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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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Go to the source code of this file.
Functions | |
| tripal_views_views_handlers () | |
| tripal_views_views_pre_render (&$view) | |
| tripal_views_views_data () | |
| tripal_views_views_data_alter (&$data) | |
| tripal_views_views_plugins () | |
| tripal_views_views_pre_view (&$view, &$display_id, &$args) | |
| tripal_views_views_pre_execute (&$view) | |
| tripal_views_views_post_render (&$view, &$output, &$cache) | |
| tripal_views_data_export_download_form (&$form_state, $view, $display_id, $args) | |
| tripal_views_data_export_download_form_submit ($form, &$form_state) | |
Tripal Views Integration
Definition in file tripal_views.views.inc.
| tripal_views_data_export_download_form | ( | &$ | form_state, |
| $ | view, | ||
| $ | display_id, | ||
| $ | args | ||
| ) |
the Download Views data export form
Definition at line 591 of file tripal_views.views.inc.
{
$form = array();
$urls = array();
// get any export_data_export displays
$displays = $view->display;
$options = array();
$default = '';
$current_display = $view->current_display;
foreach ($displays as $name => $display) {
if (preg_match("/^views_data_export/", $name)) {
// only add this display to the form if it is attached
$display_options = $display->display_options;
if (strcmp($display_options['displays'][$current_display], $current_display) != 0) {
continue;
}
// set the first item as default
if (!$default) {
$default = $display->id;
}
$path = $display->display_options['path'];
$query = $view->get_exposed_input(); // retrieves elements in $_GET array
$urls[$display->id]['path'] = $path;
$urls[$display->id]['query'] = $query;
// add the new item to the options array
$options[$display->id] = $display->display_title;
}
}
// only generate the form if we have views_data_export displays attached
// to this view
if (count($options) > 0) {
$form_state['storage']['urls'] = $urls;
$form['#cache'] = TRUE;
// we want the form to redirect to a new window
$form['#attributes']['target'] = "_blank";
// now build the form elements
$form['downloads'] = array(
'#type' => 'fieldset',
'#title' => 'Download Results',
'#collapsible' => TRUE,
'#collapsed' => FALSE
);
$form['downloads']['file_type'] = array(
'#title' => t('File format'),
'#type' => 'radios',
'#options' => $options,
'#required' => TRUE,
'#default_value' => $default,
'#description' => t('Please select a file format to download'),
);
$form['downloads']['submit'] = array(
'#value' => t('Download Results'),
'#type' => 'submit',
);
}
return $form;
}
| tripal_views_data_export_download_form_submit | ( | $ | form, |
| &$ | form_state | ||
| ) |
Submit for the Download Views data export form
Definition at line 661 of file tripal_views.views.inc.
{
$urls = $form_state['storage']['urls'];
$display_id = $form_state['values']['file_type'];
drupal_goto($urls[$display_id]['path'], $urls[$display_id]['query']);
}
| tripal_views_views_data | ( | ) |
Generates a dynamic data array for Views
Purpose: This function is a hook used by the Views module. It populates and returns a data array that specifies for the Views module the base table, the tables it joins with and handlers. The data array is populated using the data stored in the tripal_views tables.
Definition at line 225 of file tripal_views.views.inc.
{
// Make sure all chado tables are integrated
tripal_views_integrate_all_chado_tables();
// Define Global Fields
// Filter handler that lets the admin say:
// "Show no results until they enter search parameters"
$data['views']['search_results'] = array(
'title' => t('Search Results'),
'help' => t('Delay results until Apply/Search is clicked by the user.'),
'filter' => array(
'handler' => 'tripal_views_handler_filter_no_results',
),
);
$tvi_query = db_query('SELECT * FROM {tripal_views}');
while ($tvi_row = db_fetch_object($tvi_query)) {
// check to see if this is the lightest (drupal-style) priority setup for this table
// if not then don't use this definition
$lightest_priority_setup = tripal_views_is_lightest_priority_setup($tvi_row->setup_id, $tvi_row->table_name);
if (!$lightest_priority_setup) {
continue;
}
// ids we'll use for queries
$setup_id = $tvi_row->setup_id;
$mview_id = $tvi_row->mview_id;
// holds the base table name and fields
$base_table = '';
$base_fields = array();
// indicated whether the current table is a base table or not
$is_base_table = $tvi_row->base_table;
// populate the base table name and fields. If an $mview_id is given
// then get the materialized view info, otherwise get the Chado table info
if ($mview_id) {
// get the base table name from the materialized view
$sql = "SELECT name, mv_specs FROM {tripal_mviews} WHERE mview_id = %d";
$mview_table = db_fetch_object(db_query($sql, $mview_id));
$base_table = $mview_table->name;
// get the columns in this materialized view. They are separated by commas
// where the first word is the column name and the rest is the type
