Added views integration templates and instructions to all tripal modules

tripal_analysis/views/README

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+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_analysis_views_data() in ../tripal_analysis.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_analysis.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_analysis.views.inc:tripal_analysis_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_analysis/views/template.node_join.views.inc

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

tripal_analysis/views/template.table_defn.views.inc

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+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_analysis.views.inc in 
+ *        tripal_analysis_views_data() by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_analysis.views.inc --in tripal_analysis_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_analysis_views_data() --in tripal_analysis.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_contact/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_contact_views_data() in ../tripal_contact.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_contact.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_contact.views.inc:tripal_contact_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_contact/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_contact.views.inc:tripal_contact_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_contact.views.inc --in tripal_contact_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_contact_views_data() --in tripal_contact.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_contact/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_contact.views.inc:tripal_contact_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_contact.views.inc --in tripal_contact_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_contact_views_data() --in tripal_contact.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_core/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_core_views_data() in ../tripal_core.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_core.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_core.views.inc:tripal_core_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_core/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_core.views.inc:tripal_core_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_core.views.inc --in tripal_core_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_core_views_data() --in tripal_core.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_core/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_core.views.inc:tripal_core_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_core.views.inc --in tripal_core_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_core_views_data() --in tripal_core.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_cv/views/README

@@ -1,22 +1,45 @@
-This folder contains all supplementary code needed for views integration
-of the chado cvterm and related tables.
 
-File Descriptions:
-========================================================================
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
 <chado table name>.views.inc:
 	contains a single function retrieve_<chado table name>_views_data()
 	which describes that table to views. This function is called by
-	<tripal module>_views_data() in ../<tripal module>.views.inc.
+	tripal_cv_views_data() in ../tripal_cv.views.inc.
 	For more information on the form of this data array look up the
 	views2 documentation for hook_views_data() 
 	-http://views2.logrus.com/doc/html/index.html
 	
 handlers/
-	A folder which contains symbolic links to tripal_core/views_handlers/ files.
 	Each file contained within this folder defines a views handler. Only custom
 	handlers are included in this folder and each must be described in 
-	hook_views_handlers() in ../<tripal module>.views.inc.
+	hook_views_handlers() in ../tripal_cv.views.inc.
 	A views handler does one of the following:
 		1) describe the type of a field and how it should be displayed
 		2) describe a method to sort this field
-		3) describe a method to filter this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_cv.views.inc:tripal_cv_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_cv/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_cv.views.inc:tripal_cv_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_cv.views.inc --in tripal_cv_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_cv_views_data() --in tripal_cv.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_cv/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_cv.views.inc:tripal_cv_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_cv.views.inc --in tripal_cv_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_cv_views_data() --in tripal_cv.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_db/views/README

@@ -1,22 +1,45 @@
-This folder contains all supplementary code needed for views integration
-of the chado dbxref and related tables.
 
-File Descriptions:
-========================================================================
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
 <chado table name>.views.inc:
 	contains a single function retrieve_<chado table name>_views_data()
 	which describes that table to views. This function is called by
-	<tripal module>_views_data() in ../<tripal module>.views.inc.
+	tripal_db_views_data() in ../tripal_db.views.inc.
 	For more information on the form of this data array look up the
 	views2 documentation for hook_views_data() 
 	-http://views2.logrus.com/doc/html/index.html
 	
 handlers/
-	A folder which contains symbolic links to tripal_core/views_handlers/ files.
 	Each file contained within this folder defines a views handler. Only custom
 	handlers are included in this folder and each must be described in 
-	hook_views_handlers() in ../<tripal module>.views.inc.
+	hook_views_handlers() in ../tripal_db.views.inc.
 	A views handler does one of the following:
 		1) describe the type of a field and how it should be displayed
 		2) describe a method to sort this field
-		3) describe a method to filter this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_db.views.inc:tripal_db_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_db/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_db.views.inc:tripal_db_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_db.views.inc --in tripal_db_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_db_views_data() --in tripal_db.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_db/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_db.views.inc:tripal_db_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_db.views.inc --in tripal_db_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_db_views_data() --in tripal_db.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_feature/views/README

@@ -1,22 +1,45 @@
-This folder contains all supplementary code needed for views integration
-of the chado feature and related tables.
 
