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@@ -9,7 +9,7 @@
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* There are two steps to implement the ability to set custom titles for the node type:
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* 1) Add the 'chado_node_api' elements to the hook_node_info function(). These values
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* define the name of the base table and how to refer to nodes in singular and plural.
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- * There are additional paramaters that can be added to the 'chado_node_api' for
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+ * There are additional paramaters that can be added to the 'chado_node_api' for
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* syncing nodes (see documentation for the chado_node_sync_form() function for additional
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* options.
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* @code
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@@ -35,7 +35,7 @@
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);
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}
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* @endcode
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- *
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+ *
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* 2) Add the "Set Page Titles" Form to the admin settings form
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* @code
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// If the module is using the "Chado Node: Title & Path API" to allow custom titles
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@@ -186,7 +186,7 @@ function chado_add_admin_form_set_title(&$form, &$form_state, $details) {
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$tokens = array_merge($tokens, $details['custom_tokens']);
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$token_list = chado_node_format_tokens($tokens);
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$details['default_option'] = (isset($details['default_option'])) ? $details['default_option'] : chado_node_get_title_format($details['content_type'], $tokens);
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-
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+
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// FORM PROPER
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$msg = t(
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'Each synced %singular must have a unique page title, however, %plural may have the
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@@ -428,13 +428,495 @@ function chado_node_get_legacy_title_default($content_type) {
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* Set Paths
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*/
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+/**
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+ * Get the url of a node based on the url Format set in the admin
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+ * section of the module. If the format has not yet been set than
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+ * the the unique constrain and name fields will be used to generate
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+ * a default format
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+ *
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+ * @param $node
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+ * The node object
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+ *
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+ * @ingroup tripal_chado_node_api
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+ */
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+function chado_get_node_url($node) {
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+ $content_type = $node->type;
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+
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+ // Get the tokens and format
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+ $tokens = array(); // this will be set by chado_node_get_url_format
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+ $url = chado_node_get_url_format($content_type, $tokens);
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+
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+ // Determine which tokens were used in the format string
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+ if (preg_match_all('/\[[^]]+\]/', $url, $used_tokens)) {
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+
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+ // Get the value for each token used
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+ foreach ($used_tokens[0] as $token) {
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+ $token_info = $tokens[$token];
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+ if (!empty($token_info)) {
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+ $value = chado_get_token_value($token_info, $node);
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+ $url = str_replace($token, $value, $url);
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+ }
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+ }
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+ }
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+ else {
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+ return $url;
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+ }
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+
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+ return $url;
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+}
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+
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+/**
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+ * Set the URL for a given node.
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+ *
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+ * Note: This makes the old URL completely invalid which breaks bookmarks.
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+ * Furthermore, if someone attempts to go to an old URL they will get a white
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+ * screen PDO error which is not very user friendly ;-)
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+ * @todo handle re-directing for old URLs or at least ensure a page not found
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+ * error is displayed.
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+ *
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+ * @param $node
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+ * The node to set the URL for.
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+ *
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+ * @return
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+ * The URL alias that was set.
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+ */
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+function chado_set_node_url($node) {
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+
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+ // Get the global variable determining the language of the current content.
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+ global $language_content;
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+
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+ // First we need to get the URL alias.
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+ $url_alias = chado_get_node_url($node);
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+
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+ // And remove any forward slashes since those wreak havok.
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+ $url_alias = preg_replace('/^\//', '', $url_alias);
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+
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+ // Use the node to determine the source/original URL.
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+ $source_url = 'node/' . $node->nid;
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+
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+ // Only bother setting the alias if there is one.
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+ if (!empty($url_alias) AND $source_url != $url_alias) {
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+
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+ $path = array(
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+ 'source' => $source_url,
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+ 'alias' => $url_alias,
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+ 'language' => $language_content->language
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+ );
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+ path_save($path);
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+/**
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+ // Remove any existing alias.
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+ db_delete('url_alias')
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+ ->condition('source', $source_url)
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+ ->execute();
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+
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+ // Add our new one.
