From 0017f1e606631f177d3462bab0f8a4df439b03c6 Mon Sep 17 00:00:00 2001 From: Lum Date: Tue, 17 Dec 2024 16:16:49 -0800 Subject: [PATCH] repackage/clean up transform script code introduce AnalysisScript class to handle different scripting operations --- elisa/src/org/labkey/elisa/ElisaAssayProvider.java | 2 +- elisa/src/org/labkey/elisa/ElisaDataHandler.java | 2 +- .../src/org/labkey/elispot/ElispotAssayProvider.java | 2 +- .../src/org/labkey/elispot/ElispotDataHandler.java | 2 +- flow/src/org/labkey/flow/data/FlowAssayProvider.java | 7 ++++--- luminex/src/org/labkey/luminex/LuminexAssayProvider.java | 2 +- luminex/src/org/labkey/luminex/LuminexDataHandler.java | 2 +- .../api/study/assay/matrix/AbstractMatrixRunCreator.java | 4 ++-- .../microarray/matrix/ExpressionMatrixRunCreator.java | 2 +- nab/src/org/labkey/nab/SinglePlateNabDataHandler.java | 2 +- .../nab/multiplate/HighThroughputNabDataHandler.java | 2 +- viability/src/org/labkey/viability/GuavaDataHandler.java | 2 +- .../src/org/labkey/viability/ViabilityAssayProvider.java | 2 +- 13 files changed, 17 insertions(+), 16 deletions(-) diff --git a/elisa/src/org/labkey/elisa/ElisaAssayProvider.java b/elisa/src/org/labkey/elisa/ElisaAssayProvider.java index ee12f19770..d62fc11d31 100644 --- a/elisa/src/org/labkey/elisa/ElisaAssayProvider.java +++ b/elisa/src/org/labkey/elisa/ElisaAssayProvider.java @@ -49,7 +49,7 @@ import org.labkey.api.gwt.client.DefaultValueType; import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipelineProvider; -import org.labkey.api.qc.DataExchangeHandler; +import org.labkey.api.assay.transform.DataExchangeHandler; import org.labkey.api.query.FieldKey; import org.labkey.api.query.FilteredTable; import org.labkey.api.security.User; diff --git a/elisa/src/org/labkey/elisa/ElisaDataHandler.java b/elisa/src/org/labkey/elisa/ElisaDataHandler.java index c681d833a9..63a2e2b716 100644 --- a/elisa/src/org/labkey/elisa/ElisaDataHandler.java +++ b/elisa/src/org/labkey/elisa/ElisaDataHandler.java @@ -50,7 +50,7 @@ import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.qc.DataLoaderSettings; -import org.labkey.api.qc.TransformDataHandler; +import org.labkey.api.assay.transform.TransformDataHandler; import org.labkey.api.query.FieldKey; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; diff --git a/elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java b/elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java index 8d06b470fe..e6c7e429b7 100644 --- a/elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java +++ b/elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java @@ -34,7 +34,7 @@ import org.labkey.api.exp.property.PropertyService; import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipelineProvider; -import org.labkey.api.qc.DataExchangeHandler; +import org.labkey.api.assay.transform.DataExchangeHandler; import org.labkey.api.query.FieldKey; import org.labkey.api.security.User; import org.labkey.api.assay.actions.AssayRunUploadForm; diff --git a/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java b/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java index 38af5914d0..ff934acc81 100644 --- a/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java +++ b/elispotassay/src/org/labkey/elispot/ElispotDataHandler.java @@ -39,7 +39,7 @@ import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.qc.DataLoaderSettings; -import org.labkey.api.qc.TransformDataHandler; +import org.labkey.api.assay.transform.TransformDataHandler; import org.labkey.api.assay.plate.Plate; import org.labkey.api.assay.plate.PlateService; import org.labkey.api.assay.plate.Position; diff --git a/flow/src/org/labkey/flow/data/FlowAssayProvider.java b/flow/src/org/labkey/flow/data/FlowAssayProvider.java index 988191f310..dac60c5d56 100644 --- a/flow/src/org/labkey/flow/data/FlowAssayProvider.java +++ b/flow/src/org/labkey/flow/data/FlowAssayProvider.java @@ -18,6 +18,7 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.transform.AnalysisScript; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerManager; @@ -36,7 +37,7 @@ import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipelineProvider; import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.qc.DataExchangeHandler; +import org.labkey.api.assay.transform.DataExchangeHandler; import org.labkey.api.query.FieldKey; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; @@ -474,14 +475,14 @@ public List getHeaderLinks(ViewContext viewContext, ExpProtocol protoco } @Override - public ValidationException setValidationAndAnalysisScripts(ExpProtocol protocol, @NotNull List scripts) + public ValidationException setValidationAndAnalysisScripts(ExpProtocol protocol, @NotNull List scripts) { throw new UnsupportedOperationException(); } @NotNull @Override - public List getValidationAndAnalysisScripts(ExpProtocol protocol, Scope scope) + public List getValidationAndAnalysisScripts(ExpProtocol protocol, Scope scope) { throw new UnsupportedOperationException(); } diff --git a/luminex/src/org/labkey/luminex/LuminexAssayProvider.java b/luminex/src/org/labkey/luminex/LuminexAssayProvider.java index d51f746b00..852ccbe865 100644 --- a/luminex/src/org/labkey/luminex/LuminexAssayProvider.java +++ b/luminex/src/org/labkey/luminex/LuminexAssayProvider.java @@ -41,7 +41,7 @@ import org.labkey.api.exp.property.PropertyService; import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipelineProvider; -import org.labkey.api.qc.DataExchangeHandler; +import org.labkey.api.assay.transform.DataExchangeHandler; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryParam; import org.labkey.api.query.ValidationException; diff --git a/luminex/src/org/labkey/luminex/LuminexDataHandler.java b/luminex/src/org/labkey/luminex/LuminexDataHandler.java index 8fab9c4b46..7dac5bcd57 100644 --- a/luminex/src/org/labkey/luminex/LuminexDataHandler.java +++ b/luminex/src/org/labkey/luminex/LuminexDataHandler.java @@ -60,7 +60,7 @@ import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.exp.query.ExpQCFlagTable; import org.labkey.api.qc.DataLoaderSettings; -import org.labkey.api.qc.TransformDataHandler; +import org.labkey.api.assay.transform.TransformDataHandler; import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.FieldKey; import org.labkey.api.security.User; diff --git a/microarray/src/org/labkey/api/study/assay/matrix/AbstractMatrixRunCreator.java b/microarray/src/org/labkey/api/study/assay/matrix/AbstractMatrixRunCreator.java index 6139e92fa5..382ff445c4 100644 --- a/microarray/src/org/labkey/api/study/assay/matrix/AbstractMatrixRunCreator.java +++ b/microarray/src/org/labkey/api/study/assay/matrix/AbstractMatrixRunCreator.java @@ -27,8 +27,8 @@ import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.property.DomainProperty; -import org.labkey.api.qc.DefaultTransformResult; -import org.labkey.api.qc.TransformResult; +import org.labkey.api.assay.transform.DefaultTransformResult; +import org.labkey.api.assay.transform.TransformResult; import org.labkey.api.query.ValidationException; import org.labkey.api.reader.ColumnDescriptor; import org.labkey.api.reader.TabLoader; diff --git a/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixRunCreator.java b/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixRunCreator.java index de1534bbdf..94718b24b6 100644 --- a/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixRunCreator.java +++ b/microarray/src/org/labkey/microarray/matrix/ExpressionMatrixRunCreator.java @@ -19,7 +19,7 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.qc.TransformResult; +import org.labkey.api.assay.transform.TransformResult; import org.labkey.api.query.ValidationException; import org.labkey.api.assay.AssayRunUploadContext; import org.labkey.api.study.assay.matrix.AbstractMatrixRunCreator; diff --git a/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java b/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java index 6ff1b9cc61..fe4e317e78 100644 --- a/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java +++ b/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java @@ -50,7 +50,7 @@ import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.qc.DataLoaderSettings; -import org.labkey.api.qc.TransformDataHandler; +import org.labkey.api.assay.transform.TransformDataHandler; import org.labkey.api.query.FieldKey; import org.labkey.api.query.FilteredTable; import org.labkey.api.reader.ColumnDescriptor; diff --git a/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java b/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java index e2e3983178..f7a35ce0c6 100644 --- a/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java +++ b/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java @@ -36,7 +36,7 @@ import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.qc.DataLoaderSettings; -import org.labkey.api.qc.TransformDataHandler; +import org.labkey.api.assay.transform.TransformDataHandler; import org.labkey.api.reader.ColumnDescriptor; import org.labkey.api.reader.DataLoader; import org.labkey.api.reader.ExcelLoader; diff --git a/viability/src/org/labkey/viability/GuavaDataHandler.java b/viability/src/org/labkey/viability/GuavaDataHandler.java index cbe7d37957..8ab4097f5d 100644 --- a/viability/src/org/labkey/viability/GuavaDataHandler.java +++ b/viability/src/org/labkey/viability/GuavaDataHandler.java @@ -35,7 +35,7 @@ import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.qc.DataLoaderSettings; -import org.labkey.api.qc.TransformDataHandler; +import org.labkey.api.assay.transform.TransformDataHandler; import org.labkey.api.reader.ColumnDescriptor; import org.labkey.api.reader.TabLoader; import org.labkey.api.util.FileType; diff --git a/viability/src/org/labkey/viability/ViabilityAssayProvider.java b/viability/src/org/labkey/viability/ViabilityAssayProvider.java index 220cbf50ea..8c1111daed 100644 --- a/viability/src/org/labkey/viability/ViabilityAssayProvider.java +++ b/viability/src/org/labkey/viability/ViabilityAssayProvider.java @@ -38,7 +38,7 @@ import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.exp.property.PropertyService; import org.labkey.api.module.ModuleLoader; -import org.labkey.api.qc.DataExchangeHandler; +import org.labkey.api.assay.transform.DataExchangeHandler; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryView; import org.labkey.api.security.User;