Merge branch 'release26.3-SNAPSHOT' into 26.3_fb_issue_936

Author: labkey-klum

.github/pull_request_template.md

@@ -10,6 +10,6 @@
 <!-- list of standard tasks (remove this comment to enable)
 #### Tasks 📍
 - [ ] Manual Testing
-- [ ] Needs Automation
+- [ ] Test Automation
 - [ ] Verify Fix
--->
+-->

announcements/src/org/labkey/announcements/announcementThread.jsp

@@ -127,7 +127,7 @@ if (!announcementModel.getAttachments().isEmpty())
         {
             ActionURL downloadURL = AnnouncementsController.getDownloadURL(announcementModel, d.getName());
         %>
-        <a href="<%=h(downloadURL)%>"><img alt="" src="<%=getWebappURL(d.getFileIcon())%>">&nbsp;<%=h(d.getName())%></a>&nbsp;<%
+        <%=d.renderDownloadLink(downloadURL)%>&nbsp;<%
         } %>
     </div></td>
 </tr><%
@@ -210,7 +210,7 @@ if (!announcementModel.getResponses().isEmpty())
                 {
                     ActionURL downloadURL = AnnouncementsController.getDownloadURL(r, rd.getName());
                 %>
-                    <a href="<%=h(downloadURL)%>"><img alt="" src="<%=getWebappURL(rd.getFileIcon())%>">&nbsp;<%=h(rd.getName())%></a>&nbsp;<%
+                    <%=rd.renderDownloadLink(downloadURL)%>&nbsp;<%
                 }
                 %>
                 </div></td>

announcements/src/org/labkey/announcements/announcementWebPartSimple.jsp

@@ -195,7 +195,7 @@ for (AnnouncementModel a : bean.announcementModels)
         for (Attachment d : a.getAttachments())
         {
             ActionURL downloadURL = AnnouncementsController.getDownloadURL(a, d.getName());
-            %><a href="<%=h(downloadURL)%>"><img src="<%=getWebappURL(d.getFileIcon())%>">&nbsp;<%=h(d.getName())%></a>&nbsp;<%
+            %><%=d.renderDownloadLink(downloadURL)%>&nbsp;<%
         }
         %></td></tr><%
     }

announcements/src/org/labkey/announcements/announcementWebPartWithExpandos.jsp

@@ -217,7 +217,7 @@ for (AnnouncementModel a : bean.announcementModels)
         for (Attachment d : a.getAttachments())
         {
             ActionURL downloadURL = AnnouncementsController.getDownloadURL(a, d.getName());
-            %><a href="<%=h(downloadURL)%>"><img src="<%=getWebappURL(d.getFileIcon())%>">&nbsp;<%=h(d.getName())%></a>&nbsp;<%
+            %><%=d.renderDownloadLink(downloadURL)%>&nbsp;<%
         }
         %></td></tr><%
     }

announcements/src/org/labkey/announcements/update.jsp

@@ -140,7 +140,6 @@ if (settings.hasExpires())
             <tbody>
                 <%
                     int x = -1;
-                    String id;
                     for (Attachment att : ann.getAttachments())
                 {
                     x++;

api/src/org/labkey/api/assay/AbstractAssayProvider.java

@@ -124,6 +124,7 @@
 import javax.script.ScriptEngine;
 import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.net.URI;
 import java.net.URL;
 import java.sql.ResultSet;
@@ -1274,9 +1275,9 @@ public Pair<ValidationException, Pair<String, String>> setValidationAndAnalysisS
                     if (!(engine instanceof ExternalScriptEngine && ((ExternalScriptEngine) engine).isBinary(scriptFile)))
                     {
                         String scriptText;
-                        try
+                        try (InputStream is = scriptFile.openInputStream())
                         {
-                            scriptText = IOUtils.toString(scriptFile.openInputStream(), StringUtilsLabKey.DEFAULT_CHARSET);
+                            scriptText = IOUtils.toString(is, StringUtilsLabKey.DEFAULT_CHARSET);
                         }
                         catch (IOException e)
                         {

api/src/org/labkey/api/attachments/Attachment.java

@@ -21,9 +21,13 @@
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.services.ServiceRegistry;
+import org.labkey.api.util.DOM;
+import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.MemTracker;
 import org.labkey.api.util.MimeMap;
+import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
+import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewServlet;
 import org.labkey.api.webdav.WebdavResolver;
 
