GalaxyJobs Class Reference

Public Member Functions
	__construct (GalaxyInstance $galaxy)
	buildForRerun ($params)
	inputs ($params)
	outputs ($params)
	show ($params)
	index ($params)
	create ()
	search ($params)

Constructor & Destructor Documentation

GalaxyJobs::__construct

(

GalaxyInstance

$galaxy

)

The Jobs constructor.

Parameters

GalaxyInstance

$galaxy

A GalaxyInstance object.

Returns

An instance of a Jobs object.

Member Function Documentation

GalaxyJobs::buildForRerun

(

$params

)

Retreive a tool input template populated with this job's information.

Corresponds to the Galaxy Api/path at: GET /api/jobs/{encoded_job_id}/build_for_rerun This function is suitable for rerunning or rendering parameters of the job.

Parameters

$params

An associative array containing the input parameters for this function. The following parameters are available:

• id: The job id of the job whose information to retreive. The job id can be ontained from this class's index() function.

Returns

An array containing ouput informaiton of the tool that has been built.

GalaxyJobs::create

(

)

This function is not implemented by its python counterpart

NOTE: Creating/submitting a job is actually run under tools.py in the Galaxy api

Returns

FALSE

GalaxyJobs::index

(

$params

)

Retreive a list of jobs for current user.

Corresponds to the Galaxy Api method/path: GET /api/jobs

Parameters

$params

An associative array containing the input parameters for this function. The following parameters are available:

• state: filter job search by any one of these conditions: (i) 'new' (ii) 'upload' (iii) 'waiting' (iv) 'queued' (v) 'running' (vi) 'ok' (vii) 'error' (viii) 'paused' (ix) 'deleted' (x) 'deleted_now'
• tool_ids: A list of tool ids that limit the search to include only those with given tool_ids. To find tool id's, please refer to this class's index() function.
• date_range_min: Limit the search of jobs updated after this date.
• date_range_max: Limit the search of jobs updated before this date.
• history_id: Limit listing of jobs to those that match history_id. To find the history id, please refer to the history class.

Returns

An array containing a list of all the jobs that matched the given parameters.

GalaxyJobs::inputs

(

$params

)

Retreive the input datasets created from the specified job.

Corresponds to the Galaxy Api/path at: GET/api/jobs/{encoded_job_id}/inputs

Parameters

$params

An associative array containing the input parameters for this function. The following parameters are available:

• job_id: The job id of the job whose information to retreive. The job id can be ontained from this class's index() function.

Returns

An array containing ouput informaiton of the job input.

GalaxyJobs::outputs

(

$params

)

Retreive the output datasets created from the specified job.

Corresponds to the Galaxy Api/path at: GET/api/jobs/{encoded_job_id}/inputs.

Parameters

$params

An associative array containing the input parameters for this function. The following parameters are available:

• job_id: The job id of the job whose information to retreive. The job id can be ontained from this class's index() function.

Returns

An array containing ouput informaiton of the job outputs.

GalaxyJobs::search

(

$params

)

Search for previously created jobs.

Corresponds to the Galaxy api/path at: POST /api/jobs/search

This method is designed to scan the list of previously run jobs and find records of jobs that had the exact some input parameters and datasets. This can be used to minimize, the amount of repeated work, and simplyrecycle the old results.

Parameters

$params

An associative array containing the input parameters for this function. The following parameters are available:

• tool_id: Required. The tool id to execute. To find the tool id, use the index function of this class.
• inputs: Required. An associative array of key/value pairs where valid keys are 'id' and 'src' and 'id' is a tool_id (e.g. wc_gnu), and 'src' is is optional but defaults to 'hda'. Alternatively, if multiple inputs are desired, this can be an array of associative arrays.
• state: Optional. The state of the job: 'running', 'queued', 'waiting', 'ok'.

  Returns

  An array of jobs matching the provided arguments.

GalaxyJobs::show

(

$params

)

Retreive information about a specific job

Corresponds to the Galaxy API function/path: GET /api/jobs/{job_id}

Parameters

$params

An associative array containing the input parameters for this function. The following parameters are available:

• job_id: The job that you would like to see. Please see the index() function in this class to obtain job ids.

Returns

An array containing information about the specified job.

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The documentation for this class was generated from the following file:

• Jobs.inc