Support all labkey.xml/ROOT.xml settings via application.properties

api/src/org/labkey/api/data/DbScope.java

@@ -286,9 +286,9 @@ public DbScope(String dsName, LabKeyDataSource dataSource) throws ServletExcepti
      *  <p>Wraps a {@link DataSource}, validating the data source, adding LabKey-specific properties, and
      *  setting an application name that LabKey sends on every connection. With the exception of
      *  {@code ScopeQueryLoggingProfilerListener.TestCase}, there's a one-to-one correspondence between LabKeyDataSource
-     *  and valid data sources defined in labkey.xml. That's not the case with {@link DbScopeLoader} and {@link DbScope}</p>
+     *  and valid data sources defined in application.properties. That's not the case with {@link DbScopeLoader} and {@link DbScope}</p>
      *
-     *  <p>This class handles the special LabKey-specific properties that administrators can add to labkey.xml and
+     *  <p>This class handles the special LabKey-specific properties that administrators can add to application.properties and
      *  associate with a data source. To add support for a new property, simply add a getter & setter to this class and
      *  then do something with the typed value in DbScope.</p>
      *
@@ -302,7 +302,7 @@ public static class LabKeyDataSource
         public static final String CPAS_DATA_SOURCE = "cpasDataSource";
         private static final String DEFAULT_APPLICATION_NAME = "LabKey Server";
 
-        private final String _dsName; // DataSource name from labkey.xml
+        private final String _dsName; // DataSource name from application.properties
         private final DataSource _ds;
         private final DataSourcePropertyReader _dsPropertyReader;
         private final @Nullable Properties _connectionProperties;
@@ -1532,7 +1532,7 @@ private static void verifyTomcatLibJars()
 
     private static String _applicationName = null;
 
-    // Enumerate each jdbc DataSource in labkey.xml and initialize them
+    // Enumerate each jdbc DataSource and initialize them
     public static void initializeDataSources()
     {
         verifyTomcatLibJars();
@@ -1564,8 +1564,8 @@ public static void initializeDataSources()
                 }
             }
 
-            // Ensure that the labkeyDataSource (or cpasDataSource, for old installations) exists in
-            // labkey.xml / cpas.xml and create the associated database if it doesn't already exist.
+            // Ensure that the labkeyDataSource (or cpasDataSource, for old installations) exists
+            // and create the associated database if it doesn't already exist.
             LabKeyDataSource primaryDS = LabKeyDataSource.setPrimaryDataSource(dataSources);
             labkeyDsName = primaryDS.getDsName();
             // Now that we've tagged the primary datasource we can prepare them all

api/src/org/labkey/api/data/PropertyEncryption.java

@@ -96,7 +96,7 @@ public enum PropertyEncryption
                 return "Test";
             }
         },
-    /** No encryption key was specified in labkey.xml, so throw ConfigurationException */
+    /** No encryption key was specified in application.properties, so throw ConfigurationException */
     NoKey
         {
             @Override

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

@@ -1838,7 +1838,7 @@ private void afterUpgrade(boolean performedUpgrade, File lockFile)
         verifyRequiredModules();
     }
 
-    // If the "requiredModules" parameter is present in labkey.xml then fail startup if any specified module is missing.
+    // If the "requiredModules" parameter is present in application.properties then fail startup if any specified module is missing.
     // Particularly interesting for compliant deployments, e.g., <Parameter name="requiredModules" value="Compliance"/>
     private void verifyRequiredModules()
     {
@@ -1987,7 +1987,7 @@ public Collection<Module> orderModules(Collection<Module> modules)
     }
 
     // Returns a set of data source names representing all external data sources that are required for module schemas.
-    // These are just the names that modules advertise; there's no guarantee that they're defined in labkey.xml or
+    // These are just the names that modules advertise; there's no guarantee that they're defined or
     // valid. Be sure to null check after attempting to resolve each to a DbScope.
     public Set<String> getAllModuleDataSourceNames()
     {

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

@@ -236,9 +236,9 @@ interface ResetPasswordProvider extends AuthenticationProvider
     interface SecondaryAuthenticationProvider<AC extends SecondaryAuthenticationConfiguration<?>> extends AuthenticationProvider, AuthenticationConfigurationFactory<AC>
     {
         /**
-         * Bypass authentication from this provider. Might be configured via labkey.xml parameter to
-         * temporarily not require secondary authentication if this has been misconfigured or a 3rd
-         * party service provider is unavailable.
+         * 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();
     }

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

@@ -66,7 +66,7 @@
 
 /**
  * Easy to use wrappers for common encryption algorithms. Also includes related helper methods for shared operations
- * such as generating salts & keys, and for retrieving & saving the labkey.xml encryption key and standard salt.
+ * such as generating salts & keys, and for retrieving & saving the application.properties encryption key and standard salt.
  * WARNING: Do not change the core algorithms or parameters of existing implementations; changes will likely
  * render existing data irrecoverable.
 */
@@ -416,9 +416,9 @@ public DecryptionException(String message, Throwable cause)
     }
 
