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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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| tripal_contact_views_default_views | ( | ) |
Definition at line 88 of file tripal_contact.views.inc.
{
$views = array();
if (!module_exists('tripal_views')) {
return $views;
}
// Main default view
$view = new view;
$view->name = 'contact_listing';
$view->description = 'A listing of chado contacts';
$view->tag = 'chado default';
$view->base_table = 'contact';
$view->core = 6;
$view->api_version = '2';
$view->disabled = TRUE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
'name' => array(
'label' => 'Name',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name',
'table' => 'contact',
'field' => 'name',
'relationship' => 'none',
),
'name_1' => array(
'label' => 'Type',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name_1',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'none',
),
'description' => array(
'label' => 'Description',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'description',
'table' => 'contact',
'field' => 'description',
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'search_results' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
),
'id' => 'search_results',
'table' => 'views',
'field' => 'search_results',
'relationship' => 'none',
'apply_button' => 'Show',
'no_results_text' => 'Click "Show" to see a list of all contacts matching the entered criteria. If you leave a any of the criteria blank then the contacts will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all contacts will be listed.',
),
'type_id' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'type_id_op',
'identifier' => 'type_id',
'label' => 'Type',
'remember' => 0,
),
'case' => 1,
'id' => 'type_id',
'table' => 'contact',
'field' => 'type_id',
'relationship' => 'none',
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'name' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'name_op',
'identifier' => 'name',
'label' => 'Name Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'name',
'table' => 'contact',
'field' => 'name',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'description' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'description_op',
'identifier' => 'description',
'label' => 'Description Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'description',
'table' => 'contact',
'field' => 'description',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Contacts');
$handler->override_option('header', 'Click "Show" to see a list of all contacts matching the entered criteria. If you leave a any of the criteria blank then the contacts will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all contacts will be listed.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No contacts match the current 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',
'summary' => '',
'columns' => array(
'name' => 'name',
'name_1' => 'name_1',
'description' => 'description',
),
'info' => array(
'name' => array(
'sortable' => 1,
'separator' => '',
),
'name_1' => array(
'sortable' => 1,
'separator' => '',
),
'description' => array(
'sortable' => 0,
'separator' => '',
),
),
'default' => 'name',
));
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/contacts');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Contacts',
'description' => 'Contacts can be persons, institutes, groups, or organizations.',
'weight' => '10',
'name' => 'navigation',
));
$handler->override_option('tab_options', array(
'type' => 'none',
'title' => '',
'description' => '',
'weight' => 0,
'name' => 'navigation',
));
$views[$view->name] = $view;
return $views;
}
| tripal_feature_views_data | ( | ) |
Implements hook_views_data()
Purpose: Describe chado/tripal tables & fields to views
Definition at line 31 of file tripal_feature.views.inc.
{
$data = array();
if (module_exists('tripal_views')) {
$tables = array(
'feature',
);
foreach ($tables as $tablename) {
$priority = 9;
// check to see if the table is integrated. If it is then integrate it's
// corresponding 'chado_[table]' table.
if (!tripal_views_is_integrated($tablename, $priority)) {
$table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
// Add in node relationships if chado is in the same db as drupal
if (tripal_core_chado_schema_exists()) {
$integrations = tripal_views_add_node_relationship_to_chado_table_integration($table_integration_array);
foreach ($integrations as $integration) {
tripal_views_integration_add_entry($integration);
}
}
else {
tripal_views_integration_add_entry($table_integration_array);
}
}
}
$tables = array(
'feature_cvterm',
'feature_cvterm_dbxref',
'feature_cvterm_pub',
'feature_cvtermprop',
'feature_dbxref',
'feature_pub',
'feature_pubprop',
'feature_relationship',
'feature_relationship_pub',
'feature_relationshipprop',
'feature_relationshipprop_pub',
'feature_synonym',
'featureloc',
'featureloc_pub',
'featureprop',
'featureprop_pub',
'featuremap',
'featuremap_pub',
'featurepos',
'featurerange'
);
foreach ($tables as $tablename) {
$priority = 9;
if (!tripal_views_is_integrated($tablename, $priority)) {
$table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE, $priority);
tripal_views_integration_add_entry($table_integration_array);
}
}
}
return $data;
}
| tripal_feature_views_default_views | ( | ) |
$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);
Definition at line 149 of file tripal_feature.views.inc.
