Added configuration page to tripal_pub module

tripal_feature/tripal_feature.module

@@ -164,8 +164,8 @@ function tripal_feature_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_feature/configuration'] = array(
-    'title' => 'Feature Configuration',
-    'description' => 'Settings for Chado Features',
+    'title' => 'Configuration',
+    'description' => 'Configure the Tripal Feature module.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_admin'),
     'access arguments' => array('administer tripal features'),

tripal_library/tripal_library.module

@@ -117,8 +117,8 @@ function tripal_library_menu() {
   );
 
   $items['admin/tripal/tripal_library/configuration'] = array(
-    'title' => 'Library Configuration',
-    'description' => 'Manage integration of Chado libraries including associated features.',
+    'title' => 'Configuration',
+    'description' => 'Configure the Tripal Library module',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_library_admin'),
     'access arguments' => array('administer tripal libraries'),

tripal_pub/includes/pub_form.inc

@@ -253,7 +253,7 @@ function chado_pub_node_form_add_new_props(&$form, $form_state, $num_new, &$d_pr
         if (preg_match('/Abstract/', $cvterm[0]->name)) {
           $rows = 10;
         }
-        if ($cvterm[0]->name == 'Author List') {
+        if ($cvterm[0]->name == 'Authors') {
           $rows = 2;
         }
         
@@ -310,7 +310,7 @@ function chado_pub_node_form_add_new_props(&$form, $form_state, $num_new, &$d_pr
     if (preg_match('/Abstract/', $cvterm[0]->name)) {
       $rows = 10;
     }
-    if ($cvterm[0]->name == 'Author List') {
+    if ($cvterm[0]->name == 'Authors') {
       $rows = 2;
     }
     
@@ -397,7 +397,7 @@ function chado_pub_node_form_add_pubprop_table_props(&$form, $form_state, $pub_i
     if (preg_match('/Abstract/', $prop->name)) {
       $rows = 10;
     }
-    if ($prop->name == 'Author List') {
+    if ($prop->name == 'Authors') {
       $rows = 2;
     }
   
@@ -480,7 +480,7 @@ function chado_pub_node_form_add_pub_table_props(&$form, $form_state, $propertie
       if (preg_match('/Abstract/', $prop->name)) {
         $rows = 10;
       }
-      if ($prop->name == 'Author List') {
+      if ($prop->name == 'Authors') {
         $rows = 2;
       }
       

tripal_pub/includes/pub_importers.inc

@@ -0,0 +1,490 @@
+<?php
+/**
+ * A function to render a listing of all publication importers
+ *
+ * @ingroup tripal_pub
+ */
+function tripal_pub_importers_list() {
+  $header = array('', 'Importer Name', 'Database', 'Search String', 'Disabled', 'Create Contact', '');
+  $rows = array();
+  $importers = db_query("SELECT * FROM {tripal_pub_import} ORDER BY name");    
+
+  while ($importer = db_fetch_object($importers)) {
+    $criteria = unserialize($importer->criteria);
+    $num_criteria = $criteria['num_criteria'];
+    $criteria_str = '';
+    for ($i = 0; $i <= $num_criteria; $i++) {
+      $search_terms = $criteria['criteria'][$i]['search_terms'];
+      $scope = $criteria['criteria'][$i]['scope'];
+      $operation = $criteria['criteria'][$i]['operation'];
+      $criteria_str .= "$operation ($scope: $search_terms) ";
+    }
+ 
+    $rows[] = array(
+      l(t('Edit/Test'), "admin/tripal/tripal_pub/import/edit/$importer->pub_import_id"),
+      $importer->name,
+      $criteria['remote_db'],
+      $criteria_str,
+      $importer->disabled ? 'Yes' : 'No',
+      $importer->do_contact ? 'Yes' : 'No',
+      l(t('Delete'), "admin/tripal/tripal_pub/import/delete/$importer->pub_import_id"),
+    );
+  }
+
+  $rows[] = array(
+    'data' => array(
+      array('data' => l(t('Create a new publication importer.'), "admin/tripal/tripal_pub/import/new"),
+        'colspan' => 7),
+    )
+  );
+
+  $page = theme('table', $header, $rows);
+  return $page;
+}
+
+/*
+ * 
+ */
+function tripal_pub_importer_setup($action = 'new', $pub_import_id = NULL) {
+  global $pager_total, $pager_total_items;
+  
+  $pager_id = 0;
+  $limit = 10;
+  
+  // generate the search form 
+  $form = drupal_get_form('tripal_pub_importer_setup_form',  $pub_import_id, $action);
+  
+  $output = l("Return to publication importers list", "admin/tripal/tripal_pub/import_list");
+  $output .= $form;
+
+  // retrieve any results
+  $remote_db = $_SESSION['tripal_pub_search']['remote_db'];
+  $num_criteria = $_SESSION['tripal_pub_search']['num_criteria'];
+  $days = $_SESSION['tripal_pub_search']['days'];
+ 
+  $search_array = array();
+  $search_array['remote_db'] = $remote_db;
+  $search_array['num_criteria'] = $num_criteria;
+  $search_array['days'] = $days; 
+  for ($i = 0; $i <= $num_criteria; $i++) {
+    $search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'];
+    $search_array['criteria'][$i]['scope'] = $_SESSION['tripal_pub_search']['criteria'][$i]['scope'];  
+    $search_array['criteria'][$i]['operation'] = $_SESSION['tripal_pub_search']['criteria'][$i]['operation'];
+  }
+  
+    
+  if ($_SESSION['tripal_pub_search']['perform_search']) {
+    // get the list of publications from the remote database using the search criteria.  
+    $pubs = tripal_pub_get_remote_search_results($remote_db, $search_array, $limit, $pager_id);
+  
+    // generate the pager
+    $total_pages = $pager_total[$pager_id];
+    $total_items = $pager_total_items[$pager_id];
+    $page = isset($_GET['page']) ? $_GET['page'] : '0';
+    $pager = theme('pager');
+    
+    // iterate through the results and construct the table displaying the publications
+    $rows = array();
+    $i = $page * $limit + 1;
+    if (count($pubs) > 0) {
+      foreach ($pubs as $pub) {
+        $rows[] = array(number_format($i), $pub['Citation']);
+        $i++;
+      }
+    }
+    $headers = array('', 'Citation');
+    $table = theme('table', $headers, $rows);   
+  
+    // join all to form the results
+    $output .= "<br><p><b>Found " . number_format($total_items) .  
+      ". Page " . ($page + 1) . " of $total_pages. " .
+      " Results</b></br>" . $table . '</p>' . $pager;    
+  }
+  return $output;
+}
+/*
+ * 
+ */
+function theme_tripal_pub_importer_setup_form($form) {
+  $rows = array();
+  foreach ($form['criteria'] as $i => $element) {
+    if(is_numeric($i)) {
+      $rows[] = array(  
+        array('data' => drupal_render($element["operation-$i"]), 'width' => '10%'),    
+        array('data' => drupal_render($element["scope-$i"]), 'width' => '10%'),
+        drupal_render($element["search_terms-$i"]),
+        array('data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]), 'width' => '5%'),
+      );
+    }
+  } 
+  $headers = array('Operation','Scope', 'Search Terms', '');
+  
+  $markup  = '<div id="pub-search-form-row1">';
+  $markup .= '  <div id="pub-search-form-col1">' . drupal_render($form['loader_name']) . '</div>';
+  $markup .= '  <div id="pub-search-form-col2">' . drupal_render($form['remote_db']) . '</div>';
+  $markup .= '  <div id="pub-search-form-col3">' . drupal_render($form['days']) . '</div>';
+  $markup .= '</div>';
+  $markup .= '<div id="pub-search-form-row2">' . drupal_render($form['disabled']) . '</div>'; 
+  $markup .= '<div id="pub-search-form-row3">' . drupal_render($form['do_contact']) . '</div>';
+  $markup .= theme('table', $headers, $rows);
+  
+  $form['criteria'] = array(
+    '#type' => 'markup',
+    '#value' =>  $markup,
+    '#weight' => -10,
+  );
+  return drupal_render($form);
+}
+/**
+ * Purpose: Provides the form to search pubmed
+ *
+  * @ingroup tripal_pub
+ */
+function tripal_pub_importer_setup_form(&$form_state = NULL, $pub_import_id = NULL, $action = 'new') {
+  tripal_core_ahah_init_form();
+
+  dpm($form_state);
+  
+  // Set the default values. If the pub_import_id isn't already defined by the form values 
+  // and one is provided then look it up in the database
+  $criteria = NULL;
+  if ($action == "edit" and !$form_state['values']) {
+    $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = %d";
+    $importer = db_fetch_object(db_query($sql, $pub_import_id));
+    
+    $criteria       = unserialize($importer->criteria);
+    $remote_db      = $criteria['remote_db'];
+    $days           = $criteria['days'];
+    $disabled       = $criteria['disabled'];
+    $do_contact     = $criteria['do_contact'];
+    $num_criteria   = $criteria['num_criteria'];    
+    $loader_name    = $criteria['loader_name'];  
+  }
+
+  // if the session has variables then use those.  This should only happen when
+  // the 'Test Criteria' button is clicked.
+  $num_criteria = $_SESSION['tripal_pub_search']['num_criteria'] ? $_SESSION['tripal_pub_search']['num_criteria'] : $num_criteria;    
+  $loader_name  = $_SESSION['tripal_pub_search']['loader_name']  ? $_SESSION['tripal_pub_search']['loader_name']  : $loader_name;
+  $remote_db    = $_SESSION['tripal_pub_search']['remote_db']    ? $_SESSION['tripal_pub_search']['remote_db']    : $remote_db;
+  $disabled     = $_SESSION['tripal_pub_search']['disabled']     ? $_SESSION['tripal_pub_search']['disabled']     : $disabled;    
+  $do_contact   = $_SESSION['tripal_pub_search']['do_contact']   ? $_SESSION['tripal_pub_search']['do_contact']   : $do_contact;
+  $days         = $_SESSION['tripal_pub_search']['days']         ? $_SESSION['tripal_pub_search']['days']         : $days;    
+  
+  
+  // If the form_state has variables then use those.  This happens when an error occurs on the form or the 
+  // form is resbumitted using AJAX
+  $num_criteria = $form_state['values']['num_criteria'] ? $form_state['values']['num_criteria'] : $num_criteria;    
+  $loader_name  = $form_state['values']['loader_name']  ? $form_state['values']['loader_name']  : $loader_name;
+  $remote_db    = $form_state['values']['remote_db']    ? $form_state['values']['remote_db']    : $remote_db;
+  $disabled     = $form_state['values']['disabled']     ? $form_state['values']['disabled']     : $disabled;
+  $do_contact   = $form_state['values']['do_contact']   ? $form_state['values']['do_contact']   : $do_contact;
+  $days         = $form_state['values']['days']         ? $form_state['values']['days']         : $days;    
+  
+   
+  // change the number of criteria based on form_state post data.
+  if (!$num_criteria) {
+    $num_criteria = 0;
+  }
+  if($form_state['post']["add-$num_criteria"]) {    
+    $num_criteria++;
+  }
+  if($form_state['post']["remove-$num_criteria"]) {    
+    $num_criteria--;
+  }
+  
+  $form['pub_import_id'] = array(
+    '#type'          => 'hidden',
+    '#value'         => $pub_import_id,
+    '#required'      => TRUE,
+  );
+  $form['action'] = array(
+    '#type'          => 'hidden',
+    '#value'         => $action,
+    '#required'      => TRUE,
+  );
+  
+  $form['loader_name'] = array(
+    '#type'          => 'textfield',
+    '#title'         => t('Loader Name'),
+    '#description'   => t('Please provide a name for this loader setup..'),
+    '#default_value' => $loader_name,
+    '#required'      => TRUE,
+  );
+   
+  $remote_dbs = array('PMID' => 'Pubmed');
+  $form['remote_db'] = array(
+    '#title' => t('Remote Database'),
+    '#type' => 'select',
+    '#options' => $remote_dbs,
+    '#default_value' => $remote_db,
+  );
+
+  $form['num_criteria']= array(
+    '#type'          => 'hidden',
+    '#default_value' => $num_criteria,
+  );
+  $form['pub_import_id']= array(
+    '#type'          => 'hidden',
+    '#default_value' => $pub_import_id,
+  );
+  
+  $form['days'] = array(
+    '#type'          => 'textfield',
+    '#title'         => t('Days'),
+    '#description'   => t('The number of days from today to search.'),
+    '#default_value' => $days,
+    '#size'          => 5,
+  );
+  $form['disabled'] = array(
+    '#type'          => 'checkbox',
+    '#title'         => t('Disabled'),
+    '#description'   => t('Check to disable this importer.'),
+    '#default_value' => $disabled,
+  );
+  $form['do_contact'] = array(
