Merge pull request #7560 from jmchilton/refactor_security_helper

Refactor galaxy.web.security into galaxy.security.idencoding.

lib/galaxy/config.py

@@ -1126,8 +1126,8 @@ class ConfiguresGalaxyMixin(object):
         self.object_store = build_object_store_from_config(self.config, **kwds)
 
     def _configure_security(self):
-        from galaxy.web import security
-        self.security = security.SecurityHelper(id_secret=self.config.id_secret)
+        from galaxy.security import idencoding
+        self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
 
     def _configure_tool_shed_registry(self):
         import tool_shed.tool_shed_registry

lib/galaxy/security/idencoding.py

@@ -18,7 +18,7 @@ MAXIMUM_ID_SECRET_LENGTH = int(MAXIMUM_ID_SECRET_BITS / 8)
 KIND_TOO_LONG_MESSAGE = "Galaxy coding error, keep encryption 'kinds' smaller to utilize more bites of randomness from id_secret values."
 
 
-class SecurityHelper(object):
+class IdEncodingHelper(object):
 
     def __init__(self, **config):
         id_secret = config['id_secret']

lib/galaxy/webapps/reports/app.py

@@ -3,7 +3,7 @@ import sys
 import time
 
 import galaxy.model
-from galaxy.web import security
+from galaxy.security import idencoding
 from galaxy.web.stack import application_stack_instance
 from . import config
 
@@ -36,7 +36,7 @@ class UniverseApplication(object):
         else:
             self.targets_mysql = 'mysql' in self.config.database_connection
         # Security helper
-        self.security = security.SecurityHelper(id_secret=self.config.id_secret)
+        self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
         # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
         self.server_starttime = int(time.time())
 

lib/galaxy/webapps/tool_shed/app.py

@@ -11,8 +11,8 @@ import tool_shed.repository_types.registry
 from galaxy import tools
 from galaxy.config import configure_logging
 from galaxy.model.tags import CommunityTagHandler
+from galaxy.security import idencoding
 from galaxy.util.dbkeys import GenomeBuilds
-from galaxy.web import security
 from galaxy.web.stack import application_stack_instance
 from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
 from . import config
@@ -51,8 +51,7 @@ class UniverseApplication(object):
         self.model = mapping.init(self.config.file_path,
                                   db_url,
                                   self.config.database_engine_options)
-        # Initialize the Tool Shed security helper.
-        self.security = security.SecurityHelper(id_secret=self.config.id_secret)
+        self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
         # initialize the Tool Shed tag handler.
         self.tag_handler = CommunityTagHandler(self)
         # Initialize the Tool Shed tool data tables.  Never pass a configuration file here

scripts/communication/communication_server.py

@@ -50,9 +50,9 @@ from flask_socketio import (
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
 
 import galaxy.config
+from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.util.script import app_properties_from_args, populate_config_args
-from galaxy.web.security import SecurityHelper
 
 logging.basicConfig()
 log = logging.getLogger(__name__)
@@ -77,7 +77,7 @@ if "id_secret" not in app_properties:
 
 id_secret = app_properties.get('id_secret', 'dangerous_default')
 
-security_helper = SecurityHelper(id_secret=id_secret)
+security_helper = IdEncodingHelper(id_secret=id_secret)
 # And get access to the models
 # Login manager to manage current_user functionality
 login_manager = flask_login.LoginManager()

scripts/helper.py

@@ -13,8 +13,8 @@ import sys
 sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))
 
 import galaxy.config
+from galaxy.security import idencoding
 from galaxy.util.script import app_properties_from_args, populate_config_args
-from galaxy.web import security
 
 parser = argparse.ArgumentParser()
 populate_config_args(parser)
@@ -26,7 +26,7 @@ args = parser.parse_args()
 
 app_properties = app_properties_from_args(args)
 config = galaxy.config.Configuration(**app_properties)
-helper = security.SecurityHelper(id_secret=app_properties.get('id_secret'))
+helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
 model = galaxy.config.init_models_from_config(config)
 
 if args.encode_id:

scripts/pages_identifier_conversion.py

@@ -10,10 +10,10 @@ import galaxy
 import galaxy.app
 import galaxy.config
 from galaxy.objectstore import build_object_store_from_config
+from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import unicodify
 from galaxy.util.bunch import Bunch
 from galaxy.util.script import app_properties_from_args, populate_config_args
-from galaxy.web.security import SecurityHelper
 from galaxy.webapps.galaxy.controllers.page import _PageContentProcessor, _placeholderRenderForSave
 
