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@@ -1,1064 +0,0 @@
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-<?php
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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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-function tripal_ws_services_v0_1($api_url, $ws_path, $params) {
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-
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- // Set some initial variables.
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- $response = array();
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- $version = 'v0.1';
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-
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- // Set some defaults for the response.
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- $response['@context'] = array();
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-
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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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-
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- // The services is the first argument
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- $service = (count($ws_path) > 0) ? $ws_path[0] : '';
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-
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- switch ($service) {
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- case 'doc':
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- tripal_ws_services_v0_1_handle_doc_service($api_url, $response);
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- break;
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- case 'content':
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- tripal_ws_services_v0_1_handle_content_service($api_url, $response, $ws_path, $params);
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- break;
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- case 'vocab':
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- tripal_ws_services_v0_1_handle_vocab_service($api_url, $response, $ws_path);
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- break;
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- default:
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- tripal_ws_services_v0_1_handle_no_service($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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- $message = $e->getMessage();
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- drupal_add_http_header('Status', '400 Bad Request');
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-
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- }
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-
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- return $response;
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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 $ws_path
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- */
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-function tripal_ws_services_v0_1_handle_content_service($api_url, &$response, $ws_path, $params) {
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-
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- // Get the content type.
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- $ctype = (count($ws_path) > 1) ? $ws_path[1] : '';
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- $entity_id = (count($ws_path) > 2) ? $ws_path[2] : '';
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-
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- // If we have no content type then list all of the available content types.
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- if (!$ctype) {
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- tripal_ws_services_v0_1_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 !$entity_id) {
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- tripal_ws_services_v0_1_get_content_type($api_url, $response, $ws_path, $ctype, $params);
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- }
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- // If we have a content type and an entity ID then show the entity
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- else {
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- tripal_ws_services_v0_1_get_content($api_url, $response, $ws_path, $ctype, $entity_id, $params);
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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 $ws_path
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-*/
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-function tripal_ws_services_v0_1_handle_vocab_service($api_url, &$response, $ws_path) {
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-
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- // Get the vocab name.
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- $vocabulary = (count($ws_path) > 1) ? $ws_path[1] : '';
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- $accession = (count($ws_path) > 2) ? $ws_path[2] : '';
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-
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- // If we have no $vocabulary type then list all of the available vocabs.
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- if (!$vocabulary) {
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- tripal_ws_services_v0_1_get_vocabs($api_url, $response);
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- }
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- // If we don't have a $vocabulary then show a paged list of terms.
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- else if ($vocabulary and !$accession) {
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- tripal_ws_services_v0_1_get_vocab($api_url, $response, $ws_path, $vocabulary);
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- }
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- // If we have a content type and an entity ID then show the entity
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- else if ($vocabulary and $accession) {
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- tripal_ws_services_v0_1_get_term($api_url, $response, $ws_path, $vocabulary, $accession);
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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 $response
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- */
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-function tripal_ws_services_v0_1_get_vocabs($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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- $response['@id'] = url($api_url . '/vocab', array('absolute' => TRUE));
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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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- $response['member'] = array();
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-
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- $vocabs = db_select('tripal_vocab', 'tv')
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- ->fields('tv')
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- ->execute();
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- // Iterate through the vocabularies and add an entry in the collection.
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- $i = 0;
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- while ($vocab = $vocabs->fetchObject()) {
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- // Add the bundle as a content type.
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- $response['member'][] = array(
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- '@id' => url($api_url . '/vocab/' . urlencode($vocab->vocabulary), array('absolute' => TRUE)),
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- '@type' => 'vocabulary',
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- 'vocabulary' => $vocab->vocabulary,
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- );
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- $i++;
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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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- $response['@context']['description'] = 'hydra:description';
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-
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- tripal_ws_services_v0_1_write_context($response, $ctype);
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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 $ws_path
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- */
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-function tripal_ws_services_v0_1_get_vocab($api_url, &$response, $ws_path, $vocabulary) {
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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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- $response['@id'] = url($api_url . '/vocab/' . $vocabulary, array('absolute' => TRUE));
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-
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- // Get the vocabulary
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- $vocab = tripal_load_vocab_entity(array('vocabulary' => $vocabulary));
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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'] = vocabulary . " vocabulary collection";
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- $response['comment'] = 'The following list of terms may not be the full ' .
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- 'list for the vocabulary. The terms listed here are only those ' .
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- 'that have associated content on this site.';
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-
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- // Get the list of terms for this vocab.
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- $query = db_select('tripal_term', 'tt')
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- ->fields('tt', array('id'))
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- ->condition('vocab_id', $vocab->id)
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- ->orderBy('accession', 'DESC');
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-
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- // Iterate through the entities and add them to the list.
