From f08ab1c8b4809c343e038ec98f1e1784e6506b34 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Oct 2023 11:40:45 +0100
Subject: [PATCH 01/19] Fix duplicated cache key

---
 .github/workflows/toolshed.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
index f6c06663da3c..21303063345a 100644
--- a/.github/workflows/toolshed.yaml
+++ b/.github/workflows/toolshed.yaml
@@ -68,7 +68,6 @@ jobs:
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-toolshed
-          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy_root/requirements.txt') }}-toolshed
       - name: Install dependencies
         run: ./scripts/common_startup.sh --skip-client-build
         working-directory: 'galaxy root'

From 72629a4f8edc95858a110dca8cc1c1911af66ed0 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Oct 2023 11:43:02 +0100
Subject: [PATCH 02/19] Expand matrix to test all combinations on Python 3.7
 and 3.11

---
 .github/workflows/toolshed.yaml | 25 ++++++-------------------
 1 file changed, 6 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
index 21303063345a..ce985340dd0a 100644
--- a/.github/workflows/toolshed.yaml
+++ b/.github/workflows/toolshed.yaml
@@ -19,24 +19,11 @@ jobs:
     name: Test
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        include:
-        - test-install-client: 'galaxy_api'
-          python-version: '3.7'
-          shed-api: 'v1'
-          shed-browser: 'twill'
-        - test-install-client: 'standalone'
-          python-version: '3.8'
-          shed-api: 'v1'
-          shed-browser: 'twill'
-        - test-install-client: 'galaxy_api'
-          python-version: '3.9'
-          shed-api: 'v2'
-          shed-browser: 'playwright'
-        - test-install-client: 'standalone'
-          python-version: '3.10'
-          shed-api: 'v2'
-          shed-browser: 'playwright'
+        python-version: ['3.7', '3.11']
+        shed-api: ['v1', 'v2']
+        test-install-client: ['galaxy_api', 'standalone']
     services:
       postgres:
         image: postgres:13
@@ -82,10 +69,10 @@ jobs:
         env:
           TOOL_SHED_TEST_INSTALL_CLIENT: ${{ matrix.test-install-client }}
           TOOL_SHED_API_VERSION: ${{ matrix.shed-api }}
-          TOOL_SHED_TEST_BROWSER: ${{ matrix.shed-browser }}
+          TOOL_SHED_TEST_BROWSER: ${{ matrix.shed-api == 'v1' && 'twill' || 'playwright' }}
         working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v3
         if: failure()
         with:
-          name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.test-install-client }})
+          name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.shed-api }}, ${{ matrix.test-install-client }})
           path: 'galaxy root/run_toolshed_tests.html'

From 60aca1657d4ac01d3a1873529c09984709393ed8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Oct 2023 11:43:56 +0100
Subject: [PATCH 03/19] Expand ``run:`` values to multiple lines

---
 .github/workflows/toolshed.yaml | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
index ce985340dd0a..2b047a4676be 100644
--- a/.github/workflows/toolshed.yaml
+++ b/.github/workflows/toolshed.yaml
@@ -59,13 +59,19 @@ jobs:
         run: ./scripts/common_startup.sh --skip-client-build
         working-directory: 'galaxy root'
       - name: Build Frontend
-        run: '. .venv/bin/activate && cd lib/tool_shed/webapp/frontend && yarn && make client'
+        run: |
+          . .venv/bin/activate
+          cd lib/tool_shed/webapp/frontend
+          yarn
+          make client
         working-directory: 'galaxy root'
       - name: Install playwright
-        run: '. .venv/bin/activate && playwright install'
+        run: |
+          . .venv/bin/activate
+          playwright install
         working-directory: 'galaxy root'
       - name: Run tests
-        run: './run_tests.sh -toolshed'
+        run: ./run_tests.sh -toolshed
         env:
           TOOL_SHED_TEST_INSTALL_CLIENT: ${{ matrix.test-install-client }}
           TOOL_SHED_API_VERSION: ${{ matrix.shed-api }}

From 9a5a552ca74ae4b6f0680e4de5b8a80ac3043b3b Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Oct 2023 12:07:23 +0100
Subject: [PATCH 04/19] Fix issues reported by ``yarn build``

Introduced in https://github.com/galaxyproject/galaxy/pull/16787 .
---
 lib/tool_shed/webapp/frontend/src/apiUtil.ts                    | 2 +-
 .../webapp/frontend/src/components/pages/RepositoryPage.vue     | 2 +-
 lib/tool_shed/webapp/frontend/src/stores/users.store.ts         | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/tool_shed/webapp/frontend/src/apiUtil.ts b/lib/tool_shed/webapp/frontend/src/apiUtil.ts
index f14774767f97..9dfa3df9109d 100644
--- a/lib/tool_shed/webapp/frontend/src/apiUtil.ts
+++ b/lib/tool_shed/webapp/frontend/src/apiUtil.ts
@@ -2,7 +2,7 @@ import axios from "axios"
 import { RawAxiosRequestConfig } from "axios"
 import { components } from "@/schema"
 
-type User = components["schemas"]["User"]
+type User = components["schemas"]["UserV2"]
 
 export async function getCurrentUser(): Promise<User | null> {
     const conf: RawAxiosRequestConfig<unknown> = {}
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue
index 51929fc44d31..d337877ce8bd 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue
@@ -242,7 +242,7 @@ const toolsYaml = computed(
                         <revision-actions
                             :repository-id="repositoryId"
                             :current-metadata="currentMetadata"
-                            v-if="currentMetadata && can_manage"
+                            v-if="currentMetadata && canManage"
                             @update="onUpdate"
                         />
                     </revision-select>
diff --git a/lib/tool_shed/webapp/frontend/src/stores/users.store.ts b/lib/tool_shed/webapp/frontend/src/stores/users.store.ts
index 13cb403f801f..5e32f2042178 100644
--- a/lib/tool_shed/webapp/frontend/src/stores/users.store.ts
+++ b/lib/tool_shed/webapp/frontend/src/stores/users.store.ts
@@ -3,7 +3,7 @@ import { defineStore } from "pinia"
 import { fetcher, components } from "@/schema"
 const usersFetcher = fetcher.path("/api/users").method("get").create()
 
-type User = components["schemas"]["User"]
+type User = components["schemas"]["UserV2"]
 
 export const useUsersStore = defineStore({
     id: "users",

From 7dc9be43bf0e9e36d6f6e67ff273739dd5993136 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Oct 2023 12:47:56 +0100
Subject: [PATCH 05/19] Explicitly add playwright to dev dependencies

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 4794d781629d..f0729a813c1f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -140,6 +140,7 @@ lxml = "!=4.2.2"
 markdown-it-reporter = "*"
 myst-parser = "*"
 pkce = "*"
+playwright = "*"
 pytest = "*"
 pytest-asyncio = "*"
 pytest-celery = "*"

From b1d86d4bad7a96c9c9b0ac0de1f97b189b41f993 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Oct 2023 18:15:01 +0100
Subject: [PATCH 06/19] Check that TOOL_SHED_TEST_BROWSER is a valid value

---
 lib/tool_shed/test/functional/conftest.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/test/functional/conftest.py b/lib/tool_shed/test/functional/conftest.py
index 9798b868a212..2b547bfe4b51 100644
--- a/lib/tool_shed/test/functional/conftest.py
+++ b/lib/tool_shed/test/functional/conftest.py
@@ -10,13 +10,12 @@
     Browser,
     BrowserContext,
 )
-from typing_extensions import Literal
 
 from ..base.browser import ShedBrowser
 from ..base.playwrightbrowser import PlaywrightShedBrowser
 from ..base.twillbrowser import TwillShedBrowser
 
-DEFAULT_BROWSER: Literal["twill", "playwright"] = "playwright"
+DEFAULT_BROWSER = "playwright"
 
 
 def twill_browser() -> Generator[ShedBrowser, None, None]:
@@ -28,10 +27,13 @@ def playwright_browser(class_context: BrowserContext) -> Generator[ShedBrowser,
     yield PlaywrightShedBrowser(page)
 
 
-if os.environ.get("TOOL_SHED_TEST_BROWSER", DEFAULT_BROWSER) == "twill":
+test_browser = os.environ.get("TOOL_SHED_TEST_BROWSER", DEFAULT_BROWSER)
+if test_browser == "twill":
     shed_browser = pytest.fixture(scope="class")(twill_browser)
-else:
+elif test_browser == "playwright":
     shed_browser = pytest.fixture(scope="class")(playwright_browser)
+else:
+    raise ValueError(f"Unrecognized value for TOOL_SHED_TEST_BROWSER: {test_browser}")
 
 
 @pytest.fixture(scope="class")

From ed0c72e3c4b32b4b998218b5196622a72d8fd461 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 11 Oct 2023 10:44:54 +0100
Subject: [PATCH 07/19] Make owner and name parameters of
 ``get_or_create_repository()`` not optional

---
 lib/tool_shed/test/base/twilltestcase.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 2d9b5e25c86f..d03a5041fee2 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -764,7 +764,7 @@ def login(
         )
         # v2 doesn't log you in on account creation... so force a login here
         if previously_created or self.is_v2:
-            # The acount has previously been created, so just login.
+            # The account has previously been created, so just login.
             # HACK: don't use panels because late_javascripts() messes up the twill browser and it
             # can't find form fields (and hence user can't be logged in).
             params = {"use_panels": False}
@@ -1402,21 +1402,20 @@ def get_repositories_category_api(
             self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def get_or_create_repository(
-        self, category: Category, owner=None, strings_displayed=None, strings_not_displayed=None, **kwd
+        self, category: Category, owner: str, name: str, strings_displayed=None, strings_not_displayed=None, **kwd
     ) -> Optional[Repository]:
         # If not checking for a specific string, it should be safe to assume that
         # we expect repository creation to be successful.
         if strings_displayed is None:
-            strings_displayed = ["Repository", kwd["name"], "has been created"]
+            strings_displayed = ["Repository", name, "has been created"]
         if strings_not_displayed is None:
             strings_not_displayed = []
-        name = kwd["name"]
         repository = self.populator.get_repository_for(owner, name)
-        category_id = category.id
-        assert category_id
         if repository is None:
+            category_id = category.id
+            assert category_id
             self.visit_url("/repository/create_repository")
-            self.submit_form(button="create_repository_button", category_id=category_id, **kwd)
+            self.submit_form(button="create_repository_button", name=name, category_id=category_id, **kwd)
             self.check_for_strings(strings_displayed, strings_not_displayed)
             repository = self.populator.get_repository_for(owner, name)
         return repository

From 219bd20320df5adfc491860725484f3ea3091f19 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 18 Oct 2023 15:20:43 +0100
Subject: [PATCH 08/19] Fix imports

Broken in commit 3238b212805f35aa17906ee51296a08b491e0e4c .
---
 lib/tool_shed/webapp/controllers/repository.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index ce313c9d0821..110838cbabae 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -16,10 +16,6 @@
     null,
     select,
 )
-from toolshed.webapp.model import (
-    Repository,
-    RepositoryMetadata,
-)
 
 import tool_shed.grids.repository_grids as repository_grids
 import tool_shed.grids.util as grids_util
@@ -62,7 +58,9 @@
 from tool_shed.webapp.framework.decorators import require_login
 from tool_shed.webapp.model import (
     Category,
+    Repository,
     RepositoryCategoryAssociation,
+    RepositoryMetadata,
 )
 from tool_shed.webapp.util import ratings_util
 

