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@@ -46,261 +46,7 @@ function tripal_feature_admin_feature_view() {
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*/
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function tripal_feature_admin() {
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- /*
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- // before proceeding check to see if we have any
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- // currently processing jobs. If so, we don't want
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- // to give the opportunity to sync libraries
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- $active_jobs = FALSE;
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- if (tripal_get_module_active_jobs('tripal_feature')) {
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- $active_jobs = TRUE;
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- }
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- if (!$active_jobs) {
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-*/
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- get_tripal_feature_admin_form_title_set($form);
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- get_tripal_feature_admin_form_url_set($form);
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-
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- $form['browser'] = array(
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- '#type' => 'fieldset',
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- '#title' => t('Feature Browser'),
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- '#collapsible' => TRUE,
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- '#collapsed' => FALSE,
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- );
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- $allowedoptions1 = array(
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- 'show_feature_browser' => "Show the feature browser on the organism page. The browser loads when page loads. This may be slow for large sites.",
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- 'hide_feature_browser' => "Hide the feature browser on the organism page. Disables the feature browser completely.",
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- );
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- // $allowedoptions ['allow_feature_browser'] = "Allow loading of the feature browsing through AJAX. For large sites the initial page load will be quick with the feature browser loading afterwards.";
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-
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- $form['browser']['browser_desc'] = array(
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- '#markup' => t('A feature browser can be added to an organism page to allow users to quickly ' .
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- 'access a feature. This will most likely not be the ideal mechanism for accessing feature ' .
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- 'information, especially for large sites, but it will alow users exploring the site (such ' .
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- 'as students) to better understand the data types available on the site.'),
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-
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- );
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- $form['browser']['feature_types'] = array(
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- '#title' => t('Feature Types'),
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- '#type' => 'textarea',
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- '#description' => t("Enter the Sequence Ontology (SO) terms for the feature types that " .
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- "will be shown in the feature browser."),
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- '#default_value' => variable_get('chado_browser_feature_types', 'gene mRNA'),
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- );
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-
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-
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- $form['browser']['browse_features'] = array(
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- '#title' => 'Feature Browser on Organism Page',
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- '#type' => 'radios',
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- '#options' => $allowedoptions1,
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- '#default_value' => variable_get('tripal_feature_browse_setting', 'show_feature_browser'),
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- );
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-
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- $form['browser']['browse_features_library'] = array(
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- '#title' => 'Feature Browser on Library Page',
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- '#type' => 'radios',
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- '#options' => array(
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- 'show_feature_browser' => "Show the feature browse on the library page. The browser loads when page loads. This may be slow for large sites.",
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- 'hide_feature_browser' => "Hide the feature browser on the library page. Disables the feature browser completely.",
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- ),
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- '#default_value' => variable_get('tripal_library_feature_browse_setting', 'show_feature_browser'),
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- );
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-
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- $form['browser']['browse_features_analysis'] = array(
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- '#title' => 'Feature Browser on Analysis Page',
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- '#type' => 'radios',
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- '#options' => array(
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- 'show_feature_browser' => "Show the feature browse on the analysis page. The browser loads when page loads. This may be slow for large sites.",
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- 'hide_feature_browser' => "Hide the feature browser on the analysis page. Disables the feature browser completely.",
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- ),
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- '#default_value' => variable_get('tripal_analysis_feature_browse_setting', 'show_feature_browser'),
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- );
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-
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- $form['browser']['set_browse_button'] = array(
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- '#type' => 'submit',
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- '#value' => t('Set Browser'),
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- '#weight' => 2,
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- );
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-
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- $form['summary'] = array(
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- '#type' => 'fieldset',
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- '#title' => t('Feature Summary Report'),
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- '#collapsible' => TRUE,
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- '#collapsed' => FALSE,
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- );
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- $allowedoptions2 ['show_feature_summary'] = "Show the feature summary on the organism page. The summary loads when page loads.";
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- $allowedoptions2 ['hide_feature_summary'] = "Hide the feature summary on the organism page. Disables the feature summary.";
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-
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- $form['summary']['feature_summary'] = array(
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- '#title' => 'Feature Summary on Organism Page',
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- '#description' => 'A feature summary can be added to an organism page to allow users to see the ' .
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- 'type and quantity of features available for the organism.',
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- '#type' => 'radios',
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- '#options' => $allowedoptions2,
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- '#default_value' => variable_get('tripal_feature_summary_setting', 'show_feature_summary'),
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- );
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- $form['summary']['feature_mapping'] = array(
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- '#title' => 'Map feature types',
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- '#description' => t('You may specify which Sequence Ontology (SO) terms to show in the ' .
