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working on navigating schema
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@eagmon
eagmon committed Feb 14, 2024
1 parent ee6cc64 commit f545496
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Showing 2 changed files with 155 additions and 44 deletions.
21 changes: 8 additions & 13 deletions builder/builder_api.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,6 @@
from pprint import pformat as pf
import warnings

from bigraph_schema.type_system import Edge
from process_bigraph import Process, Step, Composite, ProcessTypes
from bigraph_schema.protocols import local_lookup_module
from bigraph_viz import plot_bigraph
Expand Down Expand Up @@ -92,8 +91,8 @@ def register_process(self, process_name, address):
self.core.process_registry.register(process_name, address)
# Check if address is a string
elif isinstance(address, str):
# separate out the protocol from the address
try:
# separate out the protocol from the address
protocol, addr = address.split(':', 1)
assert protocol == 'local', 'BigraphBuilder only supports local protocol in the current version'

Expand All @@ -106,7 +105,6 @@ def register_process(self, process_name, address):
Exception('only support local addresses')

except ValueError:
# Handle cases where the string does not conform to "protocol:address"
Exception(f"Address '{address}' does not contain a protocol. Registration failed.")
else:
# Handle other types if necessary
Expand All @@ -128,13 +126,13 @@ def __setitem__(self, keys, value):

first_key = keys[0]
if first_key not in self.tree:
self.tree[first_key] = Builder(core=self.core)
self.tree[first_key] = Builder(core=self.core, schema=self.schema.get(first_key, {}))

remaining = keys[1:]
if len(remaining) > 0:
self.tree[first_key].__setitem__(remaining, value)
elif isinstance(value, dict):
self.tree[first_key] = Builder(tree=value, core=self.core)
self.tree[first_key] = Builder(tree=value, core=self.core, schema=self.schema.get(first_key, {}))
else:
self.tree[first_key] = value

Expand All @@ -147,7 +145,7 @@ def __getitem__(self, keys):

first_key = keys[0]
if first_key not in self.tree:
self.tree[first_key] = Builder(parent=self, core=self.core)
self.tree[first_key] = Builder(parent=self, core=self.core, schema=self.schema.get(first_key, {}))

remaining = keys[1:]
if len(remaining) > 0:
Expand All @@ -159,10 +157,7 @@ def list_types(self):
return self.core.type_registry.list()

def list_processes(self):
types = self.core.process_registry.list()
processes = [
types for type in types if type.get('_type') in EDGE_KEYS]
return processes
print(self.core.process_registry.list())

# def register(self, name, process, force=False):
# if not self.core.access(name) and isinstance(process, Edge):
Expand Down Expand Up @@ -199,13 +194,13 @@ def add_process(
schema, state = self.core.complete(initial_schema, initial_state)

self.tree = builder_tree_from_dict(state)
self.schema = schema
self.schema = schema or {}

# reset compiled composite
self.compile()

def connect(self, port=None, target=None):
assert self.schema.get('_type') in EDGE_KEYS, f"Invalid type for connect: {self.schema}, needs to be in {EDGE_KEYS}"
# assert self.schema.get('_type', {}) in EDGE_KEYS, f"Invalid type for connect: {self.schema}, needs to be in {EDGE_KEYS}"
if port in self.schema['_inputs']:
self.tree['inputs'][port] = target
if port in self.schema['_outputs']:
Expand Down Expand Up @@ -250,7 +245,7 @@ def compile(self):
return self.compiled_composite

