Merge branch 'release_22.01' into dev

lib/galaxy/tools/__init__.py

@@ -3433,9 +3433,7 @@ class SortTool(DatabaseOperationTool):
             presort_elements = [(dce.element_identifier, dce) for dce in elements]
         elif sorttype == "numeric":
             presort_elements = [(int(re.sub("[^0-9]", "", dce.element_identifier)), dce) for dce in elements]
-        if presort_elements:
-            sorted_elements = [x[1] for x in sorted(presort_elements, key=lambda x: x[0])]
-        if sorttype == "file":
+        elif sorttype == "file":
             hda = incoming["sort_type"]["sort_file"]
             data_lines = hda.metadata.get("data_lines", 0)
             if data_lines == len(elements):
@@ -3450,8 +3448,13 @@ class SortTool(DatabaseOperationTool):
                     message = f"List of element identifiers does not match element identifiers in collection '{hdca_history_name}'"
                     raise Exception(message)
             else:
-                message = "Number of lines must match number of list elements (%i), but file has %i lines"
-                raise Exception(message % (data_lines, len(elements)))
+                message = f"Number of lines must match number of list elements ({len(elements)}), but file has {data_lines} lines"
+                raise Exception(message)
+        else:
+            raise Exception(f"Unknown sort_type '{sorttype}'")
+
+        if presort_elements:
+            sorted_elements = [x[1] for x in sorted(presort_elements, key=lambda x: x[0])]
 
         for dce in sorted_elements:
             dce_object = dce.element_object

lib/galaxy/web_stack/__init__.py

@@ -276,7 +276,7 @@ class UWSGIApplicationStack(MessageApplicationStack):
     name = "uWSGI"
     prohibited_middleware = frozenset(
         {
-            "wrap_in_static",
+            "build_url_map",
             "EvalException",
         }
     )

lib/galaxy/webapps/base/webapp.py

@@ -1044,7 +1044,7 @@ def build_native_uwsgi_app(paste_factory, config_section):
     return uwsgi_app
 
 
-def build_url_map(app, global_conf, local_conf):
+def build_url_map(app, global_conf, **local_conf):
     from paste.urlmap import URLMap
 
     from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
@@ -1076,4 +1076,4 @@ def build_url_map(app, global_conf, local_conf):
 
     if "static_local_dir" in conf:
         urlmap["/static_local"] = Static(conf["static_local_dir"], cache_time)
-    return urlmap, cache_time
+    return urlmap

lib/galaxy/webapps/galaxy/buildapp.py

@@ -25,6 +25,7 @@ from galaxy.web.framework.middleware.batch import BatchMiddleware
 from galaxy.web.framework.middleware.error import ErrorMiddleware
 from galaxy.web.framework.middleware.request_id import RequestIDMiddleware
 from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
+from galaxy.webapps.base.webapp import build_url_map
 from galaxy.webapps.util import wrap_if_allowed
 
 log = logging.getLogger(__name__)
@@ -264,13 +265,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     if kwargs.get("middleware", True):
         webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
     if asbool(kwargs.get("static_enabled", True)):
-        webapp = wrap_if_allowed(
-            webapp,
-            app.application_stack,
-            wrap_in_static,
-            args=(global_conf,),
-            kwargs=dict(plugin_frameworks=[app.visualizations_registry], **kwargs),
-        )
+        webapp = wrap_if_allowed(webapp, app.application_stack, build_url_map, args=(global_conf,), kwargs=kwargs)
     app.application_stack.register_postfork_function(postfork_setup)
 
     for th in threading.enumerate():
@@ -2010,8 +2005,3 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
 
         app = wrap_if_allowed(app, stack, SQLDebugMiddleware, args=(webapp, {}))
     return app
-
-
-def wrap_in_static(app, global_conf, plugin_frameworks=None, **local_conf):
-    urlmap, cache_time = galaxy.webapps.base.webapp.build_url_map(app, global_conf, local_conf)
-    return urlmap

lib/galaxy/webapps/reports/buildapp.py

@@ -13,6 +13,7 @@ import galaxy.model.mapping
 import galaxy.webapps.base.webapp
 from galaxy.util import asbool
 from galaxy.util.properties import load_app_properties
+from galaxy.webapps.base.webapp import build_url_map
 from galaxy.webapps.util import wrap_if_allowed
 
 log = logging.getLogger(__name__)
@@ -67,6 +68,8 @@ def app_factory(global_conf, load_app_kwds=None, **kwargs):
     # Wrap the webapp in some useful middleware
     if kwargs.get("middleware", True):
         webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
+    if asbool(kwargs.get("static_enabled", True)):
+        webapp = wrap_if_allowed(webapp, app.application_stack, build_url_map, args=(global_conf,), kwargs=kwargs)
     return webapp
 
