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Merged
labkey-danield merged 6 commits into from
Aug 25, 2025
Merged

Add test coverage for issue 53421 #2645

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da389b0
Add test coverage for issue 53421
labkey-danield Aug 22, 2025
acb046f
Corrected a type and some comments.
labkey-danield Aug 22, 2025
7d3d0b7
Added checks to a linked data class and experiment (flow).
labkey-danield Aug 22, 2025
259feb1
Changing some variable names to add clarity.
labkey-danield Aug 23, 2025
0f59fc3
Change permissions for EXTERNAL_SCHEMA_USER to be Reader.
labkey-danield Aug 25, 2025
95d7919
Added an explicit check for Issue 53784.
labkey-danield Aug 25, 2025
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191 changes: 191 additions & 0 deletions src/org/labkey/test/tests/LinkedSchemaTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,17 @@
import org.labkey.test.SortDirection;
import org.labkey.test.TestFileUtils;
import org.labkey.test.TestTimeoutException;
import org.labkey.test.WebTestHelper;
import org.labkey.test.categories.Daily;
import org.labkey.test.categories.Data;
import org.labkey.test.components.CustomizeView;
import org.labkey.test.pages.list.EditListDefinitionPage;
import org.labkey.test.pages.list.GridPage;
import org.labkey.test.pages.query.QueryMetadataEditorPage;
import org.labkey.test.params.FieldDefinition;
import org.labkey.test.params.FieldInfo;
import org.labkey.test.params.experiment.DataClassDefinition;
import org.labkey.test.params.experiment.SampleTypeDefinition;
import org.labkey.test.params.list.IntListDefinition;
import org.labkey.test.params.list.ListDefinition;
import org.labkey.test.params.list.VarListDefinition;
Expand All @@ -40,7 +44,11 @@
import org.labkey.test.util.AuditLogHelper;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.LogMethod;
import org.labkey.test.util.PortalHelper;
import org.labkey.test.util.SchemaHelper;
import org.labkey.test.util.TestDataGenerator;
import org.labkey.test.util.exp.DataClassAPIHelper;
import org.labkey.test.util.exp.SampleTypeAPIHelper;

import java.io.File;
import java.io.IOException;
Expand Down Expand Up @@ -112,6 +120,7 @@ public class LinkedSchemaTest extends BaseWebDriverTest
private static final String STUDY_FOLDER = "StudyFolder"; // Folder used to validate fix for issues 32454 & 32456
private static final String MOTHER = "Mother";
private static final String READER_USER = "reader@linkedschema.test";
private static final String EXTERNAL_SCHEMA_USER = "external@linkedschema.test";
private final AuditLogHelper _auditLogHelper = new AuditLogHelper(this);

public static final String LIST_NAME = "LinkedSchemaTestPeople";
Expand Down Expand Up @@ -401,6 +410,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException
{
super.doCleanup(afterTest);
_userHelper.deleteUsers(false, READER_USER);
_userHelper.deleteUsers(false, EXTERNAL_SCHEMA_USER);
}

@BeforeClass
Expand Down Expand Up @@ -632,8 +642,10 @@ void setupProject()
{
ApiPermissionsHelper apiPermissionsHelper = new ApiPermissionsHelper(this);
_userHelper.createUser(READER_USER);
_userHelper.createUser(EXTERNAL_SCHEMA_USER);

_containerHelper.createProject(getProjectName(), null);
apiPermissionsHelper.setUserPermissions(EXTERNAL_SCHEMA_USER, "Reader");
_containerHelper.createSubfolder(getProjectName(), SOURCE_FOLDER);
// Enable linkedschematest in source folder so the "BPeopleTemplate" is visible.
_containerHelper.enableModule("linkedschematest");
Expand Down Expand Up @@ -918,6 +930,185 @@ public void testCoreLinkedSchemaFilters()
_schemaHelper.deleteSchema(sourceContainerPath, linkedSchemaName);
}

// Issue 53421: linked schemas can't use sample type as a source in a container different from where the type is defined
@Test
public void testLinkedSchemaToExternalSubfolder() throws IOException, CommandException
{

String externalProject = "Linked Schema Other Project" + TRICKY_CHARACTERS_FOR_PROJECT_NAMES;

log(String.format("Create a separate project %s.",
externalProject));

// Delete the external project if it already exists.
_containerHelper.deleteProject(externalProject, false);
_containerHelper.createProject(externalProject, null);

// Add the Experiment module to test schemas linked to exp.
_containerHelper.enableModule("Experiment");

validateExternalLinkedSampleType(externalProject);
validateExternalLinkedExperiment(externalProject);
validateExternalLinkedDataclass(externalProject);
}

private void validateExternalLinkedSampleType(String externalProject) throws IOException, CommandException
{
String subFolder = "Sub Folder " + TRICKY_CHARACTERS_FOR_PROJECT_NAMES + " Sample Type";
String subFolderPath = externalProject + "/" + subFolder;

String sampleType = TestDataGenerator.randomDomainName("Linked Schema Test");
String strField = TestDataGenerator.randomFieldName("Str");

log(String.format("Create sub-folder %s for the sample type test.", subFolderPath));
_containerHelper.createSubfolder(externalProject, subFolder);

List<String> expectedValues = populateDomain(externalProject, subFolder, true, sampleType, strField);

String linkedSampleTypeSchema = "External_Sample_Type_Schema";
validateExternalLinkedSchema(linkedSampleTypeSchema, subFolderPath, "samples", sampleType, strField, expectedValues);

}

private void validateExternalLinkedExperiment(String externalProject)
{
String subFolder = "Sub Folder " + TRICKY_CHARACTERS_FOR_PROJECT_NAMES + " Experiment";
String subfolderPath = externalProject + "/" + subFolder;