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- $terms = $query->execute();
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- $i = 0;
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- while($term = $terms->fetchObject()) {
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- $term = tripal_load_term_entity(array('term_id' => $term->id));
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- $response['member'][] = array(
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- '@id' => url($api_url . '/vocab/' . urlencode($vocabulary) . '/' . urlencode($term->accession), array('absolute' => TRUE)),
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- '@type' => 'vocabulary_term',
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- 'vocabulary' => $vocab->vocabulary,
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- 'accession' => $term->accession,
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- 'name' => $term->name,
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- 'definition' => $term->definition,
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- );
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- $i++;
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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']['comment'] = 'rdfs:comment';
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- $response['@context']['itemPage'] = 'schema:itemPage';
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-
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- tripal_ws_services_v0_1_write_context($response, $ctype);
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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 $ws_path
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- */
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-function tripal_ws_services_v0_1_get_term($api_url, &$response, $ws_path, $vocabulary, $accession) {
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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 term.
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- $term = tripal_load_term_entity(array('vocabulary' => $vocabulary, 'accession' => $accession));
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-
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- // Next add in the ID and Type for this resources.
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- $response['@id'] = url($api_url . '/vocab/' . urlencode($vocabulary) . '/' . urlencode($accession), array('absolute' => TRUE));
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- $response['@type'] = 'vocabulary_term';
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- $response['label'] = $term->name;
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- $response['vocabulary'] = $vocabulary;
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- $response['accession'] = $accession;
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- $response['name'] = $term->name;
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- $response['definition'] = $term->definition;
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-
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- if ($term->url) {
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- $response['URL'] = $term->url;
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- }
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-
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- // Lastly, add in the terms used into the @context section.
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- $response['@context']['label'] = 'rdfs:label';
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- $response['@context']['itemPage'] = 'schema:itemPage';
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-
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- tripal_ws_services_v0_1_write_context($response, $ctype);
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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 $response
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- */
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-function tripal_ws_services_v0_1_get_content_types($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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- $response['@id'] = url($api_url . '/content', array('absolute' => TRUE));
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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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- $response['member'] = array();
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-
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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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- ->fields('tb')
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- ->orderBy('tb.label', 'ASC')
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- ->execute();
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-
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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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- $vocab = $term->vocab;
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-
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- $response['@context'][$term->name] = $term->url;
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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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- $response['member'][] = array(
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- '@id' => url($api_url . '/content/' . urlencode($bundle->label), array('absolute' => TRUE)),
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- '@type' => $term->name,
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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['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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- $response['@context']['description'] = 'hydra:description';
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-
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- tripal_ws_services_v0_1_write_context($response, $ctype);
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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 $ws_path
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- */
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-function tripal_ws_services_v0_1_get_content_type($api_url, &$response, $ws_path, $ctype, $params) {
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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 this resource.
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- $URL = url($api_url . '/content/' . $ctype, array('absolute' => TRUE));
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- $response['@id'] = $URL;
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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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- $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
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- $term = reset($term);
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- $response['@context'][$term->name] = $term->url;
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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'] = $bundle->label . " collection";
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-
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- // Iterate through the fields and create a $field_mapping array that makes
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- // it easier to determine which filter criteria belongs to which field. The
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- // key is the label for the field and the value is the field name. This way
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- // user's can use the field label or the field name to form a query.
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- $field_mapping = array();
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- $fields = field_info_fields();
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- foreach ($fields as $field) {
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- if (array_key_exists('TripalEntity', $field['bundles'])) {
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- foreach ($field['bundles']['TripalEntity'] as $bundle_name) {
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- if ($bundle_name == $bundle->name) {
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- $instance = field_info_instance('TripalEntity', $field['field_name'], $bundle_name);
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- if (array_key_exists('term_accession', $instance['settings'])){
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- $vocabulary = $instance['settings']['term_vocabulary'];
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- $accession = $instance['settings']['term_accession'];
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- $term = tripal_get_term_details($vocabulary, $accession);
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- $key = $term['name'];
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- $key = strtolower(preg_replace('/ /', '_', $key));
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- $field_mapping[$key] = $field['field_name'];
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- $field_mapping[$field['field_name']] = $field['field_name'];
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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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- // Convert the filters to their field names
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- $new_params = array();
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- $order = array();
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- $order_dir = array();
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- $URL_add = array();
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- foreach ($params as $param => $value) {
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- $URL_add[] = "$param=$value";
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-
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- // Ignore non filter parameters
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- if ($param == 'page' or $param == 'limit') {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // Handle order separately
|
|
|
- if ($param == 'order') {
|
|
|
- $temp = explode(',', $value);
|
|
|
- foreach ($temp as $key) {
|
|
|
- $matches = array();
|
|
|
- $dir = 'ASC';
|
|
|
- // The user can provide a direction by separating the field key and the
|
|
|
- // direction with a '|' character.
|
|
|
- if (preg_match('/^(.*)\|(.*)$/', $key, $matches)) {
|
|
|
- $key = $matches[1];
|
|
|
- if ($matches[2] == 'ASC' or $matches[2] == 'DESC') {
|
|
|
- $dir = $matches[2];
|
|
|
- }
|
|
|
- else {
|
|
|
- // TODO: handle error of providing an incorrect direction.
