Merge remote-tracking branch 'origin/develop' into fb_updateMessageWhen

labkey-susanh · labkey-susanh · commit f4585707664d · 2025-09-29T15:14:45.000-07:00
diff --git a/src/org/labkey/remoteapi/plate/PlateParams.java b/src/org/labkey/remoteapi/plate/PlateParams.java
@@ -2,20 +2,27 @@
 
 import org.json.JSONObject;
 
+import java.util.List;
+import java.util.Map;
+
 public class PlateParams
 {
+    private boolean _archived;
+    private String _assayType;
+    private String _barcode;
+    private int _columns;
+    private String _description;
     private String _name;
     private String _plateId;
-    private int _rowId;
     private int _plateSetId;
-    private String _description;
-    private int _rows;
-    private int _columns;
     private int _plateType;
-    private String _assayType;
+    private int _rowId;
+    private int _rows;
     private boolean _template;
-    private boolean _archived;
 
+    private PlateParams()
+    {
+    }
 
     public PlateParams(JSONObject json)
     {
@@ -45,6 +52,35 @@ public PlateParams(JSONObject json)
 
         if (json.has("archived"))
             _archived = json.getBoolean("archived");
+
+        if (json.has("barcode"))
+            _barcode = json.getString("barcode");
+    }
+
+    public static final List<String> QUERY_COLUMNS = List.of("Archived", "AssayType", "Barcode", "Description", "Name", "PlateId", "PlateSet", "PlateType", "PlateType/Columns", "PlateType/Rows", "RowId", "Template");
+
+    public static PlateParams fromQueryRow(Map<String, Object> row)
+    {
+        var params = new PlateParams();
+        params._archived = (Boolean) row.get("Archived");
+        params._assayType = (String) row.get("AssayType");
+        params._barcode = (String) row.get("Barcode");
+        params._columns = (Integer) row.get("PlateType/Columns");
+        params._description = (String) row.get("Description");
+        params._name = (String) row.get("Name");
+        params._plateId = (String) row.get("PlateId");
+        params._plateSetId = (Integer) row.get("PlateSet");
+        params._plateType = (Integer) row.get("PlateType");
+        params._rowId = (Integer) row.get("RowId");
+        params._rows = (Integer) row.get("PlateType/Rows");
+        params._template = (Boolean) row.get("Template");
+
+        return params;
+    }
+
+    public String getBarcode()
+    {
+        return _barcode;
     }
 
     public String getName()
diff --git a/src/org/labkey/remoteapi/plate/PlateSetParams.java b/src/org/labkey/remoteapi/plate/PlateSetParams.java
@@ -2,6 +2,9 @@
 
 import org.json.JSONObject;
 
+import java.util.List;
+import java.util.Map;
+
 public class PlateSetParams
 {
     private boolean _archived;
@@ -22,6 +25,10 @@ public class PlateSetParams
     private boolean _template;
     private CreatePlateSetParams.PlateSetType _plateSetType;
 
+    private PlateSetParams()
+    {
+    }
+
     public PlateSetParams(JSONObject json)
     {
         if (json.has("archived"))
@@ -58,6 +65,31 @@ public PlateSetParams(JSONObject json)
             _plateSetType = CreatePlateSetParams.PlateSetType.fromName(json.getString("type"));
     }
 