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- 'feature summary report by listing them in the following text area. Enter one per line. ' .
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- 'If left blank, all SO terms for all features will be shown in the report. Only those terms ' .
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- 'listed below will be shown in the report. Terms will appear in the report in the same order listed. To rename a ' .
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- 'SO term to be more human readable form, use an \'=\' sign after the SO term (e.g. \'polypeptide = Protein\')'),
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- '#type' => 'textarea',
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- '#rows' => 15,
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- '#default_value' => variable_get('tripal_feature_summary_report_mapping', ''),
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- );
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- $form['summary']['set_summary_button'] = array(
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- '#type' => 'submit',
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- '#value' => t('Set Summary'),
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- '#weight' => 2,
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- );
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-
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- get_tripal_feature_admin_form_taxonomy_set($form);
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-// get_tripal_feature_admin_form_reindex_set($form);
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-/* }
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- else {
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- $form['notice'] = array(
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- '#type' => 'fieldset',
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- '#title' => t('Feature Management Temporarily Unavailable'),
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- '#collapsible' => FALSE,
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- '#collapsed' => FALSE,
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- );
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- $form['notice']['message'] = array(
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- '#value' => t('Currently, feature management jobs are waiting or " .
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- "are running. Managemment features have been hidden until these " .
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- "jobs complete. Please check back later once these jobs have " .
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- "finished. You can view the status of pending jobs in the Tripal " .
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- "jobs page.'),
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- );
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- }
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- */
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- return system_settings_form($form);
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-}
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-
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-/**
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- * Validate the feature settings forms
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- *
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- * @ingroup tripal_feature
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- */
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-function tripal_feature_admin_validate($form, &$form_state) {
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- global $user; // we need access to the user info
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- $job_args = array();
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-
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- variable_set('chado_browser_feature_types', $form_state['values']['feature_types']);
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-
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- switch ($form_state['values']['op']) {
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-
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- case t('Set/Reset Taxonomy for all feature nodes') :
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- tripal_add_job('Set all feature taxonomy', 'tripal_feature',
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- 'tripal_features_set_taxonomy', $job_args, $user->uid);
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- break;
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-
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- case t('Reindex all feature nodes') :
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- tripal_add_job('Reindex all features', 'tripal_feature',
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- 'tripal_features_reindex', $job_args, $user->uid);
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- break;
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-
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- case t('Set Browser') :
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- variable_set('tripal_feature_browse_setting', $form_state['values']['browse_features']);
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- variable_set('tripal_library_feature_browse_setting', $form_state['values']['browse_features_library']);
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- variable_set('tripal_analysis_feature_browse_setting', $form_state['values']['browse_features_analysis']);
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- break;
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-
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- case t('Set Summary') :
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- variable_set('tripal_feature_summary_setting', $form_state['values']['feature_summary']);
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- variable_set('tripal_feature_summary_report_mapping', $form_state['values']['feature_mapping']);
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- break;
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-
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- case t('Set Feature URLs') :
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- variable_set('chado_feature_url', $form_state['values']['feature_url']);
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- tripal_add_job('Set Feature URLs', 'tripal_feature',
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- 'tripal_feature_set_urls', $job_args, $user->uid);
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- break;
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- }
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-
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-}
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-
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-/**
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- * Form: Reindex feature nodes for the drupal search
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- *
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- * @ingroup tripal_feature
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- */
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-function get_tripal_feature_admin_form_reindex_set(&$form) {
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- $form['reindex'] = array(
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- '#type' => 'fieldset',
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- '#title' => t('Index/Reindex'),
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- '#collapsible' => TRUE,
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- '#collapsed' => TRUE,
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- );
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- $form['reindex']['description'] = array(
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- '#type' => 'item',
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- '#value' => t("Indexing or reindexing of nodes is required for Drupal's full text searching. " .
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- "Index features for the first time to allow for searching of content, and later when content for features " .
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- "is updated. Depending on the number of features this may take " .
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- "quite a while. Click the button below to begin reindexing of " .
