File

tripal_core/api/tripal_core.chado_nodes.properties.api.inc, line 140

API to manage the chado prop table for various Tripal Node Types

Code

function chado_add_node_form_properties(&$form, &$form_state, $details) {

  // Set defaults for optional fields
  if (!array_key_exists('fieldset_title', $details)) {
    $details['fieldset_title'] = 'Properties';
  }
  if (!array_key_exists('additional_instructions', $details)) {
    $details['additional_instructions'] = '';
  }
  if (!array_key_exists('default_properties', $details)) {
    $details['default_properties'] = array();
  }
  if (!is_array($details['default_properties'])) {
    drupal_set_message("The 'default_properties' option must be an array", "error");
    tripal_report_error('tcprops_form', TRIPAL_ERROR, 
    "The 'default_properties' option must be an array", 
    array());
    return;
  }

  // make sure the property table exists before proceeding.
  if (!chado_table_exists($details['property_table'])) {
    drupal_set_message("Cannot add property elements to the form. The property table, '" .
      $details['property_table'] . "', does not exists", "error");
    tripal_report_error('tcprops_form', TRIPAL_ERROR, 
    "Cannot add property elements to the form. The property table, '%name', cannot be found.", 
    array('%name' => $details['property_table']));
    return;
  }

  // if the chado_id_field is not specified then set it using the
  // typical chado naming scheme
  if (!array_key_exists('chado_id_field', $details)) {
    $chado_id_table = preg_replace('/prop$/', '', $details['property_table']);
    $chado_id_field = $chado_id_table . '_id';
    $details['nodetype'] = $chado_id_table;
    $details['chado_id_field'] = $chado_id_field;
  }
  else {
    $details['nodetype'] = str_replace('_id', '', $details['chado_id_field']);
  }

  // make sure the specified cv exists
  if (isset($details['cv_name'])) {
    // make sure the cv_name is real
    $result = chado_select_record('cv', array('cv_id'), array('name' => $details['cv_name']));
    if (count($result) == 0) {
      drupal_set_message("Cannot add property elements to the form. The CV name, '" .
        $details['cv_name'] . "', does not exists", "error");
      tripal_report_error('tcprops_form', TRIPAL_ERROR, 
      "Cannot add property elements to the form. The CV named, '%name', cannot be found.", 
      array('%name' => $details['cv_name']));
      return;
    }
    // add the cv_id option to the details array
    $details['cv_id'] = $result[0]->cv_id;
  }
  elseif (isset($details['cv_id'])) {
    // make sure the cv_id is real
    $result = chado_select_record('cv', array('name'), array('cv_id' => $details['cv_id']));
    if (count($result) == 0) {
      drupal_set_message("Cannot add property elements to the form. The CV ID, '" .
        $details['cv_id'] . "', does not exist", "error");
      tripal_report_error('tcprops_form', TRIPAL_ERROR, 
      "Cannot add property elements to the form. The CV ID, '%id', cannot be found.", 
      array('%id' => $details['cv_id']));
      return;
    }
    // add the cv_name option to the details array
    $details['cv_name'] = $result[0]->name;
  }
  else {

    // If we didn't get given a cv identifier, then try retrieving the default one
    // using the new cv defaults api
    $default_cv = tripal_get_default_cv($details['property_table'], 'type_id');
    if (!empty($default_cv)) {
      $details['cv_id'] = $default_cv->cv_id;
      $details['cv_name'] = $default_cv->name;
    }
    else {

      $default_form_link = l('vocabulary defaults configuration page', 
      'admin/tripal/chado/tripal_cv/defaults', 
      array('attributes' => array('target' => '_blank')));
      $message = "There is not a default vocabulary set for Property Types. Please set one using the $default_form_link.";

      if (preg_match('/(\w+)_id/', $details['chado_id_field'], $matches)) {
        $table = $matches[1];
        $table = ucwords(str_replace('_', ' ', $table));
        $message = "There is not a default vocabulary set for $table Property Types. Please set one using the  $default_form_link.";
      }

      tripal_set_message($message, TRIPAL_WARNING);
      tripal_report_error('tcprops_form', TRIPAL_ERROR, 
      "Please provide either a 'cv_name' or 'cv_id' as an option for adding properties to the form", 
      array());
    }
    return;
  }

