tripal/tripal_bulk_loader/tripal_bulk_loader.admin.templates.inc

<?php

/**
 * @file
 * All functions in this file pertain to administrative management of bulk loader templates
 */

/**
 * @section
 * Modify Template
 * The main form for creating/editing templates as a whole
 */


/**
 * The main form reached at admin/tripal/tripal_bulk_loader/create and /edit
 */
function tripal_bulk_loader_modify_template_base_form($form_state = NULL, $mode) {
  $form = array();

   // get template id from path and rebuild form
  if ($_GET['template_id']) {
    if (preg_match('/^\d+$/', $_GET['template_id'])) {
      $form_state['storage']['template_id'] = $_GET['template_id'];
    }

    $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
    $result = db_fetch_object(db_query($sql, $form_state['storage']['template_id']));
    $form_state['storage']['template'] = unserialize($result->template_array);
    $form_state['storage']['template_name'] = $result->name;

    $form_state['storage']['record2priority'] = array();
    foreach ($form_state['storage']['template'] as $priority => $record_array) {
      if (!is_array($record_array)) {
        continue; }
      $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
    }
  }

  $form['mode'] = array(
    '#type' => 'hidden',
    '#value' => $mode,
  );

  if ($form_state['storage']['template_id']) {
    $form['template_name'] = array(
      '#type' => 'item',
      '#title' => 'Template',
      '#value' => $form_state['storage']['template_name'],
      '#weight' => 1,
    );
  }
  else {
    if (preg_match('/create/', $mode)) {
      $form['new_template_name'] = array(
        '#type' => 'textfield',
        '#title' => 'Template Name',
        '#weight' => 1,
      );
    }
    elseif (preg_match('/edit/', $mode)) {
      $sql = "SELECT * FROM {tripal_bulk_loader_template}";
      $resource = db_query($sql);
      $templates = array();
      $templates[''] = 'Select a Template';
      while ($r = db_fetch_object($resource)) {
        $templates[$r->template_id] = $r->name;
      }

      $form['template_id'] = array(
        '#title'         => t('Template'),
        '#description'   => t('Please select the template you would like to edit.'),
        '#type'          => 'select',
        '#options'       => $templates,
        '#default_value' => $form_state['storage']['template_id'],
        '#weight'        => 0,
        '#required'      => TRUE,
        '#weight' => 1,
      );
    }
  }

  $form['records'] = array(
    '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
    '#title' => t('Current Records'),
    '#collapsible' => TRUE,
    '#weight' => 2,
  );

  $form['records']['description'] = array(
    '#type' => 'item',
    '#value' => 'Records will be inserted into the chado database in the order listed below. To '
      .'change this order: <ul><li>Drag the rows into the correct order <br/>(If you don\'t have javascript enabled then enter '
      .'the numbers 1 and up in the Order textboxes to indicate the correct order).</li></ul>',
  );

  $form['records']['records-data'] = array(
    '#tree' => TRUE,
  );

  $form['records']['no_records'] = array(
    '#type' => 'hidden',
    '#value' => TRUE,
  );

  $form['records']['submit-new_record'] = array(
    '#type' => 'submit',
    '#value' => 'New Record/Field',
  );

  $form['records']['submit-reorder'] = array(
    '#type' => 'submit',
    '#value' => 'Save Order',
  );

  $form['fields'] = array(
    '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
    '#title' => t('Current Fields'),
    '#collapsible' => TRUE,
    '#weight' => 3,
  );

  $form['fields']['fields-data'] = array(
    '#tree' => TRUE,
  );

  if ($form_state['storage']['template']) {

    // List Current Fields -------------------------------------------------------------
    $i=1;
    foreach ($form_state['storage']['template'] as $priority => $table_array) {
      if (!is_array($table_array)) {
      continue; }

        $form['records']['no_records']['#value'] = FALSE;

        $mode_value = '';
        if ($table_array['optional']) {
          $mode_value .= 'optional ';
        }

        // for backwards compatibility we want to convert insert_unique to be 'insert'
        // and optional to 'insert'
        if (strcmp($table_array['mode'], 'insert_unique')==0) {
          $mode_value .= 'insert or select if duplicate';
        }
        elseif (strcmp($table_array['mode'], 'optional')==0) {
          $mode_value .= 'optional insert';
        }
        elseif (strcmp($table_array['mode'], 'insert_once')==0) {
          $mode_value .= 'insert once';
        }
         elseif (strcmp($table_array['mode'], 'select_once')==0) {
          $mode_value .= 'select once';
        }
        elseif ($table_array['mode']) {
          $mode_value .= $table_array['mode'];
        }
        else {
          $mode_value .= 'insert';
        }

        // add in the select if duplicate
        if ($table_array['select_if_duplicate']) {
          $mode_value .= ' or select if duplicate';
        }
        if ($table_array['select_optional']) {
          $mode_value .= ' (no fail)';
        }
        if ($table_array['update_if_duplicate']) {
          $mode_value .= ' or update if duplicate';
        }


        // add in the disabled
        if ($table_array['disable']) {
          $mode_value .= '. <font color="Red">DISABLED</font>';
        }

        $form['records']['records-data'][$priority] = array(
          'title' => array(
            '#type' => 'markup',
            '#value' => filter_xss($priority . ". " . $table_array['record_id']),
            '#prefix' => "<a name=\"record_$priority\"></a>",
            '#suffix' => "<p><a href=\"#fields_$priority\"> View Fields </a></p>",
          ),
          'chado_table' => array(
            '#type' => 'markup',
            '#value' => filter_xss($table_array['table']),
          ),
          'mode' => array(
            '#type' => 'item',
            '#value' => $mode_value,
          ),
          'new_priority' => array(
            '#type' => 'select',
            '#options' => range(1, sizeof($form_state['storage']['template'])),
            '#default_value' => $priority,
          ),
          'old_priority' => array(
            '#type' => 'hidden',
            '#value' => $priority,
          ),
          'id'  => array(
            '#type' => 'hidden',
            '#value' => $priority,
          ),
          'submit-edit_record' => array(
            '#type' => 'submit',
            '#name' => ($priority !== 0) ? (string)$priority : 'zero',
            '#value' => 'Edit Record',
          ),
          'submit-add_field' => array(
            '#type' => 'submit',
            '#name' => ($priority !== 0) ? (string)$priority : 'zero',
            '#value' => 'Add Field',
          ),
          'submit-duplicate_record' => array(
            '#type' => 'submit',
            '#name' => ($priority !== 0) ? (string)$priority : 'zero',
            '#value' => 'Duplicate Record'
          ),
        );

        foreach ($table_array['fields'] as $field_index => $field) {
          $fk_value = '';
          if ($field['foreign key']) {
            if ($field['foreign field']) {
              $fk_value = $field['foreign key'] . " (" . $field['foreign field'] . ")";
            }
            else {
              // for backwards compatibility we need to get the FK relationship to find
              // out what field we're joining on.  For templates created using a
              // previous version this information isn't stored in the template
              // so we need to get it.
              $fk_priority = $form_state['storage']['record2priority'][$field['foreign key']];
              $fk_table = $form_state['storage']['template'][$fk_priority]['table'];
              $tbl_description = tripal_core_get_chado_table_schema($table_array['table']);
              foreach ($tbl_description['foreign keys'] as $key_table => $key_array) {
                foreach ($key_array['columns'] as $left_field => $right_field) {
                  if ($key_table == $fk_table and $left_field == $field['field']) {
                    $fk_value = $field['foreign key'] . " ($right_field)";
                  }
                }
              }
            }
          }

          $form['fields']['fields-data'][$i] = array(
            'record_id' => array(
              '#type' => 'item',
              '#value' =>  $table_array['record_id'],
              '#prefix' => "<a name=\"fields_$priority\"></a>",
              '#suffix' => "<p><a href=\"#record_$priority\"> View Record </a></p>",
            ),
            'priority_hidden' => array(
              '#type' => 'hidden',
              '#value' => $priority,
            ),
            'field_name' => array(
              '#type' => 'item',
              '#value' => $field['title'],
            ),
            'chado_table_name' => array(
              '#type' => 'item',
              '#value' => $table_array['table'],
            ),
            'chado_table_hidden' => array(
              '#type' => 'hidden',
              '#value' => $table_array['table'],
            ),
            'chado_field_name' => array(
              '#type' => 'item',
              '#value' => $field['field'],
            ),
            'sheet_name' => array(
              '#type' => 'item',
              '#value' => $field['spreadsheet sheet'],
            ),
            'column_num' => array(
              '#type' => 'item',
              '#value' => $field['spreadsheet column'],
            ),
            'constant_value' => array(
              '#type' => 'item',
              '#value' => $field['constant value'],
            ),
            'field_index' => array(
              '#type' => 'hidden',
              '#value' => $field_index
            ),
            'foreign_record_id' => array(
              '#type' => 'item',
              '#value' => $fk_value,
            ),
            'edit_submit' => array(
              '#type' => 'submit',
              '#name' => (string)$i,
              '#value' => "Edit Field",
            ),
            'delete_submit' => array(
              '#type' => 'submit',
              '#name' => (string)$i,
              '#value' => "Delete Field",
            ),
          );

          $i++;
        }
    }
    $form['fields']['total_fields'] = array(
      '#type' => 'item',
      '#value' => $i,
    );

  }

  if ($form['records']['no_records']['#value']) {
    $form['records']['description'] = array(
      '#type' => 'item',
      '#value' => 'There are currently no records.',
    );
    unset($form['records']['submit-reorder']);

    $form['fields']['description'] = array(
      '#type' => 'item',
      '#value' => 'There are currently no fields.',
    );

  }

  $mode_title = (preg_match('/create/', $mode)) ? 'Create Template' : 'Edit Template';
  $value = ($form_state['storage']['template_id'])? 'Save Template' : $mode_title;
  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => $value,
    '#weight' => 4,
  );

  return $form;
}

/**
 * Submit for tripal_bulk_loader_modify_template_base_form
 */
function tripal_bulk_loader_modify_template_base_form_submit($form, &$form_state) {

  $form_state['rebuild'] = TRUE;
  if ($form_state['storage']['template_id']) {
    $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
    $result = db_fetch_object(db_query($sql, $form_state['storage']['template_id']));
    $form_state['storage']['template'] = unserialize($result->template_array);
  }

  $op = $form_state['values'][ $form_state['clicked_button']['#name'] ];

  // part of fix for 1st button set not working on records list (edit record, duplicate record, add field)
  if ($form_state['clicked_button']['#name'] === 'zero') {
    $form_state['clicked_button']['#name'] = '0';
  }

  switch ($op) {
    // Initialize after template is chosen ----------------------------------------
    case 'Edit Template':
      $form_state['storage']['template_id'] = $form_state['values']['template_id'];

      $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
      $result = db_fetch_object(db_query($sql, $form_state['storage']['template_id']));
      $form_state['storage']['template'] = unserialize($result->template_array);
      $form_state['storage']['template_name'] = $result->name;

      $form_state['storage']['record2priority'] = array();
      foreach ($form_state['storage']['template'] as $priority => $record_array) {
        if (!is_array($record_array)) {
          continue;
        }
        $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
      }
    break;

    case 'Create Template':
      $record = array(
        'name' => $form_state['values']['new_template_name'],
        'template_array' => array(),
      );
      drupal_write_record('tripal_bulk_loader_template', $record);
      $form_state['storage']['template_id'] = $record['template_id'];
      $form_state['storage']['template_name'] = $record['name'];
      $form_state['storage']['template'] = array();
    break;

