Fixed bug in MView validation. Added instructions to create MView page

tripal_core/api/tripal_core.custom_tables.api.inc

@@ -229,7 +229,7 @@ function chado_validate_custom_table_schema($schema_array) {
     return "The schema array must have key named 'table'";
   }
 
-  if (!ctype_lower($schema_array['table'])) {
+  if (preg_match('/[ABCDEFGHIJKLMNOPQRSTUVWXYZ]/', $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.";
   }
 

tripal_core/includes/tripal_core.custom_tables.inc

@@ -185,8 +185,8 @@ function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL)
     '#collapsed' => TRUE,
   );
   $form['instructions']['text'] = array(
-    '#type'          => 'item',
-    '#description'         => '<p>' . t('At times it is necessary to add a custom table
+    '#type'   => 'item',
+    '#markup' => '<p>' . t('At times it is necessary to add a custom table
        to the Chado schema. These are not offically sanctioned tables but may
        be necessary for local data requirements. Avoid creating custom tables
        when possible as other GMOD tools may not recognize these tables nor
@@ -195,7 +195,7 @@ function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL)
        libraries (e.g. library_stock). Try to model linker or propery tables
        after existing tables.  If the table already exists it will not be
        modified.  To force dropping and recreation of the table
-       click the checkbox below.  Tables are defined usign the ' .
+       click the checkbox below.  Tables are defined using the ' .
        l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7',
          array('attributes' => array('target' => '_blank'))) . '</p>' .
       '<p>Please note that table names should be all lower-case.</p>'
@@ -203,8 +203,8 @@ function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL)
   );
 
   $form['instructions']['example']= array(
-      '#type'          => 'item',
-      '#description'         => "Example library_stock table: <pre>
+      '#type'    => 'item',
+      '#markup'  => "Example library_stock table: <pre>
 array (
   'table' => 'library_stock',
   'fields' => array (

tripal_core/includes/tripal_core.mviews.inc

@@ -258,6 +258,89 @@ function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
     '#description' => l("Return to table of materialized views", "admin/tripal/schema/mviews/"),
   );
 
+  $form['instructions'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Instructions',
+    '#collapsible' => TRUE,
+    '#collapsed' => TRUE,
+  );
+  $form['instructions']['text'] = array(
+    '#type'          => 'item',
+    '#markup'   =>  t('Materialized views are used to help speed data
+      querying, particularly for searching.  A materialized view is essentially
+      a database table that is pre-populated with the desired data to search on.
+      Rows in the materialized view are typically a combination of data from
+      multiple tables with indexes on searchable columns. The table structure
+      for materialized views is defined using the ' .
+      l('Drupal Schema API', 'https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7',
+        array('attributes' => array('target' => '_blank'))) . '. '. t('Additionally,
+      an SQL statement is provided that populates the table with data. ' .
+      'Please note that table names should be all lower-case.')
+    ),
+  );
+  $form['instructions']['example_schema']= array(
+    '#type'          => 'item',
+    '#markup'         => "An example Schema API definition for a materialized view: <pre>
+array (
+  'description' => 'Stores the type and number of features per organism',
+  'table' => 'organism_feature_count',
+  'fields' => array (
+    'organism_id' => array (
+      'type' => 'int',
+      'not null' => true,
+    ),
+    'genus' => array (
+      'type' => 'varchar',
+      'length' => '255',
+      'not null' => true,
+    ),
+    'species' => array (
+      'type' => 'varchar',
+      'length' => '255',
+      'not null' => true,
+    ),
+    'common_name' => array (
+      'type' => 'varchar',
+      'length' => '255',
+      'not null' => false,
+    ),
+    'num_features' => array (
+      'type' => 'int',
+      'not null' => true,
+    ),
+    'cvterm_id' => array (
+      'type' => 'int',
+      'not null' => true,
+    ),
+    'feature_type' => array (
+      'type' => 'varchar',
+      'length' => '255',
+      'not null' => true,
+    ),
+  ),
+  'indexes' => array (
+    'organism_id_idx'  => array ('organism_id'),
+    'cvterm_id_idx'    => array ('cvterm_id'),
+    'feature_type_idx' => array ('feature_type'),
+  ),
+)
+</pre>"
+  );
+  $form['instructions']['example_sql'] = array(
+    '#type' => 'item',
+    '#markup' => "An example SQL statement to populate the table: <pre>
+SELECT
+    O.organism_id, O.genus, O.species, O.common_name,
+    count(F.feature_id) as num_features,
+    CVT.cvterm_id, CVT.name as feature_type
+ FROM organism O
+    INNER JOIN feature F  ON O.Organism_id = F.organism_id
+    INNER JOIN cvterm CVT ON F.type_id     = CVT.cvterm_id
+ GROUP BY
+    O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
+    </pre>"
+  );
+
 
