Added brackets around all table names in SQL statements throughout all of Tripal

tripal_analysis/api/tripal_analysis.api.inc

@@ -132,8 +132,8 @@ function tripal_analysis_delete_property($analysis_id, $property) {
  */
 function tripal_analysis_get_node($analysis_id) {
   $sql = "SELECT *
-           FROM chado_analysis CA
-              INNER JOIN node N on CA.nid = N.nid
+           FROM {chado_analysis} CA
+              INNER JOIN {node} N on CA.nid = N.nid
            WHERE analysis_id = %d";
   $node = db_fetch_object(db_query($sql, $analysis_id));
   return $node;

tripal_bulk_loader/tripal_bulk_loader.constants.inc

@@ -286,7 +286,7 @@ function tripal_bulk_loader_set_constants_form_validate($form, $form_state) {
         foreach ($array as $field_id) {
           if ($template[$record_id]['fields'][$field_id]['exposed_validate']) {
             $result = db_fetch_object(chado_query(
-              "SELECT 1 as valid FROM %s WHERE %s='%s'",
+              "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_bulk_loader/tripal_bulk_loader.drush.inc

@@ -171,8 +171,8 @@ function drush_tripal_bulk_loader_tripal_loader_revert ($nid) {
   $resource = db_query('SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=%d ORDER BY tripal_bulk_loader_inserted_id DESC', $nid);
   while ($r = db_fetch_object($resource)) {
     $ids = preg_split('/,/', $r->ids_inserted);
-    db_query('DELETE FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted);
-    $result = db_fetch_object(db_query('SELECT true as present FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted));
+    db_query('DELETE FROM {%s} WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted);
+    $result = db_fetch_object(db_query('SELECT true as present FROM {%s} WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted));
     if (!$result->present) {
       drush_print('Successfully Removed data Inserted into the '.$r->table_inserted_into.' table.');
       db_query('DELETE FROM {tripal_bulk_loader_inserted} WHERE tripal_bulk_loader_inserted_id=%d', $r->tripal_bulk_loader_inserted_id);

tripal_bulk_loader/tripal_bulk_loader.loader.inc

@@ -97,8 +97,8 @@ function tripal_bulk_loader_add_loader_job_form_submit($form, $form_state) {
     $resource = db_query('SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=%d ORDER BY tripal_bulk_loader_inserted_id DESC', $form_state['values']['nid']);
     while ($r = db_fetch_object($resource)) {
       $ids = preg_split('/,/', $r->ids_inserted);
-      db_query('DELETE FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted);
-      $result = db_fetch_object(db_query('SELECT true as present FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted));
+      db_query('DELETE FROM {%s} WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted);
+      $result = db_fetch_object(db_query('SELECT true as present FROM {%s} WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted));
       if (!$result->present) {
         drupal_set_message(t('Successfully Removed data Inserted into the %tableto table.', array('%tableto' => $r->table_inserted_into)));
         db_query('DELETE FROM {tripal_bulk_loader_inserted} WHERE tripal_bulk_loader_inserted_id=%d', $r->tripal_bulk_loader_inserted_id);

tripal_core/api/tripal_core_chado.api.inc

@@ -3374,11 +3374,8 @@ function tripal_get_max_chado_rank($tablename, $where_options) {
       $where[] = $key . $operator . "'" . $val_array['value'] . "'";
     }
   }
-  $previous_db = tripal_db_set_active('chado');
-  $result = db_fetch_object(db_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));
+  $sql = "SELECT max(rank) as max_rank, count(rank) as count FROM {%s} WHERE %s";
+  $result = db_fetch_object(chado_query($sql, $tablename,  implode(' AND ', $where)));
   if ($result->count > 0) {
     return $result->max_rank;
   }
@@ -3546,9 +3543,9 @@ function tripal_core_set_chado_version() {
   // because the Tripal API depends on this function to
   // tell it the version. So, we need a typical SQL statement
   $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 {chadoprop} CP "
+  ."  INNER JOIN {cvterm} CVT on CVT.cvterm_id = CP.type_id "
+  ."  INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id "
   ."WHERE CV.name = 'chado_properties' and CVT.name = 'version'";
   $previous_db = tripal_db_set_active('chado');
   $v = db_fetch_object(db_query($sql));
@@ -3666,9 +3663,9 @@ function tripal_core_clean_orphaned_nodes($table, $job_id) {
   // build the SQL statments needed to check if nodes point to valid analyses
   $dsql = "SELECT * FROM {node} WHERE type = 'chado_%s' order by nid";
   $nsql = "SELECT * FROM {node} WHERE nid = %d";
-  $csql = "SELECT * FROM {chado_%s} where nid = %d ";
+  $csql = "SELECT * FROM {chado_%s} WHERE nid = %d ";
   $clsql= "SELECT * FROM {chado_%s}";
-  $lsql = "SELECT * FROM %s where %s_id = %d ";
+  $lsql = "SELECT * FROM {%s} where %s_id = %d ";
 
   // load into nodes array
   print "Getting nodes\n";

tripal_core/includes/chado_install.php

@@ -79,10 +79,10 @@ function tripal_core_chado_load_form_submit($form, &$form_state) {
  */
 function tripal_core_install_chado($action) {
 