    // Save Reordered Records -----------------------------------------------------
    case 'Save Order':
      $new_template = $form_state['storage']['template'];
      // unset old elements
      $form_state['storage']['record2priority'] = array();
      foreach ($new_template as $priority => $record_array) {
        if (preg_match('/\d+/', $priority)) {
          unset($new_template[$priority]);
        }
      }
      //set elements in new order
      foreach ($form_state['values']['records-data'] as $item) {
        $new_template[$item['new_priority']] = $form_state['storage']['template'][$item['old_priority']];
        $record_name = $new_template[$item['new_priority']]['record_id'];
        $form_state['storage']['record2priority'][$record_name] = $item['new_priority'];
      }
      ksort($new_template);
      $form_state['storage']['template'] = $new_template;
    break;

    case 'New Record/Field':
      $query = array(
        'template_id' => $form_state['storage']['template_id'],
        'record_id' => 'NEW',
      );
      drupal_goto('admin/tripal/tripal_bulk_loader_template/add_field', $query);
    break;

    case 'Edit Record':
      $query = array(
        'template_id' => $form_state['storage']['template_id'],
        'record_id' => $form_state['clicked_button']['#name'],
      );
      drupal_goto('admin/tripal/tripal_bulk_loader_template/edit_record', $query);
    break;

    case 'Add Field':
      $query = array(
        'template_id' => $form_state['storage']['template_id'],
        'record_id' => $form_state['clicked_button']['#name'],
      );
      drupal_goto('admin/tripal/tripal_bulk_loader_template/add_field', $query);
    break;

    case 'Duplicate Record':
      // original record (one to be duplicated)
      $orig_priority = $form_state['clicked_button']['#name'];
      $record = $form_state['storage']['template'][ $orig_priority ];

      // new record
      $new_priority = sizeof($form_state['storage']['template']) + 1;
      $record['record_id'] = $record['record_id'] . '_' . date('YzHi');
      $form_state['storage']['template'][ $new_priority ] = $record;
    break;

    case 'Edit Field':
      $field_data_index = $form_state['clicked_button']['#name'];
      $query = array(
        'template_id' => $form_state['storage']['template_id'],
        'record_id' => $form_state['values']['fields-data'][$field_data_index]['priority_hidden'],
        'field_index' => $form_state['values']['fields-data'][$field_data_index]['field_index'],
      );
      drupal_goto('admin/tripal/tripal_bulk_loader_template/edit_field', $query);
    break;

    case 'Delete Field':
      $field_data = $form_state['values']['fields-data'][$form_state['clicked_button']['#name']];
      $priority = $field_data['priority_hidden'];
      $field_key = $field_data['field_index'];
      unset($form_state['storage']['template'][$priority]['fields'][$field_key]);
      if (!$form_state['storage']['template'][$priority]['fields']) {
        unset($form_state['storage']['record2priority'][$form_state['storage']['template'][$priority]['record_id']]);
        unset($form_state['storage']['template'][$priority]);
      }
      drupal_set_message(t('Deleted Field from Template.'));
    break;
  } //end of switch

  // Save Template
  $record = array(
    'template_id' => $form_state['storage']['template_id'],
    'template_array' => serialize($form_state['storage']['template'])
  );
  drupal_write_record('tripal_bulk_loader_template', $record, array('template_id'));
  drupal_set_message(t('Template Saved.'));

}

/**
 * @section
 * Delete Template
 */

/**
 * Delete Template Form
 * This form allows admin to delete already existing templates
 */
function tripal_bulk_loader_delete_template_base_form() {
  $form = array();

  $sql = "SELECT * FROM {tripal_bulk_loader_template}";
  $resource = db_query($sql);
  $templates = array();
  $templates[''] = 'Select a Template';
  while ($r = db_fetch_object($resource)) {
    $templates[$r->template_id] = $r->name;
  }
  $form['template_name'] = array(
      '#title'         => t('Template'),
      '#description'   => t('Please select the template you would like to delete.'),
      '#type'          => 'select',
      '#options'       => $templates,
      '#weight'        => 0,
      '#required'      => TRUE,
  );

  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => 'Delete Template',
  );

  return $form;
}

/**
 * Delete Template Form Submit
 *
 * @param $form
 *   The form that was submitted
 * @param $form_state
 *   The values and storage that were submitted
 */
function tripal_bulk_loader_delete_template_base_form_submit($form, &$form_state) {
  $sql = "DELETE FROM {tripal_bulk_loader_template} WHERE template_id=%d";
  db_query($sql, $form_state['values']['template_name']);
}

/**
 * @section
 * Import/Export Template
 */

/**
 * Import/Export Template Form
 *
 * On export, simply selects the serialized array from the db for a given template
 * and presents it to the user. On import, a serialized template array and a name is
 * supplied and a template record is created.
 *
 * @todo Make array presented to the user more readable. (ie: unserialize and print to the screen)
 *
 * @param $form_state
 *   The values and storage for the form
 * @param $mode
 *   Either 'import' or 'export' to indicate which function is being performed
 * @return
 *   A form array to be rendered by drupal_get_form
 */
function tripal_bulk_loader_import_export_template_form($form_state = NULL, $mode) {
  $form = array();

  $form['mode'] = array(
    '#type' => 'hidden',
    '#value' => $mode,
  );

  if (preg_match('/import/', $mode)) {
    $form['new_template_name'] = array(
      '#type' => 'textfield',
      '#title' => 'Template Name',
      '#weight' => 1,
    );
  }
  elseif (preg_match('/export/', $mode)) {
    $sql = "SELECT * FROM {tripal_bulk_loader_template}";
    $resource = db_query($sql);
    $templates = array();
    $templates[''] = 'Select a Template';
    while ($r = db_fetch_object($resource)) {
      $templates[$r->template_id] = $r->name;
    }

    $form['template_id'] = array(
      '#title'         => t('Template'),
      '#description'   => t('Please select the template you would like to edit.'),
      '#type'          => 'select',
      '#options'       => $templates,
      '#default_value' => $form_state['storage']['template_id'],
      '#weight'        => 0,
      '#required'      => TRUE,
    );
  }

  $form['template_array'] = array(
    '#type' => 'textarea',
    '#title' => 'Template Array',
    '#default_value' => $form_state['storage']['template_array'],
    '#description' => t('Use this serialized array for import.'),
    '#rows' => 15,
    '#weight' => 5,

  );

  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => 'Submit',
    '#weight' => 10,
  );

  return $form;
}

/**
 * Import/Export Template Form Submit
 *
 * @param $form
 *   The form that was submitted
 * @param $form_state
 *   The values and storage that were submitted
 */
function tripal_bulk_loader_import_export_template_form_submit($form, &$form_state) {
  switch ($form_state['values']['mode']) {
    case 'export':
      $record = db_fetch_object(db_query("SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d", $form_state['values']['template_id']));
      //$form_state['storage']['template_array'] = $record->template_array;
      $t = var_export(unserialize($record->template_array), TRUE);
      $t = preg_replace("/\n\s+array/", "array", $t); // move array( to previous line
      $t = preg_replace("/true/", "TRUE", $t); // upper case true
      $t = preg_replace("/false/", "FALSE", $t); // upper case false
      $t = preg_replace("/array\(/", "array (", $t); // put a space between array and paren

      $form_state['storage']['template_array'] = $t;
      $form_state['storage']['template_id'] = $form_state['values']['template_id'];
    break;
    case 'import':
      // get the template array, and convert from text into an array.
      $t = array();
      eval("\$t = " . $form_state['values']['template_array'] . ";");
      $record = array(
        'name' => $form_state['values']['new_template_name'],
        'template_array' => serialize($t),
      );
      drupal_write_record('tripal_bulk_loader_template', $record);
      if ($record->template_id) {
        drupal_set_message(t('Successfully imported Tripal Bulk Loader Template.'));
      }
    break;
  }
}

/**
 * @section
 * Edit Record Form
 */

/**
 * Edit Record Form
 *
 * This form is meant to be called from a bulk loader form. The following should be set
 * in the query section of the path:
 *  - template_id=\d+: the template which the edited record is part of
 *  - record_id=\d+: the priority or key in the template array of the record to be edited
 *
 * @param $form_state
 *   Contains the values and storage for the form
 * @return
 *   A form array to be rendered by drupal_get_form
 */
function tripal_bulk_loader_edit_template_record_form(&$form_state = NULL) {
  $form['#cache'] = TRUE; // Make sure the form is cached.

   // get template id from path
  $template_id = ($_GET['template_id'] !== NULL) ? $_GET['template_id'] : $form_state['values']['template_id'];

  // if there is no template supplied don't return rest of form
  if (!$template_id) {
    return $form;
  }

  // Pre-process values/defaults ---------------------------

  // If this is the first load of the form (no form state) we need to initialize some variables
  if (!$form_state['storage']['template']) {
    $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
    $template = db_fetch_object(db_query($sql, $template_id));
    $form_state['storage']['template_array'] = unserialize($template->template_array);
    $form_state['storage']['template'] = $template;

    $form_state['storage']['record2priority'] = array();
    foreach ($form_state['storage']['template_array'] as $priority => $record_array) {
      if (!is_array($record_array)) {
        continue;
      }
      $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
    }

    $form_state['storage']['referring URL'] = $_SERVER["HTTP_REFERER"];
  }
  else {
    $template = $form_state['storage']['template'];
  }

  // get the record_id from the path
  if ($_GET['record_id'] !== NULL) {
    $form_state['values']['field_group'] = $_GET['record_id'];
    $form_state['storage']['original_priority'] = $_GET['record_id'];
  }


  // Tables and default table
  $tables = tripal_core_get_chado_tables(TRUE);
  if ($form_state['values']['chado_table']) {
    $table = $form_state['values']['chado_table'];
  }
  else {
    $table = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['table'];
  }

  // get the default mode
  $mode = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['mode'];
  if (!$mode) {
     $mode = 'insert';
  }

  // get default for the select optional
  $select_optional = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['select_optional'];
  if (!isset($select_optional)) {
    $select_optional = 0;
  }

  // get default for the select if duplicate
  $select_if_duplicate = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['select_if_duplicate'];
  if (!isset($select_if_duplicate)) {
    $select_if_duplicate = 1;
  }

  // get default for the update if duplicate
  $update_if_duplicate = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['update_if_duplicate'];
  if (!isset($update_if_duplicate)) {
    $update_if_duplicate = 0;
  }

  // get default for the select if duplicate
  $optional = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['optional'];
  if (!isset($optional)) {
    $optional = 0;
  }

  // get the default for disabling the record
  $disable = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['disable'];

  // this is just for backwards compatibility. the insert_unique mode type is no longer available
  if (strcmp($mode, 'insert_unique')==0) {
     $mode = 'insert';
     $select_if_duplicate = 1;
  }

  // this is just for backwards compatibility. the insert_unique mode type is no longer available
  if (strcmp($mode, 'optional')==0) {
     $mode = 'insert';
     $optional = 1;
  }

  //dpm($form_state, 'form state');

