Added Tripal Views to Tripal v3 (non legacy) and renamed Tripal Chado Views. Fixed several bugs, removed unneeded files

legacy/tripal_analysis/tripal_analysis.info

@@ -7,6 +7,6 @@ version = 7.x-3.0-alpha1
 configure = admin/tripal/legacy/tripal_analysis/configuration
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_db
 dependencies[] = tripal_cv

legacy/tripal_contact/tripal_contact.info

@@ -6,5 +6,5 @@ package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_cv

legacy/tripal_cv/tripal_cv.info

@@ -7,5 +7,5 @@ version = 7.x-3.0-alpha1
 configure = admin/tripal/vocab
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_db

legacy/tripal_db/tripal_db.info

@@ -7,4 +7,4 @@ version = 7.x-3.0-alpha1
 configure = admin/tripal/legacy/tripal_db
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views

legacy/tripal_db/tripal_db.module

@@ -7,8 +7,6 @@
 //require_once 'api/tripal_db.api.inc';
 require_once 'api/tripal_db.DEPRECATED.inc';
 
-require_once 'includes/tripal_db.admin.inc';
-
 /**
  * @defgroup tripal_db Database Reference Module
  * @ingroup tripal_modules
@@ -29,45 +27,6 @@ require_once 'includes/tripal_db.admin.inc';
 function tripal_db_menu() {
   $items = array();
 
-
-  $items['admin/tripal/legacy/tripal_db'] = array(
-    'title' => 'Databases',
-    'description' => 'References to External Database sites such as NCBI',
-    'page callback' => 'tripal_db_admin_db_listing',
-    'access arguments' => array('administer db cross-references'),
-    'type' => MENU_NORMAL_ITEM,
-  );
-
-  $items['admin/tripal/legacy/tripal_db/help'] = array(
-    'title' => 'Help',
-    'description' => "A description of the Tripal Database module including a short description of it's usage.",
-    'page callback' => 'theme',
-    'page arguments' => array('tripal_db_admin'),
-    'access arguments' => array('administer db cross-references'),
-    'type' => MENU_LOCAL_TASK,
-    'weight' => 10
-  );
-
-  $items['admin/tripal/legacy/tripal_db/edit/%'] = array(
-    'title' => 'Edit a Database Reference',
-    'description' => 'Edit existing Database References.',
-    'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_db_db_edit_form',5),
-    'access callback' => 'user_access',
-    'access arguments' => array('administer db cross-references'),
-    'type' => MENU_CALLBACK,
-  );
-
-  $items['admin/tripal/legacy/tripal_db/add'] = array(
-    'title' => 'Create a Database Reference',
-    'description' => 'Create a new reference to an External Database.',
-    'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_db_db_add_form'),
-    'access callback' => 'user_access',
-    'access arguments' => array('administer db cross-references'),
-    'type' => MENU_CALLBACK,
-  );
-
   $items['admin/tripal/legacy/tripal_db/views/dbs/enable'] = array(
     'title' => 'Enable Database Administrative View',
     'page callback' => 'tripal_enable_view',

legacy/tripal_db/tripal_db.views_default.inc

@@ -12,379 +12,9 @@
 function tripal_db_views_default_views() {
   $views = array();
 
-  // Default Tripal Admin View: DB
-  $view = tripal_db_defaultview_admin_db_listing();
-  $view = tripal_make_view_compatible_with_external($view);
-  $views[$view->name] = $view;
 
-  // Default Tripal Admin View: DB References
-  $view = tripal_db_defaultview_admin_dbxref_listing();
-  $view = tripal_make_view_compatible_with_external($view);
-  $views[$view->name] = $view;
 
   return $views;
 }
 
-/**
- * Default Admin View for db management
- *
- * @ingroup tripal_db
- */
-function tripal_db_defaultview_admin_db_listing() {
-
-  $view = new view();
-  $view->name = 'tripal_db_admin_dbs';
-  $view->description = 'DO NOT DISABLE';
-  $view->tag = 'tripal admin';
-  $view->base_table = 'db';
-  $view->human_name = 'DB Admin';
-  $view->core = 6;
-  $view->api_version = '3.0';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-
-  /* Display: Defaults */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->display->display_options['title'] = 'Databases';
-  $handler->display->display_options['use_more_always'] = FALSE;
-  $handler->display->display_options['access']['type'] = 'perm';
-  $handler->display->display_options['access']['perm'] = 'access chado_db content';
-  $handler->display->display_options['cache']['type'] = 'none';
-  $handler->display->display_options['query']['type'] = 'views_query';
-  $handler->display->display_options['exposed_form']['type'] = 'input_required';
-  $handler->display->display_options['exposed_form']['options']['submit_button'] = 'Search';
-  $handler->display->display_options['exposed_form']['options']['text_input_required'] = 'Click search to see a listing of external databases that meet the filter requirements. Use the filters to restrict this set to a more reasonable number of databases or to find a specific database.';
-  $handler->display->display_options['exposed_form']['options']['text_input_required_format'] = 'full_html';
-  $handler->display->display_options['pager']['type'] = 'full';
-  $handler->display->display_options['pager']['options']['items_per_page'] = '50';
-  $handler->display->display_options['pager']['options']['offset'] = '0';
-  $handler->display->display_options['pager']['options']['id'] = '0';
-  $handler->display->display_options['pager']['options']['quantity'] = '9';
-  $handler->display->display_options['style_plugin'] = 'table';
-  $handler->display->display_options['style_options']['grouping'] = '';
-  $handler->display->display_options['style_options']['columns'] = array(
-    'name' => 'name',
-    'url' => 'url',
-    'urlprefix' => 'urlprefix',
-    'description' => 'description',
-  );
-  $handler->display->display_options['style_options']['default'] = 'name';
-  $handler->display->display_options['style_options']['info'] = array(
-    'name' => array(
-      'sortable' => 1,
-      'separator' => '',
-    ),
-    'url' => array(
-      'sortable' => 1,
-      'separator' => '',
-    ),
-    'urlprefix' => array(
-      'sortable' => 0,
-      'separator' => '',
-    ),
-    'description' => array(
-      'sortable' => 0,
-      'separator' => '',
-    ),
-  );
-  /* Header: Global: Action Links */
-  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
-  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
-  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
-  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
-  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
-  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
-    'label-1' => 'Add Database',
-    'path-1' => 'admin/tripal/legacy/tripal_db/add',
-  );
-  /* No results behavior: Global: Text area */
-  $handler->display->display_options['empty']['text']['id'] = 'area';
-  $handler->display->display_options['empty']['text']['table'] = 'views';
-  $handler->display->display_options['empty']['text']['field'] = 'area';
-  $handler->display->display_options['empty']['text']['content'] = 'No databases match the supplied criteria.';
-  $handler->display->display_options['empty']['text']['format'] = '2';
-  /* Field: Chado Db: Db Id */
-  $handler->display->display_options['fields']['db_id']['id'] = 'db_id';
-  $handler->display->display_options['fields']['db_id']['table'] = 'db';
-  $handler->display->display_options['fields']['db_id']['field'] = 'db_id';
-  $handler->display->display_options['fields']['db_id']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['db_id']['separator'] = '';
-  /* Field: Chado Db: Name */
-  $handler->display->display_options['fields']['name']['id'] = 'name';
-  $handler->display->display_options['fields']['name']['table'] = 'db';
-  $handler->display->display_options['fields']['name']['field'] = 'name';
-  /* Field: Chado Db: Urlprefix */
-  $handler->display->display_options['fields']['urlprefix']['id'] = 'urlprefix';
-  $handler->display->display_options['fields']['urlprefix']['table'] = 'db';
-  $handler->display->display_options['fields']['urlprefix']['field'] = 'urlprefix';
-  $handler->display->display_options['fields']['urlprefix']['exclude'] = TRUE;
-  /* Field: Chado Db: Url */
-  $handler->display->display_options['fields']['url']['id'] = 'url';
-  $handler->display->display_options['fields']['url']['table'] = 'db';
-  $handler->display->display_options['fields']['url']['field'] = 'url';
-  $handler->display->display_options['fields']['url']['alter']['alter_text'] = TRUE;
-  $handler->display->display_options['fields']['url']['alter']['text'] = '[url]<br />[urlprefix]';
-  $handler->display->display_options['fields']['url']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['url']['alter']['path'] = '[url]';
-  $handler->display->display_options['fields']['url']['alter']['absolute'] = TRUE;
-  $handler->display->display_options['fields']['url']['alter']['target'] = '_blank';
-  /* Field: Chado Db: Description */
-  $handler->display->display_options['fields']['description']['id'] = 'description';
-  $handler->display->display_options['fields']['description']['table'] = 'db';
-  $handler->display->display_options['fields']['description']['field'] = 'description';
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
-  $handler->display->display_options['fields']['nothing']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing']['label'] = 'Edit Link';
-  $handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['text'] = 'edit';
-  $handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/legacy/tripal_db/edit/[db_id]';
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
-  $handler->display->display_options['fields']['nothing_1']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing_1']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing_1']['label'] = 'View DBxrefs';
-  $handler->display->display_options['fields']['nothing_1']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['nothing_1']['alter']['text'] = 'References';
-  $handler->display->display_options['fields']['nothing_1']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/legacy/tripal_db/dbxrefs?db_name=[name]';
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing_2']['id'] = 'nothing_2';
-  $handler->display->display_options['fields']['nothing_2']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing_2']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing_2']['label'] = '';
-  $handler->display->display_options['fields']['nothing_2']['alter']['text'] = '[nothing]<br />
-    [nothing_1]';
-  $handler->display->display_options['fields']['nothing_2']['element_label_colon'] = FALSE;
-  /* Filter criterion: Chado Db: Name */
-  $handler->display->display_options['filters']['name']['id'] = 'name';
-  $handler->display->display_options['filters']['name']['table'] = 'db';
-  $handler->display->display_options['filters']['name']['field'] = 'name';
-  $handler->display->display_options['filters']['name']['operator'] = 'contains';
-  $handler->display->display_options['filters']['name']['group'] = '0';
-  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
-  $handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
-  $handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
-  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
-  $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'textfield';
-  $handler->display->display_options['filters']['name']['expose']['select_multiple'] = FALSE;
-  $handler->display->display_options['filters']['name']['expose']['select_optional'] = FALSE;
-  $handler->display->display_options['filters']['name']['expose']['max_length'] = 40;
-  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-  /* Filter criterion: Chado Db: Description */
-  $handler->display->display_options['filters']['description']['id'] = 'description';
-  $handler->display->display_options['filters']['description']['table'] = 'db';
-  $handler->display->display_options['filters']['description']['field'] = 'description';
-  $handler->display->display_options['filters']['description']['operator'] = 'contains';
-  $handler->display->display_options['filters']['description']['group'] = '0';
-  $handler->display->display_options['filters']['description']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['description']['expose']['operator_id'] = 'description_op';
-  $handler->display->display_options['filters']['description']['expose']['label'] = 'Description Contains';
-  $handler->display->display_options['filters']['description']['expose']['operator'] = 'description_op';
-  $handler->display->display_options['filters']['description']['expose']['identifier'] = 'description';
-  $handler->display->display_options['filters']['description']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-
-  /* Display: Page */
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_db/dbs';
-  $handler->display->display_options['menu']['type'] = 'default tab';
-  $handler->display->display_options['menu']['title'] = 'Databases';
-  $handler->display->display_options['menu']['description'] = 'Lists all databases available to create database references for.';
-  $handler->display->display_options['menu']['weight'] = '-8';
-  $handler->display->display_options['menu']['name'] = 'management';
-  $handler->display->display_options['menu']['context'] = 0;
-  $handler->display->display_options['menu']['context_only_inline'] = 0;
-  $handler->display->display_options['tab_options']['weight'] = '0';
-
-  return $view;
-}
 
-/**
- * Default Admin View for dbxref management
- *
- * @ingroup tripal_db
- */
-function tripal_db_defaultview_admin_dbxref_listing() {
-
-  $view = new view();
-  $view->name = 'tripal_db_admin_dbxrefs';
-  $view->description = 'DO NOT DISABLE';
-  $view->tag = 'tripal admin';
-  $view->base_table = 'dbxref';
-  $view->human_name = 'DB Reference Admin';
-  $view->core = 7;
-  $view->api_version = '3.0';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-
-  /* Display: Master */
-  $handler = $view->new_display('default', 'Master', 'default');
-  $handler->display->display_options['title'] = 'DB Reference Admin';
-  $handler->display->display_options['use_more_always'] = FALSE;
-  $handler->display->display_options['access']['type'] = 'perm';
-  $handler->display->display_options['access']['perm'] = 'administer db cross-references';
-  $handler->display->display_options['cache']['type'] = 'none';
-  $handler->display->display_options['query']['type'] = 'views_query';
-  $handler->display->display_options['exposed_form']['type'] = 'input_required';
-  $handler->display->display_options['exposed_form']['options']['submit_button'] = 'Search';
-  $handler->display->display_options['exposed_form']['options']['text_input_required'] = 'Click search to see a listing of external database references that meet the filter requirements. Use the filters to restrict this set to a more reasonable number of references or to find a specific reference.';
-  $handler->display->display_options['exposed_form']['options']['text_input_required_format'] = 'full_html';
-  $handler->display->display_options['pager']['type'] = 'full';
-  $handler->display->display_options['pager']['options']['items_per_page'] = '50';
-  $handler->display->display_options['style_plugin'] = 'table';
-  $handler->display->display_options['style_options']['columns'] = array(
-    'dbxref_id' => 'dbxref_id',
-    'name' => 'name',
-    'accession' => 'accession',
-    'description' => 'description',
-    'version' => 'version',
-  );
-  $handler->display->display_options['style_options']['default'] = '-1';
-  $handler->display->display_options['style_options']['info'] = array(
-    'dbxref_id' => array(
-      'sortable' => 0,
-      'default_sort_order' => 'asc',
-      'align' => '',
-      'separator' => '',
-      'empty_column' => 0,
-    ),
-    'name' => array(
-      'sortable' => 1,
-      'default_sort_order' => 'asc',
-      'align' => '',
-      'separator' => '',
-      'empty_column' => 0,
-    ),
-    'accession' => array(
-      'sortable' => 1,
-      'default_sort_order' => 'asc',
-      'align' => '',
-      'separator' => '',
-      'empty_column' => 0,
-    ),
-    'description' => array(
-      'sortable' => 0,
-      'default_sort_order' => 'asc',
-      'align' => '',
-      'separator' => '',
-      'empty_column' => 0,
-    ),
-    'version' => array(
-      'sortable' => 1,
-      'default_sort_order' => 'asc',
-      'align' => '',
-      'separator' => '',
-      'empty_column' => 0,
-    ),
-  );
-  /* Field: Chado Dbxref: Dbxref Id */
-  $handler->display->display_options['fields']['dbxref_id']['id'] = 'dbxref_id';
-  $handler->display->display_options['fields']['dbxref_id']['table'] = 'dbxref';
-  $handler->display->display_options['fields']['dbxref_id']['field'] = 'dbxref_id';
-  $handler->display->display_options['fields']['dbxref_id']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['dbxref_id']['separator'] = '';
-  /* Field: Chado Db: Name */
-  $handler->display->display_options['fields']['name']['id'] = 'name';
-  $handler->display->display_options['fields']['name']['table'] = 'db';
-  $handler->display->display_options['fields']['name']['field'] = 'name';
-  $handler->display->display_options['fields']['name']['label'] = 'Database';
-  /* Field: Chado Dbxref: Accession */
-  $handler->display->display_options['fields']['accession']['id'] = 'accession';
-  $handler->display->display_options['fields']['accession']['table'] = 'dbxref';
-  $handler->display->display_options['fields']['accession']['field'] = 'accession';
-  /* Field: Chado Dbxref: Description */
-  $handler->display->display_options['fields']['description']['id'] = 'description';
-  $handler->display->display_options['fields']['description']['table'] = 'dbxref';
-  $handler->display->display_options['fields']['description']['field'] = 'description';
-  /* Field: Chado Dbxref: Version */
-  $handler->display->display_options['fields']['version']['id'] = 'version';
-  $handler->display->display_options['fields']['version']['table'] = 'dbxref';
-  $handler->display->display_options['fields']['version']['field'] = 'version';
-  /* Sort criterion: Chado Db: Name */
-  $handler->display->display_options['sorts']['name']['id'] = 'name';
-  $handler->display->display_options['sorts']['name']['table'] = 'db';
-  $handler->display->display_options['sorts']['name']['field'] = 'name';
-  /* Sort criterion: Chado Dbxref: Accession */
-  $handler->display->display_options['sorts']['accession']['id'] = 'accession';
-  $handler->display->display_options['sorts']['accession']['table'] = 'dbxref';
-  $handler->display->display_options['sorts']['accession']['field'] = 'accession';
-  /* Sort criterion: Chado Dbxref: Version */
-  $handler->display->display_options['sorts']['version']['id'] = 'version';
-  $handler->display->display_options['sorts']['version']['table'] = 'dbxref';
-  $handler->display->display_options['sorts']['version']['field'] = 'version';
-  $handler->display->display_options['sorts']['version']['order'] = 'DESC';
-  /* Filter criterion: Chado Db: Name */
-  $handler->display->display_options['filters']['name']['id'] = 'name';
-  $handler->display->display_options['filters']['name']['table'] = 'db';
-  $handler->display->display_options['filters']['name']['field'] = 'name';
-  $handler->display->display_options['filters']['name']['value'] = array(
-    'All' => 'All',
-  );
-  $handler->display->display_options['filters']['name']['group'] = 1;
-  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['name']['expose']['operator_id'] = '';
-  $handler->display->display_options['filters']['name']['expose']['label'] = 'Database';
-  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'db_name';
-  $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'select';
-  $handler->display->display_options['filters']['name']['expose']['select_multiple'] = TRUE;
-  $handler->display->display_options['filters']['name']['expose']['select_optional'] = TRUE;
-  $handler->display->display_options['filters']['name']['expose']['max_length'] = 40;
-  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-  /* Filter criterion: Chado Dbxref: Accession */
-  $handler->display->display_options['filters']['accession']['id'] = 'accession';
-  $handler->display->display_options['filters']['accession']['table'] = 'dbxref';
-  $handler->display->display_options['filters']['accession']['field'] = 'accession';
-  $handler->display->display_options['filters']['accession']['operator'] = 'contains';
-  $handler->display->display_options['filters']['accession']['group'] = 1;
-  $handler->display->display_options['filters']['accession']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['accession']['expose']['operator_id'] = 'accession_op';
-  $handler->display->display_options['filters']['accession']['expose']['label'] = 'Accession Contains';
-  $handler->display->display_options['filters']['accession']['expose']['operator'] = 'accession_op';
-  $handler->display->display_options['filters']['accession']['expose']['identifier'] = 'accession';
-  $handler->display->display_options['filters']['accession']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-  /* Filter criterion: Chado Dbxref: Description */
-  $handler->display->display_options['filters']['description']['id'] = 'description';
-  $handler->display->display_options['filters']['description']['table'] = 'dbxref';
-  $handler->display->display_options['filters']['description']['field'] = 'description';
-  $handler->display->display_options['filters']['description']['operator'] = 'contains';
-  $handler->display->display_options['filters']['description']['group'] = 1;
-  $handler->display->display_options['filters']['description']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['description']['expose']['operator_id'] = 'description_op';
-  $handler->display->display_options['filters']['description']['expose']['label'] = 'Description Contains';
-  $handler->display->display_options['filters']['description']['expose']['operator'] = 'description_op';
-  $handler->display->display_options['filters']['description']['expose']['identifier'] = 'description';
-  $handler->display->display_options['filters']['description']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-
-  /* Display: Page */
-  $handler = $view->new_display('page', 'Page', 'page');
-  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_db/dbxrefs';
-  $handler->display->display_options['menu']['type'] = 'tab';
-  $handler->display->display_options['menu']['title'] = 'References';
-  $handler->display->display_options['menu']['weight'] = '0';
-  $handler->display->display_options['menu']['name'] = 'management';
-  $handler->display->display_options['menu']['context'] = 0;
-  $handler->display->display_options['menu']['context_only_inline'] = 0;
-
-  return $view;
-}

legacy/tripal_example/tripal_example.info

@@ -45,6 +45,6 @@ scripts[]          = theme/js/tripal_example.js
 ; These modules must be enabled before this module can be enabled
 ;
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_db
 dependencies[] = tripal_cv

legacy/tripal_feature/tripal_feature.info

@@ -9,7 +9,7 @@ stylesheets[all][] = theme/css/tripal_feature.css
 scripts[]          = theme/js/tripal_feature.js
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_db
 dependencies[] = tripal_cv
 dependencies[] = tripal_organism

legacy/tripal_featuremap/tripal_featuremap.info

@@ -6,7 +6,7 @@ package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_organism
 dependencies[] = tripal_feature
 dependencies[] = tripal_cv

legacy/tripal_genetic/tripal_genetic.info

@@ -6,7 +6,7 @@ package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_feature
 dependencies[] = tripal_phenotype

legacy/tripal_library/tripal_library.info

@@ -6,7 +6,7 @@ package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_organism
 dependencies[] = tripal_cv
 

legacy/tripal_natural_diversity/tripal_natural_diversity.info

@@ -6,7 +6,7 @@ package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_db
 dependencies[] = tripal_genetic

legacy/tripal_organism/tripal_organism.info

@@ -11,4 +11,4 @@ stylesheets[all][] = theme/css/tripal_organism.css
 dependencies[] = tripal_core
 dependencies[] = tripal_cv
 dependencies[] = tripal_db
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views

legacy/tripal_phenotype/tripal_phenotype.info

@@ -6,6 +6,6 @@ package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_feature

legacy/tripal_project/tripal_project.info

@@ -7,6 +7,6 @@ version = 7.x-3.0-alpha1
 configure = admin/tripal/legacy/tripal_project
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_contact

legacy/tripal_pub/tripal_pub.info

@@ -8,7 +8,7 @@ version = 7.x-3.0-alpha1
 stylesheets[all][] = theme/css/tripal_pub.css
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_db
 dependencies[] = tripal_contact

legacy/tripal_stock/tripal_stock.info

@@ -6,5 +6,5 @@ package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views
 dependencies[] = tripal_organism

tripal_bulk_loader/tripal_bulk_loader.info

@@ -6,4 +6,4 @@ package = Tripal
 version = 7.x-3.0-alpha1
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views
+dependencies[] = tripal_chado_views

tripal_chado/api/modules/tripal_chado.db.api.inc

@@ -582,4 +582,4 @@ function tripal_autocomplete_dbxref($db_id, $string = '') {
   }
 
   drupal_json_output($items);
-}
+}

tripal_chado/api/tripal_chado.schema.api.inc

@@ -489,7 +489,7 @@ function chado_get_table_names($include_custom = NULL) {
 function chado_get_schema($table) {
 
   // first get the chado version that is installed
-  $v = $GLOBALS["chado_version"];
+  $v = array_key_exists("chado_version", $GLOBALS) ? $GLOBALS["chado_version"] : '';
 
   // get the table array from the proper chado schema
   $v = preg_replace("/\./", "_", $v); // reformat version for hook name

tripal_chado/api/tripal_chado.views.api.inc

@@ -150,7 +150,7 @@ function tripal_make_view_compatible_with_external($view) {
  * @param $redirect_link
  *   The path to redirect to. FALSE if no redirect needed
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_disable_view($view_name, $redirect_link = FALSE) {
 
@@ -205,7 +205,7 @@ function tripal_disable_view($view_name, $redirect_link = FALSE) {
  * @param $redirect_link
  *   The path to redirect to. FALSE if no redirect needed
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_enable_view($view_name, $redirect_link = FALSE) {
 

tripal_chado/includes/TripalFields.old/chado_base__dbxref_id.inc

@@ -1,337 +0,0 @@
-<?php
-
-class chado_base__dbxref_id extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Accession';
-
-  // The default description for this field.
-  public static $default_description = 'The unique stable accession (ID) for
-        this record on this site.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    foreach ($items as $delta => $item) {
-      if ($item['value']) {
-        $content = $item['value']['vocabulary'] . ':' . $item['value']['accession'];
-        $element[$delta] = array(
-          '#type' => 'markup',
-          '#markup' => $content,
-        );
-      }
-    }
-  }
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the field defaults.
-    $fk_val = '';
-    $db_id = '';
-    $accession = '';
-    $version = '';
-    $description = '';
-
-    // If the field already has a value then it will come through the $items
-    // array.  This happens when editing an existing record.
-    if (count($items) > 0 and array_key_exists($delta, $items)) {
-      $fk_val = $items[$delta]['chado-' . $field_table . '__' . $field_column];
-      $db_id = $items[$delta]['db_id'];
-      $accession = $items[$delta]['accession'];
-      $version = $items[$delta]['version'];
-      $description = $items[$delta]['description'];
-    }
-
-    // Check $form_state['values'] to see if an AJAX call set the values.
-    if (array_key_exists('values', $form_state)) {
-      $fk_val = isset($form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $field_column]) ? $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $field_column] : '';
-      $db_id = isset($form_state['values'][$field_name]['und'][$delta]['db_id']) ? $form_state['values'][$field_name]['und'][$delta]['db_id'] : '';
-      $accession = isset($form_state['values'][$field_name]['und'][$delta]['accession']) ? $form_state['values'][$field_name]['und'][$delta]['accession'] : '';
-      $version = isset($form_state['values'][$field_name]['und'][$delta]['version']) ? $form_state['values'][$field_name]['und'][$delta]['version'] : '';
-      $description = isset($form_state['values'][$field_name]['und'][$delta]['description']) ? $form_state['values'][$field_name]['und'][$delta]['description'] : '';
-    }
-
-    $schema = chado_get_schema('dbxref');
-    $options = tripal_get_db_select_options();
-
-    //$widget['#element_validate'] = array('chado_base__dbxref_id_widget_validate');
-    $widget['#prefix'] =  "<span id='$field_name-dbxref--db-id'>";
-    $widget['#suffix'] =  "</span>";
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-' . $field_table . '__' . $field_column] = array(
-      '#type' => 'value',
-      '#default_value' => $fk_val,
-    );
-
-    $widget['db_id'] = array(
-      '#type' => 'select',
-      '#title' => t('Database'),
-      '#options' => $options,
-      '#required' => $element['#required'],
-      '#default_value' => $db_id,
-      '#ajax' => array(
-        'callback' => "chado_base__dbxref_id_widget_form_ajax_callback",
-        'wrapper' => "$field_name-dbxref--db-id",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-    );
-    $widget['accession'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Accession'),
-      '#default_value' => $accession,
-      '#required' => $element['#required'],
-      '#maxlength' => array_key_exists('length', $schema['fields']['accession']) ? $schema['fields']['accession']['length'] : 255,
-      '#size' => 15,
-      '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/dbxref/' . $db_id,
-      '#ajax' => array(
-        'callback' => "tripal_chado_dbxref_widget_form_ajax_callback",
-        'wrapper' => "$field_name-dbxref--db-id",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-      '#disabled' => $db_id ? FALSE : TRUE,
-    );
-    $widget['version'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Version'),
-      '#default_value' => $version,
-      '#maxlength' => array_key_exists('length', $schema['fields']['version']) ? $schema['fields']['version']['length'] : 255,
-      '#size' => 5,
-      '#disabled' => $db_id ? FALSE : TRUE,
-    );
-    $widget['description'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Description'),
-      '#default_value' => $description,
-      '#size' => 20,
-      '#disabled' => $db_id ? FALSE : TRUE,
-    );
-    $widget['links'] = array(
-      '#type' => 'item',
-      '#markup' => l('Add a new database', 'admin/tripal/legacy/tripal_db/add', array('attributes' => array('target' => '_blank')))
-    );
-  }
-
-
-  /**
-   * @see TripalField::validate()
-   */
-  public function validate($entity_type, $entity, $field, $items, &$errors) {
-
-    $field_name = $this->field['field_name'];
-    $settings = $this->field['settings'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the field values.
-    foreach ($items as $delta => $values) {
-      $fk_val = $values['chado-' . $field_table . '__' . $field_column];
-      $db_id = $values['db_id'];
-      $accession = $values['accession'];
-      $version = $values['version'];
-      $description = $values['description'];
-
-      // Make sure that if a database ID is provided that an accession is also
-      // provided.  Here we use the form_set_error function rather than the
-      // form_error function because the form_error will add a red_highlight
-      // around all of the fields in the fieldset which is confusing as it's not
-      // clear to the user what field is required and which isn't. Therefore,
-      // we borrow the code from the 'form_error' function and append the field
-      // so that the proper field is highlighted on error.
-      if (!$db_id and $accession) {
-        $errors[$field_name][$delta]['und'][] = array(
-          'message' => t("A database and the accession must both be provided for the primary cross reference."),
-          'error' => 'chado_base__dbxref',
-        );
-      }
-      if ($db_id and !$accession) {
-        $errors[$field_name][$delta]['und'][] = array(
-          'message' => t("A database and the accession must both be provided for the primary cross reference."),
-          'error' => 'chado_base__dbxref',
-        );
-      }
-      if (!$db_id and !$accession and ($version or $description)) {
-        $errors[$field_name][$delta]['und'][] = array(
-          'message' => t("A database and the accession must both be provided for the primary cross reference."),
-          'error' => 'chado_base__dbxref',
-        );
-      }
-    }
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-    $field_name = $this->field['field_name'];
-    $settings = $this->field['settings'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    $fk_val = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__' . $field_column]) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__' . $field_column] : '';
-    $db_id = isset($form_state['values'][$field_name][$langcode][$delta]['db_id']) ? $form_state['values'][$field_name][$langcode][$delta]['db_id'] : '';
-    $accession = isset($form_state['values'][$field_name][$langcode][$delta]['accession']) ? $form_state['values'][$field_name][$langcode][$delta]['accession'] : '';
-    $version = isset($form_state['values'][$field_name][$langcode][$delta]['version']) ? $form_state['values'][$field_name][$langcode][$delta]['version'] : '';
-
-    // If user did not select a database, we want to remove dbxref_id from the
-    // field.
-    if (!$db_id) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__dbxref_id'] = '__NULL__';
-    }
-    // If the dbxref_id does not match the db_id + accession then the user
-    // has selected a new dbxref record and we need to update the hidden
-    // value accordingly.
-    if ($db_id and $accession) {
-      $dbxref = chado_generate_var('dbxref', array('db_id' => $db_id, 'accession' => $accession));
-      if ($dbxref and $dbxref->dbxref_id != $fk_val) {
-        $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__dbxref_id'] = $dbxref->dbxref_id;
-      }
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-
-    // Set some defauls for the empty record
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(
-        'vocabulary' => '',
-        'accession' => '',
-        'URL' => '',
-      ),
-      'chado-' . $field_table . '__' . $field_column => '',
-      'db_id' => '',
-      'accession' => '',
-      'version' => '',
-      'description' => '',
-    );
-
-    // Get the primary dbxref record (if it's not NULL).  Because we have a
-    // dbxref_id passed in by the base record, we will only have one record.
-    if ($record->$field_column) {
-      $dbxref = $record->$field_column;
-      $value = $dbxref->db_id->name . ':' . $dbxref->accession;
-      $entity->{$field_name}['und'][0] = array(
-        'value' => array(
-          'vocabulary' => $dbxref->db_id->name,
-          'accession' => $dbxref->accession,
-          'URL' => tripal_get_dbxref_url($dbxref),
-        ),
-        'chado-' . $field_table . '__' . $field_column => $record->$field_column->$field_column,
-        'db_id'       => $dbxref->db_id->db_id,
-        'accession'   => $dbxref->accession,
-        'version'     => $dbxref->version,
-        'description' => $dbxref->description,
-      );
-    }
-  }
-}
-
-/**
- * An Ajax callback for the tripal_chado_admin_publish_form..
- */
-function chado_base__dbxref_id_widget_form_ajax_callback($form, $form_state) {
-  $field_name = $form_state['triggering_element']['#parents'][0];
-  $field = field_info_field($field_name);
-  $field_type = $field['type'];
-  $field_table = $field['settings']['chado_table'];
-  $field_column = $field['settings']['chado_column'];
-  $field_prefix = 'chado-' . $field_table . '__' . $field_column;
-
-//   $db_id = tripal_chado_get_field_form_values($field_name, $form_state, 0, $field_prefix . '--db_id');
-//   $accession = tripal_chado_get_field_form_values($field_name, $form_state, 0, $field_prefix . '--accession');
-  if ($db_id and $accession) {
-    $values = array(
-      'db_id' => $db_id,
-      'accession' => $accession,
-    );
-    $options = array('is_duplicate' => TRUE);
-    $has_duplicate = chado_select_record('dbxref', array('*'), $values, $options);
-    if (!$has_duplicate) {
-      drupal_set_message('The selected cross reference is new and will be added for future auto completions.', 'warning');
-    }
-  }
-
-  return $form[$field_name];
-}
-
-function theme_chado_base__dbxref_id_widget($variables) {
-  $element = $variables['element'];
-  $field_name = $element['#field_name'];
-  $field = field_info_field($field_name);
-  $field_type = $field['type'];
-  $field_table = $field['settings']['chado_table'];
-  $field_column = $field['settings']['chado_column'];
-  $field_prefix = 'chado-' . $field_table . '__' . $field_column;
-
-  $layout = "
-      <div class=\"primary-dbxref-widget\">
-        <div class=\"primary-dbxref-widget-item\">" .
-        drupal_render($element['db_id']) . "
-        </div>
-        <div class=\"primary-dbxref-widget-item\">" .
-        drupal_render($element['accession']) . "
-        </div>
-        <div class=\"primary-dbxref-widget-item\">" .
-        drupal_render($element['version']) . "
-        </div>
-        <div class=\"primary-dbxref-widget-item\">" .
-        drupal_render($element['description']) . "
-        </div>
-        <div class=\"primary-dbxref-widget-links\">" . drupal_render($element['links']) . "</div>
-      </div>
-    ";
-
-  $fieldset = array(
-    '#title' => $element['#title'],
-    '#value' => '',
-    '#description' => $element['#description'],
-    '#children' => $layout,
-    //    '#attributes' => array('class' => $classes),
-  );
-
-  return theme('fieldset', array('element' => $fieldset));
-}

tripal_chado/includes/TripalFields.old/chado_base__organism_id.inc

@@ -1,235 +0,0 @@
-<?php
-
-class chado_base__organism_id extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Organism';
-
-  // The default description for this field.
-  public static $default_description = 'A field for specifying an organism.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'field_display_string' => '<i>[organism.genus] [organism.species]</i>',
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    if (count($items) > 0) {
-      $content = $items[0]['value']['label'];
-      if (array_key_exists('entity', $items[0]['value'])) {
-        list($entity_type, $entity_id) = explode(':', $items[0]['value']['entity']);
-        $content = l(strip_tags($items[0]['value']['label']), 'bio_data/' . $entity_id);
-      }
-
-      // The cardinality of this field is 1 so we don't have to
-      // iterate through the items array, as there will never be more than 1.
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::widget()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $settings = $this->field['settings'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    $organism_id = 0;
-    if (count($items) > 0 and array_key_exists('chado-' . $field_table . '__organism_id', $items[0])) {
-      $organism_id = $items[0]['chado-' . $field_table . '__organism_id'];
-    }
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-    $options = tripal_get_organism_select_options(FALSE);
-    $widget['chado-' . $field_table . '__organism_id'] = array(
-      '#type' => 'select',
-      '#title' => $element['#title'],
-      '#description' => $element['#description'],
-      '#options' => $options,
-      '#default_value' => $organism_id,
-      '#required' => $element['#required'],
-      '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
-      '#delta' => $delta,
-    );
-  }
-
-  /**
-   * @see TripalField::validate()
-   */
-  public function validate($entity_type, $entity, $field, $items, &$errors) {
-
-    $settings = $this->field['settings'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the field values.
-    foreach ($items as $delta => $values) {
-
-      // Get the field values.
-      $organism_id = $values['chado-' . $field_table . '__organism_id'];
-      if (!$organism_id or $organism_id == 0) {
-        $errors[$field_name]['und'][0][] = array(
-          'message' =>  t("Please specify an organism."),
-          'error' => 'chado_base__organism_id'
-        );
-      }
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-    $settings = $this->field['settings'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(
-        'label' => '',
-        'genus' => '',
-        'species' => '',
-      ),
-      'semantic_web' => array(
-        'label' => 'rdfs:label',
-        'genus' => tripal_get_chado_semweb_term('organism', 'genus'),
-        'species' => tripal_get_chado_semweb_term('organism', 'species'),
-        'infraspecific_name' => tripal_get_chado_semweb_term('organism', 'infraspecific_name'),
-        'infraspecific_type' => tripal_get_chado_semweb_term('organism', 'type_id'),
-      ),
-      'chado_mapping' => array(
-        'genus' => 'organism_id,genus',
-        'species' => 'organism_id,genus',
-        'infraspecific_name' => 'organism_id,infraspecific_name',
-        'infraspecific_type' => 'organism_id,infraspecific_type',
-      )
-    );
-
-    if ($record) {
-      $organism = $record->organism_id;
-      $string = $settings['field_display_string'];
-      $label = tripal_replace_chado_tokens($string, $organism);
-      $entity->{$field_name}['und'][0]['value'] = array(
-        'label' => $label,
-        'genus' => $organism->genus,
-        'species' => $organism->species,
-      );
-      // The infraspecific fiels were introdcued in Chado v1.3.
-      if (property_exists($organism, 'infraspecific_name')) {
-        $entity->{$field_name}['und'][0]['value']['infraspecific_type'] = NULL;
-        $entity->{$field_name}['und'][0]['value']['infraspecific_name'] = $organism->infraspecific_name;
-        if ($organism->type_id) {
-          $entity->{$field_name}['und'][0]['value']['infraspecific_type'] =  $organism->type_id->name;
-        }
-      }
-      $entity->{$field_name}['und'][0]['chado-' . $field_table . '__organism_id'] = $organism->organism_id;
-
-      // Is there a published entity for this organism?
-      if (property_exists($entity->chado_record->$field_column, 'entity_id')) {
-        $fk_entity_id = $entity->chado_record->$field_column->entity_id;
-        $entity->{$field_name}['und'][0]['value']['entity'] = 'TripalEntity:' . $fk_entity_id;
-      }
-    }
-  }
-
-  /**
-   * @see TripalField::globalSettingsForm()
-   */
-  public function globalSettingsForm($has_data) {
-    $element = parent::globalSettingsForm($has_data);
-
-    $settings = $this->field['settings'];
-
-    $element['instructions'] = array(
-      '#type' => 'item',
-      '#markup' => 'You may rewrite the way this field is presented to the end-user.
-        The Rewrite Value field allows you to use tokens to indicate how the
-        value should be displayed.  Tokens will be substituted with appriorate
-        data from the database.  See the Available tokens list for the
-        tokens you may use.'
-    );
-
-    $element['field_display_string'] = array(
-      '#type' => 'textfield',
-      '#title' => 'Rewrite Value',
-      '#description' => t('Provide a mixture of text and/or tokens for the format.
-          For example: [organism.genus] [organism.species].  When displayed,
-          the tokens will be replaced with the actual value.'),
-      '#default_value' => $settings['field_display_string'],
-    );
-
-    $element['tokens'] = array(
-      '#type' => 'fieldset',
-      '#collapsed' => TRUE,
-      '#collapsible' => TRUE,
-      '#title' => 'Available Tokens'
-    );
-    $headers = array('Token', 'Description');
-    $rows = array();
-
-    // Here we use the tripal_get_chado_tokens rather than the
-    // tripal_get_entity_tokens because we can't gurantee that all organisms
-    // have entities.
-    $tokens = tripal_get_chado_tokens('organism');
-    foreach ($tokens as $token) {
-      $rows[] = array(
-        $token['token'],
-        $token['description'],
-      );
-    }
-
-    $table_vars = array(
-      'header'     => $headers,
-      'rows'       => $rows,
-      'attributes' => array(),
-      'sticky'     => FALSE,
-      'caption'    => '',
-      'colgroups'  => array(),
-      'empty'      => 'There are no tokens',
-    );
-    $element['tokens']['list'] = array(
-      '#type' => 'item',
-      '#markup' => theme_table($table_vars),
-    );
-
-    // Add in the semantic web fields.
-    $parent_elements = parent::settings_form($field, $instance, $has_data);
-    $element = array_merge($element, $parent_elements);
-
-    return $element;
-  }
-
-}

