Fix for issue #431

tripal_chado/api/tripal_chado.query.api.inc

@@ -349,9 +349,9 @@ function chado_set_active($dbname = 'default') {
   $search_path = chado_get_schema_name('drupal');
 
   // Change only if 'chado' has been specified.
-  // Notice that we leave the active_db set as chado but use the possibly 
-  // user-altered  schema name for the actual search path. This is to keep 
-  // outward facing mentions of chado as "chado" while still allowing the user 
+  // Notice that we leave the active_db set as chado but use the possibly
+  // user-altered  schema name for the actual search path. This is to keep
+  // outward facing mentions of chado as "chado" while still allowing the user
   // to alter the schema name used.
   if ($dbname == 'chado') {
     $active_db = 'chado';
@@ -490,7 +490,7 @@ function chado_insert_record($table, $values, $options = []) {
   // that has all the values needed for insert with all foreign relationsihps
   // resolved.
   foreach ($values as $field => $value) {
-    // Make sure the field is in the table description. If not then return an 
+    // Make sure the field is in the table description. If not then return an
     // error message.
     if (!array_key_exists($field, $table_desc['fields'])) {
       tripal_report_error('tripal_chado', TRIPAL_ERROR,
@@ -910,7 +910,7 @@ function chado_update_record($table, $match, $values, $options = NULL) {
 
   // If we have a result then add primary keys to return array.
   if ($options['return_record'] == TRUE and $result) {
-    // Only if we have a single result do we want to add the primary keys to the 
+    // Only if we have a single result do we want to add the primary keys to the
     // values array.  If the update matched many records we can't add the pkeys.
 
     if (count($pkeys) == 1) {
@@ -1430,7 +1430,7 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
         $where[] = $value;
       }
       // CASE 1c: If we have an integer indexed array and the first element is
-      // not an array then we have a simple array of values to be used for an 
+      // not an array then we have a simple array of values to be used for an
       // IN clause.
       elseif (is_int(key($value)) AND !is_array(current($value))) {
 
@@ -1453,7 +1453,7 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
             $where[] = $subvalue;
           }
         }
-        // CASE 1e: We have a multi-dimensional array that doesn't fit any of 
+        // CASE 1e: We have a multi-dimensional array that doesn't fit any of
         // the above cases then we have a foreign key definition to follow.
         else {
 
@@ -1701,7 +1701,7 @@ function chado_select_record_check_value_type(&$op, &$value, $type) {
  * $args = array( ':feature_uniquename' => $form_state['values']['uniquename']
  *   );
  * $result = chado_query($sql, $args);
- * while ($r = $results->fetchObject()) { 
+ * while ($r = $results->fetchObject()) {
  *   // Do something with the record object $r
  * }
  * @endcode
@@ -1728,30 +1728,51 @@ function chado_query($sql, $args = []) {
     // Remove carriage returns from the SQL.
     $sql = preg_replace('/\n/', ' ', $sql);
 
+    // Get the current default Chado and Drupal schema prefixes.
+    $chado_schema_name = chado_get_schema_name('chado');
+    $drupal_schema_name = chado_get_schema_name('drupal');
+
     // Prefix the tables with their correct schema.
     // Chado tables should be enclosed in curly brackets (ie: {feature} )
     // and Drupal tables should be enclosed in square brackets
     // (ie: [tripal_jobs] ).
-    $chado_schema_name = chado_get_schema_name('chado');
-    $drupal_schema_name = chado_get_schema_name('drupal');
-    $sql = preg_replace('/\{(.*?)\}/', $chado_schema_name . '.$1', $sql);
-    $sql = preg_replace('/\[(\w+)\]/', $drupal_schema_name . '.$1', $sql);
+    $matches = [];
+    if (preg_match_all('/\{(.*?)\}/', $sql, $matches)) {
+      $matches = $matches[1];
+      $chado_tables = array_unique(array_keys(chado_get_table_names(TRUE)));
+      foreach ($matches as $match) {
+        if (in_array($match, $chado_tables)) {
+          $sql = preg_replace("/\{$match\}/", $chado_schema_name . '.' . $match, $sql);
+        }
+      }
+    }
+
+    // Now set the Drupal prefix if the table is surrounded by square brakets.
+    if (preg_match_all('/\[(.*?)\]/', $sql, $matches)) {
+      $matches = $matches[1];
+      $drupal_tables = array_unique(array_keys(drupal_get_schema()));
+      foreach ($matches as $match) {
+        if (in_array($match, $drupal_tables)) {
+          $sql = preg_replace("/\[$match\]/", $drupal_schema_name . '.' . $match, $sql);
+        }
+      }
+    }
 
