Merge pull request #21922 from jmchilton/toolshed_2_cleanup_v2

Make Shed 2 the Default - Drop Legacy Shed Tests in CI

.github/workflows/toolshed.yaml

@@ -24,7 +24,6 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ['3.10', '3.14']
-        shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:
       postgres:
@@ -77,11 +76,9 @@ jobs:
         run: ./run_tests.sh -toolshed
         env:
           TOOL_SHED_TEST_INSTALL_CLIENT: ${{ matrix.test-install-client }}
-          TOOL_SHED_API_VERSION: ${{ matrix.shed-api }}
-          TOOL_SHED_TEST_BROWSER: ${{ matrix.shed-api == 'v1' && 'twill' || 'playwright' }}
         working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v6
         if: failure()
         with:
-          name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.shed-api }}, ${{ matrix.test-install-client }})
+          name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.test-install-client }})
           path: 'galaxy root/run_toolshed_tests.html'

lib/tool_shed/test/README.md

@@ -8,10 +8,10 @@ Integration and browser tests for the Tool Shed. Requires a running server.
 # From packages/tool_shed directory
 
 # Start shed in another terminal first
-TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+./run_tool_shed.sh
 
 # Run all functional tests
-TOOL_SHED_API_VERSION=v2 uv run pytest tool_shed/test/functional/ -v
+uv run pytest tool_shed/test/functional/ -v
 
 # Run specific test
 uv run pytest tool_shed/test/functional/test_frontend_login.py -v
@@ -22,6 +22,7 @@ uv run pytest tool_shed/test/functional/test_frontend_login.py -v
 ### Numbered Tests (`test_0xxx`, `test_1xxx`)
 
 Legacy comprehensive tests using Twill/API:
+
 - `test_0xxx` - Tool Shed functionality (repos, dependencies, metadata)
 - `test_1xxx` - Galaxy installation scenarios
 
@@ -31,22 +32,20 @@ These test complex multi-step workflows and dependency chains.
 
 Modern Playwright/API tests:
 
-| File | Description |
-|------|-------------|
-| `test_frontend_*.py` | Browser UI tests (Playwright) |
-| `test_shed_*.py` | API-level tests |
-| `test_repositories_integration.py` | Repository operations |
-| `test_component_showcase.py` | Component visual tests |
+| File                               | Description                   |
+| ---------------------------------- | ----------------------------- |
+| `test_frontend_*.py`               | Browser UI tests (Playwright) |
+| `test_shed_*.py`                   | API-level tests               |
+| `test_repositories_integration.py` | Repository operations         |
+| `test_component_showcase.py`       | Component visual tests        |
 
 ## Environment Variables
 
-| Variable | Default | Description |
-|----------|---------|-------------|
-| `TOOL_SHED_API_VERSION` | v1 | Set to `v2` for modern API |
-| `TOOL_SHED_TEST_BROWSER` | playwright | Browser: `playwright` or `twill` |
-| `TOOL_SHED_TEST_EXTERNAL` | - | Use external running shed |
-| `TOOL_SHED_TEST_HOST` | localhost | Host for external shed |
-| `TOOL_SHED_TEST_SCREENSHOTS` | - | Directory for test screenshots |
+| Variable                     | Default   | Description                    |
+| ---------------------------- | --------- | ------------------------------ |
+| `TOOL_SHED_TEST_EXTERNAL`    | -         | Use external running shed      |
+| `TOOL_SHED_TEST_HOST`        | localhost | Host for external shed         |
+| `TOOL_SHED_TEST_SCREENSHOTS` | -         | Directory for test screenshots |
 
 ## Test Patterns
 

lib/tool_shed/test/base/api.py

@@ -1,5 +1,4 @@
 import os
-from functools import wraps
 from typing import (
     Any,
     Optional,
@@ -102,25 +101,6 @@ class ShedGalaxyInteractorApi(GalaxyInteractorApi):
         super().__init__(**interactor_kwds)
 
 
-def make_skip_if_api_version_wrapper(version):
-    def wrapper(method):
-        @wraps(method)
-        def wrapped_method(api_test_case, *args, **kwd):
-            interactor: ShedApiInteractor = api_test_case.api_interactor
-            api_version = interactor.api_version
-            if api_version == version:
-                raise pytest.skip(f"{version} tool shed API found, skipping test")
-            return method(api_test_case, *args, **kwd)
-
-        return wrapped_method
-
-    return wrapper
-
-
-skip_if_api_v1 = make_skip_if_api_version_wrapper("v1")
-skip_if_api_v2 = make_skip_if_api_version_wrapper("v2")
-
-
 class ShedApiTestCase(ShedBaseTestCase, UsesShedApi):
     _galaxy_interactor: Optional[GalaxyInteractorApi] = None
 

lib/tool_shed/test/base/twilltestcase.py

@@ -692,7 +692,7 @@ class ShedTwillTestCase(ShedApiTestCase):
 
     @property
     def invalid_tools_labels(self) -> str:
-        return "Invalid Tools" if self.is_v2 else "Invalid tools"
+        return "Invalid Tools"
 
     def create(
         self,
@@ -702,39 +702,22 @@ class ShedTwillTestCase(ShedApiTestCase):
         username: str = "admin-user",
         redirect: Optional[str] = None,
     ) -> tuple[bool, bool, bool]:
-        # 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 = dict(cntrller=cntrller, use_panels=False)
-        self.visit_url("/user/create", params)
-        self._submit_register_form(
-            email,
-            password,
-            username,
-            redirect,
-        )
-        previously_created = False
-        username_taken = False
-        invalid_username = False
-        if not self.is_v2:
-            try:
-                self.check_page_for_string("Created new user account")
-            except AssertionError:
-                try:
-                    # May have created the account in a previous test run...
-                    self.check_page_for_string(f"User with email '{email}' already exists.")
-                    previously_created = True
-                except AssertionError:
-                    try:
-                        self.check_page_for_string("Public name is taken; please choose another")
-                        username_taken = True
-                    except AssertionError:
-                        # Note that we're only checking if the usr name is >< 4 chars here...
-                        try:
-                            self.check_page_for_string("Public name must be at least 4 characters in length")
-                            invalid_username = True
-                        except AssertionError:
-                            pass
-        return previously_created, username_taken, invalid_username
+        return self._ensure_user_via_api(email, password, username)
+
+    def _ensure_user_via_api(self, email: str, password: str, username: str) -> tuple[bool, bool, bool]:
+        """Create user via admin API if not already present.
+
+        Returns (previously_created, username_taken, invalid_username).
+        """
+        admin = self.admin_api_interactor
+        all_users = admin.get("users").json()
+        if any(u["username"] == username for u in all_users):
+            return (True, False, False)
+        response = admin.post("users", json={"email": email, "username": username, "password": password})
+        if response.status_code != 200:
+            # User creation failed (e.g. reserved username)
+            return (False, False, True)
+        return (False, False, False)
 
     def last_page(self):
         """
@@ -758,34 +741,48 @@ class ShedTwillTestCase(ShedApiTestCase):
         logout_first: bool = True,
         explicit_logout: bool = False,
     ):
-        if self.is_v2:
-            # old version had a logout URL, this one needs to check
-            # page if logged in
-            self.visit_url("/")
-
-        # Clear cookies.
+        self.visit_url("/")
         if logout_first:
             self.logout(explicit=explicit_logout)
-        # test@bx.psu.edu is configured as an admin user
+        # Ensure user exists via API
         previously_created, username_taken, invalid_username = self.create(
             email=email, password=password, username=username, redirect=redirect
         )
-        # v2 doesn't log you in on account creation... so force a login here
-        if previously_created or self.is_v2:
-            # 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}
-            self.visit_url("/user/login", params=params)
-            self.submit_form(button="login_button", login=email, redirect=redirect, password=password)
-
-    @property
-    def is_v2(self) -> bool:
-        return self.api_interactor.api_version == "v2"
+        if invalid_username:
+            return
+        # Re-visit root after logout to get fresh session + CSRF token
+        self.visit_url("/")
+        cookies = self._page.context.cookies()
+        csrf_token = ""
+        for cookie in cookies:
+            if cookie["name"] == "session_csrf_token":
+                csrf_token = cookie["value"]
+                break
+        # Establish browser session via internal login API
+        self._page.evaluate(
+            """async ([login, password, csrfToken]) => {
+                const response = await fetch('/api_internal/login', {
+                    method: 'PUT',
+                    headers: {'Content-Type': 'application/json'},
+                    body: JSON.stringify({
+                        login: login,
+                        password: password,
+                        session_csrf_token: csrfToken,
+                    })
+                });
+                if (!response.ok) {
+                    const text = await response.text();
+                    throw new Error('Login failed: ' + response.status + ' ' + text);
+                }
+                return await response.json();
+            }""",
+            [email, password, csrf_token],
+        )
+        # Reload to pick up the new session
+        self.visit_url("/")
 
     @property
     def _playwright_browser(self) -> PlaywrightShedBrowser:
-        # make sure self.is_v2
         browser = self._browser
         assert isinstance(browser, PlaywrightShedBrowser)
         return browser
@@ -802,14 +799,10 @@ class ShedTwillTestCase(ShedApiTestCase):
         and be explicit in logging out to provide extract test
         structure.
         """
-        if self.is_v2:
-            if explicit:
-                self._playwright_browser.explicit_logout()
-            else:
-                self._playwright_browser.logout_if_logged_in()
+        if explicit:
+            self._playwright_browser.explicit_logout()
         else:
-            self.visit_url("/user/logout")
-            self.check_page_for_string("You have been logged out")
+            self._playwright_browser.logout_if_logged_in()
 
     def submit_form(self, form_no=-1, button="runtool_btn", form=None, **kwd):
         """Populates and submits a form from the keyword arguments."""
@@ -860,15 +853,7 @@ class ShedTwillTestCase(ShedApiTestCase):
         self.check_for_strings(strings_displayed=["Role", "has been associated"])
 
     def browse_category(self, category: Category, strings_displayed=None, strings_not_displayed=None):
-        if self.is_v2:
-            self.visit_url(f"/repositories_by_category/{category.id}")
-        else:
-            params = {
-                "sort": "name",
-                "operation": "valid_repositories_by_category",
-                "id": category.id,
-            }
-            self.visit_url("/repository/browse_valid_categories", params=params)
+        self.visit_url(f"/repositories_by_category/{category.id}")
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_repository(self, repository: Repository, strings_displayed=None, strings_not_displayed=None):
@@ -882,10 +867,7 @@ class ShedTwillTestCase(ShedApiTestCase):
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def browse_tool_shed(self, url, strings_displayed=None, strings_not_displayed=None):
-        if self.is_v2:
-            url = "/repositories_by_category"
-        else:
-            url = "/repository/browse_valid_categories"
+        url = "/repositories_by_category"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
@@ -929,14 +911,8 @@ class ShedTwillTestCase(ShedApiTestCase):
         depends_on_changeset_revision=None,
         changeset_revision=None,
     ):
-        if not self.is_v2:
-            # v2 doesn't display repository repository dependencies, they are deprecated
-            strings_displayed = [depends_on_repository.name, depends_on_repository.owner]
-            if depends_on_changeset_revision:
-                strings_displayed.append(depends_on_changeset_revision)
-            self.display_manage_repository_page(
-                repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed
-            )
+        # v2 doesn't display repository repository dependencies, they are deprecated
+        pass
 
     def check_repository_metadata(self, repository: Repository, tip_only=True):
         if tip_only:
@@ -1228,9 +1204,7 @@ class ShedTwillTestCase(ShedApiTestCase):
         params = {"id": repository.id}
         if changeset_revision:
             params["changeset_revision"] = changeset_revision
-        url = "/repository/manage_repository"
-        if self.is_v2:
-            url = f"/repositories/{repository.id}"
+        url = f"/repositories/{repository.id}"
         self.visit_url(url, params=params)
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
@@ -1648,25 +1622,11 @@ class ShedTwillTestCase(ShedApiTestCase):
             # Changeset revision should never be provided unless repository name also is.
             assert repository_name is not None, "Changeset revision is present, but repository name is not - aborting."
             url += f"/{changeset_revision}"
-        if self.is_v2:
-            # I think pagination broke this legacy test - so I added this
-            url += "?rows_per_page=250"
+        # I think pagination broke this legacy test - so I added this
+        url += "?rows_per_page=250"
         self.visit_url(url)
         self.check_for_strings(strings_displayed, strings_not_displayed)
-        if self.is_v2:
-            self.check_for_strings(strings_displayed_in_iframe, strings_not_displayed_in_iframe)
-        else:
-            # Now load the page that should be displayed inside the iframe and check for strings.
-            if encoded_repository_id:
-                params = {"id": encoded_repository_id, "operation": "view_or_manage_repository"}
-                if changeset_revision:
-                    params["changeset_revision"] = changeset_revision
-                self.visit_url("/repository/view_repository", params=params)
-                self.check_for_strings(strings_displayed_in_iframe, strings_not_displayed_in_iframe)
-            elif encoded_user_id:
-                params = {"user_id": encoded_user_id, "operation": "repositories_by_user"}
-                self.visit_url("/repository/browse_repositories", params=params)
-                self.check_for_strings(strings_displayed_in_iframe, strings_not_displayed_in_iframe)
+        self.check_for_strings(strings_displayed_in_iframe, strings_not_displayed_in_iframe)
 
     def load_changeset_in_tool_shed(
         self, repository_id, changeset_revision, strings_displayed=None, strings_not_displayed=None
@@ -1758,13 +1718,8 @@ class ShedTwillTestCase(ShedApiTestCase):
         return tip_ctx.rev() < 0
 
     def reset_metadata_on_selected_repositories(self, repository_ids):
-        if self.is_v2:
-            for repository_id in repository_ids:
-                self.populator.reset_metadata(repository_id)
-        else:
-            self.visit_url("/admin/reset_metadata_on_selected_repositories_in_tool_shed")
-            kwd = dict(repository_ids=repository_ids)
-            self.submit_form(button="reset_metadata_on_selected_repositories_button", **kwd)
+        for repository_id in repository_ids:
+            self.populator.reset_metadata(repository_id)
 
     def reset_metadata_on_installed_repositories(self, repositories):
         assert self._installation_client

lib/tool_shed/test/functional/conftest.py

@@ -1,21 +1,10 @@
-import os
-from collections.abc import (
-    Callable,
-    Generator,
-)
+from collections.abc import Generator
 
 import pytest
 from playwright.sync_api import Browser
 
 from ..base.browser import ShedBrowser
 from ..base.playwrightbrowser import PlaywrightShedBrowser
-from ..base.twillbrowser import TwillShedBrowser
-
-DEFAULT_BROWSER = "playwright"
-
-
-def twill_browser() -> Generator[ShedBrowser, None, None]:
-    yield TwillShedBrowser()
 
 
 def playwright_browser(browser: Browser) -> Generator[ShedBrowser, None, None]:
@@ -23,10 +12,4 @@ def playwright_browser(browser: Browser) -> Generator[ShedBrowser, None, None]:
     yield PlaywrightShedBrowser(page)
 
 
-test_browser = os.environ.get("TOOL_SHED_TEST_BROWSER", DEFAULT_BROWSER)
-if test_browser == "twill":
-    shed_browser: Callable[..., Generator[ShedBrowser, None, None]] = pytest.fixture(scope="class")(twill_browser)
-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}")
+shed_browser = pytest.fixture(scope="class")(playwright_browser)

lib/tool_shed/test/functional/test_0000_basic_repository_features.py

@@ -3,7 +3,6 @@ import logging
 import pytest
 
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 repository_name = "filtering_0000"
@@ -22,15 +21,6 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         self.login(email=common.admin_email, username=common.admin_username)
 
-    @skip_if_api_v2
-    # no replicating the functionality in tool shed 2.0, use Planemo
-    # to create repositories.
-    def test_0005_create_repository_without_categories(self):
-        """Verify that a repository cannot be created unless at least one category has been defined."""
-        strings_displayed = ["No categories have been configured in this instance of the Galaxy Tool Shed"]
-        self.visit_url("/repository/create_repository")
-        self.check_for_strings(strings_displayed=strings_displayed, strings_not_displayed=[])
-
     def test_0010_create_categories(self):
         """Create categories for this test suite"""
         self.create_category(
@@ -73,13 +63,6 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
             categories_to_remove=["Test 0000 Basic Repository Features 1"],
         )
 
-    @skip_if_api_v2
-    def test_0030_grant_write_access(self):
-        """Grant write access to another user"""
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.grant_write_access(repository, usernames=[common.test_user_2_name])
-        self.revoke_write_access(repository, common.test_user_2_name)
-
     def test_0035_upload_filtering_1_1_0(self):
         """Upload filtering_1.1.0.tar to the repository"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
@@ -125,49 +108,6 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
             strings_displayed=strings,
         )
 
-    @skip_if_api_v2
-    def test_0045_alter_repository_states(self):
-        """Test toggling the malicious and deprecated repository flags."""
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.login(email=common.admin_email, username=common.admin_username)
-        self.set_repository_malicious(
-            repository, set_malicious=True, strings_displayed=["The repository tip has been defined as malicious."]
-        )
-        self.set_repository_malicious(
-            repository,
-            set_malicious=False,
-            strings_displayed=["The repository tip has been defined as <b>not</b> malicious."],
-        )
-        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
-        self.set_repository_deprecated(repository, strings_displayed=["has been marked as deprecated"])
-        strings_displayed = ["This repository has been marked as deprecated", "Mark repository as not deprecated"]
-        self.display_manage_repository_page(
-            repository,
-            strings_displayed=strings_displayed,
-            strings_not_displayed=["Reset all repository metadata"],
-        )
-        self.browse_repository(repository)
-        self.set_repository_deprecated(
-            repository, strings_displayed=["has been marked as not deprecated"], set_deprecated=False
-        )
-        strings_displayed = ["Mark repository as deprecated", "Reset all repository metadata"]
-        self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-
-    @skip_if_api_v2
-    # probably not porting this functionality - just test
-    # with Twill for older UI and drop when that is all dropped
-    def test_0050_display_repository_tip_file(self):
-        """Display the contents of filtering.xml in the repository tip revision"""
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        if self._browser.is_twill:
-            self.display_repository_file_contents(
-                repository=repository,
-                filename="filtering.xml",
-                filepath=None,
-                strings_displayed=["1.1.0"],
-                strings_not_displayed=[],
-            )
-
     def test_0055_upload_filtering_txt_file(self):
         """Upload filtering.txt file associated with tool version 1.1.0."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
@@ -201,10 +141,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         tip = self.get_repository_tip(repository)
         self.check_for_valid_tools(repository)
-        if self.is_v2:
-            strings_displayed = []
-        else:
-            strings_displayed = ["Select a revision"]
+        strings_displayed: list[str] = []
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
         self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=2)
         tool_guid = f"{self.url.replace('http://', '').rstrip('/')}/repos/user1/filtering_0000/Filter1/2.2.0"
@@ -248,16 +185,6 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
         readme_content = self._escape_page_content_if_needed("Readme file for filtering 1.1.0")
         self.display_manage_repository_page(repository, strings_displayed=[readme_content])
 
