Selenium tests for file path import

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

@@ -13,6 +13,7 @@
 import org.labkey.test.components.DomainDesignerPage;
 import org.labkey.test.components.domain.DomainFieldRow;
 import org.labkey.test.components.domain.DomainFormPanel;
+import org.labkey.test.pages.admin.FileRootsManagementPage;
 import org.labkey.test.pages.experiment.UpdateSampleTypePage;
 import org.labkey.test.params.FieldDefinition;
 import org.labkey.test.params.experiment.SampleTypeDefinition;
@@ -81,6 +82,15 @@ public void testFileFieldInSampleType()
         setFormElement(Locator.name("quf_" + fieldName), SAMPLE_FILE);
         clickButton("Submit");
 
+        assertElementPresent(Locator.tagWithAttribute("a", "title", "Download attached file"));
+
+        clickAndWait(Locator.tagWithText("a", "S1"));
+        clickAndWait(Locator.tagWithClass("a", "labkey-text-link").withText("edit"));
+        waitForElement(Locator.tagContainingText("div", "sampletype/jpg_sample.jpg"));
+        // Issue 53200: Update form incorrectly shows that a file is not available
+        assertTextNotPresent("sampletype/jpg_sample.jpg (unavailable)");
+        clickButton("Cancel");
+
         log("Verifying view in browser works");
         clickAndWait(Locator.tagWithAttributeContaining("img", "title", SAMPLE_FILE.getName()));
         Assertions.assertThat(getDriver().getCurrentUrl()).as("File field view URL.").contains("core-downloadFileLink.view");
@@ -92,6 +102,49 @@ public void testFileFieldInSampleType()
 
         File downloadedFile = doAndWaitForDownload(() -> Locator.tagWithAttributeContaining("img", "title", SAMPLE_FILE.getName()).findElement(getDriver()).click());
         Assert.assertTrue("Downloaded file is empty", downloadedFile.length() > 0);
+
+        // create a subfolder and set the Project file root to child folder file root, to simulate sample file path not under current file root
+        String subFolder = "ChildFolder";
+        _containerHelper.createSubfolder(getProjectName(), subFolder);
+        clickFolder(subFolder);
+        FileRootsManagementPage fileRootsManagementPage = goToFolderManagement().goToFilesTab();
+        String childFileRoot = fileRootsManagementPage.getRootPath();
+        goToProjectHome();
+        fileRootsManagementPage = goToFolderManagement().goToFilesTab();
+        fileRootsManagementPage.useCustomFileRoot(childFileRoot).clickSave();
+
+        // verify file path display for files that's present but outside of current file root
+        verifyUnavailableFile();
+
+        // reset file root to default
+        goToFolderManagement()
+                .goToFilesTab()
+                .selectFileRootType(FileRootsManagementPage.FileRootOption.siteDefault)
+                .clickSave();
+        goToProjectHome();
+        clickAndWait(Locator.linkWithText(sampleTypeName));
+        assertElementPresent(Locator.tagWithAttribute("a", "title", "Download attached file"));
+
+        // delete the file and verify file path that doesn't exist
+        goToModule("FileContent");
+        _fileBrowserHelper.deleteFile("sampletype");
+        verifyUnavailableFile();
+    }
+
+    private void verifyUnavailableFile()
+    {
+        String sampleTypeName = "Sample type with attachment";
+        goToProjectHome();
+        clickAndWait(Locator.linkWithText(sampleTypeName));
+        waitForElement(Locator.tagContainingText("td", "jpg_sample.jpg (unavailable)"));
+        assertElementNotPresent(Locator.tagWithAttribute("a", "title", "Download attached file"));
+
+        // "(unavailable)" suffix is present in update view
+        clickAndWait(Locator.tagWithText("a", "S1"));
+        clickAndWait(Locator.tagWithClass("a", "labkey-text-link").withText("edit"));
+        waitForElement(Locator.tagContainingText("div", "jpg_sample.jpg (unavailable)"));
+        assertElementNotPresent(Locator.tagWithAttributeContaining("img", "src", "/_icons/image.png"));
+
     }
 