-  $vsql = "INSERT INTO chadoprop (type_id, value) VALUES  " .
+  $vsql = "INSERT INTO {chadoprop} (type_id, value) VALUES  " .
           "((SELECT cvterm_id " .
-          "FROM cvterm CVT " .
-          " INNER JOIN cv CV on CVT.cv_id = CV.cv_id " .
+          "FROM {cvterm} CVT " .
+          " INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id " .
           "WHERE CV.name = 'chado_properties' AND CVT.name = 'version'), " .
           "'%s') ";
 

tripal_core/tripal_core.coder_ignores.txt

@@ -1,18 +0,0 @@
-; The file should be formatted this way :
-; file:line:warning-type
-; where warning-type is one of security, style, sql, i18n, comment, etc.
-
-; This query selects from a non-drupal schema where the database prefixes are not
-; applied and thus the curcly brackets ({}) are not needed
-tripal_core.schema.api.inc:55:sql
-tripal_core.schema.api.inc:61:sql
-tripal_core.api.inc:1060:sql
-tripal_core.api.inc:2153:sql
-
-; Only module designers can create the criteria evaluated by drupal_eval since it
-; is designed in a hook. Since module designers can already write php code to act on
-; the database and the criteria is never subject to user input, this is not a security
-; risk.
-tripal_core.api.inc:993:security
-tripal_core.api.inc:1029:security
-tripal_core.api.inc:1082:security

tripal_cv/api/tripal_cv.api.inc

@@ -466,10 +466,10 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
       PREPARE sel_cvterm_by_accession(text, text) AS
       SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname, 
         DB.name as dbname, DB.db_id, DBX.accession 
-      FROM cvterm CVT
-        INNER JOIN dbxref DBX on CVT.dbxref_id = DBX.dbxref_id
-        INNER JOIN db DB on DBX.db_id = DB.db_id
-        INNER JOIN cv CV on CV.cv_id = CVT.cv_id
+      FROM {cvterm} CVT
+        INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
+        INNER JOIN {db} DB on DBX.db_id = DB.db_id
+        INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
       WHERE DBX.accession = $1 and DB.name = $2";
     if (!tripal_core_chado_prepare('sel_cvterm_by_accession', $pcvtermsql, array('text', 'text'))) {
       watchdog('tripal_cv', "Cannot prepare statement 'sel_cvterm_by_accession'", NULL, WATCHDOG_WARNING);

tripal_cv/includes/charts.inc

@@ -74,7 +74,7 @@
  *    $analysis_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$chart_id);
  *    $type        = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$chart_id);
  *
- *    $sql = "SELECT * FROM {Analysis} WHERE analysis_id = %d";
+ *    $sql = "SELECT * FROM {analysis} WHERE analysis_id = %d";
  *    $analysis = db_fetch_object(chado_query($sql,$analysis_id));
  *
  *    if (strcmp($type,'mf')==0) {
@@ -98,9 +98,9 @@
  *          CNT.analysis_id = $analysis_id AND
  *          CNT.cvterm_id IN (
  *            SELECT CVTR.subject_id
- *            FROM {CVTerm_relationship} CVTR
- *              INNER JOIN CVTerm CVT on CVTR.object_id = CVT.cvterm_id
- *              INNER JOIN CV on CVT.cv_id = CV.cv_id
+ *            FROM {cvterm_relationship} CVTR
+ *              INNER JOIN {CVTerm} CVT on CVTR.object_id = CVT.cvterm_id
+ *              INNER JOIN {CV} on CVT.cv_id = CV.cv_id
  *            WHERE CVT.name = '$class' AND
  *                   CV.name = '$class'
  *          )

tripal_cv/includes/obo_loader.inc

@@ -310,7 +310,7 @@ function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
     } 
   }
   // empty the temp table
-  $sql = "DELETE FROM tripal_obo_temp";
+  $sql = "DELETE FROM {tripal_obo_temp}";
   chado_query($sql);
 
   // get a persistent connection
@@ -435,7 +435,7 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
 
   // iterate through each term from the OBO file and add it
   $sql = "
-    SELECT * FROM tripal_obo_temp
+    SELECT * FROM {tripal_obo_temp}
     WHERE type = 'Term'
     ORDER BY id
   ";
@@ -443,7 +443,7 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
   
   $sql = "
     SELECT count(*) as num_terms
-    FROM tripal_obo_temp
+    FROM {tripal_obo_temp}
     WHERE type = 'Term'     
   "; 
   $result = db_fetch_object(chado_query($sql));

