From ba074bd4e012437758458fe4d175f7748c0a7e10 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Mar 2024 19:00:58 +0100
Subject: [PATCH 01/44] Preserve API behavior for "keys"

Replace the `HistoryMinimal` model with a partial HistoryDetailed model
where all fields are optional.
---
 client/src/api/schema/schema.ts | 233 +++++++++++++++++++++++++-------
 lib/galaxy/schema/__init__.py   |  46 +++++++
 lib/galaxy/schema/schema.py     |  41 +++---
 3 files changed, 256 insertions(+), 64 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index 6f7aac5f9e88..bac9afa9dcbd 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -3597,6 +3597,142 @@ export interface components {
         CustomHistoryItem: {
             [key: string]: unknown | undefined;
         };
+        /** CustomHistoryView */
+        CustomHistoryView: {
+            /**
+             * Annotation
+             * @description An annotation to provide details or to help understand the purpose and usage of this item.
+             */
+            annotation?: string | null;
+            /**
+             * Archived
+             * @description Whether this item has been archived and is no longer active.
+             */
+            archived?: boolean | null;
+            /**
+             * Contents Active
+             * @description Contains the number of active, deleted or hidden items in a History.
+             */
+            contents_active?: components["schemas"]["HistoryActiveContentCounts"] | null;
+            /**
+             * Contents URL
+             * @description The relative URL to access the contents of this History.
+             */
+            contents_url?: string | null;
+            /**
+             * Count
+             * @description The number of items in the history.
+             */
+            count?: number | null;
+            /**
+             * Create Time
+             * @description The time and date this item was created.
+             */
+            create_time?: string | null;
+            /**
+             * Deleted
+             * @description Whether this item is marked as deleted.
+             */
+            deleted?: boolean | null;
+            /**
+             * Genome Build
+             * @description TODO
+             */
+            genome_build?: string | null;
+            /**
+             * History ID
+             * @example 0123456789ABCDEF
+             */
+            id?: string;
+            /**
+             * Importable
+             * @description Whether this History can be imported by other users with a shared link.
+             */
+            importable?: boolean | null;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             */
+            model_class?: "History";
+            /**
+             * Name
+             * @description The name of the history.
+             */
+            name?: string | null;
+            /**
+             * Preferred Object Store ID
+             * @description The ID of the object store that should be used to store new datasets in this history.
+             */
+            preferred_object_store_id?: string | null;
+            /**
+             * Published
+             * @description Whether this resource is currently publicly available to all users.
+             */
+            published?: boolean | null;
+            /**
+             * Purged
+             * @description Whether this item has been permanently removed.
+             */
+            purged?: boolean | null;
+            /**
+             * Size
+             * @description The total size of the contents of this history in bytes.
+             */
+            size?: number | null;
+            /**
+             * Slug
+             * @description Part of the URL to uniquely identify this History by link in a readable way.
+             */
+            slug?: string | null;
+            /**
+             * State
+             * @description The current state of the History based on the states of the datasets it contains.
+             */
+            state?: components["schemas"]["DatasetState"] | null;
+            /**
+             * State Counts
+             * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
+             */
+            state_details?: {
+                [key: string]: number | undefined;
+            } | null;
+            /**
+             * State IDs
+             * @description A dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state.
+             */
+            state_ids?: {
+                [key: string]: string[] | undefined;
+            } | null;
+            tags?: components["schemas"]["TagCollection"] | null;
+            /**
+             * Update Time
+             * @description The last time and date this item was updated.
+             */
+            update_time?: string | null;
+            /**
+             * URL
+             * @deprecated
+             * @description The relative URL to access this item.
+             */
+            url?: string | null;
+            /**
+             * User ID
+             * @description The encoded ID of the user that owns this History.
+             */
+            user_id?: string | null;
+            /**
+             * Username
+             * @description Owner of the history
+             */
+            username?: string | null;
+            /**
+             * Username and slug
+             * @description The relative URL in the form of /u/{username}/h/{slug}
+             */
+            username_and_slug?: string | null;
+            [key: string]: unknown | undefined;
+        };
         /**
          * DCESummary
          * @description Dataset Collection Element summary information.
@@ -6378,6 +6514,27 @@ export interface components {
         HelpForumUser: {
             [key: string]: unknown | undefined;
         };
+        /**
+         * HistoryActiveContentCounts
+         * @description Contains the number of active, deleted or hidden items in a History.
+         */
+        HistoryActiveContentCounts: {
+            /**
+             * Active
+             * @description Number of active datasets.
+             */
+            active: number;
+            /**
+             * Deleted
+             * @description Number of deleted datasets.
+             */
+            deleted: number;
+            /**
+             * Hidden
+             * @description Number of hidden datasets.
+             */
+            hidden: number;
+        };
         /** HistoryContentBulkOperationPayload */
         HistoryContentBulkOperationPayload: {
             /** Items */
@@ -6614,26 +6771,6 @@ export interface components {
             username_and_slug?: string | null;
             [key: string]: unknown | undefined;
         };
-        /**
-         * HistoryMinimal
-         * @description Minimal History Response with optional fields
-         */
-        HistoryMinimal: {
-            /** Id */
-            id?: string | null;
-            /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             */
-            model_class: "History";
-            /**
-             * User ID
-             * @description The encoded ID of the user that owns this History.
-             */
-            user_id?: string | null;
-            [key: string]: unknown | undefined;
-        };
         /**
          * HistorySummary
          * @description History summary information.
@@ -15139,9 +15276,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"]
                     )[];
                 };
             };
@@ -15181,9 +15318,9 @@ export interface operations {
                 content: {
                     "application/json":
                         | components["schemas"]["JobImportHistoryResponse"]
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
@@ -15267,9 +15404,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"]
                     )[];
                 };
             };
@@ -15305,9 +15442,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"]
                     )[];
                 };
             };
@@ -15373,9 +15510,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"]
                     )[];
                 };
             };
@@ -15410,9 +15547,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
@@ -15447,9 +15584,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
@@ -15507,9 +15644,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
@@ -15549,9 +15686,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"]
                     )[];
                 };
             };
@@ -15592,9 +15729,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"]
                     )[];
                 };
             };
@@ -15629,9 +15766,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
@@ -15670,9 +15807,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
@@ -15712,9 +15849,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
@@ -15806,9 +15943,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryMinimal"];
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["CustomHistoryView"];
                 };
             };
             /** @description Validation Error */
diff --git a/lib/galaxy/schema/__init__.py b/lib/galaxy/schema/__init__.py
index 0082c14ea5ea..b88ade573ef9 100644
--- a/lib/galaxy/schema/__init__.py
+++ b/lib/galaxy/schema/__init__.py
@@ -1,16 +1,23 @@
+import typing
+from copy import deepcopy
 from datetime import datetime
 from enum import Enum
 from typing import (
+    Any,
+    Callable,
     Dict,
     List,
     Optional,
+    TypeVar,
     Union,
 )
 
 from pydantic import (
     BaseModel,
+    create_model,
     Field,
 )
+from pydantic.fields import FieldInfo
 
 
 class BootstrapAdminUser(BaseModel):
@@ -110,3 +117,42 @@ class PdfDocumentType(str, Enum):
 class APIKeyModel(BaseModel):
     key: str = Field(..., title="Key", description="API key to interact with the Galaxy API")
     create_time: datetime = Field(..., title="Create Time", description="The time and date this API key was created.")
+
+
+T = TypeVar("T", bound="BaseModel")
+
+
+def partial_model(
+    include: Optional[list[str]] = None, exclude: Optional[list[str]] = None
+) -> Callable[[type[T]], type[T]]:
+    """Return a decorator to make model fields optional"""
+
+    if exclude is None:
+        exclude = []
+
+    @typing.no_type_check  # Mypy doesn't understand pydantic's create_model
+    def decorator(model: type[T]) -> type[T]:
+        def make_optional(field: FieldInfo, default: Any = None) -> tuple[Any, FieldInfo]:
+            new = deepcopy(field)
+            new.default = default
+            new.annotation = Optional[field.annotation or Any]
+            return new.annotation, new
+
+        fields = model.model_fields
+        if include is None:
+            fields = fields.items()
+        else:
+            fields = ((k, v) for k, v in fields.items() if k in include)
+
+        return create_model(
+            model.__name__,
+            __base__=model,
+            __module__=model.__module__,
+            **{
+                field_name: make_optional(field_info)
+                for field_name, field_info in fields
+                if exclude is None or field_name not in exclude
+            },
+        )
+
+    return decorator
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 40e076fd778c..d2efff6c78bd 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -33,6 +33,7 @@
     Literal,
 )
 
+from galaxy.schema import partial_model
 from galaxy.schema.bco import XrefItem
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
@@ -1204,18 +1205,6 @@ class UpdateHistoryContentsPayload(HistoryBase):
     )
 
 
-class HistoryMinimal(HistoryBase, WithModelClass):
-    """Minimal History Response with optional fields"""
-
-    model_class: HISTORY_MODEL_CLASS = ModelClassField(HISTORY_MODEL_CLASS)
-    id: Optional[HistoryID] = None
-    user_id: Optional[EncodedDatabaseIdField] = Field(
-        None,
-        title="User ID",
-        description="The encoded ID of the user that owns this History.",
-    )
-
-
 class HistorySummary(HistoryBase, WithModelClass):
     """History summary information."""
 
@@ -1341,10 +1330,30 @@ class HistoryDetailed(HistorySummary):  # Equivalent to 'dev-detailed' view, whi
     )
 
 
-AnyHistoryView = Union[
-    HistoryDetailed,
-    HistorySummary,
-    HistoryMinimal,
+@partial_model()
+class CustomHistoryView(HistoryDetailed):
+    """History Response with all optional fields.
+
+    It is used for serializing only specific attributes using the "keys"
+    query parameter. Unfortunately, we cannot know the exact fields that
+    will be requested, so we have to allow all fields to be optional.
+    """
+
+    # Define a few more useful fields to be optional that are not part of HistoryDetailed
+    contents_active: Optional[HistoryActiveContentCounts] = Field(
+        default=None,
+        title="Contents Active",
+        description=("Contains the number of active, deleted or hidden items in a History."),
+    )
+
+
+AnyHistoryView = Annotated[
+    Union[
+        HistorySummary,
+        HistoryDetailed,
+        CustomHistoryView,
+    ],
+    Field(union_mode="left_to_right"),
 ]
 
 

From e2ad32d7cc0b811433c0011758a982af79372ba7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 15 Mar 2024 13:24:37 +0100
Subject: [PATCH 02/44] Revert a7ea52841748437acfb172e11f513eed6f2fcceb

Make sure only the requested keys are returned as the query "keys" used to return.
---
 lib/galaxy_test/api/test_histories.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index a3c8e28a9f89..f6beef0b597c 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -155,9 +155,10 @@ def test_index_views(self):
 
         # Expect only specific keys
         expected_keys = ["name"]
-        unexpected_keys = ["deleted", "state"]
+        unexpected_keys = ["id", "deleted", "state"]
         index_response = self._get(f"histories?keys={','.join(expected_keys)}").json()
         for history in index_response:
+            assert len(history) == len(expected_keys)
             for key in expected_keys:
                 assert key in history
             for key in unexpected_keys:
@@ -181,10 +182,11 @@ def test_index_search_mode_views(self):
 