     @Test

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

@@ -52,6 +52,7 @@
 import java.util.List;
 import java.util.Map;
 
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.fail;
 
 public class APIAssayHelper extends AbstractAssayHelper
@@ -83,14 +84,44 @@ public ImportRunResponse importAssay(int assayID, String runFilePath, String pro
 
     @LogMethod(quiet = true)
     public ImportRunResponse importAssay(int assayID, String runName, List<Map<String, Object>> dataRows, String projectPath,
-                                         Map<String, Object> runProperties, Map<String, Object> batchProperties)  throws CommandException, IOException
+                                         Map<String, Object> runProperties, Map<String, Object> batchProperties, String errorMsg) throws CommandException, IOException
     {
         ImportRunCommand  irc = new ImportRunCommand(assayID, dataRows);
         irc.setName(runName);
         irc.setProperties(runProperties);
         irc.setBatchProperties(batchProperties);
         irc.setTimeout(180000); // Wait 3 minutes for assay import
-        return irc.execute(_test.createDefaultConnection(), projectPath);
+        if (errorMsg != null)
+        {
+            try
+            {
+                irc.execute(_test.createDefaultConnection(), projectPath);
+                throw new Exception("This should have failed");
+            }
+            catch (CommandException e)
+            {
+                Map<String, Object> responseJson = e.getProperties();
+                if (!responseJson.containsKey("exception"))
+                    throw new CommandException("Response lacks exception");
+
+                String exception = responseJson.get("exception").toString();
+                assertEquals("Invalid file path message not as expected", errorMsg, exception);
+                return null;
+            }
+            catch (Exception e)
+            {
+                throw new CommandException(e.getMessage());
+            }
+        }
+        else
+            return irc.execute(_test.createDefaultConnection(), projectPath);
+    }
+
+    @LogMethod(quiet = true)
+    public ImportRunResponse importAssay(int assayID, String runName, List<Map<String, Object>> dataRows, String projectPath,
+                                         Map<String, Object> runProperties, Map<String, Object> batchProperties) throws CommandException, IOException
+    {
+        return importAssay(assayID, runName, dataRows, projectPath, runProperties, batchProperties, null);
     }
 
     @LogMethod(quiet = true)
@@ -280,7 +311,7 @@ public static Map<String, Integer> getProtocolIds(String containerPath, Connecti
         return resultData;
     }
 
-    public void saveBatch(String assayName, String runName, Map<String, Object> runProperties, List<Map<String, Object>> resultRows, String projectName) throws IOException, CommandException
+    public void saveBatch(String assayName, String runName, Map<String, Object> runProperties, List<Map<String, Object>> resultRows, String projectName, @Nullable String errorMsg) throws Exception
     {
         int assayId = getIdFromAssayName(assayName, projectName);
 
@@ -294,14 +325,35 @@ public void saveBatch(String assayName, String runName, Map<String, Object> runP
         runs.add(run);
         batch.setRuns(runs);
 
-        saveBatch(assayId, batch, projectName);
+        saveBatch(assayId, batch, projectName, errorMsg);
     }
 
-    public void saveBatch(int assayId, Batch batch, String projectPath) throws IOException, CommandException
+    public void saveBatch(int assayId, Batch batch, String projectPath, @Nullable String errorMsg) throws Exception
     {
         SaveAssayBatchCommand cmd = new SaveAssayBatchCommand(assayId, batch);
         cmd.setTimeout(180000); // Wait 3 minutes for assay import
-        cmd.execute(_test.createDefaultConnection(), projectPath);
+        if (errorMsg != null)
+        {
+            try
+            {
+                var result = cmd.execute(_test.createDefaultConnection(), projectPath);
+                throw new Exception("This should have failed");
+            }
+            catch (CommandException e)
+            {
+                Map<String, Object> responseJson = e.getProperties();
+                if (!responseJson.containsKey("exception"))
+                    throw new Exception("Response lacks exception");
+
+                String exception = responseJson.get("exception").toString();
+                assertEquals("Invalid file path message not as expected", errorMsg, exception);
+            }
+        }
+        else
+            cmd.execute(_test.createDefaultConnection(), projectPath);
+
+
+
     }
 
