Fixed issue #1712422. Changed all Chado querie to use chado_query() rather than db_query()

tripal_analysis/includes/tripal_analysis.admin.inc

@@ -227,10 +227,8 @@ function get_tripal_analysis_admin_form_taxonomy_set(&$form) {
   );
 
   // get the list of analyses
-  $sql = "SELECT * FROM {Analysis} ORDER BY name";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $sql = "SELECT * FROM {analysis} ORDER BY name";
+  $lib_rset = chado_query($sql);
 
   // iterate through all of the libraries
   $lib_boxes = array();
@@ -282,10 +280,8 @@ function get_tripal_analysis_admin_form_reindex_set(&$form) {
   );
 
   // get the list of libraries
-  $sql = "SELECT * FROM {Analysis} ORDER BY name";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $sql = "SELECT * FROM {analysis} ORDER BY name";
+  $lib_rset = chado_query($sql);
 
   // iterate through all of the libraries
   $lib_boxes = array();
@@ -377,9 +373,7 @@ function get_tripal_analysis_admin_form_sync_set(&$form) {
 
     // get the list of analyses
     $sql = "SELECT * FROM {analysis} ORDER BY name";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $ana_rset = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $ana_rset = chado_query($sql);
 
     // if we've added any analyses to the list that can be synced
     // then we want to build the form components to allow the user
@@ -463,9 +457,7 @@ function tripal_analysis_admin_validate($form, &$form_state) {
       if ($analysis_id and preg_match("/^\d+$/i", $analysis_id)) {
         // get the list of analyses
         $sql = "SELECT * FROM {analysis} WHERE analysis_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $analysis = db_fetch_object(db_query($sql, $analysis_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $analysis = db_fetch_object(chado_query($sql, $analysis_id));
         $to_sync[$analysis_id] = $analysis->name;
       }
     }
@@ -491,9 +483,7 @@ function tripal_analysis_admin_validate($form, &$form_state) {
       if ($analysis_id and preg_match("/^\d+$/i", $analysis_id)) {
         // get the analysis info
         $sql = "SELECT * FROM {analysis} WHERE analysis_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $analysis = db_fetch_object(db_query($sql, $analysis_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $analysis = db_fetch_object(chado_query($sql, $analysis_id));
         $job_args[0] = $analysis_id;
         tripal_add_job("Reindex features for analysis: $analysis->name", 'tripal_analysis',
              'tripal_analysis_reindex_features', $job_args, $user->uid);
@@ -511,9 +501,7 @@ function tripal_analysis_admin_validate($form, &$form_state) {
       if ($analysis_id and preg_match("/^\d+$/i", $analysis_id)) {
         // get the analysis info
         $sql = "SELECT * FROM {analysis} WHERE analysis_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $analysis = db_fetch_object(db_query($sql, $analysis_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $analysis = db_fetch_object(chado_query($sql, $analysis_id));
         $job_args[0] = $analysis_id;
         tripal_add_job("Set taxonomy for features in analysis: $analysis->name", 'tripal_analysis',
              'tripal_analysis_taxonify_features', $job_args, $user->uid);

tripal_analysis/includes/tripal_analysis_privacy.inc

@@ -52,9 +52,7 @@ function tripal_analysis_set_feature_permission($analysis_id, $nid) {
 
   // Get features associated with the analysis
   $sql = "SELECT feature_id FROM {analysisfeature} WHERE analysis_id = %d";
-  $previous_db = db_set_active('chado');
-  $features = db_query($sql, $analysis_id);
-  db_set_active($previous_db);
+  $features = chado_query($sql, $analysis_id);
 
   // Convert feature_id into node_id
   $feature_nids = array();

tripal_analysis/tripal_analysis.module

@@ -220,9 +220,7 @@ function chado_analysis_delete($node) {
   db_query($sql_del, $node->nid, $node->vid);
 
   //Remove from analysis and analysisprop tables of chado database as well
-  $previous_db = tripal_db_set_active('chado');
-  db_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
-  tripal_db_set_active($previous_db);
+  chado_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
 }
 
 /**
@@ -263,11 +261,9 @@ function chado_analysis_update($node) {
            "    timeexecuted = '%s' ".
            "WHERE analysis_id = %d ";
 
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  db_query($sql, $node->analysisname, $node->description, $node->program,
-  $node->programversion, $node->algorithm, $node->sourcename,
-  $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
-    tripal_db_set_active($previous_db);  // switch back to drupal database
+  chado_query($sql, $node->analysisname, $node->description, $node->program,
+    $node->programversion, $node->algorithm, $node->sourcename,
+    $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
 
   // Create a title for the analysis node using the unique keys so when the
   // node is saved, it will have a title
@@ -498,9 +494,7 @@ function tripal_analysis_sync_analyses($analysis_id = NULL, $job_id = NULL) {
         "  programversion, algorithm, sourcename, sourceversion, sourceuri, ".
           "  timeexecuted ".
           "FROM {Analysis} ";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
   else {
     $sql = "SELECT Analysis_id, name, description, program, ".
@@ -508,9 +502,7 @@ function tripal_analysis_sync_analyses($analysis_id = NULL, $job_id = NULL) {
           "  timeexecuted ".
           "FROM {Analysis} ".
           "WHERE analysis_id = %d";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql, $analysis_id);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql, $analysis_id);
   }
 
 
@@ -538,9 +530,7 @@ function tripal_analysis_sync_analyses($analysis_id = NULL, $job_id = NULL) {
                     AND type_id =
                         (SELECT cvterm_id from {cvterm} where name = '%s')
             ";
-      $previous_db = tripal_db_set_active('chado');
-      $analysis_type = db_fetch_object(db_query($sql, $analysis->analysis_id, "analysis_type"));
-      tripal_db_set_active($previous_db);
+      $analysis_type = db_fetch_object(chado_query($sql, $analysis->analysis_id, "analysis_type"));
 
       // Get the type of analysis using cvterm_id
             // Current possibilities: kegg, unigene, interpro, blast
@@ -861,7 +851,6 @@ function get_chado_analyses() {
   if ($no_orgs != 0) {
     $sql = "SELECT analysis_id, CA.nid, type FROM {chado_analysis} CA INNER JOIN node ON CA.nid = node.nid";
     $result = db_query($sql);
-    $previous_db = tripal_db_set_active('chado');
     $sql = "SELECT Analysis_id, name, description, program,
                    programversion, algorithm, sourcename, sourceversion,
                    sourceuri, timeexecuted
@@ -869,7 +858,7 @@ function get_chado_analyses() {
     $analyses = array();
     $count = 0;
     while ($data = db_fetch_object($result)) {
-      $analysis = db_fetch_object(db_query($sql, $data->analysis_id));
+      $analysis = db_fetch_object(chado_query($sql, $data->analysis_id));
       $analysis->node_id = $data->nid;
       $analysis->node_type = $data->type;
       // Use node_type as the key so we can sort by node type
@@ -879,7 +868,6 @@ function get_chado_analyses() {
       $analyses ["$sortedBy$count"] = $analysis;
       $count ++;
     }
-    tripal_db_set_active($previous_db);
 
     //Sort analyses by time, descending order
     krsort($analyses, SORT_STRING);

tripal_bulk_loader/tripal_bulk_loader.constants.inc

@@ -274,14 +274,12 @@ function tripal_bulk_loader_set_constants_form_validate($form, $form_state) {
       foreach ($indexes as $record_id => $array) {
         foreach ($array as $field_id) {
           if ($template[$record_id]['fields'][$field_id]['exposed_validate']) {
-            $previous_db = tripal_db_set_active('chado');
-            $result = db_fetch_object(db_query(
+            $result = db_fetch_object(chado_query(
               "SELECT 1 as valid FROM %s WHERE %s='%s'",
               $template[$record_id]['table'],
               $template[$record_id]['fields'][$field_id]['field'],
               $form_state['values'][$record_id . '-' . $field_id]
             ));
-            tripal_db_set_active($previous_db);
 
             if (!$result->valid) {
               $msg = 'A ' . $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#title'] . ' of "' . $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#value'] . '" must already exist!';

tripal_cv/api/tripal_cv.api.inc

@@ -111,9 +111,7 @@ function tripal_cv_get_cv($select_values) {
  */
 function tripal_cv_get_cv_by_name($name) {
 
-  $previous_db = tripal_db_set_active('chado');
   $r = tripal_core_chado_select('cv', array('*'), array('name' => $name));
-  tripal_db_set_active($previous_db);
 
   return $r[0];
 }
@@ -134,9 +132,7 @@ function tripal_cv_get_cv_by_name($name) {
  */
 function tripal_cv_get_cv_by_id($cv_id) {
 
-  $previous_db = tripal_db_set_active('chado');
   $r = tripal_core_chado_select('cv', array('*'), array('cv_id' => $cv_id));
-  tripal_db_set_active($previous_db);
 
   return $r;
 }

tripal_cv/includes/charts.inc

@@ -75,9 +75,7 @@
  *    $type        = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$chart_id);
  *
  *    $sql = "SELECT * FROM {Analysis} WHERE analysis_id = %d";
- *    $previous_db = tripal_db_set_active('chado');  // use chado database
- *    $analysis = db_fetch_object(db_query($sql,$analysis_id));
- *    tripal_db_set_active($previous_db);  // now use drupal database
+ *    $analysis = db_fetch_object(chado_query($sql,$analysis_id));
  *
  *    if (strcmp($type,'mf')==0) {
  *       $class = 'molecular_function';
@@ -214,9 +212,7 @@ function tripal_cv_count_chart($cnt_table, $fk_column,
   ";
 
