tripal_bulk_loader.chado_node.inc
- 2.x tripal_bulk_loader/includes/tripal_bulk_loader.chado_node.inc
- 3.x tripal_bulk_loader/includes/tripal_bulk_loader.chado_node.inc
Tripal Bulk Loader Node functionality (jobs).
File
tripal_bulk_loader/includes/tripal_bulk_loader.chado_node.incView source
- <?php
-
- /**
- * @file
- * Tripal Bulk Loader Node functionality (jobs).
- *
- * @ingroup tripal_bulk_loader
- */
-
- /**
- * 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,
- 'locked' => TRUE
- );
- return $nodes;
- }
-
- /**
- * Implements hook_form().
- * Used to gather the extra details stored with a Bulk Loading Job Node
- *
- * @ingroup tripal_bulk_loader
- */
- function tripal_bulk_loader_form($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'),
- );
-
- $form['loader']['loader_name'] = array(
- '#type' => 'textfield',
- '#title' => t('Job Name'),
- '#weight' => -10,
- '#required' => TRUE,
- '#default_value' => (isset($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 hook_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' => $record->value
- );
- }
-
- }
-
- /**
- * Implements hook_node_presave().
- * Acts on all node types.
- *
- * @ingroup tripal_bulk_loader
- */
- function tripal_bulk_loader_node_presave($node) {
-
- // We need to set the title using loader details before the node is saved
- // which has already been done by the time hook_insert is called
- switch ($node->type) {
- case 'tripal_bulk_loader':
- $node->title = 'Bulk Loading Job: ' . $node->loader_name;
- break;
- }
- }
-
-
- /**
- * Implements hook_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) {
-
- db_insert('tripal_bulk_loader')->fields(array(
- 'nid' => $node->nid,
- 'loader_name' => trim($node->loader_name),
- 'template_id' => $node->template_id,
- 'file' => trim($node->file),
- 'file_has_header' => $node->has_header,
- 'job_status' => 'Initialized',
- 'keep_track_inserted' => $node->keep_track_inserted
- ))->execute();
- drupal_set_message(t('After reviewing the details, please Submit this Job (by clicking the "Submit Job" button below). No data will be loaded until the submitted job is reached in the queue.'));
-
- }
-
- /**
- * Implements hook_delete().
- * Deletes the data when the delete button on the node form is clicked
- *
- * @ingroup tripal_bulk_loader
- */
- function tripal_bulk_loader_delete($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',$node->nid)
- ->execute();
- }
- }
-
- /**
- * Implements hook_update().
- * Updates the data submitted by the node form on edit
- *
- * @ingroup tripal_bulk_loader
- */
- function tripal_bulk_loader_update($node) {
-
- // Update tripal_bulk_loader
- db_update('tripal_bulk_loader')->fields(array(
- 'nid' => $node->nid,
- 'loader_name' => trim($node->loader_name),
- 'template_id' => $node->template_id,
- 'file' => trim($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)));
- }
- }
- */
-
- }
-
- /**
- * 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) {
- $node_type = $node;
- if (is_object($node)) {
- $node_type = $node->type;
- }
-
- if($node_type == 'tripal_bulk_loader') {
- 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', $account)) {
- return NODE_ACCESS_DENY;
- }
- }
- if ($op == 'delete') {
- if (!user_access('delete tripal_bulk_loader', $account)) {
- return NODE_ACCESS_DENY;
- }
- }
- if ($op == 'view') {
- if (!user_access('access tripal_bulk_loader', $account)) {
- return NODE_ACCESS_DENY;
- }
- }
- return NODE_ACCESS_IGNORE;
- }
- }
-
-
- /**
- * Implements hook_node_view().
- * Acts on all content types.
- *
- * @ingroup tripal_feature
- */
- function tripal_bulk_loader_node_view($node, $view_mode, $langcode) {
- switch ($node->type) {
- case 'tripal_bulk_loader':
- // Show feature browser and counts
- if ($view_mode == 'full') {
-
- // we want to use the Tripal generic node template
- $node->content['#tripal_generic_node_template'] = TRUE;
-
- $node->content['tripal_bulk_loader_base'] = array(
- '#theme' => 'tripal_bulk_loader_base',
- '#node' => $node,
- '#tripal_toc_id' => 'base',
- '#tripal_toc_title' => 'Overview',
- '#tripal_template_show' => FALSE,
- '#weight' => -100,
- );
- $node->content['tripal_bulk_loader_fields'] = array(
- '#theme' => 'tripal_bulk_loader_fields',
- '#node' => $node,
- '#tripal_toc_id' => 'fields',
- '#tripal_toc_title' => 'Data Fields',
- '#tripal_template_show' => FALSE,
- );
- }
- if ($view_mode == 'teaser') {
- $node->content['tripal_bulk_loader_teaser'] = array(
- '#theme' => 'tripal_bulk_loader_teaser',
- '#node' => $node,
- );
- }
- break;
- }
- }