Setup flask migrate (#198)

Dockerfile

@@ -5,11 +5,12 @@ WORKDIR /app
 COPY requirements.txt .
 RUN pip install --no-cache-dir -r requirements.txt
 
-COPY labconnect /app/labconnect
-COPY run.py .
+COPY labconnect .
+COPY app.py .
 COPY db_init.py .
 COPY config.py .
 COPY run.sh .
+COPY migrations .
 RUN chmod +x run.sh
 
 HEALTHCHECK --interval=10s --timeout=5s --start-period=5s --retries=3 \

Makefile

@@ -5,7 +5,7 @@ clean:
 	pystarter clean
 
 run: 
-	gunicorn run:app -w 6 --preload --max-requests-jitter 300 --bind 0.0.0.0:8000
+	gunicorn app:app -w 6 --preload --max-requests-jitter 300 --bind 0.0.0.0:9000
 
 develop:
 	python3 run.py

run.py → app.py

@@ -3,4 +3,4 @@
 app = create_app()
 
 if __name__ == "__main__":
-    app.run(port=8000)
+    app.run(port=9000)

labconnect/__init__.py

@@ -5,19 +5,20 @@
 # Import Flask modules
 from flask import Flask
 from flask_cors import CORS
+
 from flask_jwt_extended import (
     JWTManager,
     create_access_token,
     get_jwt,
     get_jwt_identity,
 )
 from flask_sqlalchemy import SQLAlchemy
-
+from flask_migrate import Migrate
 from labconnect.helpers import OrJSONProvider
 
 # Create Database object
 db = SQLAlchemy()
-
+migrate = Migrate()
 jwt = JWTManager()
 
 
@@ -43,6 +44,7 @@ def initialize_extensions(app) -> None:
     # Since the application instance is now created, pass it to each Flask
     # extension instance to bind it to the Flask application instance (app)
     db.init_app(app)
+    migrate.init_app(app, db)
     jwt.init_app(app)
     app.json = OrJSONProvider(app)
 

migrations/README

@@ -0,0 +1,21 @@
+Single-database configuration for Flask.
+
+# To upgrade the database:
+
+1. Run $ flask db upgrade to apply current migration
+2. Preform any changes to labconnect/models.py
+3. Run $ flask db migrate -m "description of changes"
+4. The migration will be automatically created in migrations/versions.
+Review migration to ensure it is correct.
+5. Run $ flask db upgrade. Your changes will now be reflected in labconnect/models.py
+
+# To downgrade the database:
+This will revert the database back to the version before last upgrade
+
+1. In labconnect/models.py, view downgrade() method to see the changes 
+that will be made with this downgrade. 
+2. If these are the desired changes, run $ flask db downgrade
+
+# Official Documnetation
+https://flask-migrate.readthedocs.io/en/latest/
+

migrations/alembic.ini

@@ -0,0 +1,50 @@
+# A generic, single database configuration.
+
+[alembic]
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic,flask_migrate
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[logger_flask_migrate]
+level = INFO
+handlers =
+qualname = flask_migrate
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migrations/env.py

@@ -0,0 +1,108 @@
+import logging
+from logging.config import fileConfig
+
+from flask import current_app
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger("alembic.env")
+
+
+def get_engine():
+    try:
+        # this works with Flask-SQLAlchemy<3 and Alchemical
+        return current_app.extensions["migrate"].db.get_engine()
+    except (TypeError, AttributeError):
+        # this works with Flask-SQLAlchemy>=3
+        return current_app.extensions["migrate"].db.engine
+
+
+def get_engine_url():
+    try:
+        return get_engine().url.render_as_string(hide_password=False).replace("%", "%%")
+    except AttributeError:
+        return str(get_engine().url).replace("%", "%%")
+
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+config.set_main_option("sqlalchemy.url", get_engine_url())
+target_db = current_app.extensions["migrate"].db
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def get_metadata():
+    if hasattr(target_db, "metadatas"):
+        return target_db.metadatas[None]
+    return target_db.metadata
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(url=url, target_metadata=get_metadata(), literal_binds=True)
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    # this callback is used to prevent an auto-migration from being generated
+    # when there are no changes to the schema
+    # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+    def process_revision_directives(_unusedcontext, _unusedrevision, directives):
+        if getattr(config.cmd_opts, "autogenerate", False):
+            script = directives[0]
+            if script.upgrade_ops.is_empty():
+                directives[:] = []
+                logger.info("No changes in schema detected.")
+
+    conf_args = current_app.extensions["migrate"].configure_args
+    if conf_args.get("process_revision_directives") is None:
+        conf_args["process_revision_directives"] = process_revision_directives
+
+    connectable = get_engine()
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection, target_metadata=get_metadata(), **conf_args
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

migrations/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}