From 450e54a8a485b06fcb4956289c08b889ca63407b Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Tue, 26 Dec 2023 17:25:05 -0500 Subject: [PATCH 1/3] Migrate ONPRC repos (#257) --- SequenceAnalysis/build.gradle | 2 +- .../labkey/sequenceanalysis/OutputIntegrationTests.java | 4 ++-- .../sequenceanalysis/SequenceAnalysisController.java | 4 ++-- .../labkey/sequenceanalysis/SequenceIntegrationTests.java | 4 ++-- blast/src/org/labkey/blast/BLASTController.java | 4 ++-- blast/src/org/labkey/blast/model/BlastJob.java | 2 +- cluster/src/org/labkey/cluster/ClusterManager.java | 2 +- jbrowse/src/org/labkey/jbrowse/model/JsonFile.java | 2 +- .../src/org/labkey/jbrowse/pipeline/IndexVariantsStep.java | 7 +------ .../src/org/labkey/singlecell/SingleCellController.java | 2 +- .../singlecell/analysis/SingleCellReadsetListener.java | 2 +- singlecell/src/org/labkey/singlecell/run/NimbleHelper.java | 2 +- 12 files changed, 16 insertions(+), 21 deletions(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 055c431c9..c600a7abe 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -20,7 +20,7 @@ repositories { configurations.all { resolutionStrategy { - force "com.sun.activation:jakarta.activation:${activationVersion}" + force "jakarta.activation:jakarta.activation-api:${activationVersion}" // NOTE: this should be kept in sync with mcc module: force "jakarta.xml.bind:jakarta.xml.bind-api:${jaxbVersion}" } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java index 1a91853db..4f9a6cdaf 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java @@ -37,8 +37,8 @@ import org.springframework.mock.web.MockHttpServletResponse; import org.springframework.web.bind.annotation.RequestMethod; -import javax.servlet.http.HttpServletRequest; -import javax.servlet.http.HttpServletResponse; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; import java.io.File; import java.util.Arrays; import java.util.Collections; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index 5b8625a4a..d29e0a4b6 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java @@ -172,8 +172,8 @@ import org.springframework.web.bind.ServletRequestParameterPropertyValues; import org.springframework.web.servlet.ModelAndView; -import javax.servlet.http.HttpServletRequest; -import javax.servlet.http.HttpServletResponse; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java index 929edc204..9fc9b090c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java @@ -70,8 +70,8 @@ import org.springframework.mock.web.MockHttpServletResponse; import org.springframework.web.bind.annotation.RequestMethod; -import javax.servlet.http.HttpServletRequest; -import javax.servlet.http.HttpServletResponse; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; import java.io.BufferedReader; import java.io.File; import java.io.IOException; diff --git a/blast/src/org/labkey/blast/BLASTController.java b/blast/src/org/labkey/blast/BLASTController.java index 74e2d9815..82a453097 100644 --- a/blast/src/org/labkey/blast/BLASTController.java +++ b/blast/src/org/labkey/blast/BLASTController.java @@ -63,8 +63,8 @@ import org.springframework.web.multipart.MultipartHttpServletRequest; import org.springframework.web.servlet.ModelAndView; -import javax.servlet.http.HttpServletRequest; -import javax.servlet.http.HttpServletResponse; +import jakarta.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletResponse; import java.io.File; import java.io.IOException; import java.io.OutputStreamWriter; diff --git a/blast/src/org/labkey/blast/model/BlastJob.java b/blast/src/org/labkey/blast/model/BlastJob.java index 109d2ac91..86890a9de 100644 --- a/blast/src/org/labkey/blast/model/BlastJob.java +++ b/blast/src/org/labkey/blast/model/BlastJob.java @@ -1,5 +1,6 @@ package org.labkey.blast.model; +import jakarta.servlet.jsp.JspWriter; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; @@ -24,7 +25,6 @@ import org.labkey.blast.BLASTSchema; import org.labkey.blast.BLASTWrapper; -import javax.servlet.jsp.JspWriter; import java.io.File; import java.io.IOException; import java.io.Serializable; diff --git a/cluster/src/org/labkey/cluster/ClusterManager.java b/cluster/src/org/labkey/cluster/ClusterManager.java index