tripal/tripal_entities/includes/tripal_entities.entity_form.inc

<?php

/**
 *
 */
function tripal_entities_entity_form($form, &$form_state, $entity = NULL) {

  // Set the defaults.
  $cv_id = NULL;
  $term_name = NULL;
  $cvterm = NULL;
  $do_sync = 0;
  $terms = array();
  $num_terms = 0;

  // Set defaults if an entity was provided.
  if ($entity) {
    drupal_set_title('Edit ' .$entity->title);
    $id = $entity->id;
    $values = array('cvterm_id' => $entity->cvterm_id);
    $cvterm = chado_generate_var('cvterm', $values);
    $cv_id = $cvterm->cv_id->cv_id;
    $term_name = $cvterm->name;
    $terms[]  = $cvterm;
    $num_terms = 1;
  }

  // Set defaults using the form state.
  if (array_key_exists('storage', $form_state) and
      array_key_exists('terms', $form_state['storage'])) {
    $terms = $form_state['storage']['terms'];
    $num_terms = count($terms);
  }
  if (array_key_exists('values', $form_state) and
      array_key_exists('term_name', $form_state['values'])) {
    $term_name = $form_state['values']['term_name'];
  }
  if (array_key_exists('values', $form_state) and
      array_key_exists('do_sync', $form_state['values'])) {
    $do_sync = $form_state['values']['do_sync'];
  }

  // If no term has been selected yet then provide the auto complete field.
  if ($num_terms != 1) {
    $cvterms = tripal_entities_get_published_terms_as_select_options($cv_id);
    $form['term_name'] = array(
      '#title'       => t('Data Type'),
      '#type'        => 'textfield',
      '#description' => t("Please enter the type of data that you want to publish.  As you type, suggestions will be provided."),
      '#required'    => TRUE,
      '#default_value' => $term_name,
      '#autocomplete_path' => "admin/tripal/chado/tripal_cv/cvterm/auto_name/$cv_id",
    );
    // If we are not editing an existing entity then provide a radio button
    // to allow the user to add a new record or to sync existing records.
    if (!$entity) {
      $action = array(0 => t('Publish a new record'), 1 => t('Publish one or more existing records'));
      $form['do_sync'] = array(
        '#type' => 'radios',
        '#title' => t('Publish Action'),
        '#default_value' => $do_sync,
        '#options' => $action,
      );
    }
  }

  // If the term belongs to more than one vocabulary then add additional fields
  // to let the user select the vocabulary.
  if ($num_terms > 1) {
    $cvs = array();
    foreach ($terms as $term) {
      $cvs[$term->cv_id->cv_id] = $term->cv_id->name;
    }
    $form['cv)id'] = array(
      '#type' => 'radios',
      '#title' => t('Select the appropriate vocabulary'),
      '#options' => $cvs,
      '#description' => t('The term belongs to more than one vocabulary. Please
          indicate the proper vocabulary for the term.')
    );
  }

  // Add in the button for the cases of no terms or too many.
  if ($num_terms != 1) {
    $form['select_button'] = array(
      '#type' => 'submit',
      '#value' => t('Use this term'),
      '#name' => 'select_cvterm'
    );
  }

  // If we only have one cvterm then the user has provided a unique
  // term and we can either allow them to add a new entry or sync existing
  // records.
  if ($num_terms == 1){
    $cvterm = $terms[0];
    $bundle_id = $cvterm->dbxref_id->db_id->name .'_' .$cvterm->dbxref_id->accession;

