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Fix FileWatcherAssayIntegrationTest after FileLike refactor #7244

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Merged
labkey-jeckels merged 3 commits into from
Dec 5, 2025
+9 −16
Merged

Fix FileWatcherAssayIntegrationTest after FileLike refactor #7244

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abd4c44
Fix FileWatcherAssayIntegrationTest
labkey-jeckels Dec 4, 2025
808d958
Fix FileWatcherAssayIntegrationTest
labkey-jeckels Dec 4, 2025
cb5791a
Remove special bonus character and unused code
labkey-jeckels Dec 5, 2025
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3 changes: 2 additions & 1 deletion api/src/org/labkey/api/reader/ExcelLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@

import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
Expand Down Expand Up @@ -114,7 +115,7 @@ public static boolean isExcel(final FileLike dataFile)
{
try
{
try (InputStream inputStream = dataFile.openInputStream())
try (InputStream inputStream = new BufferedInputStream(dataFile.openInputStream()))
{
return ExcelLoader.FILE_TYPE.isType(dataFile.toNioPathForRead(), null, FileUtil.readHeader(inputStream, 8 * 1024));
}
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22 changes: 7 additions & 15 deletions assay/src/org/labkey/assay/pipeline/AssayImportRunTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,6 @@
import org.labkey.api.exp.api.ExpProtocol;
import org.labkey.api.exp.api.ExpRun;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.pipeline.XarGeneratorId;
import org.labkey.api.module.Module;
import org.labkey.api.module.ModuleLoader;
import org.labkey.api.pipeline.AbstractTaskFactory;
Expand All @@ -46,7 +45,6 @@
import org.labkey.api.pipeline.PipelineValidationException;
import org.labkey.api.pipeline.RecordedAction;
import org.labkey.api.pipeline.RecordedActionSet;
import org.labkey.api.pipeline.TaskFactory;
import org.labkey.api.pipeline.TaskId;
import org.labkey.api.pipeline.XMLBeanTaskFactoryFactory;
import org.labkey.api.pipeline.file.AbstractFileAnalysisJob;
Expand All @@ -70,6 +68,7 @@
import org.labkey.vfs.FileLike;
import org.labkey.vfs.FileSystemLike;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.IOException;
import java.net.URI;
Expand All @@ -95,7 +94,7 @@ public class AssayImportRunTask extends PipelineJob.Task<AssayImportRunTask.Fact
public static class FactoryFactory implements XMLBeanTaskFactoryFactory
{
@Override
public TaskFactory create(TaskId taskId, TaskType xobj, Path taskDir)
public Factory create(TaskId taskId, TaskType xobj, Path taskDir)
{
if (taskId.getModuleName() == null)
throw new IllegalArgumentException("Task factory must be defined by a module");
Expand Down Expand Up @@ -245,7 +244,7 @@ List<Map<String, Object>> getRawData(PipelineJob job) throws PipelineJobExceptio
{
job.getLogger().info("Processing excel file: " + dataFile.getName());
// check to see if this is a multi-sheet format
try (ExcelLoader loader = new ExcelLoader(dataFile.openInputStream(), true, null))
try (ExcelLoader loader = new ExcelLoader(new BufferedInputStream(dataFile.openInputStream()), true, null))
{
List<String> sheets = loader.getSheetNames();
if (sheets.size() > 1)
Expand Down Expand Up @@ -424,8 +423,6 @@ private FileLike getExplodedZipDir(PipelineJob job, FileLike dataFile)

public static class Factory extends AbstractTaskFactory<AssayImportRunTaskFactorySettings, Factory>
{
private final FileType _outputType = XarGeneratorId.FT_PIPE_XAR_XML;

private String _providerName = "${" + PROVIDER_NAME_PROPERTY + "}";
private String _protocolName = "${" + PROTOCOL_NAME_PROPERTY + "}";

Expand All @@ -434,7 +431,7 @@ public Factory()
super(AssayImportRunTaskId.class);
}

public Factory(Class namespaceClass)
public Factory(Class<?> namespaceClass)
{
super(namespaceClass);
}
Expand Down Expand Up @@ -468,11 +465,6 @@ public List<FileType> getInputTypes()
return Collections.emptyList();
}

public FileType getOutputType()
{
return _outputType;
}

@Override
public String getStatusName()
{
Expand Down Expand Up @@ -802,7 +794,7 @@ public RecordedActionSet run() throws PipelineJobException
createData(matchedFile, assayDataType);


AssayRunUploadContext.Factory<? extends AssayProvider, ? extends AssayRunUploadContext.Factory> factory
AssayRunUploadContext.Factory<? extends AssayProvider, ? extends AssayRunUploadContext.Factory<?, ?>> factory
= provider.createRunUploadFactory(protocol, user, container);

factory.setName(getName());
Expand All @@ -828,7 +820,7 @@ public RecordedActionSet run() throws PipelineJobException

factory.setLogger(getJob().getLogger());

AssayRunUploadContext uploadContext = factory.create();
AssayRunUploadContext<?> uploadContext = factory.create();

Long batchId = null;

Expand Down Expand Up @@ -857,7 +849,7 @@ public RecordedActionSet run() throws PipelineJobException
// }

// Check if we've been cancelled. If so, delete any newly created runs from the database
PipelineStatusFile statusFile = PipelineService.get().getStatusFile(getJob().getLogFile());
PipelineStatusFile statusFile = PipelineService.get().getStatusFile(getJob().getContainer(), getJob().getLogFileLike());
if (statusFile != null && (PipelineJob.TaskStatus.cancelled.matches(statusFile.getStatus()) || PipelineJob.TaskStatus.cancelling.matches(statusFile.getStatus())))
{
getJob().info("Deleting run " + run.getName() + " due to cancellation request");
Expand Down