Tripal Analysis adheres to Drupal coding standards

tripal_analysis/tripal_analysis.admin.inc

@@ -3,6 +3,11 @@
 // Copyright 2009 Clemson University
 //
 
+/**
+ * @file
+ * @todo Add file header description
+ */
+
 /**
  * Purpose: Provide Guidance to new Tripal Admin
  *

tripal_analysis/tripal_analysis.api.inc

@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * @todo Add file header description
+ */
+
 /**
  * @defgroup tripal_analysis_api Analysis Module API
  * @ingroup tripal_analysis

tripal_analysis/tripal_analysis.install

@@ -1,4 +1,8 @@
 <?php
+/**
+ * @file
+ * @todo Add file header description
+ */
 
 /*******************************************************************************
  * Implementation of hook_install().

tripal_analysis/tripal_analysis.module

@@ -936,7 +936,7 @@ function tripal_analyses_cleanup($dummy = NULL, $job_id = NULL) {
   while ($ca_record = db_fetch_object($results)) {
         $node = db_fetch_object(db_query($sql_drupal_node2, $ca_record->nid));
         if (!$node) {
-      db_query("DELETE FROM {chado_analysis} WHERE nid = $ca_record->nid");
+      db_query("DELETE FROM {chado_analysis} WHERE nid = %nid", $ca_record->nid);
       $message = "chado_analysis missing node.... DELETING chado_analysis record with nid: $ca_record->nid\n";
       watchdog('tripal_analysis', $message, array(), WATCHDOG_WARNING);
         }

tripal_analysis/tripal_analysis_privacy.inc

@@ -1,4 +1,8 @@
 <?php
+/**
+ * @file
+ * @todo Add file header description
+ */
 
 /*
  *  Perform permission check by analysis_id only if 'node_privacy_byrole' module is enabled
@@ -53,7 +57,7 @@ function tripal_analysis_set_feature_permission($analysis_id, $nid) {
   }
 
   //Convert analysis_id into node_id
-  $ana_nid = db_result(db_query("SELECT nid FROM {chado_analysis} WHERE analysis_id = $analysis_id"));
+  $ana_nid = db_result(db_query("SELECT nid FROM {chado_analysis} WHERE analysis_id = %analysis_id", $analysis_id));
   // Get available roles
   $roles = array_keys(user_roles());
 

tripal_analysis/views/handlers/views_handler_field_computed_analysis_nid.inc

@@ -1,4 +1,8 @@
 <?php
+/**
+ * @file
+ * @todo Add file header description
+ */
 
 /**
  *