    $form['cv_id'] = array(
      '#type' => 'hidden',
      '#value' => $cvterm->cv_id->cv_id
    );
    $form['type'] = array(
      '#type' => 'hidden',
      '#value' => $cvterm->dbxref_id->db_id->name
    );
    $form['term_name'] = array(
      '#type' => 'hidden',
      '#value' => $cvterm->name
    );
    $form['cvterm_id'] = array(
      '#type' => 'hidden',
      '#value' => $cvterm->cvterm_id
    );
    $form['bundle'] = array(
      '#type' => 'hidden',
      '#value' => $bundle_id
    );
    $form['details'] = array(
      '#type' => 'item',
      '#title' => 'Data Type',
      '#markup' => '(' . $cvterm->cv_id->name . ') ' . $cvterm->name,
      '#weight' => -1000,
    );


    if(!$do_sync) {
      tripal_entities_entity_form_add_new($bundle_id, $cvterm, $form, $form_state, $entity);
    }
    else {
      tripal_entities_entity_form_add_sync($bundle_id, $cvterm, $form, $form_state, $entity);
    }
  }

  $form['#prefix'] = '<div id="tripal-entities-entity-form">';
  $form['#suffix'] = '</div>';
  return $form;
}
/**
 * Adds fields to the tripal_entities_entity_form for syncing an entity.
 */
function tripal_entities_entity_form_add_sync($bundle_id, $cvterm, &$form, &$form_state, $entity) {
  $form['todo'] = array(
    '#type' => 'item',
    '#markup' => t('TODO: Add a form for allowing the user to filter by fields'),
  );
}
/**
 * Adds fields to the tripal_entities_entity_form for editing/adding an entity.
 */
function tripal_entities_entity_form_add_new($bundle_id, $cvterm, &$form, &$form_state, $entity) {

  // If the entity doesn't exist then create one.
  if (!$entity) {
    $entity = entity_get_controller($cvterm->dbxref_id->db_id->name)->create(array('bundle' => $bundle_id));
    field_attach_form($cvterm->dbxref_id->db_id->name, $entity, $form, $form_state);

    $form['add_button'] = array(
      '#type' => 'submit',
      '#value' => t('Add a new ' .$cvterm->name),
      '#name' => 'add_data',
      '#weight' => 1000
    );
  }
  else {
    field_attach_form($cvterm->dbxref_id->db_id->name, $entity, $form, $form_state);
    $form['entity_id'] = array(
      '#type' => 'hidden',
      '#value' => $entity->id
    );
    $form['update_button'] = array(
      '#type' => 'submit',
      '#value' => t('Update'),
      '#name' => 'update_data',
      '#weight' => 1000
    );
    $form['delete_button'] = array(
      '#type' => 'submit',
      '#value' => t('Delete'),
      '#name' => 'delete_data',
      '#weight' => 1001
    );
  }

  // The entity object must be added to the $form_state in order for
  // the Entity API to work. It must have a key of the entity name.
  $form_state[$cvterm->dbxref_id->db_id->name] = $entity;
}
/**
 * An Ajax callback for the tripal_entities_entity_form.
 */
function tripal_entities_entity_form_ajax_callback($form, $form_state) {
  // return the form so Drupal can update the content on the page
  return $form;
}

/**
 * Implements hook_validate() for the tripal_entities_entity_form.
 */
function tripal_entities_entity_form_validate($form, &$form_state) {

  // Check if this term and vocabulary is in the tripal_vocabulary usage tables.
  // If not then add it.
  if (array_key_exists('clicked_button', $form_state) and
      $form_state['clicked_button']['#name'] =='select_cvterm') {

    // First, make sure the term is unique. If not then we can't check it.
    $term_name = $form_state['values']['term_name'];
    $cv_id = array_key_exists('cv_id', $form_state['values']) ? $form_state['values']['cv_id'] : '';
    $cvterm = NULL;

    // If a term and cv_id are provided then we can look for the term using
    // both and we should find a unique term. If only ther term is provided
    // we can still look for a unique term but there must only be one.
    if ($term_name and !$cv_id) {
      $match = array(
        'name' => $term_name,
      );
    }
    else {
      $match = array(
        'name' => $term_name,
        'cv_id' => $cv_id,
      );
    }
    $terms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));

    // Add the cvterm to the storage element so we don't have to keep
    // looking it up in the submit function or on a rebuild of the form.
    $form_state['storage']['terms'] = $terms;

