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GitHub Issue 903: Remove Cross-Container Sample and Data Class Import Feature #7698

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8ec8d70
GitHub Issue 903: Remove Cross-Container Sample and Data Class Import…
XingY May 26, 2026
c6d13ee
crlf
XingY May 27, 2026
47e754c
Fix merge samples that lack read permission to
XingY May 27, 2026
73cd2b3
Fix merge source that lack read permission to, update selenium tests
XingY May 27, 2026
72d421a
dataclass existing record fix
XingY May 28, 2026
f6cebd0
merge from develop
XingY May 28, 2026
6c02b6c
CC code review
XingY May 28, 2026
661ea91
Use a seeded PRNG for jest integration fuzz tests
XingY May 28, 2026
c5d89e8
make error consistent
XingY May 28, 2026
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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/dataiterator/DataClassUpdateAddColumnsDataIterator.java
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Expand Up @@ -125,7 +125,7 @@ protected void prefetchExisting() throws BatchValidationException
}

if (!notFoundKeys.isEmpty())
_context.getErrors().addRowError(new ValidationException("Data not found for " + notFoundKeys));
_context.getErrors().addRowError(new ValidationException("Data does not exist in " + _targetContainer.getName() + ": " + notFoundKeys + "."));

resetAfterBatch();
}
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11 changes: 0 additions & 11 deletions api/src/org/labkey/api/dataiterator/DataIteratorContext.java
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Expand Up @@ -54,7 +54,6 @@ public class DataIteratorContext
LookupResolutionType _lookupResolutionType = LookupResolutionType.primaryKey;
QueryImportPipelineJob _backgroundJob = null;
boolean _crossTypeImport = false;
boolean _crossFolderImport = false;
boolean _allowCreateStorage = false;
boolean _useTransactionAuditCache = false;
private final Set<String> _passThroughBuiltInColumnNames = new CaseInsensitiveHashSet();
Expand Down Expand Up @@ -202,16 +201,6 @@ public void setCrossTypeImport(boolean crossTypeImport)
_crossTypeImport = crossTypeImport;
}

public boolean isCrossFolderImport()
{
return _crossFolderImport;
}

public void setCrossFolderImport(boolean crossFolderImport)
{
_crossFolderImport = crossFolderImport;
}

public boolean isAllowCreateStorage()
{
return _allowCreateStorage;
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6 changes: 0 additions & 6 deletions api/src/org/labkey/api/query/AbstractQueryImportAction.java
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Expand Up @@ -311,7 +311,6 @@ public enum Params
crossTypeImport,
allowCreateStorage,
importLookupByAlternateKey, // deprecated. Prefer lookupResolutionType
crossFolderImport,
useTransactionAuditCache,
lookupResolutionType,
auditDetails,
Expand All @@ -331,7 +330,6 @@ protected Map<Params, Boolean> getOptionParamsMap()
_optionParamsMap.put(Params.importIdentity, Boolean.valueOf(getParam(Params.importIdentity)));
_optionParamsMap.put(Params.crossTypeImport, Boolean.valueOf(getParam(Params.crossTypeImport)));
_optionParamsMap.put(Params.allowCreateStorage, Boolean.valueOf(getParam(Params.allowCreateStorage)));
_optionParamsMap.put(Params.crossFolderImport, Boolean.valueOf(getParam(Params.crossFolderImport)));
_optionParamsMap.put(Params.useTransactionAuditCache, Boolean.valueOf(getParam(Params.useTransactionAuditCache)));
}
return _optionParamsMap;
Expand All @@ -345,8 +343,6 @@ protected Set<String> getTransactionImportParams(String insertOption, boolean us
importParams.add("backgroundImport");
if (Boolean.valueOf(getParam(Params.crossTypeImport)))
importParams.add(Params.crossTypeImport.name());
if (Boolean.valueOf(getParam(Params.crossFolderImport)))
importParams.add(Params.crossFolderImport.name());
if (Boolean.valueOf(getParam(Params.useTransactionAuditCache)))
importParams.add(Params.useTransactionAuditCache.name());
if (Boolean.valueOf(getParam(Params.allowCreateStorage)))
Expand Down Expand Up @@ -852,7 +848,6 @@ public static DataIteratorContext createDataIteratorContext(QueryUpdateService.I
boolean importIdentity = optionParamsMap.getOrDefault(AbstractQueryImportAction.Params.importIdentity, false);
boolean crossTypeImport = optionParamsMap.getOrDefault(AbstractQueryImportAction.Params.crossTypeImport, false);
boolean allowCreateStorage = optionParamsMap.getOrDefault(AbstractQueryImportAction.Params.allowCreateStorage, false);
boolean crossFolderImport = optionParamsMap.getOrDefault(AbstractQueryImportAction.Params.crossFolderImport, false);
boolean useTransactionAuditCache = optionParamsMap.getOrDefault(Params.useTransactionAuditCache, false);

