GitHub Issue #159: Require all assay transform scripts to reside in container's @scripts dir

src/org/labkey/test/components/ui/files/AttachmentCard.java

@@ -109,6 +109,11 @@ public boolean isFileUnavailable()
         return elementCache().unavailableWarning.isPresent();
     }
 
+    public String getDescription()
+    {
+        return elementCache().description.getText();
+    }
+
     public boolean canRemove()
     {
         return getRemoveOption() != null;
@@ -146,6 +151,7 @@ protected ElementCache newElementCache()
     protected class ElementCache extends Component<?>.ElementCache
     {
         final WebElement fileSize = Locator.byClass("attachment-card__size").findWhenNeeded(this);
+        final WebElement description = Locator.byClass("attachment-card__description").refindWhenNeeded(this);
         final WebElement icon = Locator.byClass("attachment-card__icon_img").findWhenNeeded(this);
         Optional<BootstrapMenu> menu = BootstrapMenu.finder(getDriver())
                 .locatedBy(Locator.tagWithClass("div", "attachment-card__menu"))

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

@@ -29,6 +29,9 @@
 import org.labkey.test.components.ui.files.AttachmentCard;
 import org.labkey.test.pages.assay.plate.PlateTemplateListPage;
 import org.labkey.test.util.Maps;
+import org.labkey.test.util.TestLogger;
+import org.labkey.test.util.core.webdav.WebDavUploadHelper;
+import org.labkey.test.util.core.webdav.WebDavUrlFactory;
 import org.labkey.test.util.selenium.WebElementUtils;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;
@@ -256,7 +259,7 @@ public boolean getStatus()
 
     public ReactAssayDesignerPage addTransformScript(File transformScript)
     {
-        return setTransformScript(transformScript, false, null);
+        return setTransformScript(transformScript, true, null);
     }
 
     public ReactAssayDesignerPage addTransformScript(File transformScript, boolean usingFileUpload)
@@ -278,6 +281,11 @@ private ReactAssayDesignerPage setTransformScript(File transformScript, boolean
         String targetPath = transformScript.getAbsolutePath();
         if (usingFileUpload)
         {
+            // GitHub Issue #159: The upload fails if a file of the same name is already in the assay's "@scripts" dir,
+            // so remove any leftover file first.
+            if (expectedError == null)
+                removeExistingScriptFile(transformScript.getName());
+
             getWrapper().setFormElement(Locator.tagWithClass("input", "file-upload__input"), transformScript);
             targetPath = "/@scripts/" + transformScript.getName();
         }
@@ -304,6 +312,22 @@ private ReactAssayDesignerPage setTransformScript(File transformScript, boolean
         return this;
     }
 
+    /**
+     * Remove a file from the "@scripts" dir of the container that this assay design lives in, if it is present. Uses
+     * WebDav directly instead of the "Manage script files" UI, which opens in a separate browser tab.
+     * @param fileName Name of the transform script file to remove
+     */
+    private void removeExistingScriptFile(String fileName)
+    {
+        String manageScriptsUrl = elementCache().manageScriptFilesLink.getDomProperty("href");
+        WebDavUploadHelper webDavHelper = new WebDavUploadHelper(WebDavUrlFactory.fromDirectoryUrl(manageScriptsUrl));
+        if (webDavHelper.fileExists(fileName))
+        {
+            TestLogger.log("Removing existing transform script file: " + fileName);
+            webDavHelper.deleteFile(fileName);
+        }
+    }
+
     public ReactAssayDesignerPage removeTransformScript(String fileName)
     {
         AttachmentCard card = new AttachmentCard.FileAttachmentCardFinder(getDriver()).withTitle(fileName).waitFor(this);
@@ -314,6 +338,17 @@ public ReactAssayDesignerPage removeTransformScript(String fileName)
         return this;
     }
 
