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@@ -186,14 +186,25 @@ function tripal_remove_site($record_id) {
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}
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/**
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- * Retreives the full Hydra documentattion for the remote Tripal site.
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+ * Makes a request to the "content"service of a remote Tripal web site.
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*
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- * When passed a site_id from the tripal_sites table the full
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- * site's document service is returned in json format
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+ * @param $site_id
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+ * The numeric site ID for the remote Tripal site.
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+ *
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+ * @param $query
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+ * The query string. This string is added to the URL for the remote
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+ * website.
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+ *
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+ * @return
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+ * The JSON response formatted in a PHP array or FALSE if a problem occured.
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*/
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-function tripal_get_remote_site_doc($site_id) {
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+function tripal_query_remote_site($site_id, $query) {
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+ $ctype = $query;
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+ $qdata = '';
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+ if (preg_match('/\?/', $query)) {
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+ list($ctype, $qdata) = explode('?', $query);
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+ }
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- // Get the site url from the tripal_sites table.
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if ($site_id) {
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$remote_site = db_select('tripal_sites', 'ts')
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->fields('ts')
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@@ -206,10 +217,12 @@ function tripal_get_remote_site_doc($site_id) {
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$ws_version = $remote_site->version;
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$ws_url = $remote_site->url;
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$ws_url = trim($ws_url, '/');
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- $ws_url .= '/web-services/doc/' . $ws_version;
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-
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- // Build and make the request.
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- $options = [];
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+ $ws_url .= '/web-services/content/' . $ws_version . '/' . $ctype;
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+ // Build the Query and make and substitions needed.
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+ //dpm($ws_url . '?' . $query);
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+ $options = array(
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+ 'data' => $qdata,
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+ );
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$data = drupal_http_request($ws_url, $options);
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if (!$data) {
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@@ -222,8 +235,8 @@ function tripal_get_remote_site_doc($site_id) {
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// connection error (not a Tripal web servcies error).
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if (property_exists($data, 'error')) {
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tripal_report_error('tripal_ws', TRIPAL_ERROR,
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- 'Web Services error on remote site: %error.',
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- array('%error' => $data->error));
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+ 'Remote web Services reports the following error: !error. Using URL: !url',
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+ array('!error' => $error, '!url' => $ws_url));
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return FALSE;
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}
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@@ -234,8 +247,8 @@ function tripal_get_remote_site_doc($site_id) {
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if (array_key_exists('error', $data)) {
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$error = '</pre>' . print_r($data['error'], TRUE) . '</pre>';
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tripal_report_error('tripal_ws', TRIPAL_ERROR,
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- 'Web Services error on remote site: %error.',
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- array('%error' => $error));
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+ 'Tripal remote web services reports the following error: !error. Using URL: !url',
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+ array('!error' => $error, '!url' => $ws_url));
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return FALSE;
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}
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@@ -243,40 +256,113 @@ function tripal_get_remote_site_doc($site_id) {
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}
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/**
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- * Makes a request to a remote Tripal web services site.
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+ * Retrieves the JSON-LD context for any remote Tripal web service.
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*
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- * @param $query
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- * The query string. This string is added to the URL for the remote
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- * website.
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+ * @param $context_url
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+ * The Full URL for the context file on the remote Tripal site. This URL
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+ * can be found in the '@context' key of any response from a remote Tripal
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+ * web services call.
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+ * @param $cache_id
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+ * A unique ID for caching of this context result to speed furture
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+ * queries.
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+ * @return
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+ * The JSON-LD context mapping array, or FALSE if the context could not
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+ * be retrieved.
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+ */
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+function tripal_get_remote_context($context_url, $cache_id) {
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+
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+ if (!$context_url) {
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+ throw new Exception('PLease provide a context_url for the tripal_get_remote_context function.');
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+ }
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+ if (!$cache_id) {
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+ throw new Exception('PLease provide unique $cache_id for the tripal_get_remote_context function.');
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+ }
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+
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+ if ($cache = cache_get($cache_id)) {
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+ return $cache->data;
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+ }
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+
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+ $context = drupal_http_request($context_url);
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+ if (!$context) {
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+ tripal_report_error('tripal_ws', TRIPAL_ERROR,
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+ 'There was a poblem retrieving the context from the remote site: !context_url.',
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+ array('!context_url' => $context_url));
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+ return FALSE;
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+ }
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+ $context = drupal_json_decode($context->data);
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+ $context = $context['@context'];
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+ cache_set($cache_id, $context);
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+ return $context;
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+}
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+
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+/**
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+ * Retrieves the JSON-LD context for a bundle or field on a remote Tripal site.
