{
_log.debug(String.format("Total peptides inserted: %d", peptideCount));
_log.debug("Total peptides inserted: {}", peptideCount);
}
if(moleculeCount > 0)
{
_log.debug(String.format("Total molecules inserted: %d", moleculeCount));
_log.debug("Total molecules inserted: {}", moleculeCount);
}
}

Expand Down Expand Up @@ -1726,7 +1723,7 @@ private void insertLibInfo(Precursor.LibraryInfo libraryInfo, Precursor precurso
if (_missingLibraries.add(libraryInfo.getLibraryName()))
{
// Only log the first time
_log.warn("'" + libraryInfo.getLibraryName() + "' library was not found in settings.");
_log.warn("'{}' library was not found in settings.", libraryInfo.getLibraryName());
}
}
else
Expand Down Expand Up @@ -2304,7 +2301,7 @@ private void insertSampleFiles(ReplicateInfo replicateInfo, Map<Instrument, Long

if (pathToSampleFile.containsKey(sampleFile.getFilePath()))
{
_log.warn("Duplicate entries found for file path " + sampleFile.getFilePath() + ", may not resolve sample file-scoped chromatograms correctly");
_log.warn("Duplicate entries found for file path {}, may not resolve sample file-scoped chromatograms correctly", sampleFile.getFilePath());
}
else
{
Expand Down Expand Up @@ -2362,7 +2359,7 @@ private Path copyFileToCloud(Path sourcePath, Path targetParentPath) throws IOEx
{
Path dest = targetParentPath.resolve(FileUtil.getFileName(sourcePath));
Files.copy(sourcePath, dest, StandardCopyOption.REPLACE_EXISTING);
_log.info("Copied " + FileUtil.getFileName(sourcePath) + " to cloud storage.");
_log.info("Copied {} to cloud storage.", FileUtil.getFileName(sourcePath));
return dest;
}

Expand Down Expand Up @@ -2616,7 +2613,7 @@ public RunInfo prepareRun()
TargetedMSRun run = getRun();
if (run == null)
{
_log.info("Starting import from " + _expData.getName());
_log.info("Starting import from {}", _expData.getName());
run = createRun();
}

Expand Down Expand Up @@ -2685,7 +2682,7 @@ int quantifyRun(TargetedMSRun run, PeptideSettings pepSettings, Collection<Group
}
for (GroupComparisonSettings groupComparison : groupComparisons)
{
_log.debug(String.format("Calculating fold change for group comparison %s, %d of %d", groupComparison.getName(), ++i, groupComparisons.size()));
_log.debug("Calculating fold change for group comparison {}, {} of {}", groupComparison.getName(), ++i, groupComparisons.size());
for (FoldChange foldChange : quantifier.calculateFoldChanges(groupComparison))
{
Table.insert(_user, TargetedMSManager.getTableInfoFoldChange(), foldChange);
Expand Down Expand Up @@ -2928,7 +2925,7 @@ private void doUpdate(int percDone)
{
_job.setStatus(PipelineJob.TaskStatus.running + ", " + percDone + "%"); // This will throw a CancelledException if the job was cancelled.
}
_log.info(percDone + "% Done");
_log.info("{}% Done", percDone);
}


Expand Down Expand Up @@ -3043,17 +3040,15 @@ private boolean documentIsWithinLimits(File file, Container container, Logger lo
// To prevent giant DIA documents from overwhelming the DB, we skip importing TransitionChromInfos if the document
// has more than 100,000 AND has more than 1,000 precursors. We use both because a document may have a lot of
// replicates, so the TransitionChromInfo count by itself isn't sufficient to do the desired screening
log.info("Reading Skyline file, " + file.getName() + ", to determine if the TransitionChromInfos in the document should be stored...");
log.info("Reading Skyline file, {}, to determine if the TransitionChromInfos in the document should be stored...", file.getName());
boolean documentWithinLimits = new TransitionChromInfoAndPrecursorTally(maxTransitionChromInfos, maxPrecursors).isWithinLimits(file, log);
if (documentWithinLimits)
{
log.info("TransitionChromInfo counts or precursor counts are within the allowed limits. TransitionChromInfos will be stored");
}
else
{
log.info("TransitionChromInfos in the document exceed the limit of " + maxTransitionChromInfos +
", and there are more than " + maxPrecursors + " precursors." +
" TransitionChromInfos will not be stored.");
log.info("TransitionChromInfos in the document exceed the limit of {}, and there are more than {} precursors. TransitionChromInfos will not be stored.", maxTransitionChromInfos, maxPrecursors);
}
return documentWithinLimits;
}
Expand Down
6 changes: 3 additions & 3 deletions src/org/labkey/targetedms/SkylineFileUtils.java
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Expand Up @@ -65,7 +65,7 @@ public static Path getSkylineFile(@Nullable String runLSID, @NotNull Container c
TargetedMSRun run = TargetedMSManager.getRunByLsid(runLSID, container);
if (run == null)
{
LOG.warn("Run with experimentRunLSID " + runLSID + " does not exist in container " + container.getPath());
LOG.warn("Run with experimentRunLSID {} does not exist in container {}", runLSID, container.getPath());
return null;
}

Expand All @@ -79,11 +79,11 @@ public static Path getSkylineFile(@Nullable String runLSID, @NotNull Container c
}
else
{
LOG.warn("Skyline file does not exist: " + (skyDocfile != null ? FileUtil.getFileName(skyDocfile) : null) + ", referenced from " + container.getPath());
LOG.warn("Skyline file does not exist: {}, referenced from {}", skyDocfile != null ? FileUtil.getFileName(skyDocfile) : null, container.getPath());
return null;
}
}
LOG.warn("No input data found for targetedms run " + run.getId() + " in container " + container.getPath());
LOG.warn("No input data found for targetedms run {} in container {}", run.getId(), container.getPath());
return null;
}
}
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