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Fix Task registration and expand test cases #7268

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Merged
bbimber merged 1 commit into from
Dec 15, 2025
Merged

Fix Task registration and expand test cases #7268

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97 changes: 71 additions & 26 deletions experiment/src/org/labkey/experiment/pipeline/XarTestPipelineJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,11 @@
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TableSelector;
import org.labkey.api.data.WorkbookContainerType;
import org.labkey.api.exp.api.ExpData;
import org.labkey.api.exp.api.ExpRun;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.pipeline.XarGeneratorFactorySettings;
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 Down Expand Up @@ -174,20 +175,24 @@ private static TaskId getTaskFactoryId(String location)
return new TaskId(XarTestTaskFactory.class, location);
}

public static TaskId registerTaskPipeline(String location) throws CloneNotSupportedException
public static void registerTaskPipeline(String location) throws CloneNotSupportedException
{
//first register TaskFactory
TaskId taskFactoryId = getTaskFactoryId(location);
PipelineJobService.get().addTaskFactory(new XarTestTaskFactory(taskFactoryId, location));

//then TaskPipeline
TaskId taskPipelineId = getTaskIdForEngine(location);
TaskFactory<?> xarFact = PipelineJobService.get().getTaskFactory(new TaskId(XarGeneratorId.class));
if (xarFact == null)
{
throw new IllegalStateException("Unable to find TaskFactory for XarGeneratorId.class");
}

TaskPipelineSettings settings = new TaskPipelineSettings(taskPipelineId);
settings.setTaskProgressionSpec(new Object[]{taskFactoryId, getXarGenerator().getId()});
settings.setTaskProgressionSpec(new Object[]{taskFactoryId, xarFact.getId()});
settings.setDeclaringModule(ModuleLoader.getInstance().getModule(ExperimentModule.class));
PipelineJobService.get().addTaskPipeline(settings);

return taskPipelineId;
}

@Override
Expand Down Expand Up @@ -273,20 +278,6 @@ public boolean isJobComplete(PipelineJob job)
}
}

protected static XarGeneratorFactorySettings getXarGenerator() throws CloneNotSupportedException
{
XarGeneratorFactorySettings settings = new XarGeneratorFactorySettings("xarGeneratorJoin");
settings.setJoin(true);

TaskFactory<?> factory = PipelineJobService.get().getTaskFactory(settings.getCloneId());
if (factory == null)
{
PipelineJobService.get().addTaskFactory(settings);
}

return settings;
}

@Override
public String getProtocolName()
{
Expand Down Expand Up @@ -428,22 +419,76 @@ public void xarTest() throws Exception
Arrays.asList(new File("/arbitrary/path/outside/lkRoot/myFile.txt")),
Arrays.asList(new File("/another/arbitrary/path/outside/lkRoot/myFile.txt"))
);

Container project = ContainerManager.getForPath(PROJECT_NAME);
PipeRoot projectRoot = PipelineService.get().getPipelineRootSetting(project);
Assert.assertNotNull(PROJECT_NAME + " pipeline root is null", projectRoot);

// We expect /Shared to be an allowable output location:
PipeRoot sharedRoot = PipelineService.get().getPipelineRootSetting(ContainerManager.getSharedContainer());
Assert.assertNotNull("Shared pipeline root is null", sharedRoot);

// A pipeline job submitted to a project/folder should be able to access files in /Shared
doXarTest(
"XarTestJob_UsingShared",
Arrays.asList(
FileUtil.appendPath(projectRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myFileInJobFolder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(sharedRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myFileInSharedFolder.txt")).toNioPathForWrite().toFile()
),
Arrays.asList(
FileUtil.appendPath(projectRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myOutputFileInJobFolder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(sharedRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myOutputFileInSharedFolder.txt")).toNioPathForWrite().toFile()
)
);

// Now create workbooks in this folder:
Container wb1 = ContainerManager.createContainer(project, null, "WB1", null, WorkbookContainerType.NAME, TestContext.get().getUser());
Container wb2 = ContainerManager.createContainer(project, null, "WB2", null, WorkbookContainerType.NAME, TestContext.get().getUser());

PipeRoot wb1Root = PipelineService.get().getPipelineRootSetting(wb1);
Assert.assertNotNull("wb1Root is null", wb1Root);
PipeRoot wb2Root = PipelineService.get().getPipelineRootSetting(wb2);
Assert.assertNotNull("wb2Root is null", wb2Root);

// A pipeline job submitted to a workbook should be able to reference files in /Shared, the parent folder, or sibling workbooks:
doXarTest(
"XarTestJob_AcrossWorkbooks",
Arrays.asList(
FileUtil.appendPath(projectRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myFileInJobFolder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(sharedRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myFileInSharedFolder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(wb1Root.getRootFileLike(), org.labkey.api.util.Path.parse("myFileInWB1Folder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(wb2Root.getRootFileLike(), org.labkey.api.util.Path.parse("myFileInWB2Folder.txt")).toNioPathForWrite().toFile()
),
Arrays.asList(
FileUtil.appendPath(projectRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myOutputFileInJobFolder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(sharedRoot.getRootFileLike(), org.labkey.api.util.Path.parse("myOutputFileInSharedFolder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(wb1Root.getRootFileLike(), org.labkey.api.util.Path.parse("myOutputFileInWB1Folder.txt")).toNioPathForWrite().toFile(),
FileUtil.appendPath(wb2Root.getRootFileLike(), org.labkey.api.util.Path.parse("myOutputFileInWB2Folder.txt")).toNioPathForWrite().toFile()
),
wb2
);
}

@Test
public void xarTestRelativePaths() throws Exception
{
// NOTE: these will get converted to absolute paths by the pipeline code when they are saved:
doXarTest(
"XarTestJob_QuestionablePaths",
Arrays.asList(new File("../../../root/myFile.txt")),
Arrays.asList(new File("../../../users/root/anotherFile.txt"))
);
// NOTE: these will get converted to absolute paths by the pipeline code when they are saved, so this passes right now:
//Assert.assertThrows("Maybe LabKey shouldn't allow this", Exception.class, () -> {
doXarTest(
"XarTestJob_QuestionablePaths",
Arrays.asList(new File("../../../root/myFile.txt")),
Arrays.asList(new File("../../../users/root/anotherFile.txt"))
);
//});
}

private void doXarTest(String jobName, List<File> inputFiles, List<File> outputFiles) throws Exception
{
Container c = ContainerManager.getForPath(PROJECT_NAME);
doXarTest(jobName, inputFiles, outputFiles, ContainerManager.getForPath(PROJECT_NAME));
}

private void doXarTest(String jobName, List<File> inputFiles, List<File> outputFiles, Container c) throws Exception
{
PipelineJob job1 = XarTestPipelineJob.createJob(c, TestContext.get().getUser(), jobName, inputFiles, outputFiles);
PipelineService.get().queueJob(job1);
long start = System.currentTimeMillis();
Expand Down