Merge pull request #115 from TACC/development

Development

Makefile

@@ -3,14 +3,18 @@ help:  ## Display this help screen
 	@grep -E '^([a-zA-Z_-]+):.*?## .*$$|^([a-zA-Z_-]+):' $(MAKEFILE_LIST) \
 	| awk 'BEGIN {FS = ":.*?## "}; {if ($$2) {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2} else {printf "\033[36m%-30s\033[0m %s\n", $$1, "(no description)"}}'
 
-.PHONY: build
-build: ## build dev
-	docker compose -f docker-compose.yml build
-
 .PHONY: start
-start: ## start dev environment where client code changes will be automatically updated on running client
+start: ## start
 	docker compose -f docker-compose.yml up -d --build
 
 .PHONY: stop
-stop: ## stop dev
-	docker compose -f docker-compose.yml stop
+stop: ## stop
+	docker compose -f docker-compose.yml down
+
+.PHONY: start-dev
+start-dev: ## start dev environment where frontend components are mounted in container
+	docker compose -f docker-compose-dev.yml up -d --build
+
+.PHONY: stop-dev
+stop-dev: ## stop dev environment
+	docker compose -f docker-compose-dev.yml down

README.md

@@ -1,12 +1,18 @@
 # PandemicExerciseTool
 
+## Requirements
+
+* [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
+* [Docker](https://www.docker.com/products/docker-desktop/)
+
 
 ## Getting Started
 
-#### Build the production environment
+
+#### Clone the repository
 
 ```bash
-make build
+git clone https://github.com/TACC/PandemicExerciseTool
 ```
 
 #### Start the production environment

backend/backend/settings.py

@@ -25,7 +25,7 @@
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True
 
-ALLOWED_HOSTS = []
+ALLOWED_HOSTS = ['*']
 
 
 # Application definition

backend/pet/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 5.0.3 on 2024-08-30 05:51
+# Generated by Django 5.0.9 on 2024-10-22 18:41
 
 from django.db import migrations, models
 
@@ -15,21 +15,21 @@ class Migration(migrations.Migration):
             name='PET',
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('disease_name', models.CharField(max_length=100)),
+                ('disease_name', models.TextField()),
                 ('R0', models.FloatField()),
                 ('beta_scale', models.FloatField()),
                 ('tau', models.FloatField()),
                 ('kappa', models.FloatField()),
                 ('gamma', models.FloatField()),
                 ('chi', models.FloatField()),
                 ('rho', models.FloatField()),
-                ('nu', models.CharField(choices=[('high', 'high'), ('low', 'low')], max_length=4)),
+                ('nu', models.TextField()),
                 ('initial_infected', models.TextField(null=True)),
-                ('phas', models.TextField(null=True)),
+                ('npis', models.TextField(null=True)),
                 ('antiviral_effectiveness', models.FloatField(null=True)),
                 ('antiviral_wastage_factor', models.FloatField(null=True)),
                 ('antiviral_stockpile', models.TextField(null=True)),
-                ('vaccine_wastage_factor', models.FloatField(blank=True, default=None, null=True)),
+                ('vaccine_wastage_factor', models.FloatField(null=True)),
                 ('vaccine_pro_rata', models.CharField(choices=[('children', 'children'), ('pro_rata', 'pro_rata')], max_length=8, null=True)),
                 ('vaccine_adherence', models.TextField(null=True)),
                 ('vaccine_effectiveness', models.TextField(null=True)),

backend/pet/models.py

@@ -3,7 +3,7 @@
 
 class PET(models.Model):
 
-    disease_name = models.CharField(max_length=100)
+    disease_name = models.TextField()
     R0 = models.FloatField()
     beta_scale = models.FloatField()
     tau = models.FloatField()
@@ -29,134 +29,3 @@ class PET(models.Model):
     def __str__(self):
         return(f'{self.disease_name}, R0={self.R0}, nu={self.nu}') 
 
