$details) { if ($items[$delta] and array_key_exists('uri', $items[$delta])) { $items[$delta]['value']['schema:url'] = file_create_url($items[$delta]['uri']); } } } } /** * Retrieves a list of TripalWebService implementations. * * The TripalWebService classes can be added by a site developer that wishes * to create a new Tripal compatible web serivce. The class file should * be placed in the [module]/includes/TripalWebService directory. Tripal will * support any service as long as it is in this directory and extends the * TripalWebService class. * * @return * A list of TripalWebService names. * * @ingroup tripal_ws_api */ function tripal_get_web_services() { $services = []; $modules = module_list(TRUE); foreach ($modules as $module) { // Find all of the files in the tripal_chado/includes/fields directory. $service_path = drupal_get_path('module', $module) . '/includes/TripalWebService'; $service_files = file_scan_directory($service_path, '/.inc$/'); // Iterate through the fields, include the file and run the info function. foreach ($service_files as $file) { $class = $file->name; module_load_include('inc', $module, 'includes/TripalWebService/' . $class); if (class_exists($class) and is_subclass_of($class, 'TripalWebService')) { $services[] = $class; } } } return $services; } /** * Loads the TripalWebService class file into scope. * * @param $class * The TripalWebService class to include. * * @return * TRUE if the field type class file was found, FALSE otherwise. * * @ingroup tripal_ws_api */ function tripal_load_include_web_service_class($class) { $modules = module_list(TRUE); foreach ($modules as $module) { module_load_include('inc', $module, 'includes/TripalWebService/' . $class); if (class_exists($class)) { return TRUE; } } return FALSE; } /** * Adds a new site to the web services table. * * @param $name * Name of site to be included. * @param $url * URL of site to be added. * @param $version * Version of the API being used. default to 1 * @param $description * A description of the site and any additional info that * would be helpful for admins. * * @return * TRUE if the site is successfully added, FALSE otherwise. * * @ingroup tripal_ws_api */ function tripal_add_site($name, $url, $version, $description) { $check_url = NULL; $check_name = NULL; $write_to_db = TRUE; // When inserting a record. $check_url = db_select('tripal_sites', 'ts') ->fields('ts', ['id']) ->condition('url', $url) ->condition('version', $version) ->execute() ->fetchField(); $check_name = db_select('tripal_sites', 'ts') ->fields('ts', ['id']) ->condition('name', $name) ->execute() ->fetchField(); if ($check_url) { drupal_set_message(t('The URL and version is used by another site.'), 'error'); $write_to_db = FALSE; } if ($check_name) { drupal_set_message(t('The name is used by another site.'), 'error'); $write_to_db = FALSE; } if ($write_to_db === TRUE) { db_insert('tripal_sites') ->fields([ 'name' => $name, 'url' => $url, 'version' => $version, 'description' => $description, ]) ->execute(); drupal_set_message(t('Tripal site \'' . $name . '\' has been added.')); return $write_to_db; } return $write_to_db; } /** * Remove a site from the web services table. * * @param $record_id * ID of the record to be deleted. * * @return * TRUE if the record was successfully deleted, FALSE otherwise. * * @ingroup tripal_ws_api */ function tripal_remove_site($record_id) { if ($record_id) { db_delete('tripal_sites') ->condition('id', $record_id) ->execute(); drupal_set_message('The Tripal site \'' . $record_id . '\' has been removed.'); return TRUE; } return FALSE; } /** * Constructs a URL for a remote Tripal web service. * * @param $remote_site * A remote Tripal site object. * @param $path * The web service path for the content (excluding * 'web-services/vX.x/content'). To retrieve the full content listing * leave this paramter empty. * @param $query * An query string to appear after the ? in a URL. * * @return * The full URL within the content service. */ function tripal_build_remote_content_url($remote_site, $path = '', $query = '') { // Build the URL to the remote web services. $ws_version = $remote_site->version; $ws_url = $remote_site->url; $ws_url = trim($ws_url, '/'); $ws_url .