-    @skip_if_api_v2  # not re-implemented in the UI, there are API tests though
-    def test_0085_search_for_valid_filter_tool(self):
-        """Search for the filtering tool by tool ID, name, and version."""
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        tip_changeset = self.get_repository_tip(repository)
-        search_fields = dict(tool_id="Filter1", tool_name="filter", tool_version="2.2.0")
-        self.search_for_valid_tools(
-            search_fields=search_fields, strings_displayed=[tip_changeset], strings_not_displayed=[]
-        )
-
     def test_0090_verify_repository_metadata(self):
         """Verify that resetting the metadata does not change it."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
@@ -284,58 +211,12 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
         self.login(email="baduser@bx.psu.edu", username="repos")
         test_user_1 = self.test_db_util.get_user("baduser@bx.psu.edu")
         assert test_user_1 is None, 'Creating user with public name "repos" succeeded.'
-        if not self.is_v2:
-            # no longer use this terminology but the above test case ensures
-            # the important thing and caught a bug in v2
-            error_message = (
-                "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a public user name."
-            )
-            self.check_for_strings(strings_displayed=[error_message])
 
     def test_0105_contact_repository_owner(self):
         """"""
         # We no longer implement this.
         pass
 
-    @skip_if_api_v2  # v2 doesn't implement repository deleting repositories
-    def test_0110_delete_filtering_repository(self):
-        """Delete the filtering_0000 repository and verify that it no longer has any downloadable revisions."""
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.login(email=common.admin_email, username=common.admin_username)
-        self.delete_repository(repository)
-        metadata = self.populator.get_metadata(repository, downloadable_only=False)
-        for _, value in metadata.root.items():
-            assert not value.downloadable
-        # Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
-        # for metadata_revision in repository.metadata_revisions:
-        #    self.test_db_util.refresh(metadata_revision)
-        # Marking a repository as deleted should result in no metadata revisions being downloadable.
-        # assert True not in [metadata.downloadable for metadata in self._db_repository(repository).metadata_revisions]
-
-    @skip_if_api_v2  # v2 doesn't implement repository deleting repositories
-    def test_0115_undelete_filtering_repository(self):
-        """Undelete the filtering_0000 repository and verify that it now has two downloadable revisions."""
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        self.login(email=common.admin_email, username=common.admin_username)
-        self.undelete_repository(repository)
-        # Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
-        # for metadata_revision in repository.metadata_revisions:
-        #    self.test_db_util.refresh(metadata_revision)
-        # Marking a repository as undeleted should result in all previously downloadable metadata revisions being downloadable again.
-        # In this case, there should be two downloadable revisions, one for filtering 1.1.0 and one for filtering 2.2.0.
-        assert True in [metadata.downloadable for metadata in self._db_repository(repository).metadata_revisions]
-        assert len(self._db_repository(repository).downloadable_revisions) == 2
-
-    @skip_if_api_v2  # not re-implementing in tool shed 2.0
-    def test_0120_enable_email_notifications(self):
-        """Enable email notifications for test user 2 on filtering_0000."""
-        # Log in as test_user_2
-        self.login(email=common.test_user_2_email, username=common.test_user_2_name)
-        # Get the repository, so we can pass the encoded repository id and browse_repositories method to the set_email_alerts method.
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ["Total alerts added: 1, total alerts removed: 0"]
-        self.enable_email_alerts(repository, strings_displayed=strings_displayed)
-
     def test_0125_upload_new_readme_file(self):
         """Upload a new readme file to the filtering_0000 repository and verify that there is no error."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)

lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py

@@ -1,7 +1,6 @@
 import os
 
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 repository_name = "freebayes_0010"
@@ -53,9 +52,8 @@ class TestFreebayesRepository(ShedTwillTestCase):
         )
         strings_displayed = ["Metadata may have been defined", "This file requires an entry", "tool_data_table_conf"]
         self.add_file_to_repository(repository, "freebayes/freebayes.xml", strings_displayed=strings_displayed)
-        if self.is_v2:
-            # opps... not good right?
-            self.populator.reset_metadata(repository)
+        # opps... not good right?
+        self.populator.reset_metadata(repository)
         self.display_manage_repository_page(
             repository, strings_displayed=[self.invalid_tools_labels], strings_not_displayed=["Valid tools"]
         )
@@ -124,17 +122,3 @@ class TestFreebayesRepository(ShedTwillTestCase):
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         target = os.path.join("freebayes", "tool_dependencies.xml")
         self.add_file_to_repository(repository, target)
-
-    @skip_if_api_v2
-    def test_0040_verify_tool_dependencies(self):
-        """Verify that the uploaded tool_dependencies.xml specifies the correct package versions.
-
-        We are at step 7 - Check for the appropriate strings on the manage repository page.
-        Verify that the manage repository page now displays the valid tool dependencies, and that there are no invalid tools shown on the manage page.
-        """
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        strings_displayed = ["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Valid tools", "package"]
-        strings_not_displayed = [self.invalid_tools_labels]
-        self.display_manage_repository_page(
-            repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
-        )

lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py

@@ -1,5 +1,4 @@
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 column_maker_repository_name = "column_maker_0020"
@@ -69,25 +68,6 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
             repository=repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
         )
 
-    @skip_if_api_v2
-    def test_0030_verify_emboss_5_dependencies(self):
-        """Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision."""
-        repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        column_maker_repository = self._get_repository_by_name_and_owner(
-            column_maker_repository_name, common.test_user_1_name
-        )
-        changeset_revision = self.get_repository_tip(column_maker_repository)
-        strings_displayed = [
-            "Tool dependencies",
-            "emboss",
-            "5.0.0",
-            "package",
-            "user1",
-            changeset_revision,
-            "Repository dependencies",
-        ]
-        self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-
     def test_0040_verify_repository_metadata(self):
         """Verify that resetting the metadata does not change it."""
         emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)

lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py

@@ -1,5 +1,4 @@
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 column_maker_repository_name = "column_maker_0030"
@@ -160,27 +159,6 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase):
             repository=emboss_repository, repository_tuples=[emboss_tuple], filepath=repository_dependencies_path
         )
 
-    @skip_if_api_v2
-    def test_0050_verify_repository_dependency_revisions(self):
-        """Verify that different metadata revisions of the emboss repository have different repository dependencies."""
-        repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        repository_metadata = [
-            (metadata.metadata, metadata.changeset_revision) for metadata in self.get_repository_metadata(repository)
-        ]
-        column_maker_repository = self._get_repository_by_name_and_owner(
-            column_maker_repository_name, common.test_user_1_name
-        )
-        column_maker_tip = self.get_repository_tip(column_maker_repository)
-        strings_displayed = []
-        # Iterate through all metadata revisions and check for repository dependencies.
-        for _metadata, changeset_revision in repository_metadata:
-            # Add the dependency description and bismark repository details to the strings to check.
-            strings_displayed = ["column_maker_0030", "user1", column_maker_tip]
-            strings_displayed.extend(["Tool dependencies", "emboss", "5.0.0", "package"])
-            self.display_manage_repository_page(
-                repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed
-            )
-
     def test_0055_verify_repository_metadata(self):
         """Verify that resetting the metadata does not change it."""
         emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)

lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py

@@ -1,5 +1,4 @@
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 freebayes_repository_name = "freebayes_0040"
@@ -127,13 +126,3 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase):
         )
         for repository in [freebayes_repository, filtering_repository]:
             self.verify_unchanged_repository_metadata(repository)
-
-    @skip_if_api_v2
-    def test_0040_verify_tool_dependencies(self):
-        """Verify that freebayes displays tool dependencies."""
-        repository = self._get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(
-            repository,
-            strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Valid tools", "package"],
-            strings_not_displayed=["Invalid tools"],
-        )

lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py

@@ -1,5 +1,4 @@
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 emboss_repository_name = "emboss_0050"
@@ -242,24 +241,6 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
         self.check_repository_dependency(filtering_repository, emboss_repository)
         for repository in [bismark_repository, emboss_repository, column_repository]:
             self.check_repository_dependency(freebayes_repository, repository)
-        if not self.is_v2:
-            strings_displayed = ["freebayes_0050 depends on freebayes_0050, emboss_0050, column_maker_0050."]
-            self.display_manage_repository_page(freebayes_repository, strings_displayed=strings_displayed)
-
-    @skip_if_api_v2
-    def test_0050_verify_tool_dependencies(self):
-        """Check that freebayes and emboss display tool dependencies."""
-        freebayes_repository = self._get_repository_by_name_and_owner(
-            freebayes_repository_name, common.test_user_1_name
-        )
-        emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        self.display_manage_repository_page(
-            freebayes_repository,
-            strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Tool dependencies", "package"],
-        )
-        self.display_manage_repository_page(
-            emboss_repository, strings_displayed=["Tool dependencies", "emboss", "5.0.0", "package"]
-        )
 
     def test_0055_verify_repository_metadata(self):
         """Verify that resetting the metadata does not change it."""

lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py

@@ -1,8 +1,6 @@
 import logging
-import os
 
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 log = logging.getLogger(__name__)
@@ -43,11 +41,6 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase):
             strings_displayed=[],
         )
         self.add_file_to_repository(repository, "bwa/complex/tool_dependencies.xml")
-        if not self.is_v2:
-            # Visit the manage repository page for package_bwa_0_5_9_0100.
-            self.display_manage_repository_page(
-                repository, strings_displayed=["Tool dependencies", "will not be", "to this repository"]
-            )
 
     def test_0010_create_bwa_base_repository(self):
         """Create and populate bwa_base_0100."""
@@ -183,43 +176,3 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase):
             version="0.5.9",
         )
         self.check_repository_dependency(base_repository, depends_on_repository=tool_repository)
-        if not self.is_v2:
-            self.display_manage_repository_page(
-                base_repository, strings_displayed=["bwa", "0.5.9", "package", changeset_revision]
-            )
-
-    @skip_if_api_v2
-    def test_0040_generate_tool_dependency(self):
-        """Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision."""
-        # The base_repository named bwa_base_repository_0100 is the dependent repository.
-        base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
-        # The repository named package_bwa_0_5_9_0100 is the required repository.
-        tool_repository = self._get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
-        previous_changeset = self.get_repository_tip(tool_repository)
-        old_tool_dependency = self.get_filename(os.path.join("bwa", "complex", "readme", "tool_dependencies.xml"))
-        new_tool_dependency_path = self.generate_temp_path("test_1100", additional_paths=["tool_dependency"])
-        xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, "tool_dependencies.xml"))
-        # Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem.
-        open(xml_filename, "w").write(
-            open(old_tool_dependency).read().replace("__PATH__", self.get_filename("bwa/complex"))
-        )
-        self.add_file_to_repository(tool_repository, xml_filename, "tool_dependencies.xml")
-        # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
-        repository_tip = self.get_repository_tip(tool_repository)
-        strings_displayed = ["bwa", "0.5.9", "package"]
-        strings_displayed.append(repository_tip)
-        strings_not_displayed = [previous_changeset]
-        self.display_manage_repository_page(
-            tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
-        )
-        # Visit the manage page of the package_bwa_0_5_9_0100 to confirm the valid tool dependency definition.
-        self.display_manage_repository_page(
-            tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
-        )
-        # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition
-        # and the updated changeset revision (updated tip) of the package_bwa_0_5_9_0100 repository is displayed
-        # as the required repository revision.  The original revision defined in the previously uploaded
-        # tool_dependencies.xml file will be updated.
-        self.display_manage_repository_page(
-            base_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
-        )

lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py

@@ -99,8 +99,6 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
         repository = self._get_repository_by_name_and_owner(tool_repository_name, common.test_user_1_name)
         strings_displayed = ["blastxml_to_top_descr_0120", "BLAST top hit descriptions", "Make a table from BLAST XML"]
         strings_displayed.append("0.0.1")
-        if not self.is_v2:
-            strings_displayed.append("Valid tools")
         self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
 
     def test_0025_create_repository_dependency(self):

lib/tool_shed/test/functional/test_0140_tool_help_images.py

@@ -1,7 +1,6 @@
 import logging
 
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 log = logging.getLogger(__name__)
@@ -54,27 +53,3 @@ class TestToolHelpImages(ShedTwillTestCase):
             "htseq_count/htseq_count.tar",
             commit_message="Uploaded htseq_count.tar.",
         )
-
-    @skip_if_api_v2
-    def test_0010_load_tool_page(self):
-        """Load the tool page and check for the image.
-
-        We are at step 2
-        Visit the manage_repository page and the tool page, and look for the image url
-        similar to the following string:
-
-        src="/repository/static/images/<id>/count_modes.png"
-        """
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        # Get the repository tip.
-        changeset_revision = self.get_repository_tip(repository)
-        self.display_manage_repository_page(repository)
-        # Generate the image path.
-        image_path = f'src="/repository/static/images/{repository.id}/count_modes.png"'
-        # The repository uploaded in this test should only have one metadata revision, with one tool defined, which
-        # should be the tool that contains a link to the image.
-        repository_metadata = self._db_repository(repository).metadata_revisions[0].metadata
-        tool_path = repository_metadata["tools"][0]["tool_config"]
-        self.load_display_tool_page(
-            repository, tool_path, changeset_revision, strings_displayed=[image_path], strings_not_displayed=[]
-        )

lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py

@@ -123,9 +123,4 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
         matplotlib_repository = self._get_repository_by_name_and_owner(
             matplotlib_repository_name, common.test_user_1_name
         )
-        changeset_revision = self.get_repository_tip(numpy_repository)
         self.check_repository_dependency(matplotlib_repository, depends_on_repository=numpy_repository)
-        if not self.is_v2:
-            self.display_manage_repository_page(
-                matplotlib_repository, strings_displayed=["numpy", "1.7", "package", changeset_revision]
-            )

lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py

@@ -86,11 +86,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user
-        if self.is_v2:
-            strings_displayed = []
-        else:
-            strings_displayed = ["/repository/browse_repositories", encoded_user_id, "operation=repositories_by_user"]
-            strings_displayed.append(encoded_user_id)
+        strings_displayed: list[str] = []
         strings_displayed_in_iframe = ["user1", "filtering_0420", repository_description]
         self.load_citable_url(
             username="user1",
@@ -116,19 +112,13 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/bview_repository?id=<encoded repository ID>
-        if self.is_v2:
-            strings_displayed = []
-        else:
-            strings_displayed = ["/repository", "view_repository", "id=", encoded_repository_id]
+        strings_displayed: list[str] = []
         strings_displayed_in_iframe = [
             "user1",
             "filtering_0420",
             self._escape_page_content_if_needed(repository_long_description),
         ]
         strings_displayed_in_iframe.append(self.get_repository_tip(repository))
-        if not self.is_v2:
-            strings_displayed_in_iframe.append("Link to this repository:")
-            strings_displayed_in_iframe.append(f"{self.url}/view/user1/filtering_0420")
         self.load_citable_url(
             username="user1",
             repository_name="filtering_0420",
@@ -153,19 +143,13 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/view_repository?id=<encoded repository ID>
-        if self.is_v2:
-            strings_displayed = []
-        else:
-            strings_displayed = ["/repository", "view_repository", f"id={encoded_repository_id}"]
+        strings_displayed: list[str] = []
         strings_displayed_in_iframe = [
             "user1",
             "filtering_0420",
             self._escape_page_content_if_needed(repository_long_description),
             first_changeset_hash,
         ]
-        if not self.is_v2:
-            strings_displayed_in_iframe.append("Link to this repository revision:")
-            strings_displayed_in_iframe.append(f"{self.url}/view/user1/filtering_0420/{first_changeset_hash}")
         self.load_citable_url(
             username="user1",
             repository_name="filtering_0420",
@@ -183,16 +167,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         encoded_user_id = self.security.encode_id(test_user_1.id)
         encoded_repository_id = repository.id
         invalid_changeset_hash = "invalid"
-        if not self.is_v2:
-            # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
-            # then directly load the url that the iframe should be loading and check for the expected strings.
-            # The iframe should point to /repository/view_repository?id=<encoded repository ID>&status=error
-            strings_displayed = ["/repository", "view_repository", f"id={encoded_repository_id}"]
-            strings_displayed.extend(
-                ["The+change+log", "does+not+include+revision", invalid_changeset_hash, "status=error"]
-            )
-        else:
-            strings_displayed = ["The change log does not include revision " + invalid_changeset_hash]
+        strings_displayed = ["The change log does not include revision " + invalid_changeset_hash]
         self.load_citable_url(
             username="user1",
             repository_name="filtering_0420",
@@ -213,16 +188,8 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
         # then directly load the url that the iframe should be loading and check for the expected strings.
         # The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user
-        if not self.is_v2:
-            strings_displayed = ["/repository", "browse_repositories", "user1"]
-            strings_displayed.extend(
-                ["list+of+repositories+owned", "does+not+include+one+named", "%21%21invalid%21%21", "status=error"]
-            )
-            strings_displayed_in_iframe = ["user1", "filtering_0420"]
-            strings_displayed_in_iframe.append("Repositories Owned by user1")
-        else:
-            strings_displayed = ["Repository user1/!!invalid!! is not found"]
-            strings_displayed_in_iframe = []
+        strings_displayed = ["Repository user1/!!invalid!! is not found"]
+        strings_displayed_in_iframe: list[str] = []
         self.load_citable_url(
             username="user1",
             repository_name="!!invalid!!",
@@ -239,10 +206,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
         We are at step 8.
         Visit the following url and check for appropriate strings: <tool shed base url>/view/!!invalid!!
         """
-        if not self.is_v2:
-            strings_displayed = ["The tool shed", self.url, "contains no repositories owned by", "!!invalid!!"]
-        else:
-            strings_displayed = ["No repositories found"]
+        strings_displayed = ["No repositories found"]
         self.load_citable_url(
             username="!!invalid!!",
             repository_name=None,

lib/tool_shed/test/functional/test_0430_browse_utilities.py

@@ -1,7 +1,6 @@
 import logging
 
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 log = logging.getLogger(__name__)
@@ -83,37 +82,3 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
             "freebayes/freebayes.tar",
             commit_message="Uploaded freebayes.tar.",
         )
-
-    @skip_if_api_v2
-    def test_0030_browse_tools(self):
-        """Load the page to browse tools.
-
-        We are at step 3.
-        Verify the existence of emboss tools in the browse tools page.
-        """
-        repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        changeset_revision = self.get_repository_tip(repository)
-        strings_displayed = ["EMBOSS", "antigenic1", "5.0.0", changeset_revision, "user1", "emboss_0430"]
-        self.browse_tools(strings_displayed=strings_displayed)
-
-    @skip_if_api_v2
-    def test_0040_browse_tool_dependencies(self):
-        """Browse tool dependencies and look for the right versions of freebayes and samtools.
-
-        We are at step 4.
-        Verify that the browse tool dependencies page shows the correct dependencies defined for freebayes_0430.
-        """
-        freebayes_repository = self._get_repository_by_name_and_owner(
-            freebayes_repository_name, common.test_user_1_name
-        )
-        freebayes_changeset_revision = self.get_repository_tip(freebayes_repository)
-        strings_displayed = [
-            freebayes_changeset_revision,
-            "freebayes_0430",
-            "user1",
-            "0.9.4_9696d0ce8a96",
-            "freebayes",
-            "samtools",
-            "0.1.18",
-        ]
-        self.browse_tool_dependencies(strings_displayed=strings_displayed)

lib/tool_shed/test/functional/test_0460_upload_to_repository.py

@@ -125,15 +125,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url.
         """
         repository = self._get_repository_by_name_and_owner("complex_dependency_test_1_0460", common.test_user_1_name)
-        package_repository = self._get_repository_by_name_and_owner("package_bwa_0_5_9_0460", common.test_user_1_name)
         self.add_file_to_repository(repository, "0460_files/tool_dependencies.xml")
-        if not self.is_v2:
-            changeset_revision = self.get_repository_tip(package_repository)
-            strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
-            self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-            self.display_repository_file_contents(
-                repository, filename="tool_dependencies.xml", strings_displayed=[changeset_revision]
-            )
 
     def test_0025_populate_complex_dependency_test_2_0460(self):
         """Populate complex_dependency_test_2_0460.
@@ -142,19 +134,11 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url.
         """
         repository = self._get_repository_by_name_and_owner("complex_dependency_test_2_0460", common.test_user_1_name)
-        package_repository = self._get_repository_by_name_and_owner("package_bwa_0_5_9_0460", common.test_user_1_name)
         self.commit_tar_to_repository(
             repository,
             "0460_files/tool_dependencies_in_root.tar",
             commit_message="Uploaded complex repository dependency definition.",
         )
-        if not self.is_v2:
-            changeset_revision = self.get_repository_tip(package_repository)
-            strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
-            self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-            self.display_repository_file_contents(
-                repository, filename="tool_dependencies.xml", strings_displayed=[changeset_revision]
-            )
 
     def test_0030_populate_complex_dependency_test_3_0460(self):
         """Populate complex_dependency_test_3_0460.
@@ -163,22 +147,11 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         specifies a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url.
         """
         repository = self._get_repository_by_name_and_owner("complex_dependency_test_3_0460", common.test_user_1_name)
-        package_repository = self._get_repository_by_name_and_owner("package_bwa_0_5_9_0460", common.test_user_1_name)
         self.commit_tar_to_repository(
             repository,
             "0460_files/tool_dependencies_in_subfolder.tar",
             commit_message="Uploaded complex repository dependency definition.",
         )
-        changeset_revision = self.get_repository_tip(package_repository)
-        if not self.is_v2:
-            strings_displayed = ["package_bwa_0_5_9_0460", "bwa", "0.5.9", "package", changeset_revision]
-            self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-            self.display_repository_file_contents(
-                repository,
-                filename="tool_dependencies.xml",
-                filepath="subfolder",
-                strings_displayed=[changeset_revision],
-            )
 
     def test_0035_create_repositories_for_url_upload(self):
         """Create and populate hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460.
@@ -245,15 +218,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         repository = self._get_repository_by_name_and_owner(
             "repository_dependency_test_1_0460", common.test_user_1_name
         )
-        package_repository = self._get_repository_by_name_and_owner(bwa_repository_name, common.test_user_1_name)
         self.add_file_to_repository(repository, "0460_files/repository_dependencies.xml")
-        changeset_revision = self.get_repository_tip(package_repository)
-        if not self.is_v2:
-            strings_displayed = [bwa_repository_name, "user1", changeset_revision]
-            self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-            self.display_repository_file_contents(
-                repository, filename="repository_dependencies.xml", strings_displayed=[changeset_revision]
-            )
 
     def test_0060_populate_repository_dependency_test_2_0460(self):
         """Populate repository_dependency_test_2_0460.
@@ -263,19 +228,11 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         repository = self._get_repository_by_name_and_owner(
             "repository_dependency_test_2_0460", common.test_user_1_name
         )
-        package_repository = self._get_repository_by_name_and_owner(bwa_repository_name, common.test_user_1_name)
         self.commit_tar_to_repository(
             repository,
             "0460_files/in_root/repository_dependencies_in_root.tar",
             commit_message="Uploaded complex repository dependency definition.",
         )
-        changeset_revision = self.get_repository_tip(package_repository)
-        if not self.is_v2:
-            strings_displayed = [bwa_repository_name, "user1", changeset_revision]
-            self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-            self.display_repository_file_contents(
-                repository, filename="repository_dependencies.xml", strings_displayed=[changeset_revision]
-            )
 
     def test_0065_populate_repository_dependency_test_3_0460(self):
         """Populate repository_dependency_test_3_0460.
@@ -286,22 +243,11 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
         repository = self._get_repository_by_name_and_owner(
             "repository_dependency_test_3_0460", common.test_user_1_name
         )
-        package_repository = self._get_repository_by_name_and_owner(bwa_repository_name, common.test_user_1_name)
         self.commit_tar_to_repository(
             repository,
             "0460_files/in_subfolder/repository_dependencies_in_subfolder.tar",
             commit_message="Uploaded complex repository dependency definition.",
         )
-        changeset_revision = self.get_repository_tip(package_repository)
-        if not self.is_v2:
-            strings_displayed = [bwa_repository_name, "user1", changeset_revision]
-            self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
-            self.display_repository_file_contents(
-                repository,
-                filename="repository_dependencies.xml",
-                filepath="subfolder",
-                strings_displayed=[changeset_revision],
-            )
 
     def test_0070_create_repositories_for_url_upload(self):
         """Create and populate hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460.

lib/tool_shed/test/functional/test_0530_repository_admin_feature.py

@@ -1,7 +1,6 @@
 import logging
 
 from ..base import common
-from ..base.api import skip_if_api_v2
 from ..base.twilltestcase import ShedTwillTestCase
 
 log = logging.getLogger(__name__)
@@ -97,23 +96,6 @@ class TestRepositoryAdminRole(ShedTwillTestCase):
         repository = self._get_repository_by_name_and_owner("renamed_filtering_0530", common.test_user_1_name)
         assert repository.name == "renamed_filtering_0530", "Repository was not renamed to renamed_filtering_0530."
 
-    @skip_if_api_v2
-    def test_0030_verify_access_denied(self):
-        """Make sure a non-admin user can't modify the repository.
-
-        This is step 6 - Log into the Tool Shed as a user that is not the repository owner (e.g., user2) and make sure the repository
-        name and description cannot be changed.
-        """
-        self.login(email=common.test_user_2_email, username=common.test_user_2_name)
-        repository = self._get_repository_by_name_and_owner("renamed_filtering_0530", common.test_user_1_name)
-        strings_not_displayed = ["Manage repository"]
-        strings_displayed = ["View repository"]
-        self.display_manage_repository_page(repository, strings_not_displayed=strings_not_displayed)
-        self.submit_form(form_no=0, button="edit_repository_button", description="This description has been modified.")
-        strings_displayed = ["You are not the owner of this repository, so you cannot administer it."]
-        strings_not_displayed = ["The repository information has been updated."]
-        self.check_for_strings(strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)
-
     def test_0035_grant_admin_role(self):
         """Grant the repository admin role to user2.
 

lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py

@@ -68,11 +68,6 @@ class TestGetUpdatedMetadata(ShedTwillTestCase):
             freebayes_repository,
             "0550_files/package_freebayes_1_0550.tgz",
         )
-        if not self.is_v2:
-            # Visit the manage repository page for package_freebayes_0_5_9_0100.
-            self.display_manage_repository_page(
-                freebayes_repository, strings_displayed=["Tool dependencies", "will not be", "to this repository"]
-            )
 
     def test_0010_create_samtools_repository(self):
         """Create and populate the package_samtools_0550 repository."""
@@ -110,12 +105,8 @@ class TestGetUpdatedMetadata(ShedTwillTestCase):
 
     def test_0020_check_repository_dependency(self):
         """Make filtering depend on samtools and freebayes."""
-        freebayes = self._get_repository_by_name_and_owner(repositories["freebayes"]["name"], common.test_user_1_name)
-        samtools = self._get_repository_by_name_and_owner(repositories["samtools"]["name"], common.test_user_1_name)
-        filtering = self._get_repository_by_name_and_owner(repositories["filtering"]["name"], common.test_user_1_name)
-        strings_displayed = [freebayes.id, samtools.id]
-        if not self.is_v2:
-            self.display_manage_repository_page(filtering, strings_displayed=strings_displayed)
+        # Note: test not yet implemented in v2
+        pass
 
     def test_0025_update_dependent_repositories(self):
         """

lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py

@@ -41,11 +41,6 @@ class TestToolWithToolDependencies(ShedTwillTestCase):
         self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
         category = self.populator.get_category_with_name(category_name)
         self.browse_category(category, strings_displayed=[repository_name])
-        if not self.is_v2:
-            strings_displayed = [repository_name, "Valid tools", "Tool dependencies"]
-            self.preview_repository_in_tool_shed(
-                repository_name, common.test_user_1_name, strings_displayed=strings_displayed
-            )
 
     def test_0015_install_freebayes_repository(self):
         """Install the freebayes repository without installing tool dependencies."""

lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py

@@ -71,12 +71,6 @@ class TestToolWithRepositoryDependencies(ShedTwillTestCase):
         self.browse_tool_shed(url=self.url, strings_displayed=["Test 0020 Basic Repository Dependencies"])
         category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies")
         self.browse_category(category, strings_displayed=[emboss_repository_name])
-        if not self.is_v2:
-            self.preview_repository_in_tool_shed(
-                emboss_repository_name,
-                common.test_user_1_name,
-                strings_displayed=[emboss_repository_name, "Valid tools"],
-            )
 
     def test_0015_install_emboss_repository(self):
         """Install the emboss repository without installing tool dependencies."""

lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py

@@ -138,12 +138,6 @@ class TestRepositoryWithDependencyRevisions(ShedTwillTestCase):
         self.browse_tool_shed(url=self.url, strings_displayed=["Test 0030 Repository Dependency Revisions"])
         category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions")
         self.browse_category(category, strings_displayed=[emboss_repository_name])
-        if not self.is_v2:
-            self.preview_repository_in_tool_shed(
-                emboss_repository_name,
-                common.test_user_1_name,
-                strings_displayed=[emboss_repository_name, "Valid tools"],
-            )
 
     def test_0015_install_emboss_repository(self):
         """Install the emboss repository without installing tool dependencies."""

lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py

@@ -258,31 +258,11 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
         self.check_repository_dependency(filtering_repository, emboss_repository)
         for repository in [bismark_repository, emboss_repository, column_repository]:
             self.check_repository_dependency(freebayes_repository, repository)
-        freebayes_dependencies = [
-            freebayes_repository,
-            emboss_repository,
-            column_repository,
-        ]
-        strings_displayed = [
-            f"{freebayes_repository.name} depends on {', '.join(repo.name for repo in freebayes_dependencies)}."
-        ]
-        if not self.is_v2:
-            self.display_manage_repository_page(freebayes_repository, strings_displayed=strings_displayed)
 
     def test_0050_verify_tool_dependencies(self):
         """Check that freebayes and emboss display tool dependencies."""
-        freebayes_repository = self._get_repository_by_name_and_owner(
-            freebayes_repository_name, common.test_user_1_name
-        )
-        emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
-        if not self.is_v2:
-            self.display_manage_repository_page(
-                freebayes_repository,
-                strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Tool dependencies"],
-            )
-            self.display_manage_repository_page(
-                emboss_repository, strings_displayed=["Tool dependencies", "emboss", "5.0.0", "package"]
-            )
+        # Note: test not yet implemented in v2
+        pass
 
     def test_0055_install_column_repository(self):
         """Install column_maker with repository dependencies."""

lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py

@@ -71,19 +71,6 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
         Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb,
         the datatypes that are defined in datatypes_conf.xml.
         """
-        repository = self._get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_2_name)
-        strings_displayed = [
-            "BlastXml",
-            "BlastNucDb",
-            "BlastProtDb",
-            "application/xml",
-            "text/html",
-            "blastxml",
-            "blastdbn",
-            "blastdbp",
-        ]
-        if not self.is_v2:
-            self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
 
     def test_0015_create_tool_repository(self):
         """Create and populate the blastxml_to_top_descr_0120 repository

lib/tool_shed/test/functional/test_1160_tool_help_images.py

@@ -58,17 +58,6 @@ class TestToolHelpImages(ShedTwillTestCase):
 
         This is a duplicate of test method _0010 in test_0140_tool_help_images.
         """
-        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        # Get the repository tip.
-        changeset_revision = self.get_repository_tip(repository)
-        # Generate the image path.
-        image_path = f'src="/repository/static/images/{repository.id}/count_modes.png"'
-        # The repository uploaded in this test should only have one metadata revision, with one tool defined, which
-        # should be the tool that contains a link to the image.
-        repository_metadata = self._db_repository(repository).metadata_revisions[0].metadata
-        tool_path = repository_metadata["tools"][0]["tool_config"]
-        # V2 is not going to have this page right? So... do we need this test at all or that route? Likely not?
-        if self._browser.is_twill and not self.is_v2:
-            self.load_display_tool_page(
-                repository, tool_path, changeset_revision, strings_displayed=[image_path], strings_not_displayed=[]
-            )
+        # TODO: replace with API-based tool metadata check or Vue route.
+        # load_display_tool_page depends on deleted Mako route (/repository/display_tool).
+        pass

lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py

@@ -132,12 +132,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
         matplotlib_repository = self._get_repository_by_name_and_owner(
             matplotlib_repository_name, common.test_user_1_name
         )
-        changeset_revision = self.get_repository_tip(numpy_repository)
         self.check_repository_dependency(matplotlib_repository, depends_on_repository=numpy_repository)
-        if not self.is_v2:
-            self.display_manage_repository_page(
-                matplotlib_repository, strings_displayed=["numpy", "1.7", "package", changeset_revision]
-            )
 
     def test_0025_install_matplotlib_repository(self):
         """Install the package_matplotlib_1_2_0170 repository.

lib/tool_shed/test/functional/test_component_showcase.py

@@ -1,7 +1,7 @@
 """Playwright tests for component showcase screenshots.
 
 Run with:
-    TOOL_SHED_TEST_SCREENSHOTS=/tmp/component_screenshots TOOL_SHED_API_VERSION=v2 uv run pytest \
+    TOOL_SHED_TEST_SCREENSHOTS=/tmp/component_screenshots uv run pytest \
         tool_shed/test/functional/test_component_showcase.py -v
 
 Screenshots are saved to TOOL_SHED_TEST_SCREENSHOTS directory if set.
@@ -13,7 +13,6 @@ from pathlib import Path
 
 from playwright.sync_api import expect
 
-from ..base.api import skip_if_api_v1
 from ..base.playwrighttestcase import PlaywrightTestCase
 
 
@@ -47,43 +46,36 @@ class TestComponentShowcase(PlaywrightTestCase):
 
     # === General Components ===
 
-    @skip_if_api_v1
     def test_loading_div(self):
         """Screenshot LoadingDiv component."""
         self._navigate_to_showcase()
         self._screenshot_component("LoadingDiv")
 
-    @skip_if_api_v1
     def test_error_banner(self):
         """Screenshot ErrorBanner component."""
         self._navigate_to_showcase()
         self._screenshot_component("ErrorBanner")
 
-    @skip_if_api_v1
     def test_repository_link(self):
         """Screenshot RepositoryLink component."""
         self._navigate_to_showcase()
         self._screenshot_component("RepositoryLink")
 
-    @skip_if_api_v1
     def test_repository_actions(self):
         """Screenshot RepositoryActions component."""
         self._navigate_to_showcase()
         self._screenshot_component("RepositoryActions")
 
-    @skip_if_api_v1
     def test_recently_created_repositories(self):
         """Screenshot RecentlyCreatedRepositories component."""
         self._navigate_to_showcase()
         self._screenshot_component("RecentlyCreatedRepositories")
 
-    @skip_if_api_v1
     def test_landing_search_box(self):
         """Screenshot LandingSearchBox component."""
         self._navigate_to_showcase()
         self._screenshot_component("LandingSearchBox")
 
-    @skip_if_api_v1
     def test_landing_info_sections(self):
         """Screenshot LandingInfoSections component."""
         self._navigate_to_showcase()
@@ -91,37 +83,31 @@ class TestComponentShowcase(PlaywrightTestCase):
 
     # === MetadataInspector Components ===
 
-    @skip_if_api_v1
     def test_changeset_summary_table(self):
         """Screenshot ChangesetSummaryTable component."""
         self._navigate_to_showcase()
         self._screenshot_component("ChangesetSummaryTable")
 
-    @skip_if_api_v1
     def test_json_diff_viewer(self):
         """Screenshot JsonDiffViewer component."""
         self._navigate_to_showcase()
         self._screenshot_component("JsonDiffViewer")
 
-    @skip_if_api_v1
     def test_metadata_json_viewer(self):
         """Screenshot MetadataJsonViewer component."""
         self._navigate_to_showcase()
         self._screenshot_component("MetadataJsonViewer")
 
-    @skip_if_api_v1
     def test_revisions_tab(self):
         """Screenshot RevisionsTab component."""
         self._navigate_to_showcase()
         self._screenshot_component("RevisionsTab")
 
-    @skip_if_api_v1
     def test_overview_tab(self):
         """Screenshot OverviewTab component."""
         self._navigate_to_showcase()
         self._screenshot_component("OverviewTab")
 
-    @skip_if_api_v1
     def test_tool_history_tab(self):
         """Screenshot ToolHistoryTab component."""
         self._navigate_to_showcase()

lib/tool_shed/test/functional/test_frontend_admin.py

@@ -1,13 +1,12 @@
 """Playwright tests for admin-only functionality.
 
 Run with:
-    TOOL_SHED_API_VERSION=v2 uv run pytest \
+    uv run pytest \
         tool_shed/test/functional/test_frontend_admin.py -v
 """
 
 from playwright.sync_api import expect
 
-from ..base.api import skip_if_api_v1
 from ..base.playwrighttestcase import PlaywrightTestCase
 
 TEST_CATEGORY_PREFIX = "admintestcategory"
@@ -17,7 +16,6 @@ TEST_REPO_PREFIX = "admintestcolumnmaker"
 class TestFrontendAdmin(PlaywrightTestCase):
     """Frontend tests for admin-only pages and functionality."""
 