   $features = array();
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $results = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $results = chado_query($sql);
   $data = array();
   $axis = array();
   $legend = array();

tripal_cv/includes/trees.inc

@@ -193,9 +193,7 @@ function tripal_cv_init_tree($cv_id, $cnt_table = NULL, $fk_column = NULL,
     FROM {cv_root_mview} CRM
     WHERE cv_id = %d
   ";
-  $previous_db = tripal_db_set_active('chado');
-  $results = db_query($sql, $cv_id);
-  tripal_db_set_active($previous_db);
+  $results = chado_query($sql, $cv_id);
 
   // prepare the SQL statement that will allow us to pull out count
   // information for each term in the tree.
@@ -216,9 +214,7 @@ function tripal_cv_init_tree($cv_id, $cnt_table = NULL, $fk_column = NULL,
     $name = $term->name;
     $count = 0;
     if ($cnt_table) {
-      $previous_db = tripal_db_set_active('chado');
-      $cnt_results = db_query($cnt_sql, $term->cvterm_id);
-      tripal_db_set_active($previous_db);
+      $cnt_results = chado_query($cnt_sql, $term->cvterm_id);
       while ($cnt = db_fetch_object($cnt_results)) {
         $count += $cnt->cnt;
       }
@@ -264,10 +260,7 @@ function tripal_cv_get_term_children($cvterm_id, $cnt_table = NULL,
     WHERE CVTR.object_id = %d
     ORDER BY CVT1.name
   ";
-  $previous_db = tripal_db_set_active('chado');
-  $results = db_query($sql, $cvterm_id);
-  tripal_db_set_active($previous_db);
-
+  $results = chado_query($sql, $cvterm_id);
 
   // prepare the SQL statement that will allow us to pull out count
   // information for each term in the tree.
@@ -290,9 +283,7 @@ function tripal_cv_get_term_children($cvterm_id, $cnt_table = NULL,
     $name = $term->subject_name;
     $count = 0;
     if ($cnt_table) {
-      $previous_db = tripal_db_set_active('chado');
-      $cnt_results = db_query($cnt_sql, $term->subject_id);
-      tripal_db_set_active($previous_db);
+      $cnt_results = chado_query($cnt_sql, $term->subject_id);
       while ($cnt = db_fetch_object($cnt_results)) {
         $count += $cnt->num_items;
       }
@@ -300,9 +291,7 @@ function tripal_cv_get_term_children($cvterm_id, $cnt_table = NULL,
         $name .= " (" . number_format($count) . " $label)";
 
         // check if we have any children if so then set the value
-        $previous_db = tripal_db_set_active('chado');
-        $children = db_fetch_object(db_query($sql, $term->subject_id));
-        tripal_db_set_active($previous_db);
+        $children = db_fetch_object(chado_query($sql, $term->subject_id));
         $state = 'leaf';
         if ($children) {
           $state = 'closed';
@@ -319,9 +308,7 @@ function tripal_cv_get_term_children($cvterm_id, $cnt_table = NULL,
     }
     else {
       // check if we have any children if so then set the value
-      $previous_db = tripal_db_set_active('chado');
-      $children = db_fetch_object(db_query($sql, $term->subject_id));
-      tripal_db_set_active($previous_db);
+      $children = db_fetch_object(chado_query($sql, $term->subject_id));
       $state = 'leaf';
       if ($children) {
         $state = 'closed';
@@ -395,9 +382,7 @@ function tripal_cv_cvterm_info($cvterm_id) {
       INNER JOIN DB on DBX.db_id = DB.db_id
     WHERE CVT.cvterm_id = %d
   ";
-  $previous_db = tripal_db_set_active('chado');
-  $cvterm = db_fetch_object(db_query($sql, $cvterm_id));
-  tripal_db_set_active($previous_db);
+  $cvterm = db_fetch_object(chado_query($sql, $cvterm_id));
 
   $sql = "
     SELECT CVTS.synonym, CVT.name as cvname
@@ -406,9 +391,7 @@ function tripal_cv_cvterm_info($cvterm_id) {
     WHERE CVTS.cvterm_id = %d
 
   ";
-  $previous_db = tripal_db_set_active('chado');
-  $results = db_query($sql, $cvterm_id);
-  tripal_db_set_active($previous_db);
+  $results = chado_query($sql, $cvterm_id);
   while ($synonym = db_fetch_object($results)) {
     $synonym_rows .= "<b>$synonym->cvname:</b>  $synonym->synonym<br />";
   }
@@ -458,9 +441,7 @@ function tripal_cv_list_form($form_state) {
        INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
        INNER JOIN CV on CV.cv_id = CVT.cv_id
   ";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $results = db_query($sql);
-  tripal_db_set_active($previous_db);
+  $results = chado_query($sql);
 
   $blastdbs = array();
   $cvs[''] = '';

tripal_db/tripal_db.api.inc

@@ -85,11 +85,9 @@ function tripal_db_get_db($select_values) {
  */
 function tripal_db_get_db_by_db_id($db_id) {
 
-  $previous_db = tripal_db_set_active('chado');
-  $r = db_fetch_object(db_query(
+  $r = db_fetch_object(chado_query(
     "SELECT * FROM {db} WHERE db_id=%d", $db_id
   ));
-  tripal_db_set_active($previous_db);
 
   return $r;
 }
@@ -106,11 +104,9 @@ function tripal_db_get_db_by_db_id($db_id) {
  */
 function tripal_db_get_db_by_name($name) {
 
-  $previous_db = tripal_db_set_active('chado');
-  $r = db_fetch_object(db_query(
+  $r = db_fetch_object(chado_query(
     "SELECT * FROM {db} WHERE name='%s'", $name
   ));
-  tripal_db_set_active($previous_db);
 
   return $r;
 }
@@ -139,11 +135,9 @@ function tripal_db_get_db_by_name($name) {
  */
 function tripal_db_get_db_options() {
 
-  $previous_db = tripal_db_set_active('chado');
-  $result = db_query(
+  $result = chado_query(
     "SELECT db_id, name FROM {db}"
   );
-  tripal_db_set_active($previous_db);
 
   $options = array();
   while ( $r = db_fetch_object($result) ) {
@@ -256,20 +250,16 @@ function tripal_db_get_dbxref($select_values) {
 function tripal_db_get_dbxref_by_accession($accession, $db_id=0) {
 
   if (!empty($db_id)) {
-    $previous_db = tripal_db_set_active('chado');
-    $r = db_fetch_object(db_query(
+    $r = db_fetch_object(chado_query(
       "SELECT * FROM {dbxref} WHERE accession='%s' AND db_id=%d",
       $accession, $db_id
     ));
-    tripal_db_set_active($previous_db);
   }
   else {
-    $previous_db = tripal_db_set_active('chado');
-    $r = db_fetch_object(db_query(
+    $r = db_fetch_object(chado_query(
       "SELECT * FROM {dbxref} WHERE accession='%s'",
       $accession
     ));
-    tripal_db_set_active($previous_db);
   }
 
   return $r;

tripal_db/tripal_db.module

@@ -155,11 +155,9 @@ function tripal_db_admin_page() {
  */
 function tripal_db_select_form() {
 
-  $previous_db = tripal_db_set_active('chado');  // use chado database
   // get a list of db from chado for user to choose
   $sql = "SELECT * FROM {db} WHERE NOT name = 'tripal' ORDER BY name ";
-  $results = db_query($sql);
-  tripal_db_set_active($previous_db); // use drupal database
+  $results = chado_query($sql);
 
   $dbs = array();
   $dbs[] = '';
@@ -201,9 +199,7 @@ function tripal_db_form(&$form_state = NULL, $dbid = NULL) {
   // get this requested database
   if ($dbid) {
     $sql = "SELECT * FROM {db} WHERE db_id = %d ";
-    $previous_db = tripal_db_set_active('chado');
-    $db = db_fetch_object(db_query($sql, $dbid));
-    tripal_db_set_active($previous_db);
+    $db = db_fetch_object(chado_query($sql, $dbid));
 
 
     // set the default values.  If there is a value set in the
@@ -318,9 +314,7 @@ function tripal_db_form_submit($form, &$form_state) {
           urlprefix = '%s'
         WHERE db_id = %d
       ";
-      $previous_db = tripal_db_set_active('chado');
-      $db = db_query($sql, $name, $desc, $url, $urlp, $dbid);
-      tripal_db_set_active($previous_db);
+      $db = chado_query($sql, $name, $desc, $url, $urlp, $dbid);
       if ($db) {
         drupal_set_message(t("External database updated"));
       }
@@ -333,9 +327,7 @@ function tripal_db_form_submit($form, &$form_state) {
         DELETE FROM {db}
         WHERE db_id = %d
         ";
-      $previous_db = tripal_db_set_active('chado');
-      $db = db_query($sql, $dbid);
-      tripal_db_set_active($previous_db);
+      $db = chado_query($sql, $dbid);
       if ($db) {
         drupal_set_message(t("External database deleted"));
       }
@@ -351,9 +343,7 @@ function tripal_db_form_submit($form, &$form_state) {
           VALUES
           ('%s','%s','%s','%s')
           ";
-    $previous_db = tripal_db_set_active('chado');
-    $db = db_query($sql, $name, $desc, $url, $urlp);
-    tripal_db_set_active($previous_db);
+    $db = chado_query($sql, $name, $desc, $url, $urlp);
     if ($db) {
       drupal_set_message(t("External database added"));
     }

tripal_feature/includes/gff_loader.inc

@@ -266,7 +266,6 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     return 0;
   }
 
