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@@ -8,6 +8,9 @@ function tripal_ws_rest() {
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global $base_url;
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$ws_args = func_get_args();
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+ // The web services should never be cached.
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+ drupal_page_is_cacheable(FALSE);
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+
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// Set some initial variables.
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$response = array();
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$status = 'success';
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@@ -35,6 +38,7 @@ function tripal_ws_rest() {
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tripal_ws_handle_content_service($api_url, $response, $ws_args);
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break;
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case 'vocab':
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+ tripal_ws_handle_vocab_service($api_url, $response, $ws_args);
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break;
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default:
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tripal_ws_handle_no_service($api_url, $response);
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@@ -64,71 +68,6 @@ function tripal_ws_rest() {
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print drupal_json_encode($response);
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}
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-/**
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- * Provides the Hydra compatible apiDocumentation page that describes this API.
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- *
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- * @param $api_url
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- * @param $response
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- */
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-function tripal_ws_handle_doc_service($api_url, &$response) {
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- // First, add the vocabularies used into the @context section.
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- $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
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- $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
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-
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- // Next add in the ID for tihs resource.
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- $site_name = variable_get('site_name', '');
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- $response['@id'] = $api_url . '/ws-doc/';
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- $response['title'] = $site_name . ": RESTful Web Services API";
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- $response['entrypoint'] = $api_url;
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- $response['description'] = "A fully queryable REST API using JSON-LD and " .
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- "discoverable using the WC3 Hydra specification.";
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-
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- // Lastly, add in the terms used into the @context section.
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- $response['@context']['title'] = 'hydra:title';
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- $response['@context']['entrypoint'] = array(
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- "@id" => "hydra:entrypoint",
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- "@type" => "@id",
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- );
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- $response['@context']['description'] = 'hydra:description';
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-}
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-
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-/**
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- * This function specifies the types of resources avaiable via the API.
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- *
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- * @param $api_url
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- * @param $response
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- * @param $ws_args
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- */
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-function tripal_ws_handle_no_service($api_url, &$response) {
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-
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- // Add in the term's will use for keys to the context.
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- $response['@context']['itemListElement'] = 'schema:itemListElement';
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- $response['@context']['position'] = 'schema:position';
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- $response['@context']['item'] = 'schema:item';
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- $response['@context']['name'] = 'foaf:name';
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- $response['@context']['description'] = 'dc:description';
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- $response['@context']['numberOfItems'] = 'schema:numberOfItems';
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- $response['@context']['itemListOrder'] = 'schema:itemListOrder';
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- $response['@context']['numberOfItems'] = 'schema:numberOfItems';
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- $response['@context']['ListItem'] = 'schema:ListItem';
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-
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- // Start the list.
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- $response['@type'] = 'ItemList';
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- $response['itemListOrder'] = 'ItemListOrderAscending';
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- $response['numberOfItems'] = 0;
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- $response['name'] = 'Services';
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- $response['itemListElement'][] = array(
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- '@type' => 'ListItem',
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- 'position' => 1,
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- 'item' => array(
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- '@id' => $api_url . '/data/',
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- '@type' => $vocab->namespace . ':' . $term->accession,
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- 'name' => $term->name,
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- 'description' => 'This service provides acesss to the biological and ' .
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- 'anciallary data available on this site.',
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- ),
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- );
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-}
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/**
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*
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@@ -156,7 +95,64 @@ function tripal_ws_handle_content_service($api_url, &$response, $ws_args) {
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tripal_ws_get_content($api_url, $response, $ws_args, $ctype, $entity_id);
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}
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}
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+/**
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+ *
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+ * @param $api_url
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+ * @param $response
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+ * @param $ws_args
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+ */
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+function tripal_ws_handle_vocab_service($api_url, &$response, $ws_args) {
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+
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+ // Get the vocab name.
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+ $namespace = (count($ws_args) > 1) ? $ws_args[1] : '';
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+ $accession = (count($ws_args) > 2) ? $ws_args[2] : '';
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+
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+ // If we have no $namespace type then list all of the available vocabs.
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+ if (!$namespace) {
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+ tripal_ws_get_vocabs($api_url, $response);
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+ }
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+ // If we don't have a $namespace then show a paged list of terms.
