Rearranged all templates to be in a single 'templates' directory inside of each module. Added more documentation and functions to the example module.

tripal_analysis/theme/tripal_analysis/tripal_analysis_base.tpl.php → tripal_analysis/theme/templates/tripal_analysis_base.tpl.php

@@ -95,6 +95,7 @@ $table = array(
   'rows' => $rows,
   'attributes' => array(
     'id' => 'tripal_analysis-table-base',
+    'class' => 'tripal-data-table'
   ),
   'sticky' => FALSE,
   'caption' => '',

tripal_analysis/theme/tripal_analysis/tripal_analysis_properties.tpl.php → tripal_analysis/theme/templates/tripal_analysis_properties.tpl.php

@@ -33,6 +33,7 @@ if (count($properties) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_analysis-table-properties',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_analysis/tripal_analysis.module

@@ -161,34 +161,34 @@ function tripal_analysis_theme($existing, $type, $theme, $path) {
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
     'tripal_analysis_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_analysis_base',
-      'path' => "$path/theme/tripal_analysis",
+      'path' => "$path/theme/templates",
     ),
     'tripal_analysis_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_analysis_properties',
-      'path' => "$path/theme/tripal_analysis",
+      'path' => "$path/theme/templates",
     ),
     'tripal_analysis_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_analysis_teaser',
-      'path' => "$path/theme/tripal_analysis",
+      'path' => "$path/theme/templates",
     ),
     'tripal_analysis_help' => array(
       'template' => 'tripal_analysis_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
 
     // tripal_feature theme
     'tripal_feature_analyses' => array(
       'template' => 'tripal_feature_analyses',
       'variables' =>  array('node' => NULL),
-      'path' => "$path/theme/tripal_analysis",
+      'path' => "$path/theme/templates",
     ),
 
   );

tripal_contact/theme/tripal_contact/tripal_contact_base.tpl.php → tripal_contact/theme/templates/tripal_contact_base.tpl.php

@@ -58,6 +58,7 @@ $table = array(
   'rows' => $rows,
   'attributes' => array(
     'id' => 'tripal_contact-table-base',
+    'class' => 'tripal-data-table'
   ),
   'sticky' => FALSE,
   'caption' => '',

tripal_contact/theme/tripal_contact/tripal_contact_properties.tpl.php → tripal_contact/theme/templates/tripal_contact_properties.tpl.php

@@ -49,6 +49,7 @@ if (count($properties) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_contact-table-properties',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_contact/theme/tripal_contact/tripal_contact_publications.tpl.php → tripal_contact/theme/templates/tripal_contact_publications.tpl.php

@@ -69,6 +69,7 @@ if (count($pubauthor_contacts) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_contact-table-publications',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_contact/theme/tripal_contact/tripal_contact_relationships.tpl.php → tripal_contact/theme/templates/tripal_contact_relationships.tpl.php

@@ -60,6 +60,7 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
          'rows' => $rows,
          'attributes' => array(
            'id' => 'tripal_contact-table-relationship-object',
+           'class' => 'tripal-data-table'
          ),
          'sticky' => FALSE,
          'caption' => '',
@@ -109,6 +110,7 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
          'rows' => $rows,
          'attributes' => array(
            'id' => 'tripal_contact-table-relationship-subject',
+           'class' => 'tripal-data-table'
          ),
          'sticky' => FALSE,
          'caption' => '',

tripal_contact/tripal_contact.module

@@ -135,37 +135,37 @@ function tripal_contact_theme($existing, $type, $theme, $path) {
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
     'tripal_contact_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_contact_base',
-      'path' => "$path/theme/tripal_contact",
+      'path' => "$path/theme/templates",
     ),
     'tripal_contact_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_contact_properties',
-      'path' => "$path/theme/tripal_contact",
+      'path' => "$path/theme/templates",
     ),
     'tripal_contact_relationships' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_contact_relationships',
-      'path' => "$path/theme/tripal_contact",
+      'path' => "$path/theme/templates",
     ),
     'tripal_contact_publications' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_contact_publications',
-      'path' => "$path/theme/tripal_contact",
+      'path' => "$path/theme/templates",
     ),
     'tripal_contact_help' => array(
       'template' => 'tripal_contact_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
     'tripal_contact_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_contact_teaser',
-      'path' => "$path/theme/tripal_contact",
+      'path' => "$path/theme/templates",
     ),
   );
   return $items;

tripal_core/includes/custom_tables.inc

@@ -140,7 +140,7 @@ function tripal_custom_tables_list() {
   $table = array(
     'header' => $header,
     'rows' => $rows,
-    'attributes' => array(),
+    'attributes' => array('class' => 'tripal-data-table'),
     'sticky' => FALSE,
     'caption' => '',
     'colgroups' => array(),

tripal_core/includes/jobs.inc

@@ -207,7 +207,7 @@ function tripal_jobs_report() {
   $table = array(
     'header' => $header,
     'rows' => $rows,
-    'attributes' => array(),
+    'attributes' => array('class' => 'tripal-data-table'),
     'sticky' => FALSE,
     'caption' => '',
     'colgroups' => array(),
@@ -308,7 +308,7 @@ function tripal_jobs_view($job_id) {
   $table = array(
     'header' => $header,
     'rows' => $rows,
-    'attributes' => array(),
+    'attributes' => array('class' => 'tripal-data-table'),
     'sticky' => FALSE,
     'caption' => '',
     'colgroups' => array(),

tripal_core/includes/mviews.inc

@@ -114,7 +114,7 @@ function tripal_mview_report($mview_id) {
   $table = array(
     'header' => $header,
     'rows' => $rows,
-    'attributes' => array(),
+    'attributes' => array('class' => 'tripal-data-table'),
     'sticky' => FALSE,
     'caption' => '',
     'colgroups' => array(),
@@ -178,7 +178,7 @@ function tripal_mviews_report() {
   $table = array(
     'header' => $header,
     'rows' => $rows,
-    'attributes' => array(),
+    'attributes' => array('class' => 'tripal-data-table'),
     'sticky' => FALSE,
     'caption' => '',
     'colgroups' => array(),

tripal_core/tripal_core.module

@@ -420,7 +420,7 @@ function tripal_core_theme($existing, $type, $theme, $path) {
     'tripal_core_customize' => array(
       'arguments' => array('job_id' => NULL),
       'template' => 'tripal_core_customize',
-      'path' => "$path/theme"
+      'path' => "$path/theme/templates"
     ),
     'theme_file_upload_combo' => array(
       'render element' => 'element',
@@ -431,12 +431,12 @@ function tripal_core_theme($existing, $type, $theme, $path) {
     'tripal_core_jobs_help' => array(
       'template' => 'tripal_core_jobs_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme"
+      'path' => "$path/theme/templates"
     ),
     'tripal_core_customtables_help' => array(
       'template' => 'tripal_core_customtables_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme"
+      'path' => "$path/theme/templates"
     ),
 
     // Chado Node API Themes

tripal_cv/tripal_cv.module

@@ -336,7 +336,7 @@ function tripal_cv_theme($existing, $type, $theme, $path) {
     'tripal_cv_help' => array(
       'template' => 'tripal_cv_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme/"
+      'path' => "$path/theme/templates"
     )
   );
 

tripal_db/tripal_db.module

@@ -142,7 +142,7 @@ function tripal_db_theme($existing, $type, $theme, $path) {
     'tripal_db_help' => array(
       'template' => 'tripal_db_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme/"
+      'path' => "$path/theme/templates"
     )
   );
   return $items;

tripal_example/README.txt

@@ -0,0 +1,118 @@
+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 
+http://www.drupal.org but the easiest way to learn to program a Drupal module
+is to purchase the following book:
+
+  Tomlinson, VanDyk.  Pro Drupal Development. 2010. ISBN-13: 978-1430228387
+
+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
+3) Create a .module file which contains the functions used by your module
+4) Create a .install file which contains the functions used for installation,
+   enabling, disabling and uninstallation of your module.
+
+Examine the example functions and documentation in each of the files in this
+example module to learn how Tripal uses the Drupal API.
+
+-------------------------
+DIRECTORY AND FILE NAMING
+-------------------------
+When creating your Tripal Extension module, the following directory structure
+and file naming is suggested:
+
+For the required files:
+[module dir]/[module name].info
+[module dir]/[module name].module
+[module dir]/[module name].install
+
+If you want to include Drush commands for your module
+[module dir]/[module name].drush.inc
+
+If you want to integrate with Drupal Views 3.x:
+[module dir]/[module name].views.inc
+[module dir]/[module name].views_default.inc
+
+
+Include Files
+-------------
+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 
+place all of the Drupal hooks for nodes inside of an include named:
+[module dir]/includes/[module name].chado_node.inc
+
+If your module has an administrative interface, all of the functions related to
+administration should go in an include file named:
+[module dir]/includes/[module name].admin.inc
+
+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
+or periods).
+
+
+Theme Files
+-------------
+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
+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
+housed inside of a 'theme' directory with the following structure:
+[module dir]/theme
+[module dir]/theme/css      (for CSS files)
+[module dir]/theme/js       (for JS files)
+[module dir]/theme/images   (for images)
+
+All Drupal hooks and functions related to theming of content should go in the
+file named:
+[module dir]/theme/[module name].theme.inc
+
+The functions in that file will typically be functions which directly
+generate content for a page or "preprocess" hooks that prepare variables that
+are passed to templates.
+
+Template files are typically placed inside of directories named after the 
+Tripal node type to which the template adds content.  For example, the 
+tripal_pub module is responsible for interactions with the publication tables
+of Chado.  It provides it's own 'chado_pub' node type.  But it also adds 
+publication information on feature pages if there is an associated publication.
+Therefore, the tripal_pub/theme/chado_feature directory exists and 
+contains the templates responsible for adding content to the 'chado_feature' 
+node type !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+Template files are named in the following way
+[module dir]/theme/[template dir]/[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.
+
+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 
+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:
+[module dir]/api/[module name].[function].api.inc
+
+
+
+

tripal_example/includes/tripal_example.chado_node.inc

@@ -7,40 +7,48 @@
  */
 
 /**
- *  Implementation of hook_node_info().  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.
+ *  Implementation of hook_node_info().  
+ *  
+ *  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.
  *
  * @ingroup tripal_example
  */
 function tripal_example_node_info() {
   $nodes = array();
 
