updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options

tripal_analysis/includes/tripal_analysis.chado_node.inc

@@ -234,10 +234,9 @@ function chado_analysis_form($node, &$form_state) {
   // ----------------------------------
   $instructions = t('To add additional properties to the drop down. ' . l("Add terms to the analysis_property vocabulary", "admin/tripal/chado/tripal_cv/cvterm/add") . ".");
   $details = array(
-    'property_table' => 'analysisprop',             // the name of the prop table
-    'base_foreign_key' => 'analysis_id',            // the name of the key in your base chado table
-    'base_key_value' => $analysis_id,               // the value of analysis_id for this record
-    'cv_name' => 'analysis_property',               // the cv.name of the cv governing analysisprop.type_id
+    'property_table' => 'analysisprop',       // the name of the prop table
+    'chado_id' => $analysis_id,               // the value of analysis_id for this record
+    'cv_name' => 'analysis_property',         // the cv.name of the cv governing analysisprop.type_id
     'fieldset_title' => 'Properties',
     'additional_instructions' => $instructions
   );

tripal_contact/includes/tripal_contact.chado_node.inc

@@ -197,8 +197,7 @@ function chado_contact_form(&$node, $form_state) {
 
   $details = array(
     'property_table' => 'contactprop',
-    'base_foreign_key' => 'contact_id',
-    'base_key_value' => $contact_id,
+    'chado_id' => 'contact_id',
     'cv_name' => 'tripal_contact',
     'select_options' => $select_options
   );

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

@@ -32,8 +32,8 @@
 
     $details = array(
       'property_table' => 'example_property',      // the name of the table linking additional properties to this node
-      'base_foreign_key' => 'example_id',          // key to link to the chado content created by this node
-      'base_key_value' => $example_id,             // the value of the above key
+      'chado_id_field' => 'example_id',          // key to link to the chado content created by this node
+      'chado_id' => $example_id,             // the value of the above key
       'cv_name' => 'example_prop_cv',              // the name of the cv governing the _prop.type_id
       'fieldset_title' => 'Additional References', // the non-translated title for this fieldset
       'additional_instructions' => ''              // a non-stranslated string providing additional instructions
@@ -105,28 +105,82 @@
  * @param $form_state
  *   The corresponding form_state array for the form
  * @param $details
- *   An array defining details needed by this form. Required Keys are:
- *     - property_table: the name of the property linking table (ie: featureprop)
- *     - base_foreign_key: the name of the foreign key linking this table to the non-property table (ie: feature_id)
- *     - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
- *   Require ONE of the following:
- *     The controlled vocabulary governing the property types
- *       -cv_id: the unique key from the cv table
- *       -cv_name: the cv.name field uniquely identifying the controlled vocab
+ *   An array defining details used by this form. 
+ *   Required keys that are always required:
+ *     - property_table: the name of the property table (e.g.: featureprop, stockprop, etc.)
+ *   Required keys for forms that update a record.
+ *     - chado_id: the id of the record to which properties will be associated (e.g.: if a
+ *       feature has a feature_id of 999 and we want to associate properties for that feature 
+ *       then the chado_id option should be 999)
+ *   Require ONE of the following to identify the controlled vocabulary containing the properties to use:
+ *     -cv_id: the unique key from the cv table
+ *     -cv_name: the cv.name field uniquely identifying the controlled vocabulary
  *   Optional keys include:
- *     - fieldset_title: the non-translated title for this fieldset
- *     - additional_instructions: a non-translated string providing additional instructions
- *     - select_options: must be an array where the [key] is a valid cvterm_id and
- *       the [value] is the human-readable name of the option. This is generated from the cv_name/id by default
+ *     - chado_id_field: the foreign key field that links properties to the
+ *       chado_id record. If this value is not specified it is determined using the
+ *       traditional Chado naming scheme for property tables. 
  *
  * @ingroup tripal_chado_node_api
  */
 function chado_add_node_form_properties(&$form, &$form_state, $details) {
 
