Ensure Chado Prepare works in automated testing

tripal/src/TripalDBX/TripalDbxConnection.php

@@ -990,7 +990,7 @@ protected function setPrefix($prefix) {
    * @return bool
    *   TRUE if default schema is not Drupal's but the Tripal DBX managed one.
    */
-  protected function shouldUseTripalDbxSchema() :bool {
+  public function shouldUseTripalDbxSchema() :bool {
     $should = FALSE;
 
     // Check the class/object who is using Tripal DBX:
@@ -1022,15 +1022,23 @@ protected function shouldUseTripalDbxSchema() :bool {
     // Check all parents of the class who is using Tripal DBX:
     // This allows for APIs to be added to the whitelist and all children class
     // implementations to then automatically use the Tripal DBX managed schema.
-    $class = new \ReflectionClass($calling_class);
-    $inheritance_level = 0;
-    while ($parent = $class->getParentClass()) {
-      $inheritance_level++;
-      $parent_class = $parent->getName();
-      if (!empty($this->classesUsingTripalDbx[$parent_class])) {
-        $should = TRUE;
+    if (class_exists($calling_class)) {
+      $class = new \ReflectionClass($calling_class);
+      $inheritance_level = 0;
+      while ($parent = $class->getParentClass()) {
+        $inheritance_level++;
+        $parent_class = $parent->getName();
+        if (!empty($this->classesUsingTripalDbx[$parent_class])) {
+          $should = TRUE;
+        }
+        $class = $parent;
       }
-      $class = $parent;
+    }
+    // If Tripal DBX was called from a stand-alone function (i.e. not within
+    // a class) then the calling class will be empty. We do not want to throw
+    // an exception in that case.
+    elseif (!empty($calling_class)) {
+      throw new \Exception("TripalDBX unable to find class for checking inheritance. This class must exist and be available in the current application space: $calling_class. Hint: make sure to 'use' all needed classes in your application.");
     }
 
     return $should;
@@ -1218,7 +1226,9 @@ public function executeSqlQueries(
     ?string $schema_name = NULL
   ) :bool {
     // Get schema to use.
-    $schema_name = $this->getDefaultSchemaName($schema_name);
+    if (empty($schema_name)) {
+      $schema_name = $this->getDefaultSchemaName($schema_name);
+    }
     // Set search_path.
     if (!empty($schema_name)) {
       $search_path = 'SET search_path = "' . $schema_name . '";';
@@ -1239,19 +1249,29 @@ public function executeSqlQueries(
       elseif (is_array($search_path_mode)) {
         $search = [];
         $replace = [];
+
         foreach ($search_path_mode as $old_name => $replacement) {
+
+          // Ensure the replacement pattern is sanitized.
           // Secure replacement (we allow comas and spaces).
           $replacement = preg_replace(
             '/[^a-z_\\xA0-\\xFF0-9\s,]+/',
             '',
             $replacement
           );
+
+          // Find/Replace any search path queries.
           $search[] =
             '/(SET\s*search_path\s*=(?:[^;]+,)?)\s*'
             . preg_quote($old_name)
             . '\s*((?:,[^;]+)?;)(?!\s*--\s*KEEP)/im'
           ;
           $replace[] = '\1' . $replacement . '\2';
+
+          // Find/replace any in-query table prefixing.
+          $search[] = '/ '. preg_quote($old_name) . '\.(\w+) /';
+          $replace[] = ' ' . $replacement . '.\1 ';
+
         }
         $sql_queries = preg_replace(
           $search,
@@ -1299,13 +1319,15 @@ public function executeSqlQueries(
    */
   public function executeSqlFile(
     string $sql_file_path,
-    $search_path_mode = FALSE
+    $search_path_mode = FALSE,
+    ?string $schema_name = NULL
   ) :bool {
     // Retrieve the SQL file.
     $sql_queries = file_get_contents($sql_file_path);
     return $this->executeSqlQueries(
       $sql_queries,
-      $search_path_mode
+      $search_path_mode,
+      $schema_name
     );
   }
 
@@ -1341,6 +1363,16 @@ public function escapeTable($table) {
     return parent::escapeTable($table);
   }
 