$columns = explode(",", $mview_table->mv_specs);
foreach ($columns as $column) {
$column = trim($column); // trim trailing and leading spaces
preg_match("/^(.*?)\ (.*?)$/", $column, $matches);
$column_name = $matches[1];
$column_type = $matches[2];
$base_fields[$column_name] = array(
'column_name' => $column_name,
'type' => $column_type,
);
}
// get the field name and descriptions
$sql = "SELECT * FROM {tripal_views_field} WHERE setup_id=%d";
$query = db_query($sql, $setup_id);
while ($field = db_fetch_object($query)) {
$base_fields[$field->column_name]['name'] = $field->name;
$base_fields[$field->column_name]['help'] = $field->description;
}
}
// if this is not a legacy materialized view
else {
$base_table = $tvi_row->table_name;
// Check if we are trying to integrate the node table
// if we are we want to add to a current integration
// as compared to create a whole new one
if ($base_table == 'node') {
// Add any joins between the node table and other tables
$sql = "SELECT * FROM {tripal_views_join} WHERE setup_id = %d";
$joins = db_query($sql, $setup_id);
while ($join = db_fetch_object($joins)) {
$left_table = $join->left_table;
$left_field = $join->left_field;
$base_field = $join->base_field;
$handler = $join->handler;
// add join entry
$data[$base_table]['table']['join'][$left_table] = array(
'left_field' => $left_field,
'field' => $base_field,
);
if ($handler) {
$data[$base_table]['table']['join'][$left_table]['handler'] = $handler;
}
}
// Add in any handlers for node fields
$sql = "SELECT * FROM {tripal_views_handlers} WHERE setup_id=%d";
$query = db_query($sql, $setup_id);
while ($handler = db_fetch_object($query)) {
$data[$base_table][$handler->column_name][$handler->handler_type]['handler'] = $handler->handler_name;
// Add in any additional arguments
// This should be a serialized array including (at a minimum) name => <handler name>
if ($handler->arguments) {
$data[$base_table][$handler->column_name][$handler->handler_type] = array_merge($data[$base_table][$handler->column_name][$handler->handler_type], unserialize($handler->arguments));
}
}
continue;
}
// get the table description
$table_desc = tripal_core_get_chado_table_schema($base_table);
$fields = $table_desc['fields'];
if (!is_array($fields)) {
$fields = array();
watchdog('tripal_views', 'No fields were described for this table (%table) through the Tripal Schema API.', array('%table' => $base_table), WATCHDOG_ERROR);
}
foreach ($fields as $column => $attrs) {
$base_fields[$column] = array(
'column_name' => $column,
'type' => $attrs['type'],
);
}
// get the field name and descriptions
$sql = "SELECT * FROM {tripal_views_field} WHERE setup_id=%d";
$query = db_query($sql, $setup_id);
while ($field = db_fetch_object($query)) {
$base_fields[$field->column_name]['name'] = $field->name;
$base_fields[$field->column_name]['help'] = $field->description;
}
}
// Setup the base table info in the data array
$data[$base_table]['table']['group'] = t("$tvi_row->name");
if ($is_base_table) {
$data[$base_table]['table']['base'] = array(
'group' => "$tvi_row->name",
'title' => "$tvi_row->name",
'help' => $tvi_row->comment,
);
}
else {
$data[$base_table]['table'] = array(
'group' => "$tvi_row->name",
'title' => "$tvi_row->name",
'help' => $tvi_row->comment,
);
}
// first add the fields
foreach ($base_fields as $column_name => $base_field) {
$data[$base_table][$column_name] = array(
'title' => t($base_field['name']),
'help' => t($base_field['help']),
'field' => array(
'click sortable' => TRUE,
),
);
// now add the handlers
$sql = "SELECT * FROM {tripal_views_handlers} WHERE setup_id = %d AND column_name = '%s'";
$handlers = db_query($sql, $setup_id, $column_name);
while ($handler = db_fetch_object($handlers)) {
$data[$base_table][$column_name][$handler->handler_type]['handler'] = $handler->handler_name;
// Add in any additional arguments
// This should be a serialized array including (at a minimum) name => <handler name>
if ($handler->arguments) {
$data[$base_table][$column_name][$handler->handler_type] = array_merge($data[$base_table][$column_name][$handler->handler_type], unserialize($handler->arguments));
}
};
}
// now add the joins
$sql = "SELECT * FROM {tripal_views_join} WHERE setup_id = %d";
$joins = db_query($sql, $setup_id);
if (!isset($joins)) {
$joins = array();
}
while ($join = db_fetch_object($joins)) {
$left_table = $join->left_table;
$left_field = $join->left_field;
$base_field = $join->base_field;
$handler = $join->handler;
// add join entry
$data[$base_table]['table']['join'][$left_table] = array(
'left_field' => $left_field,
'field' => $base_field,
);
if ($handler) {
$data[$base_table]['table']['join'][$left_table]['handler'] = $handler;
}
}
}
// TEMPORARY: needed to join chado base tables to node linking tables
// currently done using old-style data arrays
//$data = tripal_views_TEMPORARY_chado_linking_data($data);
return $data;
}
| tripal_views_views_data_alter | ( | &$ | data | ) |
Definition at line 437 of file tripal_views.views.inc.