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+ db_insert('url_alias')
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+ ->fields(array(
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+ 'source' => $source_url,
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+ 'alias' => $url_alias,
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+ 'language' => $language_content->language
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+ ))
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+ ->execute();
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+*/
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+ }
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+
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+ return $url_alias;
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+}
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+
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+/**
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+ * Tripal Job for updating all node URLs for a particular node type.
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+ *
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+ * @param $content_type
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+ * The machine name of the node type to update URLs for.
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+ * @param $job_id
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+ * The ID of the tripal job calling this function.
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+ */
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+function chado_update_existing_node_urls($content_type, $job_id = 0) {
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+ $transaction = db_transaction();
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+
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+ print "\nNOTE: Setting of URLs is performed using a database transaction. \n" .
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+ "If the load fails or is terminated prematurely then the entire set of \n" .
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+ "new URLs will be rolled back and no changes will be made.\n\n";
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+
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+ try {
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+ // Get the number of records we need to set URLs for.
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+ $num_nodes = db_query(
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+ 'SELECT count(*) FROM {' . $content_type . '}'
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+ )->fetchField();
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+
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+ // Calculate the interval at which we will print an update on the screen.
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+ $num_set = 0;
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+ $num_per_interval = 100;
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+
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+ if ($num_nodes > 0) {
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+
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+ print "There are $num_nodes nodes to update URLs for. You will be \n"
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+ . "updated on the progress every 100 nodes.\n\n";
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+
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+ // Get the list of nodes of this particular content type.
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+ $query = new EntityFieldQuery();
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+ $result = $query->entityCondition('entity_type', 'node')
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+ ->entityCondition('bundle', $content_type)
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+ ->execute();
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+
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+ if (isset($result['node'])) {
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+ $nids = array_keys($result['node']);
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+
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+ foreach ($nids as $nid) {
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+
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+ // Load the current node.
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+ // We do it this way instead of using noad_load_multiple to load them
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+ // all at once to avoid overloading the memory.
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+ $node = node_load($nid);
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+
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+ // Now set the URL for the current node.
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+ $alias = chado_set_node_url($node);
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+
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+ // update the job status every 1% nodes
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+ if ($num_set % $num_per_interval == 0) {
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+ $percent = ($num_set / $num_nodes) * 100;
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+
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+ // Update the tripal job.
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+ if ($job_id) {
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+ tripal_set_job_progress($job_id, intval($percent));
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+ }
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+
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+ // Update the user on progress.
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+ $percent = sprintf("%.2f", $percent);
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+ print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
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+ }
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+ $num_set++;
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+ }
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+ }
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+ $percent = ($num_set / $num_nodes) * 100;
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+ tripal_set_job_progress($job_id, intval($percent));
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+ $percent = sprintf("%.2f", $percent);
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+ print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
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+ print "\nDone. Set " . number_format($num_set) . " URLs\n";
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+ }
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+ else {
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+ print "\nThere are no $content_type nodes to update. If you know there\n"
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+ . "are records of this type in chado, try sync'ing them to Drupal.\n";
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+ }
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+ }
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+ catch (Exception $e) {
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+ $transaction->rollback();
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+ print "\n"; // make sure we start errors on new line
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+ watchdog_exception('chado_node_api', $e);
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+ tripal_report_error(
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+ 'chado_node_api',
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+ TRIPAL_WARNING,
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+ 'Unable to update URLs for the :content-type Node Type. Specifically, the last URL attempted was NID=:nid and Alias=:alias',
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+ array(':content-type' => $content_type, ':nid' => $node->nid, ':alias' => $alias)
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+ );
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+ }
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+}
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+
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+/**
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+ * Generic "Set Node url" sub-form for setting the url of any chado node
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+ *
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+ * @param $form
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+ * The Drupal form array into which the property form elements will be added
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+ * @param $form_state
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+ * The corresponding form_state array for the form
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+ * @param $details
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+ * An array defining details used by this form.
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+ * Required keys that are always required:
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+ * -module: the name of the module implementing the node. For example, for features
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+ * the module is tripal_feature.
