Technical Report MORAE Notebook Demo

.gitignore

@@ -2,3 +2,4 @@
 # do not archive notebook checkpoints
 .ipynb_checkpoints
 __pycache__/
+.DS_Store

end-to-end-rest/docker-compose.yml

@@ -34,7 +34,7 @@ services:
       - "8000:8000" # Change port mapping appropriately before deploying.
     # open browser to http://127.0.0.1:8000/docs
     environment:
-      - "SKEMA_RS_ADDESS=http://skema-rs:8080"
+      - "SKEMA_RS_ADDRESS=http://skema-rs:8080"
       - "SKEMA_GRAPH_DB_PROTO=bolt://"
       - "SKEMA_GRAPH_DB_PORT=7687"
       - "SKEMA_GRAPH_DB_HOST=graphdb"
@@ -57,6 +57,7 @@ services:
       - "SKEMA_RS_PORT=8080"
       - "SKEMA_GRAPH_DB_HOST=graphdb"
       - "SKEMA_GRAPH_DB_PORT=7687"
+      - "SKEMA_GRAPH_DB_PROTO=bolt://"
 
   # We currently use Memgraph (in-memory graph database).
   graphdb:

end-to-end-rest/notebooks/M11-Q6/data/code/code1/README.md

@@ -0,0 +1 @@
+This is a readme for the SIR model in the base test scenario. This contains no code.

end-to-end-rest/notebooks/M11-Q6/data/code/code1/code.py

@@ -0,0 +1,20 @@
+# SIR model dynamics definition
+def sir(
+    s: float, i: float, r: float, beta: float, gamma: float, n: float
+) -> Tuple[float, float, float]:
+    """The SIR model, one time step."""
+    s_n = (-beta * s * i) + s
+    i_n = (beta * s * i - gamma * i) + i
+    r_n = gamma * i + r
+    scale = n / (s_n + i_n + r_n)
+    return s_n * scale, i_n * scale, r_n * scale
+
+
+if __name__ == "main":
+    # run sir model sample
+    result = sir(0.99, 0.01, 0, 0.2, 0.1, 1)
+
+    print(result)
+
+
+# 7e475a4c-cf38-44f3-b349-2badeff967e8

end-to-end-rest/notebooks/M11-Q6/data/execution_engine/complex_amr.json

@@ -0,0 +1,41 @@
+{
+    "semantics": {
+        "ode": {
+            "parameters": [
+                {"name": "a"},
+                {"name": "b"},
+                {"name": "c"},
+                {"name": "int_add"},
+                {"name": "float_add"},
+                {"name": "str_concat"},
+                {"name": "list_concat"},
+                {"name": "int_sub"},
+                {"name": "float_sub"},
+                {"name": "int_mult"},
+                {"name": "float_mult"},
+                {"name": "str_repeat"},
+                {"name": "list_repeat"},
+                {"name": "float_div"},
+                {"name": "int_floor_div"},
+                {"name": "int_mod"},
+                {"name": "int_pow"},
+                {"name": "float_pow"},
+                {"name": "int_lshift"},
+                {"name": "int_rshift"},
+                {"name": "bit_or"},
+                {"name": "bit_and"},
+                {"name": "bit_xor"},
+                {"name": "eq_int"},
+                {"name": "eq_str"},
+                {"name": "eq_list"},
+                {"name": "neq_int"},
+                {"name": "neq_str"},
+                {"name": "neq_list"},
+                {"name": "gt_int"},
+                {"name": "gte_int"},
+                {"name": "lt_int"},
+                {"name": "lte_int"}
+            ]
+        }
+    }
+}

end-to-end-rest/notebooks/M11-Q6/data/execution_engine/complex_source.py

@@ -0,0 +1,71 @@
+# Assignment types
+a = 10
+b = a
+c = a + b
+
+# Primitive addition
+int_add = 5 + 3
+float_add = 3.14 + 2.71
+str_concat = "Hello" + "World"
+list_concat = [1, 2, 3] + [4, 5, 6]
+
+# Primitive subtraction
+int_sub = 10 - 3
+float_sub = 5.5 - 2.2
+
+# Primitive multiplication
+int_mult = 4 * 7
+float_mult = 2.5 * 3.5
+str_repeat = "abc" * 3
+list_repeat = [1, 2, 3] * 2
+
+# Primitive division
+float_div = 7.5 / 2.5
+
+# Primitive floor division
+int_floor_div = 11 // 3
+
+# Primitive modulo
+int_mod = 17 % 5
+
+# Primitive exponentiation
+int_pow = 2 ** 3
+float_pow = 2.0 ** 3
+
+# Primitive left shift 
+int_lshift = 8 << 2
+
+# Primitive right shift
+int_rshift = 32 >> 2
+
+# Primitive bitwise or
+bit_or = 5 | 3
+
+# Primitive bitwise and
+bit_and = 5 & 3
+
+# Primitive bitwise xor
+bit_xor = 5 ^ 3
+
+# Primitive equality
+eq_int = 5 == 5
+eq_str = "Hello" == "World"
+eq_list = [1, 2, 3] == [1, 2, 3]
+
+# Primitive inequality
+neq_int = 5 != 3
+neq_str = "Hello" != "Hello"
+neq_list = [1, 2, 3] != [4, 5, 6]
+
+# Primitive greater than
+gt_int = 5 > 3
+
+# Primitive greater than and equal to
+gte_int = 5 >= 5
+
+# Primitive less than
+lt_int = 3 < 5
+
+# Primitive less than and equal to 
+lte_int = 5 <= 5
+