tripal_chado/includes/TripalFields.old/chado_feature__md5checksum.inc

@@ -1,92 +0,0 @@
-<?php
-
-class chado_feature__md5checksum  extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Sequence MD5 checksum';
-
-  // The default description for this field.
-  public static $default_description = 'A field for generating MD5 checksum for a sequence.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    foreach ($items as $delta => $item) {
-      $content = key_exists('value', $item) ? $item['value'] : '';
-      $element[$delta] = array(
-        // We create a render array to produce the desired markup,
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $settings = $this->field['settings'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the field defaults.
-    $md5checksum = '';
-    if (count($items) > 0 and array_key_exists('chado-feature__md5checksum', $items[0])) {
-      $md5checksum = $items[0]['chado-feature__md5checksum'];
-    }
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => $md5checksum,
-    );
-    $widget['chado-feature__md5checksum'] = array(
-      '#type' => 'value',
-      '#value' => $md5checksum,
-    );
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-    $field = $this->field;
-    $settings = $field['settings'];
-    $field_name = $field['field_name'];
-    $field_type = $field['type'];
-    $field_table = $field['settings']['chado_table'];
-    $field_column = $field['settings']['chado_column'];
-
-    // Get the residues so we can calculate teh length.
-    $residues = isset($form_state['values']['feature__residues'][$langcode][0]['chado-feature__residues']) ? $form_state['values']['feature__residues'][$langcode][0]['chado-feature__residues'] : '';
-
-    if ($residues) {
-      // Remove spaces and new lines from the residues string.
-      $residues = preg_replace('/\s/', '', $residues);
-      $form_state['values']['feature__residues'][$langcode][0]['chado-feature__residues'] = $residues;
-      $form_state['values'][$field_name][$langcode][$delta]['chado-feature__md5checksum'] = md5($residues);
-    }
-    else {
-      // Otherwise, remove the md5 value
-      $form_state['values'][$field_name][$langcode][$delta]['chado-feature__md5checksum'] = '__NULL__';
-    }
-  }
-}

tripal_chado/includes/TripalFields.old/chado_feature__residues.inc

@@ -1,618 +0,0 @@
-<?php
-
-class chado_feature__residues extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Sequences';
-
-  // The default description for this field.
-  public static $default_description = 'A field for managing nucleotide and protein residues.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-
-    $element[0] = array(
-      // We create a render array to produce the desired markup,
-      '#type' => 'markup',
-      '#markup' => '',
-    );
-
-    $num_bases = 50;
-    foreach ($items as $delta => $item) {
-      // If there are no residues then skip this one.
-      if (!is_array($item['value']) or !array_key_exists('residues', $item['value'])) {
-        continue;
-      }
-
-      $residues = $item['value']['residues'];
-      $label = $item['value']['label'];
-      $defline = $item['value']['defline'];
-
-      $content = '<p>' . $label . '<p>';
-      $content .= '<pre class="residues-formatter">';
-      $content .= '>' . $defline . "<br>";
-      $content .= wordwrap($residues, $num_bases, "<br>", TRUE);
-      $content .= '</pre>';
-
-      $element[$delta] = array(
-        // We create a render array to produce the desired markup,
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $settings = $this->field['settings'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the field defaults.
-    $residues = '';
-    if (count($items) > 0 and array_key_exists('chado-feature__residues', $items[0])) {
-      $residues = $items[0]['chado-feature__residues'];
-    }
-    if (array_key_exists('values', $form_state)) {
-      //$residues = tripal_chado_get_field_form_values($field_name, $form_state, 0, 'feature__residues');
-    }
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-    $widget['chado-feature__residues'] = array(
-      '#type' => 'textarea',
-      '#title' => $element['#title'],
-      '#description' => $element['#description'],
-      '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
-      '#default_value' => $residues,
-      '#delta' => $delta,
-      '#cols' => 30,
-    );
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    $field_name = $this->field['field_name'];
-
-    // Remove any white spaces.
-    $residues = isset($form_state['values'][$field_name][$langcode][$delta]['chado-feature__residues']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-feature__residues'] : '';
-    if ($residues) {
-      $residues = preg_replace('/\s/', '', $residues);
-      $form_state['values'][$field_name][$langcode][$delta]['chado-feature__residues'] = $residues;
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $field_name = $this->field['field_name'];
-    $feature = $details['record'];
-    $num_seqs = 0;
-
-    // We don't want to get the sequence for traditionally large types. They are
-    // too big,  bog down the web browser, take longer to load and it's not
-    // reasonable to print them on a page.
-    if(strcmp($feature->type_id->name,'scaffold') == 0 or
-       strcmp($feature->type_id->name,'chromosome') == 0 or
-       strcmp($feature->type_id->name,'supercontig') == 0 or
-       strcmp($feature->type_id->name,'pseudomolecule') == 0) {
-      $entity->{$field_name}['und'][$num_seqs]['value'] = array(
-        '@type' => 'SO:0000110',
-        'type' => 'sequence_feature',
-        'label' => 'Residues',
-        'defline' => ">This sequence is too large for this display.",
-        'residues' => '',
-      );
-      $entity->{$field_name}['und'][$num_seqs]['chado-feature__residues'] = '';
-    }
-    else {
-      $feature = chado_expand_var($feature,'field','feature.residues');
-      if ($feature->residues) {
-        $entity->{$field_name}['und'][$num_seqs]['value'] = array(
-          '@type' => 'SO:0000110',
-          'type' => 'sequence_feature',
-          'label' => 'Raw Sequence',
-          'defline' => tripal_get_fasta_defline($feature, '', NULL, '', strlen($feature->residues)),
-          'residues' => $feature->residues,
-        );
-        $entity->{$field_name}['und'][$num_seqs]['chado-feature__residues'] = $feature->residues;
-      }
-      else {
-        $entity->{$field_name}['und'][$num_seqs]['value'] = array();
-        $entity->{$field_name}['und'][$num_seqs]['chado-feature__residues'] = '';
-      }
-    }
-    $num_seqs++;
-
-    // Add in the protein sequences. It's faster to provide the SQL rather than
-    // to use chado_generate_var based on the type.
-    $sql = "
-      SELECT F.*
-      FROM {feature_relationship} FR
-        INNER JOIN {feature} F on FR.subject_id = F.feature_id
-        INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
-        INNER JOIN {cvterm} RCVT on RCVT.cvterm_id = FR.type_id
-      WHERE
-        FR.object_id = :feature_id and
-        CVT.name = 'polypeptide' and
-        RCVT.name = 'derives_from'
-      ORDER BY FR.rank ASC
-    ";
-    $results = chado_query($sql, array(':feature_id' => $feature->feature_id));
-    while ($protein = $results->fetchObject()) {
-      if ($protein->residues) {
-        $entity->{$field_name}['und'][$num_seqs++]['value'] = array(
-          '@type' => 'SO:0000104',
-          'type' => 'polypeptide',
-          'label' => 'Protein Sequence',
-          'defline' => tripal_get_fasta_defline($protein, '', NULL, '', strlen($protein->residues)),
-          'residues' => $protein->residues,
-        );
-      }
-    }
-
-
-    // Add in sequences from alignments.
-    $options = array(
-      'return_array' => 1,
-      'include_fk' => array(
-        'srcfeature_id' => array(
-          'type_id' => 1
-        ),
-        'feature_id' => array(
-          'type_id' => 1
-        ),
-      ),
-    );
-    $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
-    $featureloc_sequences = $this->get_featureloc_sequences($feature->feature_id, $feature->featureloc->feature_id);
-
-    // Add in the coding sequences. It's faster to provide the SQL rather than
-    // to use chado_generate_var based on the type.
-    $sql = "
-      SELECT F.*
-      FROM {feature_relationship} FR
-        INNER JOIN {feature} F on FR.subject_id = F.feature_id
-        INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
-        INNER JOIN {cvterm} RCVT on RCVT.cvterm_id = FR.type_id
-        INNER JOIN {featureloc} FL on FL.feature_id = F.feature_id
-      WHERE
-        FR.object_id = :feature_id and
-        CVT.name = 'CDS' and
-        RCVT.name = 'part_of'
-      ORDER BY FR.rank ASC
-    ";
-    $results = chado_query($sql, array(':feature_id' => $feature->feature_id));
-    $coding_seq = '';
-    while ($CDS = $results->fetchObject()) {
-      if ($CDS->residues) {
-        $coding_seq .= $CDS->residues;
-      }
-    }
-    if ($coding_seq) {
-      $entity->{$field_name}['und'][$num_seqs++]['value'] = array(
-        '@type' => 'SO:0000316',
-        'type' => 'coding_sequence',
-        'label' => 'Coding sequence (CDS)',
-        'defline' => tripal_get_fasta_defline($feature, 'CDS', NULL, '', strlen($coding_seq)),
-        'residues' => $coding_seq,
-      );
-    }
-
-    foreach($featureloc_sequences as $src => $attrs){
-      // the $attrs array has the following keys
-      //   * id:  a unique identifier combining the feature id with the cvterm id
-      //   * type: the type of sequence (e.g. mRNA, etc)
-      //   * location:  the alignment location
-      //   * defline: the definition line
-      //   * formatted_seq: the formatted sequences
-      //   * featureloc:  the feature object aligned to
-      $entity->{$field_name}['und'][$num_seqs++]['value'] = array(
-        'residues' => $attrs['residues'],
-        '@type' => 'SO:0000110',
-        'type' => 'sequence_feature',
-        'defline' => tripal_get_fasta_defline($feature, '', $attrs['featureloc'], 'CDS', strlen($attrs['residues'])),
-        'label' => 'Sequence from alignment at ' . $attrs['location'],
-      );
-
-
-      // check to see if this alignment has any CDS. If so, generate a CDS sequence
-      $cds_sequence = tripal_get_feature_sequences(
-        array(
-          'feature_id' => $feature->feature_id,
-          'parent_id' => $attrs['featureloc']->srcfeature_id->feature_id,
-          'name' => $feature->name,
-          'featureloc_id' => $attrs['featureloc']->featureloc_id,
-        ),
-        array(
-          'derive_from_parent' => 1, // CDS are in parent-child relationships so we want to use the sequence from the parent
-          'aggregate' => 1, // we want to combine all CDS for this feature into a single sequence
-          'sub_feature_types' => array('CDS'), // we're looking for CDS features
-          'is_html' => 0
-        )
-      );
-
-      if (count($cds_sequence) > 0) {
-        // the tripal_get_feature_sequences() function can return multiple sequences
-        // if a feature is aligned to multiple places. In the case of CDSs we expect
-        // that one mRNA is only aligned to a single location on the assembly so we
-        // can access the CDS sequence with index 0.
-        if ($cds_sequence[0]['residues']) {
-          $entity->{$field_name}['und'][$num_seqs++]['value'] = array(
-            'residues' => $cds_sequence[0]['residues'],
-            '@type' => 'SO:0000316',
-            'type' => 'coding_sequence',
-            'defline' => tripal_get_fasta_defline($feature, '', $attrs['featureloc'], 'CDS', $cds_sequence[0]['length']),
-            'label' => 'Coding sequence (CDS) from alignment at  ' . $attrs['location'],
-          );
-        }
-      }
-    }
-  }
-
-  /**
-   *
-   * @param unknown $feature_id
-   * @param unknown $featurelocs
-   * @return multitype:|Ambigous <multitype:, an>
-   */
-  private function get_featureloc_sequences($feature_id, $featurelocs) {
-
-    // if we don't have any featurelocs then no point in continuing
-    if (!$featurelocs) {
-      return array();
-    }
-
-    // get the list of relationships (including any aggregators) and iterate
-    // through each one to find information needed to color-code the reference sequence
-    $relationships = $this->get_aggregate_relationships($feature_id);
-    if (!$relationships) {
-      return array();
-    }
-
-
-    // iterate through each of the realtionships features and get their
-    // locations
-    foreach ($relationships as $rindex => $rel) {
-      // get the featurelocs for each of the relationship features
-      $rel_featurelocs = $this->get_featurelocs($rel->subject_id, 'as_child', 0);
-      foreach ($rel_featurelocs as $rfindex => $rel_featureloc) {
-        // keep track of this unique source feature
-        $src = $rel_featureloc->src_feature_id . "-" . $rel_featureloc->src_cvterm_id;
-
-        // copy over the results to the relationship object.  Since there can
-        // be more than one feature location for each relationship feature we
-        // use the '$src' variable to keep track of these.
-        $rel->featurelocs = new stdClass();
-        $rel->featurelocs->$src = new stdClass();
-        $rel->featurelocs->$src->src_uniquename = $rel_featureloc->src_uniquename;
-        $rel->featurelocs->$src->src_cvterm_id  = $rel_featureloc->src_cvterm_id;
-        $rel->featurelocs->$src->src_cvname     = $rel_featureloc->src_cvname;
-        $rel->featurelocs->$src->fmin           = $rel_featureloc->fmin;
-        $rel->featurelocs->$src->fmax           = $rel_featureloc->fmax;
-        $rel->featurelocs->$src->src_name       = $rel_featureloc->src_name;
-
-        // keep track of the individual parts for each relationship
-        $start = $rel->featurelocs->$src->fmin;
-        $end   = $rel->featurelocs->$src->fmax;
-        $type  = $rel->subject_type;
-        $rel_locs[$src]['parts'][$start][$type]['start'] = $start;
-        $rel_locs[$src]['parts'][$start][$type]['end']   = $end;
-        $rel_locs[$src]['parts'][$start][$type]['type']  = $type;
-      }
-    }
-
-    // the featurelocs array provided to the function contains the locations
-    // where this feature is found.   We want to get the sequence for each
-    // location and then annotate it with the parts found from the relationships
-    // locations determiend above.
-    $floc_sequences = array();
-    foreach ($featurelocs as $featureloc) {
-
-      // build the src name so we can keep track of the different parts for each feature
-      $src = $featureloc->srcfeature_id->feature_id . "-" . $featureloc->srcfeature_id->type_id->cvterm_id;
-
-      // orient the parts to the beginning of the feature sequence
-      if (!empty($rel_locs[$src]['parts'])) {
-        $parts = $rel_locs[$src]['parts'];
-        $rparts = array();  // we will fill this up if we're on the reverse strand
-
-        foreach ($parts as $start => $types) {
-          foreach ($types as $type_name => $type) {
-            if ($featureloc->strand >= 0) {
-              // this is on the forward strand.  We need to convert the start on the src feature to the
-              // start on this feature's sequence
-              $parts[$start][$type_name]['start'] = $parts[$start][$type_name]['start'] - $featureloc->fmin;
-              $parts[$start][$type_name]['end']   = $parts[$start][$type_name]['end'] - $featureloc->fmin;
-              $parts[$start][$type_name]['type']  = $type_name;
-            }
-            else {
-              // this is on the reverse strand.  We need to swap the start and stop and calculate from the
-              // begining of the reverse sequence
-              $size = ($featureloc->fmax - $featureloc->fmin);
-              $start_orig = $parts[$start][$type_name]['start'];
-              $end_orig = $parts[$start][$type_name]['end'];
-              $new_start = $size - ($end_orig - $featureloc->fmin);
-              $new_end = $size - ($start_orig - $featureloc->fmin);
-
-              $rparts[$new_start][$type_name]['start'] = $new_start;
-              $rparts[$new_start][$type_name]['end']   = $new_end;
-              $rparts[$new_start][$type_name]['type']  = $type_name;
-            }
-          }
-        }
-
-        // now sort the parts
-        // if we're on the reverse strand we need to resort
-        if ($featureloc->strand >= 0) {
-          usort($parts, 'chado_feature__residues_sort_rel_parts_by_start');
-        }
-        else {
-          usort($rparts, 'chado_feature__residues_sort_rel_parts_by_start');
-          $parts = $rparts;
-        }
-
-        $floc_sequences[$src]['id'] = $src;
-        $floc_sequences[$src]['type'] = $featureloc->feature_id->type_id->name;
-        $args = array(':feature_id' => $featureloc->srcfeature_id->feature_id);
-        $start = $featureloc->fmin + 1;
-        $size = $featureloc->fmax - $featureloc->fmin;
-
-        // TODO: fix the hard coded $start and $size
-        // the $start and $size variables are hard-coded in the SQL statement
-        // because the db_query function places quotes around all placeholders
-        // (e.g. :start & :size) and screws up the substring function
-        $sql = "
-          SELECT substring(residues from $start for $size) as residues
-          FROM {feature}
-          WHERE feature_id = :feature_id
-        ";
-        $sequence = chado_query($sql, $args)->fetchObject();
-        $residues = $sequence->residues;
-        if ($featureloc->strand < 0) {
-          $residues = tripal_reverse_compliment_sequence($residues);
-        }
-        $strand = '.';
-        if ($featureloc->strand == 1) {
-          $strand = '+';
-        }
-        elseif ($featureloc->strand == -1) {
-          $strand = '-';
-        }
-        $floc_sequences[$src]['location'] = tripal_get_location_string($featureloc);
-        $floc_sequences[$src]['defline'] = tripal_get_fasta_defline($featureloc->feature_id, '', $featureloc, '', strlen($residues));
-        $floc_sequences[$src]['featureloc'] = $featureloc;
-        $floc_sequences[$src]['residues'] = $residues;
-        //$floc_sequences[$src]['formatted_seq'] =  tripal_feature_color_sequence($residues, $parts, $floc_sequences[$src]['defline']);
-      }
-    }
-    return $floc_sequences;
-  }
-
-  /**
-   * Get features related to the current feature to a given depth. Recursive function.
-   *
-   * @param $feature_id
-   * @param $substitute
-   * @param $levels
-   * @param $base_type_id
-   * @param $depth
-   *
-   * @ingroup tripal_feature
-   */
-  private function get_aggregate_relationships($feature_id, $substitute=1,
-      $levels=0, $base_type_id=NULL, $depth=0) {
-
-    // we only want to recurse to as many levels deep as indicated by the
-    // $levels variable, but only if this variable is > 0. If 0 then we
-    // recurse until we reach the end of the relationships tree.
-    if ($levels > 0 and $levels == $depth) {
-      return NULL;
-    }
-
-    // first get the relationships for this feature
-    return $this->get_relationships($feature_id, 'as_object');
-
-  }
-
-  /**
-   * Get the relationships for a feature.
-   *
-   * @param $feature_id
-   *   The feature to get relationships for
-   * @param $side
-   *   The side of the relationship this feature is (ie: 'as_subject' or 'as_object')
-   *
-   * @ingroup tripal_feature
-   */
-  private function get_relationships($feature_id, $side = 'as_subject') {
-    // get the relationships for this feature.  The query below is used for both
-    // querying the object and subject relationships
-    $sql = "
-    SELECT
-      FS.name as subject_name, FS.uniquename as subject_uniquename,
-      CVTS.name as subject_type, CVTS.cvterm_id as subject_type_id,
-      FR.subject_id, FR.type_id as relationship_type_id, FR.object_id, FR.rank,
-      CVT.name as rel_type,
-      FO.name as object_name, FO.uniquename as object_uniquename,
-      CVTO.name as object_type, CVTO.cvterm_id as object_type_id
-    FROM {feature_relationship} FR
-     INNER JOIN {cvterm} CVT  ON FR.type_id    = CVT.cvterm_id
-     INNER JOIN {feature} FS  ON FS.feature_id = FR.subject_id
-     INNER JOIN {feature} FO  ON FO.feature_id = FR.object_id
-     INNER JOIN {cvterm} CVTO ON FO.type_id    = CVTO.cvterm_id
-     INNER JOIN {cvterm} CVTS ON FS.type_id    = CVTS.cvterm_id
-  ";
-    if (strcmp($side, 'as_object')==0) {
-      $sql .= " WHERE FR.object_id = :feature_id";
-    }
-    if (strcmp($side, 'as_subject')==0) {
-      $sql .= " WHERE FR.subject_id = :feature_id";
-    }
-    $sql .= " ORDER BY FR.rank";
-
-    // get the relationships
-    $results = chado_query($sql, array(':feature_id' => $feature_id));
-
-
-    // iterate through the relationships, put these in an array and add
-    // in the Drupal node id if one exists
-    $i=0;
-    $esql = "
-        SELECT entity_id
-        FROM {chado_entity}
-        WHERE data_table = 'feature' AND record_id = :feature_id";
-    $relationships = array();
-    while ($rel = $results->fetchObject()) {
-      $entity = db_query($esql, array(':feature_id' => $rel->subject_id))->fetchObject();
-      if ($entity) {
-        $rel->subject_entity_id = $entity->entity_id;
-      }
-      $entity = db_query($esql, array(':feature_id' => $rel->object_id))->fetchObject();
-      if ($entity) {
-        $rel->object_entity_id = $entity->entity_id;
-      }
-      $relationships[$i++] = $rel;
-    }
-    return $relationships;
-  }
-
-  /**
-   * Load the locations for a given feature
-   *
-   * @param $feature_id
-   *   The feature to look up locations for
-   * @param $side
-   *   Whether the feature is the scrfeature, 'as_parent', or feature, 'as_child'
-   * @param $aggregate
-   *   Whether or not to get the locations for related features
-   *
-   * @ingroup tripal_feature
-   */
-  private function get_featurelocs($feature_id, $side = 'as_parent', $aggregate = 1) {
-
-    $sql = "
-    SELECT
-       F.name, F.feature_id, F.uniquename,
-       FS.name as src_name, FS.feature_id as src_feature_id, FS.uniquename as src_uniquename,
-       CVT.name as cvname, CVT.cvterm_id,
-       CVTS.name as src_cvname, CVTS.cvterm_id as src_cvterm_id,
-       FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, FL.phase
-     FROM {featureloc} FL
-       INNER JOIN {feature} F   ON FL.feature_id = F.feature_id
-       INNER JOIN {feature} FS  ON FS.feature_id = FL.srcfeature_id
-       INNER JOIN {cvterm} CVT  ON F.type_id     = CVT.cvterm_id
-       INNER JOIN {cvterm} CVTS ON FS.type_id    = CVTS.cvterm_id
-   ";
-    if (strcmp($side, 'as_parent')==0) {
-      $sql .= "WHERE FL.srcfeature_id = :feature_id ";
-    }
-    if (strcmp($side, 'as_child')==0) {
-      $sql .= "WHERE FL.feature_id = :feature_id ";
-    }
-
-    $flresults = chado_query($sql, array(':feature_id' => $feature_id));
-
-    // copy the results into an array
-    $i=0;
-    $featurelocs = array();
-    while ($loc = $flresults->fetchObject()) {
-      // if a drupal node exists for this feature then add the nid to the
-      // results object
-
-      $loc->feid = tripal_get_chado_entity_id('feature', $loc->feature_id);
-      $loc->seid = tripal_get_chado_entity_id('feature', $loc->src_feature_id);
-      // add the result to the array
-      $featurelocs[$i++] = $loc;
-    }
-
-    // Add the relationship feature locs if aggregate is turned on
-    if ($aggregate and strcmp($side, 'as_parent')==0) {
-      // get the relationships for this feature without substituting any children
-      // for the parent. We want all relationships
-      $relationships = tripal_feature_get_aggregate_relationships($feature_id, 0);
-      foreach ($relationships as $rindex => $rel) {
-        // get the featurelocs for each of the relationship features
-        $rel_featurelocs = tripal_feature_load_featurelocs($rel->subject_id, 'as_child', 0);
-        foreach ($rel_featurelocs as $findex => $rfloc) {
-          $featurelocs[$i++] = $rfloc;
-        }
-      }
-    }
-
-    usort($featurelocs, 'chado_feature__residues_sort_locations');
-    return $featurelocs;
-  }
-}
-
-/**
- * Callback function for validating the chado_feature__residues_widget.
- */
-function chado_feature__residues_widget_validate($element, &$form_state) {
-
-}
-
-/**
- * Used to sort the list of relationship parts by start position
- *
- * @ingroup tripal_feature
- */
-function chado_feature__residues_sort_rel_parts_by_start($a, $b) {
-  foreach ($a as $type_name => $details) {
-    $astart = $a[$type_name]['start'];
-    break;
-  }
-  foreach ($b as $type_name => $details) {
-    $bstart = $b[$type_name]['start'];
-    break;
-  }
-  return strnatcmp($astart, $bstart);
-}
-/**
- * Used to sort the feature locs by start position
- *
- * @param $a
- *   One featureloc record (as an object)
- * @param $b
- *   The other featureloc record (as an object)
- *
- * @return
- *   Which feature location comes first
- *
- * @ingroup tripal_feature
- */
-function chado_feature__residues_sort_locations($a, $b) {
-  return strnatcmp($a->fmin, $b->fmin);
-}

tripal_chado/includes/TripalFields.old/chado_feature__seqlen.inc

@@ -1,83 +0,0 @@
-<?php
-
-class chado_feature__seqlen extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Sequence length';
-
-  // The default description for this field.
-  public static $default_description = 'A field for calculating the length of a sequence.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-   /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    foreach ($items as $delta => $item) {
-      $element[$delta] = array(
-        '#type' => 'markup',
-        '#markup' => $item['value'],
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-feature__seqlen'] =  array(
-      '#type' => 'value',
-      '#value' => 0,
-      '#title' => $element['#title'],
-      '#description' => $element['#description'],
-      '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
-      '#delta' => $delta,
-    );
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the residues so we can calculate teh length.
-    $residues = $form_state['values']['feature__residues']['und'][0]['chado-feature__residues'];
-    // Remove any white spaces.
-    if ($residues) {
-      $residues = preg_replace('/\s/', '', $residues);
-      $form_state['values']['feature__residues']['und'][0]['chado-feature__residues'] = $residues;
-      $items[0]['chado-feature__seqlen'] = strlen($residues);
-    }
-    else {
-      $items[0]['chado-feature__seqlen'] = '__NULL__';
-    }
-  }
-}

tripal_chado/includes/TripalFields.old/chado_gene__transcripts.inc

@@ -1,168 +0,0 @@
-<?php
-
-class chado_gene__transcripts extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Transcripts';
-
-  // The default description for this field.
-  public static $default_description = 'Transcripts of genes.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatter_settings_summary()
-   */
-  public function formatterSettingsSummary($view_mode) {
-
-  }
-
-  /**
-   * @see TripalField::formatter_settings_form()
-   */
-  public function formatterSettingsForm($view_mode, $form, &$form_state) {
-
-  }
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    // Get the settings
-    $settings = $display['settings'];
-
-    $headers = array('Transcript Name', 'Identifier', 'Type', 'Location');
-    $rows = array();
-    foreach ($items as $delta => $item) {
-
-      if (!$item['value']) {
-        continue;
-      }
-      $transcript = $item['value'];
-
-      // Get the field values
-      $feature_name = $transcript['name'];
-      $feature_uname = $transcript['identifier'];
-      $loc = $transcript['location'];
-      $type = $transcript['type'];
-
-      // Add a link i there is an entity.
-      if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
-        list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
-        $feature_name = l($feature_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
-      }
-      $rows[] = array($feature_name, $feature_uname, $type, $loc);
-    }
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'tripal_feature-table-transcripts-object',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => "",
-      'colgroups' => array(),
-      'empty' => 'This feature has no transcripts',
-    );
-    $content = theme_table($table);
-
-    // once we have our table array structure defined, we call Drupal's theme_table()
-    // function to generate the table.
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-
-    $field_name = $this->field['field_name'];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(
-        'type' => '',
-        'name' => '',
-        'identifier' => '',
-        'location' => '',
-      ),
-    );
-
-    // TODO: If the tripal_get_feature_relationships() slows this down then
-    // we may need to write a custom function to get the data.
-    $rels = tripal_get_feature_relationships($record);
-
-    // TODO: what if other transcripts names from SO are used. In that
-    // case we should support those too (using cvtermpath table to find them).
-    // mRNA should not be hard-coded below.
-
-    // Set the value to be a array of "table" rows.
-    $transcripts = array();
-    if (key_exists('part of', $rels['object']) &&
-        key_exists('mRNA', $rels['object']['part of'])) {
-     $transcripts =  $rels['object']['part of']['mRNA'];
-    }
-
-    $headers = array('Name' ,'Identifier', 'Location');
-    $rows = array();
-    $i = 0;
-    foreach ($transcripts as $transcript) {
-      // link the feature to it's node
-      $feature_name = $transcript->record->subject_id->name;
-
-      $locations = $transcript->child_featurelocs;
-      $loc = "";
-      foreach ($locations AS $location) {
-        $loc .= $location->srcfeature_name . ":" . $location->fmin . ".." . $location->fmax;
-      }
-      $type = $transcript->record->subject_id->type_id;
-      $entity->{$field_name}['und'][$i]['value'] = array(
-        'type' => $type->name,
-        'name' => $feature_name,
-        'identifier' => $transcript->record->subject_id->uniquename,
-        'location' => $loc,
-
-      );
-      // Add in the semantic web information that describes each key in the
-      // value array.
-      $entity->{$field_name}['und'][$i]['semantic_web'] = array(
-        'type' => $type->dbxref_id->db_id->name . ":" . $type->dbxref_id->accession,
-        'name' => tripal_get_chado_semweb_term('cvterm', 'name'),
-        'identifier' => tripal_get_chado_semweb_term('feature', 'uniquename'),
-        'location' => '',
-      );
-      if (property_exists($transcript->record->subject_id, 'entity_id')) {
-        $entity_id = $transcript->record->subject_id->entity_id;
-        $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $entity_id;
-      }
-      $i++;
-    }
-  }
-
-  /**
-   * We don't want a widget so override this function.
-   */
-  public static function widgetInfo() {
-    return array();
-  }
-}

tripal_chado/includes/TripalFields.old/chado_linker__contact.inc

@@ -1,312 +0,0 @@
-<?php
-
-class chado_linker__contact extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Contacts';
-
-  // The default description for this field.
-  public static $default_description = 'Associates an indviddual or organization with
-          this record';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    // Get the settings
-    $settings = $display['settings'];
-
-    $headers = array('Name', 'Description', 'Type');
-    $rows = array();
-
-    foreach ($items as $delta => $item) {
-      $contact = $item['value'];
-      if (!$contact) {
-        continue;
-      }
-
-      // Get the field values
-      $contact_name = $contact['name'];
-      $description = $contact['description'];
-      $type = $contact['type'];
-
-      // Add a link i there is an entity.
-      if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
-        list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
-        $contact_name = l($contact_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
-      }
-      $rows[] = array($contact_name, $description, $type);
-    }
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'tripal_linker-table-contact-object',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => "",
-      'colgroups' => array(),
-      'empty' => 'No contacts available',
-    );
-    $content = theme_table($table);
-
-    if (count($items) > 0) {
-      // once we have our table array structure defined, we call Drupal's theme_table()
-      // function to generate the table.
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $entity = $form['#entity'];
-    $field_name = $this->field['field_name'];
-
-    // Get the FK column that links to the base table.
-    $table_name = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Get the field defaults.
-    $record_id = '';
-    $fkey_value = $element['#entity']->chado_record_id;
-    $contact_id = '';
-    $name = '';
-
-    // If the field already has a value then it will come through the $items
-    // array.  This happens when editing an existing record.
-    if (count($items) > 0 and array_key_exists($delta, $items)) {
-      $record_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__' . $pkey, $record_id);
-      $contact_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__contact_id', $contact_id);
-      if ($contact_id) {
-        $contact = chado_generate_var('contact', array('contact_id' => $contact_id));
-        $name = $contact->name;
-      }
-    }
-
-    $schema = chado_get_schema('contact');
-
-    $widget['#table_name'] = $table_name;
-    $widget['#fkey_field'] = $fkey;
-    $widget['#theme'] = 'chado_linker__contact_widget';
-    $widget['#prefix'] =  "<span id='$table_name-$delta'>";
-    $widget['#suffix'] =  "</span>";
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-' . $table_name . '__' . $pkey] = array(
-      '#type' => 'value',
-      '#default_value' => $record_id,
-    );
-    $widget['chado-' . $table_name . '__' . $fkey] = array(
-      '#type' => 'value',
-      '#default_value' => $fkey_value,
-    );
-    $widget['chado-' . $table_name . '__contact_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $contact_id,
-    );
-
-    $widget['name'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Contact'),
-      '#default_value' => $name,
-      '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/contact',
-      '#ajax' => array(
-        'callback' => "chado_linker__contact_widget_form_ajax_callback",
-        'wrapper' => "$table_name-$delta",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-      '#maxlength' => 100000,
-    );
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    // Get the FK column that links to the base table.
-    $table_name = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-    $field_name = $this->field['field_name'];
-
-    // Get the field values.
-    $fkey_value = isset($form_state['values'][$field_name][$langcode][$delta]['value']) ? $form_state['values'][$field_name][$langcode][$delta]['value'] : '';
-    $contact_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id'] : '';
-    $name = isset($form_state['values'][$field_name][$langcode][$delta]['name']) ? $form_state['values'][$field_name][$langcode][$delta]['name'] : '';
-
-    // If the user provided a name then we want to set the foreign key
-    // value to be the chado_record_id
-    if ($name and !$contact_id) {
-      $contact = chado_generate_var('contact', array('name' => $name));
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id'] = $contact->contact_id;
-    }
-
-    // In the widgetForm function we automatically add the foreign key
-    // record.  But if the user did not provide a contact we want to take
-    // it out so that the Chado field_storage infrastructure won't try to
-    // write a record.
-    if (!$name and !$contact_id) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-    }
-
-    // If the user removed the contact from the contact_name field
-    // then we want to clear out the rest of the hidden values.
-    // Leave the primary key so the record can be deleted.
-    if (!$name and $contact_id) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id'] = '';
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $base_table = $details['record']->tablename;
-    $pkey = $schema['primary key'][0];
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-      'chado-' . $field_table . '__' . $pkey => '',
-      'chado-' . $field_table . '__' . $fkey_lcolumn => '',
-      'chado-' . $field_table . '__' . 'contact_id' => '',
-      // Ignore the synonym_sgml column for now.
-    );
-
-    $linker_table = $base_table . '_contact';
-    $options = array(
-      'return_array' => 1,
-      'include_fk' => array(
-        'contact_id' => array(
-          'type_id' => array(
-            'dbxref_id' => array(
-              'db_id' => TRUE,
-            ),
-          ),
-        ),
-        $fkey_lcolumn => TRUE,
-      ),
-    );
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-    $contact_linkers = $record->$linker_table;
-    if ($contact_linkers) {
-      foreach ($contact_linkers as $i => $contact_linker) {
-        $contact = $contact_linker->contact_id;
-        $entity->{$field_name}['und'][$i] = array(
-          'value' => array(
-            'type' => $contact->type_id ? $contact->type_id->name : '',
-            'name' => $contact->name,
-            'description' => $contact->description,
-          ),
-          // Add in the semantic web settings.  This array is expected by
-          // other Tripal modules that handle semantic web for fields.
-          'semantic_web' => array(
-            'type' => $contact->type_id ? $contact->type_id->dbxref_id->db_id->name . ':' . $contact->type_id->dbxref_id->accession : '',
-            'name' => tripal_get_chado_semweb_term('contact', 'name'),
-            'description' => tripal_get_chado_semweb_term('contact', 'description'),
-          ),
-          // Add in subfield mapping to Chado tables. This is used by the
-          // chado_field_storage for performing queries on sub element values.
-          // It should be a comma-separated list (no spacing) of the field names
-          // as foreign keys are followed starting from the Chado table to which
-          // this field maps.
-          'chado_mapping' => array(
-            'type' => 'type_id,name',
-            'name' => 'contact_id,name',
-            'description' => 'contact_id,name'
-          ),
-          'chado-' . $field_table . '__' . $pkey => $contact_linker->$pkey,
-          'chado-' . $field_table . '__' . $fkey_lcolumn => $contact_linker->$fkey_lcolumn->$fkey_lcolumn,
-          'chado-' . $field_table . '__' . 'contact_id' => $contact->contact_id
-        );
-
-        if (property_exists($contact, 'entity_id')) {
-          $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $contact->entity_id;
-        }
-      }
-    }
-  }
-}
-
-/**
- * An Ajax callback for the pub widget.
- */
-function chado_linker__contact_widget_form_ajax_callback($form, $form_state) {
-
-  $field_name = $form_state['triggering_element']['#parents'][0];
-  $delta = $form_state['triggering_element']['#parents'][2];
-
-  return $form[$field_name]['und'][$delta];
-}
-/**
- * Theme function for the pub widget.
- *
- * @param $variables
- */
-function theme_chado_linker__contact_widget($variables) {
-  $element = $variables['element'];
-
-  // These two fields were added to the widget to help identify the fields
-  // for layout.
-  $table_name = $element['#table_name'];
-  $fkey = $element['#fkey_field'];
-
-  $layout = "
-      <div class=\"pub-widget\">
-        <div class=\"pub-widget-item\">" .
-        drupal_render($element['name']) . "
-        </div>
-      </div>
-    ";
-
-  return $layout;
-}