+  // make sure the property table exists before proceeding.
+  if (!chado_table_exists($details['property_table'])) {
+    drupal_set_message("Cannot add property elements to the form. The property table, '" . 
+      $details['property_table'] . "', does not exists", "error");
+    tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add property elements to the form. 
+      The property table, '%name', cannot be found.", array('%name' => $details['property_table']));
+    return;
+  }
+  
+  // if the chado_id_field is not specified then set it using the
+  // typical chado naming scheme
+  if (!array_key_exists('chado_id_field', $details)) {
+    $chado_id_table = preg_replace('/prop$/', '', $details['property_table']);
+    $chado_id_field = $chado_id_table . '_id';
+    $details['chado_id_field'] = $chado_id_field;
+  }
+  
+  // make sure the specified cv exists
+  if (isset($details['cv_name'])) {
+    // make sure the cv_name is real
+    $result = chado_select_record('cv',array('cv_id'),array('name' => $details['cv_name']));
+    if (count($result) == 0) {
+      drupal_set_message("Cannot add property elements to the form. The CV name, '" .
+        $details['cv_name'] . "', does not exists", "error");
+      tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add property elements to the form.
+        The CV named, '%name', cannot be found.", array('%name' => $details['cv_name']));
+      return;
+    }
+    // add the cv_id option to the details array
+    $details['cv_id'] = $result[0]->cv_id;
+  }
+  elseif (isset($details['cv_id'])) {
+    // make sure the cv_id is real
+    $result = chado_select_record('cv', array('name'), array('cv_id' => $details['cv_id']));
+    if (count($result) == 0) {
+      drupal_set_message("Cannot add property elements to the form. The CV ID, '" .
+        $details['cv_id'] . "', does not exist", "error");
+      tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add property elements
+        to the form. The CV ID, '%id', cannot be found.", array('%id' => $details['cv_id']));
+      return;
+    }
+    // add the cv_name option to the details array
+    $details['cv_name'] = $result[0]->name;
+  }
+  else {
+    drupal_set_message("Please provide either a 'cv_name' or 'cv_id' as an 
+        option for adding properties to the form", "error");
+    tripal_report_error('tcprops_form', TRIPAL_ERROR, "Please provide either a 
+        'cv_name' or 'cv_id' as an option for adding properties to the form", array());
+    return;
+  }
+
   // Set Defaults for optional fields
   $details['fieldset_title'] = 'Properties';
   $details['additional_instructions'] = '';
 
+  
   // Get Property Types for the Select List
   if (isset($details['select_options'])) {
     $property_options = $details['select_options'];
@@ -137,17 +191,6 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
     // if the vocabulary name is provided in the details then use that to
     // get the terms 
     if (isset($details['cv_name'])) {
-      // make sure the cv_name is real
-      $result = chado_select_record('cv',array('cv_id'),array('name' => $details['cv_name']));
-      if (count($result) == 0) {
-        drupal_set_message("Cannot add property elements to the form. The CV name, '" . $details['cv_name'] . "', does not exists", "error");
-        tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add property elements to the form. The CV named, '%name',
-          cannot be found.", array('%name' => $details['cv_name']));
-        return;
-      }
-      // add the cv_id option to the details array
-      $details['cv_id'] = $result[0]->cv_id;
-      
       $property_options = array();
       $property_options[] = 'Select a Property';
       $sql = "
@@ -162,22 +205,10 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
       $prop_types = chado_query($sql, array(':cv_name' => $details['cv_name']));
       while ($prop = $prop_types->fetchObject()) {
         $property_options[$prop->cvterm_id] = $prop->name;
-        $details['cv_id'] = $prop->cv_id;
       }
     } 
     // if the cv_id is set in the $details array then use that to get the terms
-    elseif (isset($details['cv_id'])) {
-      // make sure the cv_id is real
-      $result = chado_select_record('cv', array('name'), array('cv_id' => $details['cv_id']));
-      if (count($result) == 0) {
-        drupal_set_message("Cannot add property elements to the form. The CV ID, '" . $details['cv_id'] . "', does not exist", "error");
-        tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add property elements to the form. The CV ID, '%id',
-          cannot be found.", array('%id' => $details['cv_id']));
-        return;
-      }
-      // add the cv_name option to the details array
-      $details['cv_name'] = $result[0]->name;
-      
+    elseif (isset($details['cv_id'])) {      
       $property_options = array();
       $property_options[] = 'Select a Property';
       $sql = "
@@ -193,8 +224,6 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
       while ($prop = $prop_types->fetchObject()) {
         $property_options[$prop->cvterm_id] = $prop->name;
       }
-      
-
     }
   }
 
