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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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Functions | |
| tripal_stock_views_data () | |
| tripal_stock_views_handlers () | |
| tripal_stock_views_pre_render (&$view) | |
| tripal_stock_views_default_views () | |
| tripal_stock_views_data | ( | ) |
Implements hook_views_data(): Describe chado/tripal tables & fields to views
Definition at line 30 of file tripal_stock.views.inc.
{
$data = array();
if (module_exists('tripal_views')) {
$tablename = 'stock';
$priority = 9;
// check to see if the table is integrated. If it is then integrate it's
// corresponding 'chado_[table]' table.
if (!tripal_views_is_integrated($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);
}
}
$tablename = 'stockcollection';
$priority = 9;
if (!tripal_views_is_integrated($tablename, $priority)) {
$table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
tripal_views_integration_add_entry($table_integration_array);
}
$tables = array(
'stock_cvterm',
'stock_dbxref',
'stock_genotype',
'stock_pub',
'stock_relationship',
'stock_relationship_pub',
'stockcollection_stock',
'stockcollectionprop',
'stockprop',
'stockprop_pub'
);
foreach ($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_stock_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 264 of file tripal_stock.views.inc.
{
$views = array();
if (!module_exists('tripal_views')) {
return $views;
}
// Main default view
$view = new view;
$view->name = 'stock_listing';
$view->description = 'This view lists all stocks by default.';
$view->tag = 'chado default';
$view->base_table = 'stock';
$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', 'Defaults', 'default');
$handler->override_option('fields', array(
'uniquename' => array(
'label' => 'Unique Name',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => '',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'link_to_node' => 1,
'exclude' => 0,
'id' => 'uniquename',
'table' => 'stock',
'field' => 'uniquename',
'relationship' => 'none',
),
'name_2' => 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_2',
'table' => 'stock',
'field' => 'name',
'relationship' => 'none',
),
'name' => array(
'label' => 'Type',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => '',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'exclude' => 0,
'id' => 'name',
'table' => 'cvterm',
'field' => 'name',
'relationship' => 'none',
),
'common_name' => array(
'label' => 'Organism',
'alter' => array(
'alter_text' => 0,
'text' => '',
'make_link' => 0,
'path' => '',
'link_class' => '',
'alt' => '',
'prefix' => '',
'suffix' => '',
'target' => '',
'help' => '',
'trim' => 0,
'max_length' => '',
'word_boundary' => 1,
'ellipsis' => 1,
'html' => 0,
'strip_tags' => 0,
),
'empty' => '',
'hide_empty' => 0,
'empty_zero' => 0,
'link_to_node' => 1,
'exclude' => 0,
'id' => 'common_name',
'table' => 'organism',
'field' => 'common_name',
'relationship' => 'none',
),
));
$handler->override_option('sorts', array(
'common_name' => array(
'order' => 'ASC',
'id' => 'common_name',
'table' => 'organism',
'field' => 'common_name',
'relationship' => 'none',
),
'uniquename' => array(
'order' => 'ASC',
'id' => 'uniquename',
'table' => 'stock',
'field' => 'uniquename',
'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_common_name',
'label' => 'Organism',
'remember' => 0,
),
'case' => 1,
'id' => 'common_name',
'table' => 'organism',
'field' => 'common_name',
'relationship' => 'none',
'values_form_type' => 'select',
'multiple' => 1,
'optional' => 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 stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks 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' => 'stock',
'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' => 'stock',
'field' => 'name',
'relationship' => 'none',
'agg' => array(
'records_with' => 1,
'aggregates_with' => 1,
),
),
));
$handler->override_option('access', array(
'type' => 'perm',
'perm' => 'access chado_stock content',
));
$handler->override_option('cache', array(
'type' => 'none',
));
$handler->override_option('title', 'Stocks');
$handler->override_option('header', 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.');
$handler->override_option('header_format', '2');
$handler->override_option('header_empty', 0);
$handler->override_option('empty', 'No stocks match the supplied criteria.');
$handler->override_option('empty_format', '1');
$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(
'uniquename' => 'uniquename',
'name_2' => 'name_2',
'name' => 'name',
'common_name' => 'common_name',
'all_dbxref' => 'all_dbxref',
'all_properties' => 'all_properties',
'all_relationships' => 'all_relationships',
),
'info' => array(
'uniquename' => array(
'sortable' => 1,
'separator' => '',
),
'name_2' => array(
'sortable' => 1,
'separator' => '',
),
'name' => array(
'sortable' => 1,
'separator' => '',
),
'common_name' => array(
'sortable' => 1,
'separator' => '',
),
'all_dbxref' => array(
'separator' => '',
),
'all_properties' => array(
'separator' => '',
),
'all_relationships' => array(
'separator' => '',
),
),
'default' => '-1',
));
$default_handler = $handler;
$handler = $view->new_display('page', 'Page', 'page_1');
$handler->override_option('path', 'chado/stocks');
$handler->override_option('menu', array(
'type' => 'normal',
'title' => 'Stocks',
'description' => 'A stock is the physical entities, either living or preserved, held by collections and can be globally identified by the combination of organism, uniquename and stock type.',
'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;
// Change analysis.name to have a link to the node
$fields['name_2']['alter']['link_to_node'] = 1;
$default_handler->override_option('fields', $fields);
// Adds stock => Node relationship
$default_handler->override_option('relationships', array(
'nid' => array(
'label' => 'Stock to Node',
'required' => 0,
'id' => 'nid',
'table' => 'chado_stock',
'field' => 'nid',
'relationship' => 'none',
),
));
// Only show records with published nodes
}
$views[$view->name] = $view;
return $views;
}
| tripal_stock_views_handlers | ( | ) |
Implements hook_views_handlers()
Purpose: Register all custom handlers with views where a handler describes either "the type of field", "how a field should be filtered", "how a field should be sorted"
Definition at line 97 of file tripal_stock.views.inc.