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+ *
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+ * The $site_id, $bundle_accession and $field_accession variables are not
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+ * needed to retrieve the context, but are used for caching the context to
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+ * make subsequent calls execute faster. This function is meant to be used
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+ * only for the 'content' service provided by Tripal.
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*
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+ * @param $site_id
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+ * The numeric site ID for the remote Tripal site.
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+ * @param $context_url
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+ * The Full URL for the context file on the remote Tripal site. This URL
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+ * can be found in the '@context' key of any response from a remote Tripal
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+ * web services call.
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+ * @param $bundle_accession
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+ * The controlled vocabulary term accession for the content type
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+ * on the remote Tripal site.
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+ * @param $field_accession
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+ * The controlled vocabulary term accession for the property (i.e. field) of
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+ * the Class (i.e. content type).
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* @return
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- * The JSON response formatted in a PHP array or FALSE if a problem occured.
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+ * The JSON-LD context mapping array.
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*/
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-function tripal_query_remote_site($site_id, $query) {
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- $ctype = $query;
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- $qdata = '';
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- if (preg_match('/\?/', $query)) {
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- list($ctype, $qdata) = explode('?', $query);
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+function tripal_get_remote_content_context($site_id, $context_url, $bundle_accession, $field_accession = '') {
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+ $cache_id = substr('trp_ws_context_' . $site_id . '-' . $bundle_accession . '-' . $field_accession, 0, 254);
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+ $context = tripal_get_remote_context($context_url, $cache_id);
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+ return $context;
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+}
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+/**
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+ * Retrieves the API documentation for a remote Tripal web service.
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+ *
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+ * @param $site_id
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+ * The numeric site ID for the remote Tripal site.
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+ * @return
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+ * The vocabulary of a remote Tripal web service, or FALSE if an error
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+ * occured.
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+ */
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+function tripal_get_remote_API_doc($site_id) {
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+ $site_doc = '';
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+
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+ if (!$site_id) {
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+ throw new Exception('PLease provide a numeric site ID for the tripal_get_remote_API_doc function.');
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}
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- if ($site_id) {
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- $remote_site = db_select('tripal_sites', 'ts')
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- ->fields('ts')
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- ->condition('ts.id', $site_id)
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- ->execute()
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- ->fetchObject();
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+ $cache_name = 'trp_ws_doc_' . $site_id;
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+ if ($cache = cache_get($cache_name)) {
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+ return $cache->data;
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+ }
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+
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+ // Get the site url from the tripal_sites table.
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+ $remote_site = db_select('tripal_sites', 'ts')
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+ ->fields('ts')
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+ ->condition('ts.id', $site_id)
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+ ->execute()
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+ ->fetchObject();
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+
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+ if (!$remote_site) {
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+ throw new Exception(t('Cannot find a remote site with id: "!id"', array('!id' => $site_id)));
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}
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// Build the URL to the remote web services.
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$ws_version = $remote_site->version;
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$ws_url = $remote_site->url;
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$ws_url = trim($ws_url, '/');
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- $ws_url .= '/web-services/content/' . $ws_version . '/' . $ctype;
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- // Build the Query and make and substitions needed.
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- //dpm($ws_url . '?' . $query);
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- $options = array(
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- 'data' => $qdata,
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- );
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+ $ws_url .= '/web-services/doc/' . $ws_version;
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+
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+ // Build and make the request.
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+ $options = [];
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$data = drupal_http_request($ws_url, $options);
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if (!$data) {
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@@ -289,22 +375,392 @@ function tripal_query_remote_site($site_id, $query) {
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// connection error (not a Tripal web servcies error).
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if (property_exists($data, 'error')) {
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tripal_report_error('tripal_ws', TRIPAL_ERROR,
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- 'Web Services error on remote site: %error.',
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- array('%error' => $data->error));
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+ 'Remote web services document reports the following error: !error. Using URL: !url',
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+ array('!error' => $error, '!url' => $ws_url));
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return FALSE;
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}
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// We got a response, so convert it to a PHP array.
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- $data = drupal_json_decode($data->data);
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+ $site_doc = drupal_json_decode($data->data);
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// Check if there was a Tripal Web Services error.
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if (array_key_exists('error', $data)) {
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$error = '</pre>' . print_r($data['error'], TRUE) . '</pre>';
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tripal_report_error('tripal_ws', TRIPAL_ERROR,
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- 'Web Services error on remote site: %error.',
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- array('%error' => $error));
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+ 'Tripal Remote web services document reports the following error: !error. Using URL: !url',
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+ array('!error' => $error, '!url' => $ws_url));
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return FALSE;
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}
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- return $data;
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+ cache_set($cache_name, $site_doc);
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+
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+ return $site_doc;
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+}
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+
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+/**
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+ * Build and return a "fake" entity for a record from a remote Tripal site.
