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@@ -75,113 +75,124 @@ function tripal_pub_menu() {
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$items['find/publications/criteria/%/%'] = array(
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'page callback' => 'tripal_pub_search_page_update_criteria',
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'page arguments' => array(5, 6),
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- 'access arguments' => array('access chado_pub content'),
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+ 'access arguments' => array('access chado_pub content'),
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'type ' => MENU_CALLBACK,
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);
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- $items['admin/tripal/tripal_pub']= array(
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+ $items['admin/tripal/chado/tripal_pub']= array(
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'title' => 'Publications',
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+ 'description' => ('A documented provenance artefact - publications, documents, personal communication.'),
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+ 'page callback' => 'tripal_pub_admin_pub_view',
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+ 'access arguments' => array('administer tripal pubs'),
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+ 'type' => MENU_NORMAL_ITEM
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+ );
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+
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+ $items['admin/tripal/chado/tripal_pub/help']= array(
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+ 'title' => 'Help',
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'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
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'page callback' => 'theme',
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'page arguments' => array('tripal_pub_help'),
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'access arguments' => array('administer tripal pubs'),
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- 'type' => MENU_NORMAL_ITEM
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+ 'type' => MENU_LOCAL_TASK,
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+ 'weight' => 10
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);
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- $items['admin/tripal/tripal_pub/configuration'] = array(
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- 'title' => 'Configuration',
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+ $items['admin/tripal/chado/tripal_pub/configuration'] = array(
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+ 'title' => 'Settings',
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'description' => 'Configure the Tripal publication module.',
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'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_pub_help'),
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+ 'page arguments' => array('tripal_pub_admin'),
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'access arguments' => array('administer tripal pubs'),
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- 'type' => MENU_NORMAL_ITEM,
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+ 'type' => MENU_LOCAL_TASK,
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+ 'weight' => 5
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);
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- $items['admin/tripal/tripal_pub/sync'] = array(
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- 'title' => ' Sync Publications',
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+ $items['admin/tripal/chado/tripal_pub/sync'] = array(
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+ 'title' => ' Sync',
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'description' => 'Sync publications in Chado with Drupal',
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'page callback' => 'drupal_get_form',
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'page arguments' => array('tripal_pub_sync_form'),
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'access arguments' => array('administer tripal pubs'),
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- 'type' => MENU_NORMAL_ITEM,
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+ 'type' => MENU_LOCAL_TASK,
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+ 'weight' => 2
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);
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-
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- $items['admin/tripal/tripal_pub/import_list'] = array(
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- 'title' => t('Importers List'),
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+ $items['admin/tripal/chado/tripal_pub/import_list'] = array(
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+ 'title' => t('Importers'),
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'description' => t('List all publication importers'),
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'page callback' => 'tripal_pub_importers_list',
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'access arguments' => array('administer tripal pubs'),
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- 'type ' => MENU_CALLBACK,
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+ 'type' => MENU_LOCAL_TASK,
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+ 'weight' => 0
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);
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- $items['admin/tripal/tripal_pub/import/new'] = array(
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+ $items['admin/tripal/chado/tripal_pub/import/new'] = array(
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'title' => t('Add an Importer'),
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'description' => t('Add a new publication importer.'),
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'page callback' => 'tripal_pub_importer_setup',
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- 'page arguments' => array(4, NULL),
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+ 'page arguments' => array(5, NULL),
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'access arguments' => array('administer tripal pubs'),
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'type ' => MENU_CALLBACK,
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);
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- $items['admin/tripal/tripal_pub/import/raw/%'] = array(
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+ $items['admin/tripal/chado/tripal_pub/import/raw/%'] = array(
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'page callback' => 'tripal_pub_get_raw_data',
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'page arguments' => array(5),
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'access arguments' => array('administer tripal pubs'),
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'type ' => MENU_CALLBACK,
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);
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- $items['admin/tripal/tripal_pub/import/edit/%'] = array(
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+ $items['admin/tripal/chado/tripal_pub/import/edit/%'] = array(
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'page callback' => 'tripal_pub_importer_setup',
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'page arguments' => array(4, 5),
