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@@ -0,0 +1,1975 @@
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+<?php
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+
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+//
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+// Copyright 2009 Clemson University
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+//
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+
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+/*************************************************************************
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+*
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+*/
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+function tripal_feature_init(){
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+
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+ // add the jGCharts JS and CSS
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+ drupal_add_js (drupal_get_path('theme', 'tripal').'/js/tripal_feature.js');
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+ drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jgcharts/jgcharts.js');
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+}
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+/************************************************************************
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+ *
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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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+ $active_jobs = TRUE;
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+ }
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+
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+ if(!$active_jobs){
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+
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+ $form['chado_feature_accession_prefix'] = array (
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+ '#title' => t('Accession Prefix'),
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+ '#type' => t('textfield'),
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+ '#description' => t("Accession numbers for features consist of the ".
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+ "chado feature_id and a site specific prefix. Set the prefix that ".
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+ "will be incorporated in front of each feature_id to form a unique ".
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+ "accession number for this site."),
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+ '#required' => TRUE,
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+ '#default_value' => variable_get('chado_feature_accession_prefix','ID'),
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+ );
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+
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+ $form['chado_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 names of the sequence types that the ".
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+ "site will support with independent pages. Pages for these data ".
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+ "types will be built automatically for features that exist in the ".
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+ "chado database. The names listed here should be spearated by ".
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+ "spaces or entered separately on new lines. The names must match ".
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+ "exactly (spelling and case) with terms in the sequence ontology'),
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+ '#required' => TRUE,
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+ '#default_value' => variable_get('chado_feature_types','EST contig'),
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+ );
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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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+ );
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+ $allowedoptions ['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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+ $allowedoptions ['hide_feature_browser'] = "Hide the feature browser on the organism page. Disables the feature browser completely.";
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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']['browse_features'] = array(
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+ '#title' => 'Feature Browser on Organism Page',
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+ '#description' => '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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+ '#type' => 'radios',
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+ '#options' => $allowedoptions,
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+ '#default_value'=>variable_get('tripal_feature_browse_setting',
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+ array('show_feature_browser')),
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+ );
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+ $form['browser']['set_browse_button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Set Browser'),
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+ '#weight' => 2,
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+ );
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+
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+ get_tripal_feature_admin_form_sync_set($form);
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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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+ get_tripal_feature_admin_form_cleanup_set($form);
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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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+ );
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+ $form['notice']['message'] = array(
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+ '#value' => t('Currently, feature management jobs are waiting or ".
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+ "are running. Managemment features have been hidden until these ".
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+ "jobs complete. Please check back later once these jobs have ".
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+ "finished. You can view the status of pending jobs in the Tripal ".
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+ "jobs page.'),
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+ );
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+ }
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+ return system_settings_form($form);
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+}
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+
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+/************************************************************************
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+ *
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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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+ $job_args = array();
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+
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+ // if the user wants to sync up the chado features then
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+ // add the job to the management queue
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+ if ($form_state['values']['op'] == t('Sync all Features')) {
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+ tripal_add_job('Sync all features','tripal_feature',
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+ 'tripal_feature_sync_features',$job_args,$user->uid);
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+ }
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+
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+ if ($form_state['values']['op'] == t('Set/Reset Taxonomy for all feature nodes')) {
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+ tripal_add_job('Set all feature taxonomy','tripal_feature',
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+ 'tripal_features_set_taxonomy',$job_args,$user->uid);
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+ }
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+
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+ if ($form_state['values']['op'] == 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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+ }
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+
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+ if ($form_state['values']['op'] == t('Clean up orphaned features')) {
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+ tripal_add_job('Cleanup orphaned features','tripal_feature',
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+ 'tripal_features_cleanup',$job_args,$user->uid);
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+ }
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+
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+ if ($form_state['values']['op'] == t('Set Browser')) {
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+ variable_set('tripal_feature_browse_setting',$form_state['values']['browse_features']);
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+ }
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+
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+
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+}
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+/************************************************************************
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+ *
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+ */
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+function get_tripal_feature_admin_form_cleanup_set(&$form) {
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+ $form['cleanup'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Clean Up')
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+ );
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+ $form['cleanup']['description'] = array(
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+ '#type' => 'item',
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+ '#value' => t("With Drupal and chado residing in different databases ".
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+ "it is possible that nodes in Drupal and features in Chado become ".
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+ "\"orphaned\". This can occur if a feature node in Drupal is ".
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+ "deleted but the corresponding chado feature is not and/or vice ".
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+ "versa. The Cleanup function will also remove nodes for features ".
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+ "that are not in the list of allowed feature types as specified ".
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+ "above. This is helpful when a feature type needs to be ".
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+ "removed but was previously present as Drupal nodes. ".
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+ "Click the button below to resolve these discrepancies."),
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+ '#weight' => 1,
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+ );
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+ $form['cleanup']['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Clean up orphaned features'),
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+ '#weight' => 2,
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+ );
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+}
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+/************************************************************************
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+ *
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+ */
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+function get_tripal_feature_admin_form_reindex_set(&$form) {
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+ $form['reindex'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Reindex')
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+ );
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+ $form['reindex']['description'] = array(
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+ '#type' => 'item',
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+ '#value' => t("Reindexing of nodes is important when content for nodes ".
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+ "is updated external to drupal, such as external uploads to chado. ".
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+ "Features need to be reindexed to ensure that updates to features ".