 
@@ -26,7 +26,7 @@ def main(argv):
     properties = app_properties_from_args(args)
     config = galaxy.config.Configuration(**properties)
     secret = args.secret_key or config.id_secret
-    security_helper = SecurityHelper(id_secret=secret)
+    security_helper = IdEncodingHelper(id_secret=secret)
     object_store = build_object_store_from_config(config)
     if not config.database_connection:
         print("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")

scripts/secret_decoder_ring.py

@@ -9,9 +9,9 @@ import sys
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
 
+from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import unicodify
 from galaxy.util.script import app_properties_from_args, populate_config_args
-from galaxy.web.security import SecurityHelper
 
 logging.basicConfig()
 log = logging.getLogger(__name__)
@@ -35,7 +35,7 @@ if "id_secret" not in app_properties:
 
 id_secret = app_properties.get('id_secret', 'dangerous_default')
 
-security_helper = SecurityHelper(id_secret=id_secret)
+security_helper = IdEncodingHelper(id_secret=id_secret)
 # And get access to the models
 # Login manager to manage current_user functionality
 

scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py

@@ -13,7 +13,7 @@ sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir,
 sys.path.insert(1, os.path.join(os.path.dirname(__file__)))
 
 import galaxy.webapps.tool_shed.config as tool_shed_config
-from galaxy.web import security
+from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.webapps.tool_shed.model import mapping
 from bootstrap_util import admin_user_info  # noqa: I100,I201
 
@@ -40,7 +40,7 @@ class BootstrapApplication(object):
                                   self.config.database_connection,
                                   engine_options={},
                                   create_tables=False)
-        self.security = security.SecurityHelper(id_secret=self.config.id_secret)
+        self.security = IdEncodingHelper(id_secret=self.config.id_secret)
         self.hgweb_config_manager = self.model.hgweb_config_manager
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
         print('Using hgweb.config file: ', self.hgweb_config_manager.hgweb_config)

test/base/testcase.py

@@ -4,8 +4,8 @@ import logging
 import os
 import unittest
 
+from galaxy.security import idencoding
 from galaxy.tools.verify.test_data import TestDataResolver
-from galaxy.web import security
 from .driver_util import GalaxyTestDriver, setup_keep_outdir, target_url_parts
 
 log = logging.getLogger(__name__)
@@ -14,8 +14,7 @@ log = logging.getLogger(__name__)
 class FunctionalTestCase(unittest.TestCase):
 
     def setUp(self):
-        # Security helper
-        self.security = security.SecurityHelper(id_secret='changethisinproductiontoo')
+        self.security = idencoding.IdEncodingHelper(id_secret='changethisinproductiontoo')
         self.history_id = os.environ.get('GALAXY_TEST_HISTORY_ID', None)
         self.host, self.port, self.url = target_url_parts()
         self.test_data_resolver = TestDataResolver()

test/shed_functional/base/twilltestcase.py

@@ -29,8 +29,8 @@ import galaxy.model.tool_shed_install as galaxy_model
 import galaxy.util
 import galaxy.webapps.tool_shed.util.hgweb_config
 from base.testcase import FunctionalTestCase  # noqa: I100,I201,I202
+from galaxy.security import idencoding  # noqa: I201
 from galaxy.util import unicodify  # noqa: I201
-from galaxy.web import security  # noqa: I201
 from tool_shed.util import hg_util, xml_util
 from tool_shed.util.encoding_util import tool_shed_encode
 from . import common, test_db_util
@@ -52,7 +52,7 @@ class ShedTwillTestCase(FunctionalTestCase):
 
     def setUp(self):
         # Security helper
-        self.security = security.SecurityHelper(id_secret='changethisinproductiontoo')
+        self.security = idencoding.IdEncodingHelper(id_secret='changethisinproductiontoo')
         self.history_id = None
         self.hgweb_config_dir = os.environ.get('TEST_HG_WEB_CONFIG_DIR')
         self.hgweb_config_manager = galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager()