{
$views = array();
if (!module_exists('tripal_views')) {
return $views;
}
// Main default view
$view = new view;
$view->name = 'feature_listing';
$view->description = 'A listing of chado sequence features.';
$view->tag = 'chado default';
$view->base_table = 'feature';
$view->core = 0;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'features_all', 'default');
$handler->override_option('fields', array(
'uniquename' => array(
'label' => 'Unique Name',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => 'node/[nid]',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'link_to_node' => 0,
'exclude' => 0,
'id' => 'uniquename',
'table' => 'feature',
'field' => 'uniquename',
'relationship' => 'none',
'override' => array(
'button' => 'Override',
),
),
'name' => array(
'label' => 'Name',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => '',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'link_to_node' => 1,
'exclude' => 0,
'id' => 'name',
'table' => 'feature',
'field' => 'name',
'relationship' => 'none',
'override' => array(
'button' => 'Override',
),
),
'name_1' => array(
'label' => 'Type',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => '',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'exclude' => 0,
'id' => 'name_1',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'none',
),
'common_name' => array(
'label' => 'Common Name',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => '',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'link_to_node' => 1,
'exclude' => 0,
'id' => 'common_name',
'table' => 'organism',
'field' => 'common_name',
'relationship' => 'none',
'override' => array(
'button' => 'Override',
),
),
'seqlen' => array(
'label' => 'Sequence Length',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => '',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'set_precision' => FALSE,
'precision' => 0,
'decimal' => '.',
'separator' => ',',
'prefix' => '',
'suffix' => '',
'exclude' => 0,
'id' => 'seqlen',
'table' => 'feature',
'field' => 'seqlen',
'relationship' => 'none',
),
'is_obsolete' => array(
'label' => 'Is Obsolete',
'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,
'type' => 'separator',
'not' => 0,
'separator' => ', ',
'exclude' => 0,
'id' => 'is_obsolete',
'table' => 'feature',
'field' => 'is_obsolete',
'relationship' => 'none',
),
'timeaccessioned' => array(
'label' => 'Accessioned On',
'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,
'date_format' => 'large',
'custom_date_format' => '',
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'timeaccessioned',
'table' => 'feature',
'field' => 'timeaccessioned',
'relationship' => 'none',
),
));
$handler->override_option('sorts', array(
'common_name' => array(
'order' => 'ASC',
'id' => 'common_name',
'table' => 'organism',
'field' => 'common_name',
'relationship' => 'none',
),
'name' => array(
'order' => 'ASC',
'id' => 'name',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'none',
),
'name_1' => array(
'order' => 'ASC',
'id' => 'name_1',
'table' => 'feature',
'field' => 'name',
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'common_name' => array(
'operator' => '=',
'value' => array(),
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'common_name_op',
'identifier' => 'organism',
'label' => 'Organism Common Name',
'remember' => 0,
),
'case' => 1,
'id' => 'common_name',
'table' => 'organism',
'field' => 'common_name',
'relationship' => 'none',
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'override' => array(
'button' => 'Override',
),
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'type_id' => array(
'operator' => '=',
'value' => array(),
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'type_id_op',
'identifier' => 'type_id',
'label' => 'Type',
'remember' => 0,
),
'case' => 1,
'id' => 'type_id',
'table' => 'feature',
'field' => 'type_id',
'relationship' => 'none',
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'name_1' => array(
'operator' => 'allwords',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'name_1_op',
'identifier' => 'name',
'label' => 'Name Contains',
'bef_filter_description' => '',
'remember' => 0,
),
'case' => 0,
'id' => 'name_1',
'table' => 'feature',
'field' => 'name',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'search_results' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
),
'id' => 'search_results',
'table' => 'views',
'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.',
),
));
$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',
),
'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' => '',
),
),
'default' => '-1',
));
$default_handler = $handler;
$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
}
$views[$view->name] = $view;
return $views;
}
| tripal_feature_views_handlers | ( | ) |
Implements hook_views_handlers()
Purpose: Register all custom handlers with views where a handler describes either "the type of field", "how a field should be filtered", "how a field should be sorted"
Definition at line 106 of file tripal_feature.views.inc.