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+ "are searchable. 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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+ $form['reindex']['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Reindex all feature nodes'),
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+ '#weight' => 2,
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+ );
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+}
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+/************************************************************************
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+ *
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+ */
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+function get_tripal_feature_admin_form_taxonomy_set (&$form) {
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+
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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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+ );
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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',''),
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+ );
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+ $form['taxonomy']['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Set/Reset Taxonomy for all feature nodes'),
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+ '#weight' => 3,
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+ );
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+
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+}
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+/************************************************************************
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+ *
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+ */
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+function get_tripal_feature_admin_form_sync_set (&$form) {
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+
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+
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+ // get the list of organisms which will be synced.
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+ $feature_sql = "SELECT * FROM {Feature} WHERE uniquename = '%s' and organism_id = %d";
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+ $previous_db = db_set_active('chado');
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+ $feature = db_fetch_object(db_query($feature_sql,$node->title,$node->organism_id));
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+ db_set_active($previous_db);
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+
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+ // define the fieldsets
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+ $form['sync'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Sync Features')
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+ );
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+
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+ $form['sync']['description'] = array(
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+ '#type' => 'item',
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+ '#value' => t("Click the 'Sync all Features' button to create Drupal ".
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+ "content for features in chado. Only features of the types listed ".
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+ "above in the Feature Types box will be synced. Depending on the ".
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+ "number of features in the chado database this may take a long ".
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+ "time to complete. "),
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+ '#weight' => 1,
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+ );
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+
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+ $orgs = tripal_organism_get_synced();
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+ $org_list = '';
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+ foreach($orgs as $org){
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+ $org_list .= "$org->genus $org->species, ";
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+ }
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+ $form['sync']['description2'] = array(
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+ '#type' => 'item',
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+ '#value' => "Only features for the following organisms will be synced: ".
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+ " $org_list",
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+ '#weight' => 1,
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+ );
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+
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+ $form['sync']['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Sync all Features'),
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+ '#weight' => 3,
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+ );
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+
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+}
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+/************************************************************************
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+ * Display help and module information
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+ * @param path which path of the site we're displaying help
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+ * @param arg array that holds the current path as would be returned from arg() function
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+ * @return help text for the path
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+ */
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+function tripal_feature_help($path, $arg) {
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+ $output = '';
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+ switch ($path) {
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+ case "admin/help#tripal_feature":
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+ $output='<p>'.t("Displays links to nodes created on this date").'</p>';
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+ break;
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+ }
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+ return $output;
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+}
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+
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+/************************************************************************
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+ * Provide information to drupal about the node types that we're creating
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+ * in this module
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+ */
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+function tripal_feature_node_info() {
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+ $nodes = array();
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+
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+ $nodes['chado_feature'] = array(
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+ 'name' => t('Feature'),
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+ 'module' => 'chado_feature',
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+ 'description' => t('A feature from the chado database'),
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+ 'has_title' => FALSE,
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+ 'title_label' => t('Feature'),
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+ 'has_body' => FALSE,
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+ 'body_label' => t('Feature Description'),
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+ 'locked' => TRUE
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+ );
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+ return $nodes;
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+}
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+
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+/************************************************************************
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+ * Set the permission types that the chado module uses. Essentially we
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+ * want permissionis that protect creation, editing and deleting of chado
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+ * data objects
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+ */
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+function tripal_feature_perm(){
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+ return array(
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+ 'access chado_feature content',
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+ 'create chado_feature content',
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+ 'delete chado_feature content',
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+ 'edit chado_feature content',
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+ );
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+}
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+
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+/************************************************************************
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+ * Set the permission types that the module uses.
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+ */
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+function chado_feature_access($op, $node, $account) {
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+ if ($op == 'create') {
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+ return user_access('create chado_feature content', $account);
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+ }
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+
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+ if ($op == 'update') {
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+ if (user_access('edit chado_feature content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ if ($op == 'delete') {
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+ if (user_access('delete chado_feature content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ if ($op == 'view') {
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+ if (user_access('access chado_feature content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ return FALSE;
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+}
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+/************************************************************************
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+ * Menu items are automatically added for the new node types created
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+ * by this module to the 'Create Content' Navigation menu item. This function
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+ * adds more menu items needed for this module.
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+ */
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+function tripal_feature_menu() {
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+ $items = array();
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+
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+ // the administative settings menu
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+ $items['admin/tripal/tripal_feature'] = array(
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+ 'title' => 'Features',
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+ 'description' => 'Settings for Chado Features',
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+ 'page callback' => 'drupal_get_form',
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+ 'page arguments' => array('tripal_feature_admin'),
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+ 'access arguments' => array('administer site configuration'),
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+ 'type' => MENU_NORMAL_ITEM,
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+ );
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+
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+ $items['admin/settings/tripal/tripal_feature/load'] = array(
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+ 'title' => 'Bulk Load',
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+ 'description' => 'Upload Data into Chado & Drupal',
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+ 'page callback' => 'tripal_feature_bulkload',
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+ 'access arguments' => array('administer site configuration'),
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+ 'type' => MENU_NORMAL_ITEM,
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+ );
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+
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+ return $items;
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+}
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+
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+/************************************************************************
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+ * When a new chado_feature node is created we also need to add information
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+ * to our chado_feature table. This function is called on insert of a new node
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+ * of type 'chado_feature' and inserts the necessary information.
