From 2b9e553ac2cfa8028cebc7df8a017100b09db468 Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Wed, 27 Aug 2025 09:46:51 -0700 Subject: [PATCH 1/4] Clean up more warnings --- .../org/labkey/ms2/pipeline/comet/CometSearchProtocol.java | 2 +- .../labkey/ms2/pipeline/mascot/MascotSearchProtocol.java | 3 +-- .../labkey/ms2/pipeline/sequest/SequestSearchProtocol.java | 6 +++--- .../labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java | 7 +------ 4 files changed, 6 insertions(+), 12 deletions(-) diff --git a/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java b/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java index 3ac389d93..07772b78d 100644 --- a/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java +++ b/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java @@ -42,7 +42,7 @@ public CometSearchProtocol(String name, String description, String xml, Containe } @Override - public AbstractFileAnalysisProtocolFactory getFactory() + public CometSearchProtocolFactory getFactory() { return CometSearchProtocolFactory.get(); } diff --git a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchProtocol.java b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchProtocol.java index 86906aae0..fae22f0de 100644 --- a/ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchProtocol.java +++ b/ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchProtocol.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol; @@ -39,7 +38,7 @@ public MascotSearchProtocol(String name, String description, String xml, Contain } @Override - public AbstractFileAnalysisProtocolFactory getFactory() + public MascotSearchProtocolFactory getFactory() { return MascotSearchProtocolFactory.get(); } diff --git a/ms2/src/org/labkey/ms2/pipeline/sequest/SequestSearchProtocol.java b/ms2/src/org/labkey/ms2/pipeline/sequest/SequestSearchProtocol.java index 79e8648fa..c0310d207 100644 --- a/ms2/src/org/labkey/ms2/pipeline/sequest/SequestSearchProtocol.java +++ b/ms2/src/org/labkey/ms2/pipeline/sequest/SequestSearchProtocol.java @@ -20,7 +20,7 @@ import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineValidationException; -import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory; +import org.labkey.api.util.FileUtil; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol; @@ -43,7 +43,7 @@ public SequestSearchProtocol(String name, String description, String xml, Contai } @Override - public AbstractFileAnalysisProtocolFactory getFactory() + public SequestSearchProtocolFactory getFactory() { return SequestSearchProtocolFactory.get(); } @@ -65,7 +65,7 @@ public void validate(PipeRoot root) throws PipelineValidationException if(dbNames.isEmpty()) throw new IllegalArgumentException("A sequence database must be selected."); - File fileSequenceDB = new File(getDirSeqRoot(), dbNames.get(0)); + File fileSequenceDB = FileUtil.appendPath(getDirSeqRoot(), org.labkey.api.util.Path.parse(dbNames.get(0))); if (!fileSequenceDB.exists()) throw new IllegalArgumentException("Sequence database '" + dbNames.get(0) + "' is not found in local FASTA root."); diff --git a/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java b/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java index 793540c99..090518689 100644 --- a/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java +++ b/ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java @@ -15,12 +15,9 @@ */ package org.labkey.ms2.pipeline.tandem; -import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol; @@ -38,15 +35,13 @@ */ public class XTandemSearchProtocol extends AbstractMS2SearchProtocol { - private static final Logger _log = LogManager.getLogger(XTandemSearchProtocol.class); - public XTandemSearchProtocol(String name, String description, String xml, Container container) { super(name, description, xml, container); } @Override - public AbstractFileAnalysisProtocolFactory getFactory() + public XTandemSearchProtocolFactory getFactory() { return XTandemSearchProtocolFactory.get(); } From c89c4018dfcad554e09e8fd33f9660ee1a27a2b4 Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Fri, 29 Aug 2025 09:35:31 -0700 Subject: [PATCH 2/4] Unused import --- ms2/src/org/labkey/ms2/pipeline/FastaCheckTask.java | 2 +- ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/ms2/src/org/labkey/ms2/pipeline/FastaCheckTask.java b/ms2/src/org/labkey/ms2/pipeline/FastaCheckTask.java index a5e6a235a..9818394ad 100644 --- a/ms2/src/org/labkey/ms2/pipeline/FastaCheckTask.java +++ b/ms2/src/org/labkey/ms2/pipeline/FastaCheckTask.java @@ -55,7 +55,7 @@ public Factory() } @Override - public PipelineJob.Task createTask(PipelineJob job) + public FastaCheckTask createTask(PipelineJob job) { return new FastaCheckTask(this, job); } diff --git a/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java b/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java index 07772b78d..75cd134d8 100644 --- a/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java +++ b/ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java @@ -19,7 +19,6 @@ import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineValidationException; -import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory; import org.labkey.api.util.FileUtil; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol; From 55f977f02c14272dd33437dae47e6e04bf52affc Mon Sep 17 00:00:00 2001 From: Josh Eckels Date: Fri, 29 Aug 2025 09:42:56 -0700 Subject: [PATCH 3/4] Make cast explicit Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> --- ms2/src/org/labkey/ms2/PeptideProphetGraphs.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ms2/src/org/labkey/ms2/PeptideProphetGraphs.java b/ms2/src/org/labkey/ms2/PeptideProphetGraphs.java index 01d85dba2..462b3656c 100644 --- a/ms2/src/org/labkey/ms2/PeptideProphetGraphs.java +++ b/ms2/src/org/labkey/ms2/PeptideProphetGraphs.java @@ -182,7 +182,7 @@ public static void renderObservedVsPPScore(HttpServletResponse response, Contain if (count == increment) { - negative += negative * ratioRandom; // add back random positives + negative += (int)(negative * ratioRandom); // add back random positives if (negative > count) negative = count; score /= (float) count; // mean score From b79696dec45a169af6aaa38edbeab09661451f05 Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Fri, 29 Aug 2025 09:45:40 -0700 Subject: [PATCH 4/4] Fix regex --- ms2/src/org/labkey/ms2/reader/MascotDatLoader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java b/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java index 95cc57e65..9b59bd48d 100644 --- a/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java +++ b/ms2/src/org/labkey/ms2/reader/MascotDatLoader.java @@ -149,7 +149,7 @@ public class MascotDatLoader extends MS2Loader implements AutoCloseable // once URL decoded, the value looks like this: // CAexample_mini.0110.0110.1 - public static final Pattern QUERY_TITLE_SCAN_REGEX = Pattern.compile("\\.??(\\d{1,6})\\.(\\d{1,6})\\.(\\d)\\.??[a-zA-z0-9_]*?$"); + public static final Pattern QUERY_TITLE_SCAN_REGEX = Pattern.compile("\\.??(\\d{1,6})\\.(\\d{1,6})\\.(\\d)\\.??[a-zA-Z0-9_]*?$"); // the title line may also look like this: // title=Spectrum270258%20scans%3a6721%2c // decoded to: