Add tool_shed_url config for explicit hostname setting

gist_implementation.diff

commit fa276e6532ba34939ce7d796370f679526e986e9
Author: John Chilton <jmchilton@gmail.com>
Date:   Fri Dec 19 11:16:09 2025 -0500

    Add tool_shed_url config for explicit hostname setting
    
    Allows admins to set a fixed base URL for clone URLs and repository
    hostnames, useful when behind proxies or needing a specific public URL.
    
    🤖 Generated with [Claude Code](https://claude.com/claude-code)
    
    Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

diff --git a/lib/galaxy/config/schemas/tool_shed_config_schema.yml b/lib/galaxy/config/schemas/tool_shed_config_schema.yml
index 0434319fd3..0725cd52c1 100644
--- a/lib/galaxy/config/schemas/tool_shed_config_schema.yml
+++ b/lib/galaxy/config/schemas/tool_shed_config_schema.yml
@@ -46,6 +46,16 @@ mapping:
           Allow pushing directly to mercurial repositories directly
           and without authentication.
 
+      tool_shed_url:
+        type: str
+        required: false
+        desc: |
+          The base URL of the Tool Shed server used for generating clone URLs
+          and repository hostnames. If set, this value will be used instead of
+          deriving the URL from the incoming request.
+
+          Example: https://toolshed.g2.bx.psu.edu
+
       file_path:
         type: str
         default: database/community_files
diff --git a/lib/tool_shed/context.py b/lib/tool_shed/context.py
index b936a7b7bf..051e7929f7 100644
--- a/lib/tool_shed/context.py
+++ b/lib/tool_shed/context.py
@@ -148,6 +148,11 @@ class SessionRequestContextImpl(SessionRequestContext):
 
     @property
     def repositories_hostname(self) -> str:
+        # Use configured tool_shed_url if available
+        tool_shed_url = self.app.config.tool_shed_url
+        if tool_shed_url:
+            return tool_shed_url.rstrip("/")
+        # Fall back to request-based URL
         return str(self.request.base).rstrip("/")
 
     @property
diff --git a/lib/tool_shed/webapp/buildapp.py b/lib/tool_shed/webapp/buildapp.py
index 16b47bc450..752f9701f5 100644
--- a/lib/tool_shed/webapp/buildapp.py
+++ b/lib/tool_shed/webapp/buildapp.py
@@ -34,6 +34,11 @@ log = logging.getLogger(__name__)
 class ToolShedGalaxyWebTransaction(GalaxyWebTransaction):
     @property
     def repositories_hostname(self) -> str:
+        # Use configured tool_shed_url if available
+        tool_shed_url = self.app.config.tool_shed_url
+        if tool_shed_url:
+            return tool_shed_url.rstrip("/")
+        # Fall back to request-based URL
         return url_for("/", qualified=True).rstrip("/")
 
     def get_or_create_default_history(self):

gist_summary.md

Add tool_shed_url Config for Explicit Hostname Setting

Overview

Add a new config variable tool_shed_url to allow administrators to explicitly set the Tool Shed's base URL. Modify repositories_hostname to use this config variable when set, falling back to request-based URL when not configured.

Problem

Currently, repositories_hostname uses the incoming request to dynamically generate the hostname. This can cause issues with clone URL generation when the Tool Shed is behind a proxy or needs a specific public URL that differs from the request URL.

Solution

1. Add optional tool_shed_url config variable to Tool Shed schema
2. Modify repositories_hostname property in both SessionRequestContextImpl and ToolShedGalaxyWebTransaction to prefer configured URL
3. Maintain backward compatibility - falls back to request-based URL when not set

Files Changed

Implementation (commit fa276e6532)

• lib/galaxy/config/schemas/tool_shed_config_schema.yml - New config option
• lib/tool_shed/context.py - Updated SessionRequestContextImpl.repositories_hostname
• lib/tool_shed/webapp/buildapp.py - Updated ToolShedGalaxyWebTransaction.repositories_hostname

Tests (new file)

• test/unit/tool_shed/test_context.py - 13 unit tests covering both context implementations