From bbb239a76be0d6fbda3cd1e1927a34e1000647fd Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 18 Oct 2023 15:29:46 +0100
Subject: [PATCH 09/19] Install node from setup-node action

---
 .github/workflows/toolshed.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
index 2b047a4676be..4e3a2b2cac8c 100644
--- a/.github/workflows/toolshed.yaml
+++ b/.github/workflows/toolshed.yaml
@@ -37,6 +37,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}

From 14e3ae32ed43c3e57ea69e5a571dedf2d2a92477 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 18 Oct 2023 13:34:10 +0100
Subject: [PATCH 10/19] Restore GET /api/categories/<encoded_id> in ToolShed
 2.0

and the deleted field in the response.

Rationale: it is not particularly useful, but both:
GET /api/categories
GET /api/categories/<encoded_id>/repositories
work on TS 2.0, so it's weird that this one is missing.

Also, it was breaking BioBlend's
https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html#bioblend.toolshed.categories.ToolShedCategoryClient.show_category
---
 lib/tool_shed/managers/categories.py          |  4 +++
 lib/tool_shed/test/base/populators.py         |  7 ++--
 .../test/functional/test_shed_categories.py   | 13 ++++++-
 lib/tool_shed/webapp/api2/categories.py       | 12 +++++++
 .../webapp/frontend/src/schema/schema.ts      | 35 +++++++++++++++++++
 lib/tool_shed_client/schema/__init__.py       |  1 +
 6 files changed, 69 insertions(+), 3 deletions(-)

diff --git a/lib/tool_shed/managers/categories.py b/lib/tool_shed/managers/categories.py
index 5341c4dea450..1d418f1aa8fa 100644
--- a/lib/tool_shed/managers/categories.py
+++ b/lib/tool_shed/managers/categories.py
@@ -26,6 +26,9 @@ class CategoryManager:
     def __init__(self, app: ToolShedApp):
         self.app = app
 
+    def get(self, encoded_category_id: str) -> Category:
+        return suc.get_category(self.app, encoded_category_id)
+
     def create(self, trans: ProvidesUserContext, category_request: CreateCategoryRequest) -> Category:
         name = category_request.name
         description = category_request.description or name
@@ -71,6 +74,7 @@ def to_model(self, category: Category) -> CategoryResponse:
             name=as_dict["name"],
             description=as_dict["description"],
             repositories=as_dict["repositories"],
+            deleted=as_dict["deleted"],
         )
 
 
diff --git a/lib/tool_shed/test/base/populators.py b/lib/tool_shed/test/base/populators.py
index 9b63e1f7a559..19b6b697b46e 100644
--- a/lib/tool_shed/test/base/populators.py
+++ b/lib/tool_shed/test/base/populators.py
@@ -266,9 +266,12 @@ def get_categories(self) -> List[Category]:
         response.raise_for_status()
         return [Category(**c) for c in response.json()]
 
-    def get_category_with_name(self, name: str) -> Optional[Category]:
-        response = self._api_interactor.get("categories")
+    def get_category_with_id(self, category_id: str) -> Category:
+        response = self._api_interactor.get(f"categories/{category_id}")
         response.raise_for_status()
+        return Category(**response.json())
+
+    def get_category_with_name(self, name: str) -> Optional[Category]:
         categories = [c for c in self.get_categories() if c.name == name]
         return categories[0] if categories else None
 
diff --git a/lib/tool_shed/test/functional/test_shed_categories.py b/lib/tool_shed/test/functional/test_shed_categories.py
index 63120b72d83c..3f9dd14fa516 100644
--- a/lib/tool_shed/test/functional/test_shed_categories.py
+++ b/lib/tool_shed/test/functional/test_shed_categories.py
@@ -10,7 +10,18 @@ def test_create_requires_name(self):
 
     def test_create_okay(self):
         name = random_name(prefix="createokay")
-        body = {"name": name, "description": "testcreateokaydescript"}
+        description = "testcreateokaydescript"
+        body = {"name": name, "description": description}
         response = self.admin_api_interactor.post("categories", json=body)
         assert response.status_code == 200
         assert response.json()["name"] == name
+
+        category = self.populator.get_category_with_name(name)
+        assert category is not None
+        assert category.name == name
+        assert category.description == description
+
+        category_id = category.id
+        category = self.populator.get_category_with_id(category_id)
+        assert category.name == name
+        assert category.description == description
diff --git a/lib/tool_shed/webapp/api2/categories.py b/lib/tool_shed/webapp/api2/categories.py
index 023242469dd1..cd8696f65cfb 100644
--- a/lib/tool_shed/webapp/api2/categories.py
+++ b/lib/tool_shed/webapp/api2/categories.py
@@ -56,6 +56,18 @@ def index(self, trans: SessionRequestContext = DependsOnTrans) -> List[CategoryR
         categories = self.category_manager.index_db(trans, deleted)
         return [self.category_manager.to_model(c) for c in categories]
 
