tripal/tripal_chado/includes/tripal_chado.custom_tables.inc

<?php
/**
 * @file
 * Contains functions for creating, editing and deleting custom tables
 * on the Tripal website.
 *
 */

/**
 * Provides a landing page for administrating custom tables.
 */
function tripal_custom_table_admin_view() {
  $output = '';

  // set the breadcrumb
  $breadcrumb = [];
  $breadcrumb[] = l('Home', '<front>');
  $breadcrumb[] = l('Administration', 'admin');
  $breadcrumb[] = l('Tripal', 'admin/tripal');
  $breadcrumb[] = l('Chado Schema', 'admin/tripal/storage/chado');
  $breadcrumb[] = l('Custom Tables', 'admin/tripal/storage/chado/custom_tables');
  drupal_set_breadcrumb($breadcrumb);

  // Add the view
  $view = views_embed_view('tripal_admin_custom_table', 'default');
  if (isset($view)) {
    $output .= $view;
  }
  else {
    $output .= '<p>The Tripal Custom Table management system uses primarily views to provide an '
      . 'administrative interface. Currently one or more views needed for this '
      . 'administrative interface are disabled. <strong>Click each of the following links to '
      . 'enable the pertinent views</strong>:</p>';
    $output .= '<ul>';
    $output .= '<li>' . l('Custom Tables View', 'admin/tripal/storage/chado/custom_tables/views/tables/enable') . '</li>';
    $output .= '</ul>';
  }

  return $output;
}

/**
 * Renders the tripal_custom_tables_form.
 *
 */
function tripal_custom_table_new_page() {

  $form = drupal_get_form('tripal_custom_tables_form');
  return drupal_render($form);
}

/**
 * A template function which returns markup to display details for the custom
 * table
 *
 * @param $table_id
 *  The unique ID of the custom table
 *
 */
function tripal_custom_table_view($table_id) {

  // get this custom_table details
  $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id";
  $results = db_query($sql, [':table_id' => $table_id]);
  $custom_table = $results->fetchObject();

  // create a table with each row containig stats for
  // an individual job in the results set.
  $return_url = url("admin/tripal/storage/chado/custom_tables");
  $output = "<p><a href=\"$return_url\">" . t("Return to list of custom tables") . "</a></p>";
  $output .= "<br />";
  $output .= "<p>Details for <b>$custom_table->table_name</b>:</p>";
  $output .= "<br />";
  $output .= "<table class=\"border-table\">";
  if ($custom_table->table_name) {
    $output .= "  <tr>" .
      "    <th>Table Name</th>" .
      "    <td>$custom_table->table_name</td>" .
      "  </tr>";
  }
  if ($custom_table->schema) {
    $output .= "  <tr>" .
      "    <th>Table Field Definitions</th>" .
      "    <td><pre>" . var_export(unserialize($custom_table->schema), 1) . "</pre></td>" .
      "  </tr>";
  }

  // build the URLs using the url function so we can handle installations where
  // clean URLs are or are not used
  $delete_url = url("admin/tripal/storage/chado/custom_tables/delete/$custom_table->table_id");
  $edit_url = url("admin/tripal/storage/chado/custom_tables/edit/$custom_table->table_id");
  $output .= "<tr><th>Actions</th>" .
    "<td>" .
    "     <a href='$edit_url'>Edit</a>, " .
    "     <a href='$delete_url'>Delete</a></td></tr>";
  $output .= "</table>";

  return $output;
}

/**
 * A Form to Create/Edit a Custom table.
 *
 * @param $form_state
 *   The current state of the form (Form API)
 * @param $table_id
 *   The unique ID of the Custom table to Edit or NULL if creating a new table
 *
 * @return
 *   A form array (Form API)
 *
 */
function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL) {

  // set the breadcrumb
  $breadcrumb = [];
  $breadcrumb[] = l('Home', '<front>');
  $breadcrumb[] = l('Administration', 'admin');
  $breadcrumb[] = l('Tripal', 'admin/tripal');
  $breadcrumb[] = l('Chado Schema', 'admin/tripal/storage/chado');
  $breadcrumb[] = l('Custom Tables', 'admin/tripal/storage/chado/custom_tables');
  drupal_set_breadcrumb($breadcrumb);

  if (!$table_id) {
    $action = 'Add';
  }
  else {
    $action = 'Edit';
  }

  // get this requested table
  $default_schema = '';
  $default_force_drop = 0;
  $default_is_base = 0;
  if (strcmp($action, 'Edit') == 0) {
    $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id ";
    $results = db_query($sql, [':table_id' => $table_id]);
    $custom_table = $results->fetchObject();

