initial setup files.

docker-compose.yml

@@ -1,4 +1,4 @@
-# docker-compose.yml for FHIRVINE
+version: '3.8'
 
 services:
   fhirvine:
@@ -9,13 +9,23 @@ services:
     volumes:
       - fhirvine_instance:/app/instance
       - fhirvine_migrations:/app/migrations
+      - ./setup/migrations:/app/setup_migrations
+      - ./setup/fhirvine.db:/app/setup_fhirvine.db
+      - ./static:/app/static
+      - ./templates:/app/templates
     environment:
       - FLASK_ENV=${FLASK_ENV:-development}
     env_file:
       - .env
     command: >
-      sh -c "flask db upgrade && waitress-serve --host=0.0.0.0 --port=5001 --call 'app:create_app'"
+      sh -c "echo 'Checking for setup migrations directory...' && ls -la /app/setup_migrations && if [ ! -d /app/migrations ]; then echo 'Copying migrations directory...' && cp -rv /app/setup_migrations /app/migrations && chown -R 1000:1000 /app/migrations && ls -la /app/migrations || { echo 'Failed to copy migrations'; exit 1; }; fi && if [ ! -f /app/instance/fhirvine.db ]; then echo 'Copying database file...' && cp -v /app/setup_fhirvine.db /app/instance/fhirvine.db && chown -R 1000:1000 /app/instance && ls -la /app/instance || { echo 'Failed to copy database'; exit 1; }; fi && echo 'Starting application...' && waitress-serve --host=0.0.0.0 --port=5001 --call 'app:create_app'"
     restart: unless-stopped
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:5001/"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+      start_period: 10s
 
 volumes:
   fhirvine_instance:

setup/migrations/README

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

setup/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

setup/migrations/env.py

@@ -0,0 +1,113 @@
+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(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.')
+
+    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()

setup/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"}

setup/migrations/versions/4e8d36d8e416_create_initial_schema_after_purge.py

@@ -0,0 +1,86 @@
+"""Create initial schema after purge
+
+Revision ID: 4e8d36d8e416
+Revises: 
+Create Date: 2025-04-23 13:08:11.515425
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '4e8d36d8e416'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('configurations',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('key', sa.String(length=100), nullable=False),
+    sa.Column('value', sa.Text(), nullable=False),
+    sa.Column('description', sa.Text(), nullable=True),
+    sa.Column('last_updated', sa.DateTime(), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('key')
+    )
+    op.create_table('oauth_tokens',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('client_id', sa.String(length=100), nullable=False),
+    sa.Column('token_type', sa.String(length=40), nullable=True),
+    sa.Column('access_token', sa.String(length=255), nullable=False),
+    sa.Column('refresh_token', sa.String(length=255), nullable=True),
+    sa.Column('scope', sa.Text(), nullable=True),
+    sa.Column('issued_at', sa.Integer(), nullable=False),
+    sa.Column('expires_in', sa.Integer(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('registered_apps',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('app_name', sa.String(length=100), nullable=False),
+    sa.Column('client_id', sa.String(length=100), nullable=False),
+    sa.Column('client_secret_hash', sa.String(length=200), nullable=False),
+    sa.Column('redirect_uris', sa.Text(), nullable=False),
+    sa.Column('scopes', sa.Text(), nullable=False),
+    sa.Column('logo_uri', sa.String(length=255), nullable=True),
+    sa.Column('contacts', sa.Text(), nullable=True),
+    sa.Column('tos_uri', sa.String(length=255), nullable=True),
+    sa.Column('policy_uri', sa.String(length=255), nullable=True),
+    sa.Column('jwks_uri', sa.String(length=255), nullable=True),
+    sa.Column('date_registered', sa.DateTime(), nullable=True),
+    sa.Column('last_updated', sa.DateTime(), nullable=True),
+    sa.Column('is_test_app', sa.Boolean(), nullable=True),
+    sa.Column('test_app_expires_at', sa.DateTime(), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('app_name'),
+    sa.UniqueConstraint('client_id')
+    )
+    op.create_table('authorization_codes',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('code', sa.String(length=255), nullable=False),
+    sa.Column('client_id', sa.String(length=100), nullable=False),
+    sa.Column('redirect_uri', sa.Text(), nullable=True),
+    sa.Column('scope', sa.Text(), nullable=True),
+    sa.Column('nonce', sa.String(length=255), nullable=True),
+    sa.Column('code_challenge', sa.String(length=255), nullable=True),
+    sa.Column('code_challenge_method', sa.String(length=10), nullable=True),
+    sa.Column('response_type', sa.String(length=40), nullable=True),
+    sa.Column('state', sa.String(length=255), nullable=True),
+    sa.Column('issued_at', sa.Integer(), nullable=False),
+    sa.Column('expires_at', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['client_id'], ['registered_apps.client_id'], name='fk_authorization_codes_client_id'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('authorization_codes')
+    op.drop_table('registered_apps')
+    op.drop_table('oauth_tokens')
+    op.drop_table('configurations')
+    # ### end Alembic commands ###

templates/base.html

@@ -245,12 +245,12 @@
         <div class="container-fluid">
             <div class="d-flex justify-content-between align-items-center">
                 <div class="footer-left">
-                    <a href="https://github.com/Sudo-JHare/FHIRVINE" target="_blank" rel="noreferrer" aria-label="Project Github">FHIRVINE Github</a>
+                    <a href="https://github.com/Sudo-JHare/FHIREVINE-Smart-Proxy" target="_blank" rel="noreferrer" aria-label="Project Github">FHIRVINE Github</a>
                     <a href="{{ url_for('about') }}" aria-label="About FHIRVINE">About FHIRVINE</a>
                     <a href="https://www.hl7.org/fhir/smart-app-launch/" target="_blank" rel="noreferrer" aria-label="SMART on FHIR">SMART on FHIR</a>
                 </div>
                 <div class="footer-right">
-                    <a href="https://github.com/Sudo-JHare/FHIRVINE/issues" target="_blank" rel="noreferrer" aria-label="Report Issue">Report Issue</a>
+                    <a href="https://github.com/Sudo-JHare/FHIREVINE-Smart-Proxy/issues" target="_blank" rel="noreferrer" aria-label="Report Issue">Report Issue</a>
                     <a href="https://github.com/Sudo-JHare" aria-label="Developer">Developer</a>
                 </div>
             </div>