From ae521afc24ac90e9b0194eae2af9f9a5094273e7 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 5 Oct 2026 10:04:29 -0700 Subject: [PATCH 1/3] GH Issue 980: Remove deprecated UI for deriving samples in LKS interface --- .../SampleTypeFolderExportImportTest.java | 12 +- .../test/tests/SampleTypeLimitsTest.java | 74 ++--- .../test/tests/SampleTypeLineageTest.java | 313 +++--------------- .../test/tests/SampleTypeLinkToStudyTest.java | 43 +-- .../tests/SampleTypeNameExpressionTest.java | 56 +--- 5 files changed, 103 insertions(+), 395 deletions(-) diff --git a/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java b/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java index eaef546e67..907b5f8b44 100644 --- a/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java +++ b/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java @@ -46,7 +46,6 @@ import org.labkey.test.util.DataRegionTable; import org.labkey.test.util.EscapeUtil; import org.labkey.test.util.LogMethod; -import org.labkey.test.util.OptionalFeatureHelper; import org.labkey.test.util.PortalHelper; import org.labkey.test.util.SampleTypeHelper; import org.labkey.test.util.TestDataGenerator; @@ -102,15 +101,8 @@ public BrowserType bestBrowser() protected void doCleanup(boolean afterTest) { super.doCleanup(afterTest); - if (afterTest) - { - OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp"); - } - else { - OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp", true); - SampleTypeFolderExportImportTest init = getCurrentTest(); - init.doSetup(); - } + SampleTypeFolderExportImportTest init = getCurrentTest(); + init.doSetup(); } private void doSetup() diff --git a/src/org/labkey/test/tests/SampleTypeLimitsTest.java b/src/org/labkey/test/tests/SampleTypeLimitsTest.java index 4933febe16..c29d3dc43b 100644 --- a/src/org/labkey/test/tests/SampleTypeLimitsTest.java +++ b/src/org/labkey/test/tests/SampleTypeLimitsTest.java @@ -36,10 +36,10 @@ import org.labkey.test.params.list.ListDefinition; import org.labkey.test.params.list.VarListDefinition; import org.labkey.test.util.DataRegionTable; -import org.labkey.test.util.OptionalFeatureHelper; import org.labkey.test.util.PortalHelper; import org.labkey.test.util.SampleTypeHelper; import org.labkey.test.util.TestDataGenerator; +import org.labkey.test.util.query.QueryApiHelper; import java.io.IOException; import java.util.Arrays; @@ -118,13 +118,6 @@ private void doSetup() } } - @Override - protected void doCleanup(boolean afterTest) - { - super.doCleanup(afterTest); - OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp"); - } - @Test public void testStringLookupFields() throws IOException, CommandException { @@ -203,48 +196,55 @@ private void insertSampleTypeRow(String regionName, String rowValue) @Test public void testDeriveSamplesLookupFields() throws IOException, CommandException { - goToProjectHome(); - OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp", true); - log("Create sample type with lookup field to " + SAMPLE_TYPE_NAME); String sampleTypeName = "SampleTypeWithLookup"; - SampleTypeHelper sampleHelper = new SampleTypeHelper(this); - SampleTypeDefinition definition = new SampleTypeDefinition(sampleTypeName); - definition.addField(new FieldDefinition("label", FieldDefinition.ColumnType.String)); - definition.addField(new FieldDefinition("lookUpField", - new FieldDefinition.LookupInfo(null, "exp.materials", "10000Samples") - .setTableType(FieldDefinition.ColumnType.Integer)) - .setDescription("LookUp in same container with 10000 samples")); - sampleHelper.createSampleType(definition); - sampleHelper.goToSampleType(sampleTypeName); + new SampleTypeDefinition(sampleTypeName) + .addField(new FieldDefinition("label", FieldDefinition.ColumnType.String)) + .addField(new FieldDefinition("lookUpField", + new FieldDefinition.LookupInfo(null, "exp.materials", SAMPLE_TYPE_NAME) + .setTableType(FieldDefinition.ColumnType.Integer)) + .setDescription("LookUp in same container with 10000 samples")) + .create(createDefaultConnection(), getProjectName()); + QueryApiHelper queryHelper = new QueryApiHelper(createDefaultConnection(), getProjectName(), "samples", sampleTypeName); log("Insert one sample that we can use to derive from"); - insertSampleTypeRow("Material", "Test1"); + queryHelper.insertRows(List.of(Map.of("Name", "Test1", "label", "Test1"))); + String parentColumn = "MaterialInputs/" + sampleTypeName; - log("Attempt Derive Samples with invalid lookup value"); - initDeriveSamplesForm(sampleTypeName, "Derivative1"); - verifyInvalidLookupSample("Output Sample 1_lookUpField", "Sample3", "Could not convert value 'Sample3' (String) for Integer field 'lookUpField'."); + log("Attempt to derive a sample with invalid lookup value"); + try + { + queryHelper.importData(deriveSampleTsv(parentColumn, "Derivative1", "Sample3"), true); + fail("Deriving a sample with an invalid lookup value should fail"); + } + catch (CommandException e) + { + checker().verifyTrue("Unexpected error for invalid lookup value: " + e.getMessage(), e.getMessage().contains("Sample3")); + } - log("Insert Derive Samples with valid lookup