Refactored pubsub module with absolute import

MDANSE/Core/ClassRegistry.py

@@ -30,29 +30,15 @@ Created on Mar 30, 2015
 :author: Eric C. Pellegrini
 '''
 
-import abc
 import glob
 import imp
 import inspect
 import os
 import sys
 
-class _Meta(type):
-    '''
-    Metaclass that allows to use the :py:meth:`__getitem__` method at a class level for the class that has been built.
-     
-    The class that uses this metaclass must define a class attribute named _registry that will be used
-    by the :py:meth:`__getitem__` method.
-    '''
-         
-    def __getitem__(self, item):
-        """
-        Returns a given item stored in the class registry
-        """
-         
-        return self._registry[item]
+from MDANSE.Core.Singleton import Singleton
     
-class ClassRegistry(abc.ABCMeta):
+class ClassRegistry(object):
     '''
     Metaclass that registers the classes that make the MDANSE framework.
 
@@ -67,49 +53,41 @@ class ClassRegistry(abc.ABCMeta):
     class attribute will not be registered.    
     '''
     
-    __metaclass__ = _Meta
+    __metaclass__ = Singleton
 
-    __interfaces = set()
+    def __init__(self):
+        
+        self._registry = {}
+        
+        self._sections = {}
+        
+    def __setitem__(self,name,cls):
 
-    _registry = {}
-                
-    def __init__(self, name, bases, namespace):
-        '''
-        Constructor
-        
-        :param name: the name of the class to be built by this metaclass
-        :type name: str
-        :param bases: the base classes of the class to be built by this metaclass
-        :type bases: tuple 
-        :param namespace: the attributes and methods of the class to be built by this metaclass
-        :type namespace: dict
-        '''
+        # The class to be registered must have a class attribute "_registry" to be registered, otherwise return       
+        clsRegistry = getattr(cls,"_registry")
+        if clsRegistry is None:
+            return
         
-        super(ClassRegistry, self).__init__(name, bases, namespace)
-            
-        # If the class objet does not have a type attribute, it will not be registered.    
-        typ = getattr(self, 'type', None)
-        if typ is None:
+        # And this attribute must be a string for the class to be registerable otherwise return
+        if not isinstance(clsRegistry,basestring):
+            return
+        
+        # Fetch the branch of the registry corresponding the one of the class to be registred, otherwise create a new branch        
+        d = self._registry.setdefault(clsRegistry,{})
+        
+        # If a class has already been registered with that name return
+        if d.has_key(name):
             return
 
-        # If the class object is metaclassed by ClassRegistry then a new section of the registry will
-        # be created with its type attribute.
-        metaClass = namespace.get("__metaclass__", None)                              
-        if metaClass is ClassRegistry:
-            ClassRegistry.__interfaces.add(self)
-            if (ClassRegistry._registry.has_key(typ)):
-                return
-            ClassRegistry._registry[typ] = {}
-
-        else:
-                                            
-            for interface in ClassRegistry.__interfaces:
-                if issubclass(self, interface):
-                    ClassRegistry._registry[interface.type][typ] = self
-                    break
-          
-    @classmethod      
-    def update_registry(cls,packageDir):
+        setattr(cls,"_type",name)
+        
+        d[name] = cls
+                
+    def __getitem__(self,name):
+        
+        return self._registry.get(name,{})
+
+    def update(self,packageDir):
         '''
         Update the classes registry by importing all the modules contained in a given package.
         
@@ -141,10 +119,8 @@ class ClassRegistry(abc.ABCMeta):
             else:
                 if os.path.abspath(os.path.dirname(mod.__file__)) != os.path.abspath(moduleDir):                    
                     print "A module with name %s is already present in your distribution with %s path." % (moduleName,moduleDir)
-
     
-    @classmethod
-    def info(cls, interface):
+    def info(self, interface):
         '''
         Returns informations about the subclasses of a given base class stored in the registry.
         