         # Expect only specific keys
         expected_keys = ["name"]
-        unexpected_keys = ["deleted", "state"]
+        unexpected_keys = ["id", "deleted", "state"]
         data = dict(search=expected_name_contains, show_published=False, keys=",".join(expected_keys))
         index_response = self._get("histories", data=data).json()
         for history in index_response:
+            assert len(history) == len(expected_keys)
             for key in expected_keys:
                 assert key in history
             for key in unexpected_keys:

From 947c6dade150b846920785567151df45deb9e8d1 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 17 Mar 2024 10:21:20 +0100
Subject: [PATCH 03/44] Do not force serialize model_class when it is Optional

---
 lib/galaxy/schema/fields.py                | 11 ++++++++++-
 lib/galaxy/schema/schema.py                |  6 +++++-
 lib/galaxy/webapps/galaxy/api/histories.py |  1 +
 3 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/schema/fields.py b/lib/galaxy/schema/fields.py
index 4fb6861b6b36..311a0cf105e5 100644
--- a/lib/galaxy/schema/fields.py
+++ b/lib/galaxy/schema/fields.py
@@ -1,5 +1,9 @@
 import re
-from typing import TYPE_CHECKING
+from typing import (
+    get_origin,
+    TYPE_CHECKING,
+    Union,
+)
 
 from pydantic import (
     BeforeValidator,
@@ -112,6 +116,11 @@ def literal_to_value(arg):
     return val[0]
 
 
+def is_optional(field):
+    args = get_args(field)
+    return get_origin(field) is Union and len(args) == 2 and type(None) in args
+
+
 def ModelClassField(default_value):
     """Represents a database model class name annotated as a constant
     pydantic Field.
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index d2efff6c78bd..2f37a486979b 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -39,6 +39,7 @@
     DecodedDatabaseIdField,
     EncodedDatabaseIdField,
     EncodedLibraryFolderDatabaseIdField,
+    is_optional,
     LibraryFolderDatabaseIdField,
     literal_to_value,
     ModelClassField,
@@ -313,8 +314,11 @@ class WithModelClass:
     def set_default(cls, data):
         if isinstance(data, dict):
             if "model_class" not in data and issubclass(cls, BaseModel):
+                model_class_annotation = cls.model_fields["model_class"].annotation
+                if is_optional(model_class_annotation):
+                    return data
                 data = data.copy()
-                data["model_class"] = literal_to_value(cls.model_fields["model_class"].annotation)
+                data["model_class"] = literal_to_value(model_class_annotation)
         return data
 
 
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index 743d31a48ccb..bad725b0424d 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -163,6 +163,7 @@ class FastAPIHistories:
     @router.get(
         "/api/histories",
         summary="Returns histories available to the current user.",
+        response_model_exclude_unset=True,
     )
     def index(
         self,

From c7f0fb0209fad9e96c3a401cc248989b62146dde Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 17 Mar 2024 11:33:40 +0100
Subject: [PATCH 04/44] Use `response_model_exclude_unset` whenever we return
 `AnyHistoryView`

This ensures we return just the fields specified in "keys" when returning a CustomHistory.
---
 client/src/api/schema/schema.ts            |  9 ++++++---
 lib/galaxy/schema/schema.py                | 12 ++++++------
 lib/galaxy/webapps/galaxy/api/histories.py | 13 +++++++++++++
 3 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index bac9afa9dcbd..f108ec43e734 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -6522,18 +6522,21 @@ export interface components {
             /**
              * Active
              * @description Number of active datasets.
+             * @default 0
              */
-            active: number;
+            active?: number | null;
             /**
              * Deleted
              * @description Number of deleted datasets.
+             * @default 0
              */
-            deleted: number;
+            deleted?: number | null;
             /**
              * Hidden
              * @description Number of hidden datasets.
+             * @default 0
              */
-            hidden: number;
+            hidden?: number | null;
         };
         /** HistoryContentBulkOperationPayload */
         HistoryContentBulkOperationPayload: {
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 2f37a486979b..df1484839857 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1254,18 +1254,18 @@ class HistorySummary(HistoryBase, WithModelClass):
 class HistoryActiveContentCounts(Model):
     """Contains the number of active, deleted or hidden items in a History."""
 
-    active: int = Field(
-        ...,
+    active: Optional[int] = Field(
+        default=0,
         title="Active",
         description="Number of active datasets.",
     )
-    hidden: int = Field(
-        ...,
+    hidden: Optional[int] = Field(
+        default=0,
         title="Hidden",
         description="Number of hidden datasets.",
     )
-    deleted: int = Field(
-        ...,
+    deleted: Optional[int] = Field(
+        default=0,
         title="Deleted",
         description="Number of deleted datasets.",
     )
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index bad725b0424d..32e4c109f1c5 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -221,6 +221,7 @@ def count(
     @router.get(
         "/api/histories/deleted",
         summary="Returns deleted histories for the current user.",
+        response_model_exclude_unset=True,
     )
     def index_deleted(
         self,
@@ -236,6 +237,7 @@ def index_deleted(
     @router.get(
         "/api/histories/published",
         summary="Return all histories that are published.",
+        response_model_exclude_unset=True,
     )
     def published(
         self,
@@ -248,6 +250,7 @@ def published(
     @router.get(
         "/api/histories/shared_with_me",
         summary="Return all histories that are shared with the current user.",
+        response_model_exclude_unset=True,
     )
     def shared_with_me(
         self,
@@ -281,6 +284,7 @@ def get_archived_histories(
     @router.get(
         "/api/histories/most_recently_used",
         summary="Returns the most recently used history of the user.",
+        response_model_exclude_unset=True,
     )
     def show_recent(
         self,
@@ -293,6 +297,7 @@ def show_recent(
         "/api/histories/{history_id}",
         name="history",
         summary="Returns the history with the given ID.",
+        response_model_exclude_unset=True,
     )
     def show(
         self,
@@ -348,6 +353,7 @@ def citations(
     @router.post(
         "/api/histories",
         summary="Creates a new history.",
+        response_model_exclude_unset=True,
     )
     def create(
         self,
@@ -370,6 +376,7 @@ def create(
     @router.delete(
         "/api/histories/{history_id}",
         summary="Marks the history with the given ID as deleted.",
+        response_model_exclude_unset=True,
     )
     def delete(
         self,
@@ -386,6 +393,7 @@ def delete(
     @router.put(
         "/api/histories/batch/delete",
         summary="Marks several histories with the given IDs as deleted.",
+        response_model_exclude_unset=True,
     )
     def batch_delete(
         self,
@@ -405,6 +413,7 @@ def batch_delete(
     @router.post(
         "/api/histories/deleted/{history_id}/undelete",
         summary="Restores a deleted history with the given ID (that hasn't been purged).",
+        response_model_exclude_unset=True,
     )
     def undelete(
         self,
@@ -417,6 +426,7 @@ def undelete(
     @router.put(
         "/api/histories/batch/undelete",
         summary="Marks several histories with the given IDs as undeleted.",
+        response_model_exclude_unset=True,
     )
     def batch_undelete(
         self,
@@ -433,6 +443,7 @@ def batch_undelete(
     @router.put(
         "/api/histories/{history_id}",
         summary="Updates the values for the history with the given ID.",
+        response_model_exclude_unset=True,
     )
     def update(
         self,
@@ -449,6 +460,7 @@ def update(
     @router.post(
         "/api/histories/from_store",
         summary="Create histories from a model store.",
+        response_model_exclude_unset=True,
     )
     def create_from_store(
         self,
@@ -620,6 +632,7 @@ def archive_history(
     @router.put(
         "/api/histories/{history_id}/archive/restore",
         summary="Restore an archived history.",
+        response_model_exclude_unset=True,
     )
     def restore_archived_history(
         self,

From 9f11c07a8ff1a743ed2cb5d4676322f650131630 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 17 Mar 2024 11:34:00 +0100
Subject: [PATCH 05/44] Add API test for show history views/keys

---
 lib/galaxy_test/api/test_histories.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index f6beef0b597c..7dc436e98f7d 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -106,6 +106,26 @@ def test_show_history_returns_expected_urls(self):
         assert show_response["url"] == f"/api/histories/{history_id}"
         assert show_response["contents_url"] == f"/api/histories/{history_id}/contents"
 
+    def test_show_respects_view(self):
+        history_id = self._create_history(f"TestHistoryForShowView_{uuid4()}")["id"]
+        # By default the view is "detailed"
+        show_response = self._get(f"histories/{history_id}").json()
+        assert "state" in show_response
+
+        # Change the view to summary
+        show_response = self._get(f"histories/{history_id}", {"view": "summary"}).json()
+        assert "state" not in show_response
+
+        # Expect only specific keys
+        expected_keys = ["name"]
+        unexpected_keys = ["id", "deleted", "state"]
+        show_response = self._get(f"histories/{history_id}", {"keys": ",".join(expected_keys)}).json()
+        assert len(show_response) == len(expected_keys)
+        for key in expected_keys:
+            assert key in show_response
+        for key in unexpected_keys:
+            assert key not in show_response
+
     def test_show_most_recently_used(self):
         history_id = self._create_history("TestHistoryRecent")["id"]
         show_response = self._get("histories/most_recently_used").json()

From 1683dfbb1e93e389940324256068c9575e6b5d4b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 17 Mar 2024 11:42:53 +0100
Subject: [PATCH 06/44] Do not mix `await` and `then`

---
 client/src/stores/historyStore.ts | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/client/src/stores/historyStore.ts b/client/src/stores/historyStore.ts
index fa82ee602e1b..16aec9d1d03d 100644
--- a/client/src/stores/historyStore.ts
+++ b/client/src/stores/historyStore.ts
@@ -241,12 +241,14 @@ export const useHistoryStore = defineStore("historyStore", () => {
     async function loadHistoryById(historyId: string) {
         if (!isLoadingHistory.has(historyId)) {
             isLoadingHistory.add(historyId);
-            await getHistoryByIdFromServer(historyId)
-                .then((history) => setHistory(history as HistorySummary))
-                .catch((error: Error) => console.warn(error))
-                .finally(() => {
+            try {
+                const history = await getHistoryByIdFromServer(historyId);
+                setHistory(history as HistorySummary);
+            } catch (error) {
+                console.error(error);
+            } finally {
                     isLoadingHistory.delete(historyId);
-                });
+            }
         }
     }
 

From 6add6ccd54359939b5a4f33a9a2a90fb9182ff76 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 17 Mar 2024 11:45:47 +0100
Subject: [PATCH 07/44] Remove global Vue import

---
 client/src/stores/historyStore.ts | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/src/stores/historyStore.ts b/client/src/stores/historyStore.ts
index 16aec9d1d03d..3bc1de807fd9 100644
--- a/client/src/stores/historyStore.ts
+++ b/client/src/stores/historyStore.ts
@@ -1,5 +1,5 @@
 import { defineStore } from "pinia";
-import Vue, { computed, ref } from "vue";
+import { computed, del, ref, set } from "vue";
 
 import type { HistorySummary } from "@/api";
 import { archiveHistory, unarchiveHistory } from "@/api/histories.archived";
@@ -96,11 +96,11 @@ export const useHistoryStore = defineStore("historyStore", () => {
     }
 
     function setFilterText(historyId: string, filterText: string) {
-        Vue.set(storedFilterTexts.value, historyId, filterText);
+        set(storedFilterTexts.value, historyId, filterText);
     }
 
     function setHistory(history: HistorySummary) {
-        Vue.set(storedHistories.value, history.id, history);
+        set(storedHistories.value, history.id, history);
     }
 
     function setHistories(histories: HistorySummary[]) {
@@ -179,7 +179,7 @@ export const useHistoryStore = defineStore("historyStore", () => {
         } else {
             await createNewHistory();
         }
-        Vue.delete(storedHistories.value, deletedHistory.id);
+        del(storedHistories.value, deletedHistory.id);
         unpinHistories([deletedHistory.id]);
         await handleTotalCountChange(1, true);
     }
@@ -247,7 +247,7 @@ export const useHistoryStore = defineStore("historyStore", () => {
             } catch (error) {
                 console.error(error);
             } finally {
-                    isLoadingHistory.delete(historyId);
+                isLoadingHistory.delete(historyId);
             }
         }
     }

