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@@ -1,1301 +1,236 @@
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<?php
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/**
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* @file
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- * Functions related to the UI for integrating tables with views
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+ * Contains functions used to manage tripal views integrations
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*/
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/**
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- * Purpose: Generates a themable table containing the list of integrated tables
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- * The look-and-feel of the table can be altered by overriding the theme for
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- * tables.
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- *
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- * @return
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- * a themed HTML table
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+ * Purpose: Deletes ALL Tripal Views Integrations.
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*
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* @ingroup tripal_views
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*/
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-function tripal_views_integration_setup_list() {
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- $output = '';
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-
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- $output .= '<ul class="action-links">';
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- $output .= '<li>' . l(t('Add a New Entry'), "admin/tripal/views-integration/new") . '</li>';
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- $output .= '<li style="float: right;">' . l(t('Delete ALL Entries'), "admin/tripal/views-integration/delete-all/confirm") . '</li>';
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- $output .= '</ul>';
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-
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- $output .= '<p>' . t('The following tables are available for integration with Drupal Views. If '
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- . 'a table is integrated more than once, then the setup with the lightest '
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- . 'priority will be used. For example, if you have created a custom setup with a priority of -5 then '
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- . 'that will be used instead of the default setup with priority 10. '
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- . 'Priorities range from -10 to +10 where a setup with -10 has '
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- . 'greater precedent than any other and +10 has the least.') . '</p>';
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-
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- // Start with materialized views
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- $output .= '<br /><h3>Legacy Materialized Views</h3>';
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- $header = array('', 'Drupal Views Type Name', 'Table Name', 'Is Legacy?', 'Priority', 'Comment');
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- $rows = array();
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-
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- // get the list of materialized views
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- $tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tc.table_id, tv.priority, tv.comment '
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- .'FROM {tripal_views} tv '
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- .'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
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- .'WHERE tv.mview_id IS NOT NULL '
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- .'ORDER BY tv.table_name ASC, tv.priority ASC');
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- foreach ($tviews as $tview) {
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- $rows[] = array(
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- l(t('Edit'), "admin/tripal/views-integration/edit/" . $tview->setup_id) . "<br />"
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- . l(t('Export'), "admin/tripal/views-integration/export/" . $tview->setup_id) . "<br />"
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- . l(t('Delete'), "admin/tripal/views-integration/delete/" . $tview->setup_id),
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- $tview->name,
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- $tview->table_name,
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- ($tview->table_id) ? 'No' : 'Yes',
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- $tview->priority,
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- $tview->comment,
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- );
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- }
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-
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- if ($rows) {
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- $output .= theme('table', array('header' => $header, 'rows' => $rows));
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- }
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- else {
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- $output .= '<p>There are currently no Materialized Views defined. ';
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-
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- }
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-
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- // Now list non-mview custom tables
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- $output .= '<br /><h3>Custom Tables & Non-Legacy Materialized Views</h3>';
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- $header = array('', 'Drupal Views Type Name', 'Table Name', 'Priority', 'Comment');
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- $rows = array();
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-
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- // get the list of chado tables
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- $tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tv.priority, tv.comment '
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- .'FROM {tripal_views} tv '
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- .'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
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- .'WHERE mview_id IS NULL AND tc.table_id IS NOT NULL '
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- .'ORDER BY table_name ASC, priority ASC');
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- foreach ($tviews as $tview) {
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- $rows[] = array(
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- l(t('Edit'), "admin/tripal/views-integration/edit/" . $tview->setup_id) . "<br />"
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- . l(t('Export'), "admin/tripal/views-integration/export/" . $tview->setup_id) . "<br />"
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- . l(t('Delete'), "admin/tripal/views-integration/delete/" . $tview->setup_id),
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- $tview->name,
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- $tview->table_name,
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- $tview->priority,
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- $tview->comment,
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- );
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- }
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-
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- if ($rows) {
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- $output .= theme('table', array('header' => $header, 'rows' => $rows));
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- }
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- else {
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- $output .= '<p>There are currently no non-Materialized View Custom Tables defined.</p>';
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- }
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-
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- // Now list chado tables
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- $output .= '<br /><h3>Chado Tables</h3>';
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- $header = array('', 'Drupal Views Type Name', 'Table Name', 'Priority', 'Comment');
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- $rows = array();
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+function tripal_views_delete_all_integrations() {
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- // get the list of chado tables
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- $tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tv.priority, tv.comment '
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- .'FROM {tripal_views} tv '
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- .'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
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- .'WHERE mview_id IS NULL AND tc.table_id IS NULL '
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- .'ORDER BY table_name ASC, priority ASC');
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- foreach ($tviews as $tview) {
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- $rows[] = array(
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- l(t('Edit'), "admin/tripal/views-integration/edit/" . $tview->setup_id) . "<br />"
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- . l(t('Export'), "admin/tripal/views-integration/export/" . $tview->setup_id) . "<br />"
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- . l(t('Delete'), "admin/tripal/views-integration/delete/" . $tview->setup_id),
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- $tview->name,
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- $tview->table_name,
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- $tview->priority,
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- $tview->comment,
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- );
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- }
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-
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- $output .= theme('table', array('header' => $header, 'rows' => $rows));
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- return $output;
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-}
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-
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-/**
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- * Purpose: Deletes integration of a table with the Views module. This
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- * function is meant to be called from a menu item. After completion it
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- * redirects the user to the views intergation page.