-  //$previous_db = tripal_db_set_active('chado');
   print "Opening $gff_file\n";
 
   //$lines = file($dfile,FILE_SKIP_EMPTY_LINES);

tripal_feature/includes/tripal_feature-db_references.inc

@@ -91,18 +91,14 @@ function tripal_feature_add_ONE_dbreference_form_validate($form, &$form_state) {
   $nid = $form_state['values']['nid'];
 
   // Check database is valid db_id in chado
-  $previous_db = tripal_db_set_active('chado');
-  $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM {db} WHERE db_id=%d", $db_id));
-  tripal_db_set_active($previous_db);
+  $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {db} WHERE db_id=%d", $db_id));
   if ($tmp_obj->count != 1) {
     form_set_error('database', 'The database you selected is not valid. Please choose another one.');
   }
 
   // Check Accession is unique for database
-  $previous_db = tripal_db_set_active('chado');
   $sql = "SELECT count(*) as count FROM {dbxref} WHERE accession='%s' and db_id = %d";
-  $tmp_obj = db_fetch_object(db_query($sql, $accession, $db_id));
-  tripal_db_set_active($previous_db);
+  $tmp_obj = db_fetch_object(chado_query($sql, $accession, $db_id));
 
   if ($tmp_obj->count > 0) {
     form_set_error('accession', 'This accession has already been assigned to another feature in the selected database.');
@@ -124,20 +120,16 @@ function tripal_feature_add_ONE_dbreference_form_submit($form, &$form_state) {
   $nid = $form_state['values']['nid'];
 
   // create dbxref
-  $previous_db = tripal_db_set_active('chado');
   $isql =  "INSERT INTO {dbxref} (db_id, accession, description) VALUES (%d, '%s', '%s')";
-  db_query($isql, $db_id, $accession, $description);
-  tripal_db_set_active($previous_db);
+  cahdo_query($isql, $db_id, $accession, $description);
 
   //create feature_dbxref
   $dbxref = tripal_db_get_dbxref( array('db_id' => array('type' => 'INT', 'value' => $form_state['values']['db_id']),
                      'accession' => array('type' => 'STRING', 'exact' => TRUE, 'value' => $form_state['values']['accession']) ) );
 
   if (!empty($dbxref->dbxref_id)) {
-    $previous_db = tripal_db_set_active('chado');
       $isql = "INSERT INTO {feature_dbxref} (feature_id, dbxref_id) VALUES (%d, %d)";
-      db_query($isql, $feature_id, $dbxref->dbxref_id);
-    tripal_db_set_active($previous_db);
+      chado_query($isql, $feature_id, $dbxref->dbxref_id);
       drupal_set_message(t('Successfully Added Database Reference'));
       drupal_goto('node/' . $nid);
   }
@@ -287,10 +279,8 @@ function tripal_feature_edit_ALL_db_references_form_submit($form, &$form_state)
  */
 function tripal_feature_update_db_reference($dbxref_id, $db_id, $accession) {
 
-  $previous_db = tripal_db_set_active('chado');
   $sql =  "UPDATE {dbxref} SET db_id=%d, accession='%s' WHERE dbxref_id=%d";
-  db_query($sql, $db_id, $accession, $dbxref_id);
-  tripal_db_set_active($previous_db);
+  chado_query($sql, $db_id, $accession, $dbxref_id);
 
 }
 
@@ -301,18 +291,15 @@ function tripal_feature_update_db_reference($dbxref_id, $db_id, $accession) {
  */
 function tripal_feature_delete_db_reference($dbxref_id) {
 
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "DELETE FROM {dbxref} WHERE dbxref_id=%d",
     $dbxref_id
   );
 
-  db_query(
+  chado_query(
     "DELETE FROM {feature_dbxref} WHERE dbxref_id=%d",
     $dbxref_id
   );
-  tripal_db_set_active($previous_db);
-
 }
 
 /**

tripal_feature/includes/tripal_feature-delete.inc

@@ -7,9 +7,7 @@
 function tripal_feature_delete_form() {
   // get the list of organisms
   $sql = "SELECT * FROM {organism} ORDER BY genus, species";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $org_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $org_rset = chado_query($sql);
   $organisms = array();
   $organisms[''] = '';
   while ($organism = db_fetch_object($org_rset)) {
@@ -49,9 +47,7 @@ function tripal_feature_delete_form() {
 
   // get the list of analyses
   $sql = "SELECT * FROM {analysis} ORDER BY name";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $org_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $org_rset = chado_query($sql);
   $analyses = array();
   $analyses[''] = '';
   while ($analysis = db_fetch_object($org_rset)) {

tripal_feature/includes/tripal_feature-relationships.inc

@@ -164,9 +164,7 @@ function tripal_feature_add_ONE_relationship_form_validate($form, &$form_state)
       form_set_error('type_id', 'Please select a type of relationship.');
     }
     else {
-      $previous_db = tripal_db_set_active('chado');
-      $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['type_id']));
-      tripal_db_set_active($previous_db);
+      $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['type_id']));
 
       if ($tmp_obj->count != 1) {
         form_set_error('type_id', 'The type you selected is not valid. Please choose another one.');
@@ -399,9 +397,7 @@ function tripal_feature_edit_ALL_relationships_form_validate($form, &$form_state
         form_set_error('type_id', 'Please select a type of relationship.');
       }
       else {
-        $previous_db = tripal_db_set_active('chado');
-        $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d" , $form_state['values']["type_id-$i"]));
-        tripal_db_set_active($previous_db);
+        $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d" , $form_state['values']["type_id-$i"]));
 
         if ($tmp_obj->count != 1) {
           form_set_error("type_id-$i", 'The type you selected is not valid. Please choose another one.');

tripal_feature/includes/tripal_feature.admin.inc

@@ -614,14 +614,12 @@ function tripal_feature_aggregator_select_form() {
   $results = db_query($sql);
 
   $sql = "SELECT * FROM {cvterm} WHERE cvterm_id = %d";
-  $previous_db = tripal_db_set_active('chado');
   $types = array();
   $types[] = '';
   while ($base = db_fetch_object($results)) {
-    $term = db_fetch_object(db_query($sql, $base->type_id));
+    $term = db_fetch_object(chado_query($sql, $base->type_id));
     $types[$base->type_id] = $term->name;
   }
-  tripal_db_set_active($previous_db);
 
   $form['type_id'] = array(
     '#title' => t('Aggregator Base Type'),
@@ -654,9 +652,7 @@ function tripal_feature_aggregator_form(&$form_state = NULL, $type_id = NULL) {
     // get the default list of terms
     $results = db_query($sql, $type_id);
     while ($type = db_fetch_object($results)) {
-      $previous_db = tripal_db_set_active('chado');
-      $term = db_fetch_object(db_query($tsql, $type->rel_type_id));
-      tripal_db_set_active($previous_db);
+      $term = db_fetch_object(chado_query($tsql, $type->rel_type_id));
       $default_others .= $term->name . " ";
     }
     $default_base = $base->name;
@@ -739,9 +735,7 @@ function tripal_feature_aggregator_form_validate($form, &$form_state) {
 
   // make sure the base type exists
   if ($base) {
-    $previous_db = tripal_db_set_active('chado');
-    $term = db_fetch_object(db_query($tsql, $base));
-    tripal_db_set_active($previous_db);
+    $term = db_fetch_object(chado_query($tsql, $base));
     if (!$term) {
       form_set_error('base', t('The specified base type is not a valid SO term'));
     }
@@ -756,9 +750,7 @@ function tripal_feature_aggregator_form_validate($form, &$form_state) {
 
   // iterate through each type to be aggregated and make sure they are valid
   foreach ($types as $type) {
-    $previous_db = tripal_db_set_active('chado');
-    $term = db_fetch_object(db_query($tsql, $type));
-    tripal_db_set_active($previous_db);
+    $term = db_fetch_object(chado_query($tsql, $type));
     if (!$term) {
       form_set_error('others', t('The specified type %type is not a valid SO term', array('%type' => $type)));
     }
@@ -796,9 +788,7 @@ function tripal_feature_aggregator_form_submit($form, &$form_state) {
   // if this is an insert then we have a base type name.  We
   // need to get the corresponding term id
   if ($base) {
-    $previous_db = tripal_db_set_active('chado');
-    $term = db_fetch_object(db_query($tsql, $base));
-    tripal_db_set_active($previous_db);
+    $term = db_fetch_object(chado_query($tsql, $base));
     $type_id = $term->cvterm_id;
   }
 
@@ -826,9 +816,7 @@ function tripal_feature_aggregator_form_submit($form, &$form_state) {
 
     // iterate through each type to be aggregated and add an entry in the table
     foreach ($types as $type) {
-      $previous_db = tripal_db_set_active('chado');
-      $term = db_fetch_object(db_query($tsql, $type));
-      tripal_db_set_active($previous_db);
+      $term = db_fetch_object(chado_query($tsql, $type));
       $result = db_query($isql, $type_id, $term->cvterm_id);
     }
     drupal_set_message(t("Aggregator added"));

tripal_featuremap/tripal_featuremap.module

@@ -403,9 +403,7 @@ function get_tripal_featuremap_admin_form_taxonomy_set(&$form) {
 
   // get the list of maps
   $sql = "SELECT * FROM {featuremap} ORDER BY name";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $lib_rset = cahdo_query($sql);
 
   // iterate through all of the maps
   $lib_boxes = array();
@@ -450,9 +448,7 @@ function get_tripal_featuremap_admin_form_reindex_set(&$form) {
 
