demo2

vivarium-collective · Jan 27, 2025 · 9636d67 · 9636d67
1 parent a3d1518
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diff --git a/.github/workflows/notebook_to_html.yml b/.github/workflows/notebook_to_html.yml
@@ -4,6 +4,7 @@ on:
   push:
     paths:
       - 'notebooks/demo.ipynb'
+      - 'notebooks/demo2.ipynb'
       - 'notebooks/cell_sorting.ipynb'
 
 jobs:
@@ -29,6 +30,7 @@ jobs:
     - name: Convert Jupyter Notebook to HTML
       run: |
         jupyter nbconvert --to html notebooks/demo.ipynb
+        jupyter nbconvert --to html notebooks/demo2.ipynb
         jupyter nbconvert --to html notebooks/cell_sorting.ipynb
 
     - name: Commit and push HTML to gh-pages branch
@@ -37,12 +39,15 @@ jobs:
         git config --local user.name "GitHub Action"
         git fetch origin
         mv notebooks/demo.html /tmp/demo.html
+        mv notebooks/demo2.html /tmp/demo2.html
         mv notebooks/cell_sorting.html /tmp/cell_sorting.html
         git checkout gh-pages || git checkout -b gh-pages
         git pull origin gh-pages
         mv /tmp/demo.html notebooks/demo.html
+        mv /tmp/demo2.html notebooks/demo2.html
         mv /tmp/cell_sorting.html notebooks/cell_sorting.html 
         git add notebooks/demo.html
+        git add notebooks/demo2.html
         git add notebooks/cell_sorting.html
         git diff-index --quiet HEAD || git commit -m "Update HTML files" 
         git push origin gh-pages || true
diff --git a/README.md b/README.md
@@ -6,6 +6,7 @@ This project contains models and schemas for validating and building JSON schema
 
 ## Notebooks
 * [Demo](https://vivarium-collective.github.io/multicell-schema/notebooks/demo.html)
+* [Demo 2](https://vivarium-collective.github.io/multicell-schema/notebooks/demo2.html)
 * [Cell Sorting](https://vivarium-collective.github.io/multicell-schema/notebooks/cell_sorting.html)
 
 ## Directory Structure

diff --git a/models/cell_sorting.json b/models/cell_sorting.json
@@ -0,0 +1,59 @@
+{
+    "id": "model_000016",
+    "name": "cell_sorting",
+    "objects": {
+        "dark": {
+            "type": "CellPopulation",
+            "attributes": {},
+            "boundary_conditions": {},
+            "contained_objects": []
+        },
+        "light": {
+            "type": "CellPopulation",
+            "attributes": {},
+            "boundary_conditions": {},
+            "contained_objects": []
+        },
+        "environment": {
+            "type": "CellField",
+            "attributes": {},
+            "boundary_conditions": {},
+            "contained_objects": [
+                "dark",
+                "light"
+            ]
+        },
+        "external_material": {
+            "type": "Material",
+            "attributes": {},
+            "boundary_conditions": {},
+            "contained_objects": []
+        }
+    },
+    "processes": {
+        "volume exclusion": {
+            "type": "VolumeExclusion",
+            "attributes": {},
+            "participating_objects": [
+                "dark",
+                "light",
+                "external_material"
+            ]
+        },
+        "contact": {
+            "type": "ContactForce",
+            "attributes": {},
+            "participating_objects": [
+                "environment"
+            ]
+        },
+        "fluctuation": {
+            "type": "MotileForce",
+            "attributes": {},
+            "participating_objects": [
+                "dark",
+                "light"
+            ]
+        }
+    }
+}
diff --git a/multicell_utils/builder.py b/multicell_utils/builder.py
@@ -51,9 +51,9 @@ def validate(self):
     def register(self, overwrite=False):
         try:
             if self.schema_type == "object":
-                schema_registry.register_object(self.schema, self.schema["type"])
+                schema_registry.register_object(self.schema, self.schema["type"], overwrite)
             elif self.schema_type == "process":
-                schema_registry.register_process(self.schema, self.schema["type"])
+                schema_registry.register_process(self.schema, self.schema["type"], overwrite)
         except ValueError as e:
             if not overwrite:
                 print(f"Failed to register schema: {e}")
@@ -67,14 +67,14 @@ def save(self, filename, directory="schema"):
         except ValidationError as e:
             raise ValidationError(f"Schema validation failed: {e.message}")
 