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+ */
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+function chado_feature_insert($node){
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+ // remove spaces, newlines from residues
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+ $residues = preg_replace("/[\n\r\s]/","",$node->residues);
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+
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+ // If this feature already exists then don't recreate it in chado
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+ // TODO: the unique index in chado for this also includes the type_id. If the site
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+ // ever needs to have the same feature name for different types then this will break.
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+ $feature_sql = "SELECT * FROM {Feature} WHERE uniquename = '%s' and organism_id = %d";
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+ $previous_db = db_set_active('chado');
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+ $feature = db_fetch_object(db_query($feature_sql,$node->title,$node->organism_id));
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+ db_set_active($previous_db);
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+
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+ // if the feature doesn't exist then let's create it in chado.
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+ if(!$feature){
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|
|
+ $sql = "INSERT INTO {feature} (organism_id, name, uniquename, residues, seqlen,".
|
|
|
+ " is_obsolete, type_id)".
|
|
|
+ " VALUES(%d,'%s','%s','%s',%d, %s, ".
|
|
|
+ " (SELECT cvterm_id ".
|
|
|
+ " FROM {CVTerm} CVT ".
|
|
|
+ " INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
|
|
|
+ " WHERE CV.name = 'sequence' and CVT.name = '%s'))";
|
|
|
+ $obsolete = 'FALSE';
|
|
|
+ if($node->is_obsolete){
|
|
|
+ $obsolete = 'TRUE';
|
|
|
+ }
|
|
|
+
|
|
|
+ // use chado database
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ db_query($sql,$node->organism_id,$node->title,$node->title,
|
|
|
+ $residues,strlen($residues),$obsolete,$node->feature_type);
|
|
|
+
|
|
|
+ // now that we've added the feature, get the feature id for this feature
|
|
|
+ $feature = db_fetch_object(db_query($feature_sql,$node->title,$node->organism_id));
|
|
|
+
|
|
|
+ // now use drupal database
|
|
|
+ db_set_active($previous_db);
|
|
|
+ }
|
|
|
+
|
|
|
+ // add the genbank accession and synonyms
|
|
|
+ chado_feature_add_synonyms($node->synonyms,$feature->feature_id);
|
|
|
+
|
|
|
+ // make sure the entry for this feature doesn't already exist in the chado_feature table
|
|
|
+ // if it doesn't exist then we want to add it.
|
|
|
+ $node_check_sql = "SELECT * FROM {chado_feature} ".
|
|
|
+ "WHERE feature_id = '%s'";
|
|
|
+ $node_check = db_fetch_object(db_query($node_check_sql,$feature->feature_id));
|
|
|
+ if(!$node_check){
|
|
|
+ // next add the item to the drupal table
|
|
|
+ $sql = "INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) ".
|
|
|
+ "VALUES (%d, %d, %d, " . time() . ")";
|
|
|
+ db_query($sql,$node->nid,$node->vid,$feature->feature_id);
|
|
|
+ }
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ */
|
|
|
+function chado_feature_delete($node){
|
|
|
+ // get feature_id so we can remove it from chado database
|
|
|
+ $sql_drupal = "SELECT feature_id ".
|
|
|
+ "FROM {chado_feature} ".
|
|
|
+ "WHERE nid = %d AND vid = %d";
|
|
|
+ $feature_id = db_result(db_query($sql_drupal, $node->nid, $node->vid));
|
|
|
+
|
|
|
+ // remove the drupal content
|
|
|
+ $sql_del = "DELETE FROM {chado_feature} ".
|
|
|
+ "WHERE nid = %d ".
|
|
|
+ "AND vid = %d";
|
|
|
+ db_query($sql_del, $node->nid, $node->vid);
|
|
|
+ $sql_del = "DELETE FROM {node} ".
|
|
|
+ "WHERE nid = %d ".
|
|
|
+ "AND vid = %d";
|
|
|
+ db_query($sql_del, $node->nid, $node->vid);
|
|
|
+ $sql_del = "DELETE FROM {node_revisions} ".
|
|
|
+ "WHERE nid = %d ".
|
|
|
+ "AND vid = %d";
|
|
|
+ db_query($sql_del, $node->nid, $node->vid);
|
|
|
+
|
|
|
+
|
|
|
+ // Remove data from feature tables of chado database. This will
|
|
|
+ // cause a cascade delete and remove all data in referencing tables
|
|
|
+ // for this feature
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ db_query("DELETE FROM {feature} WHERE feature_id = %d", $feature_id);
|
|
|
+ db_set_active($previous_db);
|
|
|
+
|
|
|
+ drupal_set_message("The feature and all associated data were removed from ".
|
|
|
+ "chado");
|
|
|
+
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ */
|
|
|
+function chado_feature_update($node){
|
|
|
+ if($node->revision){
|
|
|
+ // TODO -- decide what to do about revisions
|
|
|
+ } else {
|
|
|
+ // get the feature for this node:
|
|
|
+ $sql = 'SELECT feature_id FROM {chado_feature} WHERE vid = %d';
|
|
|
+ $feature = db_fetch_object(db_query($sql, $node->vid));
|
|
|
+
|
|
|
+ // remove spaces, newlines from residues
|
|
|
+ $residues = preg_replace("/[\n\r\s]/","",$node->residues);
|
|
|
+
|
|
|
+ $sql = "UPDATE {feature} ".
|
|
|
+ " SET residues = '%s', ".
|
|
|
+ " name = '%s', ".
|
|
|
+ " uniquename = '%s', ".
|
|
|
+ " seqlen = %d, ".
|
|
|
+ " organism_id = %d, ".
|
|
|
+ " is_obsolete = %s, ".