+    public static final List<String> QUERY_COLUMNS = List.of("Archived", "Created", "CreatedBy", "Description", "Folder/EntityId", "Folder/Name", "Folder/Path", "Modified", "ModifiedBy", "Name", "PlateCount", "PlateSetId", "PrimaryPlateSetId", "RootPlateSetId", "RowId", "Template", "Type");
+
+    public static PlateSetParams fromQueryRow(Map<String, Object> row)
+    {
+        var params = new PlateSetParams();
+        params._containerId = (String) row.get("Folder/EntityId");
+        params._containerName = (String) row.get("Folder/Name");
+        params._containerPath = (String) row.get("Folder/Path");
+        params._created = row.get("Created").toString();
+        params._createdBy = (Integer) row.get("CreatedBy");
+        params._description = (String) row.get("Description");
+        params._modified = row.get("Modified").toString();
+        params._modifiedBy = (Integer) row.get("ModifiedBy");
+        params._name = (String) row.get("Name");
+        params._plateCount = (Integer) row.get("PlateCount");
+        params._plateSetId = (String) row.get("PlateSetId");
+        params._plateSetType = CreatePlateSetParams.PlateSetType.fromName((String) row.get("Type"));
+        params._primaryPlateSetId = (Integer) row.get("PrimaryPlateSetId");
+        params._rootPlateSetId = (Integer) row.get("RootPlateSetId");
+        params._rowId = (Integer) row.get("RowId");
+        params._template = (Boolean) row.get("Template");
+
+        return params;
+    }
+
     public boolean getArchived()
     {
         return _archived;
diff --git a/src/org/labkey/test/LabKeySiteWrapper.java b/src/org/labkey/test/LabKeySiteWrapper.java
@@ -1530,26 +1530,26 @@ protected SelectRowsResponse executeSelectRowCommand(String schemaName, String q
     protected SelectRowsResponse executeSelectRowCommand(String schemaName, String queryName, ContainerFilter containerFilter,
                                                          String path, @Nullable List<Filter> filters, @Nullable List<String> requestedColumns)
     {
-        Connection cn = createDefaultConnection();
         SelectRowsCommand selectCmd = new SelectRowsCommand(schemaName, queryName);
         selectCmd.setMaxRows(-1);
         selectCmd.setContainerFilter(containerFilter);
         selectCmd.setColumns(requestedColumns);
         if (filters != null)
             selectCmd.setFilters(filters);
 
-        SelectRowsResponse selectResp;
+        return executeSelectRowCommand(path, selectCmd);
+    }
 
+    protected SelectRowsResponse executeSelectRowCommand(String containerPath, SelectRowsCommand command)
+    {
         try
         {
-            selectResp = selectCmd.execute(cn, path);
+            return command.execute(createDefaultConnection(), containerPath);
         }
         catch (CommandException | IOException e)
         {
             throw new RuntimeException(e);
         }
-
-        return selectResp;
     }
 
     // Returns the text contents of every "Status" cell in the pipeline StatusFiles grid
diff --git a/src/org/labkey/test/tests/MenuBarTest.java b/src/org/labkey/test/tests/MenuBarTest.java
@@ -88,7 +88,6 @@ public void testSteps()
         clickAndWait(Locator.linkWithText("Menu Bar"));
 
         log("Add menu bar webparts");
-        portalHelper.addWebPart("AssayList2");
         portalHelper.addWebPart("Study List");
         portalHelper.addWebPart("Wiki Menu");
 
@@ -114,7 +113,6 @@ public void testSteps()
 
         //Make sure that the menus are shown, but the content is not yet loaded.
         assertElementPresent(Locator.tagWithClass("div", "navbar-header"));
-        assertElementPresent(menuBarItem("Assays"));
         assertElementPresent(menuBarItem("Studies"));
         assertElementPresent(menuBarItem(WIKI_PAGE_TITLE));
 
@@ -125,15 +123,6 @@ public void testSteps()
 
         openMenu(WIKI_PAGE_TITLE);
         waitForElement(Locator.xpath("//div").withClass("labkey-wiki").withText(WIKI_PAGE_CONTENT));
-        openMenu("Assays");
-        waitForElement(Locator.lkButton("Manage Assays"), 3000);
-
-        _assayHelper.uploadXarFileAsAssayDesign(TestFileUtils.getSampleData("menubar/Test Assay.xar"), 1);
-        clickProject(PROJECT_NAME);
-
-        assertTextNotPresent("Test Assay");
-        openMenu("Assays");
-        waitForElement(Locator.linkWithText("Test Assay"));
 
