';
$output .= '' . l(t('Add a New Entry'), "admin/tripal/storage/chado/views-integration/new") . '';
$output .= '' . l(t('Delete ALL Entries'), "admin/tripal/storage/chado/views-integration/delete-all/confirm") . '';
$output .= '';
$output .= '' . t('The following tables are available for integration with Drupal Views. If '
. 'a table is integrated more than once, then the setup with the lightest '
. 'priority will be used. For example, if you have created a custom setup with a priority of -5 then '
. 'that will be used instead of the default setup with priority 10. '
. 'Priorities range from -10 to +10 where a setup with -10 has '
. 'greater precedent than any other and +10 has the least.') . '
';
// Start with materialized views
$output .= '
Legacy Materialized Views
';
$header = [
'',
'Drupal Views Type Name',
'Table Name',
'Is Legacy?',
'Priority',
'Comment',
];
$rows = [];
// get the list of materialized views
$tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tc.table_id, tv.priority, tv.comment '
. 'FROM {tripal_views} tv '
. 'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
. 'WHERE tv.mview_id IS NOT NULL '
. 'ORDER BY tv.table_name ASC, tv.priority ASC');
foreach ($tviews as $tview) {
$rows[] = [
l(t('Edit'), "admin/tripal/storage/chado/views-integration/edit/" . $tview->setup_id) . "
"
. l(t('Export'), "admin/tripal/storage/chado/views-integration/export/" . $tview->setup_id) . "
"
. l(t('Delete'), "admin/tripal/storage/chado/views-integration/delete/" . $tview->setup_id),
$tview->name,
$tview->table_name,
($tview->table_id) ? 'No' : 'Yes',
$tview->priority,
$tview->comment,
];
}
if ($rows) {
$output .= theme('table', ['header' => $header, 'rows' => $rows]);
}
else {
$output .= 'There are currently no Materialized Views defined. ';
}
// Now list non-mview custom tables
$output .= '
Custom Tables & Non-Legacy Materialized Views
';
$header = ['', 'Drupal Views Type Name', 'Table Name', 'Priority', 'Comment'];
$rows = [];
// get the list of chado tables
$tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tv.priority, tv.comment '
. 'FROM {tripal_views} tv '
. 'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
. 'WHERE mview_id IS NULL AND tc.table_id IS NOT NULL '
. 'ORDER BY table_name ASC, priority ASC');
foreach ($tviews as $tview) {
$rows[] = [
l(t('Edit'), "admin/tripal/storage/chado/views-integration/edit/" . $tview->setup_id) . "
"
. l(t('Export'), "admin/tripal/storage/chado/views-integration/export/" . $tview->setup_id) . "
"
. l(t('Delete'), "admin/tripal/storage/chado/views-integration/delete/" . $tview->setup_id),
$tview->name,
$tview->table_name,
$tview->priority,
$tview->comment,
];
}
if ($rows) {
$output .= theme('table', ['header' => $header, 'rows' => $rows]);
}
else {
$output .= 'There are currently no non-Materialized View Custom Tables defined.
';
}
// Now list chado tables
$output .= '
Chado Tables
';
$header = ['', 'Drupal Views Type Name', 'Table Name', 'Priority', 'Comment'];
$rows = [];
// get the list of chado tables
$tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tv.priority, tv.comment '
. 'FROM {tripal_views} tv '
. 'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
. 'WHERE mview_id IS NULL AND tc.table_id IS NULL '
. 'ORDER BY table_name ASC, priority ASC');
foreach ($tviews as $tview) {
$rows[] = [
l(t('Edit'), "admin/tripal/storage/chado/views-integration/edit/" . $tview->setup_id) . "
"
. l(t('Export'), "admin/tripal/storage/chado/views-integration/export/" . $tview->setup_id) . "
"
. l(t('Delete'), "admin/tripal/storage/chado/views-integration/delete/" . $tview->setup_id),
$tview->name,
$tview->table_name,
$tview->priority,
$tview->comment,
];
}
$output .= theme('table', ['header' => $header, 'rows' => $rows]);
return $output;
}
/**
* Purpose: Deletes integration of a table with the Views module. This
* function is meant to be called from a menu item. After completion it
* redirects the user to the views intergation page.
*
* @param $setup_id
* the unique setup id for the integrated table
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_delete($setup_id) {
tripal_remove_views_integration(['setup_id' => ($setup_id)]);
drupal_set_message(t("Record Deleted"));
drupal_goto('admin/tripal/storage/chado/views-integration');
}
/**
* Purpose: Deletes ALL Chado Views Integrations. This
* function is meant to be called from a menu item. After completion it
* redirects the user to the views intergation page.
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_delete_all_form($form, &$form_state) {
$form['extra'] = [
'#type' => 'item',
'#markup' => t('This will REMOVE ALL views integrations (both custom and default) '
. 'from your website. This allows integrations to be rebuilt to new default '
. 'settings and is especially useful after an upgrade to the views integration system.'),
];
$form['description'] = [
'#type' => 'item',
'#markup' => t('Are you sure you want to REMOVE ALL Views Integrations (including custom integrations) from your system?'),
];
$form['actions'] = ['#type' => 'actions'];
$form['actions']['submit'] = [
'#type' => 'submit',
'#value' => t('Confirm'),
];
$form['actions']['cancel'] = [
'#type' => 'link',
'#title' => t('Cancel'),
'#href' => 'admin/tripal/storage/chado/views-integration/list',
];
// By default, render the form using theme_confirm_form().
if (!isset($form['#theme'])) {
$form['#theme'] = 'confirm_form';
}
return $form;
}
/**
* Purpose: Deletes ALL Chado Views Integrations. This
* function is meant to be called from a menu item. After completion it
* redirects the user to the views intergation page.
