Include non-FastAPI routes in api/docs

lib/galaxy/app.py

@@ -705,6 +705,7 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
         self.server_starttime = int(time.time())  # used for cachebusting
         # Limit lifetime of tool shed repository cache to app startup
         self.tool_shed_repository_cache = None
+        self.api_spec = None
         log.info(f"Galaxy app startup finished {startup_timer}")
 
     def _shutdown_queue_worker(self):

lib/galaxy/webapps/base/webapp.py

@@ -5,6 +5,7 @@ import inspect
 import logging
 import os
 import random
+import re
 import socket
 import string
 import time
@@ -106,27 +107,28 @@ class WebApplication(base.WebApplication):
         Traverse all route paths starting with "api" and create an APISpec instance.
         """
         # API specification builder
-        apispec = APISpec(title=self.name,
-                          version="0.0.0-unsupported", # galaxy_app.config.version_major,
-                          openapi_version="3.0.2")
-        import re, sys
-        from apispec import yaml_utils
-        RE_URL = re.compile(r"""
+        apispec = APISpec(
+            title=self.name, version="0.0.0-unsupported", openapi_version="3.0.2"  # galaxy_app.config.version_major,
+        )
+        RE_URL = re.compile(
+            r"""
             (?::\(|{)
                 (\w*)
                 (?::.*)?
-            (?:\)|})""", re.X)
+            (?:\)|})""",
+            re.X,
+        )
         for rule in self.mapper.matchlist:
             if rule.routepath.endswith(".:(format)") or not rule.routepath.startswith("api/"):
                 continue
             # Try to replace routes various ways to encode variables with simple swagger {form}
-            swagger_path = "/%s" % RE_URL.sub(r'{\1}', rule.routepath)
-            controller = rule.defaults.get('controller', '')
-            action = rule.defaults.get('action', '')
+            swagger_path = "/%s" % RE_URL.sub(r"{\1}", rule.routepath)
+            controller = rule.defaults.get("controller", "")
+            action = rule.defaults.get("action", "")
             # Get the list of methods for the route
             methods = []
             if rule.conditions:
-                m = rule.conditions.get('method', [])
+                m = rule.conditions.get("method", [])
                 methods = type(m) is str and [m] or m
             # Find the controller class
             if controller not in self.api_controllers:
@@ -137,12 +139,14 @@ class WebApplication(base.WebApplication):
                 log.warning("No action found for '%s' in class '%s' while building API spec", action, controller_class)
                 continue
             action_method = getattr(controller_class, action)
-            # First try to load method docs from docstring
-            operations = yaml_utils.load_operations_from_docstring(action_method.__doc__)
+            operations = {}
             # Add methods that have routes but are not documents
             for method in methods:
                 if method.lower() not in operations:
-                    operations[method.lower()] = {}
+                    operations[method.lower()] = {
+                        "description": f"This route has not yet been ported to FastAPI. The documentation may not be complete.\n{action_method.__doc__}",
+                        "tags": ["routes"],
+                    }
             # Store the swagger path
             apispec.path(path=swagger_path, operations=operations)
         return apispec

lib/galaxy/webapps/galaxy/api/docs.py

@@ -1,9 +0,0 @@
-from galaxy import web
-from galaxy.webapps.base.controller import BaseAPIController
-
-
-class GenomesController(BaseAPIController):
-
-    @web.expose_api_raw
-    def index(self, trans, **kwd):
-        return trans.webapp.build_apispec().to_yaml()

lib/galaxy/webapps/galaxy/buildapp.py

@@ -260,6 +260,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     # ==== Done
     # Indicate that all configuration settings have been provided
     webapp.finalize_config()
+    app.api_spec = webapp.build_apispec()
 
     # Wrap the webapp in some useful middleware
     if kwargs.get("middleware", True):

lib/galaxy/webapps/galaxy/fast_app.py

@@ -6,12 +6,14 @@ from fastapi import (
     FastAPI,
     Request,
 )
+from fastapi.openapi.utils import get_openapi
 from starlette.middleware.cors import CORSMiddleware
 from starlette.responses import (
     FileResponse,
     Response,
 )
 
+from galaxy.version import VERSION
 from galaxy.webapps.base.api import (
     add_exception_handler,
     add_request_id_middleware,
@@ -121,6 +123,21 @@ def add_galaxy_middleware(app: FastAPI, gx_app):
             return response
 
 
+def include_legacy_openapi(app, gx_app):
+    if app.openapi_schema:
+        return app.openapi_schema
+    openapi_schema = get_openapi(
+        title="Galaxy API Documentation",
+        version=VERSION,
+        routes=app.routes,
+    )
+    legacy_openapi = gx_app.api_spec.to_dict()
+    legacy_openapi["paths"].update(openapi_schema["paths"])
+    openapi_schema["paths"] = legacy_openapi["paths"]
+    app.openapi_schema = openapi_schema
+    return app.openapi_schema
+
+
 def initialize_fast_app(gx_wsgi_webapp, gx_app):
     app = FastAPI(
         title="Galaxy API",
@@ -131,6 +148,7 @@ def initialize_fast_app(gx_wsgi_webapp, gx_app):
     add_galaxy_middleware(app, gx_app)
     add_request_id_middleware(app)
     include_all_package_routers(app, "galaxy.webapps.galaxy.api")
+    include_legacy_openapi(app, gx_app)
     wsgi_handler = WSGIMiddleware(gx_wsgi_webapp)
     app.mount("/", wsgi_handler)
     if gx_app.config.galaxy_url_prefix != "/":