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Support for running transform scripts during result updates. #833

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Merged
labkey-klum merged 2 commits into from
Jan 9, 2025
Merged

Support for running transform scripts during result updates. #833

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0ae9f00
wire up transform scripts for assay result updates
labkey-klum Jan 1, 2025
4b12c7a
Merge branch 'develop' into fb_transform_on_update_2
labkey-klum Jan 2, 2025
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22 changes: 18 additions & 4 deletions elispotassay/src/org/labkey/elispot/ElispotDataExchangeHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,10 @@
package org.labkey.elispot;

import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.assay.plate.Plate;
import org.labkey.api.assay.plate.WellGroup;
import org.labkey.api.assay.transform.DataTransformService;
import org.labkey.api.exp.api.ExpProtocol;
import org.labkey.api.exp.api.ExpRun;
import org.labkey.api.exp.property.DomainProperty;
Expand All @@ -45,7 +47,14 @@ public class ElispotDataExchangeHandler extends PlateBasedDataExchangeHandler
public static final String ANTIGEN_DATA_PROP_NAME = "antigenData";

@Override
public Pair<FileLike, Set<FileLike>> createTransformationRunInfo(AssayRunUploadContext<? extends AssayProvider> context, ExpRun run, FileLike scriptDir, Map<DomainProperty, String> runProperties, Map<DomainProperty, String> batchProperties) throws Exception
public Pair<FileLike, Set<FileLike>> createTransformationRunInfo(
DataTransformService.TransformOperation operation,
AssayRunUploadContext<? extends AssayProvider> context,
@Nullable ExpRun run,
FileLike scriptDir,
Map<DomainProperty, String> runProperties,
Map<DomainProperty, String> batchProperties
) throws Exception
{
ElispotRunUploadForm form = (ElispotRunUploadForm)context;

Expand All @@ -58,11 +67,16 @@ public Pair<FileLike, Set<FileLike>> createTransformationRunInfo(AssayRunUploadC
addSampleProperties(SAMPLE_DATA_PROP_NAME, GROUP_COLUMN_NAME, form.getSampleProperties(), template, WellGroup.Type.SPECIMEN);
addSampleProperties(ANTIGEN_DATA_PROP_NAME, GROUP_COLUMN_NAME, form.getAntigenProperties(), template, WellGroup.Type.ANTIGEN);

return super.createTransformationRunInfo(context, run, scriptDir, runProperties, batchProperties);
return super.createTransformationRunInfo(operation, context, run, scriptDir, runProperties, batchProperties);
}

@Override
public void createSampleData(@NotNull ExpProtocol protocol, ViewContext viewContext, FileLike scriptDir) throws Exception
public void createSampleData(
DataTransformService.TransformOperation operation,
@NotNull ExpProtocol protocol,
ViewContext viewContext,
FileLike scriptDir
) throws Exception
{
AssayProvider provider = AssayService.get().getProvider(protocol);
if (provider instanceof ElispotAssayProvider)
Expand All @@ -81,6 +95,6 @@ public void createSampleData(@NotNull ExpProtocol protocol, ViewContext viewCont
addSampleProperties(ANTIGEN_DATA_PROP_NAME, GROUP_COLUMN_NAME, antigens, template, WellGroup.Type.ANTIGEN);
}
}
super.createSampleData(protocol, viewContext, scriptDir);
super.createSampleData(operation, protocol, viewContext, scriptDir);
}
}
13 changes: 11 additions & 2 deletions luminex/src/org/labkey/luminex/LuminexDataExchangeHandler.java
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Expand Up @@ -18,6 +18,8 @@

import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.assay.transform.DataTransformService;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.dataiterator.DataIteratorBuilder;
import org.labkey.api.exp.ExperimentException;
Expand Down Expand Up @@ -52,7 +54,14 @@ public class LuminexDataExchangeHandler extends TsvDataExchangeHandler
private final DataSerializer _serializer = new LuminexDataSerializer();

@Override
public Pair<FileLike, Set<FileLike>> createTransformationRunInfo(AssayRunUploadContext<? extends AssayProvider> context, ExpRun run, FileLike scriptDir, Map<DomainProperty, String> runProperties, Map<DomainProperty, String> batchProperties) throws Exception
public Pair<FileLike, Set<FileLike>> createTransformationRunInfo(
DataTransformService.TransformOperation operation,
AssayRunUploadContext<? extends AssayProvider> context,
@Nullable ExpRun run,
FileLike scriptDir,
Map<DomainProperty, String> runProperties,
Map<DomainProperty, String> batchProperties
) throws Exception
{
LuminexRunContext form = (LuminexRunContext)context;
List<Map<String, Object>> analytes = new ArrayList<>();
Expand Down Expand Up @@ -80,7 +89,7 @@ public Pair<FileLike, Set<FileLike>> createTransformationRunInfo(AssayRunUploadC
List<Map<String, Object>> titrations = getTitrationMaps(form);
addSampleProperties(TITRATION_DATA_PROP_NAME, titrations);

return super.createTransformationRunInfo(context, run, scriptDir, runProperties, batchProperties);
return super.createTransformationRunInfo(operation, context, run, scriptDir, runProperties, batchProperties);
}

private static @NotNull List<Map<String, Object>> getTitrationMaps(LuminexRunContext form) throws ExperimentException
Expand Down
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