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_delete_all_form_submit($form, &$form_state) {
tripal_rebuild_views_integrations(TRUE);
$form_state['redirect'] = 'admin/tripal/storage/chado/views-integration/list';
}
/**
* Purpose: defines the web form used for specifing the base table, joins and
* handlers when integrating a table with views. This form is used for both
* creating a new record and editing an existing record.
*
* @param $form
* The form array which is passed automatically by drupal
*
* @param $form_state
* The form state which is passed automatically by drupal
*
* @return
* A proper Drupal form associative array.
*
* D7 @todo: Add ability to manage custom fields
* D7 @todo: Update relationship handler to work with the new tripal_views_join
* method
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_form($form, &$form_state) {
$data = [];
$form['#cache'] = TRUE;
if (isset($form_state['build_info']['args'][0])) {
$setup_id = $form_state['build_info']['args'][0];
}
else {
$setup_id = NULL;
}
// if Ajax is triggered to change the fields table
// then make some tweaks before the form is rendered
if (isset($form_state['triggering_element'])) {
$triggering_element = $form_state['triggering_element']['#name'];
if (($triggering_element == 'table_name' OR $triggering_element == 'mview_id')) {
$form_state['values'][$triggering_element] = $form_state['triggering_element']['#value'];
$setup_id = NULL;
}
}
// if a setup_id is provided then we want to get the form defaults
$setup_obj = [];
if (isset($setup_id)) {
// get the default setup values
$sql = "SELECT * FROM {tripal_views} WHERE setup_id = :setup";
$setup_obj = db_query($sql, [':setup' => $setup_id]);
$setup_obj = $setup_obj->fetchObject();
$mview_id = $setup_obj->mview_id;
$table_name = $setup_obj->table_name;
$form_state['values']['mview_id'] = $mview_id;
$form_state['values']['table_name'] = $table_name;
// get the default field name/description
$sql = "SELECT * FROM {tripal_views_field} WHERE setup_id=:setup";
$query = db_query($sql, [':setup' => $setup_id]);
$default_fields = [];
foreach ($query as $field) {
$default_fields[$field->column_name]['name'] = $field->name;
$default_fields[$field->column_name]['description'] = $field->description;
}
// get the default join settings and handlers
$sql = "SELECT * FROM {tripal_views_join} WHERE setup_id = :setup";
$query = db_query($sql, [':setup' => $setup_id]);
$default_joins = [];
foreach ($query as $join) {
$default_joins[$join->base_field]['left_table'] = $join->left_table;
$default_joins[$join->base_field]['left_field'] = $join->left_field;
}
// get the default handlers
$sql = "SELECT * FROM {tripal_views_handlers} WHERE setup_id = :setup";
$query = db_query($sql, [':setup' => $setup_id]);
$default_handlers = [];
foreach ($query as $handler) {
$default_handlers[$handler->column_name][$handler->handler_type]['handler_name'] = $handler->handler_name;
$default_handlers[$handler->column_name][$handler->handler_type]['arguments'] = $handler->arguments;
}
// get the default join handlers
$sql = "SELECT * FROM {tripal_views_join} WHERE setup_id = :setup";
$query = db_query($sql, [':setup' => $setup_id]);
foreach ($query as $handler) {
$default_handlers[$handler->base_field]['join']['handler_name'] = $handler->handler;
//$default_handlers[$handler->base_field]['join']['arguments'] = $handler->arguments;
}
// add in the setup_id for the form so we know this is an update not an insert
$form['setup_id'] = [
'#type' => 'hidden',
'#value' => $setup_id,
];
} // end if (isset($setup_id)) {
// add a fieldset for the MView & Chado table selectors
$form['base_table_type'] = [
'#type' => 'fieldset',
'#title' => 'Base Table',
'#description' => 'Please select either a materialized view or a Chado table for integration with ' .
'Drupal Views. In Drupal Views terminology, the selected table becomes the "base table". ' .
'After you select a table from either list, the fields from that table will appear below ' .
'and you can specify other tables to join with and handlers.',
];
// build the form element for the Chado tables
$chado_tables = chado_get_table_names(TRUE);
$chado_tables = array_merge(['Select'], $chado_tables);
$default = '';
if ($setup_id) {
$default = ($setup_obj->table_name) ? $setup_obj->table_name : '';
}
$form['base_table_type']['table_name'] = [
'#title' => t('Chado/Custom Table'),
'#type' => 'select',
'#options' => $chado_tables,
'#description' => t('Tables from Chado, custom tables and materialized view tables (non-legacy MViews) can be selected for integration.'),
'#default_value' => $default,
'#ajax' => [
//D6: 'path' => 'tripal/views-integration/ajax/view_setup_table',
'callback' => 'tripal_chado_views_integration_ajax_view_setup_table',
'wrapper' => 'tripal-views-integration-form',
'effect' => 'fade',
'event' => 'change',
'method' => 'replace',
],
];
// build the form element that lists the materialized views
$query = db_query("SELECT mview_id, name FROM {tripal_mviews} WHERE mv_schema is NULL or mv_schema = '' ORDER BY name");
$mview_tables = [];
$mview_tables['0'] = 'Select';
foreach ($query as $mview) {
$mview_tables[$mview->mview_id] = $mview->name;
}
$default = '';
$legacy_mview = FALSE;
if ($setup_id && !empty($setup_obj->mview_id)) {
$default = $setup_obj->mview_id;
}
if (isset($mview_tables[$setup_obj->mview_id])) {
$legacy_mview = TRUE;
$form['base_table_type']['mview_id'] = [
'#title' => t('Legacy Materialized View'),
'#type' => 'select',
'#options' => $mview_tables,
'#description' => 'Which materialized view to use.',
'#default_value' => $default,
'#ajax' => [
//D6: 'path' => 'tripal/views-integration/ajax/view_setup_table',
'callback' => 'tripal_chado_views_integration_ajax_view_setup_table',
'wrapper' => 'tripal-views-integration-form',
'effect' => 'fade',
'event' => 'change',
'method' => 'replace',
],
];
}
$form['views_type'] = [
'#type' => 'fieldset',
'#title' => 'View Type',
'#description' => 'Here you can provide the "type" of View you want to create.',
];
// field for the name of the
$default = '';
if ($setup_id && isset($setup_obj->name)) {
$default = $setup_obj->name;
}
$form['views_type']['row_name'] = [
'#title' => t('View Type Name'),
'#type' => 'textfield',
'#default_value' => $default,
'#size' => 60,
'#maxlength' => 128,
'#description' => 'Provide the view type name. This is the name that will appear in ' .