|
|
|
- }
|
|
|
- }
|
|
|
- if (array_key_exists($key, $field_mapping)) {
|
|
|
- $order[$field_mapping[$key]] = $key;
|
|
|
- $order_dir[] = $dir;
|
|
|
- }
|
|
|
- else {
|
|
|
- // TODO: handle error of providing a non existing field name.
|
|
|
- }
|
|
|
- }
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // Break apart any operators
|
|
|
- $key = $param;
|
|
|
- $op = '=';
|
|
|
- $matches = array();
|
|
|
- if (preg_match('/^(.+);(.+)$/', $key, $matches)) {
|
|
|
- $key = $matches[1];
|
|
|
- $op = $matches[2];
|
|
|
- }
|
|
|
-
|
|
|
- // Break apart any subkeys and pull the first one out for the term name key.
|
|
|
- $subkeys = explode(',', $key);
|
|
|
- if (count($subkeys) > 0) {
|
|
|
- $key = array_shift($subkeys);
|
|
|
- }
|
|
|
- $column_name = $key;
|
|
|
-
|
|
|
- // Map the values in the filters to their appropriate field names.
|
|
|
- if (array_key_exists($key, $field_mapping)) {
|
|
|
- $field_name = $field_mapping[$key];
|
|
|
- if (count($subkeys) > 0) {
|
|
|
- $column_name .= '.' . implode('.', $subkeys);
|
|
|
- }
|
|
|
- $new_params[$field_name]['value'] = $value;
|
|
|
- $new_params[$field_name]['op'] = $op;
|
|
|
- $new_params[$field_name]['column'] = $column_name;
|
|
|
- }
|
|
|
- else {
|
|
|
- throw new Exception("The filter term, '$key', is not available for use.");
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Get the list of entities for this bundle.
|
|
|
- $query = new TripalFieldQuery();
|
|
|
- $query->entityCondition('entity_type', 'TripalEntity');
|
|
|
- $query->entityCondition('bundle', $bundle->name);
|
|
|
- foreach($new_params as $field_name => $details) {
|
|
|
- $value = $details['value'];
|
|
|
- $column_name = $details['column'];
|
|
|
- switch ($details['op']) {
|
|
|
- case 'eq':
|
|
|
- $op = '=';
|
|
|
- break;
|
|
|
- case 'gt':
|
|
|
- $op = '>';
|
|
|
- break;
|
|
|
- case 'gte':
|
|
|
- $op = '>=';
|
|
|
- break;
|
|
|
- case 'lt':
|
|
|
- $op = '<';
|
|
|
- break;
|
|
|
- case 'lte':
|
|
|
- $op = '<=';
|
|
|
- break;
|
|
|
- case 'ne':
|
|
|
- $op = '<>';
|
|
|
- break;
|
|
|
- case 'contains':
|
|
|
- $op = 'CONTAINS';
|
|
|
- break;
|
|
|
- case 'starts':
|
|
|
- $op = 'STARTS WITH';
|
|
|
- break;
|
|
|
- default:
|
|
|
- $op = '=';
|
|
|
- }
|
|
|
-
|
|
|
- //print_r(array($field_name, $column_name, $value, $op));
|
|
|
-
|
|
|
- // We pass in the $column_name as an identifier for any sub fields
|
|
|
- // that are present for the fields.
|
|
|
- $query->fieldCondition($field_name, $column_name, $value, $op);
|
|
|
- }
|
|
|
-
|
|
|
- // Perform the query just as a count first to get the number of records.
|
|
|
- $cquery = clone $query;
|
|
|
- $cquery->count();
|
|
|
- $num_records = $cquery->execute();
|
|
|
- $num_records = count($num_records['TripalEntity']);
|
|
|
-
|
|
|
- if (!$num_records) {
|
|
|
- $num_records = 0;
|
|
|
- }
|
|
|
-
|
|
|
- // Add in the pager to the response.
|
|
|
- $response['totalItems'] = $num_records;
|
|
|
- $limit = array_key_exists('limit', $params) ? $params['limit'] : 25;
|
|
|
-
|
|
|
- $total_pages = ceil($num_records / $limit);
|
|
|
- $page = array_key_exists('page', $params) ? $params['page'] : 1;
|
|
|
- if ($num_records > 0) {
|
|
|
- $response['view'] = array(
|
|
|
- '@id' => $URL . '?' . implode('&', array_merge($URL_add, array("page=$page", "limit=$limit"))),
|
|
|
- '@type' => 'PartialCollectionView',
|
|
|
- 'first' => $URL . '?' . implode('&', array_merge($URL_add, array("page=1", "limit=$limit"))),
|
|
|
- 'last' => $URL . '?' . implode('&', array_merge($URL_add, array("page=$total_pages", "limit=$limit"))),
|
|
|
- );
|
|
|
- $prev = $page - 1;
|
|
|
- $next = $page + 1;
|
|
|
- if ($prev > 0) {
|
|
|
- $response['view']['previous'] = $URL . '?' . implode('&', array_merge($URL_add, array("page=$prev", "limit=$limit")));
|
|
|
- }
|
|
|
- if ($next < $total_pages) {
|
|
|
- $response['view']['next'] = $URL . '?' . implode('&', array_merge($URL_add, array("page=$next", "limit=$limit")));
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Set the query order
|
|
|
- $order_keys = array_keys($order);
|
|
|
- for($i = 0; $i < count($order_keys); $i++) {
|
|
|
- $query->fieldOrderBy($order_keys[$i], $order[$order_keys[$i]], $order_dir[$i]);
|
|
|
- }
|
|
|
-
|
|
|
- // Set the query range
|
|
|
- $start = ($page - 1) * $limit;
|
|
|
- $query->range($start, $limit);
|
|
|
-
|
|
|
- // Now perform the query.