+    @router.get(
+        "/api/categories/{encoded_category_id}",
+        description="show category",
+        operation_id="categories__show",
+    )
+    def show(self, encoded_category_id: str = CategoryIdPathParam) -> CategoryResponse:
+        """
+        Return a list of dictionaries that contain information about each Category.
+        """
+        category = self.category_manager.get(encoded_category_id)
+        return self.category_manager.to_model(category)
+
     @router.get(
         "/api/categories/{encoded_category_id}/repositories",
         description="display repositories by category",
diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
index 91fd9d54ea0c..c49abf299742 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/schema.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -20,6 +20,13 @@ export interface paths {
          */
         post: operations["categories__create"]
     }
+    "/api/categories/{encoded_category_id}": {
+        /**
+         * Show
+         * @description show category
+         */
+        get: operations["categories__show"]
+    }
     "/api/categories/{encoded_category_id}/repositories": {
         /**
          * Repositories
@@ -261,6 +268,8 @@ export interface components {
         }
         /** Category */
         Category: {
+            /** Deleted */
+            deleted: boolean
             /** Description */
             description: string
             /** Id */
@@ -1128,6 +1137,32 @@ export interface operations {
             }
         }
     }
+    categories__show: {
+        /**
+         * Show
+         * @description show category
+         */
+        parameters: {
+            /** @description The encoded database identifier of the category. */
+            path: {
+                encoded_category_id: string
+            }
+        }
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["Category"]
+                }
+            }
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"]
+                }
+            }
+        }
+    }
     categories__repositories: {
         /**
          * Repositories
diff --git a/lib/tool_shed_client/schema/__init__.py b/lib/tool_shed_client/schema/__init__.py
index a97ca4f3401b..2f4de2cc198f 100644
--- a/lib/tool_shed_client/schema/__init__.py
+++ b/lib/tool_shed_client/schema/__init__.py
@@ -69,6 +69,7 @@ class Category(BaseModel):
     id: str
     name: str
     description: str
+    deleted: bool
     repositories: int
 
 

From b85f2f10faeb7481ee312a8871c8ed7f19587cc9 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 18 Oct 2023 16:44:38 +0100
Subject: [PATCH 11/19] Fix `get_users_with_repo_alert()` call

Introduced in commit 1711e96dacf02724ae7d7f73d8cbc02201e88477 .
---
 lib/tool_shed/util/shed_util_common.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 3f107c652ab3..016183204139 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -11,6 +11,7 @@
     select,
     true,
 )
+from sqlalchemy.orm import scoped_session
 
 from galaxy import util
 from galaxy.tool_shed.util.shed_util_common import (
@@ -331,7 +332,7 @@ def handle_email_alerts(app, host, repository, content_alert_str="", new_repo_al
             subject = f"Galaxy tool shed alert for new repository named {str(repository.name)}"
             subject = subject[:80]
             email_alerts = []
-            for user in get_users_with_repo_alert(sa_session.query, app.model.User):
+            for user in get_users_with_repo_alert(sa_session, app.model.User):
                 if admin_only:
                     if user.email in admin_users:
                         email_alerts.append(user.email)
@@ -463,6 +464,6 @@ def tool_shed_is_this_tool_shed(toolshed_base_url, trans=None):
 )
 
 
-def get_users_with_repo_alert(session, user_model):
+def get_users_with_repo_alert(session: scoped_session, user_model):
     stmt = select(user_model).where(user_model.deleted == false()).where(user_model.new_repo_alert == true())
     return session.scalars(stmt)

From 4e7763d8468c34d013d17658ccb1a226840eb358 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 18 Oct 2023 17:05:39 +0100
Subject: [PATCH 12/19] Add type annotations. Drop unused functions and
 re-exports.

---
 lib/tool_shed/util/shed_util_common.py | 117 ++++++-------------------
 1 file changed, 27 insertions(+), 90 deletions(-)

diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 016183204139..ed4d160effda 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -3,7 +3,10 @@
 import os
 import socket
 import string
-from typing import TYPE_CHECKING
+from typing import (
+    List,
+    TYPE_CHECKING,
+)
 
 from sqlalchemy import (
     false,
@@ -14,17 +17,7 @@
 from sqlalchemy.orm import scoped_session
 
 from galaxy import util
-from galaxy.tool_shed.util.shed_util_common import (
-    can_eliminate_repository_dependency,
-    clean_dependency_relationships,
-    generate_tool_guid,
-    get_ctx_rev,
-    get_next_prior_import_or_install_required_dict_entry,
-    get_tool_panel_config_tool_path_install_dir,
-    get_user,
-    have_shed_tool_conf_for_install,
-    set_image_paths,
-)
+from galaxy.tool_shed.util.shed_util_common import get_user
 from galaxy.util import (
     checkers,
     unicodify,
@@ -39,6 +32,7 @@
 
 if TYPE_CHECKING:
     from tool_shed.structured_app import ToolShedApp
+    from tool_shed.webapp.model import Repository
 
 log = logging.getLogger(__name__)
 
@@ -118,16 +112,7 @@ def get_category_by_name(app: "ToolShedApp", name: str):
     return sa_session.scalars(stmt).first()
 
 
-def get_repository_categories(app, id):
-    """Get categories of a repository on the tool shed side from the database via id"""
-    sa_session = app.model.session
-    stmt = select(app.model.RepositoryCategoryAssociation).where(
-        app.model.RepositoryCategoryAssociation.repository_id == app.security.decode_id(id)
-    )
-    return sa_session.scalars(stmt).all()
-
-
-def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
+def get_repository_file_contents(app: "ToolShedApp", file_path: str, repository_id: str, is_admin: bool = False) -> str:
     """Return the display-safe contents of a repository file for display in a browser."""
     safe_str = ""
     if not _is_path_browsable(app, file_path, repository_id, is_admin):
@@ -188,7 +173,7 @@ def get_repository_files(folder_path):
     return contents
 
 
-def get_repository_from_refresh_on_change(app, **kwd):
+def get_repository_from_refresh_on_change(app: "ToolShedApp", **kwd):
     # The changeset_revision_select_field in several grids performs a refresh_on_change which sends in request parameters like
     # changeset_revison_1, changeset_revision_2, etc.  One of the many select fields on the grid performed the refresh_on_change,
     # so we loop through all of the received values to see which value is not the repository tip.  If we find it, we know the
@@ -206,52 +191,14 @@ def get_repository_from_refresh_on_change(app, **kwd):
     return v, None
 
 
-def get_repository_type_from_tool_shed(app, tool_shed_url, name, owner):
-    """
-    Send a request to the tool shed to retrieve the type for a repository defined by the
-    combination of a name and owner.
-    """
-    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
-    params = dict(name=name, owner=owner)
-    pathspec = ["repository", "get_repository_type"]
-    repository_type = util.url_get(
-        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
-    )
-    return repository_type
-
-
-def get_tool_dependency_definition_metadata_from_tool_shed(app, tool_shed_url, name, owner):
-    """
-    Send a request to the tool shed to retrieve the current metadata for a
-    repository of type tool_dependency_definition defined by the combination
-    of a name and owner.
-    """
-    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
-    params = dict(name=name, owner=owner)
-    pathspec = ["repository", "get_tool_dependency_definition_metadata"]
-    metadata = util.url_get(
-        tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params
-    )
-    return metadata
-
-
-def get_tool_path_by_shed_tool_conf_filename(app, shed_tool_conf):
-    """
-    Return the tool_path config setting for the received shed_tool_conf file by searching the tool box's in-memory list of shed_tool_confs for the
-    dictionary whose config_filename key has a value matching the received shed_tool_conf.
-    """
-    for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
-        config_filename = shed_tool_conf_dict["config_filename"]
-        if config_filename == shed_tool_conf:
-            return shed_tool_conf_dict["tool_path"]
-        else:
-            file_name = basic_util.strip_path(config_filename)
-            if file_name == shed_tool_conf:
-                return shed_tool_conf_dict["tool_path"]
-    return None
-
-
-def handle_email_alerts(app, host, repository, content_alert_str="", new_repo_alert=False, admin_only=False):
+def handle_email_alerts(
+    app: "ToolShedApp",
+    host: str,
+    repository: "Repository",
+    content_alert_str: str = "",
+    new_repo_alert: bool = False,
+    admin_only: bool = False,
+) -> None:
     """
     There are 2 complementary features that enable a tool shed user to receive email notification:
 
@@ -353,7 +300,7 @@ def handle_email_alerts(app, host, repository, content_alert_str="", new_repo_al
                 log.exception("An error occurred sending a tool shed repository update alert by email.")
 
 
-def _is_path_browsable(app, path, repository_id, is_admin=False):
+def _is_path_browsable(app: "ToolShedApp", path: str, repository_id: str, is_admin: bool = False) -> bool:
     """
     Detects whether the given path is browsable i.e. is within the
     allowed repository folders. Admins can additionaly browse folders
@@ -364,7 +311,7 @@ def _is_path_browsable(app, path, repository_id, is_admin=False):
     return is_path_within_repo(app, path, repository_id)
 
 
-def is_path_within_dependency_dir(app, path):
+def is_path_within_dependency_dir(app: "ToolShedApp", path: str) -> bool:
     """
     Detect whether the given path is within the tool_dependency_dir folder on the disk.
     (Specified by the config option). Use to filter malicious symlinks targeting outside paths.
@@ -378,7 +325,7 @@ def is_path_within_dependency_dir(app, path):
     return allowed
 
 
-def is_path_within_repo(app, path, repository_id):
+def is_path_within_repo(app: "ToolShedApp", path: str, repository_id: str) -> bool:
     """
     Detect whether the given path is within the repository folder on the disk.
     Use to filter malicious symlinks targeting outside paths.
@@ -388,7 +335,9 @@ def is_path_within_repo(app, path, repository_id):
     return os.path.commonprefix([repo_path, resolved_path]) == repo_path
 
 
-def open_repository_files_folder(app, folder_path, repository_id, is_admin=False):
+def open_repository_files_folder(
+    app: "ToolShedApp", folder_path: str, repository_id: str, is_admin: bool = False
+) -> List:
     """
     Return a list of dictionaries, each of which contains information for a file or directory contained
     within a directory in a repository file hierarchy.
@@ -437,33 +386,21 @@ def tool_shed_is_this_tool_shed(toolshed_base_url, trans=None):
     return cleaned_toolshed_base_url == cleaned_tool_shed
 
 
+def get_users_with_repo_alert(session: scoped_session, user_model):
+    stmt = select(user_model).where(user_model.deleted == false()).where(user_model.new_repo_alert == true())
+    return session.scalars(stmt)
+
+
 __all__ = (
-    "can_eliminate_repository_dependency",
-    "clean_dependency_relationships",
     "count_repositories_in_category",
-    "generate_tool_guid",
     "get_categories",
     "get_category",
     "get_category_by_name",
-    "get_ctx_rev",
-    "get_next_prior_import_or_install_required_dict_entry",
-    "get_repository_categories",
     "get_repository_file_contents",
-    "get_repository_type_from_tool_shed",
-    "get_tool_dependency_definition_metadata_from_tool_shed",
-    "get_tool_panel_config_tool_path_install_dir",
-    "get_tool_path_by_shed_tool_conf_filename",
     "get_user",
     "handle_email_alerts",
-    "have_shed_tool_conf_for_install",
     "is_path_within_dependency_dir",
     "is_path_within_repo",
     "open_repository_files_folder",
-    "set_image_paths",
     "tool_shed_is_this_tool_shed",
 )
-
-
-def get_users_with_repo_alert(session: scoped_session, user_model):
-    stmt = select(user_model).where(user_model.deleted == false()).where(user_model.new_repo_alert == true())
-    return session.scalars(stmt)

From 806dfae4b3ea70428c729cd9bb77d45c4703a1a8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 18 Oct 2023 17:59:47 +0100
Subject: [PATCH 13/19] Fix `index_repositories()` method