+    /**
+     * The server side path of a transform script configured on this assay design, as shown on the script's card. This
+     * is the same value as the card's "Copy path" menu option, read from the DOM to avoid a clipboard round trip.
+     * @param fileName Name of the transform script file
+     */
+    public String getTransformScriptPath(String fileName)
+    {
+        AttachmentCard card = new AttachmentCard.FileAttachmentCardFinder(getDriver()).withTitle(fileName).waitFor(this);
+        return card.getDescription();
+    }
+
     public enum MetadataInputFormat implements OptionSelect.SelectOption
     {
         MANUAL,
@@ -388,6 +423,8 @@ Locator runOnActionCheckboxLoc(String fileName, ScriptFileEvent scriptFileEvent)
         final Checkbox qcEnabledCheckbox = Checkbox(Locator.checkboxById("assay-design-qcEnabled")).findWhenNeeded(propertiesPanel);
         final Checkbox plateTemplateCheckbox = Checkbox(Locator.checkboxById("assay-design-plateMetadata")).findWhenNeeded(propertiesPanel);
         final Checkbox activeStatusCheckBox = Checkbox(Locator.checkboxById("assay-design-status")).findWhenNeeded(propertiesPanel);
+        final WebElement manageScriptFilesLink = Locator.tagWithClass("div", "transform-script--manage-link")
+                .child(Locator.linkWithText("Manage script files")).refindWhenNeeded(propertiesPanel);
 
         final WebElement hitSelectionCriteriaBtn = Locator.tagWithClass("div", "filter-criteria-input__button")
                 .child(Locator.button("Edit Criteria")).findWhenNeeded(propertiesPanel);

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

@@ -282,6 +282,22 @@ private ReactAssayDesignerPage startCreateGpatAssay(File dataFile, @LoggedParam
         return assayDesignerPage;
     }
 
+    @Test // GitHub Issue #159
+    public void testAssayTransformScriptPathError()
+    {
+        File trialData = TestFileUtils.getSampleData("GPAT/renameAssayTrial.xls");
+        String assayName = TestDataGenerator.randomDomainName();
+        log(String.format("Create an assay named '%s'.", assayName));
+        ReactAssayDesignerPage assayDesignerPage = startCreateGpatAssay(trialData, assayName);
+
+        log("Verify error message when trying to add transform script with path outside of @scripts dir");
+        assayDesignerPage.addTransformScript(RTRANSFORM_SCRIPT_FILE_NOOP, false);
+        List<String> errors = assayDesignerPage.clickSaveExpectingErrors();
+        Assert.assertTrue("Error msg not as expected during assay creation",
+                errors.contains("The transform script must exist within this folder's @scripts directory."));
+        assayDesignerPage.clickCancel();
+    }
+
     @Test
     public void testMultipleFileUploadInAssayRun()
     {

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

@@ -15,9 +15,9 @@
  */
 package org.labkey.test.tests.assay;
 
+import org.apache.commons.io.FileUtils;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
-import org.labkey.api.util.FileUtil;
 import org.labkey.test.Locator;
 import org.labkey.test.TestFileUtils;
 import org.labkey.test.categories.Assays;
@@ -26,11 +26,10 @@
 import org.labkey.test.pages.ReactAssayDesignerPage;
 import org.labkey.test.pages.assay.AssayImportPage;
 import org.labkey.test.pages.assay.AssayRunsPage;
+import org.labkey.test.pages.files.WebDavPage;
 import org.labkey.test.params.assay.GeneralAssayDesign;
 
 import java.io.File;
-import java.nio.file.Files;
-import java.nio.file.Path;
 import java.util.List;
 