   // get the list of maps
   $sql = "SELECT * FROM {featuremap} ORDER BY name";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $lib_rset = chado_query($sql);
 
   // iterate through all of the maps
   $lib_boxes = array();
@@ -495,9 +491,7 @@ function get_tripal_featuremap_admin_form_sync_set(&$form) {
 
   // get the list of maps
   $sql = "SELECT * FROM {featuremap} ORDER BY name";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $lib_rset = chado_query($sql);
 
   // if we've added any maps to the list that can be synced
   // then we want to build the form components to allow the user
@@ -574,9 +568,7 @@ function tripal_featuremap_admin_validate($form, &$form_state) {
     if ($featuremap_id and preg_match("/^\d+$/i", $featuremap_id)) {
       // get the map info
       $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = %d";
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      $featuremap = db_fetch_object(db_query($sql, $featuremap_id));
-      tripal_db_set_active($previous_db);  // now use drupal database
+      $featuremap = db_fetch_object(chado_query($sql, $featuremap_id));
       $to_sync[$featuremap_id] = $featuremap->name;
     }
   }
@@ -601,9 +593,7 @@ function tripal_featuremap_admin_validate($form, &$form_state) {
       if ($featuremap_id and preg_match("/^\d+$/i", $featuremap_id)) {
         // get the map info
         $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $featuremap = db_fetch_object(db_query($sql, $featuremap_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $featuremap = db_fetch_object(chado_query($sql, $featuremap_id));
         $job_args[0] = $featuremap_id;
         tripal_add_job("Reindex features for map: $featuremap->name", 'tripal_featuremap',
          'tripal_featuremap_reindex_features', $job_args, $user->uid);
@@ -619,9 +609,7 @@ function tripal_featuremap_admin_validate($form, &$form_state) {
       if ($featuremap_id and preg_match("/^\d+$/i", $featuremap_id)) {
         // get the map info
         $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $featuremap = db_fetch_object(db_query($sql, $featuremap_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $featuremap = db_fetch_object(chado_query($sql, $featuremap_id));
         $job_args[0] = $featuremap_id;
         tripal_add_job("Set taxonomy for features in map: $featuremap->name", 'tripal_featuremap',
          'tripal_featuremap_taxonify_features', $job_args, $user->uid);
@@ -696,18 +684,13 @@ function chado_featuremap_validate($node) {
            "{featuremap} WHERE ".
            "name = '%s' ".
            "AND NOT featuremap_id = %d";
-    $previous_db = tripal_db_set_active('chado');
-    $lib = db_fetch_object(db_query($sql, $node->name,
-    $node->featuremap_id));
-    tripal_db_set_active($previous_db);
+    $lib = db_fetch_object(chado_query($sql, $node->name, $node->featuremap_id));
   }
   else {
     $sql = "SELECT * FROM ".
            "{featuremap} ".
            "WHERE name = '%s'";
-    $previous_db = tripal_db_set_active('chado');
-    $lib = db_fetch_object(db_query($sql, $node->name));
-    tripal_db_set_active($previous_db);
+    $lib = db_fetch_object(chado_query($sql, $node->name));
   }
   if ($lib) {
     form_set_error('name', t('The unique map name already exists. '.
@@ -855,15 +838,11 @@ function tripal_featuremap_sync_featuremaps($featuremap_id = NULL, $job_id = NUL
   // get the list of featuremaps and create new nodes
   if (!$featuremap_id) {
     $sql = "SELECT * FROM {featuremap} L";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
   else {
     $sql = "SELECT * FROM {featuremap} L WHERE featuremap_id = %d";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql, $featuremap_id);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql, $featuremap_id);
   }
 
   // We'll use the following SQL statement for checking if the map
@@ -969,10 +948,8 @@ function chado_featuremap_delete(&$node) {
   db_query($sql_del, $node->nid, $node->vid);
 
   // Remove data from map and mapprop tables of chado database as well
-  $previous_db = tripal_db_set_active('chado');
-  db_query("DELETE FROM {featuremap} WHERE featuremap_id = %d", $featuremap_id);
-  db_query("DELETE FROM {featuremapprop} WHERE featuremap_id = %d", $featuremap_id);
-  tripal_db_set_active($previous_db);
+  chado_query("DELETE FROM {featuremap} WHERE featuremap_id = %d", $featuremap_id);
+  chado_query("DELETE FROM {featuremapprop} WHERE featuremap_id = %d", $featuremap_id);
 }
 
 /**

tripal_library/tripal_library.install

@@ -30,20 +30,13 @@ function tripal_library_install() {
   tripal_cv_add_cvterm(array('name' => 'yac_library', 'def' => 'YAC Library'), 'tripal', 0, 1, 'tripal');
 
   // Add the materialized view needed to count the features for the library
-  // Drop the MView table if it exists
-  $previous_db = tripal_db_set_active('chado');
-  if (db_table_exists('library_feature_count')) {
-    $sql = "DROP TABLE library_feature_count";
-    db_query($sql);
-  }
-  tripal_db_set_active($previous_db);
   // Create the MView
   tripal_add_mview('library_feature_count', 'tripal_library',
     'library_feature_count',
     'library_id integer, name character varying(255), '.
-  '  num_features integer, feature_type character varying(255)',
-   'library_id',
-   'SELECT '.
+    '  num_features integer, feature_type character varying(255)',
+    'library_id',
+    'SELECT '.
     '   L.library_id, '.
     '   L.name, '.
     '    count(F.feature_id) as num_features, '.
@@ -53,7 +46,7 @@ function tripal_library_install() {
     '    INNER JOIN Feature F           ON LF.feature_id = F.feature_id '.
     '    INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id '.
     'GROUP BY L.library_id, L.name, CVT.name',
-   ''
+    ''
   );
 
 }

tripal_library/tripal_library.module

@@ -402,22 +402,20 @@ function theme_tripal_library_search_index($node) {
   if ($node->type == 'chado_organism') {
     $content = "";
     // get the libraries for the organism
-    $previous_db = tripal_db_set_active('chado');
     $sql = "SELECT * FROM {library} L ".
             "WHERE L.organism_id = %d";
     $libraries = array();
-    $results = db_query($sql, $node->organism->organism_id);
+    $results = chado_query($sql, $node->organism->organism_id);
     while ($library = db_fetch_object($results)) {
       // get the description
       $sql = "SELECT * FROM {libraryprop} LP ".
              "  INNER JOIN CVTerm CVT ON CVT.cvterm_id = LP.type_id ".
             "WHERE LP.library_id = $library->library_id ".
             "  AND CVT.name = 'library_description'";
-      $desc = db_fetch_object(db_query($sql));
+      $desc = db_fetch_object(chado_query($sql));
       $library->description = $desc->value;
       $libraries[] = $library;
     }
-    tripal_db_set_active($previous_db);
     if (count($libraries) > 0) {
       foreach ($libraries as $library) {
         $content .= "$library->name ";
@@ -429,16 +427,14 @@ function theme_tripal_library_search_index($node) {
   elseif ($node->type == 'chado_feature') {
     $content = "";
     $organism_id = $node->feature->organism_id;
-    $previous_db = tripal_db_set_active('chado');
     $sql = "SELECT * FROM {library} L ".
            "  INNER JOIN Library_feature LF ON L.library_id = LF.library_id ".
             "WHERE LF.feature_id = " . $node->feature->feature_id;
     $libraries = array();
-    $results = db_query($sql);
+    $results = chado_query($sql);
     while ($library = db_fetch_object($results)) {
       $libraries[] = $library;
     }
-    tripal_db_set_active($previous_db);
     if (count($libraries) > 0) {
       $lib_additions = array();
       foreach ($libraries as $library) {
@@ -473,16 +469,14 @@ function theme_tripal_library_node_libraries($node) {
   // when a feature is previewed at its creation
   elseif ($node->type == 'chado_feature' && $node->feature->feature_id) {
     $organism_id = $node->feature->organism_id;
-    $previous_db = tripal_db_set_active('chado');
     $sql = "SELECT * FROM {library} L ".
            " INNER JOIN Library_feature LF ON L.library_id = LF.library_id ".
             "WHERE LF.feature_id = " . $node->feature->feature_id;
     $libraries = array();
-    $results = db_query($sql);
+    $results = chado_query($sql);
     while ($library = db_fetch_object($results)) {
       $libraries[] = $library;
-    }
-    tripal_db_set_active($previous_db);
+  }
   if (count($libraries) > 0) {
     $lib_additions = array();
     foreach ($libraries as $library) {
@@ -538,9 +532,7 @@ function get_tripal_library_admin_form_taxonomy_set(&$form) {
 
   // get the list of libraries
   $sql = "SELECT * FROM {Library} ORDER BY uniquename";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $lib_rset = chado_query($sql);
 
   // iterate through all of the libraries
   $lib_boxes = array();
@@ -585,9 +577,7 @@ function get_tripal_library_admin_form_reindex_set(&$form) {
 
   // get the list of libraries
   $sql = "SELECT * FROM {Library} ORDER BY uniquename";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $lib_rset = chado_query($sql);
 
   // iterate through all of the libraries
   $lib_boxes = array();
@@ -630,9 +620,7 @@ function get_tripal_library_admin_form_sync_set(&$form) {
 
   // get the list of libraries
   $sql = "SELECT * FROM {Library} ORDER BY uniquename";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $lib_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $lib_rset = chado_query($sql);
 