    // If we only have one term then we found a unique match and we can do
    // some further checking.
    if (count($terms) == 1) {
      $cvterm = $terms[0];
      // Make sure the term is set as published.
      tripal_entities_add_term_usage($cvterm, $form_state);
    }
    // If we do not have any terms then the term provided by the user does not
    // exists and we need to provide an error message.
    if (count($terms) == 0) {
      form_set_error('term_name', t('The term does not exist in this database.'));
    }
    // If we have more than one term then we need to set an error so that the
    // form can provide a list of vocabularies to select from.
    if (count($terms) > 1) {
      form_set_error('', t('The term is not unique. A list of vocabularies has been provided where this term is present. Please select the appropriate one.'));
    }
  }


  if (array_key_exists('clicked_button', $form_state) and
      $form_state['clicked_button']['#name'] =='add_data') {
    $tripal_entity = (object) $form_state['values'];
    $entity_type = $form_state['values']['type'];
    field_attach_form_validate($entity_type, $tripal_entity, $form, $form_state);
  }
}

/**
 * Adds a vocabulary and term to the Tripal term usage tables.
 *
 * This function is meant to be called only by the
 * tripal_entities_entity_form_validate() function. This code is
 * separated to simplify that function.  Therefore, if errors occur with adding
 * of terms then the form_set_error() is called.
 *
 * @param $cvterm
 */
function tripal_entities_add_term_usage($cvterm, &$form_state) {

  // Before creating the entity we mut add records to the tripal_vocabulary
  // tripal_vocabulary_usage, tripal_term, and tripal_term_usage tables.
  $match = array('cv_id' => $cvterm->cv_id->cv_id);
  $vocab = chado_select_record('tripal_vocabulary', array('*'), $match);
  if (count($vocab) == 0) {
    $values = array(
      'cv_id' => $cvterm->cv_id->cv_id,
      'db_id' => $cvterm->dbxref_id->db_id->db_id,
      'publish' => 1,
    );
    $values = chado_insert_record('tripal_vocabulary', $values);
    if (!$values) {
      form_set_error('', 'Could not add vocabulary to tripal_vocabluary table.');
      return FALSE;
    }
    // Convert the values array into an object.
    $vocab = new stdClass();
    $vocab->vocabulary_id = $values['vocabulary_id'];
    $vocab->cv_id = $values['cv_id'];
  }
  else {
    // Make sure the vocabulary is set to publish
    $values = array('publish' => 1);
    chado_update_record('tripal_vocabulary', $match, $values);
    $vocab = $vocab[0];
  }

  // Does this vocabulary have a record in the tripal_vocabulary_usage
  // table? If not then add one.
  $match = array('vocabulary_id' => $vocab->vocabulary_id);
  $vocab_usage = chado_select_record('tripal_vocabulary_usage', array('*'), $match);
  if (count($vocab_usage) == 0) {
    // Look to see if this vocabulary is used as a default for any table. If
    // so then we can use that to populate the tripal_vocabulary_usage table.
    $default = db_select('tripal_cv_defaults', 't')
      ->fields('t')
      ->condition('cv_id', $vocab->cv_id)
      ->execute()
      ->fetchObject();
    if ($default) {
       $values = array(
        'vocabulary_id' => $vocab->vocabulary_id,
        'data_table' => $default->table_name,
        'type_table' => $default->table_name,
        'field' =>  $default->field_name,
      );
      $values = chado_insert_record('tripal_vocabulary_usage', $values);
      if (!$values) {
        form_set_error('', 'Could not add vocabulary to tripal_vocabulary_usage table.');
        return FALSE;
      }
    }
    // If there is no default table then we have an error, and we should
    // set a variable so that the form can help the user deal with the problem.
    else {
      $form_state['storage']['cvterm_has_default'] = FALSE;
      form_set_error('', t('There is no default mapping of this term\'s
          vocabulary to a table in Chado.  Therefore, it is not possible to
          determine how to store data of this type.'));
      return FALSE;
    }
    $vocab_usage = new stdClass();
    $vocab_usage->vocabulary_id = $values['vocabulary_id'];
    $vocab_usage->data_table = $values['data_table'];
    $vocab_usage->type_table = $values['type_table'];
    $vocab_usage->field = $values['field'];
  }
  else {
    $vocab_usage = $vocab_usage[0];
  }

