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@@ -776,7 +776,7 @@ function tripal_stock_node_presave($node) {
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switch ($node->type) {
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case 'chado_stock':
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// for a form submission the fields part of the node object
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- // but for a sync the feilds are in an object of the node
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+ // but for a sync the fields are in an object of the node
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$organism_id = null;
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$sname = '';
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$uniquename = '';
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@@ -799,59 +799,13 @@ function tripal_stock_node_presave($node) {
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$values = array('organism_id' => $organism_id);
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$organism = chado_select_record('organism', array('genus','species'), $values);
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$node->title = "$sname, $uniquename ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;
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- if ($name == $uname) {
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+ if ($name == $uniquename) {
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$node->title = "$sname ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;
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}
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break;
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}
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}
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-/**
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- * Implements hook_node_insert(). Acts on all content types.
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- *
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- * @ingroup tripal_stock
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- */
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-function tripal_stock_node_insert($node) {
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- switch ($node->type) {
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- case 'chado_stock':
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- if (!$node->stock_id) {
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- $sql = "SELECT * FROM {chado_stock} WHERE nid = :nid";
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- $chado_stock = db_query($sql, array(':nid' => $node->nid))->fetchObject();
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- $node->stock_id = $chado_stock->stock_id;
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- }
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-
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- // remove any previous alias
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- db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
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-
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- // set the URL for this stock page
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- $url_alias = tripal_stock_get_stock_url($node);
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- $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
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- path_save($path_alias);
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- break;
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- }
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-}
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-
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-/**
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- * Implements hook_node_update(). Acts on all content types.
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- *
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- * @ingroup tripal_stock
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- */
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-function tripal_stock_node_update($node) {
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-
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- switch ($node->type) {
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- case 'chado_stock':
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-
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- // remove any previous alias
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- db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
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-
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- // set the URL for this stock page
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- $url_alias = tripal_stock_get_stock_url($node);
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- $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
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- path_save($path_alias);
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- break;
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- }
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-}
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-
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/**
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* Implements hook_node_view(). Acts on all content types.
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*
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@@ -916,3 +870,119 @@ function tripal_stock_node_view($node, $view_mode, $langcode) {
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break;
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}
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}
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+
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+/**
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+ * Implements hook_node_insert().
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+ * Acts on all content types.
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+ *
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+ * @ingroup tripal_stock
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+ */
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+function tripal_stock_node_insert($node) {
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+
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+ // set the URL path after inserting. We do it here because we do not
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+ // know the stock_id in the presave
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+ switch ($node->type) {
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+ case 'chado_stock':
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+
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+ // remove any previous alias
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+ db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
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+
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+ // set the URL for this stock page
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+ $url_alias = tripal_stock_get_stock_url($node);
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+ $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
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+ path_save($path_alias);
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+ break;
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+ }
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+}
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+
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+/**
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+ * Implements hook_node_update().
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+ * Acts on all content types.
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+ *
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+ * @ingroup tripal_stock
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+ */
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+function tripal_stock_node_update($node) {
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+
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+ // add items to other nodes, build index and search results
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+ switch ($node->type) {
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+ case 'chado_stock':
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+ // remove any previous alias
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+ db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
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+
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+ // set the URL for this stock page
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+ $url_alias = tripal_stock_get_stock_url($node);
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+ $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
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+ path_save($path_alias);
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+ break;
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+ }
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+}
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+/**
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+ * Return the url alias for a stock
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+ *
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+ * @param $node
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+ * A node object containing at least the stock_id and nid
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+ * @param $url_alias
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+ * Optional. This should be the URL alias syntax string that contains
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+ * placeholders such as [id], [genus], [species], [name], [uniquename],
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+ * and [type]. These placeholders will be substituted for actual values.
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+ * If this parameter is not provided then the value of the
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+ * chado_stock_url_string Drupal variable will be used.
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+ *
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+ * @ingroup tripal_stock
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+ */
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+function tripal_stock_get_stock_url($node, $url_alias = NULL) {
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+
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+ // get the starting URL alias
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+ if(!$url_alias) {
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+ $url_alias = variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]');
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+ if (!$url_alias) {
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+ $url_alias = '/stock/[genus]/[species]/[type]/[uniquename]';
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+ }
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+ $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
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+ }
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+
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+ // get the stock
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+ $values = array('stock_id' => $node->stock_id);
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+ $stock = chado_select_record('stock', array('*'), $values);
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+ if (!$stock) {
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+ tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find stock when setting URL alias for stock: %id", array('%id' => $node->stock_id));
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+ return FALSE;
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+ }
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+ $stock = (object) $stock[0];
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+
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+ // get the organism
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+ $values = array('organism_id' => $stock->organism_id);
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+ $organism = chado_select_record('organism', array('*'), $values);
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+ if (!$organism) {
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+ tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find organism when setting URL alias for stock: %id", array('%id' => $node->stock_id));
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+ return FALSE;
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+ }
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+ $genus = preg_replace('/\s/', '_', strtolower($organism[0]->genus));
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+ $species = preg_replace('/\s/', '_', strtolower($organism[0]->species));
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+
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+ // get the type
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+ $values = array('cvterm_id' => $stock->type_id);
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+ $cvterm = chado_select_record('cvterm', array('name'), $values);
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+ if (!$cvterm) {
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+ tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find type when setting URL alias for stock: %id", array('%id' => $node->stock_id));
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+ return FALSE;
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+ }
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+ $type = preg_replace('/\s/', '_', $cvterm[0]->name);
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+
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+ // now substitute in the values
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+ $url_alias = preg_replace('/\[id\]/', $stock->stock_id, $url_alias);
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+ $url_alias = preg_replace('/\[genus\]/', $genus, $url_alias);
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+ $url_alias = preg_replace('/\[species\]/', $species, $url_alias);
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+ $url_alias = preg_replace('/\[type\]/', $type, $url_alias);
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+ $url_alias = preg_replace('/\[name\]/', $stock->name, $url_alias);
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+ $url_alias = preg_replace('/\[uniquename\]/', $stock->uniquename, $url_alias);
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+
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+ // the dst field of the url_alias table is only 128 characters long.
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+ // if this is the case then simply return the node URL, we can't set this one
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+ if (strlen($url_alias) > 128) {
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+ tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot set alias longer than 128 characters: %alias.", array('%alias' => $url_alias));
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+ return "node/" . $node->nid;
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+ }
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+
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+ return $url_alias;
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+}
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Lacey Sanderson