Tripal Drush Integration

Functions
	tripal_core_drush_help ($command)
	tripal_core_drush_command ()
	drush_tripal_core_set_user ($username)
	drush_tripal_core_tripal_jobs_launch ($username)
	drush_tripal_core_tripal_jobs_rerun ($username, $job_id)
	drush_tripal_core_tripal_jobs_current ()
	drush_tripal_core_tripal_update_mview ()
	drush_tripal_core_tripal_chado_version ()
	drush_tripal_core_tripal_chadotable_desc ($table_name)
	drush_tripal_core_trp_clean_nodes ()
	drush_tripal_core_tripal_node_clean ($module)
	drush_tripal_chado_trp_clean_nodes ()
	tripal_feature_drush_help ($command)
	tripal_feature_drush_command ()
	drush_tripal_feature_tripal_get_sequence ()
	drush_tripal_feature_sync ()
	tripal_phylogeny_drush_help ($command)
	tripal_phylogeny_drush_command ()
	drush_tripal_phylogeny_trp_insert_phylotree ()
	drush_tripal_phylogeny_trp_delete_phylotree ()
	tripal_pub_drush_help ($command)
	tripal_pub_drush_command ()
	drush_tripal_pub_tripal_pubs_import ()
	drush_tripal_pub_tripal_pubs_update ()
	tripal_drush_help ($command)
	tripal_drush_command ()
	drush_tripal_set_user ($username)
	drush_tripal_trp_run_jobs_install ($username)
	drush_tripal_trp_run_jobs ()
	drush_tripal_trp_rerun_job ()
	drush_tripal_trp_get_currjob ()
	drush_tripal_trp_prepare_chado ()
	drush_tripal_trp_set_permissions ()
	drush_tripal_trp_version ()
	tripal_chado_drush_help ($command)
	tripal_chado_drush_command ()
	drush_tripal_chado_trp_import_pubs ()
	drush_tripal_chado_trp_update_pubs ()
	drush_tripal_chado_set_user ($username)
	drush_tripal_chado_trp_refresh_mview ()
	drush_tripal_chado_trp_get_cversion ()
	drush_tripal_chado_trp_get_table ()

Detailed Description

Contains function relating to drush-integration of various tripal modules.

Function Documentation

drush_tripal_chado_set_user()

drush_tripal_chado_set_user

(

$username

)

Set the user to run a drush job.

drush_tripal_chado_trp_clean_nodes()

drush_tripal_chado_trp_clean_nodes

(

)

Clean-up orphaned Drupal nodes and chado records.

drush_tripal_chado_trp_get_cversion()

drush_tripal_chado_trp_get_cversion

(

)

Returns the current version of chado.

drush_tripal_chado_trp_get_table()

drush_tripal_chado_trp_get_table

(

)

Returns the Tripal Schema API Description of the given table

drush_tripal_chado_trp_import_pubs()

drush_tripal_chado_trp_import_pubs

(

)

Imports publications into Chado

drush_tripal_chado_trp_refresh_mview()

drush_tripal_chado_trp_refresh_mview

(

)

Updates the specified materialized view

drush_tripal_chado_trp_update_pubs()

drush_tripal_chado_trp_update_pubs

(

)

Imports publications into Chado

drush_tripal_core_set_user()

drush_tripal_core_set_user

(

$username

)

Set the user to run a drush job.

drush_tripal_core_tripal_chado_version()

drush_tripal_core_tripal_chado_version

(

)

DEPRECATED. Returns the current version of chado.

drush_tripal_core_tripal_chadotable_desc()

drush_tripal_core_tripal_chadotable_desc

(

$table_name

)

DEPRECATED. Returns the Tripal Schema API Description of the given table.

Parameters

$table_name

The name of the table to return the description of

drush_tripal_core_tripal_jobs_current()

drush_tripal_core_tripal_jobs_current

(

)

DEPRECATED. Prints details about the current running job.

Executed when 'drush trpjob-curr' or 'drush tripal-current-job' is called.

drush_tripal_core_tripal_jobs_launch()

drush_tripal_core_tripal_jobs_launch

(

$username

)

DEPRECATED. Executes jobs in the Tripal Jobs Queue.

Executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called.

drush_tripal_core_tripal_jobs_rerun()

drush_tripal_core_tripal_jobs_rerun	(		$username,
			$job_id
	)

DEPRECATED. Executes jobs in the Tripal Jobs Queue.

Executed when 'drush tripal-jobs-rerun' is called.

drush_tripal_core_tripal_node_clean()

drush_tripal_core_tripal_node_clean

(

$module

)

DEPRECATED. Clean-up orphaned Drupal nodes and chado records.