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+ *
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+ * @param $remote_entity_id
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+ * Array of the remote ids.
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+ * @param $site_id
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+ * The numeric site ID for the remote Tripal site.
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+ * @param $bundle_accession
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+ * The controlled vocabulary term accession for the content type
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+ * on the remote Tripal site.
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+ * @param $field_ids
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+ * The controlled vocabulary term accessions for the fields available
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+ * on the remote content type. Any remote fields that matches these IDs will
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+ * be added to the entity returned.
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+ * @return
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+ * A fake entity object.
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+ */
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+function tripal_load_remote_entity($remote_entity_id, $site_id, $bundle_accession, $field_ids) {
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+
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+ // Get the site documentation (loads from cache if already retrieved).
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+ $site_doc = tripal_get_remote_API_doc($site_id);
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+
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+ // Get the remote entity and create the fake entity.
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+ $query = $bundle_accession . '/' . $remote_entity_id;
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+ $remote_entity = tripal_query_remote_site($site_id, $query);
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+ if (!$remote_entity) {
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+ return FALSE;
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+ }
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+
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+ // Start building the fake id.
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+ $entity = new stdClass();
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+ $entity->entityType = 'TripalEntity';
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+ $entity->entityInfo = [];
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+ $entity->id = $remote_entity_id;
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+ $entity->type = 'TripalEntity';
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+ $entity->bundle = $bundle_accession;
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+ $entity->site_id = $site_id;
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+
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+
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+ // Get the context JSON for this remote entity, we'll use it to map
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+ $context_url = $remote_entity['@context'];
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+ $context = tripal_get_remote_content_context($site_id, $context_url, $bundle_accession);
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+ if (!$context) {
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+ return $entity;
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+ }
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+
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+ // Iterate through the fields and the those values to the entity.
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+ foreach ($field_ids as $field_id) {
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+
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+ $field = tripal_get_remote_field_info($site_id, $bundle_accession, $field_id);
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+ $instance = tripal_get_remote_field_instance_info($site_id, $bundle_accession, $field_id);
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+ $field_name = $field['field_name'];
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+
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+ $field_key = '';
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+ foreach ($context as $k => $v) {
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+ if (!is_array($v) and $v == $field_id) {
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+ $field_key = $k;
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+ }
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+ }
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+
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+ // If the field is not in this remote bundle then add an empty value.
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+ if (!$field_key) {
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+ $entity->{$field_name}['und'][0]['value'] = '';
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+ continue;
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+ }
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+ if (!array_key_exists($field_key, $remote_entity)) {
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+ $entity->{$field_name}['und'][0]['value'] = '';
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+ continue;
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+ }
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+
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+ // If the key is for a field that is not "auto attached' then we need
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+ // to get that field through a separate call.
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+ $attached = TRUE;
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+ if (array_key_exists($field_id, $context) and is_array($context[$field_id]) and
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+ array_key_exists('@type', $context[$field_id]) and $context[$field_id]['@type'] == '@id'){
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+ $attached = FALSE;
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+ }
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+
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+ // Set the value for this field.
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+ $value = '';
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+ if (is_array($remote_entity[$field_key])) {
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+ $value = _tripal_update_remote_entity_field($remote_entity[$field_key], $context, 1);
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+ }
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+ else {
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+ $value = $remote_entity[$field_key];
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+ }
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+
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+ // If the field is not attached then we have to query another level.
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+ if (!$attached) {
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+
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+ $field_data = drupal_http_request($value);
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+ if (!$field_data) {
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+ tripal_report_error('tripal_ws', TRIPAL_ERROR,
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+ 'There was a poblem retrieving the unattached field, "!field:", for the remote entity: !entity_id.',
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+ array('!field' => $field_id, '!entity_id' => $remote_entity_id));
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+ $value = '';
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+ }
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+ $field_data = drupal_json_decode($field_data->data);
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+
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+ // Get the context for this field so we can map the keys to the
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+ // controlled vocabulary accessions. If it fails then skip this field.
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+ $field_context_url = $field_data['@context'];
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+ $field_context = tripal_get_remote_content_context($site_id, $field_context_url, $bundle_accession, $field_id);
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+ if (!$field_context) {
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+ continue;
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+ }
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+ $value = _tripal_update_remote_entity_field($field_data, $field_context);
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+ }
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+ $entity->{$field_name}['und'][0]['value'] = $value;
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+ }
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+ return $entity;
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+}
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+
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+/**
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+ * A helper function for the tripal_get_remote_entity() function.