'the Drupal Views interface when adding a new view. The view type name ' .
'must be unique.',
'#required' => TRUE,
];
if (isset($setup_id)) {
$form['row_name']['#attributes'] = ['readonly' => 'readonly'];
}
$priorities = [];
foreach (range(-10, 10) as $v) {
$priorities[$v] = (string) $v;
}
$default = -1;
if ($setup_id && isset($setup_obj->priority)) {
$default = $setup_obj->priority;
if ($setup_obj->priority >= 9) {
drupal_set_message('You are editing a default views integration. To ensure your changes
are used, change the priority to -10.', 'warning');
}
}
$form['views_type']['row_priority'] = [
'#type' => 'select',
'#title' => t('Priority'),
'#description' => t('The level of priority your Views integration has in relation to the '
. 'default core and module definitions. The views integration definition with the '
. 'lightest priority will be used. For example, if there is a definition created by '
. 'core with a priority of 10 and another by a custom module of 5 and yours is -1 then '
. 'your definition will be used for that table because -1 is lighter than both 5 and 10.'),
'#options' => $priorities,
'#default_value' => $default,
];
$default = TRUE;
if ($setup_id && isset($setup_obj->priority)) {
$default = ($setup_obj->priority >= 9) ? TRUE : FALSE;
}
$form['views_type']['new_integration'] = [
'#type' => 'checkbox',
'#title' => t('Create a New Chado Views Integration Record'),
'#description' => t('If this checkbox is checked then a new tripal views integration '
. 'will be created rather then overriding the current one with your changes. This '
. 'especially important if you are editing one of the default views integrations '
. '(ie: if the original priority was either 10 or 9).'),
'#default_value' => $default,
];
$default = TRUE;
if ($setup_id && isset($setup_obj->base_table)) {
$default = $setup_obj->base_table;
}
$form['views_type']['base_table'] = [
'#type' => 'checkbox',
'#title' => t('Base Table?'),
'#description' => t('If you want this table to show up as one of the options in the '
. 'add view page, then check this checkbox. It allows you to create listings '
. 'primarily from this table'),
'#default_value' => $default,
];
$default = '';
if ($setup_id && isset($setup_obj->comment)) {
$default = $setup_obj->comment;
}
$form['views_type']['row_description'] = [
'#title' => t('Comment'),
'#type' => 'textarea',
'#description' => '(Optional). Provide any details regarding this setup you would like. This ' .
'description will appear when selecting a type for a new Drupal View',
'#required' => FALSE,
'#default_value' => $default,
];
// we need a div block where the table fields will get put when the
// AHAH callback is made
$form['view_setup_table'] = [
'#type' => 'item',
'#prefix' => '',
'#suffix' => '
',
];
// add the fieldset for the table fields, but only if the $mview_id or $table_name
// is set. The only times these values are set is if we're editing an existing
// record or if the AHAH callback is being made.
if (isset($form_state['values']['mview_id']) or isset($form_state['values']['table_name'])) {
$mview_id = $form_state['values']['mview_id'];
$table_name = $form_state['values']['table_name'];
$form['view_setup_table'] = [
'#type' => 'fieldset',
'#title' => t('Table Fields'),
'#prefix' => '',
'#suffix' => '
',
'#collapsible' => TRUE,
];
// 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
$columns = [];
if ($legacy_mview) {
$sql = "SELECT mv_specs FROM {tripal_mviews} WHERE mview_id = :id";
$mview = db_query($sql, [':id' => $mview_id]);
$mview = $mview->fetchObject();
$columns = explode(",", $mview->mv_specs);
}
else {
$table_desc = chado_get_schema($table_name);
if ($table_desc) {
$fields = $table_desc['fields'];
// iterate through the columns and build the format
// compatible with the code below. The column name is first followed
// by the type with a separating space
foreach ($fields as $column => $attrs) {
$columns[] = "$column " . $attrs['type'];
}
}
}
$i = 1;
$form['view_setup_table']["instructions"] = [
'#type' => 'markup',
'#value' => filter_xss("Select an optional table to which the fields of the " .
"materialized view can join. If a field does not need to " .