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- "features. "),
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- '#weight' => 1,
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- );
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- $form['reindex']['button'] = array(
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- '#type' => 'submit',
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- '#value' => t('Reindex all feature nodes'),
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- '#weight' => 2,
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- );
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-}
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-
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-/**
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- * Form: Set taxonomy for features
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- *
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- * @ingroup tripal_feature
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- */
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-function get_tripal_feature_admin_form_taxonomy_set(&$form) {
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-
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- $form['taxonomy'] = array(
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- '#type' => 'fieldset',
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- '#title' => t('Set Taxonomy'),
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- '#collapsible' => TRUE,
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- '#collapsed' => TRUE,
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- );
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-
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- $form['taxonomy']['description'] = array(
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- '#type' => 'item',
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- '#value' => t("Drupal allows for assignment of \"taxonomy\" or " .
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- "catagorical terms to nodes. These terms allow for advanced " .
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- "filtering during searching."),
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- '#weight' => 1,
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- );
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- $tax_options = array(
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- 'organism' => t('Organism name'),
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- 'feature_type' => t('Feature Type (e.g. EST, mRNA, etc.)'),
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- 'analysis' => t('Analysis Name'),
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- 'library' => t('Library Name'),
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- );
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- $form['taxonomy']['tax_classes'] = array(
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- '#title' => t('Available Taxonomic Classes'),
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- '#type' => t('checkboxes'),
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- '#description' => t("Please select the class of terms to assign to " .
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- "chado features"),
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- '#required' => FALSE,
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- '#prefix' => '<div id="taxclass_boxes">',
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- '#suffix' => '</div>',
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- '#options' => $tax_options,
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- '#weight' => 2,
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- '#default_value' => variable_get('tax_classes', array()),
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- );
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- $form['taxonomy']['button'] = array(
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- '#type' => 'submit',
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- '#value' => t('Set/Reset Taxonomy for all feature nodes'),
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- '#weight' => 3,
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- );
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-
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-}
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-
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-/**
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- * Form: Set the definition of titles for features
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- *
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- * @ingroup tripal_feature
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- */
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-function get_tripal_feature_admin_form_title_set(&$form) {
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-
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+ // FEATURE PAGE TITLES
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$form['title'] = array(
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'#type' => 'fieldset',
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'#title' => t('Feature Page Titles'),
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@@ -308,11 +54,12 @@ function get_tripal_feature_admin_form_title_set(&$form) {
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'#collapsed' => FALSE,
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);
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$form['title']['desc'] = array(
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- '#markup' => t('Each synced feature must have a unique page title, however, features
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- may have the same name if they are of different types or from
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- different organisms. Therefore, we must be sure that the
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- page titles can uniquely identify the feature being viewed. Select
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- an option below that will uniquely identify all features on your site.'),
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+ '#markup' => t(
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+ 'Each synced feature must have a unique page title, however, features
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+ may have the same name if they are of different types or from
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+ different organisms. Therefore, we must be sure that the
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+ page titles can uniquely identify the feature being viewed. Select