   // if we've added any libraries to the list that can be synced
   // then we want to build the form components to allow the user
@@ -709,9 +697,7 @@ function tripal_library_admin_validate($form, &$form_state) {
     if ($library_id and preg_match("/^\d+$/i", $library_id)) {
       // get the library info
       $sql = "SELECT * FROM {Library} WHERE library_id = %d";
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      $library = db_fetch_object(db_query($sql, $library_id));
-      tripal_db_set_active($previous_db);  // now use drupal database
+      $library = db_fetch_object(chado_query($sql, $library_id));
       $to_sync[$library_id] = $library->name;
     }
   }
@@ -736,9 +722,7 @@ function tripal_library_admin_validate($form, &$form_state) {
       if ($library_id and preg_match("/^\d+$/i", $library_id)) {
         // get the library info
         $sql = "SELECT * FROM {Library} WHERE library_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $library = db_fetch_object(db_query($sql, $library_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $library = db_fetch_object(chado_query($sql, $library_id));
         $job_args[0] = $library_id;
         tripal_add_job("Reindex features for library: $library->name", 'tripal_library',
          'tripal_library_reindex_features', $job_args, $user->uid);
@@ -754,9 +738,7 @@ function tripal_library_admin_validate($form, &$form_state) {
       if ($library_id and preg_match("/^\d+$/i", $library_id)) {
         // get the library info
         $sql = "SELECT * FROM {Library} WHERE library_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $library = db_fetch_object(db_query($sql, $library_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $library = db_fetch_object(chado_query($sql, $library_id));
         $job_args[0] = $library_id;
         tripal_add_job("Set taxonomy for features in library: $library->name", 'tripal_library',
          'tripal_library_taxonify_features', $job_args, $user->uid);
@@ -851,18 +833,13 @@ function chado_library_validate($node) {
            "{Library} WHERE ".
            "uniquename = '%s' ".
            "AND NOT library_id = %d";
-    $previous_db = tripal_db_set_active('chado');
-    $lib = db_fetch_object(db_query($sql, $node->uniquename,
-    $node->library_id));
-    tripal_db_set_active($previous_db);
+    $lib = db_fetch_object(chado_query($sql, $node->uniquename, $node->library_id));
   }
   else {
     $sql = "SELECT * FROM ".
            "{Library} ".
            "WHERE uniquename = '%s'";
-    $previous_db = tripal_db_set_active('chado');
-    $lib = db_fetch_object(db_query($sql, $node->uniquename));
-    tripal_db_set_active($previous_db);
+    $lib = db_fetch_object(chado_query($sql, $node->uniquename));
   }
   if ($lib) {
     form_set_error('uniquename', t('The unique library name already exists. '.
@@ -1091,9 +1068,7 @@ function chado_library_form($node) {
 
   // get the list of organisms
   $sql = "SELECT * FROM {Organism}";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $org_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $org_rset = chado_query($sql);
 
   $organisms = array();
   $organisms[''] = '';
@@ -1137,15 +1112,11 @@ function tripal_library_sync_libraries($library_id = NULL, $job_id = NULL) {
   // get the list of libraries and create new nodes
   if (!$library_id) {
     $sql = "SELECT * FROM {Library} L";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
   else {
     $sql = "SELECT * FROM {Library} L WHERE library_id = %d";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql, $library_id);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql, $library_id);
   }
 
   // We'll use the following SQL statement for checking if the library
@@ -1225,13 +1196,11 @@ function chado_library_view($node, $teaser = FALSE, $page = FALSE) {
     // but not genus/species/common_name. We need to get those from chado
     // database so they will show up in preview
     if (!$node->genus) {
-      $previous_db = tripal_db_set_active('chado');
       $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
-      $data = db_fetch_object(db_query($sql, $node->organism_id));
+      $data = db_fetch_object(chado_query($sql, $node->organism_id));
       $node->genus = $data->genus;
       $node->species = $data->species;
       $node->common_name = $data->common_name;
-      tripal_db_set_active($previous_db);
     }
   }
   return $node;
@@ -1315,9 +1284,7 @@ function tripal_library_feature_set_taxonomy($library_id = NULL) {
            "INNER JOIN Library L ON LF.library_id = L.library_id ".
            "WHERE L.library_id = $library_id ".
            "ORDER BY LF.feature_id";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $features = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $features = chado_query($sql);
   }
   else {
     print "Finding features for all libraries\n";
@@ -1325,9 +1292,7 @@ function tripal_library_feature_set_taxonomy($library_id = NULL) {
            "FROM {library_feature} LF ".
            "INNER JOIN Library L ON LF.library_id = L.library_id ".
            "ORDER BY LF.feature_id";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $features = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $features = chado_query($sql);
   }
 
   $node_sql = "SELECT * FROM {chado_feature} CF ".
@@ -1359,18 +1324,14 @@ function tripal_library_reindex_features($library_id = NULL, $job_id = NULL) {
            "  INNER JOIN Library L ON LF.library_id = L.library_id ".
            "WHERE L.library_id = $library_id ".
            "ORDER BY LF.feature_id";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
   else {
     $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
            " FROM {library_feature} LF ".
            "  INNER JOIN Library L ON LF.library_id = L.library_id ".
            "ORDER BY LF.feature_id";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
 
    // load into ids array
@@ -1407,18 +1368,14 @@ function tripal_library_taxonify_features($library_id = NULL, $job_id = NULL) {
            "  INNER JOIN Library L ON LF.library_id = L.library_id ".
            "WHERE L.library_id = $library_id ".
            "ORDER BY LF.feature_id";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
   else {
     $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
            " FROM {library_feature} LF ".
            "  INNER JOIN Library L ON LF.library_id = L.library_id ".
            "ORDER BY LF.feature_id";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
 
   // load into ids array
@@ -1479,10 +1436,8 @@ function chado_library_delete(&$node) {
   db_query($sql_del, $node->nid, $node->vid);
 
   // Remove data from library and libraryprop tables of chado database as well
-  $previous_db = tripal_db_set_active('chado');
-  db_query("DELETE FROM {library} WHERE library_id = %d", $library_id);
-  db_query("DELETE FROM {libraryprop} WHERE library_id = %d", $library_id);
-  tripal_db_set_active($previous_db);
+  chado_query("DELETE FROM {library} WHERE library_id = %d", $library_id);
+  chado_query("DELETE FROM {libraryprop} WHERE library_id = %d", $library_id);
 }
 
 /**
@@ -1573,7 +1528,6 @@ function get_chado_libraries() {
     // Get library_id's from drupal
     $sql = "SELECT library_id, nid FROM {chado_library}";
     $result = db_query($sql);
-    $previous_db = tripal_db_set_active('chado');
     // Get library info from chado's library, organism, and cvterm tables
     $sql_info = "SELECT L.name, uniquename, genus, species, common_name, ".
                 "  CVT.name as type_name ".
@@ -1588,9 +1542,9 @@ function get_chado_libraries() {
                 "WHERE library_id = %d AND CVT.name = 'library_description'";
     $libraries = array();
     while ($data = db_fetch_object($result)) {
-      $library = db_fetch_object(db_query($sql_info, $data->library_id));
+      $library = db_fetch_object(chado_query($sql_info, $data->library_id));
       $library->node_id = $data->nid;
-      $desc = db_fetch_object(db_query($sql_desc, $data->library_id))->value;
+      $desc = db_fetch_object(chado_query($sql_desc, $data->library_id))->value;
       if ($desc) {
         $library->library_description = $desc;
       }
@@ -1601,7 +1555,6 @@ function get_chado_libraries() {
       $key = drupal_strtolower($library->uniquename);
       $libraries [$key] = $library;
     }
-    tripal_db_set_active($previous_db);
 
     //Sort libraries by uniquename
     ksort($libraries, SORT_STRING);

tripal_organism/tripal_organism.api.inc

@@ -16,11 +16,9 @@
  */
 function tripal_organism_get_organism_options() {
 
-  $previous_db = tripal_db_set_active('chado');
-  $result = db_query(
+  $result = chado_query(
     "SELECT organism_id, common_name FROM {organism}"
   );
-  tripal_db_set_active($previous_db);
 
   $options = array();
   while ( $r = db_fetch_object($result) ) {
@@ -148,9 +146,7 @@ function tripal_organism_get_synced() {
 
   // iterate through the organisms and build an array of those that are synced
   while ($org = db_fetch_object($orgs)) {
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $info = db_fetch_object(db_query($csql, $org->organism_id));
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $info = db_fetch_object(chado_query($csql, $org->organism_id));
     $org_list[] = $info;
   }
   return $org_list;

tripal_organism/tripal_organism.module

@@ -374,9 +374,7 @@ function get_tripal_organism_admin_form_taxonomy_set(&$form) {
 
   // get the list of libraries
   $sql = "SELECT * FROM {Organism} ORDER BY genus,species";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $org_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $org_rset = chado_query($sql);
 
   // iterate through all of the libraries
   $org_boxes = array();
@@ -421,9 +419,7 @@ function get_tripal_organism_admin_form_reindex_set(&$form) {
 
   // get the list of libraries
   $sql = "SELECT * FROM {Organism} ORDER BY genus,species";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $org_rset = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $org_rset = chado_query($sql);
 
   // iterate through all of the libraries
   $org_boxes = array();
@@ -475,9 +471,7 @@ function get_tripal_organism_admin_form_sync_set(&$form) {
 
     // get the list of organisms
     $sql = "SELECT * FROM {Organism} ORDER BY genus,species";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $org_rset = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $org_rset = chado_query($sql);
 
