tripal/tripal_bulk_loader/includes/tripal_bulk_loader.constants.inc

<?php
/**
 * @file
 * Manages the constants form added to the tripal bulk loader node form
 *
 * @ingroup tripal_bulk_loader
 */

/**
 * Inserts/Updates a tripal bulk loading job constant
 *
 * @param $nid
 *   The node ID of the the tripal bulk loading job the constant is associated
 *   with
 * @param $table
 *   The chado table the constant is associated with
 * @param $field
 *   The chado field the constant is associated with
 * @param $record_id
 *   The index in the template array for this record
 * @param $field_id
 *   The index in the template array for this field
 *
 * NOTE: $template_array[$record_id]['table'] = $table and
 *   $template_array[$record_id]['fields'][$field_id]['field'] = $field both
 *   are included as a means of double-checking the constant still is still in
 *   thesame place in the template array. For example, that the template was
 *   not edited and the records moved around after the job was submitted but
 *   before it was run.
 *
 * @return
 *   On success it returns the object (with primary key if inserted);
 *   on failure it returns FALSE
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_update_constant($nid, $group_id, $table, $field, $record_id, $field_id, $value) {

  $record = [
    'nid' => $nid,
    'group_id' => $group_id,
    'chado_table' => $table,
    'chado_field' => $field,
    'record_id' => $record_id,
    'field_id' => $field_id,
    'value' => $value,
  ];

  // Check to see if already exists
  $exists = db_select('tripal_bulk_loader_constants', 'c')
    ->fields('c', ['constant_id'])
    ->condition('nid', $record['nid'])
    ->condition('record_id', $record['record_id'])
    ->condition('field_id', $record['field_id'])
    ->condition('group_id', $record['group_id'])
    ->execute();
  $exists = $exists->fetchObject();
  if (!isset($exists)) {
    $record['constant_id'] = $exists->constant_id;
    $status = drupal_write_record('tripal_bulk_loader_constants', $record, 'constant_id');
    if ($status) {
      return $record;
    }
    else {
      return FALSE;
    }
  }
  else {

    $status = drupal_write_record('tripal_bulk_loader_constants', $record);
    if ($status) {
      return $record;
    }
    else {
      return FALSE;
    }
  }
}

/**
 * Check if a bulk loading job has exposed constants
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_has_exposed_fields($node) {

  // exposed fields isn't set
  if (!isset($node->exposed_fields)) {
    return FALSE;
  }

  // exposed fields has at least one element
  if (sizeof($node->exposed_fields) == 1) {
    // need to check if single element is an empty array
    $element = reset($node->exposed_fields);
    if ($element) {
      return TRUE;
    }
    else {
      return FALSE;
    }
  }
  elseif (sizeof($node->exposed_fields) > 1) {
    return TRUE;
  }
  else {
    return FALSE;
  }

  return FALSE;
}

///////////////////////////////////////////////////////////
// Set Constants Form (on Bulk Loader Node)
///////////////////////////////////////////////////////////

/**
 * Set constants (exposed fields in template)
 *
 * @param $form_state
 *   The current state of the form
 * @param $node
 *   The node to set constants for
 *
 * @return
 *   A form array to be rendered by drupal_get_form()
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_set_constants_form($form, &$form_state, $node) {
  $form = [];

  $form['nid'] = [
    '#type' => 'hidden',
    '#value' => $node->nid,
  ];

  $form['#attached']['css'] = [
    drupal_get_path('module', 'tripal_bulk_loader') . '/theme/tripal_bulk_loader.css',
  ];

  $form_state['node'] = $node;

  if (!tripal_bulk_loader_has_exposed_fields($node)) {
    return $form;
  }

  // Check to see if the template has changed since this node was last updated.
  // If so we need to remove the constant set since it's no longer valid.
  if ($node->template->changed >= $node->changed AND !empty($node->constants)) {

