Provided fix for issue #2446009 and issue #2430333

tripal_core/api/tripal_core.chado_nodes.title_and_path.inc

@@ -736,7 +736,7 @@ function chado_update_existing_node_urls($content_type, $job_id = 0) {
 }
 
 /**
- * Generic "Set Node url" sub-form for setting the url of any chado node
+ * Generic "Set Node URL" sub-form for setting the url of any chado node
  *
  * @param $form
  *   The Drupal form array into which the property form elements will be added
@@ -1305,7 +1305,7 @@ function chado_get_token_value($token_info, $node) {
   $token = $token_info['token'];
   $table = $token_info['table'];
   $var = $node;
-  
+
   // Iterate through each portion of the location string. An example string
   // might be:  stock > type_id > name.
   $location = explode('>', $token_info['location']);

tripal_core/api/tripal_core.jobs.api.inc

@@ -83,8 +83,11 @@ function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid, $pr
   $record->arguments = $args;
 
   if (drupal_write_record('tripal_jobs', $record)) {
-    $jobs_url = url("admin/tripal/tripal_jobs");
-    drupal_set_message(t("Job '%job_name' submitted.  Check the <a href='!jobs_url'>jobs page</a> for status", array('%job_name' => $job_name, '!jobs_url' => $jobs_url)));
+    drupal_set_message(t("Job '%job_name' submitted.", array('%job_name' => $job_name)));
+    if (user_access('administer tripal')) {
+      $jobs_url = url("admin/tripal/tripal_jobs");
+      drupal_set_message(t("Check the <a href='!jobs_url'>jobs page</a> for status", array('!jobs_url' => $jobs_url)));
+    }
   }
   else {
     drupal_set_message(t("Failed to add job %job_name.", array('%job_name' => $job_name)), 'error');

tripal_example/README.txt

@@ -1,7 +1,7 @@
-This module is provided as a template for creating a custom Tripal Extension 
+This module is provided as a template for creating a custom Tripal Extension
 Module for Drupal 7 and Tripal 2.x.
 
-Drupal does provide quite a bit of documentation on its website at 
+Drupal does provide quite a bit of documentation on its website at
 http://www.drupal.org but the easiest way to learn to program a Drupal module
 is to purchase the following book:
 
@@ -12,7 +12,7 @@ But this quick link can help get you started:
   https://drupal.org/developing/modules/7
 
 Briefly, to create a Drupal module you must
- 
+
 1) Create a directory to house all of your module's files
 2) Create a .info inside of the directory which provides information about your
    module to Drupal
@@ -44,11 +44,11 @@ If you want to integrate with Drupal Views 3.x:
 
 Include Files
 -------------
-To limit the size of files, some functionality can be placed inside of 
+To limit the size of files, some functionality can be placed inside of
 "include" files. Include files are placed inside of an 'includes' directory.
 [module dir]/includes
 
-If your module creates a node type that uses data housed in Chado, you should 
+If your module creates a node type that uses data housed in Chado, you should
 place all of the Drupal hooks for nodes inside of an include named:
 [module dir]/includes/[module name].chado_node.inc
 
@@ -60,18 +60,18 @@ All other include files should be named in the following way:
 [module dir]/includes/[module name].[function].inc
 
 where [function] is a brief description of the functionality provided by the
-include file.  Please only use underscores inside of the [function] (no dashes
+include file. Please only use underscores inside of the [function] (no dashes
 or periods).
 
 
 Theme Files
 -------------
-Tripal primarily uses template files for displaying content from Chado. This 
+Tripal primarily uses template files for displaying content from Chado. This
 allows anyone to easily change the way data is displayed without needing to
-delve into the module's source code.  A template typically provides data for
+delve into the module's source code. A template typically provides data for
 a single data type (e.g. feature) or association (e.g. properties associated to
-features, or publications associated with featurmaps, etc.).  These template
-files and any JavaScript, CSS or images needed to suppport them are all
+features, or publications associated with featurmaps, etc.). These template
+files and any JavaScript, CSS or images needed to support them are all
 housed inside of a 'theme' directory with the following structure:
 [module dir]/theme
 [module dir]/theme/css       (for CSS files)
@@ -91,18 +91,18 @@ Template files are named in the following way
 [module dir]/theme/templates/[module name]_[function].tpl.php.
 
 Notice that templates have an underscore separating the [module name] from the
-[function].  Typically a period is used (as with include files) but for
-backwards compatibility the undescores are kept.  
+[function]. Typically a period is used (as with include files) but for
+backwards compatibility the underscores are kept.
 
 API Files
 ---------
-If your module will provide a set of functions that can be used as an 
-Application Programming Intervace (API), then those functions should be placed 
+If your module will provide a set of functions that can be used as an
+Application Programming Interface (API), then those functions should be placed
 in files housed in the 'api' directory:
 [module dir]/api
 
 When creating API functions try to organize them into groups of related function
-and separate them into files by function with the following nameing:
+and separate them into files by function with the following naming:
 [module dir]/api/[module name].[function].api.inc
 
 

tripal_example/api/tripal_example.api.inc

@@ -2,7 +2,8 @@
 
 /**
  * @file
- * Provides an application programming interface (API) for working the example module
+ * Provides an application programming interface (API) for working the example
+ * module
  */
 
 /**
@@ -12,22 +13,23 @@
  * Provides an application programming interface (API) for working with features
  * @}
  */
- 
-// EXPLANATION: This file is used for housing any API function that your
-// module creates.  It is suggested you follow the naming style for Tripal 
-// API functions. Below are naming rules for Tripal API functions:
+
+// EXPLANATION: This file is used for housing any API function that your module
+// creates. It is suggested you follow the naming style for Tripal API
+// functions. Below are naming rules for Tripal API functions:
 //
 // 1) Prefix the function with 'chado_' for all insert, updates, delete or get
-//    function on a table in the chado schema.  Tripal should provide all of these 
-//    functions for tables that come with Chado.  But, you can use this prefix 
-//    for API functions on custom tables that your module may add.
+//    function on a table in the chado schema. Tripal should provide all of
+//    these functions for tables that come with Chado. But, you can use this
+//    prefix for API functions on custom tables that your module may add.
 // 2) For all other functions prefix the function with your module name. So
 //    for this example module the prefix would be 'tripal_example_'
 // 3) A 'verb' should follow the function prefix indicating the action that
 //    the function performs. Commonly used verbs are 'get', 'insert', 'update'
-//    'associate', 'execute', etc.  An exception is for functions that
-//    test state rather than perform an action (e.g. does something exist).  
-//    For functions that test state use 'does' instead of a verb 
-//    (e.g. tripal_example_does_pub_exist) 
-// 4) Follow the verb with a short predicate describing what is being acted upon.
+//    'associate', 'execute', etc. An exception is for functions that
+//    test state rather than perform an action (e.g. does something exist).
+//    For functions that test state use 'does' instead of a verb
+//    (e.g. tripal_example_does_pub_exist)
+// 4) Follow the verb with a short predicate describing what is being acted
+//    upon.
 //

tripal_example/includes/tripal_example.admin.inc

@@ -18,10 +18,9 @@ function tripal_example_admin_examples_listing() {
   drupal_set_breadcrumb($breadcrumb);
 
 
-  // EXPLANATION:  Typically for all Tripal modules the home administrative
-  // page for the module contains a search form to help the adminstrator
-  // locate records.  The following example code adds a default View to
-  // the page
+  // EXPLANATION:  Typically for all Tripal modules the home administrative page
+  // for the module contains a search form to help the adminstrator locate
+  // records. The following example code adds a default View to the page
   /*
   // Add the view
   $view = views_embed_view('tripal_example_admin_examples','default');
@@ -55,19 +54,23 @@ function tripal_example_admin() {
     '#markup' => t('There are currently no settings to configure.')
   );
 
-  // If your module is using the Chado Node: Title & Path API to allow custom titles
-  // for your node type then you need to add the configuration form for this functionality.
+  // If your module is using the Chado Node: Title & Path API to allow custom
+  // titles for your node type then you need to add the configuration form for
+  // this functionality.
   $details = array(
-    'module' => 'tripal_example',       // the name of the MODULE implementing the content type
+      // the name of the MODULE implementing the content type
+    'module' => 'tripal_example',
       // An array of options to use under "Page Titles"
-      // the key should be the token and the value should be the human-readable option
+      // the key should be the token and the value should be the human-readable
+      // option
     'options' => array(
       '[example.name]' => 'Germplasm Name Only',
       '[example.uniquename]' => 'Germplasm Unique Name Only',
         // there should always be one options matching the unique constraint.
-        // If you have a more human-readable constraint, then that is preferrable.
+        // If you have a more human-readable constraint, then that is
+        // preferable.
         // See the tripal feature module for a good example of this.
-      '[example.example_id]' => 'Unique Contraint: The Chado ID for Examples'
+      '[example.example_id]' => 'Unique Constraint: The Chado ID for Examples'
     ),
     // the token indicating the unique constraint in the options array
     'unique_option' => '[example.example_id]'
@@ -88,4 +91,3 @@ function tripal_example_admin() {
 function tripal_example_admin_validate($form, &$form_state) {
 
 }
-

tripal_example/includes/tripal_example.chado_node.inc

@@ -9,7 +9,7 @@
 /**
  *  Implementation of hook_node_info().
  *
- *  This hook provides information to drupal about any node types that are being
+ *  This hook provides information to Drupal about any node types that are being
  *  created by this module. If your module does not create any node types then
  *  this function is not required.
  *
@@ -30,22 +30,26 @@ function tripal_example_node_info() {
     'description' => t('A record from the fake chado example table'),
     'has_title'   => TRUE,
     'locked'      => TRUE,
-    // EXPLANATION: This section of the node type array specifies how Tripal will sync the node
-    // types with data in Chado. When Drupal creates a node it has no way of
-    // coordinating which node belongs to which record in Chado. Therefore,
-    // Tripal maintains tables in the Drupal schema that maps Drupal nodes
-    // to recrords in Chado.  Syncing is the process of creating Drupal nodes
-    // and linking them to the appropriate record.
+    // EXPLANATION: This section of the node type array specifies how Tripal
+    // will sync the node types with data in Chado. When Drupal creates a node
+    // it has no way of coordinating which node belongs to which record in
+    // Chado. Therefore, Tripal maintains tables in the Drupal schema that maps
+    // Drupal nodes to records in Chado. Syncing is the process of creating
+    // Drupal nodes and linking them to the appropriate record.
     'chado_node_api' => array(
-      'base_table' => 'example',       // the base table name (e.g. example, example, contact)
-      'hook_prefix' => 'chado_example',// the node type hook prefix
+      // the base table name (e.g. example, example, contact)
+      'base_table' => 'example',
+      // the node type hook prefix
+      'hook_prefix' => 'chado_example',
       'record_type_title' => array(
-        'singular' => t('Example'),    // how to refer to the record
-        'plural' => t('Examples')      // how to refer to the record in plurals
+        // how to refer to the record
+        'singular' => t('Example'),
+        // how to refer to the record in plurals
+        'plural' => t('Examples')
       ),
       'sync_filters' => array(
-        'type_id' => TRUE,             // if the record has a type_id set to TRUE
-        'organism_id' => TRUE          // if the record has an organism_id set to TRUE
+        'type_id' => TRUE,     // if the record has a type_id set to TRUE
+        'organism_id' => TRUE  // if the record has an organism_id set to TRUE
       ),
     )
   );
@@ -54,28 +58,26 @@ function tripal_example_node_info() {
 }
 
