Tripal Pub adheres to Drupal coding standards

tripal_pub/tripal_pub.install

@@ -4,8 +4,8 @@
 /**
  * @file
  * This file contains all the functions which describe and implement drupal database tables
- * needed by this module. This module was developed by Chad N.A. Krilow and Lacey-Anne Sanderson, 
- * University of Saskatchewan. 
+ * needed by this module. This module was developed by Chad N.A. Krilow and Lacey-Anne Sanderson,
+ * University of Saskatchewan.
  *
  * The project manamgenet module allows you to sync data in a chado/Tripal instance with
  * multiple project/mysql instances as well as manage and create such project instances
@@ -17,23 +17,23 @@
  */
 function tripal_pub_install() {
 
-	drupal_install_schema('tripal_pub');
-	$dbxref = array('accession' => 'abstract', 'db_id'=>array('name'=>'tripal'));
-	$success = tripal_core_chado_insert('dbxref',$dbxref);
-	if ($success) {
-		tripal_core_chado_insert('cvterm',array('name'=>'abstract','cv_id'=>array('name'=>'tripal'), 'db
-xref_id'=>$dbxref));
-	}
+  drupal_install_schema('tripal_pub');
+  $dbxref = array('accession' => 'abstract', 'db_id' => array('name' => 'tripal'));
+  $success = tripal_core_chado_insert('dbxref', $dbxref);
+  if ($success) {
+    tripal_core_chado_insert('cvterm', array('name' => 'abstract', 'cv_id' => array('name' => 'tripal'), 'db
+xref_id' => $dbxref));
+  }
 }
 
 
 /**
- * Implementation of hook_uninstall() 
+ * Implementation of hook_uninstall()
  */
 function tripal_pub_uninstall() {
-	//Remove tables
-	drupal_uninstall_schema('tripal_pub');
-	
+  //Remove tables
+  drupal_uninstall_schema('tripal_pub');
+
 }
 
 
@@ -42,49 +42,49 @@ function tripal_pub_uninstall() {
  */
 function tripal_pub_schema() {
 //specification for 'tripal_pub_instances'
-	$schema['chado_pub'] = array(
-		
-		'fields' => array(
-      
-	    //a int field that cannot be null and acts as a unique identifier for all nid's
+  $schema['chado_pub'] = array(
+
+    'fields' => array(
+
+      //a int field that cannot be null and acts as a unique identifier for all nid's
       'nid' => array(
-				'type' => 'int',
-				'unsigned' => TRUE,
-				'not null' => TRUE,
- 	 	  ),
-		
-	    //a int field that cannot be null and is vid 	  
-  		'vid' => array(
-   	   	'type' => 'int',
-   	   	'not null' => TRUE,
-  	  ),
-   	 	
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        ),
+
+      //a int field that cannot be null and is vid
+      'vid' => array(
+          'type' => 'int',
+          'not null' => TRUE,
+      ),
+
       //a intfield, not null and project_id is the unique_id of the project in chado
-    	 'pub_id' => array(
-   	   	'type' => 'int',
-   	   	'unsigned' => TRUE,
-   	   	'not null' => TRUE,
-    	),	
-    	
-    	 //a intfield, not null and project_id is the unique_id of the project in chado
-    	 'pubmed_id' => array(
-   	   	'type' => 'int',
-   	   	'unsigned' => TRUE,
-   	   	'not null' => FALSE,
-    	),
-    	'author' => array(
+       'pub_id' => array(
+          'type' => 'int',
+          'unsigned' => TRUE,
+          'not null' => TRUE,
+      ),
+
+       //a intfield, not null and project_id is the unique_id of the project in chado
+       'pubmed_id' => array(
+          'type' => 'int',
+          'unsigned' => TRUE,
+          'not null' => FALSE,
+      ),
+      'author' => array(
         'type' => 'text',
         'size' => 'normal',
         'not null' => TRUE,
         'default' => '',
         'description' => 'The Author Name.',
       ),
-  	 ), 	
+     ),
      //end of shema
-  	
-  	'primary key' => array('nid'),
-	
-	);
+
+    'primary key' => array('nid'),
+
+  );
 