tripal_chado/includes/TripalFields.old/chado_linker__cvterm.inc

@@ -1,370 +0,0 @@
-<?php
-
-class chado_linker__cvterm extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Annotations';
-
-  // The default description for this field.
-  public static $default_description = 'This record can be annotated with terms
-            from other vocabularies.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    $headers = array('Term', 'Definition', 'Is Not', 'Reference');
-    $rows = array();
-
-    $chado_table = $this->instance['settings']['chado_table'];
-    foreach ($items as $delta => $item) {
-      if ($item['chado-' . $chado_table . '__cvterm_id']) {
-        $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $item['chado-' . $chado_table . '__cvterm_id']));
-        $dbxref = $cvterm->dbxref_id;
-
-        // Build the accession.
-        $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
-        if ($dbxref->db_id->urlprefix) {
-          $accession = l($accession, tripal_get_dbxref_url($dbxref), array('attributes' => array('target' => '_blank')));
-        }
-
-        // Build the publication reference.
-        $pub_ref = '';
-        $pub_id = $item['chado-' . $chado_table . '__pub_id'];
-        if ($pub_id) {
-          $pub = chado_generate_var('pub', array('pub_id' => $pub_id));
-          $pub_ref = $pub->title;
-        }
-        $rows[] = array(
-          $accession,
-          $cvterm->definition,
-          $item['chado-' . $chado_table . '__is_not'] ? 'Yes' : '',
-          '',
-        );
-      }
-    }
-
-    // the $table array contains the headers and rows array as well as other
-    // options for controlling the display of the table.  Additional
-    // documentation can be found here:
-    // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => "$chado_table-table-terms",
-        'class' => 'tripal-data-table'
-      ),
-      'caption' => '',
-      'sticky' => FALSE,
-      'colgroups' => array(),
-      'empty' => 'There are no annotations of this type',
-    );
-
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => theme_table($table),
-      );
-    }
-  }
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $field_name = $this->field['field_name'];
-
-    $matches = array();
-    preg_match('/(.*?)__(\d+)/', $field_name, $matches);
-    // If the field name is not properly formatted then we can't tell what
-    // table and type this is.  So just return.
-    if (count($matches) != 3) {
-      return $widget;
-    }
-    $table_name = $matches[1];
-    $cv_id = $matches[2];
-
-    // Get the FK column that links to the base table.
-    $chado_table = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($chado_table);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Get the field defaults.
-    $record_id = '';
-    $fkey_value = $element['#entity']->chado_record_id;
-    $cvterm_name = '';
-    $cvterm_id = '';
-    $pub_id = '';
-    $uname = '';
-    $is_not = '';
-    $cvterm = NULL;
-
-    // If the field already has a value then it will come through the $items
-    // array.  This happens when editing an existing record.
-    if (array_key_exists($delta, $items)) {
-      $record_id = $items[$delta]['value'];
-      $cvterm_name = $items[$delta]['cvterm__name'];
-      $pub_id =$items[$delta]['chado-' . $table_name . '__pub_id'];
-      if ($pub_id && $pub_id != 1) {
-        $pub = chado_generate_var('pub', array('pub_id' => $pub_id));
-        $uname = $pub->uniquename;
-      }
-      $is_not = $items[$delta]['chado-' . $table_name . '__is_not'];
-      $cvterm_id = $items[$delta]['chado-' . $table_name . '__cvterm_id'];
-    }
-
-    // Check $form_state['values'] to see if an AJAX call set the values.
-    if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
-      // See example in chado_linker_contact.inc
-//       $record_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name);
-//       $fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
-//       $is_not = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_not');
-//       $cvterm_name = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--cvterm__name');
-    }
-
-    if ($cvterm_name) {
-      $cvterm = chado_generate_var('cvterm', array('cv_id' => $cv_id, 'name' => $cvterm_name));
-    }
-
-    $schema = chado_get_schema('cvterm');
-    $options = tripal_get_cv_select_options();
-
-    $widget['#table_name'] = $chado_table;
-    $widget['#fkey_field'] = $fkey;
-    $widget['#theme'] = 'chado_linker__cvterm_widget';
-    $widget['#prefix'] =  "<span id='$table_name-$delta'>";
-    $widget['#suffix'] =  "</span>";
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-' . $table_name . '__' . $pkey] = array(
-      '#type' => 'value',
-      '#default_value' => $record_id,
-    );
-    $widget['cv__cv_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $cv_id,
-    );
-    $widget['chado-' . $table_name . '__cvterm_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $cvterm ? $cvterm->cvterm_id : '',
-    );
-    $widget['chado-' . $table_name . '__' . $fkey] = array(
-      '#type' => 'value',
-      '#default_value' => $fkey_value,
-    );
-
-    $widget['cvterm__name'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Term Name'),
-      '#default_value' => $cvterm_name,
-      '#required' => $element['#required'],
-      '#maxlength' => array_key_exists('length', $schema['fields']['name']) ? $schema['fields']['name']['length'] : 255,
-      '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/' . $cv_id,
-      '#size' => 30
-    );
-
-    $widget['pub'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Publication'),
-      '#default_value' => $uname,
-      '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/pub',
-      '#ajax' => array(
-        'callback' => "chado_linker__pub_widget_form_ajax_callback",
-        'wrapper' => "$table_name-$delta",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-      '#maxlength' => 100000,
-    );
-
-    $widget['chado-' . $table_name . '__pub_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $pub_id ? $pub_id : 1,
-    );
-
-    $widget['chado-' . $table_name . '__is_not'] = array(
-      '#type' => 'checkbox',
-      '#title' => t('Is Not'),
-      '#default_value' => $is_not,
-      '#required' => $element['#required'],
-    );
-
-    $widget['cvterm__definition'] = array(
-      '#type' => 'item',
-      '#markup' => '',
-    );
-
-  }
-
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    $field_name = $this->field['field_name'];
-    $table_name = $this->instance['settings']['chado_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $base_table = $this->instance['settings']['base_table'];
-    $lfkey_field = key($schema['foreign keys'][$base_table]['columns']);
-    $rfkey_field = $schema['foreign keys'][$base_table]['columns'][$lfkey_field];
-
-
-    // If the form ID is field_ui_field_edit_form, then the user is editing the
-    // field's values in the manage fields form of Drupal.  We don't want
-    // to validate it as if it were being used in a data entry form.
-    if ($form_state['build_info']['form_id'] =='field_ui_field_edit_form') {
-      return;
-    }
-
-    // If the user provided a cv_id and a name then we want to set the
-    // foreign key value to be the chado_record_idd
-    $cvterm_name = isset($form_state['values'][$field_name][$langcode][$delta]['cvterm__name']) ? $form_state['values'][$field_name][$langcode][$delta]['cvterm__name'] : '';
-
-    if (!$cvterm_name) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__cvterm_id'] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $lfkey_field] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] = '';
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-
-    $matches = array();
-    preg_match('/(.*?)__(\d+)/', $field_name, $matches);
-    $table_name = $matches[1];
-    $cv_id = $matches[2];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $pkey = $schema['primary key'][0];
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-    // Set some defaults for the empty record.
-    $chado_record = $entity->chado_record;
-    $entity->{$field_name}['und'][0] = array(
-      'value' => '',
-      'chado-' . $field_table . '__' . $fkey_lcolumn => '',
-      'chado-' . $field_table . '__' . 'cvterm_id' => '',
-      // The pub column is present in the cell_line_cvterm, feature_cvterm,
-      // library_cvterm, phenotype_comparision_cvterm, phenotype_cvterm,
-      // stock_cvterm, and stock_relationship_cvterm.
-      'chado-' . $field_table . '__' . 'pub_id' => '',
-      // The is_not column is present in feature_cvterm and stock_cvterm tables.
-      'chado-' . $field_table . '__' . 'is_not' => '',
-      // The rank column is present in the cell_line_cvterm, expression_cvterm,
-      // feature_cvterm, phenotype_comparision_cvterm, phenotype_cvterm,
-      // and stock_cvterm tables.
-      'chado-' . $field_table . '__' . 'rank' => '',
-      // The cvterm_type_id is present in the expression_cvterm table.
-      'cvterm_type_id' => '',
-      // The following field are to help link the cvterm.
-      'cv__cv_id' => '',
-      'cvterm__name' => '',
-    );
-
-    // Get the annotations associated with this base record for this fields type.
-    $columns = array('*');
-    $match = array(
-      $fkey_lcolumn => $chado_record->$fkey_rcolumn,
-      'cvterm_id' => array(
-        'cv_id' => $cv_id,
-      ),
-    );
-    $options = array(
-      'return_array' => TRUE,
-      'order_by' => array('rank' => 'ASC')
-    );
-    $fcvterms = chado_select_record($field_table, $columns, $match, $options);
-    for ($i = 0; $i < count($fcvterms); $i++) {
-      $linker = $fcvterms[$i];
-      $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $linker->cvterm_id));
-      $entity->{$field_name}['und'][$i] = array(
-        'value' => $linker->$pkey,
-        'chado-' . $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn,
-        'chado-' . $field_table . '__' . 'cvterm_id' => $linker->cvterm_id,
-        'chado-' . $field_table . '__' . 'pub_id' => property_exists($linker, 'pub_id') ? $linker->pub_id : '',
-        'chado-' . $field_table . '__' . 'is_not' => property_exists($linker, 'is_not') ? $linker->is_not : '',
-        'chado-' . $field_table . '__' . 'rank' => property_exists($linker, 'rank') ? $linker->rank : '',
-        'chado-' . $field_table . '__' . 'cvterm_type_id' => property_exists($linker, 'cvterm_type_id') ? $linker->cvterm_type_id : '',
-        'cv__cv_id' => $cvterm->cv_id->cv_id,
-        'cvterm__name' => $cvterm->name,
-      );
-    }
-  }
-}
-
-/**
- * Theme function for the dbxref_id_widget.
- *
- * @param $variables
- */
-function theme_chado_linker__cvterm_widget($variables) {
-  $element = $variables['element'];
-
-  // These two fields were added to the widget to help identify the fields
-  // for layout.
-  $table_name = $element['#table_name'];
-  $fkey = $element['#fkey_field'];
-
-  $layout = "
-      <div class=\"annotation-cvterm-widget\">
-        <div class=\"annotation-cvterm-widget-item\">" .
-        drupal_render($element['cv__cv_id']) . "
-        </div>
-        <div class=\"annotation-cvterm-widget-item\">" .
-        drupal_render($element['cvterm__name']) . "
-        </div>
-        <div class=\"annotation-cvterm-widget-item\">" .
-        drupal_render($element['pub']) . "
-        </div>
-        <div class=\"annotation-cvterm-widget-item\">" .
-        drupal_render($element['chado-' . $table_name . '__is_not']) . "
-        </div>
-      </div>
-    ";
-
-  return $layout;
-}
-
-/**
- * An Ajax callback for the dbxref widget.
- */
-function chado_linker__cvterm_widget_form_ajax_callback($form, $form_state) {
-
-  $field_name = $form_state['triggering_element']['#parents'][0];
-  $delta = $form_state['triggering_element']['#parents'][2];
-
-
-  return $form[$field_name]['und'][$delta];
-}

tripal_chado/includes/TripalFields.old/chado_linker__cvterm_adder.inc

@@ -1,197 +0,0 @@
-<?php
-class chado_linker__cvterm_adder extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Add an Annotation Type';
-
-  // The default description for this field.
-  public static $default_description = 'This record may have any number of types of
-        annotations. Use this field to first add the type.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    // This field should never be viewed. It's to help add new cvterms
-    // when editing an entity.  So return nothing.
-    return '';
-  }
-
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-
-    // This field has no value field.  Just a fieldset for adding new annotation types.
-    $widget['#type'] = 'fieldset';
-    $widget['#title'] = $element['#title'];
-    $widget['#description'] = $element['#description'];
-    $widget['#group'] = 'entity_form_vtabs';
-
-    $widget['cvterm_class_adder_instructions'] = array(
-      '#type' => 'item',
-      '#markup' => t('You may add annotation types to this form by
-          providing a vocabulary name in the field above
-          and clicking the "Add Annotation Type" button.  This will add a
-          new field to the form above for the vocabulary you entered which
-          will allow users to associate terms from that vocabulary to
-          this record.'),
-    );
-
-    $options = tripal_get_cv_select_options();
-    $widget['value'] = array(
-      '#type' => 'select',
-      '#title' => t('Vocabulary'),
-      '#options' => $options,
-      '#description' => t("Please enter the vocabulary that contains terms
-          you want to allow users to use for annotations."),
-    );
-
-    //    $widget['#element_validate'] = array('chado_linker__cvterm_adder_widget_validate');
-
-    // When this button is clicked, the form will be validated and submitted.
-    // Therefore, we set custom submit and validate functions to override the
-    // default form submit.  In the validate function we set the form_state
-    // to rebuild the form so the submit function never actually gets called,
-    // but we need it or Drupal will run the default validate anyway.
-    // we also set #limit_validation_errors to empty so fields that
-    // are required that don't have values won't generate warnings.
-    $widget['cvterm_class_adder_button'] = array(
-      '#value' => t('Add Annotation Type'),
-      '#type' => 'submit',
-      '#name' => 'cvterm_class_adder_button',
-//      '#submit' => array('chado_linker__cvterm_adder_widget_submit'),
-      '#limit_validation_errors' => array(array($this->field['field_name'])),
-    );
-  }
-
-  /**
-   * @see TripalField::widgetFormValidate()
-   */
-  public function widgetFormValidate($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    if (array_key_exists('triggering_element', $form_state) and
-        $form_state['triggering_element']['#name'] == 'cvterm_class_adder_button') {
-          $this_field = $this->field;
-          $field_name = $this_field['field_name'];
-          $bundle = $entity->bundle;
-
-          // Get the base table name from the field annotations.
-          $base_table = $entity->chado_table;
-          $cvterm_class_adder = $form_state['values'][$base_table . '_cvterm'][$langcode][$delta]['value'];
-          $cv = chado_generate_var('cv', array('cv_id' => $cvterm_class_adder));
-
-          // Make sure a valid vocabulary is selected
-          if (!$cv) {
-            form_set_error("$field_name][$langcode][$delta][value", "Please select a vocabulary.");
-          }
-          else {
-            // Make sure this vocabulary doesn't already have a field
-            if (key_exists($field_name . '__' . $cv->cv_id, $form_state['values'])) {
-              form_set_error("$field_name][$langcode][$delta][wrapper][terms_name", "Field for this vocabulary already exists. Please select another vocabulary.");
-            }
-          }
-        }
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    // Add the new field to the entity
-    if (array_key_exists('triggering_element', $form_state) and
-        $form_state['triggering_element']['#name'] == 'cvterm_class_adder_button') {
-
-          $form_state['rebuild'] = TRUE;
-          $this_field = $this->field;
-          $field_name = $this_field['field_name'];
-          $bundle = $entity->bundle;
-
-          // Get the base table name from the field annotations.
-          $base_table = $entity->chado_table;
-          $cvterm_class_adder = $form_state['values'][$base_table . '_cvterm'][$langcode][$delta]['value'];
-
-          // Get the vocabulary.
-          //$cvterm_class_adder = tripal_chado_get_field_form_values($field_name, $form_state);
-          $cv = chado_generate_var('cv', array('cv_id' => $cvterm_class_adder));
-
-          if (!$cv) {
-            return;
-          }
-
-          $type_field_name = $field_name . '__' . $cv->cv_id;
-
-          // The field name is the table name in this case. We want to get the
-          // primary key as this should be the field that maps th the value.
-          $schema = chado_get_schema($field_name);
-          $pkey = $schema['primary key'][0];
-
-          // Add the field if it doesn't already exists.
-          $field = field_info_field($type_field_name);
-          if (!$field) {
-            $create_info = array(
-              'field_name' => $type_field_name,
-              'type' => 'chado_linker__cvterm',
-              'cardinality' => FIELD_CARDINALITY_UNLIMITED,
-              'locked' => FALSE,
-              'storage' => array(
-                'type' => 'field_chado_storage',
-              ),
-              'settings' => array(
-                'chado_table' => $field_name,
-                'chado_column' => $pkey,
-                'base_table' => $base_table,
-              ),
-            );
-            $field = field_create_field($create_info);
-          }
-
-          // Attach the field to the bundle if it isn't already.
-          if (!$field or !array_key_exists('bundles', $field) or
-              !array_key_exists('TripalEntity', $field['bundles']) or
-              !in_array($bundle, $field['bundles']['TripalEntity'])) {
-                $createInstanceInfo = array(
-                  'field_name' => $type_field_name,
-                  'entity_type' => 'TripalEntity',
-                  'bundle' => $bundle,
-                  'label' => ucfirst(preg_replace('/_/', ' ', $cv->name)),
-                  'description' => "Annotations from the $cv->name vocabulary",
-                  'required' => FALSE,
-                  'settings' => array(),
-                  'widget' => array(
-                    'type' => 'chado_linker__cvterm_widget',
-                    'settings' => array(
-                      'display_label' => 1,
-                    ),
-                  ),
-                  'display' => array(
-                    'default' => array(
-                      'label' => 'above',
-                      'type' => 'chado_linker__cvterm_formatter',
-                      'settings' => array(),
-                    ),
-                  ),
-                );
-                $instance = field_create_instance($createInstanceInfo);
-              }
-        }
-  }
-
-}

tripal_chado/includes/TripalFields.old/chado_linker__dbxref.inc

@@ -1,418 +0,0 @@
-<?php
-
-/**
- * This class provides fields for adding database cross-references.
- *
- * It supports two types of cross-references. The primary cross reference
- * which is usually in the base table as an FK to the dbxref table, and
- * secondary cross references which are in a linking table that connects
- * the base table with the dbxref table.
- *
- */
-class chado_linker__dbxref extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Cross references';
-
-  // The default description for this field.
-  public static $default_description = 'This record can be cross referenced with a record in
-          another online database. This field is intended for one or more
-          references.  At a minimum, the database and accession must be provided.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    $chado_table = $this->instance['settings']['chado_table'];
-    $content = '';
-    foreach ($items as $delta => $item) {
-      if (!$item['value']) {
-        continue;
-      }
-      $content = $item['value']['vocabulary'] . ':' . $item['value']['accession'];
-      if ($item['value']['URL']) {
-        $content = l($content, $item['value']['URL'], array('attributes' => array('target' => '_blank')));
-      }
-      $element[$delta] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-
-    if (count($element) == 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => '',
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the FK column that links to the base table.
-    $chado_table = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($chado_table);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Get the field defaults.
-    $record_id = '';
-    $fkey_value = $element['#entity']->chado_record_id;
-    $dbxref_id = '';
-    $db_id = '';
-    $accession = '';
-    $version = '';
-    $description = '';
-
-    // If the field already has a value then it will come through the $items
-    // array.  This happens when editing an existing record.
-    if (count($items) > 0 and array_key_exists($delta, $items)) {
-      $record_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $pkey, $record_id);
-      $fkey_value = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $fkey, $fkey_value);
-      $dbxref_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__dbxref_id', $dbxref_id);
-      $db_id = tripal_get_field_item_keyval($items, $delta, 'db_id', $db_id);
-      $accession = tripal_get_field_item_keyval($items, $delta, 'accession', $accession);
-      $version = tripal_get_field_item_keyval($items, $delta, 'version', $version);
-      $description = tripal_get_field_item_keyval($items, $delta, 'description', $description);
-    }
-
-    // Check $form_state['values'] to see if an AJAX call set the values.
-    if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
-      $record_id = $form_state['values'][$field_name]['und'][$delta][$field_table . '__' . $pkey];
-      $fkey_value = $form_state['values'][$field_name]['und'][$delta][$field_table . '__' . $fkey];
-      $dbxref_id = $form_state['values'][$field_name]['und'][$delta][$field_table . '__dbxref_id'];
-      $db_id = $form_state['values'][$field_name]['und'][$delta]['db_id'];
-      $accession = $form_state['values'][$field_name]['und'][$delta]['accession'];
-      $version = $form_state['values'][$field_name]['und'][$delta]['version'];
-      $description = $form_state['values'][$field_name]['und'][$delta]['description'];
-    }
-
-    $schema = chado_get_schema('dbxref');
-    $options = tripal_get_db_select_options();
-
-    $widget['#table_name'] = $chado_table;
-    $widget['#fkey_field'] = $fkey;
-    //$widget['#element_validate'] = array('chado_linker__dbxref_widget_validate');
-    $widget['#theme'] = 'chado_linker__dbxref_widget';
-    $widget['#prefix'] =  "<span id='$field_name-dbxref--db-id-$delta'>";
-    $widget['#suffix'] =  "</span>";
-
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-' . $field_table . '__' . $pkey] = array(
-      '#type' => 'value',
-      '#default_value' => $record_id,
-    );
-    $widget['chado-' . $field_table . '__' . $fkey] = array(
-      '#type' => 'value',
-      '#default_value' => $fkey_value,
-    );
-    $widget['chado-' . $field_table . '__dbxref_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $dbxref_id,
-    );
-    $widget['dbxref_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $dbxref_id,
-    );
-    $widget['db_id'] = array(
-      '#type' => 'select',
-      '#title' => t('Database'),
-      '#options' => $options,
-      '#required' => $element['#required'],
-      '#default_value' => $db_id,
-      '#ajax' => array(
-        'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
-        'wrapper' => "$field_name-dbxref--db-id-$delta",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-    );
-    $widget['accession'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Accession'),
-      '#default_value' => $accession,
-      '#required' => $element['#required'],
-      '#maxlength' => array_key_exists('length', $schema['fields']['accession']) ? $schema['fields']['accession']['length'] : 255,
-      '#size' => 15,
-      '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/dbxref/' . $db_id,
-      '#ajax' => array(
-        'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
-        'wrapper' => "$field_name-dbxref--db-id-$delta",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-      '#disabled' => $db_id ? FALSE : TRUE,
-    );
-    $widget['version'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Version'),
-      '#default_value' => $version,
-      '#maxlength' => array_key_exists('length', $schema['fields']['version']) ? $schema['fields']['version']['length'] : 255,
-      '#size' => 5,
-      '#disabled' => $db_id ? FALSE : TRUE,
-    );
-    $widget['description'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Description'),
-      '#default_value' => $description,
-      '#size' => 20,
-      '#disabled' => $db_id ? FALSE : TRUE,
-    );
-    if (!$db_id) {
-      $widget['links'] = array(
-        '#type' => 'item',
-        '#markup' => l('Add a database', 'admin/tripal/legacy/tripal_db/add', array('attributes' => array('target' => '_blank')))
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::validate()
-   */
-  public function validate($entity_type, $entity, $field, $items, &$errors) {
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $table_name = $this->instance['settings']['chado_table'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-
-    // Get the field values.
-    foreach ($items as $delta => $values) {
-
-      // Get the field values.
-      $dbxref_id = $values['chado-' . $field_table . '__dbxref_id'];
-      $db_id = $values['db_id'];
-      $accession = $values['accession'];
-      $version = $values['version'];
-      $description = $values['description'];
-
-      // Make sure that if a database ID is provided that an accession is also
-      // provided.  Here we use the form_set_error function rather than the
-      // form_error function because the form_error will add a red_highlight
-      // around all of the fields in the fieldset which is confusing as it's not
-      // clear to the user what field is required and which isn't. Therefore,
-      // we borrow the code from the 'form_error' function and append the field
-      // so that the proper field is highlighted on error.
-      if (!$db_id and $accession) {
-        $errors[$field_name][$delta]['und'][] = array(
-          'message' => t("A database and the accession must both be provided."),
-          'error' => 'chado_linker__dbxref',
-        );
-      }
-      if ($db_id and !$accession) {
-        $errors[$field_name][$delta]['und'][] = array(
-          'message' => t("A database and the accession must both be provided."),
-          'error' => 'chado_linker__dbxref',
-        );
-      }
-      if (!$db_id and !$accession and ($version or $description)) {
-        $errors[$field_name][$delta]['und'][] = array(
-          'message' => t("A database and the accession must both be provided."),
-          'error' => 'chado_linker__dbxref',
-        );
-      }
-    }
-  }
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $table_name = $this->instance['settings']['chado_table'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Get the field values.
-    $dbxref_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__dbxref_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__dbxref_id'] : '';
-    $db_id = isset($form_state['values'][$field_name][$langcode][$delta]['db_id']) ? $form_state['values'][$field_name][$langcode][$delta]['db_id'] : '';
-    $accession = isset($form_state['values'][$field_name][$langcode][$delta]['accession']) ? $form_state['values'][$field_name][$langcode][$delta]['accession'] : '';
-    $version = isset($form_state['values'][$field_name][$langcode][$delta]['version']) ? $form_state['values'][$field_name][$langcode][$delta]['version'] : '';
-    $description = isset($form_state['values'][$field_name][$langcode][$delta]['description']) ? $form_state['values'][$field_name][$langcode][$delta]['description'] : '';
-
-    // If the dbxref_id does not match the db_id + accession then the user
-    // has selected a new dbxref record and we need to update the hidden
-    // value accordingly.
-    if ($db_id and $accession) {
-      $dbxref = chado_generate_var('dbxref', array('db_id' => $db_id, 'accession' => $accession));
-      if ($dbxref and $dbxref->dbxref_id != $dbxref_id) {
-        $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__dbxref_id'] = $dbxref->dbxref_id;
-        $form_state['values'][$field_name][$langcode][$delta]['dbxref_id'] = $dbxref->dbxref_id;
-      }
-    }
-    // If the db_id and accession are not set, then remove the linker FK
-    // value to the base table, but leave the primary key so the record
-    // can be deleted.
-    else {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__dbxref_id'] = '';
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $record->tablename;
-
-    $schema = chado_get_schema($field_table);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-      'chado-' . $field_table . '__' . $pkey => '',
-      'chado-' . $field_table . '__' . $fkey => '',
-      'chado-' . $field_table . '__dbxref_id' => '',
-      'dbxref_id' => '',
-      'db_id' => '',
-      'accession' => '',
-      'version' => '',
-      'description' => '',
-    );
-
-    $linker_table = $base_table . '_dbxref';
-    $options = array('return_array' => 1);
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-    if (count($record->$linker_table) > 0) {
-      $i = 0;
-      foreach ($record->$linker_table as $index => $linker) {
-        $dbxref = $linker->dbxref_id;
-        $URL = tripal_get_dbxref_url($dbxref);
-        $entity->{$field_name}['und'][$i] = array(
-          'value' => array(
-            'vocabulary' => $dbxref->db_id->name,
-            'accession' => $dbxref->accession,
-            'URL' => $URL,
-          ),
-          'chado-' . $field_table . '__' . $pkey => $linker->$pkey,
-          'chado-' . $field_table . '__' . $fkey => $linker->$fkey->$fkey,
-          'chado-' . $field_table . '__dbxref_id' => $dbxref->dbxref_id,
-          'dbxref_id' => $dbxref->dbxref_id,
-          'db_id' => $dbxref->db_id->db_id,
-          'accession' => $dbxref->accession,
-          'version' => $dbxref->version,
-          'description' => $dbxref->description,
-        );
-        $i++;
-      }
-    }
-  }
-}
-/**
- * Theme function for the dbxref_id_widget.
- *
- * @param $variables
- */
-function theme_chado_linker__dbxref_widget($variables) {
-  $element = $variables['element'];
-
-  // These two fields were added to the widget to help identify the fields
-  // for layout.
-  $table_name = $element['#table_name'];
-  $fkey = $element['#fkey_field'];
-
-  $layout = "
-      <div class=\"secondary-dbxref-widget\">
-        <div class=\"secondary-dbxref-widget-item\">" .
-        drupal_render($element['db_id']) . "
-        </div>
-        <div class=\"secondary-dbxref-widget-item\">" .
-        drupal_render($element['accession']) . "
-        </div>
-        <div class=\"secondary-dbxref-widget-item\">" .
-        drupal_render($element['version']) . "
-        </div>
-        <div class=\"secondary-dbxref-widget-item\">" .
-        drupal_render($element['description']) . "
-        </div>
-        <div class=\"secondary-dbxref-widget-links\">" . drupal_render($element['links']) . "</div>
-      </div>
-    ";
-
-  return $layout;
-}
-
-/**
- * An Ajax callback for the dbxref widget.
- */
-function chado_linker__dbxref_widget_form_ajax_callback($form, $form_state) {
-
-  $field_name = $form_state['triggering_element']['#parents'][0];
-  $delta = $form_state['triggering_element']['#parents'][2];
-  $field = field_info_field($field_name);
-  $field_type = $field['type'];
-  $field_table = $field['settings']['chado_table'];
-  $field_column = $field['settings']['chado_column'];
-  $field_prefix = 'chado-' . $field_table . '__dbxref_id';
-
-  // Check to see if this dbxref already exists. If not then
-  // give a notice to the user that the dbxref will be added.
-  $db_id = $form_state['values'][$field_name]['und'][$delta]['db_id'];
-  $db_id = $form_state['values'][$field_name]['und'][$delta]['accession'];
-  if ($db_id and $accession) {
-    $values = array(
-      'db_id' => $db_id,
-      'accession' => $accession,
-    );
-    $options = array('is_duplicate' => TRUE);
-    $has_duplicate = chado_select_record('dbxref', array('*'), $values, $options);
-    if (!$has_duplicate) {
-      drupal_set_message('The selected cross reference is new and will be added for future auto completions.');
-    }
-  }
-
-  return $form[$field_name]['und'][$delta];
-}

tripal_chado/includes/TripalFields.old/chado_linker__expression.inc

@@ -1,184 +0,0 @@
-<?php
-
-class chado_linker__expression extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Expression';
-
-  // The default description for this field.
-  public static $default_description = 'Associates an expression with
-          this record.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    // Get the settings
-    $settings = $display['settings'];
-
-    $content = '';
-    $rows = array();
-    foreach ($items as $delta => $item) {
-      if (!$item['value']) {
-        continue;
-      }
-      // Iterate through all of the children of the $item['value']. Add each
-      // one as an independent row in the table.
-
-      foreach ($item['value'] as $key => $value) {
-
-        // If this key is the name, then we want to link to the entity if one
-        // exists.
-        if ($key == 'name') {
-          if (array_key_exists('entity', $item['value']) and $item['value']['$entity_id']) {
-            list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
-            $value = l($value, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
-          }
-        }
-        // If this key is the publication then we want to get the citation
-        // and link to the pub if an entity exits.
-        if ($key == 'publication') {
-          $pub = $value['Citation'];
-          if (array_key_exists('publication', $item) and array_key_exists('entity', $item['publication'][0])) {
-            $entity_id = $item['publication'][0]['entity_id'];
-            $title =  $item['value']['publication']['Title'];
-            $link = l($title, 'bio_data/' . $entity_id);
-            $pub = preg_replace("/$title/", $link, $pub);
-          }
-          $value = $pub;
-        }
-        // Add the item as a new row.
-        $rows[] = array(
-          array(
-            'data' => ucfirst(str_replace('_', ' ', $key)),
-            'header' => TRUE,
-            'width' => '20%',
-          ),
-          $value
-        );
-      }
-    }
-    $table = array(
-      'header' => array(),
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'tripal_linker-table-expression-object',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => "",
-      'colgroups' => array(),
-      'empty' => 'There is no curated expression data.',
-    );
-    $content = theme_table($table);
-    if (count($items) > 0) {
-      // once we have our table array structure defined, we call Drupal's theme_table()
-      // function to generate the table.
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-    $record = $details['record'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $base_table = $details['record']->tablename;
-    $pkey = $schema['primary key'][0];
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-    );
-
-    $linker_table = $base_table . '_expression';
-    $options = array(
-      'return_array' => 1,
-    );
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-    $exp_linkers = $record->$linker_table;
-    if ($exp_linkers) {
-      foreach ($exp_linkers as $i => $exp_linker) {
-
-        // Because the unqiuename is a text field we must expand it.
-        $expression = $exp_linker->expression_id;
-        $expression = chado_expand_var($expression, 'field', 'expression.uniquename', $options);
-
-        // Set the values that will be seen by the user on the page and in
-        // web services, or anwhere this field is viewed.
-        $entity->{$field_name}['und'][$i]['value'] = array(
-          'name' => $expression->uniquename,
-          'description' => $expression->description,
-          //'md5checksum' => $expression->md5checksum,
-        );
-
-        // Add the pub information if a real pub is associated with the record.
-        $pub = $exp_linker->pub_id;
-        if ($pub->uniquename != 'null') {
-          $pub_details = tripal_get_minimal_pub_info($pub);
-
-          $entity->{$field_name}['und'][$i]['value']['publication'] = $pub_details;
-          $entity->{$field_name}['und'][$i]['value']['publication']['type'] = $pub->type_id->name;
-          if (property_exists($pub, 'entity_id')) {
-            $entity->{$field_name}['und'][$i]['publication'][0]['value']['entity'] = 'TripalEntity:' . $pub->entity_id;
-          }
-        }
-
-        // Add the linker_expressionprop
-        $linkerprop_table =  $linker_table . 'prop';
-        if (chado_table_exists($linkerprop_table)) {
-          $exp_linker = chado_expand_var($exp_linker, 'table', $linkerprop_table, $options);
-          $exp_linkerprops = $exp_linker->feature_expressionprop;
-          if ($exp_linkerprops) {
-            foreach ($exp_linkerprops AS $linkerprop) {
-              $entity->{$field_name}['und'][$i]['value'][$linkerprop->type_id->name] = $linkerprop->value;
-            }
-          }
-        }
-        // Add the fields for the widget form.  The name requres the following
-        // format if the fields should be used as values for insertint/updating
-        // into the chado table:  [table_name]__[field_name]
-        $entity->{$field_name}['und'][$i][$linker_table . '__expression_id'] = $expression->expression_id;
-        $entity->{$field_name}['und'][$i][$linker_table . '__uniquename'] = $expression->uniquename;
-        //$entity->{$field_name}['und'][$i][$linker_table . '__md5checksum'] = $expression->md5checksum;
-        $entity->{$field_name}['und'][$i][$linker_table . '__description'] = $expression->description;
-
-      }
-    }
-  }
-
-  /**
-   * We don't want a widget so override this function.
-   */
-  public static function widgetInfo() {
-    return array();
-  }
-
-}