|
|
|
- $results = $query->execute();
|
|
|
-
|
|
|
- // Iterate through the entities and add them to the list.
|
|
|
- $i = 0;
|
|
|
- foreach ($results['TripalEntity'] as $entity_id => $stub) {
|
|
|
- $vocabulary = '';
|
|
|
- $term_name = '';
|
|
|
-
|
|
|
- // We don't need all of the attached fields for an entity so, we'll
|
|
|
- // not use the entity_load() function. Instead just pull it from the
|
|
|
- // database table.
|
|
|
- $query = db_select('tripal_entity', 'TE');
|
|
|
- $query->join('tripal_term', 'TT', 'TE.term_id = TT.id');
|
|
|
- $query->fields('TE');
|
|
|
- $query->fields('TT', array('name'));
|
|
|
- $query->condition('TE.id', $entity_id);
|
|
|
- $entity = $query->execute()->fetchObject();
|
|
|
-
|
|
|
- //$entity = tripal_load_entity('TripalEntity', array($entity->id));
|
|
|
- $response['member'][] = array(
|
|
|
- '@id' => url($api_url . '/content/' . urlencode($ctype) . '/' . $entity->id, array('absolute' => TRUE)),
|
|
|
- '@type' => $entity->name,
|
|
|
- 'label' => $entity->title,
|
|
|
- 'itemPage' => url('/bio_data/' . $entity->id, array('absolute' => TRUE)),
|
|
|
- );
|
|
|
- $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';
|
|
|
-
|
|
|
-// $response['operation'][] = array(
|
|
|
-// '@type' => 'hydra:CreateResourceOperation',
|
|
|
-// 'hydra:method' => 'PUT'
|
|
|
-// );
|
|
|
-
|
|
|
-// $response['query'] = array(
|
|
|
-// '@id' => $response['@id'],
|
|
|
-// '@type' => 'IriTemplate',
|
|
|
-// "template" => $response['@id'] . "{?name,}",
|
|
|
-// "mapping" => array(
|
|
|
-// array(
|
|
|
-// "hydra:variable" => 'name',
|
|
|
-// "hydra:property" => 'name',
|
|
|
-// )
|
|
|
-// )
|
|
|
-// );
|
|
|
-
|
|
|
- tripal_ws_services_v0_1_write_context($response, $ctype);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- * @param unknown $response
|
|
|
- * @param unknown $ws_path
|
|
|
- * @param unknown $ctype
|
|
|
- * @param unknown $entity_id
|
|
|
- * @param unknown $params
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_get_content_add_fields($entity, $bundle, $api_url, &$response, $ws_path, $ctype, $entity_id, $params) {
|
|
|
-
|
|
|
-
|
|
|
- // Get information about the fields attached to this bundle and sort them
|
|
|
- // in the order they were set for the display.
|
|
|
- $instances = field_info_instances('TripalEntity', $bundle->name);
|
|
|
-
|
|
|
- uasort($instances, function($a, $b) {
|
|
|
- $a_weight = (is_array($a) && isset($a['widget']['weight'])) ? $a['widget']['weight'] : 0;
|
|
|
- $b_weight = (is_array($b) && isset($b['widget']['weight'])) ? $b['widget']['weight'] : 0;
|
|
|
-
|
|
|
- if ($a_weight == $b_weight) {
|
|
|
- return 0;
|
|
|
- }
|
|
|
- return ($a_weight < $b_weight) ? -1 : 1;
|
|
|
- });
|
|
|
-
|
|
|
- // Iterate through the fields and add each value to the response.
|
|
|
- //$response['fields'] = $fields;
|
|
|
- foreach ($instances as $field_name => $instance) {
|
|
|
-
|
|
|
- // Ignore the content_type field provided by Tripal.
|
|
|
- if ($field_name == 'content_type') {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // Skip hidden fields.
|
|
|
- if ($instance['display']['default']['type'] == 'hidden') {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // Get the information about this field. It will have settings different
|
|
|
- // from the instance.
|
|
|
- $field = field_info_field($field_name);
|
|
|
-
|
|
|
- // By default, the label for the key in the output should be the
|
|
|
- // term from the vocabulary that the field is assigned. But in the
|
|
|
- // case that the field is not assigned a term, we must use the field name.