-File Descriptions:
-========================================================================
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
 <chado table name>.views.inc:
 	contains a single function retrieve_<chado table name>_views_data()
 	which describes that table to views. This function is called by
-	<tripal module>_views_data() in ../<tripal module>.views.inc.
+	tripal_feature_views_data() in ../tripal_feature.views.inc.
 	For more information on the form of this data array look up the
 	views2 documentation for hook_views_data() 
 	-http://views2.logrus.com/doc/html/index.html
 	
 handlers/
-	A folder which contains symbolic links to tripal_core/views_handlers/ files.
 	Each file contained within this folder defines a views handler. Only custom
 	handlers are included in this folder and each must be described in 
-	hook_views_handlers() in ../<tripal module>.views.inc.
+	hook_views_handlers() in ../tripal_feature.views.inc.
 	A views handler does one of the following:
 		1) describe the type of a field and how it should be displayed
 		2) describe a method to sort this field
-		3) describe a method to filter this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_feature.views.inc:tripal_feature_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_feature/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_feature.views.inc:tripal_feature_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_feature.views.inc --in tripal_feature_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_feature_views_data() --in tripal_feature.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_feature/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_feature.views.inc:tripal_feature_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_feature.views.inc --in tripal_feature_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_feature_views_data() --in tripal_feature.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_genetic/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_genetic_views_data() in ../tripal_genetic.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_genetic.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_genetic.views.inc:tripal_genetic_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_genetic/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_genetic.views.inc:tripal_genetic_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_genetic.views.inc --in tripal_genetic_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_genetic_views_data() --in tripal_genetic.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_genetic/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_genetic.views.inc:tripal_genetic_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_genetic.views.inc --in tripal_genetic_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_genetic_views_data() --in tripal_genetic.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_library/views/README

@@ -1,22 +1,45 @@
-This folder contains all supplementary code needed for views integration
-of the chado library and related tables.
 
-File Descriptions:
-========================================================================
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
 <chado table name>.views.inc:
 	contains a single function retrieve_<chado table name>_views_data()
 	which describes that table to views. This function is called by
-	<tripal module>_views_data() in ../<tripal module>.views.inc.
+	tripal_library_views_data() in ../tripal_library.views.inc.
 	For more information on the form of this data array look up the
 	views2 documentation for hook_views_data() 
 	-http://views2.logrus.com/doc/html/index.html
 	
 handlers/
-	A folder which contains symbolic links to tripal_core/views_handlers/ files.
 	Each file contained within this folder defines a views handler. Only custom
 	handlers are included in this folder and each must be described in 
-	hook_views_handlers() in ../<tripal module>.views.inc.
+	hook_views_handlers() in ../tripal_library.views.inc.
 	A views handler does one of the following:
 		1) describe the type of a field and how it should be displayed
 		2) describe a method to sort this field
-		3) describe a method to filter this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_library.views.inc:tripal_library_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_library/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_library.views.inc:tripal_library_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_library.views.inc --in tripal_library_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_library_views_data() --in tripal_library.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_library/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_library.views.inc:tripal_library_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_library.views.inc --in tripal_library_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_library_views_data() --in tripal_library.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_natural_diversity/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_natural_diversity_views_data() in ../tripal_natural_diversity.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_natural_diversity.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_natural_diversity.views.inc:tripal_natural_diversity_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_natural_diversity/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_natural_diversity.views.inc:tripal_natural_diversity_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_natural_diversity.views.inc --in tripal_natural_diversity_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_natural_diversity_views_data() --in tripal_natural_diversity.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_natural_diversity/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_natural_diversity.views.inc:tripal_natural_diversity_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_natural_diversity.views.inc --in tripal_natural_diversity_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_natural_diversity_views_data() --in tripal_natural_diversity.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_organism/views/README

@@ -1,22 +1,45 @@
-This folder contains all supplementary code needed for views integration
-of the chado organism and related tables.
 
-File Descriptions:
-========================================================================
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
 <chado table name>.views.inc:
 	contains a single function retrieve_<chado table name>_views_data()
 	which describes that table to views. This function is called by
-	<tripal module>_views_data() in ../<tripal module>.views.inc.
+	tripal_organism_views_data() in ../tripal_organism.views.inc.
 	For more information on the form of this data array look up the
 	views2 documentation for hook_views_data() 
 	-http://views2.logrus.com/doc/html/index.html
 	
