Assay Transform Script UX update to allow file drop and file path entry

src/org/labkey/test/pages/ReactAssayDesignerPage.java

@@ -15,13 +15,15 @@
  */
 package org.labkey.test.pages;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.test.Locator;
 import org.labkey.test.components.DomainDesignerPage;
 import org.labkey.test.components.domain.DomainFormPanel;
 import org.labkey.test.components.domain.DomainPanel;
 import org.labkey.test.components.html.Checkbox;
 import org.labkey.test.components.html.Input;
 import org.labkey.test.components.html.OptionSelect;
+import org.labkey.test.components.ui.files.AttachmentCard;
 import org.labkey.test.pages.assay.plate.PlateTemplateListPage;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;
@@ -30,7 +32,9 @@
 import java.io.File;
 import java.util.Optional;
 
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
+import static org.labkey.test.WebDriverWrapper.WAIT_FOR_JAVASCRIPT;
 import static org.labkey.test.components.html.Checkbox.Checkbox;
 import static org.labkey.test.components.html.Input.Input;
 import static org.labkey.test.components.html.SelectWrapper.Select;
@@ -206,23 +210,61 @@ public boolean getStatus()
 
     public ReactAssayDesignerPage addTransformScript(File transformScript)
     {
-        expandPropertiesPanel();
-        int index = Locator.xpath("//input[starts-with(@id, 'assay-design-protocolTransformScripts')]").findElements(getDriver()).size();
-        getWrapper().click(Locator.tagWithClass("span", "btn").containing("Add Script"));
-        return setTransformScript(transformScript, index);
+        return setTransformScript(transformScript, false, null);
     }
 
-    public ReactAssayDesignerPage setTransformScript(File transformScript)
+    public ReactAssayDesignerPage addTransformScript(File transformScript, boolean usingFileUpload)
     {
-        expandPropertiesPanel();
-        return setTransformScript(transformScript, 0);
+        return setTransformScript(transformScript, usingFileUpload, null);
     }
 
-    public ReactAssayDesignerPage setTransformScript(File transformScript, int index)
+    public ReactAssayDesignerPage addTransformScript(File transformScript, boolean usingFileUpload, @Nullable String expectedError)
+    {
+        return setTransformScript(transformScript, usingFileUpload, expectedError);
+    }
+
+    private ReactAssayDesignerPage setTransformScript(File transformScript, boolean usingFileUpload, @Nullable String expectedError)
     {
-        expandPropertiesPanel();
         assertTrue("Unable to locate the transform script: " + transformScript, transformScript.exists());
-        getWrapper().setFormElement(Locator.xpath("//input[@id='assay-design-protocolTransformScripts" + index + "']"), transformScript.getAbsolutePath());
+
+        expandPropertiesPanel();
+        getWrapper().click(Locator.tagWithClass("span", "btn").containing("Add Script"));
+        String targetPath = transformScript.getAbsolutePath();
+        if (usingFileUpload)
+        {
+            getWrapper().setFormElement(Locator.tagWithClass("input", "file-upload--input"), transformScript);
+            targetPath = "/@scripts/" + transformScript.getName();
+        }
+        else
+        {
+            getWrapper().checkRadioButton(Locator.radioButtonByNameAndValue("transformScriptAddType", "path"));
+            getWrapper().setFormElement(Locator.tagWithClass("div", "transform-script-add--path").child(Locator.tag("input")), transformScript.getAbsolutePath());
+            getWrapper().clickButton("Apply", 0);
+        }
+
+        if (expectedError == null)
+        {
+            String finalTargetPath = targetPath;
+            getWrapper().waitFor(()-> Locator.tagWithClass("div", "attachment-card__description").endsWith(finalTargetPath).isDisplayed(this),
+                    "Transform script card with expected file not found", WAIT_FOR_JAVASCRIPT);
+        }
+        else
+        {
+            getWrapper().waitFor(()-> Locator.tagWithClass("div", "alert-danger").withText(expectedError).isDisplayed(this),
+                    "Transform script expected error not found", WAIT_FOR_JAVASCRIPT);
+            getWrapper().click(Locator.tagWithClass("i", "container--removal-icon"));
+        }
+
+        return this;
+    }
+
+    public ReactAssayDesignerPage removeTransformScript(String fileName)
+    {
+        AttachmentCard card = new AttachmentCard.FileAttachmentCardFinder(getDriver()).withFile(fileName).waitFor(this);
+        int beforeCount = Locator.tagWithClass("div", "attachment-card__description").findElements(this).size();
+        card.clickRemove();
+        int afterCount = Locator.tagWithClass("div", "attachment-card__description").findElements(this).size();
+        assertEquals("Transform script count not as expected after remove.", beforeCount - 1, afterCount);
         return this;
     }
 

