updates

assets/scripts/build_all.sh

@@ -1,19 +1,25 @@
 #!/usr/bin/env bash
 
-set -e
-
 arg1="$1"
+arg2="$2"
 
 # optionally prune/clear system and cache prior to build
 if [ "$arg1" == "-p" ]; then
   yes | docker system prune -a
   yes | docker buildx prune -a
 fi
 
+# remove old spec, create new
+sudo rm compose_api/spec/openapi_3_1_0_generated.yaml
+cd compose_api && python3 openapi_spec.py && cd ..
+
 # remove pycache to clean images
 sudo rm -r compose_api/__pycache__
 sudo rm -r compose_worker/__pycache__
 
 # build and push containers
 docker compose build --no-cache
 
+if [ "$arg2" == "-r" ]; then
+  docker compose up
+fi

compose_api/main.py

@@ -2,7 +2,6 @@
 import os
 import logging
 import uuid
-from enum import Enum
 from typing import *
 
 import dotenv
@@ -13,12 +12,11 @@
 from fastapi.responses import FileResponse
 from pydantic import BeforeValidator, Field, BaseModel
 from starlette.middleware.cors import CORSMiddleware
-from sympy.multipledispatch.dispatcher import source
 
 from compatible import COMPATIBLE_VERIFICATION_SIMULATORS
-from compose_api.data_model import ObservableData
 # from bio_check import MONGO_URI
 from data_model import (
+    ObservableData,
     SimulatorRMSE,
     SmoldynJob,
     VerificationOutput,

compose_api/spec/openapi_3_1_0_generated.yaml

@@ -703,21 +703,27 @@ components:
       title: HTTPValidationError
     ObservableData:
       properties:
-        name:
+        observable_name:
           type: string
-          title: Name
+          title: Observable Name
         mse:
           type: object
           title: Mse
         proximity:
           type: object
           title: Proximity
         output_data:
+          additionalProperties:
+            anyOf:
+            - items:
+                type: number
+              type: array
+            - type: string
           type: object
           title: Output Data
       type: object
       required:
-      - name
+      - observable_name
       - mse
       - proximity
       - output_data
@@ -858,6 +864,21 @@ components:
       required:
       - name
       title: Simulator
+    SimulatorRMSE:
+      properties:
+        simulator:
+          type: string
+          title: Simulator
+        rmse_matrix:
+          additionalProperties:
+            type: number
+          type: object
+          title: Rmse Matrix
+      type: object
+      required:
+      - simulator
+      - rmse_matrix
+      title: SimulatorRMSE
     SmoldynRun:
       properties:
         job_id:
@@ -942,10 +963,13 @@ components:
           title: Requested Simulators
         results:
           anyOf:
-          - type: object
           - items:
-              $ref: '#/components/schemas/ObservableData'
+              anyOf:
+              - $ref: '#/components/schemas/ObservableData'
+              - $ref: '#/components/schemas/SimulatorRMSE'
+              - {}
             type: array
+          - type: object
           - type: 'null'
           title: Results
       type: object