Unit tests to exercise job and task mapping.
Layout models and mapping for a job metrics plugin framework.
Implement plugin framework for collecting data about runtime job execution.
An example job_metrics_conf.xml.sample is included that describes which plugins are enabled and how they are configured. This will be updated for each new plugin added. By default not instrumentation or data collection occurs - but if a job_metrics.xml file is present it will serve as the default for all job destination. Additionally, individual job destinations may disable, load a different job metrics file, or define metrics directly in job_conf.xml in an embedded fashion. See comment at top of job_metrics_conf.xml for more information.

This commit include an initial plugin (named 'core') to demonstrate the framework and capture the highest priority data - namely the number of cores allocated to the job and the runtime of the job on the cluster. These two pieces of information alone should provide a much clearer picture of what Galaxy is actually allocating cluster compute cycles to.

Current limitations - This only works with job runners utilizing the job script module and the LWR (it utilizes the job script module on the remote server), hence it won't yet work with...

 - Local job runner - I do have a downstream fork of Galaxy where I have reworked the local job runner to use the common job script template.

    https://github.com/jmchilton/galaxy-central/commits/local_job_script
    https://github.com/jmchilton/galaxy-central/commit/949db2cd14c7191cedf1febeb5f4a2f53123123e

 - CLI runner - CLI runner needs to be reworked to use the job script module anyway so GALAXY_SLOTS works - the LWR version of the CLI runner uses the job script module - this work just needs to be back ported to Galaxy.

If a job_metrics_conf.xml is present and some jobs route to the above destinations - the jobs won't fail but annoying errors will appear in the logs. Simply attach a 'metrics="off"' those these specific job destinations to disable any attempt to use metrics for these jobs and disable these errors.
Implement env job instrumentation plugin.
The 'env' plugin can collect all environment variables set at the time of job execution or just targetted environment variables. Environment variables like PATH or PYTHONPATH may be useful for debugging and environment variables such as HOSTNAME, PID, and DRM-specific variables like SLURM_JOB_ID could be useful for integrating Galaxy's view of jobs and users with external accounting/metric systems. See job_metrics.xml.sample for how to configure environment variable collection.
Implement cpuinfo job instrumentation plugin.
Implement meminfo job instrumentation plugin.
Implement uname job instrumentation plugin.
Gathers information on operating system configuration job is run on - linux only.
Implement collectl job instrumentation plugin.
This changeset documentation is an abridged form fo the documentation included in job_metrics_conf.xml.sample.

Collectl (http://collectl.sourceforge.net/) is a powerful monitoring utility capable of gathering numerous system and process level statistics of running applications. The Galaxy collectl job metrics plugin by default will grab a variety of process level metrics aggregated across all processes corresponding to a job, this behavior is highly customiziable - both using the attributes documented below or simply hacking up the code in lib/galaxy/jobs/metrics.

Warning: In order to use this plugin collectl must be available on the compute server the job runs on and on the local Galaxy server as well (unless in this latter case summarize_process_data is set to False).

Attributes (the follow describes attributes that can be used with the collectl job metrics element above to modify its behavior).

'summarize_process_data': Boolean indicating whether to run collectl
     in playback mode after jobs complete and gather process level
     statistics for the job run. These statistics can be customized
     with the 'process_statistics' attribute. (defaults to True)

'saved_logs_path': If set (it is off by default), all collectl logs
     will be saved to the specified path after jobs complete. These
     logs can later be replayed using collectl offline to generate
     full time-series data corresponding to a job run.

'subsystems': Comma separated list of collectl subystems to collect
     data for. Plugin doesn't currently expose all of them or offer
     summary data for any of them except 'process' but extensions
     would be welcome. May seem pointless to include subsystems beside
     process since they won't be processed online by Galaxy - but if
     'saved_logs_path' these files can be played back at anytime.

     Available subsystems - 'process', 'cpu', 'memory', 'network',
      'disk', 'network'. (Default 'process').

'process_statistics': If 'summarize_process_data' this attribute can
     be specified as a comma separated list to override the statistics
     that are gathered. Each statistics is of the for X_Y where X if
     one of 'min', 'max', 'count', 'avg', or 'sum' and Y is a value
     from 'S', 'VmSize', 'VmLck', 'VmRSS', 'VmData', 'VmStk', 'VmExe',
     'VmLib', 'CPU', 'SysT', 'UsrT', 'PCT', 'AccumT' 'WKB', 'RKBC',
     'WKBC', 'RSYS', 'WSYS', 'CNCL', 'MajF', 'MinF'. Consult
     lib/galaxy/jobs/metrics/collectl/processes.py for more details on
     what each of these resource types means.

     Defaults to 'max_VmSize,avg_VmSize,max_VmRSS,avg_VmRSS,sum_SysT,sum_UsrT,max_PCT avg_PCT,max_AccumT,sum_RSYS,sum_WSYS'
     as variety of statistics roughly describing CPU and memory usage of
     the program and VERY ROUGHLY describing I/O consumption.
Bugfix for multiple input data parameters.

Workflow editor would drop all but one multiple input data connections if and when the parameter itself was nested in repeats/conds.
rename biostar menu link
Fix library template functional tests. Revert change to user info tests that was breaking library template tests.
Merge stable changes into default.
History/HDA UI: pass allow_user_dataset_purge from Galaxy.config to history-panel and hda-edit and respect by not rendering purge controls if false
Unit tests for job conf parsing.
Update advanced job sample to fix "bugs" discovered during testing limit parsing.
Merge pull request #352.
Job metrics - ensure all text values are unicode before persisting.

Gets rid of the following warning: "SAWarning: Unicode type received non-unicode bind param value.".
Fix test_job_configuration.py for job metrics PR.

Still need to go in and actually write some tests for the nested parsing that can happen.
Merged in jmchilton/galaxy-central-fork-1/stable (pull request #373)

[stable] Bugfix for multiple input data parameters.
Merge stable.
Visualization framework: remove deprecated 'template_root' element left from when visualizations were loaded from galaxy's template directory