Test Summary

TestSessionRequestContextImplRepositoriesHostname (6 tests):

• Config URL used when set
• Trailing slash stripped from config
• Falls back to request.base when not configured
• Trailing slash stripped from request.base
• Empty string config falls back to request
• Config URL with port works

TestToolShedGalaxyWebTransactionRepositoriesHostname (7 tests):

• Config URL used when set
• Trailing slash stripped from config
• Falls back to url_for when not configured (mocked)
• Trailing slash stripped from url_for
• Empty string config falls back to url_for
• Config URL with port works
• url_for not called when config is set

Usage

# tool_shed.yml
tool_shed:
  tool_shed_url: https://toolshed.g2.bx.psu.edu

gist_test_context.py

"""Tests for tool_shed_url config and repositories_hostname property."""

from unittest import mock

import pytest

from tool_shed.context import SessionRequestContextImpl
from tool_shed.webapp.buildapp import ToolShedGalaxyWebTransaction
from ._util import TestToolShedApp


class ToolShedConfigWithUrl:
    """Extended config that supports tool_shed_url."""

    def __init__(self, base_config, tool_shed_url=None):
        self._base = base_config
        self._tool_shed_url = tool_shed_url

    @property
    def tool_shed_url(self):
        return self._tool_shed_url

    def __getattr__(self, name):
        return getattr(self._base, name)


class MockRequest:
    """Mock request with configurable base URL."""

    def __init__(self, base="http://request-based.example.com/"):
        self._base = base

    @property
    def base(self):
        return self._base

    @property
    def host(self):
        return "request-based.example.com"


class MockResponse:
    """Minimal mock response."""

    headers = {}


@pytest.fixture
def shed_app_with_url():
    """Factory fixture that creates app with optional tool_shed_url config."""

    def _create(tool_shed_url=None):
        app = TestToolShedApp()
        app.config = ToolShedConfigWithUrl(app.config, tool_shed_url)
        return app

    return _create


class TestSessionRequestContextImplRepositoriesHostname:
    """Tests for SessionRequestContextImpl.repositories_hostname."""

    def test_returns_config_url_when_set(self, shed_app_with_url):
        """When tool_shed_url is configured, use it."""
        app = shed_app_with_url("https://toolshed.example.com")
        request = MockRequest()
        response = MockResponse()

        ctx = SessionRequestContextImpl(app, request, response)

        assert ctx.repositories_hostname == "https://toolshed.example.com"

    def test_strips_trailing_slash_from_config_url(self, shed_app_with_url):
        """Config URL trailing slashes are stripped."""
        app = shed_app_with_url("https://toolshed.example.com/")
        request = MockRequest()
        response = MockResponse()

        ctx = SessionRequestContextImpl(app, request, response)

        assert ctx.repositories_hostname == "https://toolshed.example.com"

    def test_falls_back_to_request_base_when_not_configured(self, shed_app_with_url):
        """When tool_shed_url is not set, fall back to request.base."""
        app = shed_app_with_url(None)
        request = MockRequest("http://from-request.example.com/")
        response = MockResponse()

        ctx = SessionRequestContextImpl(app, request, response)

        assert ctx.repositories_hostname == "http://from-request.example.com"

    def test_strips_trailing_slash_from_request_base(self, shed_app_with_url):
        """Request base trailing slashes are stripped in fallback."""
        app = shed_app_with_url(None)
        request = MockRequest("http://from-request.example.com/")
        response = MockResponse()

        ctx = SessionRequestContextImpl(app, request, response)

        assert ctx.repositories_hostname == "http://from-request.example.com"

    def test_empty_string_config_falls_back_to_request(self, shed_app_with_url):
        """Empty string config is falsy, falls back to request."""
        app = shed_app_with_url("")
        request = MockRequest("http://fallback.example.com/")
        response = MockResponse()

        ctx = SessionRequestContextImpl(app, request, response)

        assert ctx.repositories_hostname == "http://fallback.example.com"

    def test_config_url_with_port(self, shed_app_with_url):
        """Config URL with port number works correctly."""
        app = shed_app_with_url("https://toolshed.example.com:8080")
        request = MockRequest()
        response = MockResponse()

        ctx = SessionRequestContextImpl(app, request, response)

        assert ctx.repositories_hostname == "https://toolshed.example.com:8080"


class TestToolShedGalaxyWebTransactionRepositoriesHostname:
    """Tests for ToolShedGalaxyWebTransaction.repositories_hostname."""