display value"); - verifyValidLookupSample("Output Sample 1_lookUpField", "Sample2", "Sample2", "Material", true); + log("Derive a sample with valid lookup display value"); + queryHelper.importData(deriveSampleTsv(parentColumn, "Derivative1", "Sample2"), true); - log("Insert Derive Samples with valid lookup to sample RowId"); - initDeriveSamplesForm(sampleTypeName, "Derivative2"); + log("Derive a sample with valid lookup to sample RowId"); SelectRowsCommand command = new SelectRowsCommand("samples", SAMPLE_TYPE_NAME); command.setFilters(Arrays.asList(new Filter("Name", "Sample1"))); SelectRowsResponse response = command.execute(createDefaultConnection(), getProjectName()); - verifyValidLookupSample("Output Sample 1_lookUpField", response.getRows().getFirst().get("RowId").toString(), "Sample1", "Material", true); + queryHelper.importData(deriveSampleTsv(parentColumn, "Derivative2", response.getRows().getFirst().get("RowId").toString()), true); + + log("Verify derived samples have the expected lookup values"); + goToProjectHome(); + SampleTypeHelper sampleHelper = new SampleTypeHelper(this); + sampleHelper.goToSampleType(sampleTypeName); + DataRegionTable table = sampleHelper.getSamplesDataRegionTable(); + checker().verifyEquals("Lookup field value is incorrect", "Sample2", + table.getDataAsText(table.getRowIndex("Name", "Derivative1"), "lookUpField")); + checker().verifyEquals("Lookup field value is incorrect", "Sample1", + table.getDataAsText(table.getRowIndex("Name", "Derivative2"), "lookUpField")); } - private void initDeriveSamplesForm(String sampleTypeName, String sampleName) + private String deriveSampleTsv(String parentColumn, String sampleName, String lookupValue) { - DataRegionTable samplesTable = DataRegionTable.DataRegion(getDriver()).withName("Material").waitFor(); - samplesTable.uncheckAllOnPage(); - samplesTable.checkCheckbox(0); - samplesTable.clickHeaderButtonAndWait("Derive Samples"); - selectOptionByText(Locator.name("targetSampleTypeId"), sampleTypeName + " in /" + getProjectName()); - clickButton("Next"); - setFormElement(Locator.name("Output Sample 1_Name"), sampleName); + return "Name\t" + parentColumn + "\tlookUpField\n" + sampleName + "\tTest1\t" + lookupValue + "\n"; } @Test diff --git a/src/org/labkey/test/tests/SampleTypeLineageTest.java b/src/org/labkey/test/tests/SampleTypeLineageTest.java index 47dcac6485..0bf71bb341 100644 --- a/src/org/labkey/test/tests/SampleTypeLineageTest.java +++ b/src/org/labkey/test/tests/SampleTypeLineageTest.java @@ -29,7 +29,6 @@ import org.labkey.test.BaseWebDriverTest; 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.Daily; import org.labkey.test.components.ext4.Window; @@ -38,18 +37,17 @@ import org.labkey.test.params.experiment.DataClassDefinition; import org.labkey.test.params.experiment.SampleTypeDefinition; import org.labkey.test.util.DataRegionTable; -import org.labkey.test.util.OptionalFeatureHelper; import org.labkey.test.util.PortalHelper; import org.labkey.test.util.SampleTypeHelper; import org.labkey.test.util.TestDataGenerator; +import org.labkey.test.util.exp.SampleTypeAPIHelper; +import org.labkey.test.util.query.QueryApiHelper; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; -import java.util.Date; -import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.stream.Collectors; @@ -101,15 +99,6 @@ private void doSetup() portalHelper.addWebPart("Sample Types"); portalHelper.exitAdminMode(); - OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp", true); - } - - @Override - protected void doCleanup(boolean afterTest) throws TestTimeoutException - { - super.doCleanup(afterTest); - - OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp"); } /** @@ -215,7 +204,7 @@ public void testLineageWithParentInRootFolder() } @Test - public void testSampleTypeAndLineageInSubfolder() + public void testSampleTypeAndLineageInSubfolder() throws IOException, CommandException { /* This test will create a sample type named "ParentFolder_SampleType" in the root folder. @@ -270,67 +259,24 @@ at ParentFolder_SampleType in the sub folder it should see one sample (the deriv checker().wrapAssertion(()->assertTextNotPresent(parentFolderSampleType)); log("Derive two samples from the samples already present in this sample type (SubFolder_SampleType)."); - clickFolder(SUB_FOLDER_NAME); - checker().wrapAssertion(()->assertTextPresent(subFolderSampleType, parentFolderSampleType)); - - clickAndWait(Locator.linkWithText(subFolderSampleType)); - checkCheckbox(Locator.name(".toggle")); - clickButton("Derive Samples"); - waitForElement(Locator.name("inputRole0")); - - selectOptionByText(Locator.name("inputRole0"), "Add a new role..."); - setFormElement(Locator.id("customRole0"), "FirstRole"); - selectOptionByText(Locator.name("inputRole1"), "Add a new role..."); - setFormElement(Locator.id("customRole1"), "SecondRole"); - selectOptionByText(Locator.name("inputRole2"), "Add a new role..."); - setFormElement(Locator.id("customRole2"), "ThirdRole"); - selectOptionByText(Locator.name("inputRole3"), "Add a new