 /**
- * Implement hook_access().  This hook provides instructions to
- * drupal for which users can access the custom content types
- * created in the function above.  The available permissions
- * are set in the chado_example_permissions() hook in the
- * tripal_example.module file.  This hook is not needed
- * if no node types were defined in the hook_node_info() hook.
+ * Implement hook_access(). This hook provides instructions to Drupal for which
+ * users can access the custom content types created in the function above. The
+ * available permissions are set in the chado_example_permissions() hook in the
+ * tripal_example.module file. This hook is not needed if no node types were
+ * defined in the hook_node_info() hook.
  *
  * @return
- * This function should return null if it does not specificially
- * deny access. This allows for other mechanisms to to deny
- * or reject access. If the return value is TRUE then access
- * is granted regardless of any other rules that might be implemented
- * by other modules.
+ * This function should return null if it does not specifically deny access.
+ * This allows for other mechanisms to to deny or reject access. If the return
+ * value is TRUE then access is granted regardless of any other rules that might
+ * be implemented by other modules.
  */
 function chado_example_node_access($node, $op, $account) {
   $node_type = $node;
   if (is_object($node)) {
     $node_type = $node->type;
   }
-  // EXPLANATION:  in the tripal_example_permissions() function we
-  // created the permission types that are used here to check for
-  // access permissions to the 'chado_exmaple' node type.
+  // EXPLANATION:  in the tripal_example_permissions() function we created the
+  // permission types that are used here to check for access permissions to the
+  // 'chado_exmaple' node type.
   if($node_type == 'chado_example') {
     if ($op == 'create') {
       if (!user_access('create chado_example content', $account)) {
@@ -111,37 +113,38 @@ function chado_example_node_access($node, $op, $account) {
  */
 function chado_example_form($node, &$form_state) {
 
-  // EXPLANATION: This function should construct a form array that is used
-  // by Drupal to contruct a form for inserting or editing our new node type.
+  // EXPLANATION: This function should construct a form array that is used by
+  // Drupal to construct a form for inserting or editing our new node type.
   // See this page for information about the Form API:
   // https://api.drupal.org/api/drupal/includes!form.inc/group/form_api/7
   //
   // The code below is laid out in the following order
   // 1) Set default values
   // 2) Add form elements used by this node type
-  // 3) Use the Tripal API to add form elemetns for properties,
+  // 3) Use the Tripal API to add form elements for properties,
   //    dbxref's and relationships
   //
-  // For the example code below we assume that the fake 'example' table
-  // only has a uniquename, organism_id, type_id and example_id.
+  // For the example code below we assume that the fake 'example' table only has
+  // a uniquename, organism_id, type_id and example_id.
 
   $form = array();
 
   // Default values can come in the following ways:
   //
-  // 1) as elements of the $node object.  This occurs when editing an existing example
-  // 2) in the $form_state['values'] array which occurs on a failed validation or
-  //    ajax callbacks from non submit form elements
-  // 3) in the $form_state['input'[ array which occurs on ajax callbacks from submit
-  //    form elements and the form is being rebuilt
+  // 1) as elements of the $node object. This occurs when editing an existing
+  //    example
+  // 2) in the $form_state['values'] array which occurs on a failed validation
+  //    or ajax callbacks from non submit form elements
+  // 3) in the $form_state['input'[ array which occurs on ajax callbacks from
+  //    submit form elements and the form is being rebuilt
   //
   // set form field defaults
 
 
   // SET FORM DEFAULTS
   //---------------------------------------------
-  $example      = null;   // holds the example object record
-  $example_id   = null;   // when editing an example record we'll have an example_id
+  $example      = null; // holds the example object record
+  $example_id   = null; // when editing an example record we'll have an example_id
 
   // initialize the defaults for the form fields
   $uniquename   = '';
@@ -164,8 +167,8 @@ function chado_example_form($node, &$form_state) {
       '#value' => $example_id,
     );
   }
-  // if we are re constructing the form from a failed validation or ajax callback
-  // then use the $form_state['values'] values
+  // if we are re constructing the form from a failed validation or ajax
+  // callback then use the $form_state['values'] values
   if (array_key_exists('values', $form_state)) {
      $uniquename   = $form_state['values']['uniquename'];
      $example_type = $form_state['values']['example_type'];
@@ -188,12 +191,12 @@ function chado_example_form($node, &$form_state) {
     '#title' => t('Unique Name'),
     '#required' => TRUE,
     '#default_value' => $uniquename,
-    '#description' => t('Enter a unique name for this example.  This name must be unique.'),
+    '#description' => t('Enter a unique name for this example. This name must be unique.'),
     '#maxlength' => 255
   );
 
-  // for the type_id we want to use the default vocabulary so that this
-  // field can have autocomplete functionality
+  // for the type_id we want to use the default vocabulary so that this field
+  // can have auto-complete functionality
   $type_cv = tripal_get_default_cv('example', 'type_id');
   $cv_id = $type_cv->cv_id;
   $form['example_type'] = array(
@@ -226,43 +229,58 @@ function chado_example_form($node, &$form_state) {
 
   // PROPERTIES FORM
   //---------------------------------------------
-  // If there is a exampleprop table and you want to allow users to add/remove entries
-  // from it through your node form then add this section to your own node form
+  // If there is a exampleprop table and you want to allow users to add/remove
+  // entries from it through your node form then add this section to your own
+  // node form
   $prop_cv = tripal_get_default_cv('exampleprop', 'type_id');
   $cv_id = $prop_cv ? $prop_cv->cv_id : NULL;
   $details = array(
-    'property_table' => 'exampleprop',      // the name of the prop table
-    'chado_id' => $example_id,              // the value of example_id for this record
-    'cv_id' => $cv_id                       // the cv.cv_id of the cv governing exampleprop.type_id
+    // the name of the prop table
+    'property_table' => 'exampleprop',
+    // the value of example_id for this record
+    'chado_id' => $example_id,
+    // the cv.cv_id of the cv governing exampleprop.type_id
+    'cv_id' => $cv_id
   );
   // Adds the form elements to your current form
   chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
-  // If there is a example_dbxref table and you want to allow users to add/remove entries
-  // from it through your node form then add this section to your own node form
+  // If there is a example_dbxref table and you want to allow users to
+  // add/remove entries from it through your node form then add this section to
+  // your own node form
   $details = array(
-    'linking_table' => 'example_dbxref',  // the name of the _dbxref table
-    'base_foreign_key' => 'example_id',   // the name of the key in your base chado table
-    'base_key_value' => $example_id       // the value of example_id for this record
+    // the name of the _dbxref table
+    'linking_table' => 'example_dbxref',
+    // the name of the key in your base chado table
+    'base_foreign_key' => 'example_id',
+    // the value of example_id for this record
+    'base_key_value' => $example_id
   );
   // Adds the form elements to your current form
   chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   // RELATIONSHIPS FORM
   //---------------------------------------------
-  // If there is a example_relationship table and you want to allow users to add/remove entries
-  // from it through your node form then add this section to your own node form
+  // If there is a example_relationship table and you want to allow users to
+  // add/remove entries from it through your node form then add this section to
+  // your own node form
   $rels_cv = tripal_get_default_cv('example_relationship', 'type_id');
   $cv_id = $rels_cv ? $rels_cv->cv_id : NULL;
   $details = array(
-    'relationship_table' => 'example_relationship', // the name of the _relationship table
-    'base_table' => 'example',                      // the name of your chado base table
-    'base_foreign_key' => 'example_id',             // the name of the key in your base chado table
-    'base_key_value' => $example_id,                // the value of example_id for this record
-    'nodetype' => 'example',                        // the human-readable name of your node type
-    'cv_id' => $cv_id                               // the cv.cv_id of the cv governing example_relationship.type_id
+    // the name of the _relationship table
+    'relationship_table' => 'example_relationship',
+    // the name of your chado base table
+    'base_table' => 'example',
+    // the name of the key in your base chado table
+    'base_foreign_key' => 'example_id',
+    // the value of example_id for this record
+    'base_key_value' => $example_id,
+    // the human-readable name of your node type
+    'nodetype' => 'example',
+    // the cv.cv_id of the cv governing example_relationship.type_id
+    'cv_id' => $cv_id
   );
   // Adds the form elements to your current form
   chado_add_node_form_relationships($form, $form_state, $details);
@@ -274,14 +292,14 @@ function chado_example_form($node, &$form_state) {
 /**
  * Implementation of hook_validate
  *
- * This function validates a form prior to insert or update. If an error
- * is detected, it sets the error using form_set_error() which takes the
- * user back to the form to make corrections.
+ * This function validates a form prior to insert or update. If an error is
+ * detected, it sets the error using form_set_error() which takes the user back
+ * to the form to make corrections.
  *
  * This validation is being used for three activities:
- *   CASE A: Update a node that exists in both drupal and chado
- *   CASE B: Synchronizing a node from chado to drupal
- *   CASE C: Inserting a new node that exists in niether drupal nor chado
+ *   CASE A: Update a node that exists in both Drupal and Chado
+ *   CASE B: Synchronizing a node from Chado to Drupal
+ *   CASE C: Inserting a new node that exists in neither Drupal nor Chado
  *
  * @param $node
  *
@@ -298,8 +316,8 @@ function chado_example_validate($node, $form, &$form_state) {
     return;
   }
 
-  // we are syncing if we do not have a node ID but we do have a example_id. We don't
-  // need to validate during syncing so just skip it.
+  // we are syncing if we do not have a node ID but we do have a example_id. We
+  // don't need to validate during syncing so just skip it.
   if (is_null($node->nid) and property_exists($node, 'example_id') and $node->example_id != 0) {
     return;
   }
@@ -322,8 +340,8 @@ function chado_example_validate($node, $form, &$form_state) {
       form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology."));
     }
 
-    // TODO: also we should check that the unique constraint is not invalidated by
-    // changing either the type_id, organism_id or uniquename.
+    // TODO: also we should check that the unique constraint is not invalidated
+    // by changing either the type_id, organism_id or uniquename.
   }
   // Validating for an insert
   else {
@@ -342,14 +360,14 @@ function chado_example_validate($node, $form, &$form_state) {
 }
 
 /**
- *  Implementation of hook_insert(). This function is called after the
- *  node is inserted into the database. We need it so that we can insert
- *  appropriate fields as provided by the user into the database. And so that
- *  we can link the new Drupal node to the data in Chado via the chado_example
- *  linking table. We can get to this function also during "syncing".
- *  With syncing, however, the data already exists in Chado and we do not want
- *  to try to re-add it. But we do need to add an entry to the chado_example table
- *  to link the Drupal node with the data in the 'example' table of Chado.
+ *  Implementation of hook_insert(). This function is called after the node is
+ * inserted into the database. We need it so that we can insert appropriate
+ * fields as provided by the user into the database. And so that we can link the
+ * new Drupal node to the data in Chado via the chado_example linking table. We
+ * can get to this function also during "syncing".
+ * With syncing, however, the data already exists in Chado and we do not want
+ * to try to re-add it. But we do need to add an entry to the chado_example
+ * table to link the Drupal node with the data in the 'example' table of Chado.
  *
  *  This function is not required if the hook_node_info() does not define
  *  any custom node types.
@@ -369,8 +387,8 @@ function chado_example_insert($node) {
   ));
 
