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

Author: labkey-susanh

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/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

api/src/org/labkey/api/module/ModuleLoader.java

@@ -580,19 +580,6 @@ private void doInit(Execution execution) throws ServletException
             throw new IllegalStateException("Core module was not first or could not find the Core module. Ensure that Tomcat user can create directories under the <LABKEY_HOME>/modules directory.");
         setProjectRoot(coreModule);
 
-        for (Module module : modules)
-        {
-            module.registerFilters(_servletContext);
-        }
-        for (Module module : modules)
-        {
-            module.registerServlets(_servletContext);
-        }
-        for (Module module : modules)
-        {
-            module.registerFinalServlets(_servletContext);
-        }
-
         // Do this after we've checked to see if we can find the core module. See issue 22797.
         verifyProductionModeMatchesBuild();
 
@@ -790,12 +777,34 @@ public void addStaticWarnings(@NotNull Warnings warnings, boolean showAllWarning
         if (!modulesRequiringUpgrade.isEmpty() || !additionalSchemasRequiringUpgrade.isEmpty())
             setUpgradeState(UpgradeState.UpgradeRequired);
 
-        // Don't accept any requests if we're bootstrapping empty schemas or migrating from SQL Server
+        // Don't accept any requests if we're bootstrapping empty schemas or doing a database migration
         if (!shouldInsertData())
             execution = Execution.Synchronous;
 
         startNonCoreUpgradeAndStartup(execution, lockFile);
 
+        // Register filters and servlets at the last minute, just before Tomcat starts. At this point, the list of
+        // modules is final. We've had one case where the CSP filter was getting initialized before the core module
+        // was initialized, GitHub Issue 1008. We have no idea how that happened, but registering late won't hurt.
+
+        _log.info("Registering filters");
+
+        for (Module module : _modules)
+        {
+            module.registerFilters(_servletContext);
+        }
+
+        _log.info("Registering servlets");
+
+        for (Module module : _modules)
+        {
+            module.registerServlets(_servletContext);
+        }
+        for (Module module : _modules)
+        {
+            module.registerFinalServlets(_servletContext);
+        }
+
         _log.info("LabKey Server startup is complete; {}", execution.getLogMessage());
     }
 

api/src/org/labkey/api/util/DOM.java

@@ -362,6 +362,54 @@ public enum Attribute
         action,
         align,
         alt,
+        aria_activedescendant,
+        aria_atomic,
+        aria_autocomplete,
+        aria_busy,
+        aria_checked,
+        aria_colcount,
+        aria_colindex,
+        aria_colspan,
+        aria_controls,
+        aria_current,
+        aria_describedby,
+        aria_details,
+        aria_disabled,
+        aria_dropeffect,
+        aria_errormessage,
+        aria_expanded,
+        aria_flowto,
+        aria_grabbed,
+        aria_haspopup,
+        aria_hidden,
+        aria_invalid,
+        aria_keyshortcuts,
+        aria_label,
+        aria_labelledby,
+        aria_level,
+        aria_live,
+        aria_modal,
+        aria_multiline,
+        aria_multiselectable,
+        aria_orientation,
+        aria_owns,
+        aria_placeholder,
+        aria_posinset,
+        aria_pressed,
+        aria_readonly,
+        aria_relevant,
+        aria_required,
+        aria_roledescription,
+        aria_rowcount,
+        aria_rowindex,
+        aria_rowspan,
+        aria_selected,
+        aria_setsize,
+        aria_sort,
+        aria_valuemax,
+        aria_valuemin,
+        aria_valuenow,
+        aria_valuetext,
         async,
         autocomplete,
         autofocus,
@@ -579,7 +627,6 @@ public _Attributes data(boolean condition, String datakey, Object value)
             }
             return this;
         }
-
         public _Attributes cl(String...names)
         {
             if (null != names)
@@ -900,7 +947,7 @@ private static Appendable appendAttribute(Appendable html, Attribute key, Object
         if (null==value)
             return html;
         html.append(" ");
-        html.append(key.name());
+        html.append(key.name().replace('_', '-'));
         html.append("=\"");
         // NOTE it is somewhat unusual to pass in a Renderable, but it is possible that we
         // want to render HTML into an attribute.  We still need to re-encode the value before trying to wrap with "".