|
|
|
- $field_name = $instance['field_name'];
|
|
|
- $vocabulary = $instance['settings']['term_vocabulary'];
|
|
|
- $accession = $instance['settings']['term_accession'];
|
|
|
- $term = tripal_get_term_details($vocabulary, $accession);
|
|
|
- if ($term) {
|
|
|
- $key = $term['name'];
|
|
|
- $key_adj = strtolower(preg_replace('/ /', '_', $key));
|
|
|
- // The term schema:url also points to a recource so we need
|
|
|
- // to make sure we set the type to be '@id'.
|
|
|
- if ($vocabulary == 'schema' and $accession == 'url') {
|
|
|
- $response['@context'][$key_adj] = array(
|
|
|
- '@id' => $term['url'],
|
|
|
- '@type' => '@id',
|
|
|
- );
|
|
|
- }
|
|
|
- else {
|
|
|
- $response['@context'][$key_adj] = $term['url'];
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // If this field should not be attached by default then just add a link
|
|
|
- // so that the caller can get the information separately.
|
|
|
- $instance_settings = $instance['settings'];
|
|
|
- if (array_key_exists('auto_attach', $instance['settings']) and
|
|
|
- $instance_settings['auto_attach'] == FALSE) {
|
|
|
- $response['@context'][$key_adj] = array(
|
|
|
- '@id' => $response['@context'][$key_adj],
|
|
|
- '@type' => '@id'
|
|
|
- );
|
|
|
- // Add a URL only if there are values. If there are no values then
|
|
|
- // don't add a URL which would make the end-user think they can get
|
|
|
- // that information.
|
|
|
- $items = field_get_items('TripalEntity', $entity, $field_name);
|
|
|
- if ($items and count($items) > 0 and $items[0]['value']) {
|
|
|
- $response[$key_adj] = url($api_url . '/content/' . $ctype . '/' . $entity->id . '/' . urlencode($key), array('absolute' => TRUE));
|
|
|
- }
|
|
|
- else {
|
|
|
- $response[$key_adj] = NULL;
|
|
|
- }
|
|
|
-
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // Get the details for this field for the JSON-LD response.
|
|
|
- tripal_ws_services_v0_1_get_content_add_field($key_adj, $entity, $field, $instance, $api_url, $response);
|
|
|
- }
|
|
|
-
|
|
|
- // Lastly, add in the terms used into the @context section.
|
|
|
- $response['@context']['label'] = 'https://www.w3.org/TR/rdf-schema/#ch_label';
|
|
|
- $response['@context']['itemPage'] = 'https://schema.org/ItemPage';
|
|
|
-
|
|
|
- // $response['operation'][] = array(
|
|
|
- // '@type' => 'hydra:DeleteResourceOperation',
|
|
|
- // 'hydra:method' => 'DELETE'
|
|
|
- // );
|
|
|
- // $response['operation'][] = array(
|
|
|
- // '@type' => 'hydra:ReplaceResourceOperation',
|
|
|
- // 'hydra:method' => 'POST'
|
|
|
- // );
|
|
|
-}
|
|
|
-/**
|
|
|
- *
|
|
|
- * @param unknown $field_arg
|
|
|
- * @param unknown $api_url
|
|
|
- * @param unknown $response
|
|
|
- * @param unknown $ws_path
|
|
|
- * @param unknown $ctype
|
|
|
- * @param unknown $entity_id
|
|
|
- * @param unknown $params
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_get_content_find_field($field_arg, $ctype, $entity_id) {
|
|
|
-
|
|
|
- $bundle = tripal_load_bundle_entity(array('label' => $ctype));
|
|
|
- $entity = tripal_load_entity('TripalEntity', array('id' => $entity_id));
|
|
|
- $entity = reset($entity);
|
|
|
- $term = NULL;
|
|
|
-
|
|
|
- // Find the field whose term matches the one provied.
|
|
|
- $value = array();
|
|
|
- $instances = field_info_instances('TripalEntity', $bundle->name);
|
|
|
- foreach ($instances as $instance) {
|
|
|
- $field_name = $instance['field_name'];
|
|
|
- $field = field_info_field($field_name);
|
|
|
- $vocabulary = $instance['settings']['term_vocabulary'];
|
|
|
- $accession = $instance['settings']['term_accession'];
|
|
|
- $temp_term = tripal_get_term_details($vocabulary, $accession);
|
|
|
- if ($temp_term['name'] == $field_arg) {
|
|
|
- return array($entity, $bundle, $field, $instance, $temp_term);
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-/**
|
|
|
- *
|
|
|
- * @param unknown $api_url
|
|
|
- * @param unknown $response
|
|
|
- * @param unknown $ws_path
|
|
|
- * @param unknown $ctype
|
|
|
- * @param unknown $entity_id
|
|
|
- * @param unknown $params
|
|
|
- * @return number
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_get_content($api_url, &$response, $ws_path, $ctype, $entity_id, $params) {
|
|
|
- // 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#';
|
|
|
-
|
|
|
- // If we have an argument in the 4th element (3rd index) then the user
|
|
|
- // is requesting to expand the details of a field that was not
|
|
|
- // initially attached to the enity.
