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Fix file path validation with non root contextPath, update error msg for saveBatch invalid file, etc #7002

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Merged
XingY merged 4 commits into from
Sep 5, 2025
Merged

Fix file path validation with non root contextPath, update error msg for saveBatch invalid file, etc #7002

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be23be8
FileBrowserHelper.getFileDetailInfo: Support more refined filtering
labkey-nicka Sep 3, 2025
e4a8145
Fix error message for saveBatch api with invalid file values
XingY Sep 4, 2025
69d74ae
Fix error message invalid file with server contextPath set
XingY Sep 5, 2025
afd6f4e
Update assay test to check QueryUpdateEvent for result edit details
XingY Sep 5, 2025
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14 changes: 10 additions & 4 deletions api/src/org/labkey/api/assay/DefaultAssayRunCreator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1223,11 +1223,17 @@ else if (!missing)
}
catch (ConversionException e)
{
String message = ConvertHelper.getStandardConversionErrorMessage(value, label, type);
if (e.getCause() instanceof ArithmeticException)
message += ": " + e.getCause().getLocalizedMessage();
String message;
if (e instanceof ConvertHelper.FileConversionException fce)
message = fce.getMessage();
else
message += ".";
{
message = ConvertHelper.getStandardConversionErrorMessage(value, label, type);
if (e.getCause() instanceof ArithmeticException)
message += ": " + e.getCause().getLocalizedMessage();
else
message += ".";
}

// Attempt to resolve lookups by display value
boolean skipError = false;
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12 changes: 7 additions & 5 deletions api/src/org/labkey/api/data/ExpDataFileConverter.java
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Expand Up @@ -364,16 +364,16 @@ public static File convertToFile(Object value, @NotNull Container container, @No

// toss in here an additional check, if starts with HTTP then try to use _webdav to resolve it
// MAKE sure that the security is in place - figure out what container it is in
String webdav = value.toString();
if (null != StringUtils.trimToNull(webdav))
String rootSubstitutedPath = getFileRootSubstitutedFilePath(value.toString(), fileRootPath);;
if (null != StringUtils.trimToNull(rootSubstitutedPath))
{
if (assayResultFileRoot != null)
{
try
{
for (int i = 0; i < 5; i++) // try up to 5 times to find a case-sensitive match
{
String resultsFileName = FileUtil.getAppendedFileName(webdav, i);
String resultsFileName = FileUtil.getAppendedFileName(rootSubstitutedPath, i);
FileLike assayResultFile = assayResultFileRoot.resolveChild(resultsFileName);

if (!assayResultFile.isFile())
Expand All @@ -390,7 +390,9 @@ public static File convertToFile(Object value, @NotNull Container container, @No

}

webdav = getFileRootSubstitutedFilePath(webdav, fileRootPath);
String webdav = rootSubstitutedPath;
if (webdav.startsWith(AppProps.getInstance().getContextPath()))
webdav = webdav.substring(AppProps.getInstance().getContextPath().length());
Path path = Path.decode(FileUtil.encodeForURL(webdav, true /*Issue 51207*/).replace(AppProps.getInstance().getBaseServerUrl() + AppProps.getInstance().getContextPath(), ""));
WebdavResource resource = WebdavService.get().getResolver().lookup(path);
if (resource != null && resource.isFile())
Expand Down Expand Up @@ -440,7 +442,7 @@ public static File convertToFile(Object value, @NotNull Container container, @No
}

// Otherwise, treat it as a plain path (processed by getFileRootSubstitutedFilePath)
return FILE_CONVERTER.convert(File.class, webdav);
return FILE_CONVERTER.convert(File.class, rootSubstitutedPath);
}

// if two files were uploaded with the same name but different casing, then the file system will uniquify the names
Expand Down
18 changes: 10 additions & 8 deletions study/test/src/org/labkey/test/tests/study/AssayTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,13 @@

import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.labkey.remoteapi.CommandException;
import org.labkey.remoteapi.assay.AssayListCommand;
import org.labkey.remoteapi.assay.AssayListResponse;
import org.labkey.test.Locator;
import org.labkey.test.TestFileUtils;
import org.labkey.test.TestTimeoutException;
import org.labkey.test.WebTestHelper;
import org.labkey.test.categories.Assays;
import org.labkey.test.categories.Daily;
import org.labkey.test.components.CustomizeView;
Expand All @@ -35,12 +37,14 @@
import org.labkey.test.params.experiment.SampleTypeDefinition;
import org.labkey.test.tests.AbstractAssayTest;
import org.labkey.test.tests.AuditLogTest;
import org.labkey.test.util.AuditLogHelper;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.LogMethod;
import org.labkey.test.util.SampleTypeHelper;
import org.labkey.test.util.StudyHelper;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

Expand Down Expand Up @@ -267,7 +271,7 @@ private void verifyWebdavTree()
}

@LogMethod
private void editResults()
private void editResults() throws IOException, CommandException
{
// Verify that the results aren't editable by default
navigateToFolder(getProjectName(), TEST_ASSAY_FLDR_LAB1);
Expand Down Expand Up @@ -310,15 +314,13 @@ private void editResults()
});

// Verify that the edit was audited
AuditLogHelper auditLogHelper = new AuditLogHelper(this, () -> WebTestHelper.getRemoteApiConnection(false));
auditLogHelper.checkAuditEventDiffCount(getProjectName(), AuditLogHelper.AuditEvent.QUERY_UPDATE_AUDIT_EVENT, List.of(0/*delete*/, 4/*edit*/));

goToSchemaBrowser();
viewQueryData("auditLog", "ExperimentAuditEvent");
assertTextPresent(
"Data row, id ",
", edited in " + TEST_ASSAY + ".",
"Specimen ID changed from 'AAA07XK5-05' to 'EditedSpecimenID'",
"Visit ID changed from '601.0' to '601.5",
"testAssayDataProp5 changed from blank to '514801'",
"Deleted data row, id ");
assertTextPresent("1 data row has been edited in " + TEST_ASSAY + ".");

}

/**
Expand Down
2 changes: 1 addition & 1 deletion study/test/src/org/labkey/test/tests/study/StudyDatasetFileFieldTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ public void testFileField() throws IOException, CommandException
File downloadedFile = doAndWaitForDownload(() -> waitAndClick(WAIT_FOR_JAVASCRIPT, Locator.tagWithAttribute("a", "title", "Download attached file"), 0));
checker().verifyTrue("Incorrect file name ", FileUtils.contentEquals(downloadedFile, inputFile));

FileBrowserHelper.FileDetailInfo fileInfoOriginalFile = _fileBrowserHelper.getFileDetailInfo(getProjectName(), "sample.txt");
FileBrowserHelper.FileDetailInfo fileInfoOriginalFile = FileBrowserHelper.getFileDetailInfo(getProjectName(), "sample.txt");

goToFolderManagement().goToExportTab();
new Checkbox(Locator.tagWithText("label", "Files").precedingSibling("input").findElement(getDriver())).check();
Expand Down