{
$tvi_query = db_query('SELECT * FROM {tripal_views}');
// iterate through the views that we manage
while ($tvi_row = db_fetch_object($tvi_query)) {
//ids we'll use for queries
$mview_id = $tvi_row->mview_id;
$setup_id = $tvi_row->setup_id;
// iterate through the columns and alter the existing data array for
// joins to other tables
$sql = "SELECT * FROM {tripal_views_join} WHERE setup_id = %d";
$joins = db_query($sql, $setup_id);
while ($join = db_fetch_object($joins)) {
$left_table = $join->left_table;
$left_field = $join->left_field;
$base_field = $join->base_field;
$base_table = $join->base_table;
// add the recipricol join entries for each column
if (array_key_exists($left_table, $data)) {
$data[$left_table]['table']['join'][$base_table] = array(
'left_field' => $base_field,
'field' => $left_field,
);
}
}
}
return $data;
}
| tripal_views_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 64 of file tripal_views.views.inc.
{
return array(
'info' => array(
'path' => drupal_get_path('module', 'tripal_views') . '/views/handlers',
),
'handlers' => array(
// Custom Tripal Filter Handlers
'tripal_views_handler_filter_file_upload' => array(
'parent' => 'views_handler_filter',
),
'tripal_views_handler_filter_textarea' => array(
'parent' => 'views_handler_filter',
),
'tripal_views_handler_filter_no_results' => array(
'parent' => 'views_handler_filter'
),
'tripal_views_handler_filter_select_cvterm' => array(
'parent' => 'views_handler_filter_string',
),
'tripal_views_handler_filter_select_string' => array(
'parent' => 'chado_views_handler_filter_string',
),
'tripal_views_handler_filter_sequence' => array(
'parent' => 'chado_views_handler_filter_string',
),
// Custom Tripal Field Handlers
'tripal_views_handler_field_aggregate' => array(
'parent' => 'chado_views_handler_field',
),
'tripal_views_handler_field_sequence' => array(
'parent' => 'chado_views_handler_field',
),
// Join Handlers
'views_handler_join_chado_aggregator' => array(
'parent' => 'views_join',
),
'views_handler_join_chado_through_linking' => array(
'parent' => 'views_join',
),
// Relationship Handlers
'chado_views_handler_relationship' => array(
'parent' => 'views_handler_relationship'
),
'chado_views_handler_relationship_to_node' => array(
'parent' => 'views_handler_relationship'
),
// Wrappers for Default Views Handlers-----
// Field Handlers
'chado_views_handler_field' => array(
'parent' => 'views_handler_field'
),
'chado_views_handler_field_boolean' => array(
'parent' => 'views_handler_field_boolean'
),
'chado_views_handler_field_counter' => array(
'parent' => 'views_handler_field_counter'
),
'chado_views_handler_field_custom' => array(
'parent' => 'views_handler_field_custom'
),
'chado_views_handler_field_date' => array(
'parent' => 'views_handler_field_date'
),
'chado_views_handler_field_markup' => array(
'parent' => 'views_handler_field_markup'
),
'chado_views_handler_field_math' => array(
'parent' => 'views_handler_field_math'
),
'chado_views_handler_field_numeric' => array(
'parent' => 'views_handler_field_numeric'
),
// Filter Handlers
'chado_views_handler_filter_string' => array(
'parent' => 'views_handler_filter_string',
),
'chado_views_handler_filter_boolean_operator_string' => array(
'parent' => 'views_handler_filter_boolean_operator_string',
),
'chado_views_handler_filter_boolean_operator' => array(
'parent' => 'views_handler_filter_boolean_operator',
),
'chado_views_handler_filter_date' => array(
'parent' => 'views_handler_filter_date',
),
'chado_views_handler_filter_equality' => array(
'parent' => 'views_handler_filter_equality',
),
'chado_views_handler_filter_float' => array(
'parent' => 'views_handler_filter_float',
),
'chado_views_handler_filter_numeric' => array(
'parent' => 'views_handler_filter_numeric',
),
// Sort Handlers
'chado_views_handler_sort' => array(
'parent' => 'views_handler_sort'
),
'chado_views_handler_sort_date' => array(
'parent' => 'views_handler_sort_date'
),
'chado_views_handler_sort_formula' => array(
'parent' => 'views_handler_sort_formula'
),
'chado_views_handler_sort_menu_hierarchy' => array(
'parent' => 'views_handler_sort_menu_hierarchy'
),
'chado_views_handler_sort_random' => array(
'parent' => 'views_handler_sort_random'
),
),
);
}
| tripal_views_views_plugins | ( | ) |
Implementation of hook_views_plugins().