tripal_chado/includes/TripalFields.old/chado_linker__featureloc.inc

@@ -1,306 +0,0 @@
-<?php
-
-class chado_linker__featureloc extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Aligned Locations';
-
-  // The default description for this field.
-  public static $default_description = 'Locations on landmark sequences where the feature is aligned.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatter_settings_summary()
-   */
-  public function formatter_settings_summary($field, $instance,
-      $view_mode) {
-
-  }
-
-  /**
-   * @see TripalField::formatter_settings_form()
-   */
-  public function formatter_settings_form($field, $instance,
-      $view_mode, $form, &$form_state) {
-
-
-
-  }
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    // Get the settings
-    $settings = $display['settings'];
-
-    $rows = array();
-    $headers = array('Aligned Feature' ,'Feature Type', 'Alignment Location');
-
-    foreach ($items as $delta => $item) {
-      if (!$item['value']) {
-        continue;
-      }
-
-      $alignment = $item['value'];
-      $feature_name = $alignment['name'];
-      $feature_loc = '';
-      $strand = '.';
-      if ($alignment['strand'] == -1) {
-        $strand = '-';
-      }
-      elseif ($alignment['strand'] == 1) {
-         $strand = '+';
-      }
-      // if this is a match then make the other location
-      if(array_key_exists('right_feature', $alignment)){
-        $rstrand = '.';
-        if ($alignment['right_strand'] == -1) {
-          $rstrand = '-';
-        }
-        elseif ($alignment['right_strand'] == 1) {
-          $rstrand = '+';
-        }
-        $feature_loc = $feature['name'] .":". ($alignment['fmin'] + 1) . ".." . $alignment['fmax'] . " " . $strand;
-        $feature_loc .= "<br>" . $alignment['name'] .":". ($alignment['right_fmin'] + 1) . ".." . $alignment['right_fmax'] . " " . $rstrand;
-      }
-      else {
-        $feature_loc = $alignment['name'] .":". ($alignment['fmin'] + 1) . ".." . $alignment['fmax'] . " " . $strand;
-      }
-
-      $rows[] = array(
-        $feature_name,
-        $alignment['type'],
-        $feature_loc
-      );
-    }
-
-
-    // the $table array contains the headers and rows array as well as other
-    // options for controlling the display of the table.  Additional
-    // documentation can be found here:
-    // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'tripal_feature-table-alignments',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => '',
-      'colgroups' => array(),
-      'empty' => 'This record is not aligned to any locations.',
-    );
-
-    // once we have our table array structure defined, we call Drupal's theme_table()
-    // function to generate the table.
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => theme_table($table),
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-    $record = $details['record'];
-    $settings = $this->field['settings'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-    );
-
-    $options = array(
-      'return_array' => TRUE,
-      'include_fk' => array(
-        'srcfeature_id' => array(
-          'type_id' => 1,
-        ),
-        'feature_id' => array(
-          'type_id' => 1
-        ),
-      )
-    );
-    $feature = chado_expand_var($record, 'table', 'featureloc', $options);
-
-    // Get alignments as child
-    $cfeaturelocs = $feature->featureloc->feature_id;
-    if (!$cfeaturelocs) {
-      $cfeaturelocs = array();
-    }
-    // Get alignment as parent
-    $pfeaturelocs = $feature->featureloc->srcfeature_id;
-    if (!$pfeaturelocs) {
-      $pfeaturelocs = array();
-    }
-
-    // Get matched alignments (those with an itermediate 'match' or 'EST_match', etc
-    $mfeaturelocs = self::get_matched_alignments($feature);
-    $feature->matched_featurelocs = $mfeaturelocs;
-
-    // Combine all three alignments into a single array for printing together in
-    // a single list
-    $alignments = array();
-    foreach ($pfeaturelocs as $featureloc) {
-      // if type is a 'match' then ignore it. We will handle those below
-      if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
-        continue;
-      }
-      $alignments[] = array(
-        'name' => $featureloc->feature_id->name,
-        'type' => $featureloc->feature_id->type_id->name,
-        'fmin' => $featureloc->fmin,
-        'fmax' => $featureloc->fmax,
-        'phase' => $featureloc->phase,
-        'strand' => $featureloc->strand,
-      );
-    }
-    foreach ($cfeaturelocs as $featureloc) {
-      // if type is a 'match' then ignore it. We will handle those below
-      if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
-        continue;
-      }
-      $alignments[] = array(
-        'name' => $featureloc->srcfeature_id->name,
-        'type' => $featureloc->srcfeature_id->type_id->name,
-        'fmin' => $featureloc->fmin,
-        'is_fmin_partial' => $featureloc->is_fmin_partial,
-        'fmax' => $featureloc->fmax,
-        'is_fmax_partial' => $featureloc->is_fmax_partial,
-        'phase' => $featureloc->phase,
-        'strand' => $featureloc->strand,
-      );
-    }
-    // in matching features, the left feature is always the feature
-    // provided to this function.
-    foreach ($mfeaturelocs as $featureloc) {
-      // get more information about the right feature
-      $select = array('feature_id' => $featureloc->right_srcfeature_id);
-      $rfeature = chado_generate_var('feature', $select);
-      // now add to the list
-      $alignments[] = array(
-        'name' => $rfeature->name,
-        'type' => $rfeature->type_id->name,
-        'fmin' => $featureloc->left_fmin,
-        'is_fmin_partial' => $featureloc->left_is_fmin_partial,
-        'fmax' => $featureloc->left_fmax,
-        'is_fmax_partial' => $featureloc->left_is_fmax_partial,
-        'phase' => $featureloc->left_phase,
-        'strand' => $featureloc->left_strand,
-        'right_fmin' => $featureloc->right_fmin,
-        'right_is_fmin_partial' => $featureloc->right_is_fmin_partial,
-        'right_fmax' => $featureloc->right_fmax,
-        'right_is_fmax_partial' => $featureloc->right_is_fmax_partial,
-        'right_phase' => $featureloc->right_phase,
-        'right_strand' => $featureloc->right_strand,
-      );
-    }
-    $i = 0;
-    foreach ($alignments as $alignment) {
-      $entity->{$field_name}['und'][$i]['value'] = $alignment;
-      $i++;
-    }
-  }
-  /**
-   * This function is for features that align through an intermediate such
-   * as 'EST_match' or 'match'.  This occurs in the case where two sequences
-   * align but where one does not align perfectly.  Some ESTs may be in a contig
-   * but not all of the EST.  Portions may overhang and not be included in the
-   * consensus if quality is bad.
-   * For example:
-   *    Feature 1: Contig --------------------
-   *    Feature 2: EST_match           -------
-   *    Feature 3: EST                 ---------
-   *
-   * The feature provided to the function will always be the feature 1.  The
-   * featureloc columns prefixed with 'right' (e.g. right_fmin) belong to the
-   * alignment of feature 3 with feature 2
-   *
-   * Features may align to more than one feature and are not matches. We do
-   * not want to include these, so we have to filter on the SO terms:
-   * match, or %_match
-   *
-   * @ingroup tripal_feature
-   */
-   static public function get_matched_alignments($feature) {
-
-     $sql = "
-       SELECT
-         FL1.featureloc_id    as left_featureloc_id,
-         FL1.srcfeature_id    as left_srcfeature_id,
-         FL1.feature_id       as left_feature_id,
-         FL1.fmin             as left_fmin,
-         FL1.is_fmin_partial  as left_is_fmin_partial,
-         FL1.fmax             as left_fmax,
-         FL1.is_fmax_partial  as left_is_fmax_partial,
-         FL1.strand           as left_strand,
-         FL1.phase            as left_phase,
-         FL1.locgroup         as left_locgroup,
-         FL1.rank             as left_rank,
-         FL2.featureloc_id    as right_featureloc_id,
-         FL2.srcfeature_id    as right_srcfeature_id,
-         FL2.feature_id       as right_feature_id,
-         FL2.fmin             as right_fmin,
-         FL2.is_fmin_partial  as right_is_fmin_partial,
-         FL2.fmax             as right_fmax,
-         FL2.is_fmax_partial  as right_is_fmax_partial,
-         FL2.strand           as right_strand,
-         FL2.phase            as right_phase,
-         FL2.locgroup         as right_locgroup,
-         FL2.rank             as right_rank
-       FROM {feature} F1
-         INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id
-         INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id
-         INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id
-         INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id
-       WHERE
-         F1.feature_id = :feature_id  AND
-         (CVT2.name = 'match' or CVT2.name like '%_match')
-       ORDER BY FL1.fmin
-     ";
-
-     $results = chado_query($sql, array(':feature_id' => $feature->feature_id));
-
-     // iterate through the results and add them to our featurelocs array
-     $featurelocs = array();
-     while ($fl = $results->fetchObject()) {
-       // ignore featurelocs where the left and right srcfeature is the same
-       if (strcmp($fl->left_srcfeature_id, $fl->right_srcfeature_id) == 0) {
-         continue;
-       }
-       $featurelocs[] = $fl ;
-     }
-     return $featurelocs;
-   }
-
-  /**
-   * We don't want a widget so override this function.
-   */
-  public static function widgetInfo() {
-    return array();
-  }
-
-}
-

tripal_chado/includes/TripalFields.old/chado_linker__featurepos.inc

@@ -1,157 +0,0 @@
-<?php
-
-class chado_linker__featurepos extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Map positions';
-
-  // The default description for this field.
-  public static $default_description = 'Map position of a sequence.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatter_settings_summary()
-   */
-  public function formatter_settings_summary($field, $instance,
-      $view_mode) {
-
-  }
-
-  /**
-   * @see TripalField::formatter_settings_form()
-   */
-  public function formatter_settings_form($field, $instance,
-      $view_mode, $form, &$form_state) {
-
-
-
-  }
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    // Get the settings
-    $settings = $display['settings'];
-
-    $rows = array();
-    $headers = array('Map', 'Mapped Feature', 'Position');
-
-    foreach ($items as $delta => $item) {
-      if (!$item['value']) {
-        continue;
-      }
-      $val = $item['value'];
-      $map_name = $val['map_name'];
-      $mapped_feature_name = $val['mapped_feature_name'];
-      $position = $val['position'];
-
-      $rows[] = array(
-        $map_name,
-        $mapped_feature_name,
-        $position
-      );
-    }
-
-
-    // the $table array contains the headers and rows array as well as other
-    // options for controlling the display of the table.  Additional
-    // documentation can be found here:
-    // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'tripal_feature-table-map-positions',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => '',
-      'colgroups' => array(),
-      'empty' => 'This record is not found on any map.',
-    );
-
-    // once we have our table array structure defined, we call Drupal's theme_table()
-    // function to generate the table.
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => theme_table($table),
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-    $record = $details['record'];
-    $settings = $this->field['settings'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-    );
-
-    $options = array(
-      'return_array' => TRUE,
-      'include_fk' => array(
-        'srcfeature_id' => array(
-          'type_id' => 1,
-        ),
-        'feature_id' => array(
-          'type_id' => 1
-        ),
-      )
-    );
-    $feature = chado_expand_var($record, 'table', 'featurepos', $options);
-
-    // iterate through the results and add them to our featureposes array
-    $featureposes = array();
-    if (isset($feature->featurepos->feature_id)) {
-       foreach ($feature->featurepos->feature_id AS $featurepos) {
-         $featuremap_id = $featurepos->featuremap_id;
-         $featuremap = chado_generate_var('featuremap', array('featuremap_id' => $featuremap_id));
-         $map_feature_id = $featurepos->map_feature_id;
-         $map_feature = chado_generate_var('feature', array('feature_id' => $map_feature_id));
-         $mappos = $featurepos->mappos;
-         $featureposes [] = array (
-           'map_name' => $featuremap->name,
-           'mapped_feature_name' => $map_feature->name,
-           'position' => $mappos
-         );
-      }
-    }
-    $i = 0;
-    foreach ($featureposes as $position) {
-      $entity->{$field_name}['und'][$i]['value'] = $position;
-      $i++;
-    }
-  }
-
-  /**
-   * We don't want a widget so override this function.
-   */
-  public static function widgetInfo() {
-    return array();
-  }
-
-}
-

tripal_chado/includes/TripalFields.old/chado_linker__genotype.inc

@@ -1,150 +0,0 @@
-<?php
-
-class chado_linker__genotype extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Genotypes';
-
-  // The default description for this field.
-  public static $default_description = 'Associates an indviddual or organization with
-          this record.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    // Get the settings
-    $settings = $display['settings'];
-
-    $headers = array('Name', 'Description', 'Type');
-    $rows = array();
-
-    foreach ($items as $delta => $item) {
-      $genotype = $item['value'];
-      if (!$genotype) {
-        continue;
-      }
-
-      // Get the field values
-      $genotype_name = $genotype['name'];
-      $description = $genotype['description'];
-      $type = $genotype['type'];
-
-      // Add a link i there is an entity.
-      if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
-        list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
-        $genotype_name = l($genotype_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
-      }
-      $rows[] = array($genotype_name, $description, $type);
-    }
-
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'tripal_linker-table-genotype-object',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => "",
-      'colgroups' => array(),
-      'empty' => 'No genotypes available.',
-    );
-    $content = theme_table($table);
-    if (count($items) > 0) {
-      // once we have our table array structure defined, we call Drupal's theme_table()
-      // function to generate the table.
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-    $record = $details['record'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $base_table = $details['record']->tablename;
-    $pkey = $schema['primary key'][0];
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-      $field_table . '__' . $pkey => '',
-      $field_table . '__' . $fkey_lcolumn => '',
-      $field_table . '__' . 'genotype_id' => '',
-      // Ignore the synonym_sgml column for now.
-    );
-
-    $linker_table = $base_table . '_genotype';
-    $options = array(
-      'return_array' => 1,
-      'include_fk' => array(
-        'genotype_id' => array(
-          'type_id' => array(
-            'dbxref_id' => array(
-              'db_id' => TRUE,
-            ),
-          ),
-        ),
-        $fkey_lcolumn => TRUE,
-      ),
-    );
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-    $genotype_linkers = $record->$linker_table->$fkey_rcolumn;
-    if ($genotype_linkers) {
-      foreach ($genotype_linkers as $i => $genotype_linker) {
-        $genotype = $genotype_linker->genotype_id;
-        $entity->{$field_name}['und'][$i] = array(
-          'value' => array(
-            '@type' => $genotype->type_id->dbxref_id->db_id->name . ':' . $genotype->type_id->dbxref_id->accession,
-            'type' => $genotype->type_id->name,
-            'name' => $genotype->name,
-            'description' => $genotype->description,
-          ),
-          $field_table . '__' . $pkey => $genotype_linker->$pkey,
-          $field_table . '__' . $fkey_lcolumn => $genotype_linker->$fkey_lcolumn->$fkey_lcolumn,
-          $field_table . '__' . 'genotype_id' => $genotype->genotype_id
-        );
-
-        if ($genotype && property_exists($genotype, 'entity_id')) {
-          $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $genotype->entity_id;
-        }
-      }
-    }
-  }
-
-  /**
-   * We don't want a widget so override this function.
-   */
-  public static function widgetInfo() {
-    return array();
-  }
-
-}

tripal_chado/includes/TripalFields.old/chado_linker__phenotype.inc

@@ -1,150 +0,0 @@
-<?php
-
-class chado_linker__phenotype extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Phenotypes';
-
-  // The default description for this field.
-  public static $default_description = 'Associates phenotypes with this record.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    // Get the settings
-    $settings = $display['settings'];
-
-    $headers = array('Name', 'Value', 'Type');
-    $rows = array();
-
-    foreach ($items as $delta => $item) {
-      $phenotype = $item['value'];
-      if (!$phenotype) {
-        continue;
-      }
-
-      // Get the field values
-      $phenotype_name = $phenotype['name'];
-      $value = $phenotype['value'];
-      $type = $phenotype['type'];
-
-      // Add a link i there is an entity.
-      if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
-        list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
-        $phenotype_name = l($phenotype_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
-      }
-      $rows[] = array($phenotype_name, $value, $type);
-    }
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'tripal_linker-table-phenotype-object',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => "",
-      'colgroups' => array(),
-      'empty' => 'No phenotypes available',
-    );
-    $content = theme_table($table);
-
-    // once we have our table array structure defined, we call Drupal's theme_table()
-    // function to generate the table.
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $base_table = $details['record']->tablename;
-    $pkey = $schema['primary key'][0];
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-      $field_table . '__' . $pkey => '',
-      $field_table . '__' . $fkey_lcolumn => '',
-      $field_table . '__' . 'phenotype_id' => '',
-      // Ignore the synonym_sgml column for now.
-    );
-
-    $linker_table = $base_table . '_phenotype';
-    $options = array(
-      'return_array' => 1,
-      'include_fk' => array(
-        'phenotype_id' => array(
-          'attr_id' => array(
-            'dbxref_id' => array(
-              'db_id' => TRUE,
-            ),
-          ),
-        ),
-        $fkey_lcolumn => TRUE,
-      ),
-    );
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-    $phenotype_linkers = $record->$linker_table;
-    if ($phenotype_linkers) {
-      foreach ($phenotype_linkers as $i => $phenotype_linker) {
-        $phenotype = $phenotype_linker->phenotype_id;
-        $entity->{$field_name}['und'][$i] = array(
-          'value' => array(
-       '@type' => $phenotype->attr_id->dbxref_id->db_id->name . ':' . $phenotype->attr_id->dbxref_id->accession,
-            'type' => $phenotype->attr_id->name,
-            'name' => $phenotype->name,
-            'value' => $phenotype->value,
-          ),
-          $field_table . '__' . $pkey => $phenotype_linker->$pkey,
-          $field_table . '__' . $fkey_lcolumn => $phenotype_linker->$fkey_lcolumn->$fkey_lcolumn,
-          $field_table . '__' . 'phenotype_id' => $phenotype->phenotype_id
-        );
-
-        if ($phenotype && property_exists($phenotype, 'entity_id')) {
-          $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $phenotype->entity_id;
-        }
-      }
-    }
-  }
-
-  /**
-   * We don't want a widget so override this function.
-   */
-  public static function widgetInfo() {
-    return array();
-  }
-
-}

tripal_chado/includes/TripalFields.old/chado_linker__prop.inc

@@ -1,204 +0,0 @@
-<?php
-
-class chado_linker__prop extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Property';
-
-  // The default description for this field.
-  public static $default_description = 'Add details about this property.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    $field_name = $this->field['field_name'];
-    $chado_table = $this->instance['settings']['chado_table'];
-
-    $properties = array();
-    foreach ($items as $delta => $item) {
-      $properties[] = $item['chado-' . $chado_table . '__value'];
-    }
-    $content = implode(', ', $properties);
-
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
-    }
-  }
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $instance = $this->instance;
-
-    // Get the table name and cvterm that this field maps to.
-    $matches = array();
-    preg_match('/(.*?)__(\d+)/', $field_name, $matches);
-    // If the field name is not properly formatted then we can't tell what
-    // table and type this is.  So just return.
-    if (count($matches) != 3) {
-      return $widget;
-    }
-    $table_name = $matches[1];
-    $cvterm_id = $matches[2];
-
-    // Get the name of the pkey field for this property table and the name
-    // of the FK field that links to the base table.
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $base_table = $this->instance['settings']['base_table'];
-    $lfkey_field = key($schema['foreign keys'][$base_table]['columns']);
-    $rfkey_field = $schema['foreign keys'][$base_table]['columns'][$lfkey_field];
-
-    // Get the field defaults.
-    $fk_value =key_exists(0, $items) ? $items[0]['chado-' . $field_table . '__' . $lfkey_field] : '';
-    $propval = '';
-    if (array_key_exists($delta, $items)) {
-      $propval = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__value', $propval);
-    }
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-' . $table_name . '__' . $pkey] = array(
-      '#type' => 'hidden',
-      '#default_value' => !empty($items[$delta]['chado-' . $field_table . '__' . $pkey]) ? $items[$delta]['chado-' . $field_table . '__' . $pkey] : '',
-    );
-    $widget['chado-' . $table_name . '__' . $lfkey_field] = array(
-      '#type' => 'hidden',
-      '#value' => $fk_value,
-    );
-    $widget['chado-' . $table_name . '__value'] = array(
-      '#type' => 'textfield',
-      '#default_value' => $propval,
-      '#title' => $instance['label'] . ' value',
-      '#description' => $instance['description'],
-    );
-    $widget['chado-' . $table_name . '__type_id'] = array(
-      '#type' => 'hidden',
-      '#value' => $cvterm_id,
-    );
-    $widget['chado-' . $table_name . '__rank'] = array(
-      '#type' => 'hidden',
-      '#value' => $delta,
-    );
-  }
-
-
-  /**
-   * @see TripalField::validate()
-   */
-  public function validate($entity_type, $entity, $field, $items, &$errors) {
-
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    $field_name = $this->field['field_name'];
-    $table_name = $this->instance['settings']['chado_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $base_table = $this->instance['settings']['base_table'];
-    $lfkey_field = key($schema['foreign keys'][$base_table]['columns']);
-    $rfkey_field = $schema['foreign keys'][$base_table]['columns'][$lfkey_field];
-
-    $prop_value = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__value']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__value'] : '';
-
-    // If the user removed the contact from the contact_name field
-    // then we want to clear out the rest of the hidden values.
-    // Leave the primary key so the record can be deleted.
-    if (!$prop_value) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $pkey] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__rank'] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__type_id'] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $lfkey_field] = '';
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-
-    $matches = array();
-    preg_match('/(.*?)__(\d+)/', $field_name, $matches);
-    $table_name = $matches[1];
-    $cvterm_id = $matches[2];
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $pkey = $schema['primary key'][0];
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-    // Set some defaults for the empty record.
-    $chado_record = $entity->chado_record;
-    $entity->{$field_name}['und'][0] = array(
-      'value' => '',
-      'chado-' . $field_table . '__' . $pkey => '',
-      'chado-' . $field_table . '__' . $fkey_lcolumn => $chado_record->{$fkey_lcolumn},
-      'chado-' . $field_table . '__value' => '',
-      'chado-' . $field_table . '__type_id' => '',
-      'chado-' . $field_table . '__rank' => '',
-    );
-
-    // Get the properties associated with this base record for this fields
-    // given type.
-    $columns = array('*');
-    $match = array(
-      $fkey_lcolumn => $chado_record->{$fkey_lcolumn},
-      'type_id' => $cvterm_id,
-    );
-    $options = array(
-      'return_array' => TRUE,
-      'order_by' => array('rank' => 'ASC')
-    );
-    $properties = chado_select_record($field_table, $columns, $match, $options);
-    for ($i = 0; $i < count($properties); $i++) {
-      $property = $properties[$i];
-      foreach ($schema['fields'] as $fname => $details) {
-        $entity->{$field_name}['und'][$i] = array(
-          'value' => array(),
-          'chado-' . $field_table . '__' . $pkey => $property->$pkey,
-          'chado-' . $field_table . '__' . $fkey_lcolumn => $property->$fkey_lcolumn,
-          'chado-' . $field_table . '__value' => $property->value,
-          'chado-' . $field_table . '__type_id' => $property->type_id,
-          'chado-' . $field_table . '__rank' => $property->rank,
-        );
-      }
-    }
-  }
-}

tripal_chado/includes/TripalFields.old/chado_linker__prop_adder.inc

@@ -1,306 +0,0 @@
-<?php
-
-class chado_linker__prop_adder extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Add a Property Type';
-
-  // The default description for this field.
-  public static $default_description = 'This record may have any number of properties. Use
-            this field to first add the type.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    // This field should never be viewed. It's to help add new properties
-    // when editing an entity.  So return nothing.
-    return '';
-  }
-
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $field_name = $widget['#field_name'];
-
-    $widget['#type'] = 'fieldset';
-    $widget['#title'] = $element['#title'];
-    $widget['#description'] = $element['#description'];
-    $widget['#group'] = 'entity_form_vtabs';
-
-
-     $widget['kvproperty_instructions'] = array(
-      '#type' => 'item',
-      '#markup' => t('You may add additional properties to this form by
-          providing a property name (from a vocabulary) in the field below
-          and clicking the "Lookup Term" button.  Terms that match the value
-          entered will be displayed for selection.  After selecting the
-          appropriate term click the "Use this term" button and a
-          new field will be added to the form above for the property you selected.
-          In the future, this field will be present for all records
-          of this type.'),
-    );
-
-    $term_name = isset($form_state['values'][$field_name]['und'][0]['wrapper']['term_name']) ? $form_state['values'][$field_name]['und'][0]['wrapper']['term_name'] : '';
-
-    // Drupal's vertical feild set is a bit quirky in that we can't just
-    // add a prefix and suffix to the weidget.  If we do, then the
-    // field doesn't show up on the page after an AJAX call.  We have to add
-    // an internal wrapper (below) for AJAX calls.
-    $widget['wrapper'] = array(
-      '#prefix' =>  "<span id='$field_name-lookup-form'>",
-      '#suffix' => '</span>',
-    );
-
-    // If no term has been selected yet then provide the auto complete field.
-    $widget['wrapper']['term_name'] = array(
-      '#title'       => t('Term'),
-      '#type'        => 'textfield',
-      '#description' => t("The content type must be the name of a term in
-        a controlled vocabulary and the controlled vocabulary should
-        already be loaded into Tripal.  For example, to create a content
-        type for storing 'genes', use the 'gene' term from the
-        Sequence Ontology (SO)."),
-      '#default_value' => $term_name,
-      '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/",
-    );
-
-    $widget['wrapper']['select_button'] = array(
-      '#type' => 'button',
-      '#value' => t('Lookup Term'),
-      '#name' => 'select_cvterm',
-      '#ajax' => array(
-        'callback' => "tripal_chado_prop_adder_form_ajax_callback",
-        'wrapper' => "$field_name-lookup-form",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-    );
-    if ($term_name) {
-      $widget['wrapper']['terms_list'] = array(
-        '#type' => 'fieldset',
-        '#title' => t('Matching Terms'),
-        '#description' => t('Please select the term the best matches the
-          content type you want to create. If the same term exists in
-          multiple vocabularies you will see more than one option below.')
-      );
-      $match = array(
-        'name' => $term_name,
-      );
-      $terms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));
-      $terms = chado_expand_var($terms, 'field', 'cvterm.definition');
-      $num_terms = 0;
-      foreach ($terms as $term) {
-        // Save the user a click by setting the default value as 1 if there's
-        // only one matching term.
-        $default = FALSE;
-        $attrs = array();
-        if ($num_terms == 0 and count($terms) == 1) {
-          $default = TRUE;
-          $attrs = array('checked' => 'checked');
-        }
-        $widget['wrapper']['terms_list']['term-' . $term->cvterm_id] = array(
-          '#type' => 'checkbox',
-          '#title' =>  $term->name,
-          '#default_value' => $default,
-          '#attributes' => $attrs,
-          '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name . ' (' . $term->dbxref_id->db_id->name . ') ' . $term->cv_id->definition .
-          '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
-          '<br><b>Definition:</b>  ' . $term->definition,
-        );
-        $num_terms++;
-      }
-      if ($num_terms == 0) {
-        $widget['wrapper']['terms_list']['none'] = array(
-          '#type' => 'item',
-          '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
-        );
-      }
-      else {
-        $widget['wrapper']['cardinality'] = array(
-          '#title'       => t('Number of Values'),
-          '#type'        => 'textfield',
-          '#description' => t("A number of 1 or more indicating the number of values allowed for this property. Enter -1 for unlimited values"),
-          '#size' => 10,
-          '#default_value' => 1,
-        );
-        // Add in the button for the cases of no terms or too many.
-        $widget['wrapper']['submit_button'] = array(
-          '#type' => 'submit',
-          '#value' => t('Use this term'),
-          '#name' => 'use_term_button',
-        );
-      }
-    }
-  }
-
-  /**
-   * @see TripalField::widgetFormValidate()
-   */
-  public function widgetFormValidate($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-    $field = $this->field;
-    $field_name = $field['field_name'];
-
-    if ($form_state['triggering_element']['#name'] == 'use_term_button') {
-      // If the user has clicked the 'user_term_button' then we need to makes
-      // sure that the cardinality textbox contains a positive integer.
-      $cardinality = $form_state['values'][$field_name][$langcode][$delta]['wrapper']['cardinality'];
-      if (!preg_match('/^-*\d+$/', $cardinality) or $cardinality < -2 or $cardinality == 0) {
-        form_set_error("$field_name][$langcode][$delta][wrapper][cardinality", "Please provide positive number for the number of values, or -1 for unlimited.");
-      }
-
-      // Get selected terms
-      $terms_list = $form_state['values'][$field_name][$langcode][$delta]['wrapper']['terms_list'];
-      $counter = 0;
-      $selected_term_id = '';
-      foreach ($terms_list AS $term => $selected) {
-        if ($selected) {
-          $selected_term_id = str_replace('term-', '', $term);
-          $counter ++;
-        }
-      }
-      // Make sure at least a term is selected
-      if ($counter == 0) {
-        form_set_error("$field_name][$langcode][$delta][wrapper][terms_list", "Please select a term.");
-      }
-      // Make sure only one term is selected
-      if ($counter > 1) {
-        form_set_error("$field_name][$langcode][$delta][wrapper][terms_list", "Please select only one term.");
-      }
-      // Make sure this property doesn't already have a field
-      if (key_exists($field_name . '__' . $selected_term_id, $form_state['values'])) {
-        form_set_error("$field_name][$langcode][$delta][wrapper][terms_name", "Property already exists. Please select another term.");
-      }
-    }
-  }
-
-  /**
-   * @see TripalField::widgetFormValidate
-   */
-  public function validate($entity_type, $entity, $field, $items, &$errors) {
-    // This form doesn't manage data in the database so we don't need to
-    // validate anything here.
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    // Add the new field to the entity but only if the property adder button
-    // was clicked
-    if (!array_key_exists('triggering_element', $form_state) or
-      $form_state['triggering_element']['#name'] != 'use_term_button') {
-      return;
-    }
-    else {
-      // Because we're going to add a new property we want to rebuild the form
-      // rather than have it fully submit.
-      $form_state['rebuild'] = TRUE;
-    }
-
-    // Get the table and base table.
-    $base_table = $this->instance['settings']['base_table'];
-
-    // Get the term for the property
-    $field = $this->field;
-    $fname = $field['field_name'];
-    $cardinality = $form_state['values'][$fname][$langcode][$delta]['wrapper']['cardinality'];
-    // Get selected terms
-    $terms_list = $form_state['values'][$fname][$langcode][$delta]['wrapper']['terms_list'];
-    $selected_term_id = '';
-    foreach ($terms_list AS $term => $selected) {
-      if ($selected) {
-        $selected_term_id = str_replace('term-', '', $term);
-      }
-    }
-    $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $selected_term_id));
-
-    // Generate the name for the property table and the field name that we'll
-    // be creating.
-    $prop_table = $base_table . 'prop';
-    $field_name = $prop_table . '__' . $cvterm->cvterm_id;
-
-    // The field name is the table name in this case. We want to get the
-    // primary key as this should be the field that maps th the value.
-    $schema = chado_get_schema($prop_table);
-    $pkey = $schema['primary key'][0];
-
-    // Add the field if it doesn't already exists.
-    $field = field_info_field($field_name);
-    if (!$field) {
-      $field = field_create_field(array(
-        'field_name' => $field_name,
-        'type' => 'chado_linker__prop',
-        'cardinality' => $cardinality,
-        'locked' => FALSE,
-        'storage' => array(
-          'type' => 'field_chado_storage',
-        ),
-        'settings' => array(
-          'chado_table' => $prop_table,
-          'chado_column' => $pkey,
-          'base_table' => $base_table,
-          'semantic_web' => $cvterm->dbxref_id->db_id->name . ':' . $cvterm->dbxref_id->accession,
-        ),
-      ));
-    }
-
-    // Create an instance of the field.
-    $instance = field_info_instance($entity_type, $field_name,  $entity->bundle);
-    if (!$instance) {
-      $instance = field_create_instance(array(
-        'field_name' => $field_name,
-        'entity_type' => 'TripalEntity',
-        'bundle' => $entity->bundle,
-        'label' => ucfirst(preg_replace('/_/', ' ', $cvterm->name)),
-        'description' => $cvterm->definition ? $cvterm->definition : '',
-        'required' => FALSE,
-        'settings' => array(
-          'auto_attach' => FALSE,
-        ),
-        'widget' => array(
-          'type' => 'chado_linker__prop_widget',
-          'settings' => array(
-            'display_label' => 1,
-          ),
-        ),
-        'display' => array(
-          'default' => array(
-            'label' => 'inline',
-            'type' => 'chado_linker__prop_formatter',
-            'settings' => array(),
-          ),
-        ),
-      ));
-    }
-  }
-}
-
-/**
- *
- */
-function tripal_chado_prop_adder_form_ajax_callback($form, $form_state) {
-  $field_name = $form_state['triggering_element']['#parents'][0];
-
-  // Because this field is inside a vertical fieldset we can't just
-  // return $form[$field_name]. We have set the AJAX call to replace
-  // everything inside of the 'wrapper' element, so we must return that.
-  return $form[$field_name]['und'][0]['wrapper'];
-}

tripal_chado/includes/TripalFields.old/chado_linker__pub.inc

@@ -1,260 +0,0 @@
-<?php
-
-class chado_linker__pub extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Publications';
-
-  // The default description for this field.
-  public static $default_description = 'Associates a publication (e.g. journal article,
-            conference proceedings, book chapter, etc.) with this record.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    $list_items = array();
-    $chado_table = $this->instance['settings']['chado_table'];
-    foreach ($items as $delta => $item) {
-      if ($item['chado-' . $chado_table . '__pub_id']) {
-        $pub = chado_generate_var('pub', array('pub_id' => $item['chado-' . $chado_table . '__pub_id']));
-        $list_items[$pub->pyear] = $pub->uniquename;
-      }
-    }
-
-    krsort($list_items, SORT_NUMERIC);
-
-    $list = array(
-      'title' => '',
-      'items' => $list_items,
-      'type' => 'ol',
-      'attributes' => array(),
-    );
-
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => theme_item_list($list),
-      );
-    }
-  }
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $entity = $form['#entity'];
-    $field_name = $this->field['field_name'];
-
-    // Get the FK column that links to the base table.
-    $table_name = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Get the field defaults.
-    $record_id = '';
-    $fkey_value = $element['#entity']->chado_record_id;
-    $pub_id = '';
-    $uname = '';
-
-    // If the field already has a value then it will come through the $items
-    // array.  This happens when editing an existing record.
-    if (count($items) > 0 and array_key_exists($delta, $items)) {
-      $record_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__' . $pkey, $record_id);
-      $pub_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__pub_id', $pub_id);
-      $uname = tripal_get_field_item_keyval($items, $delta, 'uniquename', $uname);
-    }
-
-    $schema = chado_get_schema('pub');
-
-    $widget['#table_name'] = $table_name;
-    $widget['#fkey_field'] = $fkey;
-    $widget['#theme'] = 'chado_linker__pub_widget';
-    $widget['#prefix'] =  "<span id='$table_name-$delta'>";
-    $widget['#suffix'] =  "</span>";
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-' . $table_name . '__' . $pkey] = array(
-      '#type' => 'value',
-      '#default_value' => $record_id,
-    );
-    $widget['chado-' . $table_name . '__' . $fkey] = array(
-      '#type' => 'value',
-      '#default_value' => $fkey_value,
-    );
-    $widget['chado-' . $table_name . '__pub_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $pub_id,
-    );
-
-    $widget['uniquename'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Publication'),
-      '#default_value' => $uname,
-      '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/pub',
-      '#ajax' => array(
-        'callback' => "chado_linker__pub_widget_form_ajax_callback",
-        'wrapper' => "$table_name-$delta",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-      '#maxlength' => 100000,
-    );
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-
-    // Get the FK column that links to the base table.
-    $table_name = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-    $field_name = $this->field['field_name'];
-
-    // Get the field values.
-    $fkey_value = isset($form_state['values'][$field_name][$langcode][$delta]['value']) ? $form_state['values'][$field_name][$langcode][$delta]['value'] : '';
-    $pub_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] : '';
-    $uname = isset($form_state['values'][$field_name][$langcode][$delta]['uniquename']) ? $form_state['values'][$field_name][$langcode][$delta]['uniquename'] : '';
-
-    // If the user provided a uniquename then we want to set the foreign key
-    // value to be the chado_record_id
-    if ($uname and !$pub_id) {
-      $pub = chado_generate_var('pub', array('uniquename' => $uname));
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] = $pub->pub_id;
-    }
-
-    // In the widgetFrom function we automatically add the foreign key
-    // record.  But if the user did not provide a publication we want to take
-    // it out so that the Chado field_storage infrastructure won't try to
-    // write a record.
-    if (!$uname and !$pub_id) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-    }
-
-    // If the user removed the publication from the pub_uniquename field
-    // then we want to clear out the rest of the hidden values.
-    // Leave the primary key so the record can be deleted.
-    if (!$uname and $pub_id) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] = '';
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $pkey = $schema['primary key'][0];
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-      'chado-' . $field_table . '__' . $pkey => '',
-      'chado-' . $field_table . '__' . $fkey_lcolumn => '',
-      'chado-' . $field_table . '__' . 'pub_id' => '',
-      'uniquename' => '',
-    );
-
-    $linker_table = $base_table . '_pub';
-    $options = array(
-      'return_array' => 1,
-    );
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-
-    if (count($record->$linker_table) > 0) {
-      $i = 0;
-      foreach ($record->$linker_table as $index => $linker) {
-        $pub = $linker->pub_id;
-        $pub_details = tripal_get_minimal_pub_info($pub);
-        $pub_details['@type'] = $pub->type_id->dbxref_id->db_id->name . ':' . $pub->type_id->dbxref_id->accession;
-        $pub_details['publication']['type'] = $pub->type_id->name;
-
-        $entity->{$field_name}['und'][$i]['value'] = $pub_details;
-        $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $pkey] = $linker->$pkey;
-        $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $fkey_lcolumn] = $linker->$fkey_lcolumn->$fkey_lcolumn;
-        $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . 'pub_id'] = $pub->pub_id;
-        $entity->{$field_name}['und'][$i]['uniquename'] =  $pub->uniquename;
-
-        if (property_exists($pub, 'entity_id')) {
-          $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $pub->entity_id;
-        }
-        $i++;
-      }
-    }
-  }
-}
-
-/**
- * An Ajax callback for the pub widget.
- */
-function chado_linker__pub_widget_form_ajax_callback($form, $form_state) {
-
-  $field_name = $form_state['triggering_element']['#parents'][0];
-  $delta = $form_state['triggering_element']['#parents'][2];
-
-  return $form[$field_name]['und'][$delta];
-}
-/**
- * Theme function for the pub widget.
- *
- * @param $variables
- */
-function theme_chado_linker__pub_widget($variables) {
-  $element = $variables['element'];
-
-  // These two fields were added to the widget to help identify the fields
-  // for layout.
-  $table_name = $element['#table_name'];
-  $fkey = $element['#fkey_field'];
-
-  $layout = "
-      <div class=\"pub-widget\">
-        <div class=\"pub-widget-item\">" .
-        drupal_render($element['uniquename']) . "
-        </div>
-      </div>
-    ";
-
-  return $layout;
-}