-    // Add an alter hook to allow module developers to change the query right 
+    // Add an alter hook to allow module developers to change the query right
     // before it's  executed. Since all queriying of chado by Tripal eventually
     // goes through this function, we only need to provide an alter hook at this
-    // point in order to ensure developers have complete control over the query 
-    // being executed. For example, a module developer might want to remove 
-    // schema prefixing from queries and rely on the search path. This alter 
+    // point in order to ensure developers have complete control over the query
+    // being executed. For example, a module developer might want to remove
+    // schema prefixing from queries and rely on the search path. This alter
     // hook would allow them to do that by implementing
-    // mymodule_chado_query_alter($sql, $args) and using a regular expression 
+    // mymodule_chado_query_alter($sql, $args) and using a regular expression
     // to remove table prefixing from the query.
     // @see hook_chado_query_alter().
     drupal_alter('chado_query', $sql, $args);
 
     // The featureloc table has some indexes that use function that call other
-    // functions and those calls do not reference a schema, therefore, any 
-    // tables with featureloc must automaticaly have the chado schema set as 
+    // functions and those calls do not reference a schema, therefore, any
+    // tables with featureloc must automaticaly have the chado schema set as
     // active to find.
     if (preg_match('/' . $chado_schema_name . '.featureloc/i', $sql) or preg_match('/' . $chado_schema_name . '.feature/i', $sql)) {
       $previous_db = chado_set_active('chado');
@@ -1763,7 +1784,7 @@ function chado_query($sql, $args = []) {
         throw $e;
       }
     }
-    // For all other tables we should have everything in scope so just run the 
+    // For all other tables we should have everything in scope so just run the
     // query.
     else {
       $results = db_query($sql, $args);
@@ -1817,11 +1838,11 @@ function hook_chado_query_alter(&$sql, &$args) {
 
   // The following code is an example of how this alter function might be used.
   // Say you would like only a portion of node => feature connections available
-  // for a period of time or under a specific condition. To "hide" the other 
-  // connections you might create a temporary view of the chado_feature table 
+  // for a period of time or under a specific condition. To "hide" the other
+  // connections you might create a temporary view of the chado_feature table
   // that only includes the connections you would like to be available. In order
-  // to ensure this view is used rather than the original chado_feature table 
-  // you could alter all Tripal queries referring to chado_feature to instead 
+  // to ensure this view is used rather than the original chado_feature table
+  // you could alter all Tripal queries referring to chado_feature to instead
   //refer to your view.
   if (preg_match('/(\w+)\.chado_feature/', $sql, $matches)) {
 

tripal_chado/api/tripal_chado.schema.api.inc

@@ -392,11 +392,16 @@ function chado_get_version($exact = FALSE, $warn_if_unsupported = FALSE) {
     $version = "1.11 or older";
   }
   else {
+    // We need to hardcode the schema here rather than rely on the db_query
+    // function to settle it cecause the db_query function needs to know the
+    // Chado version to make the table prefixes set properly (chicken and
+    // egg problem).
+    $chado_schema = chado_get_schema_name('chado');
     $sql = "
       SELECT value
-      FROM {chadoprop} CP
-        INNER JOIN {cvterm} CVT on CVT.cvterm_id = CP.type_id
-        INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
+      FROM $chado_schema.chadoprop CP
+        INNER JOIN $chado_schema.cvterm CVT on CVT.cvterm_id = CP.type_id
+        INNER JOIN $chado_schema.cv CV on CVT.cv_id = CV.cv_id
       WHERE CV.name = 'chado_properties' and CVT.name = 'version'
     ";
     if (!$is_local) {
@@ -498,7 +503,7 @@ function chado_get_table_names($include_custom = NULL) {
     }
   }
 
-  // now add in the custom tables too if requested
+  // Now add in the custom tables too if requested
   if ($include_custom) {
     $sql = "SELECT table_name FROM {tripal_custom_tables}";
     $resource = db_query($sql);
@@ -633,7 +638,7 @@ function chado_get_base_tables() {
   // whose foreign key constraints link to two or more base table.
   $final_list = [];
   foreach ($base_tables as $i => $tablename) {
-    // A few tables break our rule and seems to look 
+    // A few tables break our rule and seems to look
     // like a linking table, but we want to keep it as a base table.
     if ($tablename == 'biomaterial' or $tablename == 'assay' or $tablename == 'arraydesign') {
       $final_list[] = $tablename;