+    '#type'          => 'checkbox',
+    '#title'         => t('Create Contact'),
+    '#description'   => t('Check to create an entry in the contact table for each author of a matching publication during import. This allows storage of 
+       additional information such as affilation, etc. Otherwise, only authors names are retrieved.'),
+    '#default_value' => $do_contact,
+  );
+  
+  for($i = 0; $i <= $num_criteria; $i++) {
+    // if we have criteria supplied from the database then use that, othrewise look from the form_state or the session
+    if ($criteria) {
+      $search_terms = $criteria['criteria'][$i]['search_terms'];
+      $scope = $criteria['criteria'][$i]['scope'];
+      $operation = $criteria['criteria'][$i]['operation'];
+    }
+    // first populate defaults using any values in the SESSION variable
+    $search_terms = $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'] ? $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'] : $search_terms;
+    $scope        = $_SESSION['tripal_pub_search']['criteria'][$i]['scope']        ? $_SESSION['tripal_pub_search']['criteria'][$i]['scope']        : $scope;
+    $operation    = $_SESSION['tripal_pub_search']['criteria'][$i]['operation']    ? $_SESSION['tripal_pub_search']['criteria'][$i]['operation']    : $operation;
+    
+    // next populate defaults using any form values
+    $search_terms = $form_state['values']["search_terms-$i"] ? $form_state['values']["search_terms-$i"] : $search_terms;
+    $scope        = $form_state['values']["scope-$i"]        ? $form_state['values']["scope-$i"]        : $scope;
+    $operation    = $form_state['values']["operation-$i"]    ? $form_state['values']["operation-$i"]    : $operation;
+    
+    // default to searching the title and abstract
+    if (!$scope) {
+      $scope = 'abstract';
+    }
+  
+    $form['criteria'][$i]["search_terms-$i"] = array(
+      '#type'          => 'textfield',
+      '#description'   => t('Please provide a list of words for searching. You may use conjunctions such as "AND" or "OR" to separate words if they are expected in the same scope"'),
+      '#default_value' => $search_terms,
+      '#required'      => TRUE,
+    );
+    $form['criteria'][$i]["scope-$i"] = array(
+      '#type'          => 'select',
+      '#description'   => t('Please select the fields to search for this term.'),
+      '#options'       => array(
+        'any'      => 'Any Field',
+        'title'    => 'Title',
+        'abstract' => 'Title/Abstract',
+        'author'   => 'Author'),
+      '#default_value' => $scope,
+    );    
+    
+    if ($i > 0) {
+      $form['criteria'][$i]["operation-$i"] = array(
+        '#type'          => 'select',
+        '#options'       => array(
+          'AND' => 'AND',
+          'OR'  => 'OR',
+          'NOT' => 'NOT'),
+        '#default_value' => $operation,
+      );
+    }
+    if ($i == $num_criteria) {    
+      if($i > 0) {
+        $form['criteria'][$i]["remove-$i"] = array(
+          '#type'         => 'image_button',
+          '#value'        => t('Remove'),
+          '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
+          '#ahah' => array(
+            'path'    => "admin/tripal/tripal_pub/import/criteria/minus/$i",
+            'wrapper' => 'tripal-pub-importer-setup-form',
+            'event'   => 'click',
+            'method'  => 'replace',
+          ), 
+          '#attributes' => array('onClick' => 'return false;'),
+        );
+      }
+      $form['criteria'][$i]["add-$i"] = array(
+        '#type'         => 'image_button',      
+        '#value'        => t('Add'),
+        '#src'          => drupal_get_path('theme', 'tripal') . '/images/add.png',
+        '#ahah' => array(
+          'path'    => "admin/tripal/tripal_pub/import/criteria/add/$i",
+          'wrapper' => 'tripal-pub-importer-setup-form',
+          'event'   => 'click',
+          'method'  => 'replace',          
+        ),   
+        '#attributes' => array('onClick' => 'return false;'),
+      );
+    }
+  }
+  
+  $form['test'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Test Importer'),
+  );
+  $form['save'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Save Importer'),
+  );
+  $form['delete'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Delete Importer'),
+  );
+
+  return $form;
+}
+
+/**
+ *
+ */
+function tripal_pub_importer_setup_form_validate($form, &$form_state) {
+  $num_criteria = $form_state['values']['num_criteria'];
+  $remote_db =  $form_state['values']["remote_db"];
+  $days =  trim($form_state['values']["days"]);
+  $disabled =  $form_state['values']["disabled"];
+  $do_contact =  $form_state['values']["do_contact"];
+  $loader_name =  trim($form_state['values']["loader_name"]);
+
+  for ($i = 0; $i <= $num_criteria; $i++) {            
+    $search_terms =  trim($form_state['values']["search_terms-$i"]);
+    $scope =  $form_state['values']["scope-$i"];
+    $operation =  $form_state['values']["operation-$i"];
+    
+    if ($days and !is_numeric($days) or preg_match('/\./', $days)) {
+      form_set_error("days-$i", "Please enter a numeric, non decimal value, for the number of days.");
+    }
+  }
+}
+
+/**
+ *
+ */
+function tripal_pub_importer_setup_form_submit($form, &$form_state) {
+   
+  $pub_import_id = $form_state['values']['pub_import_id'];
+  $num_criteria = $form_state['values']['num_criteria'];
+  $remote_db =  $form_state['values']["remote_db"];
+  $days =  trim($form_state['values']["days"]);
+  $loader_name =  trim($form_state['values']["loader_name"]);
+  $disabled =  $form_state['values']["disabled"];
+  $do_contact =  $form_state['values']["do_contact"];
+
+  // set the session variables
+  $_SESSION['tripal_pub_search']['remote_db'] = $remote_db;
+  $_SESSION['tripal_pub_search']['days'] = $days;
+  $_SESSION['tripal_pub_search']['num_criteria'] = $num_criteria;
+  $_SESSION['tripal_pub_search']['loader_name'] = $loader_name;
+  $_SESSION['tripal_pub_search']['disabled'] = $disabled;
+  $_SESSION['tripal_pub_search']['do_contact'] = $do_contact;
+  unset($_SESSION['tripal_pub_search']['criteria']);
+  for ($i = 0; $i <= $num_criteria; $i++) {
+    $search_terms =  trim($form_state['values']["search_terms-$i"]);
+    $scope =  $form_state['values']["scope-$i"];
+    $operation =  $form_state['values']["operation-$i"];
+    
+    $_SESSION['tripal_pub_search']['criteria'][$i] = array(
+      'search_terms' => $search_terms,
+      'scope' => $scope,
+      'operation' => $operation
+    );
+  }
+
+  // now perform the appropriate action for the button clicked
+  if ($form_state['values']['op'] == 'Test Importer') {
+    $_SESSION['tripal_pub_search']['perform_search'] = 1;
+  }
+  if ($form_state['values']['op'] == 'Save Importer') {    
+    $record = array(
+      'name' => $loader_name,
+      'criteria' => serialize($_SESSION['tripal_pub_search']),
+      'disabled' => $disabled,
+      'do_contact' => $do_contact
+    );
+    // first check to see if this pub_import_id is already present. If so,
+    // do an update rather than an insert    
+    $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = %d";
+    $importer = db_fetch_object(db_query($sql, $pub_import_id));
+    if($importer) {
+      // do the update
+      $record['pub_import_id'] = $pub_import_id;
+      if(drupal_write_record('tripal_pub_import', $record, 'pub_import_id')){
+        unset($_SESSION['tripal_pub_search']);
+        drupal_set_message('Publication import settings updated.');
+        drupal_goto('admin/tripal/tripal_pub/import_list');       
+      }
+      else {
+        drupal_set_message('Could not update publication import settings.', 'error');
+      }
+    }     
+    else {         
+      // do the insert        
+      if(drupal_write_record('tripal_pub_import', $record)){
+        unset($_SESSION['tripal_pub_search']);
+        drupal_set_message('Publication import settings saved.');
+        drupal_goto('admin/tripal/tripal_pub/import_list');
+      }
+      else {
+        drupal_set_message('Could not save publication import settings.', 'error');
+      }
+    }    
+  }
+  if ($form_state['values']['op'] == 'Delete Importer') {
+    $sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = %d";
+    $success = db_query($sql, $pub_import_id);
+    if ($success) {
+      drupal_set_message('Publication importer deleted.');
+      drupal_goto('admin/tripal/tripal_pub/import_list');  
+    }
+    else {
+      drupal_set_message('Could not delete publication importer.', 'error');
+    }
+  }  
+}
+
+/*
+ * 
+ */
+function tripal_pub_importer_delete($pub_import_id) {
+  $sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = %d";
+  $success = db_query($sql, $pub_import_id);
+  if ($success) {
+    drupal_set_message('Publication importer deleted.');
+    drupal_goto('admin/tripal/tripal_pub/import_list');  
+  }
+  else {
+    drupal_set_message('Could not delete publication importer.', 'error');
+  }
+}
+/*
+ * AHAH callback
+ */
+function tripal_pub_importer_setup_page_update_criteria($action, $i) {
+  $status = TRUE;
+
+  // prepare and render the form
+  $form = tripal_core_ahah_prepare_form();   
+  $data = theme('tripal_pub_importer_setup_form', $form);  
+
+  // bind javascript events to the new objects that will be returned 
+  // so that AHAH enabled elements will work.
+  $settings = tripal_core_ahah_bind_events();
+
+  // return the updated JSON
+  drupal_json(
+    array(
+      'status'   => $status, 
+      'data'     => $data,
+      'settings' => $settings,
+    )  
+  );
+}