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'access arguments' => array('administer tripal pubs'),
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'type ' => MENU_CALLBACK,
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);
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- $items['admin/tripal/tripal_pub/import/delete/%'] = array(
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+ $items['admin/tripal/chado/tripal_pub/import/delete/%'] = array(
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'page callback' => 'tripal_pub_importer_delete',
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'page arguments' => array(5),
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'access arguments' => array('administer tripal pubs'),
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'type ' => MENU_CALLBACK,
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);
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- $items['admin/tripal/tripal_pub/import/changedb'] = array(
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+ $items['admin/tripal/chado/tripal_pub/import/changedb'] = array(
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'page callback' => 'tripal_pub_importer_setup_page_update_remotedb',
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'page arguments' => array(),
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- 'access arguments' => array('administer tripal pubs'),
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+ 'access arguments' => array('administer tripal pubs'),
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'type ' => MENU_CALLBACK,
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);
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- $items['admin/tripal/tripal_pub/import/criteria/%/%'] = array(
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+ $items['admin/tripal/chado/tripal_pub/import/criteria/%/%'] = array(
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'page callback' => 'tripal_pub_importer_setup_page_update_criteria',
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'page arguments' => array(5, 6),
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- 'access arguments' => array('administer tripal pubs'),
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+ 'access arguments' => array('administer tripal pubs'),
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'type ' => MENU_CALLBACK,
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);
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- $items['tripal_pub/properties/add'] = array(
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+ $items['tripal_pub/chado/properties/add'] = array(
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'page callback' => 'tripal_pub_property_add',
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'access arguments' => array('edit chado_pub content'),
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'type ' => MENU_CALLBACK,
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);
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- $items['tripal_pub/properties/description'] = array(
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+ $items['tripal_pub/chado/properties/description'] = array(
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'page callback' => 'tripal_pub_property_get_description',
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'access arguments' => array('edit chado_pub content'),
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'type ' => MENU_CALLBACK,
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);
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- $items['tripal_pub/properties/minus/%/%'] = array(
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+ $items['tripal_pub/chado/properties/minus/%/%'] = array(
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'page callback' => 'tripal_pub_property_delete',
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'page arguments' => array(3, 4),
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'access arguments' => array('edit chado_pub content'),
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'type ' => MENU_CALLBACK,
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);
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- $items['admin/tripal/tripal_pub/citation'] = array(
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+ $items['admin/tripal/chado/tripal_pub/citation'] = array(
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'title' => ' Create Citations',
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'description' => 'Create citations in Chado with Drupal',
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'page callback' => 'drupal_get_form',
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'page arguments' => array('tripal_pub_citation_form'),
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'access arguments' => array('administer tripal pubs'),
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- 'type' => MENU_NORMAL_ITEM,
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+ 'type' => MENU_CALLBACK,
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);
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return $items;
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@@ -253,9 +264,9 @@ function tripal_pub_theme() {
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// instructions page for the pub module
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'tripal_pub_help' => array(
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- 'template' => 'tripal_pub_help',
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- 'arguments' => array(NULL),
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- 'path' => $theme_path,
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+ 'template' => 'tripal_pub_help',
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+ 'arguments' => array(NULL),
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+ 'path' => $theme_path,
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),
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// themed forms
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@@ -282,6 +293,21 @@ function tripal_pub_help ($path, $arg) {
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return theme('tripal_pub_help', array());
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}
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}
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+
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+/**
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+ * Implements hook_views_api()
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+ * Purpose: Essentially this hook tells drupal that there is views support for
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+ * for this module which then includes tripal_db.views.inc where all the
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+ * views integration code is
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+ *
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+ * @ingroup tripal_pub
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+ */
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+function tripal_pub_views_api() {
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+ return array(
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+ 'api' => 3.0,
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+ );
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+}
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+
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/**
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* Implement hook_permissions().