end-to-end-rest/notebooks/M11-Q6/data/execution_engine/epi_model_amr.json

@@ -0,0 +1,148 @@
+{
+    "header": {
+        "name": "mathml model",
+        "schema": "https://github.com/DARPA-ASKEM/Model-Representations/blob/main/petrinet/petrinet_schema.json",
+        "schema_name": "PetriNet",
+        "description": "This is a model from equations",
+        "model_version": "0.1"
+    },
+    "model": {
+        "states": [
+            {
+                "id": "D",
+                "name": "D"
+            },
+            {
+                "id": "E",
+                "name": "E"
+            },
+            {
+                "id": "I",
+                "name": "I"
+            },
+            {
+                "id": "R",
+                "name": "R"
+            },
+            {
+                "id": "S",
+                "name": "S"
+            }
+        ],
+        "transitions": [
+            {
+                "id": "t0",
+                "input": [
+                    "I",
+                    "S"
+                ],
+                "output": [
+                    "E",
+                    "I"
+                ]
+            },
+            {
+                "id": "t1",
+                "input": [
+                    "E"
+                ],
+                "output": [
+                    "I"
+                ]
+            },
+            {
+                "id": "t2",
+                "input": [
+                    "I"
+                ],
+                "output": [
+                    "R"
+                ]
+            },
+            {
+                "id": "t3",
+                "input": [
+                    "I"
+                ],
+                "output": [
+                    "D"
+                ]
+            }
+        ]
+    },
+    "semantics": {
+        "ode": {
+            "rates": [
+                {
+                    "target": "t0",
+                    "expression": "N*beta*I*S",
+                    "expression_mathml": "<apply><times/><apply><times/><ci>I</ci><ci>beta</ci><ci>S</ci></apply><ci>N</ci></apply>"
+                },
+                {
+                    "target": "t1",
+                    "expression": "sigma*E",
+                    "expression_mathml": "<apply><times/><ci>sigma</ci><ci>E</ci></apply>"
+                },
+                {
+                    "target": "t2",
+                    "expression": "gamma*I",
+                    "expression_mathml": "<apply><times/><ci>gamma</ci><ci>I</ci></apply>"
+                },
+                {
+                    "target": "t3",
+                    "expression": "delta*I",
+                    "expression_mathml": "<apply><times/><ci>delta</ci><ci>I</ci></apply>"
+                }
+            ],
+            "initials": [
+                {
+                    "target": "S",
+                    "expression": "",
+                    "expression_mathml": ""
+                },
+                {
+                    "target": "E",
+                    "expression": "",
+                    "expression_mathml": ""
+                },
+                {
+                    "target": "I",
+                    "expression": "",
+                    "expression_mathml": ""
+                },
+                {
+                    "target": "R",
+                    "expression": "",
+                    "expression_mathml": ""
+                },
+                {
+                    "target": "D",
+                    "expression": "",
+                    "expression_mathml": ""
+                }
+            ],
+            "parameters": [
+                {
+                    "id": "N",
+                    "name": "N"
+                },
+                {
+                    "id": "beta",
+                    "name": "beta"
+                },
+                {
+                    "id": "delta",
+                    "name": "delta"
+                },
+                {
+                    "id": "gamma",
+                    "name": "gamma"
+                },
+                {
+                    "id": "sigma",
+                    "name": "sigma"
+                }
+            ]
+        }
+    }
+}

end-to-end-rest/notebooks/M11-Q6/data/execution_engine/epi_model_source.py

@@ -0,0 +1,36 @@
+import numpy as np
+from scipy.integrate import odeint
+import matplotlib.pyplot as plt
+
+def seird_model(y, t, N, beta, sigma, gamma, delta):
+    S, E, I, R, D = y
+    dSdt = -beta * S * I / N
+    dEdt = beta * S * I / N - sigma * E
+    dIdt = sigma * E - gamma * I - delta * I
+    dRdt = gamma * I
+    dDdt = delta * I
+    return dSdt, dEdt, dIdt, dRdt, dDdt
+
+N = 1000
+beta = 0.2
+sigma = 0.1
+gamma = 0.05
+delta = 0.01
+y0 = N-1, 1, 0, 0, 0
+
+t = np.linspace(0, 100, 1000)
+
+result = odeint(seird_model, y0, t, args=(N, beta, sigma, gamma, delta))
+S, E, I, R, D = result.T
+
+plt.figure(figsize=(10,6))
+plt.plot(t, S, 'b', label='Susceptible')
+plt.plot(t, E, 'y', label='Exposed')
+plt.plot(t, I, 'r', label='Infected')
+plt.plot(t, R, 'g', label='Recovered')
+plt.plot(t, D, 'k', label='Dead')
+plt.xlabel('Time')
+plt.ylabel('Population')
+plt.legend()
+plt.grid(True)
+plt.show()