Definition at line 473 of file tripal_views.views.inc.
{
$tc_path = drupal_get_path('module', 'tripal_views');
$style_defaults = array(
'path' => $tc_path . '/views_data_export/plugins',
'parent' => 'views_data_export',
'theme' => 'views_data_export',
'theme path' => $tc_path . '/views_data_export/theme',
'theme file' => 'tripal_views_data_export.theme.inc',
'uses row plugin' => FALSE,
'uses fields' => TRUE,
'uses options' => TRUE,
'type' => 'data_export',
);
// add FASTA format as a new style for the existing views_export_data Display
return array(
'style' => array(
'views_data_export_fasta' => array(
'title' => t('FASTA file'),
'help' => t('Display results in FASTA format. All fields in results are on the definition line while the feature.residues field must be present .'),
'handler' => 'tripal_views_plugin_style_export_fasta',
// Views Data Export element that will be used to set additional headers when serving the feed.
'export headers' => array('Content-type: text/plain; charset=utf-8'),
// Views Data Export element mostly used for creating some additional classes and template names.
'export feed type' => 'fasta',
'export feed text' => 'FASTA',
'export feed file' => '%view.fna',
'export feed icon' => $tc_path . '/views_data_export/images/fasta.png',
'additional themes' => array(
'views_data_export_fasta_header' => 'style',
'views_data_export_fasta_body' => 'style',
'views_data_export_fasta_footer' => 'style',
),
'additional themes base' => 'views_data_export_fasta',
) + $style_defaults,
),
);
}
| tripal_views_views_post_render | ( | &$ | view, |
| &$ | output, | ||
| &$ | cache | ||
| ) |
Implementation of hook_views_post_render().
Definition at line 579 of file tripal_views.views.inc.
{
// if the base table and the query is completed we want to set
// the search path back to the default.
$desc = tripal_core_get_chado_table_schema($view->base_table);
if ($desc) {
tripal_db_set_default_search_path();
}
}
| tripal_views_views_pre_execute | ( | &$ | view | ) |
Implementation of hook_views_pre_build(). Implementation of hook_views_pre_execute().
Definition at line 566 of file tripal_views.views.inc.
{
// if the base table is a chado table then we want to set the
// search path so it can find all of the tables.
// this will break views that use tables that have the same name
// as chado tables (e.g. contact).
$desc = tripal_core_get_chado_table_schema($view->base_table);
if ($desc) {
tripal_db_set_chado_search_path('chado');
}
}
| tripal_views_views_pre_render | ( | &$ | 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 196 of file tripal_views.views.inc.
{
// We need to unset the exposed_input for the view so we can repopulate that
// variable. This is necessary if we're using the file_upload_combo
// custom form element which adds the file_path variable to the $_GET after the
// view has populated the $view->exposed_input variable
unset($view->exposed_input);
// we want to add to the bottom of the views the form for downloading
// results in other formats (e.g. Excel, FASTA, CSV, etc.). The Views Data
// Export module provides small images at the bottom, but we want to provide
// a more intutitive interface for getting different file formats
$form = drupal_get_form('tripal_views_data_export_download_form', $view, $display_id, $args);
$view->attachment_after = $form;
}
| tripal_views_views_pre_view | ( | &$ | view, |
| &$ | display_id, | ||
| &$ | args | ||
| ) |
Implementation of hook_views_pre_view().
Definition at line 516 of file tripal_views.views.inc.
{
// merge the $_GET and $_POST into the $_GET. This is because
// Views and Views Data Export modules only uses the $_GET variable but
// file uploads require $_POST. We need to make sure these two modules
// have access to everything needed for this view to work properlys
$_GET = array_merge($_GET, $_POST);
}
1.7.4