    def test_returns_config_url_when_set(self, shed_app_with_url):
        """When tool_shed_url is configured, use it instead of url_for."""
        app = shed_app_with_url("https://toolshed.example.com")

        # Create a minimal mock transaction
        trans = mock.Mock(spec=ToolShedGalaxyWebTransaction)
        trans.app = app

        # Call the actual property implementation
        result = ToolShedGalaxyWebTransaction.repositories_hostname.fget(trans)

        assert result == "https://toolshed.example.com"

    def test_strips_trailing_slash_from_config_url(self, shed_app_with_url):
        """Config URL trailing slashes are stripped."""
        app = shed_app_with_url("https://toolshed.example.com/")

        trans = mock.Mock(spec=ToolShedGalaxyWebTransaction)
        trans.app = app

        result = ToolShedGalaxyWebTransaction.repositories_hostname.fget(trans)

        assert result == "https://toolshed.example.com"

    @mock.patch("tool_shed.webapp.buildapp.url_for")
    def test_falls_back_to_url_for_when_not_configured(self, mock_url_for, shed_app_with_url):
        """When tool_shed_url is not set, fall back to url_for."""
        app = shed_app_with_url(None)
        mock_url_for.return_value = "http://url-for-result.example.com/"

        trans = mock.Mock(spec=ToolShedGalaxyWebTransaction)
        trans.app = app

        result = ToolShedGalaxyWebTransaction.repositories_hostname.fget(trans)

        assert result == "http://url-for-result.example.com"
        mock_url_for.assert_called_once_with("/", qualified=True)

    @mock.patch("tool_shed.webapp.buildapp.url_for")
    def test_strips_trailing_slash_from_url_for(self, mock_url_for, shed_app_with_url):
        """url_for result trailing slashes are stripped."""
        app = shed_app_with_url(None)
        mock_url_for.return_value = "http://url-for-result.example.com/"

        trans = mock.Mock(spec=ToolShedGalaxyWebTransaction)
        trans.app = app

        result = ToolShedGalaxyWebTransaction.repositories_hostname.fget(trans)

        assert result == "http://url-for-result.example.com"

    @mock.patch("tool_shed.webapp.buildapp.url_for")
    def test_empty_string_config_falls_back_to_url_for(self, mock_url_for, shed_app_with_url):
        """Empty string config is falsy, falls back to url_for."""
        app = shed_app_with_url("")
        mock_url_for.return_value = "http://fallback.example.com/"

        trans = mock.Mock(spec=ToolShedGalaxyWebTransaction)
        trans.app = app

        result = ToolShedGalaxyWebTransaction.repositories_hostname.fget(trans)

        assert result == "http://fallback.example.com"
        mock_url_for.assert_called_once()

    def test_config_url_with_port(self, shed_app_with_url):
        """Config URL with port number works correctly."""
        app = shed_app_with_url("https://toolshed.example.com:8080")

        trans = mock.Mock(spec=ToolShedGalaxyWebTransaction)
        trans.app = app

        result = ToolShedGalaxyWebTransaction.repositories_hostname.fget(trans)

        assert result == "https://toolshed.example.com:8080"

    @mock.patch("tool_shed.webapp.buildapp.url_for")
    def test_url_for_not_called_when_config_set(self, mock_url_for, shed_app_with_url):
        """When config is set, url_for should not be called."""
        app = shed_app_with_url("https://configured.example.com")

        trans = mock.Mock(spec=ToolShedGalaxyWebTransaction)
        trans.app = app

        ToolShedGalaxyWebTransaction.repositories_hostname.fget(trans)

        mock_url_for.assert_not_called()