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*/
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@@ -315,7 +341,7 @@ function tripal_pub_permissions() {
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* Implement hook_access().
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*
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* This hook allows node modules to limit access to the node types they define.
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- *
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+ *
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* @param $node
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* The node on which the operation is to be performed, or, if it does not yet exist, the
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* type of node to be created
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@@ -329,7 +355,7 @@ function tripal_pub_permissions() {
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* @return
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* If the permission for the specified operation is not set then return FALSE. If the
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* permission is set then return NULL as this allows other modules to disable
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- * access. The only exception is when the $op == 'create'. We will always
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+ * access. The only exception is when the $op == 'create'. We will always
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* return TRUE if the permission is set.
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*
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*/
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@@ -379,7 +405,7 @@ function chado_pub_insert($node) {
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// we need an array suitable for the tripal_pub_create_citation() function
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// to automatically generate a citation if a uniquename doesn't already exist
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$pub_arr = array();
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-
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+
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// if a pub_id already exists for this node then it already exists in Chado and
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// we get here because we are syncing the node. Therefore, we can skip the insert
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// but we always want to set the URL path alias to be the Chado pub ID
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@@ -398,9 +424,9 @@ function chado_pub_insert($node) {
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INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
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INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
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INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
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- WHERE CV.name = 'tripal_pub' and CVTO.name = 'Publication Details' and
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+ WHERE CV.name = 'tripal_pub' and CVTO.name = 'Publication Details' and
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NOT CVTS.is_obsolete = 1
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- ORDER BY CVTS.name ASC
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+ ORDER BY CVTS.name ASC
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";
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$prop_types = chado_query($sql);
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while ($prop = $prop_types->fetchObject()) {
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@@ -434,12 +460,12 @@ function chado_pub_insert($node) {
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// iterate through all of the properties and remove those that really are
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// part of the pub table fields
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- foreach ($properties as $name => $element) {
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+ foreach ($properties as $name => $element) {
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$value = trim($element[0]);
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-
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+
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// populate our $pub_array for building a citation
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$pub_arr[$name] = $value;
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-
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+
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// remove properties that are stored in the pub table
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if ($name == "Volume") {
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$volume = $value;
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@@ -475,7 +501,7 @@ function chado_pub_insert($node) {
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$cross_refs[] = $value;
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}
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}
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- // generate a citation for this pub if one doesn't already exist
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+ // generate a citation for this pub if one doesn't already exist
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if (!$node->uniquename and array_key_exists('Citation', $properties)) {
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$pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
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$pub_arr['Title'] = $node->pubtitle;
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@@ -484,20 +510,20 @@ function chado_pub_insert($node) {
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$node->uniquename = tripal_pub_create_citation($pub_arr);
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$properties['Citation'][0] = $node->uniquename;
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}
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-
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+
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// insert the pub record
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$values = array(
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'title' => trim($node->pubtitle),
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'series_name' => substr(trim($node->series_name), 0, 255),
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'type_id' => trim($node->type_id),
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'pyear' => trim($node->pyear),
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- 'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
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+ 'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
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'uniquename' => trim($node->uniquename),
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'volumetitle' => $volumetitle,
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- 'volume' => $volume,
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- 'issue' => $issue,
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+ 'volume' => $volume,
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+ 'issue' => $issue,
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'pages' => $pages,
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- 'miniref' => substr($miniref, 0, 255),
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+ 'miniref' => substr($miniref, 0, 255),
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'publisher' => substr($publisher, 0, 255),
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'pubplace' => substr($pubplace, 0, 255),
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);
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@@ -511,7 +537,7 @@ function chado_pub_insert($node) {
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// now add in the properties
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foreach ($properties as $property => $elements) {
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foreach ($elements as $rank => $value) {
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-
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+
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$status = tripal_pub_insert_property($pub['pub_id'], $property, $value, FALSE);
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if (!$status) {
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drupal_set_message("Error cannot add property: $property", "error");
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@@ -568,7 +594,7 @@ function chado_pub_update($node) {
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// there is no way to handle revisions in Chado but leave
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// this here just to make not we've addressed it.