String subFolderRunGroup = "SubFolder Run Group";
createExperiment(externalProject, subFolder, subFolderRunGroup);

List<String> expectedValues = List.of(subFolderRunGroup);
String linkedExpRunSchema = "External_Exp_Run_Schema";

validateExternalLinkedSchema(linkedExpRunSchema, subfolderPath, "exp", "RunGroups", "Name", expectedValues);

}

private void validateExternalLinkedDataclass(String externalProject) throws IOException, CommandException
{

String subFolder = "Sub Folder " + TRICKY_CHARACTERS_FOR_PROJECT_NAMES + " DataClass";
String subfolderPath = externalProject + "/" + subFolder;

String dataClassName = TestDataGenerator.randomDomainName("Export data class");

// This is the last sscenario to run. Adding this check here will allow the other scenarios to run before the test fails.
//Issue 53784: Field name with a quote causes a "QueryParseException: syntax error" when creating a linked schema.
String strField = TestDataGenerator.randomFieldName("Str \" ");

log(String.format("Create sub-folder %s for the data classs test.", subfolderPath));
_containerHelper.createSubfolder(externalProject, subFolder);

List<String> expectedValues = populateDomain(externalProject, subFolder, false, dataClassName, strField);

String linkedDataclassSchema = "External_Dataclass_Schema";
validateExternalLinkedSchema(linkedDataclassSchema, subfolderPath, "exp.data", dataClassName, strField, expectedValues);

}

// Populating a sample type and a data class is very similar.
private List<String> populateDomain(String externalProject, String subFolder, boolean isSampleType, String query, String fieldName) throws IOException, CommandException
{

TestDataGenerator testDataGenerator;
FieldDefinition field = new FieldDefinition(fieldName);
String subFolderPath = externalProject + "/" + subFolder;
String schema;

if (isSampleType)
{
schema = "samples";
SampleTypeDefinition sampleTypeDefinition = new SampleTypeDefinition(query);
sampleTypeDefinition.setNameExpression("External ${genId}");
sampleTypeDefinition.addField(field);
testDataGenerator = SampleTypeAPIHelper.createEmptySampleType(externalProject, sampleTypeDefinition);
}
else
{
schema = "exp.data";
DataClassDefinition dataClassDefinition = new DataClassDefinition(query);
dataClassDefinition.setNameExpression("DC - ${genId}");
dataClassDefinition.addField(field);
testDataGenerator = DataClassAPIHelper.createEmptyDataClass(externalProject, dataClassDefinition);
}

for (String value : List.of("A", "B", "C", "D"))
{
testDataGenerator.addCustomRow(Map.of(fieldName, value));
}
testDataGenerator.insertRows(WebTestHelper.getRemoteApiConnection(), testDataGenerator.getRows());

// Add entries in the subfolder. Send these back as values to check.
List<String> subFolderValues = List.of("W", "X", "Y", "Z");
testDataGenerator = new TestDataGenerator(schema, query, subFolderPath);
for (String value : subFolderValues)
{
testDataGenerator.addCustomRow(Map.of(fieldName, value));
}
testDataGenerator.insertRows(WebTestHelper.getRemoteApiConnection(), testDataGenerator.getRows());

return subFolderValues;
}

private void createExperiment(String externalProject, String subFolder, String subFolderRunGroup)
{
// Create a RunGroup in the parent folder.
goToProjectHome(externalProject);
clickTab("Experiment");
waitAndClickAndWait(Locator.linkContainingText("Create Run Group"));
setFormElement(Locator.name("name"), "Parent Run Group");
clickButton("Submit");

_containerHelper.createSubfolder(externalProject, subFolder);

// Create a RunGroup in the subfolder.
clickTab("Experiment");
waitAndClickAndWait(Locator.linkContainingText("Create Run Group"));
setFormElement(Locator.name("name"), subFolderRunGroup);
clickButton("Submit");

}

private void validateExternalLinkedSchema(String linkedSchemaName, String sourceSubFolderPath, String sourceSchemaName, String sourceQueryName, String fieldName, List<String> expectedValues)
{
goToProjectHome();

log(String.format("Create a linked schema named %s that looks at %s.",
linkedSchemaName, sourceSubFolderPath));

_schemaHelper.createLinkedSchema(getProjectName(), linkedSchemaName, sourceSubFolderPath, null, sourceSchemaName, null, null);

goToProjectHome();

validateExternalLinkedData(linkedSchemaName, sourceQueryName, fieldName,
expectedValues, String.format("Data displayed for linked schema '%s' not as expected.", linkedSchemaName));

log("Impersonate a user, with no permissions in the external source project, and validate.");
goToProjectHome();
impersonate(EXTERNAL_SCHEMA_USER);
validateExternalLinkedData(linkedSchemaName, sourceQueryName, fieldName,
expectedValues, String.format("User with no permissions did not see the expected data for the linked schema '%s'.", linkedSchemaName));
stopImpersonating();
}

private void validateExternalLinkedData(String linkedSchemaName, String query, String fieldName, List<String> expectedValues, String errorMsg)
{

// Use a FieldInfo object to deal with any tricky characters.
FieldInfo fieldInfo = new FieldInfo(fieldName, FieldDefinition.ColumnType.String);
String url = WebTestHelper.buildURL("query", getProjectName(), "begin.view");
beginAt(url);
viewQueryData(linkedSchemaName, query);
DataRegionTable table = new DataRegionTable("query", getDriver());
List<String> actualValues = table.getColumnDataAsText(fieldInfo);

// Using a sort list to validate because the list should be equal and I don't want to worry about the order.
checker().withScreenshot().verifyEqualsSorted(errorMsg,
expectedValues, actualValues);

}

/*
Test coverage : Issue 45347: Audit table data not available in linked schema
*/
Expand Down