{
return array(
'info' => array(
'path' => drupal_get_path('module', 'tripal_feature') . '/views_handlers',
),
'handlers' => array(
'views_handler_field_residues' => array(
'parent' => 'views_handler_field',
),
),
);
}
| tripal_genetic_views_default_views | ( | ) |
Definition at line 95 of file tripal_genetic.views.inc.
{
$views = array();
if (!module_exists('tripal_views')) {
return $views;
}
// Main default view
$view = new view;
$view->name = 'genotype_listing';
$view->description = 'A listing of observed genotypes and the features displaying them';
$view->tag = 'chado default';
$view->base_table = 'genotype';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
'uniquename' => array(
'label' => 'Uniquename',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'uniquename',
'table' => 'genotype',
'field' => 'uniquename',
'relationship' => 'none',
),
'name' => array(
'label' => 'Name',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name',
'table' => 'genotype',
'field' => 'name',
'relationship' => 'none',
),
'description' => array(
'label' => 'Description',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'description',
'table' => 'genotype',
'field' => 'description',
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'uniquename' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'uniquename_op',
'identifier' => 'uniquename',
'label' => 'Unique Name Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'uniquename',
'table' => 'genotype',
'field' => 'uniquename',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'description' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'description_op',
'identifier' => 'description',
'label' => 'Description Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'description',
'table' => 'genotype',
'field' => 'description',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'search_results' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
),
'id' => 'search_results',
'table' => 'views',
'field' => 'search_results',
'relationship' => 'none',
'apply_button' => 'Show',
'no_results_text' => 'Click "Show" to see a list of all genotypes matching the entered criteria. If you leave a any of the criteria blank then the genotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all genotypes will be listed.',
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Genotypes Observed');
$handler->override_option('header', 'Click "Show" to see a list of all genotypes matching the entered criteria. If you leave a any of the criteria blank then the genotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all genotypes will be listed.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No genotypes match the current 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',
'summary' => '',
'columns' => array(
'uniquename' => 'uniquename',
'name' => 'name',
'description' => 'description',
),
'info' => array(
'uniquename' => array(
'sortable' => 1,
'separator' => '',
),
'name' => array(
'sortable' => 1,
'separator' => '',
),
'description' => array(
'sortable' => 1,
'separator' => '',
),
),
'default' => 'uniquename',
));
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/genotypes');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Genotypes',
'description' => 'A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.',
'weight' => '10',
'name' => 'navigation',
));
$handler->override_option('tab_options', array(
'type' => 'none',
'title' => '',
'description' => '',
'weight' => 0,
'name' => 'navigation',
));
$views[$view->name] = $view;
return $views;
}
| tripal_natural_diversity_views_default_views | ( | ) |
Created Default views related to the tables integrated by this module
Definition at line 120 of file tripal_natural_diversity.views.inc.