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+ an option below that will uniquely identify all features on your site.'),
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);
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$options = array(
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'feature_unique_name' => 'Feature unique name',
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@@ -330,22 +77,15 @@ function get_tripal_feature_admin_form_title_set(&$form) {
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'#options' => $options,
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'#default_value' => variable_get('chado_feature_title', 'unique_constraint'),
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);
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-}
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-
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-/**
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- * Form: Set the URL definition for feature nodes
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- *
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- * @ingroup tripal_feature
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- */
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-function get_tripal_feature_admin_form_url_set(&$form) {
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-
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+
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+ // FEATURE URL PATHS
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$form['url'] = array(
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'#type' => 'fieldset',
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'#title' => t('Feature URL Path'),
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'#collapsible' => TRUE,
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'#collapsed' => FALSE,
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);
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-
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+
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$options = array(
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'SID[id]' => '[id]:' . t('The Chado feature_id'),
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'feature' => 'feature:' . t('Chado table name'),
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@@ -356,23 +96,22 @@ function get_tripal_feature_admin_form_url_set(&$form) {
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'[name]' => '[name]:' . t('The feature name'),
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'reset' => t('Reset'),
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);
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-
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-
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+
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$form['url']['chado_feature_url_string'] = array(
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'#title' => 'URL Syntax',
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'#type' => 'textfield',
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'#description' => t('You may rearrange elements in this text box to
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- customize the URLs. The available tags include: [id],
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- [uniquename]. [name], [species], [genus], [type]. You can separate or
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- include any text between the tags. Click the "Set Feature URLs" button to
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- reset the URLs for all feature pages. Click the "Save Configuration" button to
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- simply save this setup. <b>Important</b>: be sure that whatever you choose will always be unique even considering
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- future data that may be added. If you include the Chado table name, genus, species, type
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- and uniquename you are guaranteed to have a unique URL. For example feature/[genus]/[species]/[type]/[uniquename]'),
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+ customize the URLs. The available tags include: [id],
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+ [uniquename]. [name], [species], [genus], [type]. You can separate or
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+ include any text between the tags. Click the "Set Feature URLs" button to
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+ reset the URLs for all feature pages. Click the "Save Configuration" button to
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+ simply save this setup. <b>Important</b>: be sure that whatever you choose will always be unique even considering
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+ future data that may be added. If you include the Chado table name, genus, species, type
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+ and uniquename you are guaranteed to have a unique URL. For example feature/[genus]/[species]/[type]/[uniquename]'),
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'#size' => 150,
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'#default_value' => variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]'),
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);
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-
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+
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$form['url']['chado_feature_url'] = array(
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'#title' => t('URL components'),
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'#type' => 'checkboxes',
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@@ -381,340 +120,154 @@ function get_tripal_feature_admin_form_url_set(&$form) {
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'#description' => t('Click the item above to make it appear in the URL Syntax box'),
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'#attributes' => array(
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'onclick' => '
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- box = $(\'#edit-chado-feature-url-string\');
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- if (this.value == \'reset\') {
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- box.val(\'\');
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- }
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- else {
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- box.val(box.val() + "/" + this.value);
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- }
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- this.checked = false;
