From 94274c45f0d42f9ffd59ef72e5cd5c84acf00a80 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 10 Feb 2023 09:05:17 -0800 Subject: [PATCH 1/7] Migrate to new JSONObject/JSONArray --- .../genotypeassays/GenotypeAssaysController.java | 2 +- .../labkey/genotypeassays/GenotypeAssaysManager.java | 7 ++++--- .../assay/DefaultGenotypeAssaysImportMethod.java | 5 +++-- .../assay/DefaultSnpAssayImportMethod.java | 2 +- .../assay/GenotypeAssayDataProvider.java | 2 +- .../genotypeassays/assay/SNPAssayDataProvider.java | 2 +- .../genotypeassays/assay/SSPAssayDataProvider.java | 2 +- .../assay/SSPAssayDefaultImportMethod.java | 2 +- .../assay/SSPPivotingImportMethod.java | 3 ++- .../labpurchasing/LabPurchasingDataProvider.java | 2 +- .../org/labkey/covidseq/CovidseqDataProvider.java | 2 +- .../elispot_assay/ELISPOT_AssayDataProvider.java | 2 +- .../labkey/elispot_assay/assay/AIDImportMethod.java | 3 ++- .../elispot_assay/assay/DefaultImportMethod.java | 11 ++++++----- .../labkey/flowassays/FlowAssaysDataProvider.java | 2 +- .../flowassays/assay/DefaultFlowImportMethod.java | 2 +- .../labkey/flowassays/assay/FlowImportHelper.java | 6 +++--- .../flowassays/assay/FlowPivotingImportMethod.java | 2 +- .../org/labkey/flowassays/assay/ICSDataProvider.java | 2 +- .../assay/ImmunophenotypingDataProvider.java | 2 +- .../columnTransforms/JBrowseSessionTransform.java | 2 +- .../src/org/labkey/mgap/pipeline/AnnotationStep.java | 2 +- .../SampleSpecificGenotypeFiltrationStep.java | 2 +- .../org/labkey/mgap/pipeline/VcfComparisonStep.java | 2 +- .../pipeline/mGapReleaseAnnotateNovelSitesStep.java | 2 +- .../mgap/pipeline/mGapReleaseComparisonStep.java | 2 +- .../labkey/mgap/pipeline/mGapReleaseGenerator.java | 10 ++++++---- .../src/org/labkey/primeseq/PrimeseqController.java | 4 ++-- .../analysis/CombineMethylationRatesHandler.java | 2 +- .../primeseq/analysis/MethylationRateComparison.java | 4 ++-- .../analysis/MethylationRateComparisonHandler.java | 4 ++-- .../org/labkey/primeseq/pipeline/BismarkWrapper.java | 2 +- .../primeseq/pipeline/ExacloudResourceSettings.java | 2 +- .../primeseq/pipeline/GeographicOriginStep.java | 2 +- .../primeseq/pipeline/MhcMigrationPipelineJob.java | 2 +- .../pipeline/SequenceJobResourceAllocator.java | 1 - tcrdb/src/org/labkey/tcrdb/TCRdbProvider.java | 2 +- .../pipeline/CellRangerVDJCellHashingHandler.java | 2 +- .../labkey/tcrdb/pipeline/CellRangerVDJUtils.java | 2 +- .../src/org/labkey/tcrdb/pipeline/MiXCRAnalysis.java | 9 +++++---- .../org/labkey/variantdb/VariantDBDataProvider.java | 2 +- .../variantdb/analysis/GBSAnalysisHandler.java | 10 +++++----- .../variantdb/analysis/ImputationAnalysis.java | 12 ++++++------ .../variantdb/analysis/MendelianAnalysisHandler.java | 10 +++++----- .../org/labkey/variantdb/run/MendelianEvaluator.java | 2 +- 45 files changed, 83 insertions(+), 76 deletions(-) diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java b/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java index 95d2250f7..e3bbfefb5 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java @@ -16,7 +16,7 @@ package org.labkey.genotypeassays; -import org.json.old.JSONArray; +import org.json.JSONArray; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.ConfirmAction; diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java b/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java index 1afe5b6f6..fc48d2aef 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java @@ -18,8 +18,8 @@ import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; -import org.json.old.JSONArray; -import org.json.old.JSONObject; +import org.json.JSONArray; +import org.json.JSONObject; import org.labkey.api.assay.AssayProtocolSchema; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayService; @@ -45,6 +45,7 @@ import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; import org.labkey.api.util.FileUtil; +import org.labkey.api.util.JsonUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.view.ViewContext; @@ -197,7 +198,7 @@ public Pair, List> cacheHaplotypes(final ViewContext ctx, Set analysisIds = new HashSet<>(); final Map> haploMap = new HashMap<>(); - for (JSONObject row : data.toJSONObjectArray()) + for (JSONObject row : JsonUtil.toJSONObjectList(data)) { Integer analysisId = row.getInt("analysisId"); analysisIds.add(analysisId); diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultGenotypeAssaysImportMethod.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultGenotypeAssaysImportMethod.java index 0612354da..dbc988df2 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultGenotypeAssaysImportMethod.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultGenotypeAssaysImportMethod.java @@ -1,7 +1,7 @@ package org.labkey.genotypeassays.assay; +import org.apache.commons.lang3.StringUtils; import org.labkey.api.data.Container; -import org.labkey.api.gwt.client.util.StringUtils; import org.labkey.api.laboratory.assay.AssayImportMethod; import org.labkey.api.laboratory.assay.AssayParser; import org.labkey.api.laboratory.assay.DefaultAssayImportMethod; @@ -27,12 +27,13 @@ public DefaultGenotypeAssaysImportMethod() super(GenotypeAssaysManager.GENOTYPE_ASSAY_PROVIDER); } + @Override public AssayParser getFileParser(Container c, User u, int assayId) { return new DefaultGenotypeAssayParser(this, c, u, assayId); } - public class DefaultGenotypeAssayParser extends DefaultAssayParser + public static class DefaultGenotypeAssayParser extends DefaultAssayParser { public DefaultGenotypeAssayParser(AssayImportMethod method, Container c, User u, int assayId) { diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultSnpAssayImportMethod.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultSnpAssayImportMethod.java index 98300e17d..13a384717 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultSnpAssayImportMethod.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultSnpAssayImportMethod.java @@ -1,6 +1,6 @@ package org.labkey.genotypeassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.laboratory.assay.DefaultAssayImportMethod; import org.labkey.api.view.ViewContext; diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/GenotypeAssayDataProvider.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/GenotypeAssayDataProvider.java index 5e9c7ebe1..55b292abd 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/GenotypeAssayDataProvider.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/GenotypeAssayDataProvider.java @@ -1,6 +1,6 @@ package org.labkey.genotypeassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.laboratory.NavItem; diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SNPAssayDataProvider.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SNPAssayDataProvider.java index f260d83ab..f525967c5 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SNPAssayDataProvider.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SNPAssayDataProvider.java @@ -1,6 +1,6 @@ package org.labkey.genotypeassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.laboratory.assay.AbstractAssayDataProvider; import org.labkey.api.module.Module; import org.labkey.api.view.ViewContext; diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDataProvider.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDataProvider.java index c66b28373..db0647d7b 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDataProvider.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDataProvider.java @@ -1,6 +1,6 @@ package org.labkey.genotypeassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.laboratory.assay.AbstractAssayDataProvider; import org.labkey.api.laboratory.assay.AssayImportMethod; import org.labkey.api.module.Module; diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java index f188ef380..9eb857fc3 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java @@ -1,6 +1,6 @@ package org.labkey.genotypeassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpProtocol; diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPPivotingImportMethod.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPPivotingImportMethod.java index 9a5be9e11..86f349db6 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPPivotingImportMethod.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPPivotingImportMethod.java @@ -1,6 +1,6 @@ package org.labkey.genotypeassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpProtocol; @@ -51,6 +51,7 @@ public JSONObject getMetadata(ViewContext ctx, ExpProtocol protocol) return _importMethod.getMetadata(ctx, protocol); } + @Override public String getTooltip() { return "Choose this option to upload data using a template with many allele typings per row"; diff --git a/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingDataProvider.java b/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingDataProvider.java index cd19f62b1..385d66541 100644 --- a/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingDataProvider.java +++ b/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingDataProvider.java @@ -1,6 +1,6 @@ package org.labkey.labpurchasing; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.laboratory.AbstractDataProvider; import org.labkey.api.laboratory.DetailsUrlWithoutLabelNavItem; diff --git a/covidseq/src/org/labkey/covidseq/CovidseqDataProvider.java b/covidseq/src/org/labkey/covidseq/CovidseqDataProvider.java index d6d86c6e3..90cf16863 100644 --- a/covidseq/src/org/labkey/covidseq/CovidseqDataProvider.java +++ b/covidseq/src/org/labkey/covidseq/CovidseqDataProvider.java @@ -1,6 +1,6 @@ package org.labkey.covidseq; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.TableInfo; import org.labkey.api.laboratory.AbstractDataProvider; diff --git a/elispot_assay/src/org/labkey/elispot_assay/ELISPOT_AssayDataProvider.java b/elispot_assay/src/org/labkey/elispot_assay/ELISPOT_AssayDataProvider.java index e9ffdc2f2..b51c387f7 100644 --- a/elispot_assay/src/org/labkey/elispot_assay/ELISPOT_AssayDataProvider.java +++ b/elispot_assay/src/org/labkey/elispot_assay/ELISPOT_AssayDataProvider.java @@ -15,7 +15,7 @@ */ package org.labkey.elispot_assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.laboratory.NavItem; diff --git a/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java b/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java index acfda9f93..4c129102e 100644 --- a/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java +++ b/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java @@ -2,7 +2,7 @@ import au.com.bytecode.opencsv.CSVWriter; import org.apache.commons.lang3.StringUtils; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpExperiment; @@ -74,6 +74,7 @@ public String getTemplateInstructions() return super.getTemplateInstructions() + "

This import path assumes you prepared this run by creating/saving a template from this site, which defines your plate layout and sample information. The results you enter below will be merged with that previously imported sample information using well. When you select a saved plate template using the \'Saved Sample Information\' section above, you should see a list of the samples you uploaded."; } + @Override public AssayParser getFileParser(Container c, User u, int assayId) { return new Parser(this, c, u, assayId); diff --git a/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java b/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java index bb426b9a7..174cab048 100644 --- a/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java +++ b/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java @@ -7,8 +7,8 @@ import org.apache.commons.math3.stat.inference.TestUtils; import org.apache.logging.log4j.Level; import org.jetbrains.annotations.Nullable; -import org.json.old.JSONArray; -import org.json.old.JSONObject; +import org.json.JSONArray; +import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; import