{
$views = array();
if (!module_exists('tripal_views')) {
return $views;
}
// Experiment Listing
$view = new view;
$view->name = 'natdiv_experiment_listing';
$view->description = 'A listing of all natural diversity experiments';
$view->tag = 'chado default';
$view->base_table = 'nd_experiment';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
'name' => array(
'label' => 'Type',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'none',
),
'description' => array(
'label' => 'Location Experiment Performed',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'description',
'table' => 'nd_geolocation',
'field' => 'description',
'relationship' => 'none',
),
));
$handler->override_option('sorts', array(
'name' => array(
'order' => 'ASC',
'id' => 'name',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'none',
),
'description' => array(
'order' => 'ASC',
'id' => 'description',
'table' => 'nd_geolocation',
'field' => 'description',
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'type_id' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'type_id_op',
'identifier' => 'type_id',
'label' => 'Experiment Type',
'remember' => 0,
),
'case' => 1,
'id' => 'type_id',
'table' => 'nd_experiment',
'field' => 'type_id',
'relationship' => 'none',
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'description' => array(
'operator' => '=',
'value' => array(),
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'description_op',
'identifier' => 'geolocation',
'label' => 'Location Experiment Performed',
'remember' => 0,
),
'case' => 1,
'id' => 'description',
'table' => 'nd_geolocation',
'field' => 'description',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
),
'search_results' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
),
'id' => 'search_results',
'table' => 'views',
'field' => 'search_results',
'relationship' => 'none',
'apply_button' => 'Show',
'no_results_text' => 'Click "Show" to see a list of all experiments matching the entered criteria. If you leave a any of the criteria blank then the experiments will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all experiments will be listed.',
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Natural Diversity Experiments');
$handler->override_option('header', 'Click "Show" to see a list of all experiments matching the entered criteria. If you leave a any of the criteria blank then the experiments will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all experiments will be listed.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No natural diversity experiments match the current 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',
'summary' => '',
'columns' => array(
'name' => 'name',
'description' => 'description',
),
'info' => array(
'name' => array(
'sortable' => 1,
'separator' => '',
),
'description' => array(
'sortable' => 1,
'separator' => '',
),
),
'default' => '-1',
));
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/natdiv_experiments');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Natural Diversity Experiments',
'description' => 'A single assay resulting in a single genotype or phenotype. Multiple assays resulting in an entire experiment should be grouped together as a project.',
'weight' => '10',
'name' => 'navigation',
));
$handler->override_option('tab_options', array(
'type' => 'none',
'title' => '',
'description' => '',
'weight' => 0,
'name' => 'navigation',
));
$views[$view->name] = $view;
// List geolocations
$view = new view;
$view->name = 'geolocation_listing';
$view->description = 'A listing of locations where natural diversity experiments took place.';
$view->tag = 'chado default';
$view->base_table = 'nd_geolocation';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
'description' => array(
'label' => 'Name',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'description',
'table' => 'nd_geolocation',
'field' => 'description',
'relationship' => 'none',
),
'latitude' => array(
'label' => 'Latitude',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'latitude',
'table' => 'nd_geolocation',
'field' => 'latitude',
'relationship' => 'none',
),
'longitude' => array(
'label' => 'Longitude',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'longitude',
'table' => 'nd_geolocation',
'field' => 'longitude',
'relationship' => 'none',
),
'altitude' => array(
'label' => 'Altitude',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'altitude',
'table' => 'nd_geolocation',
'field' => 'altitude',
'relationship' => 'none',
),
'geodetic_datum' => array(
'label' => 'Geodetic Datum',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'geodetic_datum',
'table' => 'nd_geolocation',
'field' => 'geodetic_datum',
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'geodetic_datum' => array(
'operator' => '=',
'value' => array(),
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'geodetic_datum_op',
'identifier' => 'geodetic_datum',
'label' => 'Geodetic Datum',
'remember' => 0,
),
'case' => 1,
'id' => 'geodetic_datum',
'table' => 'nd_geolocation',
'field' => 'geodetic_datum',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
),
'latitude' => array(
'operator' => '=',
'value' => array(
'value' => '',
'min' => '',
'max' => '',
),
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 1,
'operator' => 'latitude_op',
'identifier' => 'latitude',
'label' => 'Latitude',
'optional' => 0,
'remember' => 0,
),
'case' => 1,
'id' => 'latitude',
'table' => 'nd_geolocation',
'field' => 'latitude',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'longitude' => array(
'operator' => '=',
'value' => array(
'value' => '',
'min' => '',
'max' => '',
),
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 1,
'operator' => 'longitude_op',
'identifier' => 'longitude',
'label' => 'Longitude',
'optional' => 0,
'remember' => 0,
),
'case' => 1,
'id' => 'longitude',
'table' => 'nd_geolocation',
'field' => 'longitude',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'altitude' => array(
'operator' => '=',
'value' => array(
'value' => '',
'min' => '',
'max' => '',
),
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 1,
'operator' => 'altitude_op',
'identifier' => 'altitude',
'label' => 'Altitude',
'optional' => 0,
'remember' => 0,
),
'case' => 0,
'id' => 'altitude',
'table' => 'nd_geolocation',
'field' => 'altitude',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'description' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'description_op',
