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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, job_directory)[source]
static from_file(plugin_classes, conf_file, **kwargs) → JobInstrumenterI[source]
static from_dict(plugin_classes, conf_dict, **kwargs) → JobInstrumenterI[source]
class galaxy.job_metrics.Safety(value)[source]

Bases: Enum

An enumeration.

UNSAFE = 2
POTENTIALLY_SENSITVE = 4
SAFE = 6

Subpackages

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: NamedTuple

title: str

Alias for field number 0

value: str

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: str, value: Any) → FormattedMetric | None[source]

Render a metric for display, or None to record it without displaying it.

Returning None is how a plugin says “collected, but this particular value is not worth showing” – a metric that is uninteresting at some values and interesting at others. Safety levels are the other way to keep a metric out of the UI, but they decide per metric name rather than per value.

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