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@@ -7,543 +7,280 @@
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function tripal_feature_views_default_views() {
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$views = array();
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- if (!module_exists('tripal_views')) {
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- return $views;
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- }
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+ $view = tripal_feature_defaultview_admin_features();
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+ $views[$view->name] = $view;
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+
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+ return $views;
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+}
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- // Main default view
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- $view = new view;
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- $view->name = 'feature_listing';
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- $view->description = 'A listing of chado sequence features.';
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- $view->tag = 'chado default';
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+function tripal_feature_defaultview_admin_features() {
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+
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+ $view = new view();
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+ $view->name = 'tripal_feature_admin_features';
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+ $view->description = 'DO NOT DISABLE';
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+ $view->tag = 'tripal admin';
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$view->base_table = 'feature';
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+ $view->human_name = 'Feature Admin';
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$view->core = 0;
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- $view->api_version = '2';
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+ $view->api_version = '3.0';
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$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
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+
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+ /* Display: features_all */
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$handler = $view->new_display('default', 'features_all', 'default');
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- $handler->override_option('fields', array(
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- 'uniquename' => array(
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- 'label' => 'Unique Name',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => 'node/[nid]',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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- 'strip_tags' => 0,
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- ),
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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'link_to_node' => 0,
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- 'exclude' => 0,
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- 'id' => 'uniquename',
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- 'table' => 'feature',
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- 'field' => 'uniquename',
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- 'relationship' => 'none',
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- 'override' => array(
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- 'button' => 'Override',
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- ),
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+ $handler->display->display_options['title'] = 'Sequence Features';
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+ $handler->display->display_options['use_more_always'] = FALSE;
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+ $handler->display->display_options['access']['type'] = 'perm';
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+ $handler->display->display_options['access']['perm'] = 'access chado_feature content';
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+ $handler->display->display_options['cache']['type'] = 'none';
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+ $handler->display->display_options['query']['type'] = 'views_query';
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+ $handler->display->display_options['exposed_form']['type'] = 'basic';
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+ $handler->display->display_options['pager']['type'] = 'full';
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+ $handler->display->display_options['pager']['options']['items_per_page'] = '25';
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+ $handler->display->display_options['pager']['options']['offset'] = '0';
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+ $handler->display->display_options['pager']['options']['id'] = '0';
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+ $handler->display->display_options['pager']['options']['quantity'] = '9';
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+ $handler->display->display_options['style_plugin'] = 'table';
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+ $handler->display->display_options['style_options']['grouping'] = '';
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+ $handler->display->display_options['style_options']['columns'] = array(
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+ 'accession' => 'accession',
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+ 'accession_link' => 'accession_link',