"join you may leave the selection blank."),
];
$data['field_types'] = [];
$form['view_setup_table']['header'] = [
'#type' => 'markup',
'#prefix' => '',
];
$form['view_setup_table']['header']['column-1'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#markup' => 'Field',
];
$form['view_setup_table']['header']['column-2'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#markup' => 'Labels',
];
$form['view_setup_table']['header']['column-3'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#markup' => '',
];
$form['view_setup_table']['header']['column-4'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#markup' => 'Handlers',
];
// get the list of chado tables to join on
$chado_join_tables = chado_get_table_names(TRUE);
$chado_join_tables = array_merge(['Select a Join Table'], $chado_join_tables);
// get list of all handlers
$all_handlers = tripal_chado_views_integration_discover_handlers();
$handlers_fields = [0 => "Select a field handler"];
$handlers_filters = [0 => "Select a filter handler"];
$handlers_sort = [0 => "Select a sort handler"];
$handlers_argument = [0 => "Select an argument handler"];
$handlers_join = [0 => "Select a join handler"];
$handlers_rel = [0 => "Select a relationship handler"];
foreach ($all_handlers as $handler) {
if (preg_match("/views_handler_field/", $handler)) {
$handlers_fields[$handler] = $handler;
}
if (preg_match("/views_handler_filter/", $handler)) {
$handlers_filters[$handler] = $handler;
}
if (preg_match("/views_handler_sort/", $handler)) {
$handlers_sort[$handler] = $handler;
}
if (preg_match("/views_handler_argument/", $handler)) {
$handlers_argument[$handler] = $handler;
}
if (preg_match("/_join/", $handler)) {
$handlers_join[$handler] = $handler;
}
if (preg_match("/views_handler_relationship/", $handler)) {
$handlers_rel[$handler] = $handler;
}
}
// generate a unique $table_id for keeping track of the table
if ($mview_id) {
$table_id = $mview_id;
}
else {
$table_id = $table_name;
}
// Per Row (Fields) --------------
// now iterate through the columns of the materialized view or
// chado table and generate the join and handler fields
foreach ($columns as $column) {
$column = trim($column); // trim trailing and leading spaces
preg_match("/^(.*?)\ (.*?)$/", $column, $matches);
$column_name = $matches[1];
$column_type = $matches[2];
$form['view_setup_table']["$table_id-$i"] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
// COLUMN I
$form['view_setup_table']["$table_id-$i"]["fields_name_$table_id-$i"] = [
'#type' => 'item',
'#prefix' => "",
'#markup' => '' . filter_xss($column_name) . '' .
'
' . filter_xss($column_type) . '',
'#suffix' => "
",
];
$data['field_types'][$column_name] = $column_type;
// COLUMN II
$form['view_setup_table']["$table_id-$i"]['column-2'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
// set the default values for the human-readable name and description
$default_name = '';
$default_descrip = '';
if (isset($setup_id) && !isset($form_state['values']["fields_readable_name_$table_id-$i"])) {
$default_name = $default_fields[$column_name]['name'];
$default_descrip = $default_fields[$column_name]['description'];
}
elseif (isset($form_state['values']["fields_readable_name_$table_id-$i"])) {
$default_name = $form_state['values']["fields_readable_name_$table_id-$i"];
$default_descrip = $form_state['values']["fields_description_$table_id-$i"];
}
else {
$default_name = ucwords(str_replace('_', ' ', $column_name));
$default_descrip = 'TODO: please describe this field!';
}
$form['view_setup_table']["$table_id-$i"]['column-2']["fields_readable_name_$table_id-$i"] = [
'#type' => 'textfield',
'#title' => 'Human-Readable Name',
'#description' => 'This is the name of the field in the Views UI',
'#required' => TRUE,
'#default_value' => $default_name,
'#size' => 42,
];
$form['view_setup_table']["$table_id-$i"]['column-2']["fields_description_$table_id-$i"] = [
'#type' => 'textarea',
'#title' => 'Short Description',
'#description' => 'This is the field help in the Views UI',
'#required' => TRUE,
'#cols' => 42,
'#rows' => 3,
'#default_value' => $default_descrip,
];
// COLUMN III
$form['view_setup_table']["$table_id-$i"]['column-3'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
// COLUMN 4
$form['view_setup_table']["$table_id-$i"]['column-4'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
// create the handler fields
$default_field_handler = 0;
if (isset($setup_id) && !isset($form_state['values']["fields_field_handler_$table_id-$i"])) {
$default_field_handler = array_key_exists('field', $default_handlers[$column_name]) ? $default_handlers[$column_name]['field']['handler_name'] : "";
$form_state['values']["fields_field_handler_$table_id-$i"] = $default_field_handler;
}
else {
$default_field_handler = array_key_exists("fields_field_handler_$table_id-$i", $form_state['values']) ? $form_state['values']["fields_field_handler_$table_id-$i"] : '';
if (!$default_field_handler) {
if ($column_type == 'integer' or $column_type == 'int' or $column_type == 'serial') {
$default_field_handler = 'views_handler_field_numeric';
}
elseif (preg_match("/character varying/", $column_type) or $column_type == 'char' or $column_type == 'text' or $column_type == 'varchar') {
$default_field_handler = 'views_handler_field';
}
elseif ($column_type == 'boolean') {
$default_field_handler = 'views_handler_field_boolean';
}
elseif ($column_type == 'float') {
$default_field_handler = 'views_handler_field_numeric';
}
elseif ($column_type == 'datetime') {
$default_field_handler = 'views_handler_field_date';
}
}
}
$form['view_setup_table']["$table_id-$i"]['column-4']["fields_field_handler_$table_id-$i"] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_fields,
'#required' => FALSE,
'#default_value' => $default_field_handler,
];
// Assign the default filter handler for this field. Use the handler provided
// by the user through the form if provided, or set the default using the
// column type.