DataIteratorContext context = new DataIteratorContext(errors);
Expand All @@ -874,7 +869,6 @@ public static DataIteratorContext createDataIteratorContext(QueryUpdateService.I
context.setSupportAutoIncrementKey(true);
}
context.setCrossTypeImport(crossTypeImport);
context.setCrossFolderImport(crossFolderImport && container != null && container.hasProductFolders());
context.setAllowCreateStorage(allowCreateStorage);
context.setUseTransactionAuditCache(useTransactionAuditCache);
context.setLogger(logger);
Expand Down
16 changes: 6 additions & 10 deletions api/src/org/labkey/api/query/AbstractQueryUpdateService.java
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Expand Up @@ -205,6 +205,8 @@ public Map<Integer, Map<String, Object>> getExistingRows(User user, Container co
Map<Integer, Map<String, Object>> result = new LinkedHashMap<>();
for (Map.Entry<Integer, Map<String, Object>> key : keys.entrySet())
{
String keyDisplay = key.getValue().toString();
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@labkey-nicka labkey-nicka May 28, 2026

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nit: Perhaps just inline so we only need to compute once when there is an error.


Map<String, Object> row = getRow(user, container, key.getValue(), verifyNoCrossFolderData);
if (row != null && !row.isEmpty())
{
Expand All @@ -215,21 +217,15 @@ public Map<Integer, Map<String, Object>> getExistingRows(User user, Container co
if (StringUtils.isEmpty(dataContainer))
dataContainer = (String) row.get("folder");
if (!container.getId().equals(dataContainer))
throw new InvalidKeyException("Data does not belong to folder '" + container.getName() + "': " + key.getValue().values());
throw new InvalidKeyException("Data does not exist in " + container.getName() + ": " + keyDisplay + ".");
}
}
else if (verifyExisting)
throw new InvalidKeyException("Data not found for " + key.getValue().values());
throw new InvalidKeyException("Data does not exist in " + container.getName() + ": " + keyDisplay + ".");
}
return result;
}

@Override
public boolean hasExistingRowsInOtherContainers(Container container, Map<Integer, Map<String, Object>> keys)
{
return false;
}

public static TransactionAuditProvider.TransactionAuditEvent createTransactionAuditEvent(Container container, QueryService.AuditAction auditAction)
{
return createTransactionAuditEvent(container, auditAction, null);
Expand Down Expand Up @@ -408,7 +404,7 @@ protected int _importRowsUsingDIB(User user, Container container, DataIteratorBu

preImportDIBValidation(in, null);

boolean skipTriggers = context.getConfigParameterBoolean(ConfigParameters.SkipTriggers) || context.isCrossTypeImport() || context.isCrossFolderImport();
boolean skipTriggers = context.getConfigParameterBoolean(ConfigParameters.SkipTriggers) || context.isCrossTypeImport();
boolean hasTableScript = hasTableScript(container);
TriggerDataBuilderHelper helper = new TriggerDataBuilderHelper(getQueryTable(), container, user, extraScriptContext, context.getInsertOption().useImportAliases);
if (!skipTriggers)
Expand Down Expand Up @@ -1299,7 +1295,7 @@ static FileLike checkFileUnderRoot(Container container, FileLike file) throws Ex

