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@@ -208,7 +208,7 @@ function chado_project_validate($node, $form, &$form_state) {
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// trim white space from text fields
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$node->title = trim($node->title);
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$node->description = trim($node->description);
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-
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+
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$project = 0;
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// check to make sure the name on the project is unique
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// before we try to insert into chado.
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@@ -395,8 +395,8 @@ function chado_project_load($nodes) {
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if (!$project_id) {
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continue;
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}
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-
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-
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+
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+
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$values = array('project_id' => $project_id);
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$project = chado_generate_var('project', $values);
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@@ -435,26 +435,26 @@ function chado_project_node_access($node, $op, $account) {
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if (is_object($node)) {
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$node_type = $node->type;
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}
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-
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+
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if($node_type == 'chado_project') {
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if ($op == 'create') {
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- if (!user_access('create chado_project', $account)) {
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+ if (!user_access('create chado_project content', $account)) {
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return NODE_ACCESS_DENY;
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}
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return NODE_ACCESS_ALLOW;
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}
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if ($op == 'update') {
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- if (!user_access('edit chado_project', $account)) {
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+ if (!user_access('edit chado_project content', $account)) {
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return NODE_ACCESS_DENY;
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}
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}
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if ($op == 'delete') {
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- if (!user_access('delete chado_project', $account)) {
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+ if (!user_access('delete chado_project content', $account)) {
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return NODE_ACCESS_DENY;
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}
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}
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if ($op == 'view') {
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- if (!user_access('access chado_project', $account)) {
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+ if (!user_access('access chado_project content', $account)) {
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return NODE_ACCESS_DENY;
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}
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}
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@@ -507,3 +507,188 @@ function tripal_project_node_view($node, $view_mode, $langcode) {
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break;
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}
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}
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+
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+/**
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+ * Implements hook_node_insert().
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+ * Acts on all content types.
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+ *
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+ * @ingroup tripal_project
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+ */
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+function tripal_project_node_insert($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 project_id in the presave
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+ switch ($node->type) {
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+ case 'chado_project':
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+
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+ // on an insert we need to add the project_id to the node object
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+ // so that the tripal_project_get_project_url function can set the URL properly
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+ $node->project_id = chado_get_id_from_nid('project', $node->nid);
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+
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+ // remove any previous alias
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+ db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
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+
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+ // set the URL for this project page
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+ $url_alias = tripal_project_get_project_url($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_project
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+ */
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+function tripal_project_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_project':
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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 project page
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+ $url_alias = tripal_project_get_project_url($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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+ * Return the url alias for a project
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+ *
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+ * @param $node
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+ * A node object containing at least the project_id and nid
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+ * @param $url_alias
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+ * Optional. This should be the URL alias syntax string that contains
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+ * placeholders such as [id] and [name]. These placeholders will be substituted for actual values.
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+ * If this parameter is not provided then the value of the
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+ * chado_project_url_string Drupal variable will be used.
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+ *
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+ * @ingroup tripal_project
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+ */
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+function tripal_project_get_project_url($node, $url_alias = NULL) {
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+ $length_project_name = 100;
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+
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+ // get the starting URL alias
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+ if(!$url_alias) {
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+ $url_alias = variable_get('chado_project_url_string', '/project/[id]');
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+ if (!$url_alias) {
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+ $url_alias = '/project/[id]';
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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 project
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+ $values = array('project_id' => $node->project_id);
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+ $project = chado_select_record('project', array('*'), $values);
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+ if (!$project) {
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+ tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find project when setting URL alias for project: %id", array('%id' => $node->project_id));
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+ return FALSE;
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+ }
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+ $project = (object) $project[0];
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+
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+ // Sanitize project name
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+ $project_name = str_replace(' ','-', $project->name);
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+ $project_name = str_replace(',','', $project_name);
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+ $project_name = str_replace('&','and', $project_name);
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+ $project_name = substr($project_name, 0, $length_project_name);
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+
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+ // now substitute in the values
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+ $url_alias = preg_replace('/\[id\]/', $project->project_id, $url_alias);
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+ $url_alias = preg_replace('/\[name\]/', $project_name, $url_alias);
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+
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+ // the dst field of the url_alias table is only 128 characters long.
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+ // if this is the case then simply return the node URL, we can't set this one
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+ if (strlen($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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+
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+/**
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+ * Resets all of the URL alias for all projects. This function is meant to
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+ * be run using Tripal's job managmenet interface
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+ *
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+ * @param $na
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+ * Tripal expects all jobs to have at least one argument. For this function
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+ * we don't need any, so we have this dummy argument as a filler
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+ * @param $job_id
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+ *
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+ * @ingroup tripal_project
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+ */
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+function tripal_project_set_urls($na = NULL, $job = NULL) {
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+
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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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+ $csql = "SELECT count(*) FROM {chado_project}";
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+ $num_nodes = db_query($csql)->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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+ // prepare the statements which will quickly add url alias. Because these
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+ // are not Chado tables we must manually prepare them
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+ $dsql = "DELETE FROM {url_alias} WHERE source = :source";
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+ $isql = "INSERT INTO url_alias (source, alias, language) VALUES (:source, :alias, :language)";
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+
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+ // get the URL alias syntax string
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+ $url_alias = variable_get('chado_project_url_string', '/project/[id]');
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+ $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
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+
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+ // get the list of projects that have been synced
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+ $sql = "SELECT * FROM {chado_project}";
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+ $nodes = db_query($sql);
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+ foreach ($nodes as $node) {
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+
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+ // get the URL alias
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+ $src = "node/$node->nid";
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+ $dst = tripal_project_get_project_url($node, $url_alias);
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+
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+ // if the src and dst is the same (the URL alias couldn't be set)
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+ // then skip to the next one. There's nothing we can do about this one.
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+ if($src == $dst) {
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+ continue;
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+ }
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+
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+ // remove any previous alias and then add the new one
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+ db_query($dsql, array(':source' => $src));
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+ db_query($isql, array(':source' => $src, ':alias' => $dst, ':language' => LANGUAGE_NONE));
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+
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+ // update the job status every 1% projects
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+ if ($job and $num_set % $num_per_interval == 0) {
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+ $percent = ($num_set / $num_nodes) * 100;
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+ tripal_job_set_progress($job, 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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+
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+ }
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+ $num_set++;
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+ }
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+ $percent = ($num_set / $num_nodes) * 100;
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+ tripal_job_set_progress($job, 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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+ }
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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('tripal_project', $e);
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+ watchdog('trp-seturl', "Failed Removing URL Alias: %src", array('%src' => $src), WATCHDOG_ERROR);
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+ }
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+}
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Lacey Sanderson