$default_filter_handler = 0;
if (isset($setup_id) && !isset($form_state['values']["fields_filter_handler_$table_id-$i"])) {
$default_filter_handler = array_key_exists('filter', $default_handlers[$column_name]) ? $default_handlers[$column_name]['filter']['handler_name'] : "";
$form_state['values']["fields_filter_handler_$table_id-$i"] = $default_filter_handler;
}
else {
$default_filter_handler = array_key_exists("fields_filter_handler_$table_id-$i", $form_state['values']) ? $form_state['values']["fields_filter_handler_$table_id-$i"] : "";
if (!$default_filter_handler) {
if ($column_type == 'integer' or $column_type == 'int' or $column_type == 'serial') {
$default_filter_handler = 'views_handler_filter_numeric';
}
elseif (preg_match("/^character varying/", $column_type) or $column_type == 'char' or $column_type == 'text' or $column_type == 'varchar') {
$default_filter_handler = 'views_handler_filter_string';
}
elseif ($column_type == 'boolean') {
$default_filter_handler = 'views_handler_filter_boolean';
}
elseif ($column_type == 'float') {
$default_filter_handler = 'views_handler_filter_numeric';
}
elseif ($column_type == 'datetime') {
$default_filter_handler = 'views_handler_filter_date';
}
}
}
$form['view_setup_table']["$table_id-$i"]['column-4']["fields_filter_handler_$table_id-$i"] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_filters,
'#required' => FALSE,
'#default_value' => $default_filter_handler,
];
$default_sort_handler = 0;
if (isset($setup_id) && !isset($form_state['values']["fields_sort_handler_$table_id-$i"])) {
$default_sort_handler = array_key_exists('sort', $default_handlers[$column_name]) ? $default_handlers[$column_name]['sort']['handler_name'] : "";
$form_state['values']["fields_sort_handler_$table_id-$i"] = $default_sort_handler;
}
else {
$default_sort_handler = array_key_exists("fields_sort_handler_$table_id-$i", $form_state['values']) ? $form_state['values']["fields_sort_handler_$table_id-$i"] : "";
if (!$default_sort_handler) {
if ($column_type == 'integer' or $column_type == 'int' or $column_type == 'serial') {
$default_sort_handler = 'views_handler_sort';
}
elseif (preg_match("/character varying/", $column_type) or $column_type == 'char' or $column_type == 'text' or $column_type == 'varchar') {
$default_sort_handler = 'views_handler_sort';
}
elseif ($column_type == 'boolean') {
$default_sort_handler = 'views_handler_sort';
}
elseif ($column_type == 'float') {
$default_sort_handler = 'views_handler_sort';
}
elseif ($column_type == 'datetime') {
$default_sort_handler = 'views_handler_sort_date';
}
}
}
$form['view_setup_table']["$table_id-$i"]['column-4']["fields_sort_handler_$table_id-$i"] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_sort,
'#required' => FALSE,
'#default_value' => $default_sort_handler,
];
$default_argument_handler = 0;
if (isset($setup_id)
&& !isset($form_state['values']["fields_argument_handler_$table_id-$i"])
&& isset($default_handlers[$column_name]['argument'])) {
$default_argument_handler = $default_handlers[$column_name]['argument']['handler_name'];
$form_state['values']["fields_argument_handler_$table_id-$i"] = $default_argument_handler;
}
else {
if (isset($form_state['values']["fields_argument_handler_$table_id-$i"])) {
$default_argument_handler = $form_state['values']["fields_argument_handler_$table_id-$i"];
}
if (!$default_argument_handler) {
if ($column_type == 'integer' or $column_type == 'int' or $column_type == 'serial') {
$default_argument_handler = 'views_handler_argument_numeric';
}
elseif (preg_match("/character varying/", $column_type) or $column_type == 'char' or $column_type == 'text' or $column_type == 'varchar') {
$default_argument_handler = 'views_handler_argument_string';
}
elseif ($column_type == 'boolean') {
$default_argument_handler = 'views_handler_argument_numeric';
}
elseif ($column_type == 'float') {
$default_argument_handler = 'views_handler_argument_numeric';
}
elseif ($column_type == 'datetime') {
$default_argument_handler = 'views_handler_argument_date';
}
}
}
$form['view_setup_table']["$table_id-$i"]['column-4']["fields_argument_handler_$table_id-$i"] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_argument,
'#required' => FALSE,
'#default_value' => $default_argument_handler,
];
$i++;
} // end foreach ($columns as $column) {
$form['view_setup_join'] = [
'#type' => 'fieldset',
'#title' => t('Joins & Relationships'),
'#prefix' => '',
'#suffix' => '
',
'#description' => t('Below is a list of the joins/relationships between the '
. 'current base table and other chado tables.'),
'#collapsible' => TRUE,
'#collapsed' => TRUE,
];
$form['view_setup_join']['header'] = [
'#type' => 'markup',
'#prefix' => '',
];
$form['view_setup_join']['header']['column-1'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#markup' => 'Base',
];
$form['view_setup_join']['header']['column-2'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#markup' => 'Handlers',
];
$form['view_setup_join']['header']['column-3'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#markup' => 'Joined to',
];
$base_field_options = ['Select the Base Column'];
$table_desc = chado_get_schema($table_name);
foreach ($table_desc['fields'] as $column => $def) {
$base_field_options[$column] = $column;
}
$chado_join_tables[0] = 'Select the Left Table';
unset($handlers_join[0]);
$i = 0;
$query = db_select('tripal_views_join', 'tvj');
$query->fields('tvj')
->condition('tvj.setup_id', $setup_id, '=')
->orderBy('tvj.relationship_only', 'ASC')
->orderBy('tvj.base_field', 'ASC')
->orderBy('tvj.left_table', 'ASC');
foreach ($query->execute() as $i => $result) {