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+ * -options: an array of quick-choice options to supply to the user. The key should be
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+ * the token and the value should be a human-readable description of the option
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+ * Optional keys include:
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+ * -content_type: the name of the content type. Defaults to module name.
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+ * -fieldset_title: the title to use for the fieldset. Defaults to "Set Page url".
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+ * -default_option: the default format to use which matches one of those in $details['options']
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+ * -custom_tokens: an array of custom tokens that follow the same format as those
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+ * generated by chado_node_generate_tokens().
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+ *
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+ * @ingroup tripal_chado_node_api
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+ */
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+function chado_add_admin_form_set_url(&$form, &$form_state, $details) {
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+
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+ // Get Node Info
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+ if (isset($details['module'])) {
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+ $node_info = call_user_func($details['module'] . '_node_info');
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+ $chado_node_api = $node_info[ $details['content_type'] ]['chado_node_api'];
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+ }
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+ else {
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+ tripal_report_error(
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+ 'chado_node_api',
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+ TRIPAL_ERROR,
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+ "Set URL API: When calling chado_add_admin_form_set_url, you \$details array must include 'module' => [name of your module] in order to pull out all the information provided in your implementation of hook_node_info"
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+ );
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+ }
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+
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+ // Defaults
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+ $details['fieldset_title'] = (isset($details['fieldset_title'])) ? $details['fieldset_title'] : 'Set Page URLs';
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+ $details['additional_instructions'] = (isset($details['additional_instructions'])) ? $details['additional_instructions'] : '';
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+ $details['custom_tokens'] = (isset($details['custom_tokens'])) ? $details['custom_tokens'] : array();
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+ $details['content_type'] = (isset($details['content_type'])) ? $details['content_type'] : $details['module'];
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+
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+ $tokens = array();
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+ if (empty($tokens)) {
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+ $tokens = chado_node_generate_tokens($chado_node_api['base_table']);
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+ }
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+ $tokens = array_merge($tokens, $details['custom_tokens']);
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+ $token_list = chado_node_format_tokens($tokens);
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+ $current_format = chado_node_get_url_format($details['content_type'], $tokens);
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+ $details['default_option'] = (isset($details['default_option'])) ? $details['default_option'] : $current_format;
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+
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+ // FORM PROPER
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+ $msg = t(
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+ 'Each synced %singular must have a unique page URL, however, %plural may have the
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+ same name if they are of different types or from different organisms. Therefore,
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+ we must be sure that the page URLs can uniquely identify the %singular being viewed.
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+ Select an option below that will uniquely identify all %plural on your site.'
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+ . $details['additional_instructions'],
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+ array('%singular' => $chado_node_api['record_type_title']['singular'],
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+ '%plural' => $chado_node_api['record_type_title']['plural'])
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+ );
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+ $form['set_url'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t($details['fieldset_title']),
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+ '#description' => $msg,
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+ '#collapsible' => TRUE,
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+ '#collapsed' => FALSE,
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+ '#prefix' => "<div id='set_url-fieldset'>",
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+ '#suffix' => '</div>',
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+ '#weight' => 8
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+ );
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+
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+ $form['set_url']['content_type'] = array(
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+ '#type' => 'hidden',
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+ '#value' => $node_info[ $details['content_type'] ]['base'],
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+ );
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+
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+ $details['options']['custom'] = 'Custom: See the text field below.';
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+
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+ $form['set_url']['url_option'] = array(
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+ '#title' => t('%singular Page URL', array('%singular' => $chado_node_api['record_type_title']['singular'])),
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+ '#type' => 'radios',
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+ '#description' => t("Choose a URL type from the list above that is
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+ guaranteed to be unique for all %plural. If in doubt it is safest to choose
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+ the 'Unique Constaint' option as that guarantees uniqueness.",
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+ array('%plural' => $chado_node_api['record_type_title']['plural'])),
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+ '#required' => FALSE,
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+ '#options' => $details['options'],