   return $schema;
 }

tripal_pub/views/template.node_join.views.inc

@@ -5,18 +5,18 @@
  *
  *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
  *    (ie: If you want to join features to their drupal nodes then XXX=feature)
- * 
- *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *
+ *  NOTE: Creating the table definition file is not enough. You also need to call the
  *        retrieve_XXX_views_data() function from ../tripal_pub.views.inc:tripal_pub_views_data()
  *        by adding the following line:
  *           $data = array_merge($data, retrieve_XXX_views_data());
- *        to the function and including the file directly above the function (blow the function 
+ *        to the function and including the file directly above the function (blow the function
  *        header by adding:
  *           require_once('views/XXX.views.inc');
  *
  *  REMOVE THIS COMMENT IN THE COPY!
- */ 
- 
+ */
+
 /**
  *  @file
  *  This file defines the data array for a given chado table. This array
@@ -24,31 +24,31 @@
  *  with this module in:
  *  @see tripal_pub.views.inc --in tripal_pub_views_data()
  *
- *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table.
  *        This file simply defines this linking table and joins the three tables together.
  *        No modification of XXX.views.inc is needed.
  *
- *  Documentation on views integration can be found at 
+ *  Documentation on views integration can be found at
  *  http://views2.logrus.com/doc/html/index.html.
  */
- 
+
 /**
- * Purpose: this function returns the portion of the data array 
- *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ * Purpose: this function returns the portion of the data array
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it
  *   and other tables
  * @see tripal_pub_views_data() --in tripal_pub.views.inc
  *
  * The main need for description of this table to views is to join chado data with drupal nodes
  *
  */
-function retrieve_chado_XXX_views_data () {
-	global $db_url;
+function retrieve_chado_XXX_views_data() {
+  global $db_url;
   $data = array();
-  
+
   // if the chado database is not local to the drupal database
   // then we need to set the database name.  This should always
   // be 'chado'.
-  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+  if (is_array($db_url) and array_key_exists('chado', $db_url)) {
      // return empty data array b/c if chado is external then no join to the nodetable can be made
      return $data;
   }
@@ -57,28 +57,28 @@ function retrieve_chado_XXX_views_data () {
   $data['chado_XXX']['table'] = array(
     'field' => 'nid',
   );
-  
+
   //Relationship Definitions---------------------------------
   // Note: No joins need to be made from $data['XXX']['table']
-  
+
   // Join the chado_XXX table to XXX
   $data['chado_XXX']['table']['join']['XXX'] = array(
-  	'left_field' => 'XXX_id',
-  	'field' => 'XXX_id',
+    'left_field' => 'XXX_id',
+    'field' => 'XXX_id',
   );
-  
+
   // Join the node table to chado_XXX
   $data['node']['table']['join']['chado_XXX'] = array(
-  	'left_field' => 'nid',
-  	'field' => 'nid',
+    'left_field' => 'nid',
+    'field' => 'nid',
   );
-  
+
   // Join the node table to XXX
   $data['node']['table']['join']['XXX'] = array(
-  	'left_table' => 'chado_XXX',
-  	'left_field' => 'nid',
-  	'field' => 'nid',
-  );  
+    'left_table' => 'chado_XXX',
+    'left_field' => 'nid',
+    'field' => 'nid',
+  );
 
-	return $data;
-}
+  return $data;
+}

tripal_pub/views/template.table_defn.views.inc

@@ -5,7 +5,7 @@
  *
  *   - Every instance of XXX should be replaced with the name of your table
  *   - If this is a base table (you want a view where every row is a row from this table)
- *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base']
  *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
  *   - Relationships between this table and others: YYY is the table you are trying to join to this
  *     one. You want to join a table to this one if this table contains a foreign key to the other
@@ -15,18 +15,18 @@
  *   - Create a field definition for each field in this table using the example fields already
  *     listed. Match the type of the database field to the field definition listed below.
  *     (ie: for a text/varchar field from the database use plain_text_field below)
- * 
- *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *
+ *  NOTE: Creating the table definition file is not enough. You also need to call the
  *        retrieve_XXX_views_data() function from ../tripal_pub.views.inc:tripal_pub_views_data()
  *        by adding the following line:
  *           $data = array_merge($data, retrieve_XXX_views_data());
- *        to the function and including the file directly above the function (blow the function 
+ *        to the function and including the file directly above the function (blow the function
  *        header by adding:
  *           require_once('views/XXX.views.inc');
  *
  *  REMOVE THIS COMMENT IN THE COPY!
- */ 
- 
+ */
+
 /**
  *  @file
  *  This file defines the data array for a given chado table. This array
@@ -34,12 +34,12 @@
  *  with this module in:
  *  @see tripal_pub.views.inc --in tripal_pub_views_data()
  *
- *  Documentation on views integration can be found at 
+ *  Documentation on views integration can be found at
  *  http://views2.logrus.com/doc/html/index.html.
  */
 