-    @skip_if_api_v1
     def test_admin_page_loads_when_logged_in(self):
         """Verify admin page loads for admin user."""
         self.login()
@@ -28,7 +26,6 @@ class TestFrontendAdmin(PlaywrightTestCase):
         # Admin page should show re-index button
         expect(page.get_by_role("button", name="Re-index search")).to_be_visible()
 
-    @skip_if_api_v1
     def test_reindex_search(self):
         """Verify Re-index search button works and returns results."""
         self.login()
@@ -52,7 +49,6 @@ class TestFrontendAdmin(PlaywrightTestCase):
         expect(page.locator("text=repositories_indexed")).to_be_visible(timeout=30000)
         expect(page.locator("text=tools_indexed")).to_be_visible()
 
-    @skip_if_api_v1
     def test_admin_page_screenshot(self):
         """Capture screenshot of admin page with re-index results."""
         self.login()

lib/tool_shed/test/functional/test_frontend_login.py

@@ -1,7 +1,6 @@
 from playwright.sync_api import expect
 
 from galaxy_test.base.api_util import random_name
-from ..base.api import skip_if_api_v1
 from ..base.playwrightbrowser import Locators
 from ..base.playwrighttestcase import PlaywrightTestCase
 
@@ -9,7 +8,6 @@ TEST_PASSWORD = "testpass"
 
 
 class TestFrontendLogin(PlaywrightTestCase):
-    @skip_if_api_v1
     def test_register(self):
         self.visit_url("/")
         page = self._page
@@ -26,7 +24,6 @@ class TestFrontendLogin(PlaywrightTestCase):
         )
         expect(page.locator(Locators.login_submit_button)).to_be_visible()
 
-    @skip_if_api_v1
     def test_create(self):
         user = random_name(prefix="shduser")
         self.create(
@@ -35,14 +32,12 @@ class TestFrontendLogin(PlaywrightTestCase):
             username=user,
         )
 
-    @skip_if_api_v1
     def test_logout(self):
         self._create_and_login()
         self._playwright_browser.expect_logged_in()
         self._playwright_browser.logout_if_logged_in()
         self._playwright_browser.expect_not_logged_in()
 
-    @skip_if_api_v1
     def test_change_password(self):
         self._create_and_login()
 

lib/tool_shed/test/functional/test_frontend_repositories.py

@@ -1,6 +1,5 @@
 from playwright.sync_api import expect
 
-from ..base.api import skip_if_api_v1
 from ..base.playwrighttestcase import PlaywrightTestCase
 
 TEST_CATEGORY_PREFIX = "guitestcategory"
@@ -31,7 +30,6 @@ class TestFrontendRepositories(PlaywrightTestCase):
         self.visit_url(f"/repositories/{repository.id}/metadata-inspector")
         return repository
 
-    @skip_if_api_v1
     def test_metadata_inspector_loads(self):
         """Verify Metadata Inspector page loads with repository data."""
         self._setup_repo_and_visit_inspector()
@@ -43,7 +41,6 @@ class TestFrontendRepositories(PlaywrightTestCase):
         expect(page.locator("[role=tab]").filter(has_text="Tool History")).to_be_visible()
         expect(page.locator("[role=tab]").filter(has_text="Raw JSON")).to_be_visible()
 
-    @skip_if_api_v1
     def test_metadata_inspector_default_tab(self):
         """Verify Revisions is the default landing tab."""
         repository = self._setup_repo_and_visit_inspector()
@@ -52,7 +49,6 @@ class TestFrontendRepositories(PlaywrightTestCase):
         # Revisions tab active by default, repo name visible
         expect(page.locator("body")).to_contain_text(repository.name)
 
-    @skip_if_api_v1
     def test_metadata_inspector_revisions_tab(self):
         """Verify Revisions tab shows changeset data."""
         self._setup_repo_and_visit_inspector()
@@ -62,7 +58,6 @@ class TestFrontendRepositories(PlaywrightTestCase):
         # RevisionsTab uses q-list with expansion items showing changeset hashes
         expect(page.locator(".q-list")).to_be_visible()
 
-    @skip_if_api_v1
     def test_metadata_inspector_reset_tab(self):
         """Verify Reset Metadata tab with admin login."""
         self.login()
@@ -77,7 +72,6 @@ class TestFrontendRepositories(PlaywrightTestCase):
         # Preview button should be visible
         expect(page.get_by_role("button", name="Preview")).to_be_visible()
 
-    @skip_if_api_v1
     def test_metadata_inspector_screenshots(self):
         """Capture screenshots of metadata inspector tabs."""
         self.login()
@@ -114,7 +108,6 @@ class TestFrontendRepositories(PlaywrightTestCase):
         page.wait_for_selector("text=Preview Results")  # Wait for results
         self.screenshot("metadata_inspector_reset_preview")
 
-    @skip_if_api_v1
     def test_metadata_inspector_reset_full(self):
         """Perform a full metadata reset and verify completion."""
         self.login()

lib/tool_shed/test/functional/test_repositories_integration.py

@@ -15,10 +15,7 @@ from sqlalchemy import select
 from galaxy_test.base import api_asserts
 from tool_shed.test.base import test_db_util
 from tool_shed.webapp import model
-from ..base.api import (
-    ShedApiTestCase,
-    skip_if_api_v1,
-)
+from ..base.api import ShedApiTestCase
 
 CORRUPTED_PATH = "/old/wrong/path/column_maker.xml"
 
@@ -88,7 +85,6 @@ def metadata_has_valid_paths(metadata_dict: dict, invalid_prefix: str = "/old/wr
 
 
 class TestRepositoriesIntegration(ShedApiTestCase):
-    @skip_if_api_v1
     def test_reset_metadata_dry_run_shows_corrupted_path_fix(self):
         """Verify dry_run=True shows before/after diff for corrupted tool_config paths.
 
@@ -133,7 +129,6 @@ class TestRepositoriesIntegration(ShedApiTestCase):
             metadata_revision.metadata["tools"][0]["tool_config"] == fixture.corrupted_path
         ), "dry_run should not have modified the database"
 
-    @skip_if_api_v1
     def test_reset_metadata_fixes_corrupted_path_when_not_dry_run(self):
         """Verify non-dry-run reset actually fixes corrupted tool_config paths."""
         repository = self.populator.setup_column_maker_repo(prefix="integfix")

lib/tool_shed/test/functional/test_shed_repositories.py

@@ -18,11 +18,7 @@ from tool_shed_client.schema import (
     RepositoryRevisionMetadata,
     UpdateRepositoryRequest,
 )
-from ..base.api import (
-    ShedApiTestCase,
-    skip_if_api_v1,
-    skip_if_api_v2,
-)
+from ..base.api import ShedApiTestCase
 
 COLUMN_MAKER_PATH = resource_path(__name__, "../test_data/column_maker/column_maker.tar")
 
@@ -130,7 +126,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         assert repository.owner == repo.owner
         assert repository.name == repo.name
 
-    @skip_if_api_v1
     def test_index_pagination(self):
         populator = self.populator
         category1 = populator.new_category(prefix="paginatecat1")
@@ -161,7 +156,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         response = populator.repository_index_paginated(request)
         assert response.total_results == 1
 
-    @skip_if_api_v1
     def test_index_sorting(self):
         populator = self.populator
         category1 = populator.new_category(prefix="paginatecat1")
@@ -184,7 +178,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         assert "_a" in order_of_these[0]
         assert "_z" in order_of_these[1]
 
-    @skip_if_api_v1
     def test_allow_push(self):
         populator = self.populator
         request = {
@@ -216,7 +209,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         assert "sharewith" not in populator.get_usernames_allowed_to_push(repo)
         assert "alsosharewith" in populator.get_usernames_allowed_to_push(repo)
 
-    @skip_if_api_v1
     def test_set_malicious(self):
         populator = self.populator
         repository = populator.setup_column_maker_repo(prefix="repoformalicious")
@@ -231,7 +223,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         populator.unset_malicious(repository, only_revision.changeset_revision)
         assert not populator.tip_is_malicious(repository)
 
-    @skip_if_api_v1
     def test_set_deprecated(self):
         populator = self.populator
         repository = populator.setup_column_maker_repo(prefix="repofordeprecated")
@@ -300,7 +291,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
             else:
                 raise AssertionError("Wrong number of repo tars returned...")
 
-    @skip_if_api_v1
     def test_readmes(self):
         populator = self.populator
         repository = populator.setup_test_data_repo("column_maker_with_readme")
@@ -334,21 +324,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         api_asserts.assert_status_code_is_ok(response)
         populator.assert_has_n_installable_revisions(repository, 3)
 
-    @skip_if_api_v2
-    def test_reset_all_v1(self):
-        populator = self.populator
-        repository = populator.setup_test_data_repo("column_maker_with_download_gaps")
-        populator.assert_has_n_installable_revisions(repository, 3)
-        # resetting one at a time or resetting everything via the web controllers works...
-        # resetting all at once via the API does not work - it breaks the repository
-        response = self.api_interactor.post(
-            "repositories/reset_metadata_on_repositories",
-            data={"payload": "can not be empty because bug in controller"},
-        )
-        api_asserts.assert_status_code_is_ok(response)
-        populator.assert_has_n_installable_revisions(repository, 3)
-
-    @skip_if_api_v1
     def test_reset_all_v2(self):
         populator = self.populator
         repository = populator.setup_test_data_repo("column_maker_with_download_gaps")
@@ -357,7 +332,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         api_asserts.assert_status_code_is_ok(response)
         populator.assert_has_n_installable_revisions(repository, 3)
 
-    @skip_if_api_v1
     def test_reset_metadata_dry_run(self):
         """Verify dry_run=True returns success but doesn't modify repository."""
         populator = self.populator
@@ -379,7 +353,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         # Revisions should still be there (nothing changed)
         populator.assert_has_n_installable_revisions(repository, 3)
 
-    @skip_if_api_v1
     def test_reset_metadata_verbose(self):
         """Verify verbose=True returns per-changeset details."""
         populator = self.populator
@@ -401,7 +374,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
             assert "numeric_revision" in detail
             assert "comparison_result" in detail or "error" in detail
 
-    @skip_if_api_v1
     def test_reset_metadata_dry_run_and_verbose(self):
         """Verify dry_run + verbose returns details without persisting."""
         populator = self.populator
@@ -422,7 +394,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         # Verify repo unchanged
         populator.assert_has_n_installable_revisions(repository, 3)
 
-    @skip_if_api_v1
     def test_reset_metadata_legacy_endpoint_with_dry_run(self):
         """Verify legacy endpoint supports dry_run in request body."""
         populator = self.populator
@@ -438,7 +409,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         assert result["dry_run"] is True
         assert result["changeset_details"] is not None
 
-    @skip_if_api_v1
     def test_reset_metadata_verbose_includes_before_after(self):
         """Verify verbose=True returns repository_metadata_before and after snapshots."""
         populator = self.populator
@@ -469,7 +439,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
                 for tool in rev_data["tools"]:
                     assert "tool_config" in tool
 
-    @skip_if_api_v1
     def test_reset_metadata_non_verbose_omits_before_after(self):
         """Verify verbose=False (default) omits before/after metadata."""
         populator = self.populator
@@ -496,7 +465,6 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         assert only_revision
         return only_revision
 
-    @skip_if_api_v1
     def test_generate_frontend_fixtures(self):
         """Generate JSON fixture files for frontend unit tests.
 

lib/tool_shed/test/functional/test_shed_tools.py

@@ -3,10 +3,7 @@ from tool_shed_client.schema.trs import (
     ToolClass,
 )
 from tool_shed_client.trs_util import encode_identifier
-from ..base.api import (
-    ShedApiTestCase,
-    skip_if_api_v1,
-)
+from ..base.api import ShedApiTestCase
 
 
 class TestShedToolsApi(ShedApiTestCase):
@@ -41,12 +38,10 @@ class TestShedToolsApi(ShedApiTestCase):
             tool_search_hit = response.find_search_hit(repository)
             assert tool_search_hit
 
-    @skip_if_api_v1
     def test_trs_service_info(self):
         service_info = self.api_interactor.get("ga4gh/trs/v2/service-info")
         service_info.raise_for_status()
 
-    @skip_if_api_v1
     def test_trs_tool_classes(self):
         classes_response = self.api_interactor.get("ga4gh/trs/v2/toolClasses")
         classes_response.raise_for_status()
@@ -56,7 +51,6 @@ class TestShedToolsApi(ShedApiTestCase):
         class0 = classes[0]
         assert ToolClass(**class0)
 
-    @skip_if_api_v1
     def test_trs_tool_list(self):
         populator = self.populator
         repository = populator.setup_column_maker_repo(prefix="toolstrsindex")
@@ -67,7 +61,6 @@ class TestShedToolsApi(ShedApiTestCase):
         tool_response.raise_for_status()
         assert Tool(**tool_response.json())
 
-    @skip_if_api_v1
     def test_trs_tool_parameter_json_schema(self):
         populator = self.populator
         repository = populator.setup_column_maker_repo(prefix="toolsparameterschema")
@@ -77,7 +70,6 @@ class TestShedToolsApi(ShedApiTestCase):
         tool_response = self.api_interactor.get(url)
         tool_response.raise_for_status()
 
-    @skip_if_api_v1
     def test_tool_source(self):
         populator = self.populator
         repository = populator.setup_column_maker_repo(prefix="toolsource")

lib/tool_shed/test/functional/test_shed_users.py

@@ -7,10 +7,7 @@ from tool_shed_client.schema import (
     CreateUserRequest,
     User,
 )
-from ..base.api import (
-    ShedApiTestCase,
-    skip_if_api_v1,
-)
+from ..base.api import ShedApiTestCase
 from ..base.api_util import (
     email_to_username,
     ensure_user_with_email,
@@ -80,7 +77,6 @@ class TestShedUsersApi(ShedApiTestCase):
         assert show_response.json()["username"] == username
         assert show_response.json()["id"] == user_id
 
-    @skip_if_api_v1
     def test_api_key_endpoints(self):
         email = "testindexapi@bx.psu.edu"
         password = "mycoolpassword123"

lib/tool_shed/webapp/api/__init__.py

@@ -1,9 +0,0 @@
-from galaxy.webapps.base.controller import BaseAPIController
-from tool_shed.structured_app import ToolShedApp
-
-
-class BaseShedAPIController(BaseAPIController):
-    app: ToolShedApp
-
-    def __init__(self, app: ToolShedApp):
-        super().__init__(app)

lib/tool_shed/webapp/api/authenticate.py

@@ -1,44 +0,0 @@
-"""
-API key retrieval through BaseAuth
-Sample usage:
-
-.. code-block::
-
-    curl --user zipzap@foo.com:password http://localhost:9009/api/authenticate/baseauth
-
-Returns
-
-.. code-block:: json
-
-    {
-        "api_key": "<some api key>"
-    }
-
-"""
-
-import logging
-
-from galaxy.web import expose_api_anonymous_and_sessionless
-from galaxy.webapps.galaxy.api import depends
-from galaxy.webapps.galaxy.services.authenticate import AuthenticationService
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class ToolShedAuthenticationController(BaseShedAPIController):
-    authentication_service = depends(AuthenticationService)
-
-    @expose_api_anonymous_and_sessionless
-    def get_tool_shed_api_key(self, trans, **kwd):
-        """
-        GET /api/authenticate/baseauth
-
-        returns an API key for authenticated user based on BaseAuth headers
-
-        :returns: api_key in json format
-        :rtype:   dict
-
-        :raises: ObjectNotFound, HTTPBadRequest
-        """
-        return self.authentication_service.get_api_key(trans.environ, trans.request)

lib/tool_shed/webapp/api/categories.py

@@ -1,112 +0,0 @@
-import logging
-from typing import (
-    Any,
-)
-
-import tool_shed.util.shed_util_common as suc
-import tool_shed_client.schema
-from galaxy import (
-    util,
-    web,
-)
-from galaxy.web import (
-    expose_api,
-    expose_api_anonymous_and_sessionless,
-    require_admin,
-)
-from galaxy.webapps.galaxy.api import depends
-from tool_shed.managers.categories import CategoryManager
-from tool_shed.managers.repositories import repositories_by_category
-from tool_shed.webapp.model import Category
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class CategoriesController(BaseShedAPIController):
-    """RESTful controller for interactions with categories in the Tool Shed."""
-
-    category_manager: CategoryManager = depends(CategoryManager)
-
-    @expose_api
-    @require_admin
-    def create(self, trans, payload, **kwd):
-        """
-        POST /api/categories
-        Return a dictionary of information about the created category.
-        The following parameters are included in the payload:
-
-        :param name (required): the name of the category
-        :param description (optional): the description of the category (if not provided, the name will be used)
-
-        Example: POST /api/categories/?key=XXXYYYXXXYYY
-        Content-Disposition: form-data; name="name" Category_Name
-        Content-Disposition: form-data; name="description" Category_Description
-        """
-        category_dict = dict(message="", status="ok")
-        request = tool_shed_client.schema.CreateCategoryRequest(
-            name=payload.get("name"),
-            description=payload.get("description", ""),
-        )
-        category: Category = self.category_manager.create(trans, request)
-        category_dict = self.category_manager.to_dict(category)
-        category_dict["message"] = f"Category '{str(category.name)}' has been created"
-        return category_dict
-
-    @expose_api_anonymous_and_sessionless
-    def get_repositories(self, trans, category_id, **kwd):
-        """
-        GET /api/categories/{encoded_category_id}/repositories
-        Return information about the provided category and the repositories in that category.
-
-        :param id: the encoded id of the Category object
-        :param sort_key: the field by which the repositories should be sorted
-        :param sort_order: ascending or descending sort
-        :param page: the page number to return
-
-        Example: GET localhost:9009/api/categories/f9cad7b01a472135/repositories
-        """
-        installable = util.asbool(kwd.get("installable", "false"))
-        sort_key = kwd.get("sort_key", "name")
-        sort_order = kwd.get("sort_order", "asc")
-        page = kwd.get("page", None)
-        category_dict = repositories_by_category(
-            self.app,
-            category_id,
-            page=page,
-            sort_key=sort_key,
-            sort_order=sort_order,
-            installable=installable,
-        )
-        category_dict["url"] = web.url_for(controller="categories", action="show", id=category_dict["id"])
-        return category_dict
-
-    @expose_api_anonymous_and_sessionless
-    def index(self, trans, deleted=False, **kwd) -> list[dict[str, Any]]:
-        """
-        GET /api/categories
-        Return a list of dictionaries that contain information about each Category.
-
-        :param deleted: flag used to include deleted categories
-
-        Example: GET localhost:9009/api/categories
-        """
-        deleted = util.asbool(deleted)
-        return self.category_manager.index(trans, deleted)
-
-    @expose_api_anonymous_and_sessionless
-    def show(self, trans, id, **kwd):
-        """
-        GET /api/categories/{encoded_category_id}
-        Return a dictionary of information about a category.
-
-        :param id: the encoded id of the Category object
-
-        Example: GET localhost:9009/api/categories/f9cad7b01a472135
-        """
-        category = suc.get_category(self.app, id)
-        if category is None:
-            category_dict = dict(message=f"Unable to locate category record for id {str(id)}.", status="error")
-            return category_dict
-        category_dict = self.category_manager.to_dict(category)
-        return category_dict

lib/tool_shed/webapp/api/configuration.py

@@ -1,25 +0,0 @@
-"""
-API operations allowing clients to determine Tool Shed instance's
-capabilities and configuration settings.
-"""
-
-import logging
-
-from galaxy.web import expose_api_anonymous_and_sessionless
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class ConfigurationController(BaseShedAPIController):
-    @expose_api_anonymous_and_sessionless
-    def version(self, trans, **kwds):
-        """
-        GET /api/version
-        Return a description of the version_major and version of Galaxy Tool Shed
-        (e.g. 15.07 and 15.07.dev).
-
-        :rtype:     dict
-        :returns:   dictionary with versions keyed as 'version_major' and 'version'
-        """
-        return {"version_major": self.app.config.version_major, "version": self.app.config.version}