src/org/labkey/test/tests/GpatPlateTemplateTest.java

@@ -57,7 +57,7 @@ private void doSetup()
                 .createAssayDesign("General", ASSAY_NAME)
                 .setPlateMetadata(true)
                 // Regression check for Issue 48293: Standard Assay with Plate Metadata & Transformation Script throws an error
-                .addTransformScript(TRANSFORM_SCRIPT)
+                .addTransformScript(TRANSFORM_SCRIPT, true)
                 .clickFinish();
         createPlateTemplate(templateName, "blank", "Standard", true);
     }

src/org/labkey/test/tests/assay/AssayTransformWarningTest.java

@@ -27,6 +27,7 @@
 import org.labkey.test.categories.Assays;
 import org.labkey.test.categories.Daily;
 import org.labkey.test.pages.ReactAssayDesignerPage;
+import org.labkey.test.pages.files.WebDavPage;
 import org.labkey.test.params.FieldDefinition;
 import org.labkey.test.util.DataRegionTable;
 import org.labkey.test.util.QCAssayScriptHelper;
@@ -46,6 +47,7 @@ public class AssayTransformWarningTest extends BaseWebDriverTest
     public static final File JAVA_TRANSFORM_SCRIPT = TestFileUtils.getSampleData("qc/transformWarning.jar");
     public static final File R_TRANSFORM_SCRIPT = TestFileUtils.getSampleData("qc/assayTransformWarning.R");
     public static final File R_TRANSFORM_ERROR_SCRIPT = TestFileUtils.getSampleData("qc/assayTransformError.R");
+    public static final File JAVA_INVALID_TRANSFORM_SCRIPT = TestFileUtils.getSampleData("qc/src/org/labkey/AssayTransformNoOp.java");
 
     @Override
     public List<String> getAssociatedModules()
@@ -100,7 +102,7 @@ public void testJavaTransformWarning()
         String runName = "java transform run";
 
         _assayHelper.createAssayDesign("General", assayName)
-            .addTransformScript(JAVA_TRANSFORM_SCRIPT)
+            .addTransformScript(JAVA_TRANSFORM_SCRIPT, true)
             .clickFinish();
 
         clickAndWait(Locator.linkWithText(assayName));
@@ -136,7 +138,7 @@ public void testRTransformWarning()
         String runName = "R transform run";
 
         ReactAssayDesignerPage assayDesignerPage = _assayHelper.createAssayDesign("General", assayName)
-            .addTransformScript(R_TRANSFORM_SCRIPT);
+            .addTransformScript(R_TRANSFORM_SCRIPT, true);
         assayDesignerPage.goToRunFields()
             .addField("myFile")
             .setLabel("My File")
@@ -210,4 +212,32 @@ public void testRTransformError()
         assertElementPresent(Locator.tag("td").containing("Col1"));
         assertElementPresent(Locator.tag("td").containing("test2"));
     }
+
+    @Test
+    public void testTransformScriptValidation()
+    {
+        String assayName = "transformInvalid";
+        ReactAssayDesignerPage assayDesignerPage = _assayHelper.createAssayDesign("General", assayName);
+
+        // verify check for valid script engine defined for the file extension
+        assayDesignerPage.addTransformScript(JAVA_INVALID_TRANSFORM_SCRIPT, true, "Script engine for the extension '.java' has not been registered.");
+        assayDesignerPage.addTransformScript(JAVA_INVALID_TRANSFORM_SCRIPT, false, "Script engine for the extension '.java' has not been registered.");
+
+        // verify check for duplicate file in @scripts dir
+        assayDesignerPage.addTransformScript(R_TRANSFORM_ERROR_SCRIPT, true);
+        assayDesignerPage.addTransformScript(R_TRANSFORM_ERROR_SCRIPT, true, "File already exists: assayTransformError.R");
+
+        // verify that removing the transform script path does not remove file from file system
+        assayDesignerPage.removeTransformScript(R_TRANSFORM_ERROR_SCRIPT.getName());
+        WebDavPage webDavPage = WebDavPage.beginAt(this, getProjectName() + "/@scripts");
+        webDavPage.getFileBrowserHelper().waitForFileGridReady();
+        assertTrue("Transform script file not present in file system.", webDavPage.getFileBrowserHelper().getFileList(false).contains(R_TRANSFORM_ERROR_SCRIPT.getName()));
+
+        // verify file exists in @scripts dir via webdav page
+        goToProjectHome();
+        impersonateRole("Folder Administrator");
+        WebDavPage.beginAt(this, getProjectName() + "/@scripts");
+        waitForElement(Locators.labkeyErrorHeading.withText("/_webdav/" + getProjectName() + "/@scripts"));
+        stopImpersonatingHTTP();
+    }
 }