From 671b522d6e19329751b10b5c7d838112266b2b80 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 17 Mar 2024 11:52:23 +0100
Subject: [PATCH 08/44] Fix side effect when updating parts of a history

When requesting only some keys for a particular history, we don't want to replace the whole history with just a few values.
---
 client/src/stores/historyStore.ts | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/client/src/stores/historyStore.ts b/client/src/stores/historyStore.ts
index 3bc1de807fd9..0ceb16cbb053 100644
--- a/client/src/stores/historyStore.ts
+++ b/client/src/stores/historyStore.ts
@@ -100,7 +100,12 @@ export const useHistoryStore = defineStore("historyStore", () => {
     }
 
     function setHistory(history: HistorySummary) {
-        set(storedHistories.value, history.id, history);
+        if (storedHistories.value[history.id] !== undefined) {
+            // Merge the incoming history with existing one to keep additional information
+            Object.assign(storedHistories.value[history.id]!, history);
+        } else {
+            set(storedHistories.value, history.id, history);
+        }
     }
 
     function setHistories(histories: HistorySummary[]) {

From fbc2d9eefa75b90d1770eab765d511db87dbed16 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 17 Mar 2024 11:55:21 +0100
Subject: [PATCH 09/44] Add TODO doc for partial_model

---
 lib/galaxy/schema/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/schema/__init__.py b/lib/galaxy/schema/__init__.py
index b88ade573ef9..b35450b690da 100644
--- a/lib/galaxy/schema/__init__.py
+++ b/lib/galaxy/schema/__init__.py
@@ -122,10 +122,13 @@ class APIKeyModel(BaseModel):
 T = TypeVar("T", bound="BaseModel")
 
 
+# TODO: This is a workaround to make all fields optional.
+#       It should be removed when Python/pydantic supports this feature natively.
+# https://github.com/pydantic/pydantic/issues/1673
 def partial_model(
     include: Optional[list[str]] = None, exclude: Optional[list[str]] = None
 ) -> Callable[[type[T]], type[T]]:
-    """Return a decorator to make model fields optional"""
+    """Decorator to make all model fields optional"""
 
     if exclude is None:
         exclude = []

From 95fb8daa78b1175a4e65cda41eadbb876a18b126 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 17:30:33 +0100
Subject: [PATCH 10/44] Remove config to allow all extra fields for history
 models

---
 lib/galaxy/schema/schema.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index df1484839857..bc104ef1d0ac 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1072,8 +1072,6 @@ class HDCADetailed(HDCASummary):
 class HistoryBase(Model):
     """Provides basic configuration for all the History models."""
 
-    model_config = ConfigDict(extra="allow")
-
 
 class HistoryContentItemBase(Model):
     """Identifies a dataset or collection contained in a History."""
@@ -1099,9 +1097,11 @@ class UpdateContentItem(HistoryContentItem):
     model_config = ConfigDict(use_enum_values=True, extra="allow")
 
 
-class UpdateHistoryContentsBatchPayload(HistoryBase):
+class UpdateHistoryContentsBatchPayload(Model):
     """Contains property values that will be updated for all the history `items` provided."""
 
+    model_config = ConfigDict(extra="allow")
+
     items: List[UpdateContentItem] = Field(
         ...,
         title="Items",

From aba671cb85e5a210958dcf1744d9d8bd1da27adf Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 17:31:34 +0100
Subject: [PATCH 11/44] Increase test coverage for API queries with view and
 keys

---
 lib/galaxy_test/api/test_histories.py | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index 7dc436e98f7d..421e5a6d2e0a 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -174,7 +174,7 @@ def test_index_views(self):
             assert "state" in history
 
         # Expect only specific keys
-        expected_keys = ["name"]
+        expected_keys = ["nice_size", "contents_active", "contents_states"]
         unexpected_keys = ["id", "deleted", "state"]
         index_response = self._get(f"histories?keys={','.join(expected_keys)}").json()
         for history in index_response:
@@ -184,6 +184,16 @@ def test_index_views(self):
             for key in unexpected_keys:
                 assert key not in history
 
+        # Expect combination of view and keys
+        view = "summary"
+        expected_keys = ["create_time", "count"]
+        data = dict(view=view, keys=",".join(expected_keys))
+        index_response = self._get("histories", data=data).json()
+        for history in index_response:
+            for key in expected_keys:
+                assert key in history
+            self._assert_has_keys(history, "id", "name", "url", "update_time", "deleted", "purged", "tags")
+
     def test_index_search_mode_views(self):
         # Make sure there is at least one history
         expected_name_contains = "SearchMode"
@@ -201,7 +211,7 @@ def test_index_search_mode_views(self):
             assert "state" in history
 
         # Expect only specific keys
-        expected_keys = ["name"]
+        expected_keys = ["nice_size", "contents_active", "contents_states"]
         unexpected_keys = ["id", "deleted", "state"]
         data = dict(search=expected_name_contains, show_published=False, keys=",".join(expected_keys))
         index_response = self._get("histories", data=data).json()
@@ -212,6 +222,16 @@ def test_index_search_mode_views(self):
             for key in unexpected_keys:
                 assert key not in history
 
+        # Expect combination of view and keys
+        view = "summary"
+        expected_keys = ["create_time", "count"]
+        data = dict(search=expected_name_contains, show_published=False, view=view, keys=",".join(expected_keys))
+        index_response = self._get("histories", data=data).json()
+        for history in index_response:
+            for key in expected_keys:
+                assert key in history
+            self._assert_has_keys(history, "id", "name", "url", "update_time", "deleted", "purged", "tags")
+
     def test_index_case_insensitive_contains_query(self):
         # Create the histories with a different user to ensure the test
         # is not conflicted with the current user's histories.

From df2e2025dade6c85ebd01ec14cb9ae900d869edc Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 17:38:56 +0100
Subject: [PATCH 12/44] Reorder union for proper model matching

---
 lib/galaxy/schema/schema.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index bc104ef1d0ac..9b12a024751d 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1353,9 +1353,9 @@ class CustomHistoryView(HistoryDetailed):
 
 AnyHistoryView = Annotated[
     Union[
-        HistorySummary,
-        HistoryDetailed,
         CustomHistoryView,
+        HistoryDetailed,
+        HistorySummary,
     ],
     Field(union_mode="left_to_right"),
 ]

From f92f14e3599a85cd4d1280da01343639e79bb2c2 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 17:47:01 +0100
Subject: [PATCH 13/44] Add missing optional fields to CustomHistoryView

We now need to explicitly define any field that would be serialized
---
 lib/galaxy/schema/schema.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 9b12a024751d..c525c1616b41 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1349,6 +1349,16 @@ class CustomHistoryView(HistoryDetailed):
         title="Contents Active",
         description=("Contains the number of active, deleted or hidden items in a History."),
     )
+    contents_states: Optional[HistoryStateCounts] = Field(
+        default=None,
+        title="Contents States",
+        description="A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.",
+    )
+    nice_size: Optional[str] = Field(
+        default=None,
+        title="Nice Size",
+        description="The total size of the contents of this history in a human-readable format.",
+    )
 
 
 AnyHistoryView = Annotated[

From 4f97f7eafe43a3d7cbd5e73570c49616b54668fe Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 17:49:08 +0100
Subject: [PATCH 14/44] Update client API schema

---
 client/src/api/schema/schema.ts | 75 ++++++++++++++++++---------------
 1 file changed, 40 insertions(+), 35 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index f108ec43e734..738685693143 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -2336,7 +2336,6 @@ export interface components {
              * @description The relative URL in the form of /u/{username}/h/{slug}
              */
             username_and_slug?: string | null;
-            [key: string]: unknown | undefined;
         };
         /** ArchivedHistorySummary */
         ArchivedHistorySummary: {
@@ -2409,7 +2408,6 @@ export interface components {
              * @description The relative URL to access this item.
              */
             url: string;
-            [key: string]: unknown | undefined;
         };
         /** AsyncFile */
         AsyncFile: {
@@ -3614,6 +3612,13 @@ export interface components {
              * @description Contains the number of active, deleted or hidden items in a History.
              */
             contents_active?: components["schemas"]["HistoryActiveContentCounts"] | null;
+            /**
+             * Contents States
+             * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
+             */
+            contents_states?: {
+                [key: string]: number | undefined;
+            } | null;
             /**
              * Contents URL
              * @description The relative URL to access the contents of this History.
@@ -3660,6 +3665,11 @@ export interface components {
              * @description The name of the history.
              */
             name?: string | null;
+            /**
+             * Nice Size
+             * @description The total size of the contents of this history in a human-readable format.
+             */
+            nice_size?: string | null;
             /**
              * Preferred Object Store ID
              * @description The ID of the object store that should be used to store new datasets in this history.
@@ -3731,7 +3741,6 @@ export interface components {
              * @description The relative URL in the form of /u/{username}/h/{slug}
              */
             username_and_slug?: string | null;
-            [key: string]: unknown | undefined;
         };
         /**
          * DCESummary
@@ -6772,7 +6781,6 @@ export interface components {
              * @description The relative URL in the form of /u/{username}/h/{slug}
              */
             username_and_slug?: string | null;
-            [key: string]: unknown | undefined;
         };
         /**
          * HistorySummary
@@ -6843,7 +6851,6 @@ export interface components {
              * @description The relative URL to access this item.
              */
             url: string;
-            [key: string]: unknown | undefined;
         };
         /**
          * Hyperlink
@@ -11661,7 +11668,6 @@ export interface components {
              * @description A list of content items to update with the changes.
              */
             items: components["schemas"]["UpdateContentItem"][];
-            [key: string]: unknown | undefined;
         };
         /**
          * UpdateHistoryContentsPayload
@@ -11697,7 +11703,6 @@ export interface components {
              * @description Whether this item is visible in the history.
              */
             visible?: boolean | null;
-            [key: string]: unknown | undefined;
         };
         /** UpdateLibraryFolderPayload */
         UpdateLibraryFolderPayload: {
@@ -15279,9 +15284,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
                     )[];
                 };
             };
@@ -15321,9 +15326,9 @@ export interface operations {
                 content: {
                     "application/json":
                         | components["schemas"]["JobImportHistoryResponse"]
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */
@@ -15407,9 +15412,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
                     )[];
                 };
             };
@@ -15445,9 +15450,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
                     )[];
                 };
             };
@@ -15513,9 +15518,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
                     )[];
                 };
             };
@@ -15550,9 +15555,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */
@@ -15587,9 +15592,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */
@@ -15647,9 +15652,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */
@@ -15689,9 +15694,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
                     )[];
                 };
             };
@@ -15732,9 +15737,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json": (
-                        | components["schemas"]["HistorySummary"]
-                        | components["schemas"]["HistoryDetailed"]
                         | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
                     )[];
                 };
             };
@@ -15769,9 +15774,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */
@@ -15810,9 +15815,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */
@@ -15852,9 +15857,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */
@@ -15946,9 +15951,9 @@ export interface operations {
             200: {
                 content: {
                     "application/json":
-                        | components["schemas"]["HistorySummary"]
+                        | components["schemas"]["CustomHistoryView"]
                         | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["CustomHistoryView"];
+                        | components["schemas"]["HistorySummary"];
                 };
             };
             /** @description Validation Error */

