Skip to content

Commit

Permalink
Merge pull request #1 from vivarium-collective/new-schema
Browse files Browse the repository at this point in the history 
New schema
  • Loading branch information
@eagmon
eagmon authored Jan 3, 2024
2 parents fc1df5d + 6b8023b commit 1899c84
Show file tree
Hide file tree
Showing 4 changed files with 195 additions and 175 deletions.
5 changes: 4 additions & 1 deletion bigraph_viz/dict_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

pretty = pprint.PrettyPrinter(indent=2)


# TODO -- sync this up with bigraph-schema
schema_keys = [
'_super',
'_value',
Expand All @@ -26,6 +26,9 @@
]
schema_keys.extend(type_schema_keys)

# TODO -- this should come from process-bigraph
process_schema_keys = ['address', 'config', 'inputs', 'outputs', 'instance', 'interval']


def pp(x: Any) -> None:
"""Print ``x`` in a pretty format."""
Expand Down
232 changes: 136 additions & 96 deletions bigraph_viz/plot.py
View file
Original file line number Diff line number Diff line change
@@ -1,14 +1,12 @@
"""
====
Plot
====
* plot_bigraph
============
Plot Bigraph
============
"""
import copy
import os

from bigraph_viz.dict_utils import absolute_path, schema_keys
from bigraph_viz.dict_utils import absolute_path, schema_keys, process_schema_keys
import graphviz


Expand Down Expand Up @@ -39,7 +37,21 @@ def check_if_path_in_removed_nodes(path, remove_nodes):
return False


def get_bigraph_network(bigraph_dict, path=None, remove_nodes=None):
def get_state_path_extended(state_path):
if isinstance(state_path, tuple):
# support tuple paths
state_path = list(state_path)
state_path = state_path_tuple(state_path)
state_path.insert(0, '..') # go up one to the same level as the process
return state_path


def get_bigraph_network(
bigraph_dict,
path=None,
remove_nodes=None,
show_process_schema=False
):
path = path or ()

# initialize bigraph
Expand All @@ -54,94 +66,115 @@ def get_bigraph_network(bigraph_dict, path=None, remove_nodes=None):
}

for key, child in bigraph_dict.items():
if key not in schema_keys:
path_here = path + (key,)
if check_if_path_in_removed_nodes(path_here, remove_nodes):
# skip node if path in removed_nodes
continue
node = {'path': path_here}

if not isinstance(child, dict):
# this is a leaf node
node['_value'] = child
bigraph['state_nodes'] += [node]
continue

# add schema
if '_value' in child:
node['_value'] = child['_value']
if '_type' in child:
node['_type'] = child['_type']
if '_sync_step' in child:
node['sync_step'] = child['_sync_step']

# what kind of node?
if 'wires' in child or '_ports' in child:
# this is a hyperedge/process
if path_here not in bigraph['hyper_edges']:
bigraph['hyper_edges'][path_here] = {}
if 'wires' in child:
for port, state_path in child['wires'].items():
if isinstance(state_path, tuple):
# support tuple paths
state_path = list(state_path)
state_path = state_path_tuple(state_path)
state_path.insert(0, '..') # go up one to the same level as the process
bigraph['hyper_edges'][path_here][port] = state_path
if child.get('_depends_on'):
depends_on = child.get('_depends_on', [])
if path_here not in bigraph['flow']:
bigraph['flow'][path_here] = []
if isinstance(depends_on, str):
depends_on = [depends_on]
for state_path in depends_on:
if isinstance(state_path, str):
state_path = [state_path]
state_path = state_path_tuple(state_path)
state_path.insert(0, '..') # go up one to the same level as the process
bigraph['flow'][path_here].append(state_path)

# check for mismatch, there might be disconnected wires or mismatch with declared wires
wire_ports = []
if 'wires' in child:
wire_ports = child['wires'].keys()
if '_ports' in child:
# wires need to match schema
schema_ports = child['_ports'].keys()
assert all(item in schema_ports for item in wire_ports), \
f"attempting to wire undeclared process ports: " \
f"wire ports: {wire_ports}, schema ports: {schema_ports}"
disconnected_ports = [port_id for port_id in schema_ports if port_id not in wire_ports]
if disconnected_ports and path_here not in bigraph['disconnected_hyper_edges']:
bigraph['disconnected_hyper_edges'][path_here] = {}
for port in disconnected_ports:
bigraph['disconnected_hyper_edges'][path_here][port] = [port, ]
if '_tunnels' in child:
tunnels = child['_tunnels']
if path_here not in bigraph['tunnels']:
bigraph['tunnels'][path_here] = {}
for port, state_path in tunnels.items():
assert port in bigraph['disconnected_hyper_edges'][path_here].keys() or \
port in bigraph['hyper_edges'][path_here].keys(), f"tunnel '{port}' " \
f"is not declared in ports"
bigraph['tunnels'][path_here][port] = state_path_tuple(state_path)

bigraph['process_nodes'] += [node]
else:
bigraph['state_nodes'] += [node]

# check inner states
if isinstance(child, dict):
# this is a branch node
child_bigraph_network = get_bigraph_network(child, path=path_here, remove_nodes=remove_nodes)
bigraph = extend_bigraph(bigraph, child_bigraph_network)