tripal_cv/includes/trees.inc

@@ -204,7 +204,7 @@ function tripal_cv_init_tree($cv_id, $cnt_table = NULL, $fk_column = NULL,
     $cnt_sql = "
        SELECT CVT.name, CVT.cvterm_id, CNT.$cnt_column as num_items
        FROM {$cnt_table} CNT
-        INNER JOIN cvterm CVT on CNT.$fk_column = CVT.cvterm_id
+        INNER JOIN {cvterm} CVT on CNT.$fk_column = CVT.cvterm_id
        WHERE $filter AND CVT.cvterm_id = %d
        ORDER BY $cnt_column desc
     ";
@@ -253,10 +253,10 @@ function tripal_cv_get_term_children($cvterm_id, $cnt_table = NULL,
        CVT1.name as subject_name, CVT3.name as type_name, CVTR.type_id,
        CVT2.name as object_name,CVTR.object_id
     FROM {cvterm_relationship} CVTR
-       INNER JOIN CVTerm CVT1 on CVTR.subject_id = CVT1.cvterm_id
-       INNER JOIN CVTerm CVT2 on CVTR.object_id = CVT2.cvterm_id
-       INNER JOIN CVTerm CVT3 on CVTR.type_id = CVT3.cvterm_id
-       INNER JOIN CV on CV.cv_id = CVT1.cv_id
+       INNER JOIN {CVTerm} CVT1 on CVTR.subject_id = CVT1.cvterm_id
+       INNER JOIN {CVTerm} CVT2 on CVTR.object_id = CVT2.cvterm_id
+       INNER JOIN {CVTerm} CVT3 on CVTR.type_id = CVT3.cvterm_id
+       INNER JOIN {CV} on CV.cv_id = CVT1.cv_id
     WHERE CVTR.object_id = %d
     ORDER BY CVT1.name
   ";
@@ -271,7 +271,7 @@ function tripal_cv_get_term_children($cvterm_id, $cnt_table = NULL,
     $cnt_sql = "
        SELECT CVT.name, CVT.cvterm_id, CNT.$cnt_column as num_items
        FROM {$cnt_table} CNT
-        INNER JOIN cvterm CVT on CNT.$fk_column = CVT.cvterm_id
+        INNER JOIN {cvterm} CVT on CNT.$fk_column = CVT.cvterm_id
        WHERE $filter AND CVT.cvterm_id = %d
        ORDER BY $cnt_column desc
     ";
@@ -377,9 +377,9 @@ function tripal_cv_cvterm_info($cvterm_id) {
     SELECT CVT.name as cvtermname, CVT.definition, CV.name as cvname,
        DBX.accession,DB.urlprefix,DB.db_id,DB.name as dbname
     FROM {CVTerm} CVT
-      INNER JOIN CV on CVT.cv_id = CV.cv_id
-      INNER JOIN dbxref DBX on CVT.dbxref_id = DBX.dbxref_id
-      INNER JOIN DB on DBX.db_id = DB.db_id
+      INNER JOIN {CV} on CVT.cv_id = CV.cv_id
+      INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
+      INNER JOIN {DB} on DBX.db_id = DB.db_id
     WHERE CVT.cvterm_id = %d
   ";
   $cvterm = db_fetch_object(chado_query($sql, $cvterm_id));
@@ -387,7 +387,7 @@ function tripal_cv_cvterm_info($cvterm_id) {
   $sql = "
     SELECT CVTS.synonym, CVT.name as cvname
     FROM {cvtermsynonym} CVTS
-      INNER JOIN cvterm CVT on CVTS.type_id = CVT.cvterm_id
+      INNER JOIN {cvterm} CVT on CVTS.type_id = CVT.cvterm_id
     WHERE CVTS.cvterm_id = %d
 
   ";
@@ -438,8 +438,8 @@ function tripal_cv_list_form($form_state) {
   $sql = "
     SELECT DISTINCT CV.name,CV.cv_id
     FROM {cvterm_relationship} CVTR
-       INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
-       INNER JOIN CV on CV.cv_id = CVT.cv_id
+       INNER JOIN {cvterm} CVT on CVTR.object_id = CVT.cvterm_id
+       INNER JOIN {CV} on CV.cv_id = CVT.cv_id
   ";
   $results = chado_query($sql);
 

tripal_cv/includes/tripal_cv_admin.inc

@@ -430,7 +430,12 @@ function tripal_cv_cvterm_form(&$form_state, $action = 'add') {
  * @ingroup tripal_cv
  */
 function tripal_cv_cvterm_name_autocomplete($cv_id, $string = '') {
-  $sql = "SELECT cvterm_id, name FROM cvterm WHERE cv_id = %d and name like '%s%%' ORDER by name";
+  $sql = "
+    SELECT cvterm_id, name 
+    FROM {cvterm} 
+    WHERE cv_id = %d and name like '%s%%' 
+    ORDER by name
+  ";
   $results = chado_query($sql, $cv_id, $string);
   $items = array();
   while($term = db_fetch_object($results)) {

tripal_cv/tripal_cv.coder_ignores.txt

@@ -2,6 +2,3 @@
 ; file:line:warning-type
 ; where warning-type is one of security, style, sql, i18n, comment, etc.
 
-; This query selects from a non-drupal schema where the database prefixes are not
-; applied and thus the curcly brackets ({}) are not needed
-tripal_cv.module:1062:sql