@@ -155,7 +131,7 @@ class ClassRegistry(abc.ABCMeta):
         :rtype: str
         '''
                 
-        if not cls._registry.has_key(interface):
+        if not self._registry.has_key(interface):
             return "The interface " + interface + " is not registered"
 
         words = ["Name", "Class","File"]
@@ -168,7 +144,7 @@ class ClassRegistry(abc.ABCMeta):
         maxlength = -1
         
         # Loop over the registry items.
-        for i, (k, v) in enumerate(sorted(cls._registry[interface].items())):
+        for i, (k, v) in enumerate(sorted(self._registry[interface].items())):
             
             # Get the module corresponding to the job class.
             mod = inspect.getmodule(v)
@@ -185,8 +161,8 @@ class ClassRegistry(abc.ABCMeta):
                     
         return contents.format(maxlength,*words)
 
-    @classmethod
-    def get_interfaces(cls):
+    @property
+    def interfaces(self):
         '''
         Returns the interfaces that are currently registered.
         
@@ -194,4 +170,8 @@ class ClassRegistry(abc.ABCMeta):
         :rtype: list of str
         '''
         
-        return sorted(cls._registry.keys())
\ No newline at end of file
+        return sorted(self._registry.keys())
+        
+REGISTRY = ClassRegistry()
+
+                

MDANSE/Data/ElementsDatabase.py

@@ -35,6 +35,8 @@ import copy
 import csv
 import numbers
 import os
+import pkg_resources
+import sys
 import xml.etree.ElementTree as etree
 
 from MDANSE.Core.Platform import PLATFORM
@@ -111,8 +113,14 @@ class ElementsDatabase(object):
     
     __metaclass__ = Singleton
     
-    # The default path
-    _DEFAULT_DATABASE = os.path.join(os.path.dirname(__file__), "elements_database.csv")
+    try:  
+        _DEFAULT_DATABASE = pkg_resources.resource_filename(__name__,"elements_database.csv")
+    except:  
+        if hasattr(sys,'frozen'):
+            _DEFAULT_DATABASE = os.path.join(os.path.dirname(sys.executable),"elements_database.csv")
+        else:
+            raise
+
 
     # The user path
     _USER_DATABASE = os.path.join(PLATFORM.application_directory(), "elements_database.csv")

MDANSE/Externals/pubsub/__init__.py

+'''
+Publish-subscribe package.
+
+This package provides the following modules:
+
+- pub: "entry point" module for core pubsub functionality. It provides 
+  functions for sending messages and subscribing listeners and various
+  others.
+- utils: subpackage of utility functions and classes for debugging
+  messages, handling exceptions raised in listeners, and more.
+- setupv1: (deprecated) module to force pubsub to use the old,
+  "version 1" (aka v1) API (should only be useful to wxPython users
+  for legacy code).
+- setuparg1: module to setup pubsub to use "arg1" messaging protocol
+- setupkwargs: module to setup pubsub to use "kwargs" messaging protocol
+
+For instance::
+
+    from pubsub import pub
+    pub.sendMessage('topic', data1=123)
+
+:copyright: Copyright 2006-2009 by Oliver Schoenborn, all rights reserved.
+:license: BSD, see LICENSE.txt for details.
+
+Last known commit:
+- $Date: 2010-02-13 08:57:21 -0500 (Sat, 13 Feb 2010) $
+- $Revision: 249 $
+
+'''
+
+
+__all__ = [
+    'pub', 'utils',
+    'printImported', 'setupkwargs', 'setuparg1', 'setupv1',
+    ]
+
+# set our module search path in globalsettings so setup*.py modules 
+# can find and modify
+from MDANSE.Externals.pubsub import pubsubconf
+pubsubconf.setPubsubInfo(__path__, globals())
+#del pubsubconf # prevent circular ref
+
+
+def printImported():
+    '''Output a list of pubsub modules imported so far'''
+    import sys
+    ll = [mod for mod in sys.modules.keys() if mod.find('pubsub') >= 0]
+    ll.sort()
+    print '\n'.join(ll)
+
+
+def _tryAutoSetupV1():
+    '''This function is called automatically when the pubsub module is 
+    imported. It determines if the legacy "version 1" API of pubsub should
+    be used automatically, by looking for a module called 'autosetuppubsubv1'
+    on the module's search path. If this module is found, setupv1 is imported,
+    so your application will get v1 API just by doing "from pubsub import ...". 
+    If that module is not found then nothing happens and the function
+    returns; your application will get the "default" API unless you 
+    explicitly choose a different one. Note that autosetuppubsubv1 is never
+    actually imported, just searched. '''
+    try: 
+        # if autosetupv1 is importable, then it means we should
+        # automatically setup for version 1 API
+        import imp
+        imp.find_module('autosetuppubsubv1', __path__)
+        
+    except ImportError:
+        pass
+        
+    else:
+        from MDANSE.Externals.pubsub import setupv1
+        assert pub is not None
+        assert Publisher is pub.Publisher
+
+
+_tryAutoSetupV1()