# add place edges to this layer
for node in child.keys():
child_path = path_here + (node,)
if node in schema_keys or check_if_path_in_removed_nodes(child_path, remove_nodes):
continue
bigraph['place_edges'] += [(path_here, child_path)]
# skip process schema
if not show_process_schema and key in process_schema_keys:
continue
if key in schema_keys:
continue

path_here = path + (key,)
if check_if_path_in_removed_nodes(path_here, remove_nodes):
# skip node if path in removed_nodes
continue
node = {'path': path_here}

if not isinstance(child, dict):
# this is a leaf node
node['_value'] = child
bigraph['state_nodes'] += [node]
continue

# add schema
if '_value' in child:
node['_value'] = child['_value']
if '_type' in child:
node['_type'] = child['_type']
if '_sync_step' in child:
node['sync_step'] = child['_sync_step']

# what kind of node?
if ('wires' in child or
'_ports' in child or
child.get('_type') == 'process' or
child.get('_type') == 'step' or
child.get('_type') == 'edge'
):
# this is a hyperedge/process
if path_here not in bigraph['hyper_edges']:
bigraph['hyper_edges'][path_here] = {}
if 'wires' in child:
for port, state_path in child['wires'].items():
bigraph['hyper_edges'][path_here][port] = get_state_path_extended(state_path)
if 'inputs' in child:
for port, state_path in child['inputs'].items():
bigraph['hyper_edges'][path_here][port] = get_state_path_extended(state_path)
if 'outputs' in child:
for port, state_path in child['outputs'].items():
bigraph['hyper_edges'][path_here][port] = get_state_path_extended(state_path)
if '_depends_on' in child:
depends_on = child.get('_depends_on', [])
if path_here not in bigraph['flow']:
bigraph['flow'][path_here] = []
if isinstance(depends_on, str):
depends_on = [depends_on]
for state_path in depends_on:
if isinstance(state_path, str):
state_path = [state_path]
state_path = state_path_tuple(state_path)
state_path.insert(0, '..') # go up one to the same level as the process
bigraph['flow'][path_here].append(state_path)

# check for mismatch, there might be disconnected wires or mismatch with declared wires
wire_ports = []
if 'wires' in child:
wire_ports = child['wires'].keys()
if '_ports' in child:
# wires need to match schema
schema_ports = child['_ports'].keys()
assert all(item in schema_ports for item in wire_ports), \
f"attempting to wire undeclared process ports: " \
f"wire ports: {wire_ports}, schema ports: {schema_ports}"
disconnected_ports = [port_id for port_id in schema_ports if port_id not in wire_ports]
if disconnected_ports and path_here not in bigraph['disconnected_hyper_edges']:
bigraph['disconnected_hyper_edges'][path_here] = {}
for port in disconnected_ports:
bigraph['disconnected_hyper_edges'][path_here][port] = [port, ]
if '_tunnels' in child:
tunnels = child['_tunnels']
if path_here not in bigraph['tunnels']:
bigraph['tunnels'][path_here] = {}
for port, state_path in tunnels.items():
assert port in bigraph['disconnected_hyper_edges'][path_here].keys() or \
port in bigraph['hyper_edges'][path_here].keys(), f"tunnel '{port}' " \
f"is not declared in ports"
bigraph['tunnels'][path_here][port] = state_path_tuple(state_path)

bigraph['process_nodes'] += [node]
else:
bigraph['state_nodes'] += [node]

# check inner states
if isinstance(child, dict):
# this is a branch node
child_bigraph_network = get_bigraph_network(
child,
path=path_here,
remove_nodes=remove_nodes,
show_process_schema=show_process_schema)
bigraph = extend_bigraph(bigraph, child_bigraph_network)

# add place edges to this layer
for node in child.keys():

# skip process schema
if not show_process_schema and node in process_schema_keys:
continue

child_path = path_here + (node,)
if node in schema_keys or check_if_path_in_removed_nodes(child_path, remove_nodes):
continue
place_edge = [(path_here, child_path)]
bigraph['place_edges'] += place_edge

return bigraph

Expand Down Expand Up @@ -358,6 +391,7 @@ def plot_bigraph(
node_label_size='12pt',
show_values=False,
show_types=False,
show_process_schema=False,
collapse_processes=False,
port_labels=True,
port_label_size='10pt',
Expand Down Expand Up @@ -385,6 +419,7 @@ def plot_bigraph(
node_label_size (str, optional): The font size for the node labels. Default is None.
show_values (bool, optional): Display on value info in node label. Default is False.
show_types (bool, optional): Display on type info in node label. Default is False.
show_process_schema (bool, optional): Display process schema info as internal nodes. Default is False.
collapse_processes (bool, optional): Collapse rectangular process nodes to a hyperedge vertex. Default is False.
port_labels (bool, optional): Turn on port labels. Default is True.
port_label_size (str, optional): The font size of the port labels (example: '10pt'). Default is None.
Expand Down Expand Up @@ -424,9 +459,14 @@ def plot_bigraph(
out_dir = kwargs.pop('out_dir')
filename = kwargs.pop('filename')
remove_nodes = kwargs.pop('remove_nodes')
show_process_schema = kwargs.pop('show_process_schema')

# get the nodes and edges from the composite
bigraph_network = get_bigraph_network(bigraph_schema, remove_nodes=remove_nodes)
bigraph_network = get_bigraph_network(
bigraph_schema,
remove_nodes=remove_nodes,
show_process_schema=show_process_schema,
)

# make graphviz network
graph = get_graphviz_bigraph(bigraph_network, **kwargs)
Expand Down
Loading

0 comments on commit 1899c84

Please sign in to comment.