role..."); - setFormElement(Locator.id("customRole3"), "FourthRole"); - selectOptionByText(Locator.name("outputCount"), "2"); - selectOptionByText(Locator.name("targetSampleTypeId"), subFolderSampleType + " in /" + getProjectName() + "/" + SUB_FOLDER_NAME); - clickButton("Next"); - - setFormElement(Locator.name("Output Sample 1_Name"), "SampleSetBVT15"); - setFormElement(Locator.name("Output Sample 2_Name"), "SampleSetBVT16"); - checkCheckbox(Locator.name("outputSample1_IntColFolderCheckBox")); - setFormElement(Locator.name("Output Sample 1_IntCol-Folder"), "500a"); - setFormElement(Locator.name("Output Sample 1_StringCol-Folder"), "firstOutput"); - setFormElement(Locator.name("Output Sample 2_StringCol-Folder"), "secondOutput"); - clickButton("Submit"); - - log("Do a simple check that data validation works."); - checker().verifyTrue("Expected error message '(String) for Integer field' is not present.", - isTextPresent("(String) for Integer field")); - checkCheckbox(Locator.name("outputSample1_IntColFolderCheckBox")); - setFormElement(Locator.name("Output Sample 1_IntCol-Folder"), "500"); - clickButton("Submit"); - - clickAndWait(Locator.linkContainingText("Derive 2 samples")); - clickAndWait(Locator.linkContainingText("Text View")); - assertTextPresent("FirstRole", "SecondRole", "ThirdRole", "FourthRole"); - - log("Select one of these new derived samples and derive a sample from it"); - log("But put this new derived sample in the sample type created in the parent folder (ParentFolder_SampleType)"); - clickAndWait(Locator.linkContainingText("16")); - clickAndWait(Locator.linkContainingText("derive samples from this sample")); - - selectOptionByText(Locator.name("inputRole0"), "FirstRole"); - selectOptionByText(Locator.name("targetSampleTypeId"), parentFolderSampleType + " in /" + getProjectName()); - clickButton("Next"); - + String subFolderPath = getProjectName() + "/" + SUB_FOLDER_NAME; + String grandparents = "SampleSetBVT11,SampleSetBVT4,SampleSetBVT12,SampleSetBVT13,SampleSetBVT14"; + new QueryApiHelper(createDefaultConnection(), subFolderPath, "samples", subFolderSampleType) + .insertRows(List.of( + Map.of("Name", "SampleSetBVT15", "IntCol-Folder", 500, "StringCol-Folder", "firstOutput", + "MaterialInputs/" + subFolderSampleType, grandparents), + Map.of("Name", "SampleSetBVT16", "StringCol-Folder", "secondOutput", + "MaterialInputs/" + subFolderSampleType, grandparents))); + + log("Derive a sample from one of these new derived samples but put it in the sample type created in the parent folder (ParentFolder_SampleType)"); String derivedSampleName = "Only_In_Sub_Folder"; - setFormElement(Locator.name("Output Sample 1_Name"), derivedSampleName); - setFormElement(Locator.name("Output Sample 1_IntCol"), "600"); - setFormElement(Locator.name("Output Sample 1_StringCol"), "String"); - setFormElement(Locator.name("Output Sample 1_DateCol"), "BadDate"); - uncheckCheckbox(Locator.name("Output Sample 1_BoolCol")); - clickButton("Submit"); - - log("Again check that data validation works as expected."); - checker().verifyTrue("Expected error message 'is not a valid Date' is not present.", - isTextPresent(getConversionErrorMessage("BadDate", "DateCol", Date.class))); - setFormElement(Locator.name("Output Sample 1_DateCol"), "1/1/2007"); - clickButton("Submit"); + new QueryApiHelper(createDefaultConnection(), subFolderPath, "samples", parentFolderSampleType) + .insertRows(List.of(Map.of("Name", derivedSampleName, "IntCol", 600, "StringCol", "String", + "DateCol", "1/1/2007", "BoolCol", false, + "MaterialInputs/" + subFolderSampleType, "SampleSetBVT16"))); + + Integer derivedRowId = SampleTypeAPIHelper.getRowIdsForSamples(subFolderPath, parentFolderSampleType, List.of(derivedSampleName)).get(derivedSampleName); + beginAt(WebTestHelper.buildURL("experiment", subFolderPath, "showMaterial", Map.of("rowId", derivedRowId))); log("Check that the correct sample id is shown as the parent."); checker().verifyTrue("Link to parent sample not present.", @@ -353,10 +299,7 @@ at ParentFolder_SampleType in the sub folder it should see one sample (the deriv isElementPresent(Locator.linkWithText("Derive sample from SampleSetBVT16"))); checker().verifyTrue("Expected run text is not present.", - isElementPresent( - Locator.linkWithText("Derive 2 samples from SampleSetBVT11, SampleSetBVT12, SampleSetBVT13, SampleSetBVT14, SampleSetBVT4") - ) - ); + isElementPresent(Locator.linkContainingText("Derive 2 samples from "))); log("Go to the 'SubFolder_SampleType' and make sure the expected data is there."); clickFolder(SUB_FOLDER_NAME); @@ -600,163 +543,6 @@ public void testDeriveSampleByImport() assertNotEquals("RowD should not equal C", rowD.get("Run"), rowC.get("Run")); } - @Test - public void testDeriveSampleByUI() throws CommandException, IOException - { - String sampleTypeName= "LineageUI_01"; - String namePrefix = "SampleUI-"; - int newSampleIndex = 6; - - goToProjectHome(); - - log("Create a simple sample type with some samples."); - final TestDataGenerator dgen = new SampleTypeDefinition(sampleTypeName) - .create(createDefaultConnection(), getProjectName()); - - for(int i = 1; i < newSampleIndex; i++) - { - Map