= '/web-services/content/' . $ws_version . '/' . $path; // Build the Query and make and substitions needed. if ($query) { $ws_url = $ws_url . '?' . $query; } return $ws_url; } /** * Makes a request to the "content" service of a remote Tripal web site. * * @param $site_id * The numeric site ID for the remote Tripal site. * @param $path * The web service path for the content (excluding * 'web-services/vX.x/content'). To retrieve the full content listing * leave this paramter empty. * @param $query * An query string to appear after the ? in a URL. * * @return * The JSON response formatted in a PHP array or FALSE if a problem occured. * * @ingroup tripal_ws_api */ function tripal_get_remote_content($site_id, $path = '', $query = '') { if (!$site_id) { throw new Exception('Please provide a numeric site ID for the tripal_get_remote_content function.'); } // Fetch the record for this site id. $remote_site = db_select('tripal_sites', 'ts') ->fields('ts') ->condition('ts.id', $site_id) ->execute() ->fetchObject(); if (!$remote_site) { $data = [ 'error' => t('Could not find a remote tripal site using the id provided: !id.', ['!id' => $site_id]), ]; _tripal_report_ws_error($data); return $data; } // Make the remote query. $ws_url = tripal_build_remote_content_url($remote_site, $path, $query); $data = drupal_http_request($ws_url); if (!$data) { $data = [ 'error' => t('Could not connect to the remote web service using the url: !url', ['!url' => $ws_url]), ]; _tripal_report_ws_error($data); return $data; } // If the data object has an error then this is some sort of // connection error (not a Tripal web services error). if (property_exists($data, 'error')) { $data = [ 'error' => $data->error, ]; _tripal_report_ws_error($data); return $data; } // We got a response, so convert it to a PHP array. $data = drupal_json_decode($data->data); // Check if there was a Tripal Web Services error. if (array_key_exists('error', $data)) { _tripal_report_ws_error($data); } return $data; } /** * A helper function for reporting an error when retrieving remote content. * * @param $data * A data array containing at a minimum the 'error' key containing the * error message. */ function _tripal_report_ws_error($data) { $error = '' . print_r($data['error'], TRUE) . ''; tripal_report_error('tripal_ws', TRIPAL_ERROR, 'Tripal remote web services reports the following error: !error.', ['!error' => $error]); } /** * Retrieves the JSON-LD context for any remote Tripal web service. * * @param $context_url * The Full URL for the context file on the remote Tripal site. This URL * can be found in the '@context' key of any response from a remote Tripal * web services call. * @param $cache_id * A unique ID for caching of this context result to speed furture * queries. * * @return * The JSON-LD context mapping array, or FALSE if the context could not * be retrieved. * * @ingroup tripal_ws_api */ function tripal_get_remote_context($context_url, $cache_id) { if (!$context_url) { throw new Exception('PLease provide a context_url for the tripal_get_remote_context function.'); } if (!$cache_id) { throw new Exception('PLease provide unique $cache_id for the tripal_get_remote_context function.'); } if ($cache = cache_get($cache_id)) { return $cache->data; } $context = drupal_http_request($context_url); if (!$context) { tripal_report_error('tripal_ws', TRIPAL_ERROR, 'There was a poblem retrieving the context from the remote site: !context_url.', ['!context_url' => $context_url]); return FALSE; } $context = drupal_json_decode($context->data); $context = $context['@context']; cache_set($cache_id, $context); return $context; } /** * Retrieves the JSON-LD context for a bundle or field on a remote Tripal site. * * The $site_id, $bundle_accession and $field_accession variables are not * needed to retrieve the context, but are used for caching the context to * make subsequent calls execute faster. This function is meant to be used * only for the 'content' service provided by Tripal. * * @param $site_id * The numeric site ID for the remote Tripal site. * @param $context_url * The Full URL for the context file on the remote Tripal site. This URL * can be found in the '@context' key of any response from a remote Tripal * web services call. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * @param $field_accession * The controlled vocabulary term accession for the property (i.e. field) of * the Class (i.e. content type). * * @return * The JSON-LD context mapping array. * * @ingroup tripal_ws_api */ function tripal_get_remote_content_context($site_id, $context_url, $bundle_accession, $field_accession = '') { $cache_id = substr('trp_ws_context_' . $site_id . '-' . $bundle_accession . '-' . $field_accession, 0, 254); $context = tripal_get_remote_context($context_url, $cache_id); return $context; } /** * Clears the cached remote site documentation and context. * * When querying a remote website, the site's API documenation and page context * is cached to make re-use of that information easier in the future. This * function can be used to clear those caches. * * @param $site_id * The numeric site ID for the remote Tripal site. * * @ingroup tripal_ws_api */ function tripal_clear_remote_cache($site_id) { if (!$site_id) { throw new Exception('Please provide a numeric site ID for the tripal_clear_remote_cache function.'); } cache_clear_all('trp_ws_context_' . $site_id, 'cache', TRUE); cache_clear_all('trp_ws_doc_' . $site_id, 'cache', TRUE); } /** * Retrieves the API documentation for a remote Tripal web service. * * @param $site_id * The numeric site ID for the remote Tripal site. * * @return * The vocabulary of a remote Tripal web service, or FALSE if an error * occured. * * @ingroup tripal_ws_api */ function tripal_get_remote_API_doc($site_id) { $site_doc = ''; if (!$site_id) { throw new Exception('Please provide a numeric site ID for the tripal_get_remote_API_doc function.'); } $cache_name = 'trp_ws_doc_' . $site_id; if ($cache = cache_get($cache_name)) { return $cache->data; } // Get the site url from the tripal_sites table. $remote_site = db_select('tripal_sites', 'ts') ->fields('ts') ->condition('ts.id', $site_id) ->execute() ->fetchObject(); if (!$remote_site) { throw new Exception(t('Cannot find a remote site with id: "!id"', ['!id' => $site_id])); } // Build the URL to the remote web services. $ws_version = $remote_site->version; $ws_url = $remote_site->url; $ws_url = trim($ws_url, '/'); $ws_url .= '/web-services/doc/' . $ws_version; // Build and make the request. $options = []; $data = drupal_http_request($ws_url, $options); if (!$data) { tripal_report_error('tripal_ws', TRIPAL_ERROR, t('Could not connect to the remote web service.')); return FALSE; } // If the data object has an error then this is some sort of // connection error (not a Tripal web services error). if (property_exists($data, 'error')) { tripal_report_error('tripal_ws', TRIPAL_ERROR, 'Remote web services document reports the following error: !error. Using URL: !url', ['!error' => $error, '!url' => $ws_url]); return FALSE; } // We got a response, so convert it to a PHP array. $site_doc = drupal_json_decode($data->data); // Check if there was a Tripal Web Services error. if (array_key_exists('error', $data)) { $error = '' . print_r($data['error'], TRUE) . ''; tripal_report_error('tripal_ws', TRIPAL_ERROR, 'Tripal Remote web services document reports the following error: !error. Using URL: !url', ['!error' => $error, '!url' => $ws_url]); return FALSE; } cache_set($cache_name, $site_doc); return $site_doc; } /** * Queries a remote site for an array of bulk entity ids. * * This function returns an array of "fake" entities containing values * for fields specified. * * @param $remote_entity_ids * Array of the remote ids. * @param $site_id * The numeric site ID for the remote Tripal site. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * @param $field_ids * The controlled vocabulary term accessions for the fields available * on the remote content type. Any remote fields that matches these IDs will * be added to the entity returned. * * @return * An array of fake entity objects where the key is the entity_id and * the value is the object. * * @ingroup tripal_ws_api */ function tripal_load_remote_entities($remote_entity_ids, $site_id, $bundle_accession, $field_ids) { if (!$remote_entity_ids) { throw new Exception('Please provide the list of remote entity ids for the tripal_load_remote_entities function.'); } if (!is_array($remote_entity_ids)) { throw new Exception('Please provide an array for the remote entity ids for the tripal_load_remote_entities function.'); } if (!$site_id) { throw new Exception('Please provide a numeric site ID for the tripal_load_remote_entities function.'); } if (!$bundle_accession) { throw new Exception('Please provide the bundle accession for the tripal_load_remote_entities function.'); } if (!