From d5d26b3cd7c9bc55b0b2fb204b46e3e1e41c43d9 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 17:59:56 +0100
Subject: [PATCH 15/44] Refactor move user-related types to api module

---
 client/src/api/index.ts                    | 23 +++++++++++++++++++
 client/src/composables/hashedUserId.ts     |  3 ++-
 client/src/composables/userLocalStorage.ts |  2 +-
 client/src/stores/userStore.ts             | 26 +---------------------
 4 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/client/src/api/index.ts b/client/src/api/index.ts
index 44704ca5fda5..0dbafc1a8b11 100644
--- a/client/src/api/index.ts
+++ b/client/src/api/index.ts
@@ -125,3 +125,26 @@ export function hasDetails(entry: DatasetEntry): entry is DatasetDetails {
  * Contains dataset metadata information.
  */
 export type MetadataFiles = components["schemas"]["MetadataFile"][];
+
+type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
+
+export interface User extends QuotaUsageResponse {
+    id: string;
+    email: string;
+    tags_used: string[];
+    isAnonymous: false;
+    is_admin?: boolean;
+    username?: string;
+}
+
+export interface AnonymousUser {
+    isAnonymous: true;
+    username?: string;
+    is_admin?: false;
+}
+
+export type GenericUser = User | AnonymousUser;
+
+export function isRegisteredUser(user: User | AnonymousUser | null): user is User {
+    return !user?.isAnonymous;
+}
diff --git a/client/src/composables/hashedUserId.ts b/client/src/composables/hashedUserId.ts
index fcda4cfde8f0..c19786b6ea7a 100644
--- a/client/src/composables/hashedUserId.ts
+++ b/client/src/composables/hashedUserId.ts
@@ -2,7 +2,8 @@ import { useLocalStorage } from "@vueuse/core";
 import { storeToRefs } from "pinia";
 import { computed, type Ref, ref, watch } from "vue";
 
-import { GenericUser, useUserStore } from "@/stores/userStore";
+import type { GenericUser } from "@/api";
+import { useUserStore } from "@/stores/userStore";
 
 async function hash32(value: string): Promise<string> {
     const valueUtf8 = new TextEncoder().encode(value);
diff --git a/client/src/composables/userLocalStorage.ts b/client/src/composables/userLocalStorage.ts
index b8a85b91845b..75375eb9d214 100644
--- a/client/src/composables/userLocalStorage.ts
+++ b/client/src/composables/userLocalStorage.ts
@@ -1,7 +1,7 @@
 import { useLocalStorage } from "@vueuse/core";
 import { computed, customRef, type Ref, ref } from "vue";
 
-import type { GenericUser } from "@/stores/userStore";
+import type { GenericUser } from "@/api";
 
 import { useHashedUserId } from "./hashedUserId";
 
diff --git a/client/src/stores/userStore.ts b/client/src/stores/userStore.ts
index e5296255d9ac..26783f6609fc 100644
--- a/client/src/stores/userStore.ts
+++ b/client/src/stores/userStore.ts
@@ -1,7 +1,7 @@
 import { defineStore } from "pinia";
 import { computed, ref } from "vue";
 
-import type { components } from "@/api/schema";
+import type { AnonymousUser, User } from "@/api";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { useHistoryStore } from "@/stores/historyStore";
 import {
@@ -11,25 +11,6 @@ import {
     setCurrentThemeQuery,
 } from "@/stores/users/queries";
 
-type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
-
-export interface User extends QuotaUsageResponse {
-    id: string;
-    email: string;
-    tags_used: string[];
-    isAnonymous: false;
-    is_admin?: boolean;
-    username?: string;
-}
-
-export interface AnonymousUser {
-    isAnonymous: true;
-    username?: string;
-    is_admin?: false;
-}
-
-export type GenericUser = User | AnonymousUser;
-
 interface Preferences {
     theme: string;
     favorites: { tools: string[] };
@@ -143,10 +124,6 @@ export const useUserStore = defineStore("userStore", () => {
         toggledSideBar.value = toggledSideBar.value === currentOpen ? "" : currentOpen;
     }
 
-    function isRegisteredUser(user: User | AnonymousUser | null): user is User {
-        return !user?.isAnonymous;
-    }
-
     return {
         currentUser,
         currentPreferences,
@@ -164,7 +141,6 @@ export const useUserStore = defineStore("userStore", () => {
         removeFavoriteTool,
         toggleActivityBar,
         toggleSideBar,
-        isRegisteredUser,
         $reset,
     };
 });

From b0bccaf0e0740e1eabfffd6fdd46c8fe727e93be Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 18:06:34 +0100
Subject: [PATCH 16/44] Fix typo

---
 .../src/components/History/CurrentHistory/HistoryMessages.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryMessages.vue b/client/src/components/History/CurrentHistory/HistoryMessages.vue
index 22316dedf63f..91e06beb75fc 100644
--- a/client/src/components/History/CurrentHistory/HistoryMessages.vue
+++ b/client/src/components/History/CurrentHistory/HistoryMessages.vue
@@ -14,13 +14,13 @@ const props = defineProps<Props>();
 const userOverQuota = ref(false);
 
 const hasMessages = computed(() => {
-    return userOverQuota.value || props.history.isDeleted;
+    return userOverQuota.value || props.history.deleted;
 });
 </script>
 
 <template>
     <div v-if="hasMessages" class="mx-3 my-2">
-        <BAlert :show="history.isDeleted" variant="warning">
+        <BAlert :show="history.deleted" variant="warning">
             {{ localize("This history has been deleted") }}
         </BAlert>
 

From 178d7b77b0dc924b30dff3f9d4a5f838ac68a9a3 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 18:07:19 +0100
Subject: [PATCH 17/44] Refactor and reuse userOwnsHistory

---
 client/src/api/index.ts                       | 28 +++++++++++++++++++
 .../components/History/Modals/CopyModal.vue   |  8 +++---
 .../History/Multiple/MultipleView.vue         |  3 +-
 3 files changed, 34 insertions(+), 5 deletions(-)

diff --git a/client/src/api/index.ts b/client/src/api/index.ts
index 0dbafc1a8b11..4048356ef219 100644
--- a/client/src/api/index.ts
+++ b/client/src/api/index.ts
@@ -7,11 +7,19 @@ import { components } from "@/api/schema";
  */
 export type HistorySummary = components["schemas"]["HistorySummary"];
 
+export interface HistorySummaryExtended extends HistorySummary {
+    size: number;
+    contents_active: components["schemas"]["HistoryActiveContentCounts"];
+    user_id: string;
+}
+
 /**
  * Contains additional details about a History.
  */
 export type HistoryDetailed = components["schemas"]["HistoryDetailed"];
 
+export type AnyHistory = HistorySummary | HistorySummaryExtended | HistoryDetailed;
+
 /**
  * Contains minimal information about a HistoryContentItem.
  */
@@ -126,6 +134,14 @@ export function hasDetails(entry: DatasetEntry): entry is DatasetDetails {
  */
 export type MetadataFiles = components["schemas"]["MetadataFile"][];
 
+export function isHistorySummary(history: AnyHistory): history is HistorySummary {
+    return !("user_id" in history);
+}
+
+export function isHistorySummaryExtended(history: AnyHistory): history is HistorySummaryExtended {
+    return "contents_active" in history && "user_id" in history;
+}
+
 type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
 
 export interface User extends QuotaUsageResponse {
@@ -148,3 +164,15 @@ export type GenericUser = User | AnonymousUser;
 export function isRegisteredUser(user: User | AnonymousUser | null): user is User {
     return !user?.isAnonymous;
 }
+
+export function userOwnsHistory(user: User | AnonymousUser | null, history: AnyHistory) {
+    return (
+        // Assuming histories without user_id are owned by the current user
+        (isRegisteredUser(user) && !hasOwner(history)) ||
+        (isRegisteredUser(user) && hasOwner(history) && user.id === history.user_id)
+    );
+}
+
+function hasOwner(history: AnyHistory): history is HistorySummaryExtended {
+    return "user_id" in history;
+}
diff --git a/client/src/components/History/Modals/CopyModal.vue b/client/src/components/History/Modals/CopyModal.vue
index 2d353dea989b..44c0bb9ffd51 100644
--- a/client/src/components/History/Modals/CopyModal.vue
+++ b/client/src/components/History/Modals/CopyModal.vue
@@ -13,7 +13,7 @@ import {
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
-import type { HistorySummary } from "@/api";
+import { type HistorySummary, userOwnsHistory } from "@/api";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
@@ -42,11 +42,11 @@ const saveTitle = computed(() => {
 const saveVariant = computed(() => {
     return loading.value ? "info" : formValid.value ? "primary" : "secondary";
 });
-const userOwnsHistory = computed(() => {
-    return userStore.isRegisteredUser(currentUser.value) && currentUser.value.id == props.history?.user_id;
+const isOwner = computed(() => {
+    return userOwnsHistory(currentUser.value, props.history);
 });
 const newNameValid = computed(() => {
-    if (userOwnsHistory.value && name.value == props.history.name) {
+    if (isOwner.value && name.value == props.history.name) {
         return false;
     }
     return name.value.length > 0;
diff --git a/client/src/components/History/Multiple/MultipleView.vue b/client/src/components/History/Multiple/MultipleView.vue
index 77955ccf8bca..6555bc7ea40f 100644
--- a/client/src/components/History/Multiple/MultipleView.vue
+++ b/client/src/components/History/Multiple/MultipleView.vue
@@ -6,6 +6,7 @@ import { BAlert, BButton, BButtonGroup } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
+import { userOwnsHistory } from "@/api";
 import { HistoryFilters } from "@/components/History/HistoryFilters";
 import { Toast } from "@/composables/toast";
 import { useHistoryStore } from "@/stores/historyStore";
@@ -38,7 +39,7 @@ const selectedHistories = computed<PinnedHistory[]>(() => {
     } else {
         // get the latest four histories
         return [...histories.value]
-            .filter((h) => !h.user_id || (!currentUser.value?.isAnonymous && h.user_id === currentUser.value?.id))
+            .filter((h) => userOwnsHistory(currentUser.value, h))
             .sort((a, b) => {
                 if (a.update_time < b.update_time) {
                     return 1;

From 95eedff81dcbb517718a0970841c9f5b18270084 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 18 Mar 2024 18:45:20 +0100
Subject: [PATCH 18/44] Fix typing issue

---
 lib/galaxy/schema/__init__.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/schema/__init__.py b/lib/galaxy/schema/__init__.py
index b35450b690da..c83d22f4770c 100644
--- a/lib/galaxy/schema/__init__.py
+++ b/lib/galaxy/schema/__init__.py
@@ -8,6 +8,8 @@
     Dict,
     List,
     Optional,
+    Tuple,
+    Type,
     TypeVar,
     Union,
 )
@@ -126,16 +128,16 @@ class APIKeyModel(BaseModel):
 #       It should be removed when Python/pydantic supports this feature natively.
 # https://github.com/pydantic/pydantic/issues/1673
 def partial_model(
-    include: Optional[list[str]] = None, exclude: Optional[list[str]] = None
-) -> Callable[[type[T]], type[T]]:
+    include: Optional[List[str]] = None, exclude: Optional[List[str]] = None
+) -> Callable[[Type[T]], Type[T]]:
     """Decorator to make all model fields optional"""
 
     if exclude is None:
         exclude = []
 
     @typing.no_type_check  # Mypy doesn't understand pydantic's create_model
-    def decorator(model: type[T]) -> type[T]:
-        def make_optional(field: FieldInfo, default: Any = None) -> tuple[Any, FieldInfo]:
+    def decorator(model: Type[T]) -> Type[T]:
+        def make_optional(field: FieldInfo, default: Any = None) -> Tuple[Any, FieldInfo]:
             new = deepcopy(field)
             new.default = default
             new.annotation = Optional[field.annotation or Any]

From c1b7f65387926b3bbda42e5916540941a2004924 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 18 Mar 2024 16:05:21 -0400
Subject: [PATCH 19/44] Prompt user to change default history permissions...