  // Now add the tripal_term record if it doesn't already exist.
  $match = array(
    'vocabulary_id' => $vocab->vocabulary_id,
    'cvterm_id' => $cvterm->cvterm_id,
  );
  $term = chado_select_record('tripal_term', array('*'), $match);
  if (count($term) == 0) {
    $values = array(
      'vocabulary_id' => $vocab->vocabulary_id,
      'cvterm_id' => $cvterm->cvterm_id,
    );
    $values = chado_insert_record('tripal_term', $values);
    if (!$values) {
      form_set_error('', 'Could not add term to tripal_term table..');
      return FALSE;
    }
    $term = new stdClass();
    $term->term_id = $values['term_id'];
  }
  else {
    $values = array('publish' => 1);
    chado_update_record('tripal_term', $match, $values);
    $term = $term[0];
  }

  // Finally, add the tripal_term_usage record if it doesn't already exist.
  $match = array('term_id' => $term->term_id);
  $options = array('has_record' => TRUE);
  if (!chado_select_record('tripal_term_usage', array('*'), $match, $options)) {
    $values = array(
      'term_id' => $term->term_id,
      'data_table' => $vocab_usage->data_table,
      'type_table' => $vocab_usage->type_table,
      'field' =>  $vocab_usage->field,
    );
    $values = chado_insert_record('tripal_term_usage', $values);
    if (!$values) {
      form_set_error('', 'Could not add term to tripal_term table..');
      return FALSE;
    }
  }

  // Clear the entity cache so that Drupal will read our
  // hook_entity_info() implementation which now will have the entities
  // described because we set the publish column to 1 in the tripal_term
  // table.
  global $language;
  $langcode = $language->language;
  cache_clear_all("entity_info:$langcode", 'cache');

  return TRUE;
}
/**
 * Implements hook_submit() for the tripal_entities_entity_form.
 */
function tripal_entities_entity_form_submit($form, &$form_state) {
  if ($form_state['clicked_button']['#name'] =='cancel') {
    if (array_key_exists('id', $form_state['values'])) {
      $entity_id = $form_state['values']['entity_id'];
      $form_state['redirect'] = "data/$entity_id";
    }
    else {
      $form_state['redirect'] = "admin/structure/tripal_entity";
    }
    return;
  }
  if ($form_state['clicked_button']['#name'] =='select_cvterm') {
    // Check to see if the entity already exists. If not then create it.
    $cvterm = $form_state['storage']['terms'][0];
    $einfo = entity_get_info($cvterm->dbxref_id->db_id->name);
    tripal_entities_add_bundle($cvterm);

    $form_state['rebuild'] = TRUE;
  }
  if ($form_state['clicked_button']['#name'] =='update_data' or
      $form_state['clicked_button']['#name'] =='add_data') {
    // Use the Entity API to get the entity from the form state, then
    // attach the fields and save.
    $entity_type = $form_state['values']['type'];
    $entity = entity_ui_controller($entity_type)->entityFormSubmitBuildEntity($form, $form_state);
    $entity->save();
    $form_state['redirect'] = "data/$entity->id";
  }
  if ($form_state['clicked_button']['#name'] =='delete_data') {
    $entity_id = $form_state['values']['entity_id'];
    $form_state['redirect'] = 'data/' .$entity_id .'/delete';
  }
}

/**
 * Form callback: confirmation form for deleting a tripal_entity.
 *
 * @param $tripal_entity The
 *          tripal_entity to delete
 *
 * @see confirm_form()
 */
function tripal_entities_entity_delete_form($form, &$form_state, $entity) {
  $form_state['entity'] = $entity;
  $form['#submit'][] = 'tripal_entities_entity_delete_form_submit';