|
|
|
+ " type_id = (SELECT cvterm_id ".
|
|
|
+ " FROM {CVTerm} CVT ".
|
|
|
+ " INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
|
|
|
+ " WHERE CV.name = 'sequence' and CVT.name = '%s') ".
|
|
|
+ "WHERE feature_id = %d ";
|
|
|
+ $obsolete = 'FALSE';
|
|
|
+ if($node->is_obsolete){
|
|
|
+ $obsolete = 'TRUE';
|
|
|
+ }
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ db_query($sql,$residues,$node->title,$node->title,
|
|
|
+ strlen($residues),$node->organism_id,$obsolete,$node->feature_type,
|
|
|
+ $feature->feature_id);
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ // add the genbank accession & synonyms
|
|
|
+ // chado_feature_add_gbaccession($node->gbaccession,$feature->feature_id);
|
|
|
+ chado_feature_add_synonyms($node->synonyms,$feature->feature_id);
|
|
|
+ }
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_feature_add_synonyms($synonyms,$feature_id){
|
|
|
+
|
|
|
+ // make sure we only have a single space between each synonym
|
|
|
+ $synonyms = preg_replace("/[\s\n\r]+/"," ",$synonyms);
|
|
|
+ // split the synonyms into an array based on a space as the delimieter
|
|
|
+ $syn_array = array();
|
|
|
+ $syn_array = explode(" ",$synonyms);
|
|
|
+
|
|
|
+ // use the chado database
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+
|
|
|
+ // remove any old synonyms
|
|
|
+ $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d";
|
|
|
+ if(!db_query($feature_syn_dsql,$feature_id)){
|
|
|
+ $error .= "Could not remove synonyms from feature. ";
|
|
|
+ }
|
|
|
+
|
|
|
+ // return if we don't have any synonmys to add
|
|
|
+ if(!$synonyms){
|
|
|
+ db_set_active($previous_db);
|
|
|
+ return;
|
|
|
+ }
|
|
|
+ // iterate through each synonym and add it to the database
|
|
|
+ foreach($syn_array as $syn){
|
|
|
+ // skip this item if it's empty
|
|
|
+ if(!$syn){ break; }
|
|
|
+
|
|
|
+ // check to see if we have this accession number already in the database
|
|
|
+ // if so then don't add it again. it messes up drupal if the insert fails.
|
|
|
+ // It is possible for the accession number to be present and not the feature
|
|
|
+ $synonym_sql = "SELECT synonym_id FROM {synonym} ".
|
|
|
+ "WHERE name = '%s'";
|
|
|
+ $synonym = db_fetch_object(db_query($synonym_sql,$syn));
|
|
|
+ if(!$synonym){
|
|
|
+ $synonym_isql = "INSERT INTO {synonym} (name,synonym_sgml,type_id) ".
|
|
|
+ "VALUES ('%s','%s', ".
|
|
|
+ " (SELECT cvterm_id ".
|
|
|
+ " FROM {CVTerm} CVT ".
|
|
|
+ " INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
|
|
|
+ " WHERE CV.name = 'feature_property' and CVT.name = 'synonym'))";
|
|
|
+ if(!db_query($synonym_isql,$syn,$syn)){
|
|
|
+ $error .= "Could not add synonym. ";
|
|
|
+ }
|
|
|
+ // now get the synonym we just added
|
|
|
+ $synonym_sql = "SELECT synonym_id FROM {synonym} ".
|
|
|
+ "WHERE name = '%s'";
|
|
|
+ $synonym = db_fetch_object(db_query($synonym_sql,$syn));
|
|
|
+ }
|
|
|
+
|
|
|
+ // now add in our new sysnonym
|
|
|
+ $feature_syn_isql = "INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) ".
|
|
|
+ "VALUES (%d,%d,1)";
|
|
|
+ if(!db_query($feature_syn_isql,$synonym->synonym_id,$feature_id)){
|
|
|
+ $error .= "Could not add synonyms to feature. ";
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // return to the drupal database
|
|
|
+ db_set_active($previous_db);
|
|
|
+ return $error;
|
|
|
+
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_feature_add_gbaccession($accession,$feature_id){
|
|
|
+
|
|
|
+ // use chado database
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+
|
|
|
+ // remove any old accession from genbank dbEST
|
|
|
+ $fdbxref_dsql = "DELETE FROM {feature_dbxref} ".
|
|
|
+ "WHERE feature_id = %d and dbxref_id IN ".
|
|
|
+ " (SELECT DBX.dbxref_id FROM {dbxref} DBX ".
|
|
|
+ " INNER JOIN DB ON DB.db_id = DBX.db_id ".
|
|
|
+ " INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id ".
|
|
|
+ " WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)";
|
|
|
+ if(!db_query($fdbxref_dsql,$feature_id,$feature_id)){
|
|
|
+ $error .= "Could not remove accession from feature. ";
|
|
|
+ }
|
|
|
+
|
|
|
+ // if we don't have an accession number to add then just return
|
|
|
+ if(!$accession){
|
|
|
+ db_set_active($previous_db);
|
|
|
+ return;
|
|
|
+ }
|
|
|
+ // get the db_id
|
|
|
+ $db_sql = "SELECT db_id FROM {DB} ".
|
|
|
+ "WHERE name = 'DB:Genbank_est'";
|
|
|
+ $db = db_fetch_object(db_query($db_sql));
|
|
|
+
|
|
|
+ // check to see if we have this accession number already in the database
|
|
|
+ // if so then don't add it again. it messes up drupal if the insert fails.
