galaxy.job_metrics package¶

This module defines the job metrics collection framework for Galaxy jobs.

The framework consists of two parts - the JobMetrics class and individual JobInstrumenter plugins.

A JobMetrics object reads any number of plugins from a configuration source such as an XML file, a YAML file, or a dictionary.

Each JobInstrumenter plugin object describes how to inject a bits of shell code into a job scripts (before and after tool commands run) and then collect the output of these from a job directory.

class galaxy.job_metrics.JobInstrumenter(plugin_classes, plugins_source, **kwargs)[source]¶

Bases: JobInstrumenterI

__init__(plugin_classes, plugins_source, **kwargs)[source]¶

get_configured_plugin(plugin_type: str)[source]¶

pre_execute_commands(job_directory)[source]¶

post_execute_commands(job_directory)[source]¶

collect_properties(job_id, job_directory)[source]¶

static from_file(plugin_classes, conf_file, **kwargs) → JobInstrumenterI[source]¶

class galaxy.job_metrics.Safety(value)[source]¶

Bases: Enum

An enumeration.

UNSAFE = 2¶

POTENTIALLY_SENSITVE = 4¶

SAFE = 6¶

Subpackages¶

galaxy.job_metrics.instrumenters package

Submodules¶

galaxy.job_metrics.formatting module¶

Utilities related to formatting job metrics for human consumption.

class galaxy.job_metrics.formatting.FormattedMetric(title, value)[source]¶

Bases: tuple

property title¶: Alias for field number 0

property value¶: Alias for field number 1

class galaxy.job_metrics.formatting.JobMetricFormatter[source]¶

Bases: object

Format job metric key-value pairs for human consumption in Web UI.

format(key: Any, value: Any) → FormattedMetric[source]¶

galaxy.job_metrics.formatting.seconds_to_str(value: int) → str[source]¶: Convert seconds to a simple simple string describing the amount of time.

galaxy.job_metrics.safety module¶

class galaxy.job_metrics.safety.Safety(value)[source]¶

Bases: Enum

An enumeration.

UNSAFE = 2¶

POTENTIALLY_SENSITVE = 4¶

SAFE = 6¶