  $form = confirm_form($form,
      t('Click the delete button below to confirm deletion of the record titled: %title',
          array('%title' => $entity->title)), 'admin/content/tripal_entity',
      '<p>' .t('This action cannot be undone.') .'</p>', t('Delete'), t('Cancel'), 'confirm');

  return $form;
}

/**
 * Submit callback for tripal_entity_delete_form
 */
function tripal_entities_entity_delete_form_submit($form, &$form_state) {
  $entity = $form_state['entity'];

  $entity_controller = new TripalEntityController($entity->type);
  if ($entity_controller->delete($entity)) {
    drupal_set_message(t('The record title "%name" has been deleted.', array('%name' => $entity->title)));
    $form_state['redirect'] = 'admin/content/tripal_entitys';
  }
  else {
    drupal_set_message(t('The tripal_entity %name was not deleted.', array('%name' => $entity->title)), "error");
  }
}


/**
 * Implements hook_submit() for the tripal_entities_admin_publish_form.
 *
 */
function tripal_entities_add_bundle($cvterm) {

  // Create the bundle name and entity type name.
  $type = $cvterm->dbxref_id->db_id->name;
  $bundle_name = $type . '_' . $cvterm->dbxref_id->accession;
  $entity_type_name = $cvterm->dbxref_id->db_id->name;

  // Check to see if this bundle exists. If not then create it
  $bundle = db_select('tripal_bundle', 't')
    ->fields('t')
    ->condition('type', $type)
    ->condition('bundle', $bundle_name)
    ->execute()
    ->fetchObject();

  if (!$bundle) {
    // The TripalBundle Entity manages the bundles we have available.
    // Therefore, we need to add a new entity for each bundle "type".
    $vals = array(
      'label' => $bundle_name  . ' (' . $cvterm->name . ')',
      'type' => $entity_type_name,
      'bundle' => $bundle_name,
      'data' => serialize(array()),
      'module' => 'tripal_entities'
    );
    $tripal_bundle = new TripalBundle($vals, $entity_type_name . '_bundle');
    $tripal_bundle->save();

    // Allow modules to now add fields to the bundle
    module_invoke_all('add_bundle_fields', $entity_type_name, $bundle_name, $cvterm);
  }
}
/**
 *
 * @param $table
 * @param $entity_type
 * @param $bundle_name
 */
function tripal_entities_add_bundle_fields($entity_type_name, $bundle_name, $cvterm) {

  // Get the list of tables where this cvterm is used.
  $match = array('cvterm_id' => $cvterm->cvterm_id);
  $term = chado_select_record('tripal_term', array('*'), $match);
  $values = array('term_id' => $term[0]->term_id);
  $tables = chado_select_record('tripal_term_usage', array('*'), $values);

  // Iterate through the tables.
  foreach ($tables as $table) {
    $tablename = $table->data_table;
    $type_table = $table->type_table;
    $type_field = $table->field;

    // We only want to look at base tables.
    if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
        $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
        $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
        preg_match('/_cvterm$/', $tablename)) {
      continue;
    }

    // Iterate through the columns of the table and see if fields have been
    // created for each one. If not, then create them.
    $schema = chado_get_schema($tablename);
    $columns = $schema['fields'];
    foreach ($columns as $column_name => $details) {
      $field_name = $tablename . '__' . $column_name;
      $field = field_info_field($field_name);

      // Skip the primary key field.
      if ($column_name == $schema['primary key'][0]) {
        continue;
      }

      // Skip the type field.
      if ($tablename == $type_table and $column_name == $type_field) {
        continue;
      }

      // Determine if the field is required.
      $is_required = 0;
      if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
        $is_required = array_key_exists('default', $details) ? 0 : 1;
      }

      // Determine what type of field this should be.
      // Drupal data types are: https://www.drupal.org/node/159605.
      // Field types are here:  https://www.drupal.org/node/1879542

