Move dbkeys to managers

lib/galaxy/app.py

@@ -41,6 +41,7 @@
 from galaxy.managers.api_keys import ApiKeyManager
 from galaxy.managers.citations import CitationsManager
 from galaxy.managers.collections import DatasetCollectionManager
+from galaxy.managers.dbkeys import GenomeBuilds
 from galaxy.managers.folders import FolderManager
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.histories import HistoryManager
@@ -126,7 +127,6 @@
     listify,
     StructuredExecutionTimer,
 )
-from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.util.task import IntervalTask
 from galaxy.util.tool_shed import tool_shed_registry
 from galaxy.visualization.data_providers.registry import DataProviderRegistry

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -22,6 +22,7 @@
 from galaxy.job_metrics import JobMetrics
 from galaxy.jobs.manager import NoopManager
 from galaxy.managers.collections import DatasetCollectionManager
+from galaxy.managers.dbkeys import GenomeBuilds
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.histories import HistoryManager
 from galaxy.managers.jobs import JobSearch
@@ -51,7 +52,6 @@
 from galaxy.tools.data import ToolDataTableManager
 from galaxy.util import StructuredExecutionTimer
 from galaxy.util.bunch import Bunch
-from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.web.short_term_storage import (
     ShortTermStorageAllocator,
     ShortTermStorageConfiguration,

lib/galaxy/util/dbkeys.py → lib/galaxy/managers/dbkeys.py

@@ -5,6 +5,10 @@
 import os.path
 import re
 from json import loads
+from typing import (
+    Dict,
+    List,
+)
 
 from galaxy.util import (
     galaxy_directory,
@@ -17,9 +21,9 @@
 
 def read_dbnames(filename):
     """Read build names from file"""
-    db_names = []
+    db_names: List = []
     try:
-        ucsc_builds = {}
+        ucsc_builds: Dict = {}
         man_builds = []  # assume these are integers
         name_to_db_base = {}
         if filename is None:
@@ -43,9 +47,9 @@ def read_dbnames(filename):
                         ucsc_builds[db_base] = []
                         name_to_db_base[fields[1]] = db_base
                     # we want to sort within a species numerically by revision number
-                    build_rev = re.compile(r"\d+$")
+                    pattern = re.compile(r"\d+$")
                     try:
-                        build_rev = int(build_rev.findall(fields[0])[0])
+                        build_rev = int(pattern.findall(fields[0])[0])
                     except Exception:
                         build_rev = 0
                     ucsc_builds[db_base].append((build_rev, fields[0], fields[1]))

lib/galaxy/structured_app.py

@@ -14,6 +14,7 @@
 from galaxy.di import Container
 from galaxy.files import ConfiguredFileSources
 from galaxy.job_metrics import JobMetrics
+from galaxy.managers.dbkeys import GenomeBuilds
 from galaxy.model.base import (
     ModelMapping,
     SharedModelMapping,
@@ -32,7 +33,6 @@
 from galaxy.tool_util.deps.containers import ContainerFinder
 from galaxy.tool_util.deps.views import DependencyResolversView
 from galaxy.tool_util.verify import test_data
-from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.util.tool_shed.tool_shed_registry import Registry as ToolShedRegistry
 from galaxy.web_stack import ApplicationStack
 from galaxy.webhooks import WebhooksRegistry

lib/galaxy/tools/parameters/basic.py

@@ -21,6 +21,7 @@
 
 from galaxy import util
 from galaxy.files import ProvidesUserFileSourcesUserContext
+from galaxy.managers import dbkeys
 from galaxy.model import (
     cached_id,
     Dataset,
@@ -33,7 +34,6 @@
 from galaxy.schema.fetch_data import FilesPayload
 from galaxy.tool_util.parser import get_input_source as ensure_input_source
 from galaxy.util import (
-    dbkeys,
     sanitize_param,
     string_as_bool,
     string_as_bool_or_none,

lib/galaxy/tools/remote_tool_eval.py

@@ -12,6 +12,7 @@
 from galaxy.files import ConfiguredFileSources
 from galaxy.job_execution.compute_environment import SharedComputeEnvironment
 from galaxy.job_execution.setup import JobIO
+from galaxy.managers.dbkeys import GenomeBuilds
 from galaxy.metadata.set_metadata import (
     get_metadata_params,
     get_object_store,
@@ -30,7 +31,6 @@
     ToolDataTableManager,
 )
 from galaxy.util.bunch import Bunch
-from galaxy.util.dbkeys import GenomeBuilds
 
 
 class ToolAppConfig(NamedTuple):

lib/galaxy/tools/repositories.py

@@ -4,9 +4,9 @@
 import tempfile
 from contextlib import contextmanager
 
+from galaxy.managers.dbkeys import GenomeBuilds
 from galaxy.tools.data import ToolDataTableManager
 from galaxy.util.bunch import Bunch
-from galaxy.util.dbkeys import GenomeBuilds
 
 
 class ValidationContext:

lib/tool_shed/webapp/app.py

@@ -18,6 +18,7 @@
 from galaxy.config import configure_logging
 from galaxy.managers.api_keys import ApiKeyManager
 from galaxy.managers.citations import CitationsManager
+from galaxy.managers.dbkeys import GenomeBuilds
 from galaxy.managers.users import UserManager
 from galaxy.model.base import SharedModelMapping
 from galaxy.model.tags import CommunityTagHandler
@@ -27,7 +28,6 @@
 )
 from galaxy.security import idencoding
 from galaxy.structured_app import BasicSharedApp
-from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.web_stack import application_stack_instance
 from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
 from tool_shed.structured_app import ToolShedApp