<?php
/**
* @file
* The functions for the Tripal bulk loader.
*
* @defgroup tripal_bulk_loader Tripal Bulk Loader Module
* @ingroup tripal_modules
*/
include('includes/tripal_bulk_loader.loader.inc');
include('includes/tripal_bulk_loader.constants.inc');
// Administration
include('includes/tripal_bulk_loader.admin.inc');
include('includes/tripal_bulk_loader.admin.templates.inc');
// API
include('api/tripal_bulk_loader.api.templates.inc');
/**
* Implements hook_init
* Used to add stylesheets and javascript files to the header
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_init() {
// Add javascript and style sheet
drupal_add_css(drupal_get_path('theme', 'tripal') . '/css/tripal_bulk_loader.css');
drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_bulk_loader.js');
}
/**
* Implements hook_menu
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_menu() {
$items = array();
// Bulk Loading Job Node
$items['node/%node/constants/%/edit'] = array(
'title' => 'Edit Constant Set',
'description' => 'Edit a group of constants associated with the current bulk loader',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_edit_constant_set_form', 1, 3),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
$items['node/%node/constants/%/delete'] = array(
'title' => 'Delete Constant Set',
'description' => 'Delete a group of constants associated with the current bulk loader',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_delete_constant_set_form', 1, 3),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
// Admin pages -----------------
$items['admin/tripal/loaders/bulk'] = array(
'title' => 'Bulk Loader',
'description' => 'Templates for loading tab-delimited data',
'page callback' => 'tripal_bulk_loader_admin_jobs_listing',
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/loaders/bulk/configure'] = array(
'title' => 'Configure',
'description' => 'Configuration of global options related to bulk loading jobs',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_configuration_form'),
'access arguments' => array('administer tripal_bulk_loader'),
'weight' => 8,
'type' => MENU_LOCAL_TASK,
);
$items['admin/tripal/loaders/bulk/help'] = array(
'title' => 'Help',
'description' => "A description of the Tripal Bulk Loader module including a short description of it's usage.",
'page callback' => 'tripal_bulk_loader_admin_manage_templates',
'access arguments' => array('administer tripal_bulk_loader'),
'weight' => 10,
'type' => MENU_LOCAL_TASK,
);
// Enable View Callbacks
$items['admin/tripal/loaders/bulk/views/jobs/enable'] = array(
'title' => 'Enable Jobs Administrative View',
'description' => 'Enable Jobs Administrative View',
'page callback' => 'tripal_bulk_loader_admin_enable_view',
'page arguments' => array('tripal_bulk_loading_jobs'),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/views/templates/enable'] = array(
'title' => 'Enable Templates Administrative View',
'description' => 'Enable Templates Administrative View',
'page callback' => 'tripal_bulk_loader_admin_enable_view',
'page arguments' => array('tripal_bulk_loader_templates'),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
// Create/Edit Template --------
$items['admin/tripal/loaders/bulk/template/create'] = array(
'title' => 'Create Template',
'description' => 'Create loader template for loading tab-delimited data',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'create'),
'access arguments' => array('administer tripal_bulk_loader'),
'weight' => -8,
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/template/%tblid/edit'] = array(
'title' => 'Edit Template',
'description' => 'Edit loader template for loading tab-delimited data',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'edit',5),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
/**
$items['admin/tripal/loaders/bulk/template/edit'] = array(
'title' => 'Edit Template',
'description' => 'Edit loader template for loading tab-delimited data',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'edit',FALSE),
'access arguments' => array('administer tripal_bulk_loader'),
'weight' => -6,
'type' => MENU_CALLBACK,
);
*/
// Add/Edit Record -----
$items['admin/tripal/loaders/bulk/template/%tblid/add_record'] = array(
'title' => 'Add Template Field',
'description' => 'Add a template field to an existing tripal bulk loader template.',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_template_field_form','create_record',5,FALSE),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/template/%tblid/edit_record/%tblid'] = array(
'title' => 'Edit Template Record',
'description' => 'Edit a record in an existing tripal bulk loader template.',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_edit_template_record_form',5,7),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/template/%tblid/delete_record/%tblid'] = array(
'title' => 'Delete Template Record',
'description' => 'Delete a record in an existing tripal bulk loader template.',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_delete_template_record_form',5,7),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/template/%tblid/duplicate_record/%tblid'] = array(
'title' => 'Duplicate Template Record',
'description' => 'Duplicate a record in an existing tripal bulk loader template.',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_duplicate_template_record_form',5,7),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
// Add/Edit Field ------
$items['admin/tripal/loaders/bulk/template/%tblid/add_field/%tblid'] = array(
'title' => 'Add Template Field',
