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@@ -1,8 +1,12 @@
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<?php
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+/**
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+ *
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+ */
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function tripal_ws_rest() {
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global $base_url;
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+ $ws_args = func_get_args();
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// Set some initial variables.
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$response = array();
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@@ -13,26 +17,28 @@ function tripal_ws_rest() {
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$page_limit = 25;
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$pager_id = 0;
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- $response['@context'] = array(
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- 'schema' => 'http://schema.org/',
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- 'foaf' => 'http://xmlns.com/foaf/0.1/',
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- 'dc' => 'http://purl.org/dc/elements/1.1/',
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- );
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- $response['@id'] = $api_url;
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-
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- $namespace = arg(3) ? arg(3) : '';
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- $bundle_name = arg(4) ? arg(4) : '';
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+ // Set some defaults for the response.
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+ $response['@context'] = array();
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// Lump everything ito a try block so that if there is a problem we can
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// throw an error and have that returned in the response.
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try {
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- if (!$namespace) {
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- tripal_ws_get_content_types($api_url, $response);
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- }
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- if ($namespace and !$bundle_name) {
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- tripal_ws_get_content_type($api_url, $response, $namespace);
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- }
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+ // The services is the first argument
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+ $service = (count($ws_args) > 0) ? $ws_args[0] : '';
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+
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+ switch ($service) {
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+ case 'doc':
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+ tripal_ws_handle_doc_service($api_url, $response);
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+ break;
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+ case 'content':
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+ tripal_ws_handle_content_service($api_url, $response, $ws_args);
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+ break;
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+ case 'vocab':
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+ break;
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+ default:
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+ tripal_ws_handle_no_service($api_url, $response);
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+ }
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}
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catch (Exception $e) {
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watchdog('tripal_ws', $e->getMessage(), array(), WATCHDOG_ERROR);
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@@ -51,15 +57,49 @@ function tripal_ws_rest() {
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'site_slogan' => variable_get('site_slogan', 'Unspecified'),
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'site_email' => variable_get('site_mail', 'Unspecified'),
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); */
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- print drupal_json_output($response);
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+
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+ // Rather than use the drupal_json_output() funciton we manually specify
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+ // content type because we want it to be 'ld+json'.
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+ drupal_add_http_header('Content-Type', 'application/ld+json');
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+ print drupal_json_encode($response);
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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 unknown $api_url
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- * @param unknown $response
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+ * @param $api_url
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+ * @param $response
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*/
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-function tripal_ws_get_content_types($api_url, &$response) {
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+function tripal_ws_handle_doc_service($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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+ * 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, &$response) {
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// Add in the term's will use for keys to the context.
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$response['@context']['itemListElement'] = 'schema:itemListElement';
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@@ -76,7 +116,66 @@ function tripal_ws_get_content_types($api_url, &$response) {
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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'] = 'Content Types';
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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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+ *
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+ * @param $api_url
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+ * @param $response
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+ * @param $ws_args
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+ */
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+function tripal_ws_handle_content_service($api_url, &$response, $ws_args) {
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+
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+ // Get the content type.
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+ $ctype = (count($ws_args) > 1) ? $ws_args[1] : '';
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+ $entity_id = (count($ws_args) > 2) ? $ws_args[2] : '';
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+
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+ // If we have no content type then list all of the available content types.
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+ if (!$ctype) {
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+ tripal_ws_get_content_types($api_url, $response);
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+ }
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+ // If we don't have an entity ID then show a paged list of entities with
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+ // the given type.
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+ else if ($ctype and !$entity_id) {
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+ tripal_ws_get_content_type($api_url, $response, $ws_args, $ctype);
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+ }
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+ // If we have a content type and an entity ID then show the entity
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+ else {
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+ tripal_ws_get_content($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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+ * Provides a collection (list) of all of the content types.
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+ *
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+ * @param $api_url
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+ * @param $response
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+ */
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+function tripal_ws_get_content_types($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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+
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+ // Next add in the ID for tihs resource.
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+ $response['@id'] = $api_url . '/content';
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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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+ $response['label'] = 'Content Types';
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// Get the list of published terms (these are the bundle IDs)
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$bundles = db_select('tripal_bundle', 'tb')
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@@ -84,14 +183,13 @@ function tripal_ws_get_content_types($api_url, &$response) {
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->orderBy('tb.label', 'ASC')
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->execute();
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$terms = array();
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+
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+ // Iterate through the terms and add the mas a entry in the collection.
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while ($bundle = $bundles->fetchObject()) {
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$entity = entity_load('TripalTerm', array('id' => $bundle->term_id));
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- $terms[$bundle->label] = reset($entity);
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- }
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-
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- $i = 0;
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- foreach ($terms as $name => $term) {
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+ $term = reset($entity);
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$vocab = $term->vocab;
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+
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if (!array_key_exists($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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@@ -101,29 +199,154 @@ function tripal_ws_get_content_types($api_url, &$response) {
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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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- $response['itemListElement'][] = array(
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- '@type' => 'ListItem',
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- 'position' => $i + 1,
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- 'item' => array(
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- '@id' => $api_url . '/bio-data/' . $term->name,
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- '@type' => $vocab->namespace . ':' . $term->accession,
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- 'name' => $term->name,
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- 'description' => $term->definition,
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- ),
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+ // Get the bundle description. If no description is provided then
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+ // use the term definition
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+ $description = tripal_get_bundle_variable('description', $bundle->id);
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+ if (!$description) {
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+ $description = $term->definition;
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+ }
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+ // Add the bundle as a content type.
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+ $response['member'][] = array(
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+ '@id' => $api_url . '/content/' . $bundle->label,
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+ '@type' => $vocab->namespace . ':' . $term->accession,
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+ 'label' => $bundle->label,
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+ 'description' => $description,
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);
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$i++;
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}
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- $response['numberOfItems'] = $i;
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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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+/**
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+ *
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+ * @param $api_url
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+ * @param $response
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+ * @param $ws_args
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+ */
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+function tripal_ws_get_content_type($api_url, &$response, $ws_args, $ctype) {
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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']['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 . '/content/' . $ctype;
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+
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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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+ $vocab = $term->vocab;
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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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+
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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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+
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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/' . $entity->id, array('absolute' => TRUE)),
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+ );
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+ $i++;
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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']['itemPage'] = 'schema:itemPage';
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+
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}
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/**
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*
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- * @param unknown $api_url
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- * @param unknown $response
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- * @param unknown $vocab
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- * @param unknown $name
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+ * @param $api_url
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+ * @param $response
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+ * @param $ws_args
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*/
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-function tripal_ws_get_content_type($api_url, &$response, $vocab, $name) {
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+function tripal_ws_get_content($api_url, &$response, $ws_args, $ctype, $entity_id) {
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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']['schema'] = 'https://schema.org/';
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+
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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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+ $vocab = $term->vocab;
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+
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+ // Get the TripalEntity
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+ $entity = entity_load('TripalEntity', array('id' => $entity_id));
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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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+
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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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+
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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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+ }
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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']['itemPage'] = 'schema:itemPage';
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}
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Chun-Huai Cheng