  // Get property types for the select list. If the user has provided a set
  // then use those, otherwise get them from the cvterm table for specified cv.
  if (array_key_exists('select_options', $details) and 
    is_array($details['select_options'])) {
    $property_options = $details['select_options'];
  }
  // if the select options are not provided then try to get them on our own
  else {
    // if the vocabulary name is provided in the details then use that to
    // get the terms
    if (isset($details['cv_name'])) {
      $property_options = array();
      $property_options[] = 'Select a Property';
      $sql = "
        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition, CV.cv_id as cv_id
        FROM  {cvterm} CVT
          INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
        WHERE
          CV.name = :cv_name AND
          NOT CVT.is_obsolete = 1
        ORDER BY CVT.name ASC
      ";
      $prop_types = chado_query($sql, array(':cv_name' => $details['cv_name']));
      while ($prop = $prop_types->fetchObject()) {
        $property_options[$prop->cvterm_id] = $prop->name;
      }
    }
    // if the cv_id is set in the $details array then use that to get the terms
    elseif (isset($details['cv_id'])) {
      $property_options = array();
      $property_options[] = 'Select a Property';
      $sql = "
        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition, CV.name as cv_name
        FROM  {cvterm} CVT
          INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
        WHERE
          CV.cv_id = :cv_id AND
          NOT CVT.is_obsolete = 1
        ORDER BY CVT.name ASC
      ";
      $prop_types = chado_query($sql, array(':cv_id' => $details['cv_id']));
      while ($prop = $prop_types->fetchObject()) {
        $property_options[$prop->cvterm_id] = $prop->name;
      }
    }
  }

  // Tell tripal administrators how to add terms to the property types drop down.
  if (empty($property_options)) {
    $tripal_message = tripal_set_message(
    t('There are currently no property types! To add properties to the drop
        down list, you need to <a href="@cvtermlink">add a controlled vocabulary term</a>
        to the %cv_name controlled vocabulary.', 
    array(
      '%cv_name' => $details['cv_name'],
      '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/' . $details['cv_id'] . '/cvterm/add')
    )
    ), 
    TRIPAL_NOTICE, 
    array('return_html' => TRUE)
    );
  }
  else {
    $tripal_message = tripal_set_message(
    t('To add additional properties to the drop down list, you need to <a href="@cvtermlink">add
        a controlled vocabulary term</a> to the %cv_name controlled vocabulary.', 
    array(
      '%cv_name' => $details['cv_name'],
      '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/' . $details['cv_id'] . '/cvterm/add')
    )
    ), 
    TRIPAL_INFO, 
    array('return_html' => TRUE)
    );
  }

  // Group all of the chado node api fieldsets into vertical tabs.
  $form['chado_node_api'] = array(
    '#type' => 'vertical_tabs',
    '#attached' => array(
      'css' => array(
        'chado-node-api' => drupal_get_path('module', 'tripal_core') . '/theme/css/chado_node_api.css',
      ),
    ),
  );

  // the fieldset of the property elements
  $instructions = 'To add properties of the current %nodetype, select the type of 
      information from the drop-down below and enter the information in the text box before 
      clicking "Add". To remove incorrect information, click the "Remove" button. 
      Note: you cannot edit previously added information but instead need to 
      remove and re-add it.';
  $form['properties'] = array(
    '#type' => 'fieldset',
    '#title' => t($details['fieldset_title']),
    '#description' => t('<p><strong>Additional information about a 
      %nodetype.</strong></p><p>' . $instructions . $details['additional_instructions'] . '</p>', array('%nodetype' => $details['nodetype'])),
    '#collapsible' => TRUE,
    '#collapsed' => TRUE,
    '#group' => 'chado_node_api',
    '#weight' => 8,
    '#attributes' => array('class' => array('chado-node-api', 'properties')),
    '#attached' => array(
      'js' => array(
        'chado-node-api-vertical-tabs' => drupal_get_path('module', 'tripal_core') . '/theme/js/chadoNodeApi_updateVerticalTabSummary.js',
      ),
    ),
  );