tripal_feature/api/tripal_feature.api.inc

@@ -551,11 +551,11 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
                     END                   
                 END as downstream,  
                 OF.residues                                                     
-              FROM featureloc FL 
-                INNER JOIN feature SF on FL.feature_id = SF.feature_id
-                INNER JOIN cvterm SCVT on SF.type_id = SCVT.cvterm_id
-                INNER JOIN feature OF on FL.srcfeature_id = OF.feature_id                
-                INNER JOIN cvterm OCVT on OF.type_id = OCVT.cvterm_id
+              FROM {featureloc} FL 
+                INNER JOIN {feature} SF on FL.feature_id = SF.feature_id
+                INNER JOIN {cvterm} SCVT on SF.type_id = SCVT.cvterm_id
+                INNER JOIN {feature} OF on FL.srcfeature_id = OF.feature_id                
+                INNER JOIN {cvterm} OCVT on OF.type_id = OCVT.cvterm_id
               WHERE SF.feature_id = $3) as tbl1
     ';              
     $status = tripal_core_chado_prepare('sequence_by_parent', $psql, array('int', 'int', 'int'));
@@ -570,11 +570,11 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
     // feature (arg #2).
     $psql ='PREPARE sub_features (int, int) AS 
             SELECT SF.feature_id, CVT.name as type_name, SF.type_id
-            FROM feature_relationship FR
-              INNER JOIN feature SF on SF.feature_id = FR.subject_id
-              INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
-              INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
-              INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
+            FROM {feature_relationship} FR
+              INNER JOIN {feature} SF on SF.feature_id = FR.subject_id
+              INNER JOIN {cvterm} CVT on CVT.cvterm_id = SF.type_id
+              INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id
+              INNER JOIN {feature} PF on PF.feature_id = FL.srcfeature_id
             WHERE FR.object_id = $1 and PF.feature_id = $2
             ORDER BY FL.fmin ASC';            
     $status = tripal_core_chado_prepare('sub_features', $psql, array('int', 'int'));
@@ -585,11 +585,11 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
     }
     $psql ='PREPARE count_sub_features (int, int) AS 
             SELECT count(*) as num_children
-            FROM feature_relationship FR
-              INNER JOIN feature SF on SF.feature_id = FR.subject_id
-              INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
-              INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
-              INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
+            FROM {feature_relationship} FR
+              INNER JOIN {feature} SF on SF.feature_id = FR.subject_id
+              INNER JOIN {cvterm} CVT on CVT.cvterm_id = SF.type_id
+              INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id
+              INNER JOIN {feature} PF on PF.feature_id = FL.srcfeature_id
             WHERE FR.object_id = $1 and PF.feature_id = $2';            
     $status = tripal_core_chado_prepare('count_sub_features', $psql, array('int', 'int'));
     if (!$status) {
@@ -732,7 +732,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
   // if we are not getting the sequence from the parent sequence then
   // use what comes through from the feature record
   else {
-    $sql = "SELECT * FROM feature F WHERE feature_id = %d";
+    $sql = "SELECT * FROM {feature} F WHERE feature_id = %d";
     $values = db_fetch_object(chado_query($sql, $feature_id));
     $residues = $values->residues;
     if ($output_format == 'fasta_html') {

tripal_feature/includes/gff_loader.inc

@@ -307,7 +307,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     } 
   }
   // empty the temp table
-  $sql = "DELETE FROM tripal_gff_temp";
+  $sql = "DELETE FROM {tripal_gff_temp}";
   chado_query($sql);
 
   // get a persistent connection
@@ -357,8 +357,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
 
   // get the controlled vocaubulary that we'll be using.  The
   // default is the 'sequence' ontology
-  // @coder-ignore: non-drupal schema thus table prefixing does not apply
-  $sql = "SELECT * FROM cv WHERE name = '%s'";
+  $sql = "SELECT * FROM {cv} WHERE name = '%s'";
   $cv = db_fetch_object(chado_query($sql, 'sequence'));
   if (!$cv) {   
     watchdog('T_gff3_loader', "Cannot find the 'sequence' ontology", 
@@ -367,8 +366,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
   }
 
   // get the organism for which this GFF3 file belongs
-  // @coder-ignore: non-drupal schema thus table prefixing does not apply
-  $sql = "SELECT * FROM organism WHERE organism_id = %d";
+  $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
   $organism = db_fetch_object(chado_query($sql, $organism_id));
 
   $interval = intval($filesize * 0.0001);
@@ -775,18 +773,18 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     // get features in a relationship that are also children of an alignment
     $sql = "SELECT DISTINCT F.feature_id, F.organism_id, F.type_id, 
               F.uniquename, FL.strand 
-            FROM tripal_gff_temp TGT 
-              INNER JOIN feature F                ON TGT.feature_id = F.feature_id
-              INNER JOIN feature_relationship FR  ON FR.object_id = TGT.feature_id
-              INNER JOIN cvterm CVT               ON CVT.cvterm_id = FR.type_id  
-              INNER JOIN featureloc FL            ON FL.feature_id = F.feature_id    
+            FROM {tripal_gff_temp} TGT 
+              INNER JOIN {feature} F                ON TGT.feature_id = F.feature_id
+              INNER JOIN {feature_relationship} FR  ON FR.object_id = TGT.feature_id
+              INNER JOIN {cvterm} CVT               ON CVT.cvterm_id = FR.type_id  
+              INNER JOIN {featureloc} FL            ON FL.feature_id = F.feature_id    
             WHERE CVT.name = 'part_of'";
     $parents = chado_query($sql);
     
     // build and prepare the SQL for selecting the children relationship
     $sql = "SELECT DISTINCT FR.feature_relationship_id, FL.fmin, FR.rank
-            FROM feature_relationship FR              
-              INNER JOIN featureloc FL on FL.feature_id = FR.subject_id";
+            FROM {feature_relationship} FR              
+              INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id";
     if (!$connection) {
       $sql .= "WHERE FR.object_id = %d ".
               "ORDER BY FL.fmin ASC ";
@@ -942,9 +940,9 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
   if (!tripal_core_is_sql_prepared('sel_cvterm_cvname_cvtname_synonym')) {
     $psql = "PREPARE sel_cvterm_cvname_cvtname_synonym (text, text, text) AS
              SELECT CVT.cvterm_id
-             FROM cvterm CVT
-               INNER JOIN cv CV on CVT.cv_id = CV.cv_id
-               LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id
+             FROM {cvterm} CVT
+               INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
+               LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
              WHERE cv.name = $1 and (CVT.name = $2 or CVTS.synonym = $3)";
     $status = tripal_core_chado_prepare('sel_cvterm_cvname_cvtname_synonym', $psql, array('text', 'text' ,'text'));
     if (!$status) {
@@ -1298,11 +1296,11 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
       // prepare the statement
       if (!tripal_core_is_sql_prepared('ins_pub_uniquename_typeid')) {
         $psql = "PREPARE ins_pub_uniquename_typeid (text, text) AS
-                 INSERT INTO pub (uniquename,type_id) VALUES ('%s',
+                 INSERT INTO {pub} (uniquename,type_id) VALUES ('%s',
                  (SELECT cvterm_id
-                  FROM cvterm CVT
-                    INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
-                    INNER JOIN db DB on DB.db_id = DBX.db_id
+                  FROM {cvterm} CVT
+                    INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
+                    INNER JOIN {db} DB on DB.db_id = DBX.db_id
                   WHERE CVT.name = $1 and DB.name = $2)";
         $status = tripal_core_chado_prepare('ins_pub_uniquename_typeid', $psql, args('text', 'text'));
         if (!$status) {