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+ 'name' => 'name',
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+ 'uniquename' => 'uniquename',
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+ 'name_1' => 'name_1',
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+ 'common_name' => 'common_name',
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+ 'seqlen' => 'seqlen',
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+ 'is_obsolete' => 'is_obsolete',
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+ 'is_analysis' => 'is_analysis',
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+ 'nid' => 'nid',
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+ );
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+ $handler->display->display_options['style_options']['default'] = '-1';
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+ $handler->display->display_options['style_options']['info'] = array(
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+ 'accession' => array(
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+ 'sortable' => 1,
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+ 'separator' => '',
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+ ),
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+ 'accession_link' => array(
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+ 'sortable' => 1,
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+ 'separator' => '',
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),
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'name' => array(
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- 'label' => 'Name',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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- 'strip_tags' => 0,
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- ),
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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'link_to_node' => 1,
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- 'exclude' => 0,
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- 'id' => 'name',
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- 'table' => 'feature',
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- 'field' => 'name',
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- 'relationship' => 'none',
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- 'override' => array(
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- 'button' => 'Override',
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- ),
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+ 'sortable' => 1,
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+ 'separator' => '',
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+ ),
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+ 'uniquename' => array(
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+ 'sortable' => 1,
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+ 'separator' => '',
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),
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'name_1' => array(
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- 'label' => 'Type',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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- 'strip_tags' => 0,
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- ),
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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'exclude' => 0,
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- 'id' => 'name_1',
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- 'table' => 'cvterm',
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- 'field' => 'name',
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- 'relationship' => 'none',
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+ 'sortable' => 1,
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+ 'separator' => '',
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),
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'common_name' => array(
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- 'label' => 'Common Name',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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- 'strip_tags' => 0,
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- ),
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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'link_to_node' => 1,
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- 'exclude' => 0,
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- 'id' => 'common_name',
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- 'table' => 'organism',
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- 'field' => 'common_name',
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- 'relationship' => 'none',
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- 'override' => array(
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- 'button' => 'Override',
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- ),
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+ 'sortable' => 1,
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+ 'separator' => '',
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),
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'seqlen' => array(
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- 'label' => 'Sequence Length',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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- 'strip_tags' => 0,
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- ),
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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'set_precision' => FALSE,
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- 'precision' => 0,
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- 'decimal' => '.',