$form['view_setup_join']["$table_id-$i"] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
// COLUMN I
$form['view_setup_join']["$table_id-$i"]['column-1'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
];
$form['view_setup_join']["$table_id-$i"]['column-1']['join_base_table'] = [
'#type' => 'item',
'#markup' => '' . filter_xss($result->base_table) . '',
];
$form['view_setup_join']["$table_id-$i"]['column-1']["join_base_table-$i"] = [
'#type' => 'hidden',
'#value' => $result->base_table,
];
$form['view_setup_join']["$table_id-$i"]['column-1']["join_base_field-$i"] = [
'#type' => 'select',
'#options' => $base_field_options,
'#required' => FALSE,
'#default_value' => $result->base_field,
];
// COLUMN II
$form['view_setup_join']["$table_id-$i"]['column-2'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
$form['view_setup_join']["$table_id-$i"]['column-2']["join_join_handler-$i"] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_join,
'#required' => FALSE,
'#default_value' => $result->handler,
];
$form['view_setup_join']["$table_id-$i"]['column-2']["join_relationship_handler-$i"] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_rel,
'#required' => FALSE,
'#default_value' => $result->relationship_handler,
];
$form['view_setup_join']["$table_id-$i"]['column-2']["join_relationship_only-$i"] = [
'#type' => 'checkbox',
'#title' => 'Relationship Only?',
'#default_value' => $result->relationship_only,
];
// COLUMN III
$form['view_setup_join']["$table_id-$i"]['column-3'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
$form['view_setup_join']["$table_id-$i"]['column-3']["join_left_table-$i"] = [
'#type' => 'select',
'#options' => $chado_join_tables,
'#default_value' => $result->left_table,
];
$columns = [];
if ($result->left_table) {
// get the table description
$table_desc = chado_get_schema($result->left_table);
foreach ($table_desc['fields'] as $column => $def) {
$columns[$column] = $column;
}
}
else {
$columns = ['Select Left Column'];
}
$form['view_setup_join']["$table_id-$i"]['column-3']["join_left_field-$i"] = [
'#type' => 'select',
'#prefix' => " ",
'#suffix' => "
",
'#options' => $columns,
'#required' => FALSE,
'#default_value' => $result->left_field,
];
} // end foreach ($query->execute() as $i => $result) {
$form['num_joins'] = [
'#type' => 'hidden',
'#value' => $i,
];
// Form to add a new join
$form['view_setup_join']['new_join'] = [
'#type' => 'fieldset',
'#title' => 'New Join',
'#description' => "Add a new join to the $table_name table",
'#prefix' => '',
'#suffix' => '
',
];
$form['view_setup_join']['new_join']['column-1'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
];
$form['view_setup_join']['new_join']['column-1']['join_base_table'] = [
'#type' => 'item',
'#markup' => '' . $table_name . '',
];
$form['view_setup_join']['new_join']['column-1']['new_join_base_table'] = [
'#type' => 'hidden',
'#value' => $table_name,
];
$form['view_setup_join']['new_join']['column-1']['new_join_base_field'] = [
'#type' => 'select',
'#options' => $base_field_options,
'#required' => FALSE,
];
// COLUMN II
$form['view_setup_join']['new_join']['column-2'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
$form['view_setup_join']['new_join']['column-2']['new_join_join_handler'] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_join,
'#required' => FALSE,
];
$form['view_setup_join']['new_join']['column-2']['new_join_relationship_handler'] = [
'#type' => 'select',
'#prefix' => "",
'#suffix' => "
",
'#options' => $handlers_rel,
'#required' => FALSE,
'#default_value' => 'views_handler_relationship',
];
$form['view_setup_join']['new_join']['column-2']['new_join_relationship_only'] = [
'#type' => 'checkbox',
'#title' => 'Relationship Only?',
'#default_value' => TRUE,
];
// COLUMN III
$form['view_setup_join']['new_join']['column-3'] = [
'#type' => 'markup',
'#prefix' => "",
'#suffix' => "
",
'#value' => filter_xss(''),
];
$form['view_setup_join']['new_join']['column-3']['new_join_left_table'] = [
'#type' => 'select',
'#options' => $chado_join_tables,
'#ajax' => [
'callback' => 'tripal_chado_views_integration_ajax_new_join_left_field_callback',
'wrapper' => 'new-join',
],
];
$new_join_table = (isset($form_state['values']['new_join_left_table'])) ? $form_state['values']['new_join_left_table'] : FALSE;
if ($new_join_table) {
// get the table description
$table_desc = chado_get_schema($new_join_table);
foreach ($table_desc['fields'] as $column => $def) {
$columns[$column] = $column;
}
}
else {
$columns = ['Select Left Column'];
}
$form['view_setup_join']['new_join']['column-3']['new_join_left_field'] = [
'#type' => 'select',
'#prefix' => " ",
'#suffix' => "
",
'#options' => $columns,
'#required' => FALSE,
];
$form['view_setup_join']['new_join']['save'] = [
'#type' => 'submit',
'#value' => t('Save & Add Join'),
];
$form['save'] = [
'#type' => 'submit',
'#value' => t('Save'),
];
$data['row_count'] = $i - 1;
} // end of if table/mview
// use this to put values into $form_state['values']
$form['data'] = [];
// Ensure that we don't store an array
// since we will get a check_plain:htmlspecial_characters error if we do
foreach ($data as $key => $value) {
if (is_array($value)) {
$form['data'][$key] = [
'#type' => 'hidden',
'#value' => serialize($value),
];
}
else {
$form['data'][$key] = [
'#type' => 'hidden',
'#value' => $value,
];
}
}
$form['#prefix'] = '';
$form['#suffix'] = '
';
$form['#redirect'] = 'admin/tripal/storage/chado/views-integration/list';
return $form;
}
/**
* Purpose: validates the tripal_chado_views_integration_form after submission
*
* @param $form
* The form object which is passed automatically by drupal
*
* @param $form_state