tripal_chado/includes/TripalFields.old/chado_linker__relationship.inc

@@ -1,1247 +0,0 @@
-<?php
-
-class chado_linker__relationship extends TripalField {
-  // The default lable for this field.
-  public static $default_label = 'Relationships';
-
-  // The default description for this field.
-  public static $default_description = 'Relationships between records.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Provide a list of instance specific settings. These can be access within
-  // the instanceSettingsForm.  When the instanceSettingsForm is submitted
-  // then Drupal with automatically change these settings for the instnace.
-  // It is recommended to put settings at the instance level whenever possible.
-  public static $default_instance_settings = array(
-    'relationships' => array(
-      'option1_vocabs' => '',
-      'option2_vocab' => '',
-      'option2_parent' => '',
-      'relationship_types' => '',
-    ),
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    // Get the settings
-    $settings = $display['settings'];
-
-    $rows = array();
-    $headers = array('Subject' ,'Type', 'Object');
-    $headers = array('Relationship');
-
-    foreach ($items as $delta => $item) {
-      if (!$item['value']) {
-        continue;
-      }
-      $subject_name = $item['value']['subject']['name'];
-      $subject_type = $item['value']['subject']['type'];
-      $object_name = $item['value']['object']['name'];
-      $object_type = $item['value']['object']['type'];
-      $phrase = $item['value']['phrase'];
-
-      // Handle some special cases.
-      // For mRNA objects we don't want to show the CDS, exons, 5' UTR, etc.
-      // we want to show the parent gene and the protein.
-      if ($object_type == 'mRNA' and ($subject_type != 'polypeptide')) {
-        continue;
-      }
-      if ($subject_type == 'mRNA' and ($object_type != 'gene')) {
-        continue;
-      }
-
-      $phrase = preg_replace("/$subject_type/", "<b>$subject_type</b>", $phrase);
-      $phrase = preg_replace("/$object_type/", "<b>$object_type</b>", $phrase);
-
-      if (array_key_exists('entity', $item['value']['object'])) {
-        list($entity_type, $object_entity_id) = explode(':', $item['value']['object']['entity']);
-        if ($object_entity_id != $entity->id) {
-          $link = l($object_name, 'bio_data/' . $object_entity_id);
-          $phrase = preg_replace("/$object_name/", $link, $phrase);
-        }
-      }
-      if (array_key_exists('entity', $item['value']['subject'])) {
-        list($entity_type, $subject_entity_id) = explode(':', $item['value']['subject']['entity']);
-        if ($subject_entity_id != $entity->id) {
-          $link = l($subject_name, 'bio_data/' . $subject_entity_id);
-          $phrase = preg_replace("/$subject_name/", $link, $phrase);
-        }
-      }
-
-      $rows[] = array($phrase);
-    }
-
-
-    // the $table array contains the headers and rows array as well as other
-    // options for controlling the display of the table.  Additional
-    // documentation can be found here:
-    // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
-    $table = array(
-      'header' => $headers,
-      'rows' => $rows,
-      'attributes' => array(
-        'id' => 'chado-linker--relationship-table',
-        'class' => 'tripal-data-table'
-      ),
-      'sticky' => FALSE,
-      'caption' => '',
-      'colgroups' => array(),
-      'empty' => 'There are no relationships',
-    );
-
-    // once we have our table array structure defined, we call Drupal's theme_table()
-    // function to generate the table.
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => theme_table($table),
-      );
-    }
-  }
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the instance settings
-    $instance = $this->instance;
-    $settings = $instance['settings']['relationships'];
-
-    $option1_vocabs = $settings['option1_vocabs'];
-    $option2_vocab  = $settings['option2_vocab'];
-    $option2_parent = $settings['option2_parent'];
-    $option3_rtypes = $settings['relationship_types'];
-
-    // For testing if there are selected vocabs for option1 we'll copy the
-    // contents in a special variable for later.
-    $option1_test   = $option1_vocabs;
-
-    // Get the FK column that links to the base table.
-    $chado_table = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($chado_table);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Get the field defaults.
-    $record_id = '';
-    $fkey_value = $element['#entity'] ? $element['#entity']->chado_record_id : '';
-    $subject_id = '';
-    $subject_uniquename = '';
-    $type_id = '';
-    $type = '';
-    $object_id = '';
-    $object_uniquename = '';
-    $value = '';
-    $rank = '';
-
-    // Handle special cases
-    $subject_id_key = 'subject_id';
-    $object_id_key = 'object_id';
-    if ($chado_table == 'organism_relationship') {
-      $subject_id_key = 'subject_organism_id';
-      $object_id_key = 'object_organism_id';
-    }
-    else if ($chado_table == 'nd_reagent_relationship') {
-      $subject_id_key = 'subject_reagent_id';
-      $object_id_key = 'object_reagent_id';
-    }
-    else if ($chado_table == 'project_relationship') {
-      $subject_id_key = 'subject_project_id';
-      $object_id_key = 'object_project_id';
-    }
-
-    // If the field already has a value then it will come through the $items
-    // array.  This happens when editing an existing record.
-    if (array_key_exists($delta, $items)) {
-      $record_id = isset($items[$delta][$field_table . '__' . $pkey]) ? $items[$delta][$field_table . '__' . $pkey] : '';
-      $subject_id = isset($items[$delta][$field_table . '__' . $subject_id_key]) ? $items[$delta][$field_table . '__' . $subject_id_key] : '';
-      $type_id = isset($items[$delta][$field_table . '__type_id']) ? $items[$delta][$field_table . '__type_id'] : '';
-      $object_id = isset($items[$delta][$field_table . '__' . $object_id_key]) ? $items[$delta][$field_table . '__' . $object_id_key] : '';
-
-      if (isset($items[$delta][$field_table . '__value'])) {
-        $value = $items[$delta][$field_table . '__value'];
-      }
-      if (isset($items[$delta][$field_table . '__rank'])) {
-        $rank = $items[$delta][$field_table . '__rank'];
-      }
-
-      $object_uniquename = isset($items[$delta]['object_name']) ? $items[$delta]['object_name'] : '';
-      $subject_uniquename = isset($items[$delta]['subject_name']) ? $items[$delta]['subject_name'] : '';
-      $type = isset($items[$delta]['type_name']) ? $items[$delta]['type_name'] : '';
-    }
-
-    // Check $form_state['values'] to see if an AJAX call set the values.
-    if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
-//       $record_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__' . $pkey);
-//       $subject_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__subject_id');
-//       $subject_uniquename = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'subject_name');
-//       $type_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__type_id');
-//       $type = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'type_name');
-//       $object_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__object_id');
-//       $object_uniquename = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'object_name');
-//       $value = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__value');
-//       $rank = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__rank');
-    }
-
-    $widget['#table_name'] = $chado_table;
-
-    $widget['#fkeys'] = $schema['foreign keys'];
-    $widget['#base_table'] = $base_table;
-    $widget['#chado_record_id'] = isset($form['#entity']) ? $form['#entity']->chado_record_id : '';
-    //$widget['#element_validate'] = array('chado_linker__relationship_validate');
-    $widget['#theme'] = 'chado_linker__relationship_widget';
-    $widget['#prefix'] =  "<span id='$chado_table-$delta'>";
-    $widget['#suffix'] =  "</span>";
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-    $widget[$field_table . '__' . $pkey] = array(
-      '#type' => 'value',
-      '#default_value' => $record_id,
-    );
-    $widget[$field_table . '__' . $subject_id_key] = array(
-      '#type' => 'value',
-      '#default_value' => $subject_id,
-    );
-    $widget[$field_table . '__type_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $type_id,
-    );
-    $widget[$field_table . '__' . $object_id_key] = array(
-      '#type' => 'value',
-      '#default_value' => $object_id,
-    );
-    if (array_key_exists('value', $schema['fields'])) {
-      $widget[$field_table . '__value'] = array(
-        '#type' => 'value',
-        '#default_value' => $value,
-      );
-    }
-    if (array_key_exists('rank', $schema['fields'])) {
-      $widget[$field_table . '__rank'] = array(
-        '#type' => 'value',
-        '#default_value' => $rank,
-      );
-    }
-    $widget['subject_name'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Subject'),
-      '#default_value' => $subject_uniquename,
-      '#required' => $element['#required'],
-      '#maxlength' => array_key_exists('length', $schema['fields'][$subject_id_key]) ? $schema['fields'][$subject_id_key]['length'] : 255,
-      '#size' => 35,
-      '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/$base_table",
-    );
-
-    // Getting default values
-    $default_voc = '';
-    if (isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['vocabulary'])) {
-      $default_voc = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['vocabulary'];
-    }
-    $default_term = '';
-    if (isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_name'])) {
-      $default_term = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_name'];
-    }
-
-    $default_type_id = $type_id;
-    if (!$type_id && isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_id'])) {
-      $default_type_id = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_id'];
-    }
-    // Option 3: Custom list of Relationship Types
-    $rtype_options = array();
-    $rtype_options[] = 'Select a Type';
-    if ($option3_rtypes) {
-      $rtypes = explode(PHP_EOL, $option3_rtypes);
-      foreach($rtypes AS $rtype) {
-        // Ignore empty lines
-        if (trim($rtype) == '') {
-          continue;
-        }
-        $term = tripal_get_cvterm(array('name' => trim($rtype)));
-        // Try to get term with vocabulary specified
-        if (!$term) {
-          $tmp = explode('|', trim($rtype), 2);
-          $cv = tripal_get_cv(array('name' => trim($tmp[0])));
-          $rtype = trim($tmp[1]);
-          $term = tripal_get_cvterm(array('name' => $rtype, 'cv_id' => $cv->cv_id));
-        }
-        $rtype_options[$term->cvterm_id] = $term->name;
-      }
-      $widget['type_id'] = array(
-        '#type' => 'select',
-        '#title' => t('Relationship Type'),
-        '#options' => $rtype_options,
-        '#default_value' => $default_type_id,
-      );
-      if ($type_id && !key_exists($type_id, $rtype_options)) {
-        form_set_error($this->field['field_name'] . '[' . $langcode . '][' . $delta . '][type_id]', 'Illegal option detected for Relationship Type. Please contact site administrator to fix the problem');
-      }
-    }
-    // Option 2: Child terms of a selected cvterm
-    else if ($option2_vocab) {
-      $values = array(
-        'cv_id' => $option2_vocab,
-        'name' => $option2_parent
-      );
-      $parent_term = tripal_get_cvterm($values);
-
-      // If the term wasn't found then see if it's a synonym.
-      if(!$parent_term) {
-        $values = array(
-          'synonym' => array(
-            'name' => trim($option2_parent),
-          )
-        );
-        $synonym = tripal_get_cvterm($values);
-        if ($synonym && $synonym->cv_id->cv_id == $option2_vocab) {
-          $parent_term = $synonym;
-        }
-      }
-      // Get the child terms of the parent term found above.
-      $sql =
-        "SELECT
-           subject_id,
-           (SELECT name from {cvterm} where cvterm_id = subject_id) AS name
-         FROM {cvtermpath}
-         WHERE
-           object_id = :parent_cvterm_id
-         AND
-           cv_id = :parent_cv_id
-         ORDER BY name
-       ";
-      $args = array(
-        ':parent_cvterm_id' => $parent_term->cvterm_id,
-        ':parent_cv_id' => $parent_term->cv_id->cv_id
-      );
-      $results = chado_query($sql, $args);
-      while($child = $results->fetchObject()) {
-        $rtype_options[$child->subject_id] = $child->name;
-      }
-      $widget['type_id'] = array(
-        '#type' => 'select',
-        '#title' => t('Relationship Type'),
-        '#options' => $rtype_options,
-        '#default_value' => $default_type_id,
-      );
-      if ($type_id && !key_exists($type_id, $rtype_options)) {
-        form_set_error($this->field['field_name'] . '[' . $langcode . '][' . $delta . '][type_id]', 'Illegal option detected for Relationship Type. Please contact site administrator to fix the problem');
-      }
-    }
-    // Option 1: All terms of selected vocabularies
-    else if ($option1_test && array_pop($option1_test)) {
-      $sql = "SELECT cvterm_id, name FROM {cvterm} WHERE cv_id IN (:cv_id) ORDER BY name";
-      $results = chado_query($sql, array(':cv_id' => $option1_vocabs));
-      while ($obj = $results->fetchObject()) {
-        $rtype_options[$obj->cvterm_id] = $obj->name;
-      }
-      $widget['type_id'] = array(
-        '#type' => 'select',
-        '#title' => t('Relationship Type'),
-        '#options' => $rtype_options,
-        '#default_value' => $default_type_id,
-      );
-      if ($type_id && !key_exists($type_id, $rtype_options)) {
-        form_set_error($this->field['field_name'] . '[' . $langcode . '][' . $delta . '][type_id]', 'Illegal option detected for Relationship Type. Please contact site administrator to fix the problem');
-      }
-    }
-    // Default option:
-    else {
-      // Set up available cvterms for selection
-      $vocs = array(0 => 'Select a vocabulary');
-      $vocs = tripal_get_cv_select_options();
-      $cv_id = isset($form_state['values'][$field_name]['und'][0]['vocabulary']) ? $form_state['values'][$field_name]['und'][0]['vocabulary'] : 0;
-      // Try getting the cv_id from cvterm for existing records
-      if (!$cv_id && $type_id) {
-        $cvterm = tripal_get_cvterm(array('cvterm_id' => $type_id));
-        if (isset($cvterm->cv_id->cv_id)) {
-          $cv_id = $cvterm->cv_id->cv_id;
-          $default_term = $cvterm->name;
-        }
-      }
-      if (!$cv_id) {
-        $cv_id = $default_voc;
-      }
-      $widget['vocabulary'] = array(
-        '#type' => 'select',
-        '#title' => t('Vocabulary'),
-        '#options' => $vocs,
-        '#required' => $element['#required'],
-        '#default_value' => $cv_id,
-        '#ajax' => array(
-          'callback' => "chado_linker__relationship_widget_form_ajax_callback",
-          'wrapper' => "$chado_table-$delta",
-          'effect' => 'fade',
-          'method' => 'replace'
-        ),
-      );
-      if ($cv_id) {
-        $options = array();
-        $widget['type_name'] = array(
-          '#type' => 'textfield',
-          '#title' => t('Relationship Type'),
-          '#size' => 15,
-          '#default_value' => $default_term,
-          '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/$cv_id"
-        );
-      }
-    }
-
-    $widget['object_name'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Object'),
-      '#default_value' => $object_uniquename,
-      '#required' => $element['#required'],
-      '#maxlength' => array_key_exists('length', $schema['fields'][$object_id_key]) ? $schema['fields'][$object_id_key]['length'] : 255,
-      '#size' => 35,
-      '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/$base_table",
-    );
-  }
-  /**
-   * @see TripalField::validate()
-   */
-  function validate($entity_type, $entity, $langcode, $items, &$errors) {
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-
-    $schema = chado_get_schema($field_table);
-    $fkeys = $schema['foreign keys'];
-
-    // Handle special cases
-    $subject_id_key = 'subject_id';
-    $object_id_key = 'object_id';
-    if ($field_table == 'organism_relationship') {
-      $subject_id_key = 'subject_organism_id';
-      $object_id_key = 'object_organism_id';
-    }
-    else if ($field_table == 'nd_reagent_relationship') {
-      $subject_id_key = 'subject_reagent_id';
-      $object_id_key = 'object_reagent_id';
-    }
-    else if ($field_table == 'project_relationship') {
-      $subject_id_key = 'subject_project_id';
-      $object_id_key = 'object_project_id';
-    }
-
-    foreach ($items as $delta => $item) {
-      $subject_id = $item[$field_table . '__' . $subject_id_key];
-      $object_id = $item[ $field_table . '__' . $object_id_key];
-      $type_id = $item[$field_table . '__type_id'];
-      $type_id = isset($item['type_id']) ? $item['type_id'] : $type_id;
-      $type_name = isset($item['type_name']) ? $item['type_name'] : '';
-      $subject_name = $item['subject_name'];
-      $object_name = $item['object_name'];
-
-
-      // If the row is empty then just continue, there's nothing to validate.
-      if (!$type_id and !$type_name and !$subject_name and !$object_name) {
-        continue;
-      }
-
-      // Make sure we have values for all of the fields.
-      $form_error = FALSE;
-      if (!$type_name && !$type_id) {
-        $errors[$this->field['field_name']][$langcode][$delta][] = array(
-          'error' => 'chado_linker__relationship',
-          'message' => t("Please provide the type of relationship."),
-        );
-      }
-      if ($entity and !$subject_name) {
-        $errors[$this->field['field_name']][$langcode][$delta][] = array(
-          'error' => 'chado_linker__relationship',
-          'message' => t("Please provide the subject of the relationship."),
-        );
-      }
-      if ($entity and !$object_name) {
-        $errors[$this->field['field_name']][$langcode][$delta][] = array(
-          'error' => 'chado_linker__relationship',
-          'message' => t("Please provide the object of the relationship."),
-        );
-      }
-      if ($form_error) {
-        continue;
-      }
-
-      // Before submitting this form we need to make sure that our subject_id and
-      // object_ids are real values.  There are two ways to get the value, either
-      // just with the text value or with an [id: \d+] string embedded.  If the
-      // later we will pull it out.
-      $subject_id = '';
-      $fkey_rcolumn = $fkeys[$base_table]['columns'][$subject_id_key];
-      $matches = array();
-      if ($entity) {
-        if(preg_match('/\[id: (\d+)\]/', $subject_name, $matches)) {
-          $subject_id =  $matches[1];
-          $values = array($fkey_rcolumn => $subject_id);
-          $subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
-          if (count($subject) == 0) {
-            $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
-              'message' => t("The subject record cannot be found using the specified id (e.g. [id: xx])."),
-            );
-          }
-        }
-        else {
-          $values = array('uniquename' => $subject_name);
-          $subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
-          if (count($subject) == 0) {
-            $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
-              'message' => t("The subject record cannot be found. Please check spelling."),
-            );
-          }
-          elseif (count($subject) > 1) {
-            $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
-              'message' => t("The subject is not unique and therefore the relationship cannot be made."),
-            );
-          }
-        }
-      }
-
-      // Now check for a matching object.
-      $object_id = '';
-      $fkey_rcolumn = $fkeys[$base_table]['columns'][$object_id_key];
-      $matches = array();
-      if ($entity) {
-        if (preg_match('/\[id: (\d+)\]/', $object_name, $matches)) {
-          $object_id = $matches[1];
-          $values = array($fkey_rcolumn => $object_id);
-          $object = chado_select_record($base_table, array($fkey_rcolumn), $values);
-          if (count($subject) == 0) {
-            $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
-              'message' => t("The object record cannot be found using the specified id (e.g. [id: xx])."),
-            );
-          }
-        }
-        else {
-          $values = array('uniquename' => $object_name);
-          $object = chado_select_record($base_table, array($fkey_rcolumn), $values);
-          if (count($object) == 0) {
-            $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
-              'message' => t("The object record cannot be found. Please check spelling."),
-            );;
-          }
-          elseif (count($object) > 1) {
-            $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
-              'message' =>  t("The object is not unique and therefore the relationship cannot be made."),
-            );
-          }
-        }
-      }
-
-      // Make sure that either our object or our subject refers to the base record.
-      if ($entity) {
-        $chado_record_id = $entity->chado_record_id;
-        if ($object_id != $chado_record_id  and $subject_id != $chado_record_id) {
-          $errors[$this->field['field_name']][$langcode][$delta][] = array(
-            'error' => 'chado_linker__relationship',
-            'message' =>  t("Either the subject or the object in the relationship must refer to this record."),
-          );
-        }
-
-        // Make sure that the object and subject are not both the same thing.
-        if ($object_id == $subject_id) {
-          $errors[$this->field['field_name']][$langcode][$delta][] = array(
-            'error' => 'chado_linker__relationship',
-            'message' =>  t("The subject and the object in the relationship cannot both refer to the same record."),
-          );
-        }
-      }
-    }
-  }
-  /**
-   * @see TripalField::submit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-return;
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-    $chado_record_id = $entity->chado_record_id;
-
-    $schema = chado_get_schema($field_table);
-    $fkeys = $schema['foreign keys'];
-
-    $type_name = array_key_exists('type_name', $item) ? $item['type_name'] : '';
-    $subject_id = $form_state['values'][$field_name][$langcode][$delta][$field_table . '__subject_id'];
-    $object_id = $form_state['values'][$field_name][$langcode][$delta][ $field_table . '__object_id'];
-    $type_id = $form_state['values'][$field_name][$langcode][$delta][$field_table . '__type_id'];
-
-    $subject_name = $form_state['values'][$field_name][$langcode][$delta]['subject_name'];
-    $object_name = $form_state['values'][$field_name][$langcode][$delta]['object_name'];
-
-    // If the row is empty then skip this one, there's nothing to validate.
-    if (!($type_id or !$type_name) and !$subject_name and !$object_name) {
-      return;
-    }
-
-    // Get the subject ID.
-    $subject_id = '';
-    $fkey_rcolumn = $fkeys[$base_table]['columns']['subject_id'];
-    $matches = array();
-    if (preg_match('/\[id: (\d+)\]/', $subject_name, $matches)) {
-      $subject_id =  $matches[1];
-    }
-    else {
-      $values = array('uniquename' => $subject_name);
-      $subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
-      $subject_id = $subject[0]->$fkey_rcolumn;
-    }
-
-    // Get the object ID.
-    $object_id = '';
-    $fkey_rcolumn = $fkeys[$base_table]['columns']['object_id'];
-    $matches = array();
-    if (preg_match('/\[id: (\d+)\]/', $object_name, $matches)) {
-      $object_id = $matches[1];
-    }
-    else {
-      $values = array('uniquename' => $object_name);
-      $object = chado_select_record($base_table, array($fkey_rcolumn), $values);
-      $object_id = $object[0]->$fkey_rcolumn;
-    }
-
-    // Set the IDs according to the values that were determined above.
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__subject_id'] = $subject_id;
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__object_id'] = $object_id;
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__type_id'] = $type_name;
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__rank'] = $item['_weight'];
-
-  }
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-    $settings = $this->field['settings'];
-
-    $record = $details['record'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-
-    // Get the PKey for this table
-    $schema = chado_get_schema($field_table);
-    $pkey = $schema['primary key'][0];
-
-    // Get the Pkeys for the subject and object tables
-    $subject_fkey_table = '';
-    $object_fkey_table = '';
-    $fkeys = $schema['foreign keys'];
-    foreach ($fkeys as $fktable => $details) {
-      foreach ($details['columns'] as $fkey_lcolumn => $fkey_rcolumn) {
-        if ($fkey_lcolumn == 'subject_id') {
-          $subject_fkey_table = $fktable;
-        }
-        if ($fkey_lcolumn == 'object_id') {
-          $object_fkey_table = $fktable;
-        }
-      }
-    }
-    $subject_schema = chado_get_schema($subject_fkey_table);
-    $object_schema = chado_get_schema($object_fkey_table);
-    $subject_pkey = $subject_schema['primary key'][0];
-    $object_pkey = $object_schema['primary key'][0];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-      $field_table . '__' . $pkey => '',
-      $field_table . '__subject_id' => '',
-      $field_table . '__object_id' => '',
-      $field_table . '__type_id' => '',
-      // These elements don't need to follow the naming scheme above
-      // becasue we don't need the chado_field_storage to try and
-      // save these values.
-      'object_name' => '',
-      'subject_name' => '',
-      'type_name' => '',
-    );
-
-    // If the table has rank and value fields then add those to the default
-    // value array.
-    if (array_key_exists('value', $schema['fields'])) {
-      $entity->{$field_name}['und'][0][$field_table . '__value'] = '';
-    }
-    if (array_key_exists('rank', $schema['fields'])) {
-      $entity->{$field_name}['und'][0][$field_table . '__rank'] = '';
-    }
-
-    // If we have no record then just return.
-    if (!$record) {
-      return;
-    }
-
-    // Expand the object to include the relationships.
-    $options = array(
-      'return_array' => 1,
-      // we don't want to fully recurse we only need information about the
-      // relationship type and the object and subject
-      'include_fk' => array(
-        'type_id' => 1,
-        'object_id' => array(
-          'type_id' => 1,
-        ),
-        'subject_id'  => array(
-          'type_id' => 1,
-        ),
-      ),
-    );
-    $rel_table = $base_table . '_relationship';
-    $schema = chado_get_schema($rel_table);
-    if (array_key_exists('rank', $schema['fields'])) {
-      $options['order_by'] = array('rank' => 'ASC');
-    }
-    $record = chado_expand_var($record, 'table', $rel_table, $options);
-    if (!$record->$rel_table) {
-      return;
-    }
-    $srelationships = null;
-    $orelationships = null;
-    if ($rel_table == 'organism_relationship') {
-      $srelationships = $record->$rel_table->subject_organism_id;
-      $orelationships = $record->$rel_table->object_organism_id;
-    }
-    else if ($rel_table == 'nd_reagent_relationship') {
-      $srelationships = $record->$rel_table->subject_reagent_id;
-      $orelationships = $record->$rel_table->object_reagent_id;
-    }
-    else if ($rel_table == 'project_relationship') {
-      $srelationships = $record->$rel_table->subject_project_id;
-      $orelationships = $record->$rel_table->object_project_id;
-    }
-    else {
-      $srelationships = $record->$rel_table->subject_id;
-      $orelationships = $record->$rel_table->object_id;
-    }
-
-    $i = 0;
-    if ($orelationships) {
-      foreach ($orelationships as $relationship) {
-        $rel_acc = $relationship->type_id->dbxref_id->db_id->name . ':' . $relationship->type_id->dbxref_id->accession;
-        $rel_type = $relationship->type_id->name;
-        $verb = self::get_rel_verb($rel_type);
-        $subject_name = $relationship->subject_id->name;
-        $subject_type = $relationship->subject_id->type_id->name;
-        $object_name = $relationship->object_id->name;
-        $object_type = $relationship->object_id->type_id->name;
-        $entity->{$field_name}['und'][$i]['value'] = array(
-          'type' => $relationship->type_id->name,
-          'subject' => array(
-            'type' => $subject_type,
-            'name' => $subject_name,
-          ),
-          'type' => $relationship->type_id->name,
-          'object' => array(
-            'type' => $object_type,
-            'name' => $object_name,
-            'entity' => 'TripalEntity:' . $entity->id,
-          )
-        );
-        if (property_exists($relationship->subject_id, 'uniquename')) {
-          $entity->{$field_name}['und'][$i]['value']['subject']['identifier'] =  $relationship->subject_id->uniquename;;
-        }
-        if (property_exists($relationship->object_id, 'uniquename')) {
-          $entity->{$field_name}['und'][$i]['value']['object']['identifier'] = $relationship->object_id->uniquename;
-        }
-        if (property_exists($relationship->subject_id, 'entity_id')) {
-          $entity_id = $relationship->subject_id->entity_id;
-          $entity->{$field_name}['und'][$i]['value']['subject']['entity'] = 'TripalEntity:' . $entity_id;
-        }
-        $rel_type_clean = lcfirst(preg_replace('/_/', ' ', $rel_type));
-        $entity->{$field_name}['und'][$i]['value']['phrase'] = 'The ' . $subject_type . ', ' .
-          $subject_name . ', ' . $verb . ' '  . $rel_type_clean . ' this '  .
-          $object_type . '.';
-
-        $entity->{$field_name}['und'][$i]['semantic_web'] = array(
-          'type' => $rel_acc,
-          'subject' => $relationship->subject_id->type_id->dbxref_id->db_id->name . ':' . $relationship->subject_id->type_id->dbxref_id->accession,
-          'object' => $relationship->object_id->type_id->dbxref_id->db_id->name . ':' . $relationship->object_id->type_id->dbxref_id->accession,
-        );
-
-        $entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $relationship->$pkey;
-        $entity->{$field_name}['und'][$i][$field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
-        $entity->{$field_name}['und'][$i][$field_table . '__type_id'] = $relationship->type_id->cvterm_id;
-        $entity->{$field_name}['und'][$i][$field_table . '__object_id'] = $relationship->object_id->$object_pkey;
-
-        $entity->{$field_name}['und'][$i]['type_name'] = $relationship->type_id->name;
-        $entity->{$field_name}['und'][$i]['subject_name'] = $relationship->subject_id->name . ' [id: ' . $relationship->subject_id->$fkey_rcolumn . ']';
-        $entity->{$field_name}['und'][$i]['object_name'] = $relationship->object_id->name  . ' [id: ' . $relationship->object_id->$fkey_rcolumn . ']';
-        if (array_key_exists('value', $schema['fields'])) {
-          $entity->{$field_name}['und'][$i][$field_table . '__value'] = $relationship->value;
-        }
-        if (array_key_exists('rank', $schema['fields'])) {
-          $entity->{$field_name}['und'][$i][$field_table . '__rank'] = $relationship->rank;
-        }
-        $i++;
-      }
-    }
-
-    if ($srelationships) {
-      foreach ($srelationships as $relationship) {
-        $rel_acc = $relationship->type_id->dbxref_id->db_id->name . ':' . $relationship->type_id->dbxref_id->accession;
-        $rel_type = $relationship->type_id->name;
-        $verb = self::get_rel_verb($rel_type);
-        $subject_name = $relationship->subject_id->name;
-        $subject_type = $relationship->subject_id->type_id->name;
-        $object_name = $relationship->object_id->name;
-        $object_type = $relationship->object_id->type_id->name;
-        $entity->{$field_name}['und'][$i]['value'] = array(
-          '@type' => $relationship->type_id->name,
-          'subject' => array(
-            'type' => $subject_type,
-            'name' => $subject_name,
-            'entity' => 'TripalEntity:' . $entity->id,
-          ),
-          'type' => $relationship->type_id->name,
-          'object' => array(
-            'type' =>  $object_type,
-            'name' => $object_name,
-          )
-        );
-        if (property_exists($relationship->subject_id, 'uniquename')) {
-          $entity->{$field_name}['und'][$i]['value']['subject']['identifier'] = $relationship->subject_id->uniquename;
-        }
-        if (property_exists($relationship->object_id, 'uniquename')) {
-          $entity->{$field_name}['und'][$i]['value']['object']['identifier'] = $relationship->object_id->uniquename;
-        }
-        if (property_exists($relationship->object_id, 'entity_id')) {
-          $entity_id = $relationship->object_id->entity_id;
-          $entity->{$field_name}['und'][$i]['value']['object']['entity'] = 'TripalEntity:' . $entity_id;
-        }
-        $rel_type_clean = lcfirst(preg_replace('/_/', ' ', $rel_type));
-        $entity->{$field_name}['und'][$i]['value']['phrase'] = 'This  ' .
-          $subject_type . ' ' . $verb . ' '  . $rel_type_clean . ' the '  .
-          $object_type . ', ' . $object_name . '.';
-
-
-        $entity->{$field_name}['und'][$i]['semantic_web'] = array(
-          'type' => $rel_acc,
-          'subject' => $relationship->subject_id->type_id->dbxref_id->db_id->name . ':' . $relationship->subject_id->type_id->dbxref_id->accession,
-          'object' => $relationship->object_id->type_id->dbxref_id->db_id->name . ':' . $relationship->object_id->type_id->dbxref_id->accession,
-        );
-
-
-        $entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $relationship->$pkey;
-        $entity->{$field_name}['und'][$i][$field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
-        $entity->{$field_name}['und'][$i][$field_table . '__type_id'] = $relationship->type_id->cvterm_id;
-        $entity->{$field_name}['und'][$i][$field_table . '__object_id'] = $relationship->object_id->$object_pkey;
-
-        $entity->{$field_name}['und'][$i]['type_name'] = $relationship->type_id->name;
-        $entity->{$field_name}['und'][$i]['subject_name'] = $relationship->subject_id->name  . ' [id: ' . $relationship->subject_id->$fkey_rcolumn . ']';
-        $entity->{$field_name}['und'][$i]['object_name'] = $relationship->object_id->name  . ' [id: ' . $relationship->object_id->$fkey_rcolumn . ']';
-
-        if (array_key_exists('value', $schema['fields'])) {
-          $entity->{$field_name}['und'][$i][$field_table . '__value'] = $relationship->value;
-        }
-        if (array_key_exists('rank', $schema['fields'])) {
-          $entity->{$field_name}['und'][$i][$field_table . '__rank'] = $relationship->rank;
-        }
-        $i++;
-      }
-    }
-  }
-  /**
-   * A helper function to define English verbs for relationship types.
-   *
-   * @param $rel_type
-   *   The vocabulary term name for the relationship.
-   *
-   * @return
-   *   The verb to use when creating a sentence of the relationship.
-   */
-  public static function get_rel_verb($rel_type) {
-    $rel_type_clean = lcfirst(preg_replace('/_/', ' ', $rel_type));
-    $verb = $rel_type_clean;
-    switch ($rel_type_clean) {
-      case 'integral part of':
-      case 'instance of':
-        $verb = 'is an';
-        break;
-      case 'proper part of':
-      case 'transformation of':
-      case 'genome of':
-      case 'part of':
-        $verb = 'is a';
-      case 'position of':
-      case 'sequence of':
-      case 'variant of':
-        $verb = 'is a';
-        break;
-      case 'derives from':
-      case 'connects on':
-      case 'contains':
-      case 'finishes':
-      case 'guides':
-      case 'has origin':
-      case 'has part':
-      case 'has quality':
-      case 'is consecutive sequence of':
-      case 'maximally overlaps':
-      case 'overlaps':
-      case 'starts':
-        break;
-      default:
-        $verb = 'is';
-    }
-
-    return $verb;
-  }
-
-  /**
-   * @see TripalField::instanceSettingsForm()
-   */
-  public function instanceSettingsForm() {
-
-    $element = parent::instanceSettingsForm();
-
-    //$element = parent::instanceSettingsForm();
-    $element['relationships'] = array(
-      '#type' => 'fieldset',
-      '#title' => 'Allowed Relationship Types',
-      '#description' => t('There are three ways that relationship types
-          can be limited for users who have permission to add new relationships.
-          Please select the most appropriate for you use case.  By default
-          all vocabularies are provided to the user which allows use of any
-          term for the relationship type.'),
-      '#collapsed' => TRUE,
-      '#collapsible' => TRUE,
-      '#theme' => 'chado_linker__relationship_instance_settings'
-    );
-//     $element['instructions'] = array(
-//       '#type' => 'item',
-//       '#markup' => 'You may provide a list of terms that will be available in a select box
-//         as the relationship types. This select box will replace the vocabulary select box if the
-//         following value is set.'
-//     );
-    $vocs = tripal_get_cv_select_options();
-    $element['relationships']['option1'] = array(
-      '#type' => 'item',
-      '#title' => 'Option #1',
-      '#description' => t('Use this option to limit the vocabularies that a user .
-        could use to specify relationship types. With this option any term in .
-        the vocabulary can be used for the relationship type. You may select
-        more than one vocabulary.'),
-
-    );
-    $element['relationships']['option1_vocabs'] = array(
-      '#type' => 'select',
-      '#multiple' => TRUE,
-      '#options' => $vocs,
-      '#size' => 6,
-      '#default_value' => $this->instance['settings']['relationships']['option1_vocabs'],
-      // TODO add ajax here so that the relationship autocomplete below works
-    );
-
-    $element['relationships']['option2'] = array(
-      '#type' => 'item',
-      '#title' => '<b>Option #2</b>',
-      '#description' => 'Some vocabularies are heirarchichal (an ontology). Within this
-         heirarchy groups of related terms typically fall under a common parent. If you
-         wish to limit the list of terms that a user can use for the relationship type,
-         you can provide the parent term here.  Then, only that term\'s children will
-         be avilable for use as a relationship type.',
-    );
-    $element['relationships']['option2_vocab'] = array(
-      '#type' => 'select',
-      '#description' => 'Specify Default Vocabulary',
-      '#multiple' => FALSE,
-      '#options' => $vocs,
-      '#default_value' => $this->instance['settings']['relationships']['option2_vocab'],
-      '#ajax' => array(
-        'callback' => "chado_linker__relationship_instance_settings_form_ajax_callback",
-        'wrapper' => 'relationships-option2-parent',
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-    );
-    $element['relationships']['option2_parent'] = array(
-      '#type' => 'textfield',
-      '#description' => 'Specify a Heirarchical Parent Term',
-      '#default_value' => $this->instance['settings']['relationships']['option2_parent'],
-      '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/",
-      '#prefix' => '<div id=relationships-option2-parent>',
-      '#suffix' => '</div>'
-    );
-    $element['relationships']['option3'] = array(
-      '#type' => 'item',
-      '#title' => 'Option #3',
-      '#description' => 'Provide terms separated by a new line. The term provided should be
-        unique and distinguishable by the name. You can use a bar | to separate a vocabulary
-        and a term to allow more specific assignment.',
-    );
-    $element['relationships']['relationship_types'] = array(
-      '#type' => 'textarea',
-      '#default_value' => $this->instance['settings']['relationships']['relationship_types'],
-    );
-
-    return $element;
-
-  }
-  /**
-   * @see TripalField::instanceSettingsFormValidate()
-   */
-  public function instanceSettingsFormValidate($form, &$form_state) {
-
-    $element = parent::instanceSettingsFormValidate();
-
-    // Get relationships settings
-    $settings = $form_state['values']['instance']['settings']['relationships'];
-    $form_state['values']['instance']['settings']['relationships']['relationship_types']= trim($settings['relationship_types']);
-
-    // Make sure only one option is selected
-    $option1test = $settings['option1_vocabs'];
-    $option1 = isset($settings['option1_vocabs']) && array_pop($option1test);
-    $option2 = (isset($settings['option2_vocab']) && $settings['option2_vocab']) || $settings['option2_parent'];
-    $option3 = isset($settings['relationship_types']) && trim($settings['relationship_types']);
-    if ($option1 && ($option2 || $option3) == 1 ||
-         $option2 && ($option1 || $option3) == 1 ||
-          $option3 && ($option1 || $option2) == 1
-        ) {
-      form_set_error(
-        "instance][settings][relationships",
-         t("Only one option is allowed to limit the relationship types.")
-      );
-      return;
-    }
-
-    // For option3, make sure the supplied types are valid cvterms
-    if ($option3) {
-      $rel_types = explode(PHP_EOL, $settings['relationship_types']);
-      foreach($rel_types AS $type) {
-        $type =  trim($type);
-        // Ignore empty lines
-        if ($type == '') {
-          continue;
-        }
-        // Find the matching cvterm
-        $sql = "SELECT cvterm_id FROM {cvterm} WHERE name = :name";
-        $results = chado_query($sql, array(':name' => $type));
-        $terms = array();
-        while ($obj = $results->fetchObject()) {
-          $terms[] = $obj;
-        }
-        // Don't save the form  if a term can not be found or it matches more than one cvterm
-        $cv = '';
-        if (count($terms) == 0) {
-          // If a term can not be found, maybe the type contains '|', parse it as 'vocabulary|cvterm'
-          if (strpos($type, '|')) {
-            $tmp = explode('|', $type, 2);
-            $type = trim($tmp[1]);
-            $cv = tripal_get_cv(array('name' => trim($tmp[0])));
-            if($cv) {
-              $sql = "SELECT cvterm_id FROM {cvterm} WHERE name = :name AND cv_id = :cv_id";
-              $results = chado_query($sql, array(':name' => $type, ':cv_id' => $cv->cv_id));
-              while ($obj = $results->fetchObject()) {
-                $terms[] = $obj;
-              }
-            }
-            else {
-              $cv = $tmp[0];
-            }
-          }
-          if (count($terms) != 1) {
-            $message = "The term '@type' can not be found.";
-            $token = array('@type' => $type);
-            if ($cv) {
-              $message =  "The term '@type' can not be found within the vocabulary '@vocab'.";
-              $token['@vocab'] = $cv;
-            }
-            form_set_error(
-              "instance][settings][relationships][relationship_types",
-              t($message, $token)
-            );
-          }
-        }
-        else if (count($terms) > 1) {
-          // If a type matches more than one term, parse it as 'vocabulary|cvterm' and try again
-          if (strpos($type, '|')) {
-            $tmp = explode('|', $type, 2);
-            $type = trim($tmp[1]);
-            $cv = tripal_get_cv(array('name' => trim($tmp[0])));
-            if ($cv) {
-              $sql = "SELECT cvterm_id FROM {cvterm} WHERE name = :name AND cv_id = :cv_id";
-              $results = chado_query($sql, array(':name' => $type, ':cv_id' => $cv->cv_id));
-              while ($obj = $results->fetchObject()) {
-                $terms[] = $obj;
-              }
-            }
-          }
-          if(count($terms) != 1) {
-            form_set_error(
-              "instance][settings][relationships][relationship_types",
-              t("The term '@type' matches more than one term. Please specify its vocabulary in
-                  the format of 'vocabulary|@type'.", array('@type' => $type))
-            );
-          }
-        }
-      }
-    }
-
-    // For option2: Make sure the parent term is a valid cvterm
-    if ($option2) {
-      $cv_id = $settings['option2_vocab'];
-      $supertype = $settings['option2_parent'];
-      $term = tripal_get_cvterm(array(
-        'name' => trim($supertype),
-        'cv_id' => $cv_id,
-      ));
-      // Tripal cv autocomplete also allow cvterm synonyms, if the parent term doesn't match
-      // a cvterm, try cvtermsynonym
-      if (!$term) {
-        $synonym = tripal_get_cvterm(
-          array(
-            'synonym' => array(
-              'name' => trim($supertype),
-            )
-          )
-        );
-        if ($synonym && $synonym->cv_id->cv_id == $cv_id) {
-          $term = $synonym;
-        }
-      }
-      if (!isset($term->cvterm_id)) {
-        form_set_error(
-          "instance][settings][relationships][option2_parent",
-          t("The term '@type' is not a valid term for the vocabulary selected.", array('@type' => $supertype))
-        );
-      }
-    }
-  }
-}
-
-/**
- * Theme function for the chado_linker__relationship_widget.
- */
-function theme_chado_linker__relationship_widget($variables) {
-  $element = $variables['element'];
-  $field_name = $element['#field_name'];
-  $field = field_info_field($field_name);
-  $field_type = $field['type'];
-  $field_table = $field['settings']['chado_table'];
-  $field_column = $field['settings']['chado_column'];
-  $layout = "
-      <div class=\"chado-linker--relationship-widget\">
-        <div class=\"chado-linker--relationship-widget-item\">" .
-          drupal_render($element['subject_name']) . "
-        </div>
-        <div class=\"chado-linker--relationship-widget-item\">" .
-          drupal_render($element['vocabulary']) . "
-        </div>
-        <div class=\"chado-linker--relationship-widget-item\">" .
-          drupal_render($element['type_name']) . "
-        </div>
-        <div class=\"chado-linker--relationship-widget-item\">" .
-          drupal_render($element['type_id']) . "
-        </div>
-        <div class=\"chado-linker--relationship-widget-item\">" .
-          drupal_render($element['object_name']) . "
-        </div>
-      </div>
-    ";
-  return $layout;
-}
-
-function theme_chado_linker__relationship_instance_settings ($variables) {
-  $element = $variables['element'];
-  $option1 = $element['option1'];
-  $option1_vocabs = $element['option1_vocabs'];
-  $option2 = $element['option2'];
-  $option2_vocab = $element['option2_vocab'];
-  $option2_parent = $element['option2_parent'];
-  $option3 = $element['option3'];
-  $rtype = $element['relationship_types'];
-  $layout = drupal_render($option1);
-  $layout .= drupal_render($option1_vocabs);
-  $layout .=
-    drupal_render($option2) .
-    "<div class=\"chado-linker--relationship-instance-settings-option2\">" .
-        "<div class=\"chado-linker--relationship-instance-settings-option2-item\">" .
-            drupal_render($option2_vocab) .
-        "</div>" .
-        "<div class=\"chado-linker--relationship-instance-settings-option2-item\">" .
-            drupal_render($option2_parent) .
-        "</div>" .
-    "</div>";
-  $layout .= drupal_render($option3);
-  $layout .= drupal_render($rtype);
-  return $layout;
-}
-
-/**
- * An Ajax callback for the relationshp widget.
- */
-function chado_linker__relationship_widget_form_ajax_callback(&$form, $form_state) {
-
-  // Get the triggering element
-  $form_element_name = $form_state['triggering_element']['#name'];
-  preg_match('/(.+?)\[(.+?)\]\[(.+?)\]/', $form_element_name, $matches);
-  $field = $matches[1];
-  $lang = $matches[2];
-  $delta = $matches[3];
-  // Return the widget that triggered the AJAX call
-  if (isset($form[$field][$lang][$delta])) {
-    return $form[$field][$lang][$delta];
-  }
-  // Alternatively, return the default value widget for the widget setting form
-  else {
-    return $form['instance']['default_value_widget'][$field];
-  }
-}
-
-/**
- * An Ajax callback for the relationshp instance setting form.
- */
-function chado_linker__relationship_instance_settings_form_ajax_callback(&$form, &$form_state) {
-  $acpath  = $form['instance']['settings']['relationships']['option2_parent']['#autocomplete_path'];
-  $acpath .=  $form_state['values']['instance']['settings']['relationships']['option2_vocab'] . '/';
-  $urlval  = $form['instance']['settings']['relationships']['option2_parent']['#autocomplete_input']['#url_value'];
-  $urlval .=  $form_state['values']['instance']['settings']['relationships']['option2_vocab'];
-  // Reset value if a different vocabulary is selected
-  $form['instance']['settings']['relationships']['option2_parent']['#value'] = NULL;
-  $form_state['values']['instance']['settings']['relationships']['option2_parent'] = NULL;
-  $form['instance']['settings']['relationships']['option2_parent']['#autocomplete_path'] = $acpath;
-  $form['instance']['settings']['relationships']['option2_parent']['#autocomplete_input']['#url_value'] = $urlval;
-  return $form['instance']['settings']['relationships']['option2_parent'];
-}
-

