Added development db for Sanctuary

Makefile

@@ -28,13 +28,15 @@ web:
 	@docker compose up -d web
 
 mig:
-	@echo "Creating database and applying migrations..."
+	@echo "Creating database and applying migrations for medical..."
 	@docker compose up migs
+	@docker compose up migssanctuary
 
 automig:
 	@echo "Autogenerating migration in docker context"
 	@docker compose up -d --no-recreate api
-	@docker compose exec api bash -c "cd /app/api && alembic revision --autogenerate -m 'CHANGEME'"
+	@docker compose exec api bash -c "cd /app/api && alembic --name sanctuary revision --autogenerate -m 'CHANGEME'"
+	@docker compose exec api bash -c "cd /app/api && alembic --name medical revision --autogenerate -m 'CHANGEME'"
 
 prune:
 	@echo "Pruning docker artifacts..."

app/api/alembic.ini

@@ -1,16 +1,14 @@
-# A generic, single database configuration.
-
-[alembic]
+[sanctuary]
 # path to migration scripts
-script_location = alembic/
+script_location = alembic/sanctuary
 
 # template used to generate migration files
 # file_template = %%(rev)s_%%(slug)s
 file_template = %%(year)d-%%(month).2d-%%(day).2d_%%(rev)s_%%(slug)s
 
 # sys.path path, will be prepended to sys.path if present.
 # defaults to the current working directory.
-prepend_sys_path = ..
+prepend_sys_path = .., ..
 
 # timezone to use when rendering the date
 # within the migration file as well as the filename.
@@ -32,16 +30,21 @@ prepend_sys_path = ..
 # sourceless = false
 
 # version location specification; this defaults
-# to alembic//versions.  When using multiple version
+# to sanctuary/versions.  When using multiple version
 # directories, initial revisions must be specified with --version-path
-# version_locations = %(here)s/bar %(here)s/bat alembic//versions
+# version_locations = %(here)s/bar %(here)s/bat sanctuary/versions
 
 # the output encoding used when revision files
 # are written from script.py.mako
 # output_encoding = utf-8
 
 sqlalchemy.url = driver://user:pass@localhost/dbname
 
+[medical]
+script_location = alembic/medical
+sqlalchemy.url = driver://user:pass@localhost/dbname
+prepend_sys_path = .., ..
+file_template = %%(year)d-%%(month).2d-%%(day).2d_%%(rev)s_%%(slug)s
 
 [post_write_hooks]
 # post_write_hooks defines scripts or Python functions that are run

app/api/alembic/env.py → app/api/alembic/medical/env.py

@@ -22,18 +22,13 @@
 
 target_metadata = Base.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.
-
 # Environment based sqlalchemy url
 user = os.environ.get("POSTGRES_USER")
 password = os.environ.get("POSTGRES_PASSWORD")
 hostname = os.environ.get("POSTGRES_HOST")
 db = os.environ.get("POSTGRES_DB")
 SQLALCHEMY_DATABASE_URL = f"postgresql+psycopg2://{user}:{password}@{hostname}/{db}"
-config.set_main_option('sqlalchemy.url', SQLALCHEMY_DATABASE_URL)
+config.set_main_option("sqlalchemy.url", SQLALCHEMY_DATABASE_URL)
 
 
 def run_migrations_offline():
@@ -74,8 +69,7 @@ def run_migrations_online():
     )
 
     with connectable.connect() as connection:
-        context.configure(connection=connection,
-                          target_metadata=target_metadata)
+        context.configure(connection=connection, target_metadata=target_metadata)
 
         with context.begin_transaction():
             context.run_migrations()

app/api/alembic/medical/versions/2024-01-30_f2fff363a197_changeme.py

@@ -0,0 +1,52 @@
+"""CHANGEME
+
+Revision ID: f2fff363a197
+Revises: a98d7be28c23
+Create Date: 2024-01-30 00:30:26.398900
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = 'f2fff363a197'
+down_revision = 'a98d7be28c23'
+
+from alembic import op
+import sqlalchemy as sa
+
+from alembic import context
+
+
+def upgrade():
+    schema_upgrades()
+    if context.get_x_argument(as_dictionary=True).get("data", None):
+        data_upgrades()
+
+
+def downgrade():
+    if context.get_x_argument(as_dictionary=True).get("data", None):
+        data_downgrades()
+    schema_downgrades()
+
+
+def schema_upgrades():
+    """schema upgrade migrations go here."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###
+
+
+def schema_downgrades():
+    """schema downgrade migrations go here."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###
+
+
+def data_upgrades():
+    """Add any optional data upgrade migrations here!"""
+    pass
+
+
+def data_downgrades():
+    """Add any optional data downgrade migrations here!"""
+    pass

app/api/alembic/sanctuary/env.py

@@ -0,0 +1,82 @@
+import os
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+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)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+from api.main.database import BaseSanctuary
+
+# Populates Base.metadata by importing all models
+import api.models
+
+target_metadata = BaseSanctuary.metadata
+
+# Environment based sqlalchemy url
+user = os.environ.get("POSTGRES_USER")
+password = os.environ.get("POSTGRES_PASSWORD")
+hostname = os.environ.get("POSTGRES_HOST")
+db = "sanctuary"
+SQLALCHEMY_DATABASE_URL = f"postgresql+psycopg2://{user}:{password}@{hostname}/{db}"
+config.set_main_option("sqlalchemy.url", SQLALCHEMY_DATABASE_URL)
+
+
+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,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    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.
+
+    """
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(connection=connection, target_metadata=target_metadata)
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

