[bot] Merge 26.3 to develop (Conflicts)

api/src/org/labkey/api/audit/query/DefaultAuditTypeTable.java

@@ -34,9 +34,14 @@
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.query.column.BuiltInColumnTypes;
+import org.labkey.api.security.SecurityManager;
+import org.labkey.api.security.User;
 import org.labkey.api.security.UserPrincipal;
 import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.security.permissions.ReadPermission;
+import org.labkey.api.security.roles.CanSeeAuditLogRole;
+import org.labkey.api.security.roles.Role;
+import org.labkey.api.security.roles.RoleManager;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -114,7 +119,14 @@ protected void initColumns()
     @Override
     protected SimpleFilter.FilterClause getContainerFilterClause(ContainerFilter filter, FieldKey fieldKey)
     {
-        return filter.createFilterClause(getSchema(), fieldKey, CanSeeAuditLogPermission.class, Set.of());
+        // TODO: Setting a contextual role on the container filter clause should not be necessary; the user passed
+        // (separately) to the ContainerFilter should have the appropriate permission. However, some app actions
+        // (GetTransactionRowIdsAction, maybe GetLocationHistoryAction, etc.) have been relying on this behavior. Clean
+        // this up soon, but not for 26.3. Note that this is the only code path that passes contextual roles into
+        // createFilterClause(), so we could eliminate that option during clean up.
+        User user = (null == getUserSchema()) ? null : getUserSchema().getUser();
+        Set<Role> roles = SecurityManager.canSeeAuditLog(user) ? RoleManager.roleSet(CanSeeAuditLogRole.class) : null;
+        return filter.createFilterClause(getSchema(), fieldKey, CanSeeAuditLogPermission.class, roles);
     }
 
     // Subclasses may override this to provide customizations to the column

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

@@ -169,9 +169,9 @@ public SimpleFilter.FilterClause createFilterClause(DbSchema schema, FieldKey co
     }
 
     /** Create a FilterClause that restricts based on the containers that meet the filter and user that meets the permission*/
-    public SimpleFilter.FilterClause createFilterClause(DbSchema schema, FieldKey containerFilterColumn, Class<? extends Permission> permission, Set<Role> roles)
+    public SimpleFilter.FilterClause createFilterClause(DbSchema schema, FieldKey containerFilterColumn, Class<? extends Permission> permission, Set<Role> contextualRoles)
     {
-        return new ContainerClause(schema, containerFilterColumn, this, permission, roles);
+        return new ContainerClause(schema, containerFilterColumn, this, permission, contextualRoles);
     }
 
 

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

@@ -52,7 +52,7 @@ public RecordFactory(Class<K> clazz)
     {
         Object[] params = Arrays.stream(_parameters).map(p -> {
             Object value = m.get(p.getName());
-            return ConvertUtils.convert(value, p.getType());
+            return value != null ? ConvertUtils.convert(value, p.getType()) : null;
         }).toArray();
 
         try

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

@@ -221,6 +221,7 @@ public void execute()
                 {
                     LOG.info("Executing {}", upgradeMethod.getDisplayName());
                     _moduleContext.invokeUpgradeMethod(upgradeMethod);
+                    LOG.info("Finished executing {}", upgradeMethod.getDisplayName());
                 }
             }
             catch (NoSuchMethodException e)

api/src/org/labkey/api/data/dialect/PostgreSqlService.java

@@ -0,0 +1,18 @@
+package org.labkey.api.data.dialect;
+
+import org.labkey.api.services.ServiceRegistry;
+
+public interface PostgreSqlService
+{
+    static PostgreSqlService get()
+    {
+        return ServiceRegistry.get().getService(PostgreSqlService.class);
+    }
+
+    static void setInstance(PostgreSqlService impl)
+    {
+        ServiceRegistry.get().registerService(PostgreSqlService.class, impl);
+    }
+
+    BasePostgreSqlDialect getDialect();
+}

api/src/org/labkey/api/query/QueryView.java

@@ -1050,52 +1050,6 @@ public ActionButton createDeleteButton(boolean showConfirmation)
         return null;
     }
 