   // if there is an example_id in the $node object then this must be a sync so
-  // we can skip adding the example as it is already there, although
-  // we do need to proceed with the rest of the insert
+  // we can skip adding the example as it is already there, although we do need
+  // to proceed with the rest of the insert
   if (!property_exists($node, 'example_id')) {
 
     // perform the insert using the chado_insert_record function();
@@ -391,39 +409,51 @@ function chado_example_insert($node) {
     // get the example_id for linking Drupal node with Chado data
     $example_id = $example['example_id'];
 
-    // Only add to other chado tables if the base record was inserted properly
+    // Only add to other Chado tables if the base record was inserted properly
     if ($example_id > 0) {
 
-      // If you implemented the properties form in chado_example_form then you need to
-      // handle inserting these properties into your chado prop table.
+      // If you implemented the properties form in chado_example_form then you
+      // need to handle inserting these properties into your Chado prop table.
       $details = array(
-        'property_table'   => 'exampleprop',   // the name of the prop table
-        'base_table'       => 'example',       // the name of your chado base table
-        'foreignkey_name'  => 'example_id',    // the name of the key in your base table
-        'foreignkey_value' => $example_id      // the value of the example_id key
+        // the name of the prop table
+        'property_table'   => 'exampleprop',
+        // the name of your Chado base table
+        'base_table'       => 'example',
+        // the name of the key in your base table
+        'foreignkey_name'  => 'example_id',
+        // the value of the example_id key
+        'foreignkey_value' => $example_id
       );
       chado_update_node_form_properties($node, $details);
 
-      // If you implemented the dbxrefs form in chado_example_form then you need to
-      // handle inserting these database references into your chado _dbxref table.
+      // If you implemented the dbxrefs form in chado_example_form then you need
+      // to handle inserting these database references into your Chado _dbxref
+      // table.
       $details = array(
-        'linking_table'    => 'example_dbxref', // the name of your _dbxref table
-        'foreignkey_name'  => 'example_id',     // the name of the key in your base table
-        'foreignkey_value' => $example_id       // the value of the example_id key
+        // the name of your _dbxref table
+        'linking_table'    => 'example_dbxref',
+        // the name of the key in your base table
+        'foreignkey_name'  => 'example_id',
+        // the value of the example_id key
+        'foreignkey_value' => $example_id
       );
       chado_update_node_form_dbxrefs($node, $details);
 
-      // If you implemented the relationships form in chado_example_form then you need to
-      // handle inserting these relationships into your chado _relationship table.
+      // If you implemented the relationships form in chado_example_form then
+      // you need to handle inserting these relationships into your Chado
+      // _relationship table.
       $details = array(
-        'relationship_table' => 'example_relationship',  // name of the _relationship table
-        'foreignkey_value' => $example_id                // value of the example_id key
+        // name of the _relationship table
+        'relationship_table' => 'example_relationship',
+        // value of the example_id key
+        'foreignkey_value' => $example_id
       );
       chado_update_node_form_relationships($node, $details);
     }
   }
   else {
-    // the node has an example_id so get it for linking Drupal node with Chado data
+    // the node has an example_id so get it for linking Drupal node with Chado
+    // data
     $example_id = $node->example_id;
   }
 
@@ -440,12 +470,11 @@ function chado_example_insert($node) {
 }
 
 /**
- * Implementation of hook_update().  This function runs after the
- * node has been inserted into the Drupal schema and allows us to
- * update the record in Chado.
+ * Implementation of hook_update(). This function runs after the node has been
+ * inserted into the Drupal schema and allows us to update the record in Chado.
  *
- *  This function is not required if the hook_node_info() does not define
- *  any custom node types.
+ * This function is not required if the hook_node_info() does not define any
+ * custom node types.
  *
  * @ingroup tripal_example
  */
@@ -470,41 +499,44 @@ function chado_example_update($node) {
       array('%values' => print_r($values, TRUE)));
   }
 
-  // If you implemented the properties form in chado_example_form then you need to
-  // handle updating these properties into your chado prop table.
+  // If you implemented the properties form in chado_example_form then you need
+  // to handle updating these properties into your Chado prop table.
   $details = array(
-    'property_table' => 'exampleprop',   // the name of the prop table
-    'base_table' => 'example',           // the name of your chado base table
-    'foreignkey_name' => 'example_id',   // the name of the key in your base table
-    'foreignkey_value' => $example_id    // the value of the example_id key
+    'property_table' => 'exampleprop', // the name of the prop table
+    'base_table' => 'example',         // the name of your Chado base table
+    'foreignkey_name' => 'example_id', // the name of the key in your base table
+    'foreignkey_value' => $example_id  // the value of the example_id key
   );
   chado_update_node_form_properties($node, $details);
 
   // If you implemented the dbxrefs form in chado_example_form then you need to
-  // handle updating these database references into your chado _dbxref table.
+  // handle updating these database references into your Chado _dbxref table.
   $details = array(
-    'linking_table' => 'example_dbxref',   // the name of your _dbxref table
-    'foreignkey_name' => 'example_id',     // the name of the key in your base table
-    'foreignkey_value' => $example_id      // the value of the example_id key
+    'linking_table' => 'example_dbxref', // the name of your _dbxref table
+    'foreignkey_name' => 'example_id',   // the name of the key in your base table
+    'foreignkey_value' => $example_id    // the value of the example_id key
   );
   chado_update_node_form_dbxrefs($node, $details);
 
-  // If you implemented the relationships form in chado_example_form then you need to
-  // handle updating these relationships into your chado _relationship table.
+  // If you implemented the relationships form in chado_example_form then you
+  // need to handle updating these relationships into your Chado _relationship
+  // table.
   $details = array(
-    'relationship_table' => 'example_relationship',  // name of the _relationship table
-    'foreignkey_value' => $example_id                // value of the example_id key
+    // name of the _relationship table
+    'relationship_table' => 'example_relationship',
+    // value of the example_id key
+    'foreignkey_value' => $example_id
   );
   chado_update_node_form_relationships($node, $details);
 
 }
 /**
- * Implementation of hook_delete().  This function runs after the
- * node has been deleted from the Drupal schema and allows us to
- * delete the corresponding recrod in Chado.
+ * Implementation of hook_delete(). This function runs after the node has been
+ * deleted from the Drupal schema and allows us to delete the corresponding
+ * record in Chado.
  *
- * This function is not required if the hook_node_info() does not define
- * any custom node types.
+ * This function is not required if the hook_node_info() does not define any
+ * custom node types.
  *
  * @ingroup tripal_example
  */
@@ -513,18 +545,18 @@ function chado_example_delete($node) {
   // get the example id from the node
   $example_id  = chado_get_id_from_nid('example', $node->nid);
 
-  // if we don't have a example id for this node then this isn't a node of
-  // type chado_example or the entry in the chado_example table was lost.
+  // if we don't have a example id for this node then this isn't a node of type
+  // chado_example or the entry in the chado_example table was lost.
   if (!$example_id) {
     return;
   }
 
   // remove the entry in the chado_exapmle table linking the deleted
-  // Drupal node with the data in chado
+  // Drupal node with the data in Chado
   $sql_del = "DELETE FROM {chado_example} WHERE nid = :nid AND vid = :vid";
   db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
 
-  // Remove data from example tables of chado database.  This will
+  // Remove data from example tables of Chado database. This will
   // cause a cascade delete and remove all data in referencing tables
   // for this example
   chado_query("DELETE FROM {example} WHERE example_id = :example_id", array(':example_id' => $example_id));
@@ -535,25 +567,25 @@ function chado_example_delete($node) {
 }
 
 /**
- * Implementation of hook_load().  This function is necessary to load
- * into the $node object the fields of the table form Chado. For example
- * for the example table, the chado_example_load() function adds in
- * a example object which contains all of the fields and sub objects
- * for data in tables with foreign key relationships.
+ * Implementation of hook_load(). This function is necessary to load into the
+ * $node object the fields of the table form Chado. For example for the example
+ * table, the chado_example_load() function adds in a example object which
+ * contains all of the fields and sub objects for data in tables with foreign
+ * key relationships.
  *
- * This function is not required if the hook_node_info() does not define
- * any custom node types.
+ * This function is not required if the hook_node_info() does not define any
+ * custom node types.
  *
  * @ingroup tripal_example
  */
 function chado_example_load($nodes) {
 
   // EXPLANATION: when displaying or node or accessing the node in a template
-  // we need the data from Chado.  This fucntion finds the record in Chado that
+  // we need the data from Chado. This function finds the record in Chado that
   // this node belongs to and adds the record.
 
-  // there may be multiple nodes that get passed in so we have to iterate through
-  // them all
+  // there may be multiple nodes that get passed in so we have to iterate
+  // through them all
   foreach ($nodes as $nid => $node) {
     // find the example and add in the details
     $example_id = chado_get_id_from_nid('example', $nid);
@@ -568,20 +600,21 @@ function chado_example_load($nodes) {
     $values = array('example_id' => $example_id);
     $example = chado_generate_var('example', $values);
 
-    // for fields in the table that are of type 'text' you may want to include those
-    // by default, the chado_generate_var does not include text fields as
-    // they may be very large and including a large text field can slow the page load.
+    // for fields in the table that are of type 'text' you may want to include
+    // those by default, the chado_generate_var does not include text fields as
+    // they may be very large and including a large text field can slow the page
+    // load.
     // If you know a text field will never be large and it is important for the
     // other functions that will see the node to have access to a field you can
-    // include it here using the chado_expand_var() function.  In most
-    // cases it is probably best to let the end-user decide if text fields should
-    // be included by using this function in the templates.
+    // include it here using the chado_expand_var() function. In most
+    // cases it is probably best to let the end-user decide if text fields
+    // should be included by using this function in the templates.
     $example = chado_expand_var($example, 'field', 'example.description');
 
 
-    // If your module is using the Chado Node: Title & Path API to allow custom titles
-    // for your node type. Every time you want the title of the node, you need to use the
-    // following API function:
+    // If your module is using the Chado Node: Title & Path API to allow custom
+    // titles for your node type. Every time you want the title of the node, you
+    // need to use the following API function:
     $node->title = chado_get_node_title($node);
 
     // add the new example object to this node.
@@ -598,24 +631,24 @@ function chado_example_load($nodes) {
  */
 function tripal_example_node_presave($node) {
 
-  // EXPLANATION: This node is useful for
-  // making changes to the node prior to it being saved to the database.
+  // EXPLANATION: This node is useful for making changes to the node prior to it
+  // being saved to the database.
   // One useful case for this is to set the title of a node using values
   // supplied by the user.
   //
-  // This function is not required. You probably won't need it if you
-  //  don't define a custom node type in the hook_node_info() function. But
-  // it is node type agnostic, so you can use this function to change the
-  // contents of any node regardless of it's type.
+  // This function is not required. You probably won't need it if you don't
+  // define a custom node type in the hook_node_info() function. But it is node
+  // type agnostic, so you can use this function to change the contents of any
+  // node regardless of it's type.
 