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- 'separator' => ',',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'exclude' => 0,
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- 'id' => 'seqlen',
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- 'table' => 'feature',
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- 'field' => 'seqlen',
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- 'relationship' => 'none',
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+ 'sortable' => 1,
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+ 'separator' => '',
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),
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'is_obsolete' => array(
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- 'label' => 'Is Obsolete',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'absolute' => 0,
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- 'link_class' => '',
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- 'alt' => '',
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- 'rel' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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- 'strip_tags' => 0,
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- ),
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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'hide_alter_empty' => 1,
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- 'type' => 'separator',
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- 'not' => 0,
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- 'separator' => ', ',
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- 'exclude' => 0,
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- 'id' => 'is_obsolete',
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- 'table' => 'feature',
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- 'field' => 'is_obsolete',
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- 'relationship' => 'none',
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- ),
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- 'timeaccessioned' => array(
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- 'label' => 'Accessioned On',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'absolute' => 0,
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- 'link_class' => '',
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- 'alt' => '',
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- 'rel' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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- 'strip_tags' => 0,
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- ),
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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'hide_alter_empty' => 1,
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- 'date_format' => 'large',
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- 'custom_date_format' => '',
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- 'type' => 'separator',
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- 'separator' => ', ',
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- 'exclude' => 0,
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- 'id' => 'timeaccessioned',
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- 'table' => 'feature',
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- 'field' => 'timeaccessioned',
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- 'relationship' => 'none',
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- ),
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- ));
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- $handler->override_option('sorts', array(
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- 'common_name' => array(
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- 'order' => 'ASC',
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- 'id' => 'common_name',
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- 'table' => 'organism',
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- 'field' => 'common_name',
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- 'relationship' => 'none',
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- ),
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- 'name' => array(
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- 'order' => 'ASC',
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- 'id' => 'name',
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- 'table' => 'cvterm',
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- 'field' => 'name',
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- 'relationship' => 'none',
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- ),
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- 'name_1' => array(
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- 'order' => 'ASC',
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- 'id' => 'name_1',
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- 'table' => 'feature',
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- 'field' => 'name',
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- 'relationship' => 'none',
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- ),
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- ));
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- $handler->override_option('filters', array(
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- 'common_name' => array(
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- 'operator' => '=',
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- 'value' => array(),
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- 'group' => '0',
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- 'exposed' => TRUE,