org.labkey.api.data.ConvertHelper; @@ -21,6 +21,7 @@ import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; +import org.labkey.api.util.JsonUtil; import org.labkey.api.view.ViewContext; import java.text.DecimalFormat; @@ -169,14 +170,14 @@ protected List> calculatePositivity(List } } - Integer minspots = runProperties.containsKey(MIN_SPOTS_FIELD) ? Integer.valueOf(runProperties.getInt(MIN_SPOTS_FIELD)) : null; + Integer minspots = runProperties.has(MIN_SPOTS_FIELD) ? Integer.valueOf(runProperties.getInt(MIN_SPOTS_FIELD)) : null; if (minspots == null) { minspots = 0; runProperties.put(MIN_SPOTS_FIELD, minspots); } - Double threshold = runProperties.containsKey(THRESHOLD_FIELD) ? runProperties.getDouble(THRESHOLD_FIELD) : null; + Double threshold = runProperties.has(THRESHOLD_FIELD) ? runProperties.getDouble(THRESHOLD_FIELD) : null; if (threshold == null) { threshold = 0.05; @@ -295,7 +296,7 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd"); Map negCtlCounts = new HashMap(); - for (JSONObject row : rawResults.toJSONObjectArray()) + for (JSONObject row : JsonUtil.toJSONObjectList(rawResults)) { for (String prop : resultDefaults.keySet()) { diff --git a/flowassays/src/org/labkey/flowassays/FlowAssaysDataProvider.java b/flowassays/src/org/labkey/flowassays/FlowAssaysDataProvider.java index e44e6e3d4..246bb7c56 100644 --- a/flowassays/src/org/labkey/flowassays/FlowAssaysDataProvider.java +++ b/flowassays/src/org/labkey/flowassays/FlowAssaysDataProvider.java @@ -15,7 +15,7 @@ */ package org.labkey.flowassays; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.laboratory.AbstractDataProvider; diff --git a/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java b/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java index 2b85b6f69..41d236114 100644 --- a/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java +++ b/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java @@ -1,6 +1,6 @@ package org.labkey.flowassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpProtocol; diff --git a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java index 240aa58ad..7e146f1ab 100644 --- a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java +++ b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java @@ -1,10 +1,10 @@ package org.labkey.flowassays.assay; -import org.json.old.JSONObject; +import org.apache.commons.lang3.StringUtils; +import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.TableInfo; import org.labkey.api.data.TableSelector; -import org.labkey.api.gwt.client.util.StringUtils; import org.labkey.api.laboratory.assay.ImportContext; import org.labkey.flowassays.FlowAssaysSchema; @@ -159,6 +159,6 @@ public static JSONObject applyDefaultMetadata(JSONObject meta) private static JSONObject getJsonObject(JSONObject parent, String key) { - return parent.containsKey(key) ? parent.getJSONObject(key): new JSONObject(); + return parent.has(key) ? parent.getJSONObject(key): new JSONObject(); } } diff --git a/flowassays/src/org/labkey/flowassays/assay/FlowPivotingImportMethod.java b/flowassays/src/org/labkey/flowassays/assay/FlowPivotingImportMethod.java index 59810c4e4..3141dc1e7 100644 --- a/flowassays/src/org/labkey/flowassays/assay/FlowPivotingImportMethod.java +++ b/flowassays/src/org/labkey/flowassays/assay/FlowPivotingImportMethod.java @@ -1,6 +1,6 @@ package org.labkey.flowassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.laboratory.assay.AssayImportMethod; diff --git a/flowassays/src/org/labkey/flowassays/assay/ICSDataProvider.java b/flowassays/src/org/labkey/flowassays/assay/ICSDataProvider.java index 6805d04cf..94bb15eb9 100644 --- a/flowassays/src/org/labkey/flowassays/assay/ICSDataProvider.java +++ b/flowassays/src/org/labkey/flowassays/assay/ICSDataProvider.java @@ -1,6 +1,6 @@ package org.labkey.flowassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.laboratory.assay.AbstractAssayDataProvider; import org.labkey.api.laboratory.assay.AssayImportMethod; import org.labkey.api.module.Module; diff --git a/flowassays/src/org/labkey/flowassays/assay/ImmunophenotypingDataProvider.java b/flowassays/src/org/labkey/flowassays/assay/ImmunophenotypingDataProvider.java index 707453125..4288e65f9 100644 --- a/flowassays/src/org/labkey/flowassays/assay/ImmunophenotypingDataProvider.java +++ b/flowassays/src/org/labkey/flowassays/assay/ImmunophenotypingDataProvider.java @@ -1,6 +1,6 @@ package org.labkey.flowassays.assay; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.laboratory.assay.AbstractAssayDataProvider; import org.labkey.api.laboratory.assay.AssayImportMethod; import org.labkey.api.module.Module; diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index 90091442e..3dafcc084 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -1,6 +1,6 @@ package org.labkey.mgap.columnTransforms; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DbSchema; diff --git a/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java b/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java index 84c326165..d28fcb37d 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java +++ b/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java @@ -5,7 +5,7 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.Nullable; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.CompareType; import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbSchemaType; diff --git a/mGAP/src/org/labkey/mgap/pipeline/SampleSpecificGenotypeFiltrationStep.java b/mGAP/src/org/labkey/mgap/pipeline/SampleSpecificGenotypeFiltrationStep.java index f2e202d3d..6510a5204 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/SampleSpecificGenotypeFiltrationStep.java +++ b/mGAP/src/org/labkey/mgap/pipeline/SampleSpecificGenotypeFiltrationStep.java @@ -4,7 +4,7 @@ import htsjdk.variant.vcf.VCFFileReader; import htsjdk.variant.vcf.VCFHeader; import org.apache.logging.log4j.Logger; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; diff --git a/mGAP/src/org/labkey/mgap/pipeline/VcfComparisonStep.java b/mGAP/src/org/labkey/mgap/pipeline/VcfComparisonStep.java index c1f1f04c2..15419979f 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/VcfComparisonStep.java +++ b/mGAP/src/org/labkey/mgap/pipeline/VcfComparisonStep.java @@ -2,7 +2,7 @@ import htsjdk.samtools.util.Interval; import org.apache.logging.log4j.Logger; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider; diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseAnnotateNovelSitesStep.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseAnnotateNovelSitesStep.java index d77d3c95e..1e245b47f 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseAnnotateNovelSitesStep.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseAnnotateNovelSitesStep.java @@ -2,7 +2,7 @@ import htsjdk.samtools.util.Interval; import org.apache.logging.log4j.Logger; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.TableSelector; import org.labkey.api.pipeline.PipelineJob; diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseComparisonStep.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseComparisonStep.java index 88642fffe..e81600598 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseComparisonStep.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseComparisonStep.java @@ -1,7 +1,7 @@ package org.labkey.mgap.pipeline; import htsjdk.samtools.util.Interval; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index 326fb663f..09ae8a943 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -16,7 +16,8 @@ import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; -import org.json.old.JSONObject; +import org.json.JSONArray; +import org.json.JSONObject; import org.junit.Assert; import org.junit.Test; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -57,6 +58,7 @@ import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.util.GUID; +import org.labkey.api.util.JsonUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.writer.PrintWriters; import org.labkey.mgap.mGAPManager; @@ -686,12 +688,12 @@ private String getOmimJson(String input, String apiKey, Logger log, String orig) } JSONObject json = new JSONObject(response.toString()); - if (json.containsKey("omim")) + if (json.has("omim")) { json = json.getJSONObject("omim"); - if (json.containsKey("entryList")) + if (json.has("entryList")) { - for (JSONObject j : json.getJSONArray("entryList").toJSONObjectArray()) + for (JSONObject j : JsonUtil.toJSONObjectList(json.getJSONArray("entryList"))) { String val = j.getJSONObject("entry").getJSONObject("titles").optString("preferredTitle", input); if (val.contains(";")) diff --git a/primeseq/src/org/labkey/primeseq/PrimeseqController.java b/primeseq/src/org/labkey/primeseq/PrimeseqController.java index 2914f8441..2e322d6fe 100644 --- a/primeseq/src/org/labkey/primeseq/PrimeseqController.java +++ b/primeseq/src/org/labkey/primeseq/PrimeseqController.java @@ -20,7 +20,7 @@ import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.ConfirmAction; @@ -469,7 +469,7 @@ else if (!sf.lookupContainer().hasPermission(getUser(), ReadPermission.class)) { String name = jsonObj.getString("name"); String jsonName = "resourceSettings.resourceSettings." + name; - if (jobParams.containsKey(jsonName) && jobParams.get(jsonName) != null) + if (jobParams.has(jsonName) && jobParams.get(jsonName) != null) { if (!valueMap.containsKey(name)) { diff --git a/primeseq/src/org/labkey/primeseq/analysis/CombineMethylationRatesHandler.java b/primeseq/src/org/labkey/primeseq/analysis/CombineMethylationRatesHandler.java index a1cc77aec..f8c732ddb 100644 --- a/primeseq/src/org/labkey/primeseq/analysis/CombineMethylationRatesHandler.java +++ b/primeseq/src/org/labkey/primeseq/analysis/CombineMethylationRatesHandler.java @@ -2,7 +2,7 @@ import htsjdk.samtools.util.Interval; import org.apache.commons.lang3.StringUtils; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobException; diff --git a/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparison.java b/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparison.java index 9ba217d78..5ad679d29 100644 --- a/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparison.java +++ b/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparison.java @@ -1,7 +1,7 @@ package org.labkey.primeseq.analysis; import org.apache.commons.lang3.StringUtils; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleLoader; @@ -136,7 +136,7 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport throw new PipelineJobException("No parameters provided"); } - if (params.containsKey("stds")) + if (params.has("stds")) { String ampliconBorders = params.getString("ampliconBorders"); if (StringUtils.isEmpty(ampliconBorders)) diff --git a/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java b/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java index 8609ef4bb..f3d149977 100644 --- a/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java +++ b/primeseq/src/org/labkey/primeseq/analysis/MethylationRateComparisonHandler.java @@ -13,8 +13,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; -import org.json.old.JSONArray; -import org.json.old.JSONObject; +import org.json.JSONArray; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.jbrowse.JBrowseService; import org.labkey.api.module.Module; diff --git a/primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java b/primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java index 820d748d1..c83607b0f 100644 --- a/primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java +++ b/primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java @@ -5,7 +5,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.ConvertHelper; import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbSchemaType; diff --git a/primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java