    // if this is a materialized view then don't allow editing with this function
    if (property_exists($custom_table, 'mview_id') and $custom_table->mview_id) {
      drupal_set_message("This custom table is a materialized view. Please use the " . l('Materialized View', 'admin/tripal/storage/chado/mviews') . " interface to edit it.", 'error');
      drupal_goto("admin/tripal/storage/chado/custom_tables");
      return [];
    }

    // set the default values.  If there is a value set in the
    // form_state then let's use that, otherwise, we'll pull
    // the values from the database
    if (array_key_exists('values', $form_state)) {
      $default_schema = $form_state['values']['schema'];
      $default_force_drop = $form_state['values']['force_drop'];
      $default_is_base = $form_state['values']['is_base'];
    }
    else {
      $default_is_base = $custom_table->is_base;
    }

    if (!$default_schema) {
      $default_schema = var_export(unserialize($custom_table->schema), 1);
      $default_schema = preg_replace('/=>\s+\n\s+array/', '=> array', $default_schema);
    }
  }

  // Build the form
  $form['action'] = [
    '#type' => 'value',
    '#value' => $action,
  ];

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

  $form['instructions'] = [
    '#type' => 'fieldset',
    '#title' => 'Instructions',
    '#collapsible' => TRUE,
    '#collapsed' => TRUE,
  ];
  $form['instructions']['text'] = [
    '#type' => 'item',
    '#markup' => '<p>' . t('At times it is necessary to add a custom table
       to the Chado schema. These are not offically sanctioned tables but may
       be necessary for local data requirements. Avoid creating custom tables
       when possible as other GMOD tools may not recognize these tables nor
       the data in them.  Linker tables or property tables are often a good
       candidate for a custom table. For example a table to link stocks and
       libraries (e.g. library_stock). Try to model linker or propery tables
       after existing tables.  If the table already exists it will not be
       modified.  To force dropping and recreation of the table
       click the checkbox below.  Tables are defined using the ' .
        l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7',
          ['attributes' => ['target' => '_blank']]) . '</p>' .
        '<p>Please note that table names should be all lower-case.</p>'
      ),
  ];

  $form['instructions']['example'] = [
    '#type' => 'item',
    '#markup' => "Example library_stock table: <pre>
array (
  'table' => 'library_stock',
  'fields' => array (
    'library_stock_id' => array(
      'type' => 'serial',
      'not null' => TRUE,
    ),
    'library_id' => array(
      'type' => 'int',
      'not null' => TRUE,
    ),
    'stock_id' => array(
      'type' => 'int',
      'not null' => TRUE,
    ),
  ),
  'primary key' => array(
    'library_stock_id'
  ),
  'unique keys' => array(
    'library_stock_c1' => array(
      'library_id',
      'stock_id'
    ),
  ),
  'foreign keys' => array(
    'library' => array(
      'table' => 'library',
      'columns' => array(
        'library_id' => 'library_id',
      ),
    ),
    'stock' => array(
      'table' => 'stock',
      'columns' => array(
        'stock_id' => 'stock_id',
      ),
    ),
  ),
)
    </pre>",
  ];

  $form['force_drop'] = [
    '#type' => 'checkbox',
    '#title' => t('Re-create table'),
    '#description' => t('Check this box if your table already exists and you would like to drop it and recreate it.'),
    '#default_value' => $default_force_drop,
  ];
  $form['is_base'] = [
      '#type' => 'checkbox',
      '#title' => t('Is this a base table?'),
      '#description' => t('Check this box if this custom table will contain records '.
          'that can be published. For example, tables such as "feature", ' .
          '"stock", "analysis" are all tables in Chado that contain "base" ' .
          'records that can be published and anciallary data attached via '.
          'fields.  If selected, site admins can create new content types ' .
          'that resolve to this table.'),
      '#default_value' => $default_is_base,
  ];
  $form['schema'] = [
    '#type' => 'textarea',
    '#title' => t('Schema Array'),
    '#description' => t('Please enter the ' . l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7', ['attributes' => ['target' => '_blank']]) . ' compatible array that defines the table.'),
    '#required' => FALSE,
    '#default_value' => $default_schema,
    '#rows' => 25,
  ];

  if ($action == 'Edit') {
    $value = 'Save';
  }
  if ($action == 'Add') {
    $value = 'Add';
  }
  $form['submit'] = [
    '#type' => 'submit',
    '#value' => t($value),
    '#executes_submit_callback' => TRUE,
  ];
  $form['cancel'] = [
    '#type' => 'markup',
    '#markup' => l('Cancel', 'admin/tripal/storage/chado/custom_tables'),
  ];

  return $form;
}

/**
 * Implements hook_validate().
 * Validate the Create/Edit custom table form.
 *
 */
function tripal_custom_tables_form_validate($form, &$form_state) {
  $action = $form_state['values']['action'];
  $table_id = $form_state['values']['table_id'];
  $schema = $form_state['values']['schema'];
  $force_drop = $form_state['values']['force_drop'];

  if (!$schema) {
    form_set_error($form_state['values']['schema'], t('Schema array field is required.'));
  }

