Logging Configuration¶

Overview¶

There are two ways in which you can configure logging for Galaxy servers:

Basic/automatic configuration with control over log level and log destination (standard output or a named log file).
More complex configuration using the Python logging module’s logging.config.dictConfig() or 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 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:

galaxy:
    log_level: LEVEL

Or if using galaxy.ini:

[app:main]
log_level = LEVEL

Where LEVEL is one of the logging levels documented in the logging module.

Logging to a file:

To change the log file name or location, use the $GALAXY_LOG environment variable like so:

$ 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 logging are available in Galaxy:

Two custom fields (aka Python 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 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 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 logging.config.dictConfig(). This section covers a few of the most common configurations as well as Galaxy’s customizations. Consult the 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 galaxy.config.LOGGING_CONFIG_DEFAULT constant and (in YAML) below:

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
    loggers:
      galaxy:
        handlers:
        - console
        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
      level: INFO
    version: 1

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.

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 server deployment scenarios are given below:

Fact	Application server
	Paste/webless	uWSGI web worker	uWSGI mule
`server_name`	`NAME` for `[server:<NAME>]` in `galaxy.ini`	`main`, but can be modified with `server_name` in `galaxy.yml`
`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:

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 logging.config.fileConfig() configuration method for advanced logging configuration. For example:

[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.