tripal_pub/includes/pubmed.inc

@@ -299,7 +299,7 @@ function tripal_pub_PMID_parse_pubxml($pub_xml) {
       }
     }
   }
-  $pub['Citation'] = $pub['Author List'] . 
+  $pub['Citation'] = $pub['Authors'] . 
     '. <a href="http://www.ncbi.nlm.nih.gov/pubmed/' . $pub['Publication Accession'] . '" target="_blank">' . $pub['Title'] .  '</a> ' .
     $pub['Journal ISO Abbreviation']. '. ' . $pub['Publication Date'];
   if ($pub['Volume'] or $pub['Issue']) {
@@ -708,7 +708,7 @@ function tripal_pub_PMID_parse_authorlist($xml, &$pub) {
           }             
         }
         $author_list = substr($author_list, 0, -2);
-        $pub['Author List'] = $author_list;
+        $pub['Authors'] = $author_list;
         return;
       }
       // if we're at the end </Author> element then we're done with the author and we can

tripal_pub/includes/tripal_pub.admin.inc

@@ -1,491 +1,95 @@
-<?php
+<?php 
 
 /**
- * A function to render a listing of all publication importers
+ * Administrative settings form
  *
  * @ingroup tripal_pub
  */
-function tripal_pub_importers_list() {
-  $header = array('', 'Importer Name', 'Database', 'Search String', 'Disabled', 'Create Contact', '');
-  $rows = array();
-  $importers = db_query("SELECT * FROM {tripal_pub_import} ORDER BY name");    
+function tripal_pub_admin() {
+  $form = array();
+
+  // before proceeding check to see if we have any
+  // currently processing jobs. If so, we don't want
+  // to give the opportunity to sync publications
+  $active_jobs = FALSE;
+  if (tripal_get_module_active_jobs('tripal_pub')) {
+    $active_jobs = TRUE;
+  }
 