     /**
-     * Return standard AES encryption algorithm. Generates a 128-bit key from the labkey.xml encryption key. All other
-     * encryption parameters are documented in AES(). Pass in a registered EncryptionMigrationHandler to prove that you
-     * can migrate your encrypted content.
+     * Return standard AES encryption algorithm. Generates a 128-bit key from the application.properties encryption key.
+     * All other encryption parameters are documented in AES(). Pass in a registered EncryptionMigrationHandler to prove
+     * that you can migrate your encrypted content.
      */
     public static Algorithm getAES128(EncryptionMigrationHandler handler)
     {

api/src/org/labkey/api/settings/AppProps.java

@@ -194,7 +194,7 @@ static WriteableAppProps getWriteableInstance()
 
     String getBLASTServerBaseURL();
 
-    /** @return the name of the Tomcat XML deployment descriptor based on the context path for this install - typically ROOT.xml or labkey.xml */
+    /** @return the name of the Tomcat XML deployment descriptor based on the context path for this install - now always application.properties */
     String getWebappConfigurationFilename();
 
     /**

api/src/org/labkey/api/settings/AppPropsImpl.java

@@ -469,14 +469,12 @@ public UsageReportingLevel getUsageReportingLevel()
         }
     }
 
-    // Get the name of the webapp configuration file, e.g., labkey.xml, cpas.xml, or ROOT.xml.  Used in some error messages
+    // Get the name of the webapp configuration file, now always application.properties.  Used in some error messages
     //  to provide suggestions to the admin.
     @Override
     public String getWebappConfigurationFilename()
     {
-        String path = getContextPath();
-
-        return "".equals(path) ? "ROOT.xml" : path.substring(1) + ".xml";
+        return "application.properties";
     }
 
     @Override

core/src/org/labkey/core/CoreModule.java

@@ -1356,7 +1356,7 @@ public Set<DbSchema> getSchemasToTest()
     {
         Set<DbSchema> result = new LinkedHashSet<>(super.getSchemasToTest());
 
-        // Add the "labkey" schema in all module data sources as well... should match labkey.xml
+        // Add the "labkey" schema in all module data sources as well... should match application.properties
         for (String dataSourceName : ModuleLoader.getInstance().getAllModuleDataSourceNames())
         {
             DbScope scope = DbScope.getDbScope(dataSourceName);

core/src/org/labkey/core/view/template/bootstrap/CoreWarningProvider.java

@@ -234,7 +234,7 @@ private void getConnectionPoolSizeWarnings(Warnings warnings, DbScope labkeyScop
 
             if (null == maxTotal)
             {
-                warnings.add(HtmlString.of("Could not determine the connection pool size for the labkeyDataSource; verify that the connection pool is properly configured in labkey.xml"));
+                warnings.add(HtmlString.of("Could not determine the connection pool size for the labkeyDataSource; verify that the connection pool is properly configured in application.properties"));
             }
             else if (showAllWarnings || maxTotal < 20)
             {

pipeline/src/org/labkey/pipeline/cluster/ClusterStartup.java

@@ -16,6 +16,7 @@
 
 package org.labkey.pipeline.cluster;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.SystemUtils;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -41,14 +42,21 @@
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
 import java.net.InetAddress;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.TimeUnit;
+import java.util.jar.JarEntry;
+import java.util.jar.JarFile;
 
 /**
  * Entry point for pipeline jobs that are invoked on a cluster node. After completion of the job, the process
@@ -193,26 +201,26 @@ public void testSuccess() throws IOException, InterruptedException
             DummyPipelineJob job = new DummyPipelineJob(JunitUtil.getTestContainer(), TestContext.get().getUser(), DummyPipelineJob.Worker.success);
             String output = executeJobRemote(createArgs(job), 0);
             String jobLog = PageFlowUtil.getFileContentsAsString(job.getLogFile());
-            Assert.assertTrue("Couldn't find logging", jobLog.contains("Successful worker!"));
-            Assert.assertTrue("Couldn't find logging", output.contains("Exploding module archives"));
+            Assert.assertTrue("Couldn't find logging. \nProcess output: " + output + "\nJob log: " + jobLog, jobLog.contains("Successful worker!"));
+            Assert.assertTrue("Couldn't find logging. \nProcess output: " + output + "\nJob log: " + jobLog, output.contains("Exploding module archives"));
         }
 