tripal_feature/includes/indexFeatures.inc

@@ -76,7 +76,7 @@ function tripal_features_reindex($max_sync, $job_id = NULL) {
   // reindexing, but adjusted to include the chado_feature
   $sql = "SELECT N.nid, N.title, CF.feature_id ".
         "FROM {node} N ".
-        "  INNER JOIN chado_feature CF ON CF.nid = N.nid ";
+        "  INNER JOIN {chado_feature} CF ON CF.nid = N.nid ";
   $results = db_query($sql);
 
   // load into ids array

tripal_feature/includes/syncFeatures.inc

@@ -128,8 +128,8 @@ function tripal_feature_set_urls($job_id = NULL) {
   while ($node = db_fetch_object($nodes)) {
     // now get the feature details
     $sql = "SELECT * 
-            FROM feature F
-              INNER JOIN organism O on O.organism_id = F.organism_id
+            FROM {feature} F
+              INNER JOIN {organism} O on O.organism_id = F.organism_id
             WHERE F.feature_id = %d";     
     $feature = db_fetch_object(chado_query($sql, $node->feature_id));
     if ($feature) {
@@ -220,8 +220,8 @@ function tripal_feature_sync_features($max_sync = 0, $organism_id = NULL,
   // use this SQL statement to get the features that we're going to upload
   $sql = "SELECT feature_id ".
         "FROM {FEATURE} F ".
-        "  INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
-        "  INNER JOIN CV on CV.cv_id = CVT.cv_id ".
+        "  INNER JOIN {Cvterm} CVT ON F.type_id = CVT.cvterm_id ".
+        "  INNER JOIN {CV} on CV.cv_id = CVT.cv_id ".
         "WHERE ($where_cvt) AND ($where_org) AND CV.name = 'sequence' ".
         "ORDER BY feature_id";
 
@@ -302,8 +302,8 @@ function tripal_feature_sync_feature($feature_id) {
   $fsql = "SELECT F.feature_id, F.name, F.uniquename,O.genus, ".
          "    O.species,CVT.name as cvname,F.residues,F.organism_id ".
          "FROM {FEATURE} F ".
-         "  INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
-         "  INNER JOIN Organism O ON F.organism_id = O.organism_ID ".
+         "  INNER JOIN {Cvterm} CVT ON F.type_id = CVT.cvterm_id ".
+         "  INNER JOIN {Organism} O ON F.organism_id = O.organism_ID ".
          "WHERE F.feature_id = %d";
   $feature = db_fetch_object(chado_query($fsql, $feature_id));
 

tripal_feature/includes/tripal_feature.admin.inc

@@ -480,8 +480,8 @@ function tripal_feature_set_taxonomy($node, $feature_id) {
   // get the cvterm and the organism for this feature
   $sql = "SELECT CVT.name AS cvname, O.genus, O.species ".
         "FROM {CVTerm} CVT ".
-        "  INNER JOIN Feature F on F.type_id = CVT.cvterm_id ".
-        "  INNER JOIN Organism O ON F.organism_id = O.organism_id ".
+        "  INNER JOIN {Feature} F on F.type_id = CVT.cvterm_id ".
+        "  INNER JOIN {Organism} O ON F.organism_id = O.organism_id ".
         "WHERE F.feature_id = $feature_id";
   $feature = db_fetch_object(chado_query($sql));
 
@@ -498,7 +498,7 @@ function tripal_feature_set_taxonomy($node, $feature_id) {
   if ($do_lb && $lb_vid) {
     $sql = "SELECT L.name ".
            "FROM {Library} L ".
-           "  INNER JOIN Library_feature LF ON LF.library_id = L.library_id ".
+           "  INNER JOIN {Library_feature} LF ON LF.library_id = L.library_id ".
            "WHERE LF.feature_id = %d ";
     $library = db_fetch_object(chado_query($sql, $feature_id));
     $tags["$lb_vid"] = "$library->name";
@@ -514,7 +514,7 @@ function tripal_feature_set_taxonomy($node, $feature_id) {
   if ($do_an && $an_vid) {
     $sql = "SELECT A.name ".
            "FROM {Analysis} A ".
-           "  INNER JOIN Analysisfeature AF ON AF.analysis_id = A.analysis_id ".
+           "  INNER JOIN {Analysisfeature} AF ON AF.analysis_id = A.analysis_id ".
            "WHERE AF.feature_id = $feature_id ";
     $results = chado_query($sql);
     $analysis_terms = array();

tripal_feature/tripal_feature.coder_ignores.txt

@@ -2,16 +2,6 @@
 ; file:line:warning-type
 ; where warning-type is one of security, style, sql, i18n, comment, etc.
 