protected void _addSummaryAuditEvent(Container container, User user, DataIteratorContext context, int count)
{
if (!context.isCrossTypeImport() && !context.isCrossFolderImport()) // audit handled at table level
if (!context.isCrossTypeImport()) // audit handled at table level
{
AuditBehaviorType auditType = (AuditBehaviorType) context.getConfigParameter(DetailedAuditLogDataIterator.AuditConfigs.AuditBehavior);
String auditUserComment = (String) context.getConfigParameter(DetailedAuditLogDataIterator.AuditConfigs.AuditUserComment);
Expand Down
8 changes: 0 additions & 8 deletions api/src/org/labkey/api/query/CacheClearingQueryUpdateService.java
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Expand Up @@ -52,14 +52,6 @@ public List<Map<String, Object>> getRows(User user, Container container, List<Ma
return _service.getRows(user, container, keys);
}

@Override
public boolean hasExistingRowsInOtherContainers(Container container, Map<Integer, Map<String, Object>> keys)
{
var ret = _service.hasExistingRowsInOtherContainers(container, keys);
clearCache();
return ret;
}

@Override
public Map<Integer, Map<String, Object>> getExistingRows(User user, Container container, Map<Integer, Map<String, Object>> keys, boolean verifyNoCrossFolderData, boolean verifyExisting, Set<String> columns)
throws InvalidKeyException, QueryUpdateServiceException, SQLException
Expand Down
19 changes: 0 additions & 19 deletions api/src/org/labkey/api/query/DefaultQueryUpdateService.java
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Expand Up @@ -915,25 +915,6 @@ protected boolean isAttachmentProperty(String name)
return false;
}

protected void configureCrossFolderImport(DataIteratorBuilder rows, DataIteratorContext context) throws IOException
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@labkey-nicka labkey-nicka May 28, 2026

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nit: (unrelated) unused imports

{
if (!context.getInsertOption().updateOnly && context.isCrossFolderImport() && rows instanceof DataLoader dataLoader)
{
boolean hasContainerField = false;
for (ColumnDescriptor columnDescriptor : dataLoader.getColumns())
{
String fieldName = columnDescriptor.getColumnName();
if (fieldName.equalsIgnoreCase("Container") || fieldName.equalsIgnoreCase("Folder"))
{
hasContainerField = true;
break;
}
}
if (!hasContainerField)
context.setCrossFolderImport(false);
}
}

public static @Nullable String getKeyColumnAliasForUpdate(TableInfo tableInfo, @NotNull Map<String, Integer> columnNameMap)
{
// Currently, SampleUpdateAddColumnsDataIterator and DataClassUpdateAddColumnsDataIterator is being called before a translator is invoked to
Expand Down
2 changes: 0 additions & 2 deletions api/src/org/labkey/api/query/QueryUpdateService.java
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Expand Up @@ -149,8 +149,6 @@ List<Map<String, Object>> getRows(User user, Container container, List<Map<Strin
Map<Integer, Map<String, Object>> getExistingRows(User user, Container container, Map<Integer, Map<String, Object>> keys, boolean verifyNoCrossFolderData, boolean verifyExisting, @Nullable Set<String> columns)
throws InvalidKeyException, QueryUpdateServiceException, SQLException;

boolean hasExistingRowsInOtherContainers(Container container, Map<Integer, Map<String, Object>> keys);