lib/tool_shed/webapp/api/groups.py

@@ -1,180 +0,0 @@
-import logging
-from collections.abc import Callable
-
-from sqlalchemy import select
-
-from galaxy import (
-    util,
-    web,
-)
-from galaxy.exceptions import (
-    AdminRequiredException,
-    ObjectNotFound,
-    RequestParameterMissingException,
-)
-from galaxy.util import (
-    pretty_print_time_interval,
-    UNKNOWN,
-)
-from galaxy.web import (
-    expose_api,
-    expose_api_anonymous_and_sessionless,
-    require_admin,
-)
-from tool_shed.managers import groups
-from tool_shed.structured_app import ToolShedApp
-from tool_shed.webapp.model import (
-    Category,
-    Repository,
-    RepositoryCategoryAssociation,
-    RepositoryMetadata,
-    User,
-)
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class GroupsController(BaseShedAPIController):
-    """RESTful controller for interactions with groups in the Tool Shed."""
-
-    def __init__(self, app: ToolShedApp):
-        super().__init__(app)
-        self.group_manager = groups.GroupManager()
-
-    def __get_value_mapper(self, trans) -> dict[str, Callable]:
-        value_mapper = {"id": trans.security.encode_id}
-        return value_mapper
-
-    @expose_api_anonymous_and_sessionless
-    def index(self, trans, deleted=False, **kwd):
-        """
-        GET /api/groups
-        Return a list of dictionaries that contain information about each Group.
-
-        :param deleted: flag used to include deleted groups
-
-        Example: GET localhost:9009/api/groups
-        """
-        group_dicts = []
-        deleted = util.asbool(deleted)
-        if deleted and not trans.user_is_admin:
-            raise AdminRequiredException("Only administrators can query deleted groups.")
-        for group in self.group_manager.list(trans, deleted):
-            group_dicts.append(self._populate(trans, group))
-        return group_dicts
-
-    @expose_api
-    @require_admin
-    def create(self, trans, payload, **kwd):
-        """
-        POST /api/groups
-        Return a dictionary of information about the created group.
-        The following parameters are included in the payload:
-
-        :param name (required): the name of the group
-        :param description (optional): the description of the group
-
-        Example: POST /api/groups/?key=XXXYYYXXXYYY
-        Content-Disposition: form-data; name="name" Group_Name
-        Content-Disposition: form-data; name="description" Group_Description
-        """
-        group_dict = dict(message="", status="ok")
-        if name := payload.get("name", ""):
-            description = payload.get("description", "")
-            if not description:
-                description = ""
-            else:
-                # TODO add description field to the model
-                group_dict = self.group_manager.create(trans, name=name).to_dict(
-                    view="element", value_mapper=self.__get_value_mapper(trans)
-                )
-        else:
-            raise RequestParameterMissingException('Missing required parameter "name".')
-        return group_dict
-
-    @expose_api_anonymous_and_sessionless
-    def show(self, trans, encoded_id, **kwd):
-        """
-        GET /api/groups/{encoded_group_id}
-        Return a dictionary of information about a group.
-
-        :param id: the encoded id of the Group object
-
-        Example: GET localhost:9009/api/groups/f9cad7b01a472135
-        """
-        decoded_id = trans.security.decode_id(encoded_id)
-        group = self.group_manager.get(trans, decoded_id)
-        if group is None:
-            raise ObjectNotFound("Unable to locate group record with the given id.")
-        return self._populate(trans, group)
-
-    def _populate(self, trans, group):
-        """
-        Turn the given group information from DB into a dict
-        and add other characteristics like members and repositories.
-        """
-        group_dict = group.to_dict(view="collection", value_mapper=self.__get_value_mapper(trans))
-        group_members = []
-        group_repos = []
-        total_downloads = 0
-        for uga in group.users:
-            user = trans.sa_session.get(User, uga.user_id)
-            user_repos_count = 0
-            for repo in get_user_repositories(trans.sa_session, uga.user_id):
-                categories = []
-                for rca in repo.categories:
-                    cat_dict = dict(name=rca.category.name, id=trans.app.security.encode_id(rca.category.id))
-                    categories.append(cat_dict)
-                time_repo_created_full = repo.create_time.strftime("%Y-%m-%d %I:%M %p")
-                time_repo_updated_full = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
-                time_repo_created = pretty_print_time_interval(repo.create_time, True)
-                time_repo_updated = pretty_print_time_interval(repo.update_time, True)
-                # TODO add user ratings
-                total_downloads += repo.times_downloaded
-                group_repos.append(
-                    {
-                        "name": repo.name,
-                        "times_downloaded": repo.times_downloaded,
-                        "owner": repo.user.username,
-                        "time_created_full": time_repo_created_full,
-                        "time_created": time_repo_created,
-                        "time_updated_full": time_repo_updated_full,
-                        "time_updated": time_repo_updated,
-                        "description": repo.description,
-                        "categories": categories,
-                    }
-                )
-                user_repos_count += 1
-            encoded_user_id = trans.app.security.encode_id(user.id)
-            user_repos_url = web.url_for(
-                controller="repository", action="browse_repositories_by_user", user_id=encoded_user_id
-            )
-            time_created = pretty_print_time_interval(user.create_time, True)
-            member_dict = {
-                "id": encoded_user_id,
-                "username": user.username,
-                "user_repos_url": user_repos_url,
-                "user_repos_count": user_repos_count,
-                "user_tools_count": UNKNOWN,
-                "time_created": time_created,
-            }
-            group_members.append(member_dict)
-        group_dict["members"] = group_members
-        group_dict["total_members"] = len(group_members)
-        group_dict["repositories"] = group_repos
-        group_dict["total_repos"] = len(group_repos)
-        group_dict["total_downloads"] = total_downloads
-        return group_dict
-
-
-def get_user_repositories(session, user_id):
-    stmt = (
-        select(Repository)
-        .where(Repository.user_id == user_id)
-        .join(RepositoryMetadata)
-        .join(User)
-        .outerjoin(RepositoryCategoryAssociation)
-        .outerjoin(Category)
-    )
-    return session.scalars(stmt)

lib/tool_shed/webapp/api/repositories.py

@@ -1,734 +0,0 @@
-import json
-import logging
-import os
-from collections.abc import Callable
-from io import StringIO
-from time import strftime
-
-from webob.compat import cgi_FieldStorage
-
-from galaxy import (
-    util,
-    web,
-)
-from galaxy.exceptions import (
-    ActionInputError,
-    InsufficientPermissionsException,
-    MessageException,
-    ObjectNotFound,
-    RequestParameterInvalidException,
-    RequestParameterMissingException,
-)
-from galaxy.web import (
-    expose_api,
-    expose_api_anonymous_and_sessionless,
-    expose_api_raw_anonymous_and_sessionless,
-)
-from galaxy.webapps.base.controller import HTTPBadRequest
-from tool_shed.managers.repositories import (
-    can_update_repo,
-    check_updates,
-    create_repository,
-    get_install_info,
-    get_ordered_installable_revisions,
-    get_repository_metadata_dict,
-    get_value_mapper,
-    index_repositories,
-    index_tool_ids,
-    IndexRequest,
-    reset_metadata_on_repository,
-    search,
-    to_element_dict,
-    UpdatesRequest,
-    upload_tar_and_set_metadata,
-)
-from tool_shed.metadata import repository_metadata_manager
-from tool_shed.repository_types import util as rt_util
-from tool_shed.util import (
-    metadata_util,
-    repository_util,
-    tool_util,
-)
-from tool_shed.webapp import model
-from tool_shed.webapp.model.db import get_repository_by_name_and_owner
-from tool_shed_client.schema import (
-    CreateRepositoryRequest,
-    LegacyInstallInfoTuple,
-)
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class RepositoriesController(BaseShedAPIController):
-    """RESTful controller for interactions with repositories in the Tool Shed."""
-
-    @web.legacy_expose_api
-    def add_repository_registry_entry(self, trans, payload, **kwd):
-        """
-        POST /api/repositories/add_repository_registry_entry
-        Adds appropriate entries to the repository registry for the repository defined by the received name and owner.
-
-        :param key: the user's API key
-
-        The following parameters are included in the payload.
-        :param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
-        :param name (required): the name of the Repository
-        :param owner (required): the owner of the Repository
-        """
-        response_dict = {}
-        if not trans.user_is_admin:
-            response_dict["status"] = "error"
-            response_dict["message"] = "You are not authorized to add entries to this Tool Shed's repository registry."
-            return response_dict
-        tool_shed_url = payload.get("tool_shed_url", "")
-        if not tool_shed_url:
-            raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
-        tool_shed_url = tool_shed_url.rstrip("/")
-        name = payload.get("name", "")
-        if not name:
-            raise HTTPBadRequest(detail="Missing required parameter 'name'.")
-        owner = payload.get("owner", "")
-        if not owner:
-            raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
-        repository = get_repository_by_name_and_owner(self.app.model.context, name, owner)
-        if repository is None:
-            error_message = f"Cannot locate repository with name {name} and owner {owner},"
-            log.debug(error_message)
-            response_dict["status"] = "error"
-            response_dict["message"] = error_message
-            return response_dict
-        # Update the repository registry.
-        self.app.repository_registry.add_entry(repository)
-        response_dict["status"] = "ok"
-        response_dict["message"] = (
-            f"Entries for repository {name} owned by {owner} have been added to the Tool Shed repository registry."
-        )
-        return response_dict
-
-    @web.legacy_expose_api_anonymous
-    def get_ordered_installable_revisions(self, trans, name=None, owner=None, **kwd):
-        """
-        GET /api/repositories/get_ordered_installable_revisions
-
-        :param name: the name of the Repository
-        :param owner: the owner of the Repository
-
-        Returns the ordered list of changeset revision hash strings that are associated with installable revisions.
-        As in the changelog, the list is ordered oldest to newest.
-        """
-        # Example URL: http://localhost:9009/api/repositories/get_ordered_installable_revisions?name=add_column&owner=test
-        if name is None:
-            name = kwd.get("name", None)
-        if owner is None:
-            owner = kwd.get("owner", None)
-        tsr_id = kwd.get("tsr_id", None)
-        return get_ordered_installable_revisions(self.app, name, owner, tsr_id)
-
-    @web.legacy_expose_api_anonymous
-    def get_repository_revision_install_info(
-        self, trans, name, owner, changeset_revision, **kwd
-    ) -> LegacyInstallInfoTuple:
-        """
-        GET /api/repositories/get_repository_revision_install_info
-
-        :param name: the name of the Repository
-        :param owner: the owner of the Repository
-        :param changeset_revision: the changeset_revision of the RepositoryMetadata object associated with the Repository
-
-        Returns a list of the following dictionaries
-
-        - a dictionary defining the Repository.  For example::
-
-            {
-                "deleted": false,
-                "deprecated": false,
-                "description": "add_column hello",
-                "id": "f9cad7b01a472135",
-                "long_description": "add_column hello",
-                "name": "add_column",
-                "owner": "test",
-                "private": false,
-                "times_downloaded": 6,
-                "url": "/api/repositories/f9cad7b01a472135",
-                "user_id": "f9cad7b01a472135"
-            }
-
-        - a dictionary defining the Repository revision (RepositoryMetadata).  For example::
-
-            {
-                "changeset_revision": "3a08cc21466f",
-                "downloadable": true,
-                "has_repository_dependencies": false,
-                "has_repository_dependencies_only_if_compiling_contained_td": false,
-                "id": "f9cad7b01a472135",
-                "includes_datatypes": false,
-                "includes_tool_dependencies": false,
-                "includes_tools": true,
-                "includes_tools_for_display_in_tool_panel": true,
-                "includes_workflows": false,
-                "malicious": false,
-                "repository_id": "f9cad7b01a472135",
-                "url": "/api/repository_revisions/f9cad7b01a472135",
-                "valid_tools": [{u'add_to_tool_panel': True,
-                    u'description': u'data on any column using simple expressions',
-                    u'guid': u'localhost:9009/repos/enis/sample_repo_1/Filter1/2.2.0',
-                    u'id': u'Filter1',
-                    u'name': u'Filter',
-                    u'requirements': [],
-                    u'tests': [{u'inputs': [[u'input', u'1.bed'], [u'cond', u"c1=='chr22'"]],
-                    u'name': u'Test-1',
-                    u'outputs': [[u'out_file1', u'filter1_test1.bed']],
-                    u'required_files': [u'1.bed', u'filter1_test1.bed']}],
-                    u'tool_config': u'database/community_files/000/repo_1/filtering.xml',
-                    u'tool_type': u'default',
-                    u'version': u'2.2.0',
-                    u'version_string_cmd': None}]
-            }
-
-        - a dictionary including the additional information required to install the repository.  For example::
-
-            {
-                "add_column": [
-                    "add_column hello",
-                    "http://test@localhost:9009/repos/test/add_column",
-                    "3a08cc21466f",
-                    "1",
-                    "test",
-                    {},
-                    {}
-                ]
-            }
-
-        """
-        return get_install_info(trans, name, owner, changeset_revision)
-
-    @web.legacy_expose_api_anonymous
-    def get_installable_revisions(self, trans, **kwd):
-        """
-        GET /api/repositories/get_installable_revisions
-
-        :param tsr_id: the encoded toolshed ID of the repository
-
-        Returns a list of lists of changesets, in the format [ [ 0, fbb391dc803c ], [ 1, 9d9ec4d9c03e ], [ 2, 9b5b20673b89 ], [ 3, e8c99ce51292 ] ].
-        """
-        # Example URL: http://localhost:9009/api/repositories/get_installable_revisions?tsr_id=9d37e53072ff9fa4
-        if (tsr_id := kwd.get("tsr_id", None)) is not None:
-            repository = repository_util.get_repository_in_tool_shed(
-                self.app, tsr_id, eagerload_columns=[model.Repository.downloadable_revisions]
-            )
-        else:
-            error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
-            error_message += "missing or invalid parameter received."
-            log.debug(error_message)
-            return []
-        return repository.installable_revisions(self.app)
-
-    def __get_value_mapper(self, trans) -> dict[str, Callable]:
-        return get_value_mapper(self.app)
-
-    @expose_api_raw_anonymous_and_sessionless
-    def index(self, trans, deleted=False, owner=None, name=None, **kwd):
-        """
-        GET /api/repositories
-        Displays a collection of repositories with optional criteria.
-
-        :param q:        (optional)if present search on the given query will be performed
-        :type  q:        str
-
-        :param page:     (optional)requested page of the search
-        :type  page:     int
-
-        :param page_size:     (optional)requested page_size of the search
-        :type  page_size:     int
-
-        :param jsonp:    (optional)flag whether to use jsonp format response, defaults to False
-        :type  jsonp:    bool
-
-        :param callback: (optional)name of the function to wrap callback in
-                         used only when jsonp is true, defaults to 'callback'
-        :type  callback: str
-
-        :param deleted:  (optional)displays repositories that are or are not set to deleted.
-        :type  deleted:  bool
-
-        :param owner:    (optional)the owner's public username.
-        :type  owner:    str
-
-        :param name:     (optional)the repository name.
-        :type  name:     str
-
-        :param tool_ids:  (optional) a tool GUID to find the repository for
-        :param tool_ids:  str
-
-        :returns dict:   object containing list of results
-
-        Examples:
-            GET http://localhost:9009/api/repositories
-            GET http://localhost:9009/api/repositories?q=fastq
-        """
-        repository_dicts = []
-        deleted = util.asbool(deleted)
-        if q := kwd.get("q", ""):
-            page = kwd.get("page", 1)
-            page_size = kwd.get("page_size", 10)
-            try:
-                page = int(page)
-                page_size = int(page_size)
-            except ValueError:
-                raise RequestParameterInvalidException('The "page" and "page_size" parameters have to be integers.')
-            return_jsonp = util.asbool(kwd.get("jsonp", False))
-            callback = kwd.get("callback", "callback")
-            search_results = search(trans, q, page, page_size)
-            if return_jsonp:
-                response = str(f"{callback}({json.dumps(search_results)});")
-            else:
-                response = json.dumps(search_results)
-            return response
-        if (tool_ids := kwd.get("tool_ids", None)) is not None:
-            tool_ids = util.listify(tool_ids)
-            response = index_tool_ids(self.app, tool_ids)
-            return json.dumps(response)
-        else:
-            index_request = IndexRequest(owner=owner, name=name, deleted=deleted)
-            repositories = index_repositories(self.app, index_request)
-            repository_dicts = []
-            for repository in repositories:
-                repository_dict = repository.to_dict(view="collection", value_mapper=self.__get_value_mapper(trans))
-                repository_dict["category_ids"] = [
-                    trans.security.encode_id(x.category.id) for x in repository.categories
-                ]
-                repository_dicts.append(repository_dict)
-            return json.dumps(repository_dicts)
-
-    @web.legacy_expose_api
-    def remove_repository_registry_entry(self, trans, payload, **kwd):
-        """
-        POST /api/repositories/remove_repository_registry_entry
-        Removes appropriate entries from the repository registry for the repository defined by the received name and owner.
-
-        :param key: the user's API key
-
-        The following parameters are included in the payload.
-        :param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
-        :param name (required): the name of the Repository
-        :param owner (required): the owner of the Repository
-        """
-        response_dict = {}
-        if not trans.user_is_admin:
-            response_dict["status"] = "error"
-            response_dict["message"] = (
-                "You are not authorized to remove entries from this Tool Shed's repository registry."
-            )
-            return response_dict
-        tool_shed_url = payload.get("tool_shed_url", "")
-        if not tool_shed_url:
-            raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
-        tool_shed_url = tool_shed_url.rstrip("/")
-        name = payload.get("name", "")
-        if not name:
-            raise HTTPBadRequest(detail="Missing required parameter 'name'.")
-        owner = payload.get("owner", "")
-        if not owner:
-            raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
-        repository = get_repository_by_name_and_owner(self.app.model.context, name, owner)
-        if repository is None:
-            error_message = f"Cannot locate repository with name {name} and owner {owner},"
-            log.debug(error_message)
-            response_dict["status"] = "error"
-            response_dict["message"] = error_message
-            return response_dict
-        # Update the repository registry.
-        self.app.repository_registry.remove_entry(repository)
-        response_dict["status"] = "ok"
-        response_dict["message"] = (
-            f"Entries for repository {name} owned by {owner} have been removed from the Tool Shed repository registry."
-        )
-        return response_dict
-
-    @web.legacy_expose_api
-    def reset_metadata_on_repositories(self, trans, payload, **kwd):
-        """
-        POST /api/repositories/reset_metadata_on_repositories
-
-        Resets all metadata on all repositories in the Tool Shed in an "orderly fashion".  Since there are currently only two
-        repository types (tool_dependecy_definition and unrestricted), the order in which metadata is reset is repositories of
-        type tool_dependecy_definition first followed by repositories of type unrestricted, and only one pass is necessary.  If
-        a new repository type is introduced, the process will undoubtedly need to be revisited.  To facilitate this order, an
-        in-memory list of repository ids that have been processed is maintained.
-
-        :param key: the API key of the Tool Shed user.
-        :param my_writable (optional):
-            if the API key is associated with an admin user in the Tool Shed, setting this param value
-            to True will restrict resetting metadata to only repositories that are writable by the user
-            in addition to those repositories of type tool_dependency_definition.  This param is ignored
-            if the current user is not an admin user, in which case this same restriction is automatic.
-
-        :param encoded_ids_to_skip (optional): a list of encoded repository ids for repositories that should not be processed.
-        :param skip_file (optional):
-            A local file name that contains the encoded repository ids associated with repositories to skip.
-            This param can be used as an alternative to the above encoded_ids_to_skip.
-
-        """
-
-        def handle_repository(trans, repository, results):
-            log.debug(f"Resetting metadata on repository {repository.name}")
-            try:
-                rmm = repository_metadata_manager.RepositoryMetadataManager(
-                    trans,
-                    resetting_all_metadata_on_repository=True,
-                    updating_installed_repository=False,
-                    repository=repository,
-                    persist=False,
-                )
-                rmm.reset_all_metadata_on_repository_in_tool_shed()
-                rmm_invalid_file_tups = rmm.get_invalid_file_tups()
-                if rmm_invalid_file_tups:
-                    message = tool_util.generate_message_for_invalid_tools(
-                        self.app, rmm_invalid_file_tups, repository, None, as_html=False
-                    )
-                    results["unsuccessful_count"] += 1
-                else:
-                    message = f"Successfully reset metadata on repository {repository.name} owned by {repository.user.username}"
-                    results["successful_count"] += 1
-            except Exception as e:
-                message = (
-                    f"Error resetting metadata on repository {repository.name} owned by {repository.user.username}: {e}"
-                )
-                results["unsuccessful_count"] += 1
-            status = f"{repository.name} : {message}"
-            results["repository_status"].append(status)
-            return results
-
-        start_time = strftime("%Y-%m-%d %H:%M:%S")
-        results = dict(start_time=start_time, repository_status=[], successful_count=0, unsuccessful_count=0)
-        handled_repository_ids = []
-        encoded_ids_to_skip = payload.get("encoded_ids_to_skip", [])
-        skip_file = payload.get("skip_file", None)
-        if skip_file and os.path.exists(skip_file) and not encoded_ids_to_skip:
-            # Load the list of encoded_ids_to_skip from the skip_file.
-            # Contents of file must be 1 encoded repository id per line.
-            lines = open(skip_file, "rb").readlines()
-            for line in lines:
-                if line.startswith("#"):
-                    # Skip comments.
-                    continue
-                encoded_ids_to_skip.append(line.rstrip("\n"))
-        if trans.user_is_admin:
-            my_writable = util.asbool(payload.get("my_writable", False))
-        else:
-            my_writable = True
-        rmm = repository_metadata_manager.RepositoryMetadataManager(
-            trans,
-            resetting_all_metadata_on_repository=True,
-            updating_installed_repository=False,
-            persist=False,
-        )
-        # First reset metadata on all repositories of type repository_dependency_definition.
-        for repository in rmm.get_repositories_for_setting_metadata(my_writable=my_writable, order=False):
-            encoded_id = trans.security.encode_id(repository.id)
-            if encoded_id in encoded_ids_to_skip:
-                log.debug(
-                    "Skipping repository with id %s because it is in encoded_ids_to_skip %s",
-                    repository.id,
-                    encoded_ids_to_skip,
-                )
-            elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
-                results = handle_repository(trans, repository, results)
-        # Now reset metadata on all remaining repositories.
-        for repository in rmm.get_repositories_for_setting_metadata(my_writable=my_writable, order=False):
-            encoded_id = trans.security.encode_id(repository.id)
-            if encoded_id in encoded_ids_to_skip:
-                log.debug(
-                    "Skipping repository with id %s because it is in encoded_ids_to_skip %s",
-                    repository.id,
-                    encoded_ids_to_skip,
-                )
-            elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids:
-                results = handle_repository(trans, repository, results)
-        stop_time = strftime("%Y-%m-%d %H:%M:%S")
-        results["stop_time"] = stop_time
-        return json.dumps(results, sort_keys=True, indent=4)
-
-    @web.legacy_expose_api
-    def reset_metadata_on_repository(self, trans, payload, **kwd):
-        """
-        POST /api/repositories/reset_metadata_on_repository
-
-        Resets all metadata on a specified repository in the Tool Shed.
-
-        :param key: the API key of the Tool Shed user.
-
-        The following parameters must be included in the payload.
-        :param repository_id: the encoded id of the repository on which metadata is to be reset.
-        """
-        repository_id = payload.get("repository_id", None)
-        return reset_metadata_on_repository(trans, repository_id).model_dump()
-
-    @expose_api_anonymous_and_sessionless
-    def show(self, trans, id, **kwd):
-        """
-        GET /api/repositories/{encoded_repository_id}
-        Returns information about a repository in the Tool Shed.
-
-        Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
-
-        :param id: the encoded id of the Repository object
-        :type  id: encoded str
-
-        :returns:   detailed repository information
-        :rtype:     dict
-
-        :raises:  ObjectNotFound, MalformedId
-        """
-        repository = repository_util.get_repository_in_tool_shed(self.app, id)
-        if repository is None:
-            raise ObjectNotFound("Unable to locate repository for the given id.")
-        repository_dict = repository.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
-        # TODO the following property would be better suited in the to_dict method
-        repository_dict["category_ids"] = [trans.security.encode_id(x.category.id) for x in repository.categories]
-        return repository_dict
-
-    @expose_api_raw_anonymous_and_sessionless
-    def updates(self, trans, **kwd):
-        """
-        GET /api/repositories/updates
-        Return a dictionary with boolean values for whether there are updates available
-        for the repository revision, newer installable revisions available,
-        the revision is the latest installable revision, and if the repository is deprecated.
-
-        :param owner: owner of the repository
-        :type  owner: str
-        :param name: name of the repository
-        :type  name: str
-        :param changeset_revision: changeset of the repository
-        :type  changeset_revision: str
-        :param hexlify: flag whether to hexlify the response (for backward compatibility)
-        :type  changeset: boolean
-
-        :returns:   information about repository deprecations, updates, and upgrades
-        :rtype:     dict
-        """
-        name = kwd.get("name", None)
-        owner = kwd.get("owner", None)
-        changeset_revision = kwd.get("changeset_revision", None)
-        hexlify_this = util.asbool(kwd.get("hexlify", True))
-        request = UpdatesRequest(
-            name=name,
-            owner=owner,
-            changeset_revision=changeset_revision,
-            hexlify=hexlify_this,
-        )
-        return check_updates(trans.app, request)
-
-    @expose_api_anonymous_and_sessionless
-    def show_tools(self, trans, id, changeset, **kwd):
-        repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app, id, changeset)
-        if repository_metadata is not None:
-            encoded_repository_metadata_id = trans.security.encode_id(repository_metadata.id)
-            repository_metadata_dict = repository_metadata.to_dict(
-                view="collection", value_mapper=self.__get_value_mapper(trans)
-            )
-            repository_metadata_dict["url"] = web.url_for(
-                controller="repository_revisions", action="show", id=encoded_repository_metadata_id
-            )
-            if "tools" in repository_metadata.metadata:
-                repository_metadata_dict["valid_tools"] = repository_metadata.metadata["tools"]
-            return repository_metadata_dict
-        else:
-            log.debug(
-                "Unable to locate repository_metadata record for repository id %s and changeset_revision %s",
-                id,
-                changeset,
-            )
-            return {}
-
-    @expose_api_anonymous_and_sessionless
-    def metadata(self, trans, id, **kwd):
-        """
-        GET /api/repositories/{encoded_repository_id}/metadata
-        Returns information about a repository in the Tool Shed.
-
-        Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135/metadata
-
-        :param id: the encoded id of the Repository object
-
-        :param downloadable_only: Return only downloadable revisions (defaults to True).
-                                  Added for test cases - shouldn't be considered part of the stable API.
-
-        :returns:   A dictionary containing the specified repository's metadata, by changeset,
-                    recursively including dependencies and their metadata.
-
-        :not found:  Empty dictionary.
-        """
-        recursive = util.asbool(kwd.get("recursive", "True"))
-        downloadable_only = util.asbool(kwd.get("downloadable_only", "True"))
-        return get_repository_metadata_dict(self.app, id, recursive, downloadable_only)
-
-    @expose_api
-    def update(self, trans, id, **kwd):
-        """
-        PATCH /api/repositories/{encoded_repository_id}
-        Updates information about a repository in the Tool Shed.
-
-        :param id: the encoded id of the Repository object
-
-        :param payload: dictionary structure containing
-
-            'name':                  repo's name (optional)
-            'synopsis':              repo's synopsis (optional)
-            'description':           repo's description (optional)
-            'remote_repository_url': repo's remote repo (optional)
-            'homepage_url':          repo's homepage url (optional)
-            'category_ids':          list of existing encoded TS category ids the updated repo should be associated with (optional)
-
-        :type payload: dict
-
-        :returns:   detailed repository information
-        :rtype:     dict
-
-        :raises: RequestParameterInvalidException, InsufficientPermissionsException
-        """
-        payload = kwd.get("payload", None)
-        if not payload:
-            raise RequestParameterMissingException("You did not specify any payload.")
-
-        name = payload.get("name", None)
-        synopsis = payload.get("synopsis", None)
-        description = payload.get("description", None)
-        remote_repository_url = payload.get("remote_repository_url", None)
-        homepage_url = payload.get("homepage_url", None)
-        category_ids = payload.get("category_ids", None)
-        if category_ids is not None:
-            # We need to know if it was actually passed, and listify turns None into []
-            category_ids = util.listify(category_ids)
-
-        update_kwds = dict(
-            name=name,
-            description=synopsis,
-            long_description=description,
-            remote_repository_url=remote_repository_url,
-            homepage_url=homepage_url,
-            category_ids=category_ids,
-        )
-
-        repo, message = repository_util.update_repository(trans, id, **update_kwds)
-        if repo is None:
-            if "You are not the owner" in message:
-                raise InsufficientPermissionsException(message)
-            else:
-                raise ActionInputError(message)
-
-        repository_dict = repo.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
-        repository_dict["category_ids"] = [trans.security.encode_id(x.category.id) for x in repo.categories]
-        return repository_dict
-
-    @expose_api
-    def create(self, trans, **kwd):
-        """
-        POST /api/repositories:
-
-        Creates a new repository.
-        Only ``name`` and ``synopsis`` parameters are required.
-
-        :param payload: dictionary structure containing
-
-            'name':                  new repo's name (required)
-            'synopsis':              new repo's synopsis (required)
-            'description':           new repo's description (optional)
-            'remote_repository_url': new repo's remote repo (optional)
-            'homepage_url':          new repo's homepage url (optional)
-            'category_ids[]':        list of existing encoded TS category ids the new repo should be associated with (optional)
-            'type':                  new repo's type, defaults to ``unrestricted`` (optional)
-
-        :type payload: dict
-
-        :returns:   detailed repository information
-        :rtype:     dict
-
-        :raises: RequestParameterMissingException, RequestParameterInvalidException
-        """
-        payload = kwd.get("payload", None)
-        if not payload:
-            raise RequestParameterMissingException("You did not specify any payload.")
-        name = payload.get("name", None)
-        if not name:
-            raise RequestParameterMissingException("Missing required parameter 'name'.")
-        synopsis = payload.get("synopsis", None)
-        if not synopsis:
-            raise RequestParameterMissingException("Missing required parameter 'synopsis'.")
-
-        description = payload.get("description", "")
-        remote_repository_url = payload.get("remote_repository_url", "")
-        homepage_url = payload.get("homepage_url", "")
-
-        repo_type = payload.get("type", rt_util.UNRESTRICTED)
-        if repo_type not in rt_util.types:
-            raise RequestParameterInvalidException("This repository type is not valid")
-
-        request = CreateRepositoryRequest(
-            name=name,
-            synopsis=synopsis,
-            description=description,
-            remote_repository_url=remote_repository_url,
-            homepage_url=homepage_url,
-            category_ids=payload.get("category_ids[]", ""),
-            type_=repo_type,
-        )
-        repo = create_repository(trans, request)
-        return to_element_dict(self.app, repo, include_categories=True)
-
-    @web.legacy_expose_api
-    def create_changeset_revision(self, trans, id, payload, **kwd):
-        """
-        POST /api/repositories/{encoded_repository_id}/changeset_revision
-
-        Create a new tool shed repository commit - leaving PUT on parent
-        resource open for updating meta-attributes of the repository (and
-        Galaxy doesn't allow PUT multipart data anyway
-        https://trello.com/c/CQwmCeG6).
-
-        :param id: the encoded id of the Repository object
-
-        The following parameters may be included in the payload.
-        :param commit_message: hg commit message for update.
-        """
-
-        # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
-        repository = repository_util.get_repository_in_tool_shed(self.app, id)
-
-        if not can_update_repo(trans, repository):
-            trans.response.status = 400
-            return {
-                "err_msg": "You do not have permission to update this repository.",
-            }
-
-        file_data = payload.get("file")
-        # Code stolen from gx's upload_common.py
-        if isinstance(file_data, cgi_FieldStorage):
-            assert not isinstance(file_data.file, StringIO)
-            assert file_data.file.name != "<fdopen>"
-            local_filename = util.mkstemp_ln(file_data.file.name, "upload_file_data_")
-            file_data.file.close()
-            file_data = dict(filename=file_data.filename, local_filename=local_filename)
-        elif isinstance(file_data, dict) and "local_filename" not in file_data:
-            raise Exception("Uploaded file was encoded in a way not understood.")
-
-        commit_message = kwd.get("commit_message", "Uploaded")
-
-        uploaded_file_name = file_data["local_filename"]
-        try:
-            message = upload_tar_and_set_metadata(
-                trans,
-                trans.request.host,
-                repository,
-                uploaded_file_name,
-                commit_message,
-            )
-            rval = {"message": message}
-        except MessageException as e:
-            trans.response.status = e.status_code
-            rval = {"err_msg": str(e)}
-        if os.path.exists(uploaded_file_name):
-            os.remove(uploaded_file_name)
-        return rval

