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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Go to the source code of this file.
Functions | |
| tripal_core_drush_help ($command) | |
| tripal_core_drush_command () | |
| drush_tripal_core_tripal_jobs_launch ($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_tripal_node_sync ($module) | |
| drush_tripal_core_tripal_node_clean ($module) | |
Contains function relating to drush-integration of this module.
Definition in file tripal_core.drush.inc.
| drush_tripal_core_tripal_chado_version | ( | ) |
Returns the current version of chado
Definition at line 285 of file tripal_core.drush.inc.
{
$version = tripal_core_get_chado_version();
drush_print('Current Chado Version: '.$version);
}
| drush_tripal_core_tripal_chadotable_desc | ( | $ | table_name | ) |
Returns the Tripal Schema API Description of the given table
| $table_name | The name of the table to return the description of |
Definition at line 296 of file tripal_core.drush.inc.
{
$section = drush_get_option('section');
drush_print("Schema API Description for $table_name:");
$desc = tripal_core_get_chado_table_schema($table_name);
if (!empty($section)) {
drush_print("$section = ".print_r($desc[$section],TRUE));
}
else {
drush_print(print_r($desc,TRUE));
}
}
| drush_tripal_core_tripal_jobs_current | ( | ) |
Prints details about the current running job
NOTE: The following code is executed when 'drush trpjob-curr' or 'drush tripal-current-job' is called
Definition at line 220 of file tripal_core.drush.inc.
{
$sql = "SELECT * FROM {tripal_jobs} TJ ".
"WHERE TJ.end_time IS NULL and NOT TJ.start_time IS NULL ";
$jobs = db_query($sql);
while ($job = db_fetch_object($jobs)) {
$job_pid = $job->pid;
$output = "Name: " . $job->job_name . "\n"
."Submitted: " . date(DATE_RFC822, $job->submit_date) . "\n"
."Started: " . date(DATE_RFC822, $job->start_time) . "\n"
."Module: " . $job->modulename . "\n"
."Callback: " . $job->callback . "\n"
."Process ID: " . $job->pid . "\n"
."Progress: " . $job->progress . "%\n";
drush_print($output);
}
if (!$job_pid) {
drush_print('There are currently no running jobs.');
}
//log to the command line with an OK status
drush_log('Running tripal-current-job', 'ok');
}
| drush_tripal_core_tripal_jobs_launch | ( | $ | username | ) |
Executes jobs in the Tripal Jobs Queue
NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
Definition at line 176 of file tripal_core.drush.inc.
{
$parallel = drush_get_option('parallel');
$job_id = drush_get_option('job_id');
if ($username) {
global $user;
$user = user_load(array('name' => $username));
}
else {
drush_print('ERROR: Please provide a username for running this job.');
return;
}
if ($parallel) {
drush_print("Tripal Job Launcher (in parallel)");
drush_print("Running as user '$username'");
drush_print("-------------------");
tripal_jobs_launch($parallel, $job_id);
}
else {
drush_print("Tripal Job Launcher");
drush_print("Running as user '$username'");
drush_print("-------------------");
tripal_jobs_launch(0, $job_id);
}
}
| drush_tripal_core_tripal_jobs_rerun | ( | $ | username, |
| $ | job_id | ||
| ) |
Executes jobs in the Tripal Jobs Queue
NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
Definition at line 208 of file tripal_core.drush.inc.
{
$new_job_id = tripal_jobs_rerun($job_id, FALSE);
drush_tripal_core_tripal_jobs_launch($username, $new_job_id);
}
| drush_tripal_core_tripal_node_clean | ( | $ | module | ) |
Clean-up orphaned Drupal nodes and chado records.
| $module | The name of a module with nodes associated with it. For example, feature |
Definition at line 348 of file tripal_core.drush.inc.
{
tripal_core_clean_orphaned_nodes($module, 0);
}| drush_tripal_core_tripal_node_sync | ( | $ | module | ) |
Sync's chado records with drupal creating nodes for the given chado-centric module.
| $module | The name of a module with nodes associated with it. For example, feature |
Definition at line 316 of file tripal_core.drush.inc.
{
switch($module) {
case 'analysis':
call_user_func('tripal_analysis_sync_analyses');
break;
case 'feature':
call_user_func('tripal_feature_sync_features');
break;
case 'featuremap':
call_user_func('tripal_featuremap_sync_featuremaps');
break;
case 'library':
call_user_func('tripal_library_sync_libraries');
break;
case 'organism':
call_user_func('tripal_organism_sync_organisms');
break;
case 'project':
call_user_func('tripal_project_sync_all_projects');
break;
case 'stock':
call_user_func('tripal_stock_sync_stocks');
break;
}
}
| drush_tripal_core_tripal_update_mview | ( | ) |
Updates the specified materialized view
| $mview_id | The ID of the materialized view (tripal_mview.mview_id) |
| $table_name | The name of the table storing the materialized view (tripal_mview.mv_table) |
Note: Either $mview_id OR $table_name is required
Definition at line 252 of file tripal_core.drush.inc.
{
$mview_id = drush_get_option('mview_id');
$table_name = drush_get_option('table_name');
// Either table_name or mview is required
if (!$mview_id) {
if ($table_name) {
// if table_name supplied use that to get mview_id
$sql = "SELECT mview_id FROM {tripal_mviews} WHERE mv_table='%s'";
$r = db_fetch_object(db_query($sql, $table_name));
if (!$r->mview_id) {
drush_set_error('No Materialized View associated with that table_name.');
}
$mview_id=$r->mview_id;
}
else {
drush_set_error('Either mview_id OR table_name are required.');
}
}
drush_print('Updating the Materialized View with ID=' . $mview_id);
$status = tripal_update_mview($mview_id);
if ($status) {
drush_log('Materialized View Updated', 'ok');
}
else {
drush_set_error('Update failed.');
}
}
| tripal_core_drush_command | ( | ) |
Registers a drush command and constructs the full help for that command
Definition at line 43 of file tripal_core.drush.inc.