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- *
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- * @param $setup_id
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- * the unique setup id for the integrated table
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- *
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- * @ingroup tripal_views
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- */
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-function tripal_views_integration_delete($setup_id) {
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+ db_query("DELETE FROM {tripal_views}");
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+ db_query("DELETE FROM {tripal_views_field}");
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+ db_query("DELETE FROM {tripal_views_handlers}");
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+ db_query("DELETE FROM {tripal_views_join}");
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- tripal_views_integration_remove_entry_by_setup_id($setup_id);
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- drupal_set_message(t("Record Deleted"));
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- drupal_goto('admin/tripal/views-integration');
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+ drupal_set_message("Successfully deleted all views integration.");
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}
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/**
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- * Purpose: Deletes ALL Tripal Views Integrations. This
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- * function is meant to be called from a menu item. After completion it
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- * redirects the user to the views intergation page.
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+ * Integrate all chado tables in the schema api. This integration only occurs
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+ * once and sets all Chado tables to a priority of 10
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*
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* @ingroup tripal_views
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*/
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-function tripal_views_integration_delete_all_form ($form, $form_state) {
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+function tripal_views_integrate_all_chado_tables() {
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- $form['extra'] = array(
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- '#type' => 'item',
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- '#markup' => t('This will REMOVE ALL views integrations (both custom and default) '
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- . 'from your website. This allows integrations to be rebuilt to new default '
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- . 'settings and is especially useful after an upgrade to the views integration system.'),
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- );
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+ $tables = chado_get_table_names(TRUE);
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- $form['description'] = array(
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- '#type' => 'item',
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- '#markup' => t('Are you sure you want to REMOVE ALL Views Integrations (including custom integrations) from your system?'),
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+ $base_tables = array(
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+ 'acquisition', 'analysis', 'assay', 'biomaterial', 'contact', 'cv', 'cvterm',
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+ 'db', 'dbxref', 'environment', 'expression', 'feature', 'featuremap', 'genotype',
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+ 'library', 'nd_experiment', 'nd_geolocation', 'nd_protocol', 'nd_reagent',
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+ 'organism', 'phendesc', 'phenotype', 'phenstatement', 'phylonode', 'phylotree',
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+ 'project', 'protocol', 'pub', 'stock', 'study', 'synonym'
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);
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- $form['actions'] = array('#type' => 'actions');
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-
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- $form['actions']['submit'] = array(
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- '#type' => 'submit',
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- '#value' => t('Confirm'),
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- );
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-
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- $form['actions']['cancel'] = array(
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- '#type' => 'link',
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- '#title' => t('Cancel'),
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- '#href' => 'admin/tripal/views-integration/list',
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- );
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+ foreach ($tables as $tablename) {
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- // By default, render the form using theme_confirm_form().
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- if (!isset($form['#theme'])) {
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- $form['#theme'] = 'confirm_form';
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+ $priority = 10;
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+ if (!tripal_views_is_integrated($tablename, $priority)) {
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+ if (in_array($tablename, $base_tables)) {
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+ $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
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+ }
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+ else {
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+ $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE, $priority);
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+ }
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+ if ($table_integration_array) {
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+ tripal_views_integration_add_entry($table_integration_array);
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+ }
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+ }
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}
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-
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- return $form;
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-}
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-
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-/**
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- * Purpose: Deletes ALL Tripal Views Integrations. This
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- * function is meant to be called from a menu item. After completion it
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- * redirects the user to the views intergation page.
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- *
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- * @ingroup tripal_views
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- */
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-function tripal_views_integration_delete_all_form_submit ($form, &$form_state) {
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-
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- tripal_views_rebuild_views_integrations(TRUE);
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-
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- $form_state['redirect'] = 'admin/tripal/views-integration/list';
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-
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}
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/**
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- * Purpose: defines the web form used for specifing the base table, joins and
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- * handlers when integrating a table with views. This form is used for both
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- * creating a new record and editing an existing record.
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- *
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- * @param $form_state
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- * The form state which is passed automatically by drupal
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- *
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- * @param $setup_id
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- * The unique setup for an integrated table. This value is only set when
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- * the form is used for updating an existing record.
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+ * Returns the array needed to integrate a given chado table with views
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*
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+ * @param $tablename
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+ * The table to generate the tripal views integration array for
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* @return
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- * A proper Drupal form associative array.