lib/tool_shed/webapp/api/repository_revisions.py

@@ -1,214 +0,0 @@
-import logging
-from collections.abc import Callable
-
-from sqlalchemy import select
-
-from galaxy import (
-    util,
-    web,
-)
-from galaxy.webapps.base.controller import HTTPBadRequest
-from tool_shed.util import metadata_util
-from tool_shed.webapp.model import RepositoryMetadata
-from tool_shed.webapp.model.db import get_repository_by_name_and_owner
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class RepositoryRevisionsController(BaseShedAPIController):
-    """RESTful controller for interactions with tool shed repository revisions."""
-
-    def __get_value_mapper(self, trans) -> dict[str, Callable]:
-        value_mapper = {
-            "id": trans.security.encode_id,
-            "repository_id": trans.security.encode_id,
-            "user_id": trans.security.encode_id,
-        }
-        return value_mapper
-
-    @web.legacy_expose_api_anonymous
-    def index(self, trans, **kwd):
-        """
-        GET /api/repository_revisions
-        Displays a collection (list) of repository revisions.
-        """
-        # Example URL: http://localhost:9009/api/repository_revisions
-        downloadable = kwd.get("downloadable", None)
-        malicious = kwd.get("malicious", None)
-        missing_test_components = kwd.get("missing_test_components", None)
-        includes_tools = kwd.get("includes_tools", None)
-        repository_metadata_dicts = []
-        all_repository_metadata = get_repository_metadata(
-            trans.sa_session, downloadable, malicious, missing_test_components, includes_tools
-        )
-        for repository_metadata in all_repository_metadata:
-            repository_metadata_dict = repository_metadata.to_dict(
-                view="collection", value_mapper=self.__get_value_mapper(trans)
-            )
-            repository_metadata_dict["url"] = web.url_for(
-                controller="repository_revisions", action="show", id=trans.security.encode_id(repository_metadata.id)
-            )
-            repository_metadata_dicts.append(repository_metadata_dict)
-        return repository_metadata_dicts
-
-    @web.legacy_expose_api_anonymous
-    def repository_dependencies(self, trans, id, **kwd):
-        """
-        GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies
-
-        Returns a list of dictionaries that each define a specific downloadable revision of a
-        repository in the Tool Shed.  This method returns dictionaries with more information in
-        them than other methods in this controller.  The information about repository_metdata is
-        enhanced to include information about the repository (e.g., name, owner, etc) associated
-        with the repository_metadata record.
-
-        :param id: the encoded id of the `RepositoryMetadata` object
-        """
-        # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
-        repository_dependencies_dicts = []
-        repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
-        if repository_metadata is None:
-            log.debug(f"Invalid repository_metadata id received: {id}")
-            return repository_dependencies_dicts
-        metadata = repository_metadata.metadata
-        if metadata is None:
-            log.debug(f"The repository_metadata record with id {id} has no metadata.")
-            return repository_dependencies_dicts
-        if "repository_dependencies" in metadata:
-            rd_tups = metadata["repository_dependencies"]["repository_dependencies"]
-            for rd_tup in rd_tups:
-                tool_shed, name, owner, changeset_revision = rd_tup[0:4]
-                repository_dependency = get_repository_by_name_and_owner(trans.sa_session, name, owner)
-                if repository_dependency is None:
-                    log.debug(f"Cannot locate repository dependency {name} owned by {owner}.")
-                    continue
-                repository_dependency_id = trans.security.encode_id(repository_dependency.id)
-                repository_dependency_repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
-                    trans.app, repository_dependency_id, changeset_revision
-                )
-                if repository_dependency_repository_metadata is None:
-                    # The changeset_revision column in the repository_metadata table has been updated with a new
-                    # value value, so find the changeset_revision to which we need to update.
-                    new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
-                        trans.app, repository_dependency, changeset_revision
-                    )
-                    if new_changeset_revision != changeset_revision:
-                        repository_dependency_repository_metadata = (
-                            metadata_util.get_repository_metadata_by_changeset_revision(
-                                trans.app, repository_dependency_id, new_changeset_revision
-                            )
-                        )
-                        changeset_revision = new_changeset_revision
-                    else:
-                        decoded_repository_dependency_id = trans.security.decode_id(repository_dependency_id)
-                        debug_msg = (
-                            f"Cannot locate repository_metadata with id {decoded_repository_dependency_id} for repository dependency {name} owned by {owner} "
-                            f"using either of these changeset_revisions: {changeset_revision}, {new_changeset_revision}."
-                        )
-                        log.debug(debug_msg)
-                        continue
-                repository_dependency_metadata_dict = repository_dependency_repository_metadata.to_dict(
-                    view="element", value_mapper=self.__get_value_mapper(trans)
-                )
-                repository_dependency_dict = repository_dependency.to_dict(
-                    view="element", value_mapper=self.__get_value_mapper(trans)
-                )
-                # We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
-                # controller is working with repository_metadata records.  The above to_dict() method returns a dictionary
-                # with an id entry for the repository record.  However, all of the other methods in this controller have
-                # the id entry associated with a repository_metadata record id.  To avoid confusion, we'll update the
-                # repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
-                # Python dictionary update() method because we do not want to overwrite existing entries.
-                for k, v in repository_dependency_dict.items():
-                    if k not in repository_dependency_metadata_dict:
-                        repository_dependency_metadata_dict[k] = v
-                repository_dependency_metadata_dict["url"] = web.url_for(
-                    controller="repositories", action="show", id=repository_dependency_id
-                )
-                repository_dependencies_dicts.append(repository_dependency_metadata_dict)
-        return repository_dependencies_dicts
-
-    @web.legacy_expose_api_anonymous
-    def show(self, trans, id, **kwd):
-        """
-        GET /api/repository_revisions/{encoded_repository_metadata_id}
-        Displays information about a repository_metadata record in the Tool Shed.
-
-        :param id: the encoded id of the `RepositoryMetadata` object
-        """
-        # Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620
-        repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
-        if repository_metadata is None:
-            log.debug(f"Cannot locate repository_metadata with id {id}")
-            return {}
-        encoded_repository_id = trans.security.encode_id(repository_metadata.repository_id)
-        repository_metadata_dict = repository_metadata.to_dict(
-            view="element", value_mapper=self.__get_value_mapper(trans)
-        )
-        repository_metadata_dict["url"] = web.url_for(
-            controller="repositories", action="show", id=encoded_repository_id
-        )
-        return repository_metadata_dict
-
-    @web.legacy_expose_api
-    def update(self, trans, payload, **kwd):
-        """
-        PUT /api/repository_revisions/{encoded_repository_metadata_id}/{payload}
-        Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload.
-
-        :param id: the encoded id of the `RepositoryMetadata` object
-        """
-        repository_metadata_id = kwd.get("id", None)
-        if repository_metadata_id is None:
-            raise HTTPBadRequest(detail="Missing required parameter 'id'.")
-        repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
-        if repository_metadata is None:
-            decoded_repository_metadata_id = trans.security.decode_id(repository_metadata_id)
-            log.debug(f"Cannot locate repository_metadata with id {decoded_repository_metadata_id}")
-            return {}
-        else:
-            decoded_repository_metadata_id = repository_metadata.id
-        flush_needed = False
-        for key, new_value in payload.items():
-            if hasattr(repository_metadata, key):
-                # log information when setting attributes associated with the Tool Shed's install and test framework.
-                if key in ["includes_tools", "missing_test_components"]:
-                    log.debug(
-                        "Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API.",
-                        key,
-                        new_value,
-                        repository_metadata.changeset_revision,
-                    )
-                setattr(repository_metadata, key, new_value)
-                flush_needed = True
-        if flush_needed:
-            log.debug(
-                "Updating repository_metadata record with id %s and changeset_revision %s.",
-                decoded_repository_metadata_id,
-                repository_metadata.changeset_revision,
-            )
-            trans.sa_session.add(repository_metadata)
-            trans.sa_session.commit()
-            trans.sa_session.refresh(repository_metadata)
-        repository_metadata_dict = repository_metadata.to_dict(
-            view="element", value_mapper=self.__get_value_mapper(trans)
-        )
-        repository_metadata_dict["url"] = web.url_for(
-            controller="repository_revisions", action="show", id=repository_metadata_id
-        )
-        return repository_metadata_dict
-
-
-def get_repository_metadata(session, downloadable, malicious, missing_test_components, includes_tools):
-    stmt = select(RepositoryMetadata)
-    if downloadable is not None:
-        stmt = stmt.where(RepositoryMetadata.downloadable == util.asbool(downloadable))
-    if malicious is not None:
-        stmt = stmt.where(RepositoryMetadata.malicious == util.asbool(malicious))
-    if missing_test_components is not None:
-        stmt = stmt.where(RepositoryMetadata.missing_test_components == util.asbool(missing_test_components))
-    if includes_tools is not None:
-        stmt = stmt.where(RepositoryMetadata.includes_tools == util.asbool(includes_tools))
-    stmt = stmt.order_by(RepositoryMetadata.repository_id.desc())
-    return session.scalars(stmt)