   // Form Proper -------------------------------------------
  $form['template_name'] = array(
    '#type' => 'item',
    '#title' => 'Template',
    '#value' => $template->name,
  );

  $form['template_id'] = array(
    '#type' => 'hidden',
    '#value' => $template_id,
  );

  $form['edit_record'] = array(
    '#type' => 'fieldset',
  );

  // check template array for records then add one more
  if (!$form_state['storage']['record2priority']) {
    $groups = array();
  }
  else {
    $groups = array_flip($form_state['storage']['record2priority']);
  }
  $priority_default = $form_state['values']['field_group'];
  $form['edit_record']['field_group']  = array(
    '#type' => 'select',
    '#title' => 'Record',
    '#description' => 'By Changing the record here, you can move all the fields from the current record into the selected record.',
    '#options' => $groups,
    '#default_value' => $priority_default,
    '#required' => TRUE,
  );

  $form['edit_record']['record_name'] = array(
    '#type' => 'textfield',
    '#title' => 'Unique Record Name',
    '#default_value' => $groups[$priority_default],
  );

  $form['edit_record']['chado_table'] = array(
    '#type' => 'select',
    '#title' => t('Chado Table'),
    '#description' => 'This changes the chado table for all fields in this record.',
    '#options' => $tables,
    '#default_value' => $table,
  );

  $form['edit_record']['mode'] = array(
    '#type' => 'radios',
    '#title' => 'Action to take when Loading Record',
    '#options' => array(
      'select' => 'SELECT: Don\'t insert this record: it\'s used to define a foreign key in another record',
      'select_once' => 'SELECT ONCE: Select the record only once for the entire file.',
      'insert' => 'INSERT: Insert the record',
      'insert_once' => 'INSERT ONCE: Record will be inserted once for the entire file',
    ),
    '#default_value' => $mode
  );

  $form['edit_record']['select_options'] = array(
     '#type' => 'markup',
     '#value' => t('Additional Select Options:'),
  );
  $form['edit_record']['select_optional'] = array(
     '#type' => 'checkbox',
     '#title' => t('Continue if no record exists or too many exist.'),
     '#description' => t('By default if a select does not find a match the loader will fail, or if it finds too many matches it will fail.  Check here to allow the loader to continue when no match is found. In either case no value is passed on.'),
     '#default_value' => $select_optional
  );

  $form['edit_record']['insert_options'] = array(
     '#type' => 'markup',
     '#prefix' => '<br>',
     '#value' => t('Additional Insert Options:'),
  );

  $form['edit_record']['select_if_duplicate'] = array(
     '#type' => 'checkbox',
     '#title' => t('SELECT if duplicate (no insert)'),
     '#description' => t('If this is not the first time this record has been added then perform a select rather than an insert.'),
     '#default_value' => $select_if_duplicate
  );

  $form['edit_record']['update_if_duplicate'] = array(
     '#type' => 'checkbox',
     '#title' => t('UPDATE if duplicate (no insert)'),
     '#description' => t('If this is not the first time this record has been added then perform an update rather than an insert.'),
     '#default_value' => $update_if_duplicate
  );

  $form['edit_record']['optional'] = array(
     '#type' => 'checkbox',
     '#title' => t('Optional'),
     '#description' => t('The insert, update or select will only be performed only if all required data are present'),
     '#default_value' => $optional
  );
  $form['edit_record']['disable'] = array(
     '#type' => 'checkbox',
     '#title' => t('Disable this record'),
     '#description' => t("Check this box to ignore this record (not perform select or insert) during template loading.  Uncheck to re-enable the record"),
     '#default_value' => $disable,
  );

  $form['edit_record']['submit-edit_record'] = array(
      '#type' => 'submit',
      '#value' => 'Edit Record'
  );

  $form['edit_record']['submit-cancel'] = array(
      '#type' => 'submit',
      '#value' => 'Cancel'
  );

  return $form;
}

function tripal_bulk_loader_edit_template_record_form_validate($form, $form_state) {

  // Don't worry about validation when Cancel button is clicked
  if ($form_state['clicked_button']['#value'] == 'Edit Record') {
    $is_unique = tripal_bulk_loader_is_record_name_unique(
      $form_state['values']['record_name'],
      $form_state['values']['template_id'],
      $form_state['storage']['template_array'],
      $form_state['values']['field_group']
    );
    if (!$is_unique) {
      form_set_error('record_name', "New Record Name must be unique. '" . $form_state['values']['record_name'] . "' is not unique.");
    }
  }

}

/**
 * Edit Record Form Submit
 *
 * @param $form
 *   The form that was submitted
 * @param $form_state
 *   Contains the values and storage for the form
 */
function tripal_bulk_loader_edit_template_record_form_submit($form, &$form_state) {
  //dpm($form_state, 'form state -start submit');

  if (!$form_state['ahah_submission']) {
    if ($form_state['values']['op'] ==  'Edit Record') {

      $template = $form_state['storage']['template_array'];
      $original_record_name = $template[ $form_state['storage']['original_priority'] ]['record_id'];

      // Edit Record
      $record = $template[ $form_state['storage']['original_priority'] ];
      $record['record_id'] = $form_state['values']['record_name'];
      $record['mode'] = $form_state['values']['mode'];
      $record['table'] = $form_state['values']['chado_table'];
      $record['select_if_duplicate'] = $form_state['values']['select_if_duplicate'];
      $record['update_if_duplicate'] = $form_state['values']['update_if_duplicate'];
      $record['select_optional'] = $form_state['values']['select_optional'];
      $record['disable'] = $form_state['values']['disable'];
      $record['optional'] = $form_state['values']['optional'];

      if ($form_state['storage']['original_priority'] != $form_state['values']['field_group']) {
        $record['fields'] = array_merge($record['fields'], $template[ $form_state['values']['field_group'] ]['fields']);
        $template[ $form_state['values']['field_group'] ] = $record;
        unset($template[ $form_state['storage']['original_priority'] ]);
      }
      else {
        $template[ $form_state['storage']['original_priority'] ] = $record;
      }

      // Go through all records and update this record name where it was used for a foreign key
      // Foreach field in each record that is of type: foreign key
      foreach ($template as $priority => $record) {
        foreach ($record['fields'] as $field_index => $field) {
          if ($field['type'] === 'foreign key') {
            // Check if this points to the old record name and if so, update it
            if ($field['foreign key'] === $original_record_name) {
              $template[$priority]['fields'][$field_index]['foreign key'] = $form_state['values']['record_name'];
            }
          }
        }
      }

      // Save Template
      $form_state['storage']['template']->template_array = serialize($template);
      $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));

      if ($success) {
        drupal_set_message(t('Successfully Updated Template Record'));
        drupal_set_message(t('Template Saved.'));

        $path = explode('?', $form_state['storage']['referring URL']);
        parse_str($path[1], $query);
        $query['template_id'] = $form_state['storage']['template']->template_id;
        drupal_goto($path[0], $query);
      }
      else {
        drupal_set_message(t('Unable to Save Template!'), 'error');
        watchdog('T_bulk_loader',
          'Unable to save bulk loader template: %template',
          array('%template' => print_r($form_state['storage']['template'], TRUE)),
          WATCHDOG_ERROR
        );
      }
    }
    elseif ($form_state['values']['op'] ==  'Cancel') {
        $path = explode('?', $form_state['storage']['referring URL']);
        parse_str($path[1], $query);
        $query['template_id'] = $form_state['storage']['template']->template_id;
        //dpm('Redirecting to: '.$path[0].'?'.print_r($query,TRUE).' where the referring URL:'.$form_state['storage']['referring URL']);
        drupal_goto($path[0], $query);
    }
  }

}

/**
 * @section
 * Add/Edit Field Forms
 */

/**
 * Add Field Form
 *
 * This form is meant to be called from a bulk loader form. Blank Defaults are in place but you
 * can use the following in the query of the path to set defaults for a given template:
 *  - template_id=\d+: the template to add the field to
 *  - record_id=\d+: the priority or key in the template array of the record to add the field to
 *
 * @param $form_state
 *   Contains the values and storage for the form
 * @return
 *   A form array to be rendered by drupal_get_form
 */
function tripal_bulk_loader_add_template_field_form(&$form_state = NULL) {
  $form = array();
  $form['#cache'] = TRUE; // Make sure the form is cached.

  // get template id from path
  $template_id = ($_GET['template_id']) ? $_GET['template_id'] : $form_state['values']['template_id'];

  // if there is no template supplied don't return rest of form
  if (!$template_id) {
    return $form;
  }

  // Pre-set Variables needed for form proper------------------------------------------

   // If this is the first load of the form (no form state) we need to initialize some variables
  if (!$form_state['storage']['template']) {
    $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
    $template = db_fetch_object(db_query($sql, $template_id));
    $form_state['storage']['template_array'] = unserialize($template->template_array);
    $form_state['storage']['template'] = $template;

    $form_state['storage']['record2priority'] = array();
    foreach ($form_state['storage']['template_array'] as $priority => $record_array) {
      if (!is_array($record_array)) {
        continue;
      }
      $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
    }

    $form_state['storage']['referring URL'] = $_SERVER["HTTP_REFERER"];
  }
  else {
    $template = $form_state['storage']['template'];
  }

  $field_type = ($form_state['values']['field_type'])? $form_state['values']['field_type'] : 'table field';

  // Tables and default table
  $tables = tripal_core_get_chado_tables(TRUE);
  if ($form_state['values']) {
    if (!preg_match('/^' . current($tables) . '$/', $form_state['values']['chado_table'])) {
      $table = $form_state['values']['chado_table'];
    }
    elseif ($form_state['values']['record_name']) {
      $record_name = $form_state['values']['record_name'];
      $priority = $form_state['storage']['record2priority'][$record_name];
      $table = $form_state['storage']['template_array'][$priority]['table'];
    }
    else {
      $priority = $form_state['values']['field_group'];
      $table = $form_state['storage']['template_array'][$priority]['table'];
    }
  }
  if (!$table) {
    $table = reset($tables);
  }

  // get the record_id from the path
  if ($_GET['record_id'] !== NULL) {
    $form_state['values']['field_group'] = $_GET['record_id'];
    if (preg_match('/\d+/', $_GET['record_id'])) {
      $priority = $form_state['values']['field_group'];
      $table = $form_state['storage']['template_array'][$priority]['table'];
    }
  }

  $show_all = $form_state['values']['show_all_records'];

  $table_description = tripal_core_get_chado_table_schema($table);

  // Fields and foreign key / referral mappings
  // build the fields array
  $chado_fields = array();
  foreach ($table_description['fields'] as $field_name => $field_array) {
    $chado_fields[$field_name] = $field_name;
  }

  $fk_options = array();
  $fk_options['NULL'] = 'None';
  if ($field_type == 'foreign key' and !$show_all) {

    $foreign_field2table = array();
    foreach ($table_description['foreign keys'] as $key_table => $key_array) {
      foreach ($key_array['columns'] as $left_field => $right_field) {
        //$chado_fields[$left_field] = $left_field;
        $foreign_field2table[$left_field] = $key_table;
      }
    }
//   reset($chado_fields);

    // set default field
    if (empty($chado_fields)) {
      $field = NULL;
    }
    elseif ($chado_fields[$form_state['values']['chado_field']]) {
      $field = $form_state['values']['chado_field'];
    }
    else {
      $field = current($chado_fields);
    }