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- *
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- * D7 @todo: Add ability to manage custom fields
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- * D7 @todo: Update relationship handler to work with the new tripal_views_join method
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+ * The tripal views integration array which is the parameter for
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+ * tripal_views_integration_add_entry($defn_array)
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*
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* @ingroup tripal_views
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*/
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-function tripal_views_integration_form($form, $form_state, $arg) {
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-
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- $data = array();
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- $form['#cache'] = TRUE;
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- if (isset($form_state['build_info']['args'][0])) {
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- $setup_id = $form_state['build_info']['args'][0];
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- }
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- else {
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- $setup_id = NULL;
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- }
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-
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- // if Ajax is triggered to change the fields table
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- // then make some tweaks before the form is rendered
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- if (isset($form_state['triggering_element'])) {
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-
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- $triggering_element = $form_state['triggering_element']['#name'];
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- if (($triggering_element == 'table_name' OR $triggering_element == 'mview_id')) {
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- $form_state['values'][$triggering_element] = $form_state['triggering_element']['#value'];
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- $setup_id = NULL;
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- }
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- }
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-
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- // if a setup_id is provided then we want to get the form defaults
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- $setup_obj = array();
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- if (isset($setup_id)) {
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-
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- // get the default setup values
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- $sql = "SELECT * FROM {tripal_views} WHERE setup_id = :setup";
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- $setup_obj = db_query($sql, array(':setup' => $setup_id));
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- $setup_obj = $setup_obj->fetchObject();
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- $mview_id = $setup_obj->mview_id;
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- $table_name = $setup_obj->table_name;
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- $form_state['values']['mview_id'] = $mview_id;
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- $form_state['values']['table_name'] = $table_name;
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-
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- // get the default field name/description
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- $sql = "SELECT * FROM {tripal_views_field} WHERE setup_id=:setup";
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- $query = db_query($sql, array(':setup' => $setup_id));
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- $default_fields = array();
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- foreach ($query as $field) {
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- $default_fields[$field->column_name]['name'] = $field->name;
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- $default_fields[$field->column_name]['description'] = $field->description;
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- }
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-
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- // get the default join settings and handlers
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- $sql = "SELECT * FROM {tripal_views_join} WHERE setup_id = :setup";
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- $query = db_query($sql, array(':setup' => $setup_id));
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- $default_joins = array();
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- foreach ($query as $join) {
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- $default_joins[$join->base_field]['left_table'] = $join->left_table;
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- $default_joins[$join->base_field]['left_field'] = $join->left_field;
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- }
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-
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- // get the default handlers
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- $sql = "SELECT * FROM {tripal_views_handlers} WHERE setup_id = :setup";
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- $query = db_query($sql, array(':setup' => $setup_id));
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- $default_handlers = array();
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- foreach ($query as $handler) {
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- $default_handlers[$handler->column_name][$handler->handler_type]['handler_name'] = $handler->handler_name;
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- $default_handlers[$handler->column_name][$handler->handler_type]['arguments'] = $handler->arguments;
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- }
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-
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- // get the default join handlers
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- $sql = "SELECT * FROM {tripal_views_join} WHERE setup_id = :setup";
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- $query = db_query($sql, array(':setup' => $setup_id));
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- foreach ($query as $handler) {
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- $default_handlers[$handler->base_field]['join']['handler_name'] = $handler->handler;
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- //$default_handlers[$handler->base_field]['join']['arguments'] = $handler->arguments;
