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Convert ValidateReadsetFilesAction and ImportReferenceSequencesAction to use FileLike #350

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Merged
labkey-bpatel merged 6 commits into from
Apr 10, 2025
Merged

Convert ValidateReadsetFilesAction and ImportReferenceSequencesAction to use FileLike #350

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dd196e3
Update ValidateReadsetFilesAction and ImportReferenceSequencesAction …
labkey-bpatel Apr 8, 2025
21e947e
Update 'DownloadTempImageAction' to use FileLike.
labkey-bpatel Apr 8, 2025
0bbf7ea
Use getPath() in the error message.
labkey-bpatel Apr 8, 2025
f06440b
Use resolveFile()
labkey-bpatel Apr 9, 2025
e219ea4
Remove DownloadTempImageAction and ConvertTextToFileAction and its as…
labkey-bpatel Apr 9, 2025
ce11f9a
Adjust error, use resolveFile()
labkey-bpatel Apr 9, 2025
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156 changes: 23 additions & 133 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -171,6 +171,7 @@
import org.labkey.sequenceanalysis.util.FastqUtils;
import org.labkey.sequenceanalysis.util.SequenceUtil;
import org.labkey.vfs.FileLike;
import org.labkey.vfs.FileSystemLike;
import org.springframework.beans.PropertyValues;
import org.springframework.validation.BindException;
import org.springframework.validation.Errors;
Expand Down Expand Up @@ -427,80 +428,6 @@ public void addNavTrail(NavTree tree)
}
}

@RequiresPermission(ReadPermission.class)
@IgnoresTermsOfUse
public static class DownloadTempImageAction extends ExportAction<TempImageAction>
{
@Override
public void export(TempImageAction form, HttpServletResponse response, BindException errors) throws Exception
{
File parentDir = form.getDirectory() == null ? FileUtil.getTempDirectory() : new File(FileUtil.getTempDirectory(), form.getDirectory());
File targetFile = new File(parentDir, form.getFileName());
targetFile = FileUtil.getAbsoluteCaseSensitiveFile(targetFile);

if (!NetworkDrive.exists(targetFile))
{
throw new FileNotFoundException("Could not find file: " + targetFile.getPath());
}

if (parentDir.listFiles() == null)
{
throw new FileNotFoundException("Unable to list the contents of folder: " + parentDir.getPath());
}

PageFlowUtil.streamFile(response, targetFile, false);

//the file will be recreated, so delete upon running
FileUtils.deleteQuietly(targetFile);

//if the folder if empty, remove it too. other simultaneous requests might have deleted this folder before we get to it
if (parentDir != null && parentDir.exists())
{
File[] children = parentDir.listFiles();
if (children != null && children.length == 0 && !parentDir.equals(FileUtil.getTempDirectory()))
{
FileUtils.deleteQuietly(parentDir); //the Images folder
File parent = parentDir.getParentFile();
FileUtils.deleteQuietly(parent); //the file's folder

if (parent != null && parent.getParentFile() != null)
{
File[] children2 = parent.getParentFile().listFiles();
if (children2 != null && children2.length == 0)
FileUtils.deleteQuietly(parent.getParentFile()); //the file's folder
}
}
}
}
}

@RequiresPermission(ReadPermission.class)
@IgnoresTermsOfUse
public static class ConvertTextToFileAction extends ExportAction<ConvertTextToFileForm>
{
@Override
public void export(ConvertTextToFileForm form, HttpServletResponse response, BindException errors) throws Exception
{
String text = form.getText();

if (text == null)
{
errors.reject(ERROR_MSG, "Need to provide text");
return;
}
if (form.getFileName() == null)
{
errors.reject(ERROR_MSG, "Need to provide a filename");
return;
}

Map<String, String> headers = new HashMap<>();

PageFlowUtil.prepareResponseForFile(response, headers, form.getFileName(), true);
response.getOutputStream().print(text);
}
}

