Simplify embedded Tomcat configuration

api/src/org/labkey/api/security/AuthenticationProvider.java

@@ -36,6 +36,7 @@
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
+import org.labkey.bootstrap.StartupEnvironment;
 
 import java.util.Arrays;
 import java.util.Collections;
@@ -245,14 +246,18 @@ default boolean isFicamApproved()
     interface SecondaryAuthenticationProvider<SAC extends SecondaryAuthenticationConfiguration<?>> extends ConfigurableAuthenticationProvider<SAC>
     {
         String REQUIRED_FOR = "requiredFor";
-
         /**
          * Bypass authentication from this provider. Might be configured via context.bypass2FA=true property in
          * application.properties to temporarily not require secondary authentication if this has been misconfigured, or
          * a 3rd party service provider is unavailable.
          */
         boolean bypass();
 
+        static boolean isBypassConfigured()
+        {
+            return Boolean.parseBoolean(ModuleLoader.getServletContext().getInitParameter(StartupEnvironment.BYPASS_2FA_PARAMETER));
+        }
+
         default SettingsField getRequiredForField(String name)
         {
             return OptionsField.of(REQUIRED_FOR, "Require " + name + " for:", "Specifying the role option allows for a progressive roll-out of " + name + " to site users.", true, "all")

api/src/org/labkey/api/security/Directive.java

@@ -21,7 +21,7 @@
 /**
  * All CSP directives that support substitutions. These constant names are persisted to the database, so be careful
  * with any changes. If adding a Directive, make sure to add the corresponding substitutions to the appropriate CSP
- * template(s) in LabKeyServer.
+ * template(s) in server/embedded/src/main/resources/labkey-defaults.properties.
  */
 public enum Directive implements StartupProperty, SafeToRenderEnum
 {

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

@@ -30,34 +30,22 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.util.logging.LogHelper;
+import org.labkey.bootstrap.PipelineBootstrapConfig;
+import org.labkey.bootstrap.StartupEnvironment;
 import org.springframework.web.context.ContextLoaderListener;
 
 import java.util.List;
 import java.util.concurrent.CopyOnWriteArrayList;
 
-/**
- * @see org.labkey.bootstrap.PipelineBootstrapConfig
- * @see org.labkey.bootstrap.LabKeyBootstrapClassLoader
- */
 public class ContextListener implements ServletContextListener
 {
     // this is among the earliest classes loaded (except for classes loaded via annotations @ClientEndpoint @ServerEndpoint etc)
 
-    // IMPORTANT see also LabKeyBootstrapClassLoader/PipelineBootstrapConfig which duplicates this code, keep them consistent
-    // On startup on some platforms, some modules will die if java.awt.headless is not set to false.
     static
     {
-        String headless = "java.awt.headless";
-        if (System.getProperty(headless) == null)
-            System.setProperty(headless, "true");
-        // On most installs, catalina.home and catalina.base point to the same directory. However, it's possible
-        // to have multiple instances share the Tomcat binaries but have their own ./logs, ./conf, etc. directories
-        // Thus, we want to use catalina.base for our place to find log files.
-        if (LogHelper.getLabKeyLogDir() == null)
-        {
-            // Set this only if the user hasn't overridden it
-            System.setProperty(LogHelper.LOG_HOME_PROPERTY_NAME, System.getProperty("catalina.base") + "/logs");
-        }
+        StartupEnvironment.ensureHeadless();
+        // Covers launchers other than LabKeyServer.main, which sets this first
+        PipelineBootstrapConfig.ensureLogHomeSet("logs");
 
         // Adds non-standard TLDs to allowable values for Apache Commons Validator. See Issue 25041. Since this
         // is set statically, it must be called very early, before any reference to UrlValidator occurs. Any

pipeline/src/org/labkey/pipeline/api/PipelineServiceImpl.java

@@ -82,6 +82,7 @@
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.api.view.ViewContext;
 import org.labkey.bootstrap.ClusterBootstrap;
+import org.labkey.bootstrap.StartupEnvironment;
 import org.labkey.pipeline.PipelineController;
 import org.labkey.pipeline.analysis.ProtocolManagementAuditProvider;
 import org.labkey.pipeline.importer.FolderImportJob;
@@ -456,9 +457,10 @@ public List<String> getClusterStartupArguments()
     {
         List<String> args = new ArrayList<>();
         args.add(System.getProperty("java.home") + "/bin/java" + (SystemUtils.IS_OS_WINDOWS ? ".exe" : ""));
-        File labkeyBootstrap = FileUtil.appendName(new File(System.getProperty("catalina.home")), "labkeyBootstrap.jar");
+        File labkeyHome = StartupEnvironment.getLabKeyHome();
+        File labkeyBootstrap = labkeyHome == null ? null : FileUtil.appendName(labkeyHome, "labkeyBootstrap.jar");
 
-        if (!labkeyBootstrap.exists())
+        if (labkeyBootstrap == null || !labkeyBootstrap.exists())
         {
             try
             {