Fixed issue #2086459. When creating custom tables the validate routine will check to ensure the table name is not-uppercase.

tripal_core/api/tripal_core.custom_tables.api.inc

@@ -38,26 +38,26 @@ function chado_edit_custom_table($table_id, $table_name, $schema, $skip_if_exist
     $record->table_id = $table_id;
     $record->table_name = $table_name;
     $record->schema = serialize($schema);
-  
+
     // get the current custom table record
     $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id";
     $results = db_query($sql, array(':table_id' => $table_id));
     $custom_table = $results->fetchObject();
-  
+
     // if this is a materialized view then don't allow editing with this function
     if ($custom_table->mview_id) {
       tripal_report_error('tripal_core', TRIPAL_ERROR, "Please use the tripal_edit_mview() function to edit this custom table as it is a materialized view.", array());
       drupal_set_message("This custom table is a materialized view. Please use the "  . l('Materialized View', 'admin/tripal/schema/mviews') . " interface to edit it.", 'error');
       return FALSE;
     }
-    
+
     // if the user changed the table name, we want to drop the old one and force
     // creation of the new one.
     if ($custom_table->table_name != $table_name) {
       chado_query("DROP TABLE %s", $custom_table->table_name);
       $skip_if_exists = 0; // we want to create the table
     }
-  
+
     // if skip creation is not set, then drop the table from chado if it exists
     if (!$skip_if_exists) {
       if (db_table_exists($custom_table->table_name)) {
@@ -65,7 +65,7 @@ function chado_edit_custom_table($table_id, $table_name, $schema, $skip_if_exist
         drupal_set_message(t("Custom Table " . $custom_table->table_name . " dropped"));
       }
     }
-  
+
     // update the custom table record and run the create custom table function
     drupal_write_record('tripal_custom_tables', $record, 'table_id');
     $success = chado_create_custom_table ($table_name, $schema, $skip_if_exists);
@@ -90,10 +90,10 @@ function chado_edit_custom_table($table_id, $table_name, $schema, $skip_if_exist
  * table. This way the function cannot be used to accidentally alter existing
  * non custom tables.  If $skip_if_exists is set then the table is simply
  * added to the tripal_custom_tables and no table is created in Chado.
- * 
- * If you are creating a materialized view do not use this function, but rather 
+ *
+ * If you are creating a materialized view do not use this function, but rather
  * use the tripal_add_mview(). A materialized view is also considered a custom table
- * and an entry for it will be added to both the tripal_mviews and 
+ * and an entry for it will be added to both the tripal_mviews and
  * tripal_custom_tables tables, but only if the tripal_add_mview() function is
  * used. The optional $mview_id parameters in this function is intended
  * for use by the tripal_add_mview() function when it calls this function
@@ -129,20 +129,20 @@ function chado_create_custom_table($table, $schema, $skip_if_exists = 1, $mview_
     $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_name = :table_name";
     $results = db_query($sql, array(':table_name' => $table));
     $centry = $results->fetchObject();
-  
+
     // check to see if the table already exists in the chado schema
     $exists = chado_table_exists($table);
-  
+
     // if the table does not exist then create it
     if (!$exists) {
       $ret = db_create_table('chado.' . $table, $schema);
       $created = 1;
     }
-  
+
     // if the table exists in Chado and in our custom table and
     // skip creation is turned off then drop and re-create the table
     if ($exists and is_object($centry) and !$skip_if_exists) {
-  
+
       // drop the table we'll recreate it with the new schema
       chado_query('DROP TABLE {' . $table . '}');
       // remove any 'referring_tables' from the array as the db_create_table doesn't use that
@@ -153,7 +153,7 @@ function chado_create_custom_table($table, $schema, $skip_if_exists = 1, $mview_
       db_create_table('chado.' . $table, $new_schema);
       $recreated = 1;
     }
-  
+
     // add an entry in the tripal_custom_table
     $record = new stdClass();
     $record->table_name = $table;
@@ -161,17 +161,17 @@ function chado_create_custom_table($table, $schema, $skip_if_exists = 1, $mview_
     if ($mview_id) {
       $record->mview_id = $mview_id;
     }
-  
+
     // if an entry already exists then remove it
     if ($centry) {
       $sql = "DELETE FROM {tripal_custom_tables} WHERE table_name = :table_name";
       db_query($sql, array(':table_name' => $table));
     }
-    $success = drupal_write_record('tripal_custom_tables', $record); 
+    $success = drupal_write_record('tripal_custom_tables', $record);
 