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+ *
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+ * This function converts the field's key elements to their
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+ * vocabulary term accessions.
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+ *
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+ * @param $field_data
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+ * The field array as returned by web services.
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+ * @param $context
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+ * The web service JSON-LD context for the bundle to which the field belongs.
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+ */
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+function _tripal_update_remote_entity_field($field_data, $context, $depth = 0) {
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+
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+ // If depth is 0 then we are tring to find out how to deal with this field.
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+ if ($depth == 0) {
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+ // Check if this is an array.
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+ if ($field_data['@type'] == 'Collection') {
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+ $members = array();
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+ foreach ($field_data['member'] as $member) {
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+ $next_depth = $depth + 1;
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+ $members[] = _tripal_update_remote_entity_field($member, $context, $next_depth);
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+ }
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+
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+ // If we only have one item then just return it as a single item.
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+ // TODO: we may need to check cardinality of the field and be more
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+ // strict about how we return the value.
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+ if ($field_data['totalItems'] == 1){
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+ return $members[0];
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+ }
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+ else {
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+ return $members;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $next_depth = $depth + 1;
|
|
|
+ return _tripal_update_remote_entity_field($field_data, $context, $next_depth);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // If this isn't depth 0 then we are rewriting keys as CV term accession.
|
|
|
+ else {
|
|
|
+
|
|
|
+ $value = array();
|
|
|
+ foreach ($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] = $value;
|
|
|
+ }
|
|
|
+ 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 $field_accession
|
|
|
+ * The controlled vocabulary term accession for the property (i.e. field) of
|
|
|
+ * the Class (i.e. content type).
|
|
|
+ * @return
|
|
|
+ * An array similar to that returned by the field_info_field function
|
|
|
+ * of Drupal for local fields.
|
|
|
+ */
|
|
|
+function tripal_get_remote_field_info($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 = array(
|
|
|
+ 'field_name' => $field_name,
|
|
|
+ 'type' => $field_name,
|
|
|
+ 'storage' => array(
|
|
|
+ '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 $field_accession
|
|
|
+ * The controlled vocabulary term accession for the property (i.e. field) of
|
|
|
+ * the Class (i.e. content type).
|
|
|
+ * @return
|
|
|
+ * An array similar to that returned by the field_info_instance function
|
|
|
+ * of Drupal for local fields.
|
|
|
+ */
|
|
|
+function tripal_get_remote_field_instance_info($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 = array(
|
|
|
+ 'label' => $property['hydra:title'],
|
|
|
+ 'description' => $property['hydra:description'],
|
|
|
+ 'formatters' => $property['tripal_formatters'],
|
|
|
+ 'settings' => array(
|
|
|
+ 'term_vocabulary' => $vocab,
|
|
|
+ 'term_accession' => $accession
|
|
|
+ ),
|
|
|
+ 'field_name' => $field_name,
|
|
|
+ 'entity_type' => 'TripalEntity',
|
|
|
+ 'bundle_name' => $bundle_accession,
|
|
|
+ );
|
|
|
+ return $instance;
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retreive the bundle (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 $bundle_accession
|
|
|
+ * The controlled vocabulary term accession for the content type
|
|
|
+ * on the remote Tripal site.
|
|
|
+ * @return
|
|
|
+ * A PHP array corresponding to the Hydra Class stanza (i.e. a content type).
|
|
|
+ * Returns NULL if the class ID cannot be found.
|
|
|
+ */
|
|
|
+function tripal_get_remote_bundle_doc($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 $field_accession
|
|
|
+ * The controlled vocabulary term accession for the property (i.e. field) of
|
|
|
+ * the Class (i.e. content type).
|
|
|
+ * @return
|
|
|
+ * A PHP array corresponding to the Hydra property stanza (field) that
|
|
|
+ * belongs to the given Class (i.e. a content type). Retruns NULL if the
|
|
|
+ * property cannot be found.
|
|
|
+ */
|
|
|
+function tripal_get_remote_field_doc($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);
|
|
|
+
|
|
|
+ $class = tripal_get_remote_bundle_doc($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 $field_accession
|
|
|
+ * The controlled vocabulary term accession for the property (i.e. field) of
|
|
|
+ * the Class (i.e. content type).
|
|
|
+ * @return
|
|
|
+ * An array of field downloader class names that are compoatible with the
|
|
|
+ * field and which exist on this site.
|
|
|
+ */
|
|
|
+function tripal_get_remote_field_formatters($site_id, $bundle_accession, $field_accession) {
|
|
|
+
|
|
|
+ $flist = array();
|
|
|
+
|
|
|
+ // 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;
|
|
|
}
|
Stephen Ficklin