-  while ($importer = db_fetch_object($importers)) {
-    $criteria = unserialize($importer->criteria);
-    $num_criteria = $criteria['num_criteria'];
-    $criteria_str = '';
-    for ($i = 0; $i <= $num_criteria; $i++) {
-      $search_terms = $criteria['criteria'][$i]['search_terms'];
-      $scope = $criteria['criteria'][$i]['scope'];
-      $operation = $criteria['criteria'][$i]['operation'];
-      $criteria_str .= "$operation ($scope: $search_terms) ";
-    }
- 
-    $rows[] = array(
-      l(t('Edit/Test'), "admin/tripal/tripal_pub/import/edit/$importer->pub_import_id"),
-      $importer->name,
-      $criteria['remote_db'],
-      $criteria_str,
-      $importer->disabled ? 'Yes' : 'No',
-      $importer->do_contact ? 'Yes' : 'No',
-      l(t('Delete'), "admin/tripal/tripal_pub/import/delete/$importer->pub_import_id"),
+  // add the field set for syncing publications
+  if (!$active_jobs) {
+    get_tripal_pub_admin_form_cleanup_set($form);
+  }
+  else {
+    $form['notice'] = array(
+     '#type' => 'fieldset',
+     '#title' => t('Publication Management Temporarily Unavailable')
+    );
+    $form['notice']['message'] = array(
+        '#value' => t('Currently, publication management jobs are waiting or are running. . Managemment features have been hidden until these jobs complete.  Please check back later once these jobs have finished.  You can view the status of pending jobs in the Tripal jobs page.'),
     );
   }
 
-  $rows[] = array(
-    'data' => array(
-      array('data' => l(t('Create a new publication importer.'), "admin/tripal/tripal_pub/import/new"),
-        'colspan' => 7),
-    )
-  );
-
-  $page = theme('table', $header, $rows);
-  return $page;
+  return system_settings_form($form);
 }
 
-/*
- * 
- */
-function tripal_pub_importer_setup($action = 'new', $pub_import_id = NULL) {
-  global $pager_total, $pager_total_items;
-  
-  $pager_id = 0;
-  $limit = 10;
-  
-  // generate the search form 
-  $form = drupal_get_form('tripal_pub_importer_setup_form',  $pub_import_id, $action);
-  
-  $output = l("Return to publication importers list", "admin/tripal/tripal_pub/import_list");
-  $output .= $form;
 