-
-
-
-#{
-#  "output": "OUTPUT.json",
-#  "number_of_realizations": "1",
-#  "data": {
-#    "population": "data/texas/county_age_matrix_small.csv",
-#    "contact": "data/texas/contact_matrix.csv",
-#    "flow": "data/texas/work_matrix_rel.csv",
-#    "high_risk_ratios": "data/texas/high_risk_ratios.csv",
-#    "flow_reduction": "data/texas/flow_reduction.csv",
-#    "relative_susceptibility": "data/texas/relative_susceptibility.csv",
-#    "nu_value_matrix": "data/texas/nu_value_matrix.csv"
-#  },
-#  "parameters": {
-#    "R0": "1.2",
-#    "beta_scale": "10",
-#    "tau": "1.2",
-#    "kappa": "1.9",
-#    "gamma": "4.1",
-#    "chi": "1.0",
-#    "rho": "0.39",
-#    "nu": "high"
-#  },
-#  "initial_infected": [
-#    {
-#      "county": "453",
-#      "infected": "100",
-#      "age_group": "1"
-#    },
-#    {
-#      "county": "113",
-#      "infected": "100",
-#      "age_group": "1"
-#    },
-#    {
-#      "county": "201",
-#      "infected": "100",
-#      "age_group": "1"
-#    },
-#    {
-#      "county": "141",
-#      "infected": "100",
-#      "age_group": "1"
-#    },
-#    {
-#      "county": "375",
-#      "infected": "100",
-#      "age_group": "1"
-#    }
-#  ],
-#  "non_pharma_interventions": [
-#    {
-#      "day": "50",
-#      "effectiveness": "0.4",
-#      "halflife": "10.0"
-#    },
-#    {
-#      "day": "200",
-#      "effectiveness": "0.6",
-#      "halflife": "50.0"
-#    }
-#  ],
-#  "antivirals": {
-#    "antiviral_effectiveness": "1.5",
-#    "antiviral_wastage_factor": "60",
-#    "antiviral_stockpile": [
-#      {
-#        "day": "103",
-#        "amount": "17830"
-#      },
-#      {
-#        "day": "110",
-#        "amount": "65310"
-#      },
-#      {
-#        "day": "117",
-#        "amount": "33900"
-#      },
-#      {
-#        "day": "124",
-#        "amount": "92230"
-#      },
-#      {
-#        "day": "131",
-#        "amount": "48340"
-#      }
-#    ] 
-#  },
-#  "vaccines": {
-#    "vaccine_wastage_factor": "60",
-#    "vaccine_pro_rata": "children",
-#    "vaccine_adherence": [
-#      "0.4345",
-#      "0.298",
-#      "0.388",
-#      "0.450",
-#      "0.696"
-#    ],
-#    "vaccine_effectiveness": [
-#      "0.8",
-#      "0.8",
-#      "0.8",
-#      "0.8",
-#      "0.8"
-#    ],
-#    "vaccine_stockpile": [
-#      {
-#        "day": "203",
-#        "amount": "178300"
-#      },
-#      {
-#        "day": "210",
-#        "amount": "653100"
-#      },
-#      {
-#        "day": "217",
-#        "amount": "339000"
-#      },
-#      {
-#        "day": "224",
-#        "amount": "922300"
-#      },
-#      {
-#        "day": "231",
-#        "amount": "483400"
-#      }
-#    ]
-#  }
-#}

backend/pet/views.py

@@ -10,6 +10,11 @@
 import requests
 import pymongo
 
+import logging
+
+
+logger = logging.getLogger(__name__)
+
 myclient = pymongo.MongoClient("mongodb://mongo-db:27017/")
 mydb = myclient["PES"]
 mycol = mydb["days"]
@@ -34,6 +39,12 @@ def delete_job(request, task_id):
 def get_output(request, day):
     if request.method == 'GET':
         mydoc = mycol.find_one({'day': int(day)})
+        if mydoc is None:
+            logger.warning(f"Day {day} not calculated")
+            return JsonResponse(
+                {"error": f"Day {day} not calculated"},
+                status=404
+            )
         del mydoc['_id']
         return JsonResponse(mydoc, status=200)
 

backend/requirements.txt

@@ -1,7 +1,7 @@
 amqp==5.2.0
-Django==5.0.3
+Django==5.0.9
 django-cors-headers==4.3.1
-djangorestframework==3.15.1
+djangorestframework==3.15.2
 requests==2.32.3
 celery==5.4.0
 pymongo==4.8.0