    // Save all constants for display to the user.
    $form['old_constants'] = [
      '#type' => 'fieldset',
      '#title' => 'Previous Constant Set',
      '#description' => 'This constant set is no longer valid due to changes in
        the bulk loading template. As such you will need to re-enter it below.
        <strong>Please copy this information somewhere before leaving this page
        (including entering a constant set) because it will NOT BE SAVED.</strong>',
      '#prefix' => '<div id="expired-constants">',
      '#suffix' => '</div>',
    ];

    $form['old_constants']['table'] = [
      '#type' => 'markup',
      '#theme' => 'tripal_bulk_loader_constant_set',
      '#nid' => $node->nid,
      '#constants' => $node->constants,
      '#template' => $node->template,
      '#options' => ['display_operations' => FALSE],
    ];

    drupal_set_message('Template has been changed since the constant set was added; therefore,
      your constants are no longer valid. Please re-enter them before loading.',
      'warning'
    );

    // Remove all constants for this node.
    db_delete('tripal_bulk_loader_constants')
      ->condition('nid', $node->nid)
      ->execute();
    $node->constants = [];
  }

  $form['exposed_array'] = [
    '#type' => 'hidden',
    '#value' => serialize($node->exposed_fields),
  ];

  $form['exposed_fields'] = [
    '#type' => 'fieldset',
    '#title' => t('Constant Values'),
    '#collapsible' => TRUE,
    '#collapsed' => ($node->template_id) ? FALSE : TRUE,
    '#prefix' => '<div id="set-constants">',
    '#suffix' => '</div>',
  ];

  // Display table of already added constant sets with the ability to re-arrange and delete
  $first_constant = reset($node->constants);
  if (sizeof($node->constants) > 0) {
    $form['exposed_fields']['explanation-1'] = [
      '#type' => 'item',
      '#markup' => t('You have already added constants to this bulk loading job. Each '
        . 'row in the following table represents a set of constants. Each set will be used '
        . 'to load your data file with the specified template resulting in the each record '
        . 'in the template to be loaded x number of times where there are x sets of '
        . 'constants (rows in the following table).'),
    ];

    $form['exposed_fields']['existing'] = [
      '#type' => 'markup',
      '#theme' => 'tripal_bulk_loader_constant_set',
      '#nid' => $node->nid,
      '#constants' => $node->constants,
      '#template' => $node->template,
    ];
  }

  $form['exposed_fields']['new'] = [
    '#type' => 'fieldset',
    '#title' => t('New set of Constants'),
  ];

  $form['exposed_fields']['new']['explanation-2'] = [
    '#type' => 'item',
    '#markup' => t('The following fields are constants in the selected template that you need to set values for.'),
  ];

  // Add textifelds for exposed fields of the current template
  $exposed_fields = FALSE;
  $indexes = [];
  if (tripal_bulk_loader_has_exposed_fields($node)) {
    foreach ($node->exposed_fields as $exposed_id => $exposed_index) {

      $record_id = $exposed_index['record_id'];
      $field_id = $exposed_index['field_id'];
      $field = $node->template->template_array[$record_id]['fields'][$field_id];

      if ($field['exposed']) {
        $exposed_fields = TRUE;
        $indexes[$record_id][] = $field_id;

        $default_value = '';
        if (isset($node->constants[$record_id])) {
          if (isset($node->constants[$record_id][$field_id])) {
            $default_value = $node->constants[$exposed_id][$record_id][$field_id]['value'];
          }
        }
        elseif (isset($field['constant value'])) {
          $default_value = $field['constant value'];
        }
        elseif (isset($field['spreadsheet column'])) {
          $default_value = $field['spreadsheet column'];
        }

        switch ($field['type']) {
          case 'table field':
            $form['exposed_fields']['new'][$record_id . '-' . $field_id] = [
              '#type' => 'textfield',
              '#title' => t('@title', ['@title' => $field['title']]),
              '#description' => t('%exposed_description', ['%exposed_description' => $field['exposed_description']]),
              '#default_value' => $default_value,
            ];
            break;
          case 'constant':
            $form['exposed_fields']['new'][$record_id . '-' . $field_id] = [
              '#type' => 'textfield',
              '#title' => t('@title', ['@title' => $field['title']]),
              '#description' => t('Enter the case-sensitive value of this constant for your data file'),
              '#default_value' => $default_value,
            ];
            break;
        }