|
|
|
+ // It is possible for the accession number to be present and not the feature
|
|
|
+ $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
|
|
|
+ "WHERE db_id = %d and accession = '%s'";
|
|
|
+ $dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
|
|
|
+ if(!$dbxref){
|
|
|
+ // add the accession number
|
|
|
+ $dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) ".
|
|
|
+ " VALUES (%d, '%s') ";
|
|
|
+ if(!db_query($dbxref_isql,$db->db_id,$accession)){
|
|
|
+ $error .= 'Could not add accession as a database reference ';
|
|
|
+ }
|
|
|
+ // get the dbxref_id for the just added accession number
|
|
|
+ $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
|
|
|
+ "WHERE db_id = %d and accession = '%s'";
|
|
|
+ $dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
|
|
|
+ }
|
|
|
+
|
|
|
+
|
|
|
+ // associate the accession number with the feature
|
|
|
+ $feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) ".
|
|
|
+ " VALUES (%d, %d) ";
|
|
|
+ if(!db_query($feature_dbxref_isql,$feature_id,$dbxref->dbxref_id)){
|
|
|
+ $error .= 'Could not add feature database reference. ';
|
|
|
+ }
|
|
|
+
|
|
|
+ db_set_active($previous_db);
|
|
|
+ return $error;
|
|
|
+}
|
|
|
+
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_feature_form ($node,$param){
|
|
|
+ $type = node_get_types('type', $node);
|
|
|
+ $form = array();
|
|
|
+ $feature = $node->feature;
|
|
|
+ $synonyms = $node->synonyms;
|
|
|
+ $analyses = $node->analyses;
|
|
|
+ $references = $node->references;
|
|
|
+
|
|
|
+ // We need to pass above variables for preview to show
|
|
|
+ $form['feature'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#value' => $feature
|
|
|
+ );
|
|
|
+ // This field is read when previewing a node
|
|
|
+ $form['synonyms'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#value' => $synonyms
|
|
|
+ );
|
|
|
+ // This field is read when previewing a node
|
|
|
+ $form['analyses'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#value' => $analyses
|
|
|
+ );
|
|
|
+ // This field is read when previewing a node
|
|
|
+ $form['references'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#value' => $references
|
|
|
+ );
|
|
|
+
|
|
|
+ // keep track of the feature id if we have one. If we do have one then
|
|
|
+ // this would indicate an update as opposed to an insert.
|
|
|
+ $form['feature_id'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#value' => $feature->feature_id,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['title']= array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Unique Feature Name'),
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#default_value' => $feature->featurename,
|
|
|
+ '#description' => t('Enter a unique name for this feature'),
|
|
|
+ '#weight' => 1,
|
|
|
+ '#maxlength' => 255
|
|
|
+ );
|
|
|
+
|
|
|
+ // get the list of supported feature types
|
|
|
+ $ftypes = array();
|
|
|
+ $ftypes[''] = '';
|
|
|
+ $supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
|
|
|
+ foreach($supported_ftypes as $ftype){
|
|
|
+ $ftypes["$ftype"] = $ftype;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['feature_type'] = array (
|
|
|
+ '#title' => t('Feature Type'),
|
|
|
+ '#type' => t('select'),
|
|
|
+ '#description' => t("Choose the feature type."),
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#default_value' => $feature->cvname,
|
|
|
+ '#options' => $ftypes,
|
|
|
+ '#weight' => 2
|
|
|
+ );
|
|
|
+ // get the list of organisms
|
|
|
+ $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $org_rset = db_query($sql);
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ //
|
|
|
+ $organisms = array();
|
|
|
+ $organisms[''] = '';
|
|
|
+ while($organism = db_fetch_object($org_rset)){
|
|
|
+ $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['organism_id'] = array (
|
|
|
+ '#title' => t('Organism'),
|
|
|
+ '#type' => t('select'),
|
|
|
+ '#description' => t("Choose the organism with which this feature is associated "),
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#default_value' => $feature->organism_id,
|
|
|
+ '#options' => $organisms,
|
|
|
+ '#weight' => 3,
|
|
|
+ );
|
|
|
+
|
|
|
+ // Get synonyms
|
|
|
+ if ($synonyms) {
|
|
|
+ if (is_array($synonyms)) {
|
|
|
+ foreach ($synonyms as $synonym){
|
|
|
+ $syn_text .= "$synonym->name\n";
|
|
|
+ }
|
|
|
+ } else {
|
|
|
+ $syn_text = $synonyms;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ $form['synonyms']= array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#title' => t('Synonyms'),
|
|
|
+ '#required' => FALSE,
|
|
|
+ '#default_value' => $syn_text,
|
|
|
+ '#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed separated by spaces or on different lines.'),
|
|
|
+ '#weight' => 5,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['residues']= array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#title' => t('Residues'),
|
|
|
+ '#required' => FALSE,
|
|
|
+ '#default_value' => $feature->residues,
|
|
|
+ '#description' => t('Enter the nucelotide sequences for this feature'),
|
|
|
+ '#weight' => 6
|
|
|
+ );
|
|
|
+
|
|
|
+ $checked = '';
|
|
|
+ if($feature->is_obsolete == 't'){
|
|
|
+ $checked = '1';
|
|
|
+ }
|
|
|
+ $form['is_obsolete']= array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Is Obsolete'),
|
|
|
+ '#required' => FALSE,
|
|
|
+ '#default_value' => $checked,
|
|
|
+ '#description' => t('Check this box if this sequence should be retired and no longer included in further analysis.'),
|
|
|
+ '#weight' => 8
|
|
|
+ );
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_feature_validate($node){
|
|
|
+ $result = 0;
|
|
|
+
|
|
|
+ // if this is an update, we want to make sure that a different feature for
|
|
|
+ // the organism doesn't already have this uniquename. We don't want to give
|
|
|
+ // two sequences the same uniquename
|
|
|
+ if($node->feature_id){
|
|
|
+ $sql = "SELECT * FROM {Feature} WHERE uniquename = '%s' ".
