Added a mechanism to detect a corrupt/broken config database file. Fixes #6460

docs/en_US/release_notes_5_4.rst

@@ -21,6 +21,7 @@ Housekeeping
 ************
 
 | `Issue #6225 <https://redmine.postgresql.org/issues/6225>`_ -  Updated Flask-Security-Too to the latest v4.
+| `Issue #6460 <https://redmine.postgresql.org/issues/6460>`_ -  Added a mechanism to detect a corrupt/broken config database file.
 
 Bug fixes
 *********

web/pgadmin/__init__.py

@@ -14,6 +14,8 @@ import os
 import sys
 import re
 import ipaddress
+import traceback
+
 from types import MethodType
 from collections import defaultdict
 from importlib import import_module
@@ -38,8 +40,8 @@ from pgadmin.utils import PgAdminModule, driver, KeyManager
 from pgadmin.utils.preferences import Preferences
 from pgadmin.utils.session import create_session_interface, pga_unauthorised
 from pgadmin.utils.versioned_template_loader import VersionedTemplateLoader
-from datetime import timedelta
+from datetime import timedelta, datetime
-from pgadmin.setup import get_version, set_version
+from pgadmin.setup import get_version, set_version, check_db_tables
 from pgadmin.utils.ajax import internal_server_error, make_json_response
 from pgadmin.utils.csrf import pgCSRFProtect
 from pgadmin import authenticate
@@ -349,6 +351,44 @@ def create_app(app_name=None):
     ##########################################################################
     # Upgrade the schema (if required)
     ##########################################################################
+    def backup_db_file():
+        """
+        Create a backup of the current database file
+        and create new database file with default settings.
+        """
+        backup_file_name = "{0}.{1}".format(
+            SQLITE_PATH, datetime.now().strftime('%Y%m%d%H%M%S'))
+        os.rename(SQLITE_PATH, backup_file_name)
+        app.logger.error('Exception in database migration.')
+        app.logger.info('Creating new database file.')
+        try:
+            db_upgrade(app)
+            os.environ[
+                'CORRUPTED_DB_BACKUP_FILE'] = backup_file_name
+            app.logger.info('Database migration completed.')
+        except Exception as e:
+            app.logger.error('Database migration failed')
+            app.logger.error(traceback.format_exc())
+            raise RuntimeError('Migration failed')
+
+    def upgrade_db():
+        """
+        Execute the migrations.
+        """
+        try:
+            db_upgrade(app)
+            os.environ['CORRUPTED_DB_BACKUP_FILE'] = ''
+        except Exception as e:
+            backup_db_file()
+
+        # check all tables are present in the db.
+        is_db_error, invalid_tb_names = check_db_tables()
+        if is_db_error:
+            app.logger.error(
+                'Table(s) {0} are missing in the'
+                ' database'.format(invalid_tb_names))
+            backup_db_file()
+
     with app.app_context():
         # Run migration for the first time i.e. create database
         from config import SQLITE_PATH
@@ -356,25 +396,34 @@ def create_app(app_name=None):
 
         # If version not available, user must have aborted. Tables are not
         # created and so its an empty db
-        if not os.path.exists(SQLITE_PATH) or get_version() == -1:
+        version = get_version()
+        if not os.path.exists(SQLITE_PATH) or version == -1:
             # If running in cli mode then don't try to upgrade, just raise
             # the exception
             if not cli_mode:
-                db_upgrade(app)
+                upgrade_db()
             else:
                 if not os.path.exists(SQLITE_PATH):
                     raise FileNotFoundError(
                         'SQLite database file "' + SQLITE_PATH +
                         '" does not exists.')
-                raise RuntimeError('Specified SQLite database file '
+                raise RuntimeError(
-                                   'is not valid.')
+                    'The configuration database file is not valid.')
         else:
             schema_version = get_version()
 
             # Run migration if current schema version is greater than the
             # schema version stored in version table
             if CURRENT_SCHEMA_VERSION >= schema_version:
-                db_upgrade(app)
+                upgrade_db()
+            else:
+                # check all tables are present in the db.
+                is_db_error, invalid_tb_names = check_db_tables()
+                if is_db_error:
+                    app.logger.error(
+                        'Table(s) {0} are missing in the'
+                        ' database'.format(invalid_tb_names))
+                    backup_db_file()
 