-  //$nodes['chado_example'] = array(
-  //  'name'        => t('Example'),
-  //  'base'        => 'chado_example',
-  //  'description' => t('A example from the chado database'),
-  //  'has_title'   => TRUE,
-  //  'locked'      => TRUE
-  // 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.
-  //  'chado_node_api' => array(
-  //    'base_table' => 'example',       // the base table name (e.g. feature, example, contact)
-  //    'hook_prefix' => 'chado_example',// the node type hook prefix
-  //    'record_type_title' => array(
-  //      'singular' => t('Library'),    // how to refer to the record
-  //      'plural' => t('Libraries')     // how to refer to the record in plurals
-  //    ),
-  //    '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
-  //    ),
-  //  )
-  //);
+  // EXPLANATION: this array describes all of the node types that are created
+  // by this module. For many Tripal modules (e.g. tripal_example, tripal_stock,
+  // tripal_library, tripal_pub, etc.) new node types are created. It is
+  // customary to name all new node types that interact with data in Chado
+  // with a 'chado_' prefix.  
+  
+  $nodes['chado_example'] = array(
+    'name'        => t('Example'),
+    'base'        => 'chado_example',
+    '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.
+    '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
+      'record_type_title' => array(
+        'singular' => t('Example'),    // how to refer to the record
+        'plural' => t('Examples')      // how to refer to the record in plurals
+      ),
+      '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
+      ),
+    )
+  );
 
   return $nodes;
 }
@@ -65,7 +73,9 @@ function chado_example_node_access($node, $op, $account) {
   if (is_object($node)) {
     $node_type = $node->type;
   }
-  
+  // EXPLANATION:  in the tripal_example_permissions() function we 
+  // created the permission types that are used here to check for 
+  // access permissions to the 'chado_exmaple' node type.
   if($node_type == 'chado_example') {
     if ($op == 'create') {
       if (!user_access('create chado_example content', $account)) {
@@ -93,15 +103,27 @@ function chado_example_node_access($node, $op, $account) {
 }
 
 /**
- * Implementation of hook_form() when a node type of chado_example is defined.
- * If a node type is not defined then this function is not needed. The table
- * name in chado for this example module is named 'example' so there is a
- * corresponding example_id in that table (similar to feature.feature_id,
- * contact.contact_id, etc).
+ * Implementation of hook_form() 
+ * 
+ * Creates the form for editing or inserting a record 
  *
  * @ingroup tripal_example
  */
 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.
+  // 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, 
+  //    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.
 
   $form = array();
 
@@ -116,37 +138,72 @@ function chado_example_form($node, &$form_state) {
   // set form field defaults
 
 
-  // if we are editing an existing node then the example is already part of the node
+  // SET FORM DEFAULTS
+  //---------------------------------------------
+  
+  // if we are editing an existing node then the 'example' record from Chado
+  // is already part of the node, so we set the defaults from that object
   if (property_exists($node, 'example')) {
-    // $example = $node->example;
-    // $example = chado_expand_var($example, 'field', 'example.residues');
-    // $example_id   = $example->example_id;
-    // $uniquename   = $example->uniquename;
+    $example = $node->example;
+    $example = chado_expand_var($example, 'field', 'example.residues');
+    $example_id   = $example->example_id;
+    $uniquename   = $example->uniquename;
 
     // keep track of the example id
-    //$form['example_id'] = array(
-    //  '#type' => 'value',
-    //  '#value' => $example_id,
-    //);
+    $form['example_id'] = array(
+      '#type' => 'value',
+      '#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 (array_key_exists('values', $form_state)) {
-    // $uniquename   = $form_state['values']['uniquename'];
+     $uniquename   = $form_state['values']['uniquename'];
+     $example_type = $form_state['values']['example_type'];
 
   }
   // if we are re building the form from after submission (from ajax call) then
   // the values are in the $form_state['input'] array
   if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
-    // $uniquename   = $form_state['input']['uniquename'];
-
+     $uniquename   = $form_state['input']['uniquename'];
+     $example_type = $form_state['input']['example_type'];
   }
+    
   
-  // NOTE: if the table has a 'type_id' column, be sure to use the 
-  // tripal_get_default_cv('example', 'type_id') to get the site's 
-  // default vocabulary.
+  // FORM ELEMENTS 
+  //---------------------------------------------
+  $form['uniquename']= array(
+    '#type' => 'textfield',
+    '#title' => t('Unique Name'),
+    '#required' => TRUE,
+    '#default_value' => $uniquename,
+    '#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
+  $type_cv = tripal_get_default_cv('example', 'type_id');
+  $cv_id = $type_cv->cv_id;
+  $form['example_type'] = array(
+    '#title'       => t('Feature Type'),
+    '#type'        => 'textfield',
+    '#description' => t("Choose the example type."),
+    '#required'    => TRUE,
+    '#default_value' => $example_type,
+    '#autocomplete_path' => "admin/tripal/chado/tripal_cv/cvterm/auto_name/$cv_id",
+  );
+  
+  // add a select box of organisms
+  $organisms = tripal_get_organism_select_options();
+  $form['organism_id'] = array(
+    '#title'       => t('Organism'),
+    '#type'        => t('select'),
+    '#description' => t("Choose the organism with which this example is associated"),
+    '#required'    => TRUE,
+    '#default_value' => $organism_id,
+    '#options'     => $organisms,
+  );
 
   // PROPERTIES FORM
   //---------------------------------------------
@@ -198,6 +255,10 @@ 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 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
@@ -222,20 +283,20 @@ function chado_example_validate($node, $form, &$form_state) {
   }
 
   // be sure to always trim text fields
-  // $node->uniquename   = trim($node->uniquename);
+  $node->uniquename   = trim($node->uniquename);
   
   // Validating for an update. If the 'nid' property is present in the node then
   // this is an update and validation can be different for updates
   if (property_exists($node, 'nid')) {
 
     // if there is a problem with a field then you can set an error on the form
-    // form_set_error('uniquename', t("example update cannot proceed. The example name '$node->uniquename' is not unique for this organism. Please provide a unique name for this example."));
+    form_set_error('uniquename', t("example update cannot proceed. The example name '$node->uniquename' is not unique for this organism. Please provide a unique name for this example."));
   }
   // Validating for an insert
   else {
 
     // if there is a problem with a field then you can set an error on the form
-    // form_set_error('uniquename', t("example insert cannot proceed. The example name '$node->uniquename' already exists for this organism. Please provide a unique name for this example."));
+    form_set_error('uniquename', t("example insert cannot proceed. The example name '$node->uniquename' already exists for this organism. Please provide a unique name for this example."));
   }
 }
 
@@ -256,81 +317,75 @@ function chado_example_validate($node, $form, &$form_state) {
  */
 function chado_example_insert($node) {
   // be sure to always trim text fields
-  //$node->uniquename   = trim($node->uniquename);
+  $node->uniquename   = trim($node->uniquename);
 
   // if there is an example_id in the $node object then this must be a sync so
   // we can skip adding the example as it is already there, although
   // we do need to proceed with the rest of the insert
   if (!property_exists($node, 'example_id')) {
 
-    // ADD TO CHADO
-
-    // * Example Table *
     // perform the insert using the tripal_core_chado_insert function();
-    //$values = array(
-    //  'uniquename' => $node->uniquename,
-    //  'residues' => $residues,
-    //);
-    //$example = chado_select_record('example', array('*'), $values);
-    //if (!$example) {
-    //  drupal_set_message(t('Unable to add example.'), 'warning');
-    //  tripal_report_error('tripal_example', TRIPAL_WARNING, 'Insert example: Unable to create example where values: %values',
-    //    array('%values' => print_r($values, TRUE)));
-    //  return;
-    //}
+    $values = array(
+      'uniquename' => $node->uniquename,
+      'residues' => $residues,
+    );
+    $example = chado_select_record('example', array('*'), $values);
+    if (!$example) {
+      drupal_set_message(t('Unable to add example.'), 'warning');
+      tripal_report_error('tripal_example', TRIPAL_WARNING, 'Insert example: Unable to create example where values: %values',
+        array('%values' => print_r($values, TRUE)));
+      return;
+    }
 
     // get the example_id for linking Drupal node with Chado data
-    // $example_id = $example->example_id;
+    $example_id = $example->example_id;
 