MDANSE/Externals/pubsub/autosetuppubsubv1.py

+'''
+If this module is named autosetuppubsubv1, and it is in the pubsub
+package's folder, it will cause pubsub to default to "version 1" (v1)
+of the API when pub is imported. The v1 API was the version originally
+developed as part of wxPython's wx.lib library.
+
+If this module is named anything else (such as prefixed with an
+underscore) it will not be found by pubsub: the most recent pubsub
+API will be loaded upon import of the *pub* module.
+'''
\ No newline at end of file

MDANSE/Externals/pubsub/core/__init__.py

+'''
+Core package of pubsub, holding the publisher, listener, and topic
+object modules. Functions defined here are used internally by
+pubsub so that the right modules can be found later, based on the
+selected messaging protocol.
+
+Indeed some of the API depends on the messaging
+protocol used. For instance sendMessage(), defined in publisher.py,
+has a different signature (and hence implementation) for the kwargs
+protocol than for the arg1 protocol.
+
+The most convenient way to
+support this is to put the parts of the package that differ based
+on protocol in separate folders, and add one of those folders to
+the package's __path__ variable (defined automatically by the Python
+interpreter when __init__.py is executed). For instance, code
+specific to the kwargs protocol goes in the kwargs folder, and code
+specific to the arg1 protocol in the arg1 folder. Then when doing
+"from pubsub.core import listener", the correct listener.py will be
+found for the specified protocol. The default protocol is kwargs.
+
+Only one protocol can be used in an application. The default protocol,
+if none is chosen by user, is kwargs, as selected by the call to
+_prependModulePath() at end of this file. 
+
+:copyright: Copyright 2006-2009 by Oliver Schoenborn, all rights reserved.
+:license: BSD, see LICENSE.txt for details.
+
+'''
+
+from MDANSE.Externals.pubsub.core import policies
+
+def setMsgProtocol(protocol):
+    
+    policies.msgDataProtocol = protocol
+
+    # add appropriate subdir for protocol-specific implementation
+    if protocol == 'kwargs':
+        _replaceModulePath0('kwargs')
+    else:
+        _replaceModulePath0('arg1')
+
+
+def setMsgDataArgName(stage, listenerArgName, senderArgNameAny=False):
+
+    policies.senderKwargNameAny = senderArgNameAny
+    policies.msgDataArgName = listenerArgName
+    policies.msgProtocolTransStage = stage
+    #print `policies.msgProtocolTransStage`, `policies.msgDataProtocol`, \
+    #      `policies.senderKwargNameAny`, `policies.msgDataArgName`
+    #print 'override "arg1" protocol arg name:', argName
+
+
+def _replaceModulePath0(dirname):
+    '''Replace the first package-path item (in __path__) with dirname.
+    The dirname will be prepended with the package's path, assumed to
+    be the last item in __path__.'''
+    corepath = __path__
+    assert len(corepath) > 1
+    initpyLoc = corepath[-1]
+    import os
+    corepath[0] = os.path.join(initpyLoc, dirname)
+
+
+def _prependModulePath(extra):
+    '''Insert extra at beginning of package's path list. Should only be
+    called once, at package load time, to set the folder used for
+    implementation specific to the default message protocol.'''
+    corepath = __path__
+    initpyLoc = corepath[-1]
+    import os
+    corepath.insert(0, os.path.join(initpyLoc, extra))
+    
+
+# default protocol:
+_prependModulePath('kwargs')

