Merge pull request galaxyproject#17497 from mvdbeek/provide_working_u…

…rl_for_to_every_request

[23.2] Provide working routes.url_for every ASGI request

lib/galaxy/app.py

@@ -138,10 +138,7 @@
 from galaxy.visualization.data_providers.registry import DataProviderRegistry
 from galaxy.visualization.genomes import Genomes
 from galaxy.visualization.plugins.registry import VisualizationsRegistry
-from galaxy.web import (
-    legacy_url_for,
-    url_for,
-)
+from galaxy.web import url_for
 from galaxy.web.framework.base import server_starttime
 from galaxy.web.proxy import ProxyManager
 from galaxy.web.short_term_storage import (
@@ -798,7 +795,6 @@ def __init__(self, **kwargs) -> None:
         # Inject url_for for components to more easily optionally depend
         # on url_for.
         self.url_for = url_for
-        self.legacy_url_for = legacy_url_for
 
         self.server_starttime = server_starttime  # used for cachebusting
         # Limit lifetime of tool shed repository cache to app startup

lib/galaxy/datatypes/data.py

@@ -783,7 +783,7 @@ def as_display_type(self, dataset: DatasetProtocol, type: str, **kwd) -> Union[F
         return f"This display type ({type}) is not implemented for this datatype ({dataset.ext})."
 
     def get_display_links(
-        self, dataset: DatasetProtocol, type: str, app, base_url: str, request, target_frame: str = "_blank", **kwd
+        self, dataset: DatasetProtocol, type: str, app, base_url: str, target_frame: str = "_blank", **kwd
     ):
         """
         Returns a list of tuples of (name, link) for a particular display type.  No check on
@@ -794,7 +794,7 @@ def get_display_links(
         try:
             if app.config.enable_old_display_applications and type in self.get_display_types():
                 return target_frame, getattr(self, self.supported_display_apps[type]["links_function"])(
-                    dataset, type, app, base_url, request, **kwd
+                    dataset, type, app, base_url, **kwd
                 )
         except Exception:
             log.exception(

lib/galaxy/datatypes/display_applications/application.py

@@ -53,16 +53,14 @@ def __init__(self, display_application):
 
     def get_display_url(self, data, trans):
         dataset_hash, user_hash = encode_dataset_user(trans, data, None)
-        return trans.app.legacy_url_for(
-            mapper=trans.app.legacy_mapper,
+        return trans.app.url_for(
             controller="dataset",
             action="display_application",
             dataset_id=dataset_hash,
             user_id=user_hash,
             app_name=quote_plus(self.display_application.id),
             link_name=quote_plus(self.id),
             app_action=None,
-            environ=trans.request.environ,
         )
 
     def get_inital_values(self, data, trans):

lib/galaxy/datatypes/display_applications/parameters.py

@@ -274,8 +274,7 @@ def url(self):
             base_url = f"http{base_url[5:]}"
         return "{}{}".format(
             base_url,
-            self.trans.app.legacy_url_for(
-                mapper=self.trans.app.legacy_mapper,
+            self.trans.app.url_for(
                 controller="dataset",
                 action="display_application",
                 dataset_id=self._dataset_hash,
@@ -284,7 +283,6 @@ def url(self):
                 link_name=quote_plus(self.parameter.link.id),
                 app_action=self.action_name,
                 action_param=self._url,
-                environ=self.trans.request.environ,
             ),
         )
 

lib/galaxy/datatypes/genetics.py

@@ -90,7 +90,7 @@ def as_ucsc_display_file(self, dataset: DatasetProtocol, **kwd) -> Union[FileObj
         """
         return open(dataset.get_file_name(), "rb")
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         """
         from the ever-helpful angie hinrichs [email protected]
         a genome graphs call looks like this
@@ -114,17 +114,15 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
                     site_url = site_url.replace("/hgTracks?", "/hgGenome?")  # for genome graphs
-                    internal_url = "%s" % app.legacy_url_for(
-                        mapper=app.legacy_mapper,
-                        environ=request.environ,
+                    internal_url = app.url_for(
                         controller="dataset",
                         dataset_id=dataset.id,
                         action="display_at",
                         filename=f"ucsc_{site_name}",
                     )
                     display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (
                         base_url,
-                        app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                        app.url_for(controller="root"),
                         dataset.id,
                         type,
                     )

lib/galaxy/datatypes/interval.py

@@ -315,7 +315,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
             },
         )
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         """
         Generate links to UCSC genome browser sites based on the dbkey
         and content of dataset.
@@ -337,9 +337,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
         # Accumulate links for valid sites
         ret_val = []
         for site_name, site_url in valid_sites:
-            internal_url = app.legacy_url_for(
-                mapper=app.legacy_mapper,
-                environ=request.environ,
+            internal_url = app.url_for(
                 controller="dataset",
                 dataset_id=dataset.id,
                 action="display_at",
@@ -349,7 +347,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
                 "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
                 % (
                     base_url,
-                    app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                    app.url_for(controller="root"),
                     dataset.id,
                     type,
                 )
@@ -768,20 +766,26 @@ class Bed12(BedStrict):
 