|
|
|
+ " AND organism_id = %d AND NOT feature_id = %d";
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ $result = db_fetch_object(db_query($sql, $node->title,$node->organism_id,$node->feature_id));
|
|
|
+ db_set_active($previous_db);
|
|
|
+ if($result){
|
|
|
+ form_set_error('title',t("Feature update cannot proceed. The feature name '$node->title' is not unique for this organism. Please provide a unique name for this feature. "));
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // if this is an insert then we just need to make sure this name doesn't
|
|
|
+ // already exist for this organism if it does then we need to throw an error
|
|
|
+ else {
|
|
|
+ $sql = "SELECT * FROM {Feature} WHERE uniquename = '%s' AND organism_id = %d";
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ $result = db_fetch_object(db_query($sql, $node->title,$node->organism_id));
|
|
|
+ db_set_active($previous_db);
|
|
|
+ if($result){
|
|
|
+ form_set_error('title',t("Feature insert cannot proceed. The feature name '$node->title' already exists for this organism. Please provide a unique name for this feature. "));
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // we want to remove all characters except IUPAC nucleotide characters from the
|
|
|
+ // the residues. however, residues are not required so if blank then we'll skip
|
|
|
+ // this step
|
|
|
+ if($node->residues){
|
|
|
+ $residues = preg_replace("/[^\w]/",'',$node->residues);
|
|
|
+ if(!preg_match("/^[ACTGURYMKSWBDHVN]+$/i",$residues)){
|
|
|
+ form_set_error('residues',t("The residues in feature $node->title contains more than the nucleotide IUPAC characters. Only the following characters are allowed: A,C,T,G,U,R,Y,M,K,S,W,B,D,H,V,N: '" . $residues ."'"));
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // we don't allow a genbank accession number for a contig
|
|
|
+ if($node->feature_type == 'contig' and $node->gbaccession){
|
|
|
+ form_set_error('gbaccession',t("Contigs cannot have a genbank accession number. Please change the feature type or remove the accession number"));
|
|
|
+ }
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ * When a node is requested by the user this function is called to allow us
|
|
|
+ * to add auxiliary data to the node object.
|
|
|
+ */
|
|
|
+function chado_feature_load($node){
|
|
|
+ // get the feature_id for this node:
|
|
|
+ $sql = 'SELECT feature_id FROM {chado_feature} WHERE vid = %d';
|
|
|
+ $map = db_fetch_object(db_query($sql, $node->vid));
|
|
|
+
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+
|
|
|
+ // get information about this organism and add it to the items in this node
|
|
|
+ $sql = "SELECT F.feature_id, F.name as featurename, F.uniquename, ".
|
|
|
+ "F.residues, F.seqlen, O.genus, O.species, O.common_name, ".
|
|
|
+ " CVT.name as cvname, O.organism_id, F.type_id, F.is_obsolete ".
|
|
|
+ "FROM {Feature} F ".
|
|
|
+ " INNER JOIN Organism O ON F.organism_id = O.organism_id ".
|
|
|
+ " INNER JOIN CVterm CVT ON F.type_id = CVT.cvterm_id ".
|
|
|
+ "WHERE F.feature_id = %d";
|
|
|
+ $feature = db_fetch_object(db_query($sql,$map->feature_id));
|
|
|
+ $additions->feature = $feature;
|
|
|
+ $additions->seqlen = $feature->seqlen;
|
|
|
+
|
|
|
+ // get the feature synonyms
|
|
|
+ $sql = "SELECT S.name ".
|
|
|
+ "FROM {Feature_Synonym} FS ".
|
|
|
+ " INNER JOIN Synonym S ".
|
|
|
+ " ON FS.synonym_id = S.Synonym_id ".
|
|
|
+ "WHERE FS.feature_id = %d";
|
|
|
+ $results = db_query($sql,$map->feature_id);
|
|
|
+ $synonyms = array();
|
|
|
+ $i=0;
|
|
|
+ while($synonym = db_fetch_object($results)){
|
|
|
+ $synonyms[$i++] = $synonym;
|
|
|
+ }
|
|
|
+ $additions->synonyms = $synonyms;
|
|
|
+
|
|
|
+ // get feature references in external databases
|
|
|
+ $sql = "SELECT F.uniquename,F.Feature_id,DBX.accession,DB.description as dbdesc, ".
|
|
|
+ " DB.db_id, DB.name as db_name, DB.urlprefix ".
|
|
|
+ "FROM {Feature} F ".
|
|
|
+ " INNER JOIN Feature_dbxref FDBX on F.feature_id = FDBX.feature_id ".
|
|
|
+ " INNER JOIN Dbxref DBX on DBX.dbxref_id = FDBX.dbxref_id ".
|
|
|
+ " INNER JOIN DB on DB.db_id = DBX.db_id ".