    // Foreign key options
    $foreign_table = $foreign_field2table[$field];
    if ($foreign_table) {
      foreach ($form_state['storage']['record2priority'] as $record_name => $priority ) {
        if (preg_match('/^' . $foreign_table . '$/', $form_state['storage']['template_array'][$priority]['table'])) {
          $fk_options[$record_name] = $record_name;
        }
      }
    }
  }
  // the user wants to see all of the records
  elseif ($field_type == 'foreign key' and $show_all) {
    foreach ($form_state['storage']['record2priority'] as $record_name => $priority ) {
      $fk_options[$record_name] = $record_name;
    }
  }

  // build the list of referrer table fields. This list is used
  // for the referring table field drop down. It has two groups
  // one for foreign keys and another for additional fields.
  $ref_chado_fields = array();
  if ($field_type == 'foreign key') {
    $fk_rec = $form_state['values']['foreign_record'];
    if ($fk_rec and $fk_rec != 'None' and $fk_rec != 'NULL') {

      // first add in the foreign key field in the referring table
      // that corresponds to this field (if one exists).
      $fk_priority = $form_state['storage']['record2priority'][$fk_rec];
      $fk_table = $form_state['storage']['template_array'][$fk_priority]['table'];
      foreach ($table_description['foreign keys'] as $key_table => $key_array) {
        foreach ($key_array['columns'] as $left_field => $right_field) {
          if ($key_table == $fk_table and $left_field == $field) {
            $ref_chado_fields['Foreign Key'][$right_field] = $right_field;
          }
        }
      }
      // now add in the remaining fields of the referring record's table.
      $fk_description = tripal_core_get_chado_table_schema($fk_table);
      foreach ($fk_description['fields'] as $fk_field_name => $fk_farray) {
        // don't include the FK field it's included above
        if (in_array('Foreign Key', $ref_chado_fields)) {
          if (in_array($fk_field_name, $ref_chado_fields['Foreign Key'])) {
            continue;
          }
        }
        $ref_chado_fields['Additional Table Fields'][$fk_field_name] = $fk_field_name;
      }
    }
  }

  // Ensure other field type fields are reset/cleared except for those of the current type
  // ie: if the type is changed from spreadsheet column to constant, the spreadsheet column
  // fields should be cleared since they don't apply to a constant
  switch ($field_type) {
    case 'table field':
      // clear constant
      $form_state['values']['constant_value'] = NULL;
      // clear foreign key
      // clears by default :)
      break;
    case 'constant':
      // clear spreadsheet column
      $form_state['values']['column_number'] = NULL;
      $form_state['values']['column_exposed'] = NULL;
      $template_field['exposed'] = NULL;
      $form_state['values']['column_exposed_desc'] = NULL;
      $template_field['exposed_description'] = NULL;
      // clear foreign key
      // clears by default :)
      break;
    case 'foreign key':
      // clear constant
      $form_state['values']['constant_value'] = NULL;
      // clear spreadsheet column
      $form_state['values']['column_number'] = NULL;
      $form_state['values']['column_exposed'] = NULL;
      $template_field['exposed'] = NULL;
      $form_state['values']['column_exposed_desc'] = NULL;
      $template_field['exposed_description'] = NULL;
      break;
  }

  // Start of Form Proper-------------------------------------------------------------

  $form['template_name'] = array(
    '#type' => 'item',
    '#title' => 'Template',
    '#value' => $template->name,
  );

  $form['template_id'] = array(
    '#type' => 'hidden',
    '#value' => $template_id,
  );

  $form['add_fields'] = array(
    '#type' => 'fieldset',
    '#prefix' => '<div id="tripal_bulk_loader_template-add_field">',
    '#suffix' => '</div>',
  );

  $form['add_fields']['field_type'] = array(
    '#type' => 'radios',
    '#title' => t('Type of Field'),
    '#options' => array(
      'table field' => t('Data: A Field which maps to a column in the supplied file.'),
      'constant' => t('Constant: Field which remains Constant throughout the file'),
      'foreign key' => t('Record Referral: Fields which map to a record in another table'),
    ),
    '#required' => TRUE,
    '#default_value' => $field_type,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
    ),
  );

  // check template array for records then add one more
  if (!$form_state['storage']['record2priority']) {
    $groups = array();
  }
  else {
    $groups = array_flip($form_state['storage']['record2priority']);
  }
  $groups['NONE'] = 'Select a Record';
  $groups['NEW'] = 'New Record';
  $form['add_fields']['field_group']  = array(
    '#type' => 'select',
    '#title' => 'Record',
    '#description' => 'This is used to group a set of fields together allowing '
      .'multiple records to be inserted into the same table per line of the file',
    '#options' => $groups,
    '#default_value' => (preg_match('/\w+.*/', $form_state['values']['field_group'])) ? $form_state['values']['field_group'] : 'NONE',
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
    ),
    '#required' => TRUE,
  );

  $form['add_fields']['record_name'] = array(
    '#type' => (preg_match('/NEW/', $form_state['values']['field_group'])) ? 'textfield' : 'hidden',
    '#title' => 'Unique Record Name',
    '#prefix' => '<div id="tripal_bulk_loader_template-add_record">',
    '#suffix' => '</div>',
    '#default_value' => $form_state['values']['record_name'],
  );

  $form['add_fields']['field_title'] = array(
    '#type' => 'textfield',
    '#title' => t('Human-readable Title for Field'),
    '#default_value' => $form_state['values']['field_title'],
  );


  // Chado Field
  $form['add_fields']['chado'] = array(
    '#type' => 'fieldset',
    '#title' => t('Chado Field/Column Details'),
    '#description' => t('Specify the Table/Field in chado that this field maps to.'),
  );

  $form['add_fields']['chado']['chado_table'] = array(
    '#type' => 'select',
    '#title' => t('Chado Table'),
    '#options' => $tables,
    '#default_value' => $table,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
      ),
  );

  $form['add_fields']['chado']['chado_field'] = array(
    '#type' => 'select',
    '#title' => t('Chado Field/Column'),
    '#options' => $chado_fields,
    '#default_value' => $form_state['values']['chado_field'],
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
    ),
  );

  // loading file data column
  $form['add_fields']['columns'] = array(
    '#type' => 'fieldset',
    '#title' => t('Data File Column'),
    '#collapsible' => TRUE,
    '#collapsed' => ($field_type == 'table field')? FALSE : TRUE,
  );

  /**
  $form['add_fields']['columns']['sheet_name'] = array(
    '#type' => 'textfield',
    '#title' => t('Worksheet'),
    '#description' => t('Specify the name of the worksheet.'),
    '#size' => 5,
    '#default_value' => ($form_state['values']['sheet_name'])? $form_state['values']['sheet_name'] : 'Sheet1',
  );
  */

  $form['add_fields']['columns']['column_number'] = array(
    '#type' => 'textfield',
    '#title' => t('Column'),
    '#description' => t('Specify the column in the data that this field maps to where the first column is 1.'),
    '#size' => 5,
    '#default_value' => $form_state['values']['column_number'],
  );

  $form['add_fields']['columns']['column_exposed'] = array(
    '#type' => 'checkbox',
    '#title' => t('Allow Column to be set for each Bulk Loading Job'),
    '#description' => t('Adds a textbox field to the Bulk Loader Page to allow users to set this value.'),
    '#default_value' => ($form_state['values']['column_exposed']) ? $form_state['values']['column_exposed'] : $template_field['exposed'],
  );

  $form['add_fields']['columns']['column_exposed_desc'] = array(
    '#type' => 'textfield',
    '#title' => t('Description for exposed field on bulk loading job'),
    '#description' => t('This description should tell the user what column should be entered here.'),
    '#default_value' => ($form_state['values']['column_exposed_desc']) ? $form_state['values']['column_exposed_desc'] : $template_field['exposed_description'],
  );

  // Global Value
  $form['add_fields']['constant'] = array(
    '#type' => 'fieldset',
    '#title' => t('Constant'),
    '#collapsible' => TRUE,
    '#collapsed' => ($field_type == 'constant')? FALSE : TRUE,
  );

  $form['add_fields']['constant']['constant_value'] = array(
    '#type' => 'textfield',
    '#title' => t('Constant Value'),
    '#description' => t('Specify the value you wish this field to have regardless of data file value.'),
    '#default_value' => $form_state['values']['constant_value']
  );

  $form['add_fields']['constant']['constant_exposed'] = array(
    '#type' => 'checkbox',
    '#title' => t('Allow Constant to be set for each Bulk Loading Job'),
    '#description' => t('Adds a textbox field to the Create Bulk Loader Form to allow users to set this value.')
  );

  $form['add_fields']['constant']['constant_validate'] = array(
    '#type' => 'checkbox',
    '#title' => t('Ensure value is in table'),
    '#description' => t('Checks the database when a bulk loading job is created to ensure the value entered already exists in the database.'),
  );

  // Foreign Key / Referrer
  $form['add_fields']['foreign_key'] = array(
    '#type' => 'fieldset',
    '#title' => 'Record Referral',
    '#collapsible' => TRUE,
    '#collapsed' => ($field_type == 'foreign key')? FALSE : TRUE,
  );

  $form['add_fields']['foreign_key']['show_all_records'] = array(
    '#type' => 'checkbox',
    '#title' => 'Refer to any record',
    '#description' => t('By default, the bulk loader will only allow referral to records in a foreign key relationship.  To allow referral to any previous record, check this box'),
    '#default_value' => $show_all,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
    ),
  );

  $form['add_fields']['foreign_key']['foreign_record'] = array(
    '#type' => 'select',
    '#title' => 'Record to refer to',
    '#descripion' => 'Select the record that this value should refer to. The record needs to already exist.',
    '#options' => $fk_options,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
    ),
    '#default_value' => ($form_state['values']['foreign_record']) ? $form_state['values']['foreign_record'] : $template_field['foreign key'],
  );

  $form['add_fields']['foreign_key']['foreign_field'] = array(
    '#type' => 'select',
    '#title' => 'Field to refer to',
    '#descripion' => 'Select the record that this value should refer to. The record needs to already exist.',
    '#options' => $ref_chado_fields,
    '#default_value' => ($form_state['values']['foreign_field']) ? $form_state['values']['foreign_field'] : $template_field['foreign_field'],
  );


  $form['add_fields']['additional'] = array(
    '#type' => 'fieldset',
    '#title' => 'Additional Options',
  );

  $form['add_fields']['additional']['required'] = array(
    '#type' => 'checkbox',
    '#title' => 'Make this field required',
    '#default_value' => (!empty($form_state['values']['required'])) ? $form_state['values']['required'] : $template_field['required'],
  );

  $form['add_fields']['additional']['regex_transform'] = array(
    '#type' => 'fieldset',
    '#title' => 'Transform Data File Value Rules',
    '#collapsible' => TRUE,
    '#collapsed' => (!$form_state['storage']['regex']['pattern']) ? TRUE : FALSE,
  );

  $form['add_fields']['additional']['regex_transform']['regex_description'] = array(
    '#type' => 'item',
    '#value' => 'A transformation rule allows you to transform the original value '
      .'(usually from a user submitted data file) into the form you would like it stored '
      .'in the chado database. Each rule consists of a match pattern (a php regular expression '
      .'which determines which replacement patterns are applied and captures regions of the '
      .'original value) and a replacement pattern (a string which may contain capture references '
      .'that describes what the new value should be). Each rule is applied to the result of the '
      .'previous rule.'
  );