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- ',
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+ box = $(\'#edit-chado-feature-url-string\');
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+ if (this.value == \'reset\') {
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+ box.val(\'\');
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+ }
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+ else {
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+ box.val(box.val() + "/" + this.value);
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+ }
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+ this.checked = false;
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+ ',
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),
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);
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-
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+
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$form['url']['button'] = array(
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'#type' => 'submit',
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'#value' => t('Set Feature URLs'),
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);
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-}
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-
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-/**
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- * Set feature taxonomy
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- *
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- * @ingroup tripal_feature
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- */
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-function tripal_features_set_taxonomy($max_sync = 0, $job_id = NULL) {
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-
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- // make sure our vocabularies are cleaned and reset before proceeding
|
|
|
- tripal_feature_del_vocabulary();
|
|
|
- tripal_feature_set_vocabulary();
|
|
|
-
|
|
|
- // iterate through all drupal feature nodes and set the taxonomy
|
|
|
- $results = db_query("SELECT * FROM {chado_feature}");
|
|
|
- $nsql = "
|
|
|
- SELECT * FROM {node}
|
|
|
- WHERE nid = :nid
|
|
|
- ";
|
|
|
- $i = 0;
|
|
|
-
|
|
|
- // load into ids array
|
|
|
- $count = 0;
|
|
|
- $chado_features = array();
|
|
|
- while ($chado_feature = $results->fetchObject()) {
|
|
|
- $chado_features[$count] = $chado_feature;
|
|
|
- $count++;
|
|
|
- }
|
|
|
-
|
|
|
- // Iterate through features that need to be synced
|
|
|
- $interval = intval($count * 0.01);
|
|
|
- foreach ($chado_features as $chado_feature) {
|
|
|
-
|
|
|
- // update the job status every 1% features
|
|
|
- if ($job_id and $i % $interval == 0) {
|
|
|
- tripal_set_job_progress($job_id, intval(($i/$count)*100));
|
|
|
- }
|
|
|
- print "$i of $count: ";
|
|
|
- $node = db_query($nsql, array(':nid' => $chado_feature->nid))->fetchObject();
|
|
|
- tripal_feature_set_taxonomy($node, $chado_feature->feature_id);
|
|
|
-
|
|
|
- $i++;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Set taxonomy for a single feature
|
|
|
- *
|
|
|
- * @ingroup tripal_feature
|
|
|
- */
|
|
|
-function tripal_feature_set_taxonomy($node, $feature_id) {
|
|
|
-
|
|
|
- // iterate through the taxonomy classes that have been
|
|
|
- // selected by the admin user and make sure we only set those
|
|
|
- $tax_classes = variable_get('tax_classes', array());
|
|
|
- $do_ft = 0;
|
|
|
- $do_op = 0;
|
|
|
- $do_lb = 0;
|
|
|
- $do_an = 0;
|
|
|
- foreach ($tax_classes as $class) {
|
|
|
- if (strcmp($class , 'organism')==0) {
|
|
|
- $do_op = 1;
|
|
|
- }
|
|
|
- if (strcmp($class, 'feature_type')==0) {
|
|
|
- $do_ft = 1;
|
|
|
- }
|
|
|
- if (strcmp($class, 'library')==0) {
|
|
|
- $do_lb = 1;
|
|
|
- }
|
|
|
- if (strcmp($class, 'analysis')==0) {
|
|
|
- $do_an = 1;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
-
|
|
|
- // get the list of vocabularies and find our two vocabularies of interest
|
|
|
- $vocabularies = taxonomy_get_vocabularies();
|
|
|
- $ft_vid = NULL;
|
|
|
- $op_vid = NULL;
|
|
|
- $lb_vid = NULL;
|
|
|
- $an_vid = NULL;
|
|
|
- foreach ($vocabularies as $vocab) {
|
|
|
- if ($vocab->name == 'Feature Type') {
|
|
|
- $ft_vid = $vocab->vid;
|
|
|
- }
|
|
|
- if ($vocab->name == 'Organism') {
|
|
|
- $op_vid = $vocab->vid;
|
|
|
- }
|
|
|
- if ($vocab->name == 'Library') {
|
|
|
- $lb_vid = $vocab->vid;
|
|
|
- }
|
|
|
- if ($vocab->name == 'Analysis') {
|
|
|
- $an_vid = $vocab->vid;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // get the cvterm and the organism for this feature
|
|
|
- $sql = "
|
|
|
- SELECT CVT.name AS cvname, O.genus, O.species
|
|
|
- FROM {cvterm} CVT
|
|
|
- INNER JOIN {feature} F on F.type_id = CVT.cvterm_id
|
|
|
- INNER JOIN {organism} O ON F.organism_id = O.organism_id
|
|
|
- WHERE F.feature_id = :feature_id
|
|
|
- ";
|
|
|
- $feature = chado_query($sql, array(':feature_id' => $feature_id))->fetchObject();
|
|
|
-
|
|
|
- // Set the feature type for this feature
|
|
|
- if ($do_ft && $ft_vid) {
|
|
|
- $tags["$ft_vid"] = "$feature->cvname";
|
|
|
- }
|
|
|
- // Set the organism for this feature type
|
|
|
- if ($do_op && $op_vid) {
|
|
|
- $tags["$op_vid"] = "$feature->genus $feature->species";
|
|
|
- }
|
|
|
-
|
|
|
- // get the library that this feature may belong to and add it as taxonomy
|
|
|
- if ($do_lb && $lb_vid) {
|
|
|
- $sql = "
|
|
|
- SELECT L.name
|
|
|
- FROM {Library} L
|
|
|
- INNER JOIN {Library_feature} LF ON LF.library_id = L.library_id
|
|
|
- WHERE LF.feature_id = :feature_id
|
|
|
- ";
|
|
|
- $library = chado_query($sql, array(':feature_id' => $feature_id))->fetchObject();
|
|
|
- $tags["$lb_vid"] = "$library->name";
|
|
|
- }
|
|
|
-
|
|
|
- // now add the taxonomy to the node
|
|
|
- $terms['tags'] = $tags;
|
|
|
- taxonomy_node_save($node, $terms);
|
|
|
- // print "Setting $node->name: " . implode(", ",$tags) . "\n";
|
|
|
-
|
|
|
- // get the analysis that this feature may belong to and add it as taxonomy
|
|
|
- // We'll add each one individually since there may be more than one analysis
|
|
|
- if ($do_an && $an_vid) {
|
|
|
- $sql = "
|
|
|
- SELECT A.name
|
|
|
- FROM {Analysis} A
|
|
|
- INNER JOIN {analysisfeature} AF ON AF.analysis_id = A.analysis_id
|
|
|
- WHERE AF.feature_id = :feature_id
|
|
|
- ";
|
|
|
- $results = chado_query($sql, array(':feature_id' => $feature_id));
|
|
|
- $analysis_terms = array();
|
|
|
- while ($analysis = $results->fetchObject()) {
|
|
|
- $tags2["$an_vid"] = "$analysis->name";
|
|
|
- $terms['tags'] = $tags2;
|
|
|
- taxonomy_node_save($node, $terms);
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * This function is an extension of the chado_feature_view by providing
|
|
|
- * the markup for the feature object THAT WILL BE INDEXED.