     // Only add to other chado tables if the base record was inserted properly
     if ($example_id > 0) {
 
-      // * Properties Form *
       // 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' => $example_id    // the value of the example_id key
-      // );
-      // chado_update_node_form_properties($node, $details);
-
-      // * Additional DBxrefs Form *
+      $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' => $example_id    // the value of the example_id key
+      );
+      chado_update_node_form_properties($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.
-      // $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' => $example_id      // the value of the example_id key
-      // );
-      // chado_update_node_form_dbxrefs($node, $details);
-
-      // * Relationships Form *
+      $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' => $example_id      // the value of the example_id key
+      );
+      chado_update_node_form_dbxrefs($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.
-      // $details = array(
-      //   'relationship_table' => 'example_relationship',  // name of the _relationship table
-      //   'foreignkey_value' => $example_id                // value of the example_id key
-      // );
-      // chado_update_node_form_relationships($node, $details);
+      $details = array(
+        'relationship_table' => 'example_relationship',  // name of the _relationship table
+        'foreignkey_value' => $example_id                // value of the example_id key
+      );
+      chado_update_node_form_relationships($node, $details);
     }
   }
   else {
     // the node has an example_id so get it for linking Drupal node with Chado data
-    // $example_id = $node->example_id;
+    $example_id = $node->example_id;
   }
 
   // Make sure the entry for this example doesn't already exist in the
   // chado_example table if it doesn't exist then we want to add it.
   // $check_org_id = chado_get_id_from_nid('example', $node->nid);
-  //if (!$check_org_id) {
-  //  $record = new stdClass();
-  //  $record->nid = $node->nid;
-  //  $record->vid = $node->vid;
-  //  $record->example_id = $example_id;
-  //  drupal_write_record('chado_example', $record);
-  //}
+  if (!$check_org_id) {
+    $record = new stdClass();
+    $record->nid = $node->nid;
+    $record->vid = $node->vid;
+    $record->example_id = $example_id;
+    drupal_write_record('chado_example', $record);
+  }
 }
 
 /**
@@ -345,53 +400,50 @@ function chado_example_insert($node) {
  */
 function chado_example_update($node) {
   // be sure to always trim text fields
-  // $node->uniquename   = trim($node->uniquename);
+  $node->uniquename   = trim($node->uniquename);
 
   // use the chado_update_record() function to update the record
-  //$match = array(
-  //'example_id' => $example_id,
-  //);
-  //$values = array(
-  //  'uniquename' => $node->uniquename,
-  //);
-  //$options = array('return_record' => TRUE);
-  //$status = chado_update_record('example', $match, $values, $options);
-
-  //if (!$status) {
-  //  drupal_set_message(t('Unable to update example.'), 'warning');
-  //  tripal_report_error('tripal_example', TRIPAL_WARNING, 'Update example: Unable to update example where values: %values',
-  //    array('%values' => print_r($values, TRUE)));
-  //}
-
-  // * Properties Form *
+  $match = array(
+    'example_id' => $example_id,
+  );
+  $values = array(
+    'uniquename' => $node->uniquename,
+  );
+  $options = array('return_record' => TRUE);
+  $status = chado_update_record('example', $match, $values, $options);
+
+  if (!$status) {
+    drupal_set_message(t('Unable to update example.'), 'warning');
+    tripal_report_error('tripal_example', TRIPAL_WARNING, 'Update example: Unable to update example where values: %values',
+      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.
-  // $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' => $example_id    // the value of the example_id key
-  // );
-  // chado_update_node_form_properties($node, $details);
-
-  // * Additional DBxrefs Form *
+  $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' => $example_id    // the value of the example_id key
+  );
+  chado_update_node_form_properties($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.
-  // $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' => $example_id      // the value of the example_id key
-  // );
-  // chado_update_node_form_dbxrefs($node, $details);
-
-  // * Relationships Form *
+  $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' => $example_id      // the value of the example_id key
+  );
+  chado_update_node_form_dbxrefs($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.
-  // $details = array(
-  //   'relationship_table' => 'example_relationship',  // name of the _relationship table
-  //   'foreignkey_value' => $example_id                // value of the example_id key
-  // );
-  // chado_update_node_form_relationships($node, $details);
+  $details = array(
+    'relationship_table' => 'example_relationship',  // name of the _relationship table
+    'foreignkey_value' => $example_id                // value of the example_id key
+  );
+  chado_update_node_form_relationships($node, $details);
 
 }
 /**
@@ -407,7 +459,7 @@ function chado_example_update($node) {
 function chado_example_delete($node) {
 
   // get the example id from the node
-  //$example_id  = chado_get_id_from_nid('example', $node->nid);
+  $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.
@@ -417,13 +469,13 @@ function chado_example_delete($node) {
 
   // remove the entry in the chado_exapmle table linking the deleted
   // 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));
+  $sql_del = "DELETE FROM {chado_example} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
 
   // Remove data from example tables of chado database.  This will
   // 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));
+  chado_query("DELETE FROM {example} WHERE example_id = :example_id", array(':example_id' => $example_id));
 
   // inform the user that the data was deleted
   drupal_set_message(t("The example and all associated data were removed from Chado"));
@@ -433,8 +485,8 @@ function chado_example_delete($node) {
 /**
  * Implementation of hook_load().  This function is necessary to load
  * into the $node object the fields of the table form Chado. For example
- * for the feature table, the chado_feature_load() function adds in
- * a feature object which contains all of the fields and sub objects
+ * for the example table, the chado_example_load() function adds in
+ * a example object which contains all of the fields and sub objects
  * for data in tables with foreign key relationships.
  *
  * This function is not required if the hook_node_info() does not define
@@ -443,22 +495,26 @@ function chado_example_delete($node) {
  * @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 
+  // 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
   foreach ($nodes as $nid => $node) {
     // find the example and add in the details
-    //$example_id = chado_get_id_from_nid('example', $nid);
+    $example_id = chado_get_id_from_nid('example', $nid);
 
     // if the nid does not have a matching record then skip this node.
     // this can happen with orphaned nodes.
-    //if (!$example_id) {
-    //  continue;
-    //}
+    if (!$example_id) {
+      continue;
+    }
     
     // build the example variable by using the chado_generate_var() function
-    //$values = array('example_id' => $example_id);
-    //$example = chado_generate_var('example', $values);
+    $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 tripal_core_generate_chado_var does not include text fields as
@@ -468,180 +524,193 @@ function chado_example_load($nodes) {
     // include it here using the chado_expand_var() function.  In most
     // cases it is probably best to let the end-user decide if text fields should
     // be included by using this function in the templates.
-    //$example = chado_expand_var($example, 'field', 'example.residues');
+    $example = chado_expand_var($example, 'field', 'example.residues');
 
     // add the new example object to this node.
-    //$nodes[$nid]->example = $example;
+    $nodes[$nid]->example = $example;
   }
 }
 
 /**
- * Implementation of hook_node_presave().  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. In some cases
- * such as for the organism module, the title will be set depending on
- * what genus and species is provided. This hook can allow the title to
- * be set using user supplied data before the node is saved.  In practice
- * any change can be made to any fields in the node object.
- *
- * 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.
+ * Implementation of hook_node_presave().
+ * 
+ * Performs actions on a node object prior to it being saved
  *
  * @ingroup tripal_example
  */
 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.
+  // One useful case for this is to set the title of a node. In some cases
+  // such as for the organism module, the title will be set depending on
+  // what genus and species is provided. This hook can allow the title to
+  // be set using user supplied data before the node is saved.  In practice
+  // any change can be made to any fields in the node object.
+  //
+  // 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 ($node->type) {
     case 'chado_example':
-      // for a form submission the 'examplename' field will be set,
+      // for a form submission the 'uniquename' field will be set,
       // for a sync, we must pull from the example object
-      if (property_exists($node, 'examplename')) {
+      if (property_exists($node, 'uniquename')) {
         // set the title
-        $node->title = $node->examplename;
+        $node->title = $node->uniquename;
       }
       else if (property_exists($node, 'example')) {
-        $node->title = $node->example->name;
+        $node->title = $node->example->uniquename;
       }
       break;
   }
-  */
 }
 
 /**
- * Implementation of hook node_insert().  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 when you
- * can't edit the hook_insert() function of a node not defined by this
- * module, or to access values of a node when have not yet been saved.
- * 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 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.
+ * Implementation of hook node_insert(). 
+ * 
+ * Performs actions after any node has been inserted. 
  *
  * @ingroup tripal_example
  */
 function tripal_example_node_insert($node) {
-
-  // set the URL path after inserting.  We do it here because we do not know the
-  // example_id in the presave and cannot do it in the hook_insert()
-  //switch ($node->type) {
-  //  case 'chado_example':
-  //    if (!$node->example_id) {
-  //      $sql = "SELECT * FROM {chado_example} WHERE nid = :nid";
-  //      $chado_example = db_query($sql, array(':nid' => $node->nid))->fetchObject();
-  //      $node->example_id = $chado_example->example_id;
-  //    }
   