-    public ActionButton createDeleteAllRowsButton(String tableNoun)
-    {
-        ActionButton deleteAllRows = new ActionButton("Delete All Rows");
-        deleteAllRows.setDisplayPermission(AdminPermission.class);
-        deleteAllRows.setActionType(ActionButton.Action.SCRIPT);
-        deleteAllRows.setScript(
-                "LABKEY.requiresExt4Sandbox(function() {" +
-                    "Ext4.Msg.confirm('Confirm Deletion', 'Are you sure you wish to delete all rows in this " + tableNoun + "? This action cannot be undone and will result in an empty " + tableNoun + ".', function(button){" +
-                        "if (button == 'yes'){" +
-                            "var waitMask = Ext4.Msg.wait('Deleting Rows...', 'Delete Rows'); " +
-                            "Ext4.Ajax.request({ " +
-                                "url : LABKEY.ActionURL.buildURL('query', 'truncateTable'), " +
-                                "method : 'POST', " +
-                                "success: function(response) " +
-                                "{" +
-                                    "waitMask.close(); " +
-                                    "var data = Ext4.JSON.decode(response.responseText); " +
-                                    "Ext4.Msg.show({ " +
-                                        "title : 'Success', " +
-                                        "buttons : Ext4.MessageBox.OK, " +
-                                        "msg : data.deletedRows + ' rows deleted', " +
-                                        "fn: function(btn) " +
-                                        "{ " +
-                                            "if(btn == 'ok') " +
-                                            "{ " +
-                                                "window.location.reload(); " +
-                                            "} " +
-                                        "} " +
-                                    "})" +
-                                "}, " +
-                                "failure : function(response, opts) " +
-                                "{ " +
-                                    "waitMask.close(); " +
-                                    "Ext4.getBody().unmask(); " +
-                                    "LABKEY.Utils.displayAjaxErrorResponse(response, opts); " +
-                                "}, " +
-                                "jsonData : {schemaName : " + PageFlowUtil.jsString(getQueryDef().getSchema().getName()) + ", queryName : " + PageFlowUtil.jsString(getQueryDef().getName()) + "}, " +
-                                "scope : this " +
-                            "});" +
-                        "}" +
-                    "});" +
-                "});"
-        );
-        return deleteAllRows;
-    }
-
     public ActionButton createInsertMenuButton()
     {
         return createInsertMenuButton(null, null);

audit/src/org/labkey/audit/AuditController.java

@@ -383,11 +383,12 @@ public void validateForm(AuditTransactionForm form, Errors errors)
         public Object execute(AuditTransactionForm form, BindException errors)
         {
             List<Long> rowIds;
-            ContainerFilter cf = ContainerFilter.getContainerFilterByName(form.getContainerFilter(), getContainer(), getUser());
+            User elevatedUser = ElevatedUser.ensureCanSeeAuditLogRole(getContainer(), getUser());
+            ContainerFilter cf = ContainerFilter.getContainerFilterByName(form.getContainerFilter(), getContainer(), elevatedUser);
             if (form.isSampleType())
-                rowIds = AuditLogImpl.get().getTransactionSampleIds(form.getTransactionAuditId(), ElevatedUser.ensureCanSeeAuditLogRole(getContainer(), getUser()), getContainer(), cf);
+                rowIds = AuditLogImpl.get().getTransactionSampleIds(form.getTransactionAuditId(), elevatedUser, getContainer(), cf);
             else
-                rowIds = AuditLogImpl.get().getTransactionSourceIds(form.getTransactionAuditId(), ElevatedUser.ensureCanSeeAuditLogRole(getContainer(), getUser()), getContainer(), cf);
+                rowIds = AuditLogImpl.get().getTransactionSourceIds(form.getTransactionAuditId(), elevatedUser, getContainer(), cf);
 
             ApiSimpleResponse response = new ApiSimpleResponse();
             response.put("success", true);

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

@@ -77,6 +77,7 @@
 import org.labkey.api.data.TestSchema;
 import org.labkey.api.data.WorkbookContainerType;
 import org.labkey.api.data.dialect.BasePostgreSqlDialect;
+import org.labkey.api.data.dialect.PostgreSqlService;
 import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.data.dialect.SqlDialectManager;
 import org.labkey.api.data.dialect.SqlDialectRegistry;
@@ -88,6 +89,7 @@
 import org.labkey.api.files.FileBrowserConfigWriter;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.markdown.MarkdownService;
+import org.labkey.api.mcp.McpService;
 import org.labkey.api.message.settings.MessageConfigService;
 import org.labkey.api.migration.DatabaseMigrationService;
 import org.labkey.api.module.FolderType;
@@ -98,7 +100,6 @@
 import org.labkey.api.module.SchemaUpdateType;
 import org.labkey.api.module.SpringModule;
 import org.labkey.api.module.Summary;
-import org.labkey.api.mcp.McpService;
 import org.labkey.api.notification.EmailMessage;
 import org.labkey.api.notification.EmailService;
 import org.labkey.api.notification.NotificationMenuView;
@@ -253,9 +254,9 @@
 import org.labkey.core.login.DbLoginAuthenticationProvider;
 import org.labkey.core.login.DbLoginManager;
 import org.labkey.core.login.LoginController;
+import org.labkey.core.mcp.McpServiceImpl;
 import org.labkey.core.metrics.SimpleMetricsServiceImpl;
 import org.labkey.core.metrics.WebSocketConnectionManager;
-import org.labkey.core.mcp.McpServiceImpl;
 import org.labkey.core.notification.EmailPreferenceConfigServiceImpl;
 import org.labkey.core.notification.EmailPreferenceContainerListener;
 import org.labkey.core.notification.EmailPreferenceUserListener;
@@ -560,11 +561,11 @@ public QuerySchema createSchema(DefaultSchema schema, Module module)
         ScriptEngineManagerImpl.registerEncryptionMigrationHandler();
 