@@ -206,7 +235,7 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
         to the %cv_name controlled vocabulary.',
         array(
           '%cv_name' => $details['cv_name'],
-          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/'.$details['cv_id'].'/cvterm/add')
+          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/' . $details['cv_id'] . '/cvterm/add')
         )
       ),
       TRIPAL_WARNING,
@@ -219,7 +248,7 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
         a controlled vocabulary term</a> to the %cv_name controlled vocabulary.',
         array(
           '%cv_name' => $details['cv_name'],
-          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/'.$details['cv_id'].'/cvterm/add')
+          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/' . $details['cv_id'] . '/cvterm/add')
         )
       ),
       TRIPAL_INFO,
@@ -282,10 +311,10 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
         INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
         INNER JOIN {cv} CV      ON CVT.cv_id     = CV.cv_id
         WHERE
-        PP." . $details['base_foreign_key'] . " = :base_key_value AND
+        PP." . $details['chado_id_field'] . " = :chado_id AND
         CV.name = '" .$details['cv_name']. "'
         ORDER BY CVT.name, PP.rank",
-         array(':base_key_value' => $details['base_key_value'])
+         array(':chado_id' => $details['chado_id'])
       );
     } elseif (isset($details['cv_id'])) {
       $existing_properties = chado_query(
@@ -294,10 +323,10 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
         INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
         INNER JOIN {cv} CV      ON CVT.cv_id     = CV.cv_id
         WHERE
-        PP." . $details['base_foreign_key'] . " = :base_key_value AND
+        PP." . $details['chado_id_field'] . " = :chado_id AND
         CV.cv_id = '" .$details['cv_id']. "'
         ORDER BY CVT.name, PP.rank",
-         array(':base_key_value' => $details['base_key_value'])
+         array(':chado_id' => $details['chado_id'])
       );
     }
   }
@@ -508,7 +537,7 @@ function chado_add_node_form_properties_add_button_submit(&$form, &$form_state)
   $rank = chado_get_table_max_rank(
     $details['property_table'],
     array(
-      $details['base_foreign_key'] => $details['base_key_value'],
+      $details['chado_id_field'] => $details['chado_id'],
       'type_id' => $property['type_id']
     )
   );

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

@@ -106,7 +106,7 @@
  *   An array defining details needed by this form. Required Keys are:
  *     - relationship_table: the name of the relationship table (ie: feature_relationship)
  *     - base_table: the name of the base table (ie: feature)
- *     - base_foreign_key: the name of the foreign key linking this table to the non-relationship table (ie: feature_id)
+ *     - base_foreign_key: the name of the foreign key in the relationship table field linking this table to the non-relationship table (ie: feature_id)
  *     - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
  *     - nodetype: the non-translated singular title of this node type
  *   One of the following:
@@ -126,6 +126,50 @@
  */
 function chado_add_node_form_relationships(&$form, &$form_state, $details) {
 
+  // make sure the property table exists before proceeding.
+  if (!chado_table_exists($details['relationship_table'])) {
+    drupal_set_message("Cannot add relationship elements to the form. The relationship table, '" .
+      $details['relationship_table'] . "', does not exists", "error");
+    tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add relationship elements to the form.
+      The relationship table, '%name', cannot be found.", array('%name' => $details['relationship_table']));
+    return;
+  }
+  
+  // make sure the specified cv exists
+  if (isset($details['cv_name'])) {
+    // make sure the cv_name is real
+    $result = chado_select_record('cv',array('cv_id'),array('name' => $details['cv_name']));
+    if (count($result) == 0) {
+      drupal_set_message("Cannot add relationship elements to the form. The CV name, '" .
+          $details['cv_name'] . "', does not exists", "error");
+          tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add relationship elements to the form.
+        The CV named, '%name', cannot be found.", array('%name' => $details['cv_name']));
+          return;
+    }
+    // add the cv_id option to the details array
+    $details['cv_id'] = $result[0]->cv_id;
+  }
+  elseif (isset($details['cv_id'])) {
+    // make sure the cv_id is real
+    $result = chado_select_record('cv', array('name'), array('cv_id' => $details['cv_id']));
+    if (count($result) == 0) {
+      drupal_set_message("Cannot add relationship elements to the form. The CV ID, '" .
+          $details['cv_id'] . "', does not exist", "error");
+          tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add relationship elements
+        to the form. The CV ID, '%id', cannot be found.", array('%id' => $details['cv_id']));
+          return;
+    }
+    // add the cv_name option to the details array
+    $details['cv_name'] = $result[0]->name;
+  }
+  else {
+    drupal_set_message("Please provide either a 'cv_name' or 'cv_id' as an
+        option for adding relationship to the form", "error");
+    tripal_report_error('tcprops_form', TRIPAL_ERROR, "Please provide either a
+        'cv_name' or 'cv_id' as an option for adding relationship to the form", array());
+    return;
+  }
+  
   $form_state['rebuild'] = TRUE;
 