@@ -350,4 +354,29 @@ public void setDocumentSize(int documentSize)
     {
         _documentSize = documentSize;
     }
+
+    /**
+     * Returns an HtmlString rendering a download link: an anchor containing a file type icon and the filename.
+     * The icon is marked aria-hidden since it is decorative; the link text serves as the accessible name.
+     */
+    public HtmlString renderDownloadLink(ActionURL downloadURL)
+    {
+        return renderDownloadLink(downloadURL, getName());
+    }
+
+    /**
+     * Returns an HtmlString rendering a download link: an anchor containing a file type icon and custom link text.
+     * Use this overload when the visible link label differs from the filename (e.g. "Study Protocol Document").
+     * The icon is marked aria-hidden since it is decorative; linkText serves as the accessible name.
+     */
+    public HtmlString renderDownloadLink(ActionURL downloadURL, String linkText)
+    {
+        return DOM.createHtmlFragment(
+            DOM.A(DOM.at(DOM.Attribute.href, downloadURL.toString()),
+                DOM.IMG(DOM.at(DOM.Attribute.alt, "").at(DOM.Attribute.src, PageFlowUtil.staticResourceUrl(getFileIcon()))),
+                HtmlString.NBSP,
+                linkText
+            )
+        );
+    }
 }

api/src/org/labkey/api/exp/list/ListService.java

@@ -51,6 +51,7 @@ static void setInstance(ListService ls)
     boolean hasLists(Container container, boolean includeProjectAndShared);
     ListDefinition createList(Container container, String name, ListDefinition.KeyType keyType);
     ListDefinition createList(Container container, String name, ListDefinition.KeyType keyType, @Nullable TemplateInfo templateInfo, @Nullable ListDefinition.Category category);
+    void deleteLists(Container container, User user, @Nullable String auditUserComment);
     @Nullable ListDefinition getList(Container container, int listId);
     @Nullable ListDefinition getList(Container container, String name);
     @Nullable ListDefinition getList(Container container, String name, boolean includeProjectAndShared);

api/src/org/labkey/api/inventory/InventoryService.java

@@ -52,6 +52,7 @@ enum InventoryStatusColumn
         StorageColSort,
         StorageComment,
         StorageLocation,
+        StorageTerminalLocation,
         StorageRow,
         StorageRowSort,
         StoragePositionNumber,

api/src/org/labkey/api/mcp/McpService.java

@@ -29,11 +29,11 @@
 /// ### MCP Development Guide
 /// `McpService` lets you expose functionality over the MCP protocol (only simple http for now). This allows external
 /// chat sessions to pull information from LabKey Server. Exposed functionality is also made available to chat sessions
-/// hosted by LabKey (see `AbstractAgentAction``).
+/// hosted by LabKey (see `AbstractAgentAction`).
 ///
 /// ### Adding a new MCP class
 /// 1. Create a new class that implements `McpImpl` (see below) in the appropriate module
-/// 2. Register that class in your module `init()` method: `McpService.get().register(new MyMcp())`
+/// 2. Register that class in your module's `startup()` method: `McpService.get().register(new MyMcp())`
 /// 3. Add tools and resources
 ///
 /// ### Adding a new MCP tool
@@ -44,13 +44,13 @@
 ///     permission annotation is required, otherwise your tool will not be registered.**
 /// 4.  Add `ToolContext` as the first parameter to the method
 /// 5.  Add additional required or optional parameters to the method signature, as needed. Note that "required" is the
-///     default. Again here, the parameter descriptions are very important. Provide examples.
+///     default. Again here, the parameter descriptions are very important. Provide examples of parameter values.
 /// 6.  Use the helper method `getContext(ToolContext)` to retrieve the current `Container` and `User`
 /// 7.  Use the helper method `getUser(ToolContext)` in the rare cases where you need just a `User`
 /// 8.  Perform additional permissions checking (beyond what the annotations offer), where appropriate
 /// 9.  Filter all results to the current container, of course
 /// 10. For any error conditions, throw exceptions with detailed information. These will get translated into appropriate
-///     failure responses and the LLM client will attempt to correct the problem.
+///     failure responses and the LLM client will attempt to correct any problems (hopefully).
 /// 11. For success cases, return a String with a message or JSON content, for example, `JSONObject.toString()`. Spring
 ///     has some limited ability to convert other objects into JSON strings, but we haven't experimented with that. See
 ///     `DefaultToolCallResultConverter` and the ability to provide a custom result converter via the `@Tool` annotation.
@@ -126,6 +126,7 @@ static void setInstance(McpService service)
 
     boolean isReady();
 
+    // Register MCPs in Module.startup()
     default void register(McpImpl mcp)
     {
         try