 

lib/tool_shed/webapp/buildapp.py

@@ -15,6 +15,7 @@ import galaxy.webapps.base.webapp
 from galaxy import util
 from galaxy.util import asbool
 from galaxy.util.properties import load_app_properties
+from galaxy.webapps.base.webapp import build_url_map
 from galaxy.webapps.util import wrap_if_allowed
 
 log = logging.getLogger(__name__)
@@ -204,6 +205,8 @@ def app_factory(global_conf, load_app_kwds=None, **kwargs):
     # Wrap the webapp in some useful middleware
     if kwargs.get("middleware", True):
         webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
+    if asbool(kwargs.get("static_enabled", True)):
+        webapp = wrap_if_allowed(webapp, app.application_stack, build_url_map, args=(global_conf,), kwargs=kwargs)
     return webapp
 
 

run_tool_shed.sh

@@ -26,7 +26,7 @@ if [ $? -eq 0 ] ; then
 fi
 
 if [ -z "$TOOL_SHED_CONFIG_FILE" ]; then
-    TOOL_SHED_CONFIG_FILE=$(PYTHONPATH=lib python -c "from __future__ import print_function; from galaxy.util.properties import find_config_file; print(find_config_file(['tool_shed', 'tool_shed_wsgi']) or '')")
+    TOOL_SHED_CONFIG_FILE=$(PYTHONPATH=lib python -c "from __future__ import print_function; from galaxy.util.properties import find_config_file; print(find_config_file(['tool_shed', 'tool_shed_wsgi'], include_samples=True) or '')")
     export TOOL_SHED_CONFIG_FILE
 fi
 

scripts/common_startup_functions.sh

@@ -162,9 +162,11 @@ find_server() {
             gunicorn_worker="galaxy.webapps.galaxy.workers.Worker"
             ;;
         reports)
-            # TODO: don't override this var, and is this really the only way to configure the port?
-            GUNICORN_CMD_ARGS="--bind=localhost:9001"
+            # TODO: is this really the only way to configure the port?
+            GUNICORN_CMD_ARGS=${GUNICORN_CMD_ARGS:-"--bind=localhost:9001"}
             ;;
+        tool_shed)
+            GUNICORN_CMD_ARGS=${GUNICORN_CMD_ARGS:-"--bind=localhost:9009"}
     esac
 
     APP_WEBSERVER=${APP_WEBSERVER:-$default_webserver}
@@ -187,9 +189,13 @@ find_server() {
         fi
         server_args="$server_args $uwsgi_args"
     elif [ "$APP_WEBSERVER" = "gunicorn" ]; then
-        export GUNICORN_CMD_ARGS="${GUNICORN_CMD_ARGS:-\"--bind=localhost:8080\"}"
         run_server="gunicorn"
-        server_args="'galaxy.webapps.${server_app}.fast_factory:factory()' --pythonpath lib -k ${gunicorn_worker:-$default_gunicorn_worker} $gunicorn_args"
+        export GUNICORN_CMD_ARGS
+        if [ "$server_app" = "tool_shed" ]; then
+            server_args="'${server_app}.webapp.fast_factory:factory()' --pythonpath lib -k ${gunicorn_worker:-$default_gunicorn_worker} $gunicorn_args"
+        else
+            server_args="'galaxy.webapps.${server_app}.fast_factory:factory()' --pythonpath lib -k ${gunicorn_worker:-$default_gunicorn_worker} $gunicorn_args"
+        fi
         if [ "$add_pid_arg" -eq 1 ]; then
             server_args="$server_args --pid \"$PID_FILE\""
         fi