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+ '#default_value' => (isset($details['options'][$details['default_option']])) ? $details['default_option'] : 'custom',
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+ );
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+
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+ $form['set_url']['url_format_variable'] = array(
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+ '#type' => 'hidden',
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+ '#value' => $details['module'] . '_url_format'
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+ );
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+
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+ $form['set_url']['custom_url'] = array(
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+ '#type' => 'textarea',
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+ '#title' => 'Custom Page URL',
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+ '#description' => 'You may rearrange elements in this text box to customize the page
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+ URLs. The available tokens are listed below. You can separate or include any text
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+ between the tokens. <strong>Important: be sure that whatever you choose
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+ will always be unique even considering future data that may be added. If in doubt,
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+ please select the unique constraint title option above.</strong>',
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+ '#default_value' => $current_format,
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+ '#rows' => 1
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+ );
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+
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+ $form['set_url']['token_display'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'Available Tokens',
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+ '#description' => 'Copy the token and paste it into the "Custom Page URL" text field above.',
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+ '#collapsible' => TRUE,
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+ '#collapsed' => TRUE
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+ );
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+
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+ $form['set_url']['token_display']['content'] = array(
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+ '#type' => 'item',
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+ '#markup' => $token_list
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+ );
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+
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+ $form['set_url']['tokens'] = array(
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+ '#type' => 'hidden',
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+ '#value' => serialize($tokens)
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+ );
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+
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+ $form['set_url']['submit'] = array(
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+ '#type' => 'submit',
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+ '#value' => 'Set URLs',
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+ '#validate' => array('chado_add_admin_form_set_url_form_validate'),
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+ '#submit' => array('chado_add_admin_form_set_url_form_submit')
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+ );
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+
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+}
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+
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+/**
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+ * Implements hook_form_validate().
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+ * VALIDATE: validate the format.
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+ */
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+function chado_add_admin_form_set_url_form_validate($form, $form_state) {
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+
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+ // Ensure that all tokens used in the format are in the tokens list
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+ if (preg_match_all('/\[[^]]+\]/',$form_state['values']['custom_url'],$used_tokens)) {
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+ $token_list = unserialize($form_state['values']['tokens']);
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+ foreach ($used_tokens[0] as $token) {
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+ if (!array_key_exists($token,$token_list)) {
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+ form_set_error('custom_url', 'All tokens used must be in the "Available Tokens" list. Please make sure not to use [ or ] unless it\'s denoting a token');
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+ }
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+ }
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+ }
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+
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+}
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+
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+/**
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+ * Implements hook_form_submit().
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+ * SUBMIT: Actually add the format specified by chado_add_admin_form_set_title()
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+ */
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+function chado_add_admin_form_set_url_form_submit($form, $form_state) {
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+
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+ if ($form_state['values']['url_option'] == 'custom') {
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+ $format = $form_state['values']['custom_url'];
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+ }
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+ else {
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+ $format = $form_state['values']['url_option'];
|
|
|
+ }
|
|
|
+
|
|
|
+ // Add the format to the table for all new nodes.
|
|
|
+ chado_node_add_token_format(
|
|
|
+ 'url',
|
|
|
+ $form_state['values']['content_type'],
|
|
|
+ $format,
|
|
|
+ $form_state['values']['tokens']
|
|
|
+ );
|
|
|
+
|
|
|
+ // Add a job to Update all existing nodes.
|
|
|
+ global $user;
|
|
|
+ tripal_add_job(
|
|
|
+ "Set " . $form_state['values']['content_type'] . " URLs for all existing nodes.",
|
|
|
+ $form_state['values']['content_type'],
|
|
|
+ 'chado_update_existing_node_urls',
|
|
|
+ array('content_type' => $form_state['values']['content_type']),
|
|
|
+ $user->uid
|
|
|
+ );
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Get the url format for a specific content type
|
|
|
+ *
|
|
|
+ * If the url format has not yet been set then the following will be done
|
|
|
+ * 1) Check to see if there is a legacy url format set (features & stocks)
|
|
|
+ * 2) Check if there is a defined default for this content type
|
|
|
+ * 3) Create a format using any name fields and the unique constraint for the
|
|
|
+ * base table associated with this content type
|
|
|
+ *
|
|
|
+ * Define a default for a specific content type by implementing a function of the name
|
|
|
+ * [content type]_chado_node_default_url_format() that returns a string describing the
|
|
|
+ * default format.