'description' => 'Add a template field to an existing tripal bulk loader template.',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_template_field_form','create',5,7),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/template/%tblid/edit_field/%tblid/%tblid'] = array(
'title' => 'Edit Template Field',
'description' => 'Edit an existing field from a tripal bulk loader template.',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_template_field_form','edit',5,7,8),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/template/%tblid/delete_field/%tblid/%tblid'] = array(
'title' => 'Delete Template Field',
'description' => 'Delete an existing field from a tripal bulk loader template.',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_delete_template_field_form',5,7,8),
'access arguments' => array('administer tripal_bulk_loader'),
'type' => MENU_CALLBACK,
);
// Delete Template -----
$items['admin/tripal/loaders/bulk/template/%tblid/delete'] = array(
'title' => 'Delete Template',
'description' => 'Delete bulk loader template',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_delete_template_base_form',5),
'access arguments' => array('administer tripal_bulk_loader'),
'weight' => -4,
'type' => MENU_CALLBACK,
);
// Import/Export ---------
$items['admin/tripal/loaders/bulk/templates/import'] = array(
'title' => 'Import Template',
'description' => 'Import Loaders',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_import_template_form'),
'access arguments' => array('administer tripal_bulk_loader'),
'weight' => 2,
'type' => MENU_CALLBACK,
);
$items['admin/tripal/loaders/bulk/template/%tblid/export'] = array(
'title' => 'Export Template',
'description' => 'Export Loaders',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_bulk_loader_export_template_form', 5),
'access arguments' => array('administer tripal_bulk_loader'),
'weight' => 4,
'type' => MENU_CALLBACK,
);
return $items;
}
function tblid_to_arg($arg, $map, $index) {
if (preg_match('/^\d+$/', $arg)) {
return $arg;
}
}
/**
* Implements hook_views_api()
*
* Purpose: Essentially this hook tells drupal that there is views support for
* for this module which then includes tripal_views.views.inc where all the
* views integration code is
*
* @ingroup tripal_views
*/
function tripal_bulk_loader_views_api() {
return array(
'api' => 3.0,
);
}
/**
* Implements hook_theme
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_theme() {
return array(
'node__tripal_bulk_loader' => array(
'template' => 'node--tripal-bulk-loader',
'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
'render element' => 'node',
'base hook' => 'node',
),
'tripal_bulk_loader_template' => array(
'variables' => array('template_id' => NULL),
'template' => 'tripal_bulk_loader_template',
'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
),
'tripal_bulk_loader_modify_template_base_form' => array(
'template' => 'tripal_bulk_loader_modify_template_base_form',
'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
'render element' => 'form'
),
'tripal_bulk_loader_field_regex_fieldset' => array(
'file' => 'theme/tripal_bulk_loader.theme.inc',
'function' => 'tripal_bulk_loader_field_regex_fieldset',
'render element' => 'element'
),
'tripal_bulk_loader_admin' => array(
'template' => 'tripal_bulk_loader_admin',
'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
),
);
}
/**
* Implement hook_access().
*
* This hook allows node modules to limit access to the node types they define.
*
* @param $op
* The operation to be performed
*
* @param $node
* The node on which the operation is to be performed, or, if it does not yet exist, the
* type of node to be created
*
* @param $account
* A user object representing the user for whom the operation is to be performed
*
* @return
* If the permission for the specified operation is not set then return FALSE. If the
* permission is set then return NULL as this allows other modules to disable
* access. The only exception is when the $op == 'create'. We will always
* return TRUE if the permission is set.
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_node_access($node, $op, $account) {
if ($op == 'create') {
if (!user_access('create tripal_bulk_loader', $account)) {
return NODE_ACCESS_DENY;
}
return NODE_ACCESS_ALLOW;
}
if ($op == 'update') {
if (!user_access('edit tripal_bulk_loader', $account)) {
return NODE_ACCESS_DENY;
}
return NODE_ACCESS_ALLOW;
}
if ($op == 'delete') {
if (!user_access('delete tripal_bulk_loader', $account)) {
return NODE_ACCESS_DENY;
}
return NODE_ACCESS_ALLOW;
}
if ($op == 'view') {
if (!user_access('access tripal_bulk_loader', $account)) {
return NODE_ACCESS_DENY;
}
return NODE_ACCESS_ALLOW;
}
return NODE_ACCESS_IGNORE;
}
/**
* Implements hook_perm
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_permission() {
return array(
'access tripal_bulk_loader' => array(
'title' => t('View Tripal Bulk Loading Jobs'),
'description' => t('Permission to view Tripal Bulk Loader Nodes')
),
'create tripal_bulk_loader' => array(
'title' => t('Create Tripal Bulk Loading Jobs'),
'description' => t('Permission to create Tripal Bulk Loader Nodes')
),
'edit tripal_bulk_loader' => array(
'title' => t('Edit Tripal Bulk Loading Jobs'),
'description' => t('Permission to edit Tripal Bulk Loader Nodes')
),
'delete tripal_bulk_loader' => array(
'title' => t('Delete Tripal Bulk Loading Jobs'),
'description' => t('Permission to delete Tripal Bulk Loader Nodes')
),
'administer tripal_bulk_loader' => array(
'title' => t('Administrate Tripal Bulk Loader'),
'description' => t('Permission to administrate the Tripal Bulk Loader including template management.')