+  /**
+   * Retrieve a list of classes which are using Tripal DBX byb default.
+   *
+   * @return array
+   *  An array of class names including namespace.
+   */
+  public function getListClassesUsingTripalDbx() {
+    return $this->classesUsingTripalDbx;
+  }
+
   /**
    * Implements the magic __toString method.
    */

tripal/src/TripalImporter/TripalImporterBase.php

@@ -449,7 +449,7 @@ protected function setItemsHandled($total_handled) {
 
     if ($total_handled == 0) {
       $memory = number_format(memory_get_usage());
-      print t("Percent complete: 0%. Memory: " . $memory . " bytes.") . "\r";
+      $this->logger->notice(t("Percent complete: 0%. Memory: " . $memory . " bytes.") . "\r");
       return;
     }
 
@@ -462,12 +462,10 @@ protected function setItemsHandled($total_handled) {
     if ($ipercent > 0 and $ipercent != $this->reported and $ipercent % $this->interval == 0) {
       $memory = number_format(memory_get_usage());
       $spercent = sprintf("%.2f", $percent);
-      /*
-      print t("Percent complete: !percent %. Memory: !memory bytes.",
-          ['!percent' => $spercent, '!memory' => $memory]) . "\r";
-      */
-      print t("Percent complete: " . $spercent .
-        " %. Memory: " . $memory . " bytes.") . "\r";
+      $this->logger->notice(
+        t("Percent complete: " . $spercent . " %. Memory: " . $memory . " bytes.")
+         . "\r"
+      );
 
       // If we have a job the update the job progress too.
       if ($this->job) {
@@ -502,4 +500,4 @@ public function getArguments() {
     return $this->arguments;
   }
 
-}
+}

tripal_chado/src/ChadoCustomTables/ChadoCustomTable.php

@@ -59,14 +59,17 @@ public function __construct($table_name, string $chado_schema = NULL) {
     // an empty record for it.
     if (!$this->table_id) {
       $public = \Drupal::database();
-      $chado = $this->getChado();
       $insert = $public->insert('tripal_custom_tables');
       $insert->fields([
-        'table_name' => $table_name,
+        'table_name' => $this->table_name,
         'schema' => '',
-        'chado' => $chado->getSchemaName(),
+        'chado' => $this->chado_schema,
       ]);
-      $insert->execute();
+      $table_id = $insert->execute();
+      if (!$table_id) {
+        throw New \Exception('Could not add the custom table, "' . $this->table_name .
+            '" for the Chado schema "' . $this->chado_schema .'".');
+      }
       $this->setTableId();
     }
   }
@@ -97,10 +100,8 @@ private function setTableId() {
     $query->condition('ct.table_name', $this->table_name);
     $query->condition('ct.chado', $this->chado_schema);
     $results = $query->execute();
-    if ($results) {
-      $custom_table = $results->fetchObject();
-      $this->table_id = $custom_table->table_id;
-    }
+    $this->table_id = $results->fetchField();
+
   }
 
   /**
@@ -419,4 +420,4 @@ private function deleteCustomTable() {
     }
     return True;
   }
-}
+}

tripal_chado/src/ChadoCustomTables/ChadoMview.php

@@ -239,10 +239,10 @@ public function populate() {
     $transaction = $public->startTransaction();
 
     try {
-      $chado->query("DELETE FROM {" . $this->getTableName() . "}");
+      $chado->query("DELETE FROM {1:" . $this->getTableName() . "}");
       $sql_query = $this->getSqlQuery();
-      $chado->query("INSERT INTO {" . $this->getTableName() . "} ($sql_query)");
-      $results = $chado->query("SELECT COUNT(*) as num_rows FROM {" . $this->getTableName() . "}");
+      $chado->query("INSERT INTO {1:" . $this->getTableName() . "} ($sql_query)");
+      $results = $chado->query("SELECT COUNT(*) as num_rows FROM {1:" . $this->getTableName() . "}");
       $num_rows = $results->fetchField();
       $this->setStatus("Populated with " . $num_rows . " rows");
       $this->setLastUpdate(time());
@@ -288,4 +288,4 @@ public function destroy() {
 
     return parent::destroy();
   }
-}
+}