galaxy.jobs.metrics.instrumenters package

Submodules

galaxy.jobs.metrics.instrumenters.collectl module

The module describes the collectl job metrics plugin.

class galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin(**kwargs)

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Run collectl along with job to capture system and/or process data according to specified collectl subsystems.

formatter = <galaxy.jobs.metrics.instrumenters.collectl.CollectlFormatter object>

job_properties(job_id, job_directory)

Collect properties for this plugin from specified job directory. This method will run on the Galaxy server and can assume files created in job_directory with pre_execute_instrument and post_execute_instrument are available.

plugin_type = 'collectl'

post_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server after the tool defined command is ran.

pre_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server prior to the job running.

galaxy.jobs.metrics.instrumenters.core module

The module describes the core job metrics plugin.

class galaxy.jobs.metrics.instrumenters.core.CorePlugin(**kwargs)

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Simple plugin that collects data without external dependencies. In particular it currently collects value set for Galaxy slots.

formatter = <galaxy.jobs.metrics.instrumenters.core.CorePluginFormatter object>

job_properties(job_id, job_directory)

Collect properties for this plugin from specified job directory. This method will run on the Galaxy server and can assume files created in job_directory with pre_execute_instrument and post_execute_instrument are available.

plugin_type = 'core'

post_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server after the tool defined command is ran.

pre_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server prior to the job running.

galaxy.jobs.metrics.instrumenters.cpuinfo module

The module describes the cpuinfo job metrics plugin.

class galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin(**kwargs)

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Gather information about processor configuration from /proc/cpuinfo. Linux only.

formatter = <galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoFormatter object>

job_properties(job_id, job_directory)

Collect properties for this plugin from specified job directory. This method will run on the Galaxy server and can assume files created in job_directory with pre_execute_instrument and post_execute_instrument are available.

plugin_type = 'cpuinfo'

pre_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server prior to the job running.

galaxy.jobs.metrics.instrumenters.env module

The module describes the env job metrics plugin.

class galaxy.jobs.metrics.instrumenters.env.EnvPlugin(**kwargs)

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Instrumentation plugin capable of recording all or specific environment variables for a job at runtime.

formatter = <galaxy.jobs.metrics.instrumenters.env.EnvFormatter object>

job_properties(job_id, job_directory)

Recover environment variables dumped out on compute server and filter out specific variables if needed.

plugin_type = 'env'

post_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server after the tool defined command is ran.

pre_execute_instrument(job_directory)

Use env to dump all environment variables to a file.

galaxy.jobs.metrics.instrumenters.meminfo module

The module describes the meminfo job metrics plugin.

class galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin(**kwargs)

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Gather information about processor configuration from /proc/cpuinfo. Linux only.

formatter = <galaxy.jobs.metrics.instrumenters.meminfo.MemInfoFormatter object>

job_properties(job_id, job_directory)

Collect properties for this plugin from specified job directory. This method will run on the Galaxy server and can assume files created in job_directory with pre_execute_instrument and post_execute_instrument are available.

plugin_type = 'meminfo'

pre_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server prior to the job running.

galaxy.jobs.metrics.instrumenters.uname module

The module describes the uname job metrics plugin.

class galaxy.jobs.metrics.instrumenters.uname.UnamePlugin(**kwargs)

Bases: galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Use uname to gather operating system information about remote system job is running on. Linux only.

formatter = <galaxy.jobs.metrics.instrumenters.uname.UnameFormatter object>

job_properties(job_id, job_directory)

Collect properties for this plugin from specified job directory. This method will run on the Galaxy server and can assume files created in job_directory with pre_execute_instrument and post_execute_instrument are available.

plugin_type = 'uname'

pre_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server prior to the job running.

Module contents

This module describes the abstract interface for InstrumentPlugin.

These are responsible for collecting and formatting a coherent set of metrics.

class galaxy.jobs.metrics.instrumenters.InstrumentPlugin

Bases: object

Describes how to instrument job scripts and retrieve collected metrics.

formatter = <galaxy.jobs.metrics.formatting.JobMetricFormatter object>

job_properties(job_id, job_directory)

Collect properties for this plugin from specified job directory. This method will run on the Galaxy server and can assume files created in job_directory with pre_execute_instrument and post_execute_instrument are available.

plugin_type

Short string providing labelling this plugin

post_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server after the tool defined command is ran.

pre_execute_instrument(job_directory)

Optionally return one or more commands to instrument job. These commands will be executed on the compute server prior to the job running.