         _containerHelper.createSubfolder(PROJECT_NAME, PROJECT_NAME, "StudyFolder", "Study", null);
         createDefaultStudy();
@@ -218,7 +207,6 @@ public void testSteps()
         // Issue 47841: verify that menu config comes through with folder export/import (via create from template)
         UIContainerHelper uiContainerHelper = new UIContainerHelper(this);
         uiContainerHelper.createProjectFromTemplate(getAltProjectName(), "/" + getProjectName());
-        openMenu("Assays");
         openMenu("Studies");
         openMenu(WIKI_PAGE_TITLE);
         openMenu("Wiki Render Types");
diff --git a/src/org/labkey/test/tests/wiki/WikiTest.java b/src/org/labkey/test/tests/wiki/WikiTest.java
@@ -26,6 +26,7 @@
 import org.labkey.remoteapi.SimplePostCommand;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
+import org.labkey.test.TestFileUtils;
 import org.labkey.test.categories.Daily;
 import org.labkey.test.categories.Wiki;
 import org.labkey.test.pages.admin.ExternalSourcesPage;
@@ -38,6 +39,7 @@
 import org.labkey.test.util.search.SearchAdminAPIHelper;
 
 import java.io.File;
+import java.io.IOException;
 import java.time.Duration;
 import java.util.Arrays;
 import java.util.List;
@@ -240,6 +242,75 @@ public void testWikiWithComma()
         Assert.assertEquals("Incorrect result with comma", Arrays.asList(wikiTitle + "\n/" + getProjectName() + "\n" + wikiContent), getTexts(new SearchResultsPage(getDriver()).getResults()));
     }
 
+    // Issue 49321
+    @Test
+    public void testDeleteUndeleteAttachment() throws IOException
+    {
+        String wikiName = "Wiki with attachments";
+        String wikiTitle = "Attach Delete Undelete file";
+        String wikiContent = "Lorem Ipsum something";
+        String fileName = "wiki_temp_file_attachment.txt";
+        File testAttachment = TestFileUtils.writeTempFile(fileName, "it was a dark and stormy night");
+        Locator.XPathLocator attachmentParentLoc = Locator.id("wiki-ea-name-0");
+        Locator.XPathLocator removeLinkLoc = Locator.tag("td").child(Locator.linkContainingText("remove"));
+        Locator.XPathLocator deleteLinkLoc = Locator.tag("td").child(Locator.linkContainingText("delete"));
+        Locator undeleteLinkLoc = Locator.tag("td").child("a").child("span").containing("un-delete");
+        Locator filePickerLinkLoc = Locator.id("filePickerLink");
+        Locator fileInputLoc = Locator.tag("input").withAttribute("type", "file")
+                .withAttributeContaining("id", "formFile");
+
+        goToProjectHome();
+        log("Creating the wiki " + wikiTitle);
+        WikiHelper wikiHelper = new WikiHelper(this);
+        wikiHelper.createNewWikiPage("HTML");
+        wikiHelper.setWikiName(wikiName);
+        wikiHelper.setWikiTitle(wikiTitle);
+        wikiHelper.setWikiBody("<p>" + wikiContent + "</p>");
+        wikiHelper.saveWikiPage();
+        numberOfWikiCreated++;
+
+        log("adding an attachment");
+        wikiHelper.editWikiPage();
+        click(filePickerLinkLoc);
+        setFormElement(fileInputLoc, testAttachment);
+        waitForElement(removeLinkLoc);  // when just attached, 'remove' will be an option but delete will not be
+        assertElementNotPresent(deleteLinkLoc);
+        click(removeLinkLoc);   // verify remove removes the file
+        waitForElementToDisappear(Locator.linkWithText(fileName));
+        click(filePickerLinkLoc);
+        setFormElement(fileInputLoc, testAttachment);
+        wikiHelper.saveWikiPage();  // save with the attachment
+        waitForElement(Locator.linkWithText(fileName));
+
+        log("Deleting attachment");
+        wikiHelper.editWikiPage();
+        click(deleteLinkLoc);
+        waitForElement(attachmentParentLoc.withAttributeContaining("style", "text-decoration: line-through"));
+        wikiHelper.saveWikiPage();
+        // verify save while in deleted state actually deletes the attachment
+        assertElementNotPresent(Locator.linkWithText(fileName));
+
+        log("prepare to delete/undelete attachment");
+        // re-attach the file and save
+        wikiHelper.editWikiPage();
+        click(filePickerLinkLoc);
+        setFormElement(fileInputLoc, testAttachment);
+        wikiHelper.saveWikiPage();
+
+        log("Un-Deleting attachment");
+        wikiHelper.editWikiPage();
+        click(deleteLinkLoc);   // delete
+        waitForElement(attachmentParentLoc.withAttributeContaining("style", "text-decoration: line-through"));
+        waitAndClick(undeleteLinkLoc);
+        checker().awaiting(Duration.ofMillis(500), ()-> Assertions.assertThat(attachmentParentLoc.findElement(getDriver()).getAttribute("style"))
+                .as("expect strikethrough style not to be present")
+                .doesNotContain("text-decoration: line-through"));
+        wikiHelper.saveWikiPage();
+
+        // verify save after undelete persists the attachment
+        assertElementPresent(Locator.linkWithText(fileName));
+    }
+
     // Issue 51382
     @Test
     public void testCreateWikiWithHostileNameAndTitle() throws Exception
diff --git a/src/org/labkey/test/util/AuditLogHelper.java b/src/org/labkey/test/util/AuditLogHelper.java
@@ -4,6 +4,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONException;
+import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.remoteapi.CommandException;
 import org.labkey.remoteapi.Connection;
 import org.labkey.remoteapi.query.ContainerFilter;
@@ -29,10 +30,10 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
-import java.util.stream.Stream;
 