 /**
@@ -40,53 +39,63 @@
 @Category({Assays.class, Daily.class})
 public class AssayTransformMissingParentDirTest extends AbstractAssayTransformTest
 {
+    private static final File RTRANSFORM_SCRIPT_FILE_NOOP = TestFileUtils.getSampleData("qc/noopTransform.R");
+
     @Test
     public void testMissingParentDirectoryRegression() throws Exception
     {
-        // Create a nested directory and an R transform script within it
+        // create a General assay and add the transform
         String assayName = "missingParentDirAssay";
-        Path parentDir = Files.createTempDirectory("assay-transform-parent-");
-        Path nestedDir = FileUtil.createDirectories(parentDir.resolve("child"), false);
-        String scriptName = "transformMissingParent.R";
-        String transformContent = "library(Rlabkey);";
-        File transformFile = nestedDir.resolve(scriptName).toFile();
-        TestFileUtils.writeFile(transformFile, transformContent);
-
-        // Create a General assay and add the transform by absolute path (not upload)
+        String transformFileName = RTRANSFORM_SCRIPT_FILE_NOOP.getName();
         var protocolResponse = new GeneralAssayDesign(assayName).setBatchFields(List.of(), false).createAssay(getProjectName(), createDefaultConnection());
         var assayDesignerPage = ReactAssayDesignerPage.beginAt(this, getProjectName(), protocolResponse.getProtocolId(),
                 "general", "");
-        // add by path so the absolute path is stored; this allows reproducing the missing parent dir scenario
-        assayDesignerPage.addTransformScript(transformFile);
+        assayDesignerPage.addTransformScript(RTRANSFORM_SCRIPT_FILE_NOOP);
+        String transformScriptPath = assayDesignerPage.getTransformScriptPath(transformFileName);
+        assayDesignerPage.clickSave();
+
+        // move the script into a nested directory in the @scripts webdav path
+        WebDavPage webDavPage = WebDavPage.beginAt(this, getProjectName() + "/@scripts");
+        webDavPage.getFileBrowserHelper().createFolder("child");
+        File transformFile = new File(transformScriptPath);
+        File destinationFile = new File(transformFile.getParent() + "/child", transformFileName);
+        FileUtils.moveFile(transformFile, destinationFile);
+
+        // update the assay design with the new nested dir file path
+        assayDesignerPage = ReactAssayDesignerPage.beginAt(this, getProjectName(), protocolResponse.getProtocolId(),
+                "general", "");
+        assayDesignerPage.removeTransformScript(transformFileName);
+        assayDesignerPage.addTransformScript(destinationFile, false);
         assayDesignerPage.clickSave();
 
-        // Now delete the parent dir to ensure we handle it reasonably
-        TestFileUtils.deleteDirWithRetry(parentDir.toFile());
+        // Now delete the nested dir to ensure we handle it reasonably
+        File destinationDir = new File(transformFile.getParent() + "/child");
+        FileUtils.deleteDirectory(destinationDir);
 
         // Attempt to import data and verify a reasonable error message is shown
         String importData = """
                 VisitID\tParticipantID\tComment
                 1\tP1\timport after parent deleted
                 """;
 
-        new AssayRunsPage(getDriver()).getTable().clickHeaderButtonAndWait("Import Data");
+        AssayRunsPage.beginAt(this, getProjectName(), protocolResponse.getProtocolId())
+            .getTable().clickHeaderButtonAndWait("Import Data");
         var importPage = new AssayImportPage(getDriver());
         importPage.setNamedInputText("Name", "missingParentImport");
         importPage.setNamedTextAreaValue(AssayConstants.TEXT_AREA_DATA_COLLECTOR_TEXT_AREA_NAME, importData);
         importPage.clickSaveAndFinish();
 
         // Expect an error page/message indicating the transform script path cannot be used
         // Be tolerant to platform-specific phrasing; assert any of these appear
-        String expectedPath = transformFile.getAbsolutePath();
         checker().withScreenshot("missing-parent-error")
                 .verifyTrue("Expect an error message about the transform script path not being found",
-                        isTextPresent("transformMissingParent.R, configured for this assay does not exist."));
+                        isTextPresent(transformFileName + ", configured for this assay does not exist."));
 
         // Fix the assay design by removing the transform script
         goToProjectHome();
         assayDesignerPage = ReactAssayDesignerPage.beginAt(this, getProjectName(), protocolResponse.getProtocolId(),
                 "general", getURL().toString());
-        assayDesignerPage.removeTransformScript(scriptName);
+        assayDesignerPage.removeTransformScript(transformFileName);
         assayDesignerPage.clickSave();
 
         // Retry the import and verify it succeeds without the transform

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

@@ -310,7 +310,6 @@ public void testTransformScriptValidation()
 
         // 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);

src/org/labkey/test/util/core/webdav/WebDavUrlFactory.java

@@ -55,5 +55,15 @@ public static WebDavUrlFactory webFilesUrlFactory(String containerPath)
     {
         return new WebDavUrlFactory(buildBaseWebfilesUrl(containerPath));
     }
+
+    /**
+     * For cases where the WebDav directory URL is already known (e.g. taken from the 'href' of a link rendered by the
+     * server or a React component) and doesn't need to be constructed from a container path.
+     * @param directoryUrl Absolute URL of a WebDav directory
+     */
+    public static WebDavUrlFactory fromDirectoryUrl(String directoryUrl)
+    {
+        return new WebDavUrlFactory(directoryUrl);
+    }
 }