      // Create an array with information about this field.
      $field_info = array(
        'field_type' => '',
        'widget_type' => '',
        'field_settings' => array(),
        'widget_settings' => array('display_label' => 1),
        'description' => '',
        'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
        'chado_table' => $tablename,
        'chado_column' => $column_name
      );

      // Alter the field info array dependiing on the column details.
      switch($details['type']) {
        case 'char':
          $field_info['field_type'] = 'text';
          $field_info['widget_type'] = 'text_textfield';
          $field_info['field_settings']['max_length'] = $details['length'];
          break;
        case 'varchar':
          $field_info['field_type'] = 'text';
          $field_info['widget_type'] = 'text_textfield';
          $field_info['field_settings']['max_length'] = $details['length'];
          break;
        case 'text':
          $field_info['field_type'] = 'text';
          $field_info['widget_type'] = 'text_textarea';
          $field_info['field_settings']['max_length'] = 17179869184;
          break;
        case 'blob':
          // not sure how to support a blob field.
          continue;
          break;
        case 'int':
          $field_info['field_type'] = 'number_integer';
          $field_info['widget_type'] = 'number';
          break;
        case 'float':
          $field_info['field_type'] = 'number_float';
          $field_info['widget_type'] = 'number';
          $field_info['field_settings']['precision'] = 10;
          $field_info['field_settings']['scale'] = 2;
          $field_info['field_settings']['decimal_separator'] = '.';
          break;
        case 'numeric':
          $field_info['field_type'] = 'number_decimal';
          $field_info['widget_type'] = 'number';
          break;
        case 'serial':
          // Serial fields are most likely not needed as a field.
          break;
        case 'boolean':
          $field_info['field_type'] = 'list_boolean';
          $field_info['widget_type'] = 'options_onoff';
          $field_info['field_settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
          break;
        case 'datetime':
          // Use the Drupal Date and Date API to create the field/widget
          $field_info['field_type'] = 'datetime';
          $field_info['widget_type'] = 'date_select';
          $field_info['widget_settings']['increment'] = 1;
          $field_info['widget_settings']['tz_handling'] = 'none';

          // TODO: Add settings so that the minutes increment by 1.
          // And turn off the timezone, as the Chado field doesn't support it.
          break;
      }

      // If we don't have a field type then we don't need to create a field.
      if (!$field_info['field_type']) {
        // If we don't have a field type but it is required and doesn't have
        // a default value then we are in trouble.
        if ($is_required and !array_key_exists('default', $details)) {
          throw new Exception(t('The %table.%field type, %type, is not yet supported for Entity fields, but it is required,',
              array('%table' => $tablename, '%field' => $column_name, '%type' => $details['type'])));
        }
        continue;
      }

      // If this field is a foreign key field then we will have a special custom
      // field provided by Tripal.
      $is_fk = FALSE;
      if (array_key_exists('foreign keys', $schema)) {
        foreach ($schema['foreign keys'] as $remote_table => $fk_details) {
          if (array_key_exists($column_name, $fk_details['columns'])) {
            $is_fk = TRUE;
          }
        }
      }

      // Allow other modules to alter the field information array.
      drupal_alter('chado_field', $field_info);

      // If the field doesn't exist then create it.
      if (!$field) {
        $field = array(
          'field_name' => $field_name,
          'type' => $field_info['field_type'],
          'cardinality' => 1,
          'locked' => FALSE,
          'storage' => array(
            'type' => 'field_chado_storage'
          ),
          'settings' => $field_info['field_settings'],
        );
        field_create_field($field);
      }

      // Attach the field to the bundle.
      $field_instance = array(
        'field_name' => $field_name,
        'label' => $field_info['label'],
        'description' => $field_info['description'],
        'widget' => array(
          'type' => $field_info['widget_type'],
          'settings' => $field_info['widget_settings'],
        ),
        'entity_type' => $entity_type_name,
        'required' => $is_required,
        'settings' => $field_info['field_settings'],
        'bundle' => $bundle_name,
      );
      field_create_instance($field_instance);
    }
  }
}