|
|
|
- *
|
|
|
- * @ingroup tripal_feature
|
|
|
- */
|
|
|
-function theme_tripal_feature_search_index($node) {
|
|
|
- $feature = $node->feature;
|
|
|
- $content = '';
|
|
|
-
|
|
|
- // get the accession prefix
|
|
|
- $aprefix = variable_get('chado_feature_accession_prefix', 'FID');
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ // FEATURE BROWSER
|
|
|
+ $form['browser'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Feature Browser'),
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => FALSE,
|
|
|
+ );
|
|
|
+ $allowedoptions1 = array(
|
|
|
+ 'show_feature_browser' => "Show the feature browser on the organism page. The browser loads when page loads. This may be slow for large sites.",
|
|
|
+ 'hide_feature_browser' => "Hide the feature browser on the organism page. Disables the feature browser completely.",
|
|
|
+ );
|
|
|
+// $allowedoptions ['allow_feature_browser'] = "Allow loading of the feature browsing through AJAX. For large sites the initial page load will be quick with the feature browser loading afterwards.";
|
|
|
|
|
|
- $content .= "<h1>$feature->uniquename</h1>. ";
|
|
|
- $content .= "<strong>$aprefix$feature->feature_id.</strong> ";
|
|
|
- $content .= "$feature->cvname ";
|
|
|
- $content .= "$feature->common_name ";
|
|
|
+ $form['browser']['browser_desc'] = array(
|
|
|
+ '#markup' => t('A feature browser can be added to an organism page to allow users to quickly ' .
|
|
|
+ 'access a feature. This will most likely not be the ideal mechanism for accessing feature ' .
|
|
|
+ 'information, especially for large sites, but it will alow users exploring the site (such ' .
|
|
|
+ 'as students) to better understand the data types available on the site.'),
|
|
|
|
|
|
- // add the synonyms of this feature to the text for searching
|
|
|
- $synonyms = $node->synonyms;
|
|
|
- if (count($synonyms) > 0) {
|
|
|
- foreach ($synonyms as $result) {
|
|
|
- $content .= "$result->name ";
|
|
|
- }
|
|
|
- }
|
|
|
+ );
|
|
|
+ $form['browser']['feature_types'] = array(
|
|
|
+ '#title' => t('Feature Types'),
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#description' => t("Enter the Sequence Ontology (SO) terms for the feature types that " .
|
|
|
+ "will be shown in the feature browser."),
|
|
|
+ '#default_value' => variable_get('chado_browser_feature_types', 'gene mRNA'),
|
|
|
+ );
|
|
|
|
|
|
- return $content;
|
|
|
-}
|
|
|
|
|
|
-/**
|
|
|
- * This function is an extension of the chado_feature_view by providing
|
|
|
- * the markup for the feature object THAT WILL BE INDEXED.
|
|
|
- *
|
|
|
- * @ingroup tripal_feature
|
|
|
- */
|
|
|
-function theme_tripal_feature_search_results($node) {
|
|
|
- $feature = $node->feature;
|
|
|
- $content = '';
|
|
|
+ $form['browser']['browse_features'] = array(
|
|
|
+ '#title' => 'Feature Browser on Organism Page',
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#options' => $allowedoptions1,
|
|
|
+ '#default_value' => variable_get('tripal_feature_browse_setting', 'show_feature_browser'),
|
|
|
+ );
|
|
|
|
|
|
- // get the accession prefix
|
|
|
- $aprefix = variable_get('chado_feature_accession_prefix', 'FID');
|
|
|
+ $form['browser']['browse_features_library'] = array(
|
|
|
+ '#title' => 'Feature Browser on Library Page',
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#options' => array(
|
|
|
+ 'show_feature_browser' => "Show the feature browse on the library page. The browser loads when page loads. This may be slow for large sites.",
|
|
|
+ 'hide_feature_browser' => "Hide the feature browser on the library page. Disables the feature browser completely.",
|
|
|
+ ),
|
|
|
+ '#default_value' => variable_get('tripal_library_feature_browse_setting', 'show_feature_browser'),
|
|
|
+ );
|
|
|
|
|
|
- $content .= "Feature Name: <h1>$feature->uniquename</h1>. ";
|
|
|
- $content .= "<strong>Accession: $aprefix$feature->feature_id.</strong>";
|
|
|
- $content .= "Type: $feature->cvname. ";
|
|
|
- $content .= "Organism: $feature->common_name. ";
|
|
|
+ $form['browser']['browse_features_analysis'] = array(
|
|
|
+ '#title' => 'Feature Browser on Analysis Page',