MDANSE/Externals/pubsub/core/arg1/__init__.py

+'''
+This is not really a package init file, it is only here to simplify the
+packaging and installation of pubsub.core's protocol-specific subfolders
+by setuptools.  The python modules in this folder are automatically made
+part of pubsub.core via pubsub.core's __path__. Hence, this should not
+be imported directly, it is part of pubsub.core when the messaging
+protocol is "arg1" (and not usable otherwise).
+
+:copyright: Copyright 2006-2009 by Oliver Schoenborn, all rights reserved.
+:license: BSD, see LICENSE.txt for details.
+
+'''
+
+
+msg = 'Should not import this directly, used by pubsub.core if applicable'
+raise RuntimeError(msg)
\ No newline at end of file

MDANSE/Externals/pubsub/core/arg1/listenerimpl.py

+'''
+
+:copyright: Copyright 2006-2009 by Oliver Schoenborn, all rights reserved.
+:license: BSD, see LICENSE.txt for details.
+
+'''
+
+from MDANSE.Externals.pubsub.core.listenerbase import ListenerBase, ValidatorBase, ListenerInadequate
+from MDANSE.Externals.pubsub.core.callables import ListenerInadequate
+from MDANSE.Externals.pubsub.core import policies
+
+
+class Message:
+    """
+    A simple container object for the two components of a topic messages
+    in the pubsub API v1: the
+    topic and the user data. An instance of Message is given to your
+    listener when called by sendMessage(topic). The data is accessed
+    via the 'data' attribute, and can be type of object.
+    """
+    def __init__(self, topicNameTuple, data):
+        self.topic = topicNameTuple
+        self.data  = data
+
+    def __str__(self):
+        return '[Topic: '+`self.topic`+',  Data: '+`self.data`+']'
+
+
+class Listener(ListenerBase):
+    def __call__(self, actualTopic, data):
+        '''Call the listener with data. Note that it raises RuntimeError 
+        if listener is dead. Should always return True (False would require
+        the callable_ be dead but self hasn't yet been notified of it...).'''
+        kwargs = {}
+        if self._autoTopicArgName is not None:
+            kwargs[self._autoTopicArgName] = actualTopic
+        cb = self._callable()
+        if cb is None:
+            self._calledWhenDead()
+        msg = Message(actualTopic.getNameTuple(), data)
+        cb(msg, **kwargs)
+        return True
+
+
+class ListenerValidator(ValidatorBase):
+    '''
+    Accept one arg or *args; accept any **kwarg, 
+    and require that the Listener have at least all the kwargs (can 
+    have extra) of Topic.
+    '''
+    
+    def _validateArgs(self, listener, paramsInfo):
+        # accept **kwargs
+        # accept *args
+        # accept any keyword args
+
+        if (paramsInfo.getAllArgs() == ()) and paramsInfo.acceptsAllUnnamedArgs:
+            return
+
+        if paramsInfo.getAllArgs() == ():
+            msg = 'Must have at least one parameter (any name, with or without default value, or *arg)'
+            raise ListenerInadequate(msg, listener, [])
+
+        assert paramsInfo.getAllArgs()
+        #assert not paramsInfo.acceptsAllUnnamedArgs
+        
+        # verify at most one required arg
+        numReqdArgs = paramsInfo.numRequired
+        if numReqdArgs > 1:
+            allReqd = paramsInfo.getRequiredArgs()
+            msg = 'only one of %s can be a required agument' % (allReqd,)
+            raise ListenerInadequate(msg, listener, allReqd)
+
+        # if no required args but listener has *args, then we
+        # don't care about anything else:
+        if numReqdArgs == 0 and paramsInfo.acceptsAllUnnamedArgs:
+            return
+
+        # if no policy set, any name ok; otherwise validate name:
+        needArgName = policies.msgDataArgName
+        firstArgName = paramsInfo.allParams[0]
+        if (needArgName is not None) and firstArgName != needArgName:
+            msg = 'listener arg name must be "%s" (is "%s")' % (needArgName, firstArgName)
+            effTopicArgs = [needArgName]
+            raise ListenerInadequate(msg, listener, effTopicArgs)
+        
+