     // if we've added any organisms to the list that can be synced
     // then we want to build the form components to allow the user
@@ -551,9 +545,7 @@ function tripal_organism_admin_validate($form, &$form_state) {
       if ($organism_id and preg_match("/^\d+$/i" , $organism_id)) {
         // get the list of organisms
         $sql = "SELECT * FROM {Organism} WHERE organism_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $organism = db_fetch_object(db_query($sql, $organism_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $organism = db_fetch_object(chado_query($sql, $organism_id));
         $to_sync[$organism_id] = "$organism->genus $organism->species";
       }
     }
@@ -580,9 +572,7 @@ function tripal_organism_admin_validate($form, &$form_state) {
       if ($organism_id and preg_match("/^\d+$/i" , $organism_id)) {
         // get the organism info
         $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $organism = db_fetch_object(db_query($sql , $organism_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $organism = db_fetch_object(chado_query($sql , $organism_id));
         $job_args[0] = $organism_id;
         tripal_add_job("Reindex features for organism: $organism->genus ".
          "$organism->species", 'tripal_organism' ,
@@ -599,9 +589,7 @@ function tripal_organism_admin_validate($form, &$form_state) {
       if ($organism_id and preg_match("/^\d+$/i", $organism_id)) {
         // get the organism info
         $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
-        $previous_db = tripal_db_set_active('chado');  // use chado database
-        $organism = db_fetch_object(db_query($sql , $organism_id));
-        tripal_db_set_active($previous_db);  // now use drupal database
+        $organism = db_fetch_object(chado_query($sql , $organism_id));
         $job_args[0] = $organism_id;
         tripal_add_job("Set taxonomy for features in organism: ".
           "$organism->genus $organism->species" , 'tripal_organism',
@@ -679,9 +667,7 @@ function chado_organism_validate($node, &$form) {
     $sql = "SELECT *
           FROM {organism} O
           WHERE genus = '%s' and species = '%s' AND NOT organism_id = %d";
-    $previous_db = tripal_db_set_active('chado');
-    $result = db_fetch_object(db_query($sql, $node->genus, $node->species, $node->organism_id));
-    tripal_db_set_active($previous_db);
+    $result = db_fetch_object(chado_query($sql, $node->genus, $node->species, $node->organism_id));
     if ($result) {
       form_set_error('genus', t("Update cannot proceed. The organism genus
         '$node->genus' and species '$node->species' is already present in the database."));
@@ -828,10 +814,9 @@ function chado_organism_delete($node) {
   // feature depends on this organism, don't delete it
 
   $sql = "SELECT feature_id FROM {feature} WHERE organism_id = %d";
-  $previous_db = tripal_db_set_active('chado');
-  $check_feature = db_result(db_query($sql, $organism_id));
+  $check_feature = db_result(chado_query($sql, $organism_id));
   $sql = "SELECT library_id FROM {library} WHERE organism_id = %d";
-  $check_lib = db_result(db_query($sql, $organism_id));
+  $check_lib = db_result(chado_query($sql, $organism_id));
 
   if ($check_lib == 0 && $check_feature == 0) {
     tripal_core_chado_delete('organism', array('organism_id' => $organism_id));
@@ -841,7 +826,6 @@ function chado_organism_delete($node) {
                        "library or feature depends on this organism. It was ".
                "not removed from chado."));
   }
-  tripal_db_set_active($previous_db);
 }
 /**
  *
@@ -1002,15 +986,11 @@ function tripal_organism_sync_organisms($organism_id = NULL, $job_id = NULL) {
 
   if (!$organism_id) {
     $sql = "SELECT * FROM {Organism} O";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql);
   }
   else {
     $sql = "SELECT * FROM {Organism} L WHERE organism_id = %d";
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    $results = db_query($sql, $organism_id);
-    tripal_db_set_active($previous_db);  // now use drupal database
+    $results = chado_query($sql, $organism_id);
   }
 
   // We'll use the following SQL statement for checking if the organism
@@ -1085,15 +1065,14 @@ function get_chado_organisms() {
   $no_orgs = db_result(db_query($sql_drupal));
   if ($no_orgs != 0) {
     $sql = "SELECT organism_id, nid FROM {chado_organism}";
-    $result = db_query($sql);
-    $previous_db = tripal_db_set_active('chado');
+    $result = chado_query($sql);
     $sql = "SELECT genus, species, common_name, comment ".
            "FROM {Organism} ".
            "WHERE organism_id=%d";
     $organisms = array();
     $count = 0;
     while ($data = db_fetch_object($result)) {
-      $organism = db_fetch_object(db_query($sql, $data->organism_id));
+      $organism = db_fetch_object(chado_query($sql, $data->organism_id));
       $organism->node_id = $data->nid;
       // Use common_name plus $count as the key so we can sort by common
       // name later. Since common_name is not unique, we need to add $count
@@ -1102,7 +1081,6 @@ function get_chado_organisms() {
       $organisms [$key] = $organism;
       $count ++;
     }
-    tripal_db_set_active($previous_db);
 
     //Sort organisms by common name
     ksort($organisms, SORT_STRING);
@@ -1124,9 +1102,7 @@ function tripal_organism_reindex_features($organism_id = NULL, $job_id = NULL) {
         "FROM {feature} ".
         "WHERE organism_id = $organism_id ".
         "ORDER BY feature_id";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $results = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal databa  tripal_db_set_active($previous_db);  // now use drupal database
+  $results = chado_query($sql);
 
   // load into ids array
   $count = 0;
@@ -1161,9 +1137,7 @@ function tripal_organism_taxonify_features($organism_id = NULL, $job_id = NULL)
         "FROM {feature} ".
         "WHERE organism_id = $organism_id ".
         "ORDER BY feature_id";
-  $previous_db = tripal_db_set_active('chado');  // use chado database
-  $results = db_query($sql);
-  tripal_db_set_active($previous_db);  // now use drupal database
+  $results = chado_query($sql);
 
   // load into ids array
   $count = 0;

tripal_project/tripal_project.admin.inc

@@ -63,9 +63,7 @@ function tripal_project_sync_all_projects() {
 
   // retrieve all projects in chado
   $chado_projects = array();
-  $previous_db = tripal_db_set_active('chado');
-  $resource = db_query('SELECT project_id FROM {project}');
-  tripal_db_set_active($previous_db);
+  $resource = chado_query('SELECT project_id FROM {project}');
   while ($r = db_fetch_object($resource)) {
     // if not already in drupal add to list to be sync'd
     if (!isset($drupal_projects[$r->project_id])) {

tripal_stock/includes/other_module_api_functions.inc

@@ -43,13 +43,11 @@ function get_max_chado_rank($tablename, $where_options) {
     }
   }
 
-  $previous_db = tripal_db_set_active('chado');
-  $result = db_fetch_object(db_query(
+  $result = db_fetch_object(chado_query(
     "SELECT max(rank) as max_rank, count(rank) as count FROM %s WHERE %s",
     $tablename,
     implode(' AND ', $where)
   ));
-  tripal_db_set_active($previous_db);
   //drupal_set_message("Max Rank Query=SELECT max(rank) as max_rank, count(rank) as count FROM ".$tablename." WHERE ".implode(' AND ',$where));
   if ($result->count > 0) {
     return $result->max_rank;

tripal_stock/includes/tripal_stock-administration.inc

@@ -313,12 +313,10 @@ function tripal_stock_sync_stock_set($organism_id, $job_id) {
   else {
 
   // Get list of stocks to sync
-  $previous_db = tripal_db_set_active('chado');
-  $result = db_query(
+  $result = chado_query(
      "SELECT stock_id, uniquename, type_id, organism_id FROM {stock} WHERE organism_id=%d",
       $organism_id
   );
-  tripal_db_set_active($previous_db);
 
   $stocks_created_count = 0; //keeps track of total number of stocks successfully created
   $stocks_attempted = 0;

tripal_stock/includes/tripal_stock-db_references.inc

@@ -115,9 +115,7 @@ function tripal_stock_add_ONE_dbreference_form_validate($form, &$form_state) {
 
     // Check database is valid db_id in chado
     if ( $form_state['values']['database'] > 0) {
-      $previous_db = tripal_db_set_active('chado');
-      $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM {db} WHERE db_id=%d", $form_state['values']['database']));
-      tripal_db_set_active($previous_db);
+      $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {db} WHERE db_id=%d", $form_state['values']['database']));
 
       if ($tmp_obj->count != 1) {
         form_set_error('database', 'The database you selected is not valid. Please choose another one.');
@@ -128,9 +126,7 @@ function tripal_stock_add_ONE_dbreference_form_validate($form, &$form_state) {
     }
 
     // Check Accession is unique for database
-    $previous_db = tripal_db_set_active('chado');
-    $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM {dbxref} WHERE accession='%s'", $form_state['values']['accession']));
-    tripal_db_set_active($previous_db);
+    $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {dbxref} WHERE accession='%s'", $form_state['values']['accession']));
 
     if ($tmp_obj->count > 0) {
       form_set_error('accession', 'This accession has already been assigned to another stock.');
@@ -162,25 +158,21 @@ function tripal_stock_add_ONE_dbreference_form_submit($form, &$form_state) {
 
 
     // create dbxref
-    $previous_db = tripal_db_set_active('chado');
-    db_query(
+    chado_query(
       "INSERT INTO {dbxref} (db_id, accession, description) VALUES (%d, '%s', '%s')",
       $form_state['values']['database'],
       $form_state['values']['accession'],
       $form_state['values']['db_description']
     );
-    tripal_db_set_active($previous_db);
 
