Merge pull request #6 from cmu-delphi/SD-16

Change database to mySQL

Author: minhkhul

.env.example

@@ -1,7 +1,9 @@
-POSTGRES_DB=postgres_db_name
-POSTGRES_USER=postgres_db_user
-POSTGRES_PASSWORD=postgres_db_password
-POSTGRES_PORT=postgres_db_port
+MYSQL_DATABASE=mysql_database
+MYSQL_USER=mysql_user
+MYSQL_PASSWORD=mysql_password
+MYSQL_PORT=mysql_port
+MYSQL_HOST=mysql_host
+MYSQL_ROOT_PASSWORD=mysql_root_password
 
 ALLOWED_HOSTS='127.0.0.1,localhost'
 CORS_ORIGIN_WHITELIST='http://127.0.0.1:3000,http://localhost:3000'

Dockerfile

@@ -3,6 +3,9 @@ FROM python:3.10.8-alpine
 ENV PYTHONDONTWRITEBYTECODE=1
 ENV PYTHONUNBUFFERED=1
 RUN addgroup -S python && adduser -S python -G python
+RUN apk update
+RUN apk add musl-dev mariadb-dev gcc
+RUN apk add graphviz-dev
 RUN pip install -U pipenv
 USER python
 WORKDIR /home/python

Pipfile

@@ -6,7 +6,6 @@ name = "pypi"
 [packages]
 django = "*"
 django-filter = "*"
-psycopg2-binary = "*"
 django-extensions = "*"
 pillow = "*"
 pre-commit = "*"
@@ -20,8 +19,8 @@ pygraphviz = "*"
 django-bootstrap-v5 = "*"
 factory-boy = "*"
 linkpreview = "*"
-pymemcache = "*"
 django-redis = "*"
+mysqlclient = "*"
 
 [dev-packages]
 flake8 = "*"

Pipfile.lock

@@ -3,20 +3,20 @@ version: '3.8'
 services:
 
   db:
-    image: postgres:latest
+    image: mysql:latest
     container_name: signal_documentation-db
     restart: always
     env_file:
      - ./.env
     environment:
-      POSTGRES_DB: ${POSTGRES_DB}
-      POSTGRES_USER: ${POSTGRES_USER}
-      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
-      POSTGRES_HOST: ${POSTGRES_HOST}
+      MYSQL_DATABASE: ${MYSQL_DATABASE}
+      MYSQL_USER: ${MYSQL_USER}
+      MYSQL_PASSWORD: ${MYSQL_PASSWORD}
+      MYSQL_ROOT_PASSWORD: ${MYSQL_ROOT_PASSWORD}
     volumes:
-      - postgres:/var/lib/postgresql/data
+      - mysql:/var/lib/mysql/
     ports:
-      - "5432:5432"
+      - "3306:3306"
 
   webapp:
     build: .
@@ -45,5 +45,5 @@ services:
       - "6379:6379"
 
 volumes:
-  postgres:
+  mysql:
   webapp:

docker-compose.yaml

@@ -1,4 +1,4 @@
-# Generated by Django 4.2 on 2023-05-09 10:39
+# Generated by Django 4.2.2 on 2023-06-13 11:51
 
 from django.db import migrations, models
 
@@ -15,7 +15,7 @@ class Migration(migrations.Migration):
             name='Link',
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('link_type', models.CharField(choices=[('api_documentation', 'API Documentation'), ('dua', 'DUA'), ('interpreting_mask', 'Interpreting mask use in context'), ('question_text', 'Question text'), ('survey_details', 'Survey details'), ('survey_documentation', 'Survey documentation'), ('technical_description', 'Technical description'), ('wave_10_revision', 'Wave 10 revision updates'), ('wave_11_revision', 'Wave 11 revision updates'), ('other', 'Other')], help_text='Link type', max_length=128, unique=True)),
+                ('link_type', models.CharField(choices=[('api_documentation', 'API Documentation'), ('dua', 'DUA'), ('interpreting_mask', 'Interpreting mask use in context'), ('question_text', 'Question text'), ('survey_details', 'Survey details'), ('survey_documentation', 'Survey documentation'), ('technical_description', 'Technical description'), ('wave_10_revision', 'Wave 10 revision updates'), ('wave_11_revision', 'Wave 11 revision updates'), ('other', 'Other')], help_text='Link type', max_length=128)),
                 ('url', models.URLField(help_text='Link url', max_length=256, unique=True)),
             ],
         ),

src/base/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 4.2 on 2023-05-09 10:39
+# Generated by Django 4.2.2 on 2023-06-13 11:51
 
 from django.db import migrations, models
 import django.db.models.deletion

src/base/migrations/0002_alter_link_link_type.py

@@ -116,12 +116,12 @@
 
 DATABASES = {
     'default': {
-        'ENGINE': 'django.db.backends.postgresql',
-        'NAME': os.environ.get('POSTGRES_DB', None),
-        'USER': os.environ.get('POSTGRES_USER', None),
-        'PASSWORD': os.environ.get('POSTGRES_PASSWORD', None),
-        'HOST': os.environ.get('POSTGRES_HOST', 'localhost'),
-        'PORT': os.environ.get('POSTGRES_PORT', 5432),
+        'ENGINE': 'django.db.backends.mysql',
+        'NAME': os.environ.get('MYSQL_DATABASE', None),
+        'USER': os.environ.get('MYSQL_USER', None),
+        'PASSWORD': os.environ.get('MYSQL_PASSWORD', None),
+        'HOST': os.environ.get('MYSQL_HOST', 'localhost'),
+        'PORT': os.environ.get('MYSQL_PORT', 3306),
     }
 }
 

src/datasources/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 4.2 on 2023-05-09 10:39
+# Generated by Django 4.2.2 on 2023-06-13 11:51
 
 from django.db import migrations, models
 import django.db.models.deletion
@@ -22,6 +22,7 @@ class Migration(migrations.Migration):
             ],
             options={
                 'verbose_name_plural': 'geographies',
+                'ordering': ['name'],
             },
         ),
         migrations.CreateModel(
@@ -44,6 +45,9 @@ class Migration(migrations.Migration):
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('name', models.CharField(help_text='Name', max_length=128, unique=True)),
             ],
+            options={
+                'ordering': ['name'],
+            },
         ),
         migrations.CreateModel(
             name='Signal',
@@ -63,7 +67,7 @@ class Migration(migrations.Migration):
                 ('has_sample_size', models.BooleanField(default=False, help_text='Has Sample Size')),
                 ('high_values_are', models.CharField(choices=[('bad', 'Bad'), ('good', 'Good'), ('neutral', 'Neutral')], help_text='High values are', max_length=128)),
                 ('available_geography', models.ManyToManyField(help_text='Available geography', to='signals.geography')),
-                ('base', models.ForeignKey(help_text='Signal base', on_delete=django.db.models.deletion.PROTECT, related_name='base_for', to='signals.signal')),
+                ('base', models.ForeignKey(blank=True, help_text='Signal base', null=True, on_delete=django.db.models.deletion.PROTECT, related_name='base_for', to='signals.signal')),
                 ('category', models.ForeignKey(help_text='Signal Category', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='signals', to='signals.signalcategory')),
                 ('links', models.ManyToManyField(help_text='Signal links', related_name='signals', to='base.link')),
                 ('pathogen', models.ForeignKey(help_text='Pathogen/Disease Area', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='signals', to='signals.pathogen')),