   // set the node title
   switch ($node->type) {
-    // This step is for setting the title for the Drupal node.  This title
-    // is permanent and thus is created to be unique.  Title changes provided
-    // by tokens are generated on the fly dynamically, but the node title
-    // seen in the content listing needs to be set here. Do not call
-    // the chado_get_node_title() function here to set the title as the node
-    // object isn't properly filled out and the function will fail.
+    // This step is for setting the title for the Drupal node. This title is
+    // permanent and thus is created to be unique. Title changes provided by
+    // tokens are generated on the fly dynamically, but the node title seen in
+    // the content listing needs to be set here. Do not call the
+    // chado_get_node_title() function here to set the title as the node object
+    // isn't properly filled out and the function will fail.
     case 'chado_example':
       // for a form submission the 'uniquename' field will be set,
       // for a sync, we must pull from the example object
@@ -639,24 +672,23 @@ function tripal_example_node_presave($node) {
  */
 function tripal_example_node_insert($node) {
 
-  // EXPLANATION: This function is used
-  // after any a node is inserted into the database.  It is different
-  // from the hook_insert() function above in that it is called after
-  // any node is saved, regardlesss of it's type. This function is useful
-  // for making changes to the database after a node is inserted.
-  // An example comes from the tripal_feature module where the URL alias
-  // of a node cannot be set in the hook_insert() function. Therefore
-  // the tripal_feature module uses this function to set the url path
-  // of a newly inserted example node.
+  // EXPLANATION: This function is used after any a node is inserted into the
+  // database. It is different from the hook_insert() function above in that it
+  // is called after any node is saved, regardless of it's type. This function
+  // is useful for making changes to the database after a node is inserted.
+  // An example comes from the tripal_feature module where the URL alias of a
+  // node cannot be set in the hook_insert() function. Therefore the
+  // tripal_feature module uses this function to set the URL path of a newly
+  // inserted example node.
   //
-  // This function is not required. You probably won't need it if you
-  // don't define a custom node type in the hook_node_info() function. But
-  // it is node type agnostic, so you can use this function to do any
-  // activity after insert of any node.
-
-  // the Example code below will set the URL path after inserting.  We do it
-  // here because we do not know the example_id in the presave and cannot do
-  // it in the hook_insert()
+  // This function is not required. You probably won't need it if you don't
+  // define a custom node type in the hook_node_info() function. But it is node
+  // type agnostic, so you can use this function to do any activity after insert
+  // of any node.
+
+  // the Example code below will set the URL path after inserting. We do it here
+  // because we do not know the example_id in the pre-save and cannot do it in
+  // the hook_insert()
   switch ($node->type) {
     case 'chado_example':
 
@@ -668,17 +700,17 @@ function tripal_example_node_insert($node) {
       $example = chado_generate_var('example', $values);
       $node->example = $example;
 
-      // If your module is using the 'Chado Node: Title & Path API' to allow custom titles
-      // for your node type. Every time you want the title of the node, you need to use the
-      // following API function:
+      // If your module is using the 'Chado Node: Title & Path API' to allow
+      // custom titles for your node type. Every time you want the title of the
+      // node, you need to use the following API function:
       $example->title = chado_get_node_title($node);
 
       // set the URL for this example page
-      // see the code in the tripal_feature/includes/tripal_feature.chado_node.inc file
-      // in the function tripal_feature_node_insert for an example of how that
-      // module sets the URL.  It uses a configuration file to allow the user
-      // to dynmically build a URL schema and then uses that schema to generate
-      // a URL string.
+      // see the code in the tripal_feature/includes/tripal_feature.chado_node.inc
+      // file in the function tripal_feature_node_insert for an example of how
+      // that module sets the URL. It uses a configuration file to allow the
+      // user to dynamically build a URL schema and then uses that schema to
+      // generate a URL string.
       break;
   }
 }
@@ -691,35 +723,34 @@ function tripal_example_node_insert($node) {
  */
 function tripal_example_node_update($node) {
 
-  // EXPLANATION: This function is used
-  // after any a node is updated in the database.  It is different
-  // from the hook_update() function above in that it is called after
-  // any node is updated, regardlesss of it's type.
-  // An example comes from the tripal_feature module where the URL alias
-  // of a node cannot be set in the hook_update() function. Therefore
-  // the tripal_feature module uses this function to reset the url path
-  // of an updated feature node.
+  // EXPLANATION: This function is used after any a node is updated in the
+  // database. It is different from the hook_update() function above in that it
+  // is called after any node is updated, regardless of it's type.
+  // An example comes from the tripal_feature module where the URL alias of a
+  // node cannot be set in the hook_update() function. Therefore the
+  // tripal_feature module uses this function to reset the URL path of an
+  // updated feature node.
   //
-  // This function is not required. You probably won't need it if you
-  // don't define a custom node type in the hook_node_info() function. But
-  // it is node type agnostic, so you can use this function to do any
-  // activity after insert of a node.
+  // This function is not required. You probably won't need it if you don't
+  // define a custom node type in the hook_node_info() function. But it is node
+  // type agnostic, so you can use this function to do any activity after insert
+  // of a node.
 
   // add items to other nodes, build index and search results
   switch ($node->type) {
     case 'chado_example':
 
-      // If your module is using the Chado Node: Title & Path API to allow custom titles
-      // for your node type. Every time you want the title of the node, you need to use the
-      // following API function:
+      // If your module is using the Chado Node: Title & Path API to allow
+      // custom titles for your node type. Every time you want the title of the
+      // node, you need to use the following API function:
       $example->title = chado_get_node_title($node);
 
       // set the URL for this example page
-      // see the code in the tripal_feature/includes/tripal_feature.chado_node.inc file
-      // in the function tripal_feature_node_insert for an example of how that
-      // module sets the URL.  It uses a configuration file to allow the user
-      // to dynmically build a URL schema and then uses that schema to generate
-      // a URL string.
+      // see the code in the tripal_feature/includes/tripal_feature.chado_node.inc
+      // file in the function tripal_feature_node_insert for an example of how
+      // that module sets the URL. It uses a configuration file to allow the
+      // user to dynamically build a URL schema and then uses that schema to
+      // generate a URL string.
       break;
   }
 }
@@ -730,11 +761,11 @@ function tripal_example_node_update($node) {
  */
 function tripal_example_node_view($node, $view_mode, $langcode) {
 
-  // EXPLANATION: This function defines the content "blocks" that appear
-  // when thhe node is displayed. It is node type agnostic so we can add
-  // content to any node type.  So, we use this function to add the content
-  // from all of our theme templates onto our new node type. We will also
-  // use this function to add content to other node types.
+  // EXPLANATION: This function defines the content "blocks" that appear when
+  // the node is displayed. It is node type agnostic so we can add content to
+  // any node type. So, we use this function to add the content from all of our
+  // theme templates onto our new node type. We will also use this function to
+  // add content to other node types.
 
   switch ($node->type) {
     case 'chado_example':
@@ -742,24 +773,25 @@ function tripal_example_node_view($node, $view_mode, $langcode) {
       // supports full page view and teaser view.
       if ($view_mode == 'full') {
 
-        // If you want to use the default Tripal node template then you need to tell
-        // tripal to generate the Table of Contents. This is done by setting the following
-        // to TRUE. If your content type follows the chado_<base table> convention
-        // then this is the default. In this case if you don't want to use the default
-        // template then you need to set the following to FALSE.
+        // If you want to use the default Tripal node template then you need to
+        // tell Tripal to generate the Table of Contents. This is done by
+        // setting the following to TRUE. If your content type follows the
+        // chado_<base table> convention then this is the default. In this case
+        // if you don't want to use the default template then you need to set
+        // the following to FALSE.
         $node->content['#tripal_generic_node_template'] = TRUE;
 
-        // There is always a base template.  This is the template that
-        // is first shown when the example node type is first displayed.
-        // if you are using the default Tripal node template, then you should
+        // There is always a base template. This is the template that is first
+        // shown when the example node type is first displayed.
+        // If you are using the default Tripal node template, then you should
         // also set two additional items in each array:  tripal_toc_id and
-        // tripal_toc_title.  The tripal_tock_id should be a single unqiue
+        // tripal_toc_title. The tripal_tock_id should be a single unique
         // world that is used to reference the template. This ID is used for
-        // constructing URLs for the content.  The tripal_toc_title contains
+        // constructing URLs for the content. The tripal_toc_title contains
         // the title that should appear in the table of contents for this
-        // content.  You should only set the '#weight' element for the
-        // base template (or Overview) to ensure that it appears at the top of
-        // the list. Otherwise items are sorted alphabetically.
+        // content. You should only set the '#weight' element for the base
+        // template (or Overview) to ensure that it appears at the top of the
+        // list. Otherwise items are sorted alphabetically.
         $node->content['tripal_example_base'] = array(
           '#theme' => 'tripal_example_base',
           '#node' => $node,
@@ -788,11 +820,11 @@ function tripal_example_node_view($node, $view_mode, $langcode) {
           '#tripal_toc_title' => 'Relationships',
         );
 
-        // Note: if you create a template that you do not want a user to
-        // know where it is (discourage editing of it), you can add the following
-        // key:  '#tripal_template_show' => FALSE. If this key/value is set
-        // the the administrator message that Tripal provides indicating
-        // where the template is housed will not be shown.
+        // Note: if you create a template that you do not want a user to know
+        // where it is (discourage editing of it), you can add the following
+        // key:  '#tripal_template_show' => FALSE. If this key/value is set the
+        // administrator message that Tripal provides indicating where the
+        // template is housed will not be shown.
       }
       // set the content for the teaser view
       if ($view_mode == 'teaser') {
@@ -803,8 +835,8 @@ function tripal_example_node_view($node, $view_mode, $langcode) {
         );
       }
       break;
-    // you can add custom content to any node type by adding
-    // content to the node in the same way as above.
+    // you can add custom content to any node type by adding content to the node
+    // in the same way as above.
     case 'chado_organism':
       if ($view_mode == 'full') {
         $node->content['tripal_organism_examples'] = array(

tripal_example/theme/templates/tripal_example_base.tpl.php

@@ -2,18 +2,18 @@
 $example  = $variables['node']->example;  ?>
 
 <div class="tripal_example-data-block-desc tripal-data-block-desc"></div> <?php
- 
-// the $headers array is an array of fields to use as the colum headers. 
-// additional documentation can be found here 
+
+// the $headers array is an array of fields to use as the column headers.
+// additional documentation can be found here
 // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
 // This table for the analysis has a vertical header (down the first column)
 // so we do not provide headers here, but specify them in the $rows array below.
 $headers = array();
 
 // the $rows array contains an array of rows where each row is an array
-// of values for each column of the table in that row.  Additional documentation
+// of values for each column of the table in that row. Additional documentation
 // can be found here:
-// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7 
+// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
 $rows = array();
 
 // Unique Name row
@@ -36,7 +36,7 @@ $rows[] = array(
 $organism = $example->organism_id->genus ." " . $example->organism_id->species ." (" . $example->organism_id->common_name .")";
 if (property_exists($example->organism_id, 'nid')) {
   $organism = l("<i>" . $example->organism_id->genus . " " . $example->organism_id->species . "</i> (" . $example->organism_id->common_name .")", "node/".$example->organism_id->nid, array('html' => TRUE));
-} 
+}
 $rows[] = array(
   array(
     'data' => 'Organism',
@@ -46,7 +46,7 @@ $rows[] = array(
 );
 
 // allow site admins to see the example ID
-if (user_access('view ids')) { 
+if (user_access('view ids')) {
   // Feature ID
   $rows[] = array(
     array(
@@ -62,9 +62,9 @@ if (user_access('view ids')) {
 }
 
 
-// the $table array contains the headers and rows array as well as other
-// options for controlling the display of the table.  Additional
-// documentation can be found here:
+// the $table array contains the headers and rows array as well as other options
+// for controlling the display of the table. Additional documentation can be
+// found here:
 // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
 $table = array(
   'header' => $headers,
@@ -79,7 +79,7 @@ $table = array(
   'empty' => '',
 );
 
