Add type annotations to initial keyword args

lib/galaxy/files/sources/__init__.py

@@ -36,11 +36,15 @@ class FilesSourceProperties(TypedDict):
     file_sources_config: NotRequired["ConfiguredFileSourcesConfig"]
     id: NotRequired[str]
     label: NotRequired[str]
-    doc: NotRequired[str]
+    doc: NotRequired[Optional[str]]
     scheme: NotRequired[str]
     writable: NotRequired[bool]
-    required_roles: NotRequired[List[str]]
-    requires_groups: NotRequired[List[str]]
+    requires_roles: NotRequired[Optional[str]]
+    requires_groups: NotRequired[Optional[str]]
+    # API helper values
+    uri_root: NotRequired[str]
+    type: NotRequired[str]
+    browsable: NotRequired[bool]
 
 
 class FilesSourceOptions:
@@ -100,7 +104,7 @@ class SingleFileSource(metaclass=abc.ABCMeta):
         returned unchanged."""
 
     @abc.abstractmethod
-    def to_dict(self, for_serialization=False, user_context=None):
+    def to_dict(self, for_serialization=False, user_context=None) -> FilesSourceProperties:
         """Return a dictified representation of this FileSource instance.
 
         If ``user_context`` is supplied, properties should be written so user
@@ -114,7 +118,7 @@ class SupportsBrowsing(metaclass=abc.ABCMeta):
         """Return a prefix for the root (e.g. gxfiles://prefix/)."""
 
     @abc.abstractmethod
-    def list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None) -> dict:
         """Return dictionary of 'Directory's and 'File's."""
 
 
@@ -175,7 +179,7 @@ class BaseFilesSource(FilesSource):
         uri_root = self.get_uri_root()
         return uri_join(uri_root, path)
 
-    def _parse_common_config_opts(self, kwd: dict):
+    def _parse_common_config_opts(self, kwd: FilesSourceProperties):
         self._file_sources_config = kwd.pop("file_sources_config")
         self.id = kwd.pop("id")
         self.label = kwd.pop("label", None) or self.id
@@ -191,8 +195,8 @@ class BaseFilesSource(FilesSource):
         kwd.pop("browsable", None)
         return kwd
 
-    def to_dict(self, for_serialization=False, user_context=None):
-        rval = {
+    def to_dict(self, for_serialization=False, user_context=None) -> FilesSourceProperties:
+        rval: FilesSourceProperties = {
             "id": self.id,
             "type": self.plugin_type,
             "label": self.label,

lib/galaxy/files/sources/_pyfilesystem2.py

@@ -13,10 +13,12 @@ from typing import (
 
 import fs
 from fs.base import FS
+from typing_extensions import Unpack
 
 from . import (
     BaseFilesSource,
     FilesSourceOptions,
+    FilesSourceProperties,
 )
 
 log = logging.getLogger(__name__)
@@ -28,7 +30,7 @@ class PyFilesystem2FilesSource(BaseFilesSource):
     required_module: ClassVar[Optional[Type[FS]]]
     required_package: ClassVar[str]
 
-    def __init__(self, **kwd):
+    def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         if self.required_module is None:
             raise Exception(PACKAGE_MESSAGE % self.required_package)
         props = self._parse_common_config_opts(kwd)

lib/galaxy/files/sources/base64.py

@@ -2,9 +2,12 @@ import base64
 import logging
 from typing import Optional
 
+from typing_extensions import Unpack
+
 from . import (
     BaseFilesSource,
     FilesSourceOptions,
+    FilesSourceProperties,
 )
 
 log = logging.getLogger(__name__)
@@ -13,11 +16,11 @@ log = logging.getLogger(__name__)
 class Base64FilesSource(BaseFilesSource):
     plugin_type = "base64"
 
-    def __init__(self, label="Base64 encoded string", doc="Base64 string handler", **kwd):
-        kwds = dict(
+    def __init__(self, **kwd: Unpack[FilesSourceProperties]):
+        kwds: FilesSourceProperties = dict(
             id="_base64",
-            label=label,
-            doc=doc,
+            label="Base64 encoded string",
+            doc="Base64 string handler",
             writable=False,
         )
         kwds.update(kwd)

lib/galaxy/files/sources/drs.py

@@ -1,10 +1,13 @@
 import logging
 from typing import Optional
 
+from typing_extensions import Unpack
+
 from galaxy.util.drs import fetch_drs_to_file
 from . import (
     BaseFilesSource,
     FilesSourceOptions,
+    FilesSourceProperties,
 )
 
 log = logging.getLogger(__name__)
@@ -13,11 +16,11 @@ log = logging.getLogger(__name__)
 class DRSFilesSource(BaseFilesSource):
     plugin_type = "drs"
 
-    def __init__(self, label="DRS file", doc="DRS file handler", **kwd):
-        kwds = dict(
+    def __init__(self, **kwd: Unpack[FilesSourceProperties]):
+        kwds: FilesSourceProperties = dict(
             id="_drs",
-            label=label,
-            doc=doc,
+            label="DRS file",
+            doc="DRS file handler",
             writable=False,
         )
         kwds.update(kwd)

lib/galaxy/files/sources/http.py

@@ -7,6 +7,8 @@ from typing import (
     Optional,
 )
 
+from typing_extensions import Unpack
+
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     get_charset_from_http_headers,
@@ -29,8 +31,8 @@ class HTTPFilesSourceProperties(FilesSourceProperties, total=False):
 class HTTPFilesSource(BaseFilesSource):
     plugin_type = "http"
 
-    def __init__(self, **kwd):
-        kwds = dict(
+    def __init__(self, **kwd: Unpack[FilesSourceProperties]):
+        kwds: FilesSourceProperties = dict(
             id="_http",
             label="HTTP File",
             doc="Default HTTP file handler",

lib/galaxy/files/sources/posix.py

@@ -8,6 +8,8 @@ from typing import (
     Optional,
 )
 
+from typing_extensions import Unpack
+
 from galaxy import exceptions
 from galaxy.util.path import (
     safe_contains,
@@ -42,7 +44,7 @@ class PosixFilesSource(BaseFilesSource):
     #    handle = OSFS(**self._props)
     #    return handle
 
-    def __init__(self, **kwd):
+    def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
         props = self._parse_common_config_opts(kwd)
         self.root = props["root"]
         self.enforce_symlink_security = props.get("enforce_symlink_security", DEFAULT_ENFORCE_SYMLINK_SECURITY)

lib/galaxy/files/sources/s3fs.py

@@ -9,6 +9,8 @@ from typing import (
     Optional,
 )
 
+from typing_extensions import Unpack
+
 from . import (
     FilesSourceOptions,
     FilesSourceProperties,
@@ -38,7 +40,7 @@ class S3FsFilesSourceProperties(FilesSourceProperties, total=False):
 class S3FsFilesSource(BaseFilesSource):
     plugin_type = "s3fs"
 
-    def __init__(self, **kwd):
+    def __init__(self, **kwd: Unpack[S3FsFilesSourceProperties]):
         if s3fs is None:
             raise Exception("Package s3fs unavailable but required for this file source plugin.")
         props: S3FsFilesSourceProperties = cast(S3FsFilesSourceProperties, self._parse_common_config_opts(kwd))