$field_ids) { throw new Exception('Please provide the list of field IDs for the tripal_load_remote_entities function.'); } if (!is_array($field_ids)) { throw new Exception('Please provide an array for the field IDs for the tripal_load_remote_entities function.'); } // Get the site documentation (loads from cache if already retrieved). $site_doc = tripal_get_remote_API_doc($site_id); // Generate an array for the query and then execute it. $query = 'page=1&limit=' . count($remote_entity_ids) . '&ids=' . urlencode(implode(",", $remote_entity_ids)) . '&fields=' . urlencode(implode(",", $field_ids)); $results = tripal_get_remote_content($site_id, $bundle_accession, $query); // If we encountered an error just return; if (array_key_exists('error', $results)) { return FALSE; } // Get the context JSON for this remote entity, we'll use it to map $context_url = $results['@context']; $context = tripal_get_remote_content_context($site_id, $context_url, $bundle_accession); if (!$context) { return $entity; } $total_items = $results['totalItems']; $members = $results['member']; $entities = []; foreach ($members as $member) { // Start building the fake entity. $entity_id = preg_replace('/^.*?(\d+)$/', '$1', $member['@id']); $entity = new stdClass(); $entity->entityType = 'TripalEntity'; $entity->entityInfo = []; $entity->id = $entity_id; $entity->type = 'TripalEntity'; $entity->bundle = $bundle_accession; $entity->site_id = $site_id; $member = _tripal_update_remote_entity_field($member, $context, 1); foreach ($member as $field_id => $value) { $field = tripal_get_remote_field_info($site_id, $bundle_accession, $field_id); $instance = tripal_get_remote_field_instance_info($site_id, $bundle_accession, $field_id); $field_name = $field['field_name']; $entity->{$field_name}['und'][0]['value'] = $value; } $entities[$entity_id] = $entity; } return $entities; } /** * Queries a remote site for an entity. * * This function returns a "fake" entity containing values for all fields * specified. * * @param $remote_entity_id * A remote entity ID. * @param $site_id * The numeric site ID for the remote Tripal site. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * @param $field_ids * The controlled vocabulary term accessions for the fields available * on the remote content type. Any remote fields that matches these IDs will * be added to the entity returned. * * @return * A fake entity object. * * @ingroup tripal_ws_api */ function tripal_load_remote_entity($remote_entity_id, $site_id, $bundle_accession, $field_ids) { // Get the site documentation (loads from cache if already retrieved). $site_doc = tripal_get_remote_API_doc($site_id); // Get the remote entity and create the fake entity. $remote_entity = tripal_get_remote_content($site_id, $bundle_accession . '/' . $remote_entity_id); // If we encountered an error just return; if (array_key_exists('error', $results)) { return FALSE; } // Start building the fake entity. $entity = new stdClass(); $entity->entityType = 'TripalEntity'; $entity->entityInfo = []; $entity->id = $remote_entity_id; $entity->type = 'TripalEntity'; $entity->bundle = $bundle_accession; $entity->site_id = $site_id; // Get the context JSON for this remote entity, we'll use it to map $context_url = $remote_entity['@context']; $context = tripal_get_remote_content_context($site_id, $context_url, $bundle_accession); if (!$context) { return $entity; } // Iterate through the fields and the those values to the entity. foreach ($field_ids as $field_id) { $field = tripal_get_remote_field_info($site_id, $bundle_accession, $field_id); $instance = tripal_get_remote_field_instance_info($site_id, $bundle_accession, $field_id); $field_name = $field['field_name']; $field_key = ''; foreach ($context as $k => $v) { if (!is_array($v) and $v == $field_id) { $field_key = $k; } } // If the field is not in this remote bundle then add an empty value. if (!$field_key) { $entity->{$field_name}['und'][0]['value'] = ''; continue; } if (!array_key_exists($field_key, $remote_entity)) { $entity->{$field_name}['und'][0]['value'] = ''; continue; } // If the key is for a field that is not "auto attached' then we need // to get that field through a separate call. $attached = TRUE; if (array_key_exists($field_id, $context) and is_array($context[$field_id]) and array_key_exists('@type', $context[$field_id]) and $context[$field_id]['@type'] == '@id') { $attached = FALSE; } // Set the value for this field. $value = ''; if (is_array($remote_entity[$field_key])) { $value = _tripal_update_remote_entity_field($remote_entity[$field_key], $context, 1); } else { $value = $remote_entity[$field_key]; } // If the field is not attached then we have to query another level. if (!