-  // retrieve any results
-  $remote_db = $_SESSION['tripal_pub_search']['remote_db'];
-  $num_criteria = $_SESSION['tripal_pub_search']['num_criteria'];
-  $days = $_SESSION['tripal_pub_search']['days'];
- 
-  $search_array = array();
-  $search_array['remote_db'] = $remote_db;
-  $search_array['num_criteria'] = $num_criteria;
-  $search_array['days'] = $days; 
-  for ($i = 0; $i <= $num_criteria; $i++) {
-    $search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'];
-    $search_array['criteria'][$i]['scope'] = $_SESSION['tripal_pub_search']['criteria'][$i]['scope'];  
-    $search_array['criteria'][$i]['operation'] = $_SESSION['tripal_pub_search']['criteria'][$i]['operation'];
-  }
-  
-    
-  if ($_SESSION['tripal_pub_search']['perform_search']) {
-    // get the list of publications from the remote database using the search criteria.  
-    $pubs = tripal_pub_get_remote_search_results($remote_db, $search_array, $limit, $pager_id);
-  
-    // generate the pager
-    $total_pages = $pager_total[$pager_id];
-    $total_items = $pager_total_items[$pager_id];
-    $page = isset($_GET['page']) ? $_GET['page'] : '0';
-    $pager = theme('pager');
-    
-    // iterate through the results and construct the table displaying the publications
-    $rows = array();
-    $i = $page * $limit + 1;
-    if (count($pubs) > 0) {
-      foreach ($pubs as $pub) {
-        $rows[] = array(number_format($i), $pub['Citation']);
-        $i++;
-      }
-    }
-    $headers = array('', 'Citation');
-    $table = theme('table', $headers, $rows);   
-  
-    // join all to form the results
-    $output .= "<br><p><b>Found " . number_format($total_items) .  
-      ". Page " . ($page + 1) . " of $total_pages. " .
-      " Results</b></br>" . $table . '</p>' . $pager;    
-  }
-  return $output;
-}
-/*
- * 
- */
-function theme_tripal_pub_importer_setup_form($form) {
-  $rows = array();
-  foreach ($form['criteria'] as $i => $element) {
-    if(is_numeric($i)) {
-      $rows[] = array(  
-        array('data' => drupal_render($element["operation-$i"]), 'width' => '10%'),    
-        array('data' => drupal_render($element["scope-$i"]), 'width' => '10%'),
-        drupal_render($element["search_terms-$i"]),
-        array('data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]), 'width' => '5%'),
-      );
-    }
-  } 
-  $headers = array('Operation','Scope', 'Search Terms', '');
-  
-  $markup  = '<div id="pub-search-form-row1">';
-  $markup .= '  <div id="pub-search-form-col1">' . drupal_render($form['loader_name']) . '</div>';
-  $markup .= '  <div id="pub-search-form-col2">' . drupal_render($form['remote_db']) . '</div>';
-  $markup .= '  <div id="pub-search-form-col3">' . drupal_render($form['days']) . '</div>';
-  $markup .= '</div>';
-  $markup .= '<div id="pub-search-form-row2">' . drupal_render($form['disabled']) . '</div>'; 
-  $markup .= '<div id="pub-search-form-row3">' . drupal_render($form['do_contact']) . '</div>';
-  $markup .= theme('table', $headers, $rows);
-  
-  $form['criteria'] = array(
-    '#type' => 'markup',
-    '#value' =>  $markup,
-    '#weight' => -10,
-  );
-  return drupal_render($form);
-}
 /**
- * Purpose: Provides the form to search pubmed
  *
-  * @ingroup tripal_pub
+ *
+ * @ingroup tripal_pub
  */
-function tripal_pub_importer_setup_form(&$form_state = NULL, $pub_import_id = NULL, $action = 'new') {
-  tripal_core_ahah_init_form();
-
-  dpm($form_state);
-  
-  // Set the default values. If the pub_import_id isn't already defined by the form values 
-  // and one is provided then look it up in the database
-  $criteria = NULL;
-  if ($action == "edit" and !$form_state['values']) {
-    $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = %d";
-    $importer = db_fetch_object(db_query($sql, $pub_import_id));
-    
-    $criteria       = unserialize($importer->criteria);
-    $remote_db      = $criteria['remote_db'];
-    $days           = $criteria['days'];
-    $disabled       = $criteria['disabled'];
-    $do_contact     = $criteria['do_contact'];
-    $num_criteria   = $criteria['num_criteria'];    
-    $loader_name    = $criteria['loader_name'];  
-  }
-
-  // if the session has variables then use those.  This should only happen when
-  // the 'Test Criteria' button is clicked.
-  $num_criteria = $_SESSION['tripal_pub_search']['num_criteria'] ? $_SESSION['tripal_pub_search']['num_criteria'] : $num_criteria;    
-  $loader_name  = $_SESSION['tripal_pub_search']['loader_name']  ? $_SESSION['tripal_pub_search']['loader_name']  : $loader_name;
-  $remote_db    = $_SESSION['tripal_pub_search']['remote_db']    ? $_SESSION['tripal_pub_search']['remote_db']    : $remote_db;
-  $disabled     = $_SESSION['tripal_pub_search']['disabled']     ? $_SESSION['tripal_pub_search']['disabled']     : $disabled;    
-  $do_contact   = $_SESSION['tripal_pub_search']['do_contact']   ? $_SESSION['tripal_pub_search']['do_contact']   : $do_contact;
-  $days         = $_SESSION['tripal_pub_search']['days']         ? $_SESSION['tripal_pub_search']['days']         : $days;    
-  
-  
-  // If the form_state has variables then use those.  This happens when an error occurs on the form or the 
-  // form is resbumitted using AJAX
-  $num_criteria = $form_state['values']['num_criteria'] ? $form_state['values']['num_criteria'] : $num_criteria;    
-  $loader_name  = $form_state['values']['loader_name']  ? $form_state['values']['loader_name']  : $loader_name;
-  $remote_db    = $form_state['values']['remote_db']    ? $form_state['values']['remote_db']    : $remote_db;
-  $disabled     = $form_state['values']['disabled']     ? $form_state['values']['disabled']     : $disabled;
-  $do_contact   = $form_state['values']['do_contact']   ? $form_state['values']['do_contact']   : $do_contact;
-  $days         = $form_state['values']['days']         ? $form_state['values']['days']         : $days;    
-  
-   
-  // change the number of criteria based on form_state post data.
-  if (!$num_criteria) {
-    $num_criteria = 0;
-  }
-  if($form_state['post']["add-$num_criteria"]) {    
-    $num_criteria++;
-  }
-  if($form_state['post']["remove-$num_criteria"]) {    
-    $num_criteria--;
-  }
-  
-  $form['pub_import_id'] = array(
-    '#type'          => 'hidden',
-    '#value'         => $pub_import_id,
-    '#required'      => TRUE,
-  );
-  $form['action'] = array(
-    '#type'          => 'hidden',
-    '#value'         => $action,
-    '#required'      => TRUE,
+function get_tripal_pub_admin_form_cleanup_set(&$form) {
+  $form['cleanup'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Clean Up')
   );
-  
-  $form['loader_name'] = array(
-    '#type'          => 'textfield',
-    '#title'         => t('Loader Name'),
-    '#description'   => t('Please provide a name for this loader setup..'),
-    '#default_value' => $loader_name,
-    '#required'      => TRUE,
+  $form['cleanup']['description'] = array(
+     '#type' => 'item',
+     '#value' => t("With Drupal and chado residing in different databases ".
+        "it is possible that nodes in Drupal and publications in Chado become ".
+        "\"orphaned\".  This can occur if an pub node in Drupal is ".
+        "deleted but the corresponding chado pub is not and/or vice ".
+        "versa. Click the button below to resolve these discrepancies."),
+     '#weight' => 1,
   );
-   
-  $remote_dbs = array('PMID' => 'Pubmed');
-  $form['remote_db'] = array(
-    '#title' => t('Remote Database'),
-    '#type' => 'select',
-    '#options' => $remote_dbs,
-    '#default_value' => $remote_db,
+  $form['cleanup']['button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Clean up orphaned publications'),
+    '#weight' => 2,
   );
-
-  $form['num_criteria']= array(
-    '#type'          => 'hidden',
-    '#default_value' => $num_criteria,
-  );
-  $form['pub_import_id']= array(
-    '#type'          => 'hidden',
-    '#default_value' => $pub_import_id,
-  );
-  
-  $form['days'] = array(
-    '#type'          => 'textfield',
-    '#title'         => t('Days'),
-    '#description'   => t('The number of days from today to search.'),
-    '#default_value' => $days,
-    '#size'          => 5,
-  );
-  $form['disabled'] = array(
-    '#type'          => 'checkbox',
-    '#title'         => t('Disabled'),
-    '#description'   => t('Check to disable this importer.'),
-    '#default_value' => $disabled,
-  );
-  $form['do_contact'] = array(
-    '#type'          => 'checkbox',
-    '#title'         => t('Create Contact'),
-    '#description'   => t('Check to create an entry in the contact table for each author of a matching publication during import. This allows storage of 
-       additional information such as affilation, etc. Otherwise, only authors names are retrieved.'),
-    '#default_value' => $do_contact,
-  );
-  
-  for($i = 0; $i <= $num_criteria; $i++) {
-    // if we have criteria supplied from the database then use that, othrewise look from the form_state or the session
-    if ($criteria) {
-      $search_terms = $criteria['criteria'][$i]['search_terms'];
-      $scope = $criteria['criteria'][$i]['scope'];
-      $operation = $criteria['criteria'][$i]['operation'];
-    }
-    // first populate defaults using any values in the SESSION variable
-    $search_terms = $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'] ? $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'] : $search_terms;
-    $scope        = $_SESSION['tripal_pub_search']['criteria'][$i]['scope']        ? $_SESSION['tripal_pub_search']['criteria'][$i]['scope']        : $scope;
-    $operation    = $_SESSION['tripal_pub_search']['criteria'][$i]['operation']    ? $_SESSION['tripal_pub_search']['criteria'][$i]['operation']    : $operation;
-    
-    // next populate defaults using any form values
-    $search_terms = $form_state['values']["search_terms-$i"] ? $form_state['values']["search_terms-$i"] : $search_terms;
-    $scope        = $form_state['values']["scope-$i"]        ? $form_state['values']["scope-$i"]        : $scope;
-    $operation    = $form_state['values']["operation-$i"]    ? $form_state['values']["operation-$i"]    : $operation;
-    
-    // default to searching the title and abstract
-    if (!$scope) {
-      $scope = 'abstract';
-    }
-  
-    $form['criteria'][$i]["search_terms-$i"] = array(
-      '#type'          => 'textfield',
-      '#description'   => t('Please provide a list of words for searching. You may use conjunctions such as "AND" or "OR" to separate words if they are expected in the same scope"'),
-      '#default_value' => $search_terms,
-      '#required'      => TRUE,
-    );
-    $form['criteria'][$i]["scope-$i"] = array(
-      '#type'          => 'select',
-      '#description'   => t('Please select the fields to search for this term.'),
-      '#options'       => array(
-        'any'      => 'Any Field',
-        'title'    => 'Title',
-        'abstract' => 'Title/Abstract',
-        'author'   => 'Author'),
-      '#default_value' => $scope,
-    );    
-    
-    if ($i > 0) {
-      $form['criteria'][$i]["operation-$i"] = array(
-        '#type'          => 'select',
-        '#options'       => array(
-          'AND' => 'AND',
-          'OR'  => 'OR',
-          'NOT' => 'NOT'),
-        '#default_value' => $operation,
-      );
-    }
-    if ($i == $num_criteria) {    
-      if($i > 0) {
-        $form['criteria'][$i]["remove-$i"] = array(
-          '#type'         => 'image_button',
-          '#value'        => t('Remove'),
-          '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
-          '#ahah' => array(
-            'path'    => "admin/tripal/tripal_pub/import/criteria/minus/$i",
-            'wrapper' => 'tripal-pub-importer-setup-form',
-            'event'   => 'click',
-            'method'  => 'replace',
-          ), 
-          '#attributes' => array('onClick' => 'return false;'),
-        );
-      }
-      $form['criteria'][$i]["add-$i"] = array(
-        '#type'         => 'image_button',      
-        '#value'        => t('Add'),
-        '#src'          => drupal_get_path('theme', 'tripal') . '/images/add.png',
-        '#ahah' => array(
-          'path'    => "admin/tripal/tripal_pub/import/criteria/add/$i",
-          'wrapper' => 'tripal-pub-importer-setup-form',
-          'event'   => 'click',
-          'method'  => 'replace',          
-        ),   
-        '#attributes' => array('onClick' => 'return false;'),
-      );
-    }
-  }
-  
-  $form['test'] = array(
-    '#type'         => 'submit',
-    '#value'        => t('Test Importer'),
-  );
-  $form['save'] = array(
-    '#type'         => 'submit',
-    '#value'        => t('Save Importer'),
-  );
-  $form['delete'] = array(
-    '#type'         => 'submit',
-    '#value'        => t('Delete Importer'),
-  );
-
-  return $form;
 }
 
