Notes Architecture Code

## Benutzerschnitstellen

1. Web Front-end

    ```
    Enter Variant [chr9:1234A>C] [SUBMIT]
    
    =>
    
    Ja, Variante gefunden/Nein Variante nicht gefunden.
    ```

2. REST API

    ```
    GET /api/<variant> HTTP/1.1
    
    =>
    
    200 OK
    
    {"message": "Yes, variant found"}
    ```

3. Command line interface (CLI)

    ```
    host:~$ beacon-query
    Bitte Variante eingeben> chr9:1234A>C
    Ja, deine Variante wurde gefunden
    ```

4. Administrations/Wartungsinterface

    - Datenbank anlegen

        ```
        host:~$ beacon-admin setup-database path/to/db.sqlite3
        ...
        host:~$ ls path/to/db.sqlite3
        path/to/db.sqlite3
        ```
    
    - VCF Importieren mit Ersetzen
    
        ```
        host:~$ beacon-admin vcf-import --method=replace path/to/db.sqlite3 path/to/input.vcf
        ...
        2345 records successfully imported, replaced previous 123 ones
        ```
    
    - VCF Importieren mit Hinzufuegen

        ```
        host:~$ beacon-admin vcf-import --method=add path/to/db.sqlite3 path/to/input.vcf
        ...
        2300 records successfully imported, updated, 45 updated, left 78 untouched
        ```

    - Nach Duplikaten Suchen

        ```
        host:~$ beacon-admin search-dupalictes path/to/db.sqlite3
        ...
        20 duplicates found, remove with beacon-admin fix-duplicates path/to/db.sqlite3
        ```

## Design

flask_app user_cli database admin_cli

module beacon.flask_app

"""Provides the front-end for both web UI and REST API."""

flask = ....

db_connectioin = ...

@route("/"): def render_form(): pass

@route("/query"): def handle_form_submission(): pass

@route("/api/query/<var_str>"): def api_query(var_str): # var = ... parse ... var_str # db_connection.run_query(var) pass

module beacon.user_cli

"""Provide the user query command line interface."""

import argparse

def main(): parser = argparse.ArgumentParser() # ... args = parser.parse_args() # var_str = args.variant var_str = input("Enter variant please") # ...

module beacon.admin_cli

"""Provides administrative commands."""

class CreateDbCommand: pass

class ImportVcfCommand: replace = True/False

class SearchDuplicatesCommand: pass

def main(): parser = argparse.ArgumentParser() # ... args = parser.parse_args()

if args.command == "create-db":
     CreateDbCommand().run()
elif args.command == "import-vcf":
     ImportVcfCommand().run()
# ....

module beacon.common

"""Provides common data structures and operations."""

class Variant: pass

class AnnotatedVariant: pass

class VariantStringParser: def parse_var(var_str): # -> Variant pass

module beacon.database

"""Provides internal API to database."""

class DatabaseConnection: def run_query(var): # => [AnnotatedVariant] pass

```bash
## file beacon/settings.py

PATH_DATABASE = None

## file beacon/flask_app.py

from . import settings

app = Flask(__name__)

db_connection = DatabaseConnection(settings.PATH_DATABASE)

## beacon/flask_app.py

from . import settings

def run():
    # ...
    args = parser.parse_args() # ...
    settings.PATH_DATABASE = args.path_database
    from . flask_app import app
    app.run_server() # ...

if __name__ == "__main__":
    run()