 /*************************************************************************
- * Purpose: this function returns the portion of the data array 
+ * Purpose: this function returns the portion of the data array
  *   which describes the XXX table, it's fields and any joins between it and other tables
  * @see tripal_pub_views_data() --in tripal_pub.views.inc
  *
@@ -55,23 +55,23 @@
   // if the chado database is not local to the drupal database
   // then we need to set the database name.  This should always
   // be 'chado'.
-  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+  if (is_array($db_url) and array_key_exists('chado', $db_url)) {
     $database = 'chado';
   }
-   
+
   //Basic table definition-----------------------------------
   $data['XXX']['table']['group'] = t('Chado XXX');
-  
+
   $data['XXX']['table'] = array(
     'field' => 'primary_id',
     'title' => t('Chado XXX'),
     'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
   );
-  if($database){
+  if ($database) {
      $data['XXX']['table']['database'] = $database;
   }
 
-  
+
   //Relationship Definitions---------------------------------
   //Join: YYY => XXX
   // Notice that this relationship tells the primary table to show it's fields to the
@@ -80,16 +80,16 @@
   $data['XXX']['table']['join']['YYY'] = array(
     'left_field' => 'foreign key in YYY table',
     'field' => 'primary key in XXX table',
-  );  
-  
+  );
+
   //Join: XXX => XY => YYY
   // This relationship should be described in both directions
-  // in the appropriate files (ie: for feature => library 
+  // in the appropriate files (ie: for feature => library
   // describe in both feature.views.inc and library.views.inc)
   $data['XXX']['table']['join']['XY'] = array(
     'left_field' => 'matching XXX key in the XY table',
     'field' => 'primary key in XXX table',
-  );  
+  );
   $data['XXX']['table']['join']['YYY'] = array(
     'left_table' => 'XY',
     'left_field' => 'matching XXX key in the XY table',
@@ -99,9 +99,9 @@
     'left_field' => 'primary key in YYY table',
     'field' => 'matching YYY key in the XY table',
   );
-   
+
   //Table Field Definitions----------------------------------
-      
+
   //Field: XXX_id (primary key)
   $data['XXX']['field_name'] = array(
     'title' => t('XXX Primary Key'),
@@ -123,7 +123,7 @@
    * Remove this section when done
    */
 
-  //Field: plain_text_field (chado datatype)   
+  //Field: plain_text_field (chado datatype)
   $data['XXX']['plain_text_field'] = array(
     'title' => t('Human-Readable Name'),
     'help' => t('Description of this field.'),
@@ -142,7 +142,7 @@
     ),
   );
 
-  //Field: numeric_field (chado datatype)   
+  //Field: numeric_field (chado datatype)
   $data['XXX']['numeric_field'] = array(
     'title' => t('Human-Readable Name'),
     'help' => t('Description of this field.'),
@@ -158,7 +158,7 @@
     ),
   );
 
-  //Field: boolean_field (chado datatype)   
+  //Field: boolean_field (chado datatype)
   $data['XXX']['boolean_field'] = array(
     'title' => t('Human-Readable Name'),
     'help' => t('Description of this field.'),
@@ -174,7 +174,7 @@
     ),
   );
 
-  //Field: unix_timestamp (chado datatype)   
+  //Field: unix_timestamp (chado datatype)
   $data['XXX']['unix_timestamp'] = array(
     'title' => t('Human-Readable Name'),
     'help' => t('Description of this field.'),
@@ -190,7 +190,7 @@
     ),
   );
 
-  //Field: human_readable_date (chado datatype)   
+  //Field: human_readable_date (chado datatype)
   $data['XXX']['human_readable_date'] = array(
     'title' => t('Human-Readable Name'),
     'help' => t('Description of this field.'),
@@ -202,10 +202,10 @@
       'handler' => 'views_handler_sort_date',
     ),
   );
-   
+
    /*
     * End of Example Field definitions
     */
-    
+
   return $data;
-}
+}