-        # directory = os.path.join(project_root, directory, self.schema_type) # objects or processes
-        directory = os.path.join(directory, self.schema_type)
-
-        if not os.path.exists(directory):
-            os.makedirs(directory)
-        with open(os.path.join(directory, filename), 'w') as file:
+        # make absolute path to directory
+        absolute_directory = os.path.join(project_root, directory, self.schema_type) # objects or processes
+        local_directory = os.path.join(directory, self.schema_type)
+        if not os.path.exists(absolute_directory):
+            os.makedirs(absolute_directory)
+        with open(os.path.join(absolute_directory, filename), 'w') as file:
             json.dump(self.schema, file, indent=4)
-            print(f"Schema saved to {os.path.join(directory, filename)}")
+            print(f"Schema saved to {os.path.join(local_directory, filename)}")
 
     def load_from_json(self, json_path, name):
         assert name is not None, "Name must be provided when loading from JSON"
@@ -230,10 +230,11 @@ def save(self, filename, directory="models"):
             print(f"Model validation failed: {e.message}")
             return
 
-        # absolute_directory = os.path.join(project_root, directory)
-        if not os.path.exists(directory):
-            os.makedirs(directory)
-        with open(os.path.join(directory, filename), 'w') as file:
+        # make absolute path to directory
+        absolute_directory = os.path.join(project_root, directory)
+        if not os.path.exists(absolute_directory):
+            os.makedirs(absolute_directory)
+        with open(os.path.join(absolute_directory, filename), 'w') as file:
             json.dump(self.model, file, indent=4)
         print(f"Model saved to {os.path.join(directory, filename)}")
 

diff --git a/multicell_utils/registry.py b/multicell_utils/registry.py
@@ -126,10 +126,10 @@ def validate_containment(self, model):
                     if not any(base_type in allowed_children_types for base_type in self.object_inheritance.get(child_type, [])):
                         print(f"Invalid containment: {child_type} object is not contained by {parent_type}")
 
-    def register_object(self, schema, object_type):
+    def register_object(self, schema, object_type, overwrite=False):
         if 'type' in schema:
             object_type = schema['type']
-        if object_type in self.object_types:
+        if object_type in self.object_types and not overwrite:
             raise ValueError(f"Object schema '{object_type}' is already registered.")
         try:
             self.validate_schema(schema, self.object_meta_schema)
@@ -151,10 +151,10 @@ def register_object(self, schema, object_type):
         self.object_inheritance[object_type] = inherits_from
 
 
-    def register_process(self, schema, process_type=None):
+    def register_process(self, schema, process_type=None, overwrite=False):
         if 'type' in schema:
             process_type = schema['type']
-        if process_type in self.process_types:
+        if process_type in self.process_types and not overwrite:
             raise ValueError(f"Process schema type '{process_type}' is already registered.")
         try:
             self.validate_schema(schema, self.process_meta_schema)
@@ -174,9 +174,11 @@ def register_process(self, schema, process_type=None):
             self.process_inheritance[process_type] = schema.get('inherits_from', [])
 
         except ValidationError as e:
-            print(f"Failed to register process schema '{process_name}': {e.message}")
+            print(f"Failed to register process schema '{process_type}': {e.message}")
+
 
     def register_template(self, schema, template_name):
+        # TODO implement template registration
         schema_name = schema['name']
         pass
 

