repackage/clean up transform script code (#828)

labkey-klum · web-flow · commit ba27d784c3cc · 2024-12-20T15:10:41.000-08:00
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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<NavTree> getHeaderLinks(ViewContext viewContext, ExpProtocol protoco
     }
 
     @Override
-    public ValidationException setValidationAndAnalysisScripts(ExpProtocol protocol, @NotNull List<File> scripts)
+    public ValidationException setValidationAndAnalysisScripts(ExpProtocol protocol, @NotNull List<AnalysisScript> scripts)
     {
         throw new UnsupportedOperationException();
     }
 
     @NotNull
     @Override
-    public List<File> getValidationAndAnalysisScripts(ExpProtocol protocol, Scope scope)
+    public List<AnalysisScript> 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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;

Original file line number	Diff line number	Diff line change
`@@ -18,6 +18,7 @@`
`18`	`18`
`19`	`19`	`import org.jetbrains.annotations.NotNull;`
`20`	`20`	`import org.jetbrains.annotations.Nullable;`
	`21`	`+import org.labkey.api.assay.transform.AnalysisScript;`
`21`	`22`	`import org.labkey.api.data.Container;`
`22`	`23`	`import org.labkey.api.data.ContainerFilter;`
`23`	`24`	`import org.labkey.api.data.ContainerManager;`
`@@ -36,7 +37,7 @@`
`36`	`37`	`import org.labkey.api.module.ModuleLoader;`
`37`	`38`	`import org.labkey.api.pipeline.PipelineProvider;`
`38`	`39`	`import org.labkey.api.pipeline.PipelineService;`
`39`		`-import org.labkey.api.qc.DataExchangeHandler;`
	`40`	`+import org.labkey.api.assay.transform.DataExchangeHandler;`
`40`	`41`	`import org.labkey.api.query.FieldKey;`
`41`	`42`	`import org.labkey.api.query.ValidationException;`
`42`	`43`	`import org.labkey.api.security.User;`
`@@ -474,14 +475,14 @@ public List<NavTree> getHeaderLinks(ViewContext viewContext, ExpProtocol protoco`
`474`	`475`	`}`
`475`	`476`
`476`	`477`	`@Override`
`477`		`- public ValidationException setValidationAndAnalysisScripts(ExpProtocol protocol, @NotNull List<File> scripts)`
	`478`	`+ public ValidationException setValidationAndAnalysisScripts(ExpProtocol protocol, @NotNull List<AnalysisScript> scripts)`
`478`	`479`	`{`
`479`	`480`	`throw new UnsupportedOperationException();`
`480`	`481`	`}`
`481`	`482`
`482`	`483`	`@NotNull`
`483`	`484`	`@Override`
`484`		`- public List<File> getValidationAndAnalysisScripts(ExpProtocol protocol, Scope scope)`
	`485`	`+ public List<AnalysisScript> getValidationAndAnalysisScripts(ExpProtocol protocol, Scope scope)`
`485`	`486`	`{`
`486`	`487`	`throw new UnsupportedOperationException();`
`487`	`488`	`}`