  $form['add_fields']['additional']['regex_transform']['regex-data'] = array(
    '#tree' => TRUE,
  );
  if (!$form_state['storage']['regex']['pattern']) {
    $form_state['storage']['regex']['pattern'] = array();
  }
  foreach ($form_state['storage']['regex']['pattern'] as $index => $pattern) {
    $data_element = array(
      'pattern' => array(
        '#type' => 'item',
        '#value' => $pattern,
      ),
      'replace' => array(
        '#type' => 'item',
        '#value' => $form_state['storage']['regex']['replace'][$index],
      ),
      'old_index' => array(
        '#type' => 'hidden',
        '#value' => $index,
      ),
      'new_index' => array(
        '#type' => 'select',
        '#options' => range(0, sizeof($form_state['storage']['regex']['pattern'])-1),
        '#default_value' => $index,
      ),
      'id' => array(
        '#type' => 'hidden',
        '#value' => $index,
      ),
      'submit-delete' => array(
        '#type' => 'submit',
        '#value' => 'Delete Transformation',
        '#name' => $index,
      ),
    );
    $form['add_fields']['additional']['regex_transform']['regex-data'][$index] = $data_element;
  }

  $form['add_fields']['additional']['regex_transform']['submit-reorder_regex'] = array(
    '#type' => ($form_state['storage']['regex']['pattern']) ? 'submit' : 'hidden',
    '#value' => 'Save Transformation Rule Order'
  );

  $form['add_fields']['additional']['regex_transform']['new_regex'] = array(
    '#type' => 'fieldset',
    '#title' => 'Add a new Transformation Rule',
  );

  $form['add_fields']['additional']['regex_transform']['new_regex']['pattern'] = array(
    '#type' => 'textfield',
    '#title' => 'Match Pattern',
    '#description' => 'You can use standard php regular expressions in this field to specify a '
      .'pattern. Only if this pattern matches the value in the data file does the replacement '
      .'pattern get applied to the value. To capture a section of your value for use in the '
      .'replacement patten surround with round brackets. For example, <i>GI:(\d+)</i> will match '
      .' NCBI gi numbers and will capture the numerical digits for use in the replacement pattern. '
      .' To match and capture any value use <i>.*</i>',
  );

  $form['add_fields']['additional']['regex_transform']['new_regex']['replace'] = array(
    '#type' => 'textfield',
    '#title' => 'Replacement Pattern',
    '#description' => 'This pattern should contain the text you want to replace the match pattern '
    .'mentioned above. It can include references of the form \n where n is the number of the '
    .'capture in the match pattern. For example, \1 will be replaced with the text matched in your '
    .'first set of round brackets.',
  );

  if ($field_type == 'table field') {
    $tab = '&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp';
    $form['add_fields']['additional']['regex_transform']['new_regex']['replace']['#description'] .= '<p>'
      .'The following references are also available for data file fields: <b><#column:<i>number</i>#></b>. '
      .'This allows you to substitute other data file values into the current field. For example, '
      .'if you had the following line:<br />'
      . $tab . 'SNP' . $tab . '15-Jan-2011' . $tab . '1' . $tab . '54' . $tab . 'Contig34355'
      .'<br /> and your current field is for column #1 and you\'re inserting into the chado field '
      .'feature.uniquename then you might want to add in the data to ensure your uniquename is '
      .'unique. The Match Pattern is (.*) to select all the first column and the Replacement '
      .'Pattern could be \1_<#column:2#> which would insert SNP_15-Jan-2011 into the database.</p>';
  }

  $form['add_fields']['additional']['regex_transform']['new_regex']['submit-add_transform'] = array(
    '#type' => 'submit',
    '#value' => 'Add Transformation',
  );

  $form['add_fields']['additional']['regex_transform']['test_regex'] = array(
    '#type' => 'fieldset',
    '#title' => 'Test Transformation Rules',
  );

  $form['add_fields']['additional']['regex_transform']['test_regex']['test_string'] = array(
    '#type' => 'textfield',
    '#title' => 'Test Value',
    '#description' => 'This should be a value that you expect the above transformation rules '
      .'to be applied to.',
    '#default_value' => $form_state['storage']['test_regex_test'],
  );

  $form['add_fields']['additional']['regex_transform']['test_regex']['test_result'] = array(
    '#type' => 'textfield',
    '#title' => 'Test Result',
    '#description' => 'This is the value that would be saved to the database after the above transformation '
      .'riles were applied to the Test Value.',
    '#default_value' => $form_state['storage']['test_regex_result'],
  );

  $form['add_fields']['additional']['regex_transform']['test_regex']['submit-test'] = array(
    '#type' => 'submit',
    '#value' => 'Test Transformation Rules'
  );

  $form['add_fields']['submit-add_field'] = array(
      '#type' => 'submit',
      '#value' => 'Save Changes'
  );

  $form['add_fields']['submit-cancel'] = array(
      '#type' => 'submit',
      '#value' => 'Cancel'
  );

  return $form;
}

function tripal_bulk_loader_add_template_field_form_validate($form, $form_state) {

  // Don't worry about validation when Cancel button is clicked
  if ($form_state['clicked_button']['#value'] == 'Save Changes') {
    $is_unique = tripal_bulk_loader_is_record_name_unique(
      $form_state['values']['record_name'],
      $form_state['values']['template_id'],
      $form_state['storage']['template_array']
    );
    $new_record = ($form_state['values']['field_group'] == 'NEW') ? TRUE : FALSE;
    if ((!$is_unique) AND $new_record) {
      form_set_error('record_name', "New Record Name must be unique. '" . $form_state['values']['record_name'] . "' is not unique.");
    }
  }

}

/**
 * Add Field Submit
 *
 * @param $form
 *   The form that was submitted
 * @param $form_state
 *   The values and storage for the form
 */
function tripal_bulk_loader_add_template_field_form_submit($form, &$form_state) {

  $op = $form_state['values'][ $form_state['clicked_button']['#name'] ];

  if (!$form_state['ahah_submission']) {
    if ($op ==  'Save Changes') {

      $template = $form_state['storage']['template_array'];

       // If new record
      if (preg_match('/NEW/', $form_state['values']['field_group'])) {
        $record_name = $form_state['values']['record_name'];
        $priority = sizeof($form_state['storage']['template_array']) + 1;
        $record2priority[$record_name] = $priority;
        $template[$priority]['table'] = $form_state['values']['chado_table'];
        $template[$priority]['record_id'] = $record_name;

      }
      else {
        $priority = $form_state['values']['field_group'];
        $record_name = $record2priority[$priority];
      }

      // Add field to template array
      if ($form_state['values']['field_type'] == 'table field') {
        $field = array(
          'type' => 'table field',
          'title' => $form_state['values']['field_title'],
          'field' => $form_state['values']['chado_field'],
          'required' => $form_state['values']['required'],
          //'allowed values' => empty by default,
          'spreadsheet column' => $form_state['values']['column_number'],
          'exposed' => $form_state['values']['column_exposed'],
          'exposed_description' => $form_state['values']['column_exposed_desc'],
        );
      }
      elseif ($form_state['values']['field_type'] == 'constant') {
        $field = array(
          'type' => 'constant',
          'title' => $form_state['values']['field_title'],
          'field' => $form_state['values']['chado_field'],
          'required' => $form_state['values']['required'],
          //'allowed values' => empty by default,
          'constant value' => $form_state['values']['constant_value'],
          'exposed' => $form_state['values']['constant_exposed'],
          'exposed_validate' => $form_state['values']['constant_validate'],
        );
      }
      elseif ($form_state['values']['field_type'] == 'foreign key') {
        $field = array(
          'type' => 'foreign key',
          'title' => $form_state['values']['field_title'],
          'field' => $form_state['values']['chado_field'],
          'show_all_records' => $form_state['values']['show_all_records'],
          'foreign key' => $form_state['values']['foreign_record'],
          'foreign field' => $form_state['values']['foreign_field'],
          'required' => $form_state['values']['required'],
        );
      }

      // Deal with any additional options
      if ($form_state['storage']['regex']) {
        $field['regex'] = $form_state['storage']['regex'];
      }

      // Save Template
      $template[$priority]['fields'][] = $field;
      $form_state['storage']['template']->template_array = serialize($template);
      $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));

      if ($success) {
        drupal_set_message(t('Successfully Added Field to Template'));
        drupal_set_message(t('Template Saved.'));

        $path = explode('?', $form_state['storage']['referring URL']);
        parse_str($path[1], $query);
        $query['template_id'] = $form_state['storage']['template']->template_id;
        drupal_goto($path[0], $query);
      }
      else {
        drupal_set_message(t('Unable to Save Template!'), 'error');
        watchdog('T_bulk_loader',
          'Unable to save bulk loader template: %template',
          array('%template' => print_r($form_state['storage']['template'], TRUE)),
          WATCHDOG_ERROR
        );
      }
    }
    elseif ($op ==  'Cancel') {
        $path = explode('?', $form_state['storage']['referring URL']);
        parse_str($path[1], $query);
        $query['template_id'] = $form_state['storage']['template']->template_id;
        drupal_goto($path[0], $query);
    }
    elseif ($op == 'Add Transformation') {

      // Add transformation rule to original field
      $form_state['storage']['regex']['pattern'][] = '/' . $form_state['values']['pattern'] . '/';
      $form_state['storage']['regex']['replace'][] = $form_state['values']['replace'];
      drupal_set_message(t('Successfully Added Transformation Rule'));

    }
    elseif ($op == 'Save Transformation Rule Order') {

      // Generate new regex array
      $new_regex = array();
      $old_regex = $form_state['storage']['regex'];
      foreach ($form_state['values']['regex-data'] as $key => $element) {
        $new_regex['pattern'][ $element['new_index'] ] = $old_regex['pattern'][ $element['old_index'] ];
        $new_regex['replace'][ $element['new_index'] ] = $old_regex['replace'][ $element['old_index'] ];
      }

      // sort new regex arrays
      ksort($new_regex['pattern']);
      ksort($new_regex['replace']);

      $form_state['storage']['regex'] = $new_regex;
    }
    elseif ($op == 'Delete Transformation') {

      // Unset regex rule
      $index = $form_state['clicked_button']['#name'];
      unset($form_state['storage']['regex']['pattern'][$index]);
      unset($form_state['storage']['regex']['replace'][$index]);

    }
    elseif ($op == 'Test Transformation Rules') {

      $patterns = $form_state['storage']['regex']['pattern'];
      $replaces = $form_state['storage']['regex']['replace'];
      $test_string = $form_state['values']['test_string'];
      $form_state['storage']['test_regex_result'] = preg_replace($patterns, $replaces, $test_string);
      $form_state['storage']['test_regex_test'] = $test_string;
    }
  }

}

/**
 * Edit Field Form
 *
 * This form is meant to be called from a bulk loader form. The following should be set
 * in the query section of the path:
 *  - template_id=\d+: the template which the edited field is part of
 *  - record_id=\d+: the priority or key in the template array of the record the field
 *      is currently part of
 *  - field_index=\d+: the key of the field in the fields array of the previously
 *      specified record
 *
 * @param $form_state
 *   Contains the values and storage for the form
 * @return
 *   A form array to be rendered by drupal_get_form
 */
function tripal_bulk_loader_edit_template_field_form(&$form_state = NULL) {
  $form = array();
  $form['#cache'] = TRUE; // Make sure the form is cached.

