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Merged
labkey-jeckels merged 4 commits into from
Oct 16, 2025
Merged

Improve file path validation #181

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2832ba7
Checkpoint FileLike migration
labkey-jeckels Oct 5, 2025
8583884
ExperimentDataHandler File->FileLike
labkey-jeckels Oct 11, 2025
30b9e22
Test cleanup
labkey-jeckels Oct 13, 2025
d68ca93
Merge branch 'develop' into fb_adoptFileLike
labkey-jeckels Oct 14, 2025
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19 changes: 6 additions & 13 deletions genotyping/src/org/labkey/genotyping/HaplotypeAssayProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
import org.labkey.api.assay.AssayUrls;
import org.labkey.api.study.assay.ParticipantVisitResolverType;
import org.labkey.api.util.FileType;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.view.ActionURL;
Expand Down Expand Up @@ -135,7 +136,7 @@ public String getName()
@Override
public HttpView<?> getDataDescriptionView(AssayRunUploadForm form)
{
return new HtmlView("");
return new HtmlView(HtmlString.EMPTY_STRING);
}

@Override
Expand Down Expand Up @@ -205,26 +206,18 @@ protected Map<String, Set<String>> getRequiredDomainProperties()
{
Map<String, Set<String>> domainMap = super.getRequiredDomainProperties();

Set<String> runProperties = domainMap.get(ExpProtocol.ASSAY_DOMAIN_RUN);
if (runProperties == null)
{
runProperties = new HashSet<>();
domainMap.put(ExpProtocol.ASSAY_DOMAIN_RUN, runProperties);
}
Set<String> runProperties = domainMap.computeIfAbsent(ExpProtocol.ASSAY_DOMAIN_RUN, k -> new HashSet<>());
runProperties.add(ENABLED_PROPERTY_NAME);
for (String propName : getColumnMappingProperties(true).keySet())
{
runProperties.add(propName);
}
runProperties.addAll(getColumnMappingProperties(true).keySet());
runProperties.add(SPECIES_COLUMN.getName());

return domainMap;
}

@Override
public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, File> uploadedFiles, AssayRunUploadForm context)
public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, org.labkey.vfs.FileLike> uploadedFiles, AssayRunUploadForm context)
{
return Collections.singletonList(new HaplotypeDataCollector());
return Collections.singletonList(new HaplotypeDataCollector<>());
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java
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Expand Up @@ -43,7 +43,7 @@ public class HaplotypeDataCollector<ContextType extends AssayRunUploadContext<Ha
private Map<String, String> _reshowMap;

@Override
public HttpView getView(ContextType context)
public HttpView<?> getView(ContextType context)
{
// if reshowing on error, get the data param out of the context for the JSP to use
HttpServletRequest request = context.getRequest();
Expand Down
9 changes: 5 additions & 4 deletions genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@
import org.labkey.api.assay.AssayService;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.io.IOException;
Expand All @@ -70,17 +71,17 @@ public DataType getDataType()
}

@Override
public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
{
if (!dataFile.exists())
{
log.warn("Could not find file " + dataFile.getAbsolutePath() + " on disk for data with LSID " + data.getLSID());
log.warn("Could not find file " + dataFile + " on disk for data with LSID " + data.getLSID());
return;
}
ExpRun expRun = data.getRun();
if (expRun == null)
{
throw new ExperimentException("Could not load haplotype file " + dataFile.getAbsolutePath() + " because it is not owned by an experiment run");
throw new ExperimentException("Could not load haplotype file " + dataFile + " because it is not owned by an experiment run");
}

try
Expand All @@ -100,7 +101,7 @@ public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgr
Map<String, String> animalIds = new CaseInsensitiveTreeMap<>();
List<HaplotypeIdentifier> haplotypes = new ArrayList<>();
List<HaplotypeAssignmentDataRow> dataRows = new ArrayList<>();
TabLoader tabLoader = new TabLoader(dataFile, true);
TabLoader tabLoader = new TabLoader(dataFile.openInputStream(), true, data.getContainer());
List<Map<String, Object>> rowsMap = tabLoader.load();
parseHaplotypeData(protocol, rowsMap, runPropertyValues, animalIds, haplotypes, dataRows);