 /**
  *
+ * @ingroup tripal_pub
  */
-function tripal_pub_importer_setup_form_validate($form, &$form_state) {
-  $num_criteria = $form_state['values']['num_criteria'];
-  $remote_db =  $form_state['values']["remote_db"];
-  $days =  trim($form_state['values']["days"]);
-  $disabled =  $form_state['values']["disabled"];
-  $do_contact =  $form_state['values']["do_contact"];
-  $loader_name =  trim($form_state['values']["loader_name"]);
+function tripal_pub_admin_validate($form, &$form_state) {
+  global $user;  // we need access to the user info
+  $job_args = array();
 
-  for ($i = 0; $i <= $num_criteria; $i++) {            
-    $search_terms =  trim($form_state['values']["search_terms-$i"]);
-    $scope =  $form_state['values']["scope-$i"];
-    $operation =  $form_state['values']["operation-$i"];
-    
-    if ($days and !is_numeric($days) or preg_match('/\./', $days)) {
-      form_set_error("days-$i", "Please enter a numeric, non decimal value, for the number of days.");
-    }
+
+  // -------------------------------------
+  // Submit the Cleanup Job if selected
+  if ($form_state['values']['op'] == t('Clean up orphaned publications')) {
+    tripal_add_job('Cleanup orphaned publications', 'tripal_pub',
+       'tripal_pub_cleanup', $job_args, $user->uid);
   }
 }
 