  // this form element is a tree, so that we don't puke all of the values into then node variable
  // it is set as a tree, and keeps them in the $form_state['values']['property_table'] heading.
  $form['properties']['property_table'] = array(
    '#type' => 'markup',
    '#tree' => TRUE,
    '#prefix' => '<div id="tripal-generic-edit-properties-table">',
    '#suffix' => '</div>',
    '#theme' => 'chado_node_properties_form_table'
  );

  // We need to provide feedback to the user that changes made
  // are not saved until the node is saved.
  $form['properties']['property_table']['save_warning'] = array(
    '#type' => 'markup',
    '#prefix' => '<div id="property-save-warning" class="messages warning" style="display:none;">',
    '#suffix' => '</div>',
    '#markup' => '* The changes to these properties will not be saved until the 
      "Save" button at the bottom of this form is clicked. <span class="specific-changes"></span>',
    '#attached' => array(
      'js' => array(
        'chado-node-api-unsaved' => drupal_get_path('module', 'tripal_core') . '/theme/js/chadoNodeApi_unsavedNotify.js',
      ),
    ),
  );

  // Add defaults into form_state to be used elsewhere
  $form['properties']['property_table']['details'] = array(
    '#type' => 'hidden',
    '#value' => serialize($details)
  );

  /* Properties can come to us in two ways:
   * 1) As entries in the $details['default_properties'] option
   *
   * 2) In the form state in the $form_state['chado_properties']. Data is in this field
   *    when an AJAX call updates the form state or a validation error.
   *
   * 3) Directly from the database if the record already has properties associated.  This
   *    data is only used the first time the form is loaded. On AJAX calls or validation
   *    errors the fields on the form are populated from the $form_state['chado_properties']
   *    entry.
   */
  if (isset($form_state['chado_properties'])) {
    $existing_properties = $form_state['chado_properties'];
  }
  else {

    // build the SQL for extracting properties already assigned to this record
    $sql_args = array();
    $sql_args[':chado_id'] = $details['chado_id'];
    if (array_key_exists('cv_name', $details)) {
      $cv_where = "CV.name = :cvname";
      $sql_args[':cvname'] = $details['cv_name'];
    }
    elseif (array_key_exists('cv_id', $details)) {
      $cv_where = "CV.cv_id = :cvid";
      $sql_args[':cvid'] = $details['cv_id'];
    }
    $existing_properties = chado_query(
    "SELECT
         PP." . $details['property_table'] . "_id property_id,
         CVT.cvterm_id as type_id,
         CVT.name as type_name,
         CVT.definition,
         PP.value,
         PP.rank
       FROM {" . $details['property_table'] . "} PP
         INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
         INNER JOIN {cv} CV      ON CVT.cv_id     = CV.cv_id
       WHERE
         PP." . $details['chado_id_field'] . " = :chado_id AND
         $cv_where
       ORDER BY CVT.name, PP.rank", $sql_args)->fetchAll();

    // next add in any default properties
    if (array_key_exists('default_properties', $details)) {

      // next iterate through each of the default properties and create a new
      // stdClass array that contains the fields needed.
      foreach ($details['default_properties'] as $property) {
        $new_prop = new stdClass();
        $new_prop->type_id = $property['cvterm']->cvterm_id;
        $new_prop->type_name = $property['cvterm']->name;
        $new_prop->definition = $property['cvterm']->definition;
        $new_prop->value = $property['value'];
        $new_prop->property_id = 'TEMP' . uniqid();
        $new_prop->rank = 'TEMP' . uniqid();
        $existing_properties[] = $new_prop;
      }
    }
  }

