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Resolve SequenceAnalysis pipeline paths through PipeRoot #450

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Merged
labkey-matthewb merged 1 commit into from
Oct 29, 2026
Merged

Resolve SequenceAnalysis pipeline paths through PipeRoot #450

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24 changes: 18 additions & 6 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1073,7 +1073,13 @@ public ApiResponse execute(ValidateReadsetImportForm form, BindException errors)
FileLike base = root.getRootFileLike();

if (form.getPath() != null)
base = base.resolveFile(new Path(form.getPath()));
{
base = root.resolvePathToFileLike(form.getPath());
if (null == base)
{
throw new PipelineJobException("Invalid path: " + form.getPath());
}
}

for (String fileName : form.getFileNames())
{
Expand All @@ -1088,7 +1094,7 @@ 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(FileSystemLike.toFile(root.getRootFileLike())).getPath(), FileUtil.getAbsoluteCaseSensitiveFile(f).getPath()));
map.put("relPath", root.relativePath(f));
map.put("container", getContainer().getId());
map.put("containerPath", getContainer().getPath());
String basename = SequenceTaskHelper.getUnzippedBaseName(fileName);
Expand Down Expand Up @@ -1925,12 +1931,13 @@ else if (!d.getContainer().hasPermission(u, ReadPermission.class))
else if (o.has("relPath") || o.has("fileName"))
{
FileLike f;
if (o.opt("relPath") == null)
if (o.isNull("relPath"))
{
if (path != null)
if (StringUtils.isNotEmpty(path))
{
f = pr.resolvePathToFileLike(path);
f = f.resolveFile(Path.parse(o.getString("fileName")));
if (f != null)
f = f.resolveFile(Path.parse(o.getString("fileName")));
}
else
{
Expand Down Expand Up @@ -2231,7 +2238,12 @@ public Object execute(ImportFastaSequencesForm form, BindException errors) throw
return null;
}

FileLike baseDir = StringUtils.trimToNull(form.getPath()) == null ? root.getRootFileLike() : root.getRootFileLike().resolveFile(new Path(form.getPath()));
FileLike baseDir = StringUtils.trimToNull(form.getPath()) == null ? root.getRootFileLike() : root.resolvePathToFileLike(form.getPath());
if (baseDir == null)
{
errors.reject(ERROR_MSG, "Invalid path: " + form.getPath());
return null;
}

if (!baseDir.exists())
{
Expand Down
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