|
|
|
- $field_arg = '';
|
|
|
- if (array_key_exists(3, $ws_path)) {
|
|
|
-
|
|
|
- $field_arg = urldecode($ws_path[3]);
|
|
|
- list($entity, $bundle, $field, $instance, $term) = tripal_ws_services_v0_1_get_content_find_field($field_arg, $ctype, $entity_id);
|
|
|
-
|
|
|
- // If we couldn't match this field argument to a field and entity then return
|
|
|
- if (!$entity or !$field) {
|
|
|
- return;
|
|
|
- }
|
|
|
-
|
|
|
- // Next add in the ID and Type for this resources.
|
|
|
- $key = $term['name'];
|
|
|
- $key_adj = strtolower(preg_replace('/ /', '_', $term['name']));
|
|
|
- $response['@context'][$key_adj] = $term['url'];
|
|
|
- $response['@id'] = url($api_url . '/content/' . $ctype . '/' . $entity->id . '/' . urlencode($key), array('absolute' => TRUE));
|
|
|
-
|
|
|
- // Attach the field and then add it's values to the response.
|
|
|
- field_attach_load($entity->type, array($entity->id => $entity),
|
|
|
- FIELD_LOAD_CURRENT, array('field_id' => $field['id']));
|
|
|
-
|
|
|
- tripal_ws_services_v0_1_get_content_add_field($key_adj, $entity, $field, $instance, $api_url, $response, TRUE);
|
|
|
- tripal_ws_services_v0_1_write_context($response, $ctype);
|
|
|
- return;
|
|
|
- }
|
|
|
-
|
|
|
- // If we don't have a 4th argument then we're loading the base record.
|
|
|
- // Get the TripalBundle, TripalTerm and TripalVocab type for this type.
|
|
|
- $bundle = tripal_load_bundle_entity(array('label' => $ctype));
|
|
|
- $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
|
|
|
- $term = reset($term);
|
|
|
- $vocab = $term->vocab;
|
|
|
-
|
|
|
- // Add the vocabulary for this content type to the @context section.
|
|
|
- if (!array_key_exists($vocab->vocabulary, $response['@context'])) {
|
|
|
- // If there is no URL prefix then use this API's vocabulary API
|
|
|
- if (property_exists($term, 'urlprefix')) {
|
|
|
- $response['@context'][$vocab->vocabulary] = $term->urlprefix;
|
|
|
- }
|
|
|
- else {
|
|
|
- $response['@context'][$vocab->vocabulary] = url($api_url . '/vocab/' . $vocab->vocabulary . '/', array('absolute' => TRUE));
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Get the TripalEntity
|
|
|
- $entity = tripal_load_entity('TripalEntity', array('id' => $entity_id));
|
|
|
- $entity = reset($entity);
|
|
|
-
|
|
|
- // Next add in the ID and Type for this resources.
|
|
|
- $response['@id'] = url($api_url . '/content/' . $ctype . '/' . $entity_id, array('absolute' => TRUE));
|
|
|
- $response['@type'] = $term->name;
|
|
|
- $response['@context'][$term->name] = $term->url;
|
|
|
- $response['label'] = $entity->title;
|
|
|
- $response['itemPage'] = url('/bio_data/' . $entity->id, array('absolute' => TRUE));
|
|
|
-
|
|
|
- tripal_ws_services_v0_1_get_content_add_fields($entity, $bundle, $api_url, $response, $ws_path, $ctype, $entity_id, $params);
|
|
|
- tripal_ws_services_v0_1_write_context($response, $ctype);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- * @param $response
|
|
|
- * @param $ctype
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_write_context(&$response, $ctype) {
|
|
|
- // Save the response '@context' into a temporary file
|
|
|
- $context = array('@context' => $response['@context']);
|
|
|
- $file_name = drupal_tempnam(file_default_scheme() . '://', 'tws_context-') . '.json';
|
|
|
- $context_file = file_save_data(json_encode($context), $file_name, FILE_EXISTS_REPLACE );
|
|
|
-
|
|
|
- // Mark the file as temporary by setting it's status
|
|
|
- $context_file->status = 0;
|
|
|
- file_save($context_file);
|
|
|
-
|
|
|
- // Return the response with the '@context' section replaced with the file URL.
|
|
|
- $response['@context'] = file_create_url($context_file->uri);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_get_content_add_field($key, $entity, $field, $instance, $api_url, &$response, $is_field_page = NULL) {
|
|
|
- // Get the field settings.
|
|
|
- $field_name = $field['field_name'];
|
|
|
- $field_settings = $field['settings'];
|
|
|
-
|
|
|
- $items = field_get_items('TripalEntity', $entity, $field_name);
|
|
|
- if (!$items) {
|
|
|
- return;
|
|
|
- }
|
|
|
-
|
|
|
- // Give modules the opportunity to edit values for web services. This hook
|
|
|
- // really should be used sparingly. Where it helps is with non Tripal fields
|
|
|
- // that are added to a TripalEntity content type and it doesn't follow
|
|
|
- // the rules (e.g. Image field).