/**
* Inserts or merges the given values into the source table of this query.
* The operation to be performed and import behavior is configured by the <code>context</code> parameter.
Expand Down
8 changes: 4 additions & 4 deletions experiment/package-lock.json
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2 changes: 1 addition & 1 deletion experiment/package.json
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Expand Up @@ -17,7 +17,7 @@
},
"devDependencies": {
"@labkey/build": "9.1.4",
"@labkey/test": "1.13.2",
"@labkey/test": "1.14.0-fb-dropCrossFolder.1",
"@types/jest": "30.0.0",
"@types/react": "18.3.27",
"@types/react-dom": "18.3.7",
Expand Down
5 changes: 3 additions & 2 deletions experiment/src/client/test/integration/AssayDesignCrud.ispec.ts
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@@ -1,4 +1,4 @@
import { hookServer, RequestOptions, selectRandomN, successfulResponse } from '@labkey/test';
import { hookServer, RequestOptions, selectRandomN, successfulResponse, testSeed } from '@labkey/test';

import {
deleteAssayDesign,
Expand All @@ -12,7 +12,8 @@ import { ASSAY_DESIGNER_ROLE } from '@labkey/components';

// @ts-expect-error process is not available in a browser environment
const server = hookServer(process.env);
const PROJECT_NAME = 'DataClassCrudJestProject';
const PROJECT_NAME = 'AssayDesignCrudJestProject';
console.log(`[AssayDesignCrud] Random seed: ${testSeed} (rerun with: TEST_SEED=${testSeed})`);
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@labkey-nicka labkey-nicka May 28, 2026

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Perhaps we console log this during init() in integrationUtils.ts like we do the server and container path? Then each test would not need to log it themselves.

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@XingY XingY May 28, 2026

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Yep, it's already logged in init(). I decided to also log it individually for ease of locating the seed as teamcity build log could get long and/or corrupted.


let readerUser, readerUserOptions;
let editorUser, editorUserOptions;
Expand Down
5 changes: 4 additions & 1 deletion experiment/src/client/test/integration/AssayImportRunAction.ispec.ts
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@@ -1,4 +1,4 @@
import { hookServer, IntegrationTestServer, RequestOptions, successfulResponse } from '@labkey/test';
import { hookServer, IntegrationTestServer, RequestOptions, successfulResponse, testSeed } from '@labkey/test';
import mock from 'mock-fs';

import {
Expand Down Expand Up @@ -27,6 +27,9 @@ import {
// @ts-expect-error process is not available in a browser environment
const server = hookServer(process.env);
const PROJECT_NAME = 'ArrayImportRunActionTest Project';

console.log(`[ArrayImportRunAction] Random seed: ${testSeed} (rerun with: TEST_SEED=${testSeed})`);

const BATCH_FILE_FIELD_NAME = 'batchFileField';
const BATCH_FILE_FIELD_TWO_NAME = 'batchFile2Field';
const RUN_FILE_FIELD_NAME = 'runFileField';
Expand Down
15 changes: 8 additions & 7 deletions experiment/src/client/test/integration/DataClassCrud.ispec.ts
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Expand Up @@ -4,7 +4,8 @@ import {
getEscapedNameExpression,
hookServer,
RequestOptions,
successfulResponse
successfulResponse,
testSeed
} from '@labkey/test';
import mock from 'mock-fs';
import {
Expand All @@ -22,6 +23,7 @@ import {
import { caseInsensitive, DATA_CLASS_DESIGNER_ROLE } from '@labkey/components';
const server = hookServer(process.env);
const PROJECT_NAME = 'DataClassCrudJestProject';
console.log(`[DataClassCrud] Random seed: ${testSeed} (rerun with: TEST_SEED=${testSeed})`);

let readerUser, readerUserOptions;
let editorUser, editorUserOptions;
Expand Down Expand Up @@ -278,8 +280,7 @@ describe('Import with update / merge', () => {
it ("Issue 52922: Blank sample id in the file are getting ignored in update from file", async () => {
const BLANK_KEY_UPDATE_ERROR_NO_EXPRESSION = 'Missing value for required property: Name';
const BLANK_KEY_UPDATE_ERROR_WITH_EXPRESSION = 'Name value not provided on row ';
const BOGUS_KEY_UPDATE_ERROR = 'Data not found for ';
const DUPLICATE_KEY_ERROR = 'duplicate key value';
const BOGUS_KEY_UPDATE_ERROR = 'Data does not exist in ';