'identifier' => 'description',
'label' => 'Name Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'description',
'table' => 'nd_geolocation',
'field' => 'description',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
'values_form_type' => 'textfield',
'multiple' => 0,
'optional' => 0,
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Geographical Locations');
$handler->override_option('header', 'Use the following criteria to limit the locations listed. If you leave a any of the criteria blank then the locations will be not be filtered based on that field.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No locations matched the current 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',
'summary' => '',
'columns' => array(
'description' => 'description',
'latitude' => 'latitude',
'longitude' => 'longitude',
'altitude' => 'altitude',
'geodetic_datum' => 'geodetic_datum',
),
'info' => array(
'description' => array(
'sortable' => 1,
'separator' => '',
),
'latitude' => array(
'sortable' => 1,
'separator' => '',
),
'longitude' => array(
'sortable' => 1,
'separator' => '',
),
'altitude' => array(
'sortable' => 1,
'separator' => '',
),
'geodetic_datum' => array(
'sortable' => 1,
'separator' => '',
),
),
'default' => 'description',
));
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/natdiv_geolocations');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Locations',
'description' => 'Geographical locations in which natural diversity experiments might be performed.',
'weight' => '10',
'name' => 'navigation',
));
$handler->override_option('tab_options', array(
'type' => 'none',
'title' => '',
'description' => '',
'weight' => 0,
'name' => 'navigation',
));
$views[$view->name] = $view;
// List protocols
$view = new view;
$view->name = 'natdiv_protocol_listing';
$view->description = 'A listing of protocols used for natural diversity experiments';
$view->tag = 'chado default';
$view->base_table = 'nd_protocol';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
'name' => array(
'label' => 'Name',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name',
'table' => 'nd_protocol',
'field' => 'name',
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'name' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'name_op',
'identifier' => 'name',
'label' => 'Name Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'name',
'table' => 'nd_protocol',
'field' => 'name',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'search_results' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
),
'id' => 'search_results',
'table' => 'views',
'field' => 'search_results',
'relationship' => 'none',
'apply_button' => 'Show',
'no_results_text' => 'Click "Show" to see a list of all protocols matching the entered criteria. If you leave a any of the criteria blank then the protocols will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all protocols will be listed.',
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Protocols');
$handler->override_option('header', 'Click "Show" to see a list of all protocols matching the entered criteria. If you leave a any of the criteria blank then the protocols will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all protocols will be listed.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No protocols match the current 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',
'summary' => '',
'columns' => array(
'name' => 'name',
),
'info' => array(
'name' => array(
'sortable' => 1,
'separator' => '',
),
),
'default' => 'name',
));
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/natdiv_protocols');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Protocols',
'description' => 'The protcols used for natural diversity experiments',
'weight' => '10',
'name' => 'navigation',
));
$handler->override_option('tab_options', array(
'type' => 'none',
'title' => '',
'description' => '',
'weight' => 0,
'name' => 'navigation',
));
$views[$view->name] = $view;
// List Reagents
$view = new view;
$view->name = 'natdiv_reagent_listing';
$view->description = 'A listing of reagents used in natural diversity experiments';
$view->tag = 'chado default';
$view->base_table = 'nd_reagent';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
'name_1' => array(
'label' => 'Name',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name_1',
'table' => 'nd_reagent',
'field' => 'name',
'relationship' => 'none',
),
'name' => array(
'label' => 'Type',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'type_id' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'type_id_op',
'identifier' => 'type_id',
'label' => 'Type',
'remember' => 0,
),
'case' => 1,
'id' => 'type_id',
'table' => 'nd_reagent',
'field' => 'type_id',
'relationship' => 'none',
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'search_results' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
),
'id' => 'search_results',
'table' => 'views',
'field' => 'search_results',
'relationship' => 'none',
'apply_button' => 'Show',
'no_results_text' => 'Click "Show" to see a list of all reagents matching the entered criteria. If you leave a any of the criteria blank then the reagents will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all reagents will be listed.',
),
'name' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'name_op',
'identifier' => 'name',
'label' => 'Name Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'name',
'table' => 'nd_reagent',
'field' => 'name',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Reagents');
$handler->override_option('header', 'Click "Show" to see a list of all reagents matching the entered criteria. If you leave a any of the criteria blank then the reagents will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all reagents will be listed.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No reagents match the current 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 = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/natdiv_reagents');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Reagents',
'description' => 'Reagents used in natural diversity experiments',
'weight' => '10',
'name' => 'navigation',
));
$handler->override_option('tab_options', array(
'type' => 'none',
'title' => '',
'description' => '',
'weight' => 0,
'name' => 'navigation',
));
$views[$view->name] = $view;
return $views;
}
| tripal_phenotype_views_default_views | ( | ) |
Definition at line 96 of file tripal_phenotype.views.inc.