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- 'expose' => array(
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- 'use_operator' => 0,
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- 'operator' => 'common_name_op',
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- 'identifier' => 'organism',
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- 'label' => 'Organism Common Name',
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- 'remember' => 0,
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- ),
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- 'case' => 1,
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- 'id' => 'common_name',
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- 'table' => 'organism',
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- 'field' => 'common_name',
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- 'relationship' => 'none',
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- 'values_form_type' => 'select',
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- 'multiple' => 1,
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- 'optional' => 0,
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- 'override' => array(
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- 'button' => 'Override',
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- ),
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- 'agg' => array(
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- 'records_with' => 1,
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- 'aggregates_with' => 1,
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- ),
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- ),
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- 'type_id' => array(
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- 'operator' => '=',
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- 'value' => array(),
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- 'group' => '0',
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- 'exposed' => TRUE,
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- 'expose' => array(
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- 'use_operator' => 0,
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- 'operator' => 'type_id_op',
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- 'identifier' => 'type_id',
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- 'label' => 'Type',
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- 'remember' => 0,
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- ),
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- 'case' => 1,
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- 'id' => 'type_id',
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- 'table' => 'feature',
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- 'field' => 'type_id',
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- 'relationship' => 'none',
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- 'values_form_type' => 'select',
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- 'multiple' => 1,
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- 'optional' => 0,
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- 'show_all' => 0,
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- 'agg' => array(
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- 'records_with' => 1,
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- 'aggregates_with' => 1,
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- ),
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- ),
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- 'name_1' => array(
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- 'operator' => '~',
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- 'value' => '',
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- 'group' => '0',
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- 'exposed' => TRUE,
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- 'expose' => array(
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- 'use_operator' => 0,
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- 'operator' => 'name_1_op',
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- 'identifier' => 'name',
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- 'label' => 'Name Contains',
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- 'bef_filter_description' => '',
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- 'remember' => 0,
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- ),
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- 'case' => 0,
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- 'id' => 'name_1',
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- 'table' => 'feature',
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- 'field' => 'name',
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- 'relationship' => 'none',
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- 'agg' => array(
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- 'records_with' => 1,
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- 'aggregates_with' => 1,
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- ),
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- ),
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- 'search_results' => array(
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- 'operator' => '=',
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- 'value' => '',
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- 'group' => '0',
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- 'exposed' => FALSE,
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- 'expose' => array(
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- 'operator' => FALSE,
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- 'label' => '',