{
return array(
'info' => array(
'path' => drupal_get_path('module', 'tripal_stock') . '/views/handlers',
),
'handlers' => array(
'views_handler_field_computed_stock_nid' => array(
'parent' => 'views_handler_field_numeric',
),
'views_handler_field_stockprop_by_type' => array(
'parent' => 'views_handler_field_prerender_list',
),
'views_handler_field_stockprop_all' => array(
'parent' => 'views_handler_field_prerender_list',
),
'views_handler_field_stockrel_by_type' => array(
'parent' => 'views_handler_field_prerender_list',
),
'views_handler_field_stockrel_all' => array(
'parent' => 'views_handler_field_prerender_list',
),
'views_handler_field_stock_dbxref_by_type' => array(
'parent' => 'views_handler_field_prerender_list',
),
'views_handler_field_stock_dbxref_all' => array(
'parent' => 'views_handler_field_prerender_list',
),
'views_handler_filter_stockprop_id' => array(
'parent' => 'views_handler_filter',
),
'views_handler_filter_stock_dbxref_id' => array(
'parent' => 'views_handler_filter',
),
'views_handler_filter_stock_relationship_id' => array(
'parent' => 'views_handler_filter',
),
'views_handler_argument_stockprop_id' => array(
'parent' => 'views_handler_argument_string',
),
),
);
}
| tripal_stock_views_pre_render | ( | &$ | view | ) |
Implements hook_views_pre_render
Purpose: Intercepts the view after the query has been executed All the results are stored in $view->result Looking up the NID here ensures the query is only executed once for all stocks in the table.
Definition at line 178 of file tripal_stock.views.inc.
{
if (preg_match('/stock/', $view->base_table)) {
//-----Node IDs---------------------------------------------
// @see tripal_core.views.inc, tripal_core_add_node_ids_to_view()
// retrieve the stock_id for each record in the views current page
$stock_ids = array();
foreach ($view->result as $row_num => $row) {
$stock_ids[$row_num] = $row->stock_id;
}
if (sizeof($stock_ids)) {
//-----Properties------------------------------------------
$field_names = array_keys($view->field);
//if any property fields are in the current view
$property_field_names = preg_grep('/properties/', $field_names);
if (!empty($property_field_names)) {
$sql = "SELECT stockprop.*, cvterm.name as type_name FROM {stockprop} "
."INNER JOIN cvterm cvterm ON stockprop.type_id=cvterm.cvterm_id "
."WHERE stockprop.stock_id IN (" . implode(',', $stock_ids) . ")";
$resource = chado_query($sql);
$view->result[$key]->properties = array();
while ($r = db_fetch_object($resource)) {
$key = array_search($r->stock_id, $stock_ids);
$view->result[$key]->properties[] = $r;
}
}
//-----Relationships----------------------------------------
//if any relationship fields are in the current view
$relationship_field_names = preg_grep('/relationships/', $field_names);
if (!empty($relationship_field_names)) {
$sql = "SELECT stock_relationship.*, cvterm.name as type_name, "
."subject_stock.name as subject_name, object_stock.name as object_name "
."FROM stock_relationship "
."LEFT JOIN stock subject_stock ON stock_relationship.subject_id=subject_stock.stock_id "
."LEFT JOIN stock object_stock ON stock_relationship.object_id=object_stock.stock_id "
."LEFT JOIN cvterm cvterm ON stock_relationship.type_id = cvterm.cvterm_id "
."WHERE stock_relationship.subject_id IN (" . implode(',', $stock_ids) . ") "
."OR stock_relationship.object_id IN (" . implode(',', $stock_ids) . ") ";
$resource = chado_query($sql);
while ($r = db_fetch_object($resource)) {
if (in_array($r->subject_id, $stock_ids)) {
$key = array_search($r->subject_id, $stock_ids);
$r->stock_id = $r->subject_id;
$view->result[$key]->relationships[] = clone $r;
}
if (in_array($r->object_id, $stock_ids)) {
$key = array_search($r->object_id, $stock_ids);
$r->stock_id = $r->object_id;
$view->result[$key]->relationships[] = clone $r;
}
}
}
//-----DB References--------------------------------------------
//if any dbxref fields are in the current view
$dbxref_field_names = preg_grep('/dbxref/', $field_names);
if (!empty($dbxref_field_names)) {
$sql = "SELECT stock_dbxref.*, dbxref.db_id, db.name as db_name, db.urlprefix, "
."dbxref.accession, dbxref.version, dbxref.description "
."FROM stock_dbxref "
."LEFT JOIN dbxref dbxref ON stock_dbxref.dbxref_id=dbxref.dbxref_id "
."LEFT JOIN db db ON dbxref.db_id=db.db_id "
."WHERE stock_dbxref.stock_id IN (" . implode(',', $stock_ids) . ")";
$resource = chado_query($sql);
$view->result[$key]->dbxref = array();
while ($r = db_fetch_object($resource)) {
$key = array_search($r->stock_id, $stock_ids);
$view->result[$key]->dbxref[] = $r;
}
}
} //if there are stocks
} //if we're dealing with a stock view
}
1.7.4