Logging Configuration ======================================== Overview ---------------------------- There are two ways in which you can configure logging for Galaxy servers: 1. Basic/automatic configuration with control over log level and log destination (standard output or a named log file). 2. More complex configuration using the Python :mod:`logging` module's :func:`logging.config.dictConfig` or :func:`logging.config.fileConfig`. By default, Galaxy logs all messages to standard output at the ``DEBUG`` logging level, unless the ``--daemon`` argument is passed to ``run.sh``, in which case, output is logged to the file ``galaxy.log`` in the current directory. The way in which you configure logging depends on whether you are using a YAML or INI configuration file, and also on whether you are using the uWSGI application server, or Python Paste. Galaxy servers that were created starting with Galaxy Release 18.01 or later use a YAML configuration file with uWSGI. Galaxy servers that were created with 17.09 or older use an INI configuration file, and Python Paste by default, but they could be configured to run under uWSGI (and this was the recommendation for production servers). If you upgrade a pre-18.01 server running under Paste to 18.01 or later but do not convert your INI config (``galaxy.ini``) to a YAML config (``galaxy.yml``), the INI config and Paste will still be used. uWSGI, Paste, and related terminology are explained in detail in the :doc:`Scaling and Load Balancing ` documentation. Basic Configuration ---------------------------- Basic logging configuration can be used to modify the level of log messages and the file to which Galaxy logs. The level is controlled by the ``log_level`` configuration option. If not set, Galaxy logs all messages at the ``DEBUG`` level (versions prior to 18.01 defaulted to ``INFO`` if unset, but the default config file shipped with ``log_level`` explicitly set to ``DEBUG`` for development purposes). Galaxy logs all messages to standard output by default if running in the foreground. If running in the background (``sh run.sh --daemon``) under uWSGI, the log is written to ``galaxy.log`` in the current directory. If running in the background under Paste, the log is written to ``paster.log``. **Setting the log level:** In ``galaxy.yml``, set ``log_level``: .. code-block:: yaml galaxy: log_level: LEVEL Or if using ``galaxy.ini``: .. code-block:: ini [app:main] log_level = LEVEL Where ``LEVEL`` is one of the `logging levels`_ documented in the :mod:`logging` module. **Logging to a file:** To change the log file name or location, use the ``$GALAXY_LOG`` environment variable like so: .. code-block:: shell-session $ GALAXY_LOG=/path/to/galaxy/logfile sh run.sh --daemon Advanced Configuration ---------------------------- For more useful and manageable logging when running Galaxy with forking application stacks (e.g. uWSGI) where multiple Galaxy server processes are forked after the Galaxy application is loaded, some extensions to standard Python :mod:`logging` are available in Galaxy: - Two custom fields (aka Python :class:`logging.LogRecord` attributes) identifying the uWSGI worker ID and mule ID can be added to log messages: ``%(worker_id)s`` and ``%(mule_id)s``. These fields aid in associating log messages with the Galaxy server processes that emitted them. They are included in the default log format (found in :data:`galaxy.web.stack.UWSGIApplicationStack.log_format`) when using uWSGI and are available for use in custom log formats. - A custom ``filename_template`` config option is available to :class:`logging.FileHandler` (or derivative class) log handler definitions so that multiple file logging is possible. Without this custom option, all forked Galaxy server processes would only be able to log to a single combined log file, which can be very difficult to work with. YAML ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Advanced logging configuration is performed under the ``logging`` key in the ``galaxy`` section of ``galaxy.yml``. The syntax is a YAML dictionary in the syntax of Python's :func:`logging.config.dictConfig`. This section covers a few of the most common configurations as well as Galaxy's customizations. Consult the :func:`logging.config.dictConfig` documentation for a complete explanation of the syntax and possibilities. Default ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The default as of this Galaxy release can be found (in Python syntax) in the :data:`galaxy.config.LOGGING_CONFIG_DEFAULT` constant and (in YAML) below: .. include:: config_logging_default_yaml.rst Split Logfiles ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Using ``run.sh --daemon`` causes Galaxy to log to ``galaxy.log``, but this is done using uWSGI's logging functionality and does not