     public Protocol createAssayDesignWithDefaults(String containerPath, String providerName, String assayName) throws IOException, CommandException

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

@@ -38,6 +38,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 import java.util.regex.Pattern;
 
 import static org.junit.Assert.fail;
@@ -206,6 +207,35 @@ public static void injectCookies(@NotNull String username, HttpUriRequest method
             method.setHeader(session.getName(), session.getValue());
     }
 
+    /*
+        reads a script result object, returns a string representation of an exception if it exists.
+        calling code should check the result and assert accordingly.
+        an exception means there was a server-side exception, rather than a script error.
+    */
+    static public String parseScriptResult(Map<String, Object> scriptResult)
+    {
+        if (scriptResult.containsKey("exception"))
+        {
+            String exType = (String)scriptResult.get("exception");
+            if (exType.contains("ERROR:"))
+                return exType;      // not an exception, but a friendly error message
+
+            ArrayList<String> frames = (ArrayList<String>)scriptResult.get("stackTrace");
+
+            StringBuilder builder = new StringBuilder();
+            if (null != frames)
+            {
+                for (String frame : frames)
+                {
+                    builder.append(frame + "\n");
+                }
+                return "An exception of type [" + exType + "] occurred while executing the script.\n[ " + builder + " ]";
+            }
+        }
+
+        return null;
+    }
+
     public static class ApiTestCase
     {
         private String _name;

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

@@ -28,6 +28,31 @@
 
 public class EscapeUtil
 {
+    static public String toJSONStr(String str)
+    {
+        if (str == null) return null;
+        StringBuilder escaped = new StringBuilder();
+        for (char c : str.toCharArray()) {
+            switch (c) {
+                case '"': escaped.append("\\\""); break;
+                case '\\': escaped.append("\\\\"); break;
+                case '\b': escaped.append("\\b"); break;
+                case '\f': escaped.append("\\f"); break;
+                case '\n': escaped.append("\\n"); break;
+                case '\r': escaped.append("\\r"); break;
+                case '\t': escaped.append("\\t"); break;
+                default:
+                    // Escape control characters (ASCII 0-31) and ensure Unicode compatibility
+                    if (c < 32) {
+                        escaped.append(String.format("\\u%04x", (int) c));
+                    } else {
+                        escaped.append(c);
+                    }
+            }
+        }
+        return escaped.toString();
+    }
+
     static public String jsString(String s)
     {
         if (s == null)

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

@@ -20,11 +20,17 @@
 import org.apache.commons.lang3.mutable.MutableObject;
 import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
+import org.labkey.remoteapi.CommandException;
+import org.labkey.remoteapi.Connection;
+import org.labkey.remoteapi.query.Filter;
+import org.labkey.remoteapi.query.SelectRowsCommand;
+import org.labkey.remoteapi.query.SelectRowsResponse;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.SortDirection;
 import org.labkey.test.TestProperties;
 import org.labkey.test.WebDriverWrapper;
+import org.labkey.test.WebTestHelper;
 import org.labkey.test.components.DomainDesignerPage;
 import org.labkey.test.components.ext4.Checkbox;
 import org.labkey.test.components.ext4.RadioButton;
@@ -40,6 +46,7 @@
 import org.openqa.selenium.support.ui.WebDriverWait;
 
 import java.io.File;
+import java.io.IOException;
 import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
 import java.time.Duration;
@@ -873,6 +880,58 @@ public void openFolderTree()
         }
     }
 