 import static java.lang.Integer.parseInt;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 import static org.labkey.test.WebDriverWrapper.WAIT_FOR_JAVASCRIPT;
@@ -85,16 +86,19 @@ public enum AuditBehaviorType
 
     public enum AuditEvent
     {
-        SAMPLE_TIMELINE_EVENT("SampleTimelineEvent"),
-        SOURCES_AUDIT_EVENT("SourcesAuditEvent"), // avaialble with SampleManagement module
+        ASSAY_AUDIT_EVENT("AssayAuditEvent"), // available with SampleManagement module
+        ASSAY_RESULT_AUDIT_EVENT("AssayResultAuditEvent"), // available with SampleManagement module
+        EXPERIMENT_AUDIT_EVENT("ExperimentAuditEvent"),
+        FILE_SYSTEM_EVENT("FileSystem"),
         INVENTORY_AUDIT_EVENT("InventoryAuditEvent"),
         LIST_AUDIT_EVENT("ListAuditEvent"),
-        ASSAY_AUDIT_EVENT("AssayAuditEvent"), // avaialble with SampleManagement module
-        ASSAY_RESULT_AUDIT_EVENT("AssayResultAuditEvent"), // avaialble with SampleManagement module
-        EXPERIMENT_AUDIT_EVENT("ExperimentAuditEvent"),
-        SAMPLE_WORKFLOW_AUDIT_EVENT("SamplesWorkflowAuditEvent"),
+        PLATE_AUDIT_EVENT("PlateEvent"), // available in Biologics module
+        PLATE_DATA_AUDIT_EVENT("PlateDataAuditEvent"), // available in Biologics module
+        PLATE_SET_AUDIT_EVENT("PlateSetEvent"), // available in Biologics module
         QUERY_UPDATE_AUDIT_EVENT("QueryUpdateAuditEvent"),
-        FILE_SYSTEM_EVENT("FileSystem");
+        SAMPLE_TIMELINE_EVENT("SampleTimelineEvent"),
+        SAMPLE_WORKFLOW_AUDIT_EVENT("SamplesWorkflowAuditEvent"),
+        SOURCES_AUDIT_EVENT("SourcesAuditEvent"); // available with SampleManagement module
 
         private final String _name;
 
@@ -257,16 +261,16 @@ public void checkAuditEventDiffCount(String containerPath, AuditEvent auditEvent
             boolean isInventoryUpdateType = event.get("InventoryUpdateType") != null;
             int expectedDiffCount = isInventoryUpdateType ? 0 : expectedDiffCounts.get(i);
             String dataChangesStr = (String) event.get(eventDiffFieldName);
-            String[] dataChanges = dataChangesStr != null ? dataChangesStr.split("&") : new String[0];
+            Map<String, String> dataChanges = decodeValues(dataChangesStr);
 
