Allow Interventions (#16)

* interventions

* Create empty interventions by default

* Add logging of interventions

* Strip interventions from calibrate

* Fix typo

* Fix logging message

* Reinclude docker network

---------

Co-authored-by: Five Grant <5@fivegrant.com>

api/models.py

@@ -91,12 +91,17 @@ class Dataset(BaseModel):
  example={'postive_tests': 'infected'},
  )
 
+class InterventionObject(BaseModel):
+ timestep: float
+ name: str
+ value: float
 
 class SimulatePostRequest(BaseModel):
  engine: Engine = Field(..., example="ciemss")
  username: str = Field("not_provided", example="not_provided")
  model_config_id: str = Field(..., example="ba8da8d4-047d-11ee-be56")
  timespan: Timespan
+ interventions: List[InterventionObject] = Field(default_factory=list, example=[{"timestep":1,"name":"beta","value":.4}])
  extra: SimulateExtra = Field(
  None,
  description="optional extra system specific arguments for advanced use cases",

api/server.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import logging
 from fastapi import FastAPI, Response, status
 from fastapi.middleware.cors import CORSMiddleware
 
@@ -13,6 +14,9 @@
 )
 
 
+logging.basicConfig()
+logging.getLogger().setLevel(logging.DEBUG)
+
 def build_api(*args) -> FastAPI:
 
  api = FastAPI(
@@ -53,7 +57,7 @@ def get_status(simulation_id: str) -> StatusSimulationIdGetResponse:
  from utils import fetch_job_status
 
  status = fetch_job_status(simulation_id)
- print(status)
+ logging.info(status)
  if not isinstance(status, str):
  return status
 
@@ -72,6 +76,10 @@ def simulate_model(body: SimulatePostRequest) -> JobResponse:
  username = body.username
  start = body.timespan.start
  end = body.timespan.end
+ interventions = [
+ (intervention.timestep, intervention.name, intervention.value) for intervention in body.interventions 
+ ]
+
 
  operation_name = "operations.simulate"
  options = {
@@ -81,11 +89,14 @@ def simulate_model(body: SimulatePostRequest) -> JobResponse:
  "start": start,
  "end": end,
  "extra": body.extra.dict(),
- "visual_options": True
+ "visual_options": True,
+ "interventions": interventions
  }
 
  resp = create_job(operation_name=operation_name, options=options)
 
+ if len(interventions) > 0:
+ logging.info(f"{resp['id']} used interventions: {interventions}")
  response = {"simulation_id": resp["id"]}
 
  return response
@@ -99,7 +110,7 @@ def calibrate_model(body: CalibratePostRequest) -> JobResponse:
  from utils import create_job
 
  # Parse request body
- print(body)
+ logging.info(body)
  engine = str(body.engine).lower()
  username = body.username
  model_config_id = body.model_config_id
@@ -108,7 +119,6 @@ def calibrate_model(body: CalibratePostRequest) -> JobResponse:
  end = body.timespan.end
  extra = body.extra.dict()
 
-
  operation_name = "operations.calibrate_then_simulate"
  options = {
  "engine": engine,
@@ -118,7 +128,7 @@ def calibrate_model(body: CalibratePostRequest) -> JobResponse:
  "end": end,
  "dataset": dataset.dict(),
  "extra": extra,
- "visual_options": True
+ "visual_options": True,
  }
 
  resp = create_job(operation_name=operation_name, options=options)
@@ -139,3 +149,4 @@ def create_ensemble(body: EnsemblePostRequest) -> JobResponse:
  )
 
 
+

api/utils.py

@@ -53,7 +53,7 @@ def create_job(operation_name: str, options: Optional[Dict[Any, Any]] = None):
  job = q.fetch_job(job_id)
 
  if STANDALONE:
- print(f"OPTIONS: {options}")
+ logging.info(f"OPTIONS: {options}")
  ex_payload = {
  "engine": "ciemss",
  "model_config_id": options.get("model_config_id"),
@@ -73,9 +73,9 @@ def create_job(operation_name: str, options: Optional[Dict[Any, Any]] = None):
  "engine": "ciemss",
  "workflow_id": job_id,
  }
- print(payload)
+ logging.info(payload)
  sys.stdout.flush()
- print(requests.put(post_url, json=json.loads(json.dumps(payload))).content)
+ logging.info(requests.put(post_url, json=json.loads(json.dumps(payload))).content)
 
  if job and force_restart:
  job.cleanup(ttl=0) # Cleanup/remove data immediately