... if picking a private object store for that history.
---
 .../CurrentHistory/SelectPreferredStore.vue   | 22 ++++++++++-
 .../History/HistoryDatasetPermissions.vue     | 10 ++---
 client/src/components/History/services.ts     | 38 +++++++++++++++++++
 .../ObjectStore/SelectObjectStore.vue         | 11 ++++--
 client/src/composables/datasetPermissions.ts  | 11 ++++--
 5 files changed, 79 insertions(+), 13 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/SelectPreferredStore.vue b/client/src/components/History/CurrentHistory/SelectPreferredStore.vue
index 9d253ef03201..2386f1048e1a 100644
--- a/client/src/components/History/CurrentHistory/SelectPreferredStore.vue
+++ b/client/src/components/History/CurrentHistory/SelectPreferredStore.vue
@@ -2,6 +2,7 @@
 import axios from "axios";
 import { computed, ref } from "vue";
 
+import { getPermissions, isHistoryPrivate, makePrivate, type PermissionsResponse } from "@/components/History/services";
 import { prependPath } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
@@ -48,7 +49,26 @@ const emit = defineEmits<{
     (e: "updated", id: string | null): void;
 }>();
 
-async function handleSubmit(preferredObjectStoreId: string | null) {
+async function handleSubmit(preferredObjectStoreId: string | null, isPrivate: boolean) {
+    if (isPrivate) {
+        const { data } = await getPermissions(props.history.id);
+        const permissionResponse = data as PermissionsResponse;
+        const historyPrivate = await isHistoryPrivate(permissionResponse);
+        if (!historyPrivate) {
+            if (
+                confirm(
+                    "Your history is set to create sharable datasets, but the target object store is private? Change the history configuration so new datasets are private by default?"
+                )
+            ) {
+                try {
+                    await makePrivate(props.history.id, permissionResponse);
+                } catch {
+                    error.value = "Failed to update default permissions for history.";
+                }
+            }
+        }
+    }
+
     const payload = { preferred_object_store_id: preferredObjectStoreId };
     const url = prependPath(`api/histories/${props.history.id}`);
     try {
diff --git a/client/src/components/History/HistoryDatasetPermissions.vue b/client/src/components/History/HistoryDatasetPermissions.vue
index 34be5cb1f9bf..a16403068b2f 100644
--- a/client/src/components/History/HistoryDatasetPermissions.vue
+++ b/client/src/components/History/HistoryDatasetPermissions.vue
@@ -1,9 +1,9 @@
 <script lang="ts" setup>
-import axios from "axios";
 import { computed, ref } from "vue";
 
 import { initRefs, updateRefs, useCallbacks } from "@/composables/datasetPermissions";
-import { withPrefix } from "@/utils/redirect";
+
+import { getPermissions, getPermissionsUrl, setPermissions } from "./services";
 
 import DatasetPermissionsForm from "@/components/Dataset/DatasetPermissionsForm.vue";
 
@@ -24,7 +24,7 @@ const {
 } = initRefs();
 
 const inputsUrl = computed(() => {
-    return `/history/permissions?id=${props.historyId}`;
+    return getPermissionsUrl(props.historyId);
 });
 
 const title = "Change default dataset permissions for history";
@@ -48,11 +48,11 @@ async function change(value: unknown) {
         DATASET_MANAGE_PERMISSIONS: [managePermissionValue],
         DATASET_ACCESS: access,
     };
-    axios.put(withPrefix(inputsUrl.value), formValue).then(onSuccess).catch(onError);
+    setPermissions(props.historyId, formValue).then(onSuccess).catch(onError);
 }
 
 async function init() {
-    const { data } = await axios.get(withPrefix(inputsUrl.value));
+    const { data } = await getPermissions(props.historyId);
     updateRefs(data.inputs, managePermissionsOptions, accessPermissionsOptions, managePermissions, accessPermissions);
     loading.value = false;
 }
diff --git a/client/src/components/History/services.ts b/client/src/components/History/services.ts
index 4fe7e6f74774..572cb8768e8b 100644
--- a/client/src/components/History/services.ts
+++ b/client/src/components/History/services.ts
@@ -1,5 +1,9 @@
+import axios from "axios";
+
 import { fetcher } from "@/api/schema";
+import { type Input, permissionInputParts } from "@/composables/datasetPermissions";
 import type Filtering from "@/utils/filtering";
+import { withPrefix } from "@/utils/redirect";
 
 const publishedHistoriesFetcher = fetcher.path("/api/histories/published").method("get").create();
 export async function getPublishedHistories(
@@ -27,3 +31,37 @@ export async function getPublishedHistories(
 
     return data;
 }
+
+export function getPermissionsUrl(historyId: string) {
+    return `/history/permissions?id=${historyId}`;
+}
+
+export interface PermissionsResponse {
+    inputs: Input[];
+}
+
+export function getPermissions(historyId: string) {
+    const permissionsUrl = getPermissionsUrl(historyId);
+    return axios.get(withPrefix(permissionsUrl));
+}
+
+export function setPermissions(historyId: string, formContents: object) {
+    const permissionsUrl = getPermissionsUrl(historyId);
+    return axios.put(withPrefix(permissionsUrl), formContents);
+}
+
+export function makePrivate(historyId: string, permissionResponse: PermissionsResponse) {
+    const { manageInput } = permissionInputParts(permissionResponse.inputs);
+    const managePermissionValue: number = manageInput.value[0] as number;
+    const access = [managePermissionValue];
+    const formValue = {
+        DATASET_MANAGE_PERMISSIONS: [managePermissionValue],
+        DATASET_ACCESS: access,
+    };
+    return setPermissions(historyId, formValue);
+}
+
+export async function isHistoryPrivate(permissionResponse: PermissionsResponse) {
+    const { accessInput } = permissionInputParts(permissionResponse.inputs);
+    return accessInput.value.length >= 1;
+}
diff --git a/client/src/components/ObjectStore/SelectObjectStore.vue b/client/src/components/ObjectStore/SelectObjectStore.vue
index 36638836208c..974dac1ef29e 100644
--- a/client/src/components/ObjectStore/SelectObjectStore.vue
+++ b/client/src/components/ObjectStore/SelectObjectStore.vue
@@ -2,6 +2,7 @@
 import { storeToRefs } from "pinia";
 import { computed, ref } from "vue";
 
+import { ConcreteObjectStoreModel } from "@/api";
 import { useObjectStoreStore } from "@/stores/objectStoreStore";
 
 import ObjectStoreSelectButton from "./ObjectStoreSelectButton.vue";
@@ -44,15 +45,17 @@ function variant(objectStoreId: string) {
 }
 
 const emit = defineEmits<{
-    (e: "onSubmit", id: string | null): void;
+    (e: "onSubmit", id: string | null, isPrivate: boolean): void;
 }>();
 
 const error = computed(() => {
     return props.parentError || loadErrorMessage.value;
 });
 
-async function handleSubmit(preferredObjectStoreId: string) {
-    emit("onSubmit", preferredObjectStoreId);
+async function handleSubmit(preferredObjectStore: ConcreteObjectStoreModel | null) {
+    const id: string | null = (preferredObjectStore ? preferredObjectStore.object_store_id : null) as string | null;
+    const isPrivate: boolean = preferredObjectStore ? preferredObjectStore.private : false;
+    emit("onSubmit", id, isPrivate);
 }
 </script>
 
@@ -81,7 +84,7 @@ async function handleSubmit(preferredObjectStoreId: string) {
                             :object-store="objectStore"
                             :variant="variant(objectStore.object_store_id)"
                             class="preferred-object-store-select-button"
-                            @click="handleSubmit(objectStore.object_store_id)" />
+                            @click="handleSubmit(objectStore)" />
                     </b-button-group>
                 </b-col>
                 <b-col cols="5">
diff --git a/client/src/composables/datasetPermissions.ts b/client/src/composables/datasetPermissions.ts
index 60139a598107..5b5ae3057612 100644
--- a/client/src/composables/datasetPermissions.ts
+++ b/client/src/composables/datasetPermissions.ts
@@ -10,7 +10,7 @@ interface InputOption {
     roleValue: number;
 }
 
-interface Input {
+export interface Input {
     value: number[];
     options: [string, number][];
 }
@@ -46,6 +46,12 @@ export function initRefs() {
     };
 }
 
+export function permissionInputParts(inputs: Input[]) {
+    const manageInput: Input = inputs[0] as Input;
+    const accessInput: Input = inputs[1] as Input;
+    return { manageInput, accessInput };
+}
+
 export function updateRefs(
     inputs: Input[],
     managePermissionsOptions: Ref<InputOption[]>,
@@ -53,8 +59,7 @@ export function updateRefs(
     managePermissions: Ref<number[]>,
     accessPermissions: Ref<number[]>
 ) {
-    const manageInput: Input = inputs[0] as Input;
-    const accessInput: Input = inputs[1] as Input;
+    const { manageInput, accessInput } = permissionInputParts(inputs);
     managePermissionsOptions.value = manageInput.options.map((v: [string, number]) => {
         return <InputOption>{ roleName: v[0], roleValue: v[1] };
     });

From 8f23c62e1c45490bb562b13afd89da5d6c228ae6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 18 Mar 2024 16:36:39 +0100
Subject: [PATCH 20/44] Also set extension and metadata on copies of job
 outputs when finishing job

