tripal/tripal_ws/includes/tripal_ws.rest.inc

<?php

/**
 *
 */
function tripal_ws_rest() {

  global $base_url;
  $ws_args = func_get_args();

  // Set some initial variables.
  $response = array();
  $status = 'success';
  $version = 'v0.1';
  $message = '';
  $api_url = $base_url . '/ws/' . $version;
  $page_limit = 25;
  $pager_id = 0;

  // Set some defaults for the response.
  $response['@context'] =  array();

  // Lump everything ito a try block so that if there is a problem we can
  // throw an error and have that returned in the response.
  try {

    // The services is the first argument
    $service = (count($ws_args) > 0) ? $ws_args[0] : '';

    switch ($service) {
      case 'doc':
        tripal_ws_handle_doc_service($api_url, $response);
        break;
      case 'content':
        tripal_ws_handle_content_service($api_url, $response, $ws_args);
        break;
      case 'vocab':
        break;
      default:
        tripal_ws_handle_no_service($api_url, $response);
    }
  }
  catch (Exception $e) {
    watchdog('tripal_ws', $e->getMessage(), array(), WATCHDOG_ERROR);
    $message = $e->getMessage();
    $status = 'error';
  }

  // The responses follow a similar format as the AGAVE API with a
  // status, message, version and all data in the 'result' object.
/*   $response['status']  = $status;
  $response['message'] = $message;
  $response['api_version'] = $version;
  $response['source'] = array(
    'site_name' => variable_get('site_name', 'Unspecified'),
    'site_url' => $base_url,
    'site_slogan' => variable_get('site_slogan', 'Unspecified'),
    'site_email' =>  variable_get('site_mail', 'Unspecified'),
  ); */

  // Rather than use the drupal_json_output() funciton we manually specify
  // content type because we want it to be 'ld+json'.
  drupal_add_http_header('Content-Type', 'application/ld+json');
  print drupal_json_encode($response);
}

/**
 * Provides the Hydra compatible apiDocumentation page that describes this API.
 *
 * @param $api_url
 * @param $response
 */
function tripal_ws_handle_doc_service($api_url, &$response) {
  // First, add the vocabularies used into the @context section.
  $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
  $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';

  // Next add in the ID for tihs resource.
  $site_name = variable_get('site_name', '');
  $response['@id'] = $api_url . '/ws-doc/';
  $response['title'] =  $site_name . ": RESTful Web Services API";
  $response['entrypoint'] = $api_url;
  $response['description'] = "A fully queryable REST API using JSON-LD and " .
    "discoverable using the WC3 Hydra specification.";

  // Lastly, add in the terms used into the @context section.
  $response['@context']['title'] = 'hydra:title';
  $response['@context']['entrypoint'] = array(
    "@id" => "hydra:entrypoint",
    "@type" => "@id",
  );
  $response['@context']['description'] = 'hydra:description';
}

/**
 * This function specifies the types of resources avaiable via the API.
 *
 * @param $api_url
 * @param $response
 * @param $ws_args
 */
function tripal_ws_handle_no_service($api_url, &$response) {

  // Add in the term's will use for keys to the context.
  $response['@context']['itemListElement'] = 'schema:itemListElement';
  $response['@context']['position'] = 'schema:position';
  $response['@context']['item'] = 'schema:item';
  $response['@context']['name'] = 'foaf:name';
  $response['@context']['description'] = 'dc:description';
  $response['@context']['numberOfItems'] = 'schema:numberOfItems';
  $response['@context']['itemListOrder'] = 'schema:itemListOrder';
  $response['@context']['numberOfItems'] = 'schema:numberOfItems';
  $response['@context']['ListItem'] = 'schema:ListItem';

  // Start the list.
  $response['@type'] = 'ItemList';
  $response['itemListOrder'] = 'ItemListOrderAscending';
  $response['numberOfItems'] = 0;
  $response['name'] = 'Services';
  $response['itemListElement'][] = array(
    '@type' => 'ListItem',
    'position' => 1,
    'item' => array(
      '@id' => $api_url . '/data/',
      '@type' => $vocab->namespace . ':' . $term->accession,
      'name' => $term->name,
      'description' => 'This service provides acesss to the biological and ' .
        'anciallary data available on this site.',
    ),
  );
}