  // get template id from path
  $template_id = ($_GET['template_id']) ? $_GET['template_id'] : $form_state['values']['template_id'];

  // if there is no template supplied don't return rest of form
  if (!$template_id) {
    return $form;
  }

  // Pre-set Variables needed for form proper------------------------------------------

  // If this is the first load of the form (no form state) we need to initialize some variables
  if (!$form_state['storage']['template']) {
    $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
    $template = db_fetch_object(db_query($sql, $template_id));
    $form_state['storage']['template_array'] = unserialize($template->template_array);
    $form_state['storage']['template'] = $template;

    $form_state['storage']['record2priority'] = array();
    foreach ($form_state['storage']['template_array'] as $priority => $record_array) {
      if (!is_array($record_array)) {
        continue;
      }
      $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
    }

    $form_state['storage']['referring URL'] = $_SERVER["HTTP_REFERER"];
  }
  else {
    $template = $form_state['storage']['template'];
  }

  // get the field from the path
  if (!($_GET['record_id']===NULL || $_GET['field_index']===NULL)) {
    $priority = $_GET['record_id'];
    $field_index = $_GET['field_index'];
    $template_field = $form_state['storage']['template_array'][$priority]['fields'][$field_index];
    $form_state['storage']['original_field'] = $template_field;
    $form_state['storage']['original_field']['priority'] = $priority;
    $form_state['storage']['original_field']['field_index'] = $field_index;
  }
  // get field from the form_state
  elseif (!empty($form_state['storage']['original_field']['priority']) && !empty($form_state['storage']['original_field']['field_index'])) {
    $priority = $form_state['storage']['original_field']['priority'];
    $field_index = $form_state['storage']['original_field']['field_index'];
    $template_field = $form_state['storage']['template_array'][$priority]['fields'][$field_index];
  }

  $field_type = ($form_state['values']['field_type'])? $form_state['values']['field_type'] : $template_field['type'];

  // Get the tables array and default table
  $tables = tripal_core_get_chado_tables(TRUE);
  if ($form_state['values']) {
    $table = $form_state['values']['chado_table'];
  }
  else {
    $table = $form_state['storage']['template_array'][$priority]['table'];
  }

  $show_all = ($form_state['values']['show_all_records'] ? $form_state['values']['show_all_records'] : $template_field['show_all_records']);
  $table_description = tripal_core_get_chado_table_schema($table);

  // Fields and foreign key / referral mappings
  // build the fields array
  $chado_fields = array();
  foreach ($table_description['fields'] as $field_name => $field_array) {
    $chado_fields[$field_name] = $field_name;
  }

  $ref_chado_fields = array();
  $fk_options = array();
  $fk_options['NULL'] = 'None';
  if ($field_type == 'foreign key' and !$show_all) {

    $foreign_field2table = array();
    foreach ($table_description['foreign keys'] as $key_table => $key_array) {
      foreach ($key_array['columns'] as $left_field => $right_field) {
        //$chado_fields[$left_field] = $left_field;
        $foreign_field2table[$left_field] = $key_table;
      }
    }
//    reset($chado_fields);

    // set default field
    if (empty($chado_fields)) {
      $field = NULL;
    }
    elseif ($chado_fields[$form_state['values']['chado_field']]) {
      $field = $form_state['values']['chado_field'];
    }
    elseif ($template_field['field']) {
      $field = $template_field['field'];
    }
    else {
      $field = current($chado_fields);
    }

    // Foreign key options
    $foreign_table = $foreign_field2table[$field];
    if ($foreign_table) {
      foreach ($form_state['storage']['record2priority'] as $record_name_ => $priority_ ) {
        if (preg_match('/^' . $foreign_table . '$/', $form_state['storage']['template_array'][$priority_]['table'])) {
          $fk_options[$record_name_] = $record_name_;
        }
      }
    }
  }
  // the user wants to see all of the records
  elseif ($field_type == 'foreign key' and $show_all) {
    foreach ($form_state['storage']['record2priority'] as $record_name => $priority ) {
      $fk_options[$record_name] = $record_name;
    }
  }

  // build the list of referrer table fields
  if ($field_type == 'foreign key') {
    $fk_rec = $form_state['values']['foreign_record'] ?  $form_state['values']['foreign_record'] : $template_field['foreign key'];
    if ($fk_rec and $fk_rec != 'None' and $fk_rec != 'NULL') {

      // first add in the foreign keys
      $fk_priority = $form_state['storage']['record2priority'][$fk_rec];
      $fk_table = $form_state['storage']['template_array'][$fk_priority]['table'];
      foreach ($table_description['foreign keys'] as $key_table => $key_array) {
        foreach ($key_array['columns'] as $left_field => $right_field) {
          if ($key_table == $fk_table and $left_field == $field) {
            $ref_chado_fields['Foreign Key'][$right_field] = $right_field;
          }
        }
      }
      $fk_description = tripal_core_get_chado_table_schema($fk_table);
      foreach ($fk_description['fields'] as $fk_field_name => $fk_farray) {
         // don't include the FK field it's included above
         if (in_array('Foreign Key', $ref_chado_fields) and
             in_array($fk_field_name, $ref_chado_fields['Foreign Key'])) {
           continue;
         }
         $ref_chado_fields['Additional Table Fields'][$fk_field_name] = $fk_field_name;
      }
    }
  }

  // Ensure other field type fields are reset/cleared except for those of the current type
  // ie: if the type is changed from spreadsheet column to constant, the spreadsheet column
  // fields should be cleared since they don't apply to a constant
  switch ($field_type) {
    case 'table field':
      // clear constant
      $form_state['values']['constant_value'] = NULL;
      $template_field['constant value'] = NULL;
      $form_state['values']['constant_exposed'] = NULL;
      $template_field['exposed'] = NULL;
      $form_state['values']['constant_validate'] = NULL;
      $template_field['exposed_validate'] = NULL;
      // clear foreign key
      // clears by default :)
      break;
    case 'constant':
      // clear spreadsheet column
      $form_state['values']['column_number'] = NULL;
      $form_state['values']['column_exposed'] = NULL;
      $template_field['exposed'] = NULL;
      $form_state['values']['column_exposed_desc'] = NULL;
      $template_field['exposed_description'] = NULL;
      // clear foreign key
      // clears by default :)
      break;
    case 'foreign key':
      // clear constant
      $form_state['values']['constant_value'] = NULL;
      $template_field['constant value'] = NULL;
      $form_state['values']['constant_exposed'] = NULL;
      $template_field['exposed'] = NULL;
      $form_state['values']['constant_validate'] = NULL;
      $template_field['exposed_validate'] = NULL;
      // clear spreadsheet column
      $form_state['values']['column_number'] = NULL;
      $form_state['values']['column_exposed'] = NULL;
      $template_field['exposed'] = NULL;
      $form_state['values']['column_exposed_desc'] = NULL;
      $template_field['exposed_description'] = NULL;
      break;
  }

  // Start of Form Proper--------------------------------------------------------------

  $form['template_name'] = array(
    '#type' => 'item',
    '#title' => 'Template',
    '#value' => $template->name,
  );

  $form['template_id'] = array(
    '#type' => 'hidden',
    '#value' => $template_id,
  );

  $form['edit_fields'] = array(
    '#type' => 'fieldset',
    '#prefix' => '<div id="tripal_bulk_loader_template-edit_field">',
    '#suffix' => '</div>',
  );

  $form['edit_fields']['field_type'] = array(
    '#type' => 'radios',
    '#title' => t('Type of Field'),
    '#options' => array(
      'table field' => t('Data Field: Fields which maps to a data file column'),
      'constant' => t('Constant: Field which remains Constant throughout the data file'),
      'foreign key' => t('Record Referral: Fields which map to a record in another table'),
    ),
    '#required' => TRUE,
    '#default_value' => $field_type,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-edit_field',
      'effect' => 'fade'
    ),
  );

  // check template array for records then edit one more
  if (!$form_state['storage']['record2priority']) {
    $groups = array();
  }
  else {
    $groups = array_flip($form_state['storage']['record2priority']);
  }
  $groups['NONE'] = 'Select a Record';
  $groups['NEW'] = 'New Record';
  $form['edit_fields']['field_group']  = array(
    '#type' => 'select',
    '#title' => 'Record',
    '#description' => 'This is used to group a set of fields together allowing '
      .'multiple records to be inserted into the same table per line of the data file',
    '#options' => $groups,
    '#default_value' => (preg_match('/(\d+|\w+)/', $form_state['values']['field_group'])) ? $form_state['values']['field_group'] : $priority,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-edit_field',
      'effect' => 'fade'
    ),
    '#required' => TRUE,
  );

  $form['edit_fields']['record_name'] = array(
    '#type' => (preg_match('/NEW/', $form_state['values']['field_group'])) ? 'textfield' : 'hidden',
    '#title' => 'Unique Record Name',
    '#prefix' => '<div id="tripal_bulk_loader_template-edit_record">',
    '#suffix' => '</div>',
    '#default_value' => $form_state['values']['record_name'],
  );

  $form['edit_fields']['field_title'] = array(
    '#type' => 'textfield',
    '#title' => t('Human-readable Title for Field'),
    '#default_value' => ($form_state['values']['field_title']) ? $form_state['values']['field_title'] : $template_field['title'],
  );

   // Chado Field
  $form['edit_fields']['chado'] = array(
    '#type' => 'fieldset',
    '#title' => t('Chado Field/Column Details'),
    '#description' => t('Specify the Table/Field in chado that this field maps to.'),
  );

  $form['edit_fields']['chado']['chado_table'] = array(
    '#type' => 'select',
    '#title' => t('Chado Table'),
    '#options' => $tables,
    '#default_value' => $table,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-edit_field',
      'effect' => 'fade'
      ),
  );

  $form['edit_fields']['chado']['chado_field'] = array(
    '#type' => 'select',
    '#title' => t('Chado Field/Column'),
    '#options' => $chado_fields,
    '#default_value' => ($form_state['values']['chado_field']) ? $form_state['values']['chado_field'] : $template_field['field'],
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-edit_field',
      'effect' => 'fade'
    ),
  );

  // data file column
  $form['edit_fields']['columns'] = array(
    '#type' => 'fieldset',
    '#title' => t('Data File Column'),
    '#collapsible' => TRUE,
    '#collapsed' => ($field_type == 'table field')? FALSE : TRUE,
  );

  /**
  $form['edit_fields']['columns']['sheet_name'] = array(
    '#type' => 'textfield',
    '#title' => t('Worksheet'),
    '#description' => t('Specify the name of the worksheet.'),
    '#size' => 5,
    '#default_value' => ($form_state['values']['sheet_name'])? $form_state['values']['sheet_name'] : $template_field['spreadsheet sheet'],
  );
  */

  $form['edit_fields']['columns']['column_number'] = array(
    '#type' => 'textfield',
    '#title' => t('Column'),
    '#description' => t('Specify the column in the data file that this field maps to where the first column is 1.'),
    '#size' => 5,
    '#default_value' => ($form_state['values']['column_number']) ? $form_state['values']['column_number'] : $template_field['spreadsheet column'],
  );