     //create stock_dbxref
     $dbxref = tripal_db_get_dbxref_by_accession($form_state['values']['accession'], $form_state['values']['database']);
     if (!empty($dbxref->dbxref_id)) {
-      $previous_db = tripal_db_set_active('chado');
-      db_query(
+      chado_query(
         "INSERT INTO {stock_dbxref} (stock_id, dbxref_id) VALUES (%d, %d)",
         $form_state['values']['db_stock_id'],
         $dbxref->dbxref_id
       );
-      tripal_db_set_active($previous_db);
 
       drupal_set_message(t('Successfully Added Database Reference'));
     }
@@ -356,14 +348,12 @@ function tripal_stock_edit_ALL_db_references_form_submit($form, &$form_state) {
  */
 function tripal_stock_update_db_reference($dbxref_id, $database_id, $accession) {
 
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "UPDATE {dbxref} SET db_id=%d, accession='%s' WHERE dbxref_id=%d",
     $database_id,
     $accession,
     $dbxref_id
   );
-  tripal_db_set_active($previous_db);
 
 }
 
@@ -380,17 +370,15 @@ function tripal_stock_update_db_reference($dbxref_id, $database_id, $accession)
  */
 function tripal_stock_delete_db_reference($dbxref_id) {
 
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "DELETE FROM {dbxref} WHERE dbxref_id=%d",
     $dbxref_id
   );
 
-  db_query(
+  chado_query(
     "DELETE FROM {stock_dbxref} WHERE dbxref_id=%d",
     $dbxref_id
   );
-  tripal_db_set_active($previous_db);
 
 }
 

tripal_stock/includes/tripal_stock-properties.inc

@@ -99,9 +99,7 @@ function tripal_stock_add_ONE_property_form_validate($form, &$form_state) {
     }
     else {
       // Check that type is in chado
-      $previous_db = tripal_db_set_active('chado');
-      $num_rows = db_fetch_object(db_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['prop_type_id']));
-      tripal_db_set_active($previous_db);
+      $num_rows = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['prop_type_id']));
       if ( $num_rows->count != 1) {
         form_set_error('prop_type_id', "The type you selected is not valid. Please choose another one. (CODE:$num_rows)");
       } // end of if more or less than 1 row
@@ -137,15 +135,13 @@ function tripal_stock_add_ONE_property_form_submit($form, &$form_state) {
     }
     else { $rank = $max_rank+1; }
 
-    $previous_db = tripal_db_set_active('chado');
-    db_query(
+    chado_query(
       "INSERT INTO {stockprop} (stock_id, type_id, value, rank) VALUES (%d, %d, '%s', %d)",
       $form_state['values']['prop_stock_id'],
       $form_state['values']['prop_type_id'],
       $form_state['values']['prop_value'],
       $rank
     );
-    tripal_db_set_active($previous_db);
 
     drupal_set_message(t("Successfully Added Property"));
 
@@ -291,21 +287,17 @@ function tripal_stock_edit_ALL_properties_form_submit($form, &$form_state) {
  */
 function tripal_stock_update_property($stockprop_id, $cvterm_id, $value, $preferred, $nid) {
 
-  $previous_db = tripal_db_set_active('chado');
-  $old_obj = db_fetch_object(db_query("SELECT * FROM {stockprop} WHERE stockprop_id=%d", $stockprop_id));
-  tripal_db_set_active($previous_db);
+  $old_obj = db_fetch_object(chado_query("SELECT * FROM {stockprop} WHERE stockprop_id=%d", $stockprop_id));
 
   // if they changed the type need to check rank
   //   (if there is another property of the same type then rank needs to be increased to prevent collisions)
   if ($cvterm_id == $old_obj->type_id) {
-    $previous_db = tripal_db_set_active('chado');
-    db_query(
+    chado_query(
       "UPDATE {stockprop} SET type_id=%d, value='%s' WHERE stockprop_id=%d",
       $cvterm_id,
       $value,
       $stockprop_id
     );
-    tripal_db_set_active($previous_db);
   }
   else {
       //determine the rank for this property
@@ -313,18 +305,16 @@ function tripal_stock_update_property($stockprop_id, $cvterm_id, $value, $prefer
                                   array('stock_id' => array('type' => 'INT', 'value' => $old_obj->stock_id),
                                         'type_id' => array('type' => 'INT', 'value' => $cvterm_id ) ));
     if ($max_rank == -1) {
-    $rank = 0;
+      $rank = 0;
     }
     else { $rank = $max_rank+1; }
-    $previous_db = tripal_db_set_active('chado');
-    db_query(
-      "UPDATE {stockprop} SET type_id=%d, value='%s', rank=%d WHERE stockprop_id=%d",
-      $cvterm_id,
-      $value,
-      $rank,
-      $stockprop_id
-    );
-    tripal_db_set_active($previous_db);
+      chado_query(
+        "UPDATE {stockprop} SET type_id=%d, value='%s', rank=%d WHERE stockprop_id=%d",
+        $cvterm_id,
+        $value,
+        $rank,
+        $stockprop_id
+     );
   }
 
   // Set Preferred Synonym
@@ -350,12 +340,10 @@ function tripal_stock_update_property($stockprop_id, $cvterm_id, $value, $prefer
  */
 function tripal_stock_delete_property($stockprop_id) {
 
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "DELETE FROM {stockprop} WHERE stockprop_id=%d",
     $stockprop_id
   );
-  tripal_db_set_active($previous_db);
 
 }
 

tripal_stock/includes/tripal_stock-relationships.inc

@@ -154,9 +154,7 @@ function tripal_stock_add_ONE_relationship_form_validate($form, &$form_state) {
       form_set_error('type_id', 'Please select a type of relationship.');
     }
     else {
-      $previous_db = tripal_db_set_active('chado');
-      $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['type_id']));
-      tripal_db_set_active($previous_db);
+      $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['type_id']));
 
       if ($tmp_obj->count != 1) {
         form_set_error('type_id', 'The type you selected is not valid. Please choose another one.');
@@ -180,15 +178,13 @@ function tripal_stock_add_ONE_relationship_form_validate($form, &$form_state) {
 function tripal_stock_add_ONE_relationship_form_submit($form, &$form_state) {
 
   if ($form_state['values']['subject_id'] > 0) {
-    $previous_db = tripal_db_set_active('chado');
-    db_query(
+    chado_query(
       "INSERT INTO {stock_relationship} (subject_id, type_id, object_id, value) VALUES (%d, %d, %d, '%s')",
       $form_state['values']['subject_id'],
       $form_state['values']['type_id'],
       $form_state['values']['object_id'],
       $form_state['values']['r_description']
     );
-    tripal_db_set_active($previous_db);
 
     drupal_set_message(t('Successfully Added Relationship.'));
   } //end of insert relationship
@@ -385,9 +381,7 @@ function tripal_stock_edit_ALL_relationships_form_validate($form, &$form_state)
         form_set_error('type_id', 'Please select a type of relationship.');
       }
       else {
-        $previous_db = tripal_db_set_active('chado');
-        $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']["type_id-$i"]));
-        tripal_db_set_active($previous_db);
+        $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']["type_id-$i"]));
 
         if ($tmp_obj->count != 1) {
           form_set_error("type_id-$i", 'The type you selected is not valid. Please choose another one.');
@@ -452,15 +446,13 @@ function tripal_stock_edit_ALL_relationships_form_submit($form, &$form_state) {
  */
 function tripal_stock_update_relationship($stock_relationship_id, $subject_id, $cvterm_id, $object_id) {
 
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "UPDATE {stock_relationship} SET subject_id=%d, type_id=%d, object_id=%d WHERE stock_relationship_id=%d",
     $subject_id,
     $cvterm_id,
     $object_id,
     $stock_relationship_id
   );
-  tripal_db_set_active($previous_db);
 
 }
 
@@ -471,12 +463,10 @@ function tripal_stock_update_relationship($stock_relationship_id, $subject_id, $
  */
 function tripal_stock_delete_relationship($stock_relationship_id) {
 
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "DELETE FROM {stock_relationship} WHERE stock_relationship_id=%d",
     $stock_relationship_id
   );
-  tripal_db_set_active($previous_db);
 
 }
 

tripal_stock/includes/tripal_stock-secondary_tables.inc

@@ -223,12 +223,10 @@ function tripal_stock_is_obsolete_form($node, $stock_id) {
  */
 function tripal_stock_is_obsolete_form_submit($form, &$form_state) {
 
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "UPDATE {stock} SET is_obsolete='t' WHERE stock_id=%d",
     $form_state['values']['make_obsolete_stock_id']
   );
-  tripal_db_set_active($previous_db);
 
 }
 

tripal_stock/tripal_stock.module

@@ -509,9 +509,7 @@ function chado_stock_validate($node, &$form) {
 
   // Validate Uniquename only if add
   if (empty($node->stock_id)) {
-    $previous_db = tripal_db_set_active('chado');
-    $chado_row = db_fetch_object(db_query("SELECT * FROM {stock} WHERE uniquename='" . $node->uniquename . "'"));
-    tripal_db_set_active($previous_db);
+    $chado_row = db_fetch_object(chado_query("SELECT * FROM {stock} WHERE uniquename='" . $node->uniquename . "'"));
     if (!empty($chado_row->stock_id)) {
       $drupal_row = db_fetch_object(db_query("SELECT * FROM {chado_stock} WHERE stock_id=" . $chado_row->stock_id));
       if (!empty($drupal_row->nid)) {
@@ -530,9 +528,7 @@ function chado_stock_validate($node, &$form) {
     form_set_error('type_id', 'Please select a type of stock.');
   }
   else {
-    $previous_db = tripal_db_set_active('chado');
-    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'cvterm', 'cvterm_id', $node->type_id));
-    tripal_db_set_active($previous_db);
+    $num_rows = db_fetch_object(chado_query($int_in_chado_sql, 'cvterm', 'cvterm_id', $node->type_id));
     if ( $num_rows->count != 1) {
       form_set_error('type_id', "The type you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
   }
@@ -542,9 +538,7 @@ function chado_stock_validate($node, &$form) {
     form_set_error('organism_id', 'Please select a source organism for this stock');
   }
   else {
-    $previous_db = tripal_db_set_active('chado');
-    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'organism', 'organism_id', $node->organism_id));
-    tripal_db_set_active($previous_db);
+    $num_rows = db_fetch_object(chado_query($int_in_chado_sql, 'organism', 'organism_id', $node->organism_id));
     if ( $num_rows->count != 1 ) {
       form_set_error('organism_id', "The organism you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
   }
@@ -565,9 +559,7 @@ function chado_stock_validate($node, &$form) {
 
