feat: add DatabaseEmitter implementation class

.gitignore

@@ -3,6 +3,8 @@ __pycache__/
 .idea/
 *.ipynb_checkpoints/
 dist/
+.DS_Store
+.empty
 build/
 
 process_bigraph.egg-info/

README.md

@@ -34,6 +34,77 @@ You can install `process-bigraph` using pip:
 pip install process-bigraph
 ```
 
+MongoDB
+-------
+
+We use a MongoDB database to store the data collected from running
+simulations via the `DatabaseEmitter` class. The use of this class is specified in the
+`'emitter'` section of the instance declaration for a given process as such:
+
+    ...,
+    'emitter': {
+                    '_type': 'step',
+                    'address': 'local:database-emitter',
+                    'config': {
+                        'ports': {
+                            'inputs': {
+                                'table': 'string',
+
+. This can be a remote server, but for this guide we will
+run a MongoDB server locally.
+
+**Note**: MongoDB is only required if you want to store data in MongoDB
+or want to run experiments that do so via the declaration shown above. You don't need MongoDB to work
+through this guide.
+
+*Check Installation*
+
+    $ mongod --version
+    db version v4.2.3
+    ...
+
+Make sure you see a version at least 3.2.
+
+*Install*
+
+If you are on macOS, you can install MongoDB using [Homebrew](https://brew.sh). You will need to add the MongoDB tap following the
+instructions [here](https://github.com/mongodb/homebrew-brew).
+
+If you are on Linux, see the MongoDB documentation's [instructions](https://docs.mongodb.com/manual/administration/install-on-linux/).
+
+*Setup*
+
+You can get a MongoDB server up and running locally any number of ways.
+Here is one:
+
+1. Create a folder ``process_bigraph_work/mongodb``. This is where MongoDB will
+   store the database We store the database here instead of at the
+   default location in ``/usr/local/var/mongodb`` to avoid permissions
+   issues if you are not running as an administrator.
+2. Make a copy of the ``mongod`` configuration file so we can make
+   changes:
+
+       $ cp /usr/local/etc/mongod.conf process_bigraph_work/mongod.conf
+
+   Note that your configuration file may be somewhere slightly
+   different. Check the MongoDB documentation for your system.
+3. In ``process_bigraph_work/mongod.conf`` change the path after ``dbPath:`` to
+   point to ``process_bigraph_work/mongodb``.
+4. Create a shell script ``process_bigraph_work/mongo.sh`` with the following
+   content:
+
+       #!/bin/bash
+
+       mongod --config mongod.conf
+
+5. Make the script executable:
+
+        $ chmod 700 process_bigraph_work/mongo.sh
+
+6. Now you can launch MongoDB by running this script:
+
+        $ process_bigraph_work/mongo.sh
+
 ## Tutorial
 
 To get started with Bigraph-viz, explore our resources: 

process_bigraph/__init__.py

@@ -1,15 +1,40 @@
-from process_bigraph.composite import Process, Step, Composite
-from process_bigraph.type_system import types
+import pprint
 from process_bigraph.protocols import local_lookup
 from process_bigraph.registry import protocol_registry, process_registry
-from process_bigraph.emitter import ConsoleEmitter, RAMEmitter
+from process_bigraph.emitter import ConsoleEmitter, RAMEmitter, DatabaseEmitter
+from process_bigraph.composite import Process, Step, Composite
+from process_bigraph.type_system import types
+
+
+__all__ = [
+    'Process',
+    'Step',
+    'Composite',
+    'types',
+    'pp',
+    'pf',
+    'protocol_registry',
+    'process_registry'
+]
+
+
+pretty = pprint.PrettyPrinter(indent=2)
+
+
+def pp(x):
+    """Print ``x`` in a pretty format."""
+    pretty.pprint(x)
+
+
+def pf(x):
+    """Format ``x`` for display."""
+    return pretty.pformat(x)
 
 
 # register protocols
 protocol_registry.register('local', local_lookup)
 
-# register processes
-# TODO
+# register emitters
 process_registry.register('console-emitter', ConsoleEmitter)
 process_registry.register('ram-emitter', RAMEmitter)
-
+process_registry.register('database-emitter', DatabaseEmitter)

process_bigraph/composite.py

@@ -224,7 +224,6 @@ def find_instances(state, instance_type='process_bigraph.composite.Process'):
     for key, inner in state.items():
         if isinstance(inner, dict) and isinstance(inner.get('instance'), process_class):
             found[key] = inner
-
     return found
 
 
@@ -383,20 +382,24 @@ def find_downstream(steps, nodes, upstream):
         down = set([])
         for step_path in downstream:
             if step_path not in visited:
-                for output in steps[step_path]['output_paths']:
+                step_outputs = steps[step_path]['output_paths']
+                if step_outputs is None:
+                    step_outputs = []  # Ensure step_outputs is always an iterable
+                for output in step_outputs:
                     for dependent in nodes[output]['after']:
                         down.add(dependent)
                 visited.add(step_path)
-        downstream ^= down
+        downstream |= down
 
     return downstream
 
 
 def determine_steps(steps, remaining, fulfilled):
     to_run = []
-
     for step_path in remaining:
         step_inputs = steps[step_path]['input_paths']
+        if step_inputs is None:
+            step_inputs = []
         all_fulfilled = True
         for input in step_inputs:
             if len(fulfilled[input]) > 0:
@@ -407,6 +410,8 @@ def determine_steps(steps, remaining, fulfilled):
     for step_path in to_run:
         remaining.remove(step_path)
         step_outputs = steps[step_path]['output_paths']
+        if step_outputs is None:
+            step_outputs = []
         for output in step_outputs:
             fulfilled[output].remove(step_path)
 
@@ -459,7 +464,7 @@ def __init__(self, config=None, local_types=None):
         composition_schema = types.access(composition)
         self.composition = copy.deepcopy(composition_schema)
 
-        # find all processes, steps, and emitters in the state
+        # find all processes, steps, and emitter in the state
         self.process_paths = find_instance_paths(
             state,
             'process_bigraph.composite.Process')
@@ -833,7 +838,7 @@ def trigger_steps(self, update_paths):
 
     def gather_results(self, queries=None):
         '''
-        a map of paths to emitters --> queries for the emitter at that path
+        a map of paths to emitter --> queries for the emitter at that path
         '''
 
         if queries is None: