Improve type hints in manager classes

client/src/api/schema/schema.ts

@@ -4019,14 +4019,10 @@ export interface components {
             /**
              * Source
              * @description The source of this dataset, either `hda` or `ldda` depending of its origin.
+             * @enum {string}
              */
-            src: components["schemas"]["DatasetSourceType"];
+            src: "hda" | "ldda";
         };
-        /**
-         * DatasetSourceType
-         * @enum {string}
-         */
-        DatasetSourceType: "hda" | "ldda";
         /**
          * DatasetState
          * @enum {string}
@@ -4645,8 +4641,9 @@ export interface components {
             /**
              * Source
              * @description The source of this dataset, either `hda` or `ldda` depending of its origin.
+             * @enum {string}
              */
-            src: components["schemas"]["DatasetSourceType"];
+            src: "hda" | "ldda";
         };
         /** EncodedHdcaSourceId */
         EncodedHdcaSourceId: {
@@ -5605,7 +5602,7 @@ export interface components {
              * HDA or LDDA
              * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
              */
-            hda_ldda?: components["schemas"]["DatasetSourceType"] | null;
+            hda_ldda?: components["schemas"]["DataItemSourceType"] | null;
             /**
              * HID
              * @description The index position of this item in the History.
@@ -5851,7 +5848,7 @@ export interface components {
              * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
              * @default hda
              */
-            hda_ldda?: components["schemas"]["DatasetSourceType"];
+            hda_ldda?: components["schemas"]["DataItemSourceType"];
             /**
              * HID
              * @description The index position of this item in the History.
@@ -6000,7 +5997,7 @@ export interface components {
              * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
              * @default hda
              */
-            hda_ldda?: components["schemas"]["DatasetSourceType"];
+            hda_ldda?: components["schemas"]["DataItemSourceType"];
             /**
              * History ID
              * @example 0123456789ABCDEF
@@ -9370,8 +9367,9 @@ export interface components {
             /**
              * Source
              * @description The source of the content. Can be other history element to be copied or library elements.
+             * @enum {string}
              */
-            source: components["schemas"]["DatasetSourceType"];
+            source: "hda" | "ldda";
         };
         /** MessageNotificationContent */
         MessageNotificationContent: {
@@ -13847,7 +13845,7 @@ export interface operations {
             /** @description View to be passed to the serializer */
             /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                hda_ldda?: "hda" | "ldda";
                 data_type?: components["schemas"]["RequestDataType"] | null;
                 view?: string | null;
                 keys?: string | null;
@@ -14148,7 +14146,7 @@ export interface operations {
         parameters: {
             /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                hda_ldda?: "hda" | "ldda";
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -14184,7 +14182,7 @@ export interface operations {
         parameters: {
             /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                hda_ldda?: "hda" | "ldda";
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -14218,7 +14216,7 @@ export interface operations {
         parameters: {
             /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                hda_ldda?: "hda" | "ldda";
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -14287,7 +14285,7 @@ export interface operations {
         parameters: {
             /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                hda_ldda?: "hda" | "ldda";
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -14353,7 +14351,7 @@ export interface operations {
         parameters: {
             /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                hda_ldda?: "hda" | "ldda";
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -19697,7 +19695,7 @@ export interface operations {
              * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
              */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"] | null;
+                hda_ldda?: ("hda" | "ldda") | null;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -19798,7 +19796,7 @@ export interface operations {
              * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
              */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"] | null;
+                hda_ldda?: ("hda" | "ldda") | null;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {

lib/galaxy/app.py

@@ -47,7 +47,7 @@
 from galaxy.files.templates import ConfiguredFileSourceTemplates
 from galaxy.job_metrics import JobMetrics
 from galaxy.jobs.manager import JobManager
-from galaxy.managers.api_keys import ApiKeyManager
+from galaxy.managers.api_keys import GalaxyApiKeyManager
 from galaxy.managers.citations import CitationsManager
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.dbkeys import GenomeBuilds
@@ -722,7 +722,7 @@ def __init__(self, **kwargs) -> None:
         self.test_data_resolver = self._register_singleton(
             TestDataResolver, TestDataResolver(file_dirs=self.config.tool_test_data_directories)
         )
-        self.api_keys_manager = self._register_singleton(ApiKeyManager)
+        self.api_keys_manager = self._register_singleton(GalaxyApiKeyManager)
 
         # Tool Data Tables
         self._configure_tool_data_tables(from_shed_config=False)

lib/galaxy/celery/tasks.py

@@ -196,7 +196,7 @@ def set_metadata(
     try:
         if overwrite:
             hda_manager.overwrite_metadata(dataset_instance)
-        dataset_instance.datatype.set_meta(dataset_instance)  # type:ignore [arg-type]
+        dataset_instance.datatype.set_meta(dataset_instance)
         dataset_instance.set_peek()
         # Reset SETTING_METADATA state so the dataset instance getter picks the dataset state
         dataset_instance.set_metadata_success_state()

lib/galaxy/datatypes/binary.py

@@ -69,7 +69,6 @@
     MetadataParameter,
 )
 from galaxy.datatypes.protocols import (
-    DatasetHasHidProtocol,
     DatasetProtocol,
     HasExtraFilesAndMetadata,
     HasFileName,
@@ -692,7 +691,7 @@ def get_chunk(self, trans, dataset: HasFileName, offset: int = 0, ck_size: Optio
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,
@@ -2094,7 +2093,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,

lib/galaxy/datatypes/blast.py

@@ -40,10 +40,7 @@
     Optional,
 )
 