     // now add any foreign key constraints
     if (($created or !$skip_if_exists) and array_key_exists('foreign keys', $schema)) {
-  
+
       // iterate through the foreign keys and add each one
       $fkeys = $schema['foreign keys'];
       foreach ($fkeys as $fktable => $fkdetails) {
@@ -192,7 +192,7 @@ function chado_create_custom_table($table, $schema, $skip_if_exists = 1, $mview_
     $transaction->rollback();
     watchdog_exception('tripal_core', $e);
     $error = _drupal_decode_exception($e);
-    drupal_set_message(t("Could not add custom table '%table_name': %message.", 
+    drupal_set_message(t("Could not add custom table '%table_name': %message.",
       array('%table_name' => $table, '%message' => $error['!message'])), 'error');
     return FALSE;
   }
@@ -209,25 +209,31 @@ function chado_create_custom_table($table, $schema, $skip_if_exists = 1, $mview_
 }
 
 /**
- * This function is used to validate a Drupal Schema API array prior to 
+ * This function is used to validate a Drupal Schema API array prior to
  * passing it ot the chado_create_custom_table_schema().  This function
  * can be used in a form validate function or whenver a schema is provided by
  * a user and needs validation.
- * 
+ *
  * @param $schema_array
  *   the Drupal Schema API compatible array
- *   
+ *
  * @return
  *   An empty string for success or a message string for failure
- * 
+ *
  * @ingroup tripal_custom_tables_api
  */
 function chado_validate_custom_table_schema($schema_array) {
 
+
   if (is_array($schema_array) and !array_key_exists('table', $schema_array)) {
     return "The schema array must have key named 'table'";
   }
-  
+
+  if (!ctype_lower($schema_array['table'])) {
+    return "Postgres will automatically change the table name to lower-case. To prevent unwanted side-effects, please rename the table with all lower-case characters.";
+  }
+
+
   // check index length
   if (array_key_exists('indexes', $schema_array)) {
     foreach ($schema_array['indexes'] as $index_name => $details) {
@@ -239,7 +245,7 @@ function chado_validate_custom_table_schema($schema_array) {
       }
     }
   }
-  
+
   // check unique key length
   if (array_key_exists('unique keys', $schema_array)) {
     foreach ($schema_array['unique keys'] as $index_name => $details) {
@@ -251,7 +257,7 @@ function chado_validate_custom_table_schema($schema_array) {
       }
     }
   }
-  
+
 }
 /**
  * Retrieve the custom table id given the name

tripal_core/includes/tripal_core.custom_tables.inc

@@ -57,7 +57,7 @@ function tripal_custom_table_admin_view() {
  * @ingroup tripal_custom_tables
  */
 function tripal_custom_table_new_page() {
- 
+
   $form = drupal_get_form('tripal_custom_tables_form');
   return drupal_render($form);
 }
@@ -140,7 +140,7 @@ function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL)
     $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id ";
     $results = db_query($sql, array(':table_id' => $table_id));
     $custom_table = $results->fetchObject();
-    
+
     // if this is a materialized view then don't allow editing with this function
     if (property_exists($custom_table, 'mview_id') and $custom_table->mview_id) {
       drupal_set_message("This custom table is a materialized view. Please use the "  . l('Materialized View', 'admin/tripal/schema/mviews') . " interface to edit it.", 'error');
@@ -161,7 +161,7 @@ function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL)
       $default_schema = preg_replace('/=>\s+\n\s+array/', '=> array', $default_schema);
     }
   }
-  
+
   $form['return'] = array(
     '#type' => 'markup',
     '#markup' => "<p>" . l("Return to list of custom tables", "admin/tripal/schema/custom_tables") . "</p>",
@@ -178,49 +178,33 @@ function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL)
     '#value' => $table_id
   );
 
-  $form['instructions']= array(
+  $form['instructions'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Instructions',
+    '#collapsible' => TRUE,
+    '#collapsed' => TRUE,
+  );
+  $form['instructions']['text'] = array(
     '#type'          => 'item',
-    '#description'         => t('At times it is necessary to add a custom table to the Chado schema.
-       These are not offically sanctioned tables but may be necessary for local data requirements.
-       Avoid creating custom tables when possible as other GMOD tools may not recognize these tables
-       nor the data in them.  Linker tables or property tables are often a good candidate for
-       a custom table. For example a table to link stocks and libraries (e.g. library_stock). 
-       Try to model linker or propery tables after existing tables.  If the
-       table already exists it will not be modified.  To force dropping and recreation of the table
-       click the checkbox below.  Tables are defined usign the ' . l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7', array('attributes' => array('target' => '_blank')))
+    '#description'         => '<p>' . t('At times it is necessary to add a custom table
+       to the Chado schema. These are not offically sanctioned tables but may
+       be necessary for local data requirements. Avoid creating custom tables
+       when possible as other GMOD tools may not recognize these tables nor
+       the data in them.  Linker tables or property tables are often a good
+       candidate for a custom table. For example a table to link stocks and
+       libraries (e.g. library_stock). Try to model linker or propery tables
+       after existing tables.  If the table already exists it will not be
+       modified.  To force dropping and recreation of the table
+       click the checkbox below.  Tables are defined usign the ' .
+       l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7',
+         array('attributes' => array('target' => '_blank'))) . '</p>' .
+      '<p>Please note that table names should be all lower-case.</p>'
     ),
   );
 