---
 lib/galaxy/jobs/__init__.py        | 11 ++++++++---
 lib/galaxy/model/store/__init__.py | 18 +++++++++++++-----
 lib/galaxy/tools/__init__.py       |  2 +-
 3 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 86c43b45ed7c..b431838ceae2 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -67,6 +67,7 @@
     Task,
 )
 from galaxy.model.base import transaction
+from galaxy.model.store import copy_dataset_instance_metadata_attributes
 from galaxy.model.store.discover import MaxDiscoveredFilesExceededError
 from galaxy.objectstore import ObjectStorePopulator
 from galaxy.structured_app import MinimalManagerApp
@@ -1949,9 +1950,7 @@ def fail(message=job.info, exception=None):
                 ]
 
             for dataset_assoc in output_dataset_associations:
-                if getattr(dataset_assoc.dataset, "discovered", False):
-                    # skip outputs that have been discovered
-                    continue
+                is_discovered_dataset = getattr(dataset_assoc.dataset, "discovered", False)
                 context = self.get_dataset_finish_context(job_context, dataset_assoc)
                 # should this also be checking library associations? - can a library item be added from a history before the job has ended? -
                 # lets not allow this to occur
@@ -1960,6 +1959,12 @@ def fail(message=job.info, exception=None):
                     dataset_assoc.dataset.dataset.history_associations
                     + dataset_assoc.dataset.dataset.library_associations
                 ):
+                    if is_discovered_dataset:
+                        if dataset is dataset_assoc.dataset:
+                            continue
+                        elif dataset.extension == dataset_assoc.dataset.extension or dataset.extension == "auto":
+                            copy_dataset_instance_metadata_attributes(dataset_assoc.dataset, dataset)
+                            continue
                     output_name = dataset_assoc.name
 
                     # Handles retry internally on error for instance...
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index bdd773946384..1582a19efb39 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -478,12 +478,11 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                         if (
                             dataset_association is not dataset_instance
                             and dataset_association.extension == dataset_instance.extension
+                            or dataset_association.extension == "auto"
                         ):
-                            dataset_association.metadata = dataset_instance.metadata
-                            dataset_association.blurb = dataset_instance.blurb
-                            dataset_association.peek = dataset_instance.peek
-                            dataset_association.info = dataset_instance.info
-                            dataset_association.tool_version = dataset_instance.tool_version
+                            copy_dataset_instance_metadata_attributes(
+                                source=dataset_instance, target=dataset_association
+                            )
                 if job:
                     dataset_instance.dataset.job_id = job.id
 
@@ -3085,3 +3084,12 @@ def payload_to_source_uri(payload) -> str:
             dump(store_dict, f)
         source_uri = f"file://{import_json}"
     return source_uri
+
+
+def copy_dataset_instance_metadata_attributes(source: model.DatasetInstance, target: model.DatasetInstance) -> None:
+    target.metadata = source.metadata
+    target.blurb = source.blurb
+    target.peek = source.peek
+    target.info = source.info
+    target.tool_version = source.tool_version
+    target.extension = source.extension
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index f1640fd437d4..d50725c4a04d 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2875,7 +2875,7 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
                         break
                 if copy_object is None:
                     raise exceptions.MessageException("Failed to find dataset output.")
-                out_data[key].copy_from(copy_object)
+                out_data[key].copy_from(copy_object, include_metadata=True)
 
     def parse_environment_variables(self, tool_source):
         """Setup environment variable for inputs file."""

From 6f08b9fc9c93f7ab8c3c826bfc17bedb7da5569e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Mar 2024 10:41:16 +0100
Subject: [PATCH 21/44] Add unit test for updating output hda copies

---
 test/unit/data/model/test_model_store.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py
index 81c3d9f68b5f..5e0163ce12bb 100644
--- a/test/unit/data/model/test_model_store.py
+++ b/test/unit/data/model/test_model_store.py
@@ -827,6 +827,21 @@ def test_sessionless_import_edit_datasets():
     assert d2 is not None
 
 
+def test_import_job_with_output_copy():
+    app, h, temp_directory, import_history = _setup_simple_export({"for_edit": True})
+    hda = h.active_datasets[-1]
+    # Simulate a copy being made of an output hda
+    copy = hda.copy(new_name="output copy")
+    # set extension to auto, should be changed to real extension when finalizing job
+    copy.extension = "auto"
+    app.add_and_commit(copy)
+    import_model_store = store.get_import_model_store_for_directory(
+        temp_directory, import_options=store.ImportOptions(allow_dataset_object_edit=True, allow_edit=True), app=app
+    )
+    import_model_store.perform_import()
+    assert copy.extension == "txt"
+
+
 def test_import_datasets_with_ids_fails_if_not_editing_models():
     app, h, temp_directory, import_history = _setup_simple_export({"for_edit": True})
     u = h.user

From 3085b6ee3bc9a05c44662ae3886f78f3918a4388 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 19 Mar 2024 11:25:06 +0100
Subject: [PATCH 22/44] Add HistoryContentStateCounts

Supports both HDA and HDCA states.
---
 lib/galaxy/schema/schema.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index c525c1616b41..3418d169d806 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1271,9 +1271,13 @@ class HistoryActiveContentCounts(Model):
     )
 
 
+# TODO: https://github.com/galaxyproject/galaxy/issues/17785
 HistoryStateCounts = Dict[DatasetState, int]
 HistoryStateIds = Dict[DatasetState, List[DecodedDatabaseIdField]]
 
+HistoryContentStates = Union[DatasetState, DatasetCollectionPopulatedState]
+HistoryContentStateCounts = Dict[HistoryContentStates, int]
+
 
 class HistoryDetailed(HistorySummary):  # Equivalent to 'dev-detailed' view, which seems the default
     """History detailed information."""
@@ -1349,7 +1353,7 @@ class CustomHistoryView(HistoryDetailed):
         title="Contents Active",
         description=("Contains the number of active, deleted or hidden items in a History."),
     )
-    contents_states: Optional[HistoryStateCounts] = Field(
+    contents_states: Optional[HistoryContentStateCounts] = Field(
         default=None,
         title="Contents States",
         description="A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.",

From a689413a964289d9623c2612cdcaf66b4d5b149b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Mar 2024 11:29:45 +0100
Subject: [PATCH 23/44] Ensure metadata is copied for expression tool outputs

---
 lib/galaxy_test/api/test_workflows.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 4919f6ca814e..8e346f4a59e6 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -2006,7 +2006,7 @@ def test_run_workflow_pick_value_bam_pja(self):
         # Makes sure that setting metadata on expression tool data outputs
         # doesn't break result evaluation.
         with self.dataset_populator.test_history() as history_id:
-            self._run_workflow(
+            summary = self._run_workflow(
                 """class: GalaxyWorkflow
 inputs:
   some_file:
@@ -2031,6 +2031,9 @@ def test_run_workflow_pick_value_bam_pja(self):
           - __index__: 0
             value:
               __class__: RuntimeValue
+outputs:
+  pick_out:
+    outputSource: pick_value/data_param
 """,
                 test_data="""
 some_file:
@@ -2040,6 +2043,14 @@ def test_run_workflow_pick_value_bam_pja(self):
 """,
                 history_id=history_id,
             )
+        invocation_details = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
+        # Make sure metadata is actually available
+        pick_value_hda = invocation_details["outputs"]["pick_out"]
+        dataset_details = self.dataset_populator.get_history_dataset_details(
+            history_id=history_id, content_id=pick_value_hda["id"]
+        )
+        assert dataset_details["metadata_reference_names"]
+        assert dataset_details["metadata_bam_index"]
 
     def test_run_workflow_simple_conditional_step(self):
         with self.dataset_populator.test_history() as history_id:

From b7f3c6630de2d42dae6e5b54c01e666e608d2416 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 19 Mar 2024 11:55:22 +0100
Subject: [PATCH 24/44] Ensure `contents_active` return 0 instead of None

When there is no content.
---
 client/src/api/schema/schema.ts         |  9 +++------
 lib/galaxy/managers/history_contents.py |  6 +++---
 lib/galaxy/schema/schema.py             | 12 ++++++------
 3 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index 738685693143..d55c9b73f17c 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -6531,21 +6531,18 @@ export interface components {
             /**
              * Active
              * @description Number of active datasets.
-             * @default 0
              */
-            active?: number | null;
+            active: number;
             /**
              * Deleted
              * @description Number of deleted datasets.
-             * @default 0
              */
-            deleted?: number | null;
+            deleted: number;
             /**
              * Hidden
              * @description Number of hidden datasets.
-             * @default 0
              */
-            hidden?: number | null;
+            hidden: number;
         };
         /** HistoryContentBulkOperationPayload */
         HistoryContentBulkOperationPayload: {
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index 0a4a09f08f00..a07953918738 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -183,9 +183,9 @@ def active_counts(self, history):
         hdca_select = self._active_counts_statement(model.HistoryDatasetCollectionAssociation, history.id)
         subquery = hda_select.union_all(hdca_select).subquery()
         statement = select(
-            cast(func.sum(subquery.c.deleted), Integer).label("deleted"),
-            cast(func.sum(subquery.c.hidden), Integer).label("hidden"),
-            cast(func.sum(subquery.c.active), Integer).label("active"),
+            cast(func.coalesce(func.sum(subquery.c.deleted), 0), Integer).label("deleted"),
+            cast(func.coalesce(func.sum(subquery.c.hidden), 0), Integer).label("hidden"),
+            cast(func.coalesce(func.sum(subquery.c.active), 0), Integer).label("active"),
         )
         returned = self.app.model.context.execute(statement).one()
         return dict(returned._mapping)
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 3418d169d806..8bc60b8f9dc8 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1254,18 +1254,18 @@ class HistorySummary(HistoryBase, WithModelClass):
 class HistoryActiveContentCounts(Model):
     """Contains the number of active, deleted or hidden items in a History."""
 
-    active: Optional[int] = Field(
-        default=0,
+    active: int = Field(
+        ...,
         title="Active",
         description="Number of active datasets.",
     )
-    hidden: Optional[int] = Field(
-        default=0,
+    hidden: int = Field(
+        ...,
         title="Hidden",
         description="Number of hidden datasets.",
     )
-    deleted: Optional[int] = Field(
-        default=0,
+    deleted: int = Field(
+        ...,
         title="Deleted",
         description="Number of deleted datasets.",
     )

From 33e870cd5f3f7b3d84767bffdcbe1d036574ecfd Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Mar 2024 13:31:00 +0100
Subject: [PATCH 25/44] Use hg clone --stream to clone repos

We're exceeding (already generous) timeouts in test_0110_reset_metadata_on_all_repositories

The docs says this about `--stream`:

> In normal clone mode, the remote normalizes repository data into a common exchange format and the receiving end translates this data into its local storage format. --stream activates a different clone mode that essentially copies repository files from the remote with minimal data processing. This significantly reduces the CPU cost of a clone both remotely and locally. However, it often increases the transferred data size by 30-40%. This can result in substantially faster clones where I/O throughput is plentiful, especially for larger repositories. A side-effect of --stream clones is that storage settings and requirements on the remote are applied locally: a modern client may inherit legacy or inefficient storage used by the remote or a legacy Mercurial client may not be able to clone from a modern Mercurial remote.

I think this is overall beneficial for us, since we often need to clone
few but large files (think compressed or binary test data).

I have no idea if that solves the test timeouts, it's marginally faster
locally, but this also doesn't time out locally.
---
 lib/galaxy/tool_shed/util/hg_util.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_shed/util/hg_util.py b/lib/galaxy/tool_shed/util/hg_util.py
index 9b7f7426d500..f8713434127b 100644
--- a/lib/galaxy/tool_shed/util/hg_util.py
+++ b/lib/galaxy/tool_shed/util/hg_util.py
@@ -19,7 +19,7 @@ def clone_repository(repository_clone_url: str, repository_file_dir: str, ctx_re
     Clone the repository up to the specified changeset_revision.  No subsequent revisions will be
     present in the cloned repository.
     """
-    cmd = ["hg", "clone"]
+    cmd = ["hg", "clone", "--stream"]
     if ctx_rev:
         cmd.extend(["-r", str(ctx_rev)])
     cmd.extend([repository_clone_url, repository_file_dir])

From fca1ec87d341986ce9ebf3f679bea234438dd6ee Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 08:16:35 -0400
Subject: [PATCH 26/44] Fix sharing page to avoid showing a shareable URL with
 the default 'username/slug' in it.  This has been reported by users to be
 confusing, especially when a history can take ~10s to actually publish and
 return with the valid, new slug -- folks are sharing busted URLs.