allow for splitting logging in to multiple files. The following logging definition uses the ``filename_template`` custom handler configuration option to split logging in to the files ``galaxy_web_0.log`` (the combined messages of all web workers) and ``galaxy_job-handlers_N.log`` where ``N`` is the instance ID of the server process in its pool (aka the mule's position in its farm argument). In addition to the split file logging, the combined output is also still logged to standard error. .. code-block:: yaml galaxy: logging: filters: stack: (): galaxy.web.stack.application_stack_log_filter formatters: stack: (): galaxy.web.stack.application_stack_log_formatter handlers: console: class: logging.StreamHandler filters: - stack formatter: stack level: DEBUG stream: ext://sys.stderr files: class: logging.FileHandler filters: - stack level: DEBUG formatter: stack filename: galaxy_default.log filename_template: galaxy_{pool_name}_{server_id}.log loggers: galaxy: handlers: - console - files level: DEBUG propagate: 0 qualname: galaxy paste.httpserver.ThreadPool: level: WARN qualname: paste.httpserver.ThreadPool routes.middleware: level: WARN qualname: routes.middleware root: handlers: - console - files level: INFO version: 1 The list of available template facts for use in ``filename_template`` with all Galaxy application server types, and their values under the various possible :doc:`server deployment scenarios ` are given below: +-------------------+-----------------------------------------------------------------------------------------------+ | Fact | Application server | +-------------------+-------------------------------+-------------------------------+-------------------------------+ | | Paste/webless | uWSGI web worker | uWSGI mule | +===================+===============================+===============================+===============================+ | ``server_name`` | ``NAME`` for | ``main``, but can be modified with ``server_name`` in | | | ``[server:]`` in | ``galaxy.yml`` | | | ``galaxy.ini`` | | +-------------------+-------------------------------+-------------------------------+-------------------------------+ | ``server_id`` | ``None`` | 1-indexed worker ID | 1-indexed mule ID | +-------------------+-------------------------------+-------------------------------+-------------------------------+ | ``pool_name`` | ``None`` | ``web`` | Mule's farm name | +-------------------+-------------------------------+-------------------------------+-------------------------------+ | ``instance_id`` | ``None`` | Same as ``server_id`` | Mule's 1-indexed position in | | | | | its defined farm | +-------------------+-------------------------------+-------------------------------+-------------------------------+ | ``fqdn`` | Fully-qualified domain name of the host on which Galaxy is running | +-------------------+-----------------------------------------------------------------------------------------------+ | ``hostname`` | "Short" hostname (with domain portion stripped) of the host on which Galaxy is running | +-------------------+-----------------------------------------------------------------------------------------------+ The log message format can be customized by adding a (or modifying the default) formatter as in the following (partial) example. Note that in addition to the new format, the value of ``formatter`` in the ``console`` handler has been changed: .. code-block:: yaml galaxy: logging: formatters: myformat: (): '%(name)s %(levelname)s %(asctime)s [p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] [%(threadName)s] %(message)s' handlers: console: class: logging.StreamHandler filters: - stack formatter: myformat level: DEBUG stream: ext://sys.stderr INI ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ With an INI Galaxy configuration, it is possible to use Python's :func:`logging.config.fileConfig` configuration method for advanced logging configuration. For example: .. code-block:: ini [loggers] keys = root, galaxy [handlers] keys = console [formatters] keys = generic [logger_root] level = INFO handlers = console [logger_galaxy] level = DEBUG handlers = console qualname = galaxy propagate = 0 [handler_console] class = StreamHandler args = (sys.stderr,) level = DEBUG formatter = generic [formatter_generic] format = %(name)s %(levelname)-5.5s %(asctime)s [p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] [%(threadName)s] %(message)s While Galaxy's custom log format fields can be used (as seen in the example), the ``filename_template`` handler configuration extension is only available in the YAML format configuration file. .. _logging levels: https://docs.python.org/2/library/logging.html#logging-levels .. _fileConfig file format: https://docs.python.org/2/library/logging.config.html#configuration-file-format