/**
 *
 * @param $api_url
 * @param $response
 * @param $ws_args
 */
function tripal_ws_handle_content_service($api_url, &$response, $ws_args) {

  // Get the content type.
  $ctype     = (count($ws_args) > 1) ? $ws_args[1] : '';
  $entity_id = (count($ws_args) > 2) ? $ws_args[2] : '';

  // If we have no content type then list all of the available content types.
  if (!$ctype) {
    tripal_ws_get_content_types($api_url, $response);
  }
  // If we don't have an entity ID then show a paged list of entities with
  // the given type.
  else if ($ctype and !$entity_id) {
    tripal_ws_get_content_type($api_url, $response, $ws_args, $ctype);
  }
  // If we have a content type and an entity ID then show the entity
  else {
    tripal_ws_get_content($api_url, $response, $ws_args, $ctype, $entity_id);
  }
}

/**
 * Provides a collection (list) of all of the content types.
 *
 * @param $api_url
 * @param $response
 */
function tripal_ws_get_content_types($api_url, &$response) {

  // First, add the vocabularies used into the @context section.
  $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
  $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';

  // Next add in the ID for tihs resource.
  $response['@id'] = $api_url . '/content';

  // Start the list.
  $response['@type'] = 'Collection';
  $response['totalItems'] = 0;
  $response['label'] = 'Content Types';

  // Get the list of published terms (these are the bundle IDs)
  $bundles = db_select('tripal_bundle', 'tb')
    ->fields('tb')
    ->orderBy('tb.label', 'ASC')
    ->execute();
  $terms = array();

  // Iterate through the terms and add the mas a entry in the collection.
  while ($bundle = $bundles->fetchObject()) {
    $entity =  entity_load('TripalTerm', array('id' => $bundle->term_id));
    $term = reset($entity);
    $vocab = $term->vocab;

    if (!array_key_exists($vocab->namespace, $response['@context'])) {
      // If there is no URL prefix then use this API's vocabulary API
      if ($term->urlprefix) {
        $response['@context'][$vocab->namespace] = $term->urlprefix;
      }
      else {
        $response['@context'][$vocab->namespace] = $api_url . '/vocab/' . $vocab->namespace . '/';
      }
    }
    // Get the bundle description. If no description is provided then
    // use the term definition
    $description = tripal_get_bundle_variable('description', $bundle->id);
    if (!$description) {
      $description = $term->definition;
    }
    // Add the bundle as a content type.
    $response['member'][] = array(
      '@id' => $api_url . '/content/' . $bundle->label,
      '@type' => $vocab->namespace . ':' . $term->accession,
      'label' => $bundle->label,
      'description' => $description,
    );
    $i++;
  }
  $response['totalItems'] = $i;

  // Lastly, add in the terms used into the @context section.
  $response['@context']['Collection'] = 'hydra:Collection';
  $response['@context']['totalItems'] = 'hydra:totalItems';
  $response['@context']['member'] = 'hydra:member';
  $response['@context']['label'] = 'rdfs:label';
  $response['@context']['description'] = 'hydra:description';
}

/**
 *
 * @param $api_url
 * @param $response
 * @param $ws_args
 */
function tripal_ws_get_content_type($api_url, &$response, $ws_args, $ctype) {

  // First, add the vocabularies used into the @context section.
  $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
  $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
  $response['@context']['schema'] = 'https://schema.org/';

  // Next add in the ID for tihs resource.
  $response['@id'] = $api_url . '/content/' . $ctype;

  // Get the TripalBundle, TripalTerm and TripalVocab type for this type.
  $bundle = tripal_load_bundle_entity(array('label' => $ctype));
  $entity =  entity_load('TripalTerm', array('id' => $bundle->term_id));
  $term = reset($entity);
  $vocab = $term->vocab;