        $form['exposed_fields']['new'][$record_id . '-' . $field_id . '-table'] = [
          '#type' => 'hidden',
          '#value' => $node->template->template_array[$record_id]['table'],
        ];
        $form['exposed_fields']['new'][$record_id . '-' . $field_id . '-field'] = [
          '#type' => 'hidden',
          '#value' => $field['field'],
        ];
        $form['exposed_fields']['new'][$record_id . '-' . $field_id . '-type'] = [
          '#type' => 'hidden',
          '#value' => $field['type'],
        ];

      }
    }
  }
  $form['template'] = [
    '#type' => 'hidden',
    '#value' => serialize($node->template->template_array),
  ];

  $form['exposed_fields']['new']['indexes'] = [
    '#type' => 'hidden',
    '#value' => serialize($indexes),
  ];

  if (!$exposed_fields) {
    $form['exposed_fields']['new']['explanation'] = [
      '#type' => 'item',
      '#value' => t('There are no exposed fields for this template.'),
    ];
  }

  $form['exposed_fields']['new']['submit-2'] = [
    '#type' => 'submit',
    '#name' => 'add_constant',
    '#value' => t('Add Constant Set'),
  ];

  return $form;
}

/**
 * Validate that the values entered exist in the database
 * if indicated in hte template array
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_set_constants_form_validate($form, $form_state) {

  $template = unserialize($form_state['values']['template']);
  $indexes = unserialize($form_state['values']['indexes']);

  $op = $form_state['values'][$form_state['clicked_button']['#name']];
  if (strcmp('Add Constant Set', $op) == 0) {
    foreach ($indexes as $record_id => $array) {
      foreach ($array as $field_id) {
        if (isset($template[$record_id]['fields'][$field_id]['exposed_validate'])) {
          if ($template[$record_id]['fields'][$field_id]['exposed_validate']) {
            $result = chado_query(
              'SELECT 1 as valid FROM {' . $template[$record_id]['table'] . '} WHERE ' . $template[$record_id]['fields'][$field_id]['field'] . '=:value',
              [':value' => $form_state['values'][$record_id . '-' . $field_id]]
            )->fetchField();

            if (!$result) {
              $msg = 'A ' . $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#title'] . ' of "' . $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#value'] . '" must already exist!';
              form_set_error($record_id . '-' . $field_id, $msg);
            }
            else {
              drupal_set_message(
                t(
                  'Confirmed a %title of "%value" already exists.',
                  [
                    '%title' => $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#title'],
                    '%value' => $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#value'],
                  ]
                )
              );
            }
          }
        }
      }
    }
  }

}

/**
 * Insert/update the constants associated with this node
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_set_constants_form_submit($form, $form_state) {

  // Insert/Update constants
  $template = unserialize($form_state['values']['template']);
  $indexes = unserialize($form_state['values']['indexes']);

  $op = $form_state['values'][$form_state['clicked_button']['#name']];
  if (strcmp('Add Constant Set', $op) == 0) {
    $max_group = db_query("SELECT max(group_id) as value FROM {tripal_bulk_loader_constants} WHERE nid=:nid", [':nid' => $form_state['values']['nid']])->fetchObject();
    foreach ($indexes as $record_id => $array) {
      foreach ($array as $field_id) {
        tripal_bulk_loader_update_constant(
          $form_state['values']['nid'],
          $max_group->value + 1,
          $form_state['values'][$record_id . '-' . $field_id . '-table'],
          $form_state['values'][$record_id . '-' . $field_id . '-field'],
          $record_id,
          $field_id,
          $form_state['values'][$record_id . '-' . $field_id]
        );
      }
    }

    // Update the node so that the constant set isn't immediatly erased...
    $node = $form_state['node'];
    $node->has_header = $node->file_has_header;
    if ($node = node_submit($node)) {
      node_save($node);
    }
  }

}

///////////////////////////////////////////////////////////
// Set Constants Form (on Bulk Loader Node)
///////////////////////////////////////////////////////////

