removed some .orig files remaining from a merge

tripal_library/tripal_library.views.inc.orig

@@ -1,425 +0,0 @@
-<?php
-
-/**
- *  @file
- *  This file contains the basic functions for views integration of
- *  chado/tripal organism tables. Supplementary functions can be found in
- *  ./views/
- *
- *  Documentation on views integration can be found at
- *  http://views2.logrus.com/doc/html/index.html.
- */
-
-/**
- * @defgroup tripal_library_views Library Views Integration
- * @ingroup views
- * @ingroup tripal_library
- */
-
-<<<<<<< HEAD
-=======
-require_once('views/library.views.inc');
-require_once('views/chado_library.views.inc');
-require_once('views/misc_tables.views.inc');
->>>>>>> 6.x-0.4-dev
-/*************************************************************************
- * Implements hook_views_data()
- * Purpose: Describe chado/tripal tables & fields to views
- * @return: a data array which follows the structure outlined in the
- *   views2 documentation for this hook. Essentially, it's an array of table
- *   definitions keyed by chado/tripal table name. Each table definition
- *   includes basic details about the table, fields in that table and
- *   relationships between that table and others (joins)
- *
- * @ingroup tripal_library_views
- */
-function tripal_library_views_data()  {
-  $data = array();
-
-<<<<<<< HEAD
-  if (module_exists('tripal_views')) {
-    $tables = array(
-      'library'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,TRUE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-
-    $tables = array(
-      'library_cvterm',
-      'library_feature',
-      'library_pub',
-      'library_synonym',
-      'libraryprop'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,FALSE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-  }
-=======
-  $data = array_merge($data, retrieve_library_views_data());
-  $data = array_merge($data, retrieve_chado_library_views_data());
-  $data = array_merge($data, retrieve_library_misc_tables_views_data());
->>>>>>> 6.x-0.4-dev
-
-  return $data;
-}
-
-/*************************************************************************
- * Implements hook_views_handlers()
- * Purpose: Register all custom handlers with views
- *   where a handler describes either "the type of field",
- *   "how a field should be filtered", "how a field should be sorted"
- * @return: An array of handler definitions
- *
- * @ingroup tripal_library_views
- */
-function tripal_library_views_handlers() {
- return array(
-   'info' => array(
-     'path' => drupal_get_path('module', 'tripal_library') . '/views/handlers',
-   ),
-   'handlers' => array(
-     'views_handler_field_computed_library_nid' => array(
-       'parent' => 'views_handler_field_numeric',
-     ),
-   ),
- );
-}
-
-/**
- * Implementation of hook_views_data_alter().
- */
-function tripal_library_views_data_alter(&$data) {
-
-  if ( !(is_array($db_url) and array_key_exists('chado', $db_url)) ) {
-
-    // Add featuer relationship to node
-    $data['node']['library_chado_nid'] = array(
-      'group' => 'Library',
-      'title' => 'Library Node',
-      'help' => 'Links Chado Library Fields/Data to the Nodes in the current View.',
-      'real field' => 'nid',
-      'relationship' => array(
-        'handler' => 'views_handler_relationship',
-        'title' => t('Node => Chado'),
-        'label' => t('Node => Chado'),
-        'real field' => 'nid',
-        'base' => 'chado_library',
-        'base field' => 'nid'
-      ),
-    );
-  }
-
-}
-
-/**
- *
- *
- * @ingroup tripal_library_views
- */
-function tripal_library_views_default_views() {
-  $views = array();
-
-  // Main default view
-  // List all cvterms based on cv
-  $view = new view;
-  $view->name = 'all_libraries';
-  $view->description = 'A listing of all libraries';
-  $view->tag = 'chado';
-  $view->view_php = '';
-  $view->base_table = 'library';
-  $view->is_cacheable = FALSE;
-  $view->api_version = 2;
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    'uniquename' => array(
-      'label' => 'Unique Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'uniquename',
-      'table' => 'library',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-    ),
-    'name_1' => array(
-      'label' => 'Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'name_1',
-      'table' => 'library',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'common_name' => array(
-      'label' => 'Organism',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-    'name' => array(
-      'label' => 'Type',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'name',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'is_obsolete' => array(
-      'label' => 'Is Obsolete?',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'type' => 'yes-no',
-      'not' => 0,
-      'exclude' => 0,
-      'id' => 'is_obsolete',
-      'table' => 'library',
-      'field' => 'is_obsolete',
-      'relationship' => 'none',
-    ),
-    'num_features' => array(
-      'label' => 'Number of Features',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'num_features',
-      'table' => 'library',
-      'field' => 'num_features',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'common_name' => array(
-      'operator' => '=',
-      'value' => 'All',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'common_name_op',
-        'identifier' => 'organism_common_name',
-        'label' => 'Organism',
-        'optional' => 1,
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_library content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Libraries');
-  $handler->override_option('empty', 'There are no libraries matching the current criteria. If you think there should be, check that all chado libraries are sync\'d with your website.');
-  $handler->override_option('empty_format', '1');
-  $handler->override_option('use_pager', '1');
-  $handler->override_option('style_plugin', 'table');
-  $handler->override_option('style_options', array(
-    'grouping' => '',
-    'override' => 1,
-    'sticky' => 0,
-    'order' => 'asc',
-    'columns' => array(
-      'name' => 'name',
-      'timeaccessioned' => 'timeaccessioned',
-      'timelastmodified' => 'timelastmodified',
-      'is_obsolete' => 'is_obsolete',
-      'name_1' => 'name_1',
-      'uniquename' => 'uniquename',
-      'common_name' => 'common_name',
-      'num_libraries' => 'num_libraries',
-    ),
-    'info' => array(
-      'name' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'timeaccessioned' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'timelastmodified' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'is_obsolete' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'name_1' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'uniquename' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'common_name' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'num_libraries' => array(
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'libraries');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Sequence Libraries',
-    'description' => '',
-    'weight' => '0',
-    'name' => 'primary-links',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_natural_diversity/tripal_natural_diversity.views.inc.orig