{
$views = array();
if (!module_exists('tripal_views')) {
return $views;
}
// Main default view
$view = new view;
$view->name = 'phenotype_listing';
$view->description = 'A listing of chado phenotypes';
$view->tag = 'chado default';
$view->base_table = 'phenotype';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('relationships', array(
'assay_id' => array(
'label' => 'assay_id to cvterm',
'required' => 0,
'id' => 'assay_id',
'table' => 'phenotype',
'field' => 'assay_id',
'relationship' => 'none',
),
'attr_id' => array(
'label' => 'attr_id to cvterm',
'required' => 0,
'id' => 'attr_id',
'table' => 'phenotype',
'field' => 'attr_id',
'relationship' => 'none',
),
'cvalue_id' => array(
'label' => 'cvalue_id to cvterm',
'required' => 0,
'id' => 'cvalue_id',
'table' => 'phenotype',
'field' => 'cvalue_id',
'relationship' => 'none',
),
'observable_id' => array(
'label' => 'observable_id to cvterm',
'required' => 0,
'id' => 'observable_id',
'table' => 'phenotype',
'field' => 'observable_id',
'relationship' => 'none',
),
));
$handler->override_option('fields', array(
'uniquename' => array(
'label' => 'Unique Name',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'uniquename',
'table' => 'phenotype',
'field' => 'uniquename',
'relationship' => 'none',
),
'name_1' => array(
'label' => 'Phenotypic Attribute',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name_1',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'attr_id',
),
'name_3' => array(
'label' => 'Controlled Value',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name_3',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'cvalue_id',
),
'value' => array(
'label' => 'Value',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'value',
'table' => 'phenotype',
'field' => 'value',
'relationship' => 'none',
),
'name_2' => array(
'label' => 'Observation Type',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name_2',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'observable_id',
),
'name' => array(
'label' => 'Evidence Type',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'assay_id',
),
));
$handler->override_option('filters', array(
'search_results' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
),
'id' => 'search_results',
'table' => 'views',
'field' => 'search_results',
'relationship' => 'none',
'apply_button' => 'Show',
'no_results_text' => 'Click "Show" to see a list of all phenotypes matching the entered criteria. If you leave a any of the criteria blank then the phenotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all phenotypes will be listed.',
),
'attr_id' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'attr_id_op',
'identifier' => 'attr_id',
'label' => 'Phenotypic Attribute',
'remember' => 0,
),
'case' => 1,
'id' => 'attr_id',
'table' => 'phenotype',
'field' => 'attr_id',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
),
'cvalue_id' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'cvalue_id_op',
'identifier' => 'cvalue_id',
'label' => 'Controlled Value',
'remember' => 0,
),
'case' => 1,
'id' => 'cvalue_id',
'table' => 'phenotype',
'field' => 'cvalue_id',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
),
'observable_id' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'observable_id_op',
'identifier' => 'observable_id',
'label' => 'Observation Type',
'remember' => 0,
),
'case' => 1,
'id' => 'observable_id',
'table' => 'phenotype',
'field' => 'observable_id',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
),
'assay_id' => array(
'operator' => '=',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'assay_id_op',
'identifier' => 'assay_id',
'label' => 'Evidence Type',
'remember' => 0,
),
'case' => 1,
'id' => 'assay_id',
'table' => 'phenotype',
'field' => 'assay_id',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 0,
'show_all' => 0,
),
'uniquename' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'uniquename_op',
'identifier' => 'uniquename',
'label' => 'Unique Name Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'uniquename',
'table' => 'phenotype',
'field' => 'uniquename',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'value' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'value_op',
'identifier' => 'phen_value',
'label' => 'Value Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'value',
'table' => 'phenotype',
'field' => 'value',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Phenotypes');
$handler->override_option('header', 'Click "Show" to see a list of all phenotypes matching the entered criteria. If you leave a any of the criteria blank then the phenotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all phenotypes will be listed.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No phenotypes match 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',
'summary' => '',
'columns' => array(
'uniquename' => 'uniquename',
'value' => 'value',
),
'info' => array(
'uniquename' => array(
'sortable' => 1,
'separator' => '',
),
'value' => array(
'sortable' => 1,
'separator' => '',
),
),
'default' => 'uniquename',
));
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/phenotypes');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Phenotypes',
'description' => 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function.',
'weight' => '10',
'name' => 'navigation',
));
$handler->override_option('tab_options', array(
'type' => 'none',
'title' => '',
'description' => '',
'weight' => 0,
'name' => 'navigation',
));
$views[$view->name] = $view;
return $views;
}
| tripal_project_views_default_views | ( | ) |
$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);
Definition at line 93 of file tripal_project.views.inc.