 class _RemoteCallMixin:
     def _get_remote_call_url(
-        self, redirect_url: str, site_name: str, dataset: HasId, type: str, app, base_url: str, request
+        self,
+        redirect_url: str,
+        site_name: str,
+        dataset: HasId,
+        type: str,
+        app,
+        base_url: str,
     ) -> str:
         """Retrieve the URL to call out to an external site and retrieve data.
         This routes our external URL through a local galaxy instance which makes
         the data available, followed by redirecting to the remote site with a
         link back to the available information.
         """
-        internal_url = f"{app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
+        internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
         base_url = app.config.get("display_at_callback", base_url)
         display_url = quote_plus(
             "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
             % (
                 base_url,
-                app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                app.url_for(controller="root"),
                 dataset.id,
                 type,
             )
@@ -969,7 +973,7 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
@@ -978,11 +982,11 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
                     redirect_url = quote_plus(
                         f"{site_url}db={dataset.dbkey}&position={seqid}:{start}-{stop}&hgt.customText=%s"
                     )
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
-    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
@@ -991,7 +995,7 @@ def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str,
                     if seqid.startswith("chr") and len(seqid) > 3:
                         seqid = seqid[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={seqid}:{start}..{stop}&eurl=%s")
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -1371,7 +1375,7 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
@@ -1380,11 +1384,11 @@ def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str,
                     if chrom.startswith("chr") and len(chrom) > 3:
                         chrom = chrom[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={chrom}:{start}..{stop}&eurl=%s")
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
@@ -1393,7 +1397,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
                     redirect_url = quote_plus(
                         f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s"
                     )
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -1553,18 +1557,18 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
-                    internal_url = f"{app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
+                    internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
                     display_url = quote_plus(
                         "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
                         % (
                             base_url,
-                            app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                            app.url_for(controller="root"),
                             dataset.id,
                             type,
                         )

lib/galaxy/managers/hdas.py

@@ -642,7 +642,10 @@ def serialize_old_display_applications(self, item, key, trans=None, **context):
         display_link_fn = hda.datatype.get_display_links
         for display_app in hda.datatype.get_display_types():
             target_frame, display_links = display_link_fn(
-                hda, display_app, self.app, trans.request.base, request=trans.request
+                hda,
+                display_app,
+                self.app,
+                trans.request.base,
             )
 
             if len(display_links) > 0:

lib/galaxy/web/__init__.py

@@ -2,10 +2,7 @@
 The Galaxy web application framework
 """
 
-from .framework import (
-    legacy_url_for,
-    url_for,
-)
+from .framework import url_for
 from .framework.base import httpexceptions
 from .framework.decorators import (
     do_not_cache,
@@ -48,6 +45,5 @@
     "legacy_expose_api_raw_anonymous",
     "require_admin",
     "require_login",
-    "legacy_url_for",
     "url_for",
 )

lib/galaxy/web/framework/__init__.py

@@ -1,9 +1,6 @@
 """
 Galaxy web application framework
 """
-
-from routes import request_config
-
 from . import base
 
 DEPRECATED_URL_ATTRIBUTE_MESSAGE = "*deprecated attribute, URL not filled in by server*"
@@ -21,19 +18,4 @@ def handle_url_for(*args, **kwargs) -> str:
         return DEPRECATED_URL_ATTRIBUTE_MESSAGE
 
 
-def legacy_url_for(mapper, *args, **kwargs) -> str:
-    """
-    Re-establishes the mapper for legacy WSGI routes.
-    """
-    rc = request_config()
-    environ = kwargs.pop("environ", None)
-    rc.mapper = mapper
-    if environ:
-        rc.environ = environ
-        if hasattr(rc, "using_request_local"):
-            rc.request_local = lambda: rc
-            rc = request_config()
-    return base.routes.url_for(*args, **kwargs)
-
-
 url_for = handle_url_for

lib/galaxy/webapps/galaxy/api/__init__.py

@@ -41,6 +41,10 @@
 from fastapi_utils.inferring_router import InferringRouter
 from pydantic import ValidationError
 from pydantic.main import BaseModel
+from routes import (
+    Mapper,
+    request_config,
+)
 from starlette.datastructures import Headers
 from starlette.routing import (
     Match,
@@ -306,6 +310,15 @@ def get_current_history_from_session(galaxy_session: Optional[model.GalaxySessio
     return None
 
 
+def fix_url_for(mapper: Mapper, galaxy_request: GalaxyASGIRequest):
+    rc = request_config()
+    rc.environ = galaxy_request.environ
+    rc.mapper = mapper
+    if hasattr(rc, "using_request_local"):
+        rc.request_local = lambda: rc
+        rc = request_config()
+
+
 def get_trans(
     request: Request,
     response: Response,
@@ -316,6 +329,9 @@ def get_trans(
     url_builder = UrlBuilder(request)
     galaxy_request = GalaxyASGIRequest(request)
     galaxy_response = GalaxyASGIResponse(response)
+    mapper = getattr(app, "legacy_mapper", None)
+    if mapper:
+        fix_url_for(mapper, galaxy_request)
     return SessionRequestContext(
         app=app,
         user=user,