Fix for issue #322... still working on unit testing for it

tests/tripal_chado/api/TripalChadoCustomTablesAPITest.php

@@ -5,15 +5,149 @@ use StatonLab\TripalTestSuite\DBTransaction;
 use StatonLab\TripalTestSuite\TripalTestCase;
 
 class TripalChadoCustomTablesAPITest extends TripalTestCase {
-  // Uncomment to auto start and rollback db transactions per test method.
-  // use DBTransaction;
 
+  use DBTransaction;
+
+  /**
+   * Test creation of a new materialized view.
+   * 
+   * @group api
+   */
+  public function test_chado_add_mview() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  /**
+   * Test deletion of a materialized view.
+   * 
+   * @group api
+   */
+  public function test_chado_delete_mview() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  /**
+   * Test modifications to a materialized view
+   * 
+   * @group api
+   */
+  public function test_chado_edit_mview() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  /**
+   * Test adding a Tripal Job to re-populate a materialized view
+   *
+   * @group api
+   */
+  public function test_chado_refresh_mview() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  /**
+   * Test re-populating a materialized view.
+   *
+   * @group api
+   */
+  public function test_chado_populate_mview() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  /**
+   * Test modifications to a materialized view
+   *
+   * @group api
+   */
+  public function test_chado_get_mview_id() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  /**
+   * Test retrieving names of the materialized views.
+   *
+   * @group api
+   */
+  public function test_chado_get_mview_table_names() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  /**
+   * Test retrieving all materialized view objects.
+   *
+   * @group api
+   */
+  public function test_chado_get_mviews() {
+    // TODO: this is currently a stub for a test function that neds
+    // implementation. For now it returns true to get past unit testing.
+    $this->assertTrue(true);
+  }
+  
   /**
-   * Basic test example.
-   * Tests must begin with the word "test".
-   * See https://phpunit.readthedocs.io/en/latest/ for more information.
+   * Issue 322 reported the problem of re-adding a materialized view after 
+   * the actual table had been manually removed outside of Tripal.  The
+   * function reported errors.
+   * 
+   * @ticket 322
    */
-  public function testBasicExample() {
+  public function test_re_adding_deleted_mview_issue_322() {
+    $mview_table = 'analysis_organism';
+    $mview_sql = "
+      SELECT DISTINCT A.analysis_id, O.organism_id
+      FROM analysis A
+        INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id
+        INNER JOIN feature F          ON AF.feature_id = F.feature_id
+        INNER JOIN organism O         ON O.organism_id = F.organism_id
+    ";
+    $mview_schema = "array (
+      'table' => 'analysis_organism',
+      'description' => 'This view is for associating an organism (via it\'s associated features) to an analysis.',
+      'fields' => array (
+        'analysis_id' => array (
+          'size' => 'big',
+          'type' => 'int',
+          'not null' => true,
+        ),
+        'organism_id' => array (
+          'size' => 'big',
+          'type' => 'int',
+          'not null' => true,
+        ),
+      ),
+      'indexes' => array (
+        'networkmod_qtl_indx0' => array (
+          0 => 'analysis_id',
+        ),
+        'networkmod_qtl_indx1' => array (
+          0 => 'organism_id',
+        ),
+      ),
+      'foreign keys' => array (
+        'analysis' => array (
+          'table' => 'analysis',
+          'columns' => array (
+            'analysis_id' => 'analysis_id',
+          ),
+        ),
+        'organism' => array (
+          'table' => 'organism',
+          'columns' => array (
+            'organism_id' => 'organism_id',
+          ),
+        ),
+      ),
+    )";
+    
+    // First add the mview normally:
+    chado_add_mview($mview_table, 'tripal_chado', $mview_schema, $mview_sql, NULL, FALSE);
+    
+      
     $this->assertTrue(true);
   }
 }

tests/tripal_chado/api/TripalChadoMViewsAPITest.php

@@ -0,0 +1,19 @@
+<?php
+namespace Tests\tripal_chado\api;
+
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
+
+class TripalChadoMViewsAPITest extends TripalTestCase {
+  // Uncomment to auto start and rollback db transactions per test method.
+  // use DBTransaction;
+
+  /**
+   * Basic test example.
+   * Tests must begin with the word "test".
+   * See https://phpunit.readthedocs.io/en/latest/ for more information.
+   */
+  public function testBasicExample() {
+    $this->assertTrue(true);
+  }
+}

tripal_chado/api/tripal_chado.mviews.api.inc

@@ -52,6 +52,15 @@ function chado_add_mview($name, $modulename, $mv_schema, $query, $comment = NULL
 
   $mv_table = $mv_schema['table'];
 
+  // Check that the materialized view actually exists and if not,
+  // remove the entry from tripal_mviews.
+  if ($mview_id AND !chado_table_exists($name)) {
+    db_query(
+      'DELETE FROM {tripal_mviews} WHERE mview_id = :id',
+      array(':id' => $mview_id))->execute();
+      $mview_id = FALSE;
+  }
+  
   // See if the mv_table name already exsists.
   $mview_id = db_query(
     'SELECT mview_id FROM {tripal_mviews} WHERE name = :name',