+    private String stringOrNull(Object value)
+    {
+        if (value == null)
+            return null;
+        return (String) value;
+    }
+
+    public record FileDetailInfo(String fileName, String absoluteFilePath, String dataFileUrl, String webDavUrl, String webDavUrlRelative)
+    {
+    }
+
+    public FileDetailInfo getFileDetailInfo(String containerPath, String fileName)
+    {
+        List<String> filePathColumns = List.of("AbsoluteFilePath", "FileExists", "DataFileUrl", "WebDavUrl", "WebDavUrlRelative");
+        try
+        {
+            Connection cn = WebTestHelper.getRemoteApiConnection();
+            SelectRowsCommand cmd = new SelectRowsCommand("exp", "files");
+            cmd.addFilter("Name", fileName, Filter.Operator.EQUAL);
+            cmd.setColumns(filePathColumns);
+            SelectRowsResponse response = cmd.execute(cn, "/" + containerPath);
+
+            for (Map<String, Object> row: response.getRows())
+            {
+                if (!(Boolean) row.get("FileExists"))
+                    continue;
+                Object absoluteFilePath = row.get("AbsoluteFilePath");
+                Object dataFileUrl = row.get("DataFileUrl");
+                Object webDavUrl = row.get("WebDavUrl");
+                Object webDavUrlRelative = row.get("WebDavUrlRelative");
+                return new FileDetailInfo(fileName, stringOrNull(absoluteFilePath), stringOrNull(dataFileUrl), stringOrNull(webDavUrl), stringOrNull(webDavUrlRelative));
+            }
+        }
+        catch (CommandException ce)
+        {
+            if (ce.getStatusCode() == 404)
+            {
+                return null;
+            }
+            else
+            {
+                throw new RuntimeException(ce);
+            }
+        }
+        catch (IOException ioe)
+        {
+            throw new RuntimeException(ioe);
+        }
+
+        return null;
+    }
+
     // See PageFlowUtil.encodeURIComponent()
     private static final Map<String, String> DECODE_UNRESERVED_MARKS = Map.of(
         "!", "%21",

src/org/labkey/test/util/data/TestDataUtils.java

@@ -14,7 +14,6 @@
 import org.labkey.serverapi.reader.TabLoader;
 import org.labkey.test.TestFileUtils;
 import org.labkey.test.params.FieldDefinition;
-import org.labkey.test.util.EscapeUtil;
 import org.labkey.test.util.TestDataGenerator;
 import org.labkey.test.util.TestLogger;
 
@@ -296,6 +295,12 @@ public static String tsvStringFromRowMaps(List<Map<String, Object>> rowMaps, Lis
         return stringFromRowMaps(rowMaps, columns, includeHeaders, CSVFormat.TDF);
     }
 
+    public static String tsvStringFromRowMapsEscapeBackslash(List<Map<String, Object>> rowMaps, List<String> columns,
+                                                             boolean includeHeaders)
+    {
+        return stringFromRowMaps(rowMaps, columns, includeHeaders, CSVFormat.MYSQL);
+    }
+
     public static <T> List<Map<String, T>> mapsFromRows(List<List<T>> allRows)
     {
         List<Map<String, T>> rowMaps = new ArrayList<>();
@@ -439,6 +444,12 @@ public static <T> File writeRowsToTsv(String fileName, List<List<T>> rows) throw
         return writeRowsToFile(fileName, rows, CSVFormat.TDF);
     }
 
+    public static <T> File writeRowsToTsvEscapeBackslash(String fileName, List<List<T>> rows) throws IOException
+    {
+        return writeRowsToFile(fileName, rows, CSVFormat.MYSQL);
+    }
+
+
     public static <T> File writeRowsToCsv(String fileName, List<List<T>> rows) throws IOException
     {
         return writeRowsToFile(fileName, rows, CSVFormat.DEFAULT);