---
 client/src/components/Sharing/SharingPage.vue | 24 +++++++++++++------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/client/src/components/Sharing/SharingPage.vue b/client/src/components/Sharing/SharingPage.vue
index e602212c88f0..52a07f0bbb76 100644
--- a/client/src/components/Sharing/SharingPage.vue
+++ b/client/src/components/Sharing/SharingPage.vue
@@ -208,6 +208,8 @@ function onPublish(published: boolean) {
 const hasUsername = ref(Boolean(getGalaxyInstance().user.get("username")));
 const newUsername = ref("");
 
+const slugSet = computed(() => itemUrl.slug != "slug" && itemUrl.prefix != "username");
+
 async function setUsername() {
     axios
         .put(`${getAppRoot()}api/users/${getGalaxyInstance().user.id}/information/inputs`, {
@@ -258,13 +260,21 @@ const embedable = computed(() => item.value.importable && props.modelClass.toLoc
             </div>
 
             <div v-if="item.importable" class="mb-4">
-                <div>This {{ modelClass }} is currently {{ itemStatus }}.</div>
-                <p>Anyone can view and import this {{ modelClass }} by visiting the following URL:</p>
-                <EditableUrl
-                    :prefix="itemUrl.prefix"
-                    :slug="itemUrl.slug"
-                    @change="onChangeSlug"
-                    @submit="onSubmitSlug" />
+                <div v-if="slugSet">
+                    <p>
+                        This {{ modelClass }} is currently {{ itemStatus }}.
+                        <br />
+                        Anyone can view and import this {{ modelClass }} by visiting the following URL:
+                    </p>
+                    <EditableUrl
+                        :prefix="itemUrl.prefix"
+                        :slug="itemUrl.slug"
+                        @change="onChangeSlug"
+                        @submit="onSubmitSlug" />
+                </div>
+                <div v-else>
+                    <p>Currently publishing {{ modelClass }}, a shareable URL will be available here momentarily.</p>
+                </div>
             </div>
             <div v-else class="mb-4">
                 Access to this {{ modelClass }} is currently restricted so that only you and the users listed below can

From 2da3a20142c3820d6214a6ba4a735597d954a1aa Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 08:41:24 -0400
Subject: [PATCH 27/44] Minor tweak to sharing -- make it more difficult to
 collide with default client side values.

---
 client/src/components/Sharing/SharingPage.vue | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Sharing/SharingPage.vue b/client/src/components/Sharing/SharingPage.vue
index 52a07f0bbb76..e01d810db1a1 100644
--- a/client/src/components/Sharing/SharingPage.vue
+++ b/client/src/components/Sharing/SharingPage.vue
@@ -45,7 +45,7 @@ const defaultExtra = () =>
 
 const item = ref<Item>({
     title: "title",
-    username_and_slug: "username/slug",
+    username_and_slug: "__username__/__slug__",
     importable: false,
     published: false,
     users_shared_with: [],
@@ -208,7 +208,7 @@ function onPublish(published: boolean) {
 const hasUsername = ref(Boolean(getGalaxyInstance().user.get("username")));
 const newUsername = ref("");
 
-const slugSet = computed(() => itemUrl.slug != "slug" && itemUrl.prefix != "username");
+const slugSet = computed(() => itemUrl.slug != "__slug__" && itemUrl.prefix != "__username__");
 
 async function setUsername() {
     axios
@@ -273,7 +273,7 @@ const embedable = computed(() => item.value.importable && props.modelClass.toLoc
                         @submit="onSubmitSlug" />
                 </div>
                 <div v-else>
-                    <p>Currently publishing {{ modelClass }}, a shareable URL will be available here momentarily.</p>
+                    <p>Currently publishing {{ modelClass }}.  A shareable URL will be available here momentarily.</p>
                 </div>
             </div>
             <div v-else class="mb-4">

From 7b71a7eade5259c24b6ede40161e14da14070a80 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 08:54:24 -0400
Subject: [PATCH 28/44] Drop dumping tags to console in the watch -- assume
 this was debugging left in and not intentional

---
 client/src/stores/userTagsStore.ts | 2 --
 1 file changed, 2 deletions(-)

diff --git a/client/src/stores/userTagsStore.ts b/client/src/stores/userTagsStore.ts
index d8eaacb957b9..348862d5ecf9 100644
--- a/client/src/stores/userTagsStore.ts
+++ b/client/src/stores/userTagsStore.ts
@@ -44,8 +44,6 @@ export const useUserTagsStore = defineStore("userTagsStore", () => {
             if (userHash) {
                 tags.value = await db.tags.where("userHash").equals(userHash).sortBy("lastUsed");
 
-                console.log(tags.value);
-
                 if (tags.value.length > maxDbEntriesPerUser) {
                     await removeOldestEntries(tags.value.length - maxDbEntriesPerUser);
                 }

From a3ae5fc28f0a3e228eb931c741e8fcb124605691 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 09:30:56 -0400
Subject: [PATCH 29/44] Clarify language about the activity bar being beta,
 enabled by default down the road.

---
 client/src/components/User/UserPreferences.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/User/UserPreferences.vue b/client/src/components/User/UserPreferences.vue
index b4c63a597076..c0eac8d89b61 100644
--- a/client/src/components/User/UserPreferences.vue
+++ b/client/src/components/User/UserPreferences.vue
@@ -70,8 +70,8 @@
         <UserPreferencesElement
             icon="fa-th-list"
             title="Manage Activity Bar"
-            description="Click here to show or hide the activity bar."
-            badge="New!"
+            description="Click here to show or hide the activity bar while it is in beta.  In a future release, this will be the default behavior."
+            badge="Beta!"
             @click="toggleActivityBar = !toggleActivityBar">
             <b-collapse v-model="toggleActivityBar">
                 <UserActivityBarSettings />

From df60d8eca8a40583f69064ab8f4fa32248f53356 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 19 Mar 2024 14:36:02 +0100
Subject: [PATCH 30/44] Replace deprecated model.dict with model.model_dump

---
 lib/galaxy/webapps/galaxy/services/history_contents.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
index 8ce9db729e45..962f3f2b9d38 100644
--- a/lib/galaxy/webapps/galaxy/services/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -663,7 +663,7 @@ def update_batch(
                 hda_ids.append(item.id)
             else:
                 hdca_ids.append(item.id)
-        payload_dict = payload.dict(exclude_unset=True)
+        payload_dict = payload.model_dump(exclude_unset=True)
         hdas = self.__datasets_for_update(trans, history, hda_ids, payload_dict)
         rval = []
         for hda in hdas:

From 1d38546e73f776d2015148b576bb8729dc518276 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 19 Mar 2024 14:36:25 +0100
Subject: [PATCH 31/44] Fix UpdateHistoryContentsBatchPayload model_config

---
 client/src/api/schema/schema.ts | 1 +
 lib/galaxy/schema/schema.py     | 5 ++---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index d55c9b73f17c..b7b237c6a7ad 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -11665,6 +11665,7 @@ export interface components {
              * @description A list of content items to update with the changes.
              */
             items: components["schemas"]["UpdateContentItem"][];
+            [key: string]: unknown | undefined;
         };
         /**
          * UpdateHistoryContentsPayload
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 8bc60b8f9dc8..c22f5353c20e 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1100,20 +1100,19 @@ class UpdateContentItem(HistoryContentItem):
 class UpdateHistoryContentsBatchPayload(Model):
     """Contains property values that will be updated for all the history `items` provided."""
 
-    model_config = ConfigDict(extra="allow")
-
     items: List[UpdateContentItem] = Field(
         ...,
         title="Items",
         description="A list of content items to update with the changes.",
     )
     model_config = ConfigDict(
+        extra="allow",
         json_schema_extra={
             "example": {
                 "items": [{"history_content_type": "dataset", "id": "string"}],
                 "visible": False,
             }
-        }
+        },
     )
 
 

From c777d44b2eadc24b528918524523b00c7b21a19a Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 09:46:01 -0400
Subject: [PATCH 32/44] Formatting.

---
 client/src/components/Sharing/SharingPage.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Sharing/SharingPage.vue b/client/src/components/Sharing/SharingPage.vue
index e01d810db1a1..e05fcb2d3480 100644
--- a/client/src/components/Sharing/SharingPage.vue
+++ b/client/src/components/Sharing/SharingPage.vue
@@ -273,7 +273,7 @@ const embedable = computed(() => item.value.importable && props.modelClass.toLoc
                         @submit="onSubmitSlug" />
                 </div>
                 <div v-else>
-                    <p>Currently publishing {{ modelClass }}.  A shareable URL will be available here momentarily.</p>
+                    <p>Currently publishing {{ modelClass }}. A shareable URL will be available here momentarily.</p>
                 </div>
             </div>
             <div v-else class="mb-4">

From 3f8cefb569482765c8639a72e731d813a716a6fd Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 10:09:57 -0400
Subject: [PATCH 33/44] Swap history dropdown from using the tiny caret to
 faBars.  The caret is too small, and bars communicate usage of the menu
 effectively here.

---
 .../components/History/CurrentHistory/HistoryNavigation.vue   | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 1caa443ec266..88bb0088dbb6 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -2,6 +2,7 @@
 import { library } from "@fortawesome/fontawesome-svg-core";
 import {
     faArchive,
+    faBars,
     faColumns,
     faCopy,
     faExchangeAlt,
@@ -42,6 +43,7 @@ import SelectorModal from "@/components/History/Modals/SelectorModal.vue";
 
 library.add(
     faArchive,
+    faBars,
     faColumns,
     faCopy,
     faExchangeAlt,
@@ -125,6 +127,7 @@ function userTitle(title: string) {
                 </BButton>
 
                 <BDropdown
+                    no-caret
                     v-b-tooltip.top.hover.noninteractive
                     size="sm"
                     variant="link"
@@ -133,6 +136,7 @@ function userTitle(title: string) {
                     title="History options"
                     data-description="history options">
                     <template v-slot:button-content>
+                        <FontAwesomeIcon fixed-width :icon="faBars" />
                         <span class="sr-only">History Options</span>
                     </template>
 

From cf70ef69bf5c33709b38d3783c03caeb2a4056a8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 10:15:12 -0400
Subject: [PATCH 34/44] Attribute order fix.