   // Set Defaults for optional fields
@@ -147,17 +191,6 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
   }
   else {
     if (isset($details['cv_name'])) {
-      // make sure the cv_name is real
-      $result = chado_select_record('cv',array('cv_id'),array('name' => $details['cv_name']));
-      if (count($result) == 0) {
-        drupal_set_message("Cannot add relationship elements to the form. The CV name, '" . $details['cv_name'] . "', does not exists", "error");
-        tripal_report_error('tcrels_form', TRIPAL_ERROR, "Cannot add relationship elements to the form. The CV named, '%name',
-          cannot be found.", array('%name' => $details['cv_name']));
-        return;
-      }
-      // add the cv_id option to the details array
-      $details['cv_id'] = $result[0]->cv_id;
-      
       $type_options = array();
       $type_options[] = 'Select a Property';
       $sql = "
@@ -176,17 +209,6 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
       }
     } 
     elseif (isset($details['cv_id'])) {
-      // make sure the cv_id is real
-      $result = chado_select_record('cv', array('name'), array('cv_id' => $details['cv_id']));
-      if (count($result) == 0) {
-        drupal_set_message("Cannot add relationships elements to the form. The CV ID, '" . $details['cv_id'] . "', does not exist", "error");
-        tripal_report_error('tcprops_form', TRIPAL_ERROR, "Cannot add relationship elements to the form. The CV ID, '%id',
-          cannot be found.", array('%id' => $details['cv_id']));
-        return;
-      }
-      // add the cv_name option to the details array
-      $details['cv_name'] = $result[0]->name;
-      
       $type_options = array();
       $type_options[] = 'Select a Property';
       $sql = "
@@ -209,7 +231,7 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
   // Tell tripal administrators how to add terms to the property types drop down.
   if (empty($type_options)) {
     $tripal_message = tripal_set_message(
-      t('There are currently no proeprty types! To add additional properties to the drop
+      t('There are currently no property types! To add additional properties to the drop
         down list, you need to <a href="@cvtermlink">add a controlled vocabulary term</a>
         to the %cv_name controlled vocabulary.',
         array(
@@ -227,7 +249,7 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
         a controlled vocabulary term</a> to the %cv_name controlled vocabulary.',
         array(
           '%cv_name' => $details['cv_name'],
-          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/'.$details['cv_id'].'/cvterm/add')
+          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/' . $details['cv_id'] . '/cvterm/add')
         )
       ),
       TRIPAL_INFO,
@@ -294,9 +316,9 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
           base2.".$details['base_name_field']." as subject_name,
           cvterm.name as type_name
         FROM {".$details['relationship_table']."} rel
-        LEFT JOIN {".$details['base_table']."} base1 ON base1.".$details['base_foreign_key']." = rel.".$details['object_field_name']."
-        LEFT JOIN {".$details['base_table']."} base2 ON base2.".$details['base_foreign_key']." = rel.".$details['subject_field_name']."
-        LEFT JOIN {cvterm} cvterm ON cvterm.cvterm_id = rel.type_id
+          LEFT JOIN {".$details['base_table']."} base1 ON base1.".$details['base_foreign_key']." = rel.".$details['object_field_name']."
+          LEFT JOIN {".$details['base_table']."} base2 ON base2.".$details['base_foreign_key']." = rel.".$details['subject_field_name']."
+          LEFT JOIN {cvterm} cvterm ON cvterm.cvterm_id = rel.type_id
         WHERE rel.".$details['object_field_name']." = :base_key_value
             OR rel.".$details['subject_field_name']." = :base_key_value",
         array(':base_key_value' => $details['base_key_value'])