-// once we have our table array structure defined, we call Drupal's theme_table()
-// function to generate the table.
+// once we have our table array structure defined, we call Drupal's
+// theme_table() function to generate the table.
 print theme_table($table); ?>
 <div style="text-align: justify"><?php print $example->description ?></div>

tripal_example/theme/templates/tripal_example_properties.tpl.php

@@ -11,24 +11,25 @@ $exampleprops = $example->exampleprop;
 $properties = array();
 
 if (count($properties)) { ?>
-  <div class="tripal_example-data-block-desc tripal-data-block-desc">Additional details for this example include:</div> <?php 
+  <div class="tripal_example-data-block-desc tripal-data-block-desc">Additional details for this example include:</div> <?php
 
-  // the $headers array is an array of fields to use as the colum headers.
+  // the $headers array is an array of fields to use as the column headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Property Name', 'Value');
-  
+
   // the $rows array contains an array of rows where each row is an array
-  // of values for each column of the table in that row.  Additional documentation
-  // can be found here:
+  // of values for each column of the table in that row. Additional
+  // documentation can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   $keywords = array();
   foreach ($properties as $property) {
-    // each keyword is stored as a seperate properties. We want to show them
-    // only in a single field not as a bunc of individual properties, so when we see one, 
-    // save it in an array for later and down't add it yet to the table yet.
+    // each keyword is stored as a separate properties. We want to show them
+    // only in a single field not as a bunch of individual properties, so when
+    // we see one, save it in an array for later and don't add it yet to the
+    // table yet.
     if ($property->type_id->name == 'Keywords') {
       $keywords[] = $property->value;
       continue;
@@ -44,11 +45,11 @@ if (count($properties)) { ?>
       'Keywords',
       implode(', ', $keywords),
     );
-  } 
+  }
 
   // the $table array contains the headers and rows array as well as other
-  // options for controlling the display of the table.  Additional
-  // documentation can be found here:
+  // options for controlling the display of the table. Additional documentation
+  // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $table = array(
     'header' => $headers,
@@ -62,8 +63,8 @@ if (count($properties)) { ?>
     'colgroups' => array(),
     'empty' => '',
   );
-  
-  // once we have our table array structure defined, we call Drupal's theme_table()
-  // function to generate the table.
+
+  // once we have our table array structure defined, we call Drupal's
+  // theme_table() function to generate the table.
   print theme_table($table);
 }

tripal_example/theme/templates/tripal_example_references.tpl.php

@@ -1,36 +1,37 @@
 <?php
 $example = $variables['node']->example;
 
-// expand the example object to include the records from the example_dbxref table
+// expand the example object to include the records from the example_dbxref
+// table
 $options = array('return_array' => 1);
 $example = chado_expand_var($example, 'table', 'example_dbxref', $options);
 $example_dbxrefs = $example->example_dbxref;
 
 $references = array();
 if (count($example_dbxrefs) > 0 ) {
-  foreach ($example_dbxrefs as $example_dbxref) {    
+  foreach ($example_dbxrefs as $example_dbxref) {
     $references[] = $example_dbxref->dbxref_id;
   }
 }
 
 if(count($references) > 0){ ?>
-  <div class="tripal_example-data-block-desc tripal-data-block-desc">This example is also available in the following databases:</div><?php 
-  
+  <div class="tripal_example-data-block-desc tripal-data-block-desc">This example is also available in the following databases:</div><?php
+
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Database', 'Accession');
-  
+
   // the $rows array contains an array of rows where each row is an array
-  // of values for each column of the table in that row.  Additional documentation
-  // can be found here:
+  // of values for each column of the table in that row. Additional
+  // documentation can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   foreach ($references as $dbxref){
     $database = $dbxref->db_id->name . ': ' . $dbxref->db_id->description;
     if ($dbxref->db_id->url) {
-      $database = l($dbxref->db_id->name, $dbxref->db_id->url, array('attributes' => array('target' => '_blank'))) . ': ' . $dbxref->db_id->description; 
+      $database = l($dbxref->db_id->name, $dbxref->db_id->url, array('attributes' => array('target' => '_blank'))) . ': ' . $dbxref->db_id->description;
     }
     $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
     if ($dbxref->db_id->urlprefix) {
@@ -39,15 +40,15 @@ if(count($references) > 0){ ?>
     if (property_exists($dbxref, 'is_primary')) {
       $accession .= " <i>(primary cross-reference)</i>";
     }
-    
+
     $rows[] = array(
       $database,
       $accession
     );
   }
   // the $table array contains the headers and rows array as well as other
-  // options for controlling the display of the table.  Additional
-  // documentation can be found here:
+  // options for controlling the display of the table. Additional documentation
+  // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $table = array(
     'header' => $headers,
@@ -61,7 +62,7 @@ if(count($references) > 0){ ?>
     'colgroups' => array(),
     'empty' => '',
   );
-  
+
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);

tripal_example/theme/templates/tripal_example_relationships.tpl.php

@@ -1,20 +1,21 @@
 <?php
 /* Typically in a Tripal template, the data needed is retrieved using a call to
- * chado_expand_var function.  For example, to retrieve all 
- * of the example relationships for this node, the following function call would be made:
- * 
+ * chado_expand_var function. For example, to retrieve all of the example
+ * relationships for this node, the following function call would be made:
+ *
  *   $example = chado_expand_var($example,'table','example_relationship');
- * 
- * However, this function call can be extremely slow when there are numerous relationships.
- * This is because the chado_expand_var function is recursive and expands 
- * all data following the foreign key relationships tree.  Therefore, to speed retrieval
- * of data, a special variable is provided to this template:
- * 
+ *
+ * However, this function call can be extremely slow when there are numerous
+ * relationships. This is because the chado_expand_var function is recursive and
+ * expands all data following the foreign key relationships tree. Therefore, to
+ * speed retrieval of data, a special variable is provided to this template:
+ *
  *   $example->all_relationships;
- *   
- * This variable is an array with two sub arrays with the keys 'object' and 'subject'.  The array with
- * key 'object' contains relationships where the example is the object, and the array with
- * the key 'subject' contains relationships where the example is the subject
+ *
+ * This variable is an array with two sub arrays with the keys 'object' and
+ * 'subject'. The array with key 'object' contains relationships where the
+ * example is the object, and the array with the key 'subject' contains
+ * relationships where the example is the subject.
  */
 $example = $variables['node']->example;
 
@@ -24,30 +25,30 @@ $subject_rels = $all_relationships['subject'];
 
 if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
   <div class="tripal_example-data-block-desc tripal-data-block-desc"></div> <?php
-  
-  // first add in the subject relationships.  
+
+  // first add in the subject relationships.
   foreach ($subject_rels as $rel_type => $rels){
     foreach ($rels as $obj_type => $objects){ ?>
       <p>This <?php print $example->type_id->name;?> is <?php print $rel_type ?> the following <b><?php print $obj_type ?></b> example(s): <?php
-       
+
       // the $headers array is an array of fields to use as the colum headers.
       // additional documentation can be found here
       // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
       $headers = array('Publication');
-      
+
       // the $rows array contains an array of rows where each row is an array
-      // of values for each column of the table in that row.  Additional documentation
-      // can be found here:
+      // of values for each column of the table in that row. Additional
+      // documentation can be found here:
       // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
       $rows = array();
-      
+
       foreach ($objects as $object){
         // link the example to it's node
         $title = $object->record->object_id->title;
         if (property_exists($object->record, 'nid')) {
           $title = l($title, "node/" . $object->record->nid, array('attributes' => array('target' => "_blank")));
         }
-        
+
         // get the citation
         $values = array(
           'example_id' => $object->record->object_id->example_id,
@@ -57,13 +58,13 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
         );
         $citation = chado_generate_var('exampleprop', $values);
         $citation = chado_expand_var($citation, 'field', 'exampleprop.value');
-        
+
         $rows[] = array(
           $title . '<br>' . htmlspecialchars($citation->value),
-        ); 
-       } 
+        );
+       }
        // the $table array contains the headers and rows array as well as other
-       // options for controlling the display of the table.  Additional
+       // options for controlling the display of the table. Additional
        // documentation can be found here:
        // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
        $table = array(
@@ -78,37 +79,37 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
          'colgroups' => array(),
          'empty' => '',
        );
-       
-       // once we have our table array structure defined, we call Drupal's theme_table()
-       // function to generate the table.
+
+       // once we have our table array structure defined, we call Drupal's
+       // theme_table() function to generate the table.
        print theme_table($table); ?>
        </p>
        <br><?php
      }
   }
-  
-  // second add in the object relationships.  
+
+  // second add in the object relationships.
   foreach ($object_rels as $rel_type => $rels){
     foreach ($rels as $subject_type => $subjects){?>
-      <p>The following <b><?php print $subjects[0]->record->subject_id->type_id->name ?></b> example(s) are <?php print $rel_type ?> this <?php print $example->type_id->name;?>: <?php 
+      <p>The following <b><?php print $subjects[0]->record->subject_id->type_id->name ?></b> example(s) are <?php print $rel_type ?> this <?php print $example->type_id->name;?>: <?php
       // the $headers array is an array of fields to use as the colum headers.
       // additional documentation can be found here
       // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
       $headers = array('Publication');
-      
+
       // the $rows array contains an array of rows where each row is an array
-      // of values for each column of the table in that row.  Additional documentation
-      // can be found here:
+      // of values for each column of the table in that row. Additional
+      // documentation can be found here:
       // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
       $rows = array();
-      
+
       foreach ($subjects as $subject){
         // link the example to it's node
         $title = $subject->record->subject_id->title;
         if (property_exists($subject->record, 'nid')) {
           $title = l($title, "node/" . $subject->record->nid, array('attributes' => array('target' => "_blank")));
         }
-        
+
         // get the citation
         $values = array(
           'example_id' => $subject->record->subject_id->example_id,
@@ -118,13 +119,13 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
         );
         $citation = chado_generate_var('exampleprop', $values);
         $citation = chado_expand_var($citation, 'field', 'exampleprop.value');
-        
+
         $rows[] = array(
           $title . '<br>' . htmlspecialchars($citation->value),
         );
-       } 
+       }
        // the $table array contains the headers and rows array as well as other
-       // options for controlling the display of the table.  Additional
+       // options for controlling the display of the table. Additional
        // documentation can be found here:
        // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
        $table = array(
@@ -139,9 +140,9 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
          'colgroups' => array(),
          'empty' => '',
        );
-       
-       // once we have our table array structure defined, we call Drupal's theme_table()
-       // function to generate the table.
+
+       // once we have our table array structure defined, we call Drupal's
+       // theme_table() function to generate the table.
        print theme_table($table); ?>
        </p>
        <br><?php

tripal_example/theme/tripal_example.theme.inc

@@ -2,40 +2,41 @@
 
 /**
  * @file
- * 
- * This file should contain all Drupal hooks for theming content.  For templates 
+ *
+ * This file should contain all Drupal hooks for theming content. For templates
  * that need specific the hook_preprocess functions should be included here
  *
  */
 
 /**
  * implementation of hook_preprocess_HOOK()
- * 
- * Used to alter or add to theme variables.  The variables are passed into
- * templates when prossing.  This function organizes the relationships
+ *
+ * Used to alter or add to theme variables. The variables are passed into
+ * templates when processing. This function organizes the relationships
  * into more simple structures for parsing in the template file.
  *
  * @ingroup tripal_example
  */
 function tripal_example_preprocess_tripal_example_relationships(&$variables) {
-  // EXPLANATION:  If you have implmented a new chado node type and the record
+  // EXPLANATION:  If you have implemented a new Chado node type and the record
   // that belongs to the node has a corresponding xxxx_relationship table
   // this this function can be used to provide relationships to the template
-  // in a format that is easier to parse.  This is one example where specific SQL
-  // statements can improve performance over Tripal API calls.  SQL is not 
+  // in a format that is easier to parse. This is one example where specific SQL
+  // statements can improve performance over Tripal API calls. SQL is not
   // recommended inside of template files, but rather the Tripal API calls only.
   // Therefore, this function queries the relationships and then organizes them
-  // into arrays that are easier and faster to parse.  You should be able to
-  // copy the content of this function 
-  // and adjust as necessary to change table names if your record has relationships.
+  // into arrays that are easier and faster to parse. You should be able to
+  // copy the content of this function and adjust as necessary to change table
+  // names if your record has relationships.
 
   $example = $variables['node']->example;
-  
+
    // expand the example object to include the example relationships.
   $options = array(
     'return_array' => 1,
-    // we don't want to fully recurse we only need information about the
-    // relationship type and the object and subject examples (including example type)
+    // we don't want to fully recurs we only need information about the
+    // relationship type and the object and subject examples (including example
+    // type)
     'include_fk' => array(
       'type_id' => 1,
       'object_id' => array(
@@ -52,7 +53,7 @@ function tripal_example_preprocess_tripal_example_relationships(&$variables) {
   $srelationships = $example->example_relationship->subject_id;
   $orelationships = $example->example_relationship->object_id;
 
-  // combine both object and subject relationshisp into a single array
+  // combine both object and subject relationships into a single array
   $relationships = array();
   $relationships['object'] = array();
   $relationships['subject'] = array();
@@ -62,11 +63,11 @@ function tripal_example_preprocess_tripal_example_relationships(&$variables) {
     foreach ($orelationships as $relationship) {
       $rel = new stdClass();
       $rel->record = $relationship;
-       
+
       // get the relationship and child types
       $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
       $child_type = $relationship->subject_id->type_id->name;
-       
+
       // get the node id of the subject
       $sql = "SELECT nid FROM {chado_example} WHERE example_id = :example_id";
       $n = db_query($sql, array(':example_id' => $relationship->subject_id->example_id))->fetchObject();
@@ -91,14 +92,14 @@ function tripal_example_preprocess_tripal_example_relationships(&$variables) {
       $rel->record = $relationship;
       $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
       $parent_type = $relationship->object_id->type_id->name;
-       
+
       // get the node id of the subject
       $sql = "SELECT nid FROM {chado_example} WHERE example_id = :example_id";
       $n = db_query($sql, array(':example_id' => $relationship->object_id->example_id))->fetchObject();
       if ($n) {
         $rel->record->nid = $n->nid;
       }
-       
+
       if (!array_key_exists($rel_type, $relationships['subject'])) {
         $relationships['subject'][$rel_type] = array();
       }

tripal_example/tripal_example.info

@@ -1,6 +1,6 @@
 ;
 ; Provide details about your module in this file. Instruction for setup of this
-; file can be found here:  https:;drupal.org/node/542202
+; file can be found here: https://drupal.org/node/542202
 ;
 name = Tripal Example
 description = An example module that can be used as a template for anyone wanting to create a custom extension module for Tripal.
@@ -17,30 +17,30 @@ project = tripal_example
 
 ;
 ; In order for this module to appear in the 'Tripal Extensions' section when
-; viewing the module administrative page, the package must be set to 
+; viewing the module administrative page, the package must be set to
 ; 'Tripal Extensions'
-; 
+;
 package = Tripal Extensions
 
 ;
 ; Follow these instructions when specifying the version:
-; https:;drupal.org/node/1015226
-; 
+; https://drupal.org/node/1015226
+;
 version = 7.x-2.0-rc1
 
 ;
-; Stylesheets containing CSS that should always be available for the
-; module should be specified here.  
+; Style-sheets containing CSS that should always be available for the
+; module should be specified here.
 ;
 stylesheets[all][] = theme/css/tripal_example.css
 
 ;
 ; Javascript files that should always be available for the
-; module should be specified here.  
+; module should be specified here.
 ;
 scripts[]          = theme/js/tripal_example.js
 
-; 
+;
 ; Add additional dependencies for other modules using the module project name.
 ; These modules must be enabled before this module can be enabled
 ;

tripal_example/tripal_example.install

@@ -13,12 +13,12 @@
  */
 function tripal_example_disable() {
 
-  // EXPLANATION: If you are using Drupal Views you want to ensure
-  // that any default views that your module provides are disabled
-  // when the module is disabled.  Default views are specified in the
-  // [module name].views.default.inc file.  The following code will disable
-  // these views.  If your module does not create any default views you
-  // can remove the following code.
+  // EXPLANATION: If you are using Drupal Views you want to ensure that any
+  // default views that your module provides are disabled when the module is
+  // disabled. Default views are specified in the
+  // [module name].views.default.inc file. The following code will disable these
+  // views. If your module does not create any default views you can remove the
+  // following code.
 
   // Disable all default views provided by this module
   require_once("tripal_example.views_default.inc");
@@ -33,8 +33,8 @@ function tripal_example_disable() {
  * Implements hook_requirements().
  *
  * Performs check to see if all required dependencies are met. Drupal will
- * automatically check for module dependencies but here you can check for
- * other requirements.
+ * automatically check for module dependencies but here you can check for other
+ * requirements.
  *
  * @ingroup tripal_example
  */
@@ -44,9 +44,9 @@ function tripal_example_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // EXPLANATION: It is essential that Chado be installed for almost all
-    // Tripal modules. Therefore, the following code checks to ensure Chado
-    // is installed and available.  If your module does not require that
-    // Chado be installed, you can remove the following check.
+    // Tripal modules. Therefore, the following code checks to ensure Chado is
+    // installed and available. If your module does not require that Chado be
+    // installed, you can remove the following check.
 
     // make sure chado is installed
     if (!$GLOBALS["chado_is_installed"]) {
@@ -71,17 +71,16 @@ function tripal_example_install() {
 
   // EXPLANATION: If your module will making data publicly available for
   // download or use by the site you can create the directory using the
-  // tripal_create_files_dir() function.  This will create a directory
-  // in the public access directory which will typcially be in
+  // tripal_create_files_dir() function. This will create a directory in the
+  // public access directory which will typically be in
   // sites/default/files/tripal/[module name]/
 
   // create the module's data directory
   tripal_create_files_dir('tripal_example');
 
-  // EXPLANATION: Here is a good place to add any materialized views,
-  // controlled vocabularies CV, databases or CV terms needed by your module.
-  // To keep this module code short, create functions to do each of those
-  // tasks
+  // EXPLANATION: Here is a good place to add any materialized views, controlled
+  // vocabularies CV, databases or CV terms needed by your module.
+  // To keep this module code short, create functions to do each of those tasks
 
   // add any materialized view
   tripal_example_add_mviews();
@@ -91,11 +90,11 @@ function tripal_example_install() {
 
   // add any controlled vocabularies used by the example module. You may need
   // to add a vocabulary if you to set it as default (see next lines of code).
-  // For example, the Sequence Ontology (SO) is used by the feature module as the
-  // default vocabulary for the feature type_id field.  But, that vocabulary
-  // does not yet exist in Chado until after the SO is loaded using the
-  // Tripal OBO loader.  But, we can add it here as a placeholder so that we can
-  // then set it as a default vocabulary (see below).
+  // For example, the Sequence Ontology (SO) is used by the feature module as
+  // the default vocabulary for the feature type_id field. But, that vocabulary
+  // does not yet exist in Chado until after the SO is loaded using the Tripal
+  // OBO loader. But, we can add it here as a place-holder so that we can then
+  // set it as a default vocabulary (see below).
   tripal_example_add_cvs();
 
 
@@ -103,12 +102,12 @@ function tripal_example_install() {
   tripal_example_add_cvterms();
 
   // EXPLANATION: Many tables in Chado have a 'type_id' column which allows for
-  // association of controlled vocabulries to describe the record.   Chado
-  // places no restrictions on which vocabularies can be used, but Tripal can
-  // be instructed to provide a default vocabulary for any given field. For
-  // example, the feature.type_id column will typically use the Sequence Ontology
-  // In that case, we can use the tripal_set_default_cv() function to specify
-  // the Sequence Ontology (sequence) as the default vocabulary.
+  // association of controlled vocabularies to describe the record. Chado places
+  // no restrictions on which vocabularies can be used, but Tripal can be
+  // instructed to provide a default vocabulary for any given field. For
+  // example, the feature.type_id column will typically use the Sequence
+  // Ontology. In that case, we can use the tripal_set_default_cv() function to
+  // specify the Sequence Ontology (sequence) as the default vocabulary.
   tripal_set_default_cv('example', 'type_id', 'example_type');
   tripal_set_default_cv('exampleprop', 'type_id', 'example_property');
   tripal_set_default_cv('example_relationship', 'type_id', 'example_relationship');
@@ -133,9 +132,9 @@ function tripal_example_uninstall() {
 /**
  * Implementation of hook_schema().
  *
- * Provides a list of tables to be created inside of the Drupal schema
- * (the 'public' schema by default). It uses the Drupal Schema API
- * array structure to define the table, its indexes and constraints.
+ * Provides a list of tables to be created inside of the Drupal schema (the
+ * 'public' schema by default). It uses the Drupal Schema API array structure to
+ * define the table, its indexes and constraints.
  *
  * Schema API documentation is here:
  * https://api.drupal.org/api/drupal/includes%21database%21schema.inc/group/schemaapi/7
@@ -145,12 +144,11 @@ function tripal_example_uninstall() {
 function tripal_example_schema() {
 
   // EXPLANATION: If your module creates a node type for data in the Chado
-  // database then you probably need to link Drupal nodes with a respective
-  // ID in the Chado table.  The following is an example array for a table
-  // that will link the 'chado_example' node type (created by this example
-  // module) with a record in the fake Chado example table.  This table
-  // will link the 'nid' of the node with the 'example_id' of the eample
-  // record.
+  // database then you probably need to link Drupal nodes with a respective ID
+  // in the Chado table. The following is an example array for a table that will
+  // link the 'chado_example' node type (created by this example module) with a
+  // record in the fake Chado example table. This table will link the 'nid' of
+  // the node with the 'example_id' of the example record.
   $schema['chado_example'] = array(
     'fields' => array(
       'vid' => array(
@@ -190,16 +188,17 @@ function tripal_example_schema() {
 };
 
 /**
- * Creates a materialized view that stores the type & number of examples per organism
+ * Creates a materialized view that stores the type & number of examples per
+ * organism.
  *
  * @ingroup tripal_example
  */
 function tripal_example_add_mviews() {
 
-  // EXPLANATION: use the tripal_add_mview() function to add a materialized
-  // view needed by your module.  If you have more than one materialized view
-  // it is best to create a single function for each one and call each
-  // function here. Otherwise this function can become quite long.
+  // EXPLANATION: use the tripal_add_mview() function to add a materialized view
+  // needed by your module. If you have more than one materialized view it is
+  // best to create a single function for each one and call each function here.
+  // Otherwise this function can become quite long.
 
 }
 /**
@@ -208,9 +207,9 @@ function tripal_example_add_mviews() {
  * @ingroup tripal_example
  */
 function tripal_example_add_dbs() {
-  // EXPLANATION: use the tripal_insert_db() function to add any
-  // external databases needed by your module.  If the database already
-  // exists then the function will gracefully return.
+  // EXPLANATION: use the tripal_insert_db() function to add any external
+  // databases needed by your module. If the database already exists then the
+  // function will gracefully return.
 
   tripal_insert_db(array(
     'name' => 'example_db',
@@ -224,10 +223,10 @@ function tripal_example_add_dbs() {
  */
 function tripal_example_add_cvs() {
 
-  // EXPLANATION: use the tripal_insert_cv() function to add any
-  // controlled vocabularies needed by your module.  If the vocabulary already
-  // exists then the function will gracefully return.  Chado convensions
-  // use a singluar name for CV names (not plural)/
+  // EXPLANATION: use the tripal_insert_cv() function to add any controlled
+  // vocabularies needed by your module. If the vocabulary already exists then
+  // the function will gracefully return. Chado conventions use a singular name
+  // for CV names (not plural).
 
   tripal_insert_cv(
     'example_property',
@@ -253,15 +252,15 @@ function tripal_example_add_cvs() {
  */
 function tripal_example_add_cvterms() {
 
-  // EXPLANATION:  for our test module to work we need to add some terms to our example_type
-  // controlled vocabulary.  Ideally we should have a full OBO file for loading
-  // but sometimes we just have a small list that won't really change so
-  // we can add those terms here.
+  // EXPLANATION: for our test module to work we need to add some terms to our
+  // example_type controlled vocabulary. Ideally we should have a full OBO file
+  // for loading but sometimes we just have a small list that won't really
+  // change so we can add those terms here.
   tripal_insert_cvterm(array(
     'id'         => 'test',         // the term accession
     'name'       => 'Test type',    // the human readable term name
     'cv_name'    => 'example_type', // the CV name this term belongs to.
-    'definition' => 'A test type for the example modlue.',
+    'definition' => 'A test type for the example module.',
     'db_name'    => 'example_db',   // the database in which the term is found.
   ));
 }
@@ -281,7 +280,7 @@ function tripal_example_add_custom_tables() {
   //   3) example_relationship (for storing relationships about examples)
   //   4) example_dbxref (for storing cross-references about an example)
   //
-  // To make the code easier to read, each table is created by a separte
+  // To make the code easier to read, each table is created by a separate
   // function called here:
 
   tripal_example_add_example_table();
@@ -289,6 +288,7 @@ function tripal_example_add_custom_tables() {
   tripal_example_add_example_relationship_table();
   tripal_example_add_example_dbxref_table();
 }
+
 /**
  * Adds the 'example' custom table to Chado.
  *
@@ -353,10 +353,9 @@ function tripal_example_add_example_table() {
         ),
       ),
     ),
-    // EXPLANATION: the 'referring_tables' array is the list of tables
-    // that have a foreign key relationships with this table. This
-    // information is required for the Tripal API to be able to expand
-    // tables in templates.
+    // EXPLANATION: the 'referring_tables' array is the list of tables that have
+    // a foreign key relationships with this table. This information is required
+    // for the Tripal API to be able to expand tables in templates.
     'referring_tables' => array(
       0 => 'example_relationship',
       1 => 'exampleprop',
@@ -584,8 +583,8 @@ function tripal_example_update_7200() {
   // https://api.drupal.org/api/drupal/modules%21system%21system.api.php/function/hook_update_N/7
   //
   // It is best not to use Tripal API calls inside of this function because an
-  // upgarde from Drupal 6 to Drupal 7 requires that all modules be disabled
-  // which means the Tripal API is not available.  This is an unfortunate
+  // upgrade from Drupal 6 to Drupal 7 requires that all modules be disabled
+  // which means the Tripal API is not available. This is an unfortunate
   // requirement, but will prevent errors during a major upgrade.
 
   // it is good to wrap any database changes inside of a try catch block:
@@ -599,17 +598,17 @@ function tripal_example_update_7200() {
 }
 
 /**
- * Implementation of hook_update_dependencies().  It specifies a list of
- * other modules whose updates must be run prior to this one.
+ * Implementation of hook_update_dependencies(). It specifies a list of other
+ * modules whose updates must be run prior to this one.
  */
 function tripal_example_update_dependencies() {
   $dependencies = array();
 
-  // EXPLANATION: here we can specify which modules must be updated prior
-  // to applying the updates in this module.  This is useful because it
-  // prevents updates from being executed out of order.  The following
-  // example code shows that the 'tripal_example' module update number 7200
-  // must be executed after the 'tripal_cv' module's 7200 update.
+  // EXPLANATION: here we can specify which modules must be updated prior to
+  // applying the updates in this module. This is useful because it prevents
+  // updates from being executed out of order. The following example code shows
+  // that the 'tripal_example' module update number 7200 must be executed after
+  // the 'tripal_cv' module's 7200 update.
   $dependencies['tripal_example'][7200] = array(
     'tripal_cv' => 7200
   );

tripal_example/tripal_example.module

@@ -2,14 +2,14 @@
 
 /**
  * @file
- * This file contains all Drupal hooks for the module other than any
- * node hooks and block hooks. Those go in the [module name].chado_node.inc file
- * and [module_name].blocks.inc respectively
+ * This file contains all Drupal hooks for the module other than any node hooks
+ * and block hooks. Those go in the [module name].chado_node.inc file and
+ * [module_name].blocks.inc respectively
  *
  */
 
-// EXPLANATION: include any files needed for this module.  That includes any 
-// API file, the theme file, or include files.
+// EXPLANATION: include any files needed for this module. That includes any API
+// file, the theme file, or include files.
 require('api/tripal_example.api.inc');
 require('theme/tripal_example.theme.inc');
 require('includes/tripal_example.admin.inc');
@@ -18,21 +18,20 @@ require('includes/tripal_example.chado_node.inc');
 
 /**
  * Implementation of hook_permissions()
- * 
+ *
  * Set the permission types that this module uses.
- * 
+ *
  * @ingroup tripal_example
  */
 function tripal_example_permission() {
-  
-  // EXPLANATION:  here we want to setup any of the permission types
-  // that this module needs.  Our exmample module creates a new
-  // chado node type called 'chado_example'.  Therefore, we need 
-  // permissions to view, edit, delete, create our new node type.  Additionally,
-  // we want to add a permission that allows for administration of this 
-  // module.  These permissions will appear in the 'People' -> 'Permissions'
-  // configuration page and allow the site admin to specify which user roles
-  // are allowed to perform specific actions.
+
+  // EXPLANATION:  here we want to setup any of the permission types that this
+  // module needs. Our example module creates a new chado node type called
+  // 'chado_example'. Therefore, we need permissions to view, edit, delete,
+  // create our new node type. Additionally, we want to add a permission that
+  // allows for administration of this module. These permissions will appear in
+  // the 'People' -> 'Permissions' configuration page and allow the site admin
+  // to specify which user roles are allowed to perform specific actions.
   return array(
     'access chado_example content' => array(
       'title' => t('View Examples'),
@@ -59,32 +58,32 @@ function tripal_example_permission() {
 
 /**
  * Implements hook_menu()
- * 
+ *
  * Specifies menu items and URLs used by this module.
  *
  * @ingroup tripal_example
  */
 function tripal_example_menu() {
   $items = array();
-  
-  // EXPLANATION:  the $items array should be popluated to contain a list of 
-  // menu items or URL callbacks that our module needs.  
-  // all Tripal Extension modules shoudl provide at least these menu items:
+
+  // EXPLANATION:  the $items array should be populated to contain a list of
+  // menu items or URL callbacks that our module needs.
+  // all Tripal Extension modules should provide at least these menu items:
   //  * A menu item for an administrative home page
   //  * A menu item for 'Help' documentation
   //  * A menu item for a module configuration page
   //
   // Additionally, if your module defines a custom node type that is linked
   // to a record in Chado:
-  //  * A menu item for syncing drupal nodes with Chado records.   
-  //    
-  
+  //  * A menu item for syncing drupal nodes with Chado records.
+  //
+
   // EXPLANATION:  all extension modules should have an administrative menu item
-  // with the path set to 'admin/tripal/extension/[module name]'.  This will
-  // place the menu item in the 'Tripal' -> 'Extesion Modules' page.  Because this
-  // is an administrative menu item we must be sure to set the 'access arguments'
-  // to be 'administer tripal example' which is a permission type we created
-  // in the tripal_example_permissions() function above.
+  // with the path set to 'admin/tripal/extension/[module name]'. This will
+  // place the menu item in the 'Tripal' -> 'Extension Modules' page. Because
+  // this is an administrative menu item we must be sure to set the
+  // 'access arguments' to be 'administer tripal example' which is a permission
+  // type we created in the tripal_example_permissions() function above.
   $items['admin/tripal/extension/tripal_example'] = array(
     'title' => 'Examples',
     'description' => 'Example module for help with development of new extension modules.',
@@ -93,14 +92,14 @@ function tripal_example_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
-  // EXPLANATION: all extension modules should provide help documentation to 
+  // EXPLANATION: all extension modules should provide help documentation to
   // describe the functionality of the module and any installation or setup
-  // tasks that may be required.  The menu 'type' is MENU_LOCAL_TASK so that
-  // the link appears in a tab on the extension module's administrative page.
-  // here the 'page callback' specifies that we are using Drupal's theme 
+  // tasks that may be required. The menu 'type' is MENU_LOCAL_TASK so that the
+  // link appears in a tab on the extension module's administrative page.
+  // Here the 'page callback' specifies that we are using Drupal's theme
   // function and the 'page_arguments' indicate the name of the template file
-  // Thus, all help documentation should be provided in the 
-  // [module name]/theme/tripal_example_help.tpl.php file. 
+  // Thus, all help documentation should be provided in the
+  // [module name]/theme/tripal_example_help.tpl.php file.
   $items['admin/tripal/extension/tripal_example/help'] = array(
     'title' => 'Help',
     'description' => 'Basic Description of Tripal Library Module Functionality',
@@ -111,14 +110,14 @@ function tripal_example_menu() {
     'weight' => 10
   );
 