baadc6199..a7e034c5a 100644 --- a/cluster/src/org/labkey/cluster/ClusterManager.java +++ b/cluster/src/org/labkey/cluster/ClusterManager.java @@ -19,6 +19,7 @@ import org.apache.commons.lang3.StringUtils; 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.data.ContainerManager; import org.labkey.api.module.Module; @@ -36,7 +37,6 @@ import org.quartz.TriggerBuilder; import org.quartz.impl.StdSchedulerFactory; -import javax.annotation.Nullable; import java.util.Arrays; import java.util.List; diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java index e4c6353d2..86546b93d 100644 --- a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java +++ b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java @@ -12,6 +12,7 @@ import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; +import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.json.JSONException; import org.json.JSONObject; @@ -56,7 +57,6 @@ import org.labkey.jbrowse.pipeline.JBrowseLucenePipelineJob; import org.labkey.sequenceanalysis.run.util.TabixRunner; -import javax.annotation.Nullable; import java.io.File; import java.io.IOException; import java.nio.file.Files; diff --git a/jbrowse/src/org/labkey/jbrowse/pipeline/IndexVariantsStep.java b/jbrowse/src/org/labkey/jbrowse/pipeline/IndexVariantsStep.java index e0e8ef5cc..407136745 100644 --- a/jbrowse/src/org/labkey/jbrowse/pipeline/IndexVariantsStep.java +++ b/jbrowse/src/org/labkey/jbrowse/pipeline/IndexVariantsStep.java @@ -1,9 +1,8 @@ package org.labkey.jbrowse.pipeline; import htsjdk.samtools.util.Interval; -import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.lang3.SystemUtils; +import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider; import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; @@ -14,12 +13,8 @@ import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl; import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper; -import org.labkey.api.writer.PrintWriters; -import javax.annotation.Nullable; import java.io.File; -import java.io.IOException; -import java.io.PrintWriter; import java.util.Arrays; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java index 160240070..13bef2154 100644 --- a/singlecell/src/org/labkey/singlecell/SingleCellController.java +++ b/singlecell/src/org/labkey/singlecell/SingleCellController.java @@ -63,7 +63,7 @@ import org.springframework.validation.BindException; import org.springframework.web.servlet.ModelAndView; -import javax.servlet.http.HttpServletResponse; +import jakarta.servlet.http.HttpServletResponse; import java.io.File; import java.io.FileInputStream; import java.io.IOException; diff --git a/singlecell/src/org/labkey/singlecell/analysis/SingleCellReadsetListener.java b/singlecell/src/org/labkey/singlecell/analysis/SingleCellReadsetListener.java index 55481651e..3ed45bb93 100644 --- a/singlecell/src/org/labkey/singlecell/analysis/SingleCellReadsetListener.java +++ b/singlecell/src/org/labkey/singlecell/analysis/SingleCellReadsetListener.java @@ -2,6 +2,7 @@ import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -22,7 +23,6 @@ import org.labkey.singlecell.SingleCellModule; import org.labkey.singlecell.SingleCellSchema; -import javax.annotation.Nullable; import java.sql.SQLException; import java.util.ArrayList; import java.util.List; diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java index 99274666b..031ec4dd3 100644 --- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java +++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java @@ -5,6 +5,7 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.io.output.StringBuilderWriter; import org.apache.commons.lang3.StringUtils; +import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.data.ColumnInfo; @@ -31,7 +32,6 @@ import org.labkey.api.util.PageFlowUtil; import org.labkey.api.writer.PrintWriters; -import javax.annotation.Nullable; import java.io.BufferedReader; import java.io.File; import java.io.IOException; From 8e8a8b1fc5b324aea4e87be651887a4ba3d52b09 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Fri, 12 Jan 2024 17:26:34 -0500 Subject: [PATCH 2/3] Use the correct @Nullable annotation (#260) --- .../sequenceanalysis/run/variant/GenotypeConcordanceStep.java | 2 +- .../sequenceanalysis/run/variant/GenotypeFiltrationStep.java | 2 +- .../labkey/sequenceanalysis/run/variant/KingInferenceStep.java | 3 +-- .../run/variant/MendelianViolationReportStep.java | 2 +- .../run/variant/OutputVariantsStartingInIntervalsStep.java | 3 +-- 5 files changed, 5 insertions(+), 7 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java index d9e2785ea..0ee8d3488 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java @@ -7,6 +7,7 @@ import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFFileReader; import htsjdk.variant.vcf.VCFHeader; +import org.jetbrains.annotations.Nullable; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; @@ -22,7 +23,6 @@ import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper; import org.labkey.sequenceanalysis.run.util.VariantAnnotatorWrapper; -import javax.annotation.Nullable; import java.io.File; import java.io.IOException; import java.util.ArrayList; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java index 37c754704..8b63d72eb 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java @@ -1,6 +1,7 @@ package org.labkey.sequenceanalysis.run.variant; import htsjdk.samtools.util.Interval; +import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; @@ -16,7 +17,6 @@ import org.labkey.api.sequenceanalysis.run.VariantFiltrationWrapper; import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper; -import javax.annotation.Nullable; import java.io.File; import java.util.ArrayList; import java.util.Arrays; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java index 831631723..aa7d6da7b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java @@ -8,6 +8,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; @@ -22,11 +23,9 @@ import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; -import javax.annotation.Nullable; import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; public class KingInferenceStep extends AbstractCommandPipelineStep implements VariantProcessingStep diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java index 052a1a982..b29befc8a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java @@ -1,6 +1,7 @@ package org.labkey.sequenceanalysis.run.variant; import htsjdk.samtools.util.Interval; +import org.jetbrains.annotations.Nullable; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep; @@ -14,7 +15,6 @@ import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl; import org.labkey.sequenceanalysis.pipeline.ProcessVariantsHandler; -import javax.annotation.Nullable; import java.io.File; import java.util.ArrayList; import java.util.Arrays; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java index 15174dfcd..2d02bc997 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java @@ -2,6 +2,7 @@ import htsjdk.samtools.util.Interval; import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep; @@ -14,12 +15,10 @@ import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper; import org.labkey.api.writer.PrintWriters; -import javax.annotation.Nullable; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; /** From 1ec9f71228659e154974f2578962262072e87e44 Mon Sep 17 00:00:00 2001 From: Josh Eckels Date: Fri, 19 Jan 2024 15:12:37 -0800 Subject: [PATCH 3/3] Support all labkey.xml/ROOT.xml settings via application.properties (#267) --- cluster/resources/web/cluster/htcondor/pipelineConfig.xml | 2 +- cluster/resources/web/cluster/slurm/pipelineConfig.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cluster/resources/web/cluster/htcondor/pipelineConfig.xml b/cluster/resources/web/cluster/htcondor/pipelineConfig.xml index 44d6d328f..36f8e6c7a 100644 --- a/cluster/resources/web/cluster/htcondor/pipelineConfig.xml +++ b/cluster/resources/web/cluster/htcondor/pipelineConfig.xml @@ -3,7 +3,7 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd"> - + diff --git a/cluster/resources/web/cluster/slurm/pipelineConfig.xml b/cluster/resources/web/cluster/slurm/pipelineConfig.xml index 4abf517c8..4c6c5e279 100644 --- a/cluster/resources/web/cluster/slurm/pipelineConfig.xml +++ b/cluster/resources/web/cluster/slurm/pipelineConfig.xml @@ -3,7 +3,7 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd"> - +