lib/tool_shed/webapp/api/tools.py

@@ -1,92 +0,0 @@
-import json
-import logging
-
-from galaxy import (
-    exceptions,
-    util,
-)
-from galaxy.web import (
-    expose_api,
-    expose_api_raw_anonymous_and_sessionless,
-    require_admin,
-)
-from tool_shed.managers.tools import search
-from tool_shed.util.shed_index import build_index
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class ToolsController(BaseShedAPIController):
-    """RESTful controller for interactions with tools in the Tool Shed."""
-
-    @expose_api
-    @require_admin
-    def build_search_index(self, trans, **kwd):
-        """
-        PUT /api/tools/build_search_index
-
-        Not part of the stable API, just something to simplify bootstrapping tool sheds,
-        scripting, testing, etc...
-        """
-        repos_indexed, tools_indexed = build_index(
-            trans.app.config.whoosh_index_dir,
-            trans.app.config.file_path,
-            trans.app.config.hgweb_config_dir,
-            trans.app.config.hgweb_repo_prefix,
-            trans.app.config.database_connection,
-        )
-        return {
-            "repositories_indexed": repos_indexed,
-            "tools_indexed": tools_indexed,
-        }
-
-    @expose_api_raw_anonymous_and_sessionless
-    def index(self, trans, **kwd):
-        """
-        GET /api/tools
-        Displays a collection of tools with optional criteria.
-
-        :param q:        (optional)if present search on the given query will be performed
-        :type  q:        str
-
-        :param page:     (optional)requested page of the search
-        :type  page:     int
-
-        :param page_size:     (optional)requested page_size of the search
-        :type  page_size:     int
-
-        :param jsonp:    (optional)flag whether to use jsonp format response, defaults to False
-        :type  jsonp:    bool
-
-        :param callback: (optional)name of the function to wrap callback in
-                         used only when jsonp is true, defaults to 'callback'
-        :type  callback: str
-
-        :returns dict:   object containing list of results and metadata
-
-        Examples:
-            GET http://localhost:9009/api/tools
-            GET http://localhost:9009/api/tools?q=fastq
-        """
-        q = kwd.get("q", "")
-        if not q:
-            raise exceptions.NotImplemented(
-                'Listing of all the tools is not implemented. Provide parameter "q" to search instead.'
-            )
-        else:
-            page = kwd.get("page", 1)
-            page_size = kwd.get("page_size", 10)
-            try:
-                page = int(page)
-                page_size = int(page_size)
-            except ValueError:
-                raise exceptions.RequestParameterInvalidException('The "page" and "page_size" have to be integers.')
-            return_jsonp = util.asbool(kwd.get("jsonp", False))
-            callback = kwd.get("callback", "callback")
-            search_results = search(trans, q, page, page_size)
-            if return_jsonp:
-                response = str(f"{callback}({json.dumps(search_results)});")
-            else:
-                response = json.dumps(search_results)
-            return response

lib/tool_shed/webapp/api/users.py

@@ -1,87 +0,0 @@
-import logging
-
-import tool_shed.util.shed_util_common as suc
-from galaxy import (
-    util,
-    web,
-)
-from tool_shed.managers.users import (
-    api_create_user,
-    index,
-)
-from tool_shed_client.schema import CreateUserRequest
-from . import BaseShedAPIController
-
-log = logging.getLogger(__name__)
-
-
-class UsersController(BaseShedAPIController):
-    """RESTful controller for interactions with users in the Tool Shed."""
-
-    @web.expose_api
-    @web.require_admin
-    def create(self, trans, payload, **kwd):
-        """
-                POST /api/users
-                Returns a dictionary of information about the created user.
-
-        :       param key: the current Galaxy admin user's API key
-
-                The following parameters are included in the payload.
-                :param email (required): the email address of the user
-                :param password (required): the password of the user
-                :param username (required): the public username of the user
-        """
-        # Get the information about the user to be created from the payload.
-        email = payload.get("email", "")
-        password = payload.get("password", "")
-        username = payload.get("username", "")
-        # Create the user.
-        request = CreateUserRequest(
-            email=email,
-            username=username,
-            password=password,
-        )
-        user = api_create_user(trans, request)
-        user_dict = user.dict()
-        user_dict["message"] = f"User '{str(user.username)}' has been created."
-        user_dict["url"] = web.url_for(controller="users", action="show", id=trans.security.encode_id(user.id))
-        return user_dict
-
-    def __get_value_mapper(self, trans):
-        value_mapper = {"id": trans.security.encode_id}
-        return value_mapper
-
-    @web.expose_api_anonymous_and_sessionless
-    def index(self, trans, deleted=False, **kwd):
-        """
-        GET /api/users
-        Returns a list of dictionaries that contain information about each user.
-        """
-        # Example URL: http://localhost:9009/api/users
-        user_dicts = []
-        deleted = util.asbool(deleted)
-        for user in index(trans.app, deleted):
-            user_dict = user.dict()
-            user_dict["url"] = web.url_for(controller="users", action="show", id=trans.security.encode_id(user.id))
-            user_dicts.append(user_dict)
-        return user_dicts
-
-    @web.expose_api_anonymous_and_sessionless
-    def show(self, trans, id, **kwd):
-        """
-        GET /api/users/{encoded_user_id}
-        GET /api/users/current
-        Returns a dictionary of information about a user.
-
-        :param id: the encoded id of the User object.
-        """
-        user = None
-        # user is requesting data about themselves
-        user = trans.user if id == "current" else suc.get_user(trans.app, id)
-        if user is None:
-            user_dict = dict(message=f"Unable to locate user record for id {str(id)}.", status="error")
-            return user_dict
-        user_dict = user.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
-        user_dict["url"] = web.url_for(controller="users", action="show", id=trans.security.encode_id(user.id))
-        return user_dict

lib/tool_shed/webapp/app.py

@@ -105,10 +105,7 @@ class UniverseApplication(ToolShedApp, SentryClientMixin, HaltableContainer):
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
         self.hgweb_config_manager.hgweb_repo_prefix = self.config.hgweb_repo_prefix
         # Initialize the repository registry.
-        if config.SHED_API_VERSION != "v2":
-            self.repository_registry = tool_shed.repository_registry.Registry(self)
-        else:
-            self.repository_registry = tool_shed.repository_registry.NullRepositoryRegistry(self)
+        self.repository_registry = tool_shed.repository_registry.NullRepositoryRegistry(self)
         # Configure Sentry client if configured
         self.configure_sentry_client()
         #  used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.

lib/tool_shed/webapp/buildapp.py

@@ -26,7 +26,6 @@ from galaxy.webapps.base.webapp import (
     GalaxyWebTransaction,
 )
 from galaxy.webapps.util import wrap_if_allowed
-from .config import SHED_API_VERSION
 
 log = logging.getLogger(__name__)
 
@@ -125,130 +124,6 @@ def app_pair(global_conf, load_app_kwds=None, **kwargs):
     webapp.add_route("/{action}", controller="repository", action="index")
     # Enable 'hg clone' functionality on repos by letting hgwebapp handle the request
     webapp.add_route("/repos/*path_info", controller="hg", action="handle_request", path_info="/")
-    # Add the web API.  # A good resource for RESTful services - https://routes.readthedocs.io/en/latest/restful.html
-    if SHED_API_VERSION == "v1":
-        webapp.add_api_controllers("tool_shed.webapp.api", app)
-        webapp.mapper.connect(
-            "api_key_retrieval",
-            "/api/authenticate/baseauth/",
-            controller="authenticate",
-            action="get_tool_shed_api_key",
-            conditions=dict(method=["GET"]),
-        )
-        webapp.mapper.connect(
-            "group", "/api/groups/", controller="groups", action="index", conditions=dict(method=["GET"])
-        )
-        webapp.mapper.connect(
-            "group", "/api/groups/", controller="groups", action="create", conditions=dict(method=["POST"])
-        )
-        webapp.mapper.connect(
-            "group", "/api/groups/{encoded_id}", controller="groups", action="show", conditions=dict(method=["GET"])
-        )
-        webapp.mapper.resource(
-            "category",
-            "categories",
-            controller="categories",
-            name_prefix="category_",
-            path_prefix="/api",
-            parent_resources=dict(member_name="category", collection_name="categories"),
-        )
-        webapp.mapper.connect(
-            "repositories_in_category",
-            "/api/categories/{category_id}/repositories",
-            controller="categories",
-            action="get_repositories",
-            conditions=dict(method=["GET"]),
-        )
-        webapp.mapper.connect(
-            "show_updates_for_repository",
-            "/api/repositories/updates",
-            controller="repositories",
-            action="updates",
-            conditions=dict(method=["GET"]),
-        )
-        webapp.mapper.resource(
-            "repository",
-            "repositories",
-            controller="repositories",
-            collection={
-                "add_repository_registry_entry": "POST",
-                "get_repository_revision_install_info": "GET",
-                "get_ordered_installable_revisions": "GET",
-                "get_installable_revisions": "GET",
-                "remove_repository_registry_entry": "POST",
-                "reset_metadata_on_repositories": "POST",
-                "reset_metadata_on_repository": "POST",
-            },
-            name_prefix="repository_",
-            path_prefix="/api",
-            parent_resources=dict(member_name="repository", collection_name="repositories"),
-        )
-        webapp.mapper.resource(
-            "repository_revision",
-            "repository_revisions",
-            member={"repository_dependencies": "GET", "export": "POST"},
-            controller="repository_revisions",
-            name_prefix="repository_revision_",
-            path_prefix="/api",
-            parent_resources=dict(member_name="repository_revision", collection_name="repository_revisions"),
-        )
-        webapp.mapper.resource(
-            "user",
-            "users",
-            controller="users",
-            name_prefix="user_",
-            path_prefix="/api",
-            parent_resources=dict(member_name="user", collection_name="users"),
-        )
-        webapp.mapper.connect(
-            "update_repository",
-            "/api/repositories/{id}",
-            controller="repositories",
-            action="update",
-            conditions=dict(method=["PATCH", "PUT"]),
-        )
-        webapp.mapper.connect(
-            "repository_create_changeset_revision",
-            "/api/repositories/{id}/changeset_revision",
-            controller="repositories",
-            action="create_changeset_revision",
-            conditions=dict(method=["POST"]),
-        )
-        webapp.mapper.connect(
-            "repository_get_metadata",
-            "/api/repositories/{id}/metadata",
-            controller="repositories",
-            action="metadata",
-            conditions=dict(method=["GET"]),
-        )
-        webapp.mapper.connect(
-            "repository_show_tools",
-            "/api/repositories/{id}/{changeset}/show_tools",
-            controller="repositories",
-            action="show_tools",
-            conditions=dict(method=["GET"]),
-        )
-        webapp.mapper.connect(
-            "create_repository",
-            "/api/repositories",
-            controller="repositories",
-            action="create",
-            conditions=dict(method=["POST"]),
-        )
-        webapp.mapper.connect(
-            "tools",
-            "/api/tools/build_search_index",
-            controller="tools",
-            action="build_search_index",
-            conditions=dict(method=["PUT"]),
-        )
-        webapp.mapper.connect(
-            "tools", "/api/tools", controller="tools", action="index", conditions=dict(method=["GET"])
-        )
-        webapp.mapper.connect(
-            "version", "/api/version", controller="configuration", action="version", conditions=dict(method=["GET"])
-        )
-
     webapp.finalize_config()
     # Wrap the webapp in some useful middleware
     if kwargs.get("middleware", True):

lib/tool_shed/webapp/config.py

@@ -27,7 +27,6 @@ from galaxy.version import (
 log = logging.getLogger(__name__)
 
 TOOLSHED_APP_NAME = "tool_shed"
-SHED_API_VERSION = os.environ.get("TOOL_SHED_API_VERSION", "v1")
 
 
 class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):

lib/tool_shed/webapp/fast_app.py

@@ -12,10 +12,7 @@ from fastapi import (
     Depends,
     FastAPI,
 )
-from fastapi.responses import (
-    HTMLResponse,
-    RedirectResponse,
-)
+from fastapi.responses import HTMLResponse
 from fastapi.staticfiles import StaticFiles
 from slowapi import (
     _rate_limit_exceeded_handler,
@@ -61,7 +58,7 @@ api_tags_metadata = [
 # Run vite with:
 #   pnpm dev
 # Start tool shed with:
-#   TOOL_SHED_VITE_PORT=4040 TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+#   TOOL_SHED_VITE_PORT=4040 ./run_tool_shed.sh
 TOOL_SHED_VITE_PORT: Optional[str] = os.environ.get("TOOL_SHED_VITE_PORT", None)
 TOOL_SHED_FRONTEND_TARGET: str = os.environ.get("TOOL_SHED_FRONTEND_TARGET") or "auto"  # auto, src, or node
 TOOL_SHED_USE_HMR: bool = TOOL_SHED_VITE_PORT is not None
@@ -111,12 +108,6 @@ def frontend_controller(app):
     return app, index
 
 
-def redirect_route(app, from_url: str, to_url: str):
-    @app.get(from_url)
-    def redirect():
-        return RedirectResponse(to_url)
-
-
 def frontend_route(controller, path):
     app, index = controller
     app.get(path, response_class=HTMLResponse)(index)
@@ -148,11 +139,6 @@ FRONT_END_ROUTES = [
     "/view/{username}/{repository_name}",
     "/view/{username}/{repository_name}/{changeset_revision}",
 ]
-LEGACY_ROUTES = {
-    "/user/create": "/register",  # for twilltestcase
-    "/user/login": "/login",  # for twilltestcase
-}
-
 
 limiter = Limiter(key_func=get_remote_address)
 
@@ -163,29 +149,23 @@ def initialize_fast_app(gx_webapp, tool_shed_app):
     add_request_id_middleware(app)
     app.state.limiter = limiter
     app.add_exception_handler(RateLimitExceeded, _rate_limit_exceeded_handler)  # type: ignore[arg-type]
-    from .config import SHED_API_VERSION
 
     def mount_static(directory: Path):
         name = directory.name
         if directory.exists():
             app.mount(f"/{name}", StaticFiles(directory=directory), name=name)
 
-    if SHED_API_VERSION == "v2":
-        controller = frontend_controller(app)
-        for route in FRONT_END_ROUTES:
-            frontend_route(controller, route)
+    controller = frontend_controller(app)
+    for route in FRONT_END_ROUTES:
+        frontend_route(controller, route)
 
-        for from_route, to_route in LEGACY_ROUTES.items():
-            redirect_route(app, from_route, to_route)
+    mount_static(FRONTEND / "static")
+    if TOOL_SHED_USE_HMR:
+        mount_static(FRONTEND / "node_modules")
+    else:
+        mount_static(find_frontend_target() / "assets")
 
-        mount_static(FRONTEND / "static")
-        if TOOL_SHED_USE_HMR:
-            mount_static(FRONTEND / "node_modules")
-        else:
-            mount_static(find_frontend_target() / "assets")
-
-    routes_package = "tool_shed.webapp.api" if SHED_API_VERSION == "v1" else "tool_shed.webapp.api2"
-    include_all_package_routers(app, routes_package)
+    include_all_package_routers(app, "tool_shed.webapp.api2")
     wsgi_handler = WSGIMiddleware(gx_webapp)
     tool_shed_app.haltables.append(("WSGI Middleware threadpool", wsgi_handler.executor.shutdown))
     # https://github.com/abersheeran/a2wsgi/issues/44

lib/tool_shed/webapp/frontend/CLAUDE.md

@@ -3,6 +3,7 @@
 Vue 3 + TypeScript frontend for the Galaxy Tool Shed.
 
 ## Stack
+
 - **Framework**: Vue 3 (Composition API + Options API mix)
 - **Build**: Vite 4
 - **UI**: Quasar 2
@@ -11,6 +12,7 @@ Vue 3 + TypeScript frontend for the Galaxy Tool Shed.
 - **Router**: vue-router 4
 
 ## Structure
+
 ```
 src/
 ├── api/           # API wrapper functions
@@ -43,29 +45,33 @@ pnpm lint
 pnpm format
 ```
 
-Backend must be running with `TOOL_SHED_API_VERSION=v2`:
+Backend must be running:
+
 ```shell
 # From galaxy root
-TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+./run_tool_shed.sh
 ```
 
 For rapid local dev with bootstrapped data:
+
 ```shell
 TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey \
 TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV=1 \
 TOOL_SHED_VITE_PORT=4040 \
-TOOL_SHED_API_VERSION=v2 \
 ./run_tool_shed.sh
 ```
 
 ## API Pattern
+
 API calls use openapi-fetch typed client via `ToolShedApi()` in `src/schema/client.ts`:
+
 ```typescript
 import { ToolShedApi } from "@/schema"
 const { data } = await ToolShedApi().GET("/api/repositories", { params: { query: params } })
 ```
 
 ## Key Components
+
 - `ShedToolbar.vue` - Main navigation toolbar
 - `RepositoryPage.vue` - Single repository view
 - `LandingPage.vue` - Homepage
@@ -73,7 +79,9 @@ const { data } = await ToolShedApi().GET("/api/repositories", { params: { query:
 - `ComponentsShowcase.vue` - Developer page for widget demos
 
 ## Component Showcase
+
 When creating reusable UI components, add examples to `src/components/pages/ComponentsShowcase.vue`. This page (accessible via `/showcase`) helps developers see components in isolation. Pattern:
+
 ```vue
 <component-showcase title="MyComponent">
     <component-showcase-example title="default">
@@ -86,6 +94,7 @@ When creating reusable UI components, add examples to `src/components/pages/Comp
 ```
 
 When writing unit tests that cover special cases (edge cases, error states, long content, special characters, etc.), consider adding those same cases to the Component Showcase. This helps developers:
+
 - Visually verify the component handles edge cases correctly
 - See how the component looks in various states during development
 - Document expected behavior for different scenarios
@@ -93,11 +102,13 @@ When writing unit tests that cover special cases (edge cases, error states, long
 For example, if you test a component with long text or special characters, add showcase examples demonstrating those cases.
 
 ## Path Alias
+
 `@/` maps to `src/` directory.
 
 ## Accessibility (WCAG 2.1 AA)
 
 ### Key Patterns
+
 - **Skip link**: `App.vue` - hidden until focused, targets `#main-content`
 - **Landmarks**: `role="banner"` on header, `role="main"` on page container
 - **Live regions**: `ErrorBanner.vue` uses `role="alert"`, `LoadingDiv.vue` uses `role="status"`
@@ -105,22 +116,25 @@ For example, if you test a component with long text or special characters, add s
 - **Focus indicators**: Global `:focus-visible` styles in `App.vue`
 
 ### Components with ARIA
-| Component | ARIA Attrs |
-|-----------|------------|
-| `App.vue` | Skip link, landmarks, focus CSS |
-| `ShedToolbar.vue` | `aria-label` on icon buttons, `aria-haspopup` on dropdowns |
-| `ErrorBanner.vue` | `role="alert"`, `aria-live="assertive"` |
-| `LoadingDiv.vue` | `role="status"`, `aria-live="polite"` |
-| `RepositoryExplore.vue` | `aria-label` on FAB and icon buttons |
-| `PaginatedRepositoriesGrid.vue` | `aria-label` on table |
+
+| Component                       | ARIA Attrs                                                 |
+| ------------------------------- | ---------------------------------------------------------- |
+| `App.vue`                       | Skip link, landmarks, focus CSS                            |
+| `ShedToolbar.vue`               | `aria-label` on icon buttons, `aria-haspopup` on dropdowns |
+| `ErrorBanner.vue`               | `role="alert"`, `aria-live="assertive"`                    |
+| `LoadingDiv.vue`                | `role="status"`, `aria-live="polite"`                      |
+| `RepositoryExplore.vue`         | `aria-label` on FAB and icon buttons                       |
+| `PaginatedRepositoriesGrid.vue` | `aria-label` on table                                      |
 
 ### Quasar Notes
+
 - `q-btn-dropdown` auto-manages `aria-expanded`
 - `q-select` has built-in label association
 - Use `aria-label` on icon-only `q-btn` components
 - FABs (`q-fab`) need explicit `aria-label` on trigger
 
 ### Notification System
+
 - `util.ts` `notify()` - uses Quasar Notify (toast messages)
 - `ErrorBanner.vue` - inline persistent errors with dismiss
 - `LoadingDiv.vue` - spinner with status message
@@ -128,30 +142,35 @@ For example, if you test a component with long text or special characters, add s
 ## Testing (Vitest + Vue Test Utils)
 
 ### Setup
+
 Tests use Vitest with `@vue/test-utils` for component testing. Test files should be co-located with components (e.g., `MyComponent.vue` → `MyComponent.test.ts`) or in a `__tests__` directory.
 