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- ),
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- 'id' => 'search_results',
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- 'table' => 'views',
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- 'field' => 'search_results',
|
|
|
- 'relationship' => 'none',
|
|
|
- 'apply_button' => 'Show',
|
|
|
- 'no_results_text' => 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.',
|
|
|
+ 'sortable' => 1,
|
|
|
+ 'separator' => '',
|
|
|
),
|
|
|
- ));
|
|
|
- $handler->override_option('access', array(
|
|
|
- 'type' => 'perm',
|
|
|
- 'perm' => 'access chado_feature content',
|
|
|
- ));
|
|
|
- $handler->override_option('cache', array(
|
|
|
- 'type' => 'none',
|
|
|
- ));
|
|
|
- $handler->override_option('title', 'Sequence Features');
|
|
|
- $handler->override_option('header', 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.');
|
|
|
- $handler->override_option('header_format', '2');
|
|
|
- $handler->override_option('header_empty', 0);
|
|
|
- $handler->override_option('empty', 'No features matched the supplied criteria.');
|
|
|
- $handler->override_option('empty_format', '2');
|
|
|
- $handler->override_option('items_per_page', 50);
|
|
|
- $handler->override_option('use_pager', '1');
|
|
|
- $handler->override_option('style_plugin', 'table');
|
|
|
- $handler->override_option('style_options', array(
|
|
|
- 'grouping' => '',
|
|
|
- 'override' => 1,
|
|
|
- 'sticky' => 0,
|
|
|
- 'order' => 'asc',
|
|
|
- 'columns' => array(
|
|
|
- 'accession' => 'accession',
|
|
|
- 'accession_link' => 'accession_link',
|
|
|
- 'name' => 'name',
|
|
|
- 'uniquename' => 'uniquename',
|
|
|
- 'name_1' => 'name_1',
|
|
|
- 'common_name' => 'common_name',
|
|
|
- 'seqlen' => 'seqlen',
|
|
|
- 'is_obsolete' => 'is_obsolete',
|
|
|
- 'is_analysis' => 'is_analysis',
|
|
|
- 'nid' => 'nid',
|
|
|
+ 'is_analysis' => array(
|
|
|
+ 'sortable' => 1,
|
|
|
+ 'separator' => '',
|
|
|
),
|
|
|
- 'info' => array(
|
|
|
- 'accession' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'accession_link' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'name' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'uniquename' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'name_1' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'common_name' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'seqlen' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'is_obsolete' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'is_analysis' => array(
|
|
|
- 'sortable' => 1,
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
- 'nid' => array(
|
|
|
- 'separator' => '',
|
|
|
- ),
|
|
|
+ 'nid' => array(
|
|
|
+ 'separator' => '',
|
|
|
),
|
|
|
- 'default' => '-1',
|
|
|
- ));
|
|
|
- $default_handler = $handler;
|
|
|
+ );
|
|
|
+ /* 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'] = 'Add/Import';
|
|
|
+ $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
|
|
|
+ $handler->display->display_options['header']['action_links_area']['link-1'] = array(
|
|
|
+ 'label-1' => 'Add Feature',
|
|
|
+ 'path-1' => 'node/add/tripal-feature',
|
|
|
+ );
|
|
|
+ $handler->display->display_options['header']['action_links_area']['link-2'] = array(
|
|
|
+ 'label-2' => 'Import via FASTA file',
|
|
|
+ 'path-2' => 'admin/tripal/loaders/fasta_loader',
|
|
|
+ );
|
|
|
+ $handler->display->display_options['header']['action_links_area']['link-3'] = array(
|
|
|
+ 'label-3' => 'Import via GFF3 file',
|
|
|
+ 'path-3' => 'admin/tripal/loaders/gff3_load',
|
|
|
+ );
|
|
|
+ $handler->display->display_options['header']['action_links_area']['link-4'] = array(
|
|
|
+ 'label-4' => '',
|
|
|
+ 'path-4' => '',
|
|
|
+ );
|
|
|
+ /* Header: Global: Action Links */
|
|
|
+ $handler->display->display_options['header']['action_links_area_1']['id'] = 'action_links_area_1';
|
|
|
+ $handler->display->display_options['header']['action_links_area_1']['table'] = 'views';
|
|
|
+ $handler->display->display_options['header']['action_links_area_1']['field'] = 'action_links_area';
|
|
|
+ $handler->display->display_options['header']['action_links_area_1']['label'] = 'Extract';
|
|
|
+ $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' => 'Retrieve Sequences',
|
|
|
+ 'path-1' => 'find/sequences',
|
|
|
+ );
|
|
|
+ $handler->display->display_options['header']['action_links_area_1']['link-2'] = array(
|
|
|
+ 'label-2' => '',
|
|
|
+ 'path-2' => '',
|
|
|
+ );
|
|
|
+ $handler->display->display_options['header']['action_links_area_1']['link-3'] = array(
|
|
|
+ 'label-3' => '',
|
|
|
+ 'path-3' => '',
|
|
|
+ );
|
|
|
+ $handler->display->display_options['header']['action_links_area_1']['link-4'] = array(
|
|
|
+ 'label-4' => '',
|
|
|
+ 'path-4' => '',
|
|
|
+ );
|
|
|
+ /* 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 features matched the supplied criteria.';
|
|
|
+ $handler->display->display_options['empty']['text']['format'] = '2';
|
|
|
+ /* Relationship: Feature: Feature => Node */
|
|
|
+ $handler->display->display_options['relationships']['feature_id']['id'] = 'feature_id';
|
|
|
+ $handler->display->display_options['relationships']['feature_id']['table'] = 'chado_feature';
|
|
|
+ $handler->display->display_options['relationships']['feature_id']['field'] = 'feature_id';
|
|
|
+ /* Field: Content: Nid */
|
|
|
+ $handler->display->display_options['fields']['nid']['id'] = 'nid';
|
|
|
+ $handler->display->display_options['fields']['nid']['table'] = 'node';
|
|
|
+ $handler->display->display_options['fields']['nid']['field'] = 'nid';
|
|
|
+ $handler->display->display_options['fields']['nid']['relationship'] = 'feature_id';
|
|
|
+ $handler->display->display_options['fields']['nid']['exclude'] = TRUE;
|
|
|
+ /* Field: Chado Feature: Uniquename */
|
|
|
+ $handler->display->display_options['fields']['uniquename']['id'] = 'uniquename';
|
|
|
+ $handler->display->display_options['fields']['uniquename']['table'] = 'feature';
|
|
|
+ $handler->display->display_options['fields']['uniquename']['field'] = 'uniquename';
|
|
|
+ $handler->display->display_options['fields']['uniquename']['label'] = 'Unique Name';
|
|
|
+ $handler->display->display_options['fields']['uniquename']['alter']['path'] = 'node/[nid]';
|
|
|
+ /* Field: Chado Feature: Name */
|
|
|
+ $handler->display->display_options['fields']['name']['id'] = 'name';
|
|
|
+ $handler->display->display_options['fields']['name']['table'] = 'feature';
|
|
|
+ $handler->display->display_options['fields']['name']['field'] = 'name';
|
|
|
+ /* Field: Chado Cvterm: Name */
|
|
|
+ $handler->display->display_options['fields']['name_1']['id'] = 'name_1';
|
|
|
+ $handler->display->display_options['fields']['name_1']['table'] = 'cvterm';
|
|
|
+ $handler->display->display_options['fields']['name_1']['field'] = 'name';
|
|
|
+ $handler->display->display_options['fields']['name_1']['label'] = 'Type';
|
|
|
+ /* Field: Chado Organism: Common Name */
|
|
|
+ $handler->display->display_options['fields']['common_name']['id'] = 'common_name';
|
|
|
+ $handler->display->display_options['fields']['common_name']['table'] = 'organism';
|
|
|
+ $handler->display->display_options['fields']['common_name']['field'] = 'common_name';
|
|
|
+ /* Field: Chado Feature: Seqlen */
|
|
|
+ $handler->display->display_options['fields']['seqlen']['id'] = 'seqlen';
|
|
|
+ $handler->display->display_options['fields']['seqlen']['table'] = 'feature';
|
|
|
+ $handler->display->display_options['fields']['seqlen']['field'] = 'seqlen';
|
|
|
+ $handler->display->display_options['fields']['seqlen']['label'] = 'Sequence Length';
|
|
|
+ /* Field: Chado Feature: Is Obsolete */
|
|
|
+ $handler->display->display_options['fields']['is_obsolete']['id'] = 'is_obsolete';
|
|
|
+ $handler->display->display_options['fields']['is_obsolete']['table'] = 'feature';
|
|
|
+ $handler->display->display_options['fields']['is_obsolete']['field'] = 'is_obsolete';
|
|
|
+ $handler->display->display_options['fields']['is_obsolete']['type'] = 'separator';
|
|
|
+ $handler->display->display_options['fields']['is_obsolete']['not'] = 0;
|
|
|
+ /* Field: Content: Delete link */
|
|
|
+ $handler->display->display_options['fields']['delete_node']['id'] = 'delete_node';
|
|
|
+ $handler->display->display_options['fields']['delete_node']['table'] = 'views_entity_node';
|
|
|
+ $handler->display->display_options['fields']['delete_node']['field'] = 'delete_node';
|
|
|
+ $handler->display->display_options['fields']['delete_node']['relationship'] = 'feature_id';
|
|
|
+ $handler->display->display_options['fields']['delete_node']['exclude'] = TRUE;
|
|
|
+ /* Field: Content: Edit link */
|
|
|
+ $handler->display->display_options['fields']['edit_node']['id'] = 'edit_node';
|
|
|
+ $handler->display->display_options['fields']['edit_node']['table'] = 'views_entity_node';
|
|
|
+ $handler->display->display_options['fields']['edit_node']['field'] = 'edit_node';
|
|
|
+ $handler->display->display_options['fields']['edit_node']['relationship'] = 'feature_id';
|
|
|
+ $handler->display->display_options['fields']['edit_node']['exclude'] = TRUE;
|
|
|
+ /* 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'] = '';
|
|
|
+ $handler->display->display_options['fields']['nothing']['alter']['text'] = '[edit_node] [delete_node]';
|
|
|
+ $handler->display->display_options['fields']['nothing']['element_label_colon'] = FALSE;
|
|
|
+ /* Sort criterion: Chado Organism: Common Name */
|
|
|
+ $handler->display->display_options['sorts']['common_name']['id'] = 'common_name';
|
|
|
+ $handler->display->display_options['sorts']['common_name']['table'] = 'organism';
|
|
|
+ $handler->display->display_options['sorts']['common_name']['field'] = 'common_name';
|
|
|
+ /* Sort criterion: Chado Cvterm: Name */
|
|
|
+ $handler->display->display_options['sorts']['name']['id'] = 'name';
|
|
|
+ $handler->display->display_options['sorts']['name']['table'] = 'cvterm';
|
|
|
+ $handler->display->display_options['sorts']['name']['field'] = 'name';
|
|
|
+ /* Sort criterion: Chado Feature: Name */
|
|
|
+ $handler->display->display_options['sorts']['name_1']['id'] = 'name_1';
|
|
|
+ $handler->display->display_options['sorts']['name_1']['table'] = 'feature';
|
|
|
+ $handler->display->display_options['sorts']['name_1']['field'] = 'name';
|
|
|
+ /* Filter criterion: Chado Organism: Common Name */
|
|
|
+ $handler->display->display_options['filters']['common_name']['id'] = 'common_name';
|
|
|
+ $handler->display->display_options['filters']['common_name']['table'] = 'organism';
|
|
|
+ $handler->display->display_options['filters']['common_name']['field'] = 'common_name';
|
|
|
+ $handler->display->display_options['filters']['common_name']['value'] = array();
|
|
|
+ $handler->display->display_options['filters']['common_name']['group'] = '0';
|
|
|
+ $handler->display->display_options['filters']['common_name']['exposed'] = TRUE;
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['operator_id'] = 'common_name_op';
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['label'] = 'Organism Common Name';
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['operator'] = 'common_name_op';
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['identifier'] = 'organism';
|
|
|
+ /* Filter criterion: Chado Feature: Type Id */
|
|
|
+ $handler->display->display_options['filters']['type_id']['id'] = 'type_id';
|
|
|
+ $handler->display->display_options['filters']['type_id']['table'] = 'feature';
|
|
|
+ $handler->display->display_options['filters']['type_id']['field'] = 'type_id';
|
|
|
+ $handler->display->display_options['filters']['type_id']['value'] = array();
|
|
|