|
|
|
+ "WHERE F.feature_id = %d";
|
|
|
+ $results = db_query($sql,$map->feature_id);
|
|
|
+ $references = array();
|
|
|
+ $i=0;
|
|
|
+ while($accession = db_fetch_object($results)){
|
|
|
+ $references[$i++] = $accession;
|
|
|
+ // we want to specifically pull out the genbank id
|
|
|
+ if(preg_match("/Genbank_est/",$accession->db_name)){
|
|
|
+ $additions->gbaccession = $accession;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ $additions->references = $references;
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ // get organism node nid
|
|
|
+ $sql = "SELECT nid FROM {chado_organism} WHERE organism_id = %d";
|
|
|
+ $org_nid = db_result(db_query($sql, $additions->feature->organism_id));
|
|
|
+ $additions->org_nid = $org_nid;
|
|
|
+ return $additions;
|
|
|
+}
|
|
|
+
|
|
|
+/************************************************************************
|
|
|
+ * This function customizes the view of the chado_feature node. It allows
|
|
|
+ * us to generate the markup.
|
|
|
+ */
|
|
|
+function chado_feature_view ($node, $teaser = FALSE, $page = FALSE) {
|
|
|
+
|
|
|
+ if (!$teaser) {
|
|
|
+ // use drupal's default node view:
|
|
|
+ $node = node_prepare($node, $teaser);
|
|
|
+
|
|
|
+ // if we're building the node for searching then
|
|
|
+ // we want to handle this within the module and
|
|
|
+ // not allow theme customization. We don't want to
|
|
|
+ // index all items (such as DNA sequence).
|
|
|
+ if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
|
|
|
+ $node->content['index_version'] = array(
|
|
|
+ '#value' => theme('tripal_feature_search_index',$node),
|
|
|
+ '#weight' => 1,
|
|
|
+ );
|
|
|
+ }
|
|
|
+ else if($node->build_mode == NODE_BUILD_SEARCH_RESULT){
|
|
|
+ $node->content['index_version'] = array(
|
|
|
+ '#value' => theme('tripal_feature_search_results',$node),
|
|
|
+ '#weight' => 1,
|
|
|
+ );
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ // do nothing here, let the theme derived template handle display
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return $node;
|
|
|
+}
|
|
|
+
|
|
|
+/*******************************************************************************
|
|
|
+ * Display feature information for associated organisms. This function also
|
|
|
+ * provides contents for indexing
|
|
|
+ */
|
|
|
+function tripal_feature_nodeapi(&$node, $op, $teaser, $page) {
|
|
|
+
|
|
|
+ switch ($op) {
|
|
|
+ // Note that this function only adds feature view to an organism node.
|
|
|
+ // The view of a feature node is controled by the theme *.tpl file
|
|
|
+ case 'view':
|
|
|
+ // Set the node types for showing feature information
|
|
|
+ $types_to_show = array('chado_organism', 'chado_library');
|
|
|
+
|
|
|
+ // Abort if this node is not one of the types we should show.
|
|
|
+ if (!in_array($node->type, $types_to_show, TRUE)) {
|
|
|
+ break;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Add feature to the content item if it's not a teaser
|
|
|
+ if (!$teaser) {
|
|
|
+
|
|
|
+ // Show feature browser
|
|
|
+ $node->content['tripal_feature_browser'] = array(
|
|
|
+ '#value' => theme('tripal_feature_browser', $node),
|
|
|
+ '#weight' => 5
|
|
|
+ );
|
|
|
+ $node->content['tripal_feature_org_counts'] = array(
|
|
|
+ '#value' => theme('tripal_feature_counts', $node),
|
|
|
+ '#weight' => 4
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ * We need to let drupal know about our theme functions and their arguments.
|
|
|
+ * We create theme functions to allow users of the module to customize the
|
|
|
+ * look and feel of the output generated in this module
|
|
|
+ */
|
|
|
+function tripal_feature_theme () {
|
|
|
+ return array(
|
|
|
+ 'tripal_feature_search_index' => array (
|
|
|
+ 'arguments' => array('node'),
|
|
|
+ ),
|
|
|
+ 'tripal_feature_search_results' => array (
|
|
|
+ 'arguments' => array('node'),
|
|
|
+ ),
|
|
|
+ 'tripal_feature_browser' => array (
|
|
|
+ 'arguments' => array('node'),
|
|
|
+ ),
|
|
|
+ 'tripal_feature_counts' => array (
|
|
|
+ 'arguments' => array('node'),
|
|
|
+ )
|
|
|
+ );
|
|
|
+}
|
|
|
+/*******************************************************************************
|
|
|
+ * create a list of features for the organism and pie chart
|
|
|
+ */
|
|
|
+function theme_tripal_feature_counts($node){
|
|
|
+
|
|
|
+ // get the feature counts. This is dependent on a materialized view
|
|
|
+ // installed with the organism module
|
|
|
+ $content = '';
|
|
|
+ if ($node->organism_id && $node->type == 'chado_organism') {
|
|
|
+ $sql = "SELECT * FROM {organism_feature_count} ".
|
|
|
+ "WHERE organism_id = %d AND NOT feature_type = 'EST_match' ".
|
|
|
+ "ORDER BY num_features desc";
|
|
|
+ $features = array();
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $results = db_query($sql,$node->organism_id);
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+ $feature = db_fetch_object($results); // retrieve the first result
|
|
|
+ if ($feature) {
|
|
|
+ $content .= "<div class=\"tripal_feature_summary-info-box\"><br>
|
|
|
+ <div class=\"tripal_expandableBox\">".