   $form['name']= array(
     '#type'          => 'textfield',
@@ -279,7 +362,7 @@ function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
   $form['schema'] = array(
     '#type' => 'fieldset',
     '#title' => 'Table Schema',
-    '#description' => t('Use a ' . l("Drupal Schema API", "https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7", array('attributes' => array('target' => '_blank'))) . 
+    '#description' => t('Use a ' . l("Drupal Schema API", "https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7", array('attributes' => array('target' => '_blank'))) .
         ' array to describe the table. See the bottom of this page for an example.'),
     '#collapsible' => 1,
     '#collapsed' => $schema_collapsed ,
@@ -288,7 +371,7 @@ function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
   $form['schema']['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'))) . 
+    '#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. There must also be a "table" key with the name of the table as the value. See the example at the bottom of this page.'),
     '#required'      => FALSE,
     '#default_value' => $default_schema,
@@ -370,55 +453,8 @@ function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
     '#value'        => t($value),
     '#executes_submit_callback' => TRUE,
   );
-  
-  $form['example']= array(
-    '#type'          => 'item',
-    '#description'         => "<br>An example Schema API definition for a materialized view: <pre>
-array (
-  'description' => 'Stores the type and number of features per organism',
-  'table' => 'organism_feature_count',
-  'fields' => array (
-    'organism_id' => array (
-      'type' => 'int',
-      'not null' => true,
-    ),
-    'genus' => array (
-      'type' => 'varchar',
-      'length' => '255',
-      'not null' => true,
-    ),
-    'species' => array (
-      'type' => 'varchar',
-      'length' => '255',
-      'not null' => true,
-    ),
-    'common_name' => array (
-      'type' => 'varchar',
-      'length' => '255',
-      'not null' => false,
-    ),
-    'num_features' => array (
-      'type' => 'int',
-      'not null' => true,
-    ),
-    'cvterm_id' => array (
-      'type' => 'int',
-      'not null' => true,
-    ),
-    'feature_type' => array (
-      'type' => 'varchar',
-      'length' => '255',
-      'not null' => true,
-    ),
-  ),
-  'indexes' => array (
-    'organism_id_idx'  => array ('organism_id'),
-    'cvterm_id_idx'    => array ('cvterm_id'),
-    'feature_type_idx' => array ('feature_type'),
-  ),
-)
-</pre>"
-  );
+
+
   return $form;
 }
 
@@ -429,14 +465,14 @@ array (
  * @ingroup tripal_mviews
  */
 function tripal_mviews_form_validate($form, &$form_state) {
-  
-  
+
+
   $action    = $form_state['values']['action'];
   $mview_id  = $form_state['values']['mview_id'];
   $name      = trim($form_state['values']['name']);
   $is_legacy = $form_state['values']['is_legacy'];
   $query     = $form_state['values']['mvquery'];
-  
+
   // if this is a legacy materialized view (no longer supported in Tripal v2.0
   // but code left just in case)
   if ($is_legacy) {
@@ -453,7 +489,7 @@ function tripal_mviews_form_validate($form, &$form_state) {
   }
   $comment = trim($form_state['values']['comment']);
   $schema  = $form_state['values']['schema'];
-  
+
   // validate the contents of the array
   $schema_array = array();
   $success = eval("\$schema_array = $schema;");
@@ -469,7 +505,7 @@ function tripal_mviews_form_validate($form, &$form_state) {
       t('You can create an MView using the Drupal Schema API method or the ' .
         'traditional method but not both.'));
   }
-  
+
   // if we don't have a schema and are missing fields for the legacy views then
   // inform the user.
   if (!$schema) {
@@ -508,7 +544,7 @@ function tripal_mviews_form_validate($form, &$form_state) {
 function tripal_mviews_form_submit($form, &$form_state) {
 
   $ret = array();
-  
+
   $action     = $form_state['values']['action'];
   $mview_id   = $form_state['values']['mview_id'];
   $name       = trim($form_state['values']['name']);
@@ -521,7 +557,7 @@ function tripal_mviews_form_submit($form, &$form_state) {
   $mv_specs = '';
   $indexed = '';
   $special_index = '';
-  
+
   // if this is a legacy materialized view (no longer supported in Tripal v2.0
   // but code left just in case)
   if ($is_legacy) {
@@ -611,11 +647,11 @@ function tripal_mviews_delete_form_submit($form, &$form_state) {
 /**
  * A wrapper for the tripal_refresh_mview() API function, which
  * then redirects back to the admin page for mviews.
- * 
+ *
  * @param $mview_id
  */
 function tripal_mviews_add_populate_job($mview_id) {
-  
+
   tripal_refresh_mview($mview_id);
   drupal_goto("admin/tripal/schema/mviews");
 }