tripal_chado/includes/TripalFields.old/chado_linker__synonym.inc

@@ -1,331 +0,0 @@
-<?php
-
-class chado_linker__synonym extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Synonyms';
-
-  // The default description for this field.
-  public static $default_description = 'Adds an alternative name (synonym or alias) to this record.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::formatterView()
-   */
-  public function formatterView(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    $chado_table = $this->instance['settings']['chado_table'];
-    foreach ($items as $delta => $item) {
-      if (array_key_exists('chado-' . $chado_table . '__synonym_id', $item) and
-          $item['chado-' . $chado_table . '__synonym_id']) {
-        $synonym = chado_generate_var('synonym', array('synonym_id' => $item['chado-' . $chado_table . '__synonym_id']));
-        $name = $synonym->name;
-        if ($synonym->type_id->name != 'exact') {
-          $name .= ' (<i>' . $synonym->type_id->name . '</i>)';
-        }
-        $element[$delta] = array(
-          '#type' => 'markup',
-          '#markup' => $name,
-        );
-      }
-    }
-  }
-  /**
-   * @see TripalField::widgetForm()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $entity = $form['#entity'];
-    $field_name = $this->field['field_name'];
-
-    // Get the FK column that links to the base table.
-    $table_name = $this->instance['settings']['chado_table'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    // Get the field defaults.
-    $record_id = '';
-    $fkey_value = $element['#entity']->chado_record_id;
-    $synonym_id = '';
-    $pub_id = '';
-    $is_current = TRUE;
-    $is_internal = FALSE;
-    $syn_name = '';
-    $syn_type = '';
-
-    // If the field already has a value then it will come through the $items
-    // array.  This happens when editing an existing record.
-    if (array_key_exists($delta, $items)) {
-      $record_id = $items[$delta]['chado-' . $table_name . '__' . $pkey];
-      $synonym_id = $items[$delta]['chado-' . $table_name . '__synonym_id'];
-      $pub_id = $items[$delta]['chado-' . $table_name . '__pub_id'];
-      $is_current = $items[$delta]['chado-' . $table_name . '__is_current'];
-      $is_internal = $items[$delta]['chado-' . $table_name . '__is_internal'];
-      $syn_name = $items[$delta]['name'];
-      $syn_type = $items[$delta]['type_id'];
-    }
-
-    // Check $form_state['values'] to see if an AJAX call set the values.
-    if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
-      $record_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__' . $pkey];
-      $synonym_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__synonym_id'];
-      $pub_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__pub_id'];
-      $is_current = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__is_current'];
-      $is_internal = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__is_internal'];
-      $syn_name = $form_state['values'][$field_name]['und'][$delta]['name'];
-      $syn_type = $form_state['values'][$field_name]['und'][$delta]['type_id'];
-    }
-
-    $options = array();
-    $value = array('cv_id' => array('name' => 'synonym_type'));
-    $op = array('return_array' => 1);
-    $types = chado_generate_var('cvterm', $value, $op);
-    if ($types) {
-      foreach($types AS $type) {
-        $options[$type->cvterm_id] = $type->name;
-      }
-    }
-
-    // Get the schema for the synonym table so we can make sure we limit the
-    // size of the name field to the proper size.
-    $schema = chado_get_schema('synonym');
-
-    $widget['#table_name'] = $table_name;
-    $widget['#fkey_field'] = $fkey;
-    $widget['#theme'] = 'chado_linker__synonym_widget';
-    $widget['#prefix'] =  "<span id='$table_name-$delta'>";
-    $widget['#suffix'] =  "</span>";
-
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $widget['chado-' . $table_name . '__' . $pkey] = array(
-      '#type' => 'value',
-      '#default_value' => $record_id,
-    );
-    $widget['chado-' . $table_name . '__synonym_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $synonym_id,
-    );
-    $widget['chado-' . $table_name . '__' . $fkey] = array(
-      '#type' => 'value',
-      '#default_value' => $fkey_value,
-    );
-    // TODO: add a widget for selecting a publication.
-    $widget['chado-' . $table_name . '__pub_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $pub_id,
-    );
-    $widget['type_id'] = array(
-      '#type' => 'select',
-      '#title' => t('Type'),
-      '#options' => $options,
-      '#default_value' => $syn_type,
-    );
-    $widget['name'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Synonym Name'),
-      '#default_value' => $syn_name,
-      '#size' => 25,
-    );
-
-    $widget['chado-' . $table_name . '__is_current'] = array(
-      '#type' => 'checkbox',
-      '#title' => t('Is Current'),
-      '#default_value' => $is_current,
-      '#required' => $element['#required'],
-    );
-
-    $widget['chado-' . $table_name . '__is_internal'] = array(
-      '#type' => 'checkbox',
-      '#title' => t('Is Internal'),
-      '#default_value' => $is_internal,
-      '#required' => $element['#required'],
-    );
-  }
-
-  /**
-   * @see TripalField::widgetFormSubmit()
-   */
-  public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $table_name = $this->instance['settings']['chado_table'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-    $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
-    $fkey = $fkeys[0];
-
-    $record_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $pkey]) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $pkey] : '';
-    $fkey_value = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey]) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] : '';
-    $synonym_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__synonym_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__synonym_id'] : '';
-    $pub_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] : '';
-    $is_current = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_current']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_current'] : '';
-    $is_internal = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_internal']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_internal'] : '';
-    $syn_name = isset($form_state['values'][$field_name][$langcode][$delta]['name']) ? $form_state['values'][$field_name][$langcode][$delta]['name'] : '';
-    $syn_type = isset($form_state['values'][$field_name][$langcode][$delta]['type_id']) ? $form_state['values'][$field_name][$langcode][$delta]['type_id'] : '';
-
-    // If the user provided a $syn_name and a $syn_type then we want to set
-    // the foreign key value to be the chado_record_id.
-    if ($syn_name and $syn_type) {
-
-      // Get the synonym. If one with the same name and type is already present
-      // then use that. Otherwise, insert a new one.
-      if (!$synonym_id) {
-        $synonym = chado_generate_var('synonym', array('name' => $syn_name, 'type_id' => $syn_type));
-        if (!$synonym) {
-          $synonym = chado_insert_record('synonym', array(
-            'name' => $syn_name,
-            'type_id' => $syn_type,
-            'synonym_sgml' => '',
-          ));
-          $synonym = (object) $synonym;
-        }
-
-        // Set the synonym_id and FK value
-        $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__synonym_id'] = $synonym->synonym_id;
-      }
-
-      if (!$pub_id) {
-        $pub = chado_generate_var('pub', array('uniquename' => 'null'));
-        $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] = $pub->pub_id;
-      }
-    }
-    else {
-      // If the $syn_name is not set, then remove the linker FK value to the base table.
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__synonym_id'] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_internal'] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_current'] = '';
-    }
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-    $base_table = $this->instance['settings']['base_table'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Get the PKey for this table
-    $schema = chado_get_schema($field_table);
-    $pkey = $schema['primary key'][0];
-
-    // Get the FK that links to the base record.
-    $schema = chado_get_schema($field_table);
-    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
-    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => array(),
-      'chado-' . $field_table . '__' . $pkey => '',
-      'chado-' . $field_table . '__' . $fkey_lcolumn => '',
-      'chado-' . $field_table . '__' . 'synonym_id' => '',
-      'chado-' . $field_table . '__' . 'pub_id' => '',
-      'chado-' . $field_table . '__' . 'is_current' => TRUE,
-      'chado-' . $field_table . '__' . 'is_internal' => '',
-      'name' => '',
-      'type_id' => '',
-      // Ignore the synonym_sgml column for now.
-    );
-
-    $linker_table = $base_table . '_synonym';
-    $options = array('return_array' => 1);
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-    if (count($record->$linker_table) > 0) {
-      $i = 0;
-      foreach ($record->$linker_table as $index => $linker) {
-        $synonym = $linker->synonym_id;
-        $entity->{$field_name}['und'][$i] = array(
-          'value' => array(
-            '@type' => $synonym->type_id->dbxref_id->db_id->name . ':' . $synonym->type_id->dbxref_id->accession,
-            'type' => $synonym->type_id->name,
-            'name' => $synonym->name,
-          ),
-          'chado-' . $field_table . '__' . $pkey => $linker->$pkey,
-          'chado-' . $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
-          'chado-' . $field_table . '__' . 'synonym_id' => $synonym->synonym_id,
-          'chado-' . $field_table . '__' . 'pub_id' => $linker->pub_id->pub_id,
-          'chado-' . $field_table . '__' . 'is_current' => $linker->is_current,
-          'chado-' . $field_table . '__' . 'is_internal' => $linker->is_internal,
-          'name' => $synonym->name,
-          'type_id' => $synonym->type_id->cvterm_id,
-        );
-        $i++;
-      }
-    }
-  }
-}
-
-/**
- * Theme function for the synonym widget.
- *
- * @param $variables
- */
-function theme_chado_linker__synonym_widget($variables) {
-  $element = $variables['element'];
-
-  // These two fields were added to the widget to help identify the fields
-  // for layout.
-  $table_name = $element['#table_name'];
-  $fkey = $element['#fkey_field'];
-
-  $layout = "
-      <div class=\"synonym-widget\">
-        <div class=\"synonym-widget-item\">" .
-          drupal_render($element['name']) . "
-        </div>
-        <div>" .
-          drupal_render($element['type_id']) . "
-        </div>
-        <div class=\"synonym-widget-item\">" .
-          drupal_render($element['chado-' . $table_name . '__is_internal']) . "
-        </div>
-        <div>" .
-          drupal_render($element['chado-' . $table_name . '__is_current']) . "
-        </div>
-      </div>
-    ";
-
-  return $layout;
-}
-
-/**
- * An Ajax callback for the synonym widget.
- */
-function chado_linker__synonym_widget_form_ajax_callback($form, $form_state) {
-
-  $field_name = $form_state['triggering_element']['#parents'][0];
-  $delta = $form_state['triggering_element']['#parents'][2];
-
-  return $form[$field_name]['und'][$delta];
-}

tripal_chado/includes/TripalFields.old/chado_organism__type_id.inc

@@ -1,90 +0,0 @@
-<?php
-
-class chado_organism__type_id extends TripalField {
-
-  // The default lable for this field.
-  public static $default_label = 'Infraspecific Type';
-
-  // The default description for this field.
-  public static $default_description = 'Specifies the infraspecific type of an organism.';
-
-  // Add any default settings elements.  If you override the globalSettingsForm()
-  // or the instanceSettingsForm() functions then you need to be sure that
-  // any settings you want those functions to manage are listed in this
-  // array.
-  public static $default_settings = array(
-    'chado_table' => '',
-    'chado_column' => '',
-    'base_table' => '',
-  );
-
-  // Set this to the name of the storage backend that by default will support
-  // this field.
-  public static $default_storage = 'field_chado_storage';
-
-  /**
-   * @see TripalField::widget()
-   */
-  public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
-    $settings = $this->field['settings'];
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    $type_id = 0;
-    if (count($items) > 0 and array_key_exists('organism__type_id', $items[0])) {
-      $type_id = $items[0]['organism__type_id'];
-    }
-
-    $form['value'] = array(
-      '#type' => 'value',
-      '#value' =>  array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
-    );
-
-    $cv = tripal_get_default_cv($field_table, $field_column);
-    $options = array();
-    if ($cv) {
-      $options = tripal_get_cvterm_select_options($cv->cv_id);
-    }
-    $widget['organism__type_id'] = array(
-      '#type' => 'select',
-      '#title' => $element['#title'],
-      '#description' => $element['#description'],
-      '#options' => $options,
-      '#default_value' => $type_id,
-      '#required' => $element['#required'],
-      '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
-      '#delta' => $delta,
-    );
-  }
-
-  /**
-   * @see TripalField::load()
-   */
-  public function load($entity, $details = array()) {
-
-    $record = $details['record'];
-    $settings = $this->field['settings'];
-
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
-    $field_table = $this->instance['settings']['chado_table'];
-    $field_column = $this->instance['settings']['chado_column'];
-
-    // Set some defaults for the empty record.
-    $entity->{$field_name}['und'][0] = array(
-      'value' => '',
-      'organism__type_id' => '',
-    );
-
-    if ($record->type_id) {
-      $entity->{$field_name}['und'][0]['value'] = $record->type_id->name;
-      $entity->{$field_name}['und'][0]['organism__type_id'] = $record->type_id->cvterm_id;
-    }
-  }
-
-}
-

tripal_chado/includes/TripalFields/data__accession/data__accession_widget.inc

@@ -106,7 +106,7 @@ class data__accession_widget extends ChadoFieldWidget {
     );
     $widget['links'] = array(
       '#type' => 'item',
-      '#markup' => l('Add a new database', 'admin/tripal/legacy/tripal_db/add', array('attributes' => array('target' => '_blank')))
+      '#markup' => l('Add a new database', 'admin/tripal/storage/chado/db/add', array('attributes' => array('target' => '_blank')))
     );
   }
 
@@ -183,7 +183,7 @@ class data__accession_widget extends ChadoFieldWidget {
  * An Ajax callback for the tripal_chado_admin_publish_form..
  */
 function data__accession_widget_form_ajax_callback($form, $form_state) {
-  
+
   $instance = $form['#instance'];
   $field_name = $form_state['triggering_element']['#parents'][0];
   $field = field_info_field($field_name);

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference.inc

@@ -103,6 +103,13 @@ class sbo__database_cross_reference extends ChadoField {
       $i = 0;
       foreach ($record->$linker_table as $index => $linker) {
         $dbxref = $linker->dbxref_id;
+
+        // Ignore the GFF_source database. This is a weird thing required by
+        // GBrowse and is added by the GFF loader. We don't want to show it.
+        if ($dbxref->db_id->name == 'GFF_source') {
+          continue;
+        }
+
         $URL = tripal_get_dbxref_url($dbxref);
         $entity->{$field_name}['und'][$i] = array(
           'value' => array(

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference_widget.inc

@@ -136,7 +136,7 @@ class sbo__database_cross_reference_widget extends ChadoFieldWidget {
     if (!$db_id) {
       $widget['links'] = array(
         '#type' => 'item',
-        '#markup' => l('Add a database', 'admin/tripal/legacy/tripal_db/add', array('attributes' => array('target' => '_blank')))
+        '#markup' => l('Add a database', 'admin/tripal/storage/chado/db/add', array('attributes' => array('target' => '_blank')))
       );
     }
   }

tripal_chado/includes/TripalFields/schema__publication/schema__publication_formatter.inc

@@ -45,13 +45,11 @@ class schema__publication_formatter extends ChadoFieldFormatter {
         'type' => 'ol',
         'attributes' => array(),
       );
+      $list = theme_item_list($list);
     }
-
-    if (count($items) > 0) {
-      $element[0] = array(
-        '#type' => 'markup',
-        '#markup' => theme_item_list($list),
-      );
-    }
+    $element[0] = array(
+      '#type' => 'markup',
+      '#markup' => $list,
+    );
   }
 }

legacy/tripal_db/includes/tripal_db.admin.inc → tripal_chado/includes/tripal_chado.db.inc

@@ -1,15 +1,11 @@
 <?php
-/**
- * @file
- * Provide administration of dbs & dbxrefs
- */
 
 /**
  * Launchpad for database reference administration
  *
  * @ingroup tripal_db
  */
-function tripal_db_admin_db_listing() {
+function tripal_chado_admin_db_listing() {
   $output = '';
 
   // set the breadcrumb
@@ -17,8 +13,9 @@ function tripal_db_admin_db_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado Modules', 'admin/tripal/legacy');
-  $breadcrumb[] = l('Databases', 'admin/tripal/legacy/tripal_db');
+  $breadcrumb[] = l('Data Storage', 'admin/tripal/storage');
+  $breadcrumb[] = l('Chado', 'admin/tripal/storage/chado');
+  $breadcrumb[] = l('Databases', 'admin/tripal/storage/chado/db');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -29,15 +26,15 @@ function tripal_db_admin_db_listing() {
   }
   else {
     $output .= '<p>The Tripal DB Module uses primarily views to provide an '
-      . 'administrative interface. Currently one or more views needed for this '
-      . 'administrative interface are disabled. <strong>Click each of the following links to '
-      . 'enable the pertinent views</strong>:</p>';
+        . 'administrative interface. Currently one or more views needed for this '
+            . 'administrative interface are disabled. <strong>Click each of the following links to '
+                . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
     if (!isset($dbs_view)) {
-      $output .= '<li>'.l('DB Admin', 'admin/tripal/legacy/tripal_db/views/dbs/enable').'</li>';
+      $output .= '<li>'.l('DB Admin', 'admin/tripal/storage/chado/db/views/dbs/enable').'</li>';
     }
     if (!isset($dbxrefs_view)) {
-      $output .= '<li>'.l('DB Reference Admin', 'admin/tripal/legacy/tripal_db/views/dbxrefs/enable').'</li>';
+      $output .= '<li>'.l('DB Reference Admin', 'admin/tripal/storage/chado/db/views/dbxrefs/enable').'</li>';
     }
     $output .= '</ul>';
   }
@@ -51,7 +48,7 @@ function tripal_db_admin_db_listing() {
  *
  * @ingroup tripal_db
  */
-function tripal_db_db_edit_form($form, &$form_state) {
+function tripal_chado_db_edit_form($form, &$form_state) {
 
   // get the dbid if form was submitted via AJAX
   $dbid = 0;
@@ -77,7 +74,7 @@ function tripal_db_db_edit_form($form, &$form_state) {
     '#type' => 'select',
     '#options' => $dbs,
     '#ajax' => array(
-      'callback' => 'tripal_db_edit_form_ajax',
+      'callback' => 'tripal_chado_edit_form_ajax',
       'wrapper'  => 'db-edit-div',
       'effect'   => 'fade',
       'event'    => 'change',
@@ -90,7 +87,7 @@ function tripal_db_db_edit_form($form, &$form_state) {
   // if we don't have a db_id then we can  return the form, otherwise
   // add in the other fields
   if ($dbid) {
-    tripal_db_add_db_form_fields($form, $form_state, $dbid);
+    tripal_chado_add_db_form_fields($form, $form_state, $dbid);
 
     $form['update'] = array(
       '#type'         => 'submit',
@@ -120,10 +117,10 @@ function tripal_db_db_edit_form($form, &$form_state) {
  *
  * @ingroup tripal_db
  */
-function tripal_db_db_add_form($form, &$form_state) {
+function tripal_chado_db_add_form($form, &$form_state) {
 
   // add in the form fields to this form
-  tripal_db_add_db_form_fields($form, $form_state);
+  tripal_chado_add_db_form_fields($form, $form_state);
 
   $form['add'] = array(
     '#type'         => 'submit',
@@ -138,7 +135,7 @@ function tripal_db_db_add_form($form, &$form_state) {
  *
  * @ingroup tripal_db
  */
-function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
+function tripal_chado_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
 
   $default_db        = '';
   $default_desc      = '';
@@ -201,8 +198,8 @@ function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
  *
  * @ingroup tripal_db
  */
-function tripal_db_db_add_form_validate($form, &$form_state) {
-  tripal_db_form_fields_validate($form, $form_state);
+function tripal_chado_db_add_form_validate($form, &$form_state) {
+  tripal_chado_db_form_fields_validate($form, $form_state);
 }
 
 /**
@@ -210,8 +207,8 @@ function tripal_db_db_add_form_validate($form, &$form_state) {
  *
  * @ingroup tripal_db
  */
-function tripal_db_db_edit_form_validate($form, &$form_state) {
-  tripal_db_form_fields_validate($form, $form_state);
+function tripal_chado_db_edit_form_validate($form, &$form_state) {
+  tripal_chado_db_form_fields_validate($form, $form_state);
 }
 
 /**
@@ -219,7 +216,7 @@ function tripal_db_db_edit_form_validate($form, &$form_state) {
  *
  * @ingroup tripal_db
  */
-function tripal_db_form_fields_validate($form, &$form_state) {
+function tripal_chado_db_form_fields_validate($form, &$form_state) {
   $name =  array_key_exists('name', $form_state['values'])        ? trim($form_state['values']['name']) : '';
   $desc =  array_key_exists('description', $form_state['values']) ? trim($form_state['values']['description']) : '';
   $url  =  array_key_exists('url', $form_state['values'])         ? trim($form_state['values']['url']) : '';
@@ -237,9 +234,8 @@ function tripal_db_form_fields_validate($form, &$form_state) {
 /**
  * Submit for add db form
  *
- * @ingroup tripal_db
  */
-function tripal_db_db_add_form_submit($form, &$form_state) {
+function tripal_chado_db_add_form_submit($form, &$form_state) {
 
   $name =  array_key_exists('name', $form_state['values'])        ? trim($form_state['values']['name']) : '';
   $desc =  array_key_exists('description', $form_state['values']) ? trim($form_state['values']['description']) : '';
@@ -264,9 +260,8 @@ function tripal_db_db_add_form_submit($form, &$form_state) {
 /**
  * Submit for edit db form
  *
- * @ingroup tripal_db
  */
-function tripal_db_db_edit_form_submit($form, &$form_state) {
+function tripal_chado_db_edit_form_submit($form, &$form_state) {
 
   $name =  array_key_exists('name', $form_state['values'])        ? trim($form_state['values']['name']) : '';
   $desc =  array_key_exists('description', $form_state['values']) ? trim($form_state['values']['description']) : '';
@@ -287,6 +282,7 @@ function tripal_db_db_edit_form_submit($form, &$form_state) {
     $success = chado_update_record('db', $match, $values);
     if ($success) {
       drupal_set_message(t("External database updated"));
+      drupal_goto('admin/tripal/storage/chado/db');
     }
     else {
       drupal_set_message(t("Failed to update external database."));
@@ -297,6 +293,7 @@ function tripal_db_db_edit_form_submit($form, &$form_state) {
     $success = chado_delete_record('db', $match);
     if ($success) {
       drupal_set_message(t("External database deleted"));
+      drupal_goto('admin/tripal/storage/chado/db');
     }
     else {
       drupal_set_message(t("Failed to delete external database."));
@@ -305,11 +302,10 @@ function tripal_db_db_edit_form_submit($form, &$form_state) {
 }
 
 /**
- * Ajax callback for the tripal_db_form
+ * Ajax callback for the tripal_chado_db_form
  *
- * @ingroup tripal_db
  */
-function tripal_db_edit_form_ajax($form, $form_state) {
+function tripal_chado_db_edit_form_ajax($form, $form_state) {
 
   $elements = array();
 
@@ -320,7 +316,7 @@ function tripal_db_edit_form_ajax($form, $form_state) {
     $elements['delete'] = $form['delete'];
   }
 
-   // add back in the db-edit-div that is used for the next round of AJAX
+  // add back in the db-edit-div that is used for the next round of AJAX
   $elements['fields']['#prefix'] =  '<div id="db-edit-div">';
   $elements['fields']['#suffix'] =  '</div">';
 
@@ -333,4 +329,4 @@ function tripal_db_edit_form_ajax($form, $form_state) {
   //drupal_set_message('<pre>' . print_r($elements, TRUE) . '</pre>', "status");
 
   return $elements;
-}
+}

tripal_chado/includes/tripal_chado.install.inc

@@ -140,9 +140,9 @@ function tripal_chado_load_form_validate($form, &$form_state) {
       $form_state['values']['action_to_do'] == "Install Chado v1.11") {
 
     $modules = system_get_info('module');
-    // The tripal_views module should not be included as it's a rquired
+    // The tripal_chado_iews module should not be included as it's a required
     // dependency of tripal_chado
-    unset($modules['tripal_views']);
+    unset($modules['tripal_chado_views']);
     $list = array();
     foreach ($modules as $mname => $module) {
       if (array_key_exists('dependencies', $module) and in_array('tripal_chado', $module['dependencies'])) {

tripal_chado/includes/tripal_chado.semweb.inc

@@ -5,20 +5,6 @@
  */
 function tripal_chado_populate_chado_semweb_table() {
 
-  // Insert commonly used ontologies into the tables.
-  $ontologies = array(
-    // array('Relationship Ontology', 'http://purl.obolibrary.org/obo/ro.obo'),
-    array('Relationship Ontology (legacy)', '{tripal_chado}/files/legacy_ro.obo'),
-    array('Sequence Ontology', 'http://purl.obolibrary.org/obo/so.obo'),
-    array('Gene Ontology', 'http://purl.obolibrary.org/obo/go.obo'),
-    //    array('Cell Ontology', 'https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl.obo'),
-    //    array('Plant Structure Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co'),
-    //    array('Plant Growth and Development Stages Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_temporal.obo?view=co')
-  );
-  foreach ($ontologies as $o) {
-  db_query("INSERT INTO {tripal_cv_obo} (name,path) VALUES (:name, :path)", array(':name' => $o[0], ':path' => $o[1]));
-  }
-
   // Add in all tables and fields into the chado_semweb table.
   $chado_tables = chado_get_table_names(TRUE);
   foreach ($chado_tables as $chado_table) {
@@ -48,53 +34,10 @@ function tripal_chado_populate_chado_semweb_table() {
   tripal_chado_populate_vocab_SO();
   tripal_chado_populate_vocab_SWO();
   tripal_chado_populate_vocab_TAXRANK();
+  tripal_chado_populate_vocab_TCONTACT();
   tripal_chado_populate_vocab_TPUB();
   tripal_chado_populate_vocab_UO();
 
-  // Add TAXRANK vocabulary for full import.
-  $obo_id = tripal_insert_obo('Taxonomic Rank', 'http://purl.obolibrary.org/obo/taxrank.obo');
-  $cv = chado_select_record('cv', array('name'), array('name' => 'taxonomic_rank'));
-  if (count($cv) == 0 and $obo_id) {
-    tripal_chado_load_obo_v1_2_id($obo_id);
-  }
-  //tripal_submit_obo_job(array('obo_id' => $obo_id));
-
-  // Add Tripal Contact vocabulary for full import.
-  $obo_path = '{tripal_chado}/files/tcontact.obo';
-  $obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
-  $cv = chado_select_record('cv', array('name'), array('name' => 'tripal_contact'));
-  if (count($cv) == 0 and $obo) {
-    tripal_chado_load_obo_v1_2_id($obo_id);
-  }
-  //tripal_submit_obo_job(array('obo_id' => $obo_id));
-
-  // Add Tripal Publication vocabulary for full import.
-  $obo_path = '{tripal_chado}/files/tpub.obo';
-  $obo_id = tripal_insert_obo('Tripal Publication', $obo_path);
-  $cv = chado_select_record('cv', array('name'), array('name' => 'tripal_pub'));
-  if (count($cv) == 0 and $obo) {
-    tripal_chado_load_obo_v1_2_id($obo_id);
-  }
-
-  // Load the sequence ontology if it isn't already loaded
-  $cv = chado_select_record('cv', array('name'), array('name' => 'sequence'));
-  $obo = tripal_get_obo(array('obo_name' => 'Sequence Ontology'));
-  if (count($cv) == 0 and $obo) {
-    print "Installing the Sequence Ontology... This may take a while...\n";
-    tripal_chado_load_obo_v1_2_id($obo->obo_id);
-  }
-
-  // Add the Chado ontology CV.
-  //$obo_path = '{tripal_chado}/files/cv_property.obo';
-  //$obo_id = tripal_insert_obo('Chado CV Properties', $obo_path);
-  //tripal_chado_load_obo_v1_2_id($obo_id);
-  //tripal_submit_obo_job(array('obo_id' => $obo_id));
-
-  // $obo_path = '{tripal_feature}/files/feature_property.obo';
-  // $obo_id = tripal_insert_obo('Chado Feature Properties', $obo_path);
-  // tripal_chado_load_obo_v1_2_id($obo_id);
-  //// tripal_submit_obo_job(array('obo_id' => $obo_id));
-
 }
 
 /**
@@ -473,6 +416,10 @@ function tripal_chado_populate_vocab_IAO() {
  */
 function tripal_chado_populate_vocab_LOCAL() {
 
+  tripal_insert_db(array(
+    'name' => 'null',
+    'description' => 'No online database.'
+  ));
   tripal_insert_db(array(
     'name' => 'local',
     'description' => 'Terms created for this site.',
@@ -1235,9 +1182,42 @@ function tripal_chado_populate_vocab_SWO() {
 }
 
 /**
- * Adds the pub table mapping.
+ * Adds the contact table mapping.
+ */
+function tripal_chado_populate_vocab_TCONTACT() {
+  tripal_insert_db(array(
+    'name' => 'TContact',
+    'description' => 'The Tripal Contact controlled vocabulary.',
+  ));
+}
+
+/**
+ * Adds the pub table mappings.
  */
 function tripal_chado_populate_vocab_TPUB() {
+
+  tripal_insert_db(array(
+    'name' => 'TPUB',
+    'description' => 'The Tripal Publication controlled vocabulary.',
+  ));
+  // make sure we have our supported databases
+  tripal_insert_db(
+      array(
+        'name' => 'PMID',
+        'description' => 'PubMed',
+        'url' => 'http://www.ncbi.nlm.nih.gov/pubmed',
+        'urlprefix' => 'http://www.ncbi.nlm.nih.gov/pubmed/'
+      ),
+      array('update_existing' => TRUE)
+  );
+  tripal_insert_db(
+      array(
+        'name' => 'AGL',
+        'description' => 'USDA National Agricultural Library',
+        'url' => 'http://agricola.nal.usda.gov/'
+      ),
+      array('update_existing' => TRUE)
+  );
   $term = tripal_get_cvterm(array('id' => 'TPUB:0000039'));
   tripal_associate_chado_semweb_term('pub', 'title', $term);
 

tripal_chado/includes/tripal_chado.setup.inc

@@ -63,163 +63,123 @@ function tripal_chado_prepare_form_submit($form, $form_state) {
    }
 }
 
+/**
+ *
+ */
+function tripal_chado_load_ontologies() {
+
+  // Insert commonly used ontologies into the tables.
+  $ontologies = array(
+    array(
+      'name' => 'Relationship Ontology (legacy)',
+      'path' => '{tripal_chado}/files/legacy_ro.obo',
+      'auto_load' => FALSE,
+    ),
+    array(
+      'name' => 'Gene Ontology',
+      'path' => 'http://purl.obolibrary.org/obo/go.obo',
+      'auto_load' => FALSE,
+    ),
+    array(
+      'name' => 'Taxonomic Rank',
+      'path' => 'http://purl.obolibrary.org/obo/taxrank.obo',
+      'auto_load' => TRUE,
+    ),
+    array(
+      'name' => 'Tripal Contact',
+      'path' => '{tripal_chado}/files/tcontact.obo',
+      'auto_load' => TRUE,
+    ),
+    array(
+      'name' => 'Tripal Publication',
+      'path' => '{tripal_chado}/files/tpub.obo',
+      'auto_load' => TRUE,
+    ),
+    array(
+      'name' => 'Sequence Ontology',
+      'path' => 'http://purl.obolibrary.org/obo/so.obo',
+      'auto_load' => TRUE,
+    ),
+
+  );
+  for ($i = 0; $i < count($ontologies); $i++) {
+    $obo_id = tripal_insert_obo($ontologies[$i]['name'], $ontologies[$i]['path']);
+    if ($ontologies[$i]['auto_load'] == TRUE) {
+      tripal_chado_load_obo_v1_2_id($obo_id);
+    }
+  }
+}
 /**
  * Prepares Chado for use by Tripal.
  */
 function tripal_chado_prepare_chado() {
 
   try {
-    // we want to force the version of Chado to be set properly
-    $real_version = chado_get_version(TRUE);
 
-    // get the effective version.  Pass true as second argument
-    // to warn the user if the current version is not compatible
+    // Get the effective version.  Pass true as second argument
+    // to warn the user if the current version is not compatible.
     $version = chado_get_version(FALSE, FALSE);
 
+    // We want to force the version of Chado to be set properly.
+    $real_version = chado_get_version(TRUE);
+
+    // Import commonly used ontologies if needed.
+    tripal_chado_load_ontologies();
 
-    ///////////////////////////////////////////////////////////////////////////
-    //                          Chado DB Module
-    ///////////////////////////////////////////////////////////////////////////
-    tripal_insert_db(array(
-      'name' => 'null',
-      'description' => 'No online database.'
-    ));
-    tripal_insert_db(array(
-      'name' => 'local',
-      'description' => variable_get('site_name', 'This site.'),
-    ));
+    // Populate the semantic web associations for Chado tables/fields.
+    module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.semweb');
+    tripal_chado_populate_chado_semweb_table();
 
-    ///////////////////////////////////////////////////////////////////////////
-    //                          Chado CV Module
-    ///////////////////////////////////////////////////////////////////////////
-    // Add the cv_root_mview.
-    tripal_cv_add_cv_root_mview();
+    // Initialize the population of the chado_cvterm_mapping table.  This will
+    // map existing data types already in Chado so that when users want to
+    // add new content types it simplifies the form for them.
+    tripal_chado_map_cvterms();
 
+    // Add the cv_root_mview.
+    tripal_chado_add_cv_root_mview_mview();
 
     // Create the temp table we will use for loading OBO files.
-    tripal_cv_create_tripal_obo_temp();
+    tripal_chado_add_tripal_obo_temp_table();
 