 handlers/
-	A folder which contains symbolic links to tripal_core/views_handlers/ files.
 	Each file contained within this folder defines a views handler. Only custom
 	handlers are included in this folder and each must be described in 
-	hook_views_handlers() in ../<tripal module>.views.inc.
+	hook_views_handlers() in ../tripal_organism.views.inc.
 	A views handler does one of the following:
 		1) describe the type of a field and how it should be displayed
 		2) describe a method to sort this field
-		3) describe a method to filter this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_organism.views.inc:tripal_organism_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_organism/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_organism.views.inc:tripal_organism_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_organism.views.inc --in tripal_organism_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_organism_views_data() --in tripal_organism.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_organism/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_organism.views.inc:tripal_organism_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_organism.views.inc --in tripal_organism_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_organism_views_data() --in tripal_organism.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_phenotype/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_phenotype_views_data() in ../tripal_phenotype.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_phenotype.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_phenotype.views.inc:tripal_phenotype_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_phenotype/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_phenotype.views.inc:tripal_phenotype_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_phenotype.views.inc --in tripal_phenotype_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_phenotype_views_data() --in tripal_phenotype.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_phenotype/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_phenotype.views.inc:tripal_phenotype_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_phenotype.views.inc --in tripal_phenotype_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_phenotype_views_data() --in tripal_phenotype.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_project/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_project_views_data() in ../tripal_project.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_project.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_project.views.inc:tripal_project_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_project/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_project.views.inc:tripal_project_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_project.views.inc --in tripal_project_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_project_views_data() --in tripal_project.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_project/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_project.views.inc:tripal_project_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_project.views.inc --in tripal_project_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_project_views_data() --in tripal_project.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_pub/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_pub_views_data() in ../tripal_pub.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_pub.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_pub.views.inc:tripal_pub_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_pub/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_pub.views.inc:tripal_pub_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_pub.views.inc --in tripal_pub_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_pub_views_data() --in tripal_pub.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_pub/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_pub.views.inc:tripal_pub_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_pub.views.inc --in tripal_pub_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_pub_views_data() --in tripal_pub.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}

tripal_stock/views/README

@@ -0,0 +1,45 @@
+
+This directory contains all additional views code needed to integrate this module with views2.
+
+FILE/FOLDER DESCRIPTIONS
+---------------------------
+<chado table name>.views.inc:
+	contains a single function retrieve_<chado table name>_views_data()
+	which describes that table to views. This function is called by
+	tripal_stock_views_data() in ../tripal_stock.views.inc.
+	For more information on the form of this data array look up the
+	views2 documentation for hook_views_data() 
+	-http://views2.logrus.com/doc/html/index.html
+	
+handlers/
+	Each file contained within this folder defines a views handler. Only custom
+	handlers are included in this folder and each must be described in 
+	hook_views_handlers() in ../tripal_stock.views.inc.
+	A views handler does one of the following:
+		1) describe the type of a field and how it should be displayed
+		2) describe a method to sort this field
+		3) describe a method to filter this field
+
+
+STANDARDS TO FOLLOW
+---------------------------
+
+1. All table definition files should be named tablename.views.inc
+2. All handlers should be in a handlers sub-directory and follow the naming convention of
+   views handlers (ie: views_handler_field/filter/sort_handlername.inc )
+
+Views Table Definitions:
+- Please use the template files provided whenever you are describing a new table to views.
+   For any table in chado simply copy template.table_defn.views.inc to tablename.views.inc and 
+   follow the instructions listed at the top of the template file.
+- ONLY ONE TABLE DEFINITION PER FILE
+- To join a chado table to it's drupal node simply copy template.node_join.views.inc to 
+   basetablename.views.inc and replace all XXX with basetablename.
+   
+   NOTE: Creating the table definition file is not enough. You also need to call the 
+         retrieve_XXX_views_data() function from ../tripal_stock.views.inc:tripal_stock_views_data()
+         by adding the following line:
+            $data = array_merge($data, retrieve_XXX_views_data());
+         to the function and including the file directly above the function (blow the function 
+         header by adding:
+            require_once('views/XXX.views.inc');

tripal_stock/views/template.node_join.views.inc

@@ -0,0 +1,84 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *  - simply replace all XXX with the original chado table you want to join to it's drupal nodes.
+ *    (ie: If you want to join features to their drupal nodes then XXX=feature)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_stock.views.inc:tripal_stock_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_stock.views.inc --in tripal_stock_views_data()
+ *
+ *  Note: All chado tables are joined to their drupal nodes through the chado_XXX linking table. 
+ *        This file simply defines this linking table and joins the three tables together.
+ *        No modification of XXX.views.inc is needed.
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the chado_XXX drupal table, it's fields and any joins between it 
+ *   and other tables
+ * @see tripal_stock_views_data() --in tripal_stock.views.inc
+ *
+ * The main need for description of this table to views is to join chado data with drupal nodes
+ *
+ */
+function retrieve_chado_XXX_views_data () {
+	global $db_url;
+  $data = array();
+  
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  //Basic table definition-----------------------------------
+  $data['chado_XXX']['table'] = array(
+    'field' => 'nid',
+  );
+  
+  //Relationship Definitions---------------------------------
+  // Note: No joins need to be made from $data['XXX']['table']
+  
+  // Join the chado_XXX table to XXX
+  $data['chado_XXX']['table']['join']['XXX'] = array(
+  	'left_field' => 'XXX_id',
+  	'field' => 'XXX_id',
+  );
+  
+  // Join the node table to chado_XXX
+  $data['node']['table']['join']['chado_XXX'] = array(
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );
+  
+  // Join the node table to XXX
+  $data['node']['table']['join']['XXX'] = array(
+  	'left_table' => 'chado_XXX',
+  	'left_field' => 'nid',
+  	'field' => 'nid',
+  );  
+
+	return $data;
+}