-  //    // on an insert we need to add the feature_id to the node object
-  //    // so that the tripal_example_get_example_url function can set the URL properly
-  //    $node->example_id = chado_get_id_from_nid('example', $node->nid);
-
-  //    // remove any previous alias
-  //    db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
-
-  //    // set the URL for this example page
-  //    $url_alias = tripal_example_get_example_url($node);
-  //    $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
-  //    path_save($path_alias);
-  //    break;
-  //}
+  // 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.
+  //
+  // 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()
+  switch ($node->type) {
+    case 'chado_example':
+      
+      // if we do not have an record ID for this node then get it
+      if (!$node->example_id) {
+        $node->example_id = chado_get_id_for_node('example', $node);
+      }
+
+      // set the URL for this example page
+      // see the code in the tripal_feature/includes/tripal_feature.chado_node.inc file
+      // in the function tripal_feature_node_insert for an example of how that
+      // module sets the URL.  It uses a configuration file to allow the user
+      // to dynmically build a URL schema and then uses that schema to generate 
+      // a URL string.
+      break;
+  }
 }
+
 /**
- * Implementation of hook node_update().  This function is used
- * after any a node is updated in the database.  It is different
- * from the hook_update() function above in that it is called after
- * any node is updated, regardlesss of it's type. This function is useful
- * for making changes to the database after a node is updated when you
- * can't perform changes in the hook_upate() function of a node not defined by this
- * module, or to access values of a node when have not yet been updated.
- * An example comes from the tripal_feature module where the URL alias
- * of a node cannot be set in the hook_update() function. Therefore
- * the tripal_feature module uses this function to reset the url path
- * of an updated feature node.
- *
- * This function is not required. You probably won't need it if you
- * don't define a custom node type in the hook_node_info() function. But
- * it is node type agnostic, so you can use this function to do any
- * activity after insert of a node.
+ * Implementation of hook node_update().
+ * 
+ * Performs actions after any node has been updated. 
  *
  */
 function tripal_example_node_update($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.
+  //
+  // 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 ($node->type) {
     case 'chado_example':
-      // remove any previous alias
-      //db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
-
       // set the URL for this example page
-      //$url_alias = tripal_example_get_example_url($node);
-      //$path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
-      //path_save($path_alias);
+      // 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.
       break;
   }
 }
 /**
- * Implementation of hook_node_view().  This function allows you to
- * add custom content to any node page.  It is node type agnostic.
- * Here we typically use it to add content to our custom node type or
- * to other Tripal node types. Typically for Tripal, a content "block"
- * (e.g. feature properties, feature dbxref, feature pub) has a corresponding
- * template file.  Those template files are first defined to Drupal using
- * the hook_theme() function defined in the tripal_example.module file.  Here
- * we can add items to a node's content by calling those templates as needed.
+ * Implementation of hook_node_view().  
  *
  * @ingroup tripal_example
  */
 function tripal_example_node_view($node, $view_mode, $langcode) {
+  
+  // EXPLANATION: This function defines the content "blocks" that appear 
+  // when thhe node is displayed. It is node type agnostic so we can add
+  // content to any node type.  So, we use this function to add the content
+  // from all of our theme templates onto our new node type. We will also
+  // use this function to add content to other node types.
+          
   switch ($node->type) {
     case 'chado_example':
       // there are different ways a node can be viewed. Primarily Tripal
       // supports full page view and teaser view.
       if ($view_mode == 'full') {
-        // there is always a base template.  This is the template that
-        // is first shown when the example node type is first displayed
-        //$node->content['tripal_example_base'] = array(
-        //  '#markup' => theme('tripal_example_base', array('node' => $node)),
-        //  '#tripal_toc_id'    => 'base',
-        //  '#tripal_toc_title' => 'Overview',
-        //  '#weight' => -100,
-        //);
-        // we can add other templates as well.
-        //$node->content['tripal_example_properties'] = array(
-        //  '#markup' => theme('tripal_example_properties', array('node' => $node)),
-        //  '#tripal_toc_id'    => 'properties',
-        //  '#tripal_toc_title' => 'Properties',
-        //);
-        //$node->content['tripal_example_publications'] = array(
-        //  '#markup' => theme('tripal_example_publications', array('node' => $node)),
-        //  '#tripal_toc_id'    => 'publications',
-        //  '#tripal_toc_title' => 'Publications',
-        //);
-        //$node->content['tripal_example_references'] = array(
-        //  '#markup' => theme('tripal_example_references', array('node' => $node)),
-        //  '#tripal_toc_id'    => 'references',
-        //  '#tripal_toc_title' => 'Cross References',
-        //);
+        
+        // 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
+        // world that is used to reference the template. This ID is used for
+        // 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.
+        $node->content['tripal_example_base'] = array(
+          '#markup' => theme('tripal_example_base', array('node' => $node)),
+          '#tripal_toc_id'    => 'base',
+          '#tripal_toc_title' => 'Overview',
+          '#weight' => -100,
+        );
+        // we can add other templates as well for properties, publications,
+        // dbxrefs, etc...
+        $node->content['tripal_example_properties'] = array(
+          '#markup' => theme('tripal_example_properties', array('node' => $node)),
+          '#tripal_toc_id'    => 'properties',
+          '#tripal_toc_title' => 'Properties',
+        );
+        $node->content['tripal_example_references'] = array(
+          '#markup' => theme('tripal_feature_references', array('node' => $node)),
+          '#tripal_toc_id'    => 'references',
+          '#tripal_toc_title' => 'Cross References',
+        );
+        $node->content['tripal_example_relationships'] = array(
+          '#markup' => theme('tripal_feature_relationships', array('node' => $node)),
+          '#tripal_toc_id'    => 'relationships',
+          '#tripal_toc_title' => 'Relationships',
+        );
       }
       // set the content for the teaser view
       if ($view_mode == 'teaser') {
-        //$node->content['tripal_example_teaser'] = array(
-        //  '#value' => theme('tripal_example_teaser', array('node' => $node)),
-        //);
+        // The teaser is also a required template
+        $node->content['tripal_example_teaser'] = array(
+          '#value' => theme('tripal_example_teaser', array('node' => $node)),
+        );
       }
       break;
-    // you can add custom content to any tripal node type by adding
+    // you can add custom content to any node type by adding
     // content to the node in the same way as above.
     case 'chado_organism':
       break;

tripal_example/theme/templates/tripal_example_help.tpl.php

@@ -0,0 +1,8 @@
+<h3>Module Description:</h3>
+<p>Place details about this module here.</p>
+
+<h3>Setup Instructions:</h3>
+<p>Instructions for setup of this module go here.</p>
+
+<h3>Features of this Module:</h3>
+<p>A description of this module's features go here.</p>

tripal_example/theme/templates/tripal_example_properties.tpl.php

@@ -0,0 +1,85 @@
+<?php
+$pub = $node->pub;
+
+// expand the pub to include the properties.
+$options = array(
+  'return_array' => 1,
+  'order_by' => array('rank' => 'ASC'),
+);
+$pub = tripal_core_expand_chado_vars($pub,'table', 'pubprop', $options);
+$pubprops = $pub->pubprop;
+$properties = array();
+if (is_array($pubprops)) {
+  foreach ($pubprops as $property) {
+    // skip the following properties as those are already on other templates
+    if ($property->type_id->name == 'Abstract' or
+        $property->type_id->name == 'Citation' or
+        $property->type_id->name == 'Publication Dbxref' or
+        $property->type_id->name == 'Authors' or
+        $property->type_id->name == 'Structured Abstract Part')  {
+      continue;
+    }
+    $property = tripal_core_expand_chado_vars($property,'field','pubprop.value');
+    $properties[] = $property;
+  }
+}
+// we'll keep track of the keywords so we can lump them into a single row
+$keywords = array(); 
+
+if (count($properties)) { ?>
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc">Additional details for this publication include:</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('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:
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $rows = array();
+  
+  $keywords = array();
+  foreach ($properties as $property) {
+    // each keyword is stored as a seperate properties. We want to show them
+    // only in a single field not as a bunc of individual properties, so when we see one, 
+    // save it in an array for later and down't add it yet to the table yet.
+    if ($property->type_id->name == 'Keywords') {
+      $keywords[] = $property->value;
+      continue;
+    }
+    $rows[] = array(
+      $property->type_id->name,
+      $property->value
+    );
+  }
+  // now add in a single row for all keywords
+  if (count($keywords) > 0) {
+    $rows[] = array(
+      '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:
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $table = array(
+    'header' => $headers,
+    'rows' => $rows,
+    'attributes' => array(
+      'id' => 'tripal_pub-table-properties',
+      'class' => 'tripal-data-table'
+    ),
+    'sticky' => FALSE,
+    'caption' => '',
+    'colgroups' => array(),
+    'empty' => '',
+  );
+  
+  // once we have our table array structure defined, we call Drupal's theme_table()
+  // function to generate the table.
+  print theme_table($table);
+}