-
-    /////////////////////////////////////////////////////////////////////////////
-    //                        Chado CompAnalysis Module
-    /////////////////////////////////////////////////////////////////////////////
+    // Support for Analyses
     // we may need the analysisfeatureprop table if it doesn't already exist
-    tripal_analysis_create_analysisfeatureprop();
+    tripal_chado_add_analysisfeatureprop_table();
 
     // add materialized views
-    tripal_analysis_add_mview_analysis_organism();
-
-    // set the default vocabularies
-    //tripal_set_default_cv('analysisprop', 'type_id', 'analysis_property');
+    tripal_chado_add_analysis_organism_mview();
 
-    /////////////////////////////////////////////////////////////////////////////
-    //                        Chado Contact Module
-    /////////////////////////////////////////////////////////////////////////////
+    // Support for Contacts
     // Add the contactprop table to Chado.
-    tripal_contact_add_custom_tables();
-
-    tripal_insert_db(array(
-      'name' => 'TContact',
-      'description' => 'The Tripal Contact controlled vocabulary.',
-    ));
-    tripal_insert_db(array(
-      'name' => 'TPUB',
-      'description' => 'The Tripal Publication controlled vocabulary.',
-    ));
-
-    // Set the default vocabularies.
-    //('contact', 'type_id', 'tripal_contact');
-    //tripal_set_default_cv('contactprop', 'type_id', 'tripal_contact');
-    //tripal_set_default_cv('contact_relationship', 'type_id', 'contact_relationship');
-
-    /////////////////////////////////////////////////////////////////////////////
-    //                        Chado Feature Module
-    /////////////////////////////////////////////////////////////////////////////
-    // Note: the feature_property OBO that came with Chado v1.2 should not
-    // be automatically installed.  Some of the terms are duplicates of
-    // others in better maintained vocabularies.  New Tripal sites should
-    // use those.
+    tripal_chado_add_contactprop_table();
 
+    // Support for Features
     // Add the materialized view.
-    tripal_feature_add_organism_count_mview();
-
-    // Add the custom tables.
-    tripal_feature_add_tripal_gff_temp_table();
-    tripal_feature_add_tripal_gffcds_temp_table();
-    tripal_feature_add_tripal_gffprotein_temp_table();
+    tripal_chado_add_organism_feature_count_mview();
 
-    // Set the default vocabularies.
-    //tripal_set_default_cv('feature', 'type_id', 'sequence');
-    //tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
-    //tripal_set_default_cv('feature_relationship', 'type_id', 'feature_relationship');
+    // Add the custom tables for the GFF loader.
+    tripal_chado_add_tripal_gff_temp_table();
+    tripal_chado_add_tripal_gffcds_temp_table();
+    tripal_chado_add_tripal_gffprotein_temp_table();
 
-    /////////////////////////////////////////////////////////////////////////////
-    //                            Chado Map Module
-    /////////////////////////////////////////////////////////////////////////////
+    // Support for FeatureMaps.
     // add the featuremapprop table to Chado
-    tripal_featuremap_add_custom_tables();
+    tripal_chado_add_featuremap_dbxref_table();
+    tripal_chado_add_featuremapprop_table();
+    tripal_chado_add_featuremappos_table();
 
-    // set the default vocabularies
-    //tripal_set_default_cv('featuremapprop', 'type_id', 'featuremap_property');
-    //tripal_set_default_cv('featureposprop', 'type_id', 'featurepos_property');
-    //tripal_set_default_cv('featuremap', 'unittype_id', 'featuremap_units');
-
-    /////////////////////////////////////////////////////////////////////////////
-    //                          Chado Library Module
-    /////////////////////////////////////////////////////////////////////////////
+    // Support for Libraries.
     // add the materialized view
-    tripal_library_add_mview_library_feature_count();
-
-    // set the default vocabularies
-    //tripal_set_default_cv('libraryprop', 'type_id', 'library_property');
-    //tripal_set_default_cv('library', 'type_id', 'library_type');
-
-
-    /////////////////////////////////////////////////////////////////////////////
-    //                          Chado Project Module
-    /////////////////////////////////////////////////////////////////////////////
-
-    // set the default vocabularies
-    //tripal_set_default_cv('projectprop', 'type_id', 'project_property');
-    ///tripal_set_default_cv('project_relationship', 'type_id', 'project_relationship');
-
-    /////////////////////////////////////////////////////////////////////////////
-    //                          Chado Pub Module
-    /////////////////////////////////////////////////////////////////////////////
-    global $base_path;
-
-    tripal_pub_add_dbs();
+    tripal_chado_add_library_feature_count_mview();
 
+    // Support for Pubs.
     // add the custom tables
-    tripal_pub_add_custom_tables();
-
-    // set the default vocabularies
-    //tripal_set_default_cv('pub', 'type_id', 'tripal_pub');
-    //tripal_set_default_cv('pubprop', 'type_id', 'tripal_pub');
-    //tripal_set_default_cv('pub_relationship', 'type_id', 'pub_relationship');
-
+    tripal_chado_add_pubauthor_contact_table();
     // Add the supported loaders
     variable_set('tripal_pub_supported_dbs', array('PMID', 'AGL'));
 
-    /////////////////////////////////////////////////////////////////////////////
-      //                          Chado Stock Module
-      /////////////////////////////////////////////////////////////////////////////
-    // set the default vocabularies
-    //tripal_set_default_cv('stock', 'type_id', 'stock_type');
-    //tripal_set_default_cv('stockprop', 'type_id', 'stock_property');
-    //tripal_set_default_cv('stock_relationship', 'type_id', 'stock_relationship');
-
+    // Support for Stocks.
     // add the materialized view
-    tripal_stock_add_organism_count_mview();
-
-    /////////////////////////////////////////////////////////////////////////////
-    //                              Entity Bundles
-    /////////////////////////////////////////////////////////////////////////////
-
-    // First, populate the semantic web associations for Chado tables/fields.
-    module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.semweb');
-    tripal_chado_populate_chado_semweb_table();
-
+    tripal_chado_add_organism_stock_count_mview();
 
     // We want to provide a set of commonly used entity types by default. This
     // way when a user first installs Tripal there are some commonly used
@@ -327,9 +287,6 @@ function tripal_chado_prepare_chado() {
       throw new Exception($error['!message']);
     }
 
-    // Initialize the population of the chado_cvterm_mapping table.
-    tripal_chado_map_cvterms();
-
     // Set a variable to indicate the site is prepared.
     variable_set('tripal_chado_is_prepared', TRUE);
   }
@@ -343,7 +300,7 @@ function tripal_chado_prepare_chado() {
  *
  * @ingroup tripal_stock
  */
-function tripal_stock_add_organism_count_mview() {
+function tripal_chado_add_organism_stock_count_mview() {
   $view_name = 'organism_stock_count';
   $comment = 'Stores the type and number of stocks per organism';
 
@@ -414,7 +371,7 @@ function tripal_stock_add_organism_count_mview() {
  *
  * @ingroup tripal_pub
  */
-function tripal_pub_add_custom_tables() {
+function tripal_chado_add_pubauthor_contact_table() {
   $schema = array (
     'table' => 'pubauthor_contact',
     'fields' => array (
@@ -458,38 +415,13 @@ function tripal_pub_add_custom_tables() {
   chado_create_custom_table('pubauthor_contact', $schema, TRUE);
 }
 
-/**
- * Adds dbs related to publications
- *
- * @ingroup tripal_pub
- */
-function tripal_pub_add_dbs() {
-  // make sure we have our supported databases
-  tripal_insert_db(
-      array(
-        'name' => 'PMID',
-        'description' => 'PubMed',
-        'url' => 'http://www.ncbi.nlm.nih.gov/pubmed',
-        'urlprefix' => 'http://www.ncbi.nlm.nih.gov/pubmed/'
-      ),
-      array('update_existing' => TRUE)
-  );
-  tripal_insert_db(
-      array(
-        'name' => 'AGL',
-        'description' => 'USDA National Agricultural Library',
-        'url' => 'http://agricola.nal.usda.gov/'
-      ),
-      array('update_existing' => TRUE)
-  );
-}
 
 /**
  * Adds a materialized view keeping track of the type of features associated with each library
  *
  * @ingroup tripal_library
  */
-function tripal_library_add_mview_library_feature_count(){
+function tripal_chado_add_library_feature_count_mview(){
   $view_name = 'library_feature_count';
   $comment = 'Provides count of feature by type that are associated with all libraries';
 
@@ -545,7 +477,7 @@ function tripal_library_add_mview_library_feature_count(){
  *
  * @ingroup tripal_featuremap
  */
-function tripal_featuremap_add_custom_tables(){
+function tripal_chado_add_featuremapprop_table(){
   // add the featuremaprop table to Chado
   $schema = array (
     'table' => 'featuremapprop',
@@ -606,7 +538,11 @@ function tripal_featuremap_add_custom_tables(){
     ),
   );
   chado_create_custom_table('featuremapprop', $schema, TRUE);
-
+}
+/**
+ *
+ */
+function tripal_chado_add_featuremap_dbxref_table(){
   // add the featuremap_dbxref table to Chado
   $schema = array (
     'table' => 'featuremap_dbxref',
@@ -658,7 +594,11 @@ function tripal_featuremap_add_custom_tables(){
     'referring_tables' => NULL,
   );
   chado_create_custom_table('featuremap_dbxref', $schema, TRUE);
-
+}
+/**
+ *
+ */
+function tripal_chado_add_featureposprop_table(){
   $schema = array (
     'table' => 'featureposprop',
     'fields' => array (
@@ -723,7 +663,7 @@ function tripal_featuremap_add_custom_tables(){
 /**
  *
  */
-function tripal_feature_add_tripal_gff_temp_table() {
+function tripal_chado_add_tripal_gff_temp_table() {
   $schema = array(
     'table' => 'tripal_gff_temp',
     'fields' => array(
@@ -761,7 +701,7 @@ function tripal_feature_add_tripal_gff_temp_table() {
 /**
  *
  */
-function tripal_feature_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
+function tripal_chado_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
   $schema = array(
     'table' => 'tripal_gffcds_temp',
     'fields' => array(
@@ -801,7 +741,7 @@ function tripal_feature_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
 /**
  *
  */
-function tripal_feature_add_tripal_gffprotein_temp_table() {
+function tripal_chado_add_tripal_gffprotein_temp_table() {
   $schema = array(
     'table' => 'tripal_gffprotein_temp',
     'fields' => array(
@@ -837,7 +777,7 @@ function tripal_feature_add_tripal_gffprotein_temp_table() {
  *
  * @ingroup tripal_feature
  */
-function tripal_feature_add_organism_count_mview() {
+function tripal_chado_add_organism_feature_count_mview() {
   $view_name = 'organism_feature_count';
   $comment = 'Stores the type and number of features per organism';
 
@@ -907,7 +847,7 @@ function tripal_feature_add_organism_count_mview() {
  *
  * @ingroup tripal_contact
  */
-function tripal_contact_add_custom_tables(){
+function tripal_chado_add_contactprop_table(){
   $schema = array (
     'table' => 'contactprop',
     'fields' => array (
@@ -974,7 +914,7 @@ function tripal_contact_add_custom_tables(){
  *
  * @ingroup tripal_analysis
  */
-function tripal_analysis_create_analysisfeatureprop() {
+function tripal_chado_add_analysisfeatureprop_table() {
 
   // Create analysisfeatureprop table in chado.  This is needed for Chado
   // version 1.11, the table exists in Chado 1.2.
@@ -999,7 +939,7 @@ function tripal_analysis_create_analysisfeatureprop() {
  *
  * @ingroup tripal_analysis
  */
-function tripal_analysis_add_mview_analysis_organism() {
+function tripal_chado_add_analysis_organism_mview() {
   $view_name = 'analysis_organism';
   $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
 
@@ -1059,7 +999,7 @@ function tripal_analysis_add_mview_analysis_organism() {
  *
  * @ingroup tripal_cv
  */
-function tripal_cv_add_cv_root_mview() {
+function tripal_chado_add_cv_root_mview_mview() {
   $mv_name = 'cv_root_mview';
   $comment = 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';
   $schema = array(
@@ -1110,7 +1050,7 @@ function tripal_cv_add_cv_root_mview() {
  *
  * @ingroup tripal_cv
  */
-function tripal_cv_create_tripal_obo_temp() {
+function tripal_chado_add_tripal_obo_temp_table() {
   // the tripal_obo_temp table is used for temporary housing of records when loading OBO files
   // we create it here using plain SQL because we want it to be in the chado schema but we
   // do not want to use the Tripal Custom Table API because we don't want it to appear in the

tripal_chado/tripal_chado.info

@@ -14,4 +14,5 @@ stylesheets[all][] = theme/css/tripal_chado.css
 
 dependencies[] = tripal
 dependencies[] = date
-dependencies[] = image
+dependencies[] = image
+dependencies[] = tripal_chado_views

tripal_chado/tripal_chado.module

@@ -585,8 +585,45 @@ function tripal_chado_menu() {
     'file path' => drupal_get_path('module', 'tripal_chado'),
     'type' => MENU_CALLBACK,
   );
-  return $items;
 
+
+  //////////////////////////////////////////////////////////////////////////////
+  //                           Databases
+  //////////////////////////////////////////////////////////////////////////////
+  $items['admin/tripal/storage/chado/db'] = array(
+    'title' => 'Databases',
+    'description' => 'References to External Database sites such as NCBI',
+    'page callback' => 'tripal_chado_admin_db_listing',
+    'access arguments' => array('administer db cross-references'),
+    'file' => 'includes/tripal_chado.db.inc',
+    'file path' => drupal_get_path('module', 'tripal_chado'),
+    'type' => MENU_NORMAL_ITEM,
+  );
+  $items['admin/tripal/storage/chado/db/edit/%'] = array(
+    'title' => 'Edit a Database Reference',
+    'description' => 'Edit existing Database References.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_chado_db_edit_form',6),
+    'access callback' => 'user_access',
+    'access arguments' => array('administer db cross-references'),
+    'file' => 'includes/tripal_chado.db.inc',
+    'file path' => drupal_get_path('module', 'tripal_chado'),
+    'type' => MENU_CALLBACK,
+  );
+
+  $items['admin/tripal/storage/chado/db/add'] = array(
+    'title' => 'Create a Database Reference',
+    'description' => 'Create a new reference to an External Database.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_chado_db_add_form'),
+    'access callback' => 'user_access',
+    'access arguments' => array('administer db cross-references'),
+    'file' => 'includes/tripal_chado.db.inc',
+    'file path' => drupal_get_path('module', 'tripal_chado'),
+    'type' => MENU_CALLBACK,
+  );
+
+  return $items;
 }
 
 /**

tripal_chado/tripal_chado.views_default.inc

@@ -30,6 +30,16 @@ function tripal_chado_views_default_views() {
   $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
+  // Default Tripal Admin View: DB
+  $view = tripal_chado_defaultview_admin_db_listing();
+  $view = tripal_make_view_compatible_with_external($view);
+  $views[$view->name] = $view;
+
+  // Default Tripal Admin View: DB References
+  $view = tripal_chado_defaultview_admin_dbxref_listing();
+  $view = tripal_make_view_compatible_with_external($view);
+  $views[$view->name] = $view;
+
   return $views;
 }
 
@@ -867,5 +877,340 @@ function tripal_chado_defaultview_admin_cvterms_listing() {
    $handler->display->display_options['filters']['name_1']['expose']['max_length'] = 40;
    */
 
+  return $view;
+}
+/**
+ * Default Admin View for db management
+ *
+ * @ingroup tripal_db
+ */
+function tripal_chado_defaultview_admin_db_listing() {
+
+  $view = new view();
+  $view->name = 'tripal_db_admin_dbs';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
+  $view->base_table = 'db';
+  $view->human_name = 'DB Admin';
+  $view->core = 6;
+  $view->api_version = '3.0';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Defaults */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->display->display_options['title'] = 'Databases';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'access chado_db content';
+  $handler->display->display_options['cache']['type'] = 'none';
+  $handler->display->display_options['query']['type'] = 'views_query';
+  $handler->display->display_options['exposed_form']['type'] = 'input_required';
+  $handler->display->display_options['exposed_form']['options']['submit_button'] = 'Search';
+  $handler->display->display_options['exposed_form']['options']['text_input_required'] = 'Click search to see a listing of external databases that meet the filter requirements. Use the filters to restrict this set to a more reasonable number of databases or to find a specific database.';
+  $handler->display->display_options['exposed_form']['options']['text_input_required_format'] = 'full_html';
+  $handler->display->display_options['pager']['type'] = 'full';
+  $handler->display->display_options['pager']['options']['items_per_page'] = '50';
+  $handler->display->display_options['pager']['options']['offset'] = '0';
+  $handler->display->display_options['pager']['options']['id'] = '0';
+  $handler->display->display_options['pager']['options']['quantity'] = '9';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['grouping'] = '';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'name' => 'name',
+    'url' => 'url',
+    'urlprefix' => 'urlprefix',
+    'description' => 'description',
+  );
+  $handler->display->display_options['style_options']['default'] = 'name';
+  $handler->display->display_options['style_options']['info'] = array(
+    'name' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'description' => array(
+      'sortable' => 0,
+      'separator' => '',
+    ),
+  );
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Database',
+    'path-1' => 'admin/tripal/storage/chado/db/add',
+  );
+  /* No results behavior: Global: Text area */
+  $handler->display->display_options['empty']['text']['id'] = 'area';
+  $handler->display->display_options['empty']['text']['table'] = 'views';
+  $handler->display->display_options['empty']['text']['field'] = 'area';
+  $handler->display->display_options['empty']['text']['content'] = 'No databases match the supplied criteria.';
+  $handler->display->display_options['empty']['text']['format'] = '2';
+  /* Field: Chado Db: Db Id */
+  $handler->display->display_options['fields']['db_id']['id'] = 'db_id';
+  $handler->display->display_options['fields']['db_id']['table'] = 'db';
+  $handler->display->display_options['fields']['db_id']['field'] = 'db_id';
+  $handler->display->display_options['fields']['db_id']['exclude'] = TRUE;
+  $handler->display->display_options['fields']['db_id']['separator'] = '';
+  /* Field: Chado Db: Name */
+  $handler->display->display_options['fields']['name']['id'] = 'name';
+  $handler->display->display_options['fields']['name']['table'] = 'db';
+  $handler->display->display_options['fields']['name']['field'] = 'name';
+  /* Field: Chado Db: Description */
+  $handler->display->display_options['fields']['description']['id'] = 'description';
+  $handler->display->display_options['fields']['description']['table'] = 'db';
+  $handler->display->display_options['fields']['description']['field'] = 'description';
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['label'] = 'Edit Link';
+  $handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
+  $handler->display->display_options['fields']['nothing']['alter']['text'] = 'edit';
+  $handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
+  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/storage/chado/db/edit/[db_id]';
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
+  $handler->display->display_options['fields']['nothing_1']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing_1']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing_1']['label'] = 'View DBxrefs';
+  $handler->display->display_options['fields']['nothing_1']['exclude'] = TRUE;
+  $handler->display->display_options['fields']['nothing_1']['alter']['text'] = 'items';
+  $handler->display->display_options['fields']['nothing_1']['alter']['make_link'] = TRUE;
+  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/storage/chado/db/dbxrefs?db_name=[name]';
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing_2']['id'] = 'nothing_2';
+  $handler->display->display_options['fields']['nothing_2']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing_2']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing_2']['label'] = 'Actions';
+  $handler->display->display_options['fields']['nothing_2']['alter']['text'] = '[nothing] | [nothing_1]';
+  $handler->display->display_options['fields']['nothing_2']['element_label_colon'] = FALSE;
+  /* Filter criterion: Chado Db: Name */
+  $handler->display->display_options['filters']['name']['id'] = 'name';
+  $handler->display->display_options['filters']['name']['table'] = 'db';
+  $handler->display->display_options['filters']['name']['field'] = 'name';
+  $handler->display->display_options['filters']['name']['operator'] = 'contains';
+  $handler->display->display_options['filters']['name']['group'] = '0';
+  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
+  $handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
+  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Db: Description */
+  $handler->display->display_options['filters']['description']['id'] = 'description';
+  $handler->display->display_options['filters']['description']['table'] = 'db';
+  $handler->display->display_options['filters']['description']['field'] = 'description';
+  $handler->display->display_options['filters']['description']['operator'] = 'contains';
+  $handler->display->display_options['filters']['description']['group'] = '0';
+  $handler->display->display_options['filters']['description']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['description']['expose']['operator_id'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['label'] = 'Description Contains';
+  $handler->display->display_options['filters']['description']['expose']['operator'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['identifier'] = 'description';
+  $handler->display->display_options['filters']['description']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /* Display: Page */
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->display->display_options['path'] = 'admin/tripal/storage/chado/db/dbs';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Databases';
+  $handler->display->display_options['menu']['description'] = 'Lists all databases available to create database references for.';
+  $handler->display->display_options['menu']['weight'] = '-8';
+  $handler->display->display_options['menu']['name'] = 'management';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['tab_options']['weight'] = '0';
+
+  return $view;
+}
+
+/**
+ * Default Admin View for dbxref management
+ *
+ * @ingroup tripal_db
+ */
+function tripal_chado_defaultview_admin_dbxref_listing() {
+
+  $view = new view();
+  $view->name = 'tripal_db_admin_dbxrefs';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
+  $view->base_table = 'dbxref';
+  $view->human_name = 'DB Reference Admin';
+  $view->core = 7;
+  $view->api_version = '3.0';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Master */
+  $handler = $view->new_display('default', 'Master', 'default');
+  $handler->display->display_options['title'] = 'DB Reference Admin';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'administer db cross-references';
+  $handler->display->display_options['cache']['type'] = 'none';
+  $handler->display->display_options['query']['type'] = 'views_query';
+  $handler->display->display_options['exposed_form']['type'] = 'input_required';
+  $handler->display->display_options['exposed_form']['options']['submit_button'] = 'Search';
+  $handler->display->display_options['exposed_form']['options']['text_input_required'] = 'Click search to see a listing of external database references that meet the filter requirements. Use the filters to restrict this set to a more reasonable number of references or to find a specific reference.';
+  $handler->display->display_options['exposed_form']['options']['text_input_required_format'] = 'full_html';
+  $handler->display->display_options['pager']['type'] = 'full';
+  $handler->display->display_options['pager']['options']['items_per_page'] = '50';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'dbxref_id' => 'dbxref_id',
+    'name' => 'name',
+    'accession' => 'accession',
+    'description' => 'description',
+    'version' => 'version',
+  );
+  $handler->display->display_options['style_options']['default'] = '-1';
+  $handler->display->display_options['style_options']['info'] = array(
+    'dbxref_id' => array(
+      'sortable' => 0,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'name' => array(
+      'sortable' => 1,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'accession' => array(
+      'sortable' => 1,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'description' => array(
+      'sortable' => 0,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'version' => array(
+      'sortable' => 1,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+  );
+  /* Field: Chado Dbxref: Dbxref Id */
+  $handler->display->display_options['fields']['dbxref_id']['id'] = 'dbxref_id';
+  $handler->display->display_options['fields']['dbxref_id']['table'] = 'dbxref';
+  $handler->display->display_options['fields']['dbxref_id']['field'] = 'dbxref_id';
+  $handler->display->display_options['fields']['dbxref_id']['exclude'] = TRUE;
+  $handler->display->display_options['fields']['dbxref_id']['separator'] = '';
+  /* Field: Chado Db: Name */
+  $handler->display->display_options['fields']['name']['id'] = 'name';
+  $handler->display->display_options['fields']['name']['table'] = 'db';
+  $handler->display->display_options['fields']['name']['field'] = 'name';
+  $handler->display->display_options['fields']['name']['label'] = 'Database';
+  /* Field: Chado Dbxref: Accession */
+  $handler->display->display_options['fields']['accession']['id'] = 'accession';
+  $handler->display->display_options['fields']['accession']['table'] = 'dbxref';
+  $handler->display->display_options['fields']['accession']['field'] = 'accession';
+  /* Field: Chado Dbxref: Description */
+  $handler->display->display_options['fields']['description']['id'] = 'description';
+  $handler->display->display_options['fields']['description']['table'] = 'dbxref';
+  $handler->display->display_options['fields']['description']['field'] = 'description';
+  /* Field: Chado Dbxref: Version */
+  $handler->display->display_options['fields']['version']['id'] = 'version';
+  $handler->display->display_options['fields']['version']['table'] = 'dbxref';
+  $handler->display->display_options['fields']['version']['field'] = 'version';
+  /* Sort criterion: Chado Db: Name */
+  $handler->display->display_options['sorts']['name']['id'] = 'name';
+  $handler->display->display_options['sorts']['name']['table'] = 'db';
+  $handler->display->display_options['sorts']['name']['field'] = 'name';
+  /* Sort criterion: Chado Dbxref: Accession */
+  $handler->display->display_options['sorts']['accession']['id'] = 'accession';
+  $handler->display->display_options['sorts']['accession']['table'] = 'dbxref';
+  $handler->display->display_options['sorts']['accession']['field'] = 'accession';
+  /* Sort criterion: Chado Dbxref: Version */
+  $handler->display->display_options['sorts']['version']['id'] = 'version';
+  $handler->display->display_options['sorts']['version']['table'] = 'dbxref';
+  $handler->display->display_options['sorts']['version']['field'] = 'version';
+  $handler->display->display_options['sorts']['version']['order'] = 'DESC';
+  /* Filter criterion: Chado Db: Name */
+  $handler->display->display_options['filters']['name']['id'] = 'name';
+  $handler->display->display_options['filters']['name']['table'] = 'db';
+  $handler->display->display_options['filters']['name']['field'] = 'name';
+  $handler->display->display_options['filters']['name']['value'] = array(
+    'All' => 'All',
+  );
+  $handler->display->display_options['filters']['name']['group'] = 1;
+  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['operator_id'] = '';
+  $handler->display->display_options['filters']['name']['expose']['label'] = 'Database';
+  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'db_name';
+  $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['name']['expose']['select_multiple'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['max_length'] = 40;
+  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Dbxref: Accession */
+  $handler->display->display_options['filters']['accession']['id'] = 'accession';
+  $handler->display->display_options['filters']['accession']['table'] = 'dbxref';
+  $handler->display->display_options['filters']['accession']['field'] = 'accession';
+  $handler->display->display_options['filters']['accession']['operator'] = 'contains';
+  $handler->display->display_options['filters']['accession']['group'] = 1;
+  $handler->display->display_options['filters']['accession']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['accession']['expose']['operator_id'] = 'accession_op';
+  $handler->display->display_options['filters']['accession']['expose']['label'] = 'Accession Contains';
+  $handler->display->display_options['filters']['accession']['expose']['operator'] = 'accession_op';
+  $handler->display->display_options['filters']['accession']['expose']['identifier'] = 'accession';
+  $handler->display->display_options['filters']['accession']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Dbxref: Description */
+  $handler->display->display_options['filters']['description']['id'] = 'description';
+  $handler->display->display_options['filters']['description']['table'] = 'dbxref';
+  $handler->display->display_options['filters']['description']['field'] = 'description';
+  $handler->display->display_options['filters']['description']['operator'] = 'contains';
+  $handler->display->display_options['filters']['description']['group'] = 1;
+  $handler->display->display_options['filters']['description']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['description']['expose']['operator_id'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['label'] = 'Description Contains';
+  $handler->display->display_options['filters']['description']['expose']['operator'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['identifier'] = 'description';
+  $handler->display->display_options['filters']['description']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /* Display: Page */
+  $handler = $view->new_display('page', 'Page', 'page');
+  $handler->display->display_options['path'] = 'admin/tripal/storage/chado/db/dbxrefs';
+  $handler->display->display_options['menu']['type'] = 'tab';
+  $handler->display->display_options['menu']['title'] = 'References';
+  $handler->display->display_options['menu']['weight'] = '0';
+  $handler->display->display_options['menu']['name'] = 'management';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+
   return $view;
 }

legacy/tripal_views/api/tripal_views.DEPRECATED.inc → tripal_chado_views/api/tripal_chado_views.DEPRECATED.inc

@@ -11,7 +11,7 @@
  *
  * @see tripal_enable_view().
  */
-function tripal_views_admin_enable_view($view_name, $redirect_link) {
+function tripal_chado_views_admin_enable_view($view_name, $redirect_link) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -33,7 +33,7 @@ function tripal_views_admin_enable_view($view_name, $redirect_link) {
  *
  * @see tripal_disable_view().
  */
-function tripal_views_admin_disable_view($view_name, $redirect_link) {
+function tripal_chado_views_admin_disable_view($view_name, $redirect_link) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -55,7 +55,7 @@ function tripal_views_admin_disable_view($view_name, $redirect_link) {
  *
  * @see tripal_make_view_compatible_with_external().
  */
-function tripal_views_make_view_compatible_with_external($view) {
+function tripal_chado_views_make_view_compatible_with_external($view) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -77,7 +77,7 @@ function tripal_views_make_view_compatible_with_external($view) {
  *
  * @see tripal_get_lightest_views_integration_priority().
  */
-function tripal_views_get_table_lightest_priority($table_name) {
+function tripal_chado_views_get_table_lightest_priority($table_name) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -99,7 +99,7 @@ function tripal_views_get_table_lightest_priority($table_name) {
  *
  * @see tripal_get_lightest_views_integration_setup().
  */
-function tripal_views_get_lightest_priority_setup($table_name) {
+function tripal_chado_views_get_lightest_priority_setup($table_name) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -121,7 +121,7 @@ function tripal_views_get_lightest_priority_setup($table_name) {
  *
  * @see tripal_get_views_integration_setup_id().
  */
-function tripal_views_get_setup_id($table_name, $priority) {
+function tripal_chado_views_get_setup_id($table_name, $priority) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -143,7 +143,7 @@ function tripal_views_get_setup_id($table_name, $priority) {
  *
  * @see tripal_is_table_integrated().
  */
-function tripal_views_is_integrated($table_name, $priority = NULL) {
+function tripal_chado_views_is_integrated($table_name, $priority = NULL) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -165,7 +165,7 @@ function tripal_views_is_integrated($table_name, $priority = NULL) {
  *
  * @see tripal_is_lightest_priority_setup().
  */
-function tripal_views_is_lightest_priority_setup($setup_id, $table_name) {
+function tripal_chado_views_is_lightest_priority_setup($setup_id, $table_name) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -187,7 +187,7 @@ function tripal_views_is_lightest_priority_setup($setup_id, $table_name) {
  *
  * @see tripal_rebuild_views_integrations().
  */
-function tripal_views_rebuild_views_integrations($delete_first = FALSE) {
+function tripal_chado_views_rebuild_views_integrations($delete_first = FALSE) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -209,7 +209,7 @@ function tripal_views_rebuild_views_integrations($delete_first = FALSE) {
  *
  * @see tripal_add_views_integration().
  */
-function tripal_views_integration_add_entry($defn_array, $setup_id = FALSE) {
+function tripal_chado_views_integration_add_entry($defn_array, $setup_id = FALSE) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -231,7 +231,7 @@ function tripal_views_integration_add_entry($defn_array, $setup_id = FALSE) {
  *
  * @see tripal_export_views_integration().
  */
-function tripal_views_integration_export_entry($setup_id) {
+function tripal_chado_views_integration_export_entry($setup_id) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -253,7 +253,7 @@ function tripal_views_integration_export_entry($setup_id) {
  *
  * @see tripal_remove_views_integration().
  */
-function tripal_views_integration_remove_entry_by_table_name($table_name, $priority) {
+function tripal_chado_views_integration_remove_entry_by_table_name($table_name, $priority) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -275,7 +275,7 @@ function tripal_views_integration_remove_entry_by_table_name($table_name, $prior
  *
  * @see tripal_remove_views_integration().
  */
-function tripal_views_integration_remove_entry_by_setup_id($setup_id) {
+function tripal_chado_views_integration_remove_entry_by_setup_id($setup_id) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -297,7 +297,7 @@ function tripal_views_integration_remove_entry_by_setup_id($setup_id) {
  *
  * @see tripal_update_views_integration().
  */
-function tripal_views_integration_update_entry($setup_id, $defn_array) {
+function tripal_chado_views_integration_update_entry($setup_id, $defn_array) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -319,7 +319,7 @@ function tripal_views_integration_update_entry($setup_id, $defn_array) {
  *
  * @see tripal_clone_views_integration().
  */
-function tripal_views_clone_integration($table_name, $new_priority = NULL, $template_priority = NULL) {
+function tripal_chado_views_clone_integration($table_name, $new_priority = NULL, $template_priority = NULL) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -341,7 +341,7 @@ function tripal_views_clone_integration($table_name, $new_priority = NULL, $temp
  *
  * @see tripal_add_field_to_views_integration().
  */
-function tripal_views_add_field_to_integration($table_name, $priority, $field) {
+function tripal_chado_views_add_field_to_integration($table_name, $priority, $field) {
 
   tripal_report_error(
     'tripal_deprecated',
@@ -363,7 +363,7 @@ function tripal_views_add_field_to_integration($table_name, $priority, $field) {
  *
  * @see tripal_remove_join_from_views_integration().
  */
-function tripal_views_remove_join_from_integration($setup_id, $base_table, $base_field, $left_table, $left_field) {
+function tripal_chado_views_remove_join_from_integration($setup_id, $base_table, $base_field, $left_table, $left_field) {
 
   tripal_report_error(
     'tripal_deprecated',

legacy/tripal_views/api/tripal_views.api.inc → tripal_chado_views/api/tripal_chado_views.api.inc

@@ -5,7 +5,7 @@
  */
 
  /**
- * @defgroup tripal_views_api Tripal Views Module API
+ * @defgroup tripal_chado_views_api Tripal Views Module API
  * @ingroup tripal_api
  * @{
  * Provides functions to help extension modules add their own tripal views integrations
@@ -193,7 +193,7 @@ function mymodule_admin_landing_page() {
  *   returns the lowest priority.  If the table has not been integrated, a priority of 10
  *   is returned.
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_get_lightest_views_integration_priority($table_name) {
 
@@ -223,7 +223,7 @@ function tripal_get_lightest_views_integration_priority($table_name) {
  * @return
  *   On success, the setup_id to use for integration of this table; otherwise FALSE
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_get_lightest_views_integration_setup($table_name) {
 
@@ -251,7 +251,7 @@ function tripal_get_lightest_views_integration_setup($table_name) {
  * @return
  *   On success, the setup_id to use for integration of this table; otherwise FALSE
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_get_views_integration_setup_id($table_name, $priority) {
 
@@ -280,7 +280,7 @@ function tripal_get_views_integration_setup_id($table_name, $priority) {
  *  record is returned (If priority is not specified this will be the lightest record);
  *  Otherwise the table is not already integrated and FALSE is returned.
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_is_table_integrated($table_name, $priority = NULL) {
 
@@ -315,7 +315,7 @@ function tripal_is_table_integrated($table_name, $priority = NULL) {
  *
  * @return TRUE is this is the lightest priority; FALSE otherwise
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_is_lightest_priority_setup($setup_id, $table_name) {
 
@@ -341,15 +341,15 @@ function tripal_is_lightest_priority_setup($setup_id, $table_name) {
  * @param $delete_first
  *   If TRUE then all integrations are first deleted.
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_rebuild_views_integrations($delete_first = FALSE) {
 
   if ($delete_first) {
-    tripal_views_delete_all_integrations();
+    tripal_chado_views_delete_all_integrations();
   }
 
-  tripal_views_integrate_all_chado_tables();
+  tripal_chado_views_integrate_all_chado_tables();
 
   // TODO: the function above should have a return value from which we can
   // determine if the message below is approprite.
@@ -414,7 +414,7 @@ function tripal_rebuild_views_integrations($delete_first = FALSE) {
   tripal_add_views_integration($defn_array);
  * @endcode
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_add_views_integration($defn_array, $setup_id = FALSE) {
   $no_errors = TRUE;
@@ -630,7 +630,7 @@ function tripal_add_views_integration($defn_array, $setup_id = FALSE) {
  * @return
  *   A views integration definition array as used by tripal_add_views_integration()
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_export_views_integration($setup_id) {
 
@@ -703,7 +703,7 @@ function tripal_export_views_integration($setup_id) {
  * @return
  *   TRUE on Success; FALSE otherwise
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_remove_views_integration($identifiers, $options = array()) {
 
@@ -750,7 +750,7 @@ function tripal_remove_views_integration($identifiers, $options = array()) {
  *   An array describing the structure and fields of the table as is used in
  *   tripal_add_views_integration().
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_update_views_integration($setup_id, $defn_array) {
 
@@ -774,7 +774,7 @@ function tripal_update_views_integration($setup_id, $defn_array) {
  *   The priority of the template to be used for the clone; this is an existing integration.
  *   If no priority is supplied then the lightest priority will be used.
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_clone_views_integration($table_name, $new_priority = NULL, $template_priority = NULL) {
 
@@ -833,7 +833,7 @@ function tripal_clone_views_integration($table_name, $new_priority = NULL, $temp
  * @return
  *   TRUE if the field was added successfully; FALSE otherwise
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_add_field_to_views_integration($table_name, $priority, $field) {
   $no_errors = TRUE;
@@ -1014,7 +1014,7 @@ function tripal_add_field_to_views_integration($table_name, $priority, $field) {
  * @return
  *   TRUE if the field was added successfully; FALSE otherwise
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_add_join_to_views_integration($table_name, $priority, $join) {
   $no_errors = TRUE;
@@ -1061,7 +1061,7 @@ function tripal_add_join_to_views_integration($table_name, $priority, $join) {
  * @param $left_field
  *   The name of the field from the other table involved in the join
  *
- * @ingroup tripal_views_api
+ * @ingroup tripal_chado_views_api
  */
 function tripal_remove_join_from_views_integration($setup_id, $base_table, $base_field, $left_table, $left_field) {
   db_query(

legacy/tripal_views/includes/tripal_views_integration.inc → tripal_chado_views/includes/tripal_chado_views_integration.inc