|
|
|
+ *
|
|
|
+ * @param $content_type
|
|
|
+ * The name of the content (node) type you are interested in (ie: chado_feature)
|
|
|
+ * @param $tokens
|
|
|
+ * An array, passed by reference that is filled to include the tokens for this
|
|
|
+ * node type. Each token is an array with the following keys:
|
|
|
+ * -table: the name of the chado table
|
|
|
+ * -field: the name of the field in the above table
|
|
|
+ * -token: the token string (ie: [stock.stock_id])
|
|
|
+ * -description: a very short description of the token (displayed when tokens are listed)
|
|
|
+ * -location: the location of the value in a chado node variable with each level
|
|
|
+ * separated by an arrow (->) symbol. For example, the location for $node->feature->type_id->name
|
|
|
+ * is feature>type_id>name
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A string containing tokens describing the default format for the url of nodes
|
|
|
+ * of the specified content type.
|
|
|
+ */
|
|
|
+function chado_node_get_url_format($content_type, &$tokens, $base_table = NULL) {
|
|
|
+ $format = '';
|
|
|
+
|
|
|
+ // Is there a url format set?
|
|
|
+ $format_record = chado_node_get_token_format('url', $content_type, array('return_record' => TRUE));
|
|
|
+ if (!empty($format_record)) {
|
|
|
+ $format = $format_record->format;
|
|
|
+ $tokens = $format_record->tokens;
|
|
|
+ }
|
|
|
+
|
|
|
+ // All three options below need the tokens to be generated so do that now
|
|
|
+ if (empty($format)) {
|
|
|
+ if (empty($base_table)) {
|
|
|
+ $base_table = chado_node_get_base_table($content_type);
|
|
|
+ }
|
|
|
+ if (empty($tokens)) {
|
|
|
+ $tokens = chado_node_generate_tokens($base_table);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // 1) Check for legacy format
|
|
|
+ if (empty($format)) {
|
|
|
+ $format = chado_node_get_legacy_url_default($content_type);
|
|
|
+ }
|
|
|
+
|
|
|
+ // 2) Module-defined default format
|
|
|
+ if (empty($format)) {
|
|
|
+ $hook = $content_type . '_chado_node_default_url_format';
|
|
|
+ if (function_exists($hook)) {
|
|
|
+ $format = call_user_func($hook);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // 3) Create unique constraint format
|
|
|
+ if (empty($format)) {
|
|
|
+ if (empty($base_table)) {
|
|
|
+ $base_table = chado_node_get_base_table($content_type);
|
|
|
+ }
|
|
|
+ $format = chado_node_get_unique_constraint_format($base_table, 'url');
|
|
|
+ }
|
|
|
+
|
|
|
+ // Add the format to table so we can use it later
|
|
|
+ chado_node_add_token_format('url', $content_type, $format, $tokens);
|
|
|
+
|
|
|
+ return $format;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Handles legacy URL options
|
|
|
+ *
|
|
|
+ * Features, Projects & Stocks already had custom functionality to handle URL
|
|
|
+ * setting before this API was created. That has since been removed but
|
|
|
+ * to remain backwards compatible this function checks for those
|
|
|
+ * old settings and translates them into new defaults.