MDANSE/Externals/pubsub/core/arg1/publisher.py

+'''
+Mixin for publishing messages to a topic's listeners. This will be
+mixed into topicobj.Topic so that a user can use a Topic object to
+send a message to the topic's listeners via a publish() method.
+
+:copyright: Copyright 2006-2009 by Oliver Schoenborn, all rights reserved.
+:license: BSD, see LICENSE.txt for details.
+
+'''
+
+
+from MDANSE.Externals.pubsub.core.publisherbase import PublisherBase
+
+
+class Publisher(PublisherBase):
+    '''
+    Publisher that allows old-style Message.data messages to be sent
+    to listeners. Listeners take one arg (required, unless there is an
+    *arg), but can have kwargs (since they have default values).
+    '''
+
+    def sendMessage(self, topicName, data=None):
+        '''Send message of type topicName to all subscribed listeners,
+        with message data. If topicName is a subtopic, listeners
+        of topics more general will also get the message.
+
+        Note that any listener that lets a raised exception escape will
+        interrupt the send operation, unless an exception handler was
+        specified via pub.setListenerExcHandler().
+        '''
+        topicMgr = self.getTopicMgr()
+        topicObj = topicMgr.getOrCreateTopic(topicName)
+
+        # don't care if topic not final: topicObj.getListeners()
+        # will return nothing if not final but notification will still work
+
+        topicObj.publish(data)
+
+    def getMsgProtocol(self):
+        return 'arg1'
+

MDANSE/Externals/pubsub/core/arg1/publishermixin.py

+'''
+Mixin for publishing messages to a topic's listeners. This will be
+mixed into topicobj.Topic so that a user can use a Topic object to
+send a message to the topic's listeners via a publish() method.
+
+Note that it is important that the PublisherMixin NOT modify any
+state data during message sending, because in principle it could
+happen that a listener causes another message of same topic to be
+sent (presumably, the listener has a way of preventing infinite
+loop).
+
+:copyright: Copyright 2006-2009 by Oliver Schoenborn, all rights reserved.
+:license: BSD, see LICENSE.txt for details.
+
+'''
+
+
+class PublisherMixin:
+    def __init__(self):
+        pass
+
+    def publish(self, data=None):
+        self._publish(data)
+
+    ############## IMPLEMENTATION ###############
+
+    def _mix_prePublish(self, data, topicObj=None, iterState=None):
+        '''Called just before the __sendMessage, to perform any argument
+        checking, set iterState, etc'''
+        return None
+
+    def _mix_callListener(self, listener, data, iterState):
+        '''Send the data to given listener.'''
+        listener(self, data)

MDANSE/Externals/pubsub/core/arg1/topicargspecimpl.py

+'''
+
+:copyright: Copyright 2006-2009 by Oliver Schoenborn, all rights reserved.
+:license: BSD, see LICENSE.txt for details.
+
+'''
+
+import weakref
+from MDANSE.Externals.pubsub.core.topicutils import WeakNone
+
+class SenderMissingReqdArgs(RuntimeError):
+    '''
+    Ignore: Not used for this message protocol.
+    '''
+    pass
+
+
+class SenderUnknownOptArgs(RuntimeError):
+    '''
+    Ignore: Not used for this message protocol.
+    '''
+    pass
+
+
+class ArgsInfo:
+    '''
+    Encode the Listener Function Parameter Specification (LPS) for a given
+    topic. In the DataMsg API of pubsub, this is the same for all
+    topics, so this is quite a simple class, required only because
+    the part of pubsub that uses ArgsInfos supports several API
+    versions using one common API. So the only difference between
+    an ArgsInfo and an ArgSpecGiven is that ArgsInfo refers to
+    parent topic's ArgsInfo; other data members are the same.
+
+    Note that the LPS is always complete because it is known:
+    it consists of one required argument named 'data' and no