Broken in commit 77df9c9a73e6efd5233ec881a555855e913b3aaf .
---
 lib/tool_shed/managers/repositories.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
index 596aca642b0e..9d83144c258e 100644
--- a/lib/tool_shed/managers/repositories.py
+++ b/lib/tool_shed/managers/repositories.py
@@ -20,6 +20,7 @@
     false,
     select,
 )
+from sqlalchemy.orm import scoped_session
 
 from galaxy import web
 from galaxy.exceptions import (
@@ -254,7 +255,9 @@ def index_tool_ids(app: ToolShedApp, tool_ids: List[str]) -> Dict[str, Any]:
 
 
 def index_repositories(app: ToolShedApp, name: Optional[str], owner: Optional[str], deleted: bool):
-    return list(_get_repository_by_name_and_owner_and_deleted(app.model.context, name, owner, deleted, app.model.User))
+    return list(
+        _get_repositories_by_name_and_owner_and_deleted(app.model.context, name, owner, deleted, app.model.User)
+    )
 
 
 def can_manage_repo(trans: ProvidesUserContext, repository: Repository) -> bool:
@@ -579,7 +582,7 @@ def upload_tar_and_set_metadata(
     return message
 
 
-def _get_repository_by_name_and_owner(session, name, owner, user_model):
+def _get_repository_by_name_and_owner(session: scoped_session, name: str, owner: str, user_model):
     stmt = (
         select(Repository)
         .where(Repository.deprecated == false())
@@ -592,12 +595,14 @@ def _get_repository_by_name_and_owner(session, name, owner, user_model):
     return session.scalars(stmt).first()
 
 
-def _get_repository_by_name_and_owner_and_deleted(session, name, owner, deleted, user_model):
+def _get_repositories_by_name_and_owner_and_deleted(
+    session: scoped_session, name: Optional[str], owner: Optional[str], deleted: bool, user_model
+):
     stmt = select(Repository).where(Repository.deprecated == false()).where(Repository.deleted == deleted)
     if owner is not None:
         stmt = stmt.where(user_model.username == owner)
         stmt = stmt.where(Repository.user_id == user_model.id)
     if name is not None:
         stmt = stmt.where(Repository.name == name)
-    stmt = stmt.order_by(Repository.name).limit(1)
-    return session.scalars(stmt).first()
+    stmt = stmt.order_by(Repository.name)
+    return session.scalars(stmt)

From e5bec6ad71494034a90926e5efbc4103e6490aea Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 19 Oct 2023 11:07:15 +0100
Subject: [PATCH 14/19] Fix typo in query

Introduced in commit 3238b212805f35aa17906ee51296a08b491e0e4c .
---
 lib/tool_shed/webapp/controllers/repository.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 110838cbabae..baee2f6123ba 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -2659,7 +2659,7 @@ def validate_changeset_revision(self, trans, changeset_revision, repository_id):
 
 def get_first_repository_metadata(session):
     stmt = select(RepositoryMetadata).limit(1)
-    return session.select(stmt).first()
+    return session.scalars(stmt).first()
 
 
 def get_current_repositories(session):

From b5013aa57a4199537ef09a4427968ec3f365605f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 19 Oct 2023 11:54:43 +0100
Subject: [PATCH 15/19] Fix another typo

Introduced in commit 70c7f03be9ef02bcdd405820ad68f1772f43a25d .
---
 lib/tool_shed/test/base/twilltestcase.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index d03a5041fee2..9568aac837df 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -2092,7 +2092,7 @@ def get_installed_repository(session, name, owner, changeset):
     if owner is not None:
         stmt = stmt.where(ToolShedRepository.owner == owner)
     if changeset is not None:
-        stmt = stmt.wehre(ToolShedRepository.changeset_revision == changeset)
+        stmt = stmt.where(ToolShedRepository.changeset_revision == changeset)
     stmt = stmt.where(ToolShedRepository.deleted == false())
     stmt = stmt.where(ToolShedRepository.uninstalled == false())
     return session.scalars(stmt).one_or_none()

From bab9753aebe6c16ac0466217cda36f4b1dacf382 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 19 Oct 2023 12:45:59 +0100
Subject: [PATCH 16/19] Fix another typo

Introduced in commit 68831ddcfc661ca13ce7b26cc7383589f185c65a .
---
 lib/tool_shed/metadata/repository_metadata_manager.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 03c5562d5c02..2bc5e756a0d0 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -1097,7 +1097,7 @@ def get_current_repositories(session, order=False):
 
 
 def get_filtered_repositories(session, repo_ids, order):
-    stmt = select(Repository).where(Repository.in_(repo_ids))
+    stmt = select(Repository).where(Repository.id.in_(repo_ids))
     if order:
         stmt = stmt.order_by(Repository.name, Repository.user_id)
     return session.scalars(stmt)

From e34089513411032d28721fd063653e485998841f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 19 Oct 2023 16:52:22 +0100
Subject: [PATCH 17/19] Type annotation fixes