             # Update schema version to the latest
             if CURRENT_SCHEMA_VERSION > schema_version:

web/pgadmin/browser/__init__.py

@@ -342,6 +342,7 @@ class BrowserModule(PgAdminModule):
             list: a list of url endpoints exposed to the client.
         """
         return [BROWSER_INDEX, 'browser.nodes',
+                'browser.check_corrupted_db_file',
                 'browser.check_master_password',
                 'browser.set_master_password',
                 'browser.reset_master_password',
@@ -951,6 +952,19 @@ def form_master_password_response(existing=True, present=False, errmsg=None):
     })
 
 
+@blueprint.route("/check_corrupted_db_file",
+                 endpoint="check_corrupted_db_file", methods=["GET"])
+def check_corrupted_db_file():
+    """
+    Get the corrupted database file path.
+    """
+    file_location = os.environ['CORRUPTED_DB_BACKUP_FILE'] \
+        if 'CORRUPTED_DB_BACKUP_FILE' in os.environ else ''
+    # reset the corrupted db file path in env.
+    os.environ['CORRUPTED_DB_BACKUP_FILE'] = ''
+    return make_json_response(data=file_location)
+
+
 @blueprint.route("/master_password", endpoint="check_master_password",
                  methods=["GET"])
 def check_master_password():

web/pgadmin/browser/static/js/browser.js

@@ -594,7 +594,7 @@ define('pgadmin.browser', [
       }, 300000);
 
       obj.set_master_password('');
-
+      obj.check_corrupted_db_file();
       obj.Events.on('pgadmin:browser:tree:add', obj.onAddTreeNode, obj);
       obj.Events.on('pgadmin:browser:tree:update', obj.onUpdateTreeNode, obj);
       obj.Events.on('pgadmin:browser:tree:refresh', obj.onRefreshTreeNode, obj);
@@ -607,7 +607,35 @@ define('pgadmin.browser', [
       obj.register_to_activity_listener(document);
       obj.start_inactivity_timeout_daemon();
     },
+    check_corrupted_db_file: function() {
+      $.ajax({
+        url: url_for('browser.check_corrupted_db_file'),
+        type: 'GET',
+        dataType: 'json',
+        contentType: 'application/json',
+      }).done((res)=> {
+        if(res.data.length > 0) {
 
+          Alertify.alert(
+            'Warning',
+            'pgAdmin detected unrecoverable corruption in it\'s SQLite configuration database. ' +
+            'The database has been backed up and recreated with default settings. '+
+            'It may be possible to recover data such as query history manually from '+
+            'the original/corrupt file using a tool such as DB Browser for SQLite if desired.'+
+            '<br><br>Original file: ' + res.data + '<br>Replacement file: ' +
+            res.data.substring(0, res.data.length - 14)
+          )
+            .set({'closable': true,
+              'onok': function() {
+              },
+            });
+
+
+        }
+      }).fail(function(xhr, status, error) {
+        Alertify.alert(error);
+      });
+    },
     init_master_password: function() {
       let self = this;
       // Master password dialog

web/pgadmin/setup/__init__.py

@@ -11,3 +11,4 @@ from .user_info import user_info
 from .db_version import get_version, set_version
 from .db_upgrade import db_upgrade
 from .data_directory import create_app_data_directory
+from .db_table_check import check_db_tables

web/pgadmin/setup/db_table_check.py

@@ -0,0 +1,32 @@
+##########################################################################
+#
+# pgAdmin 4 - PostgreSQL Tools
+#
+# Copyright (C) 2013 - 2021, The pgAdmin Development Team
+# This software is released under the PostgreSQL Licence
+#
+##########################################################################
+
+from pgadmin.model import Version
+from pgadmin.model import db
+
+
+def get_db_table_names():
+    db_table_names = db.metadata.tables.keys() if db.metadata.tables else 0
+    return db_table_names
+
+
+def check_db_tables():
+    is_error = False
+    invalid_tb_names = list()
+    db_table_names = get_db_table_names()
+    # check table is actually present in the db.
+    for table_name in db_table_names:
+        if not db.engine.dialect.has_table(db.engine, table_name):
+            invalid_tb_names.append(table_name)
+            is_error = True
+
+    if is_error:
+        return True, invalid_tb_names
+    else:
+        return False, invalid_tb_names

web/pgadmin/setup/db_version.py

@@ -16,7 +16,10 @@ def get_version():
     except Exception:
         return -1
 
+    if version:
         return version.value
+    else:
+        return -1
 
 
 def set_version(new_version):