),
);
}
//////////////////////////////////////////////////////////////////////////////////////////////
// Node Functions
//////////////////////////////////////////////////////////////////////////////////////////////
/**
* Implements hook_node_info
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_node_info() {
$nodes = array();
$nodes['tripal_bulk_loader'] = array(
'name' => t('Bulk Loading Job'),
'base' => 'tripal_bulk_loader',
'description' => t('A bulk loader for inserting tab-delimited data into chado database'),
'has_title' => TRUE,
'has_body' => FALSE,
'locked' => TRUE
);
return $nodes;
}
/**
* Implements node_form
* Used to gather the extra details stored with a Bulk Loading Job Node
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_form($node, $form_state) {
$form = array();
if (isset($form_state['values'])) {
$node = $form_state['values'] + (array)$node;
$node = (object) $node;
}
$results = db_select('tripal_bulk_loader_template', 't')
->fields('t', array('template_id','name'))
->execute();
$templates = array();
foreach ($results as $template) {
$templates [$template->template_id] = $template->name;
}
if (!$templates) {
$form['label'] = array(
'#type' => 'item',
'#description' => t("Loader template needs to be created before any bulk loader can be added. Go to 'Tripal Management > Bulk Loader Template' to create the template."),
'#weight' => -10,
);
return $form;
}
$form['loader'] = array(
'#type' => 'fieldset',
'#title' => t('Basic Details'),
);
$form['loader']['loader_name'] = array(
'#type' => 'textfield',
'#title' => t('Loading Job Name'),
'#weight' => -10,
'#required' => TRUE,
'#default_value' => (isset($node->loader_name)) ? $node->loader_name : ''
);
$form['loader']['template_id'] = array(
'#type' => 'select',
'#title' => t('Template'),
'#description' => t('Please specify a template for this loader'),
'#options' => $templates,
'#weight' => -9,
'#required' => TRUE,
'#default_value' => (isset($node->template_id)) ? $node->template_id : current($templates),
);
$form['loader']['file']= array(
'#type' => 'textfield',
'#title' => t('Data File'),
'#description' => t('Please specify the data file to be loaded. This must be a tab-delimited text file with UNIX line endings.'),
'#weight' => -8,
'#default_value' => (isset($node->file)) ? $node->file : '',
'#maxlength' => 1024,
);
$form['loader']['has_header'] = array(
'#type' => 'radios',
'#title' => t('File has a Header'),
'#options' => array( 1 => 'Yes', 2 => 'No'),
'#weight' => -7,
'#default_value' => (isset($node->file_has_header)) ? $node->file_has_header : 1,
);
$form['loader']['keep_track_inserted'] = array(
'#type' => 'radios',
'#title' => t('Keep track of inserted record IDs'),
'#description' => t('This enables the ability to revert an entire loading job even if '
.'it completed successfully. Furthermore, it displays the number of records '
.'successfully inserted into each table.'),
'#options' => array( 1 => 'Yes', 0 => 'No'),
'#weight' => -7,
'#default_value' => (isset($node->keep_track_inserted)) ? $node->keep_track_inserted : variable_get('tripal_bulk_loader_keep_track_inserted', 0),
);
return $form;
}
/**
* Implements node_load
*
* D7 Changes: now loads all $nodes at once so need to add loops
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_load($nodes) {
// Loading Job Details
// Add fields from the tripal_bulk_loader
$result = db_select('tripal_bulk_loader', 'tbl')
->fields('tbl')
->condition('nid',array_keys($nodes),'IN')
->execute();
foreach ($result as $record) {
$nodes[$record->nid]->loader_name = $record->loader_name;
$nodes[$record->nid]->template_id = $record->template_id;
$nodes[$record->nid]->file = $record->file;
$nodes[$record->nid]->job_id = $record->job_id;
$nodes[$record->nid]->job_status = $record->job_status;
$nodes[$record->nid]->file_has_header = $record->file_has_header;
$nodes[$record->nid]->keep_track_inserted = $record->keep_track_inserted;
$nodes[$record->nid]->exposed_fields = array();
$nodes[$record->nid]->constants = array();
}
// Job Details
// Add fields from tripal_jobs
$result = db_query('SELECT tbl.nid, tj.* FROM {tripal_jobs} tj '
. 'LEFT JOIN {tripal_bulk_loader} tbl ON tbl.job_id=tj.job_id '
. 'WHERE tbl.nid IN (:nids)',
array(':nids' => array_keys($nodes))
);
foreach ($result as $record) {
$nodes[$record->nid]->job = $record;
}
// Add the Loader Template
// Add fields from tripal_bulk_loader_template
$result = db_query('SELECT tbl.nid, tblt.* FROM {tripal_bulk_loader_template} tblt '
. 'LEFT JOIN {tripal_bulk_loader} tbl ON tbl.template_id=tblt.template_id '
. 'WHERE tbl.nid IN (:nids)',
array(':nids' => array_keys($nodes))
);
foreach ($result as $dbrecord) {
