galaxy.jobs.metrics.instrumenters package¶
Submodules¶
galaxy.jobs.metrics.instrumenters.collectl module¶
The module describes the collectl
job metrics plugin.
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class
galaxy.jobs.metrics.instrumenters.collectl.
CollectlPlugin
(**kwargs)[source]¶ Bases:
galaxy.jobs.metrics.instrumenters.InstrumentPlugin
Run collectl along with job to capture system and/or process data according to specified collectl subsystems.
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formatter
= <galaxy.jobs.metrics.instrumenters.collectl.CollectlFormatter object>¶
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job_properties
(job_id, job_directory)[source]¶ 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.
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plugin_type
= 'collectl'¶
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galaxy.jobs.metrics.instrumenters.core module¶
The module describes the core
job metrics plugin.
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class
galaxy.jobs.metrics.instrumenters.core.
CorePlugin
(**kwargs)[source]¶ Bases:
galaxy.jobs.metrics.instrumenters.InstrumentPlugin
Simple plugin that collects data without external dependencies. In particular it currently collects value set for Galaxy slots.
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formatter
= <galaxy.jobs.metrics.instrumenters.core.CorePluginFormatter object>¶
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job_properties
(job_id, job_directory)[source]¶ 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.
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plugin_type
= 'core'¶
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galaxy.jobs.metrics.instrumenters.cpuinfo module¶
The module describes the cpuinfo
job metrics plugin.
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class
galaxy.jobs.metrics.instrumenters.cpuinfo.
CpuInfoPlugin
(**kwargs)[source]¶ Bases:
galaxy.jobs.metrics.instrumenters.InstrumentPlugin
Gather information about processor configuration from /proc/cpuinfo. Linux only.
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formatter
= <galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoFormatter object>¶
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job_properties
(job_id, job_directory)[source]¶ 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.
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plugin_type
= 'cpuinfo'¶
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galaxy.jobs.metrics.instrumenters.env module¶
The module describes the env
job metrics plugin.
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class
galaxy.jobs.metrics.instrumenters.env.
EnvPlugin
(**kwargs)[source]¶ Bases:
galaxy.jobs.metrics.instrumenters.InstrumentPlugin
Instrumentation plugin capable of recording all or specific environment variables for a job at runtime.
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formatter
= <galaxy.jobs.metrics.instrumenters.env.EnvFormatter object>¶
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job_properties
(job_id, job_directory)[source]¶ Recover environment variables dumped out on compute server and filter out specific variables if needed.
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plugin_type
= 'env'¶
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galaxy.jobs.metrics.instrumenters.meminfo module¶
The module describes the meminfo
job metrics plugin.
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class
galaxy.jobs.metrics.instrumenters.meminfo.
MemInfoPlugin
(**kwargs)[source]¶ Bases:
galaxy.jobs.metrics.instrumenters.InstrumentPlugin
Gather information about processor configuration from /proc/cpuinfo. Linux only.
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formatter
= <galaxy.jobs.metrics.instrumenters.meminfo.MemInfoFormatter object>¶
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job_properties
(job_id, job_directory)[source]¶ 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.
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plugin_type
= 'meminfo'¶
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galaxy.jobs.metrics.instrumenters.uname module¶
The module describes the uname
job metrics plugin.
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class
galaxy.jobs.metrics.instrumenters.uname.
UnamePlugin
(**kwargs)[source]¶ Bases:
galaxy.jobs.metrics.instrumenters.InstrumentPlugin
Use uname to gather operating system information about remote system job is running on. Linux only.
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formatter
= <galaxy.jobs.metrics.instrumenters.uname.UnameFormatter object>¶
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job_properties
(job_id, job_directory)[source]¶ 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.
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plugin_type
= 'uname'¶
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Module contents¶
This module describes the abstract interface for InstrumentPlugin
.
These are responsible for collecting and formatting a coherent set of metrics.
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class
galaxy.jobs.metrics.instrumenters.
InstrumentPlugin
[source]¶ Bases:
object
Describes how to instrument job scripts and retrieve collected metrics.
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formatter
= <galaxy.jobs.metrics.formatting.JobMetricFormatter object>¶
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job_properties
(job_id, job_directory)[source]¶ 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.
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plugin_type
¶ Short string providing labelling this plugin
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