             // filter out SampleStateLabel as that is not a change, it is added for display purposes
-            dataChanges = Stream.of(dataChanges).filter(s -> !s.toLowerCase().startsWith("samplestatelabel=")).toArray(String[]::new);
+            dataChanges.remove("SampleStateLabel");
             // filter out RowId as that is not a change, it is added for display purposes
-            dataChanges = Stream.of(dataChanges).filter(s -> !s.toLowerCase().startsWith("rowid=")).toArray(String[]::new);
+            dataChanges.remove("RowId");
 
             log("Audit record data changes diff count check (" + eventDiffFieldName + "): " + dataChangesStr);
-            assertEquals("Audit record data changes did not include the expected number of diffs in " + eventDiffFieldName + ", expected " + expectedDiffCount + " but was " + dataChanges.length + ": " + dataChangesStr,
-                    expectedDiffCount, dataChanges.length);
+            assertEquals("Audit record data changes did not include the expected number of diffs in " + eventDiffFieldName + ", expected " + expectedDiffCount + " but was " + dataChanges.size() + ": " + dataChangesStr,
+                    expectedDiffCount, dataChanges.size());
         }
     }
 
@@ -527,6 +531,24 @@ public String getLogString()
         }
     }
 
+    public static Map<String, String> decodeValues(String recordMapString)
+    {
+        if (recordMapString == null || recordMapString.isEmpty())
+            return Collections.emptyMap();
+
+        Map<String, String> recordMap = new CaseInsensitiveHashMap<>();
+        for (String part : recordMapString.split("&"))
+        {
+            String[] keyValue = part.split("=");
+            String key = EscapeUtil.decode(keyValue[0]);
+            assertFalse(String.format("Audit record map already contains key for %s", key), recordMap.containsKey(key));
+
+            recordMap.put(key, keyValue.length > 1 ? EscapeUtil.decode(keyValue[1]) : null);
+        }
+
+        return recordMap;
+    }
+
     /**
      * URL-encode fields and values for {@link DetailedAuditEventRow#newValues} or {@link DetailedAuditEventRow#oldValues}
      * @param pairs alternating field names and their associated values

Original file line number	Diff line number	Diff line change
`@@ -1530,26 +1530,26 @@ protected SelectRowsResponse executeSelectRowCommand(String schemaName, String q`
`1530`	`1530`	`protected SelectRowsResponse executeSelectRowCommand(String schemaName, String queryName, ContainerFilter containerFilter,`
`1531`	`1531`	`String path, @Nullable List<Filter> filters, @Nullable List<String> requestedColumns)`
`1532`	`1532`	`{`
`1533`		`- Connection cn = createDefaultConnection();`
`1534`	`1533`	`SelectRowsCommand selectCmd = new SelectRowsCommand(schemaName, queryName);`
`1535`	`1534`	`selectCmd.setMaxRows(-1);`
`1536`	`1535`	`selectCmd.setContainerFilter(containerFilter);`
`1537`	`1536`	`selectCmd.setColumns(requestedColumns);`
`1538`	`1537`	`if (filters != null)`
`1539`	`1538`	`selectCmd.setFilters(filters);`
`1540`	`1539`
`1541`		`- SelectRowsResponse selectResp;`
	`1540`	`+ return executeSelectRowCommand(path, selectCmd);`
	`1541`	`+ }`
`1542`	`1542`
	`1543`	`+ protected SelectRowsResponse executeSelectRowCommand(String containerPath, SelectRowsCommand command)`
	`1544`	`+ {`
`1543`	`1545`	`try`
`1544`	`1546`	`{`
`1545`		`- selectResp = selectCmd.execute(cn, path);`
	`1547`	`+ return command.execute(createDefaultConnection(), containerPath);`
`1546`	`1548`	`}`
`1547`	`1549`	`catch (CommandException \| IOException e)`
`1548`	`1550`	`{`
`1549`	`1551`	`throw new RuntimeException(e);`
`1550`	`1552`	`}`
`1551`		`-`
`1552`		`- return selectResp;`
`1553`	`1553`	`}`
`1554`	`1554`
`1555`	`1555`	`// Returns the text contents of every "Status" cell in the pipeline StatusFiles grid`