-; This query selects from a non-drupal schema where the database prefixes are not
-; applied and thus the curcly brackets ({}) are not needed
-fasta_loader.php:655:sql
-fasta_loader.php:659:sql
-fasta_loader.php:672:sql
-fasta_loader.php:676:sql
-gff_loader.php:243:sql
-gff_loader.php:252:sql
-gff_loader.php:919:sql
-
 ; This is a multi-line conditional that needs to be re-written to be more readable
 gff_loader.php:166:style
 gff_loader.php:167:style

tripal_feature/tripal_feature.drush.inc

@@ -94,12 +94,12 @@ function drush_tripal_feature_tripal_get_sequence() {
   // get the list of features
   $vars = array();
   $sql  = "SELECT DISTINCT F.feature_id, F.name, F.uniquename, O.genus, O.species, CVT.name as feature_type ".
-          "FROM feature F ".
-          "  INNER JOIN organism O on O.organism_id = F.organism_id ".
-          "  INNER JOIN cvterm CVT on CVT.cvterm_id = F.type_id ";
+          "FROM {feature} F ".
+          "  INNER JOIN {organism} O on O.organism_id = F.organism_id ".
+          "  INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id ";
   if ($analysis_name) {
-     $sql .= "  INNER JOIN analysisfeature AF on AF.feature_id = F.feature_id ".
-             "  INNER JOIN analysis A on AF.analysis_id = A.analysis_id ";
+     $sql .= "  INNER JOIN {analysisfeature} AF on AF.feature_id = F.feature_id ".
+             "  INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id ";
   }         
   $sql .= "WHERE (1=1) ";
   if ($org_commonname) {

tripal_feature/tripal_feature.install

@@ -83,7 +83,7 @@ function tripal_feature_add_organism_count_mview() {
     'SELECT O.organism_id, O.genus, O.species, O.common_name,
         count(F.feature_id) as num_features,
         CVT.cvterm_id, CVT.name as feature_type
-     FROM {Organism} O
+     FROM Organism O
         INNER JOIN Feature F           ON O.Organism_id = F.organism_id
         INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id
      GROUP BY O.Organism_id, O.genus, O.species, O.common_name,

tripal_feature/tripal_feature.module

@@ -1402,12 +1402,12 @@ function tripal_feature_get_matched_alignments($feature) {
           "   FL2.phase            as right_phase, ".
           "   FL2.locgroup         as right_locgroup, ".
           "   FL2.rank             as right_rank ".
-          "FROM feature F1 ".
-          "  INNER JOIN featureloc FL1 on FL1.srcfeature_id = F1.feature_id ".
-          "  INNER JOIN feature F2 on FL1.feature_id = F2.feature_id ".
-          "  INNER JOIN featureloc FL2 on FL2.feature_id = F2.feature_id ".
-          "  INNER JOIN feature F3 on FL2.srcfeature_id = F3.feature_id ".
-          "  INNER JOIN cvterm CVT2 on F2.type_id = CVT2.cvterm_id ".
+          "FROM {feature} F1 ".
+          "  INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id ".
+          "  INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id ".
+          "  INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id ".
+          "  INNER JOIN {feature} F3 on FL2.srcfeature_id = F3.feature_id ".
+          "  INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id ".
           "WHERE F1.feature_id = %d and NOT F3.feature_id = %d ".
           "  AND (CVT2.name = 'match' or CVT2.name like '%_match') ".
           "ORDER BY FL1.fmin";
@@ -2255,11 +2255,11 @@ function tripal_feature_match_features_page($id) {
       CVT.cvterm_id, CVT.name as type_name,
       CF.nid,
       array_agg(S.name) as synonyms
-    FROM feature F
-      INNER JOIN organism O on F.organism_id = O.organism_id
-      INNER JOIN cvterm CVT on CVT.cvterm_id = F.type_id
-      LEFT JOIN feature_synonym FS on FS.feature_id = F.feature_id
-      LEFT JOIN synonym S on S.synonym_id = FS.synonym_id
+    FROM {feature} F
+      INNER JOIN {organism} O on F.organism_id = O.organism_id
+      INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
+      LEFT JOIN {feature_synonym} FS on FS.feature_id = F.feature_id
+      LEFT JOIN {synonym} S on S.synonym_id = FS.synonym_id
       INNER JOIN public.chado_feature CF on CF.feature_id = F.feature_id
     WHERE
       F.uniquename = '%s' or

tripal_library/tripal_library.install

@@ -29,7 +29,7 @@ function tripal_library_install() {
     '   L.name, '.
     '    count(F.feature_id) as num_features, '.
     '    CVT.name as feature_type '.
-    'FROM {Library} L '.
+    'FROM Library L '.
     '    INNER JOIN Library_Feature LF  ON LF.library_id = L.library_id '.
     '    INNER JOIN Feature F           ON LF.feature_id = F.feature_id '.
     '    INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id '.