|
|
|
- drupal_alter('tripal_ws_value', $items, $field, $instance);
|
|
|
-
|
|
|
- $values = array();
|
|
|
- for ($i = 0; $i < count($items); $i++) {
|
|
|
- $values[$i] = tripal_ws_services_v0_1_rewrite_field_items_keys($items[$i]['value'], $response, $api_url);
|
|
|
- }
|
|
|
-
|
|
|
- // If the field cardinality is 1
|
|
|
- if ($field[cardinality] == 1) {
|
|
|
- // If the value is an array and this is the field page then all of those
|
|
|
- // key/value pairs should be added directly to the response.
|
|
|
- if (is_array($values[0])) {
|
|
|
- if ($is_field_page) {
|
|
|
- foreach ($values[0] as $k => $v) {
|
|
|
- $response[$k] = $v;
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $response[$key] = $values[0];
|
|
|
- }
|
|
|
- }
|
|
|
- // If the value is not an array it's a scalar so add it as is to the
|
|
|
- // response.
|
|
|
- else {
|
|
|
- $response[$key] = $values[0];
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // If the field cardinality is > 1
|
|
|
- if ($field[cardinality] != 1) {
|
|
|
-
|
|
|
- // If this is the field page then the Collection is added directly to the
|
|
|
- // response, otherwise, it's added under the field $key.
|
|
|
- if ($is_field_page) {
|
|
|
- $response['@type'] = 'Collection';
|
|
|
- $response['totalItems'] = count($values);
|
|
|
- $response['label'] = $instance['label'];
|
|
|
- $response['member'] = $values;
|
|
|
- }
|
|
|
- else {
|
|
|
- $response[$key] = array(
|
|
|
- '@type' => 'Collection',
|
|
|
- 'totalItems' => count($values),
|
|
|
- 'label' => $instance['label'],
|
|
|
- 'member' => $values,
|
|
|
- );
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_rewrite_field_items_keys($value, &$response, $api_url) {
|
|
|
-
|
|
|
- $new_value = '';
|
|
|
- // If the value is an array rather than a scalar then map the sub elements
|
|
|
- // to controlled vocabulary terms.
|
|
|
- if (is_array($value)) {
|
|
|
- $temp = array();
|
|
|
- foreach ($value as $k => $v) {
|
|
|
- $matches = array();
|
|
|
- if (preg_match('/^(.+):(.+)$/', $k, $matches)) {
|
|
|
- $vocabulary = $matches[1];
|
|
|
- $accession = $matches[2];
|
|
|
- $term = tripal_get_term_details($vocabulary, $accession);
|
|
|
- $key_adj = strtolower(preg_replace('/ /', '_', $term['name']));
|
|
|
- if (is_array($v)) {
|
|
|
- $temp[$key_adj] = tripal_ws_services_v0_1_rewrite_field_items_keys($v, $response, $api_url);
|
|
|
- }
|
|
|
- else {
|
|
|
- $temp[$key_adj] = $v !== "" ? $v : NULL;
|
|
|
- }
|
|
|
- // The term schema:url also points to a recource so we need
|
|
|
- // to make sure we set the type to be '@id'.
|
|
|
- if ($vocabulary == 'schema' and $accession == 'url') {
|
|
|
- $response['@context'][$key_adj] = array(
|
|
|
- '@id' => $term['url'],
|
|
|
- '@type' => '@id',
|
|
|
- );
|
|
|
- }
|
|
|
- else {
|
|
|
- $response['@context'][$key_adj] = $term['url'];
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $temp[$k] = $v;
|
|
|
- }
|
|
|
- }
|
|
|
- $new_value = $temp;
|
|
|
-
|
|
|
- // Recurse through the values array and set the entity elements
|
|
|
- // and add the fields to the context.
|
|
|
- tripal_ws_services_v0_1_rewrite_field_items_entity($new_value, $response, $api_url);
|
|
|
-
|
|
|
- }
|
|
|
- else {
|
|
|
- $new_value = $value !== "" ? $value : NULL;
|
|
|
- }
|
|
|
-
|
|
|
- return $new_value;
|
|
|
-}
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_rewrite_field_items_entity(&$items, &$response, $api_url) {
|
|
|
-
|
|
|
- if (!$items) {
|
|
|
- return;
|
|
|
- }
|
|
|
- foreach ($items as $key => $value) {
|
|
|
- if (is_array($value)) {
|
|
|
- tripal_ws_services_v0_1_rewrite_field_items_entity($items[$key], $response, $api_url);
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- if ($key == 'entity') {
|
|
|
- list($item_etype, $item_eid) = explode(':', $items['entity']);
|
|
|
- if ($item_eid) {
|
|
|
- $item_entity = tripal_load_entity($item_etype, array($item_eid));
|
|
|
- $item_entity = reset($item_entity);
|
|
|
- $bundle = tripal_load_bundle_entity(array('name' => $item_entity->bundle));
|
|
|
- $items['@id'] = url($api_url . '/content/' . $bundle->label . '/' . $item_eid, array('absolute' => TRUE));
|
|
|
- }
|
|
|
- unset($items['entity']);
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Provides the Hydra compatible apiDocumentation page that describes this API.