tripal_example/theme/templates/tripal_example_references.tpl.php

@@ -0,0 +1,70 @@
+<?php
+$pub = $variables['node']->pub;
+
+
+// expand the pub object to include the records from the pub_dbxref table
+$options = array('return_array' => 1);
+$pub = tripal_core_expand_chado_vars($pub, 'table', 'pub_dbxref', $options);
+$pub_dbxrefs = $pub->pub_dbxref;
+
+$references = array();
+if (count($pub_dbxrefs) > 0 ) {
+  foreach ($pub_dbxrefs as $pub_dbxref) {    
+    $references[] = $pub_dbxref->dbxref_id;
+  }
+}
+
+if(count($references) > 0){ ?>
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication 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:
+  // 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; 
+    }
+    $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
+    if ($dbxref->db_id->urlprefix) {
+      $accession = l($accession, $dbxref->db_id->urlprefix . $dbxref->accession, array('attributes' => array('target' => '_blank')));
+    }
+    if (property_exists($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:
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $table = array(
+    'header' => $headers,
+    'rows' => $rows,
+    'attributes' => array(
+      'id' => 'tripal_pub-table-references',
+      'class' => 'tripal-data-table'
+    ),
+    'sticky' => FALSE,
+    'caption' => '',
+    'colgroups' => array(),
+    'empty' => '',
+  );
+  
+  // once we have our table array structure defined, we call Drupal's theme_table()
+  // function to generate the table.
+  print theme_table($table);
+}
+

tripal_example/theme/templates/tripal_example_relationships.tpl.php

@@ -0,0 +1,150 @@
+<?php
+/* Typically in a Tripal template, the data needed is retrieved using a call to
+ * tripal_core_expand_chado_vars function.  For example, to retrieve all 
+ * of the pub relationships for this node, the following function call would be made:
+ * 
+ *   $pub = tripal_core_expand_chado_vars($pub,'table','pub_relationship');
+ * 
+ * However, this function call can be extremely slow when there are numerous relationships.
+ * This is because the tripal_core_expand_chado_vars 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:
+ * 
+ *   $pub->all_relationships;
+ *   
+ * This variable is an array with two sub arrays with the keys 'object' and 'subject'.  The array with
+ * key 'object' contains relationships where the pub is the object, and the array with
+ * the key 'subject' contains relationships where the pub is the subject
+ */
+$pub = $variables['node']->pub;
+
+$all_relationships = $pub->all_relationships;
+$object_rels = $all_relationships['object'];
+$subject_rels = $all_relationships['subject'];
+
+if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc"></div> <?php
+  
+  // first add in the subject relationships.  
+  foreach ($subject_rels as $rel_type => $rels){
+    foreach ($rels as $obj_type => $objects){ ?>
+      <p>This <?php print $pub->type_id->name;?> is <?php print $rel_type ?> the following <b><?php print $obj_type ?></b> pub(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:
+      // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+      $rows = array();
+      
+      foreach ($objects as $object){
+        // link the pub 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(
+          'pub_id' => $object->record->object_id->pub_id,
+          'type_id' => array(
+            'name' => 'Citation',
+          ),
+        );
+        $citation = tripal_core_generate_chado_var('pubprop', $values);
+        $citation = tripal_core_expand_chado_vars($citation, 'field', 'pubprop.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
+       // documentation can be found here:
+       // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+       $table = array(
+         'header' => $headers,
+         'rows' => $rows,
+         'attributes' => array(
+           'id' => 'tripal_pub-table-relationship-object',
+           'class' => 'tripal-data-table'
+         ),
+         'sticky' => FALSE,
+         'caption' => '',
+         'colgroups' => array(),
+         'empty' => '',
+       );
+       
+       // once we have our table array structure defined, we call Drupal's theme_table()
+       // function to generate the table.
+       print theme_table($table); ?>
+       </p>
+       <br><?php
+     }
+  }
+  
+  // 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> pub(s) are <?php print $rel_type ?> this <?php print $pub->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:
+      // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+      $rows = array();
+      
+      foreach ($subjects as $subject){
+        // link the pub 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(
+          'pub_id' => $subject->record->subject_id->pub_id,
+          'type_id' => array(
+            'name' => 'Citation',
+          ),
+        );
+        $citation = tripal_core_generate_chado_var('pubprop', $values);
+        $citation = tripal_core_expand_chado_vars($citation, 'field', 'pubprop.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
+       // documentation can be found here:
+       // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+       $table = array(
+         'header' => $headers,
+         'rows' => $rows,
+         'attributes' => array(
+           'id' => 'tripal_pub-table-relationship-subject',
+           'class' => 'tripal-data-table'
+         ),
+         'sticky' => FALSE,
+         'caption' => '',
+         'colgroups' => array(),
+         'empty' => '',
+       );
+       
+       // once we have our table array structure defined, we call Drupal's theme_table()
+       // function to generate the table.
+       print theme_table($table); ?>
+       </p>
+       <br><?php
+     }
+  }
+}

tripal_example/theme/tripal_example.theme.inc

@@ -1 +1,112 @@
 <?php
+
+/**
+ * @file
+ * 
+ * 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
+ * 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
+  // 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 
+  // 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.
+
+  $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)
+    'include_fk' => array(
+      'type_id' => 1,
+      'object_id' => array(
+        'type_id' => 1,
+      ),
+      'subject_id'  => array(
+        'type_id' => 1,
+      ),
+    ),
+  );
+  $example = chado_expand_var($example, 'table', 'example_relationship', $options);
+
+  // get the subject relationships
+  $srelationships = $example->example_relationship->subject_id;
+  $orelationships = $example->example_relationship->object_id;
+
+  // combine both object and subject relationshisp into a single array
+  $relationships = array();
+  $relationships['object'] = array();
+  $relationships['subject'] = array();
+
+  // iterate through the object relationships
+  if ($orelationships) {
+    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' => $relationship->subject_id->example_id))->fetchObject();
+      if ($n) {
+        $rel->record->nid = $n->nid;
+      }
+
+      if (!array_key_exists($rel_type, $relationships['object'])) {
+        $relationships['object'][$rel_type] = array();
+      }
+      if (!array_key_exists($child_type, $relationships['object'][$rel_type])) {
+        $relationships['object'][$rel_type][$child_type] = array();
+      }
+      $relationships['object'][$rel_type][$child_type][] = $rel;
+    }
+  }
+
+  // now add in the subject relationships
+  if ($srelationships) {
+    foreach ($srelationships as $relationship) {
+      $rel = new stdClass();
+      $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();
+      }
+      if (!array_key_exists($parent_type, $relationships['subject'][$rel_type])) {
+        $relationships['subject'][$rel_type][$parent_type] = array();
+      }
+      $relationships['subject'][$rel_type][$parent_type][] = $rel;
+    }
+  }
+  $example->all_relationships = $relationships;
+}

tripal_example/tripal_example.info

@@ -0,0 +1,50 @@
+;
+; Provide details about your module in this file. Instruction for setup of this
+; 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.
+
+;
+; The version of Drupal with which this module is compatible.
+;
+core = 7.x
+
+;
+; The computer-readable name for this module
+;
+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 
+; 'Tripal Extensions'
+; 
+package = Tripal Extensions
+
+;
+; Follow these instructions when specifying the version:
+; https:;drupal.org/node/1015226
+; 
+version = 7.x-2.0
+
+;
+; Stylesheets containing CSS that should always be available for the
+; module should be specified here.  
+;
+stylesheets[all][] = theme/css/tripal_feature.css
+
+;
+; Javascript files that should always be available for the
+; module should be specified here.  
+;
+scripts[]          = theme/js/tripal_feature.js
+
+; 
+; Add additional dependencies for other modules using the module project name.
+; These modules must be enabled before this module can be enabled
+;
+dependencies[] = tripal_core
+dependencies[] = tripal_views
+dependencies[] = tripal_db
+dependencies[] = tripal_cv

tripal_example/tripal_example.install

@@ -1 +1,251 @@
 <?php
+/**
+ * @file
+ * Installation of the example module
+ */
+
+/**
+ * Implements hook_disable().
+ *
+ * Perform actions when the module is disabled by the site administrator
+ *
+ * @ingroup tripal_example
+ */
+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.
+
+  // Disable all default views provided by this module
+  require_once("tripal_example.views_default.inc");
+  $views = tripal_example_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
+/**
+ * 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. 
+ *
+ * @ingroup tripal_example
+ */
+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.
+    
+    // make sure chado is installed
+    if (!$GLOBALS["chado_is_installed"]) {
+      $requirements ['tripal_example'] = array(
+          'title' => "tripal_example",
+          'value' => "ERROR: Chado must be installed before this module can be enabled",
+          'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
+
+/**
+ * Implements hook_install().
+ * 
+ * Performs actions when the modules is first installed. 
+ *
+ * @ingroup tripal_example
+ */
+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
+  // 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
+  
+  // add any materialized view
+  tripal_example_add_mviews();
+
+  // add any external databases used by the example module.
+  tripal_example_add_dbs();
+  
+  // 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).
+  tripal_example_add_cvs();
+  
+  // 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.  
+  tripal_set_default_cv('example', 'type_id', 'sequence');
+  tripal_set_default_cv('exampleprop', 'type_id', 'example_property');
+  tripal_set_default_cv('example_relationship', 'type_id', 'example_relationship');
+}
+
+/**
+ * Implements hook_uninstall().
+ * 
+ * Performs actions when the modules is uninstalled.
+ * 
+ * @ingroup tripal_example
+ */
+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.
+ * 
+ * Schema API documentation is here:
+ * https://api.drupal.org/api/drupal/includes%21database%21schema.inc/group/schemaapi/7
+ *
+ * @ingroup tripal_example
+ */
+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.
+  $schema['chado_example'] = array(
+    'fields' => array(
+      'vid' => array(
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'default' => 0
+       ),
+      'nid' => array(
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'default' => 0
+       ),
+      'example_id' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+        'default' => 0
+      ),
+      'sync_date' => array(
+        'type' => 'int',
+        'not null' => FALSE,
+        'description' => 'UNIX integer sync date/time'
+      ),
+    ),
+    'indexes' => array(
+      'chado_example_idx1' => array('example_id')
+    ),
+    'unique keys' => array(
+      'chado_example_uq1' => array('nid', 'vid'),
+      'chado_example_uq2' => array('vid')
+    ),
+    'primary key' => array('nid'),
+  );
+
+  return $schema;
+};
+
+/**
+ * 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.
+  
+}
+/**
+ * Add cvs related to publications
+ *
+ * @ingroup tripal_pub
+ */
+function tripal_example_add_cvs() {
+
+  // EXPLANATION: use the tripal_cv_add_cv() function to add any 
+  // controlled vocabularies needed by your module.  If the vocabulary already
+  // exists then the function will gracefully return.  
+}
+
+/**
+ * This is the required update for tripal_example.
+ */
+function tripal_example_update_7200() {
+  // EXPLANATION: as you create new releases of your module you may find that 
+  // tables your module created, or data may need to be adjusted. This function 
+  // allows you to do that. This function is executed using the 
+  // http://[your site]/update.php  URL or using the drush command 'updatedb'.
+  // This function should be named according to the instructions provided here: 
+  // 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
+  // requirement, but will prevent errors during a major upgrade.
+
+  // it is good to wrap any database changes inside of a try catch block:
+  try {
+   // perform database changes
+  }
+  catch (\PDOException $e) {
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not apply updates: '. $error);
+  }
+}
+
+/**
+ * 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. 
+  $dependencies['tripal_example'][7200] = array(
+    'tripal_cv' => 7200
+  );
+
+  return $dependencies;
+}

