Fixed bugs in pub module with checking for duplicates. Also updated dbxref and relationships API to clear out new fields on AJAX callback

tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc

@@ -434,6 +434,13 @@ function chado_add_node_form_dbxrefs_add_button_submit(&$form, &$form_state) {
   $key = $dbxref['db_id'] . '-' . $version;
   $form_state['chado_additional_dbxrefs'][$key] = (object) $dbxref;
 
+  
+  // we don't want the new element to pick up the values from the previous element so wipe them out
+  unset($form_state['input']['dbxref_table']['new']['db']);
+  unset($form_state['input']['dbxref_table']['new']['db_name']);
+  unset($form_state['input']['dbxref_table']['new']['dbxref_version']);
+  unset($form_state['input']['dbxref_table']['new']['dbxref_accession']);
+  
   $form_state['rebuild'] = TRUE;
 }
 

tripal_core/api/tripal_core.chado_nodes.properties.api.inc

@@ -633,8 +633,7 @@ function chado_add_node_form_properties_add_button_submit(&$form, &$form_state)
   $key = $property['type_id'] . '-' . $property['rank'];
   $form_state['chado_properties'][$key] = (object) $property;
   
-  // we don't want the new element to pick up the values from the previous element
-  // so wipe them out
+  // we don't want the new element to pick up the values from the previous element so wipe them out
   unset($form_state['input']['property_table']['new']['type']);
   unset($form_state['input']['property_table']['new']['type_name']);
   unset($form_state['input']['property_table']['new']['definition']);

tripal_core/api/tripal_core.chado_nodes.relationships.api.inc

@@ -619,9 +619,11 @@ function chado_add_node_form_relationships_add_button_submit(&$form, &$form_stat
 
   $name = (isset($form_state['node']->{$details['base_table']}->uniquename)) ? $form_state['node']->{$details['base_table']}->uniquename : 'CURRENT';
 
+
+
+  
   // get details for the new relationship
   if ($form_state['values']['relationship_table']['new']['subject_is_current']) {
-
     $relationship = array(
       'type_id' => $form_state['values']['relationship_table']['new']['type_id'],
       'type_name' => $form_state['values']['relationship_table']['new']['type_name'],
@@ -631,6 +633,9 @@ function chado_add_node_form_relationships_add_button_submit(&$form, &$form_stat
       'subject_name' => $name,
       'rank' => '0',
     );
+    // we don't want the new element to pick up the values from the previous element so wipe them out
+    unset($form_state['input']['relationship_table']['new']['object_id']);
+    unset($form_state['input']['relationship_table']['new']['object_name']);
   }
   else {
     $relationship = array(
@@ -642,11 +647,18 @@ function chado_add_node_form_relationships_add_button_submit(&$form, &$form_stat
       'subject_name' => $form_state['values']['relationship_table']['new']['subject_name'],
       'rank' => '0',
     );
+    // we don't want the new element to pick up the values from the previous element so wipe them out
+    unset($form_state['input']['relationship_table']['new']['subject_id']);
+    unset($form_state['input']['relationship_table']['new']['subject_name']);
   }
-
+  
   $key = $relationship['type_id'] . '-' . $relationship['rank'];
   $form_state['chado_relationships'][$key] = (object) $relationship;
 
+  // we don't want the new element to pick up the values from the previous element so wipe them out
+  unset($form_state['input']['relationship_table']['new']['type_id']);
+  unset($form_state['input']['relationship_table']['new']['type_name']);
+  
   $form_state['rebuild'] = TRUE;
 }
 

tripal_pub/api/tripal_pub.api.inc

@@ -411,7 +411,8 @@ function tripal_get_publication($identifiers, $options = array()) {
  *     'Year':               The published year of the publication
  *     'Publication Type':   An array of publication types. A publication can have more than one type.
  *     'Series Name':        The series name of the publication
- *     'Journal Name':       An alternative to 'Series Name' is 'Journal Name'
+ *     'Journal Name':       An alternative to 'Series Name'
+ *     'Conference Name':    An alternative to 'Series Name'
  *     'Citation':           The publication citation (this is the value saved in the pub.uniquename field and must be unique)
  *   If this key is present it will also be checked
  *     'Publication Dbxref': A database cross reference of the form DB:ACCESSION where DB is the name
@@ -472,14 +473,16 @@ function tripal_publication_exists($pub_details) {
 
   // get the series name.  The pub.series_name field is only 255 chars so we must truncate to be safe
   $series_name = '';
-  if (array_key_exists('Series_Name', $pub_details)) {
+  if (array_key_exists('Series Name', $pub_details)) {
     $series_name = substr($pub_details['Series Name'], 0, 255);
   }
   if (array_key_exists('Journal Name', $pub_details)) {
     $series_name = substr($pub_details['Journal Name'], 0, 255);
   }
-
-
+  if (array_key_exists('Conference Name', $pub_details)) {
+    $series_name = substr($pub_details['Conference Name'], 0, 255);
+  }
+  
   // make sure the publication is unique using the prefereed import duplication check
   $import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media');
   $pubs = array();

tripal_pub/includes/tripal_pub.chado_node.inc

@@ -151,12 +151,6 @@ function chado_pub_form($node, $form_state) {
     $is_obsolete  = $form_state['input']['is_obsolete'];
   }
 
-  // a drupal title can only be 255 characters, but the Chado title can be much longer.
-  // we use the publication title as the drupal title, but we'll need to truncate it.
-  $form['title'] = array(
-    '#type' => 'hidden',
-    '#value' => substr($title, 0, 255),
-  );
   $form['pubtitle'] = array(
     '#type' => 'textarea',
     '#title' => t('Publication Title'),
@@ -387,21 +381,6 @@ function chado_pub_validate($node, $form, &$form_state) {
 