@@ -1,105 +0,0 @@
-<?php
-
-/**
- *  @file
- *  This file contains the basic functions for views integration of
- *  chado/tripal_natural_diversity tables. Supplementary functions can be found in
- *  ./views/
- *
- *  Documentation on views integration can be found at
- *  http://views2.logrus.com/doc/html/index.html.
- */
-
-/*************************************************************************
- * Implements hook_views_data()
- * Purpose: Describe chado/tripal tables & fields to views
- *
- * @return: a data array which follows the structure outlined in the
- *   views2 documentation for this hook. Essentially, it's an array of table
- *   definitions keyed by chado/tripal table name. Each table definition
- *   includes basic details about the table, fields in that table and
- *   relationships between that table and others (joins)
- */
-function tripal_natural_diversity_views_data()  {
-  $data = array();
-
-<<<<<<< HEAD
-  if (module_exists('tripal_views')) {
-    $tables = array(
-      'nd_experiment',
-      'nd_geolocation',
-      'nd_protocol',
-      'nd_reagent'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,TRUE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-
-    $tables = array(
-      'nd_experiment_contact',
-      'nd_experiment_dbxref',
-      'nd_experiment_genotype',
-      'nd_experiment_phenotype',
-      'nd_experiment_project',
-      'nd_experiment_protocol',
-      'nd_experiment_pub',
-      'nd_experiment_stock',
-      'nd_experiment_stock_dbxref',
-      'nd_experiment_stockprop',
-      'nd_experimentprop',
-      'nd_geolocationprop',
-      'nd_protocol_reagent',
-      'nd_protocolprop',
-      'nd_reagent_relationship',
-      'nd_reagentprop'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,FALSE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-  }
-=======
-  //EXPERIMENT
-  $data = array_merge($data, retrieve_nd_experiment_views_data());
-  $data = array_merge($data, retrieve_nd_experimentprop_views_data());
-
-  // GEOLOCATION
-  $data = array_merge($data, retrieve_nd_geolocation_views_data());
-  $data = array_merge($data, retrieve_nd_geolocationprop_views_data());
-
-  // REAGENTS
-  $data = array_merge($data, retrieve_nd_reagent_views_data());
-  $data = array_merge($data, retrieve_nd_reagentprop_views_data());
->>>>>>> 6.x-0.4-dev
-
-  return $data;
-}
-
-/*************************************************************************
- * Implements hook_views_handlers()
- * Purpose: Register all custom handlers with views
- *   where a handler describes either "the type of field",
- *   "how a field should be filtered", "how a field should be sorted"
- *
- * @return: An array of handler definitions
- */
-function tripal_natural_diversity_views_handlers() {
- return array(
-   'info' => array(
-     'path' => drupal_get_path('module', 'tripal_natural_diversity') . '/views/handlers',
-   ),
-   'handlers' => array(
-  'views_handler_field_chado_relationship_all' => array(
-       'parent' => 'views_handler_field_prerender_list',
-     ),
-  'views_handler_field_chado_relationship_by_type' => array(
-       'parent' => 'views_handler_field_prerender_list',
-     ),
-   ),
- );
-}

