mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
Move RequiredAppT back into galaxy packages.
Follow up from #19642. I'm trying to get all the Galaxy type annotations to only use Galaxy code.
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@@ -76,6 +76,7 @@ class BasicSharedApp(Container):
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auth_manager: AuthManager
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security_agent: Any
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quota_agent: QuotaAgent
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tool_data_tables: "ToolDataTableManager"
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@property
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def toolbox(self) -> "ToolBox":
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@@ -112,7 +113,6 @@ class MinimalManagerApp(MinimalApp):
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genome_builds: GenomeBuilds
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geographical_server_location_name: str
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dataset_collection_manager: "DatasetCollectionManager"
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tool_data_tables: "ToolDataTableManager"
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history_manager: "HistoryManager"
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hda_manager: "HDAManager"
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workflow_manager: "WorkflowsManager"
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@@ -4,6 +4,7 @@ import shutil
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from typing import (
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List,
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TYPE_CHECKING,
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Union,
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)
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from galaxy.tool_shed.galaxy_install.client import InstallationTarget
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@@ -16,14 +17,17 @@ from galaxy.util.tool_shed import xml_util
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if TYPE_CHECKING:
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from galaxy.model.tool_shed_install import ToolShedRepository
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from galaxy.structured_app import BasicSharedApp
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from galaxy.util.path import StrPath
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from tool_shed.structured_app import RequiredAppT
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log = logging.getLogger(__name__)
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RequiredAppT = Union["BasicSharedApp", InstallationTarget]
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class BaseShedToolDataTableManager:
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def __init__(self, app: "RequiredAppT"):
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def __init__(self, app: RequiredAppT):
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self.app = app
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def handle_sample_tool_data_table_conf_file(self, filename: "StrPath", persist: bool = False):
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@@ -1,7 +1,9 @@
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import logging
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from typing import TYPE_CHECKING
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from galaxy.tool_shed.tools.data_table_manager import BaseShedToolDataTableManager
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from galaxy.tool_shed.tools.data_table_manager import (
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BaseShedToolDataTableManager,
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RequiredAppT,
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)
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from galaxy.tool_shed.util import (
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basic_util,
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hg_util,
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@@ -14,14 +16,11 @@ from galaxy.tools import (
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)
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from galaxy.tools.parameters import dynamic_options
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if TYPE_CHECKING:
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from tool_shed.structured_app import RequiredAppT
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log = logging.getLogger(__name__)
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class ToolValidator:
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def __init__(self, app: "RequiredAppT"):
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def __init__(self, app: RequiredAppT):
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self.app = app
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self.stdtm = BaseShedToolDataTableManager(self.app)
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@@ -34,7 +34,7 @@ from galaxy.util.tool_shed.tool_shed_registry import Registry
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if TYPE_CHECKING:
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from galaxy.tool_shed.galaxy_install.client import InstallationTarget
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from tool_shed.structured_app import RequiredAppT
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from galaxy.tool_shed.tools.data_table_manager import RequiredAppT
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log = logging.getLogger(__name__)
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@@ -1,12 +1,8 @@
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from typing import (
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TYPE_CHECKING,
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Union,
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)
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from typing import TYPE_CHECKING
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from galaxy.structured_app import BasicSharedApp
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if TYPE_CHECKING:
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from galaxy.tool_shed.galaxy_install.client import InstallationTarget
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from galaxy.tools.data import ToolDataTableManager
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from tool_shed.managers.model_cache import ModelCache
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from tool_shed.repository_registry import RegistryInterface
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@@ -24,6 +20,3 @@ class ToolShedApp(BasicSharedApp):
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security_agent: "CommunityRBACAgent"
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model_cache: "ModelCache"
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tool_data_tables: "ToolDataTableManager"
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RequiredAppT = Union[ToolShedApp, "InstallationTarget"]
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