def update_tree(self, schema=None, state=None):
self.schema = schema
self.schema = schema or self.schema
state = state or {}
for k, i in state.items():
if isinstance(i, dict):
Expand Down
178 changes: 147 additions & 31 deletions notebooks/demo.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,22 +10,9 @@
"start_time": "2024-01-21T21:29:13.531449Z"
}
},
"outputs": [
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'builder'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mbuilder\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Builder, Process\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mbiosimulator_processes\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m process_registry\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'builder'"
]
}
],
"outputs": [],
"source": [
"from builder import Builder, Process\n",
"from biosimulator_processes import process_registry"
"from builder import Builder, Process"
]
},
{
Expand All @@ -40,7 +27,7 @@
},
"outputs": [],
"source": [
"b = Builder(process_registry=process_registry)"
"b = Builder()"
]
},
{
Expand All @@ -59,24 +46,141 @@
},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'Builder' object has no attribute 'process_registry_list'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprocess_registry_list\u001b[49m()\n",
"\u001b[0;31mAttributeError\u001b[0m: 'Builder' object has no attribute 'process_registry_list'"
"name": "stdout",
"output_type": "stream",
"text": [
"['ram-emitter', 'console-emitter']\n"
]
}
],
"source": [
"b.process_registry_list()"
"b.list_processes()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "5bff2ea4-42f9-430e-b1cc-f0581510ec8d",
"metadata": {},
"outputs": [],
"source": [
"from process_bigraph.experiments.minimal_gillespie import GillespieEvent , GillespieInterval\n",
"b.register_process('GillespieEvent', GillespieEvent)\n",
"b.register_process('GillespieInterval', GillespieInterval)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "40cde984-cfdf-4571-af9c-3a3755e3763c",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['GillespieEvent', 'ram-emitter', 'GillespieInterval', 'console-emitter']\n"
]
}
],
"source": [
"b.list_processes()"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "503863ee-0a58-44b3-accc-20e0167b947b",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Unexpected exception formatting exception. Falling back to standard exception\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Traceback (most recent call last):\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 3550, in run_code\n",
" exec(code_obj, self.user_global_ns, self.user_ns)\n",
" File \"/var/folders/vy/vr0_ytms6m95qrnk7xnh0bth0000gq/T/ipykernel_53425/3145499072.py\", line 2, in <module>\n",
" b['event_process'].add_process(\n",
" File \"/Users/eranagmon/code/bigraph-builder/builder/builder_api.py\", line 201, in add_process\n",
" File \"/Users/eranagmon/code/bigraph-builder/builder/builder_api.py\", line 235, in compile\n",
" else:\n",
" File \"/Users/eranagmon/code/bigraph-builder/builder/builder_api.py\", line 241, in compile\n",
" File \"/Users/eranagmon/code/process-bigraph/process_bigraph/composite.py\", line 731, in __init__\n",
" super().__init__(config, core)\n",
" File \"/Users/eranagmon/code/process-bigraph/process_bigraph/composite.py\", line 440, in __init__\n",
" self.config = self.core.fill(\n",
"AttributeError: 'NoneType' object has no attribute 'fill'\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/interactiveshell.py\", line 2144, in showtraceback\n",
" stb = self.InteractiveTB.structured_traceback(\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1435, in structured_traceback\n",
" return FormattedTB.structured_traceback(\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1326, in structured_traceback\n",
" return VerboseTB.structured_traceback(\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1173, in structured_traceback\n",
" formatted_exception = self.format_exception_as_a_whole(etype, evalue, etb, number_of_lines_of_context,\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 1088, in format_exception_as_a_whole\n",
" frames.append(self.format_record(record))\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 970, in format_record\n",
" frame_info.lines, Colors, self.has_colors, lvals\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/IPython/core/ultratb.py\", line 792, in lines\n",
" return self._sd.lines\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/stack_data/utils.py\", line 145, in cached_property_wrapper\n",
" value = obj.__dict__[self.func.__name__] = self.func(obj)\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/stack_data/core.py\", line 734, in lines\n",
" pieces = self.included_pieces\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/stack_data/utils.py\", line 145, in cached_property_wrapper\n",
" value = obj.__dict__[self.func.__name__] = self.func(obj)\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/stack_data/core.py\", line 681, in included_pieces\n",
" pos = scope_pieces.index(self.executing_piece)\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/stack_data/utils.py\", line 145, in cached_property_wrapper\n",
" value = obj.__dict__[self.func.__name__] = self.func(obj)\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/stack_data/core.py\", line 660, in executing_piece\n",
" return only(\n",
" File \"/Users/eranagmon/code/bigraph-builder/venv/lib/python3.9/site-packages/executing/executing.py\", line 116, in only\n",
" raise NotOneValueFound('Expected one value, found 0')\n",
"executing.executing.NotOneValueFound: Expected one value, found 0\n"
]
}
],
"source": [
"## add processes\n",
"b['event_process'].add_process(\n",
" name='GillespieEvent',\n",
" kdeg=1.0, # kwargs fill parameters in the config\n",
")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2f1f606b-160c-4158-9a54-54dba22f0732",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "a93508ae-95d3-4a7f-ae18-54c17e6f409e",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 6,
"id": "a84d340622208914",
"metadata": {
"ExecuteTime": {
Expand All @@ -95,7 +199,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"id": "235efcd79c0f13c1",
"metadata": {
"ExecuteTime": {
Expand All @@ -113,7 +217,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"id": "1ee84904801a9ab",
"metadata": {
"ExecuteTime": {
Expand Down Expand Up @@ -155,7 +259,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 9,
"id": "dae8ca8db70c4845",
"metadata": {
"ExecuteTime": {
Expand All @@ -166,7 +270,19 @@
"outputs_hidden": false
}
},
"outputs": [],
"outputs": [
{
"ename": "AttributeError",
"evalue": "'Builder' object has no attribute 'process_registry_list'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[9], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprocess_registry_list\u001b[49m()\n",
"\u001b[0;31mAttributeError\u001b[0m: 'Builder' object has no attribute 'process_registry_list'"
]
}
],
"source": [
"b.process_registry_list()"
]
Expand Down Expand Up @@ -319,9 +435,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python (venv)",
"display_name": "venv",
"language": "python",
"name": "venv_kernel"
"name": "venv"
},
"language_info": {
"codemirror_mode": {
Expand Down

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