-  // EXPLANATION: all extension modules should provide a configuration page. 
+  // EXPLANATION: all extension modules should provide a configuration page.
   // Even if your module does not need configuration the menu item and page
   // should be created. This helps users recognize that the module is installed
-  // and working.  The configuration page can simply state that no 
-  // configuration settings are available.  Typically a form is provided for the 
-  // module's configuration settings. Therefore the 'page callback' uses the
+  // and working. The configuration page can simply state that no configuration
+  // settings are available. Typically a form is provided for the module's
+  // configuration settings. Therefore the 'page callback' uses the
   // drupal_get_form() function and the 'page argument' indicates the form
-  // to call is named 'tripal_eample_admin'.  The function that describes
+  // to call is named 'tripal_eample_admin'. The function that describes
   // to form is in the includes/tripal_example.admin.inc file.
   $items['admin/tripal/extension/tripal_example/configuration'] = array(
     'title' => 'Settings',
@@ -129,10 +128,10 @@ function tripal_example_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
-  
+
   // EXPLANATION: If your module defines a new chado node type and that node
   // type directly links to a record in Chado, then you can use the Tripal API
-  // to quickly provide syncing functionality.  See the API documentation here
+  // to quickly provide syncing functionality. See the API documentation here
   // for more information on how that is setup:
   // http://api.tripal.info/api/tripal/tripal_core%21api%21tripal_core.chado_nodes.api.inc/function/chado_node_sync_form/2.x
   $items['admin/tripal/extension/tripal_example/sync'] = array(
@@ -144,15 +143,15 @@ function tripal_example_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 2
   );
-  
+
   // EXPLANATION: If your module defines a new node type that uses the default
-  // table of contents (left-side bar of content panes on a page). Then a 
-  // 'TOC' link will automatically appear on the node page to allow for 
-  // customization of the TOC.  However those customizations are only node
-  // specific.  To provide a tab in the module's administrative pages add the
-  // following menu item. This menu will provide a form similar to the one
-  // found on the node that allows the user to set global TOC settings for the
-  // content type.  Be sure to always use a menu path of the form:
+  // table of contents (left-side bar of content panes on a page). Then a 'TOC'
+  // link will automatically appear on the node page to allow for customization
+  // of the TOC. However those customizations are only node specific. To provide
+  // a tab in the module's administrative pages add the following menu item.
+  // This menu will provide a form similar to the one found on the node that
+  // allows the user to set global TOC settings for the content type. Be sure to
+  // always use a menu path of the form:
   //   admin/tripal/chado/[module name]/[content type name]_toc
   // this allows for a module to support TOC management when there are multiple
   // content types provided by the module, as the content type is specified
@@ -168,16 +167,16 @@ function tripal_example_menu() {
     'file path' => drupal_get_path('module', 'tripal_core'),
     'weight' => 3
   );
-  
+
   return $items;
 }
 
 /**
  * Implements hook_views_api()
- * 
- * This hook tells drupal that there is views support for
- * for this module which then automatically includes the tripal_db.views.inc 
- * where all the views integration code is found.
+ *
+ * This hook tells Drupal that there is views support for this module which then
+ * automatically includes the tripal_db.views.inc where all the views
+ * integration code is found.
  *
  * @ingroup tripal_example
  */
@@ -189,35 +188,34 @@ function tripal_example_views_api() {
 
 
 /**
- *  We need to let drupal know about our theme functions and their arguments.
- *  We create theme functions to allow users of the module to customize the
- *  look and feel of the output generated in this module
+ * We need to let Drupal know about our theme functions and their arguments.
+ * We create theme functions to allow users of the module to customize the look
+ * and feel of the output generated in this module.
  *
  * @ingroup tripal_example
  */
 function tripal_example_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
 
-  // EXPLANATION: this function defines all of the functions and templates
-  // that this module needs to provide content.  These details are provided
-  // in the form of an array the indicates which functions or templates
-  // provide content.  Please see the Drupal theming guide for an in-depth
-  // description for how theming works in Drupal:
+  // EXPLANATION: this function defines all of the functions and templates that
+  // this module needs to provide content. These details are provided in the
+  // form of an array the indicates which functions or templates provide
+  // content. Please see the Drupal theming guide for an in-depth description
+  // for how theming works in Drupal:
   // https://drupal.org/documentation/theme
-  
+
   $items = array(
-    
-    // EXPLANATION:  If this module defines a new node type that displays
-    // Chado data then we should use Tripal's default node template.  This
-    // template ensures that all content provided by Tripal and Tripal 
-    // extension modules has the same look and feel.  It is designed to be
-    // generic such that it won't intefer with the look-and-feel of the default
-    // theme.  This generic template will organize the node into a table
-    // of contents found on the left-side of the page and place the content
-    // in the center of the page.  User's will cycle through content on the 
-    // page by clicking the links in the table of contents. If you do not want
-    // to use the default Tripal template you can change this array to your
-    // liking.
+
+    // EXPLANATION:  If this module defines a new node type that displays Chado
+    // data then we should use Tripal's default node template. This template
+    // ensures that all content provided by Tripal and Tripal extension modules
+    // has the same look and feel. It is designed to be generic such that it
+    // won't interfere with the look-and-feel of the default theme. This generic
+    // template will organize the node into a table of contents found on the
+    // left-side of the page and place the content in the center of the page.
+    // User's will cycle through content on the page by clicking the links in
+    // the table of contents. If you do not want to use the default Tripal
+    // template you can change this array to your liking.
     'node__chado_example' => array(
       'template' => 'node--chado-generic',
       'render element' => 'node',
@@ -230,12 +228,12 @@ function tripal_example_theme($existing, $type, $theme, $path) {
     // correspond directly to a file with the extension '.tpl.php'. For example
     // the 'tripal_example_base' template will have a corresponding
     // tripal_example_base.tpl.php file where the display code is housed.
-    // The only required templates are the 'base',  'help' and 'teaseer' templates.
-    // The base template provides the basic information about the record in 
-    // in Chado.  The 'help' template provides the adminstrative help documenation,
-    // and the teaser provides a brief summary of the record that can be used
-    // as short description of the record in aggregated lists.
-    
+    // The only required templates are the 'base',  'help' and 'teaser'
+    // templates. The base template provides the basic information about the
+    // record in Chado. The 'help' template provides the administrative help
+    // documentation, and the teaser provides a brief summary of the record that
+    // can be used as short description of the record in aggregated lists.
+
     // the base template
     'tripal_example_base' => array(
       'variables' => array('node' => NULL),
@@ -254,13 +252,14 @@ function tripal_example_theme($existing, $type, $theme, $path) {
       'template' => 'tripal_example_teaser',
       'path' => "$path/theme/templates",
     ),
-    
-    
-    // EXPLANATION: Typically, a different template is created for each subset of data.
-    // for example, most Chado tables have a 'XXXXprop', 'XXXX_cvterm',
+
+
+    // EXPLANATION: Typically, a different template is created for each subset
+    // of data.
+    // For example, most Chado tables have a 'XXXXprop', 'XXXX_cvterm',
     // 'XXXX_dbxref', 'XXXX_synonyms', 'XXXX_relationships' tables. Therefore,
     // a template is created to display data from each of these tables.
-    
+
     'tripal_example_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_example_properties',
@@ -279,11 +278,11 @@ function tripal_example_theme($existing, $type, $theme, $path) {
 
     // EXPLANATION: sometimes a module may want to add content to another
     // modules' node types. For example, the feature module does this by
-    // adding a 'feature summary' data to an organism.  To add data to another
-    // module's node, the templates belong to this module and are 
-    // specified in the same way as above.  However, the naming of the 
-    // template is changed to include the name of the module that supplies
-    // the node type followed by our record name: 
+    // adding a 'feature summary' data to an organism. To add data to another
+    // module's node, the templates belong to this module and are specified in
+    // the same way as above. However, the naming of the template is changed to
+    // include the name of the module that supplies the node type followed by
+    // our record name:
 
     // tripal_organism templates
     'tripal_organism_examples' => array(
@@ -292,25 +291,24 @@ function tripal_example_theme($existing, $type, $theme, $path) {
       'path' => "$path/theme/templates",
     ),
   );
-  
+
   return $items;
 }
 
 /**
  * Implements hook_help()
- * 
+ *
  * Adds a help page to the module list
  */
 function tripal_example_help ($path, $arg) {
-  
-  // EXPLANATION: in the tripal_example_menu() function above we created 
-  // a menu item for the help documentation.  The menu item specified 
-  // a function that should be called when the menu item is clicked.  This 
-  // is that function.  But, rather than place HTML code in this function
-  // we want to have our help documentation in a template file.  We 
-  // specified in the tripal_example_theme() function that we have a template
-  // file so now we want to use get the contents of that template file and
-  // return it.
+
+  // EXPLANATION: in the tripal_example_menu() function above we created a menu
+  // item for the help documentation. The menu item specified a function that
+  // should be called when the menu item is clicked. This is that function. But,
+  // rather than place HTML code in this function we want to have our help
+  // documentation in a template file. We specified in the
+  // tripal_example_theme() function that we have a template file so now we want
+  // to use get the contents of that template file and return it.
   if ($path == 'admin/help#tripal_example') {
     return theme('tripal_example_help', array());
   }
@@ -324,38 +322,38 @@ function tripal_example_help ($path, $arg) {
  */
 function tripal_example_cron() {
 
-  // EXPLANATION: here we can add any code that needs to be executed when
-  // the Drupal cron is run.
+  // EXPLANATION: here we can add any code that needs to be executed when the
+  // Drupal cron is run.
 }
 
 
 /**
  * Implementation of hook_form_alter()
- * 
+ *
  * Allows a module to alter any form prior to it being rendered. For more
  * details about Drupal's Form API see this page:
- * 
+ *
  * https://api.drupal.org/api/drupal/includes!form.inc/group/form_api/7
  *
  */
 function tripal_example_form_alter(&$form, &$form_state, $form_id) {
-  
+
   if ($form_id == "chado_example_node_form") {
-    
-    // EXPLANATION:  The hook_form_alter() Drupal hook is used to alter
-    // a form before it is displayed.  This allows any module to provide new
-    // form elements or change the form that another module creates.  We do
-    // not need to alter a form created by another module, but we do want to
-    // alter the form for our new node type.  For example, all node types
-    // will automatically have a 'Preview' button.  For inserting or updating
-    // data for Chado we don't really need a Preview button and it complicates
-    // the form.  So, we use the following code to disable the Preview button.
-    // if you want to keep the preview button then remove this code.
-    // turn of preview button for insert/updates
+
+    // EXPLANATION:  The hook_form_alter() Drupal hook is used to alter a form
+    // before it is displayed. This allows any module to provide new form
+    // elements or change the form that another module creates. We do not need
+    // to alter a form created by another module, but we do want to alter the
+    // form for our new node type. For example, all node types will
+    // automatically have a 'Preview' button. For inserting or updating data
+    // for Chado we don't really need a Preview button and it complicates the
+    // form. So, we use the following code to disable the Preview button. If
+    // you want to keep the preview button then remove this code. turn of
+    // preview button for insert/updates
     $form['actions']['preview']['#access'] = FALSE;
-    
+
     // EXPLANATION: Drupal always adds a 'body' field to all node types.
-    // Our node type doens't use the 'body' field so we remove it from the form.
+    // Our node type doesn't use the 'body' field so we remove it from the form.
     unset($form['body']);
   }
 }

tripal_example/tripal_example.views.inc

@@ -1,8 +1,8 @@
 <?php
 /**
  *  @file
- *  This file contains the basic functions for views integration of
- *  chado/tripal example tables
+ *  This file contains the basic functions for views integration of chado/tripal
+ *  example tables
  */
 
 // EXPLANATION: see another tripal module (e.g. tripal_feature) for example

tripal_example/tripal_example.views_default.inc

@@ -11,15 +11,15 @@
 */
 function tripal_example_views_default_views() {
   $views = array();
-  
-  // EXPLANATION:  use this function to programmatically define any default
-  // Drupal views that your module will provide automatically.  Typically
-  // there are two default views: 1) one for the administrator to quickly
-  // find data managed by your module, or 2) one for users to be able to
-  // search for public data.  
+
+  // EXPLANATION: use this function to programmatically define any default
+  // Drupal views that your module will provide automatically. Typically there
+  // are two default views: 1) one for the administrator to quickly find data
+  // managed by your module, or 2) one for users to be able to search for public
+  // data.
   //
-  // See another Tripal module such as tripal_feature for an example 
-  // of how to setup a default views.
-  
+  // See another Tripal module such as tripal_feature for an example of how to
+  // setup a default views.
+
   return $views;
 }