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- }
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-
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- // add in the setup_id for the form so we know this is an update not an insert
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- $form['setup_id'] = array(
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- '#type' => 'hidden',
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- '#value' => $setup_id,
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- );
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-
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- }
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-
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- // add a fieldset for the MView & Chado table selectors
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- $form['base_table_type'] = array(
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- '#type' => 'fieldset',
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- '#title' => 'Base Table',
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- '#description' => 'Please select either a materialized view or a Chado table for integration with '.
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- 'Drupal Views. In Drupal Views terminology, the selected table becomes the "base table". '.
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- 'After you select a table from either list, the fields from that table will appear below '.
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- 'and you can specify other tables to join with and handlers.',
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- );
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-
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- // build the form element for the Chado tables
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- $chado_tables = chado_get_table_names(TRUE);
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- $chado_tables = array_merge(array('Select'), $chado_tables);
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- $default = '';
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- if ($setup_id) {
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- $default = (!$setup_obj->mview_id) ? $setup_obj->table_name : '';
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- }
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- $form['base_table_type']['table_name'] = array(
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- '#title' => t('Chado/Custom Table'),
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- '#type' => 'select',
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- '#options' => $chado_tables,
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- '#description' => t('Tables from Chado, custom tables and materialized view tables (non-legacy MViews) can be selected for integration.'),
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- '#default_value' => $default,
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- '#ajax' => array(
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- //D6: 'path' => 'tripal/views-integration/ajax/view_setup_table',
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- 'callback' => 'tripal_views_integration_ajax_view_setup_table',
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- 'wrapper' => 'fieldset-table-rows-wrapper',
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- 'effect' => 'fade',
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- 'event' => 'change',
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- 'method' => 'replace',
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- ),
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- );
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-
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-
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- // build the form element that lists the materialized views
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- // D7 TODO: Check DBTNG changes work
|
|
|
- $query = db_query("SELECT mview_id, name FROM {tripal_mviews} WHERE mv_schema is NULL or mv_schema = '' ORDER BY name");
|
|
|
- $mview_tables = array();
|
|
|
- $mview_tables['0'] = 'Select';
|
|
|
- foreach ($query as $mview) {
|
|
|
- $mview_tables[$mview->mview_id] = $mview->name;
|
|
|
- }
|
|
|
- $default = '';
|
|
|
- if ($setup_id && isset($setup_obj->mview_id)) {
|
|
|
- $default = $setup_obj->mview_id;
|
|
|
- }
|
|
|
- $form['base_table_type']['mview_id'] = array(
|
|
|
- '#title' => t('Legacy Materialized View'),
|
|
|
- '#type' => 'select',
|
|
|
- '#options' => $mview_tables,
|
|
|
- '#description' => 'Which materialized view to use.',
|
|
|
- '#default_value' => $default,
|
|
|
- '#ajax' => array(
|
|
|
- //D6: 'path' => 'tripal/views-integration/ajax/view_setup_table',
|
|
|
- 'callback' => 'tripal_views_integration_ajax_view_setup_table',
|
|
|
- 'wrapper' => 'fieldset-table-rows-wrapper',
|
|
|
- 'effect' => 'fade',
|
|
|
- 'event' => 'change',
|
|
|
- 'method' => 'replace',
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- $form['views_type'] = array(
|
|
|
- '#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'] = array(
|
|
|
- '#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'] = array('readonly' => 'readonly');
|
|
|
- }
|
|
|
-
|
|
|
- $priorities = array();
|
|
|
- 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'] = array(
|
|
|
- '#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 '
|
|
|
- .'you definition will be used for that table because -1 is lighter then 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'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Create a New Tripal 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'] = array(
|
|
|
- '#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'] = array(
|
|
|
- '#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
|
|
|
- $form['view_setup_table'] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#prefix' => '<div id="fieldset-table-rows-wrapper">',
|
|
|
- '#suffix' => '</div>',
|
|
|
+function tripal_views_get_integration_array_for_chado_table($table_name, $base_table = TRUE, $priority = 9) {
|
|
|
+
|
|
|
+ // Get the schema for this table (via the chado schema api)
|
|
|
+ $schema = chado_get_schema($table_name);
|
|
|
+
|
|
|
+ // Base definition array
|
|
|
+ $defn_array = array(
|
|
|
+ 'table' => $table_name,
|
|
|
+ 'type' => 'chado',
|
|
|
+ 'name' => 'Chado ' . ucwords(str_replace('_', ' ', $table_name)),
|
|
|
+ 'description' => (!empty($schema['description'])) ? $schema['description'] : ' ',
|
|
|
+ 'priority' => $priority,
|
|
|
+ 'base_table' => $base_table,
|
|
|
+ 'fields' => array(),
|
|
|
);
|
|
|
-
|
|
|
-
|
|
|
- // 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'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t('Table Fields'),
|
|
|