tripal_example/tripal_example.module

@@ -8,26 +8,31 @@
  *
  */
 
-/* 
-// include any files that might be required
+// 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');
 require('includes/tripal_example.chado_node.inc');
-*/
-
-
 
 
 /**
- * Set the permission types that the chado module uses.  Essentially we
- * want permissionis that protect creation, editing and deleting of chado
- * data objects
- *
+ * Implementation of hook_permissions()
+ * 
+ * Set the permission types that this module uses.
+ * 
  * @ingroup tripal_example
  */
 function tripal_example_permisssions() {
-  /*
+  
+  // 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.
   return array(
     'access chado_example content' => array(
       'title' => t('View Examples'),
@@ -50,22 +55,37 @@ function tripal_example_permisssions() {
       'description' => t('Allow users to administer all examples.'),
     ),
   );
-  */
 }
 
 /**
- * Menu items are automatically added for the new node types created
- * by this module to the 'Create Content' Navigation menu item.  This function
- * adds more menu items needed for this module.
+ * Implements hook_menu()
+ * 
+ * Specifies menu items and URLs used by this module.
  *
  * @ingroup tripal_example
  */
 function tripal_example_menu() {
   $items = array();
   
-  /*
-  // The administative settings menu
-  $items['admin/tripal/chado/tripal_example'] = 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:
+  //  * 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.   
+  //    
+  
+  // EXPLANATION:  all extension modules should have an administrative menu item
+  // with the path set to 'admin/tripal/extesion/[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.
+  $items['admin/tripal/extension/tripal_example'] = array(
     'title' => 'Examples',
     'description' => 'Any example.',
     'page callback' => 'tripal_example_admin_examples_listing',
@@ -73,6 +93,14 @@ function tripal_example_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
+  // 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 
+  // 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. 
   $items['admin/tripal/chado/tripal_example/help'] = array(
     'title' => 'Help',
     'description' => 'Basic Description of Tripal Library Module Functionality',
@@ -83,6 +111,15 @@ function tripal_example_menu() {
     'weight' => 10
   );
 
+  // 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
+  // drupal_get_form() function and the 'page argument' indicates the form
+  // 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/chado/tripal_example/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Configure the Tripal Library module',
@@ -92,6 +129,12 @@ 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
+  // 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/chado/tripal_example/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for examples stored in Chado',
@@ -101,24 +144,16 @@ function tripal_example_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 2
   );
-
-  $items['admin/tripal/chado/tripal_example/views/examples/enable'] = array(
-    'title' => 'Enable Library Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
-    'page arguments' => array('tripal_example_admin_examples', 'admin/tripal/chado/tripal_example'),
-    'access arguments' => array('administer tripal example'),
-    'type' => MENU_CALLBACK,
-  );
-  */
-
+  
   return $items;
 }
 
 /**
  * Implements hook_views_api()
- * Purpose: Essentially this hook tells drupal that there is views support for
- *  for this module which then includes tripal_db.views.inc where all the
- *  views integration code is
+ * 
+ * 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.
  *
  * @ingroup tripal_example
  */
@@ -139,83 +174,136 @@ function tripal_example_views_api() {
 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:
+  // https://drupal.org/documentation/theme
+  
   $items = array(
+    
+    // EXPLANATION:  If this module defines a new node type that displays
+    // Chado data then we should use Tripal's default node template.  This
+    // template ensures that all content provided by Tripal and Tripal 
+    // extension modules has the same look and feel.  It is designed to be
+    // generic such that it won't intefer with the look-and-feel of the default
+    // theme.  This generic template will organize the node into a table
+    // of contents found on the left-side of the page and place the content
+    // in the center of the page.  User's will cycle through content on the 
+    // page by clicking the links in the table of contents. If you do not want
+    // to use the default Tripal template you can change this array to your
+    // liking.
     'node__chado_example' => array(
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
 
-    // tripal_example templates
+    // EXPLANATION: the following defines all of the template files used for
+    // this module. Templates are named with underscores separating words, and
+    // 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 base template
     'tripal_example_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_example_base',
-      'path' => "$path/theme/tripal_example",
+      'path' => "$path/theme/templates",
+    ),
+    // the help template
+    'tripal_example_help' => array(
+      'template' => 'tripal_example_help',
+      'variables' =>  array(NULL),
+      'path' => "$path/theme",
     ),
+    // the teaser template.
+    'tripal_example_teaser' => array(
+      'variables' => array('node' => NULL),
+      'template' => 'tripal_example_teaser',
+      'path' => "$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',
+    // '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',
-      'path' => "$path/theme/tripal_example",
+      'path' => "$path/theme/templates",
     ),
     'tripal_example_publications' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_example_publications',
-      'path' => "$path/theme/tripal_example",
+      'path' => "$path/theme/templates",
     ),
     'tripal_example_references' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_example_references',
-      'path' => "$path/theme/tripal_example",
+      'path' => "$path/theme/templates",
     ),
     'tripal_example_synonyms' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_example_synonyms',
-      'path' => "$path/theme/tripal_example",
+      'path' => "$path/theme/templates",
     ),
     'tripal_example_terms' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_example_terms',
-      'path' => "$path/theme/tripal_example",
-    ),
-    'tripal_example_help' => array(
-      'template' => 'tripal_example_help',
-      'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
 
-    // teaser
-    'tripal_example_teaser' => array(
-      'variables' => array('node' => NULL),
-      'template' => 'tripal_example_teaser',
-      'path' => "$path/theme/tripal_example",
-    ),
+    // 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: 
 
     // tripal_organism templates
     'tripal_organism_examples' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_examples',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
 
     // tripal_feature templates
     'tripal_feature_examples' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_examples',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
 
   );
-  */
   return $items;
 }
 
 /**
  * Implements hook_help()
- * Purpose: Adds a help page to the module list
+ * 
+ * Adds a help page to the module list
  */
 function tripal_example_help ($path, $arg) {
+  
+  // EXPLANATION: in the tripal_example_menu() function above we created 
+  // a menu item for the help documentation.  The menu item specified 
+  // a function that should be called when the menu item is clicked.  This 
+  // is that function.  But, rather than place HTML code in this function
+  // we want to have our help documentation in a template file.  We 
+  // specified in the tripal_example_theme() function that we have a template
+  // file so now we want to use get the contents of that template file and
+  // return it.
   if ($path == 'admin/help#tripal_example') {
     return theme('tripal_example_help', array());
   }
@@ -223,28 +311,44 @@ function tripal_example_help ($path, $arg) {
 
 
 /**
+ * Implements hook_cron()
  *
  * @ingroup tripal_example
  */
 function tripal_example_cron() {
 
+  // 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
  *
- * @param $form
- * @param $form_state
- * @param $form_id
  */
 function tripal_example_form_alter(&$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
     $form['actions']['preview']['#access'] = FALSE;
     
-    //remove the body field
+    // 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.
     unset($form['body']);
   }
 }

tripal_example/tripal_example.views.inc

@@ -0,0 +1 @@
+<?php

tripal_example/tripal_example.views_default.inc

@@ -0,0 +1 @@
+<?php

tripal_feature/theme/tripal_feature/tripal_feature_alignments.tpl.php → tripal_feature/theme/templates/tripal_feature_alignments.tpl.php

@@ -116,6 +116,7 @@ if(count($alignments) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-alignments',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_analyses.tpl.php → tripal_feature/theme/templates/tripal_feature_analyses.tpl.php

@@ -39,6 +39,7 @@ if (count($analyses) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-analyses',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_base.tpl.php → tripal_feature/theme/templates/tripal_feature_base.tpl.php