const dataType = "NoExpressionNameRequired52922";
const createPayload = {
Expand Down Expand Up @@ -349,9 +350,9 @@ describe('Import with update / merge', () => {
successResp = await ExperimentCRUDUtils.importData(server, "Name\tDescription\n\tisBlank", dataTypeWithExpression, "MERGE", subfolder1Options, editorUserOptions);
expect(successResp.text.indexOf('"success" : true') > -1).toBeTruthy();

// cross folder update not supported when folder type is "Collaboration"
// cross folder update not supported
let crossFolderErrorResp = await ExperimentCRUDUtils.importData(server, "Name\tDescription\nData1\tNotblank\n\tisBlank", dataTypeWithExpression, "MERGE", subfolder1Options, editorUserOptions);
expect(crossFolderErrorResp.text.indexOf(DUPLICATE_KEY_ERROR) > -1).toBeTruthy();
expect(crossFolderErrorResp.text.indexOf(BOGUS_KEY_UPDATE_ERROR) > -1).toBeTruthy();
crossFolderErrorResp = await ExperimentCRUDUtils.importData(server, "Name\tDescription\nData1\tNotblank", dataTypeWithExpression, "UPDATE", subfolder1Options, editorUserOptions);
expect(crossFolderErrorResp.text.indexOf(BOGUS_KEY_UPDATE_ERROR) > -1).toBeTruthy();

Expand Down Expand Up @@ -1140,12 +1141,12 @@ describe('Data CRUD', () => {
}]
}, { ...topFolderOptions, ...editorUserOptions }).expect((result) => {
const errorResp = JSON.parse(result.text);
expect(errorResp['exception']).toContain('Data not found for [' + row3RowId + ']');
expect(errorResp['exception']).toContain('Data does not exist in ' + PROJECT_NAME + ': {RowId=' + row3RowId + '}.');
});

// using update from file, verify update using rowId for data that doesn't exist on this dataclass should fail.
errorResp = await ExperimentCRUDUtils.importData(server, "RowId\tDescription\n" + row3RowId + "\tupdate\n", emptyDataClass, "UPDATE", topFolderOptions, editorUserOptions);
expect(errorResp.text).toContain('Data not found for [' + row3RowId + ']');
expect(errorResp.text).toContain('Data does not exist in ' + PROJECT_NAME + ': {RowId=' + row3RowId + '}.');

});

Expand Down
22 changes: 15 additions & 7 deletions experiment/src/client/test/integration/SampleTypeCrud.ispec.ts
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@@ -1,4 +1,11 @@
import { ExperimentCRUDUtils, hookServer, RequestOptions, selectRandomN, successfulResponse } from '@labkey/test';
import {
ExperimentCRUDUtils,
hookServer,
RequestOptions,
selectRandomN,
successfulResponse,
testSeed
} from '@labkey/test';
import mock from 'mock-fs';
import {
checkDomainName,
Expand All @@ -15,6 +22,8 @@ const { importSample, insertRows } = ExperimentCRUDUtils;
const server = hookServer(process.env);
const PROJECT_NAME = 'SampleTypeCrudJestProject';

console.log(`[SampleTypeCrud] Random seed: ${testSeed} (rerun with: TEST_SEED=${testSeed})`);

