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Remove code to lookup runs in the source container when aligning data…
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…fileUrls. This should not be required anymore due to LabKey/targetedms#724.

Set filePathRoot on the copied expRun to be the target container's file root.
Log error if the data file path is unexpected, i.e. it does not contain "Run<runid>"
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@vagisha
vagisha committed May 25, 2023
1 parent 613d6a1 commit 5d7ab66
Showing 1 changed file with 32 additions and 58 deletions.
90 changes: 32 additions & 58 deletions panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicFileImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
import org.labkey.api.admin.ImportException;
import org.labkey.api.admin.SubfolderWriter;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerService;
import org.labkey.api.exp.api.ExpData;
import org.labkey.api.exp.api.ExpRun;
import org.labkey.api.exp.api.ExperimentService;
Expand All @@ -25,6 +24,7 @@
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.List;
import java.util.Objects;

/**
* This importer does a file move instead of copy to the temp directory and creates a symlink in place of the original
Expand Down Expand Up @@ -88,86 +88,60 @@ public void process(@Nullable PipelineJob job, FolderImportContext ctx, VirtualF
log.info("Moving files and creating sym links in folder " + ctx.getContainer().getPath());
PanoramaPublicSymlinkManager.get().moveAndSymLinkDirectory(expJob.getUser(), expJob.getContainer(), sourceFiles, targetFiles, false, log);

String sourceContainerPath = Paths.get(expJob.getExportSourceContainer().getPath(), subProject).toString().replace(File.separator, "/");
Container resolvedSourceContainer = ContainerService.get().getForPath(sourceContainerPath);

if (null == resolvedSourceContainer)
{
throw new ImportException("Invalid source container found for aligning data file urls: " + sourceContainerPath);
}

alignDataFileUrls(expJob.getUser(), ctx.getContainer(), resolvedSourceContainer, log);
alignDataFileUrls(expJob.getUser(), ctx.getContainer(), log);
}
}

private void alignDataFileUrls(User user, Container targetContainer, Container sourceContainer, Logger log) throws BatchValidationException, ImportException
private void alignDataFileUrls(User user, Container targetContainer, Logger log) throws BatchValidationException, ImportException
{
log.info("Aligning data files urls in folder: " + targetContainer.getPath());

FileContentService fcs = FileContentService.get();
if (null == fcs)
return;

ExperimentService expService = ExperimentService.get();
List<? extends ExpRun> runs = expService.getExpRuns(targetContainer, null, null);
boolean errors = false;

// Get all source and target container runs
List<? extends ExpRun> sourceRuns = ExperimentService.get().getExpRuns(sourceContainer, null, null);
for (ExpRun run : ExperimentService.get().getExpRuns(targetContainer, null, null))
Path fileRootPath = fcs.getFileRootPath(targetContainer, FileContentService.ContentType.files);
if(fileRootPath == null || !Files.exists(fileRootPath))
{
// Find matching source run
ExpRun sourceRun = sourceRuns.stream().filter(r -> r.getName().equals(run.getName())).findFirst().orElse(null);
if (null == sourceRun)
{
log.error("Source run not found for run: " + run.getName());
errors = true;
continue;
}

Path targetRootPath = fcs.getFileRootPath(run.getContainer(), FileContentService.ContentType.files);
if(targetRootPath == null || !Files.exists(targetRootPath))
{
throw new ImportException("Target file root path for container " + run.getContainer().getPath() + " does not exist: " + targetRootPath);
}

// Get source path relative to file root and apply to target file root
String sourcePath = sourceRun.getFilePathRootPath().toString();
String relativeSource = sourcePath.substring(sourcePath.lastIndexOf(FileContentService.FILES_LINK) + FileContentService.FILES_LINK.length());
Path targetRunPath = Paths.get(targetRootPath.toString(), relativeSource);
throw new ImportException("File root path for container " + targetContainer.getPath() + " does not exist: " + fileRootPath);
}

// Update run file path
if (targetRunPath.toFile().exists())
{
run.setFilePathRoot(targetRunPath.toFile());
run.save(user);
log.debug("Updated copied run: " + run.getName() + " with file path: " + targetRunPath);
}
else
{
log.error("Run file path not found: " + targetRunPath);
errors = true;
}
for (ExpRun run : runs)
{
run.setFilePathRootPath(fileRootPath);
run.save(user);
log.debug("Setting filePathRoot on copied run: " + run.getName() + " to: " + fileRootPath);

// Update data file urls
for (ExpData data : run.getAllDataUsedByRun())
{
// Find matching source data
ExpData sourceData = sourceRun.getAllDataUsedByRun().stream().filter(d -> d.getName().equals(data.getName())).findFirst().orElse(null);
if (null != sourceData && null != sourceData.getDataFileUrl())
if (null != data.getRun() && data.getDataFileUrl().contains(FileContentService.FILES_LINK))
{
// Get source data path relative to file root and apply to target data file root
String sourceDataName = sourceData.getDataFileUrl().substring(sourceData.getDataFileUrl().lastIndexOf(FileContentService.FILES_LINK) + FileContentService.FILES_LINK.length());
Path targetDataPath = Paths.get(targetRootPath.toString(), sourceDataName);
String[] parts = Objects.requireNonNull(data.getFilePath()).toString().split("Run\\d+");

// Update data file url
if (targetDataPath.toFile().exists())
if (parts.length > 1)
{
data.setDataFileURI(targetDataPath.toUri());
data.save(user);
log.debug("Updated copied data: " + data.getName() + " with file path: " + targetDataPath);
String fileName = parts[1];
Path newDataPath = Paths.get(fileRootPath.toString(), fileName);

if (newDataPath.toFile().exists())
{
data.setDataFileURI(newDataPath.toUri());
data.save(user);
log.debug("Setting dataFileUri on copied data: " + data.getName() + " to: " + newDataPath);
}
else
{
log.error("Data file not found: " + newDataPath.toUri());
errors = true;
}
}
else
{
log.error("Data file url not found: " + sourceData.getDataFileUrl());
log.error("Unexpected data file path. Could not align dataFileUri. " + data.getFilePath().toString());
errors = true;
}
}
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