@@ -7,9 +7,9 @@
 /**
  * Purpose: Deletes ALL Tripal Views Integrations.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_delete_all_integrations() {
+function tripal_chado_views_delete_all_integrations() {
 
   db_query("DELETE FROM {tripal_views}");
   db_query("DELETE FROM {tripal_views_field}");
@@ -24,10 +24,10 @@ function tripal_views_delete_all_integrations() {
  * Integrate all chado tables in the schema api.  This integration only occurs
  * once and sets all Chado tables to a priority of 10
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integrate_all_chado_tables() {
-return;
+function tripal_chado_views_integrate_all_chado_tables() {
+
   // First integrate all of the Chado tables. Those that are base tables
   // get special treatment.
   $tables = chado_get_table_names(TRUE);
@@ -58,10 +58,10 @@ return;
       // Assuming that we have a default chado table, genereate an integration
       // array describing it's Tripal Views integration.
       if (in_array($tablename, $base_tables) OR (is_array($mview_tables) and in_array($tablename, $mview_tables))) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
+        $table_integration_array = tripal_chado_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
       }
       else {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE, $priority);
+        $table_integration_array = tripal_chado_views_get_integration_array_for_chado_table($tablename, FALSE, $priority);
       }
 
       // Check to see if this table is a Materialized view and if it is,
@@ -88,9 +88,9 @@ return;
  *   The tripal views integration array which is the parameter for
  *   tripal_add_views_integration($defn_array)
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_get_integration_array_for_chado_table($table_name, $base_table = TRUE, $priority = 9) {
+function tripal_chado_views_get_integration_array_for_chado_table($table_name, $base_table = TRUE, $priority = 9) {
 
   // Get the schema for this table (via the chado schema api)
   $schema = chado_get_schema($table_name);
@@ -107,7 +107,7 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
   );
   // Add fields
   if (!isset($schema['fields'])) {
-    tripal_report_error('tripal_views', TRIPAL_NOTICE,
+    tripal_report_error('tripal_chado_views', TRIPAL_NOTICE,
       'There are no fields defined for %table in the Chado Schema API.', array('%table' => $table_name));
     return FALSE;
   }

legacy/tripal_views/includes/tripal_views_integration_UI.inc → tripal_chado_views/includes/tripal_chado_views_integration_UI.inc

@@ -12,15 +12,15 @@
  * @return
  *    a themed HTML table
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_setup_list() {
+function tripal_chado_views_integration_setup_list() {
   $output = '';
 
   // TODO: change the following to use theme_item_list()
   $output .= '<ul class="action-links">';
-  $output .=  '<li>' . l(t('Add a New Entry'), "admin/tripal/views-integration/new") . '</li>';
-  $output .=  '<li style="float: right;">' . l(t('Delete ALL Entries'), "admin/tripal/views-integration/delete-all/confirm") . '</li>';
+  $output .=  '<li>' . l(t('Add a New Entry'), "admin/tripal/storage/chado/views-integration/new") . '</li>';
+  $output .=  '<li style="float: right;">' . l(t('Delete ALL Entries'), "admin/tripal/storage/chado/views-integration/delete-all/confirm") . '</li>';
   $output .= '</ul>';
 
   $output .= '<p>' . t('The following tables are available for integration with Drupal Views. If '
@@ -43,9 +43,9 @@ function tripal_views_integration_setup_list() {
                      .'ORDER BY tv.table_name ASC, tv.priority ASC');
   foreach ($tviews as $tview) {
     $rows[] = array(
-      l(t('Edit'), "admin/tripal/views-integration/edit/" . $tview->setup_id) . "<br />"
-        . l(t('Export'), "admin/tripal/views-integration/export/" . $tview->setup_id) . "<br />"
-        . l(t('Delete'), "admin/tripal/views-integration/delete/" . $tview->setup_id),
+      l(t('Edit'), "admin/tripal/storage/chado/views-integration/edit/" . $tview->setup_id) . "<br />"
+        . l(t('Export'), "admin/tripal/storage/chado/views-integration/export/" . $tview->setup_id) . "<br />"
+        . l(t('Delete'), "admin/tripal/storage/chado/views-integration/delete/" . $tview->setup_id),
       $tview->name,
       $tview->table_name,
       ($tview->table_id) ? 'No' : 'Yes',
@@ -75,9 +75,9 @@ function tripal_views_integration_setup_list() {
                      .'ORDER BY table_name ASC, priority ASC');
   foreach ($tviews as $tview) {
     $rows[] = array(
-      l(t('Edit'), "admin/tripal/views-integration/edit/" . $tview->setup_id) . "<br />"
-        . l(t('Export'), "admin/tripal/views-integration/export/" . $tview->setup_id) . "<br />"
-        . l(t('Delete'), "admin/tripal/views-integration/delete/" . $tview->setup_id),
+      l(t('Edit'), "admin/tripal/storage/chado/views-integration/edit/" . $tview->setup_id) . "<br />"
+        . l(t('Export'), "admin/tripal/storage/chado/views-integration/export/" . $tview->setup_id) . "<br />"
+        . l(t('Delete'), "admin/tripal/storage/chado/views-integration/delete/" . $tview->setup_id),
       $tview->name,
       $tview->table_name,
       $tview->priority,
@@ -105,9 +105,9 @@ function tripal_views_integration_setup_list() {
                      .'ORDER BY table_name ASC, priority ASC');
   foreach ($tviews as $tview) {
     $rows[] = array(
-      l(t('Edit'), "admin/tripal/views-integration/edit/" . $tview->setup_id) . "<br />"
-        . l(t('Export'), "admin/tripal/views-integration/export/" . $tview->setup_id) . "<br />"
-        . l(t('Delete'), "admin/tripal/views-integration/delete/" . $tview->setup_id),
+      l(t('Edit'), "admin/tripal/storage/chado/views-integration/edit/" . $tview->setup_id) . "<br />"
+        . l(t('Export'), "admin/tripal/storage/chado/views-integration/export/" . $tview->setup_id) . "<br />"
+        . l(t('Delete'), "admin/tripal/storage/chado/views-integration/delete/" . $tview->setup_id),
       $tview->name,
       $tview->table_name,
       $tview->priority,
@@ -127,13 +127,13 @@ function tripal_views_integration_setup_list() {
  * @param $setup_id
  *    the unique setup id for the integrated table
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_delete($setup_id) {
+function tripal_chado_views_integration_delete($setup_id) {
 
   tripal_remove_views_integration(array('setup_id' => ($setup_id)));
   drupal_set_message(t("Record Deleted"));
-  drupal_goto('admin/tripal/views-integration');
+  drupal_goto('admin/tripal/storage/chado/views-integration');
 
 }
 
@@ -142,9 +142,9 @@ function tripal_views_integration_delete($setup_id) {
  *   function is meant to be called from a menu item. After completion it
  *   redirects the user to the views intergation page.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_delete_all_form($form, &$form_state) {
+function tripal_chado_views_integration_delete_all_form($form, &$form_state) {
 
   $form['extra'] = array(
     '#type' => 'item',
@@ -168,7 +168,7 @@ function tripal_views_integration_delete_all_form($form, &$form_state) {
   $form['actions']['cancel'] = array(
     '#type' => 'link',
     '#title' => t('Cancel'),
-    '#href' => 'admin/tripal/views-integration/list',
+    '#href' => 'admin/tripal/storage/chado/views-integration/list',
   );
 
   // By default, render the form using theme_confirm_form().
@@ -184,13 +184,13 @@ function tripal_views_integration_delete_all_form($form, &$form_state) {
  *   function is meant to be called from a menu item. After completion it
  *   redirects the user to the views intergation page.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_delete_all_form_submit($form, &$form_state) {
+function tripal_chado_views_integration_delete_all_form_submit($form, &$form_state) {
 
   tripal_rebuild_views_integrations(TRUE);
 
-  $form_state['redirect'] = 'admin/tripal/views-integration/list';
+  $form_state['redirect'] = 'admin/tripal/storage/chado/views-integration/list';
 
 }
 
@@ -211,9 +211,9 @@ function tripal_views_integration_delete_all_form_submit($form, &$form_state) {
  * D7 @todo: Add ability to manage custom fields
  * D7 @todo: Update relationship handler to work with the new tripal_views_join method
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_form($form, &$form_state) {
+function tripal_chado_views_integration_form($form, &$form_state) {
 
   $data = array();
   $form['#cache'] = TRUE;
@@ -316,7 +316,7 @@ function tripal_views_integration_form($form, &$form_state) {
     '#default_value' => $default,
     '#ajax' => array(
        //D6: 'path' => 'tripal/views-integration/ajax/view_setup_table',
-       'callback' => 'tripal_views_integration_ajax_view_setup_table',
+       'callback' => 'tripal_chado_views_integration_ajax_view_setup_table',
        'wrapper' => 'tripal-views-integration-form',
        'effect' => 'fade',
        'event' => 'change',
@@ -348,7 +348,7 @@ function tripal_views_integration_form($form, &$form_state) {
       '#default_value' => $default,
       '#ajax' => array(
          //D6: 'path' => 'tripal/views-integration/ajax/view_setup_table',
-         'callback' => 'tripal_views_integration_ajax_view_setup_table',
+         'callback' => 'tripal_chado_views_integration_ajax_view_setup_table',
          'wrapper' => 'tripal-views-integration-form',
          'effect' => 'fade',
          'event' => 'change',
@@ -541,7 +541,7 @@ function tripal_views_integration_form($form, &$form_state) {
     $chado_join_tables = array_merge(array('Select a Join Table'), $chado_join_tables);
 
     // get list of all handlers
-    $all_handlers = tripal_views_integration_discover_handlers();
+    $all_handlers = tripal_chado_views_integration_discover_handlers();
     $handlers_fields = array(0 => "Select a field handler");
     $handlers_filters = array(0 => "Select a filter handler");
     $handlers_sort = array(0 => "Select a sort handler");
@@ -1042,7 +1042,7 @@ function tripal_views_integration_form($form, &$form_state) {
       '#type' => 'select',
       '#options' => $chado_join_tables,
       '#ajax' => array(
-        'callback' => 'tripal_views_integration_ajax_new_join_left_field_callback',
+        'callback' => 'tripal_chado_views_integration_ajax_new_join_left_field_callback',
         'wrapper' => 'new-join',
       )
     );
@@ -1102,12 +1102,12 @@ function tripal_views_integration_form($form, &$form_state) {
   $form['#prefix'] = '<div id="tripal-views-integration-form">';
   $form['#suffix'] = '</div>';
 
-  $form['#redirect'] = 'admin/tripal/views-integration/list';
+  $form['#redirect'] = 'admin/tripal/storage/chado/views-integration/list';
   return $form;
 }
 
 /**
- * Purpose: validates the tripal_views_integration_form after submission
+ * Purpose: validates the tripal_chado_views_integration_form after submission
  *
  * @param $form
  *    The form object which is passed automatically by drupal
@@ -1115,9 +1115,9 @@ function tripal_views_integration_form($form, &$form_state) {
  * @param $form_state
  *    The form state pbject which is passed automatically by drupal
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_form_validate($form, &$form_state) {
+function tripal_chado_views_integration_form_validate($form, &$form_state) {
   $name_array = explode(" ", $form_state['values']['row_name']);
   $mview_id = $form_state['values']['mview_id'];
   $table_name = $form_state['values']['table_name'];
@@ -1161,9 +1161,9 @@ function tripal_views_integration_form_validate($form, &$form_state) {
  * @param $form_state
  *    The form state pbject which is passed automatically by drupal
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_form_submit($form, &$form_state) {
+function tripal_chado_views_integration_form_submit($form, &$form_state) {
   $name       = trim($form_state['values']['row_name']);
   $mview_id   = $form_state['values']['mview_id'];
   $table_name = $form_state['values']['table_name'];
@@ -1321,7 +1321,7 @@ function tripal_views_integration_form_submit($form, &$form_state) {
     drupal_set_message(t('Record Added'));
   }
 
-  $form_state['redirect'] = 'admin/tripal/views-integration/integrations';
+  $form_state['redirect'] = 'admin/tripal/storage/chado/views-integration/integrations';
 
   // now clear all the caches so that Drupal views picks up our chages
   views_invalidate_cache();
@@ -1329,9 +1329,9 @@ function tripal_views_integration_form_submit($form, &$form_state) {
 
 /**
  * AJAX callback to replace the left field select list in the new join fieldset of the
- * tripal_views_integration_form form
+ * tripal_chado_views_integration_form form
  */
-function tripal_views_integration_ajax_new_join_left_field_callback($form, $form_state) {
+function tripal_chado_views_integration_ajax_new_join_left_field_callback($form, $form_state) {
   return $form['view_setup_join']['new_join'];
 }
 
@@ -1343,9 +1343,9 @@ function tripal_views_integration_ajax_new_join_left_field_callback($form, $form
  * @return
  *   Returns an array of handler names
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_discover_handlers() {
+function tripal_chado_views_integration_discover_handlers() {
 
   $handlers = array();
 
@@ -1420,9 +1420,9 @@ function tripal_views_integration_discover_handlers() {
  * Ajax Callback: Tripal Views Integration Form
  * Replaces the entire fields table when the table or materialized view is set/changed
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_ajax_view_setup_table($form, $form_state) {
+function tripal_chado_views_integration_ajax_view_setup_table($form, $form_state) {
   //return $form['view_setup_table'];
   return $form;
 }
@@ -1431,9 +1431,9 @@ function tripal_views_integration_ajax_view_setup_table($form, $form_state) {
  * Ajax Callback: Tripal Views Integration Form
  * Replaces the join db field dropdown when the join table dropdown is changed
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_ajax_join_field($form, $form_state) {
+function tripal_chado_views_integration_ajax_join_field($form, $form_state) {
 
   // Determine which row we are dealing with from the name of the triggering element
   if (preg_match('/fields_join_(\w+-\d+)/', $form_state['triggering_element']['#name'], $matches)) {

legacy/tripal_views/includes/tripal_views_integration_port.inc → tripal_chado_views/includes/tripal_chado_views_integration_port.inc

@@ -16,9 +16,9 @@
  * @param $setup_id
  *   The tripal views integration setup id
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_export_form($form, &$form_state, $setup_id) {
+function tripal_chado_views_integration_export_form($form, &$form_state, $setup_id) {
   $form = array();
 
   $defn_array = tripal_export_views_integration($setup_id);
@@ -44,9 +44,9 @@ function tripal_views_integration_export_form($form, &$form_state, $setup_id) {
 /**
  * Form: Imports a tripal views integration
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_import_form() {
+function tripal_chado_views_integration_import_form() {
   $form = array();
 
   $form['name'] = array(
@@ -92,9 +92,9 @@ function tripal_views_integration_import_form() {
  * @param $form
  * @param $form_state
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_integration_import_form_submit($form, &$form_state) {
+function tripal_chado_views_integration_import_form_submit($form, &$form_state) {
 
   //$defn_array = unserialize($form_state['values']['import']);
   // convert the array into a real PHP array

legacy/tripal_views/tripal_views.coder_ignores.txt → tripal_chado_views/tripal_chado_views.coder_ignores.txt

@@ -3,7 +3,7 @@
 ; where warning-type is one of security, style, sql, i18n, comment, etc.
 
 ; All variables are filtered
-tripal_views_integration.inc:814:security
+tripal_chado_iews_integration.inc:814:security
 
 
 ; SQL queries the pg_tables table to check if a table exists in chado; drupal

legacy/tripal_views/tripal_views.info → tripal_chado_views/tripal_chado_views.info

@@ -1,10 +1,10 @@
-name = Tripal Views
+name = Tripal Chado Views
 description = Integrates all Chado tables with Drupal Views and provides basic searching for administrators and site visitors and provides a range of flexibility for creating custom pages without the need for programming.
 core = 7.x
 project = tripal
-package = Tripal v2 Legacy
+package = Tripal
 version = 7.x-3.0-alpha1
-configure = admin/tripal/views-integration
+configure = admin/tripal/storage/chado/views-integration
 
 files[] = views/handlers/tripal_views_handler_filter_textarea.inc
 files[] = views/handlers/tripal_views_handler_filter_file_upload.inc

legacy/tripal_views/tripal_views.install → tripal_chado_views/tripal_chado_views.install

@@ -7,15 +7,15 @@
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_requirements($phase) {
+function tripal_chado_views_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
     if (!$GLOBALS["chado_is_installed"]) {
-      $requirements ['tripal_views'] = array(
-        'title' => "tripal_views",
+      $requirements ['tripal_chado_views'] = array(
+        'title' => "tripal_chado_views",
         'value' => "ERROR: Chado must be installed before this module can be enabled",
         'severity' => REQUIREMENT_ERROR,
       );
@@ -27,9 +27,9 @@ function tripal_views_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_install() {
+function tripal_chado_views_install() {
 
   // we want views to pick up our changes
   views_invalidate_cache();
@@ -39,10 +39,10 @@ function tripal_views_install() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_schema() {
-  $schema = tripal_views_get_schemas();
+function tripal_chado_views_schema() {
+  $schema = tripal_chado_views_get_schemas();
   return $schema;
 }
 
@@ -52,12 +52,12 @@ function tripal_views_schema() {
  * can easily provide the entire list for hook_install or individual
  * tables for an update.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_get_schemas() {
+function tripal_chado_views_get_schemas() {
   $schema = array();
 
-  $temp = tripal_views_views_schema();
+  $temp = tripal_chado_views_views_schema();
   foreach ($temp as $table => $arr) {
     $schema[$table] = $arr;
   }
@@ -65,100 +65,6 @@ function tripal_views_get_schemas() {
   return $schema;
 }
 
-/**
- * Tripal Views Update for 6.x-0.4
- *   - Add priority field to tripal_views
- *   - Add handler field to tripal_views_join
- *   - Add tripal_views_field table to keep track of fields for views integration
- *
- * @ingroup tripal_views
- */
-function tripal_views_update_6040() {
-
-  // Add Priority to tripal_views
-  db_add_field(
-    'tripal_views',
-    'priority',
-    array('type' => 'int')
-  );
-  db_add_unique_key('tripal_views', 'priority', array('table_name', 'priority'));
-  db_add_index('tripal_views', 'priority', array('table_name', 'priority'));
-
-  // Add handler to tripal_views_join
-  db_add_field(
-    'tripal_views_join',
-    'handler',
-    array(
-      'type' => 'varchar',
-      'length' => '255',
-      'not null' => TRUE,
-      'default' => ''
-    )
-  );
-
-  // Add tripal_views_field to keep track of fields for views integration
-  $schema = tripal_views_views_schema();
-  db_create_table('tripal_views_field', $schema['tripal_views_field']);
-
-  // Add base_table TRUE/FALSE to tripal_views
-  db_add_field(
-    'tripal_views',
-    'base_table',
-    array(
-      'type' => 'int',
-      'not null ' => TRUE,
-      'default' => 1
-    )
-  );
-
-  // Add arguments to joins
-  db_add_field(
-    'tripal_views_join',
-    'arguments',
-    array(
-      'description' => 'arguments that may get passed to the handler',
-      'type' => 'text',
-      'size' => 'normal'
-    )
-  );
-
-  return t('Updated Tripal Views to handle multiple Integrations and keep track of fields.');
-}
-
-/**
- * Tripal Views Update for 7.x-2.0
- *   - Add relationship_only field to tripal_views_join
- *   - Add relationship_handler field to tripal_views_join
- *
- */
-function tripal_views_update_7200() {
-
-  // Add relationship_handler to tripal_views_join
-  db_add_field(
-    'tripal_views_join',
-    'relationship_handler',
-    array(
-      'type' => 'varchar',
-      'length' => '255',
-      'not null' => TRUE,
-      'default' => 'views_handler_relationship'
-    )
-  );
-
-  // Add relationship_only to tripal_views_join
-  db_add_field(
-    'tripal_views_join',
-    'relationship_only',
-    array(
-      'type' => 'int',
-      'not null ' => TRUE,
-      'default' => 0
-    )
-  );
-
-  return t('Updated Tripal Views to better handle relationships. Relationships are now handled through joins rather than handlers (backwards compatible).');
-}
-
 /**
  * Describe the Tripal Views Schema
  *
@@ -169,9 +75,9 @@ function tripal_views_update_7200() {
  *       and other tables.
  *   - tripal_views_handlers: keeps track of which handlers to use for a given field
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_schema() {
+function tripal_chado_views_views_schema() {
   $schema = array();
   $schema['tripal_views'] = array(
     'description' => 'contains the setups, their materialized view id and base table name that was used.',

legacy/tripal_views/tripal_views.module → tripal_chado_views/tripal_chado_views.module

@@ -5,36 +5,36 @@
  */
 
 /**
- * @defgroup tripal_views Tripal Views Module
+ * @defgroup tripal_chado_views Tripal Chado Views Module
  * @ingroup tripal_modules
  * @{
  * Provides functions for integrating chado with Drupal Views.
  * @}
  */
 
-require_once 'api/tripal_views.api.inc';
-//require_once 'api/tripal_views.DEPRECATED.inc';
+require_once 'api/tripal_chado_views.api.inc';
+//require_once 'api/tripal_chado_views.DEPRECATED.inc';
 
-require_once 'tripal_views.views.inc';
+require_once 'tripal_chado_views.views.inc';
 
-require_once 'includes/tripal_views_integration.inc';
-require_once 'includes/tripal_views_integration_UI.inc';
-require_once 'includes/tripal_views_integration_port.inc';
+require_once 'includes/tripal_chado_views_integration.inc';
+require_once 'includes/tripal_chado_views_integration_UI.inc';
+require_once 'includes/tripal_chado_views_integration_port.inc';
 
 /**
  * Implements hook_menu().
  * This hook provides details about new menu items added by this module
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_menu() {
+function tripal_chado_views_menu() {
   $items = array();
 
   $items['chado'] = array(
     'title' => 'Search Data',
     'description' => 'Listings of the various biological data available categorized by type.',
     'page callback' => 'theme',
-    'page arguments' => array('tripal_views_search_biological_content'),
+    'page arguments' => array('tripal_chado_views_search_biological_content'),
     'access arguments' => array('access content'),
     'expanded' => TRUE,
     'type' => MENU_NORMAL_ITEM,
@@ -44,17 +44,17 @@ function tripal_views_menu() {
   $items['admin/tripal/storage/chado/views-integration'] = array(
     'title' => 'Views Integration',
     'description' => 'Integration of all the chado tables and fields with Drupal Views.',
-    'page callback' => 'tripal_views_admin_integration_view',
+    'page callback' => 'tripal_chado_views_admin_integration_view',
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => 10
   );
 
   /**
-  $items['admin/tripal/views-integration/list'] = array(
+  $items['admin/tripal/storage/chado/views-integration/list'] = array(
     'title' => 'List of Integrated Tables',
     'description' => 'Provide a list of all integrated tables and allows for adding new tables or editing already integrated tables.',
-    'page callback' => 'tripal_views_integration_setup_list',
+    'page callback' => 'tripal_chado_views_integration_setup_list',
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => 0,
@@ -74,14 +74,14 @@ function tripal_views_menu() {
   $items['admin/tripal/storage/chado/views-integration/edit/%'] = array(
     'title' => 'Edit Views Integration',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_views_integration_form', 4),
+    'page arguments' => array('tripal_chado_views_integration_form', 4),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
   );
 
   $items['admin/tripal/storage/chado/views-integration/delete/%'] = array(
     'title' => 'Delete Views Integration',
-    'page callback' => 'tripal_views_integration_delete',
+    'page callback' => 'tripal_chado_views_integration_delete',
     'page arguments' => array(4),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
@@ -90,7 +90,7 @@ function tripal_views_menu() {
   $items['admin/tripal/storage/chado/views-integration/delete-all/confirm'] = array(
     'title' => 'Delete ALL Views Integration',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_views_integration_delete_all_form'),
+    'page arguments' => array('tripal_chado_views_integration_delete_all_form'),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
   );
@@ -99,7 +99,7 @@ function tripal_views_menu() {
     'title' => 'Import Views Integration',
     'description' => 'Import a Tripal Views Integration from another site.',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_views_integration_import_form'),
+    'page arguments' => array('tripal_chado_views_integration_import_form'),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
     'weight' => 2,
@@ -109,7 +109,7 @@ function tripal_views_menu() {
     'title' => 'Export Views Integration',
     'description' => 'Export a Tripal Views Integration for use in another Tripal site',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_views_integration_export_form', 4),
+    'page arguments' => array('tripal_chado_views_integration_export_form', 4),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
     'weight' => 3,
@@ -119,16 +119,16 @@ function tripal_views_menu() {
     'title' => 'Export Views Integration',
     'description' => 'Export a Tripal Views Integration for use in another Tripal site',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_views_integration_export_form', 4),
+    'page arguments' => array('tripal_chado_views_integration_export_form', 4),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
   );
 
   $items['admin/tripal/storage/chado/views-integration/help'] = array(
     'title' => 'Help',
-    'description' => "A description of the Tripal Views module including a short description of it's usage.",
+    'description' => "A description of the Tripal Chado Views module including a short description of it's usage.",
     'page callback' => 'theme',
-    'page arguments' => array('tripal_views_help'),
+    'page arguments' => array('tripal_chado_views_help'),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10,
@@ -137,7 +137,7 @@ function tripal_views_menu() {
   $items['admin/tripal/storage/chado/views-integrations/views/integrations/enable'] = array(
     'title' => 'Enable Integrations Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_views_admin_integrations', 'admin/tripal/views-integrations'),
+    'page arguments' => array('tripal_chado_views_admin_integrations', 'admin/tripal/storage/chado/views-integration'),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
   );
@@ -148,9 +148,9 @@ function tripal_views_menu() {
 /**
  * Implements hook_init().
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_init() {
+function tripal_chado_views_init() {
 return;
   // Need to ensure that all chado tables are integrated w/out making
   // the user go to views UI. It would be ideal to do this in a hook called only once
@@ -169,9 +169,9 @@ return;
  * Implements hook_help().
  * Adds a help page to the module list
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_help ($path, $arg) {
+function tripal_chado_views_help ($path, $arg) {
   if ($path == 'admin/help#tripal_views') {
     return theme('tripal_views_help', array());
   }
@@ -182,13 +182,13 @@ function tripal_views_help ($path, $arg) {
  *
  * Set the permission types that the chado module uses.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_permission() {
+function tripal_chado_views_permission() {
   return array(
     'manage tripal_views_integration' => array(
-      'title' => t('Administrate Tripal Views Integration'),
-      'description' => t('Permission to manage Tripal Views Integration.')
+      'title' => t('Administrate Tripal Chado Views Integration'),
+      'description' => t('Permission to manage Tripal Chado Views Integration.')
     ),
   );
 }
@@ -197,12 +197,12 @@ function tripal_views_permission() {
  * Implements hook_views_api().
  *
  * Purpose: Essentially this hook tells drupal that there is views support for
- *  for this module which then includes tripal_views.views.inc where all the
+ *  for this module which then includes tripal_chado_views.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_api() {
+function tripal_chado_views_views_api() {
   return array(
     'api' => 3.0,
   );
@@ -214,12 +214,12 @@ function tripal_views_views_api() {
  * This hook provides details about themable objects added by
  *   this module
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_theme($existing, $type, $theme, $path) {
+function tripal_chado_views_theme($existing, $type, $theme, $path) {
   return array(
-    'tripal_views_integration_form' => array(
-      'template'  => 'tripal_views_integration_fields_form',
+    'tripal_chado_views_integration_form' => array(
+      'template'  => 'tripal_chado_views_integration_fields_form',
       'render element'=> 'form',
     ),
     'file_upload_combo' => array(
@@ -229,16 +229,16 @@ function tripal_views_theme($existing, $type, $theme, $path) {
       'variables' => array('element' => NULL)
     ),
     // instructions page for the views module
-    'tripal_views_help' => array(
-      'template' => 'tripal_views_help',
+    'tripal_chado_views_help' => array(
+      'template' => 'tripal_chado_views_help',
       'variables' =>  array(NULL),
-      'path' => drupal_get_path('module', 'tripal_views') . '/theme'
+      'path' => drupal_get_path('module', 'tripal_chado_views') . '/theme'
     ),
     // search biological content page
-    'tripal_views_search_biological_content' => array(
-      'template' => 'tripal_views_search_biological_content',
+    'tripal_chado_views_search_biological_content' => array(
+      'template' => 'tripal_chado_views_search_biological_content',
       'variables' =>  array(NULL),
-      'path' => drupal_get_path('module', 'tripal_views') . '/theme'
+      'path' => drupal_get_path('module', 'tripal_chado_views') . '/theme'
     ),
   );
 }
@@ -247,9 +247,9 @@ function tripal_views_theme($existing, $type, $theme, $path) {
  * Implements hook_coder_ignore().
  * Defines the path to the file (tripal_views.coder_ignores.txt) where ignore rules for coder are stored
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_coder_ignore() {
+function tripal_chado_views_coder_ignore() {
   return array(
     'path' => drupal_get_path('module', 'tripal_views'),
     'line prefix' => drupal_get_path('module', 'tripal_views'),
@@ -260,9 +260,9 @@ function tripal_views_coder_ignore() {
  * A landing page for all views of chado content. Simply lists all menu items that
  * are children of it.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_biological_data_page() {
+function tripal_chado_views_biological_data_page() {
   $output = '';
 
   $item = menu_get_item();
@@ -281,9 +281,9 @@ function tripal_views_biological_data_page() {
 /**
  * Admin launchpad
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_admin_integration_view() {
+function tripal_chado_views_admin_integration_view() {
   $output = '';
 
   // set the breadcrumb
@@ -291,7 +291,9 @@ function tripal_views_admin_integration_view() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Intgrations', 'admin/tripal/views-integrations');
+  $breadcrumb[] = l('Data Storage', 'admin/tripal/storage');
+  $breadcrumb[] = l('Chado', 'admin/tripal/storage/chado');
+  $breadcrumb[] = l('Views Integration', 'admin/tripal/storage/chado/views-integration');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -300,12 +302,12 @@ function tripal_views_admin_integration_view() {
     $output .= $view;
   }
   else {
-    $output .= '<p>The Tripal Views Module uses primarily views to provide an '
+    $output .= '<p>The Tripal Chado Views Module uses primarily views to provide an '
       . 'administrative interface. Currently one or more views needed for this '
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Tripal Views Admin', 'admin/tripal/views-integrations/views/integrations/enable').'</li>';
+      $output .= '<li>'.l('Tripal Views Admin', 'admin/tripal/storage/chado/views-integration/views/integrations/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_views/tripal_views.views.inc → tripal_chado_views/tripal_chado_views.views.inc

@@ -16,13 +16,13 @@ include 'views/handlers/tripal_views_handler_area_action_links.inc';
  * @return
  *   An array of handler definitions
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_handlers() {
+function tripal_chado_views_views_handlers() {
 
   return array(
     'info' => array(
-      'path' => drupal_get_path('module', 'tripal_views') . '/views/handlers',
+      'path' => drupal_get_path('module', 'tripal_chado_views') . '/views/handlers',
     ),
     'handlers' => array(
 
@@ -77,9 +77,9 @@ function tripal_views_views_handlers() {
  *   Looking up the NID here ensures the query is only executed once
  *   for all stocks in the table.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_pre_render(&$view) {
+function tripal_chado_views_views_pre_render(&$view) {
 
   // We need to unset the exposed_input for the view so we can repopulate that
   // variable. This is necessary if we're using the file_upload_combo
@@ -89,7 +89,7 @@ function tripal_views_views_pre_render(&$view) {
 
   // Add css if tripal admin tagged view
   if ($view->tag == 'tripal admin') {
-    $tripal_admin_view_css = drupal_get_path('module', 'tripal_views') . '/theme/css/tripal_views_admin_views.css';
+    $tripal_admin_view_css = drupal_get_path('module', 'tripal_chado_views') . '/theme/css/tripal_views_admin_views.css';
     drupal_add_css($tripal_admin_view_css);
   }
 
@@ -109,16 +109,16 @@ function tripal_views_views_pre_render(&$view) {
  *
  * D7 @todo: Add support for materialized views relationships using the new method
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_data() {
+function tripal_chado_views_views_data() {
   $data = array();
 
   // Manually integrate the drupal.tripal_views* tables
-  $data = tripal_views_views_data_tripal_views_tables($data);
+  $data = tripal_chado_views_views_data_tripal_views_tables($data);
 
   // MAKE SURE ALL CHADO TABLES ARE INTEGRATED
-  tripal_views_integrate_all_chado_tables();
+  tripal_chado_views_integrate_all_chado_tables();
 
   // DEFINE GLOBAL FIELDS
   // Filter handler that lets the admin say:
@@ -263,7 +263,7 @@ function tripal_views_views_data() {
         );
 
         tripal_report_error(
-          'tripal_views',
+          'tripal_chado_views',
           TRIPAL_WARNING,
           "The name and help were not set for %table.%column. As a consequence the column
             name has been used... You should ensure that the 'name' and 'help' keys for
@@ -304,7 +304,7 @@ function tripal_views_views_data() {
       // If there were no handlers applied to the current field then warn the administrator!
       if ($num_handlers == 0) {
         tripal_report_error(
-          'tripal_views',
+          'tripal_chado_views',
           TRIPAL_WARNING,
           "No handlers were registered for %table.%column. This means there is no views
             functionality for this column. To register handlers, make sure the 'handlers'
@@ -360,7 +360,7 @@ function tripal_views_views_data() {
 
       // warn if deprecated method of relationship addition was used (ie: through handlers)
       if (isset($data[$base_table][$base_field]['relationship'])) {
-        tripal_report_error('tripal_views', TRIPAL_NOTICE,
+        tripal_report_error('tripal_chado_views', TRIPAL_NOTICE,
           'DEPRECATED: Currently using tripal_views_handlers to store relationship for %base => %left when you should be using tripal_views_joins.',
           array('%base' => $base_table, '%left' => $left_table));
       }
@@ -416,9 +416,9 @@ function tripal_views_views_data() {
 /**
  * Describes the tripal views integration tables to views for the administration views
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_data_tripal_views_tables($data) {
+function tripal_chado_views_views_data_tripal_views_tables($data) {
 
   $data['tripal_views']['table']['group'] = t('Tripal Views Integration');
   $data['tripal_views']['table']['base'] = array(
@@ -568,9 +568,9 @@ function tripal_views_views_data_tripal_views_tables($data) {
  * Used to add Chado <-> Node Joins & Relationships
  *   since you need to add to the $data['node'] to do this
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_data_alter(&$data) {
+function tripal_chado_views_views_data_alter(&$data) {
 
     // ADD IN NODE JOINS & RELATIONSHIPS
     // D7 @todo: Create custom handler to allow join from Node => Base (ie: organism)
@@ -659,8 +659,8 @@ function tripal_views_views_data_alter(&$data) {
  * file uploads require $_POST. We need to make sure these two modules
  * have access to everything needed for this view to work properly.
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_pre_view(&$view, &$display_id, &$args) {
+function tripal_chado_views_views_pre_view(&$view, &$display_id, &$args) {
   $_GET = array_merge($_GET, $_POST);
 }

legacy/tripal_views/tripal_views.views_default.inc → tripal_chado_views/tripal_chado_views.views_default.inc

@@ -6,12 +6,12 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_views_default_views() {
+function tripal_chado_views_views_default_views() {
   $views = array();
 
-  $view = tripal_views_defaultview_admin_integrations();
+  $view = tripal_chado_views_defaultview_admin_integrations();
   $views[$view->name] = $view;
 
   return $views;
@@ -20,9 +20,9 @@ function tripal_views_views_default_views() {
 /**
  * Default integrations administration view
  *
- * @ingroup tripal_views
+ * @ingroup tripal_chado_views
  */
-function tripal_views_defaultview_admin_integrations() {
+function tripal_chado_views_defaultview_admin_integrations() {
 
   $view = new view();
   $view->name = 'tripal_views_admin_integrations';
@@ -116,11 +116,11 @@ function tripal_views_defaultview_admin_integrations() {
   $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
   $handler->display->display_options['header']['action_links_area']['link-1'] = array(
     'label-1' => 'Add New Integration',
-    'path-1' => 'admin/tripal/views-integration/new',
+    'path-1' => 'admin/tripal/storage/chado/views-integration/new',
   );
   $handler->display->display_options['header']['action_links_area']['link-2'] = array(
     'label-2' => 'Import Integration',
-    'path-2' => 'admin/tripal/views-integration/import',
+    'path-2' => 'admin/tripal/storage/chado/views-integration/import',
   );
   $handler->display->display_options['header']['action_links_area']['link-3'] = array(
     'label-3' => '',
@@ -138,7 +138,7 @@ function tripal_views_defaultview_admin_integrations() {
   $handler->display->display_options['header']['action_links_area_1']['empty'] = TRUE;
   $handler->display->display_options['header']['action_links_area_1']['link-1'] = array(
     'label-1' => 'Delete ALL Integrations',
-    'path-1' => 'admin/tripal/views-integration/delete-all/confirm',
+    'path-1' => 'admin/tripal/storage/chado/views-integration/delete-all/confirm',
   );
   $handler->display->display_options['header']['action_links_area_1']['link-2'] = array(
     'label-2' => '',
@@ -193,7 +193,7 @@ function tripal_views_defaultview_admin_integrations() {
   $handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
   $handler->display->display_options['fields']['nothing']['alter']['text'] = 'edit';
   $handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/views-integration/edit/[setup_id]';
+  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/storage/chado/views-integration/edit/[setup_id]';
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
   $handler->display->display_options['fields']['nothing_1']['table'] = 'views';
@@ -202,7 +202,7 @@ function tripal_views_defaultview_admin_integrations() {
   $handler->display->display_options['fields']['nothing_1']['exclude'] = TRUE;
   $handler->display->display_options['fields']['nothing_1']['alter']['text'] = 'delete';
   $handler->display->display_options['fields']['nothing_1']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/views-integration/delete/[setup_id]';
+  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/storage/chado/views-integration/delete/[setup_id]';
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing_2']['id'] = 'nothing_2';
   $handler->display->display_options['fields']['nothing_2']['table'] = 'views';
@@ -211,7 +211,7 @@ function tripal_views_defaultview_admin_integrations() {
   $handler->display->display_options['fields']['nothing_2']['exclude'] = TRUE;
   $handler->display->display_options['fields']['nothing_2']['alter']['text'] = 'export';
   $handler->display->display_options['fields']['nothing_2']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing_2']['alter']['path'] = 'admin/tripal/views-integration/export/[setup_id]';
+  $handler->display->display_options['fields']['nothing_2']['alter']['path'] = 'admin/tripal/storage/chado/views-integration/export/[setup_id]';
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing_3']['id'] = 'nothing_3';
   $handler->display->display_options['fields']['nothing_3']['table'] = 'views';