tripal_stock/views/template.table_defn.views.inc

@@ -0,0 +1,205 @@
+<?php
+
+/*************************************************************************
+ * @file: THIS IS A TEMPLATE AND SHOULD NOT BE INCLUDED IN THE MODULE CODE
+ *
+ *   - Every instance of XXX should be replaced with the name of your table
+ *   - If this is a base table (you want a view where every row is a row from this table)
+ *     then change $data['XXX']['table'] to $data['XXX']['table']['base'] 
+ *     and $data['XXX']['table']['database'] to $data['XXX']['table']['base']['database']
+ *   - Relationships between this table and others: YYY is the table you are trying to join to this
+ *     one. You want to join a table to this one if this table contains a foreign key to the other
+ *     table. If the join between this table and another is through a linking table
+ *     (ie: library-XXX/YYY => library_feature-XY => feature-XXX/YYY) then make the join in both
+ *     directions (ie: in the file XXX.views.inc and the file YYY.views.inc
+ *   - Create a field definition for each field in this table using the example fields already
+ *     listed. Match the type of the database field to the field definition listed below.
+ *     (ie: for a text/varchar field from the database use plain_text_field below)
+ * 
+ *  NOTE: Creating the table definition file is not enough. You also need to call the 
+ *        retrieve_XXX_views_data() function from ../tripal_stock.views.inc:tripal_stock_views_data()
+ *        by adding the following line:
+ *           $data = array_merge($data, retrieve_XXX_views_data());
+ *        to the function and including the file directly above the function (blow the function 
+ *        header by adding:
+ *           require_once('views/XXX.views.inc');
+ *
+ *  REMOVE THIS COMMENT IN THE COPY!
+ */ 
+ 
+/**
+ *  @file
+ *  This file defines the data array for a given chado table. This array
+ *  is merged into a larger array containing definitions of all tables associated
+ *  with this module in:
+ *  @see tripal_stock.views.inc --in tripal_stock_views_data()
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+
+/*************************************************************************
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the XXX table, it's fields and any joins between it and other tables
+ * @see tripal_stock_views_data() --in tripal_stock.views.inc
+ *
+ * Table: XXX
+ * @code
+ * XXX-Copy/Paste Table SQL code here-XXX
+ * @endcode
+ */
+ function retrieve_XXX_views_data() {
+  global $db_url;
+  $data = array();
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+    $database = 'chado';
+  }
+   
+  //Basic table definition-----------------------------------
+  $data['XXX']['table']['group'] = t('Chado XXX');
+  
+  $data['XXX']['table'] = array(
+    'field' => 'primary_id',
+    'title' => t('Chado XXX'),
+    'help' => t('Enter some user-friendly description of this tables purpose to the user.'),
+  );
+  if($database){
+     $data['XXX']['table']['database'] = $database;
+  }
+
+  
+  //Relationship Definitions---------------------------------
+  //Join: XXX => YYY
+  $data['XXX']['table']['join']['YYY'] = array(
+    'left_field' => 'primary key in YYY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  
+  //Join: XXX => XY => YYY
+  $data['XXX']['table']['join']['XY'] = array(
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );  
+  $data['XXX']['table']['join']['YYY'] => array(
+    'left_table' => 'XY',
+    'left_field' => 'matching XXX key in the XY table',
+    'field' => 'foreign key in XXX table',
+  );
+  $data['XY']['table']['join']['YYY'] = array(
+    'left_field' => 'foreign key in YYY table',
+    'field' => 'matching YYY key in the XY table',
+  );
+   
+  //Table Field Definitions----------------------------------
+      
+  //Field: XXX_id (primary key)
+  $data['XXX']['field_name'] = array(
+    'title' => t('XXX Primary Key'),
+    'help' => t('A unique index for every XXX.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  /*.......................................................
+   * Beginning of Example Field definitions
+   * Remove this section when done
+   */
+
+  //Field: plain_text_field (chado datatype)   
+  $data['XXX']['plain_text_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: numeric_field (chado datatype)   
+  $data['XXX']['numeric_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_numeric',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_numeric',
+    ),
+  );
+
+  //Field: boolean_field (chado datatype)   
+  $data['XXX']['boolean_field'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_boolean',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_boolean_operator',
+    ),
+  );
+
+  //Field: unix_timestamp (chado datatype)   
+  $data['XXX']['unix_timestamp'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_date',
+    ),
+  );
+
+  //Field: human_readable_date (chado datatype)   
+  $data['XXX']['human_readable_date'] = array(
+    'title' => t('Human-Readable Name'),
+    'help' => t('Description of this field.'),
+    'field' => array(
+      'handler' => 'views_handler_field_readble_date',
+      'click sortable' => TRUE,
+     ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+   
+   /*
+    * End of Example Field definitions
+    *......................................................./
+    
+  return $data;
+}