tripal_library/tripal_library.module

@@ -266,7 +266,7 @@ function theme_tripal_library_search_index($node) {
     while ($library = db_fetch_object($results)) {
       // get the description
       $sql = "SELECT * FROM {libraryprop} LP ".
-             "  INNER JOIN CVTerm CVT ON CVT.cvterm_id = LP.type_id ".
+             "  INNER JOIN {CVTerm} CVT ON CVT.cvterm_id = LP.type_id ".
             "WHERE LP.library_id = $library->library_id ".
             "  AND CVT.name = 'library_description'";
       $desc = db_fetch_object(chado_query($sql));
@@ -285,7 +285,7 @@ function theme_tripal_library_search_index($node) {
     $content = "";
     $organism_id = $node->feature->organism_id;
     $sql = "SELECT * FROM {library} L ".
-           "  INNER JOIN Library_feature LF ON L.library_id = LF.library_id ".
+           "  INNER JOIN {Library_feature} LF ON L.library_id = LF.library_id ".
             "WHERE LF.feature_id = " . $node->feature->feature_id;
     $libraries = array();
     $results = chado_query($sql);

tripal_project/tripal_project.module

@@ -498,18 +498,18 @@ function tripal_project_preprocess_tripal_project_relationships(&$variables) {
   $sql = "
     SELECT P.name, P.project_id, CP.nid, CVT.name as rel_type
     FROM project_relationship PR
-      INNER JOIN project P       ON PR.object_project_id = P.project_id
-      INNER JOIN cvterm CVT      ON PR.type_id           = CVT.cvterm_id
-      LEFT JOIN chado_project CP ON P.project_id         = CP.project_id
+      INNER JOIN {project} P       ON PR.object_project_id = P.project_id
+      INNER JOIN {cvterm} CVT      ON PR.type_id           = CVT.cvterm_id
+      LEFT JOIN public.chado_project CP ON P.project_id         = CP.project_id
     WHERE PR.subject_project_id = %d
   ";
   $as_subject = chado_query($sql, $project->project_id);
   $sql = "
     SELECT P.name, P.project_id, CP.nid, CVT.name as rel_type
     FROM project_relationship PR
-      INNER JOIN project P       ON PR.subject_project_id = P.project_id
-      INNER JOIN cvterm CVT      ON PR.type_id            = CVT.cvterm_id
-      LEFT JOIN chado_project CP ON P.project_id          = CP.project_id
+      INNER JOIN {project P}       ON PR.subject_project_id = P.project_id
+      INNER JOIN {cvterm CVT}      ON PR.type_id            = CVT.cvterm_id
+      LEFT JOIN public.chado_project CP ON P.project_id          = CP.project_id
     WHERE PR.object_project_id = %d
   ";
   $as_object = chado_query($sql, $project->project_id);

tripal_stock/includes/other_module_api_functions.inc

@@ -44,7 +44,7 @@ function get_max_chado_rank($tablename, $where_options) {
   }
 
   $result = db_fetch_object(chado_query(
-    "SELECT max(rank) as max_rank, count(rank) as count FROM %s WHERE %s",
+    "SELECT max(rank) as max_rank, count(rank) as count FROM {%s} WHERE %s",
     $tablename,
     implode(' AND ', $where)
   ));

tripal_stock/includes/tripal_stock-administration.inc

@@ -270,7 +270,7 @@ function tripal_stock_sync_stock_set($organism_id, $job_id) {
           //Add stock id to chado_stock table
           /**
            db_query(
-             "INSERT INTO chado_stock (stock_id, nid, vid) VALUES (%d, %d, %d)",
+             "INSERT INTO {chado_stock} (stock_id, nid, vid) VALUES (%d, %d, %d)",
              $r->stock_id,
              $node->nid,
              $node->vid

tripal_stock/tripal_stock.module

@@ -515,8 +515,8 @@ function chado_stock_form($node, $form_state) {
  */
 function chado_stock_validate($node, &$form) {
 
-  $int_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s=%d";
-  $string_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s='%s'";
+  $int_in_chado_sql = "SELECT count(*) as count FROM {%s} WHERE %s=%d";
+  $string_in_chado_sql = "SELECT count(*) as count FROM {%s} WHERE %s='%s'";
 
   // Validate Uniquename only if add
   if (empty($node->stock_id)) {
@@ -981,11 +981,11 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
       S.name, S.uniquename, S.stock_id, CS.nid, 
       CVT.name as rel_type, CVTs.name as obj_type,
       SR.value
-    FROM stock_relationship SR
-      INNER JOIN stock S on SR.object_id = S.stock_id
-      INNER JOIN cvterm CVT on SR.type_id = CVT.cvterm_id
-      INNER JOIN cvterm CVTs on S.type_id = CVTs.cvterm_id
-      LEFT JOIN chado_stock CS on S.stock_id = CS.stock_id
+    FROM {stock_relationship} SR
+      INNER JOIN {stock} S on SR.object_id = S.stock_id
+      INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
+      INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
+      LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
     WHERE SR.subject_id = %d      
   ";
   $as_subject = chado_query($sql, $stock->stock_id);
@@ -994,11 +994,11 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
       S.name, S.uniquename,  S.stock_id, CS.nid, 
       CVT.name as rel_type, CVTs.name as sub_type,
       SR.value
-    FROM stock_relationship SR
-      INNER JOIN stock S on SR.subject_id = S.stock_id
-      INNER JOIN cvterm CVT on SR.type_id = CVT.cvterm_id
-      INNER JOIN cvterm CVTs on S.type_id = CVTs.cvterm_id
-      LEFT JOIN chado_stock CS on S.stock_id = CS.stock_id
+    FROM {stock_relationship} SR
+      INNER JOIN {stock} S on SR.subject_id = S.stock_id
+      INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
+      INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
+      LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
     WHERE SR.object_id = %d      
   ";
   $as_object = chado_query($sql, $stock->stock_id);   