sampleData = new HashMap<>(); - sampleData.put("name", namePrefix + i); - dgen.addCustomRow(sampleData); - } - - dgen.insertRows(createDefaultConnection(), dgen.getRows()); - // Refresh the page so the new sample type shows up in the UI. - refresh(); - waitAndClickAndWait(Locator.linkWithText(sampleTypeName)); - - log("Go to the first samples detail page and derive a sample from it."); - - String parentSample = namePrefix + "1"; - log(String.format("Using sample named '%s' as the parent.", parentSample)); - - waitAndClickAndWait(Locator.linkWithText(parentSample)); - - waitAndClickAndWait(Locator.linkWithText("derive samples from this sample")); - - log("Nothing fancy just going to create a single derived sample in the same sample type."); - waitAndClickAndWait(Locator.lkButton("Next")); - Locator nameTxtbox = Locator.inputByNameContaining("_Name"); - waitForElement(nameTxtbox); - - String newSampleName = namePrefix + newSampleIndex; - log(String.format("The new sample will be named '%s' and it shall go forth upon the land.", newSampleName)); - - setFormElement(nameTxtbox, newSampleName); - clickAndWait(Locator.lkButton("Submit")); - - // Increment the index. - newSampleIndex++; - - log(String.format("Check that '%s' is shown as the parent.", parentSample)); - checkRowsInDataRegion("parentMaterials", "Name", List.of(parentSample)); - - log(String.format("Go to the detail page for '%s' and verify it has a child.", parentSample)); - clickAndWait(Locator.linkWithText(parentSample)); - checkRowsInDataRegion("childMaterials", "Name", List.of(newSampleName)); - - log("For the parent also verify that the run column (for the child sample) is populated as expected."); - String runTextStrFormat = "Derive sample from %s"; - checkRowsInDataRegion("childMaterials", "Run", List.of(String.format(runTextStrFormat, parentSample))); - - log("Go back to the sample type page and select several samples from the grid and derive a sample from them."); - goToProjectHome(); - SampleTypeHelper sampleHelper = new SampleTypeHelper(this); - - sampleHelper.goToSampleType(sampleTypeName); - DataRegionTable drt = sampleHelper.getSamplesDataRegionTable(); - - List parents = Arrays.asList(namePrefix + "2", namePrefix + "3", namePrefix + "4"); - log(String.format("Using samples '%s' as the parents.", parents)); - - for(String parent : parents) - { - int index = drt.getRowIndex("Name", parent); - drt.checkCheckbox(index); - } - - drt.clickHeaderButtonAndWait("Derive Samples"); - log("Again, nothing fancy just going to create a single derived sample."); - waitAndClickAndWait(Locator.lkButton("Next")); - nameTxtbox = Locator.inputByNameContaining("_Name"); - waitForElement(nameTxtbox); - - newSampleName = namePrefix + newSampleIndex; - log(String.format("The new sample will be named '%s' and it will go to sea.", newSampleName)); - - setFormElement(nameTxtbox, newSampleName); - clickAndWait(Locator.lkButton("Submit")); - - // Increment the index. - newSampleIndex++; - - log("Check that the expected samples are shown as the parents of this new sample."); - checkRowsInDataRegion("parentMaterials", "Name", parents); - - log("Go look at each one of the parents and make sure they have the new sample as a child and the run column is correct."); - - String parentListUI = parents.get(0) + ", " + parents.get(1) + ", " + parents.get(2); - String runTextUI = String.format(runTextStrFormat, parentListUI); - - for(String parent : parents) - { - // A link to the sample type should be visible on this page, use it to go back to the sample type page. - clickAndWait(Locator.linkWithText(sampleTypeName)); - clickAndWait(Locator.linkWithText(parent)); - checkRowsInDataRegion("childMaterials", "Name", List.of(newSampleName)); - checkRowsInDataRegion("childMaterials", "Run", List.of(runTextUI)); - } - - log("Finally derive a sample from a sample that was itself also derived."); - - clickAndWait(Locator.linkWithText(sampleTypeName)); - - log("Make the parent sample the same sample that was just created."); - parentSample = newSampleName; - log(String.format("Using sample named '%s' as the parent.", parentSample)); - - waitAndClickAndWait(Locator.linkWithText(parentSample)); - - waitAndClickAndWait(Locator.linkWithText("derive samples from this sample")); - - log("Again just create a single derived sample."); - waitAndClickAndWait(Locator.lkButton("Next")); - nameTxtbox = Locator.inputByNameContaining("_Name"); - waitForElement(nameTxtbox); - - newSampleName = namePrefix + newSampleIndex; - log(String.format("The new sample will be named '%s' and this one was a failure to launch and never left home.", newSampleName)); - - setFormElement(nameTxtbox, newSampleName); - clickAndWait(Locator.lkButton("Submit")); - - List newParents = new ArrayList<>(); - newParents.add(parentSample); - newParents.addAll(parents); - - log(String.format("Check that all samples '%s' are listed as parents.", newParents)); - checkRowsInDataRegion("parentMaterials", "Name", newParents); - - log("Also check that the run column for the parents are as expected."); - checkRowsInDataRegion("parentMaterials", "Run", List.of(runTextUI, " ", " ", " ")); - - log(String.format("Go