/**
 * Edit a constant set (exposed fields in template)
 *
 * @param $form_state
 *   The current state of the form
 * @param $node
 *   The node to set constants for
 * @param $group_id
 *   The constant set to edit
 *
 * @return
 *   A form array to be rendered by drupal_get_form()
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_edit_constant_set_form($form, &$form_state, $node, $group_id) {
  $form = [];

  $form['nid'] = [
    '#type' => 'hidden',
    '#value' => $node->nid,
  ];

  $form['group_id'] = [
    '#type' => 'hidden',
    '#value' => $group_id,
  ];


  $form['explanation'] = [
    '#type' => 'item',
    '#value' => t('The following fields are constants in the selected template that you need to set values for.'),
  ];

  // Add textifelds for exposed fields of the current template
  $exposed_fields = FALSE;
  $indexes = [];
  if (tripal_bulk_loader_has_exposed_fields($node)) {
    foreach ($node->exposed_fields as $exposed_index) {

      $record_id = $exposed_index['record_id'];
      $record = $node->template->template_array[$record_id];
      $field_id = $exposed_index['field_id'];
      $field = $node->template->template_array[$record_id]['fields'][$field_id];

      if ($field['exposed']) {
        $exposed_fields = TRUE;
        $indexes[$record_id][] = $field_id;

        switch ($field['type']) {
          case 'table field':
            $form[$record_id . '-' . $field_id] = [
              '#type' => 'textfield',
              '#title' => t('%title', ['%title' => $field['title']]),
              '#description' => t('%exposed_description', ['%exposed_description' => $field['exposed_description']]),
              '#default_value' => (isset($node->constants[$group_id][$record_id][$field_id]['value'])) ? $node->constants[$group_id][$record_id][$field_id]['value'] : $field['constant value'],
            ];
            break;
          case 'constant':
            $form[$record_id . '-' . $field_id] = [
              '#type' => 'textfield',
              '#title' => t('%title', ['%title' => $field['title']]),
              '#description' => t('Enter the case-sensitive value of this constant for your data file'),
              '#default_value' => (isset($node->constants[$group_id][$record_id][$field_id]['value'])) ? $node->constants[$group_id][$record_id][$field_id]['value'] : $field['constant value'],
            ];
            break;
        }

        $form[$record_id . '-' . $field_id . '-table'] = [
          '#type' => 'hidden',
          '#value' => $record['table'],
        ];
        $form[$record_id . '-' . $field_id . '-field'] = [
          '#type' => 'hidden',
          '#value' => $field['field'],
        ];
        $form[$record_id . '-' . $field_id . '-type'] = [
          '#type' => 'hidden',
          '#value' => $field['type'],
        ];
      }

    }
  }
  $form['template'] = [
    '#type' => 'hidden',
    '#value' => serialize($node->template->template_array),
  ];

  $form['indexes'] = [
    '#type' => 'hidden',
    '#value' => serialize($indexes),
  ];

  $form['save'] = [
    '#type' => 'submit',
    '#value' => 'Save',
  ];

  $form['cancel'] = [
    '#type' => 'link',
    '#title' => 'Cancel',
    '#href' => 'node/' . $node->nid,
  ];

  return $form;
}

/**
 * Edit constants in the current constant set
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_edit_constant_set_form_submit($form, &$form_state) {

  // Update constants
  $template = unserialize($form_state['values']['template']);
  $indexes = unserialize($form_state['values']['indexes']);
  $nid = $form_state['values']['nid'];

  $op = $form_state['values'][$form_state['clicked_button']['#name']];
  if (strcmp('Save', $op) == 0) {
    $form_state['redirect'] = 'node/' . $nid;
    $form_state['rebuild'] = FALSE;

    foreach ($indexes as $record_id => $array) {
      foreach ($array as $field_id) {
        tripal_bulk_loader_update_constant(
          $form_state['values']['nid'],
          $form_state['values']['group_id'],
          $form_state['values'][$record_id . '-' . $field_id . '-table'],
          $form_state['values'][$record_id . '-' . $field_id . '-field'],
          $record_id,
          $field_id,
          $form_state['values'][$record_id . '-' . $field_id]
        );
      }
    }
    drupal_set_message(t('The constant set was successfully updated.'));

