mypy typing for galaxy-web-stack.

lib/galaxy/web_stack/__init__.py

@@ -5,6 +5,7 @@ import inspect
 import json
 import logging
 import os
+from typing import Callable, Dict, FrozenSet, List, Optional, Tuple, Type
 from urllib.request import install_opener
 
 # The uwsgi module is automatically injected by the parent uwsgi process and only exists that way.  If anything works,
@@ -43,10 +44,10 @@ class UWSGILogFilter(logging.Filter):
 
 
 class ApplicationStack:
-    name = None
-    prohibited_middleware = frozenset()
+    name: Optional[str] = None
+    prohibited_middleware: FrozenSet[str] = frozenset()
     transport_class = ApplicationStackTransport
-    log_filter_class = ApplicationStackLogFilter
+    log_filter_class: Type[logging.Filter] = ApplicationStackLogFilter
     log_format = '%(name)s %(levelname)s %(asctime)s %(message)s'
     # TODO: this belongs in the pool configuration
     server_name_template = '{server_name}'
@@ -235,7 +236,7 @@ class UWSGIApplicationStack(MessageApplicationStack):
     log_format = '%(name)s %(levelname)s %(asctime)s [p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] [%(threadName)s] %(message)s'
     server_name_template = '{server_name}.{pool_name}.{instance_id}'
 
-    postfork_functions = []
+    postfork_functions: List[Tuple[Callable, List, Dict]] = []
 
     localhost_addrs = ('127.0.0.1', '[::1]')
     bind_all_addrs = ('', '0.0.0.0', '[::]')

lib/galaxy/web_stack/message.py

@@ -4,6 +4,7 @@
 import json
 import logging
 import types
+from typing import Optional, Tuple
 
 log = logging.getLogger(__name__)
 
@@ -46,7 +47,7 @@ class ApplicationStackMessageDispatcher:
 
 
 class ApplicationStackMessage(dict):
-    target = None
+    _target: Optional[str] = None
     default_handler = None
     _validate_kwargs = ('target',)
 
@@ -96,17 +97,17 @@ class ApplicationStackMessage(dict):
 
     @property
     def target(self):
-        return self['target']
+        return self['_target']
 
     @target.setter
-    def set_target(self, target):
-        self['target'] = target
+    def target(self, target):
+        self['_target'] = target
 
 
 class ParamMessage(ApplicationStackMessage):
     _validate_kwargs = ('params',)
-    _validate_params = ()
-    _exclude_params = ()
+    _validate_params: Tuple[str, ...] = ()
+    _exclude_params: Tuple[str, ...] = ()
 
     def __init__(self, target=None, params=None, **kwargs):
         super().__init__(target=target)
@@ -126,7 +127,7 @@ class ParamMessage(ApplicationStackMessage):
         return d
 
     @params.setter
-    def set_params(self, params):
+    def params(self, params):
         self['params'] = params
 
 
@@ -151,12 +152,12 @@ class TaskMessage(ParamMessage):
 
 
 class JobHandlerMessage(TaskMessage):
-    target = 'job_handler'
+    _target = 'job_handler'
     _validate_params = ('job_id',)
 
 
 class WorkflowSchedulingMessage(TaskMessage):
-    target = 'workflow_scheduling'
+    _target = 'workflow_scheduling'
     _validate_params = ('workflow_invocation_id',)
 
 

lib/galaxy/web_stack/transport.py

@@ -3,6 +3,7 @@
 
 import logging
 import threading
+from typing import List
 
 from galaxy.util import unicodify
 
@@ -70,7 +71,7 @@ class UWSGIFarmMessageTransport(ApplicationStackTransport):
     """ Communication via uWSGI Mule Farm messages. Communication is unidirectional (workers -> mules).
     """
     # Define any static lock names here, additional locks will be appended for each configured farm's message handler
-    _locks = []
+    _locks: List[str] = []
 
     def init_late_prefork(self):
         num = int(uwsgi.opt.get('locks', 0)) + 1

packages/test.sh

@@ -34,7 +34,7 @@ PACKAGE_DIRS=(
 # tool_util not yet working 100%,
 # data has many problems quota, tool shed install database, etc..
 RUN_TESTS=(1 1 1 1 1 1 1 1 1 1 0 0)
-RUN_MYPY=(1 1 1 1 1 1 1 1 0 0 0 0)
+RUN_MYPY=(1 1 1 1 1 1 1 1 1 0 0 0)
 for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
     package_dir=${PACKAGE_DIRS[$i]}
     run_tests=${RUN_TESTS[$i]}

packages/web_stack/galaxy/__init__.py

@@ -1 +1 @@
-__path__ = __import__('pkgutil').extend_path(__path__, __name__)
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)  # type: ignore