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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)

Bases: JobInstrumenterI

__init__(plugin_classes, plugins_source, **kwargs)

get_configured_plugin(plugin_type: str)

pre_execute_commands(job_directory)

post_execute_commands(job_directory)

collect_properties(job_id, job_directory)

static from_file(plugin_classes, conf_file, **kwargs) → JobInstrumenterI

static from_dict(plugin_classes, conf_dict, **kwargs) → JobInstrumenterI

class galaxy.job_metrics.Safety(value)

Bases: Enum

An enumeration.

UNSAFE = 2

POTENTIALLY_SENSITVE = 4

SAFE = 6

Subpackages

• galaxy.job_metrics.instrumenters package
  • InstrumentPlugin
    • InstrumentPlugin.formatter
    • InstrumentPlugin.default_safety
    • InstrumentPlugin.plugin_type
    • InstrumentPlugin.pre_execute_instrument()
    • InstrumentPlugin.post_execute_instrument()
    • InstrumentPlugin.job_properties()
    • InstrumentPlugin.safety()
  • Submodules
  • galaxy.job_metrics.instrumenters.cgroup module
    • CgroupPlugin
      • CgroupPlugin.plugin_type
      • CgroupPlugin.formatter
      • CgroupPlugin.__init__()
      • CgroupPlugin.post_execute_instrument()
      • CgroupPlugin.job_properties()
  • galaxy.job_metrics.instrumenters.core module
    • CorePlugin
      • CorePlugin.plugin_type
      • CorePlugin.formatter
      • CorePlugin.default_safety
      • CorePlugin.__init__()
      • CorePlugin.pre_execute_instrument()
      • CorePlugin.post_execute_instrument()
      • CorePlugin.job_properties()
      • CorePlugin.get_container_file_path()
  • galaxy.job_metrics.instrumenters.cpuinfo module
    • CpuInfoPlugin
      • CpuInfoPlugin.plugin_type
      • CpuInfoPlugin.formatter
      • CpuInfoPlugin.__init__()
      • CpuInfoPlugin.pre_execute_instrument()
      • CpuInfoPlugin.job_properties()
  • galaxy.job_metrics.instrumenters.env module
    • EnvPlugin
      • EnvPlugin.plugin_type
      • EnvPlugin.formatter
      • EnvPlugin.default_safety
      • EnvPlugin.__init__()
      • EnvPlugin.variables
      • EnvPlugin.pre_execute_instrument()
      • EnvPlugin.post_execute_instrument()
      • EnvPlugin.job_properties()
  • galaxy.job_metrics.instrumenters.hostname module
    • HostnamePlugin
      • HostnamePlugin.plugin_type
      • HostnamePlugin.__init__()
      • HostnamePlugin.pre_execute_instrument()
      • HostnamePlugin.job_properties()
  • galaxy.job_metrics.instrumenters.meminfo module
    • MemInfoPlugin
      • MemInfoPlugin.plugin_type
      • MemInfoPlugin.formatter
      • MemInfoPlugin.default_safety
      • MemInfoPlugin.__init__()
      • MemInfoPlugin.pre_execute_instrument()
      • MemInfoPlugin.job_properties()
  • galaxy.job_metrics.instrumenters.uname module
    • UnamePlugin
      • UnamePlugin.plugin_type
      • UnamePlugin.formatter
      • UnamePlugin.__init__()
      • UnamePlugin.pre_execute_instrument()
      • UnamePlugin.job_properties()

Submodules

galaxy.job_metrics.formatting module

Utilities related to formatting job metrics for human consumption.

class galaxy.job_metrics.formatting.FormattedMetric(title, value)

Bases: NamedTuple

title: str

Alias for field number 0

value: str

Alias for field number 1

class galaxy.job_metrics.formatting.JobMetricFormatter

Bases: object

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

format(key: str, value: Any) → FormattedMetric

galaxy.job_metrics.formatting.seconds_to_str(value: int) → str

Convert seconds to a simple simple string describing the amount of time.

galaxy.job_metrics.safety module

class galaxy.job_metrics.safety.Safety(value)

Bases: Enum

An enumeration.

UNSAFE = 2

POTENTIALLY_SENSITVE = 4

SAFE = 6