* The form state pbject which is passed automatically by drupal
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_form_validate($form, &$form_state) {
$name_array = explode(" ", $form_state['values']['row_name']);
$mview_id = $form_state['values']['mview_id'];
$table_name = $form_state['values']['table_name'];
// if (count($name_array) > 1) {
// form_set_error($form_state['values']['row_name'], 'The View type name must be a single word only.');
// }
if ($mview_id and $table_name) {
form_set_error('mview_id', 'Please select either a materialized view or a Chado table but not both');
}
if (!$mview_id and !$table_name) {
form_set_error('mview_id', 'Please select either a materialized view or a Chado table');
}
// Ensure that users don't override the default integrations
if ($form_state['values']['row_priority'] >= 9) {
form_set_error('row_priority', 'A priority of 10 or 9 is reserved for default tripal '
. 'views integrations created by core modules. Please set the priority between '
. '0 and -10 to ensure your changes are used rather over the defaults.');
}
// Check that if some fields for a new join are entered, all of them are
if (!empty($form_state['values']['new_join_base_field'])
OR !empty($form_state['values']['new_join_left_table'])
OR !empty($form_state['values']['new_join_left_field'])) {
if (!(!empty($form_state['values']['new_join_base_field'])
AND !empty($form_state['values']['new_join_left_table'])
AND !empty($form_state['values']['new_join_left_field']))) {
form_set_error('new_join_base_field', 'You need to select the Base Column, Left Table and Left Column to create a new join');
}
}
}
/**
* Purpose: inserts or updates the record in the tripal views integration
* tables. This function is only called if validation is passed.
*
* @param $form
* The form object which is passed automatically by drupal
*
* @param $form_state
* The form state pbject which is passed automatically by drupal
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_form_submit($form, &$form_state) {
$name = trim($form_state['values']['row_name']);
$mview_id = $form_state['values']['mview_id'];
$table_name = $form_state['values']['table_name'];
$setup_id = array_key_exists('setup_id', $form_state['values']) ? $form_state['values']['setup_id'] : "";
$priority = $form_state['values']['row_priority'];
$comment = $form_state['values']['row_description'];
// get details about this mview
if ($mview_id) {
// D7 TODO: Check DBTNG changes work
$sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = :id";
$mview = db_query($sql, [':id' => $mview_id]);
$mview = $mview->fetchObject();
$table_name = $mview->mv_table;
$table_id = $mview_id;
$type = 'mview';
}
else {
$type = 'chado';
$table_id = $table_name;
}
// If this is for a materialized view then we want to add/update that record
$tripal_views_record = [];
if ($mview_id) {
// get details about this mview
// D7 TODO: Check DBTNG changes work
$sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = :id";
$mview = db_query($sql, [':id' => $mview_id]);
$mview = $mview->fetchObject();
// build the record for insert/update
$tripal_views_record = [
'mview_id' => $mview_id,
'table_name' => $mview->mv_table,
'name' => $name,
'priority' => $priority,
'comment' => $comment,
'base_table' => $form_state['values']['base_table'],
];
}
// if a chado table then...
else {
// build the record for insert/update
$tripal_views_record = [
'table_name' => $table_name,
'name' => $name,
'priority' => $priority,
'comment' => $comment,
'base_table' => $form_state['values']['base_table'],
];
}
// perform the insert or update
if (!$setup_id) { // this is an insert
if (!drupal_write_record('tripal_views', $tripal_views_record)) {
drupal_set_message(t("Failed to add record."), 'error');
return;
}
}
else { // this is an update
// check to see if it was specified to create a new integration
if ($form_state['values']['new_integration']) {
$setup_id = NULL;
if (!drupal_write_record('tripal_views', $tripal_views_record)) {
drupal_set_message(t("Failed to add record."), 'error');
return;
}
}
else {
$tripal_views_record['setup_id'] = $setup_id;
if (!drupal_write_record('tripal_views', $tripal_views_record, ['setup_id'])) {
drupal_set_message(t("Failed to update record."), 'error');
return;
}
}
}
// if this is an update then clean out the existing joins and handlers so we can add new ones
if ($setup_id) {
db_query("DELETE FROM {tripal_views_field} WHERE setup_id = :setup", [':setup' => $setup_id]);
db_query("DELETE FROM {tripal_views_join} WHERE setup_id = :setup", [':setup' => $setup_id]);
db_query("DELETE FROM {tripal_views_handlers} WHERE setup_id = :setup", [':setup' => $setup_id]);
}
// iterate through the columns of the form and add
// the joins if provided, and the handlers
$i = 1;
foreach (unserialize($form_state['values']['field_types']) as $key => $value) {
// add the field definition
$view_field_record = [
'setup_id' => $tripal_views_record['setup_id'],
'column_name' => $key,
'name' => $form_state['values']["fields_readable_name_$table_id-$i"],
'description' => $form_state['values']["fields_description_$table_id-$i"],
'type' => $value,
];
drupal_write_record('tripal_views_field', $view_field_record);
// add the hanlders
$handlers = ['filter', 'field', 'sort', 'argument'];
foreach ($handlers as $handler) {
$handler_name = $form_state['values']["fields_" . $handler . "_handler_$table_id-$i"];
if ($handler_name) {
$handler_record = [
'setup_id' => $tripal_views_record['setup_id'],
'column_name' => $key,
'handler_type' => $handler,
'handler_name' => $handler_name,
];
drupal_write_record('tripal_views_handlers', $handler_record);