app/api/alembic/sanctuary/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"}

app/api/alembic/sanctuary/versions/2024-01-30_e7a96dd328c5_changeme.py

@@ -0,0 +1,64 @@
+"""CHANGEME
+
+Revision ID: e7a96dd328c5
+Revises: 
+Create Date: 2024-01-30 00:30:20.784035
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = 'e7a96dd328c5'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('intakes',
+    sa.Column('created_timestamp', sa.DateTime(), nullable=True),
+    sa.Column('last_updated_timestamp', sa.DateTime(), nullable=True),
+    sa.Column('deleted', sa.Boolean(), nullable=True),
+    sa.Column('intake_uuid', postgresql.UUID(as_uuid=True), nullable=False),
+    sa.Column('user_uuid', postgresql.UUID(as_uuid=True), nullable=True),
+    sa.Column('guest_rfid', sa.String(), nullable=True),
+    sa.Column('arrival_date', sa.DateTime(), nullable=True),
+    sa.Column('arrival_time', sa.DateTime(), nullable=True),
+    sa.Column('arrival_method', sa.String(), nullable=True),
+    sa.Column('identified_gender', sa.String(), nullable=True),
+    sa.Column('first_visit', sa.Boolean(), nullable=True),
+    sa.Column('presenting_complaint', sa.String(), nullable=True),
+    sa.Column('guest_consciousness_level', sa.String(), nullable=True),
+    sa.Column('guest_emotional_state', sa.String(), nullable=True),
+    sa.Column('substance_categories', sa.String(), nullable=True),
+    sa.Column('time_since_last_dose', sa.Integer(), nullable=True),
+    sa.Column('discharge_date', sa.DateTime(), nullable=True),
+    sa.Column('discharge_time', sa.DateTime(), nullable=True),
+    sa.Column('discharge_method', sa.String(), nullable=True),
+    sa.PrimaryKeyConstraint('intake_uuid'),
+    sa.UniqueConstraint('intake_uuid')
+    )
+    op.create_table('users',
+    sa.Column('created_timestamp', sa.DateTime(), nullable=True),
+    sa.Column('last_updated_timestamp', sa.DateTime(), nullable=True),
+    sa.Column('deleted', sa.Boolean(), nullable=True),
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('user_uuid', postgresql.UUID(as_uuid=True), nullable=True),
+    sa.Column('email', sa.String(), nullable=True),
+    sa.Column('hashed_password', sa.String(), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('user_uuid')
+    )
+    op.create_index(op.f('ix_users_id'), 'users', ['id'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_users_id'), table_name='users')
+    op.drop_table('users')
+    op.drop_table('intakes')
+    # ### end Alembic commands ###

app/api/main/database.py

@@ -20,13 +20,21 @@
     f"postgresql+psycopg2://{user}:{password}@{hostname}:{port}/{db}"
 )
 
-engine = create_engine(SQLALCHEMY_DATABASE_URL, pool_pre_ping=True)
-if not database_exists(engine.url): # Check if the db exists
-        create_database(engine.url)     # Create new DB    
+# TODO: rename "example" database to medical
+# Engine for the 'medical' database
+engine_example = create_engine(
+    f"postgresql+psycopg2://{user}:{password}@{hostname}:{port}/example"
+)
+if not database_exists(engine_example.url):  # Check if the db exists
+    create_database(engine_example.url)  # Create new DB
 
-SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+# TODO: Rename sessionLocal to sessionLocalMedical
+SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine_example)
 
+# TODO: rename this to MedicalBase
 Base = declarative_base()
+BaseSanctuary = declarative_base()
+
 
 def get_db() -> Generator:
     db = SessionLocal()
@@ -35,9 +43,13 @@ def get_db() -> Generator:
     finally:
         db.close()
 
+
+# TODO: implement engine and session for sanctuary
 def create_all_tables() -> None:
-    Base.metadata.create_all(engine, checkfirst=True)
+    Base.metadata.create_all(engine_example, checkfirst=True)
+#    BaseSanctuary.metadata.create_all(engine_example, checkfirst=True)
 
 
 def drop_all_tables(check_first: bool = False) -> None:
-    Base.metadata.drop_all(engine, checkfirst=check_first)
+    Base.metadata.drop_all(engine_example, checkfirst=check_first)
+#    BaseSanctuary.metadata.drop_all(engine_example, checkfirst=check_first)

app/api/models/__init__.py

@@ -1,6 +1,3 @@
-from api.models.user import User
+from api.models.user import User, UserSanctuary, UserMedical
 from api.models.patient_encounter import PatientEncounter
-
-# TODO: uncomment this for sanctuary dev db
-# Ticket: https://mediform.atlassian.net/browse/MEDI-30
-# from api.models.intake import Intake
+from api.models.intake import Intake

app/api/models/intake.py

@@ -8,12 +8,12 @@
 from sqlalchemy.dialects.postgresql import UUID
 from sqlalchemy.orm import Session
 
-from api.main.database import Base
+from api.main.database import BaseSanctuary
 from api.models.mixins import BasicMetrics
 
 logger = logging.getLogger(__name__)
 
-class Intake(Base, BasicMetrics):
+class Intake(BaseSanctuary, BasicMetrics):
     __tablename__ = "intakes"
 
     intake_uuid = Column(UUID(as_uuid=True), primary_key=True, default=uuid.uuid4, unique=True)