tripal_core/theme/css/tripal.css

@@ -192,9 +192,12 @@ div.messages.tripal-site-admin-only{
   background-color: #cce3ff;
   margin-top: 10px;
   margin-bottom: 10px;
+  margin-left: 0px;
+  margin-right: 0px;
   border: 1px solid #7DA1D4;
-  min-height: 50px;
+  min-height: 65px;
   clear: both;
+  padding: 0px;
 }
 
 .tripal-serverity-string {
@@ -210,7 +213,7 @@ div.messages.tripal-site-admin-only{
 }
 
 .tripal-site-admin-message {
-   padding: 10px 10px 10px 55px;
+   padding: 15px 10px 10px 70px;
    font-style: italic;
 }
 

tripal_core/tripal_core.module

@@ -639,12 +639,13 @@ function tripal_core_node_view_alter(&$build) {
 
           $path = $cache->data[$key]['path'] . '/' . $key . '.tpl.php';
 
-          $path = theme('tripal_admin_message', array('message' => "Administrators, you can
+          $path = tripal_set_message("Administrators, you can
             customize the way the content above is presented.  Tripal provides a template
             file for each block of content.  To customize, copy the template file to your
             site's default theme, edit then " .
             l('clear the Drupal cache', 'admin/config/development/performance', array('attributes' => array('target' => '_blank'))) . ".
-            Currently, the content above is provided by this template: <br><br>$path")
+            Currently, the content above is provided by this template: <br><br>$path",
+            TRIPAL_INFO, array('return_html' => 1)
           );
         }
 

tripal_example/includes/tripal_example.chado_node.inc

@@ -145,8 +145,7 @@ function chado_example_form($node, &$form_state) {
   // from it through your node form then add this section to your own node form
   $details = array(
     'property_table' => 'exampleprop',      // the name of the prop table
-    'base_foreign_key' => 'example_id',     // the name of the key in your base chado table
-    'base_key_value' => $example_id,        // the value of example_id for this record
+    'chado_id' => $example_id,              // the value of example_id for this record
     'cv_name' => 'example_property_types'   // the cv.name of the cv governing exampleprop.type_id
   );
   // Adds the form elements to your current form

tripal_feature/includes/tripal_feature.chado_node.inc

@@ -217,8 +217,7 @@ function chado_feature_form($node, &$form_state) {
   //---------------------------------------------
   $details = array(
     'property_table' => 'featureprop',      // the name of the prop table
-    'base_foreign_key' => 'feature_id',     // the name of the key in your base chado table
-    'base_key_value' => $feature_id,        // the value of feature_id for this record
+    'chado_id' => $feature_id,              // the value of feature_id for this record
     'cv_name' => 'feature_property'         // the cv.name of the cv governing featureprop.type_id
   );
   // Adds the form elements to your current form

tripal_featuremap/includes/tripal_featuremap.chado_node.inc

@@ -138,8 +138,7 @@ function chado_featuremap_form($node, &$form_state) {
   $instructions = t('To add additional properties to the drop down. ' . l("Add terms to the featuremap_property vocabulary", "admin/tripal/chado/tripal_cv/cvterm/add") . ".");
   $details = array(
     'property_table' => 'featuremapprop',
-    'base_foreign_key' => 'featuremap_id',
-    'base_key_value' => $featuremap_id,
+    'chado_id' => $featuremap_id,
     'cv_name' => 'featuremap_property',
     'fieldset_name' => 'Additional Details',
     'additional_instructions' => $instructions

tripal_library/includes/tripal_library.chado_node.inc

@@ -184,8 +184,7 @@ function chado_library_form($node, &$form_state) {
 
   $details = array(
     'property_table' => 'libraryprop',      // the name of the prop table
-    'base_foreign_key' => 'library_id',     // the name of the key in your base chado table
-    'base_key_value' => $library_id,        // the value of library_id for this record
+    'chado_id' => $library_id,              // the value of library_id for this record
     'cv_name' => 'library_property',        // the cv.name of the cv governing libraryprop.type_id
     'select_options' => $select_options
   );