+ $handler->display->display_options['filters']['type_id']['group'] = '0';
|
|
|
+ $handler->display->display_options['filters']['type_id']['exposed'] = TRUE;
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['operator_id'] = 'type_id_op';
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['label'] = 'Type';
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['operator'] = 'type_id_op';
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['identifier'] = 'type_id';
|
|
|
+ /* Filter criterion: Chado Feature: Name */
|
|
|
+ $handler->display->display_options['filters']['name_1']['id'] = 'name_1';
|
|
|
+ $handler->display->display_options['filters']['name_1']['table'] = 'feature';
|
|
|
+ $handler->display->display_options['filters']['name_1']['field'] = 'name';
|
|
|
+ $handler->display->display_options['filters']['name_1']['operator'] = '~';
|
|
|
+ $handler->display->display_options['filters']['name_1']['group'] = '0';
|
|
|
+ $handler->display->display_options['filters']['name_1']['exposed'] = TRUE;
|
|
|
+ $handler->display->display_options['filters']['name_1']['expose']['operator_id'] = 'name_1_op';
|
|
|
+ $handler->display->display_options['filters']['name_1']['expose']['label'] = 'Name Contains';
|
|
|
+ $handler->display->display_options['filters']['name_1']['expose']['operator'] = 'name_1_op';
|
|
|
+ $handler->display->display_options['filters']['name_1']['expose']['identifier'] = 'name';
|
|
|
+
|
|
|
+ /** MANUALLY ADD since filter handler no exporting correctly */
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'select';
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = TRUE;
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['values_form_type'] = 'select';
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['select_multiple'] = FALSE;
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['select_optional'] = TRUE;
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['max_length'] = 40;
|
|
|
+
|
|
|
+ /* Display: Page */
|
|
|
$handler = $view->new_display('page', 'Page', 'page_1');
|
|
|
- $handler->override_option('path', 'chado/features');
|
|
|
- $handler->override_option('menu', array(
|
|
|
- 'type' => 'normal',
|
|
|
- 'title' => 'Features',
|
|
|
- 'description' => 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on.',
|
|
|
- 'weight' => '10',
|
|
|
- 'name' => 'navigation',
|
|
|
- ));
|
|
|
- $handler->override_option('tab_options', array(
|
|
|
- 'type' => 'none',
|
|
|
- 'title' => '',
|
|
|
- 'description' => '',
|
|
|
- 'weight' => 0,
|
|
|
- 'name' => 'navigation',
|
|
|
- ));
|
|
|
- // Add code specific to a local chado installation
|
|
|
- // NOTE: Edit $handler above to $default_handler for the default display
|
|
|
- if (tripal_core_chado_schema_exists()) {
|
|
|
- // Add nid field
|
|
|
- $fields = $view->get_items('field', 'default');
|
|
|
- $new_fields = array(
|
|
|
- 'nid' => array(
|
|
|
- 'label' => 'Nid',
|
|
|
- 'alter' => array(
|
|
|
- 'alter_text' => 0,
|
|
|
- 'text' => '',
|
|
|
- 'make_link' => 0,
|
|
|
- 'path' => '',
|
|
|
- 'absolute' => 0,
|
|
|
- 'link_class' => '',
|
|
|
- 'alt' => '',
|
|
|
- 'rel' => '',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'target' => '',
|
|
|
- 'help' => '',
|
|
|
- 'trim' => 0,
|
|
|
- 'max_length' => '',
|
|
|
- 'word_boundary' => 1,
|
|
|
- 'ellipsis' => 1,
|
|
|
- 'html' => 0,
|
|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'hide_alter_empty' => 1,
|
|
|
- 'link_to_node' => 0,
|
|
|
- 'exclude' => 1,
|
|
|
- 'id' => 'nid',
|
|
|
- 'table' => 'node',
|
|
|
- 'field' => 'nid',
|
|
|
- 'relationship' => 'none',
|
|
|
- )
|
|
|
- );
|
|
|
- $fields = $new_fields + $fields;
|
|
|
- // Adds feature => Node relationship
|
|
|
- $default_handler->override_option('relationships', array(
|
|
|
- 'nid' => array(
|
|
|
- 'label' => 'Feature to Node',
|
|
|
- 'required' => 0,
|
|
|
- 'id' => 'nid',
|
|
|
- 'table' => 'chado_feature',
|
|
|
- 'field' => 'nid',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- ));
|
|
|
- // Change analysis.name to have a link to the node
|
|
|
- $fields['name']['alter']['link_to_node'] = 1;
|
|
|
- $default_handler->override_option('fields', $fields);
|
|
|
- // Only show records with published nodes
|
|
|
- /**
|
|
|
- $filters = $view->get_items('filter', 'default');
|
|
|
- $filters['status'] = array(
|
|
|
- 'operator' => '=',
|
|
|
- 'value' => '1',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => FALSE,
|
|
|
- 'expose' => array(
|
|
|
- 'operator' => FALSE,
|
|
|
- 'label' => '',
|
|
|
- ),
|
|
|
- 'id' => 'status',
|
|
|
- 'table' => 'node',
|
|
|
- 'field' => 'status',
|
|
|
- 'relationship' => 'none',
|
|
|
- );
|
|
|
- $default_handler->override_option('filters', $filters);
|
|
|
- */
|
|
|
- }
|
|
|
- $views[$view->name] = $view;
|
|
|
+ $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_feature/features';
|
|
|
+ $handler->display->display_options['menu']['type'] = 'default tab';
|
|
|
+ $handler->display->display_options['menu']['title'] = 'Features';
|
|
|
+ $handler->display->display_options['menu']['description'] = 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections.';
|
|
|
+ $handler->display->display_options['menu']['weight'] = '-10';
|
|
|
+ $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 $views;
|
|
|
+ /** MANUALLY ADD since filter handler no exporting correctly
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'select';
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = TRUE;
|
|
|
+ $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['values_form_type'] = 'select';
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['select_multiple'] = FALSE;
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['select_optional'] = TRUE;
|
|
|
+ $handler->display->display_options['filters']['type_id']['expose']['max_length'] = 40;
|
|
|
+ */
|
|
|
+
|
|
|
+ return $view;
|
|
|
}
|