---
 lib/tool_shed/test/base/twilltestcase.py      |  3 +-
 .../test_0300_reset_all_metadata.py           | 34 +++++++++++++++++--
 .../test/functional/test_shed_repositories.py |  1 +
 3 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 9568aac837df..e7d32c23e153 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -1040,7 +1040,7 @@ def create_category(self, **kwd) -> Category:
 
     def create_repository_dependency(
         self,
-        repository: Optional[Repository] = None,
+        repository: Repository,
         repository_tuples=None,
         filepath=None,
         prior_installation_required=False,
@@ -1050,7 +1050,6 @@ def create_repository_dependency(
         strings_displayed=None,
         strings_not_displayed=None,
     ):
-        assert repository
         repository_tuples = repository_tuples or []
         repository_names = []
         if complex:
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 f20c29b08cbd..e28d653c4c41 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
@@ -1,3 +1,5 @@
+from typing import Dict
+
 from ..base.twilltestcase import (
     common,
     ShedTwillTestCase,
@@ -63,6 +65,7 @@ def test_0005_create_filtering_repository(self):
             owner=common.test_user_1_name,
             category=category_0000,
         )
+        assert repository
         if self.repository_is_new(repository):
             running_standalone = True
             self.commit_tar_to_repository(
@@ -90,6 +93,7 @@ def test_0010_create_freebayes_repository(self):
             strings_displayed=[],
         )
         if running_standalone:
+            assert repository
             self.setup_freebayes_0010_repo(repository)
 
     def test_0015_create_datatypes_0020_repository(self):
@@ -110,6 +114,7 @@ def test_0015_create_datatypes_0020_repository(self):
                 category=category_0020,
                 strings_displayed=[],
             )
+            assert repository
             self.commit_tar_to_repository(
                 repository,
                 "column_maker/column_maker.tar",
@@ -134,6 +139,7 @@ def test_0020_create_emboss_0020_repository(self):
                 category=category_0020,
                 strings_displayed=[],
             )
+            assert repository
             self.commit_tar_to_repository(
                 repository,
                 "emboss/emboss.tar",
@@ -158,6 +164,7 @@ def test_0025_create_emboss_datatypes_0030_repository(self):
                 category=category_0030,
                 strings_displayed=[],
             )
+            assert column_maker_repository
             self.commit_tar_to_repository(
                 column_maker_repository,
                 "column_maker/column_maker.tar",
@@ -182,6 +189,7 @@ def test_0030_create_emboss_5_repository(self):
                 category=category_0030,
                 strings_displayed=[],
             )
+            assert emboss_5_repository
             self.commit_tar_to_repository(
                 emboss_5_repository,
                 "emboss/emboss.tar",
@@ -206,6 +214,7 @@ def test_0035_create_emboss_6_repository(self):
                 category=category_0030,
                 strings_displayed=[],
             )
+            assert emboss_6_repository
             self.commit_tar_to_repository(
                 emboss_6_repository,
                 "emboss/emboss.tar",
@@ -230,6 +239,7 @@ def test_0040_create_emboss_0030_repository(self):
                 category=category_0030,
                 strings_displayed=[],
             )
+            assert emboss_repository
             self.commit_tar_to_repository(
                 emboss_repository,
                 "emboss/emboss.tar",
@@ -243,9 +253,13 @@ def test_0045_create_repository_dependencies_for_0030(self):
             column_maker_repository = self._get_repository_by_name_and_owner(
                 "column_maker_0030", common.test_user_1_name
             )
+            assert column_maker_repository
             emboss_repository = self._get_repository_by_name_and_owner("emboss_0030", common.test_user_1_name)
+            assert emboss_repository
             emboss_5_repository = self._get_repository_by_name_and_owner("emboss_5_0030", common.test_user_1_name)
+            assert emboss_5_repository
             emboss_6_repository = self._get_repository_by_name_and_owner("emboss_6_0030", common.test_user_1_name)
+            assert emboss_6_repository
             repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss"])
             column_maker_tuple = (
                 self.url,
@@ -299,6 +313,7 @@ def test_0050_create_freebayes_repository(self):
             category=category_0040,
             strings_displayed=[],
         )
+        assert repository
         if running_standalone:
             self.commit_tar_to_repository(
                 repository,
@@ -324,6 +339,7 @@ def test_0055_create_filtering_repository(self):
                 category=category_0040,
                 strings_displayed=[],
             )
+            assert repository
             self.commit_tar_to_repository(
                 repository,
                 "filtering/filtering_1.1.0.tar",
@@ -335,7 +351,9 @@ def test_0060_create_dependency_structure(self):
         global running_standalone
         if running_standalone:
             freebayes_repository = self._get_repository_by_name_and_owner("freebayes_0040", common.test_user_1_name)
+            assert freebayes_repository
             filtering_repository = self._get_repository_by_name_and_owner("filtering_0040", common.test_user_1_name)
+            assert filtering_repository
             repository_dependencies_path = self.generate_temp_path("test_0340", additional_paths=["dependencies"])
             freebayes_tuple = (
                 self.url,
@@ -375,6 +393,7 @@ def test_0065_create_convert_repository(self):
                 category=category,
                 strings_displayed=[],
             )
+            assert repository
             self.commit_tar_to_repository(
                 repository,
                 "convert_chars/convert_chars.tar",
@@ -396,6 +415,7 @@ def test_0070_create_column_repository(self):
                 category=category,
                 strings_displayed=[],
             )
+            assert repository
             self.commit_tar_to_repository(
                 repository,
                 "column_maker/column_maker.tar",
@@ -420,6 +440,7 @@ def test_0080_create_emboss_repository(self):
                 category=category,
                 strings_displayed=[],
             )
+            assert repository
             self.commit_tar_to_repository(
                 repository,
                 "emboss/emboss.tar",
@@ -441,6 +462,7 @@ def test_0085_create_filtering_repository(self):
                 category=category,
                 strings_displayed=[],
             )
+            assert filtering_repository
             self.commit_tar_to_repository(
                 filtering_repository,
                 "filtering/filtering_1.1.0.tar",
@@ -462,6 +484,7 @@ def test_0090_create_freebayes_repository(self):
                 category=category,
                 strings_displayed=[],
             )
+            assert repository
             self.commit_tar_to_repository(
                 repository,
                 "freebayes/freebayes.tar",
@@ -483,6 +506,7 @@ def test_0095_create_bismark_repository(self):
                 category=category,
                 strings_displayed=[],
             )
+            assert repository
             self.user_populator().setup_bismark_repo(repository, end=1)
 