tripal_organism/includes/tripal_organism.chado_node.inc

@@ -176,8 +176,7 @@ function chado_organism_form($node, $form_state) {
   //---------------------------------------------
   $details = array(
     'property_table' => 'organismprop',      // the name of the prop table
-    'base_foreign_key' => 'organism_id',     // the name of the key in your base chado table
-    'base_key_value' => $organism_id,        // the value of organism_id for this record
+    'chado_id' => $organism_id,              // the value of organism_id for this record
     'cv_name' => 'organism_property'         // the cv.name of the cv governing organismprop.type_id
   );
   // Adds the form elements to your current form

tripal_project/includes/tripal_project.chado_node.inc

@@ -152,8 +152,7 @@ function chado_project_form(&$node, $form_state) {
   $instructions = t('To add properties to the drop down list, you must ' . l("add terms to the project_property vocabulary", "admin/tripal/chado/tripal_cv/cvterm/add") . ".");
   $details = array(
     'property_table' => 'projectprop',
-    'base_foreign_key' => 'project_id',
-    'base_key_value' => $project_id,
+    'chado_id' => $project_id,
     'cv_name' => 'project_property',
     'additional_instructions' => $instructions,
     'select_options' => $select_options

tripal_pub/api/tripal_pub.api.inc

@@ -9,6 +9,9 @@
  * @ingroup tripal_api
  * @{
  * Provides an application programming interface (API) to manage chado publications
+ * 
+ * @stephen add documentation here for how to add a new importer.
+ * 
  * @}
  */
 

tripal_pub/includes/tripal_pub.chado_node.inc

@@ -250,8 +250,7 @@ function chado_pub_form($node, $form_state) {
 
   $details = array(
     'property_table' => 'pubprop',
-    'base_foreign_key' => 'pub_id',
-    'base_key_value' => $pub_id,
+    'chado_id' => $pub_id,
     'cv_name' => 'tripal_pub',
     'select_options' => $select_options,
   );
@@ -260,13 +259,11 @@ function chado_pub_form($node, $form_state) {
   // RELATIONSHIPS FORM
   //---------------------------------------------
   // We want to use the contact_relationship_types cv if there are any terms available
-  // and if not, to default to the relationship ontology
+  // and if not, then default to the relationship ontology
   $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'pub_relationship_types'));
-  $cv_id = $cv_result[0]->cv_id;
-  $select_options = tripal_cv_get_cvterm_options($cv_id);
-  if (empty($select_options)) {
-    $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'relationship'));
+  if (count($cv_result) > 0) {
     $cv_id = $cv_result[0]->cv_id;
+    $cv_name = 'pub_relationship_types';
     $select_options = tripal_cv_get_cvterm_options($cv_id);
   }
   // D7 @TODO: tell tripal admin's about this
@@ -277,7 +274,7 @@ function chado_pub_form($node, $form_state) {
     'base_foreign_key' => 'pub_id',             // the name of the key in your base chado table
     'base_key_value' => $pub_id,                // the value of example_id for this record
     'nodetype' => 'pub',                        // the human-readable name of your node type
-    'cv_name' => 'pub_relationship_types',      // the cv.name of the cv governing example_relationship.type_id
+    'cv_name' => $cv_name,                      // the cv.name of the cv containing the properties
     'base_name_field' => 'uniquename',          // the base table field you want to be used as the name
     'select_options' => $select_options
   );

tripal_stock/includes/tripal_stock.chado_node.inc

@@ -300,15 +300,13 @@ function chado_stock_form($node, $form_state) {
   //---------------------------------------------
   $details = array(
     'property_table' => 'stockprop',
-    'base_foreign_key' => 'stock_id',
-    'base_key_value' => $stock_id,
+    'chado_id' => $stock_id,
     'cv_id' => variable_get('chado_stock_prop_types_cv', FALSE)
   );
   chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
-
   $details = array(
     'linking_table' => 'stock_dbxref',
     'base_foreign_key' => 'stock_id',
@@ -318,7 +316,6 @@ function chado_stock_form($node, $form_state) {
 
   // RELATIONSHIPS FORM
   //---------------------------------------------
-
   $details = array(
     'relationship_table' => 'stock_relationship',
     'base_table' => 'stock',