     $pub_id = $node->pub_id;
 
-    // first get the original title, type and year before it was changed
-    $values = array('pub_id' => $pub_id);
-    $columns = array('title', 'pyear', 'type_id', 'series_name');
-    $options = array('statement_name' => 'sel_pub_id');
-    $pub = chado_select_record('pub', $columns, $values, $options);
-
-    // if the title, type,  year or series_name have changed then check the pub
-    // to see if it is a duplicate of another
-    if((strcmp(strtolower($pub[0]->title), strtolower($title)) == 0) and
-       (strcmp(strtolower($pub[0]->series_name), strtolower($series_name)) == 0) and
-       ($pub[0]->type_id == $type_id) and
-       ($pub[0]->pyear == $pyear)) {
-      $skip_duplicate_check = 1;
-    }
-
     // check to see if a duplicate publication already exists
     if (!$skip_duplicate_check) {
       chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm[0], $pub_id);
@@ -467,13 +446,11 @@ function chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvter
     'Series Name' => $series_name,
     'Publication Type' => $cvterm->name,
   );
+  // TODO: need to include the Publication Dbxref in the $pub_details as well
   $pub_ids = tripal_publication_exists($pub_details);
-//  dpm($pub_ids);
-//  dpm($pub_details);
   
-  // if we found only one publication and it is our publication then 
-  // return, we're good.
-  if (count($pub_ids) == 1 and !in_array($pub_id, $pub_ids)) {
+  // if we found only one publication and it is our publication then return, we're good.
+  if (count($pub_ids) == 1 and in_array($pub_id, $pub_ids)) {
     return;
   }
   if (count($pub_ids) == 0) {
@@ -561,9 +538,9 @@ function chado_pub_node_access($node, $op, $account) {
  */
 function chado_pub_insert($node) {
 
-  $title        = trim($node->pubtitle);
-  $pyear        = trim($node->pyear);
-  $uniquename   = trim($node->uniquename);
+  $node->pubtitle     = trim($node->pubtitle);
+  $node->pyear        = trim($node->pyear);
+  $node->uniquename   = trim($node->uniquename);
   $is_obsolete  = $node->is_obsolete;
   $type_id      = $node->type_id;
 
@@ -766,11 +743,11 @@ function chado_pub_insert($node) {
  * @ingroup tripal_pub
  */
 function chado_pub_update($node) {
-  $title        = trim($node->pubtitle);
-  $pyear        = trim($node->pyear);
-  $uniquename   = trim($node->uniquename);
-  $is_obsolete  = $node->is_obsolete;
-  $type_id      = $node->type_id;
+  $node->pubtitle   = trim($node->pubtitle);
+  $node->pyear      = trim($node->pyear);
+  $node->uniquename = trim($node->uniquename);
+  $is_obsolete      = $node->is_obsolete;
+  $type_id          = $node->type_id;
 
   // we need an array suitable for the tripal_pub_create_citation() function
   // to automatically generate a citation if a uniquename doesn't already exist

tripal_pub/includes/tripal_pub.pub_citation.inc

@@ -212,7 +212,11 @@ function tripal_pub_create_citation($pub) {
   // Journal Article
   //----------------------
   if ($pub_type == 'Journal Article') {
-    $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
+    if (array_key_exists('Authors', $pub)) {
+      $citation = $pub['Authors'] . '. ';
+    }
+    
+    $citation .= $pub['Title'] .  '. ';
 
     if (array_key_exists('Journal Name', $pub)) {
       $citation .= $pub['Journal Name'] . '. ';
@@ -253,7 +257,11 @@ function tripal_pub_create_citation($pub) {
   // Review
   //----------------------
   if ($pub_type == 'Review') {
-    $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
+    if (array_key_exists('Authors', $pub)) {
+      $citation = $pub['Authors'] . '. ';
+    }
+    
+    $citation .= $pub['Title'] .  '. ';
 
     if (array_key_exists('Journal Name', $pub)) {
       $citation .= $pub['Journal Name'] . '. ';
@@ -294,7 +302,11 @@ function tripal_pub_create_citation($pub) {
   // Research Support, Non-U.S. Gov't
   //----------------------
   elseif ($pub_type == "Research Support, Non-U.S. Gov't") {
-    $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
+    if (array_key_exists('Authors', $pub)) {
+      $citation = $pub['Authors'] . '. ';
+    }
+    
+    $citation .= $pub['Title'] .  '. ';
 
     if (array_key_exists('Journal Name', $pub)) {
       $citation .= $pub['Journal Name'] . '. ';
@@ -311,8 +323,11 @@ function tripal_pub_create_citation($pub) {
   // Letter
   //----------------------
   elseif ($pub_type == 'Letter') {
-    $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
-
+    if (array_key_exists('Authors', $pub)) {
+      $citation = $pub['Authors'] . '. ';
+    }
+    
+    $citation .= $pub['Title'] .  '. ';
     if (array_key_exists('Journal Name', $pub)) {
       $citation .= $pub['Journal Name'] . '. ';
     }
@@ -364,8 +379,11 @@ function tripal_pub_create_citation($pub) {
   // Conference Proceedings
   //----------------------
   elseif ($pub_type == 'Conference Proceedings') {
-    $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
-
+    if (array_key_exists('Authors', $pub)) {
+      $citation = $pub['Authors'] . '. ';
+    }
+    
+    $citation .= $pub['Title'] .  '. ';
     if (array_key_exists('Conference Name', $pub)) {
       $citation .= $pub['Conference Name'] . '. ';
     }