  /* The format of the $existing_properties array is either:
   *
   * From the chado_properties array:
   * $form_state['chado_properties'] = array(
   *   '[type_id]-[rank]' => array(
   *     'type_id' => [the cvterm.cvterm_id value]
   *     'type_name' => [the cvterm.name value]
   *     'property_id' => [the property.property_id value, or temporary value if it doesn't yet exist],
   *     'value' => [the BASEprop.value value],
   *     'rank' => [the BASEprop.rank value or NULL if not saved yet],
   *   ),
   * );
   *
   * OR
   * Populated from the database:
   * $existing_property = array(
   *   0 => array(
   *     'property_id' => [the property.property_id value],
   *     'type_id' => [the cvterm.cvterm_id value]
   *     'type_name' => [the cvterm.name value]
   *     'value' => [the BASEprop.value value],
   *     'rank' => [the BASEprop.rank value],
   *   ),
   * );
   *
   * NOTE: The main difference is the key
   *
   * Loop on the array elements of the $existing_properties array and add
   * an element to the form for each one as long as it's also in the
   * $properties_options array.
   */
  $num_properties = 0;
  foreach ($existing_properties as $property) {
    if (array_key_exists($property->type_id, $property_options)) {
      $num_properties++;

      $form['properties']['property_table'][$property->type_id]['#type'] = 'markup';
      $form['properties']['property_table'][$property->type_id]['#value'] = '';

      $form['properties']['property_table'][$property->type_id][$property->property_id]['#type'] = 'markup';
      $form['properties']['property_table'][$property->type_id][$property->property_id]['#value'] = '';
      $form['properties']['property_table'][$property->type_id][$property->property_id]['#attributes'] = array(
        'class' => array('property', 'saved')
      );

      // Determine whether this property is unsaved or not.
      // We can tell this by looking at the property_id: if it's not
      // saved yet we will have entered a TEMP###.
      if (preg_match('/^TEMP/', $property->property_id)) {
        $form['properties']['property_table'][$property->type_id][$property->property_id]['#attributes'] = array(
          'class' => array('property', 'unsaved')
        );
      }

      $form['properties']['property_table'][$property->type_id][$property->property_id]['prop_type_id'] = array(
        '#type' => 'hidden',
        '#value' => $property->type_id
      );

      $form['properties']['property_table'][$property->type_id][$property->property_id]['prop_value'] = array(
        '#type' => 'hidden',
        '#value' => $property->value
      );

      $form['properties']['property_table'][$property->type_id][$property->property_id]['prop_rank'] = array(
        '#type' => 'hidden',
        '#value' => $property->rank
      );

      $form['properties']['property_table'][$property->type_id][$property->property_id]['property_id'] = array(
        '#type' => 'hidden',
        '#value' => $property->property_id
      );

      $form['properties']['property_table'][$property->type_id][$property->property_id]['type'] = array(
        '#type' => 'markup',
        '#markup' => $property->type_name,
        '#prefix' => '<span class="row-unsaved-warning"></span>'
      );
      // If a definition is available we want to add that to the type column
      // to make it easier for users to determine what an added property means.
      if (isset($property->definition)) {
        $form['properties']['property_table'][$property->type_id][$property->property_id]['type']['#markup'] = $property->type_name . '<br><i>' . $property->definition . '</i>';
      }

      $form['properties']['property_table'][$property->type_id][$property->property_id]['value'] = array(
        '#type' => 'markup',
        '#markup' => $property->value,
      );