Expand Down
40 changes: 11 additions & 29 deletions genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java
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Expand Up @@ -214,7 +214,7 @@ else if (reader.getLineNumber() == 1 && totalReads == 0 && !f.getName().contains
sampleId = _sampleNameToIdMap.get(sampleName);
}
String name = (_outputPrefix == null ? "Reads" : _outputPrefix) + "-R" + pairNumber + "-" + (sampleIdx == 0 ? "Control" : sampleId) + ".fastq.gz";
File newFile = new File(targetDir, name);
File newFile = FileUtil.appendName(targetDir, name);

if (!f.equals(newFile))
{
Expand Down Expand Up @@ -408,9 +408,7 @@ public void testHeaders() throws PipelineJobException, IOException
{
Module module = ModuleLoader.getInstance().getModule("genotyping");
File newHeaderPath = JunitUtil.getSampleData(module, "genotyping/illumina_newHeader");
String newHeaderSampledataLoc = newHeaderPath.toString();
File oldHeaderPath = JunitUtil.getSampleData(module, "genotyping");
String oldHeaderSampledataLoc = oldHeaderPath.toString();
final List<String> filenamesOldHeader = Arrays.asList(
"IlluminaSamples-R1-4892.fastq.gz",
"IlluminaSamples-R1-4893.fastq.gz",
Expand Down Expand Up @@ -472,8 +470,7 @@ public void testHeaders() throws PipelineJobException, IOException
"IlluminaSamplesNewHeader-R2-4905.fastq.gz"
);

final Pair[] pairs =
{
final var pairs = List.of(
new Pair<>(4892, 1),
new Pair<>(4893, 1),
new Pair<>(4894, 1),
Expand Down Expand Up @@ -501,11 +498,10 @@ public void testHeaders() throws PipelineJobException, IOException
new Pair<>(4902, 2),
new Pair<>(4903, 2),
new Pair<>(4904, 2),
new Pair<>(4905, 2)
};
new Pair<>(4905, 2));

int i = 0;
int numOfPairs = pairs.length;
int numOfPairs = pairs.size();
Set<Pair<Integer, Integer>> expectedOutputs = new HashSet<>();
Map<Integer, Integer> sampleIndexToIdMap = new IntHashMap<>();
sampleIndexToIdMap.put(0, 0);
Expand All @@ -516,15 +512,15 @@ public void testHeaders() throws PipelineJobException, IOException

for (String fn : filenamesOldHeader)
{
File target = new File(_testRoot, fn);
FileUtils.copyFile(new File(oldHeaderSampledataLoc, fn), target);
expectedOutputs.add((Pair<Integer, Integer>) pairs[i]);
File target = FileUtil.appendName(_testRoot, fn);
FileUtils.copyFile(FileUtil.appendName(oldHeaderPath, fn), target);
expectedOutputs.add(pairs.get(i));
oldHeaderFiles.add(target);

if (i < (numOfPairs / 2))
{
sampleIndexToIdMap.put(i + 1, (Integer)pairs[i].getKey());
sampleIdToIndexMap.put((Integer)pairs[i].getKey(), i + 1);
sampleIndexToIdMap.put(i + 1, pairs.get(i).getKey());
sampleIdToIndexMap.put(pairs.get(i).getKey(), i + 1);
}
i++;
}
Expand All @@ -537,29 +533,15 @@ public void testHeaders() throws PipelineJobException, IOException

for (String fn : filenamesNewHeader)
{
File target = new File(_testRoot, fn);
FileUtils.copyFile(new File(newHeaderSampledataLoc, fn), target);
File target = FileUtil.appendName(_testRoot, fn);
FileUtils.copyFile(FileUtil.appendName(newHeaderPath, fn), target);
newHeaderFiles.add(target);
}

parser = new IlluminaFastqParser(null, sampleIndexToIdMap, sampleIdToIndexMap, Collections.emptyMap(), LogManager.getLogger(HeaderTestCase.class), newHeaderFiles);
outputs = parser.parseFastqFiles(null);
Assert.assertEquals("Outputs from parseFastqFiles with new headers were not as expected.", expectedOutputs, outputs.keySet());
}

// @After // TODO: Disabling to debug gradle failure on TeamCity
public void cleanup() throws IOException
{
if (container != null)
{
ContainerManager.delete(container, TestContext.get().getUser());
}

if (_testRoot != null)
{
FileUtils.deleteDirectory(_testRoot);
}
}
}
}

Expand Down