b/primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java index 5d6fef6a7..438512477 100644 --- a/primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java +++ b/primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java @@ -1,6 +1,6 @@ package org.labkey.primeseq.pipeline; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.module.ModuleLoader; import org.labkey.api.sequenceanalysis.pipeline.JobResourceSettings; diff --git a/primeseq/src/org/labkey/primeseq/pipeline/GeographicOriginStep.java b/primeseq/src/org/labkey/primeseq/pipeline/GeographicOriginStep.java index 9ec2d0a61..e53c9d905 100644 --- a/primeseq/src/org/labkey/primeseq/pipeline/GeographicOriginStep.java +++ b/primeseq/src/org/labkey/primeseq/pipeline/GeographicOriginStep.java @@ -2,7 +2,7 @@ import htsjdk.samtools.util.Interval; import org.apache.logging.log4j.Logger; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep; import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider; diff --git a/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java b/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java index 099546d0c..d86a3d977 100644 --- a/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java +++ b/primeseq/src/org/labkey/primeseq/pipeline/MhcMigrationPipelineJob.java @@ -1,7 +1,7 @@ package org.labkey.primeseq.pipeline; import org.apache.commons.io.FileUtils; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayService; import org.labkey.api.collections.CaseInsensitiveHashMap; diff --git a/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java b/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java index be53cf762..2e498022f 100644 --- a/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java +++ b/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java @@ -3,7 +3,6 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.NotNull; -import org.json.old.JSONObject; import org.labkey.api.cluster.ClusterResourceAllocator; import org.labkey.api.data.ConvertHelper; import org.labkey.api.pipeline.PipelineJob; diff --git a/tcrdb/src/org/labkey/tcrdb/TCRdbProvider.java b/tcrdb/src/org/labkey/tcrdb/TCRdbProvider.java index 62b9c9964..0359e45a7 100644 --- a/tcrdb/src/org/labkey/tcrdb/TCRdbProvider.java +++ b/tcrdb/src/org/labkey/tcrdb/TCRdbProvider.java @@ -1,6 +1,6 @@ package org.labkey.tcrdb; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.laboratory.LaboratoryService; diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJCellHashingHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJCellHashingHandler.java index d4a798c2b..5faba6b7f 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJCellHashingHandler.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJCellHashingHandler.java @@ -3,7 +3,7 @@ import au.com.bytecode.opencsv.CSVReader; import au.com.bytecode.opencsv.CSVWriter; import org.apache.commons.lang3.StringUtils; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.ConvertHelper; import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipelineJob; diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java index fb24af03c..431fdd624 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java @@ -4,7 +4,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.assay.AssayProtocolSchema; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayService; diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/MiXCRAnalysis.java b/tcrdb/src/org/labkey/tcrdb/pipeline/MiXCRAnalysis.java index 75abc6d8c..e9d3c0f1d 100644 --- a/tcrdb/src/org/labkey/tcrdb/pipeline/MiXCRAnalysis.java +++ b/tcrdb/src/org/labkey/tcrdb/pipeline/MiXCRAnalysis.java @@ -7,8 +7,8 @@ import htsjdk.samtools.fastq.FastqWriterFactory; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.DateUtils; -import org.json.old.JSONArray; -import org.json.old.JSONObject; +import org.json.JSONArray; +import org.json.JSONObject; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayService; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -47,6 +47,7 @@ import org.labkey.api.sequenceanalysis.run.PicardWrapper; import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper; import org.labkey.api.util.FileUtil; +import org.labkey.api.util.JsonUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.util.Path; @@ -295,7 +296,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc Map>> totalReadsInExportedAlignments = new HashMap<>(); Map>> totalReadsInExportedClones = new HashMap<>(); - for (JSONObject library : libraries.toJSONObjectArray()) + for (JSONObject library : JsonUtil.toJSONObjectList(libraries)) { String species = library.getString("species"); Integer rowid = library.optInt("rowid"); @@ -782,7 +783,7 @@ public Output performAnalysisPerSampleLocal(AnalysisModel model, File inputBam, { getPipelineCtx().getLogger().warn("no clones exported: " + table.getPath()); JSONArray libraries = getTcrDbs(); - for (JSONObject library : libraries.toJSONObjectArray()) + for (JSONObject library : JsonUtil.toJSONObjectList(libraries)) { String species = library.getString("species"); Integer rowid = library.optInt("rowid"); diff --git a/variantdb/src/org/labkey/variantdb/VariantDBDataProvider.java b/variantdb/src/org/labkey/variantdb/VariantDBDataProvider.java index 2ca106695..086ef54c4 100644 --- a/variantdb/src/org/labkey/variantdb/VariantDBDataProvider.java +++ b/variantdb/src/org/labkey/variantdb/VariantDBDataProvider.java @@ -1,7 +1,7 @@ package org.labkey.variantdb; import org.jetbrains.annotations.NotNull; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.laboratory.DetailsUrlWithoutLabelNavItem; diff --git a/variantdb/src/org/labkey/variantdb/analysis/GBSAnalysisHandler.java b/variantdb/src/org/labkey/variantdb/analysis/GBSAnalysisHandler.java index 00f8c0a80..c630356ee 100644 --- a/variantdb/src/org/labkey/variantdb/analysis/GBSAnalysisHandler.java +++ b/variantdb/src/org/labkey/variantdb/analysis/GBSAnalysisHandler.java @@ -3,7 +3,7 @@ import org.apache.commons.codec.binary.Base64; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.module.Module; @@ -84,7 +84,7 @@ public void init(JobContext ctx, List inputFiles, List inputFiles, JobContext c arguments.add(g.getWorkingFastaFile().getPath()); } - if (ctx.getParams().containsKey("vcfFile") && !StringUtils.isEmpty(ctx.getParams().getString("vcfFile"))) + if (ctx.getParams().has("vcfFile") && !StringUtils.isEmpty(ctx.getParams().getString("vcfFile"))) { arguments.add("-v"); File f = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("vcfFile")); @@ -153,7 +153,7 @@ public void processFilesRemote(List inputFiles, JobContext c arguments.add(f.getPath()); } - if (ctx.getParams().containsKey("maskFile") && !StringUtils.isEmpty(ctx.getParams().getString("maskFile"))) + if (ctx.getParams().has("maskFile") && !StringUtils.isEmpty(ctx.getParams().getString("maskFile"))) { arguments.add("-m"); File f = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("maskFile")); @@ -164,7 +164,7 @@ public void processFilesRemote(List inputFiles, JobContext c arguments.add(f.getPath()); } - if (ctx.getParams().containsKey("cutSitesFile") && !StringUtils.isEmpty(ctx.getParams().getString("cutSitesFile"))) + if (ctx.getParams().has("cutSitesFile") && !StringUtils.isEmpty(ctx.getParams().getString("cutSitesFile"))) { arguments.add("-c"); File f = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("cutSitesFile")); diff --git a/variantdb/src/org/labkey/variantdb/analysis/ImputationAnalysis.java b/variantdb/src/org/labkey/variantdb/analysis/ImputationAnalysis.java index 5850d9a05..c85319226 100644 --- a/variantdb/src/org/labkey/variantdb/analysis/ImputationAnalysis.java +++ b/variantdb/src/org/labkey/variantdb/analysis/ImputationAnalysis.java @@ -14,8 +14,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.math3.stat.StatUtils; import org.apache.logging.log4j.Logger; -import org.json.old.JSONArray; -import org.json.old.JSONObject; +import org.json.JSONArray; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.ConvertHelper; import org.labkey.api.data.SimpleFilter; @@ -762,9 +762,9 @@ private List getSampleSets(JSONObject params) { List ret = new ArrayList<>(); - if (params.containsKey("sampleSets")) + if (params.has("sampleSets")) { - for (Object o : params.getJSONArray("sampleSets").toArray()) + for (Object o : params.getJSONArray("sampleSets").toList()) { ret.add(new SampleSet((JSONArray) o)); } @@ -1242,9 +1242,9 @@ private static List generatePedigree(PipelineJob job, JSONObject Map subjectToReadsetNameMap = new HashMap<>(); TableInfo subjectTable = QueryService.get().getUserSchema(job.getUser(), (job.getContainer().isWorkbook() ? job.getContainer().getParent() : job.getContainer()), "laboratory").getTable("subjects"); TableInfo readsetTable = QueryService.get().getUserSchema(job.getUser(), job.getContainer(), "sequenceanalysis").getTable("sequence_readsets"); - if (params.containsKey("sampleSets")) + if (params.has("sampleSets")) { - for (Object o : params.getJSONArray("sampleSets").toArray()) + for (Object o : params.getJSONArray("sampleSets").toList()) { JSONArray arr = (JSONArray) o; for (int i = 0; i < arr.length(); i++) diff --git a/variantdb/src/org/labkey/variantdb/analysis/MendelianAnalysisHandler.java b/variantdb/src/org/labkey/variantdb/analysis/MendelianAnalysisHandler.java index dc34bb6b6..12b3d59f2 100644 --- a/variantdb/src/org/labkey/variantdb/analysis/MendelianAnalysisHandler.java +++ b/variantdb/src/org/labkey/variantdb/analysis/MendelianAnalysisHandler.java @@ -3,7 +3,7 @@ import org.apache.commons.codec.binary.Base64; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.json.old.JSONObject; +import org.json.JSONObject; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.module.Module; @@ -81,7 +81,7 @@ public void init(JobContext ctx, List inputFiles, List inputFiles, JobContext c arguments.add(g.getWorkingFastaFile().getPath()); } - if (ctx.getParams().containsKey("vcfFile") && !StringUtils.isEmpty(ctx.getParams().getString("vcfFile"))) + if (ctx.getParams().has("vcfFile") && !StringUtils.isEmpty(ctx.getParams().getString("vcfFile"))) { arguments.add("-v"); File f = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("vcfFile")); @@ -151,7 +151,7 @@ public void processFilesRemote(List inputFiles, JobContext c arguments.add(f.getPath()); } - if (ctx.getParams().containsKey("maskFile") && !StringUtils.isEmpty(ctx.getParams().getString("maskFile"))) + if (ctx.getParams().has("maskFile") && !StringUtils.isEmpty(ctx.getParams().getString("maskFile"))) { arguments.add("-m"); File f = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("maskFile")); @@ -162,7 +162,7 @@ public void processFilesRemote(List inputFiles, JobContext c arguments.add(f.getPath()); } - if (ctx.getParams().containsKey("cutSitesFile") && !StringUtils.isEmpty(ctx.getParams().getString("cutSitesFile"))) + if (ctx.getParams().has("cutSitesFile") && !StringUtils.isEmpty(ctx.getParams().getString("cutSitesFile"))) { arguments.add("-c"); File f = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("cutSitesFile")); diff --git a/variantdb/src/org/labkey/variantdb/run/MendelianEvaluator.java b/variantdb/src/org/labkey/variantdb/run/MendelianEvaluator.java index 81bf3eae6..b64119009 100644 --- a/variantdb/src/org/labkey/variantdb/run/MendelianEvaluator.java +++ b/variantdb/src/org/labkey/variantdb/run/MendelianEvaluator.java @@ -12,8 +12,8 @@ import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; -import org.labkey.api.gwt.client.util.StringUtils; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.reader.Readers; import org.labkey.api.util.Pair; From 7277eaecc9c8c649850d7d56cf6ef38b79c94f3a Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 10 Feb 2023 12:32:05 -0800 Subject: [PATCH 2/7] Add dependency --- primeseq/build.gradle | 1 + 1 file changed, 1 insertion(+) diff --git a/primeseq/build.gradle