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}
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-
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+
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// we need an array suitable for the tripal_pub_create_citation() function
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// to automatically generate a citation if a uniquename doesn't already exist
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$pub_arr = array();
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@@ -578,7 +604,7 @@ function chado_pub_update($node) {
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$properties = array(); // stores all of the properties we need to add
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$cross_refs = array(); // stores any cross references for this publication
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-
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+
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// get the list of properties for easy lookup (without doing lots of database queries
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$properties_list = array();
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$sql = "
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@@ -587,10 +613,10 @@ function chado_pub_update($node) {
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INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
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INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
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INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
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- WHERE CV.name = 'tripal_pub' and
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- (CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and
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+ WHERE CV.name = 'tripal_pub' and
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+ (CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and
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NOT CVTS.is_obsolete = 1
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- ORDER BY CVTS.name ASC
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+ ORDER BY CVTS.name ASC
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";
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$prop_types = chado_query($sql);
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while ($prop = $prop_types->fetchObject()) {
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@@ -635,7 +661,7 @@ function chado_pub_update($node) {
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foreach ($element as $index => $value) {
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// populate our $pub_array for building a citation
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$pub_arr[$name] = $value;
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-
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+
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// remove properties that are stored in the pub table
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if ($name == "Volume") {
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$volume = $value;
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@@ -672,7 +698,7 @@ function chado_pub_update($node) {
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}
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}
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}
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- // generate a citation for this pub if one doesn't already exist
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+ // generate a citation for this pub if one doesn't already exist
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if (!$node->uniquename) {
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$pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
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$pub_arr['Title'] = $node->pubtitle;
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@@ -690,14 +716,14 @@ function chado_pub_update($node) {
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'title' => trim($node->pubtitle),
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'type_id' => trim($node->type_id),
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'pyear' => trim($node->pyear),
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- 'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
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+ 'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
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'uniquename' => trim($node->uniquename),
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'series_name' => trim($node->series_name),
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'volumetitle' => $volumetitle,
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- 'volume' => $volume,
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- 'issue' => $issue,
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+ 'volume' => $volume,
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+ 'issue' => $issue,
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'pages' => $pages,
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- 'miniref' => $miniref,
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+ 'miniref' => $miniref,
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'publisher' => $publisher,
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'pubplace' => $pubplace,
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);
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@@ -815,10 +841,10 @@ function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
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// the form to the ahah callback URL. We need to set it back
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// to the normal form URL
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if ($form_state['values']['action'] == 'edit') {
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- $form['#action'] = url("admin/tripal/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
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+ $form['#action'] = url("admin/tripal/chado/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
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}
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if ($form_state['values']['action'] == 'new') {
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- $form['#action'] = url("admin/tripal/tripal_pub/import/new");
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+ $form['#action'] = url("admin/tripal/chado/tripal_pub/import/new");
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}
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}
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if ($form_id == "tripal_pub_search_form") {
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@@ -923,7 +949,7 @@ function tripal_pub_mail($key, &$message, $params) {
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}
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/**
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- *
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+ *
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* @param $node
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*/
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function tripal_pub_node_insert($node) {
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@@ -939,7 +965,7 @@ function tripal_pub_node_insert($node) {
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}
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}
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/**
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- *
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+ *
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* @param $node
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* @param $types
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*/
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@@ -968,7 +994,7 @@ function tripal_pub_node_update($node) {
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// node that will still work too (e.g. http://[base url]/node/[node id]
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// so the nodeapi function ensures that the URL path is set after insert or update
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// of the node and when the node is loaded if it hasn't yet been set.
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- if ($node->type == 'chado_pub') {
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+ if ($node->type == 'chado_pub') {
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$pub_id = chado_get_id_for_node('pub', $node->nid);
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tripal_pub_set_pub_url($node, $pub_id);
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}
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Stephen Ficklin