tripal_views/api/tripal_views.api.inc

@@ -750,7 +750,7 @@ function tripal_views_clone_integration($table_name, $new_priority = NULL, $temp
   }
 
   tripal_views_integration_add_entry($defn_array);
-  $setup_id = db_result(db_query("SELECT setup_id FROM tripal_views WHERE table_name='%s' AND priority=%d", $table_name, $new_priority));
+  $setup_id = db_result(db_query("SELECT setup_id FROM {tripal_views} WHERE table_name='%s' AND priority=%d", $table_name, $new_priority));
 
   if (empty($setup_id)) {
     watchdog('tripal_views','Unable to clone the setup for %table in order to add the following field to the integration: %field.',
@@ -791,7 +791,7 @@ function tripal_views_add_field_to_integration($table_name, $priority, $field) {
   }
 
   // First get the setup_id
-  $setup_id = db_result(db_query("SELECT setup_id FROM tripal_views WHERE table_name='%s' AND priority=%d", $table_name, $priority));
+  $setup_id = db_result(db_query("SELECT setup_id FROM {tripal_views} WHERE table_name='%s' AND priority=%d", $table_name, $priority));
 
   // If there isn't an integration matching that table/priority combination
   // then clone the lightest priority integration

tripal_views/tripal_views.coder_ignores.txt

@@ -5,15 +5,6 @@
 ; All variables are filtered
 tripal_views_integration.inc:814:security
 
-; SQL queries the chado database which does not use the drupal prefixing functionality
-; therefore, curly brackets ({}) are not appropriate.
-views/handlers/views_handler_filter_chado_select_cvterm_name.inc:62:sql
-views/handlers/views_handler_field_dbxref_accession_link.inc:32:sql
-views/handlers/views_handler_filter_stockprop_id.inc:105:sql
-views/handlers/views_handler_filter_stock_relationship_id.inc:24:sql
-views/handlers/views_handler_filter_stock_relationship_id.inc:74:sql
-views/handlers/views_handler_filter_stock_relationship_id.inc:82:sql
-views/handlers/views_handler_argument_stockprop_id.inc:22:sql
 
 ; SQL queries the pg_tables table to check if a table exists in chado; drupal
 ; prefixing is not appropriate

tripal_views/views/handlers/deprecated/views_handler_field_dbxref_accession_link.inc

@@ -28,7 +28,7 @@ class views_handler_field_dbxref_accession_link extends views_handler_field {
 
     if (!empty($db_id) AND !empty($accession)) {
       // @coder-ignore: non-drupal schema therefore table prefixing does not apply
-      $result = db_fetch_object(chado_query('SELECT urlprefix FROM db WHERE db_id=%d', $db_id));
+      $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

@@ -33,13 +33,13 @@ class views_handler_filter_chado_select_cvterm_name extends views_handler_filter
       else {
         //get a list of cvs currently used
         if ($this->view->base_table == 'cvterm') {
-          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
-            .' LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
+          $sql = 'SELECT distinct(cv.cv_id) FROM {' . $this->view->base_table . '}'
+            .' LEFT JOIN {cv} cv ON cv.cv_id=cvterm.cv_id';
         }
         else {
-          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
-            .' 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';
+          $sql = 'SELECT distinct(cv.cv_id) FROM {' . $this->view->base_table . '}'
+            .' 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';
         }
         $resource = chado_query($sql);
         $cvterms = array();
@@ -57,7 +57,7 @@ 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)";
+      $sql = "SELECT cvterm_id, name FROM {cvterm} WHERE cvterm_id IN (SELECT distinct(type_id) FROM {%s})";
       $resource = chado_query($sql, $this->table);
       $cvterms = array();
       while ( $r = db_fetch_object($resource) ) {

tripal_views/views/handlers/tripal_views_handler_field_sequence.inc

@@ -68,7 +68,7 @@ class tripal_views_handler_field_sequence extends chado_views_handler_field {
          'fasta_html' => 'FASTA in HTML format',
          'fasta_txt'  => 'FASTA in text format',
       ),
-      '#description' => t('Select an output format.  Raw output cannot be used when the sequence is derived from the parent.'),
+      '#description' => t('Choose an output format.  Raw output cannot be used when the sequence is derived from the parent.'),
       '#default_value' => $default_ouput_format,
     );
   }  

tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc

@@ -36,11 +36,11 @@ class tripal_views_handler_filter_select_cvterm extends views_handler_filter_str
       else {
         //get a list of cvs currently used
         if ($this->view->base_table == 'cvterm') {
-          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
+          $sql = 'SELECT distinct(cv.cv_id) FROM {' . $this->view->base_table . '}' 
             .' LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
         }
         else {
-          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
+          $sql = 'SELECT distinct(cv.cv_id) FROM {' . $this->view->base_table . '}'
             .' 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';
         }
@@ -60,7 +60,7 @@ 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)";
+      $sql = "SELECT cvterm_id, name FROM {cvterm} WHERE cvterm_id IN (SELECT distinct(%s) FROM {%s})";
       $resource = chado_query($sql, $this->field, $this->table);
       $cvterms = array();
       while ( $r = db_fetch_object($resource) ) {

tripal_views/views/handlers/tripal_views_handler_filter_select_string.inc

@@ -93,7 +93,7 @@ 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";
+      $sql = "SELECT $this->real_field FROM {$this->table} $where ORDER BY $this->field ASC";
       $results = chado_query($sql);
 
       // Build the select box options