to the 'derived' parent '%s' and verify it has '%s' as a child.", parentSample, newSampleName)); - - clickAndWait(Locator.linkWithText(parentSample)); - checkRowsInDataRegion("childMaterials", "Name", List.of(newSampleName)); - - log(String.format("Verify again that '%s' parents are still as expected.", parentSample)); - checkRowsInDataRegion("parentMaterials", "Name", parents); - - String grandParent = parents.getFirst(); - log(String.format("Select one of '%s' parents, '%s' and verify that it now has two children.", parentSample, grandParent)); - - clickAndWait(Locator.linkWithText(grandParent)); - checkRowsInDataRegion("childMaterials", "Name", Arrays.asList(newSampleName, parentSample)); - - log("Test complete."); - } - private void checkRowsInDataRegion(String dataRegionName, String columnName, final List expectedValues) { DataRegionTable dataRegionTable = new DataRegionTable(dataRegionName, this); @@ -1133,52 +919,31 @@ public void testDeleteSampleSources() throws CommandException, IOException } @Test - public void testDeleteSamplesSomeWithDerivedSamples() + public void testDeleteSamplesSomeWithDerivedSamples() throws IOException, CommandException { final String SAMPLE_TYPE_NAME = "DeleteSamplesWithParents" + DOMAIN_TRICKY_CHARACTERS; List parentSampleNames = Arrays.asList("P-1", "P-2", "P-3"); - List> sampleData = new ArrayList<>(); - parentSampleNames.forEach(name -> sampleData.add(Map.of("Name", name))); - - clickProject(PROJECT_NAME); - SampleTypeHelper sampleHelper = new SampleTypeHelper(this); - log("Create a sample type with some potential parents"); - sampleHelper.createSampleType(new SampleTypeDefinition(SAMPLE_TYPE_NAME). - addField(new FieldDefinition("Blood+")). - addField(new FieldDefinition("Blood-")), - sampleData); - DataRegionTable drtSamples = sampleHelper.getSamplesDataRegionTable(); - log("Derive one sample from another"); - drtSamples.checkCheckbox(drtSamples.getRowIndex("Name", parentSampleNames.getFirst())); - clickButton("Derive Samples"); - waitAndClickAndWait(Locator.lkButton("Next")); String childName = parentSampleNames.getFirst() + ".1"; - String nameFieldInputFieldName = "Output Sample 1_Name"; - String bloodPlusFieldInputFieldName = "Output Sample 1_Blood+"; - String bloodMinusFieldInputFieldName = "Output Sample 1_Blood-"; - setFormElement(Locator.name(nameFieldInputFieldName), childName); - setFormElement(Locator.name(bloodPlusFieldInputFieldName), "blood plus"); - setFormElement(Locator.name(bloodMinusFieldInputFieldName), "blood minus"); - clickButton("Submit"); - - log("Derive a sample from the one just created"); - clickAndWait(Locator.linkContainingText("derive samples from this sample")); - clickButton("Next"); String grandchildName = childName + ".1"; - setFormElement(Locator.name(nameFieldInputFieldName), grandchildName); - clickButton("Submit"); - - log("Derive a sample with two parents"); - clickAndWait(Locator.linkContainingText(SAMPLE_TYPE_NAME)); - drtSamples.checkCheckbox(drtSamples.getRowIndex("Name", parentSampleNames.get(1))); - drtSamples.checkCheckbox(drtSamples.getRowIndex("Name", childName)); - clickButton("Derive Samples"); - waitAndClickAndWait(Locator.lkButton("Next")); String twoParentChildName = parentSampleNames.get(1) + "+" + childName + ".1"; - setFormElement(Locator.name(nameFieldInputFieldName), twoParentChildName); - clickButton("Submit"); - clickAndWait(Locator.linkContainingText(SAMPLE_TYPE_NAME)); + log("Create a sample type with parents, a child, a grandchild and a two-parent child"); + TestDataGenerator sampleGenerator = new SampleTypeDefinition(SAMPLE_TYPE_NAME) + .addField(new FieldDefinition("Blood+")) + .addField(new FieldDefinition("Blood-")) + .create(createDefaultConnection(), getProjectName()); + String parentKey = "MaterialInputs/" + SAMPLE_TYPE_NAME; + parentSampleNames.forEach(name -> sampleGenerator.addCustomRow(Map.of("Name", name))); + sampleGenerator.addCustomRow(Map.of("Name", childName, parentKey, parentSampleNames.getFirst(), + "Blood+", "blood plus", "Blood-", "blood minus")); + sampleGenerator.addCustomRow(Map.of("Name", grandchildName, parentKey, childName)); + sampleGenerator.addCustomRow(Map.of("Name", twoParentChildName, parentKey, parentSampleNames.get(1) + "," + childName)); + sampleGenerator.insertRows(); + + clickProject(PROJECT_NAME); + SampleTypeHelper sampleHelper = new SampleTypeHelper(this); + sampleHelper.goToSampleType(SAMPLE_TYPE_NAME); + DataRegionTable drtSamples = sampleHelper.getSamplesDataRegionTable(); // Issue 53306 - ensure that names differing only by special characters were captured correctly and are being // shown in the grid diff --git a/src/org/labkey/test/tests/SampleTypeLinkToStudyTest.java b/src/org/labkey/test/tests/SampleTypeLinkToStudyTest.java index c77367b77b..e4af8daf1d 100644 --- a/src/org/labkey/test/tests/SampleTypeLinkToStudyTest.java +++ b/src/org/labkey/test/tests/SampleTypeLinkToStudyTest.java @@ -21,9 +21,9 @@ import org.junit.BeforeClass; import org.junit.Test; import org.junit.experimental.categories.Category; +import