{
$views = array();
if (!module_exists('tripal_views')) {
return $views;
}
$description_type_id = tripal_core_chado_select('cvterm',array('cvterm_id'),array('name' => 'project_description'));
$description_type_id = $description_type_id[0]->cvterm_id;
// Main default view
$view = new view;
$view->name = 'project_listing';
$view->description = 'A listing of chado projects';
$view->tag = 'chado default';
$view->base_table = 'project';
$view->core = 6;
$view->api_version = '2';
$view->disabled = FALSE;
$handler = $view->new_display('default', 'Defaults', 'default');
$handler->override_option('fields', array(
'name' => array(
'label' => 'Name',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'name',
'table' => 'project',
'field' => 'name',
'relationship' => 'none',
),
'value' => array(
'label' => 'Description',
'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,
'type' => 'separator',
'separator' => ', ',
'exclude' => 0,
'id' => 'value',
'table' => 'projectprop',
'field' => 'value',
'override' => array(
'button' => 'Override',
),
'relationship' => 'none',
),
));
$handler->override_option('filters', array(
'name' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'name_op',
'identifier' => 'name',
'label' => 'Name Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'name',
'table' => 'project',
'field' => 'name',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
'type_id' => array(
'operator' => '=',
'value' => $description_type_id,
'group' => '0',
'exposed' => FALSE,
'expose' => array(
'operator' => FALSE,
'label' => '',
'optional' => FALSE,
),
'case' => 1,
'id' => 'type_id',
'table' => 'projectprop',
'field' => 'type_id',
'override' => array(
'button' => 'Override',
),
'relationship' => 'none',
'values_form_type' => 'select',
'multiple' => 0,
'optional' => 0,
'show_all' => 0,
'agg' => array(
'records_with' => 0,
'aggregates_with' => 1,
),
),
'value' => array(
'operator' => '~',
'value' => '',
'group' => '0',
'exposed' => TRUE,
'expose' => array(
'use_operator' => 0,
'operator' => 'value_op',
'identifier' => 'description',
'label' => 'Description Contains',
'remember' => 0,
),
'case' => 0,
'id' => 'value',
'table' => 'projectprop',
'field' => 'value',
'override' => array(
'button' => 'Override',
),
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access chado_projects',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Projects');
$handler->override_option('empty', 'No projects match 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',
'summary' => '',
'columns' => array(
'name' => 'name',
'description' => 'description',
),
'info' => array(
'name' => array(
'sortable' => 1,
'separator' => '',
),
'description' => array(
'sortable' => 0,
'separator' => '',
),
),
'default' => 'name',
));
$default_handler = $handler;
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/projects');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Projects',
'description' => 'A project is a collection of data resulting from a biological experiment.',
'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 project => Node relationship
$default_handler->override_option('relationships', array(
'nid' => array(
'label' => 'Project to Node',
'required' => 0,
'id' => 'nid',
'table' => 'chado_project',
'field' => 'nid',
'relationship' => 'none',
),
));
// Change project.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
}
$views[$view->name] = $view;
return $views;
}
1.7.4