     def test_0100_create_and_upload_dependency_definitions(self):
@@ -491,19 +515,25 @@ def test_0100_create_and_upload_dependency_definitions(self):
         if running_standalone:
             self.login(email=common.test_user_1_email, username=common.test_user_1_name)
             column_repository = self._get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
+            assert column_repository
             convert_repository = self._get_repository_by_name_and_owner(
                 convert_repository_name, common.test_user_1_name
             )
+            assert convert_repository
             emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
+            assert emboss_repository
             filtering_repository = self._get_repository_by_name_and_owner(
                 filtering_repository_name, common.test_user_1_name
             )
+            assert filtering_repository
             freebayes_repository = self._get_repository_by_name_and_owner(
                 freebayes_repository_name, common.test_user_1_name
             )
+            assert freebayes_repository
             bismark_repository = self._get_repository_by_name_and_owner(
                 bismark_repository_name, common.test_user_1_name
             )
+            assert bismark_repository
             dependency_xml_path = self.generate_temp_path("test_0050", additional_paths=["freebayes"])
             # convert_chars depends on column_maker
             # column_maker depends on convert_chars
@@ -562,8 +592,8 @@ def test_0100_create_and_upload_dependency_definitions(self):
     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)
-        old_metadata = dict()
-        new_metadata = dict()
+        old_metadata: Dict[str, Dict] = dict()
+        new_metadata: Dict[str, Dict] = dict()
         repositories = self.test_db_util.get_all_repositories()
         for repository in repositories:
             old_metadata[self.security.encode_id(repository.id)] = dict()
diff --git a/lib/tool_shed/test/functional/test_shed_repositories.py b/lib/tool_shed/test/functional/test_shed_repositories.py
index 90e9b8134059..ac58f44d07d6 100644
--- a/lib/tool_shed/test/functional/test_shed_repositories.py
+++ b/lib/tool_shed/test/functional/test_shed_repositories.py
@@ -83,6 +83,7 @@ def test_index_simple(self):
         assert repository_id in repository_ids
 
         repository = self.populator.get_repository_for(repo.owner, repo.name)
+        assert repository
         assert repository.owner == repo.owner
         assert repository.name == repo.name
 

From bdcc33195a54391f09012a429f0369f56fdbe4ab Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 20 Oct 2023 11:14:05 +0100
Subject: [PATCH 18/19] Remove unused test config option

---
 lib/galaxy_test/driver/driver_util.py | 1 -
 lib/tool_shed/test/base/driver.py     | 1 -
 2 files changed, 2 deletions(-)

diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index ef9d6c4988bc..6bd109e76039 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -227,7 +227,6 @@ def setup_galaxy_config(
         template_cache_path=template_cache_path,
         tool_config_file=tool_config_file,
         tool_data_table_config_path=tool_data_table_config_path,
-        tool_parse_help=False,
         tool_path=tool_path,
         update_integrated_tool_panel=update_integrated_tool_panel,
         use_tasked_jobs=True,
diff --git a/lib/tool_shed/test/base/driver.py b/lib/tool_shed/test/base/driver.py
index 7dc778643e81..6f56751f39cc 100644
--- a/lib/tool_shed/test/base/driver.py
+++ b/lib/tool_shed/test/base/driver.py
@@ -103,7 +103,6 @@ def _setup_local(self):
             shed_tool_data_table_config=shed_tool_data_table_conf_file,
             smtp_server="smtp.dummy.string.tld",
             email_from="functional@localhost",
-            tool_parse_help=False,
             use_heartbeat=False,
         )
         kwargs.update(toolshed_database_conf)

From 048d79242f3c2619423be59a82f4503b9c4d1044 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 20 Oct 2023 11:23:35 +0100
Subject: [PATCH 19/19] Configure temporary whoosh_index_dir for tests

Otherwise a `<GALAXY_ROOT>/database/toolshed_whoosh_indexes` would
be reused, leading to failing tests when running tests locally.
---
 lib/tool_shed/test/base/driver.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/test/base/driver.py b/lib/tool_shed/test/base/driver.py
index 6f56751f39cc..b342a749f591 100644
--- a/lib/tool_shed/test/base/driver.py
+++ b/lib/tool_shed/test/base/driver.py
@@ -80,11 +80,11 @@ def _setup_local(self):
             os.environ["GALAXY_TEST_TOOL_DATA_PATH"] = tool_data_path
         galaxy_db_path = driver_util.database_files_path(tool_shed_test_tmp_dir)
         shed_file_path = os.path.join(shed_db_path, "files")
-        hgweb_config_file_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
+        whoosh_index_dir = os.path.join(shed_db_path, "toolshed_whoosh_indexes")
+        hgweb_config_dir = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
         new_repos_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
         galaxy_shed_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
         galaxy_migrated_tool_path = tempfile.mkdtemp(dir=tool_shed_test_tmp_dir)
-        hgweb_config_dir = hgweb_config_file_path
         os.environ["TEST_HG_WEB_CONFIG_DIR"] = hgweb_config_dir
         print("Directory location for hgweb.config:", hgweb_config_dir)
         toolshed_database_conf = driver_util.database_conf(shed_db_path, prefix="TOOL_SHED")
@@ -104,6 +104,7 @@ def _setup_local(self):
             smtp_server="smtp.dummy.string.tld",
             email_from="functional@localhost",
             use_heartbeat=False,
+            whoosh_index_dir=whoosh_index_dir,
         )
         kwargs.update(toolshed_database_conf)
         # Generate the tool_data_table_conf.xml file.