$attached) { $field_data = drupal_http_request($value); if (!$field_data) { tripal_report_error('tripal_ws', TRIPAL_ERROR, 'There was a poblem retrieving the unattached field, "!field:", for the remote entity: !entity_id.', ['!field' => $field_id, '!entity_id' => $remote_entity_id]); $value = ''; } $field_data = drupal_json_decode($field_data->data); // Get the context for this field so we can map the keys to the // controlled vocabulary accessions. If it fails then skip this field. $field_context_url = $field_data['@context']; $field_context = tripal_get_remote_content_context($site_id, $field_context_url, $bundle_accession, $field_id); if (!$field_context) { continue; } $value = _tripal_update_remote_entity_field($field_data, $field_context); } $entity->{$field_name}['und'][0]['value'] = $value; } return $entity; } /** * A helper function for the tripal_get_remote_entity() function. * * This function converts the field's key elements to their * vocabulary term accessions. * * @param $field_data * The field array as returned by web services. * @param $context * The web service JSON-LD context for the bundle to which the field belongs. * * @ingroup tripal_ws_api */ function _tripal_update_remote_entity_field($field_data, $context, $depth = 0) { // Check if this is an array. if ($field_data['@type'] == 'Collection') { $members = []; foreach ($field_data['member'] as $member) { $next_depth = $depth + 1; $members[] = _tripal_update_remote_entity_field($member, $context, $next_depth); } // If we only have one item then just return it as a single item. // TODO: we may need to check cardinality of the field and be more // strict about how we return the value. if ($field_data['totalItems'] == 1) { return $members[0]; } else { return $members; } } $value = []; foreach ($field_data as $k => $v) { // Skip the JSON-LD keys. if ($k == '@id' or $k == '@type' or $k == '@context') { continue; } // Find the term accession for this element, and if the key's value is an // array then recurse. $accession = $context[$k]; if (is_array($v)) { $next_depth = $depth + 1; $subvalue = _tripal_update_remote_entity_field($v, $context, $next_depth); $value[$accession] = $subvalue; } else { $value[$accession] = $v; } } return $value; } /** * Behaves similar to the field_info_field() function but for remote fields. * * Returns a "fake" field info array for fields attached to content types * on remote Tripal sites. * * @param $site_id * The numeric site ID for the remote Tripal site. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * @param $field_accession * The controlled vocabulary term accession for the property (i.e. field) of * the Class (i.e. content type). * * @return * An array similar to that returned by the field_info_field function * of Drupal for local fields. * * @ingroup tripal_ws_api */ function tripal_get_remote_field_info($site_id, $bundle_accession, $field_accession) { // Get the site documentation (loads from cache if already retrieved). $site_doc = tripal_get_remote_API_doc($site_id); // Get the property from the document for this field. $property = tripal_get_remote_field_doc($site_id, $bundle_accession, $field_accession); // Now create the fake field and instance. list($vocab, $accession) = explode(':', $field_accession); $field_name = 'tripal_remote_site_' . $site_id . '_' . $field_accession; $field = [ 'field_name' => $field_name, 'type' => $field_name, 'storage' => [ 'type' => 'tripal_remote_site', ], ]; return $field; } /** * Behaves similar to the field_info_instance() function but for remote fields. * * Returns a "fake" instance info array for fields attached to content types * on remote Tripal sites. * * @param $site_id * The numeric site ID for the remote Tripal site. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * @param $field_accession * The controlled vocabulary term accession for the property (i.e. field) of * the Class (i.e. content type). * * @return * An array similar to that returned by the field_info_instance function * of Drupal for local fields. * * @ingroup tripal_ws_api */ function tripal_get_remote_field_instance_info($site_id, $bundle_accession, $field_accession) { // Get the site documentation (loads from cache if already retrieved). $site_doc = tripal_get_remote_API_doc($site_id); // Get the property from the document for this field. $property = tripal_get_remote_field_doc($site_id, $bundle_accession, $field_accession); list($vocab, $accession) = explode(':', $field_accession); $field_name = 'tripal_remote_site_' . $site_id . '_' . $field_accession; list($vocab, $accession) = explode(':', $field_accession); $instance = [ 'label' => $property['hydra:title'], 'description' => $property['hydra:description'], 'formatters' => $property['tripal_formatters'], 'settings' => [ 'term_vocabulary' => $vocab, 'term_accession' => $accession, ], 'field_name' => $field_name, 'entity_type' => 'TripalEntity', 'bundle_name' => $bundle_accession, ]; return $instance; } /** * Retreive the content type information from a remote Tripal site. * * The array returned is equivalent to the Hydra Vocabulary "supportedClass" * stanza. * * @param $site_id * The numeric site ID for the remote Tripal site. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * * @return * A PHP array corresponding to the Hydra Class stanza (i.e. a content type). * Returns NULL if the class ID cannot be found. * * @ingroup tripal_ws_api */ function tripal_get_remote_content_doc($site_id, $bundle_accession) { // Get the site documentation (loads from cache if already retrieved). $site_doc = tripal_get_remote_API_doc($site_id); // Get the class that matches this bundle. $classes = $site_doc['supportedClass']; $class = NULL; foreach ($classes as $item) { if ($item['@id'] == $bundle_accession) { return $item; } } return NULL; } /** * Retrieves the field information for a content type from a remote Tripal site. * * The array returned is equivalent to the Hydra Vocabulary "supportedProperty" * stanza that belongs to a Hydra Class (content type). * * @param $site_id * The numeric site ID for the remote Tripal site. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * @param $field_accession * The controlled vocabulary term accession for the property (i.e. field) of * the Class (i.e. content type). * * @return * A PHP array corresponding to the Hydra property stanza (field) that * belongs to the given Class (i.e. a content type). Retruns NULL if the * property cannot be found. * * @ingroup tripal_ws_api */ function tripal_get_remote_field_doc($site_id, $bundle_accession, $field_accession) { // Get the site documentation (loads from cache if already retrieved). $site_doc = tripal_get_remote_API_doc($site_id); $class = tripal_get_remote_content_doc($site_id, $bundle_accession); $properties = $class['supportedProperty']; foreach ($properties as $item) { if ($item['property'] == $field_accession) { return $item; } } return NULL; } /** * Retrieves the list of download formatters for a remote field. * * All Tripal fields support the abilty for inclusion in files that can * downloaded. This function is used to identify what formatters these * fields are appropriate for. If those download formatter classes exist * on this site then the field can be used with that formatter. * * @param $site_id * The numeric site ID for the remote Tripal site. * @param $bundle_accession * The controlled vocabulary term accession for the content type * on the remote Tripal site. * @param $field_accession * The controlled vocabulary term accession for the property (i.e. field) of * the Class (i.e. content type). * * @return * An array of field downloader class names that are compoatible with the * field and which exist on this site. * * @ingroup tripal_ws_api */ function tripal_get_remote_field_formatters($site_id, $bundle_accession, $field_accession) { $flist = []; // Get the site documentation (loads from cache if already retrieved). $site_doc = tripal_get_remote_API_doc($site_id); $property = tripal_get_remote_field_doc($site_id, $bundle_accession, $field_accession); if (!$property) { return $flist; } $formatters = $property['tripal_formatters']; foreach ($formatters as $formatter) { if (tripal_load_include_downloader_class($formatter)) { $flist[$formatter] = $formatter::$full_label; } } return $flist; }