@RequiresPermission(ReadPermission.class)
public static class FindOrphanFilesAction extends ConfirmAction<Object>
{
Expand Down Expand Up @@ -1119,14 +1046,21 @@ public ApiResponse execute(ValidateReadsetImportForm form, BindException errors)
if (form.getFileNames() != null)
{
//TODO: consider proper container??
File root = PipelineService.get().findPipelineRoot(getContainer()).getRootPath();
File base = root;
PipeRoot root = PipelineService.get().findPipelineRoot(getContainer());

if (null == root)
{
throw new PipelineJobException("Unable to find pipeline root for container: " + getContainer().getPath());
}

FileLike base = root.getRootFileLike();

if (form.getPath() != null)
base = new File(base, form.getPath());
base = base.resolveFile(new Path(form.getPath()));

for (String fileName : form.getFileNames())
{
File f = new File(base, fileName);
File f = FileSystemLike.toFile(base.resolveChild(fileName));
ExpData data = ExperimentService.get().getExpDataByURL(f, getContainer());
if (data != null)
{
Expand All @@ -1137,7 +1071,7 @@ public ApiResponse execute(ValidateReadsetImportForm form, BindException errors)
Map<String, Object> map = new HashMap<>();
map.put("fileName", fileName);
map.put("filePath", f.getPath());
map.put("relPath", FileUtil.relativePath(FileUtil.getAbsoluteCaseSensitiveFile(root).getPath(), FileUtil.getAbsoluteCaseSensitiveFile(f).getPath()));
map.put("relPath", FileUtil.relativePath(FileUtil.getAbsoluteCaseSensitiveFile(FileSystemLike.toFile(root.getRootFileLike())).getPath(), FileUtil.getAbsoluteCaseSensitiveFile(f).getPath()));
map.put("container", getContainer().getId());
map.put("containerPath", getContainer().getPath());
String basename = SequenceTaskHelper.getUnzippedBaseName(fileName);
Expand Down Expand Up @@ -1649,58 +1583,6 @@ public void setZipFileName(String zipFileName)
}
}

public static class ConvertTextToFileForm
{
private String _text;
private String _fileName;

public String getText()
{
return _text;
}

public void setText(String text)
{
_text = text;
}

public String getFileName()
{
return _fileName;
}

public void setFileName(String fileName)
{
_fileName = fileName;
}
}

public static class TempImageAction
{
String _fileName;
String _directory;

public String getFileName()
{
return _fileName;
}

public void setFileName(String fileName)
{
_fileName = fileName;
}

public String getDirectory()
{
return _directory;
}

public void setDirectory(String directory)
{
_directory = directory;
}
}

public static class FastqcForm
{
private String[] _filenames;
Expand Down Expand Up @@ -2320,7 +2202,15 @@ public Object execute(ImportFastaSequencesForm form, BindException errors) throw
//resolve files
List<File> files = new ArrayList<>();
PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
File baseDir = StringUtils.trimToNull(form.getPath()) == null ? root.getRootPath() : new File(root.getRootPath(), form.getPath());

if (root == null)
{
errors.reject(ERROR_MSG, "Pipeline root not configured");
return null;
}

FileLike baseDir = StringUtils.trimToNull(form.getPath()) == null ? root.getRootFileLike() : root.getRootFileLike().resolveFile(new Path(form.getPath()));

if (!baseDir.exists())
{
errors.reject(ERROR_MSG, "Unable to find directory: " + baseDir.getPath());
Expand All @@ -2335,7 +2225,7 @@ public Object execute(ImportFastaSequencesForm form, BindException errors) throw

for (String fn : form.getFileNames())
{
File f = new File(baseDir, fn);
File f = FileSystemLike.toFile(baseDir.resolveChild(fn));
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@labkey-matthewb labkey-matthewb Apr 10, 2025

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No need to convert back to File here. FileLike.exists() should work

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@labkey-matthewb labkey-matthewb Apr 10, 2025

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nevermind I see that this gets passed to the job. That's a future story.

if (f.exists())
{
files.add(f);
Expand Down