- '#prefix' => '<div id="fieldset-table-rows-wrapper">',
|
|
|
- '#suffix' => '</div>',
|
|
|
- '#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
|
|
|
- $columns = array();
|
|
|
- if ($mview_id) {
|
|
|
- // D7 TODO: Check DBTNG changes work
|
|
|
- $sql = "SELECT mv_specs FROM {tripal_mviews} WHERE mview_id = :id";
|
|
|
- $mview = db_query($sql, array(':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"] = array(
|
|
|
- '#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'] = array();
|
|
|
-
|
|
|
- $form['view_setup_table']['header'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => '<div class="joins-new-row field-headers">',
|
|
|
- '#suffix' => '</div>',
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_table']['header']['column-1'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"column-one\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#markup' => 'Field'
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_table']['header']['column-2'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"column-two\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#markup' => 'Labels'
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_table']['header']['column-3'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"column-three\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#markup' => ''
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_table']['header']['column-4'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"column-four\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#markup' => 'Handlers'
|
|
|
- );
|
|
|
-
|
|
|
- // get the list of chado tables to join on
|
|
|
- $chado_join_tables = chado_get_table_names(TRUE);
|
|
|
- $chado_join_tables = array_merge(array('Select a Join Table'), $chado_join_tables);
|
|
|
-
|
|
|
- // get list of all handlers
|
|
|
- $all_handlers = tripal_views_integration_discover_handlers();
|
|
|
- $handlers_fields = array(0 => "Select a field handler");
|
|
|
- $handlers_filters = array(0 => "Select a filter handler");
|
|
|
- $handlers_sort = array(0 => "Select a sort handler");
|
|
|
- $handlers_argument = array(0 => "Select an argument handler");
|
|
|
- $handlers_join = array(0 => "Select a join handler");
|
|
|
- $handlers_rel = array(0 => "Select a relationship handler");
|
|
|
- foreach ($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"] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"fields-new-row\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#value' => filter_xss('')
|
|
|
- );
|
|
|
-
|
|
|
- // COLUMN I
|
|
|
- $form['view_setup_table']["$table_id-$i"]["fields_name_$table_id-$i"] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#prefix' => "<div class=\"column-one\">",
|
|
|
- '#markup' => '<span class="column-name">' . filter_xss($column_name) . '</span>'.
|
|
|
- '<br /><span class="column-type">' . filter_xss($column_type) . '</span>',
|
|
|
- '#suffix' => "</div>",
|
|
|
- );
|
|
|
- $data['field_types'][$column_name] = $column_type;
|
|
|
-
|
|
|
- // COLUMN II
|
|
|
- $form['view_setup_table']["$table_id-$i"]['column-2'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"column-two\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#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"] = array(
|
|
|
- '#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"] = array(
|
|
|
- '#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'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"column-three\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#value' => filter_xss('')
|
|
|
- );
|
|
|
-
|
|
|
- // COLUMN 4
|
|
|
- $form['view_setup_table']["$table_id-$i"]['column-4'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"column-four\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#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 = $default_handlers[$column_name]['field']['handler_name'];
|
|
|
- $form_state['values']["fields_field_handler_$table_id-$i"] = $default_field_handler;
|
|
|
- }
|
|
|
- else {
|
|
|
- $default_field_handler = $form_state['values']["fields_field_handler_$table_id-$i"];
|
|
|
- if (!$default_field_handler) {
|
|
|
- if ($column_type == 'integer' or $column_type == 'int' or $column_type == 'serial') {
|
|
|
- $default_field_handler = 'chado_views_handler_field_numeric';
|
|
|
- }
|
|
|
- elseif (preg_match("/character varying/", $column_type) or $column_type == 'char' or $column_type == 'text' or $column_type == 'varchar') {
|
|
|
- $default_field_handler = 'chado_views_handler_field';
|
|
|
- }
|
|
|
- elseif ($column_type == 'boolean') {
|
|
|
- $default_field_handler = 'chado_views_handler_field_boolean';
|
|
|
- }
|
|
|
- elseif ($column_type == 'float') {
|
|
|
- $default_field_handler = 'chado_views_handler_field_numeric';
|
|
|
- }
|
|
|
- elseif ($column_type == 'datetime') {
|
|
|
- $default_field_handler = 'chado_views_handler_field_date';
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- $form['view_setup_table']["$table_id-$i"]['column-4']["fields_field_handler_$table_id-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#prefix' => "<div class=\"fields-field-handler\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#options' => $handlers_fields,
|
|
|
- '#required' => FALSE,
|
|
|
- '#default_value' => $default_field_handler,
|
|
|
- );
|
|
|
-
|
|
|
- $default_filter_handler = 0;
|
|
|
- if (isset($setup_id) && !isset($form_state['values']["fields_filter_handler_$table_id-$i"])) {
|
|
|
- $default_filter_handler = $default_handlers[$column_name]['filter']['handler_name'];
|
|
|
- $form_state['values']["fields_filter_handler_$table_id-$i"]= $default_filter_handler;
|
|
|
+ // Add fields
|
|
|
+ if (!isset($schema['fields'])) {
|
|
|
+ tripal_report_error('tripal_views', TRIPAL_NOTICE,
|
|
|
+ 'There are no fields defined for %table in the Chado Schema API.', array('%table' => $table_name));
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ foreach ($schema['fields'] as $field_name => $field_schema) {
|
|
|
+
|
|
|
+ // Base field definition
|
|
|
+ if (!empty($field_name) && !empty($field_schema['type'])) {
|
|
|
+ $defn_array['fields'][$field_name] = array(
|
|
|
+ 'name' => $field_name,
|
|
|
+ 'title' => ucwords(str_replace('_', ' ', $field_name)),
|
|
|
+ 'type' => $field_schema['type'],
|
|
|
+ 'description' => (isset($field_schema['description'])) ? $field_schema['description'] : ucwords(str_replace('_', ' ', $field_name)),
|
|
|
+ 'handlers' => array(),
|
|
|
+ 'joins' => array()
|
|
|
+ );
|
|
|
+
|
|
|
+ // Add handlers based on type
|
|
|
+ if (preg_match('/^int/', $field_schema['type'])) {
|
|
|
+ $defn_array['fields'][$field_name]['handlers'] = array(
|
|
|
+ /** D6
|
|
|
+ 'field' => array('name' => 'chado_views_handler_field_numeric'),
|
|
|
+ 'filter' => array('name' => 'chado_views_handler_filter_numeric'),
|
|
|
+ 'sort' => array('name' => 'chado_views_handler_sort'),
|
|
|
+ */
|
|
|
+ 'field' => array('name' => 'views_handler_field_numeric'),
|
|
|