  $form['edit_fields']['columns']['column_exposed'] = array(
    '#type' => 'checkbox',
    '#title' => t('Allow Column to be set for each Bulk Loading Job'),
    '#description' => t('Adds a textbox field to the Bulk Loader Page to allow users to set this value.'),
    '#default_value' => ($form_state['values']['column_exposed']) ? $form_state['values']['column_exposed'] : $template_field['exposed'],
  );

  $form['edit_fields']['columns']['column_exposed_desc'] = array(
    '#type' => 'textfield',
    '#title' => t('Description for exposed field on bulk loading job'),
    '#description' => t('This description should tell the user what column should be entered here.'),
    '#default_value' => ($form_state['values']['column_exposed_desc']) ? $form_state['values']['column_exposed_desc'] : $template_field['exposed_description'],
  );

  // Global Value
  $form['edit_fields']['constant'] = array(
    '#type' => 'fieldset',
    '#title' => t('Constant'),
    '#collapsible' => TRUE,
    '#collapsed' => ($field_type == 'constant')? FALSE : TRUE,
  );

  $form['edit_fields']['constant']['constant_value'] = array(
    '#type' => 'textfield',
    '#title' => t('Constant Value'),
    '#description' => t('Specify the value you wish this field to have regardless of data file value.'),
    '#default_value' => ($form_state['values']['constant_value']) ? $form_state['values']['constant_value'] : $template_field['constant value'],
  );

  $form['edit_fields']['constant']['constant_exposed'] = array(
    '#type' => 'checkbox',
    '#title' => t('Allow Constant to be set for each Bulk Loading Job'),
    '#description' => t('Adds a textbox field to the Create Bulk Loader Form to allow users to set this value.'),
    '#default_value' => ($form_state['values']['constant_exposed']) ? $form_state['values']['constant_exposed'] : $template_field['exposed'],
  );

  $form['edit_fields']['constant']['constant_validate'] = array(
    '#type' => 'checkbox',
    '#title' => t('Ensure value is in table'),
    '#description' => t('Checks the database when a bulk loading job is created to ensure the value entered already exists in the database.'),
    '#default_value' => ($form_state['values']['constant_validate']) ? $form_state['values']['constant_validate'] : $template_field['exposed_validate'],
  );

  // Foreign Key / Referrer
  $form['edit_fields']['foreign_key'] = array(
    '#type' => 'fieldset',
    '#title' => 'Record Referral',
    '#collapsible' => TRUE,
    '#collapsed' => ($field_type == 'foreign key')? FALSE : TRUE,
  );

  $form['edit_fields']['foreign_key']['show_all_records'] = array(
    '#type' => 'checkbox',
    '#title' => 'Refer to any record',
    '#description' => t('By default, the bulk loader will only allow referral to records in a foreign key relationship.  To allow referral to any previous record, check this box'),
    '#default_value' => $show_all,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
    ),
  );

  $form['edit_fields']['foreign_key']['foreign_record'] = array(
    '#type' => 'select',
    '#title' => 'Record to refer to',
    '#descripion' => 'Select the record that this value should refer to. The record needs to already exist.',
    '#options' => $fk_options,
    '#ahah' => array(
      'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
      'wrapper' => 'tripal_bulk_loader_template-add_field',
      'effect' => 'fade'
    ),
    '#default_value' => ($form_state['values']['foreign_record']) ? $form_state['values']['foreign_record'] : $template_field['foreign key'],
  );

  $form['edit_fields']['foreign_key']['foreign_field'] = array(
    '#type' => 'select',
    '#title' => 'Field to refer to',
    '#descripion' => 'Select the record that this value should refer to. The record needs to already exist.',
    '#options' => $ref_chado_fields,
    '#default_value' => ($form_state['values']['foreign_field']) ? $form_state['values']['foreign_field'] : $template_field['foreign field'],
  );



  $form['edit_fields']['additional'] = array(
    '#type' => 'fieldset',
    '#title' => 'Additional Options',
  );

  $form['edit_fields']['additional']['required'] = array(
    '#type' => 'checkbox',
    '#title' => 'Make this field required',
    '#default_value' => (!empty($form_state['values']['required'])) ? $form_state['values']['required'] : $template_field['required'],
  );

  $form['edit_fields']['additional']['regex_transform'] = array(
    '#type' => 'fieldset',
    '#title' => 'Transform Data File Value Rules',
    '#collapsible' => TRUE,
    '#collapsed' => (!$template_field['regex']['pattern']) ? TRUE : FALSE,
  );

  $transformation_msg = '<p>A transformation rule allows you to transform the original value '
      .'(usually from a user submitted data file) into the form you would like it stored '
      .'in the chado database. Each rule consists of a match pattern (a php regular expression '
      .'which determines which replacement patterns are applied and captures regions of the '
      .'original value) and a replacement pattern (a string which may contain capture references '
      .'that describes what the new value should be). Each rule is applied to the result of the '
      .'previous rule.<p>';
  $form['edit_fields']['additional']['regex_transform']['regex_description'] = array(
    '#type' => 'item',
    '#value' => $transformation_msg,
  );

  $form['edit_fields']['additional']['regex_transform']['regex-data'] = array(
    '#tree' => TRUE,
  );

  if (!is_array($template_field['regex']['pattern'])) {
    $template_field['regex']['pattern'] = array();
  }
  $key_options = array();
  foreach ($template_field['regex']['pattern'] as $k => $v) {
    $key_options[$k] = $k;
  }
  foreach ($template_field['regex']['pattern'] as $index => $pattern) {
    $data_element = array(
      'pattern' => array(
        '#type' => 'item',
        '#value' => $pattern,
      ),
      'replace' => array(
        '#type' => 'item',
        '#value' => $template_field['regex']['replace'][$index],
      ),
      'old_index' => array(
        '#type' => 'hidden',
        '#value' => $index,
      ),
      'new_index' => array(
        '#type' => 'select',
        '#options' => $key_options,
        '#default_value' => $index,
      ),
      'id' => array(
        '#type' => 'hidden',
        '#value' => $index,
      ),
      'submit-delete' => array(
        '#type' => 'submit',
        '#value' => 'Delete Transformation',
        '#name' => $index,
      ),
    );
    $form['edit_fields']['additional']['regex_transform']['regex-data'][$index] = $data_element;
  }

  $form['edit_fields']['additional']['regex_transform']['submit-reorder_regex'] = array(
    '#type' => 'submit',
    '#value' => 'Save Transformation Rule Order'
  );

  $form['edit_fields']['additional']['regex_transform']['new_regex'] = array(
    '#type' => 'fieldset',
    '#title' => 'Add a new Transformation Rule',
  );

  $form['edit_fields']['additional']['regex_transform']['new_regex']['pattern'] = array(
    '#type' => 'textfield',
    '#title' => 'Match Pattern',
    '#description' => 'You can use standard <b>php regular expressions</b> in this field to specify a '
      .'pattern. Only if this pattern matches the value in the data file does the replacement '
      .'pattern get applied to the value. To capture a section of your value for use in the '
      .'replacement patten surround with round brackets. For example, <i>GI:(\d+)</i> will match '
      .' NCBI gi numbers and will capture the numerical digits for use in the replacement pattern. '
      .' To match and capture any value use <i>.*</i>',
  );

  $form['edit_fields']['additional']['regex_transform']['new_regex']['replace'] = array(
    '#type' => 'textfield',
    '#title' => 'Replacement Pattern',
    '#description' => '<p>This pattern should contain the text you want to replace the match pattern '
    .'mentioned above. It can include references of the form <b>\n</b> where n is the number of the '
    .'capture in the match pattern. For example, \1 will be replaced with the text matched in your '
    .'first set of round brackets.</p>',
  );

  if ($field_type == 'table field') {
    $tab = '&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp';
    $form['edit_fields']['additional']['regex_transform']['new_regex']['replace']['#description'] .= '<p>'
      .'The following references are also available for data file fields: <b><#column:<i>number</i>#></b>. '
      .'This allows you to substitute other data file values into the current field. For example, '
      .'if you had the following line:<br />'
      . $tab . 'SNP' . $tab . '15-Jan-2011' . $tab . '1' . $tab . '54' . $tab . 'Contig34355'
      .'<br /> and your current field is for column #1 and you\'re inserting into the chado field '
      .'feature.uniquename then you might want to add in the data to ensure your uniquename is '
      .'unique. The Match Pattern is (.*) to select all the first column and the Replacement '
      .'Pattern could be \1_<#column:2#> which would insert SNP_15-Jan-2011 into the database.</p>';
  }

  $form['edit_fields']['additional']['regex_transform']['new_regex']['submit-add_transform'] = array(
    '#type' => 'submit',
    '#value' => 'Add Transformation',
  );

  $form['edit_fields']['additional']['regex_transform']['test_regex'] = array(
    '#type' => 'fieldset',
    '#title' => 'Test Transformation Rules',
  );

  $form['edit_fields']['additional']['regex_transform']['test_regex']['test_string'] = array(
    '#type' => 'textfield',
    '#title' => 'Test Value',
    '#description' => 'This should be a value that you expect the above transformation rules '
      .'to be applied to.',
    '#default_value' => $form_state['storage']['test_regex_test'],
  );

  $form['edit_fields']['additional']['regex_transform']['test_regex']['test_result'] = array(
    '#type' => 'textfield',
    '#title' => 'Test Result',
    '#description' => 'This is the value that would be saved to the database after the above transformation '
      .'riles were applied to the Test Value.',
    '#default_value' => $form_state['storage']['test_regex_result'],
  );

  $form['edit_fields']['additional']['regex_transform']['test_regex']['submit-test'] = array(
    '#type' => 'submit',
    '#value' => 'Test Transformation Rules'
  );

  $form['edit_fields']['submit-edit_field'] = array(
      '#type' => 'submit',
      '#value' => 'Save Changes'
  );

  $form['edit_fields']['submit-cancel'] = array(
      '#type' => 'submit',
      '#value' => 'Cancel'
  );

  return $form;
}

function tripal_bulk_loader_edit_template_field_form_validate($form, $form_state) {

  // Don't worry about validation when Cancel button is clicked
  if ($form_state['clicked_button']['#value'] == 'Save Changes') {
    $is_unique = tripal_bulk_loader_is_record_name_unique(
      $form_state['values']['record_name'],
      $form_state['values']['template_id'],
      $form_state['storage']['template_array']
    );
    $new_record = ($form_state['values']['field_group'] == 'NEW') ? TRUE : FALSE;
    if ((!$is_unique) AND $new_record) {
      form_set_error('record_name', "New Record Name must be unique. '" . $form_state['values']['record_name'] . "' is not unique.");
    }
  }

}

/**
 * Edit Field Form Submit
 *
 * @param $form
 *   The form that was submitted
 * @param $form_state
 *   The values and storage for the form
 */
function tripal_bulk_loader_edit_template_field_form_submit($form, &$form_state) {

  $op = $form_state['values'][ $form_state['clicked_button']['#name'] ];