}
}
$i++;
}
// Now add all the joins
for ($i = 0; $i <= $form_state['values']['num_joins']; $i++) {
if (isset($form_state['values']["join_base_table-$i"])) {
$join_record = [
'setup_id' => $tripal_views_record['setup_id'],
'base_table' => $form_state['values']["join_base_table-$i"],
'base_field' => $form_state['values']["join_base_field-$i"],
'left_table' => $form_state['values']["join_left_table-$i"],
'left_field' => $form_state['values']["join_left_field-$i"],
'handler' => $form_state['values']["join_join_handler-$i"],
'relationship_handler' => $form_state['values']["join_relationship_handler-$i"],
'relationship_only' => $form_state['values']["join_relationship_only-$i"],
];
drupal_write_record('tripal_views_join', $join_record);
}
}
// Now add the new join if there is one
if ($form_state['values']['new_join_base_field']) {
$join_record = [
'setup_id' => $tripal_views_record['setup_id'],
'base_table' => $form_state['values']["new_join_base_table"],
'base_field' => $form_state['values']["new_join_base_field"],
'left_table' => $form_state['values']["new_join_left_table"],
'left_field' => $form_state['values']["new_join_left_field"],
'handler' => $form_state['values']["new_join_join_handler"],
'relationship_handler' => $form_state['values']["new_join_relationship_handler"],
'relationship_only' => $form_state['values']["new_join_relationship_only"],
];
drupal_write_record('tripal_views_join', $join_record);
}
if ($setup_id) {
drupal_set_message(t('Record Updated'));
}
else {
drupal_set_message(t('Record Added'));
}
$form_state['redirect'] = 'admin/tripal/storage/chado/views-integration/integrations';
// now clear all the caches so that Drupal views picks up our chages
views_invalidate_cache();
}
/**
* AJAX callback to replace the left field select list in the new join fieldset
* of the tripal_chado_views_integration_form form
*/
function tripal_chado_views_integration_ajax_new_join_left_field_callback($form, $form_state) {
return $form['view_setup_join']['new_join'];
}
/**
* Purpose: this function queries all modules currently enabled on the site
* looking for custom handlers and returns a list of all available handerls.
* The base View handlers are also included.
*
* @return
* Returns an array of handler names
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_discover_handlers() {
$handlers = [];
// Get handlers from all modules.
foreach (module_implements('views_handlers') as $module) {
$function = $module . '_views_handlers';
$result = $function();
if (!is_array($result)) {
continue;
}
foreach ($result['handlers'] as $handler => $parent) {
$handlers[] = $handler;
}
}
// these handlers are hard coded because I could not
// get the views_handlers() function to be called
// in the code above. However, we will be creating
// Chado wrappers for many of these and once that work
// is done these will no longer be needed.
// argument handlers
$handlers[] = 'views_handler_argument';
$handlers[] = 'views_handler_argument_numeric';
$handlers[] = 'views_handler_argument_formula';
$handlers[] = 'views_handler_argument_date';
$handlers[] = 'views_handler_argument_string';
$handlers[] = 'views_handler_argument_many_to_one';
$handlers[] = 'views_handler_argument_null';
// field handlers
$handlers[] = 'views_handler_field';
$handlers[] = 'views_handler_field_date';
$handlers[] = 'views_handler_field_boolean';
$handlers[] = 'views_handler_field_markup';
$handlers[] = 'views_handler_field_xss';
$handlers[] = 'views_handler_field_url';
$handlers[] = 'views_handler_field_file_size';
$handlers[] = 'views_handler_field_prerender_list';
$handlers[] = 'views_handler_field_numeric';
$handlers[] = 'views_handler_field_custom';
$handlers[] = 'views_handler_field_counter';
// filter handlers
$handlers[] = 'views_handler_filter';
$handlers[] = 'views_handler_filter_equality';
$handlers[] = 'views_handler_filter_string';
$handlers[] = 'views_handler_filter_boolean_operator';
$handlers[] = 'views_handler_filter_boolean_operator_string';
$handlers[] = 'views_handler_filter_in_operator';
$handlers[] = 'views_handler_filter_numeric';
$handlers[] = 'views_handler_filter_date';
$handlers[] = 'views_handler_filter_many_to_one';
// relationship handlers
$handlers[] = 'views_handler_relationship';
// sort handlers
$handlers[] = 'views_handler_sort';
$handlers[] = 'views_handler_sort_formula';
$handlers[] = 'views_handler_sort_date';
$handlers[] = 'views_handler_sort_menu_hierarchy';
$handlers[] = 'views_handler_sort_random';
// join handler
$handlers[] = 'views_join';
return $handlers;
}
/*
* Ajax Callback: Chado Views Integration Form
* Replaces the entire fields table when the table or materialized view is set/changed
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_ajax_view_setup_table($form, $form_state) {
//return $form['view_setup_table'];
return $form;
}
/*
* Ajax Callback: Chado Views Integration Form
* Replaces the join db field dropdown when the join table dropdown is changed
*
* @ingroup tripal_chado_views
*/
function tripal_chado_views_integration_ajax_join_field($form, $form_state) {
// Determine which row we are dealing with from the name of the triggering element
if (preg_match('/fields_join_(\w+-\d+)/', $form_state['triggering_element']['#name'], $matches)) {
$field = $matches[1];
$join_field = 'fields_join_column_' . $matches[1];
// return the form element to be updated
return $form['view_setup_table'][$field]['column-3'][$join_field];
}
else {
tripal_report_error('tripal_views', TRIPAL_ERROR,
'Chado Views Integration Ajax failed due to being unable to determine which row needs updating', []);
return $form;
}
}