@@ -97,6 +97,7 @@ $table = array(
   'rows' => $rows,
   'attributes' => array(
     'id' => 'tripal_feature-table-base',
+    'class' => 'tripal-data-table'
   ),
   'sticky' => FALSE,
   'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_properties.tpl.php → tripal_feature/theme/templates/tripal_feature_properties.tpl.php

@@ -38,6 +38,7 @@ if(count($properties) > 0){
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-properties',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_publications.tpl.php → tripal_feature/theme/templates/tripal_feature_publications.tpl.php

@@ -69,6 +69,7 @@ if (count($feature_pubs) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-publications',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_references.tpl.php → tripal_feature/theme/templates/tripal_feature_references.tpl.php

@@ -72,6 +72,7 @@ if(count($references) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-references',
+      'class' => 'tripal-data-table' 
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_relationships.tpl.php → tripal_feature/theme/templates/tripal_feature_relationships.tpl.php

@@ -69,6 +69,7 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
          'rows' => $rows,
          'attributes' => array(
            'id' => 'tripal_feature-table-relationship-object',
+           'class' => 'tripal-data-table'
          ),
          'sticky' => FALSE,
          'caption' => '',
@@ -127,6 +128,7 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
          'rows' => $rows,
          'attributes' => array(
            'id' => 'tripal_feature-table-relationship-subject',
+           'class' => 'tripal-data-table'
          ),
          'sticky' => FALSE,
          'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_synonyms.tpl.php → tripal_feature/theme/templates/tripal_feature_synonyms.tpl.php

@@ -37,6 +37,7 @@ if(count($synonyms) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-synonyms',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/theme/tripal_feature/tripal_feature_terms.tpl.php → tripal_feature/theme/templates/tripal_feature_terms.tpl.php

@@ -64,6 +64,7 @@ if (count($s_terms) > 0) { ?>
       'rows' => $rows,
       'attributes' => array(
         'id' => "tripal_feature-table-terms-$i",
+        'class' => 'tripal-data-table'
       ),
       'sticky' => FALSE,
       'caption' => 'Vocabulary:  <b>' . ucwords(preg_replace('/_/', ' ', $cv)) . '</b> ' . $configure_link,

tripal_feature/theme/tripal_organism/tripal_organism_feature_browser.tpl.php → tripal_feature/theme/templates/tripal_organism_feature_browser.tpl.php

@@ -89,6 +89,7 @@ if (count($features) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_organism-table-features',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/theme/tripal_organism/tripal_organism_feature_counts.tpl.php → tripal_feature/theme/templates/tripal_organism_feature_counts.tpl.php

@@ -54,6 +54,7 @@ if (count($types) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_organism-table-features',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_feature/tripal_feature.module

@@ -245,79 +245,79 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
     'tripal_feature_alignments' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_alignments',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_analyses' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_analyses',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_base',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_sequence' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_sequence',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_proteins' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_proteins',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_publications' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_publications',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_synonyms' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_synonyms',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_references' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_references',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_properties',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_terms' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_terms',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_relationships' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_relationships',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_feature_help' => array(
       'template' => 'tripal_feature_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme/"
+      'path' => "$path/theme/templates"
     ),
 
     // template for the organism page
     'tripal_organism_feature_browser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_feature_browser',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
     'tripal_organism_feature_counts' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_feature_counts',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
 
     // themed forms
@@ -329,7 +329,7 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
     'tripal_feature_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_teaser',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
   );
 
@@ -1156,9 +1156,7 @@ function tripal_feature_match_features_page($id) {
     return "<p>No features matched the given name '$id'</p>";
   }
 
-  $table_attrs = array(
-    'class' => 'tripal-table tripal-table-horz'
-  );
+  $table_attrs = array('class' => 'tripal-data-table');
   $output = "<p>The following features match the name '$id'.</p>";
   $output .= theme_table($header, $rows, $table_attrs, $caption);
   return $output;

tripal_featuremap/theme/tripal_feature/tripal_feature_featurepos.tpl.php → tripal_featuremap/theme/templates/tripal_feature_featurepos.tpl.php

@@ -117,6 +117,7 @@ if(count($map_positions) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-featurepos',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_base.tpl.php → tripal_featuremap/theme/templates/tripal_featuremap_base.tpl.php

@@ -62,6 +62,7 @@ $table = array(
   'rows' => $rows,
   'attributes' => array(
     'id' => 'tripal_featuremap-table-base',
+    'class' => 'tripal-data-table'
   ),
   'sticky' => FALSE,
   'caption' => '',

tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_featurepos.tpl.php → tripal_featuremap/theme/templates/tripal_featuremap_featurepos.tpl.php

@@ -125,6 +125,7 @@ if(count($feature_positions) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_featuremap-table-featurepos',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_properties.tpl.php → tripal_featuremap/theme/templates/tripal_featuremap_properties.tpl.php

@@ -34,6 +34,7 @@ if(count($properties) > 0){
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_featuremap-table-properties',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_publication.tpl.php → tripal_featuremap/theme/templates/tripal_featuremap_publication.tpl.php

@@ -69,6 +69,7 @@ if (count($featuremap_pubs) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_featuremap-table-publications',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_references.tpl.php → tripal_featuremap/theme/templates/tripal_featuremap_references.tpl.php

@@ -52,6 +52,7 @@ if(count($references) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_featuremap-table-references',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_featuremap/tripal_featuremap.module

@@ -196,49 +196,49 @@ function tripal_featuremap_theme($existing, $type, $theme, $path) {
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
     'tripal_featuremap_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_featuremap_base',
-      'path' => "$path/theme/tripal_featuremap",
+      'path' => "$path/theme/templates",
     ),
     'tripal_featuremap_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_featuremap_properties',
-      'path' => "$path/theme/tripal_featuremap",
+      'path' => "$path/theme/templates",
     ),
     'tripal_featuremap_featurepos' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_featuremap_featurepos',
-      'path' => "$path/theme/tripal_featuremap",
+      'path' => "$path/theme/templates",
     ),
     'tripal_featuremap_publication' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_featuremap_publication',
-      'path' => "$path/theme/tripal_featuremap",
+      'path' => "$path/theme/templates",
     ),
     'tripal_featuremap_references' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_featuremap_references',
-      'path' => "$path/theme/tripal_featuremap",
+      'path' => "$path/theme/templates",
     ),
     'tripal_featuremap_help' => array(
       'template' => 'tripal_featuremap_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
     'tripal_featuremap_teaser' => array(
       'template' => 'tripal_featuremap_teaser',
       'variables' =>  array(NULL),
-      'path' => "$path/theme/tripal_featuremap",
+      'path' => "$path/theme/templates",
     ),
 
     // templates for the chado_feature nodes:
     'tripal_feature_featurepos' => array(
       'arguments' => array('node' => NULL),
       'template' => 'tripal_feature_featurepos',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
   );
   return $items;

tripal_genetic/theme/tripal_feature/tripal_feature_genotypes.tpl.php → tripal_genetic/theme/templates/tripal_feature_genotypes.tpl.php

@@ -128,6 +128,7 @@ if (count($feature_genotypes) > 0) {?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_genetic-table-genotypes',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_genetic/theme/tripal_stock/tripal_stock_genotypes.tpl.php → tripal_genetic/theme/templates/tripal_stock_genotypes.tpl.php

@@ -124,6 +124,7 @@ if (count($stock_genotypes) > 0) {?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_genetic-table-genotypes',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_genetic/tripal_genetic.module

@@ -118,17 +118,17 @@ function tripal_genetic_theme($existing, $type, $theme, $path) {
     'tripal_feature_genotypes' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_genotypes',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_stock_genotypes' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_stock_genotypes',
-      'path' => "$path/theme/tripal_stock",
+      'path' => "$path/theme/templates",
     ),
     'tripal_genetic_help' => array(
       'template' => 'tripal_genetic_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme/",
+      'path' => "$path/theme/templates",
     ),
   );
   return $items;

tripal_library/theme/tripal_feature/tripal_feature_libraries.tpl.php → tripal_library/theme/templates/tripal_feature_libraries.tpl.php

@@ -53,6 +53,7 @@ if (count($library_features) > 0) {?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-libraries',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_library/theme/tripal_library/tripal_library_base.tpl.php → tripal_library/theme/templates/tripal_library_base.tpl.php

@@ -85,6 +85,7 @@ $table = array(
   'rows' => $rows,
   'attributes' => array(
     'id' => 'tripal_library-table-base',
+    'class' => 'tripal-data-table'
   ),
   'sticky' => FALSE,
   'caption' => '',

tripal_library/theme/tripal_library/tripal_library_properties.tpl.php → tripal_library/theme/templates/tripal_library_properties.tpl.php

@@ -45,6 +45,7 @@ if(count($properties) > 0){
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_library-table-properties',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_library/theme/tripal_library/tripal_library_publications.tpl.php → tripal_library/theme/templates/tripal_library_publications.tpl.php

@@ -69,6 +69,7 @@ if (count($library_pubs) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_library-table-publications',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_library/theme/tripal_library/tripal_library_references.tpl.php → tripal_library/theme/templates/tripal_library_references.tpl.php

@@ -53,6 +53,7 @@ if(count($references) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_library-table-references',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_library/theme/tripal_library/tripal_library_synonyms.tpl.php → tripal_library/theme/templates/tripal_library_synonyms.tpl.php