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#options' => array(
|
|
|
+ 'show_feature_browser' => "Show the feature browse on the analysis page. The browser loads when page loads. This may be slow for large sites.",
|
|
|
+ 'hide_feature_browser' => "Hide the feature browser on the analysis page. Disables the feature browser completely.",
|
|
|
+ ),
|
|
|
+ '#default_value' => variable_get('tripal_analysis_feature_browse_setting', 'show_feature_browser'),
|
|
|
+ );
|
|
|
|
|
|
- // add the synonyms of this feature to the text for searching
|
|
|
- $synonyms = $node->synonyms;
|
|
|
- if (count($synonyms) > 0) {
|
|
|
- $content .= "Synonyms: ";
|
|
|
- foreach ($synonyms as $result) {
|
|
|
- $content .= "$result->name, ";
|
|
|
- }
|
|
|
- }
|
|
|
+ $form['browser']['set_browse_button'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => t('Set Browser'),
|
|
|
+ '#weight' => 2,
|
|
|
+ );
|
|
|
|
|
|
- return $content;
|
|
|
+ // FEATURE SUMMARY REPORT
|
|
|
+ $form['summary'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Feature Summary Report'),
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => FALSE,
|
|
|
+ );
|
|
|
+ $allowedoptions2 ['show_feature_summary'] = "Show the feature summary on the organism page. The summary loads when page loads.";
|
|
|
+ $allowedoptions2 ['hide_feature_summary'] = "Hide the feature summary on the organism page. Disables the feature summary.";
|
|
|
+
|
|
|
+ $form['summary']['feature_summary'] = array(
|
|
|
+ '#title' => 'Feature Summary on Organism Page',
|
|
|
+ '#description' => 'A feature summary can be added to an organism page to allow users to see the ' .
|
|
|
+ 'type and quantity of features available for the organism.',
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#options' => $allowedoptions2,
|
|
|
+ '#default_value' => variable_get('tripal_feature_summary_setting', 'show_feature_summary'),
|
|
|
+ );
|
|
|
+ $form['summary']['feature_mapping'] = array(
|
|
|
+ '#title' => 'Map feature types',
|
|
|
+ '#description' => t('You may specify which Sequence Ontology (SO) terms to show in the ' .
|
|
|
+ 'feature summary report by listing them in the following text area. Enter one per line. ' .
|
|
|
+ 'If left blank, all SO terms for all features will be shown in the report. Only those terms ' .
|
|
|
+ 'listed below will be shown in the report. Terms will appear in the report in the same order listed. To rename a ' .
|
|
|
+ 'SO term to be more human readable form, use an \'=\' sign after the SO term (e.g. \'polypeptide = Protein\')'),
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#rows' => 15,
|
|
|
+ '#default_value' => variable_get('tripal_feature_summary_report_mapping', ''),
|
|
|
+ );
|
|
|
+ $form['summary']['set_summary_button'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => t('Set Summary'),
|
|
|
+ '#weight' => 2,
|
|
|
+ );
|
|
|
+
|
|
|
+ return system_settings_form($form);
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
- * Set the vocabulary to use taxonomy terms from
|
|
|
+ * Validate the feature settings forms
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_set_vocabulary() {
|
|
|
-
|
|
|
- //include the file containing the required functions for adding taxonomy vocabs
|
|
|
- module_load_include('inc', 'taxonomy', 'taxonomy.admin');
|
|
|
+function tripal_feature_admin_validate($form, &$form_state) {
|
|
|
+ global $user; // we need access to the user info
|
|
|
+ $job_args = array();
|
|
|
|
|
|
- // get the vocabularies so that we make sure we don't recreate
|
|
|
- // the vocabs that already exist
|
|
|
- $vocabularies = taxonomy_get_vocabularies();
|
|
|
- $ft_vid = NULL;
|
|
|
- $op_vid = NULL;
|
|
|
- $lb_vid = NULL;
|
|
|
- $an_vid = NULL;
|
|
|
+ variable_set('chado_browser_feature_types', $form_state['values']['feature_types']);
|
|
|
|
|
|
- // These taxonomic terms are hard coded because we
|
|
|
- // konw we have these relationships in the chado tables
|
|
|
- // through foreign key relationships. The tripal
|
|
|
- // modules that correspond to these chado "modules" don't
|
|
|
- // need to be installed for the taxonomy to work.