      $form['properties']['property_table'][$property->type_id][$property->property_id]['rank'] = array(
        '#type' => 'markup',
        '#markup' => $property->rank
      );
      // remove button
      $form['properties']['property_table'][$property->type_id][$property->property_id]['property_action'] = array(
        '#type' => 'submit',
        '#value' => t('Remove'),
        '#name' => "properties_remove-" . $property->type_id . '-' . $property->property_id,
        '#ajax' => array(
          'callback' => "chado_add_node_form_subtable_ajax_update",
          'wrapper' => 'tripal-generic-edit-properties-table',
          'effect' => 'fade',
          'method' => 'replace',
          'prevent' => 'click'
        ),
        // When this button is clicked, the form will be validated and submitted.
        // Therefore, we set custom submit and validate functions to override the
        // default node form submit.  In the validate function we validate only the
        // property fields and in the submit we remove the indicated property
        // from the chado_properties array. In order to keep validate errors
        // from the node form validate and Drupal required errors for non-property fields
        // preventing the user from removing properties we set the #limit_validation_errors below
        '#validate' => array('chado_add_node_form_subtables_remove_button_validate'),
        '#submit' => array('chado_add_node_form_subtables_remove_button_submit'),
        // Limit the validation of the form upon clicking this button to the property_table tree
        // No other fields will be validated (ie: no fields from the main form or any other api
        // added form).
        '#limit_validation_errors' => array(
          array('property_table') // Validate all fields within $form_state['values']['property_table']
        ),
      );
    }
  }

  // Quickly add a hidden field stating how many properties are currently added.
  $form['properties']['num_properties'] = array(
    '#type' => 'hidden',
    '#value' => $num_properties,
    '#attributes' => array('class' => 'num-properties')
  );

  // Form elements for adding a new property
  //---------------------------------------------
  $form['properties']['property_table']['new'] = array(
    '#type' => 'markup',
    '#prefix' => '<span class="addtl-properties-add-new-property">',
    '#suffix' => '</span>'
  );

  // get the value selected (only works on AJAX call) and print the
  // description
  $type_desc = '';
  if (isset($form_state['input']['property_table']['new']['type'])) {
    $new_type_id = $form_state['input']['property_table']['new']['type'];
    $new_term = tripal_get_cvterm(array('cvterm_id' => $new_type_id));
    if ($new_term) {
      $type_desc = $new_term->definition;
    }
  }
  $form['properties']['property_table']['new']['type'] = array(
    '#type' => 'select',
    '#options' => $property_options, // Set at top of form
    '#prefix' => '<span id="tripal-generic-edit-properties-new-desc">',
    '#suffix' => '<i>' . $type_desc . '</i></span>',
    '#ajax' => array(
      'callback' => "chado_add_node_form_properties_ajax_desc",
      'wrapper' => 'tripal-generic-edit-properties-new-desc',
      'effect' => 'fade',
      'method' => 'replace',
    ),
  );

  $form['properties']['property_table']['new']['value'] = array(
    '#type' => 'textarea',
    '#rows' => 2,
  );

  // add button
  $form['properties']['property_table']['new']['property_action'] = array(
    '#type' => 'submit',
    '#value' => t('Add'),
    '#name' => "properties-add",
    '#ajax' => array(
      'callback' => "chado_add_node_form_subtable_ajax_update",
      'wrapper' => 'tripal-generic-edit-properties-table',
      'effect' => 'fade',
      'method' => 'replace',
      'prevent' => 'click'
    ),
    // When this button is clicked, the form will be validated and submitted.
    // Therefore, we set custom submit and validate functions to override the
    // default node form submit.  In the validate function we validate only the
    // additional property fields and in the submit we add them to the chado_properties
    // array. In order to keep validate errors from the node form validate and Drupal
    // required errors for non-property fields preventing the user from adding properties we
    // set the #limit_validation_errors below
    '#validate' => array('chado_add_node_form_subtables_add_button_validate'),
    '#submit' => array('chado_add_node_form_subtables_add_button_submit'),
    // Limit the validation of the form upon clicking this button to the property_table tree
    // No other fields will be validated (ie: no fields from the main form or any other api
    // added form).
    '#limit_validation_errors' => array(
      array('property_table') // Validate all fields within $form_state['values']['property_table']
    )
  );

  $form['properties']['admin_message'] = array(
    '#type' => 'markup',
    '#markup' => $tripal_message
  );
}