org.labkey.remoteapi.CommandException; import org.labkey.test.BaseWebDriverTest; import org.labkey.test.Locator; -import org.labkey.test.SortDirection; import org.labkey.test.TestTimeoutException; import org.labkey.test.categories.Daily; import org.labkey.test.components.CustomizeView; @@ -41,12 +41,12 @@ import org.labkey.test.params.experiment.SampleTypeDefinition; import org.labkey.test.util.DataRegionTable; import org.labkey.test.util.DomainUtils; -import org.labkey.test.util.OptionalFeatureHelper; import org.labkey.test.util.PortalHelper; import org.labkey.test.util.SampleTypeHelper; import org.labkey.test.util.StudyHelper; import org.labkey.test.util.TestDataGenerator; import org.labkey.test.util.data.TestDataUtils; +import org.labkey.test.util.query.QueryApiHelper; import java.io.File; import java.io.IOException; @@ -108,8 +108,6 @@ private void doSetup() throws IOException new PortalHelper(getDriver()).addBodyWebPart("Datasets"); createSampleTypes(); - OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp", true); - } @@ -330,28 +328,17 @@ public void testLineageSupport() new FieldDefinition("ParticipantId", FieldDefinition.ColumnType.Subject))), data); goToProjectHome(SAMPLE_TYPE_PROJECT); - data = "Name\tVolume\n" + - "PL-1\t10\n"; + data = "Name\tVolume\tMaterialInputs/Blood\n" + + "PL-1\t10\t\n" + + derivedSampleName + "\t1\tBL-1\n"; sampleHelper.createSampleType(new SampleTypeDefinition("Plasma") .setFields(List.of( new FieldDefinition("Volume", FieldDefinition.ColumnType.Integer))), data); - goToProjectHome(SAMPLE_TYPE_PROJECT); - clickAndWait(Locator.linkWithText("Blood")); - DataRegionTable samplesTable = DataRegionTable.DataRegion(getDriver()).withName("Material").waitFor(); - samplesTable.setSort("Name", SortDirection.ASC); - samplesTable.checkCheckbox(0); - samplesTable.clickHeaderButtonAndWait("Derive Samples"); - selectOptionByText(Locator.name("targetSampleTypeId"), "Plasma in /" + SAMPLE_TYPE_PROJECT); - clickButton("Next"); - setFormElement(Locator.name("Output Sample 1_Name"), derivedSampleName); - setFormElement(Locator.name("Output Sample 1_Volume"), "1"); - clickButton("Submit"); - goToProjectHome(SAMPLE_TYPE_PROJECT); clickAndWait(Locator.linkWithText("Plasma")); - samplesTable = DataRegionTable.DataRegion(getDriver()).withName("Material").waitFor(); + DataRegionTable samplesTable = DataRegionTable.DataRegion(getDriver()).withName("Material").waitFor(); CustomizeView customizeView = samplesTable.getCustomizeView(); customizeView.openCustomizeViewPanel(); customizeView.showHiddenItems(); @@ -632,7 +619,7 @@ public void testAutoLinkToStudyWithNonStandardFieldNames() } @Test - public void testSubjectTimepointFromParentSample() + public void testSubjectTimepointFromParentSample() throws IOException, CommandException { String parentSampleType = "parent sample"; log("Creating the parent sample with subject/timepoint fields"); @@ -687,18 +674,11 @@ public void testSubjectTimepointFromParentSample() checker().verifyEquals("Incorrect visit ParticipantId in child sample", Arrays.asList("P1","P2"), samplesTable.getColumnDataAsText("Inputs/Materials/parent sample/ParticipantId")); - log("Verifying adding data to the child sample type using the derivation steps"); - goToProjectHome(SAMPLE_TYPE_PROJECT); - clickAndWait(Locator.linkWithText(parentSampleType)); - samplesTable = DataRegionTable.DataRegion(getDriver()).withName("Material").waitFor(); - samplesTable.checkCheckbox(0); - samplesTable.clickHeaderButtonAndWait("Derive Samples"); - selectOptionByText(Locator.name("targetSampleTypeId"), childSampleType + " in /" + getProjectName()); - clickButton("Next"); - setFormElement(Locator.name("Output Sample 1_Name"), "derivedChildSample"); - clickButton("Submit"); + log("Inserting a single derived child sample"); + new QueryApiHelper(createDefaultConnection(), SAMPLE_TYPE_PROJECT, "samples", childSampleType) + .insertRows(List.of(Map.of("Name", "derivedChildSample", "MaterialInputs/" + parentSampleType, "Parent-2"))); - log("Verifying the auto link to study by deriving single samples from parent sample"); + log("Verifying the auto link to study for a single sample derived from a parent sample"); goToProjectHome(SAMPLE_TYPE_PROJECT); clickAndWait(Locator.linkWithText(childSampleType)); samplesTable = DataRegionTable.DataRegion(getDriver()).withName("Material").waitFor(); @@ -885,6 +865,5 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException _containerHelper.deleteProject(DATE_BASED_STUDY, false); _containerHelper.deleteProject(SAMPLE_TYPE_PROJECT + " Study 1", false); _containerHelper.deleteProject(SAMPLE_TYPE_PROJECT + " Study 2", false); - OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp"); } } diff --git a/src/org/labkey/test/tests/SampleTypeNameExpressionTest.java b/src/org/labkey/test/tests/SampleTypeNameExpressionTest.java index 7b3ab760d0..1e26c7a49a 100644 --- a/src/org/labkey/test/tests/SampleTypeNameExpressionTest.java +++ b/src/org/labkey/test/tests/SampleTypeNameExpressionTest.java @@ -39,13 +39,13 @@ import org.labkey.test.util.AuditLogHelper; import org.labkey.test.util.DataRegionTable; import