         @Test
         public void testFailure() throws IOException, InterruptedException
         {
             DummyPipelineJob job = new DummyPipelineJob(JunitUtil.getTestContainer(), TestContext.get().getUser(), DummyPipelineJob.Worker.failure);
-            executeJobRemote(createArgs(job), 1);
+            String output = executeJobRemote(createArgs(job), 1);
             String jobLog = PageFlowUtil.getFileContentsAsString(job.getLogFile());
-            Assert.assertTrue("Couldn't find logging", jobLog.contains("Oopsies"));
-            Assert.assertTrue("Couldn't find logging", jobLog.contains("java.lang.UnsupportedOperationException"));
+            Assert.assertTrue("Couldn't find logging.\nProcess output: " + output + "\nJob log: " + jobLog, jobLog.contains("Oopsies"));
+            Assert.assertTrue("Couldn't find logging.\nProcess output: " + output + "\nJob log: " + jobLog, jobLog.contains("java.lang.UnsupportedOperationException"));
         }
 
         @Test
         public void testExtractOnly() throws IOException, InterruptedException
         {
             List<String> args = createArgs(null);
             String output = executeJobRemote(args, 0);
-            Assert.assertTrue("Couldn't find logging", output.contains("Exploding module archives"));
+            Assert.assertTrue("Couldn't find logging. \nProcess output: " + output, output.contains("Exploding module archives"));
         }
 
         @Test
@@ -223,7 +231,7 @@ public void testBadPath() throws IOException, InterruptedException
             // Last argument is supposed to be the URI to the serialized job's file, hack it to something else
             args.set(args.size() - 1, "NotAValidURI.json");
             String output = executeJobRemote(args, 1);
-            Assert.assertTrue("Couldn't find logging", output.contains("Could not find serialized job file"));
+            Assert.assertTrue("Couldn't find logging. \nProcess output: " + output, output.contains("Could not find serialized job file"));
         }
 
         protected String executeJobRemote(List<String> args, int expectedExitCode) throws IOException, InterruptedException
@@ -254,9 +262,9 @@ protected String executeJobRemote(List<String> args, int expectedExitCode) throw
             if (!proc.waitFor(1, TimeUnit.MINUTES))
             {
                 proc.destroy();
-                Assert.fail("Process did not complete. Output:\n" + sb.toString());
+                Assert.fail("Process did not complete. Output:\n" + sb);
             }
-            Assert.assertEquals("Wrong exit code, output: " + sb.toString(), expectedExitCode, proc.exitValue());
+            Assert.assertEquals("Wrong exit code, output: " + sb, expectedExitCode, proc.exitValue());
             return sb.toString();
         }
 
@@ -267,6 +275,15 @@ private List<String> createArgs(@Nullable PipelineJob job) throws IOException
             args.add(System.getProperty("java.home") + "/bin/java" + (SystemUtils.IS_OS_WINDOWS ? ".exe" : ""));
             File labkeyBootstrap = new File(new File(new File(System.getProperty("catalina.home")), "lib"), "labkeyBootstrap.jar");
 
+            if (!labkeyBootstrap.exists())
+            {
+                labkeyBootstrap = extractBootstrapFromEmbedded();
+                if (labkeyBootstrap == null || !labkeyBootstrap.exists())
+                {
+                    throw new IllegalStateException("Couldn't find labkeyBootstrap.jar");
+                }
+            }
+
             // Uncomment this line if you want to debug the forked process
 //            args.add("-agentlib:jdwp=transport=dt_socket,server=n,suspend=y,address=*:5005");
             args.add("-cp");
@@ -286,5 +303,35 @@ private List<String> createArgs(@Nullable PipelineJob job) throws IOException
 
             return args;
         }
+
+        private File extractBootstrapFromEmbedded() throws IOException
+        {
+            // Look through the JAR files in the working directory, which is expected to contain the Spring Boot entrypoint
+            File pwd = new File(".");
+            File[] jars = pwd.listFiles(f -> f.getName().toLowerCase().endsWith(".jar"));
+            for (File jar : jars)
+            {
+                try (JarFile j = new JarFile(jar))
+                {
+                    // Look inside the JAR for a labkeyBootstrap*.jar file
+                    Iterator<JarEntry> entries = j.entries().asIterator();
+                    while (entries.hasNext())
+                    {
+                        JarEntry entry = entries.next();
+                        if (entry.getName().contains("labkeyBootstrap") && entry.getName().toLowerCase().endsWith(".jar"))
+                        {
+                            File result = new File("labkeyBootstrap.jar");
+                            try (InputStream in = j.getInputStream(entry);
+                                 OutputStream out = new FileOutputStream(result))
+                            {
+                                IOUtils.copy(in, out);
+                            }
+                            return FileUtil.getAbsoluteCaseSensitiveFile(result);
+                        }
+                    }
+                }
+            }
+            return null;
+        }
     }
 }