tripal/tripal_bulk_loader/tripal_bulk_loader.loader.inc

<?php

/**
 * Add Loader Job Form
 *
 * This form is meant to be included on the node page to allow users to submit/re-submit 
 * loading jobs
 */
function tripal_bulk_loader_add_loader_job_form ($form_state, $node) {
  $form = array();
  
  $form['nid'] = array(
    '#type' => 'hidden',
    '#value' => $node->nid,
  ); 
  
  $form['file'] = array(
  	'#type' => 'hidden',
  	'#value' => $node->file
  );
  
  $form['job_id'] = array(
    '#type' => 'hidden',
    '#value' => $node->job_id,
  );
  
  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => ($node->job_id) ? 'Re-Submit Job' : 'Submit Job',
  );

  $form['submit-cancel'] = array(
    '#type' => ($node->job_id)? 'submit' : 'hidden',
    '#value' => 'Cancel Job',
  );
  
  return $form;
}

/**
 * Add Loader Job Form (Submit)
 */
function tripal_bulk_loader_add_loader_job_form_submit ($form, $form_state) {
  global $user;
  
  if (preg_match('/Submit Job/', $form_state['values']['op'])) {
    //Submit Tripal Job
		$job_args[1] = $form_state['values']['nid'];
		if (is_readable($form_state['values']['file'])) {
			$fname = basename($form_state['values']['file']);
			$job_id = tripal_add_job("Bulk Loading Job: $fname",'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
			
			// add job_id to bulk_loader node
      $record = node_load($form_state['values']['nid']);
      $record->job_id = $job_id;
      drupal_write_record('tripal_bulk_loader', $record, 'nid');

      // Add Sync Features Job
      tripal_add_job('Sync all features','tripal_feature',
        'tripal_feature_sync_features',$job_args,$user->uid);			
		} else {
			drupal_set_message("Can not open ".$form_state['values']['file'].". Job not scheduled.");
		}    
  } elseif (preg_match('/Re-Submit Job/', $form_state['values']['op'])) {
    tripal_jobs_rerun($form_state['values']['job_id']);
  } elseif (preg_match('/Cancel Job/', $form_state['values']['op'])) {
    tripal_jobs_cancel($form_state['values']['job_id']);
  }

}

/**
 * Tripal Bulk Loader
 *
 * This is the function that's run by tripal_launch_jobs to bulk load chado data.
 * @param $nid
 *   The Node ID of the bulk loading job node to be loaded. All other needed data is expected to be 
 *   in the node (ie: template ID and file)
 *
 * Note: Instead of returning a value this function updates the tripal_bulk_loader.status and
 *   Enters errors into tripal_bulk_loader_errors if they are encountered.
 */
function tripal_bulk_loader_load_data($nid) {
  
  $node = node_load($nid);
  print "Template: ".$node->template->name." (".$node->template_id.")\n";
  print "File: ".$node->file."\n";
  
  // Prep Work ==================================================================================
  // Generate default values array
  $default_data = array();
  $field2column = array();
  $record2priority = array();
  foreach ($node->template->template_array as $priority => $record_array) {
    if (!is_array($record_array)) { continue; }
    
    foreach ($record_array['fields'] as $field_index => $field_array) {
      $default_data[$priority]['table'] = $record_array['table'];
      $record2priority[$record_array['record_id']] = $priority;
      
      if (preg_match('/table field/', $field_array['type'])) {
        $default_data[$priority]['values_array'][$field_array['field']] = '';
        $default_data[$priority]['need_further_processing'] = TRUE;
        $field2column[$priority][$field_array['field']] = $field_array['spreadsheet column'];
        
      } elseif (preg_match('/constant/', $field_array['type'])) {
        $default_data[$priority]['values_array'][$field_array['field']] = $field_array['constant value'];
        
      } elseif (preg_match('/foreign key/', $field_array['type'])) {
        $default_data[$priority]['values_array'][$field_array['field']] = array();
        $default_data[$priority]['values_array'][$field_array['field']]['foreign record'] = $field_array['foreign key'];
        $default_data[$priority]['need_further_processing'] = TRUE;
        
      } else {
        print 'WARNING: Unsupported type: '. $field_array['type'] . ' for ' . $table . '.' . $field_array['field']."!\n";
      }    
    } // end of foreach field
  } //end of foreach record