@@ -37,6 +37,7 @@ if(count($synonyms) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_library-table-synonyms',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_library/theme/tripal_library/tripal_library_terms.tpl.php → tripal_library/theme/templates/tripal_library_terms.tpl.php

@@ -55,6 +55,7 @@ if (count($s_terms) > 0) { ?>
       'rows' => $rows,
       'attributes' => array(
         'id' => "tripal_library-table-terms-$i",
+        'class' => 'tripal-data-table'
       ),
       'sticky' => FALSE,
       'caption' => '<b>Vocabulary: ' . ucwords(preg_replace('/_/', ' ', $cv)) . '</b>',

tripal_library/theme/tripal_organism/tripal_organism_libraries.tpl.php → tripal_library/theme/templates/tripal_organism_libraries.tpl.php

@@ -53,6 +53,7 @@ if (count($libraries) > 0) {?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_organism-table-libraries',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_library/tripal_library.module

@@ -161,65 +161,65 @@ function tripal_library_theme($existing, $type, $theme, $path) {
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
 
     // tripal_library templates
     'tripal_library_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library_base',
-      'path' => "$path/theme/tripal_library",
+      'path' => "$path/theme/templates",
     ),
     'tripal_library_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library_properties',
-      'path' => "$path/theme/tripal_library",
+      'path' => "$path/theme/templates",
     ),
     'tripal_library_publications' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library_publications',
-      'path' => "$path/theme/tripal_library",
+      'path' => "$path/theme/templates",
     ),
     'tripal_library_references' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library_references',
-      'path' => "$path/theme/tripal_library",
+      'path' => "$path/theme/templates",
     ),
     'tripal_library_synonyms' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library_synonyms',
-      'path' => "$path/theme/tripal_library",
+      'path' => "$path/theme/templates",
     ),
     'tripal_library_terms' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library_terms',
-      'path' => "$path/theme/tripal_library",
+      'path' => "$path/theme/templates",
     ),
     'tripal_library_help' => array(
       'template' => 'tripal_library_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
 
     // teaser
     'tripal_library_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library_teaser',
-      'path' => "$path/theme/tripal_library",
+      'path' => "$path/theme/templates",
     ),
 
     // tripal_organism templates
     'tripal_organism_libraries' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_libraries',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
 
     // tripal_feature templates
     'tripal_feature_libraries' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_libraries',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
 
   );

tripal_natural_diversity/theme/tripal_feature/tripal_feature_nd_genotypes.tpl.php → tripal_natural_diversity/theme/templates/tripal_feature_nd_genotypes.tpl.php

@@ -182,6 +182,7 @@ if (count($feature_genotypes) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_natural_diversity-table-genotypes',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_natural_diversity/theme/tripal_stock/tripal_stock_nd_genotypes.tpl.php → tripal_natural_diversity/theme/templates/tripal_stock_nd_genotypes.tpl.php

@@ -211,6 +211,7 @@ if (count($genotypes) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_natural_diversity-table-genotypes',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_natural_diversity/theme/tripal_stock/tripal_stock_nd_phenotypes.tpl.php → tripal_natural_diversity/theme/templates/tripal_stock_nd_phenotypes.tpl.php

@@ -168,6 +168,7 @@ if (count($phenotypes) > 0) {?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_natural_diversity-table-phenotypes',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_natural_diversity/tripal_natural_diversity.module

@@ -104,23 +104,23 @@ function tripal_natural_diversity_theme($existing, $type, $theme, $path) {
     'tripal_feature_nd_genotypes' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_nd_genotypes',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     // tripal_stock templates
     'tripal_stock_nd_genotypes' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_stock_nd_genotypes',
-      'path' => "$path/theme/tripal_stock",
+      'path' => "$path/theme/templates",
     ),
     'tripal_stock_nd_phenotypes' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_stock_nd_phenotypes',
-      'path' => "$path/theme/tripal_stock",
+      'path' => "$path/theme/templates",
     ),
     'tripal_natural_diversity_help' => array(
       'template' => 'tripal_natural_diversity_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
   );
   return $items;

tripal_organism/theme/tripal_organism/tripal_organism_properties.tpl.php → tripal_organism/theme/templates/tripal_organism_properties.tpl.php

@@ -35,6 +35,7 @@ if(count($properties) > 0){
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_organism-table-properties',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_organism/theme/tripal_organism/tripal_organism_references.tpl.php → tripal_organism/theme/templates/tripal_organism_references.tpl.php

@@ -66,6 +66,7 @@ if(count($references) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_organism-table-references',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_organism/tripal_organism.module

@@ -163,32 +163,32 @@ function tripal_organism_theme($existing, $type, $theme, $path) {
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
     'tripal_organism_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_base',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
     'tripal_organism_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_properties',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
     'tripal_organism_references' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_references',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
     'tripal_organism_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_teaser',
-      'path' => "$path/theme/tripal_organism",
+      'path' => "$path/theme/templates",
     ),
     'tripal_organism_help' => array(
       'template' => 'tripal_organism_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
   );
   return $items;

tripal_phenotype/theme/tripal_feature/tripal_feature_phenotypes.tpl.php → tripal_phenotype/theme/templates/tripal_feature_phenotypes.tpl.php

@@ -65,6 +65,7 @@ if(count($feature_phenotypes) > 0){ ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_feature-table-phenotypes',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_phenotype/tripal_phenotype.module

@@ -102,12 +102,12 @@ function tripal_phenotype_theme($existing, $type, $theme, $path) {
     'tripal_feature_phenotypes' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature_phenotypes',
-      'path' => "$path/theme/tripal_feature",
+      'path' => "$path/theme/templates",
     ),
     'tripal_phenotype_help' => array(
       'template' => 'tripal_phenotype_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
   );
   return $items;

tripal_project/theme/tripal_project/tripal_project_base.tpl.php → tripal_project/theme/templates/tripal_project_base.tpl.php

@@ -70,6 +70,7 @@ $table = array(
   'rows' => $rows,
   'attributes' => array(
     'id' => 'tripal_project-table-base',
+    'class' => 'tripal-data-table'
   ),
   'sticky' => FALSE,
   'caption' => '',

tripal_project/theme/tripal_project/tripal_project_contact.tpl.php → tripal_project/theme/templates/tripal_project_contact.tpl.php

@@ -64,6 +64,7 @@ if (count($project_contacts) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_pub-table-contacts',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_project/theme/tripal_project/tripal_project_properties.tpl.php → tripal_project/theme/templates/tripal_project_properties.tpl.php

@@ -50,6 +50,7 @@ if (count($properties) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_project-table-properties',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_project/theme/tripal_project/tripal_project_publications.tpl.php → tripal_project/theme/templates/tripal_project_publications.tpl.php

@@ -69,6 +69,7 @@ if (count($project_pubs) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_project-table-publications',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_project/theme/tripal_project/tripal_project_relationships.tpl.php → tripal_project/theme/templates/tripal_project_relationships.tpl.php

@@ -72,6 +72,7 @@ if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
     'rows' => $rows,
     'attributes' => array(
       'id' => 'tripal_project-table-relationship-subject',
+      'class' => 'tripal-data-table'
     ),
     'sticky' => FALSE,
     'caption' => '',

tripal_project/tripal_project.module

@@ -166,42 +166,42 @@ function tripal_project_theme($existing, $type, $theme, $path) {
       'template' => 'node--chado-generic',
       'render element' => 'node',
       'base hook' => 'node',
-      'path' => "$core_path/theme",
+      'path' => "$core_path/theme/templates",
     ),
     'tripal_project_base' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_project_base',
-      'path' => "$path/theme/tripal_project",
+      'path' => "$path/theme/templates",
     ),
     'tripal_project_contact' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_project_contact',
-      'path' => "$path/theme/tripal_project",
+      'path' => "$path/theme/templates",
     ),
     'tripal_project_properties' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_project_properties',
-      'path' => "$path/theme/tripal_project",
+      'path' => "$path/theme/templates",
     ),
     'tripal_project_publications' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_project_publications',
-      'path' => "$path/theme/tripal_project",
+      'path' => "$path/theme/templates",
     ),
     'tripal_project_relationships' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_project_relationships',
-      'path' => "$path/theme/tripal_project",
+      'path' => "$path/theme/templates",
     ),
     'tripal_project_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_project_teaser',
-      'path' => "$path/theme/tripal_project",
+      'path' => "$path/theme/templates",
     ),
     'tripal_project_help' => array(
       'variables' => 'tripal_project_help',
       'variables' =>  array(NULL),
-      'path' => "$path/theme",
+      'path' => "$path/theme/templates",
     ),
   );
   return $items;

tripal_pub/includes/tripal_pub.pub_importers.inc

@@ -171,6 +171,7 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
         'rows' => $rows,
         'attributes' => array(
           'id' => 'tripal_pub-importer-test',
+          'class' => 'tripal-data-table'
         ),
         'sticky' => FALSE,
         'caption' => '',
@@ -775,7 +776,7 @@ function theme_tripal_pub_importer_setup_form_elements($variables) {
   $table = array(
     'header' => $headers,
     'rows' => $rows,
-    'attributes' => array(),
+    'attributes' => array('class' => 'tripal-data-table'),
     'sticky' => TRUE,
     'caption' => '',
     'colgroups' => array(),