+ 'filter' => array('name' => 'views_handler_filter_numeric'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort'),
|
|
|
+ );
|
|
|
}
|
|
|
- else {
|
|
|
- $default_filter_handler = $form_state['values']["fields_filter_handler_$table_id-$i"];
|
|
|
- if (!$default_filter_handler) {
|
|
|
- if ($column_type == 'integer' or $column_type == 'int' or $column_type == 'serial') {
|
|
|
- $default_filter_handler = 'chado_views_handler_filter_numeric';
|
|
|
- }
|
|
|
- elseif (preg_match("/^character varying/", $column_type) or $column_type == 'char' or $column_type == 'text' or $column_type == 'varchar') {
|
|
|
- $default_filter_handler = 'chado_views_handler_filter_string';
|
|
|
- }
|
|
|
- elseif ($column_type == 'boolean') {
|
|
|
- $default_filter_handler = 'chado_views_handler_filter_boolean';
|
|
|
- }
|
|
|
- elseif ($column_type == 'float') {
|
|
|
- $default_filter_handler = 'chado_views_handler_filter_float';
|
|
|
- }
|
|
|
- elseif ($column_type == 'datetime') {
|
|
|
- $default_filter_handler = 'chado_views_handler_filter_date';
|
|
|
- }
|
|
|
- }
|
|
|
+ elseif (preg_match('/^serial/', $field_schema['type'])) {
|
|
|
+ $defn_array['fields'][$field_name]['handlers'] = array(
|
|
|
+ /** D6
|
|
|
+ 'field' => array('name' => 'chado_views_handler_field_numeric'),
|
|
|
+ 'filter' => array('name' => 'chado_views_handler_filter_numeric'),
|
|
|
+ 'sort' => array('name' => 'chado_views_handler_sort'),
|
|
|
+ */
|
|
|
+ 'field' => array('name' => 'views_handler_field_numeric'),
|
|
|
+ 'filter' => array('name' => 'views_handler_filter_numeric'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort'),
|
|
|
+ );
|
|
|
+ $defn_array['fields'][$field_name]['type'] = 'int';
|
|
|
+ }
|
|
|
+ elseif (preg_match('/^varchar/', $field_schema['type'])) {
|
|
|
+ $defn_array['fields'][$field_name]['handlers'] = array(
|
|
|
+ /** D6
|
|
|
+ 'field' => array('name' => 'chado_views_handler_field'),
|
|
|
+ 'filter' => array('name' => 'chado_views_handler_filter_string'),
|
|
|
+ 'sort' => array('name' => 'chado_views_handler_sort'),
|
|
|
+ */
|
|
|
+ 'field' => array('name' => 'views_handler_field'),
|
|
|
+ 'filter' => array('name' => 'views_handler_filter_string'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort'),
|
|
|
+ );
|
|
|
}
|
|
|
- $form['view_setup_table']["$table_id-$i"]['column-4']["fields_filter_handler_$table_id-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#prefix' => "<div class=\"fields-filter-handler\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#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 = $default_handlers[$column_name]['sort']['handler_name'];
|
|
|
- $form_state['values']["fields_sort_handler_$table_id-$i"] = $default_sort_handler;
|
|
|
+ elseif (preg_match('/^text/', $field_schema['type'])) {
|
|
|
+ $defn_array['fields'][$field_name]['handlers'] = array(
|
|
|
+ /** D6
|
|
|
+ 'field' => array('name' => 'chado_views_handler_field'),
|
|
|
+ 'filter' => array('name' => 'chado_views_handler_filter_string'),
|
|
|
+ 'sort' => array('name' => 'chado_views_handler_sort'),
|
|
|
+ */
|
|
|
+ 'field' => array('name' => 'views_handler_field'),
|
|
|
+ 'filter' => array('name' => 'views_handler_filter_string'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort'),
|
|
|
+ );
|
|
|
}
|
|
|
- else {
|
|
|
- $default_sort_handler = $form_state['values']["fields_sort_handler_$table_id-$i"];
|
|
|
- if (!$default_sort_handler) {
|
|
|
- if ($column_type == 'integer' or $column_type == 'int' or $column_type == 'serial') {
|
|
|
- $default_sort_handler = 'chado_views_handler_sort';
|
|
|
- }
|
|
|
- elseif (preg_match("/character varying/", $column_type) or $column_type == 'char' or $column_type == 'text' or $column_type == 'varchar') {
|
|
|
- $default_sort_handler = 'chado_views_handler_sort';
|
|
|
- }
|
|
|
- elseif ($column_type == 'boolean') {
|
|
|
- $default_sort_handler = 'chado_views_handler_sort';
|
|
|
- }
|
|
|
- elseif ($column_type == 'float') {
|
|
|
- $default_sort_handler = 'chado_views_handler_sort';
|
|
|
- }
|
|
|
- elseif ($column_type == 'datetime') {
|
|
|
- $default_sort_handler = 'chado_views_handler_sort_date';
|
|
|
- }
|
|
|
- }
|
|
|
+ elseif (preg_match('/^boolean/', $field_schema['type'])) {
|
|
|
+ $defn_array['fields'][$field_name]['handlers'] = array(
|
|
|
+ /**
|
|
|
+ 'field' => array('name' => 'chado_views_handler_field_boolean'),
|
|
|
+ 'filter' => array('name' => 'chado_views_handler_filter_boolean_operator'),
|
|
|
+ 'sort' => array('name' => 'chado_views_handler_sort'),
|
|
|
+ */
|
|
|
+ 'field' => array('name' => 'views_handler_field_boolean'),
|
|
|
+ 'filter' => array('name' => 'views_handler_filter_boolean_operator'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort'),
|
|
|
+ );
|
|
|
}
|
|
|
- $form['view_setup_table']["$table_id-$i"]['column-4']["fields_sort_handler_$table_id-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#prefix' => "<div class=\"fields-sort-handler\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#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 ;
|
|
|
+ elseif (preg_match('/^datetime/', $field_schema['type'])) {
|
|
|
+ $defn_array['fields'][$field_name]['handlers'] = array(
|
|
|
+ /** D6
|
|
|
+ 'field' => array('name' => 'chado_views_handler_field_date'),
|
|
|
+ 'filter' => array('name' => 'chado_views_handler_filter_date'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort_date'),
|
|
|
+ */
|
|
|
+ 'field' => array('name' => 'views_handler_field_date'),
|
|
|
+ 'filter' => array('name' => 'views_handler_filter_date'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort_date'),
|
|
|
+ );
|
|
|
}
|
|
|
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';
|
|
|
- }
|
|
|
- }
|
|
|
+ $defn_array['fields'][$field_name]['handlers'] = array(
|
|
|
+ /** D6
|
|
|
+ 'field' => array('name' => 'chado_views_handler_field'),
|
|
|
+ 'filter' => array('name' => 'chado_views_handler_filter_string'),
|
|
|
+ 'sort' => array('name' => 'chado_views_handler_sort'),
|
|
|
+ */
|
|
|
+ 'field' => array('name' => 'views_handler_field'),
|
|
|
+ 'filter' => array('name' => 'views_handler_filter_string'),
|
|
|
+ 'sort' => array('name' => 'views_handler_sort'),
|
|
|
+ );
|
|
|
}
|
|
|
- $form['view_setup_table']["$table_id-$i"]['column-4']["fields_argument_handler_$table_id-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#prefix' => "<div class=\"fields-argument-handler\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#options' => $handlers_argument,
|
|
|
- '#required' => FALSE,
|
|
|
- '#default_value' => $default_argument_handler,
|
|
|
- );
|
|
|
-
|
|
|
- $i++;
|
|
|
- }
|
|
|
-
|
|
|
- $form['view_setup_join'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t('Joins & Relationships'),
|
|
|
- '#prefix' => '<div id="fieldset-join-rows-wrapper">',
|
|
|
- '#suffix' => '</div>',
|
|
|
- '#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'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => '<div class="joins-new-row field-headers">',
|
|
|
- '#suffix' => '</div>',