b/primeseq/build.gradle index 3c5635ae8..7eba545e3 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -20,6 +20,7 @@ dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" implementation "net.sf.opencsv:opencsv:${opencsvVersion}" BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile") + BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "runtimeElements") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:cluster", depProjectConfig: "apiJarFile") From 49bf092886714dfd8e51cbcdedd3bcb163167b58 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 12 Feb 2023 08:22:37 -0800 Subject: [PATCH 3/7] Another bugfix related to JSONObject migration --- .../genotypeassays/assay/SSPAssayDefaultImportMethod.java | 2 +- .../src/org/labkey/genotypeassays/assay/SSPImportHelper.java | 2 +- .../org/labkey/flowassays/assay/DefaultFlowImportMethod.java | 2 +- .../src/org/labkey/flowassays/assay/FlowImportHelper.java | 4 ++-- variantdb/src/org/labkey/variantdb/VariantDBManager.java | 2 +- .../src/org/labkey/variantdb/pipeline/DbSnpImportTask.java | 4 ++-- .../src/org/labkey/variantdb/pipeline/VariantImportTask.java | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java index 9eb857fc3..e3e2576ec 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java @@ -72,7 +72,7 @@ protected List> processRowsFromFile(List while (rowsIter.hasNext()) { - Map row = new CaseInsensitiveHashMap(rowsIter.next()); + Map row = new CaseInsensitiveHashMap<>(rowsIter.next()); appendPromotedResultFields(row, context); helper.normalizeResultField(row, context); diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPImportHelper.java b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPImportHelper.java index a0528f5bc..44e12a731 100644 --- a/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPImportHelper.java +++ b/GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPImportHelper.java @@ -84,7 +84,7 @@ private Map getResultValues() TableSelector ts = new TableSelector(ti); Map[] rows = ts.getMapArray(); - Map ret = new CaseInsensitiveHashMap(); + Map ret = new CaseInsensitiveHashMap<>(); for (Map row : rows) { ret.put((String)row.get("result"), (String)row.get("result")); diff --git a/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java b/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java index 41d236114..ac543fde1 100644 --- a/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java +++ b/flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java @@ -64,7 +64,7 @@ protected List> processRowsFromFile(List while (rowsIter.hasNext()) { - Map row = new CaseInsensitiveHashMap(rowsIter.next()); + Map row = new CaseInsensitiveHashMap<>(rowsIter.next()); appendPromotedResultFields(row, context); helper.normalizePopulationField(row, "population", context); diff --git a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java index 7e146f1ab..bd542569c 100644 --- a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java +++ b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java @@ -79,7 +79,7 @@ public String guessPopulation(String population) public Map getGuessedValues(Map allowable) { - Map guesses = new CaseInsensitiveHashMap(); + Map guesses = new CaseInsensitiveHashMap<>(); for (String key : allowable.keySet()) { String guess = key.replaceAll(" ", ""); @@ -103,7 +103,7 @@ private Map getResultValues() TableInfo ti = FlowAssaysSchema.getInstance().getTable(FlowAssaysSchema.TABLE_POPULATIONS); TableSelector ts = new TableSelector(ti); Map[] rows = ts.getMapArray(); - Map ret = new CaseInsensitiveHashMap(); + Map ret = new CaseInsensitiveHashMap<>(); for (Map row : rows) { ret.put((String)row.get(NAME_FIELD), (String)row.get(NAME_FIELD)); diff --git a/variantdb/src/org/labkey/variantdb/VariantDBManager.java b/variantdb/src/org/labkey/variantdb/VariantDBManager.java index 8a5445e20..3d162f13b 100644 --- a/variantdb/src/org/labkey/variantdb/VariantDBManager.java +++ b/variantdb/src/org/labkey/variantdb/VariantDBManager.java @@ -139,7 +139,7 @@ public void exec(ResultSet rs) throws SQLException ) { log.info("querying/updating variants"); - CaseInsensitiveHashMap batchRow = new CaseInsensitiveHashMap(); + CaseInsensitiveHashMap batchRow = new CaseInsensitiveHashMap<>(); final String batchId = new GUID().toString(); batchRow.put("batchId", batchId); batchRow.put("description", "Liftover of local variants"); diff --git a/variantdb/src/org/labkey/variantdb/pipeline/DbSnpImportTask.java b/variantdb/src/org/labkey/variantdb/pipeline/DbSnpImportTask.java index 760d4927a..1499f0dff 100644 --- a/variantdb/src/org/labkey/variantdb/pipeline/DbSnpImportTask.java +++ b/variantdb/src/org/labkey/variantdb/pipeline/DbSnpImportTask.java @@ -192,11 +192,11 @@ private void processVariantsFromFile(String batchId, File localFile) throws Pipe new BaseColumnInfo("status", JdbcType.VARCHAR) )); - try (FeatureReader reader = AbstractFeatureReader.getFeatureReader(localFile.getAbsolutePath(), new VCFCodec(), false)) + try (FeatureReader reader = AbstractFeatureReader.getFeatureReader(localFile.getAbsolutePath(), new VCFCodec(), false)) { VCFHeader header = (VCFHeader)reader.getHeader(); - CaseInsensitiveHashMap batchRow = new CaseInsensitiveHashMap(); + CaseInsensitiveHashMap batchRow = new CaseInsensitiveHashMap<>(); batchRow.put("batchId", batchId); batchRow.put("description", "Automatic import of data from the NCBI/dbSNP FTP site"); batchRow.put("source", "dbSNP"); diff --git a/variantdb/src/org/labkey/variantdb/pipeline/VariantImportTask.java b/variantdb/src/org/labkey/variantdb/pipeline/VariantImportTask.java index f2978975b..bdd9089ce 100644 --- a/variantdb/src/org/labkey/variantdb/pipeline/VariantImportTask.java +++ b/variantdb/src/org/labkey/variantdb/pipeline/VariantImportTask.java @@ -142,7 +142,7 @@ private String createBatch() { String batchId = new GUID().toString(); - CaseInsensitiveHashMap batchRow = new