const SAMPLE_ALIQUOT_IMPORT_TYPE_NAME = "SampleType_Aliquots_Import";
const SAMPLE_ALIQUOT_REQ_IMPORT_TYPE_NAME = "Aliquot_Import_RequiredProp";
const SAMPLE_ALIQUOT_IMPORT_NO_NAME_PATTERN_NAME = "SampleType_Aliquots_Import_NoExpression";
Expand Down Expand Up @@ -318,8 +327,7 @@ describe('Import with update / merge', () => {
it ("Issue 52922: Blank sample id in the file are getting ignored in update from file", async () => {
const BLANK_KEY_UPDATE_ERROR = 'Name value not provided';
const BLANK_KEY_MERGE_ERROR_NO_EXPRESSION = 'SampleID or Name is required for sample';
const BOGUS_KEY_UPDATE_ERROR = 'Sample does not exist: bogus.';
const CROSS_FOLDER_UPDATE_NOT_SUPPORTED_ERROR = "Sample does not belong to ";
const BOGUS_KEY_UPDATE_ERROR = 'Sample does not exist in ';

const dataType = SAMPLE_ALIQUOT_IMPORT_NO_NAME_PATTERN_NAME;
const dataName = "Data1";
Expand Down Expand Up @@ -369,11 +377,11 @@ describe('Import with update / merge', () => {
successResp = await ExperimentCRUDUtils.importSample(server, "Name\tDescription\n\tisBlank", dataTypeWithExpression, "MERGE", subfolder1Options, editorUserOptions);
expect(successResp.text.indexOf('"success" : true') > -1).toBeTruthy();

// cross folder update not supported when folder type is "Collaboration"
// cross folder update not supported
let crossFolderUpdateErrorResp = await ExperimentCRUDUtils.importSample(server, "Name\tDescription\nData1\tNotblank", dataTypeWithExpression, "UPDATE", subfolder1Options, editorUserOptions);
expect(crossFolderUpdateErrorResp.text.indexOf(CROSS_FOLDER_UPDATE_NOT_SUPPORTED_ERROR) > -1).toBeTruthy();
expect(crossFolderUpdateErrorResp.text.indexOf(BOGUS_KEY_UPDATE_ERROR) > -1).toBeTruthy();
let crossFolderMergeErrorResp = await ExperimentCRUDUtils.importSample(server, "Name\tDescription\nData1\tNotblank\n\tisBlank", dataTypeWithExpression, "MERGE", subfolder1Options, editorUserOptions);
expect(crossFolderMergeErrorResp.text.indexOf(CROSS_FOLDER_UPDATE_NOT_SUPPORTED_ERROR) > -1).toBeTruthy();
expect(crossFolderMergeErrorResp.text.indexOf(BOGUS_KEY_UPDATE_ERROR) > -1).toBeTruthy();

// bogus name
bogusKeyProvidedError = await ExperimentCRUDUtils.importSample(server, "Name\tDescription\nbogus\tisBogus", dataTypeWithExpression, "UPDATE", topFolderOptions, editorUserOptions);
Expand Down Expand Up @@ -487,7 +495,7 @@ describe('Import with update / merge', () => {
// Assert
// Verify that these rows are not updated
expect(resp.body.success).toEqual(false);
expect(resp.body.exception).toContain('Sample does not exist: (RowId)');
expect(resp.body.exception).toContain('Sample does not exist in ' + PROJECT_NAME + ': (RowId)');
})
});

Expand Down
3 changes: 2 additions & 1 deletion experiment/src/client/test/integration/utils.ts
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Expand Up @@ -2,6 +2,7 @@ import {
ExperimentCRUDUtils,
generateFieldName,
IntegrationTestServer,
random,
RequestOptions,
selectRandomN,
successfulResponse,
Expand Down Expand Up @@ -632,7 +633,7 @@ export async function verifyRequiredLineageInsertUpdate(server: IntegrationTestS
const dataType = "withRequired" + (isParentSample ? 'SampleParent' : 'DataParent');
let childDomainId = -1, childDomainURI = '';

const useLowerCase = Math.random() < 0.5;
const useLowerCase = random() < 0.5;
// test both lower case and upper case prefix
const parentInput = (isParentSample ? (useLowerCase ? 'materialInputs/' : 'MaterialInputs/') : (useLowerCase ? 'dataInputs/' : 'DataInputs/')) + parentDataType;
await server.post('property', 'createDomain', {
Expand Down
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