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']['header']['column-1'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"join-column-one\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#markup' => 'Base'
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']['header']['column-2'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"join-column-two\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#markup' => 'Handlers'
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']['header']['column-3'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"join-column-three\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#markup' => 'Joined to'
|
|
|
- );
|
|
|
-
|
|
|
- $base_field_options = array('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]);
|
|
|
-
|
|
|
- $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"] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"joins-new-row\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#value' => filter_xss('')
|
|
|
- );
|
|
|
-
|
|
|
- // COLUMN I
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-1'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"join-column-one\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-1']['join_base_table'] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#markup' => '<span class="column-name">' . filter_xss($result->base_table) . '</span>'
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-1']["join_base_table-$i"] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $result->base_table
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-1']["join_base_field-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#options' => $base_field_options,
|
|
|
- '#required' => FALSE,
|
|
|
- '#default_value' => $result->base_field
|
|
|
- );
|
|
|
-
|
|
|
- // COLUMN II
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-2'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"join-column-two\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#value' => filter_xss('')
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-2']["join_join_handler-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#prefix' => "<div class=\"fields-join-handler\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#options' => $handlers_join,
|
|
|
- '#required' => FALSE,
|
|
|
- '#default_value' => $result->handler,
|
|
|
- );
|
|
|
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-2']["join_relationship_handler-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#prefix' => "<div class=\"fields-relationship-handler\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#options' => $handlers_rel,
|
|
|
- '#required' => FALSE,
|
|
|
- '#default_value' => $result->relationship_handler,
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-2']["join_relationship_only-$i"] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => 'Relationship Only?',
|
|
|
- '#default_value' => $result->relationship_only
|
|
|
- );
|
|
|
-
|
|
|
- // COLUMN III
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-3'] = array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#prefix' => "<div class=\"join-column-three\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#value' => filter_xss('')
|
|
|
- );
|
|
|
-
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-3']["join_left_table-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#options' => $chado_join_tables,
|
|
|
- '#default_value' => $result->left_table,
|
|
|
- );
|
|
|
-
|
|
|
- $columns = array();
|
|
|
- if ($result->left_table) {
|
|
|
- // get the table description
|
|
|
- $table_desc = chado_get_schema($result->left_table);
|
|
|
- foreach ($table_desc['fields'] as $column => $def) {
|
|
|
- $columns[$column] = $column;
|
|
|
- }
|
|
|
+ // Specify specialty handlers
|
|
|
+ if ($field_name == 'type_id' OR $field_name == 'cvterm_id') {
|
|
|
+ $defn_array['fields'][$field_name]['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_cvterm';
|
|
|
}
|
|
|
- else {
|
|
|
- $columns = array('Select Left Column');
|
|
|
+ if (preg_match('/name/',$field_name)) {
|
|
|
+ $defn_array['fields'][$field_name]['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_string';
|
|
|
}
|
|
|
- $form['view_setup_join']["$table_id-$i"]['column-3']["join_left_field-$i"] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#prefix' => " <div id=\"fields-column-join-column-$table_id-$i\" class=\"fields-column-join-column\">",
|
|
|
- '#suffix' => "</div>",
|
|
|
- '#options' => $columns,
|
|
|
- '#required' => FALSE,
|
|
|
- '#default_value' => $result->left_field
|
|
|
- );
|
|
|
- }
|
|
|
-
|
|
|
- $form['num_joins'] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $i
|
|
|
- );
|
|
|
-
|
|
|
- $form['save'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => t('Save'),
|
|
|
- );
|
|
|
-
|
|
|
- $data['row_count'] = $i - 1;
|
|
|
- } //end of if table/mview
|
|
|
-
|
|
|
- //use this to put values into $form_state['values']
|
|
|
- $form['data'] = array();
|
|
|
-
|
|
|
- // Ensure that we don't store an array
|
|
|
- // since we will get a check_plain:htmlspecial_characters error if we do
|
|
|
- foreach ($data as $key => $value) {
|
|
|
- if (is_array($value)) {
|
|
|
- $form['data'][$key] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => serialize($value),
|
|
|
- );
|
|
|
- }
|
|
|
- else {
|
|
|
- $form['data'][$key] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $value,
|
|
|
- );
|
|
|
}
|
|
|
}
|
|
|
|
|
|
- $form['#redirect'] = 'admin/tripal/views-integration/list';
|
|
|
-
|
|
|
- return $form;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Purpose: validates the tripal_views_integration_form after submission
|
|
|
- *
|
|
|
- * @param $form
|
|
|
- * The form object which is passed automatically by drupal
|
|
|
- *
|
|
|
- * @param $form_state
|
|
|
- * The form state pbject which is passed automatically by drupal
|
|
|
- *
|
|
|
- * @ingroup tripal_views
|
|
|
- */
|
|
|
-function tripal_views_integration_form_validate($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.');
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * 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 $form_state
|
|
|
- * The form state pbject which is passed automatically by drupal
|
|
|
- *
|
|
|
- * @ingroup tripal_views
|
|
|
- */
|
|
|
-function tripal_views_integration_form_submit($form, &$form_state) {
|
|
|
- $name = $form_state['values']['row_name'];
|
|
|
- $mview_id = $form_state['values']['mview_id'];
|
|
|
- $table_name = $form_state['values']['table_name'];
|
|
|
- $setup_id = $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, array(':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
|
|
|
- $tripal_views_record = array();
|
|
|
- if ($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, array(':id' => $mview_id));
|
|
|
- $mview = $mview->fetchObject();
|
|
|
-
|
|
|
- // build the record for insert/update
|
|
|
- $tripal_views_record = array(
|
|
|
- '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 = array(