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+ else if ($namespace and !$accession) {
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+ }
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+ // If we have a content type and an entity ID then show the entity
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+ else {
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+ }
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+}
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+
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+/**
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+ *
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+ * @param $api_url
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+ * @param $response
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+ */
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+function tripal_ws_get_vocabs($api_url, &$response) {
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+ // First, add the vocabularies used into the @context section.
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+ $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
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+ $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
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+
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+ // Next add in the ID for tihs resource.
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+ $response['@id'] = $api_url . '/vocab';
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+ // Start the list.
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+ $response['@type'] = 'Collection';
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+ $response['totalItems'] = 0;
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+ $response['label'] = 'Content Types';
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+ $response['member'] = array();
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+
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+ // TODO: determine how to get the list of in-house terms that are used
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+ // on the site. This should really only include terms that are used
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+ // as TripalEntity bundle types and that aren't part of another published
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+ // vocabulary.
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+
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+
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+ //$response['totalItems'] = $i;
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+
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+ // Lastly, add in the terms used into the @context section.
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+ $response['@context']['Collection'] = 'hydra:Collection';
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+ $response['@context']['totalItems'] = 'hydra:totalItems';
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+ $response['@context']['member'] = 'hydra:member';
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+ $response['@context']['label'] = 'rdfs:label';
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+ $response['@context']['description'] = 'hydra:description';
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+}
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/**
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* Provides a collection (list) of all of the content types.
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*
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@@ -176,6 +172,7 @@ function tripal_ws_get_content_types($api_url, &$response) {
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$response['@type'] = 'Collection';
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$response['totalItems'] = 0;
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$response['label'] = 'Content Types';
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+ $response['member'] = array();
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// Get the list of published terms (these are the bundle IDs)
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$bundles = db_select('tripal_bundle', 'tb')
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@@ -184,7 +181,8 @@ function tripal_ws_get_content_types($api_url, &$response) {
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->execute();
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$terms = array();
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- // Iterate through the terms and add the mas a entry in the collection.
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+ // Iterate through the terms and add an entry in the collection.
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+ $i = 0;
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while ($bundle = $bundles->fetchObject()) {
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$entity = entity_load('TripalTerm', array('id' => $bundle->term_id));
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$term = reset($entity);
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@@ -242,16 +240,24 @@ function tripal_ws_get_content_type($api_url, &$response, $ws_args, $ctype) {
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// Get the TripalBundle, TripalTerm and TripalVocab type for this type.
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$bundle = tripal_load_bundle_entity(array('label' => $ctype));
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- $entity = entity_load('TripalTerm', array('id' => $bundle->term_id));
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- $term = reset($entity);
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+ $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
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+ $term = reset($term);
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$vocab = $term->vocab;
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+ if (!array_key_exists($vocab->namespace, $response['@context'])) {
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+ // If there is no URL prefix then use this API's vocabulary API
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+ if ($term->urlprefix) {
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+ $response['@context'][$vocab->namespace] = $term->urlprefix;
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+ }
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+ else {
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+ $response['@context'][$vocab->namespace] = $api_url . '/vocab/' . $vocab->namespace . '/';
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+ }
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+ }
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+
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// Start the list.
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$response['@type'] = 'Collection';
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$response['totalItems'] = 0;
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- // TODO: perhaps we should also have a plural label and get rid of the word
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- // 'records'.
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- $response['label'] = $bundle->label . " records";
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+ $response['label'] = $bundle->label . " collection";
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// Get the list of entities for this bundle.
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$query = new EntityFieldQuery;
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@@ -267,7 +273,7 @@ function tripal_ws_get_content_type($api_url, &$response, $ws_args, $ctype) {
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$entities = entity_load('TripalEntity', array_keys($results['TripalEntity']));
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foreach ($entities as $entity) {
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$response['member'][] = array(
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- '@id' => $api_url . '/content/' . $ctype . '/' . $bundle->id,
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+ '@id' => $api_url . '/content/' . $ctype . '/' . $entity->id,
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'@type' => $vocab->namespace . ':' . $term->accession,
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'label' => $entity->title,
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'itemPage' => url('/bio-data/' . $entity->id, array('absolute' => TRUE)),
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@@ -301,52 +307,176 @@ function tripal_ws_get_content($api_url, &$response, $ws_args, $ctype, $entity_i
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// Get the TripalBundle, TripalTerm and TripalVocab type for this type.