-  $form['force_drop']= array(
-    '#type'          => 'checkbox',
-    '#title'         => t('Re-create table'),
-    '#description'   => t('Check this box if your table already exists and you would like to drop it and recreate it.'),
-    '#default_value' => $default_force_drop,
-  );
-  $form['schema']= array(
-    '#type'          => 'textarea',
-    '#title'         => t('Schema Array'),
-    '#description'   => t('Please enter the ' . l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7', array('attributes' => array('target' => '_blank'))) . ' compatible array that defines the table.'),
-    '#required'      => FALSE,
-    '#default_value' => $default_schema,
-    '#rows'          => 25,
-  );
-
-  if ($action == 'Edit') {
-    $value = 'Save';
-  }
-  if ($action == 'Add') {
-    $value = 'Add';
-  }
-  $form['submit'] = array(
-    '#type'         => 'submit',
-    '#value'        => t($value),
-    '#executes_submit_callback' => TRUE,
-  );
-
-  $form['example']= array(
-    '#type'          => 'item',
-    '#description'         => "<br>Example library_stock table: <pre>
+  $form['instructions']['example']= array(
+      '#type'          => 'item',
+      '#description'         => "Example library_stock table: <pre>
 array (
   'table' => 'library_stock',
   'fields' => array (
@@ -264,6 +248,35 @@ array (
     </pre>",
   );
 
+  $form['force_drop']= array(
+    '#type'          => 'checkbox',
+    '#title'         => t('Re-create table'),
+    '#description'   => t('Check this box if your table already exists and you would like to drop it and recreate it.'),
+    '#default_value' => $default_force_drop,
+  );
+  $form['schema']= array(
+    '#type'          => 'textarea',
+    '#title'         => t('Schema Array'),
+    '#description'   => t('Please enter the ' . l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7', array('attributes' => array('target' => '_blank'))) . ' compatible array that defines the table.'),
+    '#required'      => FALSE,
+    '#default_value' => $default_schema,
+    '#rows'          => 25,
+  );
+
+  if ($action == 'Edit') {
+    $value = 'Save';
+  }
+  if ($action == 'Add') {
+    $value = 'Add';
+  }
+  $form['submit'] = array(
+    '#type'         => 'submit',
+    '#value'        => t($value),
+    '#executes_submit_callback' => TRUE,
+  );
+
+
+
 
   return $form;
 }
@@ -301,13 +314,13 @@ function tripal_custom_tables_form_validate($form, &$form_state) {
       if (is_array($schema_array) and !array_key_exists('table', $schema_array)) {
         form_set_error('schema', t("The schema array must have key named 'table'"));
       }
-      
+
       // validate the contents of the array
       $error = chado_validate_custom_table_schema($schema_array);
       if ($error) {
         form_set_error('schema', $error);
       }
-      
+
       if ($action == 'Edit') {
         // see if the table name has changed. If so, then check to make sure
         // it doesn't already exists. We don't want to drop a table we didn't mean to
@@ -359,7 +372,7 @@ function tripal_custom_tables_form_submit($form, &$form_state) {
   else {
     drupal_set_message(t("No action performed."));
   }
-  
+
   drupal_goto("admin/tripal/schema/custom_tables");
 }
 
@@ -369,26 +382,26 @@ function tripal_custom_tables_form_submit($form, &$form_state) {
  * @ingroup tripal_custom_tables
  */
 function tripal_custom_tables_delete_form($form, &$form_state, $table_id) {
-  
+
   // get details about this table entry
   $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id";
   $results = db_query($sql, array(':table_id' => $table_id));
   $entry = $results->fetchObject();
-  
+
   // if this is a materialized view then don't allow editing with this function
   if ($entry->mview_id) {
     drupal_set_message("This custom table is a materialized view. Please use the "  . l('Materialized View', 'admin/tripal/schema/mviews') . " interface to delete it.", 'error');
     drupal_goto("admin/tripal/schema/custom_tables");
     return array();
   }
-  
-  
+
+
   $form = array();
   $form['table_id'] = array(
     '#type' => 'value',
     '#value' => $table_id
   );
-  
+
   $form['sure'] = array(
     '#type' => 'markup',
     '#markup' => '<p>Are you sure you want to delete the "' . $entry->table_name . '" custom table?</p>'
@@ -406,14 +419,14 @@ function tripal_custom_tables_delete_form($form, &$form_state, $table_id) {
 
 /**
  * form submit hook for the tripal_custom_tables_delete_form form.
- * 
+ *
  * @param $form
  * @param $form_state
  */
 function tripal_custom_tables_delete_form_submit($form, &$form_state) {
   $action   = $form_state['clicked_button']['#value'];
   $table_id = $form_state['values']['table_id'];
-    
+
   if (strcmp($action, 'Delete') == 0) {
     chado_delete_custom_table($table_id);
   }