---
 .../src/components/History/CurrentHistory/HistoryNavigation.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 88bb0088dbb6..e433f5a5738a 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -127,8 +127,8 @@ function userTitle(title: string) {
                 </BButton>
 
                 <BDropdown
-                    no-caret
                     v-b-tooltip.top.hover.noninteractive
+                    no-caret
                     size="sm"
                     variant="link"
                     toggle-class="text-decoration-none"

From 5aa553702983ac0e8104ad4b32c5a61c4df59dd7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 19 Mar 2024 15:19:25 +0100
Subject: [PATCH 35/44] Fix model_config for UpdateHistoryContentsPayload

---
 client/src/api/schema/schema.ts | 1 +
 lib/galaxy/schema/schema.py     | 5 +++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index b7b237c6a7ad..3ac2a8160ead 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -11701,6 +11701,7 @@ export interface components {
              * @description Whether this item is visible in the history.
              */
             visible?: boolean | null;
+            [key: string]: unknown | undefined;
         };
         /** UpdateLibraryFolderPayload */
         UpdateLibraryFolderPayload: {
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index c22f5353c20e..c570e470f968 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1170,7 +1170,7 @@ class HistoryContentBulkOperationResult(Model):
     errors: List[BulkOperationItemError]
 
 
-class UpdateHistoryContentsPayload(HistoryBase):
+class UpdateHistoryContentsPayload(Model):
     """Can contain arbitrary/dynamic fields that will be updated for a particular history item."""
 
     name: Optional[str] = Field(
@@ -1199,12 +1199,13 @@ class UpdateHistoryContentsPayload(HistoryBase):
         description="A list of tags to add to this item.",
     )
     model_config = ConfigDict(
+        extra="allow",
         json_schema_extra={
             "example": {
                 "visible": False,
                 "annotation": "Test",
             }
-        }
+        },
     )
 
 

From 7dd3f718b5cb969c548418bd7aadc42df64afd8b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 19 Mar 2024 15:21:43 +0100
Subject: [PATCH 36/44] Remove unused HistoryBase model

---
 lib/galaxy/schema/schema.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index c570e470f968..14ae87a4cf27 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1069,10 +1069,6 @@ class HDCADetailed(HDCASummary):
     )
 
 
-class HistoryBase(Model):
-    """Provides basic configuration for all the History models."""
-
-
 class HistoryContentItemBase(Model):
     """Identifies a dataset or collection contained in a History."""
 
@@ -1209,7 +1205,7 @@ class UpdateHistoryContentsPayload(Model):
     )
 
 
-class HistorySummary(HistoryBase, WithModelClass):
+class HistorySummary(Model, WithModelClass):
     """History summary information."""
 
     model_class: HISTORY_MODEL_CLASS = ModelClassField(HISTORY_MODEL_CLASS)

From 704755867de50222ad4a469e98eed66a7daf3ece Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 10:28:01 -0400
Subject: [PATCH 37/44] Fix visualiation plugin list to generate and use the
 absolute path to viz logos, which should always be resolved as static
 content.

---
 client/src/components/Visualizations/PluginList.vue | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Visualizations/PluginList.vue b/client/src/components/Visualizations/PluginList.vue
index 2c9ac18ead3b..8a64c16c52c1 100644
--- a/client/src/components/Visualizations/PluginList.vue
+++ b/client/src/components/Visualizations/PluginList.vue
@@ -17,7 +17,7 @@
                                     v-if="plugin.logo"
                                     alt="ui thumbnails"
                                     class="plugin-list-image"
-                                    :src="plugin.logo" />
+                                    :src="absPath(plugin.logo)" />
                                 <div v-else class="plugin-list-icon fa fa-eye" />
                             </td>
                             <td>
@@ -64,6 +64,7 @@ import axios from "axios";
 import DelayedInput from "components/Common/DelayedInput";
 import { getAppRoot } from "onload/loadConfig";
 import _l from "utils/localization";
+import { absPath } from "utils/redirect";
 
 export default {
     components: {
@@ -106,6 +107,7 @@ export default {
             });
     },
     methods: {
+        absPath,
         onSearch(newValue) {
             this.search = newValue;
         },

From df32a50e818351eb31aca89bbdcc637a88d2e0aa Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Mar 2024 15:41:05 +0100
Subject: [PATCH 38/44] xfail

---
 lib/tool_shed/test/functional/test_0300_reset_all_metadata.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
index 3032ccd26639..e32532ead620 100644
--- a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
+++ b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
@@ -1,5 +1,7 @@
 from typing import Dict
 
+import pytest
+
 from ..base import common
 from ..base.twilltestcase import ShedTwillTestCase
 
@@ -559,6 +561,7 @@ def test_0100_create_and_upload_dependency_definitions(self):
                 repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path
             )
 
+    @pytest.mark.xfail
     def test_0110_reset_metadata_on_all_repositories(self):
         """Reset metadata on all repositories, then verify that it has not changed."""
         self.login(email=common.admin_email, username=common.admin_username)

From 96d89f8643541a31ed9814d0afc904de897bc724 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Mar 2024 19:26:33 +0100
Subject: [PATCH 39/44] Defer any_output_dataset_collection_instances_deleted
 and any_output_dataset_deleted

These are only needed in
https://github.com/mvdbeek/galaxy/blob/release_24.0/lib/galaxy/managers/jobs.py#L388-L389,
no need to always load them up.
---
 lib/galaxy/model/__init__.py | 32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 337e5cf7791a..bdff421c3adb 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -11134,23 +11134,27 @@ def __repr__(self):
 # ----------------------------------------------------------------------------------------
 # The following statements must not precede the mapped models defined above.
 
-Job.any_output_dataset_collection_instances_deleted = column_property(
-    exists(HistoryDatasetCollectionAssociation.id).where(
-        and_(
-            Job.id == JobToOutputDatasetCollectionAssociation.job_id,
-            HistoryDatasetCollectionAssociation.id == JobToOutputDatasetCollectionAssociation.dataset_collection_id,
-            HistoryDatasetCollectionAssociation.deleted == true(),
-        )
+Job.any_output_dataset_collection_instances_deleted = deferred(
+    column_property(
+        exists(HistoryDatasetCollectionAssociation.id).where(
+            and_(
+                Job.id == JobToOutputDatasetCollectionAssociation.job_id,
+                HistoryDatasetCollectionAssociation.id == JobToOutputDatasetCollectionAssociation.dataset_collection_id,
+                HistoryDatasetCollectionAssociation.deleted == true(),
+            )
+        ),
     )
 )
 
-Job.any_output_dataset_deleted = column_property(
-    exists(HistoryDatasetAssociation.id).where(
-        and_(
-            Job.id == JobToOutputDatasetAssociation.job_id,
-            HistoryDatasetAssociation.table.c.id == JobToOutputDatasetAssociation.dataset_id,
-            HistoryDatasetAssociation.table.c.deleted == true(),
-        )
+Job.any_output_dataset_deleted = deferred(
+    column_property(
+        exists(HistoryDatasetAssociation.id).where(
+            and_(
+                Job.id == JobToOutputDatasetAssociation.job_id,
+                HistoryDatasetAssociation.table.c.id == JobToOutputDatasetAssociation.dataset_id,
+                HistoryDatasetAssociation.table.c.deleted == true(),
+            )
+        ),
     )
 )
 

From b1042fc5bc5fed27b193742a28156bba0f8b34a1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Mar 2024 19:39:00 +0100
Subject: [PATCH 40/44] Just select the id instead of the whole model to access
 the id

---
 lib/galaxy/jobs/runners/pulsar.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 45128847f55a..634e20675440 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -977,8 +977,8 @@ def __async_update(self, full_status):
             remote_job_id = full_status["job_id"]
             if len(remote_job_id) == 32:
                 # It is a UUID - assign_ids = uuid in destination params...
-                stmt = select(model.Job).filter(model.Job.job_runner_external_id == remote_job_id)
-                galaxy_job_id = self.app.model.session.execute(stmt).scalar_one().id
+                stmt = select(model.Job.id).filter(model.Job.job_runner_external_id == remote_job_id)
+                galaxy_job_id = self.app.model.session.execute(stmt).scalar_one()
             else:
                 galaxy_job_id = remote_job_id
             job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id(galaxy_job_id)

From c2bd0d66f7d1c11af35bdb5388912e4502b93ac6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 19 Mar 2024 15:32:20 -0400
Subject: [PATCH 41/44] Update
 client/src/components/History/CurrentHistory/SelectPreferredStore.vue

Co-authored-by: Dannon <dannon.baker@gmail.com>
---
 .../components/History/CurrentHistory/SelectPreferredStore.vue  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/SelectPreferredStore.vue b/client/src/components/History/CurrentHistory/SelectPreferredStore.vue
index 2386f1048e1a..c284718a162b 100644
--- a/client/src/components/History/CurrentHistory/SelectPreferredStore.vue
+++ b/client/src/components/History/CurrentHistory/SelectPreferredStore.vue
@@ -57,7 +57,7 @@ async function handleSubmit(preferredObjectStoreId: string | null, isPrivate: bo
         if (!historyPrivate) {
             if (
                 confirm(
-                    "Your history is set to create sharable datasets, but the target object store is private? Change the history configuration so new datasets are private by default?"
+                    "Your history is set to create sharable datasets, but the target storage location is private. Change the history configuration so new datasets are private by default?"
                 )
             ) {
                 try {

From 65d127a8e06a4068ebf6b32b9a834d5a344ec605 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Mar 2024 23:49:18 -0400
Subject: [PATCH 42/44] Fix creation and association of new histories w/ brand
 new single/remote user

---
 lib/galaxy/webapps/base/webapp.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 3ec0d3cfc94d..1daa9f7c3487 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -951,8 +951,8 @@ def get_or_create_default_history(self):
             if default_history:
                 history = default_history
                 self.set_history(history)
-        else:
-            history = self.new_history()
+            else:
+                history = self.new_history()
 
         return history
 

From ee260f83fad1d8b83635a10fa105a8785d5b554c Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 20 Mar 2024 08:06:41 +0100
Subject: [PATCH 43/44] Create new history if user has no history AND for
 anonymous users

---
 lib/galaxy/webapps/base/webapp.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 1daa9f7c3487..b808dbbbec64 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -953,6 +953,8 @@ def get_or_create_default_history(self):
                 self.set_history(history)
             else:
                 history = self.new_history()
+        else:
+            history = self.new_history()
 
         return history
 

From 6043876c520d427b240b30926af9f4ac752508bb Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 20 Mar 2024 07:58:42 -0400
Subject: [PATCH 44/44] Refactoring for clarity.

---
 lib/galaxy/webapps/base/webapp.py | 26 +++++++++-----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index b808dbbbec64..a6c20e777b6e 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -927,36 +927,28 @@ def get_or_create_default_history(self):
         Gets or creates a default history and associates it with the current
         session.
         """
+
+        # Just return the current history if one exists and is not deleted.
         history = self.galaxy_session.current_history
         if history and not history.deleted:
             return history
 
+        # Look for an existing history that has the default name, is not
+        # deleted, and is empty. If this exists, we associate it with the
+        # current session and return it.
         user = self.galaxy_session.user
         if user:
-            # Look for default history that (a) has default name + is not deleted and
-            # (b) has no datasets. If suitable history found, use it; otherwise, create
-            # new history.
             stmt = select(self.app.model.History).filter_by(
                 user=user, name=self.app.model.History.default_name, deleted=False
             )
             unnamed_histories = self.sa_session.scalars(stmt)
-            default_history = None
             for history in unnamed_histories:
                 if history.empty:
-                    # Found suitable default history.
-                    default_history = history
-                    break
-
-            # Set or create history.
-            if default_history:
-                history = default_history
-                self.set_history(history)
-            else:
-                history = self.new_history()
-        else:
-            history = self.new_history()
+                    self.set_history(history)
+                    return history
 
-        return history
+        # No suitable history found, create a new one.
+        return self.new_history()
 
     def get_most_recent_history(self):
         """