Re-arranged file structure for tripal_analysis and tripal_cv. Also fixed but in tripal core

tripal_analysis/tripal_analysis.module

@@ -11,8 +11,8 @@
  * @ingroup tripal_modules
  */
 
-require('tripal_analysis.api.inc');
-require('tripal_analysis_privacy.inc');
+require('api/tripal_analysis.api.inc');
+require('includes/tripal_analysis_privacy.inc');
 
 /**
  * Register tripal_analysis sub-modules
@@ -72,7 +72,7 @@ function tripal_analysis_menu() {
       'page callback' => 'tripal_analysis_module_description_page',
       'access arguments' => array('administer site configuration'),
       'type' => MENU_NORMAL_ITEM,
-      'file' => 'tripal_analysis.admin.inc',
+      'file' => 'includes/tripal_analysis.admin.inc',
   );
 
   $items['admin/tripal/tripal_analysis/configuration'] = array(
@@ -82,7 +82,7 @@ function tripal_analysis_menu() {
       'page arguments' => array('tripal_analysis_admin'),
       'access arguments' => array('administer site configuration'),
       'type' => MENU_NORMAL_ITEM,
-      'file' => 'tripal_analysis.admin.inc',
+      'file' => 'includes/tripal_analysis.admin.inc',
   );
   return $items;
 }

tripal_core/api/tripal_core.api.inc

@@ -207,7 +207,10 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
           $ukselect_vals[$field] = $insert_values[$field];
         }
         // now check the constraint
-        $coptions = array('statement_name' => 'uqsel_' . $table . '_' . $name);
+        $coptions = array();
+        if ($options['statement_name']) {
+          $coptions = array('statement_name' => 'uqsel_' . $table . '_' . $name);
+        }
         if (tripal_core_chado_select($table, $ukselect_cols, $ukselect_vals, $coptions)) {
           watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate record into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
           return FALSE;
@@ -1941,10 +1944,10 @@ function tripal_core_insert_property($basetable, $record_id, $property,
   // insert
   $props = tripal_core_get_property($basetable, $record_id, $property, $cv_name);
   if (!is_array($props)) {
-  $props = array($props);
+    $props = array($props);
   }
   $rank = 0;
-  if (count($props)>0) {
+  if (count($props) > 0) {
     if ($update_if_present) {
       return tripal_core_update_property($basetable, $record_id, $property, $cv_name, $value);
     }
@@ -1963,7 +1966,12 @@ function tripal_core_insert_property($basetable, $record_id, $property,
       // now add 1 to the rank
       $rank++;
     }
+  } 
+  else {
+    watchdog('tripal_core', "Cannot find property '!prop_name'.",
+        array('!prop_name' => $property), WATCHDOG_ERROR);
   }
+  
 
   // get the foreign key for this property table
   $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');

tripal_cv/tripal_cv.module

@@ -1,9 +1,9 @@
 <?php
 
-require_once "charts.php";
-require_once "trees.php";
-require_once "obo_loader.php";
-require_once "tripal_cv.api.inc";
+require_once "includes/charts.inc";
+require_once "includes/trees.inc";
+require_once "includes/obo_loader.inc";
+require_once "api/tripal_cv.api.inc";
 
 /**
  * @defgroup tripal_cv CV Module
@@ -1002,7 +1002,9 @@ function tripal_cv_cvtermpath_form() {
     '#title' => t('Controlled Vocabulary/Ontology Name'),
     '#type' => 'select',
     '#options' => $cvs,
-    '#description' => t('Select a controlled vocabulary for which you would like to upate the cvtermpath.'),
+    '#description' => t('The Chado cvtermpath is a database table that provides lineage for ontology terms 
+      and is useful for quickly finding any ancestor parent of a term.  This table must be populated for each
+      ontology.  Select a controlled vocabulary for which you would like to upate the cvtermpath.'),
   );
 
   $form['description'] = array(