|
|
|
- foreach ($vocabularies as $vocab) {
|
|
|
- if ($vocab->name == 'Feature Type') {
|
|
|
- $ft_vid = $vocab->vid;
|
|
|
- }
|
|
|
- if ($vocab->name == 'Organism') {
|
|
|
- $op_vid = $vocab->vid;
|
|
|
- }
|
|
|
- if ($vocab->name == 'Library') {
|
|
|
- $lb_vid = $vocab->vid;
|
|
|
- }
|
|
|
- if ($vocab->name == 'Analysis') {
|
|
|
- $an_vid = $vocab->vid;
|
|
|
- }
|
|
|
- }
|
|
|
+ switch ($form_state['values']['op']) {
|
|
|
|
|
|
- if (!$ft_vid) {
|
|
|
- $form_state = array();
|
|
|
- $values = array(
|
|
|
- 'name' => t('Feature Type'),
|
|
|
- 'nodes' => array('chado_feature' => 'chado_feature'),
|
|
|
- 'description' => t('The feature type (or SO cvterm for this feature).'),
|
|
|
- 'help' => t('Select the term that matches the feature'),
|
|
|
- 'tags' => 0,
|
|
|
- 'hierarchy' => 1,
|
|
|
- 'relations' => 1,
|
|
|
- 'multiple' => 0,
|
|
|
- 'required' => 0,
|
|
|
- 'weight' => 1,
|
|
|
- );
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state, $values);
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state);
|
|
|
- }
|
|
|
+ case t('Set Browser') :
|
|
|
+ variable_set('tripal_feature_browse_setting', $form_state['values']['browse_features']);
|
|
|
+ variable_set('tripal_library_feature_browse_setting', $form_state['values']['browse_features_library']);
|
|
|
+ variable_set('tripal_analysis_feature_browse_setting', $form_state['values']['browse_features_analysis']);
|
|
|
+ break;
|
|
|
|
|
|
- if (!$op_vid) {
|
|
|
- $form_state = array();
|
|
|
- $values = array(
|
|
|
- 'name' => t('Organism'),
|
|
|
- 'nodes' => array('chado_feature' => 'chado_feature'),
|
|
|
- 'description' => t('The organism to which this feature belongs.'),
|
|
|
- 'help' => t('Select the term that matches the feature'),
|
|
|
- 'tags' => 0,
|
|
|
- 'hierarchy' => 1,
|
|
|
- 'relations' => 1,
|
|
|
- 'multiple' => 0,
|
|
|
- 'required' => 0,
|
|
|
- 'weight' => 2,
|
|
|
- );
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state, $values);
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state);
|
|
|
- }
|
|
|
+ case t('Set Summary') :
|
|
|
+ variable_set('tripal_feature_summary_setting', $form_state['values']['feature_summary']);
|
|
|
+ variable_set('tripal_feature_summary_report_mapping', $form_state['values']['feature_mapping']);
|
|
|
+ break;
|
|
|
|
|
|
- if (!$lb_vid) {
|
|
|
- $form_state = array();
|
|
|
- $values = array(
|
|
|
- 'name' => t('Library'),
|
|
|
- 'nodes' => array('chado_feature' => 'chado_feature'),
|
|
|
- 'description' => t('Chado features associated with a library are assigned the term associated with the library'),
|
|
|
- 'help' => t('Select the term that matches the feature'),
|
|
|
- 'tags' => 0,
|
|
|
- 'hierarchy' => 1,
|
|
|
- 'relations' => 1,
|
|
|
- 'multiple' => 0,
|
|
|
- 'required' => 0,
|
|
|
- 'weight' => 3,
|
|
|
- );
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state, $values);
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state);
|
|
|
+ case t('Set Feature URLs') :
|
|
|
+ variable_set('chado_feature_url', $form_state['values']['feature_url']);
|
|
|
+ tripal_add_job('Set Feature URLs', 'tripal_feature',
|
|
|
+ 'tripal_feature_set_urls', $job_args, $user->uid);
|
|
|
+ break;
|
|
|
}
|
|
|
|
|
|
- if (!$an_vid) {
|
|
|
- $form_state = array();
|
|
|
- $values = array(
|
|
|
- 'name' => t('Analysis'),
|
|
|
- 'nodes' => array('chado_feature' => 'chado_feature'),
|
|
|
- 'description' => t('Any analysis to which this feature belongs.'),
|
|
|
- 'help' => t('Select the term that matches the feature'),
|
|
|
- 'tags' => 0,
|
|
|
- 'hierarchy' => 1,
|
|
|
- 'relations' => 1,
|
|
|
- 'multiple' => 1,
|
|
|
- 'required' => 0,
|
|
|
- 'weight' => 4,
|
|
|
- );
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state, $values);
|
|
|
- drupal_form_submit('taxonomy_form_vocabulary', $form_state);
|
|
|
- }
|
|
|
}
|
Stephen Ficklin