  // make sure the array is valid
  $schema_array = [];
  if ($schema) {
    $success = preg_match('/^\s*array/', $schema);
    if (!$success) {
      form_set_error($form_state['values']['schema'],
        t("The schema array should begin with the word 'array'."));
    }
    else {
      $success = eval("\$schema_array = $schema;");
      if ($success === FALSE) {
        $error = error_get_last();
        form_set_error('schema', t("The schema array is improperly formatted. Parse Error : " . $error["message"]));
      }
      if (is_array($schema_array) and !array_key_exists('table', $schema_array)) {
        form_set_error('schema', t("The schema array must have key named 'table'"));
      }

      // validate the contents of the array
      $error = chado_validate_custom_table_schema($schema_array);
      if ($error) {
        form_set_error('schema', $error);
      }

      if ($action == 'Edit') {
        // see if the table name has changed. If so, then check to make sure
        // it doesn't already exists. We don't want to drop a table we didn't mean to
        $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id";
        $results = db_query($sql, [':table_id' => $table_id]);
        $ct = $results->fetchObject();
        if ($ct->table_name != $schema_array['table']) {
          $exists = chado_table_exists($schema_array['table']);
          if ($exists) {
            form_set_error($form_state['values']['schema'],
              t("The table name already exists, please choose a different name."));
          }
        }
      }
    }
  }
}

/**
 * Submit the Create/Edit Custom table form
 * Implements hook_form_submit().
 *
 */
function tripal_custom_tables_form_submit($form, &$form_state) {

  $ret = [];
  $action = $form_state['values']['action'];
  $table_id = $form_state['values']['table_id'];
  $schema = $form_state['values']['schema'];
  $force_drop = $form_state['values']['force_drop'];
  $is_base = $form_state['values']['is_base'];

  $skip_creation = 1;
  if ($force_drop) {
    $skip_creation = 0;
  }

  // convert the schema into a PHP array
  $schema_arr = [];
  eval("\$schema_arr = $schema;");


  if (strcmp($action, 'Edit') == 0) {
    chado_edit_custom_table($table_id, $schema_arr['table'], $schema_arr, $skip_creation, $is_base);
  }
  elseif (strcmp($action, 'Add') == 0) {
    chado_create_custom_table($schema_arr['table'], $schema_arr, $skip_creation,
        NULL, FALSE, $is_base);
  }
  else {
    drupal_set_message(t("No action performed."));
  }

  if ($is_base == 1) {
    drupal_set_message(t("The custom table is a base table. Before you can use this
      table for content publication you must 1) be sure to map
      the controlled vocabulary terms for the columns of this table prior
      to creating a new content type for this table. You can set the
      terms at !link",
        ['!link' => l('Admin > Tripal > Data Storage > Chado > Semantic Web', 'admin/tripal/storage/chado/semweb/' . $schema_arr['table'])]
     ));
  }

  drupal_goto("admin/tripal/storage/chado/custom_tables");
}

/**
 * Just a simple form for confirming deletion of a custom table
 *
 */
function tripal_custom_tables_delete_form($form, &$form_state, $table_id) {

  // get details about this table entry
  $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id";
  $results = db_query($sql, [':table_id' => $table_id]);
  $entry = $results->fetchObject();

  // if this is a materialized view then don't allow editing with this function
  if ($entry->mview_id) {
    drupal_set_message("This custom table is a materialized view. Please use the " . l('Materialized View', 'admin/tripal/storage/chado/mviews') . " interface to delete it.", 'error');
    drupal_goto("admin/tripal/storage/chado/custom_tables");
    return [];
  }


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

  $form['sure'] = [
    '#type' => 'markup',
    '#markup' => '<p>Are you sure you want to delete the "' . $entry->table_name . '" custom table?</p>',
  ];
  $form['submit'] = [
    '#type' => 'submit',
    '#value' => 'Delete',
  ];
  $form['cancel'] = [
    '#type' => 'submit',
    '#value' => 'Cancel',
  ];
  return $form;
}

/**
 * form submit hook for the tripal_custom_tables_delete_form form.
 *
 * @param $form
 * @param $form_state
 */
function tripal_custom_tables_delete_form_submit($form, &$form_state) {
  $action = $form_state['clicked_button']['#value'];
  $table_id = $form_state['values']['table_id'];

  if (strcmp($action, 'Delete') == 0) {
    chado_delete_custom_table($table_id);
  }
  else {
    drupal_set_message(t("No action performed."));
  }
  drupal_goto("admin/tripal/storage/chado/custom_tables");
}