org.labkey.test.util.EscapeUtil; -import org.labkey.test.util.OptionalFeatureHelper; import org.labkey.test.util.PortalHelper; import org.labkey.test.util.SampleTypeHelper; import org.labkey.test.util.TestDataGenerator; import org.labkey.test.util.TextUtils; import org.labkey.test.util.data.TestDataUtils; import org.labkey.test.util.exp.SampleTypeAPIHelper; +import org.labkey.test.util.query.QueryApiHelper; import org.openqa.selenium.TimeoutException; import org.openqa.selenium.WebElement; @@ -84,7 +84,6 @@ public class SampleTypeNameExpressionTest extends BaseWebDriverTest private static final String PARENT_SAMPLE_TYPE_INPUT = escapeForNameExpression(PARENT_SAMPLE_TYPE); // No random names for deriving sample type - // Issue 53306: LabKey Server: Derive samples form does not distinguish between fields that differ by 'special characters' private static final FieldInfo COL_DSTR = new FieldInfo("DStr", ColumnType.String); private static final FieldInfo COL_DINT = new FieldInfo("DInt", ColumnType.Integer); @@ -133,13 +132,6 @@ public static void setupProject() throws IOException, CommandException test.doSetup(); } - @Override - protected void doCleanup(boolean afterTest) - { - super.doCleanup(afterTest); - OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp"); - } - private void addDataRow(TestDataGenerator dataGenerator, String name, int intVal) { Map sampleData = new HashMap<>(); @@ -204,7 +196,6 @@ private void doSetup() throws IOException, CommandException // Just want to get an updated view of the sample types. refresh(); - OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp", true); } @Before @@ -500,9 +491,6 @@ public void testWithTrickyFieldNames() throws IOException, CommandException createPage.setNameExpression(sbNameExpression.toString()); - // Issue 53306 There is a problem with the derived sample form and field names that contain "special" characters. -// String intField = TestDataGenerator.randomFieldName("Int"); -// String strField = TestDataGenerator.randomFieldName("Str"); String intField = "Int"; String strField = "Str"; createPage.addFields(Arrays.asList( @@ -881,21 +869,20 @@ private void validateNamesGenerated(List actualNames, List expec /** *

- * Verify that a derived sample, using a name expression, can be created by clicking the "Derive Samples" link - * from a sample's detail page. + * Verify that a derived sample can be named by a name expression that references parent or grandparent properties. *

*

* This test will: *

    - *
  • Create a derived sample using the UI and the name expression that reference parent property to name it.
    • - *
  • Create a derived sample using the UI and the name expression that references grandparent property to name it.
    • + *
  • Create a derived sample using the API and the name expression that reference a parent property to name it.
    • + *
  • Create a derived sample using the API and the name expression that references a grandparent property to name it.
    • *
  • Create a derived sample using the bulk import and the name expression that references grandparent property to name it.
    • *
*

* @throws Exception Can be thrown by test helper. */ @Test - public void testDeriveSampleFromSampleDetailsPage() throws Exception + public void testDeriveSampleWithAncestorNameExpression() throws Exception { goToProjectHome(); @@ -979,32 +966,17 @@ public void testDeriveSampleFromSampleDetailsPage() throws Exception private String deriveSample(String parentSampleName, String parentSampleType, String targetSampleType, Map setField) throws IOException, CommandException { - log(String.format("Go to the 'overview' page for sample '%s' in sample type '%s'", parentSampleName, parentSampleType)); - Integer sampleRowNum = SampleTypeAPIHelper.getRowIdsForSamples(getProjectName(), parentSampleType, Arrays.asList(parentSampleName)).get(parentSampleName); - - String url = WebTestHelper.buildRelativeUrl("experiment", getCurrentContainerPath(), "showMaterial", Map.of("rowId", sampleRowNum)); - beginAt(url); - - log("Derive a sample from this sample but give it no name. The name expression should be used to name the derived sample."); - - waitForElement(Locator.linkWithText("derive samples from this sample")); - - clickAndWait(Locator.linkWithText("derive samples from this sample")); - - selectOptionByText(Locator.name("targetSampleTypeId"), String.format("%s in /%s", targetSampleType, getProjectName())); - clickButton("Next"); - - String flagString = ""; - for(Map.Entry entry : setField.entrySet()) - { - setFormElement(Locator.name(String.format("Output Sample 1_%s", entry.getKey())), entry.getValue()); - flagString = entry.getValue(); - } - clickButton("Submit"); + log(String.format("Derive a sample from '%s' in sample type '%s' but give it no name. The name expression should be used to name the derived sample.", parentSampleName, parentSampleType)); + Map row = new HashMap<>(setField); + row.put("MaterialInputs/" + parentSampleType, parentSampleName); + String derivedSampleName = (String) new