  // Start the list.
  $response['@type'] = 'Collection';
  $response['totalItems'] = 0;
  // TODO: perhaps we should also have a plural label and get rid of the word
  // 'records'.
  $response['label'] = $bundle->label . " records";

  // Get the list of entities for this bundle.
  $query = new EntityFieldQuery;
  $query->entityCondition('entity_type', 'TripalEntity')
    ->entityCondition('bundle', $bundle->name)
    ->propertyOrderBy('title', 'DESC')
    ->pager(10);

  // Iterate through the entities and add them to the list.
  $results = $query->execute();
  $i = 0;
  if (isset($results['TripalEntity'])) {
    $entities = entity_load('TripalEntity', array_keys($results['TripalEntity']));
    foreach ($entities as $entity) {
      $response['member'][] = array(
        '@id' => $api_url . '/content/' . $ctype . '/' .  $bundle->id,
        '@type' => $vocab->namespace . ':' . $term->accession,
        'label' => $entity->title,
        'itemPage' => url('/bio-data/' . $entity->id, array('absolute' => TRUE)),
      );
      $i++;
    }
  }
  $response['totalItems'] = $i;

  // Lastly, add in the terms used into the @context section.
  $response['@context']['Collection'] = 'hydra:Collection';
  $response['@context']['totalItems'] = 'hydra:totalItems';
  $response['@context']['member'] = 'hydra:member';
  $response['@context']['label'] = 'rdfs:label';
  $response['@context']['itemPage'] = 'schema:itemPage';

}

/**
 *
 * @param $api_url
 * @param $response
 * @param $ws_args
 */
function tripal_ws_get_content($api_url, &$response, $ws_args, $ctype, $entity_id) {

  // First, add the vocabularies used into the @context section.
  $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
  $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
  $response['@context']['schema'] = 'https://schema.org/';

  // Get the TripalBundle, TripalTerm and TripalVocab type for this type.
  $bundle = tripal_load_bundle_entity(array('label' => $ctype));
  $entity =  entity_load('TripalTerm', array('id' => $bundle->term_id));
  $term = reset($entity);
  $vocab = $term->vocab;

  // Get the TripalEntity
  $entity = entity_load('TripalEntity', array('id' => $entity_id));
  $entity = reset($entity);

  // Next add in the ID and Type for this resources.
  $response['@id'] = $api_url . '/content/' . $ctype . '/' . $entity_id;
  $response['@type'] = $vocab->namespace . ':' . $term->accession,;
  $response['totalItems'] = 0;
  // TODO: perhaps we should also have a plural label and get rid of the word
  // 'records'.
  $response['label'] = $bundle->label . " records";

  // Get the list of entities for this bundle.
  $query = new EntityFieldQuery;
  $query->entityCondition('entity_type', 'TripalEntity')
  ->entityCondition('bundle', $bundle->name)
  ->propertyOrderBy('title', 'DESC')
  ->pager(10);

  // Iterate through the entities and add them to the list.
  $results = $query->execute();
  $i = 0;
  if (isset($results['TripalEntity'])) {
    $entities = entity_load('TripalEntity', array_keys($results['TripalEntity']));
    foreach ($entities as $entity) {
      $response['member'][] = array(
        '@id' => $api_url . '/content/' . $ctype . '/' .  $bundle->id,
        '@type' => $vocab->namespace . ':' . $term->accession,
        'label' => $entity->title,
        'itemPage' => url('/bio-data/' . $bundle->id, array('absolute' => TRUE)),
      );
      $i++;
    }
  }
  $response['totalItems'] = $i;

  // Lastly, add in the terms used into the @context section.
  $response['@context']['Collection'] = 'hydra:Collection';
  $response['@context']['totalItems'] = 'hydra:totalItems';
  $response['@context']['member'] = 'hydra:member';
  $response['@context']['label'] = 'rdfs:label';
  $response['@context']['itemPage'] = 'schema:itemPage';

}