CaseInsensitiveHashMap(); + CaseInsensitiveHashMap batchRow = new CaseInsensitiveHashMap<>(); batchRow.put("batchId", batchId); batchRow.put("description", "Import of data from local VCF files"); batchRow.put("source", "Local VCF"); From c52f478f4d3e12f49b2e379cbb8727a1956d9773 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 12 Feb 2023 08:55:20 -0800 Subject: [PATCH 4/7] Bugfix related to JSON migration --- .../src/org/labkey/flowassays/assay/FlowImportHelper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java index bd542569c..7dc68f1eb 100644 --- a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java +++ b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java @@ -28,7 +28,7 @@ public FlowImportHelper() public void normalizePopulationField(Map row, String populationField, ImportContext context) { - if (!row.containsKey(populationField)) + if (!row.containsKey(populationField) || row.get(populationField) == null) return; String population = StringUtils.trimToNull((String) row.get(populationField)); From 58938e8cdf68fc284345d6fbbc3668a2314af4de Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 12 Feb 2023 10:14:12 -0800 Subject: [PATCH 5/7] Fix string cast --- .../src/org/labkey/flowassays/assay/FlowImportHelper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java index 7dc68f1eb..3fbf89071 100644 --- a/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java +++ b/flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java @@ -31,7 +31,7 @@ public void normalizePopulationField(Map row, String populationF if (!row.containsKey(populationField) || row.get(populationField) == null) return; - String population = StringUtils.trimToNull((String) row.get(populationField)); + String population = row.get(populationField) == null ? null : StringUtils.trimToNull(row.get(populationField).toString()); if (population == null) return; From 33afea03787b86e5113fbc7f67a0250231168403 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 12 Feb 2023 10:26:40 -0800 Subject: [PATCH 6/7] Convert JSONObject to Map to avoid null vs. JSONObject$Null issues --- .../elispot_assay/assay/DefaultImportMethod.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java b/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java index 174cab048..7b3b552c8 100644 --- a/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java +++ b/elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java @@ -107,12 +107,12 @@ protected List> calculatePositivity(List { String delim = "/"; - JSONObject runProperties = context.getRunProperties(); - List> newRows = new ArrayList>(); - Map> negWellMap = new CaseInsensitiveHashMap>(); - Map sampleKeyToNegCtlKey = new HashMap(); + Map runProperties = context.getRunProperties(); + List> newRows = new ArrayList<>(); + Map> negWellMap = new CaseInsensitiveHashMap<>(); + Map sampleKeyToNegCtlKey = new HashMap<>(); - Map>> map = new CaseInsensitiveHashMap>>(); + Map>> map = new CaseInsensitiveHashMap<>(); for (Map row : rows) { //build a map of rows, grouped by id/date/peptide @@ -124,7 +124,7 @@ protected List> calculatePositivity(List List> foundRows = map.get(key); if (foundRows == null) - foundRows = new ArrayList>(); + foundRows = new ArrayList<>(); foundRows.add(row); map.put(key, foundRows); @@ -170,14 +170,14 @@ protected List> calculatePositivity(List } } - Integer minspots = runProperties.has(MIN_SPOTS_FIELD) ? Integer.valueOf(runProperties.getInt(MIN_SPOTS_FIELD)) : null; + Integer minspots = runProperties.get(MIN_SPOTS_FIELD) != null ? Integer.valueOf(runProperties.get(MIN_SPOTS_FIELD).toString()) : null; if (minspots == null) { minspots = 0; runProperties.put(MIN_SPOTS_FIELD, minspots); } - Double threshold = runProperties.has(THRESHOLD_FIELD) ? runProperties.getDouble(THRESHOLD_FIELD) : null; + Double threshold = runProperties.get(THRESHOLD_FIELD) != null ? Double.parseDouble(runProperties.get(THRESHOLD_FIELD).toString()) : null; if (threshold == null) { threshold = 0.05; From 1a3586f67555687ce6610b193017cbce9d6a67c7 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 13 Feb 2023 10:52:24 -0800 Subject: [PATCH 7/7] Remove warnings --- .../resources/assay/GenotypeAssay/queries/Batches.query.xml | 2 +- .../resources/assay/GenotypeAssay/queries/Runs.query.xml | 2 +- .../resources/assay/SnpAssay/queries/Batches.query.xml | 2 +- GenotypeAssays/resources/assay/SnpAssay/queries/Runs.query.xml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/GenotypeAssays/resources/assay/GenotypeAssay/queries/Batches.query.xml b/GenotypeAssays/resources/assay/GenotypeAssay/queries/Batches.query.xml index d3c2e0d7a..eb0f691b5 100644 --- a/GenotypeAssays/resources/assay/GenotypeAssay/queries/Batches.query.xml +++ b/GenotypeAssays/resources/assay/GenotypeAssay/queries/Batches.query.xml @@ -11,7 +11,7 @@ false - + false diff --git a/GenotypeAssays/resources/assay/GenotypeAssay/queries/Runs.query.xml b/GenotypeAssays/resources/assay/GenotypeAssay/queries/Runs.query.xml index e2efbcce5..bfd28b383 100644 --- a/GenotypeAssays/resources/assay/GenotypeAssay/queries/Runs.query.xml +++ b/GenotypeAssays/resources/assay/GenotypeAssay/queries/Runs.query.xml @@ -7,7 +7,7 @@ Run Name - + Run Description true diff --git a/GenotypeAssays/resources/assay/SnpAssay/queries/Batches.query.xml b/GenotypeAssays/resources/assay/SnpAssay/queries/Batches.query.xml index d3c2e0d7a..eb0f691b5 100644 --- a/GenotypeAssays/resources/assay/SnpAssay/queries/Batches.query.xml +++ b/GenotypeAssays/resources/assay/SnpAssay/queries/Batches.query.xml @@ -11,7 +11,7 @@ false - + false diff --git a/GenotypeAssays/resources/assay/SnpAssay/queries/Runs.query.xml b/GenotypeAssays/resources/assay/SnpAssay/queries/Runs.query.xml index e2efbcce5..bfd28b383 100644 --- a/GenotypeAssays/resources/assay/SnpAssay/queries/Runs.query.xml +++ b/GenotypeAssays/resources/assay/SnpAssay/queries/Runs.query.xml @@ -7,7 +7,7 @@ Run Name - + Run Description true