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$bundle = tripal_load_bundle_entity(array('label' => $ctype));
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- $entity = entity_load('TripalTerm', array('id' => $bundle->term_id));
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- $term = reset($entity);
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+ $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
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+ $term = reset($term);
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$vocab = $term->vocab;
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- // Get the TripalEntity
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+ if (!array_key_exists($vocab->namespace, $response['@context'])) {
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+ // If there is no URL prefix then use this API's vocabulary API
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+ if ($term->urlprefix) {
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+ $response['@context'][$vocab->namespace] = $term->urlprefix;
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+ }
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+ else {
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+ $response['@context'][$vocab->namespace] = $api_url . '/vocab/' . $vocab->namespace . '/';
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+ }
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+ }
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+
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+ // Get the TripalEntity and attach all the fields.
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$entity = entity_load('TripalEntity', array('id' => $entity_id));
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+ field_attach_load('TripalEntity', $entity);
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$entity = reset($entity);
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+
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// Next add in the ID and Type for this resources.
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$response['@id'] = $api_url . '/content/' . $ctype . '/' . $entity_id;
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- $response['@type'] = $vocab->namespace . ':' . $term->accession,;
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- $response['totalItems'] = 0;
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- // TODO: perhaps we should also have a plural label and get rid of the word
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- // 'records'.
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- $response['label'] = $bundle->label . " records";
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+ $response['@type'] = $vocab->namespace . ':' . $term->accession;
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+ $response['label'] = $entity->title;
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+ $response['itemPage'] = url('/bio-data/' . $bundle->id, array('absolute' => TRUE));
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+
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+ // Get information about the fields attached to this bundle and sort them
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+ // in the order they were set for the display.
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+ // TODO: should we allow for custom ordering of fields for web services
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+ // or use the default display ordering?
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+ $fields = field_info_instances('TripalEntity', $bundle->name);
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+ uasort($fields, function($a, $b) {
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+ $a_weight = (is_array($a) && isset($a['display']['default']['weight'])) ? $a['display']['default']['weight'] : 0;
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+ $b_weight = (is_array($b) && isset($b['display']['default']['weight'])) ? $b['display']['default']['weight'] : 0;
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+
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+ if ($a_weight == $b_weight) {
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+ return 0;
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+ }
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+ return ($a_weight < $b_weight) ? -1 : 1;
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+ });
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+
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+ // Iterate throught the fields and add each value to the response.
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+ //$response['fields'] = $fields;
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+ foreach ($fields as $field_name => $field) {
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+ $field_value = $entity->$field_name;
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+
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+ // Get the semantic web settings for this field
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+ $field_type = '';
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+ if (array_key_exists('semantic_web', $field['settings'])) {
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+ $field_type = $field['settings']['semantic_web']['type'];
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+ if ($field_type) {
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+ $ns = $field['settings']['semantic_web']['ns'];
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+ $nsurl = $field['settings']['semantic_web']['nsurl'];
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+ $response['@context'][$ns] = $nsurl;
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+ $response['@context'][$field['label']] = $ns . ':' .$field_type;
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+ }
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+ }
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- // Get the list of entities for this bundle.
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- $query = new EntityFieldQuery;
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- $query->entityCondition('entity_type', 'TripalEntity')
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- ->entityCondition('bundle', $bundle->name)
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- ->propertyOrderBy('title', 'DESC')
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- ->pager(10);
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+ // TODO: need a way to hide fields.
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- // Iterate through the entities and add them to the list.
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- $results = $query->execute();
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- $i = 0;
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- if (isset($results['TripalEntity'])) {
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- $entities = entity_load('TripalEntity', array_keys($results['TripalEntity']));
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- foreach ($entities as $entity) {
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- $response['member'][] = array(
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- '@id' => $api_url . '/content/' . $ctype . '/' . $bundle->id,
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- '@type' => $vocab->namespace . ':' . $term->accession,
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- 'label' => $entity->title,
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- 'itemPage' => url('/bio-data/' . $bundle->id, array('absolute' => TRUE)),
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- );
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- $i++;
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+ // Get the values based on cardinality
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+ $items = field_get_items('TripalEntity', $entity, $field_name);
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+ $values = '';
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+ if (array_key_exists('und', $field_value) and count($field_value['und']) == 1) {
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+ $values = $field_value['und'][0]['value'];
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+ }
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+ // If cardinality is greater than 1 then the value should be an array
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+ else {
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+ $values = array();
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+ for ($i = 0; $i < count($field_value); $i++) {
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+ $values[] = $field_value['und'][$i]['value'];
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+ }
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}
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+ $response[$field['label']] = $values;
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}
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- $response['totalItems'] = $i;
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+
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+ //$response['fields'] = $fields;
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// Lastly, add in the terms used into the @context section.
