Create a uWSGI postfork function registry. Also, start the tool conf

watcher thread post-fork.

.ci/flake8_lint_include_list.txt

@@ -292,6 +292,7 @@ lib/galaxy/util/multi_byte.py
 lib/galaxy/util/odict.py
 lib/galaxy/util/pastescript/__init__.py
 lib/galaxy/util/plugin_config.py
+lib/galaxy/util/postfork.py
 lib/galaxy/util/simplegraph.py
 lib/galaxy_utils/__init__.py
 lib/galaxy/util/sleeper.py

lib/galaxy/app.py

@@ -5,13 +5,6 @@
 import time
 import os
 
-try:
-    from uwsgidecorators import postfork
-except:
-    def pf_dec(func):
-        return func
-    postfork = pf_dec
-
 from galaxy import config, jobs
 import galaxy.model
 import galaxy.security
@@ -31,6 +24,7 @@ def pf_dec(func):
 from galaxy.web.proxy import ProxyManager
 from galaxy.queue_worker import GalaxyQueueWorker
 from galaxy.util import heartbeat
+from galaxy.util.postfork import register_postfork_function
 from tool_shed.galaxy_install import update_repository_manager
 
 
@@ -154,12 +148,7 @@ def __init__( self, **kwargs ):
                     fname=self.config.heartbeat_log
                 )
                 self.heartbeat.daemon = True
-
-                @postfork
-                def _start():
-                    self.heartbeat.start()
-                if not config.process_is_uwsgi:
-                    _start()
+                register_postfork_function(self.heartbeat.start)
         if self.config.sentry_dsn:
             import raven
             self.sentry_client = raven.Client(self.config.sentry_dsn)

lib/galaxy/config.py

@@ -28,17 +28,6 @@
 
 log = logging.getLogger( __name__ )
 
-# The uwsgi module is automatically injected by the parent uwsgi
-# process and only exists that way.  If anything works, this is a
-# uwsgi-managed process.
-try:
-    import uwsgi
-    if uwsgi.numproc:
-        process_is_uwsgi = True
-except ImportError:
-    # This is not a uwsgi process, or something went horribly wrong.
-    process_is_uwsgi = False
-
 
 def resolve_path( path, root ):
     """If 'path' is relative make absolute by prepending 'root'"""

lib/galaxy/queues.py

@@ -4,7 +4,7 @@
 
 """
 
-from galaxy.config import process_is_uwsgi
+from galaxy.util.postfork import process_is_uwsgi
 
 from kombu import Exchange, Queue, Connection
 

lib/galaxy/tools/toolbox/base.py

@@ -15,6 +15,7 @@
 from galaxy.util import parse_xml
 from galaxy.util import string_as_bool
 from galaxy.util.bunch import Bunch
+from galaxy.util.postfork import register_postfork_function
 
 from .parser import get_toolbox_parser, ensure_tool_conf_item
 
@@ -103,6 +104,7 @@ def _init_tools_from_configs( self, config_filenames ):
                 self._init_tools_from_config( config_filename )
             except:
                 log.exception( "Error loading tools defined in config %s", config_filename )
+        register_postfork_function(self._tool_conf_watcher.start)
 
     def _init_tools_from_config( self, config_filename ):
         """

lib/galaxy/tools/toolbox/watcher.py

@@ -65,7 +65,7 @@ def __init__(self, reload_callback):
         self.paths = {}
         self._active = False
         self._lock = threading.Lock()
-        self.thread = threading.Thread(target=self.check)
+        self.thread = threading.Thread(target=self.check, name="ToolConfWatcher.thread")
         self.thread.daemon = True
         self.event_handler = ToolConfFileEventHandler(reload_callback)
 
@@ -107,7 +107,6 @@ def monitor(self, path):
             mod_time = time.ctime(os.path.getmtime(path))
         with self._lock:
             self.paths[path] = mod_time
-        self.start()
 
     def watch_file(self, tool_conf_file):
         self.monitor(tool_conf_file)

lib/galaxy/util/postfork.py

@@ -0,0 +1,35 @@
+"""
+Handle postfork functions under uWSGI
+"""
+
+# The uwsgi module is automatically injected by the parent uwsgi
+# process and only exists that way.  If anything works, this is a
+# uwsgi-managed process.
+try:
+    import uwsgi
+    from uwsgidecorators import postfork
+    if uwsgi.numproc:
+        process_is_uwsgi = True
+except ImportError:
+    # This is not a uwsgi process, or something went horribly wrong.
+    process_is_uwsgi = False
+
+    def pf_dec(func):
+        return func
+    postfork = pf_dec
+
+
+postfork_functions = []
+
+
+@postfork
+def do_postfork():
+    for f, args, kwargs in [ t for t in postfork_functions ]:
+        f(*args, **kwargs)
+
+
+def register_postfork_function(f, *args, **kwargs):
+    if process_is_uwsgi:
+        postfork_functions.append((f, args, kwargs))
+    else:
+        f(*args, **kwargs)

lib/galaxy/webapps/galaxy/buildapp.py

@@ -13,7 +13,6 @@
 
 
 import galaxy.app
-from galaxy.config import process_is_uwsgi
 import galaxy.model
 import galaxy.model.mapping
 import galaxy.datatypes.registry
@@ -22,22 +21,14 @@
 from galaxy.webapps.util import build_template_error_formatters
 from galaxy import util
 from galaxy.util import asbool
+from galaxy.util.postfork import process_is_uwsgi, register_postfork_function
 from galaxy.util.properties import load_app_properties
 
 from paste import httpexceptions
 
 import logging
 log = logging.getLogger( __name__ )
 
-try:
-    from uwsgidecorators import postfork
-except:
-    # TODO:  Make this function more like flask's @before_first_request w/
-    # registered methods etc.
-    def pf_dec(func):
-        return func
-    postfork = pf_dec
-
 
 class GalaxyWebApplication( galaxy.web.framework.webapp.WebApplication ):
     pass
@@ -135,8 +126,7 @@ def paste_app_factory( global_conf, **kwargs ):
     except:
         log.exception("Unable to dispose of pooled toolshed install model database connections.")
 
-    if not process_is_uwsgi:
-        postfork_setup()
+    register_postfork_function(postfork_setup)
 
     # Return
     return webapp
@@ -158,7 +148,6 @@ def uwsgi_app_factory():
     return app_factory(global_conf, **kwargs)
 
 
-@postfork
 def postfork_setup():
     from galaxy.app import app
     if process_is_uwsgi:

lib/galaxy/webapps/reports/buildapp.py

@@ -10,8 +10,8 @@
 
 from paste import httpexceptions
 
-from galaxy.config import process_is_uwsgi
 from galaxy.util import asbool
+from galaxy.util.postfork import process_is_uwsgi
 from galaxy.webapps.util import build_template_error_formatters
 
 import galaxy.model

lib/galaxy/webapps/tool_shed/buildapp.py

@@ -15,7 +15,7 @@
 from galaxy.webapps.util import build_template_error_formatters
 from galaxy.webapps.tool_shed.framework.middleware import hg
 from galaxy import util
-from galaxy.config import process_is_uwsgi
+from galaxy.util.postfork import process_is_uwsgi
 from galaxy.util.properties import load_app_properties
 
 log = logging.getLogger( __name__ )