  }

}

/**
 * Delete a constant set (exposed fields in template)
 *
 * @param $form_state
 *   The current state of the form
 * @param $node
 *   The node to set constants for
 * @param $group_id
 *   The constant set to delete
 *
 * @return
 *   A form array to be rendered by drupal_get_form()
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_delete_constant_set_form($form, &$form_state, $node, $group_id) {
  $form = [];

  $form['nid'] = [
    '#type' => 'value',
    '#value' => $node->nid,
  ];

  $form['group_id'] = [
    '#type' => 'hidden',
    '#value' => $group_id,
  ];

  return confirm_form($form,
    t('Are you sure you want to delete this constant set?'),
    'node/' . $node->nid,
    t('This action cannot be undone.'),
    t('Delete'),
    t('Cancel')
  );

}

/**
 * Delete the current constant set
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_delete_constant_set_form_submit($form, &$form_state) {

  $group_id = $form_state['values']['group_id'];
  $nid = $form_state['values']['nid'];
  if ($nid && $form_state['values']['confirm']) {
    $form_state['redirect'] = 'node/' . $nid;
    $form_state['rebuild'] = FALSE;

    db_delete('tripal_bulk_loader_constants')
      ->condition('nid', $nid)
      ->condition('group_id', $group_id)
      ->execute();
    drupal_set_message(t('Constant set successfully deleted.'));
  }

}

/**
 * Display a constant set.
 *
 * @param $varaibles
 *   An array of variables that are available:
 *    -nid: the NID of the bulk loading job node the constants are for.
 *    -constants: An array of constants as loaded by tripal_bulk_loader_load().
 *    -template: An object containing the template record with unserialized
 *     template_array.
 *    -options: An optional array of options.
 *
 * @return
 *   Rendered HTML.
 */
function theme_tripal_bulk_loader_constant_set($variables) {

  // Check that there are constants to render.
  if (empty($variables['constants'])) {
    return '';
  }

  // Set Defaults.
  $variables['options'] = (isset($variables['options'])) ? $variables['options'] : [];
  $variables['options']['display_operations'] = (isset($variables['options']['display_operations'])) ?
    $variables['options']['display_operations'] : TRUE;

  // Get all the rows.
  $rows = [];
  foreach ($variables['constants'] as $group_id => $set) {
    $row = [];
    $row['group_id'] = $group_id;
    foreach ($set as $record) {
      foreach ($record as $field) {
        $index = $field['record_id'] . '-' . $field['field_id'];
        $row[$index] = $field['value'];
      }
    }
    if ($variables['options']['display_operations']) {
      $row['operations'] = filter_xss(l(t('Edit'), 'node/' . $variables['nid'] . '/constants/' . $group_id . '/edit') . '  |  ' .
        l(t('Delete'), 'node/' . $variables['nid'] . '/constants/' . $group_id . '/delete'));
    }

    $rows[] = $row;
  }

  // Get the header using the last constant set.
  $header = [];
  $header[0]['group_id'] = [
    'data' => t('Group'),
    'header' => TRUE,
    'rowspan' => 2,
  ];
  foreach ($set as $record) {
    foreach ($record as $field) {

      $index = $field['record_id'] . '-' . $field['field_id'];

      $header[0][$field['record_id']] = [
        'data' => $variables['template']->template_array[$field['record_id']]['record_id'],
        'header' => TRUE,
        'colspan' => sizeof($record),
      ];

      $header[1][$index] = [
        'data' => $variables['template']->template_array[$field['record_id']]['fields'][$field['field_id']]['title'],
        'header' => TRUE,
      ];
    }
  }

  if ($variables['options']['display_operations']) {
    $header[0]['operations'] = [
      'data' => t('Operations'),
      'header' => TRUE,
      'rowspan' => 2,
    ];
  }

  return theme(
    'table',
    [
      'header' => [],
      'rows' => array_merge($header, $rows),
    ]
  );
}