   // Check database is valid db_id in chado ( $form['values']['database_reference']['database'] )
   if ( $node->database > 0) {
-    $previous_db = tripal_db_set_active('chado');
-    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'db', 'db_id', $node->database));
-    tripal_db_set_active($previous_db);
+    $num_rows = db_fetch_object(chado_query($int_in_chado_sql, 'db', 'db_id', $node->database));
     if ($num_rows->count != 1) {
       form_set_error('database', 'The database you selected is not valid. Please choose another one.'); }
   }
@@ -828,12 +820,10 @@ function chado_stock_update($node) {
 function chado_stock_delete($node) {
 
   // Set stock in chado: is_obsolete = TRUE
-  $previous_db = tripal_db_set_active('chado');
-  db_query(
+  chado_query(
     "DELETE FROM {stock} WHERE stock_id=%d",
     $node->stock->stock_id
   );
-  tripal_db_set_active($previous_db);
 
   //remove drupal node and all revisions
   db_query(

tripal_stock/tripal_stock.views.inc

@@ -198,9 +198,7 @@ function tripal_stock_views_pre_render  (&$view) {
         $sql = "SELECT stockprop.*, cvterm.name as type_name FROM {stockprop} "
           ."INNER JOIN cvterm cvterm ON stockprop.type_id=cvterm.cvterm_id "
           ."WHERE stockprop.stock_id IN (" . implode(',', $stock_ids) . ")";
-        $previous_db = tripal_db_set_active('chado');
-        $resource = db_query($sql);
-        tripal_db_set_active($previous_db);
+        $resource = chado_query($sql);
 
         $view->result[$key]->properties = array();
         while ($r = db_fetch_object($resource)) {
@@ -221,9 +219,7 @@ function tripal_stock_views_pre_render  (&$view) {
           ."LEFT JOIN cvterm cvterm ON stock_relationship.type_id = cvterm.cvterm_id "
           ."WHERE stock_relationship.subject_id IN (" . implode(',', $stock_ids) . ") "
           ."OR stock_relationship.object_id IN (" . implode(',', $stock_ids) . ") ";
-        $previous_db = tripal_db_set_active('chado');
-        $resource = db_query($sql);
-        tripal_db_set_active($previous_db);
+        $resource = chado_query($sql);
 
         while ($r = db_fetch_object($resource)) {
           if (in_array($r->subject_id, $stock_ids)) {
@@ -249,9 +245,7 @@ function tripal_stock_views_pre_render  (&$view) {
           ."LEFT JOIN dbxref dbxref ON stock_dbxref.dbxref_id=dbxref.dbxref_id "
           ."LEFT JOIN db db ON dbxref.db_id=db.db_id "
           ."WHERE stock_dbxref.stock_id IN (" . implode(',', $stock_ids) . ")";
-        $previous_db = tripal_db_set_active('chado');
-        $resource = db_query($sql);
-        tripal_db_set_active($previous_db);
+        $resource = chado_query($sql);
 
         $view->result[$key]->dbxref = array();
         while ($r = db_fetch_object($resource)) {

tripal_views/views/handlers/deprecated/views_handler_field_chado_count.inc

@@ -46,14 +46,12 @@ class views_handler_field_chado_count extends views_handler_field {
 
       //Select count from database
       $sql = 'SELECT count(*) as count FROM %s WHERE %s=%d';
-      $previous_db = tripal_db_set_active('chado');
-      $result = db_fetch_object(db_query(
+      $result = db_fetch_object(chado_query(
         $sql,
         $this->aliases['current_table'],
         $this->aliases['foreign_key'],
         $primary_id
       ));
-      tripal_db_set_active($previous_db);
 
       //Add to view results
       $this->view->result[$key]->{$this->field} = $result->count;

tripal_views/views/handlers/deprecated/views_handler_field_dbxref_accession_link.inc

@@ -27,10 +27,8 @@ class views_handler_field_dbxref_accession_link extends views_handler_field {
     $db_id = $values->{$this->aliases['db_id']};
 
     if (!empty($db_id) AND !empty($accession)) {
-      $previous_db = tripal_db_set_active('chado');
       // @coder-ignore: non-drupal schema therefore table prefixing does not apply
-      $result = db_fetch_object(db_query('SELECT urlprefix FROM db WHERE db_id=%d', $db_id));
-      tripal_db_set_active($previous_db);
+      $result = db_fetch_object(chado_query('SELECT urlprefix FROM db WHERE db_id=%d', $db_id));
       $urlprefix = $result->urlprefix;
 
       if (!empty($urlprefix)) {

tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_cvterm_name.inc

@@ -41,9 +41,7 @@ class views_handler_filter_chado_select_cvterm_name extends views_handler_filter
             .' LEFT JOIN cvterm cvterm ON cvterm.cvterm_id=' . $this->view->base_table . '.type_id '
             .'LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
         }
-        $previous_db = tripal_db_set_active('chado');
-        $resource = db_query($sql);
-        tripal_db_set_active($previous_db);
+        $resource = chado_query($sql);
         $cvterms = array();
         while ( $r = db_fetch_object($resource) ) {
           $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $r->cv_id));
@@ -60,9 +58,7 @@ class views_handler_filter_chado_select_cvterm_name extends views_handler_filter
     else {
       // @coder-ignore: non-drupal schema therefore table prefixing does not apply
       $sql = "SELECT cvterm_id, name FROM cvterm WHERE cvterm_id IN (SELECT distinct(type_id) FROM %s)";
-      $previous_db = tripal_db_set_active('chado');
-      $resource = db_query($sql, $this->table);
-      tripal_db_set_active($previous_db);
+      $resource = chado_query($sql, $this->table);
       $cvterms = array();
       while ( $r = db_fetch_object($resource) ) {
         $cvterms[$r->cvterm_id] = $r->name;

tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_string.inc

@@ -94,9 +94,7 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
 
       // get the values from the table
       $sql = "SELECT $this->real_field FROM $this->table $where ORDER BY $this->field ASC";
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      $results = db_query($sql);
-      tripal_db_set_active($previous_db);  // now use drupal database
+      $results = chado_query($sql);
 
       // Build the select box options
       $max_length = $this->options['max_length'];

tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc

@@ -44,9 +44,7 @@ class tripal_views_handler_filter_select_cvterm extends views_handler_filter_str
             .' LEFT JOIN cvterm cvterm ON cvterm.cvterm_id=' . $this->view->base_table . '.type_id '
             .'LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
         }
-        $previous_db = tripal_db_set_active('chado');
-        $resource = db_query($sql);
-        tripal_db_set_active($previous_db);
+        $resource = chado_query($sql);
         $cvterms = array();
         while ( $r = db_fetch_object($resource) ) {
           $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $r->cv_id));
@@ -63,9 +61,7 @@ class tripal_views_handler_filter_select_cvterm extends views_handler_filter_str
     else {
       // @coder-ignore: non-drupal schema therefore table prefixing does not apply
       $sql = "SELECT cvterm_id, name FROM cvterm WHERE cvterm_id IN (SELECT distinct(%s) FROM %s)";
-      $previous_db = tripal_db_set_active('chado');
-      $resource = db_query($sql, $this->field, $this->table);
-      tripal_db_set_active($previous_db);
+      $resource = chado_query($sql, $this->field, $this->table);
       $cvterms = array();
       while ( $r = db_fetch_object($resource) ) {
         $cvterms[$r->cvterm_id] = $r->name;

tripal_views/views/handlers/tripal_views_handler_filter_select_string.inc

@@ -94,9 +94,7 @@ class tripal_views_handler_filter_select_string extends chado_views_handler_filt
 
       // get the values from the table
       $sql = "SELECT $this->real_field FROM $this->table $where ORDER BY $this->field ASC";
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      $results = db_query($sql);
-      tripal_db_set_active($previous_db);  // now use drupal database
+      $results = chado_query($sql);
 
       // Build the select box options
       $max_length = $this->options['max_length'];

tripal_views/views/handlers/views_handler_join_chado_aggregator.inc

@@ -202,9 +202,7 @@ class views_handler_join_chado_aggregator extends views_join {
               WHERE typname='nd_genotype_experiment'
                 AND attrelid=typrelid
                 AND attname NOT IN ('cmin','cmax','ctid','oid','tableoid','xmin','xmax')";
-      $previous_db = tripal_db_set_active('chado');
-      $resource = db_query($sql);
-      tripal_db_set_active($previous_db);
+      $resource = chado_query($sql);
       while ($r = db_fetch_object($resource)) {
         $table = $opt['table'];
         $alias = ''; //no alias needed if table is current table (only option if no schema api definition)