|
|
|
+ */
|
|
|
+function chado_node_get_legacy_url_default($content_type) {
|
|
|
+
|
|
|
+ if ($content_type == 'chado_feature') {
|
|
|
+ $legacy_format = variable_get('chado_feature_url_string', NULL);
|
|
|
+ $legacy_tokens = array(
|
|
|
+ '[id]' => '[feature.feature_id]',
|
|
|
+ '[genus]' => '[feature.organism_id>organism.genus]',
|
|
|
+ '[species]' => '[feature.organism_id>organism.species]',
|
|
|
+ '[type]' => '[feature.type_id>cvterm.name]',
|
|
|
+ '[uniquename]' => '[feature.uniquename]',
|
|
|
+ '[name]' => '[feature.name]',
|
|
|
+ );
|
|
|
+ if ($legacy_format) {
|
|
|
+ return str_replace(array_keys($legacy_tokens),$legacy_tokens, $legacy_format);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ elseif ($content_type == 'chado_stock') {
|
|
|
+
|
|
|
+ }
|
|
|
+ elseif ($content_type == 'chado_project') {
|
|
|
+
|
|
|
+ }
|
|
|
+
|
|
|
+ return FALSE;
|
|
|
+}
|
|
|
+
|
|
|
/**
|
|
|
* @section
|
|
|
* Tokens
|
|
|
*/
|
|
|
|
|
|
/**
|
|
|
- * Save a format to be used by chado_get_node_title() or chado_get_node_path()
|
|
|
+ * Save a format to be used by chado_get_node_title() or chado_get_node_url()
|
|
|
*
|
|
|
* @param $application
|
|
|
* What the format is to be applied to. For example 'title' for generating node titles
|
|
|
@@ -515,11 +997,13 @@ function chado_node_get_token_format($application, $content_type, $options = arr
|
|
|
*
|
|
|
* @param $base_table
|
|
|
* The base table to generate the unique constraint format for
|
|
|
+ * @param $format_type
|
|
|
+ * The type of format to return. This should be one of 'title' or 'url'.
|
|
|
* @return
|
|
|
* A format string including tokens describing the unique constraint
|
|
|
* including all name fields
|
|
|
*/
|
|
|
-function chado_node_get_unique_constraint_format($base_table) {
|
|
|
+function chado_node_get_unique_constraint_format($base_table, $format_type = 'title') {
|
|
|
|
|
|
$table_descrip = chado_get_schema($base_table);
|
|
|
|
|
|
@@ -529,6 +1013,7 @@ function chado_node_get_unique_constraint_format($base_table) {
|
|
|
if (preg_match('/name/',$field_name)) {
|
|
|
$names[$field_name] = "[$base_table.$field_name]";
|
|
|
}
|
|
|
+
|
|
|
}
|
|
|
uksort($names, 'tripal_sort_key_length_asc');
|
|
|
|
|
|
@@ -553,7 +1038,25 @@ function chado_node_get_unique_constraint_format($base_table) {
|
|
|
}
|
|
|
}
|
|
|
|
|
|
- $format = implode(', ',$names) . ' (' . implode(', ',$tokens) . ')';
|
|
|
+ if ($format_type == 'title') {
|
|
|
+ $format = implode(', ',$names) . ' (' . implode(', ',$tokens) . ')';
|
|
|
+ }
|
|
|
+ elseif ($format_type == 'url') {
|
|
|
+ // We don't want to put more than one name in the URL. Thus we are
|
|
|
+ // arbitrarily grabbing the longest name token since it it likely the
|
|
|
+ // uniquename.
|
|
|
+ $format = implode('/',$tokens) . '/' . array_pop($names);
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $format = FALSE;
|
|
|
+ tripal_report_error(
|
|
|
+ 'tripal_node_api',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'Unable to determine the format for the unique contraint since the format type (%format-type) is not supported (only "title" and "url" are at this time).',
|
|
|
+ array('%format-type' => $format_type)
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
return $format;
|
|
|
}
|
|
|
|
|
|
@@ -663,7 +1166,7 @@ function chado_get_token_value($token_info, $node) {
|
|
|
$index = trim($index);
|
|
|
|
|
|
// if $var is an object then it is the $node object or a table
|
|
|
- // that has been expanded. On a node_insert then the fields are
|
|
|
+ // that has been expanded. On a node_insert then the fields are
|
|
|
if (is_object($var)) {
|
|
|
// check to see if the index is a member of the object. If so,
|
|
|
// then reset the $var to this value.
|
Lacey Sanderson