Add flask-migrate

README.md

@@ -33,7 +33,8 @@ cp .env.example .env
 vi .env 
 
 # Initialize database
-flask init-db
+flask init-db # Only the first time to seed the first data
+flask db upgrade # At each woodcamrm version upgrade
 
 # Run application
 flask run
@@ -90,7 +91,8 @@ sudo systemctl start woodcamrm.service
 docker-compose up -d
 
 # Create database
-docker exec woodcam-rm_app_1 flask init-db -y
+docker exec woodcam-rm_app_1 flask init-db # Only the first time to seed the first data
+docker exec woodcam-rm_app_1 flask db upgrade # At each woodcamrm version upgrade
 
 # Restart services
 docker-compose restart

migrations/README

@@ -0,0 +1 @@
+Single-database configuration for Flask.

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 +1,98 @@
+from __future__ import with_statement
+
+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')
+
+# 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',
+    str(current_app.extensions['migrate'].db.get_engine().url).replace(
+        '%', '%%'))
+target_metadata = current_app.extensions['migrate'].db.metadata
+
+# 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 include_object(object, name, type_, reflected, compare_to):    
+    if type_ == "table" and name == 'spatial_ref_sys':
+        return False
+    else:
+        return True
+
+
+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=target_metadata, literal_binds=True, include_object=include_object
+    )
+
+    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(context, revision, 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.')
+
+    connectable = current_app.extensions['migrate'].db.get_engine()
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            process_revision_directives=process_revision_directives,
+            include_object=include_object,
+            **current_app.extensions['migrate'].configure_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"}

migrations/versions/6d037e99c04d_initial_migration.py

@@ -0,0 +1,28 @@
+"""initial migration
+
+Revision ID: 6d037e99c04d
+Revises: 
+Create Date: 2022-04-26 13:25:12.988954
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '6d037e99c04d'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index('idx_stations_geom', table_name='stations')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_index('idx_stations_geom', 'stations', ['geom'], unique=False)
+    # ### end Alembic commands ###

migrations/versions/77b752ddd223_add_recording_parameters.py

@@ -0,0 +1,34 @@
+"""add recording parameters
+
+Revision ID: 77b752ddd223
+Revises: 6d037e99c04d
+Create Date: 2022-04-26 13:31:59.356854
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '77b752ddd223'
+down_revision = '6d037e99c04d'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('stations', sa.Column('rec_resolution', sa.String(length=12), nullable=True))
+    op.add_column('stations', sa.Column('rec_fps', sa.Integer(), nullable=True))
+    op.add_column('stations', sa.Column('rec_codec', sa.String(length=12), nullable=True))
+    op.add_column('stations', sa.Column('rec_compression', sa.Integer(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('stations', 'rec_compression')
+    op.drop_column('stations', 'rec_codec')
+    op.drop_column('stations', 'rec_fps')
+    op.drop_column('stations', 'rec_resolution')
+    # ### end Alembic commands ###

setup.py

@@ -13,6 +13,7 @@
         'flask-mqtt',
         'flask-mail',
         'flask-wtf',
+        'flask-migrate',
         'psycopg2-binary',
         'requests',
         'python-dotenv',

tests/conftest.py

@@ -2,10 +2,7 @@
 
 import pytest
 from woodcamrm import create_app
-from woodcamrm.db import get_db, init_db
-
-with open(os.path.join(os.path.dirname(__file__), 'data.sql'), 'rb') as f:
-    _data_sql = f.read().decode('utf8')
+from woodcamrm.db import init_db
 
 
 @pytest.fixture
@@ -18,11 +15,6 @@ def app():
 
     with app.app_context():
         init_db()
-        db = get_db()
-        cur = db.cursor()
-        cur.execute(_data_sql)
-        cur.close()
-        db.commit()
 
     yield app
 
@@ -41,7 +33,7 @@ class AuthActions(object):
     def __init__(self, client):
         self._client = client
 
-    def login(self, username='test', password='test'):
+    def login(self, username=app.config['DEFAULT_USER'], password=app.config['DEFAULT_PASSWORD']):
         return self._client.post(
             '/auth/login',
             data={'username': username, 'password': password}

tests/test_db.py

@@ -1,22 +1,4 @@
-import psycopg2
-
 import pytest
-from woodcamrm.db import get_db
-
-
-# def test_get_close_db(app):
-#     with app.app_context():
-#         db = get_db()
-#         assert db is get_db()
-
-#     with pytest.raises(psycopg2.ProgrammingError) as e:
-#         cur = db.cursor()
-#         db.execute('SELECT 1;')
-#         cur.close()
-#         db.commit()
-
-#     assert 'closed' in str(e.value)
-
 
 def test_init_db_command(runner, monkeypatch):
     class Recorder(object):
@@ -26,6 +8,6 @@ def fake_init_db():
         Recorder.called = True
 
     monkeypatch.setattr('woodcamrm.db.init_db', fake_init_db)
-    result = runner.invoke(args=['init-db'])
-    assert 'Initialized' in result.output
+    result = runner.invoke(args=['init-db -y'])
+    assert 'Initialized the database.' in result.output
     assert Recorder.called

woodcamrm/__init__.py

@@ -12,7 +12,7 @@
 
 from celery import Celery
 
-from woodcamrm.extensions import mqtt, dbsql, scheduler, mail
+from woodcamrm.extensions import mqtt, dbsql, scheduler, mail, migrate
 from woodcamrm.db import Stations
 
 
@@ -51,6 +51,7 @@ def create_app(test_config=None):
 
     dbsql.init_app(app)
     db.init_app(app)
+    migrate.init_app(app, dbsql)
 
     with app.app_context():
         try:

woodcamrm/db.py

@@ -82,6 +82,11 @@ class Stations(dbsql.Model):
     sd_disruption = dbsql.Column(dbsql.Integer, nullable=False, default=0)
     tampering = dbsql.Column(dbsql.Integer, nullable=False, default=0)
 
+    rec_resolution = dbsql.Column(dbsql.String(12))
+    rec_fps = dbsql.Column(dbsql.Integer, default=3)
+    rec_codec = dbsql.Column(dbsql.String(12), default="h264")
+    rec_compression = dbsql.Column(dbsql.Integer, default=30)
+
     jan_threshold = dbsql.Column(dbsql.Numeric)
     feb_threshold = dbsql.Column(dbsql.Numeric)
     mar_threshold = dbsql.Column(dbsql.Numeric)

woodcamrm/extensions.py

@@ -1,9 +1,11 @@
 from flask_sqlalchemy import SQLAlchemy
+from flask_migrate import Migrate
 from flask_apscheduler import APScheduler
 from flask_mqtt import Mqtt
 from flask_mail import Mail
 
 dbsql = SQLAlchemy()
 scheduler = APScheduler()
 mqtt = Mqtt()
-mail = Mail()
+mail = Mail()
+migrate = Migrate()

woodcamrm/station.py

@@ -36,6 +36,7 @@ class StationForm(FlaskForm):
     installation_port = IntegerField('Installation ping port', validators=[Optional()])
     snmp_received = StringField('SNMP MIB for received data', validators=[Optional()])
     snmp_transmitted = StringField('SNMP MIB for transmitted data', validators=[Optional()])
+
     jan_threshold = DecimalField('Water level threshold january (mm)', validators=[Optional()]) 
     feb_threshold = DecimalField('Water level threshold february (mm)', validators=[Optional()]) 
     mar_threshold = DecimalField('Water level threshold march (mm)', validators=[Optional()])