|
|
|
- *
|
|
|
- * @param $api_url
|
|
|
- * @param $response
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_handle_doc_service($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', '');
|
|
|
- $response['@id'] = url($api_url . '/doc/', array('absolute' => TRUE));
|
|
|
- $response['title'] = $site_name . ": RESTful Web Services API";
|
|
|
- $response['entrypoint'] = url($api_url, array('absolute' => TRUE));
|
|
|
- $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",
|
|
|
- );
|
|
|
- $response['@context']['description'] = 'hydra:description';
|
|
|
-
|
|
|
- tripal_ws_services_v0_1_write_context($response, $ctype);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * This function specifies the types of resources avaiable via the API.
|
|
|
- *
|
|
|
- * @param $api_url
|
|
|
- * @param $response
|
|
|
- * @param $ws_path
|
|
|
- */
|
|
|
-function tripal_ws_services_v0_1_handle_no_service($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#';
|
|
|
- $response['@context']['dc'] = 'http://purl.org/dc/dcmitype/';
|
|
|
- $response['@context']['schema'] = 'https://schema.org/';
|
|
|
-
|
|
|
- // Next add in the ID for tihs resource.
|
|
|
- $response['@id'] = url($api_url, array('absolute' => TRUE));
|
|
|
-
|
|
|
- // Start the list.
|
|
|
- $response['@type'] = 'Collection';
|
|
|
- $response['totalItems'] = 0;
|
|
|
- $response['label'] = 'Services';
|
|
|
- $response['member'] = array();
|
|
|
-
|
|
|
- // Start the list.
|
|
|
- $response['member'][] = array(
|
|
|
- '@id' => url($api_url . '/content/', array('absolute' => TRUE)),
|
|
|
- '@type' => 'Service',
|
|
|
- 'label' => 'Content Types',
|
|
|
- 'description' => 'Provides acesss to the biological and ' .
|
|
|
- 'ancilliary data available on this site. Each content type ' .
|
|
|
- 'represents biological data that is defined in a controlled vocabulary '.
|
|
|
- '(e.g. Sequence Ontology term: gene (SO:0000704)).',
|
|
|
- );
|
|
|
- $response['member'][] = array(
|
|
|
- '@id' => url($api_url . '/doc/', array('absolute' => TRUE)),
|
|
|
- '@type' => 'Service',
|
|
|
- 'label' => 'API Documentation',
|
|
|
- 'description' => 'The WC3 Hydra compatible documentation for this API.',
|
|
|
- );
|
|
|
- $response['member'][] = array(
|
|
|
- '@id' => url($api_url . '/vocab/', array('absolute' => TRUE)),
|
|
|
- '@type' => 'Service',
|
|
|
- 'label' => 'Vocabulary',
|
|
|
- 'description' => 'Defines in-house locally defined vocabulary terms that ' .
|
|
|
- 'have been added specifically for this site. These terms are typically ' .
|
|
|
- 'added because no other appropriate term exists in another community-vetted '.
|
|
|
- 'controlled vocabulary.',
|
|
|
- );
|
|
|
-
|
|
|
- $response['totalItems'] = count($response['member']);
|
|
|
-
|
|
|
- $response['@context']['Collection'] = 'hydra:Collection';
|
|
|
- $response['@context']['totalItems'] = 'hydra:totalItems';
|
|
|
- $response['@context']['member'] = 'hydra:member';
|
|
|
- $response['@context']['Service'] = 'dc:Service';
|
|
|
- $response['@context']['label'] = 'rdfs:label';
|
|
|
- $response['@context']['description'] = 'hydra:description';
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_tripal_ws_value_alter().
|
|
|
- *
|
|
|
- * The hook_tripal_ws_value_alter is a hook created by the Tripal WS module.
|
|
|
- * It allows the modules to adjust the values of a field for display in
|
|
|
- * web services. This hook should be used sparingly. It is meant primarily
|
|
|
- * to adjust 3rd Party (non Tripal) fields so that they work with web
|
|
|
- * services.
|
|
|
- */
|
|
|
-function tripal_ws_tripal_ws_value_alter(&$items, $field, $instance) {
|
|
|
- // The image module doesn't properly set the 'value' field, so we'll do it
|
|
|
- // here.
|
|
|
- if($field['type'] == 'image' and $field['module'] == 'image') {
|
|
|
- foreach ($items as $delta => $details) {
|
|
|
- if ($items[$delta] and array_key_exists('uri', $items[$delta])) {
|
|
|
- $items[$delta]['value']['schema:url'] = file_create_url($items[$delta]['uri']);
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
Stephen Ficklin