|
|
|
- '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', $tripal_views_record)) {
|
|
|
- drupal_set_message(t("Failed to add record."), 'error');
|
|
|
- return;
|
|
|
- }
|
|
|
+ // Add Joins & Relationships for foreign keys to fields
|
|
|
+ if (!isset($schema['foreign keys'])) {
|
|
|
+ $schema['foreign keys'] = array();
|
|
|
}
|
|
|
- else { // this is an update
|
|
|
- // check to see if it was specified to create a new integration
|
|
|
- if ($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', $tripal_views_record, array('setup_id'))) {
|
|
|
- drupal_set_message(t("Failed to update record."), 'error');
|
|
|
- return;
|
|
|
- }
|
|
|
+ foreach ($schema['foreign keys'] as $foreign_key_schema) {
|
|
|
+ foreach ($foreign_key_schema['columns'] as $left_field => $right_field) {
|
|
|
+ // Join
|
|
|
+ $defn_array['fields'][$left_field]['joins'][ $foreign_key_schema['table'] ] = array(
|
|
|
+ 'table' => $foreign_key_schema['table'],
|
|
|
+ 'field' => $right_field,
|
|
|
+ /**D6 'handler' => 'views_handler_join_chado_aggregator'*/
|
|
|
+ 'handler' => 'views_handler_join',
|
|
|
+ 'relationship_handler' => 'views_handler_relationship',
|
|
|
+ );
|
|
|
}
|
|
|
}
|
|
|
|
|
|
- // if this is an update then clean out the existing joins and handlers so we can add new ones
|
|
|
- if ($setup_id) {
|
|
|
- db_query("DELETE FROM {tripal_views_field} WHERE setup_id = :setup", array(':setup' => $setup_id));
|
|
|
- db_query("DELETE FROM {tripal_views_join} WHERE setup_id = :setup", array(':setup' => $setup_id));
|
|
|
- db_query("DELETE FROM {tripal_views_handlers} WHERE setup_id = :setup", array(':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 = array(
|
|
|
- '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', $view_field_record);
|
|
|
+ // Add in reverse relationships
|
|
|
+ if (isset($schema['referring_tables'])) {
|
|
|
+ foreach ($schema['referring_tables'] as $referring_table) {
|
|
|
|
|
|
- // add the hanlders
|
|
|
- $handlers = array('filter', 'field', 'sort', 'argument');
|
|
|
-
|
|
|
- foreach ($handlers as $handler) {
|
|
|
- $handler_name = $form_state['values']["fields_" . $handler . "_handler_$table_id-$i"];
|
|
|
- if ($handler_name) {
|
|
|
- $handler_record = array(
|
|
|
- 'setup_id' => $tripal_views_record['setup_id'],
|
|
|
- 'column_name' => $key,
|
|
|
- 'handler_type' => $handler,
|
|
|
- 'handler_name' => $handler_name,
|
|
|
+ // D7 @todo: fix referring_tables in schema to list the keys like foreign keys does
|
|
|
+ $referring_schema = chado_get_schema($referring_table);
|
|
|
+ $referring_schema_fk_columns = $referring_schema['foreign keys'][$table_name]['columns'];
|
|
|
+ foreach ($referring_schema_fk_columns as $left_field => $right_field) {
|
|
|
+ $defn_array['fields'][$right_field]['joins'][ $referring_table ] = array(
|
|
|
+ 'table' => $referring_table,
|
|
|
+ 'field' => $left_field,
|
|
|
+ 'relationship_handler' => 'views_handler_relationship',
|
|
|
+ 'relationship_only' => 1
|
|
|
);
|
|
|
- drupal_write_record('tripal_views_handlers', $handler_record);
|
|
|
}
|
|
|
}
|
|
|
- $i++;
|
|
|
- }
|
|
|
-
|
|
|
- // Now add all the joins
|
|
|
- for($i = 0; $i <= $form_state['values']['num_joins']; $i++) {
|
|
|
- $join_record = array(
|
|
|
- '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', $join_record);
|
|
|
- }
|
|
|
-
|
|
|
- if ($setup_id) {
|
|
|
- drupal_set_message(t('Record Updated'));
|
|
|
- }
|
|
|
- else {
|
|
|
- drupal_set_message(t('Record Added'));
|
|
|
- }
|
|
|
-
|
|
|
- $form_state['redirect'] = 'admin/tripal/views-integration/list';
|
|
|
-
|
|
|
- // now clear all the caches so that Drupal views picks up our chages
|
|
|
- views_invalidate_cache();
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * 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_views
|
|
|
- */
|
|
|
-function tripal_views_integration_discover_handlers() {
|
|
|
-
|
|
|
- $handlers = array();
|
|
|
-
|
|
|
- // 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_float';
|
|
|
- $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 $handlers;
|
|
|
-}
|
|
|
-
|
|
|
-/*
|
|
|
- * Ajax Callback: Tripal Views Integration Form
|
|
|
- * Replaces the entire fields table when the table or materialized view is set/changed
|
|
|
- *
|
|
|
- * @ingroup tripal_views
|
|
|
- */
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-function tripal_views_integration_ajax_view_setup_table($form, $form_state) {
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- return $form['view_setup_table'];
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|
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-}
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-
|
|
|
-/*
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|
- * Ajax Callback: Tripal Views Integration Form
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|
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- * Replaces the join db field dropdown when the join table dropdown is changed
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- *
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- * @ingroup tripal_views
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|
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- */
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-function tripal_views_integration_ajax_join_field($form, $form_state) {
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-
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- // Determine which row we are dealing with from the name of the triggering element
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- if (preg_match('/fields_join_(\w+-\d+)/', $form_state['triggering_element']['#name'], $matches)) {
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- $field = $matches[1];
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- $join_field = 'fields_join_column_' . $matches[1];
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- // return the form element to be updated
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- return $form['view_setup_table'][$field]['column-3'][$join_field];
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|
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- }
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- else {
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|
- tripal_report_error('tripal_views', TRIPAL_ERROR,
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|
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- 'Tripal Views Integration Ajax failed due to being unable to determine which row needs updating', array());
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- return $form;
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|
|
- }
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-}
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+ return $defn_array;
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+}
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Lacey Sanderson