$nodes[$dbrecord->nid]->template = $dbrecord;
$nodes[$dbrecord->nid]->template->template_array = unserialize($dbrecord->template_array);
// Add exposed field list
$template = $nodes[$dbrecord->nid]->template->template_array;
$nodes[$dbrecord->nid]->exposed_fields = array();
if ($template) {
foreach ($template as $record_id => $record) {
foreach ($record['fields'] as $field_id => $field) {
if (isset($field['exposed'])) {
if ($field['exposed']) {
$nodes[$dbrecord->nid]->exposed_fields[] = array(
'record_id' => $record_id,
'field_id' => $field_id,
'title' => $field['title'],
);
}
}
}
}
}
}
// Add inserted records
// Add fields from tripal_bulk_loader_inserted
$result = db_query('SELECT tbli.* FROM {tripal_bulk_loader_inserted} tbli '
. 'WHERE tbli.nid IN (:nids)',
array(':nids' => array_keys($nodes))
);
foreach ($result as $record) {
$record->num_inserted = sizeof(preg_split('/,/', $record->ids_inserted));
$nodes[$record->nid]->inserted_records->{$record->table_inserted_into} = $record;
}
// Add constants
// Add fields from tripal_bulk_loader_constants
$result = db_query('SELECT tblc.* FROM {tripal_bulk_loader_constants} tblc '
. 'WHERE tblc.nid IN (:nids) '
. 'ORDER BY group_id, record_id, field_id',
array(':nids' => array_keys($nodes))
);
foreach ($result as $record) {
$nodes[$record->nid]->constants[$record->group_id][$record->record_id][$record->field_id] = array(
'constant_id' => $record->constant_id,
'group_id' => $record->group_id,
'chado_table' => $record->chado_table,
'chado_field' => $record->chado_field,
'record_id' => $record->record_id,
'field_id' => $record->field_id,
'value' => $record->value
);
}
}
/**
* Implements node_insert
* Insert the data from the node form on Create content
*
* D7 Changes: seems to need db_insert; not recommended to change $node
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_insert($node) {
$node->title = $node->loader_name;
db_insert('tripal_bulk_loader')->fields(array(
'nid' => $node->nid,
'loader_name' => $node->loader_name,
'template_id' => $node->template_id,
'file' => $node->file,
'file_has_header' => $node->has_header,
'job_status' => 'Initialized',
'keep_track_inserted' => $node->keep_track_inserted
))->execute();
drupal_set_message(t('After reviewing the details, please Submit this Job (by clicking the "Submit Job" button below). No data will be loaded until the submitted job is reached in the queue.'));
}
/**
* Implements node_delete
* Deletes the data when the delete button on the node form is clicked
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_delete($node) {
$tables = array();
$tables[] = 'tripal_bulk_loader';
$tables[] = 'tripal_bulk_loader_constants';
$tables[] = 'tripal_bulk_loader_inserted';
foreach($tables as $table) {
db_delete($table)
->condition('nid',$node->nid)
->execute();
}
}
/**
* Implements node_update
* Updates the data submitted by the node form on edit
*
* D7 Changes: db_update is much easier
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_update($node) {
// Update tripal_bulk_loader
db_update('tripal_bulk_loader')->fields(array(
'nid' => $node->nid,
'loader_name' => $node->loader_name,
'template_id' => $node->template_id,
'file' => $node->file,
'file_has_header' => $node->has_header,
'keep_track_inserted' => $node->keep_track_inserted
))->condition('nid',$node->nid)->execute();
// Add a job if the user want to load the data
/**
No job checkbox in the form
global $user;
if ($node->job) {
$job_args[0] =$node->loader_name;
$job_args[1] = $node->template_id;
$job_args[2] = $node->file;
if (is_readable($node->file)) {
$fname = preg_replace("/.*\/(.*)/", "$1", $node->file);
tripal_add_job("Bulk Load: $fname", 'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
}
else {
drupal_set_message(t("Can not open %file. Job not scheduled.", array('%file' => $node->file)));
}
}
*/
}
///////////////////////////////////////////////////////////
/**
* Preprocessor function for the tripal_bulk_loader template
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_preprocess_tripal_bulk_loader_template(&$variables) {
$resource = db_select('tripal_bulk_loader_template','t')
->fields('t')
->condition('template_id', $variables['template_id'])
->execute();
$template = $resource->fetchObject();
$template->template_array = unserialize($template->template_array);
$variables['template'] = $template;
}
/**
* Get the progress of the current constant set from the progress file
*
* When transactions are used, database updates to drupal cannot be made. Thus a separate
* method to keep track of progress was implemented: save a period to the file for each
* record successfully inserted; each line in the file represents a processed line.