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- $response['@context']['Collection'] = 'hydra:Collection';
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- $response['@context']['totalItems'] = 'hydra:totalItems';
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- $response['@context']['member'] = 'hydra:member';
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$response['@context']['label'] = 'rdfs:label';
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$response['@context']['itemPage'] = 'schema:itemPage';
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+}
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+
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+
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+
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+/**
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+ * Provides the Hydra compatible apiDocumentation page that describes this API.
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+ *
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+ * @param $api_url
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+ * @param $response
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+ */
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+function tripal_ws_handle_doc_service($api_url, &$response) {
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+ // First, add the vocabularies used into the @context section.
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+ $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
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+ $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
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+ // Next add in the ID for tihs resource.
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+ $site_name = variable_get('site_name', '');
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+ $response['@id'] = $api_url . '/doc/';
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+ $response['title'] = $site_name . ": RESTful Web Services API";
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+ $response['entrypoint'] = $api_url;
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+ $response['description'] = "A fully queryable REST API using JSON-LD and " .
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+ "discoverable using the WC3 Hydra specification.";
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+
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+ // Lastly, add in the terms used into the @context section.
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+ $response['@context']['title'] = 'hydra:title';
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+ $response['@context']['entrypoint'] = array(
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+ "@id" => "hydra:entrypoint",
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+ "@type" => "@id",
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+ );
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+ $response['@context']['description'] = 'hydra:description';
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}
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+/**
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+ * This function specifies the types of resources avaiable via the API.
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+ *
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+ * @param $api_url
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+ * @param $response
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+ * @param $ws_args
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+ */
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+function tripal_ws_handle_no_service($api_url, &$response) {
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+
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+ // First, add the vocabularies used into the @context section.
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+ $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
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+ $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
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+ $response['@context']['dc'] = 'http://purl.org/dc/dcmitype/';
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+ $response['@context']['schema'] = 'https://schema.org/';
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+
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+ // Next add in the ID for tihs resource.
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+ $response['@id'] = $api_url;
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+
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+
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+ // Start the list.
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+ $response['@type'] = 'Collection';
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+ $response['totalItems'] = 0;
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+ $response['label'] = 'Services';
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+ $response['member'] = array();
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+
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+ // Start the list.
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+ $response['member'][] = array(
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+ '@id' => $api_url . '/content/',
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+ '@type' => 'Service',
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+ 'label' => 'Content Types',
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+ 'description' => 'Provides acesss to the biological and ' .
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+ 'ancilliary data available on this site. Each content type ' .
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+ 'represents biological data that is defined in a controlled vocabulary '.
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+ '(e.g. Sequence Ontology term: gene (SO:0000704)).',
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+ );
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+ $response['member'][] = array(
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+ '@id' => $api_url . '/doc/',
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+ '@type' => 'Service',
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+ 'label' => 'API Documentation',
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+ 'description' => 'The WC3 Hydra compatible documentation for this API.',
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+ );
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+ $response['member'][] = array(
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+ '@id' => $api_url . '/vocab/',
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+ '@type' => 'Service',
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+ 'label' => 'Vocabulary',
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+ 'description' => 'Defines in-house locally defined vocabulary terms that ' .
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+ 'have been added specifically for this site. These terms are typically ' .
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+ 'added because no other appropriate term exists in another community-vetted '.
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+ 'controlled vocabulary.',
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+ );
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+
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+ $response['totalItems'] = count($response['member']);
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+
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+ $response['@context']['Collection'] = 'hydra:Collection';
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+ $response['@context']['totalItems'] = 'hydra:totalItems';
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+ $response['@context']['member'] = 'hydra:member';
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+ $response['@context']['Service'] = 'dc:Service';
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+ $response['@context']['label'] = 'rdfs:label';
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+ $response['@context']['description'] = 'hydra:description';
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+}
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Stephen Ficklin