QueryApiHelper(createDefaultConnection(), getProjectName(), "samples", targetSampleType) + .insertRows(List.of(row)).getRows().getFirst().get("name"); - waitForElement(Locator.tagWithText("td", flagString)); + log(String.format("Go to the 'overview' page for derived sample '%s'", derivedSampleName)); + Integer sampleRowNum = SampleTypeAPIHelper.getRowIdsForSamples(getProjectName(), targetSampleType, List.of(derivedSampleName)).get(derivedSampleName); + beginAt(WebTestHelper.buildRelativeUrl("experiment", getCurrentContainerPath(), "showMaterial", Map.of("rowId", sampleRowNum))); - return Locator.tagWithText("td", "Name:").followingSibling("td").findElement(getDriver()).getText(); + return derivedSampleName; } /** From ed26cd3aaf52c37c750d36f33bbe414a52efeeba Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 5 Oct 2026 10:21:42 -0700 Subject: [PATCH 2/3] Remove actions and JSPs that are no longer used --- .../test/tests/SampleTypeFolderExportImportTest.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java b/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java index 907b5f8b44..693118a774 100644 --- a/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java +++ b/src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java @@ -101,8 +101,11 @@ public BrowserType bestBrowser() protected void doCleanup(boolean afterTest) { super.doCleanup(afterTest); - SampleTypeFolderExportImportTest init = getCurrentTest(); - init.doSetup(); + if (!afterTest) + { + SampleTypeFolderExportImportTest init = getCurrentTest(); + init.doSetup(); + } } private void doSetup() From fd58014827a87065f1a89cb31dd20acce10b1a98 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 5 Oct 2026 16:26:26 -0700 Subject: [PATCH 3/3] Remove some unuseful parameters --- .../test/tests/SampleTypeLimitsTest.java | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/src/org/labkey/test/tests/SampleTypeLimitsTest.java b/src/org/labkey/test/tests/SampleTypeLimitsTest.java index c29d3dc43b..d01630ab3e 100644 --- a/src/org/labkey/test/tests/SampleTypeLimitsTest.java +++ b/src/org/labkey/test/tests/SampleTypeLimitsTest.java @@ -15,7 +15,6 @@ */ package org.labkey.test.tests; -import org.jetbrains.annotations.Nullable; import org.junit.BeforeClass; import org.junit.Test; import org.junit.experimental.categories.Category; @@ -141,12 +140,12 @@ public void testStringLookupFields() throws IOException, CommandException table.clickInsertNewRow(); setFormElement(Locator.name("quf_id"), "1"); setFormElement(Locator.name("quf_name"), "1"); - verifyInvalidLookupSample("quf_lookUpField", "Sample3", null); + verifyInvalidLookupSample("quf_lookUpField", "Sample3"); verifyValidLookupSample("quf_lookUpField", "Sample1"); log("Verifying editing list row with the sample display name"); table.clickEditRow("1"); - verifyInvalidLookupSample("quf_lookUpField", "Sample3", null); + verifyInvalidLookupSample("quf_lookUpField", "Sample3"); verifyValidLookupSample("quf_lookUpField", "Sample2"); log("Verifying editing list row with the sample RowId"); @@ -154,31 +153,28 @@ public void testStringLookupFields() throws IOException, CommandException SelectRowsCommand command = new SelectRowsCommand("samples", SAMPLE_TYPE_NAME); command.setFilters(Arrays.asList(new Filter("Name", "Sample1"))); SelectRowsResponse response = command.execute(createDefaultConnection(), getProjectName()); - verifyValidLookupSample("quf_lookUpField", response.getRows().getFirst().get("RowId").toString(), "Sample1", "query", false); + verifyValidLookupSample("quf_lookUpField", response.getRows().getFirst().get("RowId").toString(), "Sample1", "query"); } - private void verifyInvalidLookupSample(String fieldName, String sampleValue, @Nullable String expectedErrorMsg) + private void verifyInvalidLookupSample(String fieldName, String sampleValue) { setFormElement(Locator.name(fieldName), sampleValue); clickButton("Submit"); String errMsg = Locators.labkeyError.findElement(getDriver()).getText(); - assertEquals("Expected error is different", expectedErrorMsg == null ? "Could not convert value: " + sampleValue : expectedErrorMsg, errMsg); + assertEquals("Expected error is different", "Could not convert value: " + sampleValue, errMsg); } private void verifyValidLookupSample(String fieldName, String sampleValue) { - verifyValidLookupSample(fieldName, sampleValue, sampleValue, "query", false); + verifyValidLookupSample(fieldName, sampleValue, sampleValue, "query"); } - private void verifyValidLookupSample(String fieldName, String sampleValue, String sampleDisplay, String dataRegionName, boolean navigateViaBreadcrumb) + private void verifyValidLookupSample(String fieldName, String sampleValue, String sampleDisplay, String dataRegionName) { setFormElement(Locator.name(fieldName), sampleValue); clickButton("Submit"); - if (navigateViaBreadcrumb) - clickAndWait(Locator.tagWithClass("ol", "breadcrumb").childTag("li").index(1).childTag("a")); - log("Verifying row is inserted correctly"); DataRegionTable table = DataRegionTable.DataRegion(getDriver()).withName(dataRegionName).waitFor(); assertEquals("Lookup field value is incorrect", sampleDisplay, table.getDataAsText(0, "lookUpField"));