tripal_organism/tripal_organism.views.inc.orig

@@ -1,410 +0,0 @@
-<?php
-
-/**
- *  @file
- *  This file contains the basic functions for views integration of
- *  chado/tripal organism tables. Supplementary functions can be found in
- *  ./views/
- *
- *  Documentation on views integration can be found at
- *  http://views2.logrus.com/doc/html/index.html.
- */
-
-/**
- * @defgroup tripal_organism_views Organism Views Integration
- * @ingroup views
- * @ingroup tripal_organism
- */
-
-<<<<<<< HEAD
-=======
-require_once('views/organism.views.inc');
-require_once('views/chado_organism.views.inc');
->>>>>>> 6.x-0.4-dev
-/**
- * Implements hook_views_data()
- * Purpose: Describe chado/tripal tables & fields to views
- * @return: a data array which follows the structure outlined in the
- *   views2 documentation for this hook. Essentially, it's an array of table
- *   definitions keyed by chado/tripal table name. Each table definition
- *   includes basic details about the table, fields in that table and
- *   relationships between that table and others (joins)
- *
- * @ingroup tripal_organism_views
- */
-function tripal_organism_views_data()  {
-  $data = array();
-
-<<<<<<< HEAD
-  if (module_exists('tripal_views')) {
-    // Base Table
-    $tables = array(
-      'organism'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,TRUE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-
-    // Additional Tables
-    $tables = array(
-      'organismprop',
-      'organism_dbxref'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,FALSE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-  }
-=======
-  $data = array_merge($data, retrieve_organism_views_data());
-  $data = array_merge($data, retrieve_chado_organism_views_data());
->>>>>>> 6.x-0.4-dev
-
-  return $data;
-}
-
-/**
- * Implements hook_views_handlers()
- * Purpose: Register all custom handlers with views
- *   where a handler describes either "the type of field",
- *   "how a field should be filtered", "how a field should be sorted"
- * @return: An array of handler definitions
- *
- * @ingroup tripal_organism_views
- */
-function tripal_organism_views_handlers() {
- return array(
-   'info' => array(
-     'path' => drupal_get_path('module', 'tripal_organism') . '/views/handlers',
-   ),
-   'handlers' => array(
-     'views_handler_field_computed_organism_nid' => array(
-       'parent' => 'views_handler_field_numeric',
-     ),
-     'views_handler_filter_organism_common_name' => array(
-      'parent' => 'views_handler_filter_string',
-     ),
-   ),
- );
-}
-
-/**
- * Implementation of hook_views_data_alter().
- */
-function tripal_organism_views_data_alter(&$data) {
-
-  if ( !(is_array($db_url) and array_key_exists('chado', $db_url)) ) {
-
-    // Add featuer relationship to node
-    $data['node']['organism_chado_nid'] = array(
-      'group' => 'Organism',
-      'title' => 'Organism Node',
-      'help' => 'Links Chado Organism Fields/Data to the Nodes in the current View.',
-      'real field' => 'nid',
-      'relationship' => array(
-        'handler' => 'views_handler_relationship',
-        'title' => t('Node => Chado'),
-        'label' => t('Node => Chado'),
-        'real field' => 'nid',
-        'base' => 'chado_organism',
-        'base field' => 'nid'
-      ),
-    );
-  }
-
-}
-
-/**
- *
- * @ingroup tripal_organism_views
- */
-function tripal_organism_views_default_views() {
-  $views = array();
-
-  // Main default view
-  // List all cvterms based on cv
-  $view = new view;
-  $view->name = 'all_organisms';
-  $view->description = 'A listing of all organism in chado';
-  $view->tag = 'chado';
-  $view->view_php = '';
-  $view->base_table = 'organism';
-  $view->is_cacheable = FALSE;
-  $view->api_version = 2;
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    'common_name' => array(
-      'label' => 'Common Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-    'abbreviation' => array(
-      'label' => 'Abbreviation',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 0,
-      'exclude' => 0,
-      'id' => 'abbreviation',
-      'table' => 'organism',
-      'field' => 'abbreviation',
-      'relationship' => 'none',
-    ),
-    'genus' => array(
-      'label' => 'Genus',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'genus',
-      'table' => 'organism',
-      'field' => 'genus',
-      'relationship' => 'none',
-    ),
-    'species' => array(
-      'label' => 'Species',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'species',
-      'table' => 'organism',
-      'field' => 'species',
-      'relationship' => 'none',
-    ),
-    'num_features' => array(
-      'label' => 'Number of Features',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'num_features',
-      'table' => 'organism',
-      'field' => 'num_features',
-      'relationship' => 'none',
-    ),
-    'num_stocks' => array(
-      'label' => 'Number of Stocks',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'num_stocks',
-      'table' => 'organism',
-      'field' => 'num_stocks',
-      'relationship' => 'none',
-    ),
-    'num_libraries' => array(
-      'label' => 'Number of Libraries',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'num_libraries',
-      'table' => 'organism',
-      'field' => 'num_libraries',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_organism content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Organisms');
-  $handler->override_option('empty', 'No organism currently in your chado database.');
-  $handler->override_option('empty_format', '1');
-  $handler->override_option('items_per_page', 0);
-  $handler->override_option('style_plugin', 'table');
-  $handler->override_option('style_options', array(
-    'grouping' => '',
-    'override' => 1,
-    'sticky' => 0,
-    'order' => 'asc',
-    'columns' => array(
-      'abbreviation' => 'abbreviation',
-      'common_name' => 'common_name',
-      'genus' => 'genus',
-      'species' => 'species',
-    ),
-    'info' => array(
-      'abbreviation' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'common_name' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'genus' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'species' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'organisms');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Organisms',
-    'description' => '',
-    'weight' => '0',
-    'name' => 'primary-links',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  $views[$view->name] = $view;
-
-  return $views;
-}