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Logging

py4cytoscape logging is based on the Python logging package, which is based on Java's logging framework. py4cytoscape emits log entries in SysLog format. For example:

[INFO] py4...S:  ǀHTTP DELETE(http://localhost:1234/v1/networks)
[INFO] py4...S:  ǀOK[200]

[INFO] is the priority level.

py4...S the name of the py4cytoscape package.

The count of | indicates the nesting level of the currently executing code, where || indicates log entries called from code at the | level.

The remainder of the message contains the logged information. In the example above, an HTTP DELETE call is logged along with the HTTP server's reply.

Logger configuration is available in the py4cytoscape_logger_settings.py module. py4cytoscape emits two independent logging streams: Summary (to the console) and Detail (to a file in the logs directory).

By default, Summary logging is the short form (priority INFO), which shows HTTP calls and results. You can disable Summary logging by setting _SUMMARY_LOG_LEVEL to NOTSET, and you can enable full logging by setting it to DEBUG.

By default, Detail logging is the long form (priority DEBUG), and is controlled by the _DETAIL_LOG_LEVEL setting.

Here is an example of Detail logging involving nested calls:

2020-06-06 15:29:55,721 [DEBUG] py4...: ǀCalling cytoscape_version_info(base_url='http://localhost:1234/v1')
2020-06-06 15:29:55,721 [DEBUG] py4...: ǀǀCalling cyrest_get('version', base_url='http://localhost:1234/v1')
2020-06-06 15:29:55,721 [DEBUG] py4...: ǀǀHTTP GET(http://localhost:1234/v1/version)
2020-06-06 15:29:55,737 [DEBUG] py4...: ǀǀOK[200], content: {"apiVersion":"v1","cytoscapeVersion":"3.9.0-SNAPSHOT"}
2020-06-06 15:29:55,738 [DEBUG] py4...: ǀǀReturning 'cyrest_get': {'apiVersion': 'v1', 'cytoscapeVersion': '3.9.0-SNAPSHOT'}
2020-06-06 15:29:55,738 [DEBUG] py4...: ǀReturning 'cytoscape_version_info': {'apiVersion': 'v1', 'cytoscapeVersion': '3.9.0-SNAPSHOT'}

py4cytoscape logs are stored in the logs directory relative to the Python workflow's current directory. The logs directory can be overridden by setting the PY4CYTOSCAPE_DETAIL_LOGGER environment variable. For example:

set PY4CYTOSCAPE_DETAIL_LOGGER_DIR=/tmp/p4clogs

Runtime Control

For convenience, Summary logging can be controlled using an environment variable or at execution time. By default, Summary logging is disabled, but can be enabled:

set PY4CYTOSCAPE_SUMMARY_LOGGER=True

At execution time, it can be enabled by calling set_summary_logger(). This is handy within a busy code block or when running in a Notebook environment. For example:

old_state = set_summary_logger(True)
  # ... make several py4cytoscape calls ...
set_summary_logger(old_state)