*
* @param $job_id
* The id of the tripal job to check the progress of
* @param $node
* The tripal_bulk_loader node associated with the job
*
* @return
* An array with the following keys:
* num_lines = the number of lines in the file processed so far
* total_lines = the total number of lines in the input file
* percent_file = the percent the input file has been loaded
* num_records = the number of records successfully inserted
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_progess_file_get_progress($job_id, $update_progress = TRUE) {
$filename = '/tmp/tripal_bulk_loader_progress-' . $job_id . '.out';
if (!file_exists($filename)) {
return (object) array();
}
$num_lines = trim(`wc --lines < $filename`);
$num_records = trim(`grep -o "." $filename | wc --lines`);
$job = db_query("SELECT j.*, b.file, b.file_has_header, c.num as num_constant_sets
FROM {tripal_jobs} j
LEFT JOIN {tripal_bulk_loader} b ON b.job_id=j.job_id
LEFT JOIN (
SELECT nid, count(distinct(group_id)) as num
FROM {tripal_bulk_loader_constants}
GROUP BY nid
) c ON c.nid=b.nid
WHERE j.job_id=:job", array(':job' =>$job_id))->execute();
if ($job->num_constant_sets) {
$num_constant_sets_loaded = round($job->progress / (100 / $job->num_constant_sets), 4);
// If the next constant set has started loading
if ($job->num_constant_sets != $num_constant_sets_loaded) {
// total lines in input file
$total_lines = trim(`wc --lines < $job->file`);
if ($job->file_has_header) {
$total_lines--;
}
// percent of the current constant set loaded
$percent = round($num_lines/$total_lines * 100, 2);
// percent of the total job = (<# fully loaded constant sets> * 100 )
// + <percent of current constant set>
// / <total number of constant sets>
$total_percent = (($num_constant_sets_loaded * 100) + $percent) / $job->num_constant_sets;
// update the progress of the job
if ($update_progress AND ($percent != 0 OR $percent != 100)) {
tripal_job_set_progress($job_id, round($total_percent, 0));
}
}
}
return (object) array(
'num_lines' => $num_lines,
'total_lines' => $total_lines,
'percent_file' => $percent,
'num_constant_sets_loaded' => $num_constant_sets_loaded,
'total_percent' => $total_percent,
'num_records' => $num_records
);
}
/**
* Implements hook_job_describe_args()
* Specifically to make viewing past tripal jobs more readable for jobs registered by this module
*
* @params $callback
* The callback passed into tripal_add_job()
* @param $args
* The arguements passed into tripal_add_job()
* @return
* An array where keys are the human readable headers describing each arguement
* and the value is the aguement passed in after formatting
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_job_describe_args($callback, $args) {
$new_args = array();
if ($callback == 'tripal_bulk_loader_load_data') {
//1st arg is the nid for a bulk loader node
$node = node_load($args[0]);
$new_args['Bulk Loading Job'] = l($node->title, 'node/' . $args[0]);
return $new_args;
}
}
/**
* Implements hook_coder_ignore().
* Defines the path to the file (tripal_bulk_loader.coder_ignores.txt) where ignore rules for coder are stored
*
* @ingroup tripal_bulk_loader
*/
function tripal_bulk_loader_coder_ignore() {
return array(
'path' => drupal_get_path('module', 'tripal_bulk_loader'),
'line prefix' => drupal_get_path('module', 'tripal_bulk_loader'),
);
}