Parameters

$module

The name of a module with nodes associated with it. For example, feature

drush_tripal_core_tripal_update_mview()

drush_tripal_core_tripal_update_mview

(

)

DEPRECATED. Updates the specified materialized view.

drush_tripal_core_trp_clean_nodes()

drush_tripal_core_trp_clean_nodes

(

)

Clean-up orphaned Drupal nodes and chado records.

drush_tripal_feature_sync()

drush_tripal_feature_sync

(

)

Sync Chado Features with Drupal (ie: create nodes)

drush_tripal_feature_tripal_get_sequence()

drush_tripal_feature_tripal_get_sequence

(

)

Retrieves the sequence of the indicated features

drush_tripal_phylogeny_trp_delete_phylotree()

drush_tripal_phylogeny_trp_delete_phylotree

(

)

Deletes a phylotree record.

Executed when 'drush trp-delete-phylotree' is called.

drush_tripal_phylogeny_trp_insert_phylotree()

drush_tripal_phylogeny_trp_insert_phylotree

(

)

Inserts a phylotree record.

Executed when 'drush trp-insert-phylotree' is called.

drush_tripal_pub_tripal_pubs_import()

drush_tripal_pub_tripal_pubs_import

(

)

DEPRECATED. Imports publications into Chado

drush_tripal_pub_tripal_pubs_update()

drush_tripal_pub_tripal_pubs_update

(

)

DEPRECATED. Imports publications into Chado

drush_tripal_set_user()

drush_tripal_set_user

(

$username

)

Set the user to run a drush job.

drush_tripal_trp_get_currjob()

drush_tripal_trp_get_currjob

(

)

Prints details about the current running job.

Executed when 'drush trp-get-currjob' is called.

drush_tripal_trp_prepare_chado()

drush_tripal_trp_prepare_chado

(

)

Prepares content types on the site after chado installation.

Executed when 'drush trp-prepare-chado' is called.

drush_tripal_trp_rerun_job()

drush_tripal_trp_rerun_job

(

)

Executes jobs in the Tripal Jobs Queue.

Executed when 'drush trp-rerun-job' is called.

drush_tripal_trp_run_jobs()

drush_tripal_trp_run_jobs

(

)

Executes jobs in the Tripal Jobs Queue.

Executed when 'drush trp-run-job' is called.

drush_tripal_trp_run_jobs_install()

drush_tripal_trp_run_jobs_install

(

$username

)

Executes jobs in the Tripal Jobs Queue.

Executed when 'drush trp-run-job' is called.

drush_tripal_trp_set_permissions()

drush_tripal_trp_set_permissions

(

)

Sets permissions for the content types on the site.

Executed when 'drush trp-set-permissions' is called.

drush_tripal_trp_version()

drush_tripal_trp_version

(

)

Returns the current version of Tripal

Executed when 'drush trp-version' is called.

Returns

string

tripal_chado_drush_command()

tripal_chado_drush_command

(

)

Registers a drush command and constructs the full help for that command.

Returns

And array of command descriptions

tripal_chado_drush_help()

tripal_chado_drush_help

(

$command

)

Describes each drush command implemented by the module

Returns

The first line of description when executing the help for a given command

tripal_core_drush_command()

tripal_core_drush_command

(

)

Registers a drush command and constructs the full help for that command.

Returns

And array of command descriptions

tripal_core_drush_help()

tripal_core_drush_help

(

$command

)

Describes each drush command implemented by the module

Returns

The first line of description when executing the help for a given command

tripal_drush_command()

tripal_drush_command

(

)

Registers a drush command and constructs the full help for that command.

Returns

And array of command descriptions

tripal_drush_help()

tripal_drush_help

(

$command

)

Describes each drush command implemented by the module

Returns

The first line of description when executing the help for a given command

tripal_feature_drush_command()

tripal_feature_drush_command

(

)

Registers a drush command and constructs the full help for that command

Returns

And array of command descriptions

tripal_feature_drush_help()

tripal_feature_drush_help

(

$command

)

Describes each drush command implemented by the module

Returns

The first line of description when executing the help for a given command

tripal_phylogeny_drush_command()

tripal_phylogeny_drush_command

(

)

Registers a drush command and constructs the full help for that command

Returns

And array of command descriptions

tripal_phylogeny_drush_help()

tripal_phylogeny_drush_help

(

$command

)

Describes each drush command implemented by the module

Returns

The first line of description when executing the help for a given command

tripal_pub_drush_command()

tripal_pub_drush_command

(

)

Registers a drush command and constructs the full help for that command

Returns

And array of command descriptions

tripal_pub_drush_help()

tripal_pub_drush_help

(

$command

)

Describes each drush command implemented by the module

Returns

The first line of description when executing the help for a given command