  //Clear Test
  $form_state['storage']['test_regex_result'] = NULL;
  $form_state['storage']['test_regex_test'] = NULL;

  if (!$form_state['ahah_submission']) {
    if ($op ==  'Save Changes') {

      // If new record
      if (preg_match('/NEW/', $form_state['values']['field_group'])) {
        // add new record
        $record_name = $form_state['values']['record_name'];
        $priority = sizeof($form_state['storage']['template_array']) + 1;
        $old_priority = $form_state['storage']['original_field']['priority'];
        $field_index = $form_state['storage']['original_field']['field_index'];
        $form_state['storage']['record2priority'][$record_name] = $priority;
        $form_state['storage']['template_array'][$priority]['table'] = $form_state['values']['chado_table'];
        $form_state['storage']['template_array'][$priority]['record_id'] = $record_name;

      }
      else {
        $priority = $form_state['values']['field_group'];
        $old_priority = $form_state['storage']['original_field']['priority'];
        $field_index = $form_state['storage']['original_field']['field_index'];
        $record_name = $form_state['storage']['record2priority'][$priority];
      }

      $field = $form_state['storage']['original_field'];
      if ($form_state['values']['field_type'] == 'table field') {
          $field['type'] = 'table field';
          $field['title'] = $form_state['values']['field_title'];
          $field['field'] = $form_state['values']['chado_field'];
          $field['required'] = $form_state['values']['required'];
          //$field['allowed values'] = empty by default;
          $field['spreadsheet column'] = $form_state['values']['column_number'];
          $field['exposed'] = $form_state['values']['column_exposed'];
          $field['exposed_description'] = $form_state['values']['column_exposed_desc'];
      }
      elseif ($form_state['values']['field_type'] == 'constant') {
          $field['type'] = 'constant';
          $field['title'] = $form_state['values']['field_title'];
          $field['field'] = $form_state['values']['chado_field'];
          $field['required'] = $form_state['values']['required'];
          //$field['allowed values'] = empty by default;
          $field['constant value'] = $form_state['values']['constant_value'];
          $field['exposed_validate'] = $form_state['values']['constant_validate'];
          $field['exposed'] = $form_state['values']['constant_exposed'];
      }
      elseif ($form_state['values']['field_type'] == 'foreign key') {
          $field['type'] = 'foreign key';
          $field['title'] = $form_state['values']['field_title'];
          $field['field'] = $form_state['values']['chado_field'];
          $field['show_all_records'] = $form_state['values']['show_all_records'];
          $field['foreign key'] = $form_state['values']['foreign_record'];
          $field['foreign field'] = $form_state['values']['foreign_field'];

          $field['required'] = $form_state['values']['required'];
      }

      // Deal with any additional options

      // if the record has changed...
      $form_state['storage']['template_array'][$priority]['table'] = $form_state['values']['chado_table'];
      if ($old_priority != $priority) {
        $form_state['storage']['template_array'][$priority]['fields'][] = $field;
        unset($form_state['storage']['template_array'][$old_priority]['fields'][$field_index]);

        // if there are no fields left delete the old record
        if (!$form_state['storage']['template_array'][$old_priority]['fields']) {
          unset($form_state['storage']['template_array'][$old_priority]);
        }
      }
      else {
        $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $field;
      }

      // Save Template
      $form_state['storage']['template']->template_array = serialize($form_state['storage']['template_array']);
      $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));

      if ($success) {
        drupal_set_message(t('Successfully Updated Field'));
        drupal_set_message(t('Template Saved.'));

        $path = explode('?', $form_state['storage']['referring URL']);
        parse_str($path[1], $query);
        $query['template_id'] = $form_state['storage']['template']->template_id;
        drupal_goto($path[0], $query);
      }
      else {
        drupal_set_message(t('Unable to Save Template!'), 'error');
        watchdog('T_bulk_loader',
          'Unable to save bulk loader template: %template',
          array('%template' => print_r($form_state['storage']['template'], TRUE)),
          WATCHDOG_ERROR
        );
      }

    }
    elseif ($op ==  'Cancel') {

        $path = explode('?', $form_state['storage']['referring URL']);
        parse_str($path[1], $query);
        $query['template_id'] = $form_state['storage']['template']->template_id;
        drupal_goto($path[0], $query);

    }
    elseif ($op == 'Add Transformation') {

      // Add transformation rule to original field
      $form_state['storage']['original_field']['regex']['pattern'][] = '/' . $form_state['values']['pattern'] . '/';
      $form_state['storage']['original_field']['regex']['replace'][] = $form_state['values']['replace'];

      // Add original field back into template
      $priority = $form_state['storage']['original_field']['priority'];
      $field_index = $form_state['storage']['original_field']['field_index'];
      $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $form_state['storage']['original_field'];

    }
    elseif ($op == 'Save Transformation Rule Order') {

      // Generate new regex array
      $new_regex = array();
      $old_regex = $form_state['storage']['original_field']['regex'];
      foreach ($form_state['values']['regex-data'] as $key => $element) {
        $new_regex['pattern'][ $element['new_index'] ] = $old_regex['pattern'][ $element['old_index'] ];
        $new_regex['replace'][ $element['new_index'] ] = $old_regex['replace'][ $element['old_index'] ];
      }

      // sort new regex arrays
      ksort($new_regex['pattern']);
      ksort($new_regex['replace']);

      // Add back to original field
      $form_state['storage']['original_field']['regex'] = $new_regex;
      $priority = $form_state['storage']['original_field']['priority'];
      $field_index = $form_state['storage']['original_field']['field_index'];
      $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $form_state['storage']['original_field'];

      /**
      // Save Template
      $form_state['storage']['template']->template_array = serialize($form_state['storage']['template_array']);
      $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));

      if ($success) {
        drupal_set_message(t('Successfully Reordered Transformation Rules'));
        drupal_set_message(t('Template Saved.'));
      }
      else {
        drupal_set_message(t('Unable to Save Template!'), 'error');
        watchdog('T_bulk_loader',
          'Unable to save bulk loader template: %template',
          array('%template' => print_r($form_state['storage']['template'], TRUE)),
          WATCHDOG_ERROR
        );
      }
      */
    }
    elseif ($op == 'Delete Transformation') {

      // Unset regex rule
      $index = $form_state['clicked_button']['#name'];
      unset($form_state['storage']['original_field']['regex']['pattern'][$index]);
      unset($form_state['storage']['original_field']['regex']['replace'][$index]);

      $priority = $form_state['storage']['original_field']['priority'];
      $field_index = $form_state['storage']['original_field']['field_index'];
      $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $form_state['storage']['original_field'];

      /**
      // Save Template
      $form_state['storage']['template']->template_array = serialize($form_state['storage']['template_array']);
      $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));

      if ($success) {
        drupal_set_message(t('Successfully Reordered Transformation Rules'));
        drupal_set_message(t('Template Saved.'));
      }
      else {
        drupal_set_message(t('Unable to Save Template!'), 'error');
        watchdog('T_bulk_loader',
          'Unable to save bulk loader template: %template',
          array('%template' => print_r($form_state['storage']['template'], TRUE)),
          WATCHDOG_ERROR
        );
      }
      */

    }
    elseif ($op == 'Test Transformation Rules') {

      $patterns = $form_state['storage']['original_field']['regex']['pattern'];
      $replaces = $form_state['storage']['original_field']['regex']['replace'];
      $test_string = $form_state['values']['test_string'];
      $form_state['storage']['test_regex_result'] = preg_replace($patterns, $replaces, $test_string);
      $form_state['storage']['test_regex_test'] = $test_string;
    }
  }

}

/**
 * @section
 * Helper Functions
 */

/**
 * Meant to be called from a form_validate function to ensure a newly added bulk loader record
 * name is unique and not empty.
 *
 * @param $new_record_name
 *   The record name to check for uniqueness
 * @param $template_id
 *   The template_id of the template to add the record to
 * @param $template_array
 *   The array describing the template. Optional -will be loaded using template_id if not provided
 * @param $current_priority
 *   The priority of the already existing record -checks that the name only occurs on this particular record
 *
 * @return
 *   TRUE if the record name is not empty and not already in the template_array; FALSE otherwise
 */
function tripal_bulk_loader_is_record_name_unique($new_record_name, $template_id, $template_array = NULL, $current_priority = NULL) {

  // get the template array if it's not supplied
  if (empty($template_array)) {
    $template = db_fetch_object(db_query("SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d", $template_id));
    $template_array = unserialize($template->template_array);
    if (!is_array($template_array)) {
      watchdog(
        'tripal_bulk_loader',
        'Unable to retrieve template array from database where template_id=%template_id',
        array('%template_id' => $template_id),
        WATCHDOG_WARNING
      );
      return FALSE;
    }
  }

  // Check that the new record name is not empty
  if (empty($new_record_name)) {
    return FALSE;
  }

  // Check the new record name is unique
  foreach ($template_array as $priority => $t) {
    if (strcmp($t['record_id'], $new_record_name) == 0) {
    	if (($priority != $current_priority) AND ($current_priority !== NULL)) {
	      return FALSE;
	    }
    }
  }
  return TRUE;
}

/**
 * @section
 * AHAH Callbacks
 */

/**
 * AHAH Function: Replace $form['add_fields'] in tripal_bulk_loader_add_template_field_form
 *
 * @return
 *  JSON Data printed to the screen
 */
function tripal_bulk_loader_add_field_ahah() {

  $form_state = array('storage' => NULL, 'submitted' => FALSE);
  $form_build_id = filter_xss($_POST['form_build_id']);
  $form = form_get_cache($form_build_id, $form_state);
  $args = $form['#parameters'];
  $form_id = array_shift($args);
  $form_state['post'] = $form['#post'] = $_POST;

  // Enable the submit/validate handlers to determine whether AHAH-submittted.
  $form_state['ahah_submission'] = TRUE;

  $form['#programmed'] = $form['#redirect'] = FALSE;
  drupal_process_form($form_id, $form, $form_state);
  $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);

  $form_element = $form['add_fields'];
  // Remove the wrapper so we don't double it up.
  //unset($form_element['#prefix'], $form_element['#suffix']);

  $output = theme('status_messages');
  $output .= drupal_render($form_element);

  // Final rendering callback.
  print drupal_json(array('status' => TRUE, 'data' => $output));
  exit();

}

/**
 * AHAH Function: Replace $form['edit_fields'] in tripal_bulk_loader_edit_template_field_form
 *
 * @return
 *  JSON Data printed to the screen
 */
function tripal_bulk_loader_edit_field_ahah() {

  $form_state = array('storage' => NULL, 'submitted' => FALSE);
  $form_build_id = filter_xss($_POST['form_build_id']);
  $form = form_get_cache($form_build_id, $form_state);
  $args = $form['#parameters'];
  $form_id = array_shift($args);
  $form_state['post'] = $form['#post'] = $_POST;

  // Enable the submit/validate handlers to determine whether AHAH-submittted.
  $form_state['ahah_submission'] = TRUE;

  $form['#programmed'] = $form['#redirect'] = FALSE;
  drupal_process_form($form_id, $form, $form_state);
  $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);

  $form_element = $form['edit_fields'];
  // Remove the wrapper so we don't double it up.
  unset($form_element['#prefix'], $form_element['#suffix']);

  $output = theme('status_messages');
  $output .= drupal_render($form_element);

  // Final rendering callback.
  print drupal_json(array('status' => TRUE, 'data' => $output));
  exit();

}