src/org/labkey/test/tests/elispotassay/ElispotAssayTest.java

@@ -68,6 +68,8 @@ public class ElispotAssayTest extends AbstractAssayTest
     protected static final File TEST_ASSAY_ELISPOT_FILE5 = TestFileUtils.getSampleData("Elispot/AID_0161456 W8.txt");
     protected static final File TEST_ASSAY_ELISPOT_FILE6 = TestFileUtils.getSampleData("Elispot/AID_TNTC.txt");
 
+    private static final File TRANSFORM_SCRIPT_FILE = TestFileUtils.getSampleData("qc/transform.jar");
+
     private static final String PLATE_TEMPLATE_NAME = "ElispotAssayTest Template";
 
     protected static final String TEST_ASSAY_FLUOROSPOT = "TestAssayFluorospot";
@@ -495,7 +497,7 @@ protected void runTransformTest()
 
 
         ReactAssayDesignerPage assayDesigner = _assayHelper.clickEditAssayDesign();
-        assayDesigner.addTransformScript(TestFileUtils.getSampleData("qc/transform.jar"));
+        assayDesigner.addTransformScript(TRANSFORM_SCRIPT_FILE, true);
         assayDesigner.clickFinish();
         DataRegionTable.DataRegion(getDriver()).withName("Runs").waitFor();
 
@@ -525,9 +527,9 @@ protected void removeTransformScript()
     {
         clickProject(TEST_ASSAY_PRJ_ELISPOT);
         clickAndWait(Locator.linkWithText(TEST_ASSAY_ELISPOT));
-        ReactAssayDesignerPage assayDesignerPage = _assayHelper.clickEditAssayDesign();
-        waitAndClick(Locator.tagWithClass("i", "container--removal-icon")); // TODO add a specific class to the transform script removal icon
-        assayDesignerPage.clickFinish();
+        _assayHelper.clickEditAssayDesign()
+                .removeTransformScript(TRANSFORM_SCRIPT_FILE.getName())
+                .clickFinish();
         DataRegionTable.DataRegion(getDriver()).withName("Runs").waitFor();
     }
 

src/org/labkey/test/tests/nab/NabAssayTest.java

@@ -702,7 +702,7 @@ protected void runTransformTest()
         clickAndWait(Locator.linkWithText(TEST_ASSAY_NAB));
 
         _assayHelper.clickEditAssayDesign()
-                .addTransformScript(TestFileUtils.getSampleData("qc/transform.jar"))
+                .addTransformScript(TestFileUtils.getSampleData("qc/transform.jar"), true)
                 .clickFinish();
 
         navigateToFolder(TEST_ASSAY_PRJ_NAB, TEST_ASSAY_FLDR_NAB);

src/org/labkey/test/tests/viability/ViabilityTest.java

@@ -245,7 +245,7 @@ protected void runTransformTest()
         clickAndWait(Locator.linkWithText(getAssayName()));
         ReactAssayDesignerPage assayDesigner = _assayHelper.clickEditAssayDesign(true);
 
-        assayDesigner.addTransformScript(TestFileUtils.getSampleData("qc/transform.jar"));
+        assayDesigner.addTransformScript(TestFileUtils.getSampleData("qc/transform.jar"), true);
         assayDesigner.clickFinish();
 
         final String runName = "transformed assayId";

src/org/labkey/test/util/FileBrowserHelper.java

@@ -369,7 +369,12 @@ public void refreshFileList()
 
     public List<String> getFileList()
     {
-        return getTexts(Locators.gridRow().childTag("td").position(3).findElements(getDriver()));
+        return getFileList(true);
+    }
+
+    public List<String> getFileList(boolean hasCheckboxColumn)
+    {
+        return getTexts(Locators.gridRow().childTag("td").position(hasCheckboxColumn ? 3 : 2).findElements(getDriver()));
     }
 
     public void createFolder(String folderName)