  //print "\nDefault Values Array: ".print_r($default_data, TRUE)."\n";
  //print "\nField to Column Mapping: ".print_r($field2column, TRUE)."\n";
  
  // Parse File adding records as we go ========================================================
  $file_handle = fopen($node->file, 'r');
  if (preg_match('/(t|true|1)/', $node->file_has_header)) { fgets($file_handle, 4096); }
  $num_records = 0;
  $num_lines = 0;
  $num_errors = 0;
  while (!feof($file_handle)) {
    $line = array();
    $raw_line = fgets($file_handle, 4096);
    $raw_line = trim($raw_line);
    $line = preg_split("/\t/", $raw_line);
    $num_lines++;

    $data = $default_data;
    
    foreach ($data as $priority => $table_data) {
      $table = $table_data['table'];
      $values = $table_data['values_array'];
      if ($table_data['need_further_processing']) {
        $values = tripal_bulk_loader_add_spreadsheetdata_to_values ($values, $line, $field2column[$priority]);
        $values = tripal_bulk_loader_add_foreignkey_to_values($values, $data, $record2priority);
      }
      
      // add new values array into the data array
      $data[$priority]['values_array'] = $values;
       
      // first check if it already exists
      $exists = tripal_core_chado_select($table, array_keys($values), $values, array('has_record'=>TRUE));
      if ($exists) {
          watchdog('T_bulk_loader', 
            'Record already exists in %table: %record',
            array('%table' => $table, '%record' => tripal_bulk_loader_flatten_array($values)),
            'WATCHDOG_WARNING'
          );      
      } else {
        // if it doesn't exist already then insert it
        $success = tripal_core_chado_insert($table, $values);
        if (!$success) {
          watchdog('T_bulk_loader', 
            'Unable to insert the following record into %table: %record',
            array('%table' => $table, '%record' => tripal_bulk_loader_flatten_array($values)),
            'WATCHDOG_ERROR'
          );
        }
      }// end of if/not record exists
    } // end of foreach table in default data array

  } //end of foreach line of file
  
}

/**
 * This function adds the file data to the values array
 *
 * @param $values
 *   The default values array -contains all constants
 * @param $line
 *   An array of values for the current line
 * @param $field2column
 *   An array mapping values fields to line columns
 * @return 
 *   Supplemented values array
 */
function tripal_bulk_loader_add_spreadsheetdata_to_values ($values, $line, $field2column) {

  foreach ($values as $field => $value) {
    if (is_array($value)) { continue; }
    
    $column = $field2column[$field] - 1;
    if ($line[$column] OR (!$values[$field])) {
      $values[$field] = $line[$column];
    }
  }
  
  return $values;
}

/**
 * Handles foreign keys in the values array.
 *
 * Specifically, if the value for a field is an array then it is assumed that the array contains
 * the name of the record whose values array should be substituted here. Thus the foreign
 * record is looked up and the values array is substituted in.
 *
 */
function tripal_bulk_loader_add_foreignkey_to_values($values, $data, $record2priority) {

  foreach ($values as $field => $value) {
    if (is_array($value)) {
      $foreign_record = $value['foreign record'];
      $foreign_priority = $record2priority[$foreign_record];
      $foreign_values = $data[$foreign_priority]['values_array'];
      
      //add to current values array
      $values[$field] = $foreign_values;
    }
  }

  return $values;
}

/**
 * Flattens an array up to two levels
 * Used for printing of arrays without taking up much space
 */
function tripal_bulk_loader_flatten_array ($values) {
  $flattened_values = array();
  
  foreach ($values as $k => $v) {
    if (is_array($v)) {
      $vstr = array();
      foreach ($v as $vk => $vv) {
        if (strlen($vv) > 20) {
          $vstr[] = $vk .'=>'. substr($vv, 0, 20) . '...';
        } else {
          $vstr[] = $vk .'=>'. $vv;
        }
      }
      $v = '{'. implode(',',$vstr) .'}';
    } elseif (strlen($v) > 20) {
      $v = substr($v, 0, 20) . '...';
    }
    $flattened_values[] = $k .'=>'. $v;
  }
  
  return implode(', ',$flattened_values);
}