diff --git a/notebooks/cell_sorting.ipynb b/notebooks/cell_sorting.ipynb
@@ -6,8 +6,8 @@
    "metadata": {
     "collapsed": true,
     "ExecuteTime": {
-     "end_time": "2025-01-26T16:42:13.442699Z",
-     "start_time": "2025-01-26T16:42:13.380688Z"
+     "end_time": "2025-01-27T16:30:26.830260Z",
+     "start_time": "2025-01-27T16:30:26.769855Z"
     }
    },
    "source": [
@@ -36,8 +36,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-26T16:42:13.448126Z",
-     "start_time": "2025-01-26T16:42:13.445524Z"
+     "end_time": "2025-01-27T16:30:26.898720Z",
+     "start_time": "2025-01-27T16:30:26.895943Z"
     }
    },
    "cell_type": "code",
@@ -59,8 +59,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-26T16:42:13.495657Z",
-     "start_time": "2025-01-26T16:42:13.491402Z"
+     "end_time": "2025-01-27T16:30:26.947836Z",
+     "start_time": "2025-01-27T16:30:26.943558Z"
     }
    },
    "cell_type": "code",
@@ -72,8 +72,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-26T16:42:13.504588Z",
-     "start_time": "2025-01-26T16:42:13.499796Z"
+     "end_time": "2025-01-27T16:30:26.955825Z",
+     "start_time": "2025-01-27T16:30:26.951474Z"
     }
    },
    "cell_type": "code",
@@ -93,8 +93,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-26T16:42:13.526863Z",
-     "start_time": "2025-01-26T16:42:13.509757Z"
+     "end_time": "2025-01-27T16:30:26.976223Z",
+     "start_time": "2025-01-27T16:30:26.959334Z"
     }
    },
    "cell_type": "code",
@@ -105,7 +105,7 @@
      "data": {
       "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n<!-- Generated by graphviz version 9.0.0 (0)\n -->\n<!-- Pages: 1 -->\n<svg width=\"733pt\" height=\"505pt\"\n viewBox=\"0.00 0.00 733.25 505.13\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 501.13)\">\n<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-501.13 729.25,-501.13 729.25,4 -4,4\"/>\n<!-- dark -->\n<g id=\"node1\" class=\"node\">\n<title>dark</title>\n<ellipse fill=\"none\" stroke=\"black\" cx=\"308.39\" cy=\"-176.39\" rx=\"81.34\" ry=\"81.34\"/>\n<text text-anchor=\"middle\" x=\"308.39\" y=\"-172.19\" font-family=\"Times,serif\" font-size=\"14.00\">dark:CellPopulation</text>\n</g>\n<!-- volume exclusion -->\n<g id=\"node5\" class=\"node\">\n<title>volume 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358.46,-240.61\"/>\n</g>\n<!-- environment&#45;&gt;light -->\n<g id=\"edge8\" class=\"edge\">\n<title>environment&#45;&gt;light</title>\n<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M489.39,-316.6C489.39,-297.45 489.39,-277.31 489.39,-258.48\"/>\n</g>\n<!-- contact -->\n<g id=\"node6\" class=\"node\">\n<title>contact</title>\n<polygon fill=\"none\" stroke=\"black\" points=\"725.25,-194.39 589.52,-194.39 589.52,-158.39 725.25,-158.39 725.25,-194.39\"/>\n<text text-anchor=\"middle\" x=\"657.39\" y=\"-172.19\" font-family=\"Times,serif\" font-size=\"14.00\">contact:ContactForce</text>\n</g>\n<!-- environment&#45;&gt;contact -->\n<g id=\"edge4\" class=\"edge\">\n<title>environment&#45;&gt;contact</title>\n<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M549.16,-324.63C583.83,-277.47 624.51,-222.13 644.69,-194.66\"/>\n<polygon fill=\"black\" stroke=\"black\" points=\"546.54,-322.28 543.44,-332.41 552.18,-326.43 546.54,-322.28\"/>\n</g>\n<!-- 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       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x10458b190>"
+       "<graphviz.graphs.Digraph at 0x114eb54d0>"
       ]
      },
      "execution_count": 5,
@@ -118,8 +118,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-26T16:42:13.534693Z",
-     "start_time": "2025-01-26T16:42:13.532329Z"
+     "end_time": "2025-01-27T16:30:26.983095Z",
+     "start_time": "2025-01-27T16:30:26.980842Z"
     }
    },
    "cell_type": "code",
@@ -129,7 +129,7 @@
     {
      "data": {
       "text/plain": [
-       "ModelBuilder({ 'id': 'model_000006',\n",
+       "ModelBuilder({ 'id': 'model_000016',\n",
        "  'name': 'cell_sorting',\n",
        "  'objects': { 'dark': { 'attributes': {},\n",
        "                         'boundary_conditions': {},\n",
@@ -170,8 +170,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-01-26T16:42:13.603866Z",
-     "start_time": "2025-01-26T16:42:13.602653Z"
+     "end_time": "2025-01-27T16:30:26.988508Z",
+     "start_time": "2025-01-27T16:30:26.987299Z"
     }
    },
    "cell_type": "code",