         McpService.get().register(new CoreMcp());
+        PostgreSqlService.setInstance(PostgreSqlDialectFactory::getLatestSupportedDialect);
 
         deleteTempFiles();
     }
 
-
     private void deleteTempFiles()
     {
         try

core/src/org/labkey/core/admin/sql/SqlScriptController.java

@@ -1605,6 +1605,7 @@ public boolean handlePost(UpgradeCodeForm form, BindException errors) throws Exc
         {
             LOG.info("Executing {}.{}(ModuleContext moduleContext)", _method.getDeclaringClass().getSimpleName(), _method.getName());
             _method.invoke(_code, _ctx);
+            LOG.info("Finished executing {}.{}(ModuleContext moduleContext)", _method.getDeclaringClass().getSimpleName(), _method.getName());
             return true;
         }
 

core/src/org/labkey/core/dialect/PostgreSqlDialectFactory.java

@@ -24,6 +24,7 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.data.dialect.AbstractDialectRetrievalTestCase;
+import org.labkey.api.data.dialect.BasePostgreSqlDialect;
 import org.labkey.api.data.dialect.DatabaseNotSupportedException;
 import org.labkey.api.data.dialect.JdbcHelperTest;
 import org.labkey.api.data.dialect.PostgreSqlServerType;
@@ -145,6 +146,11 @@ public static PostgreSql_13_Dialect getOldestSupportedDialect()
         return new PostgreSql_13_Dialect();
     }
 
+    public static BasePostgreSqlDialect getLatestSupportedDialect()
+    {
+        return new PostgreSql_18_Dialect();
+    }
+
     public static class DialectRetrievalTestCase extends AbstractDialectRetrievalTestCase
     {
         @Override

experiment/resources/schemas/dbscripts/sqlserver/exp-26.004-26.005.sql

@@ -0,0 +1,2 @@
+-- SQL Server only
+EXEC core.executeJavaUpgradeCode 'shortenAllStorageNames';

experiment/src/client/test/integration/AssayImportRunAction.ispec.ts

@@ -118,7 +118,7 @@ async function verifyPropertiesFilesOnServer(
             // Note: this is a hack to allow us to make requests to the webdav controller. The IntegrationTestServer
             // request method uses ActionURL to generate URLS, but webdav URLs are not ActionURLs, so we need to
             // override the AgentProvider to generate the proper webdav URL.
-            url = `/_webdav/${requestOptions.containerPath}/%40files/assaydata?method=JSON`;
+            url = `${LABKEY.contextPath}/_webdav/${requestOptions.containerPath}/%40files/assaydata?method=JSON`;
             return agent.get(url);
         },
         requestOptions

experiment/src/org/labkey/experiment/DataClassMigrationSchemaHandler.java

@@ -178,11 +178,12 @@ public void afterSchema(DatabaseMigrationConfiguration configuration, DbSchema s
 
         DbScope sourceScope = configuration.getSourceScope();
         DbScope targetScope = configuration.getTargetScope();
-        DbSchema biologicsSourceSchema = sourceScope.getSchema("biologics", DbSchemaType.Migration);
-        DbSchema biologicsTargetSchema = targetScope.getSchema("biologics", DbSchemaType.Module);
 
-        if (biologicsSourceSchema.existsInDatabase() && biologicsTargetSchema.existsInDatabase())
+        if (sourceScope.getSchemaNames().contains("biologics") && targetScope.getSchemaNames().contains("biologics"))
         {
+            DbSchema biologicsSourceSchema = sourceScope.getSchema("biologics", DbSchemaType.Migration);
+            DbSchema biologicsTargetSchema = targetScope.getSchema("biologics", DbSchemaType.Module);
+
             TableInfo sourceTable = biologicsSourceSchema.getTable("SequenceIdentity");
             TableInfo targetTable = biologicsTargetSchema.getTable("SequenceIdentity");
 

experiment/src/org/labkey/experiment/ExperimentModule.java

@@ -205,7 +205,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.004;
+        return 26.005;
     }
 
     @Nullable