-from galaxy.datatypes.protocols import (
-    DatasetHasHidProtocol,
-    DatasetProtocol,
-)
+from galaxy.datatypes.protocols import DatasetProtocol
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
@@ -210,7 +207,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,

lib/galaxy/datatypes/data.py

@@ -422,7 +422,7 @@ def __archive_extra_files_path(self, extra_files_path: str) -> Generator[Tuple[s
                 yield fpath, rpath
 
     def _serve_raw(
-        self, dataset: DatasetHasHidProtocol, to_ext: Optional[str], headers: Headers, **kwd
+        self, dataset: DatasetProtocol, to_ext: Optional[str], headers: Headers, **kwd
     ) -> Tuple[IO, Headers]:
         headers["Content-Length"] = str(os.stat(dataset.get_file_name()).st_size)
         headers["content-type"] = (
@@ -516,7 +516,7 @@ def _serve_file_contents(self, trans, data, headers, preview, file_size, max_pee
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,
@@ -648,7 +648,7 @@ def _yield_user_file_content(self, trans, from_dataset: HasCreatingJob, filename
 
     def _download_filename(
         self,
-        dataset: DatasetHasHidProtocol,
+        dataset: Union[DatasetProtocol, DatasetHasHidProtocol],
         to_ext: Optional[str] = None,
         hdca: Optional[DatasetHasHidProtocol] = None,
         element_identifier: Optional[str] = None,
@@ -665,7 +665,7 @@ def escape(raw_identifier):
         template_values = {
             "name": escape(dataset.name),
             "ext": to_ext,
-            "hid": dataset.hid,
+            "hid": getattr(dataset, "hid", "-library"),
         }
 
         if not filename_pattern:

lib/galaxy/datatypes/isa.py

@@ -28,7 +28,6 @@
 from galaxy import util
 from galaxy.datatypes.data import Data
 from galaxy.datatypes.protocols import (
-    DatasetHasHidProtocol,
     DatasetProtocol,
     HasExtraFilesAndMetadata,
     HasExtraFilesPath,
@@ -266,7 +265,7 @@ def groom_dataset_content(self, file_name: str) -> None:
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,

lib/galaxy/datatypes/protocols.py

@@ -2,10 +2,16 @@
 Location of protocols used in datatypes
 """
 
-from typing import Any
+from typing import (
+    Any,
+    TYPE_CHECKING,
+)
 
 from typing_extensions import Protocol
 
+if TYPE_CHECKING:
+    from sqlalchemy.orm.base import Mapped
+
 
 class HasClearAssociatedFiles(Protocol):
     def clear_associated_files(self, metadata_safe: bool = False, purge: bool = False) -> None: ...
@@ -35,7 +41,7 @@ class HasHid(Protocol):
 
 
 class HasId(Protocol):
-    id: int
+    id: "Mapped[int]"
 
 
 class HasInfo(Protocol):

lib/galaxy/datatypes/sequence.py

@@ -31,7 +31,6 @@
     MetadataElement,
 )
 from galaxy.datatypes.protocols import (
-    DatasetHasHidProtocol,
     DatasetProtocol,
     HasMetadata,
 )
@@ -766,7 +765,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,

lib/galaxy/datatypes/spaln.py

@@ -14,7 +14,6 @@
 from galaxy.datatypes.data import Data
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.protocols import (
-    DatasetHasHidProtocol,
     DatasetProtocol,
     HasExtraFilesAndMetadata,
 )
@@ -117,7 +116,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,

lib/galaxy/datatypes/tabular.py

@@ -53,7 +53,6 @@
     MetadataParameter,
 )
 from galaxy.datatypes.protocols import (
-    DatasetHasHidProtocol,
     DatasetProtocol,
     HasFileName,
     HasMetadata,
@@ -168,7 +167,7 @@ def _read_chunk(self, trans, dataset: HasFileName, offset: int, ck_size: Optiona
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,

lib/galaxy/datatypes/text.py

@@ -27,7 +27,6 @@
     MetadataParameter,
 )
 from galaxy.datatypes.protocols import (
-    DatasetHasHidProtocol,
     DatasetProtocol,
     HasCreatingJob,
     HasExtraFilesAndMetadata,
@@ -208,7 +207,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
     def display_data(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,
@@ -224,7 +223,7 @@ def display_data(
     def _display_data_trusted(
         self,
         trans,
-        dataset: DatasetHasHidProtocol,
+        dataset: DatasetProtocol,
         preview: bool = False,
         filename: Optional[str] = None,
         to_ext: Optional[str] = None,