 /**
+ * Remove orphaned drupal nodes
+ *
+ * @param $dummy
+ *   Not Used -kept for backwards compatibility
+ * @param $job_id
+ *   The id of the tripal job executing this function
  *
+ * @ingroup tripal_pub
  */
-function tripal_pub_importer_setup_form_submit($form, &$form_state) {
-   
-  $pub_import_id = $form_state['values']['pub_import_id'];
-  $num_criteria = $form_state['values']['num_criteria'];
-  $remote_db =  $form_state['values']["remote_db"];
-  $days =  trim($form_state['values']["days"]);
-  $loader_name =  trim($form_state['values']["loader_name"]);
-  $disabled =  $form_state['values']["disabled"];
-  $do_contact =  $form_state['values']["do_contact"];
-
-  // set the session variables
-  $_SESSION['tripal_pub_search']['remote_db'] = $remote_db;
-  $_SESSION['tripal_pub_search']['days'] = $days;
-  $_SESSION['tripal_pub_search']['num_criteria'] = $num_criteria;
-  $_SESSION['tripal_pub_search']['loader_name'] = $loader_name;
-  $_SESSION['tripal_pub_search']['disabled'] = $disabled;
-  $_SESSION['tripal_pub_search']['do_contact'] = $do_contact;
-  unset($_SESSION['tripal_pub_search']['criteria']);
-  for ($i = 0; $i <= $num_criteria; $i++) {
-    $search_terms =  trim($form_state['values']["search_terms-$i"]);
-    $scope =  $form_state['values']["scope-$i"];
-    $operation =  $form_state['values']["operation-$i"];
-    
-    $_SESSION['tripal_pub_search']['criteria'][$i] = array(
-      'search_terms' => $search_terms,
-      'scope' => $scope,
-      'operation' => $operation
-    );
-  }
-
-  // now perform the appropriate action for the button clicked
-  if ($form_state['values']['op'] == 'Test Importer') {
-    $_SESSION['tripal_pub_search']['perform_search'] = 1;
-  }
-  if ($form_state['values']['op'] == 'Save Importer') {    
-    $record = array(
-      'name' => $loader_name,
-      'criteria' => serialize($_SESSION['tripal_pub_search']),
-      'disabled' => $disabled,
-      'do_contact' => $do_contact
-    );
-    // first check to see if this pub_import_id is already present. If so,
-    // do an update rather than an insert    
-    $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = %d";
-    $importer = db_fetch_object(db_query($sql, $pub_import_id));
-    if($importer) {
-      // do the update
-      $record['pub_import_id'] = $pub_import_id;
-      if(drupal_write_record('tripal_pub_import', $record, 'pub_import_id')){
-        unset($_SESSION['tripal_pub_search']);
-        drupal_set_message('Publication import settings updated.');
-        drupal_goto('admin/tripal/tripal_pub/import_list');       
-      }
-      else {
-        drupal_set_message('Could not update publication import settings.', 'error');
-      }
-    }     
-    else {         
-      // do the insert        
-      if(drupal_write_record('tripal_pub_import', $record)){
-        unset($_SESSION['tripal_pub_search']);
-        drupal_set_message('Publication import settings saved.');
-        drupal_goto('admin/tripal/tripal_pub/import_list');
-      }
-      else {
-        drupal_set_message('Could not save publication import settings.', 'error');
-      }
-    }    
-  }
-  if ($form_state['values']['op'] == 'Delete Importer') {
-    $sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = %d";
-    $success = db_query($sql, $pub_import_id);
-    if ($success) {
-      drupal_set_message('Publication importer deleted.');
-      drupal_goto('admin/tripal/tripal_pub/import_list');  
-    }
-    else {
-      drupal_set_message('Could not delete publication importer.', 'error');
-    }
-  }  
-}
+function tripal_pub_cleanup($dummy = NULL, $job_id = NULL) {
 
-/*
- * 
- */
-function tripal_pub_importer_delete($pub_import_id) {
-  $sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = %d";
-  $success = db_query($sql, $pub_import_id);
-  if ($success) {
-    drupal_set_message('Publication importer deleted.');
-    drupal_goto('admin/tripal/tripal_pub/import_list');  
-  }
-  else {
-    drupal_set_message('Could not delete publication importer.', 'error');
-  }
+  return tripal_core_clean_orphaned_nodes('pub', $job_id);
+  
 }
-/*
- * AHAH callback
- */
-function tripal_pub_importer_setup_page_update_criteria($action, $i) {
-  $status = TRUE;
-
-  // prepare and render the form
-  $form = tripal_core_ahah_prepare_form();   
-  $data = theme('tripal_pub_importer_setup_form', $form);  
 
-  // bind javascript events to the new objects that will be returned 
-  // so that AHAH enabled elements will work.
-  $settings = tripal_core_ahah_bind_events();
-
-  // return the updated JSON
-  drupal_json(
-    array(
-      'status'   => $status, 
-      'data'     => $data,
-      'settings' => $settings,
-    )  
-  );
-}

tripal_pub/tpub.obo

@@ -161,8 +161,8 @@ def:  The date the work was published.  This should be in the format: YYYY Mon D
 id: TPUB:0000047
 name: Authors
 relationship: part_of TPUB:0000037 ! Publication Details
-is_obsolete: true
-def:  This term is deprecated.  Please use the 'Authors List' term.
+synonym: "Author List" EXACT []
+def:  The list of authors of the publication. For PubMed style citations list each author with the last name first, followed by initials. Each author should be separated by a comma.
 
 [Term]
 id: TPUB:0000048
@@ -1312,12 +1312,6 @@ def: For publications noted as supported by US Government.
 subset: MeSH_Publication_Type
 is_a: TPUB:0000015 ! Publication Type
 
-[Term]
-id: TPUB:0000240
-name: Author List
-relationship: part_of TPUB:0000037 ! Publication Details
-synonym: "Authors" EXACT []
-def:  The list of authors of the publication. For PubMed style citations list each author with the last name first, followed by initials. Each author should be separated by a comma.
 
 [Term]
 id: TPUB:0000241

tripal_pub/tripal_pub.module

@@ -2,10 +2,11 @@
 
 require_once "api/tripal_pub.api.inc";
 require_once "includes/tripal_pub.admin.inc";
-require_once "includes/pubmed.inc";
 require_once "includes/pub_sync.inc";
 require_once "includes/pub_form.inc";
-
+require_once "includes/pub_importers.inc";
+require_once "includes/pubmed.inc";
+require_once "includes/agricola.inc";
 /**
  * @file
  *
@@ -58,10 +59,9 @@ function tripal_pub_node_info() {
  *   as the program is ran
  */
 function tripal_pub_menu() {
-
   $items = array();
-
-  $items[ 'admin/tripal/tripal_pub' ]= array(
+  
+  $items['admin/tripal/tripal_pub' ]= array(
     'title' => 'Publications',
     'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
     'page callback' => 'theme',
@@ -70,6 +70,15 @@ function tripal_pub_menu() {
     'type' => MENU_NORMAL_ITEM
   );
   
+  $items['admin/tripal/tripal_pub/configuration'] = array(
+    'title' => 'Configuration',
+    'description' => 'Configure the Tripal publication module.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_pub_admin'),
+    'access arguments' => array('administer tripal pubs'),
+    'type' => MENU_NORMAL_ITEM,
+  );
+  
   $items['admin/tripal/tripal_pub/sync'] = array(
     'title' => ' Sync Publications',
     'description' => 'Sync publications in Chado with Drupal',