Bug fix in chado_select_record() and some in-line document changes

tripal_core/api/tripal_core.chado_query.api.inc

@@ -1082,11 +1082,12 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
 
   // Get the table description.
   $table_desc = chado_get_schema($table);
-  if (empty($table_desc)) {
-    tripal_report_error('tripal_core', TRIPAL_WARNING,
+  if (!is_array($table_desc)) {
+    tripal_report_error('tripal_chado', TRIPAL_WARNING,
       'chado_insert_record; There is no table description for !table_name',
       array('!table_name' => $table), array('print' => $print_errors)
     );
+    return FALSE;
   }
 
   $select = '';

tripal_cv/api/tripal_cv.api.inc

@@ -128,30 +128,31 @@ function tripal_get_cv_select_options() {
  * Retrieves a chado controlled vocabulary term variable
  *
  * @param $identifier
- *   An array with the key stating what the identifier is. Supported keys (only one of the
- *   following unique keys are required):
- *    - cvterm_id: the chado cv.cvterm_id primary key
- *    - name: the chado cvterm.name field (assume unique)
- *   There are also some specially handled keys. They are:
- *    - cv_id:  an integer indicating the cv_id or an array with 'name' => the name of the cv.
- *    - synonym: an array with 'name' => the name of the synonym of the cvterm you want
- *        returned; 'cv_id' => the cv_id of the synonym; 'cv_name' => the name of the cv
- *        of the synonym
- *    - property: An array/object describing the property to select records for. It
- *      should at least have either a type_name (if unique across cvs) or type_id. Other
- *      supported keys include: cv_id/cv_name (of the type), value and rank
+ *   An array apropriate for use with the chado_generate_var for uniquely
+ *   identifying a cvterm record. Alternativley, there are also some specially
+ *   handled keys. They are:
+ *    - cv_id:  an integer indicating the cv_id or an array with 'name' => the
+ *      name of the cv.
+ *    - synonym: an array with 'name' => the name of the synonym of the cvterm
+ *      you want returned; 'cv_id' => the cv_id of the synonym; 'cv_name' =>
+ *      the name of the cv of the synonym
+ *    - property: An array/object describing the property to select records
+ *      for. It should at least have either a type_name (if unique across cvs)
+ *      or type_id. Other supported keys include: cv_id/cv_name (of the type),
+ *      value and rank
  * @param $options
  *   An array of options. Supported keys include:
- *     - Any keys supported by chado_generate_var(). See that function definition for
- *       additional details.
+ *     - Any keys supported by chado_generate_var(). See that function
+ *       definition for additional details.
  *
- * NOTE: the $identifier parameter can really be any array similar to $values passed into
- *   chado_select_record(). It should fully specify the cvterm record to be returned.
+ * NOTE: the $identifier parameter can really be any array similar to $values
+ *   passed into chado_select_record(). It should fully specify the cvterm
+ *   record to be returned.
  *
  * @return
- *   If unique values were passed in as an identifier then an object describing the cvterm
- *   will be returned (will be a chado variable from chado_generate_var()). Otherwise,
- *   FALSE will be returned.
+ *   If unique values were passed in as an identifier then an object describing
+ *   the cvterm will be returned (will be a chado variable from
+ *   chado_generate_var()). Otherwise, FALSE will be returned.
  *
  * @ingroup tripal_cv_api
  */
@@ -1082,7 +1083,19 @@ function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE) {
 }
 
 /**
- * Retreives the default vocabulary for a given table and field
+ * Retreives the default vocabulary for a given table and field.
+ *
+ * Each table in Chado that has a 'type_id' (or foreign key constraint to
+ * the cvterm table) will have a default vocabulary assigned. This indicates to
+ * Tripal that terms in that vocabulary are used to set the type_id for that
+ * table. An example where this is used is the
+ * tripal_get_cvterm_select_options() function which generates a list of options
+ * for a select box used in a Drupal form.  The select box will list the terms
+ * from the default vocabulary in the drop down.
+ *
+ * This function uses the Chado table and field name (e.g. 'type_id') to
+ * retreive the vocabulary assgined.
+ *
  * @param $table
  *   The name of the table that contains a field with a foreign key
  *   relationship to the cvterm table

tripal_db/api/tripal_db.api.inc

@@ -141,7 +141,7 @@ function tripal_get_db_select_options() {
 
   $options = array();
   $options[] = 'Select a Database';
-  
+
   foreach ($dbs as $db) {
     $options[$db->db_id] = $db->name;
   }
@@ -179,10 +179,12 @@ function tripal_get_db_select_options() {
  * @endcode
  *
  * @param $identifier
- *   An array with the key stating what the identifier is. Supported keys (only one of the
- *   following unique keys is required):
- *    - dbxref_id: the chado dbxref.dbxref_id primary key
- *    - accession: the chado dbxref.accession field (assume unique)
+ *   An array apropriate for use with the chado_generate_var for uniquely
+ *   identifying a dbxref record. Alternatively, there are also some specially
+ *   handled keys. They are:
+ *    - property: An array/object describing the property to select records for. It
+ *      should at least have either a type_name (if unique across cvs) or type_id. Other
+ *      supported keys include: cv_id/cv_name (of the type), value and rank
  *   There are also some specially handled keys. They are:
  *    - property: An array/object describing the property to select records for. It
  *      should at least have either a type_name (if unique across cvs) or type_id. Other
@@ -240,7 +242,7 @@ function tripal_get_dbxref($identifiers, $options = array()) {
     $property = $identifiers['property'];
     unset($identifiers['property']);
     $dbxref = chado_get_record_with_property(
-      array('table' => 'dbxref', 'base_records' => $identifiers), 
+      array('table' => 'dbxref', 'base_records' => $identifiers),
       array('type_name' => $property),
       $options
     );