{
$items = array();
// Materialized Views
$items['tripal-mview-update'] = array(
// used by drush help
'description' => dt('Updates the specified materialized view.'),
'arguments' => array(
'mview_id' => dt('The ID of the materialized view to update'),
'table_name' => dt('The name of the materialized view table to update.'),
),
'examples' => array(
'By Materialized View ID' => 'drush tripal-update-mview --mview_id=5',
'By Table Name' => 'drush tripal-update-mview --table_name=organism_feature_count'
),
// supply options
'options' => array(
'mview_id',
'table_name'
),
'aliases' => array('trpmv-up', 'tripal-update-mview')
);
// Jobs
$items['tripal-jobs-current'] = array(
'description' => dt('Returns details about the currently running tripal job including percent complete.'),
'arguments' => array(
),
'examples' => array(
'Standard example' => 'drush tripal-jobs-current',
),
'aliases' => array('trpjob-cur','tripal-current-job'),
);
$items['tripal-jobs-launch'] = array(
// used by drush help
'description' => dt('Lauches any jobs waiting in the queue.'),
'examples' => array(
'Normal Job' => 'drush tripal-jobs-launch admin',
'Parallel Job' => 'drush tripal-jobs-launch admin --parallel=1'
),
'arguments' => array(
'user' => dt('The Drupal username under which the job should be run. The permissions for this user will be used.'),
),
// supply options
'options' => array(
'parallel' => dt('Normally jobs are executed one at a time. But if you are certain no conflicts will occur with other currently running jobs you may set this argument to a value of 1 to make the job run in parallel with other running jobs.'),
'job_id' => dt('Provide a job_id to run a specific job. Only jobs that have not been run already can be used'),
),
'aliases' => array('trpjob-run','tripal-launch-jobs')
);
$items['tripal-jobs-rerun'] = array(
// used by drush help
'description' => dt('Rerun any job in the queue.'),
'examples' => array(
'Normal Job' => 'drush tripal-jobs-rerun admin 2',
'Parallel Job' => 'drush tripal-jobs-rerun admin 2 --parallel=1'
),
'arguments' => array(
'user' => dt('The Drupal username under which the job should be run. The permissions for this user will be used.'),
'job_id' => dt('The job ID to run.'),
),
// supply options
'options' => array(
'parallel' => dt('Normally jobs are executed one at a time. But if you are certain no conflicts will occur with other currently running jobs you may set this argument to a value of 1 to make the job run in parallel with other running jobs.'),
),
'aliases' => array('trpjob-rerun','tripal-rerun-job')
);
// Chado-specific
$items['tripal-chado-version'] = array(
// used by drush help
'description' => dt('Returns the current version of chado associated with this drupal site.'),
'arguments' => array(
),
'examples' => array(
'Standard Example' => 'drush tripal-chado-version',
),
'aliases' => array('trpchado-ver')
);
$items['tripal-chadotable-desc'] = array(
// used by drush help
'description' => dt('Returns the table description as specified in the Tripal Schema API for the supplied table.'),
'arguments' => array(
'table_name' => dt('The name of the chado table.'),
),
'examples' => array(
'By Table Name' => 'drush tripal-chadotable-desc --table_name=feature'
),
// supply options
'options' => array(
'section' => dt('Only return the specified section of the schema table description. Possible sections include: description, fields, primary key, unique keys, foreign keys, indexes, referring_tables.'),
),
'aliases' => array('trpschema-tbl')
);
// Tripal Node-Module Specific
$items['tripal-node-sync'] = array(
// used by drush help
'description' => dt('Sync\'s chado records with drupal creating nodes for the given chado-centric module.'),
'arguments' => array(
'module' => dt('The name of the chado-centric module to sync.'),
),
'examples' => array(
'By Module' => 'drush tripal-node-sync feature'
),
// supply options
'options' => array(
),
'aliases' => array('trpnode-sync')
);
$items['tripal-node-clean'] = array(
// used by drush help
'description' => dt('Clean-up orphaned Drupal nodes and chado records.'),
'arguments' => array(
'module' => dt('The name of the chado-centric module to clean-up.'),
),
'examples' => array(
'By Table Name' => 'drush tripal-node-clean feature'
),
// supply options
'options' => array(
),
'aliases' => array('trpnode-cln')
);
return $items;
}
| tripal_core_drush_help | ( | $ | command | ) |
Describes each drush command implemented by the module
Definition at line 14 of file tripal_core.drush.inc.
{
switch ($command) {
// Tripal Materialized Views
case 'drush:tripal-update-mview':
return dt('Updates the specified materialized view.');
// Tripal Jobs
case 'drush:tripal-launch-jobs':
return dt('Launches any Tripal jobs waiting in the queue.');
case 'drush:tripal-current-job':
return dt('Returns details about the currently running tripal job including percent complete.');
case 'drush:tripal-rerun-job':
return dt('Rerun any tripal job in the queue.');
// Chado-specific
case 'drush:tripal-chado-version':
return dt('Returns the current version of chado associated with this drupal site.');
case 'drush:tripal-chadotable-desc':
return dt('Returns the table description as specified in the Tripal Schema API for the supplied table.');
}
}
1.7.4