Forgot ot add legacy CV API file

legacy/tripal_cv/api/tripal_cv.api.inc

@@ -0,0 +1,117 @@
+<?php
+/**
+ * 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
+ * @param $field
+ *   The table field name that has the foreign key relationship to the
+ *   cvterm table for which the default vocabulary will be set
+ *
+ * @return
+ *   The cv object of the default vocabulary or an empty array if not
+ *   available.
+ */
+function tripal_get_default_cv($table, $field) {
+  $sql = "
+    SELECT cv_id
+    FROM {tripal_cv_defaults}
+    WHERE table_name = :table and field_name = :field
+  ";
+  $cv_id = db_query($sql, array(':table' => $table, ':field' => $field))->fetchField();
+
+  return tripal_get_cv(array('cv_id' => $cv_id));
+}
+
+/**
+ * Retrieves the Chado table to which a vocbulary is set as default.
+ *
+ * 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 vocabulary ID to get the Chado table to which it
+ * is assigned.
+ *
+ * @param $cv_id
+ *  The ID of the vocabulary.
+ *
+ * @return
+ *   If an assignment is present, an object containing the 'table_name' and
+ *   'field_name' is returned.
+ */
+function tripal_get_default_cv_table($cv_id) {
+  $default = db_select('tripal_cv_defaults', 't')
+    ->fields('t', array('table_name', 'field_name'))
+    ->condition('cv_id', $cv_id)
+    ->execute()
+    ->fetchObject();
+  return $default;
+}
+
+/**
+ * Create an options array to be used in a form element
+ * which provides a list of all chado cvterms. Unlike the
+ * tripal_get_cvterm_select_option, this function retreives the cvterms using
+ * the default vocabulary set for a given table and field.  It will also
+ * notify the administrative user if a default vocabulary is missing for the
+ * field and if the vocabulary is empty.
+ *
+ * @param $table
+ *   The name of the table that contains the field with a foreign key
+ *   relationship to the cvterm table
+ * @param $field
+ *   The table field name that has the foreign key relationship to the
+ *   cvterm table for which the default vocabulary will be set
+ * @param $field_desc
+ *   A human readable descriptive name for the field
+ *
+ * @return
+ *   An array(cvterm_id => name)
+ *   for each cvterm in the chado cvterm table where cv_id=that supplied
+ */
+function tripal_get_cvterm_default_select_options($table, $field, $field_desc) {
+
+  $default_cv = tripal_get_default_cv($table, $field);
+  $options = array();
+
+  if ($default_cv) {
+    $options = tripal_get_cvterm_select_options($default_cv->cv_id);
+
+    if (count($options) == 0) {
+      tripal_set_message('There are no ' . $field_desc . '. Please ' .
+          l('add terms',
+              'admin/tripal/vocab/cv/' .$default_cv->cv_id. '/cvterm/add',
+              array('attributes' => array('target' => '_blank'))) . ' to the ' .
+          $default_cv->name .' vocabulary.',
+          TRIPAL_WARNING);
+    }
+
+  }
+  else {
+    tripal_set_message('There is not a default vocabulary set for ' . $field_desc . '. '.
+        'Please set one using the ' .
+        l('vocabulary defaults configuration page',
+            'admin/tripal/vocab/defaults',
+            array('attributes' => array('target' => '_blank'))) . '.',
+        TRIPAL_WARNING);
+  }
+
+  return $options;
+}

tripal_chado/api/modules/tripal_chado.cv.api.inc

@@ -1155,53 +1155,3 @@ function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE) {
 }
 
 
-/**
- * Create an options array to be used in a form element
- * which provides a list of all chado cvterms. Unlike the
- * tripal_get_cvterm_select_option, this function retreives the cvterms using
- * the default vocabulary set for a given table and field.  It will also
- * notify the administrative user if a default vocabulary is missing for the
- * field and if the vocabulary is empty.
- *
- * @param $table
- *   The name of the table that contains the field with a foreign key
- *   relationship to the cvterm table
- * @param $field
- *   The table field name that has the foreign key relationship to the
- *   cvterm table for which the default vocabulary will be set
- * @param $field_desc
- *   A human readable descriptive name for the field
- *
- * @return
- *   An array(cvterm_id => name)
- *   for each cvterm in the chado cvterm table where cv_id=that supplied
- */
-function tripal_get_cvterm_default_select_options($table, $field, $field_desc) {
-
-  $default_cv = tripal_get_default_cv($table, $field);
-  $options = array();
-
-  if ($default_cv) {
-    $options = tripal_get_cvterm_select_options($default_cv->cv_id);
-
-    if (count($options) == 0) {
-      tripal_set_message('There are no ' . $field_desc . '. Please ' .
-        l('add terms',
-          'admin/tripal/vocab/cv/' .$default_cv->cv_id. '/cvterm/add',
-           array('attributes' => array('target' => '_blank'))) . ' to the ' .
-        $default_cv->name .' vocabulary.',
-        TRIPAL_WARNING);
-    }
-
-  }
-  else {
-    tripal_set_message('There is not a default vocabulary set for ' . $field_desc . '. '.
-      'Please set one using the ' .
-      l('vocabulary defaults configuration page',
-        'admin/tripal/vocab/defaults',
-        array('attributes' => array('target' => '_blank'))) . '.',
-      TRIPAL_WARNING);
-  }
-
-  return $options;
-}