 ### Best Practices for AI-Developed Tests
 
 #### 1. Test Behavior, Not Implementation
+
 Focus on what the component does from a user's perspective, not internal implementation details:
+
 ```typescript
 // ✅ Good: Tests user-visible behavior
-test('displays error message when API fails', async () => {
-  vi.mocked(ToolShedApi).mockReturnValue({ error: { status: 500 } })
-  const wrapper = mount(MyComponent)
-  await flushPromises()
-  expect(wrapper.text()).toContain('Error loading data')
+test("displays error message when API fails", async () => {
+    vi.mocked(ToolShedApi).mockReturnValue({ error: { status: 500 } })
+    const wrapper = mount(MyComponent)
+    await flushPromises()
+    expect(wrapper.text()).toContain("Error loading data")
 })
 
 // ❌ Bad: Tests implementation details
-test('calls fetchData method', () => {
-  const fetchDataSpy = vi.spyOn(wrapper.vm, 'fetchData')
-  // ...
+test("calls fetchData method", () => {
+    const fetchDataSpy = vi.spyOn(wrapper.vm, "fetchData")
+    // ...
 })
 ```
 
 #### 2. Use Real Queries Over Test IDs
+
 Prefer semantic queries (text, labels, roles) over test IDs:
+
 ```typescript
 // ✅ Good: Uses accessible queries
 const button = wrapper.find('button[aria-label="Submit"]')
@@ -162,204 +181,228 @@ const button = wrapper.find('[data-testid="submit-btn"]')
 ```
 
 #### 3. Mock External Dependencies
-Mock API calls, router, and Pinia stores at the module level:
-```typescript
-import { vi } from 'vitest'
-import { ToolShedApi } from '@/schema'
 
-vi.mock('@/schema', () => ({
-  ToolShedApi: vi.fn(),
+Mock API calls, router, and Pinia stores at the module level:
+
+```typescript
+import { vi } from "vitest"
+import { ToolShedApi } from "@/schema"
+
+vi.mock("@/schema", () => ({
+    ToolShedApi: vi.fn(),
 }))
 
-test('loads repository data', async () => {
-  vi.mocked(ToolShedApi).mockReturnValue({
-    GET: vi.fn().mockResolvedValue({ data: { name: 'test-repo' } }),
-  })
-  // ...
+test("loads repository data", async () => {
+    vi.mocked(ToolShedApi).mockReturnValue({
+        GET: vi.fn().mockResolvedValue({ data: { name: "test-repo" } }),
+    })
+    // ...
 })
 ```
 
 #### 4. Test Composition API Components Properly
-For Composition API components, use `mount()` and interact with the component as a user would:
-```typescript
-import { mount } from '@vue/test-utils'
-import { describe, it, expect, vi, beforeEach } from 'vitest'
-import MyComponent from '@/components/MyComponent.vue'
 
-describe('MyComponent', () => {
-  it('updates count when button clicked', async () => {
-    const wrapper = mount(MyComponent)
-    const button = wrapper.find('button')
-    await button.trigger('click')
-    expect(wrapper.text()).toContain('Count: 1')
-  })
+For Composition API components, use `mount()` and interact with the component as a user would:
+
+```typescript
+import { mount } from "@vue/test-utils"
+import { describe, it, expect, vi, beforeEach } from "vitest"
+import MyComponent from "@/components/MyComponent.vue"
+
+describe("MyComponent", () => {
+    it("updates count when button clicked", async () => {
+        const wrapper = mount(MyComponent)
+        const button = wrapper.find("button")
+        await button.trigger("click")
+        expect(wrapper.text()).toContain("Count: 1")
+    })
 })
 ```
 
 #### 5. Test Options API Components
+
 For Options API components, avoid accessing `wrapper.vm` directly. Test through the template:
+
 ```typescript
 // ✅ Good: Tests through template
-test('shows message prop', () => {
-  const wrapper = mount(MyComponent, {
-    props: { message: 'Hello' },
-  })
-  expect(wrapper.text()).toContain('Hello')
+test("shows message prop", () => {
+    const wrapper = mount(MyComponent, {
+        props: { message: "Hello" },
+    })
+    expect(wrapper.text()).toContain("Hello")
 })
 
 // ❌ Avoid: Direct vm access
-expect(wrapper.vm.message).toBe('Hello')
+expect(wrapper.vm.message).toBe("Hello")
 ```
 
 #### 6. Mock Quasar Components When Needed
+
 Quasar components can be mocked if they're not the focus of the test:
+
 ```typescript
-import { mount, config } from '@vue/test-utils'
+import { mount, config } from "@vue/test-utils"
 
 config.global.stubs = {
-  'q-btn': { template: '<button><slot /></button>' },
-  'q-input': { template: '<input />' },
+    "q-btn": { template: "<button><slot /></button>" },
+    "q-input": { template: "<input />" },
 }
 ```
 
 #### 7. Test Pinia Stores in Isolation
+
 Test stores separately from components:
+
 ```typescript
-import { setActivePinia, createPinia } from 'pinia'
-import { useAuthStore } from '@/stores/auth.store'
+import { setActivePinia, createPinia } from "pinia"
+import { useAuthStore } from "@/stores/auth.store"
 
-describe('auth store', () => {
-  beforeEach(() => {
-    setActivePinia(createPinia())
-  })
+describe("auth store", () => {
+    beforeEach(() => {
+        setActivePinia(createPinia())
+    })
 
-  it('sets user on login', () => {
-    const store = useAuthStore()
-    store.setUser({ id: 1, username: 'test' })
-    expect(store.user?.username).toBe('test')
-  })
+    it("sets user on login", () => {
+        const store = useAuthStore()
+        store.setUser({ id: 1, username: "test" })
+        expect(store.user?.username).toBe("test")
+    })
 })
 ```
 
 #### 8. Use `flushPromises()` for Async Operations
-Wait for async operations to complete:
-```typescript
-import { flushPromises } from '@vue/test-utils'
 
-test('loads data asynchronously', async () => {
-  const wrapper = mount(MyComponent)
-  await flushPromises()
-  expect(wrapper.text()).toContain('Loaded')
+Wait for async operations to complete:
+
+```typescript
+import { flushPromises } from "@vue/test-utils"
+
+test("loads data asynchronously", async () => {
+    const wrapper = mount(MyComponent)
+    await flushPromises()
+    expect(wrapper.text()).toContain("Loaded")
 })
 ```
 
 #### 9. Test Router Navigation
+
 Mock `vue-router` and verify navigation calls:
+
 ```typescript
-import { vi } from 'vitest'
+import { vi } from "vitest"
 const mockPush = vi.fn()
 
-vi.mock('vue-router', () => ({
-  useRouter: () => ({ push: mockPush }),
+vi.mock("vue-router", () => ({
+    useRouter: () => ({ push: mockPush }),
 }))
 
-test('navigates on click', async () => {
-  const wrapper = mount(MyComponent)
-  await wrapper.find('a').trigger('click')
-  expect(mockPush).toHaveBeenCalledWith('/expected-route')
+test("navigates on click", async () => {
+    const wrapper = mount(MyComponent)
+    await wrapper.find("a").trigger("click")
+    expect(mockPush).toHaveBeenCalledWith("/expected-route")
 })
 ```
 
 #### 10. Keep Tests Focused and Independent
+
 Each test should verify one behavior and be independent:
+
 ```typescript
 // ✅ Good: Focused test
-test('displays loading state', () => {
-  const wrapper = mount(MyComponent, {
-    props: { loading: true },
-  })
-  expect(wrapper.find('[role="status"]').exists()).toBe(true)
+test("displays loading state", () => {
+    const wrapper = mount(MyComponent, {
+        props: { loading: true },
+    })
+    expect(wrapper.find('[role="status"]').exists()).toBe(true)
 })
 
 // ❌ Bad: Multiple concerns
-test('component does everything', () => {
-  // Tests loading, error, success, navigation...
+test("component does everything", () => {
+    // Tests loading, error, success, navigation...
 })
 ```
 
 #### 11. Use Descriptive Test Names
+
 Test names should clearly describe what is being tested:
+
 ```typescript
 // ✅ Good: Clear and descriptive
-test('displays error banner when API returns 500', async () => {})
-test('hides submit button when form is invalid', () => {})
+test("displays error banner when API returns 500", async () => {})
+test("hides submit button when form is invalid", () => {})
 
 // ❌ Bad: Vague
-test('works correctly', () => {})
-test('component test', () => {})
+test("works correctly", () => {})
+test("component test", () => {})
 ```
 
 #### 12. Clean Up After Tests
+
 Reset mocks and clear state between tests:
+
 ```typescript
-import { beforeEach, afterEach, vi } from 'vitest'
+import { beforeEach, afterEach, vi } from "vitest"
 
 beforeEach(() => {
-  vi.clearAllMocks()
+    vi.clearAllMocks()
 })
 
 afterEach(() => {
-  vi.restoreAllMocks()
+    vi.restoreAllMocks()
 })
 ```
 
 ### Common Patterns
 
 #### Testing Components with Props
+
 ```typescript
-test('renders with required props', () => {
-  const wrapper = mount(MyComponent, {
-    props: {
-      title: 'Test Title',
-      count: 5,
-    },
-  })
-  expect(wrapper.text()).toContain('Test Title')
+test("renders with required props", () => {
+    const wrapper = mount(MyComponent, {
+        props: {
+            title: "Test Title",
+            count: 5,
+        },
+    })
+    expect(wrapper.text()).toContain("Test Title")
 })
 ```
 
 #### Testing User Interactions
+
 ```typescript
-test('calls handler on button click', async () => {
-  const handleClick = vi.fn()
-  const wrapper = mount(MyComponent, {
-    props: { onClick: handleClick },
-  })
-  await wrapper.find('button').trigger('click')
-  expect(handleClick).toHaveBeenCalledTimes(1)
+test("calls handler on button click", async () => {
+    const handleClick = vi.fn()
+    const wrapper = mount(MyComponent, {
+        props: { onClick: handleClick },
+    })
+    await wrapper.find("button").trigger("click")
+    expect(handleClick).toHaveBeenCalledTimes(1)
 })
 ```
 
 #### Testing Conditional Rendering
+
 ```typescript
-test('shows content when condition is true', () => {
-  const wrapper = mount(MyComponent, {
-    props: { show: true },
-  })
-  expect(wrapper.find('.content').exists()).toBe(true)
+test("shows content when condition is true", () => {
+    const wrapper = mount(MyComponent, {
+        props: { show: true },
+    })
+    expect(wrapper.find(".content").exists()).toBe(true)
 })
 
-test('hides content when condition is false', () => {
-  const wrapper = mount(MyComponent, {
-    props: { show: false },
-  })
-  expect(wrapper.find('.content').exists()).toBe(false)
+test("hides content when condition is false", () => {
+    const wrapper = mount(MyComponent, {
+        props: { show: false },
+    })
+    expect(wrapper.find(".content").exists()).toBe(false)
 })
 ```
 
 ### AI-Specific Guidelines
 
 When generating tests with AI:
+
 1. **Avoid over-testing**: Don't test every method or computed property. Focus on user-facing behavior.
 2. **Don't test framework code**: Vue, Quasar, and Pinia are already tested. Test your application logic.
 3. **Test edge cases**: Include tests for error states, empty data, and boundary conditions.

lib/tool_shed/webapp/frontend/Makefile

@@ -16,7 +16,7 @@ lint:
 # how to get a test server running and populated with some initial data
 # for the new tool shed frontend.
 run_test_backend:
-	cd $(GALAXY_ROOT); TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey TOOL_SHED_VITE_PORT=4040 TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+	cd $(GALAXY_ROOT); TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey TOOL_SHED_VITE_PORT=4040 ./run_tool_shed.sh
 
 bootstrap_test_backend:
 	cd $(GALAXY_ROOT); . .venv/bin/activate; python scripts/bootstrap_test_shed.py

lib/tool_shed/webapp/frontend/README.md

@@ -4,7 +4,7 @@ You will need to start the Tool Shed backend from the galaxy root directory.
 This is required if you want to develop against a local tool shed.
 
 ```shell
-TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+./run_tool_shed.sh
 ```
 
 Start the HMR dev server.
@@ -27,5 +27,5 @@ To run a local toolshed patched for rapid bootstrapping and in local Vite dev se
 the following command should work.
 
 ```shell
-TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV=1 TOOL_SHED_VITE_PORT=4040 TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
-```
+TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV=1 TOOL_SHED_VITE_PORT=4040 ./run_tool_shed.sh
+```

lib/tool_shed/webapp/frontend/src/components/MetadataInspector/__fixtures__/index.ts

@@ -4,7 +4,6 @@
  * To regenerate these fixtures, run from packages/tool_shed:
  *
  *   TOOL_SHED_FIXTURE_OUTPUT_DIR=lib/tool_shed/webapp/frontend/src/components/MetadataInspector/__fixtures__ \
- *   TOOL_SHED_API_VERSION=v2 \
  *   uv run pytest tool_shed/test/functional/test_shed_repositories.py::TestShedRepositoriesApi::test_generate_frontend_fixtures -v
  */
 
@@ -120,7 +119,7 @@ export function getFirstRevision(metadata: RepositoryMetadata): RepositoryRevisi
 
 /** Get all tools from all revisions in metadata */
 export function getAllTools(
-    metadata: RepositoryMetadata
+    metadata: RepositoryMetadata,
 ): Array<{ tool: components["schemas"]["RepositoryTool"]; revisionKey: string }> {
     const tools: Array<{ tool: components["schemas"]["RepositoryTool"]; revisionKey: string }> = []
     for (const [key, revision] of Object.entries(metadata)) {

packages/tool_shed/.claude/commands/regenerate-fixtures.md

@@ -3,15 +3,13 @@ Regenerate API test fixtures for MetadataInspector frontend components.
 # Command
 
 Run from `packages/tool_shed`:
+
 ```bash
 TOOL_SHED_FIXTURE_OUTPUT_DIR=tool_shed/webapp/frontend/src/components/MetadataInspector/__fixtures__ \
-TOOL_SHED_API_VERSION=v2 \
 uv run pytest tool_shed/test/functional/test_shed_repositories.py::TestShedRepositoriesApi::test_generate_frontend_fixtures -v &&
 cd tool_shed/webapp/frontend && npm run format
 ```
 
-
-
 # Generated files
 
 - `repository_metadata_column_maker.json` - Multi-revision repo with tools (RepositoryMetadata)

packages/tool_shed/CLAUDE.md

@@ -3,6 +3,7 @@
 Backend services for the Galaxy Tool Shed.
 
 ## Structure
+
 ```
 tool_shed/
 ├── managers/         # Business logic (repositories, users, categories)
@@ -25,6 +26,7 @@ subproject (the directory where this file is located).
 Always use `uv run python` and `uv run pytest` to run commands in this directory to ensure the correct environment is used.
 
 Example:
+
 ```bash
 uv run python -c "from selenium.webdriver.common.by import By; print(By.CLASS_NAME)"
 uv run pytest tests/seleniumtests/test_has_driver.py -v
@@ -41,21 +43,21 @@ Run from this directory (`packages/tool_shed`):
 uv run pytest tests/tool_shed/
 
 # Functional tests (requires running shed)
-TOOL_SHED_API_VERSION=v2 uv run pytest tool_shed/test/functional/test_shed_repositories.py -v
+uv run pytest tool_shed/test/functional/test_shed_repositories.py -v
 ```
 
 ### Test Categories
 
-| Type | Location | Server Required | Description |
-|------|----------|-----------------|-------------|
-| Unit | `tests/tool_shed/` | No | In-memory SQLite, mock app |
-| Functional | `tool_shed/test/functional/` | Yes | API + Playwright browser tests |
+| Type       | Location                     | Server Required | Description                    |
+| ---------- | ---------------------------- | --------------- | ------------------------------ |
+| Unit       | `tests/tool_shed/`           | No              | In-memory SQLite, mock app     |
+| Functional | `tool_shed/test/functional/` | Yes             | API + Playwright browser tests |
 
 ### Quick Start: Functional Tests
 
 ```shell
-# Terminal 1: Start shed with v2 API
-TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+# Terminal 1: Start shed
+./run_tool_shed.sh
 
 # Terminal 2: Run tests
 uv run pytest tool_shed/test/functional/test_frontend_login.py -v
@@ -71,13 +73,13 @@ uv run pytest tool_shed/test/functional/test_frontend_login.py -v
 ### Component Showcase & Fixtures
 
 The component showcase (`/_component_showcase`) displays UI components with real API data from generated fixtures. These fixtures are shared between:
+
 - **ComponentsShowcase.vue** - Live demos at `/_component_showcase`
 - **Vitest unit tests** - Frontend component tests
 
 ```shell
 # Regenerate fixtures from real API responses
 TOOL_SHED_FIXTURE_OUTPUT_DIR=tool_shed/webapp/frontend/src/components/MetadataInspector/__fixtures__ \
-TOOL_SHED_API_VERSION=v2 \
 uv run pytest tool_shed/test/functional/test_shed_repositories.py::TestShedRepositoriesApi::test_generate_frontend_fixtures -v
 
 # Format generated files
@@ -85,7 +87,6 @@ cd tool_shed/webapp/frontend && npm run format
 
 # Capture component screenshots
 TOOL_SHED_TEST_SCREENSHOTS=/tmp/screenshots \
-TOOL_SHED_API_VERSION=v2 \
 uv run pytest tool_shed/test/functional/test_component_showcase.py -v
 ```
 
@@ -95,19 +96,19 @@ Regenerate fixtures after: schema changes, API response changes, or metadata bug
 
 ```shell
 # From galaxy root
-TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+./run_tool_shed.sh
 
 # With dev conveniences (admin key, hg config, frontend dev server)
 TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey \
 TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV=1 \
 TOOL_SHED_VITE_PORT=4040 \
-TOOL_SHED_API_VERSION=v2 \
 ./run_tool_shed.sh
 ```
 
 ## API Schema
 
 OpenAPI schema generated from FastAPI endpoints. To regenerate TypeScript types:
+
 ```shell
 # From galaxy root
 make update-client-api-schema
@@ -125,6 +126,7 @@ Frontend types live in `tool_shed/webapp/frontend/src/schema/schema.ts`.
 ## Frontend
 
 See [tool_shed/webapp/frontend/CLAUDE.md](tool_shed/webapp/frontend/CLAUDE.md) for:
+
 - Vue 3 / Quasar architecture
 - Component patterns
 - API client usage