test/unit/test_id_encode_decode.py

@@ -1,23 +1,23 @@
 # -*- coding: utf-8 -*-
 
-from galaxy.web import security
+from galaxy.security import idencoding
 
 
-test_helper_1 = security.SecurityHelper(id_secret="secu1")
-test_helper_2 = security.SecurityHelper(id_secret="secu2")
+test_helper_1 = idencoding.IdEncodingHelper(id_secret="secu1")
+test_helper_2 = idencoding.IdEncodingHelper(id_secret="secu2")
 
 
 def test_maximum_length_handling_ascii():
     # Test that id secrets can be up to 56 characters long.
-    longest_id_secret = "m" * security.MAXIMUM_ID_SECRET_LENGTH
-    helper = security.SecurityHelper(id_secret=longest_id_secret)
+    longest_id_secret = "m" * idencoding.MAXIMUM_ID_SECRET_LENGTH
+    helper = idencoding.IdEncodingHelper(id_secret=longest_id_secret)
     helper.encode_id(1)
 
     # Test that security helper will catch if the id secret is too long.
     threw_exception = False
-    longer_id_secret = "m" * (security.MAXIMUM_ID_SECRET_LENGTH + 1)
+    longer_id_secret = "m" * (idencoding.MAXIMUM_ID_SECRET_LENGTH + 1)
     try:
-        security.SecurityHelper(id_secret=longer_id_secret)
+        idencoding.IdEncodingHelper(id_secret=longer_id_secret)
     except Exception:
         threw_exception = True
 
@@ -44,14 +44,14 @@ def test_maximum_length_handling_ascii():
 
 def test_maximum_length_handling_nonascii():
     longest_id_secret = "◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎"
-    helper = security.SecurityHelper(id_secret=longest_id_secret)
+    helper = idencoding.IdEncodingHelper(id_secret=longest_id_secret)
     helper.encode_id(1)
 
     # Test that security helper will catch if the id secret is too long.
     threw_exception = False
     longer_id_secret = "◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎"
     try:
-        security.SecurityHelper(id_secret=longer_id_secret)
+        idencoding.IdEncodingHelper(id_secret=longer_id_secret)
     except Exception:
         threw_exception = True
 

test/unit/unittest_utils/galaxy_mock.py

@@ -14,10 +14,10 @@ from galaxy.auth import AuthManager
 from galaxy.datatypes import registry
 from galaxy.jobs.manager import NoopManager
 from galaxy.model import mapping, tags
+from galaxy.security import idencoding
 from galaxy.tools.deps.containers import NullContainerFinder
 from galaxy.util.bunch import Bunch
 from galaxy.util.dbkeys import GenomeBuilds
-from galaxy.web import security
 from galaxy.web.stack import ApplicationStack
 
 
@@ -110,7 +110,7 @@ class MockAppConfig(Bunch):
     def __init__(self, root=None, **kwargs):
         Bunch.__init__(self, **kwargs)
         root = root or '/tmp'
-        self.security = security.SecurityHelper(id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
+        self.security = idencoding.IdEncodingHelper(id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
         self.use_remote_user = kwargs.get('use_remote_user', False)
         self.file_path = '/tmp'
         self.jobs_directory = '/tmp'
@@ -155,7 +155,7 @@ class MockWebapp(object):
 
     def __init__(self, **kwargs):
         self.name = kwargs.get('name', 'galaxy')
-        self.security = security.SecurityHelper(id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
+        self.security = idencoding.IdEncodingHelper(id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
 
 
 class MockTrans(object):

test/unit/workflows/workflow_support.py

@@ -4,8 +4,8 @@ import yaml
 
 from galaxy import model
 from galaxy.model import mapping
+from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import bunch
-from galaxy.web.security import SecurityHelper
 
 
 class MockTrans(object):
@@ -47,7 +47,7 @@ class TestApp(object):
         )
         self.toolbox = TestToolbox()
         self.datatypes_registry = TestDatatypesRegistry()
-        self.security = SecurityHelper(id_secret="testing")
+        self.security = IdEncodingHelper(id_secret="testing")
 
 
 class TestDatatypesRegistry(object):