megaqc package

Subpackages

• megaqc.api package
  • Submodules
  • megaqc.api.constants module
  • megaqc.api.utils module
  • megaqc.api.views module
  • Module contents
• megaqc.model package
  • Submodules
  • megaqc.model.models module
  • Module contents
• megaqc.public package
  • Submodules
  • megaqc.public.forms module
  • megaqc.public.views module
  • Module contents
• megaqc.report_plot package
  • Submodules
  • megaqc.report_plot.views module
  • Module contents
• megaqc.rest_api package
  • Submodules
  • megaqc.rest_api.content module
  • megaqc.rest_api.fields module
  • megaqc.rest_api.filters module
  • megaqc.rest_api.outlier module
  • megaqc.rest_api.plot module
  • megaqc.rest_api.schemas module
  • megaqc.rest_api.utils module
  • megaqc.rest_api.views module
  • megaqc.rest_api.webarg_parser module
  • Module contents
• megaqc.user package
  • Submodules
  • megaqc.user.forms module
  • megaqc.user.models module
  • megaqc.user.views module
  • Module contents
• megaqc.utils package
  • Submodules
  • megaqc.utils.settings module
  • Module contents

Submodules

megaqc.app module

MegaQC: A web-based tool to collect and visualise data from multiple MultiQC reports.

This file contains the app module, with the app factory function.

megaqc.app.create_app(config_object)

An application factory, as explained here: http://flask.pocoo.org/docs/patterns/appfactories/.

Parameters

config_object – The configuration object to use.

megaqc.app.register_blueprints(app)

Register Flask blueprints.

megaqc.app.register_commands(app)

Register Click commands.

megaqc.app.register_errorhandlers(app)

Register error handlers.

megaqc.app.register_extensions(app)

Register Flask extensions.

megaqc.app.register_shellcontext(app)

Register shell context objects.

megaqc.cli module

MegaQC: a web application that collects results from multiple runs of MultiQC and allows bulk visualisation.

megaqc.cli.create_megaqc_app()

megaqc.cli.main()

megaqc.commands module

Click commands.

megaqc.commands.megaqc_date_type(arg)

megaqc.compat module

Python 2/3 compatibility module.

megaqc.database module

Database module, including the SQLAlchemy database object and DB-related utilities.

class megaqc.database.CRUDMixin

Bases: object

Mixin that adds convenience methods for CRUD (create, read, update, delete) operations.

classmethod create(**kwargs)

Create a new record and save it the database.

delete(commit=True)

Remove the record from the database.

classmethod get_or_create(kwargs)

property primary_key

classmethod primary_key_columns()

classmethod primary_key_name()

save(commit=True)

Save the record.

update(commit=True, **kwargs)

Update specific fields of a record.

class megaqc.database.Model(**kwargs)

Bases: megaqc.database.CRUDMixin, sqlalchemy.orm.decl_api.Model

Base model class that includes CRUD convenience methods.

class megaqc.database.SurrogatePK

Bases: object

A mixin that adds a surrogate integer ‘primary key’ column named id to any declarative-mapped class.

classmethod get_by_id(record_id)

Get record by ID.

id = Column(None, Integer(), table=None, primary_key=True, nullable=False)

megaqc.database.init_db(url)

Initialise a new database.

megaqc.database.postgres_create_database(conn, cur, database, user)

Create a Postgres database, with the given owner.

megaqc.database.postgres_create_user(username, conn, cur, password=None)

Create a postgres user, including a password if provided.

megaqc.extensions module

Extensions module.

Each extension is initialized in the app factory located in app.py.

megaqc.scheduler module

megaqc.scheduler.init_scheduler(app)

megaqc.scheduler.upload_reports_job()

megaqc.settings module

Application configuration.

class megaqc.settings.Config

Bases: object

Base configuration.

APP_DIR = '/home/runner/work/MegaQC/MegaQC/megaqc'

CACHE_TYPE = 'simple'

DB_PATH = None

DEBUG_TB_ENABLED = False

DEBUG_TB_INTERCEPT_REDIRECTS = False

EXTRA_CONFIG = None

JOBS = [{'id': 'job1', 'func': <function upload_reports_job>, 'trigger': 'interval', 'seconds': 30}]

LOG_LEVEL = 20

PROJECT_ROOT = '/home/runner/work/MegaQC/MegaQC'

SCHEDULER_API_ENABLED = True

SECRET_KEY = 'secret-key'

SERVER_NAME = None

SQLALCHEMY_DATABASE = 'megaqc'

SQLALCHEMY_DBMS = None

SQLALCHEMY_HOST = 'localhost:5432'

SQLALCHEMY_PASS = ''

SQLALCHEMY_TRACK_MODIFICATIONS = False

SQLALCHEMY_USER = 'megaqc_user'

UPLOAD_FOLDER = '/home/runner/work/MegaQC/MegaQC/uploads'

USER_REGISTRATION_APPROVAL = True

update_db_uri()

class megaqc.settings.DevConfig

Bases: megaqc.settings.Config

Development configuration.

CACHE_TYPE = 'simple'

DB_NAME = 'megaqc.db'

DB_PATH = '/home/runner/work/MegaQC/MegaQC/megaqc.db'

DEBUG = True

DEBUG_TB_ENABLED = True

ENV = 'dev'

LOG_LEVEL = 10

SQLALCHEMY_DBMS = 'sqlite'

SQLALCHEMY_ECHO = True

SQLALCHEMY_RECORD_QUERIES = True

WTF_CSRF_ENABLED = False

class megaqc.settings.ProdConfig

Bases: megaqc.settings.Config

Production configuration.

DEBUG = False

DEBUG_TB_ENABLED = False

ENV = 'prod'

SQLALCHEMY_DATABASE = 'megaqc'

SQLALCHEMY_DBMS = 'postgresql'

SQLALCHEMY_HOST = 'localhost:5432'

SQLALCHEMY_PASS = 'megaqcpswd'

SQLALCHEMY_USER = 'megaqc'

class megaqc.settings.TestConfig

Bases: megaqc.settings.Config

Test configuration.

DB_NAME = 'megaqc.db'

DB_PATH = '/tmp/tmpa0x_owth/megaqc.db'

DEBUG = True

DEBUG_TB_ENABLED = False

LOG_LEVEL = 10

SQLALCHEMY_DBMS = 'sqlite'

TESTING = True

WTF_CSRF_ENABLED = False

megaqc.wsgi module

Module contents

Main application package.