|
|
|
+ "<h3>Feature Summary</h3>".
|
|
|
+ "</div>";
|
|
|
+ $content .= "<div class=\"tripal_expandableBoxContent\">";
|
|
|
+ $content .= "<table class=\"tripal_table_horz\">";
|
|
|
+ $content .= " <tr>";
|
|
|
+ $content .= " <th class=\"dbfieldname\">Type</th>";
|
|
|
+ $content .= " <th class=\"dbfieldname\">Number</th>";
|
|
|
+ $content .= " </tr>";
|
|
|
+ do {
|
|
|
+ $content .= "<tr>";
|
|
|
+ $content .= " <td>$feature->feature_type</td>";
|
|
|
+ $content .= " <td>". number_format($feature->num_features) . "</td>";
|
|
|
+ $content .= "</tr>";
|
|
|
+ } while($feature = db_fetch_object($results));
|
|
|
+ $content .= "</table>";
|
|
|
+ $content .= "
|
|
|
+ <img class=\"tripal_cv_chart\" id=\"tripal_feature_cv_chart_$node->organism_id\" src=\"\" border=\"0\">
|
|
|
+ ";
|
|
|
+ $content .= "</div></div>";
|
|
|
+ }
|
|
|
+ }
|
|
|
+ return $content;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_cv_chart($chart_id){
|
|
|
+
|
|
|
+ // The CV module will create the JSON array necessary for buillding a
|
|
|
+ // pie chart using jgChart and Google Charts. We have to pass to it
|
|
|
+ // a table that contains count information, tell it which column
|
|
|
+ // contains the cvterm_id and provide a filter for getting the
|
|
|
+ // results we want from the table.
|
|
|
+ $organism_id = preg_replace("/^tripal_feature_cv_chart_(\d+)$/","$1",$chart_id);
|
|
|
+ $options = array(
|
|
|
+ count_mview => 'organism_feature_count',
|
|
|
+ cvterm_id_column => 'cvterm_id',
|
|
|
+ count_column => 'num_features',
|
|
|
+ filter => "CNT.organism_id = $organism_id AND NOT feature_type = 'EST_match' ",
|
|
|
+ );
|
|
|
+ return $options;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_cv_tree($tree_id){
|
|
|
+
|
|
|
+ // The CV module will create the JSON array necessary for buillding a
|
|
|
+ // pie chart using jgChart and Google Charts. We have to pass to it
|
|
|
+ // a table that contains count information, tell it which column
|
|
|
+ // contains the cvterm_id and provide a filter for getting the
|
|
|
+ // results we want from the table.
|
|
|
+ $organism_id = preg_replace("/^tripal_feature_cv_tree_(\d+)$/","$1",$tree_id);
|
|
|
+ $options = array(
|
|
|
+ cv_id => tripal_cv_get_cv_id('sequence'),
|
|
|
+ count_mview => 'organism_feature_count',
|
|
|
+ cvterm_id_column => 'cvterm_id',
|
|
|
+ count_column => 'num_features',
|
|
|
+ filter => "CNT.organism_id = $organism_id",
|
|
|
+ label => 'Features',
|
|
|
+ );
|
|
|
+ return $options;
|
|
|
+}
|
|
|
+/*******************************************************************************
|
|
|
+ * create a simple paged feature browser
|
|
|
+ */
|
|
|
+function theme_tripal_feature_browser($node){
|
|
|
+
|
|
|
+ // don't show the browser if the settings in the admin page is turned off
|
|
|
+ $show_browser = variable_get('tripal_feature_browse_setting',array('show_feature_browser'));
|
|
|
+
|
|
|
+ if(strcmp($show_browser,'show_feature_browser')!=0){
|
|
|
+ return;
|
|
|
+ }
|
|
|
+ if ($node->organism_id && $node->type == 'chado_organism') {
|
|
|
+ # get the list of available sequence ontology terms for which
|
|
|
+ # we will build drupal pages from features in chado. If a feature
|
|
|
+ # is not one of the specified typse we won't build a node for it.
|
|
|
+ $allowed_types = variable_get('chado_feature_types','EST contig');
|
|
|
+ $allowed_types = preg_replace("/[\s\n\r]+/"," ",$allowed_types);
|
|
|
+ $so_terms = split(' ',$allowed_types);
|
|
|
+ $where_cvt = "";
|
|
|
+ foreach ($so_terms as $term){
|
|
|
+ $where_cvt .= "CVT.name = '$term' OR ";
|
|
|
+ }
|
|
|
+ $where_cvt = substr($where_cvt,0,strlen($where_cvt)-3); # strip trailing 'OR'
|
|
|
+
|
|
|
+ // get the features for this organism
|
|
|
+ $sql = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname ".
|
|
|
+ "FROM {feature} F ".
|
|
|
+ " INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
|
|
|
+ "WHERE organism_id = $node->organism_id and ($where_cvt) ".
|
|
|
+ "ORDER BY feature_id ASC";
|
|
|
+
|
|
|
+ // the counting SQL
|
|
|
+ $csql = "SELECT count(*) ".
|
|
|
+ "FROM {feature} F".
|
|
|
+ " INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
|
|
|
+ "WHERE organism_id = $node->organism_id and ($where_cvt) ".
|
|
|
+ "GROUP BY organism_id ";
|
|
|
+
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $features = pager_query($sql,10,0,$csql);
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ $content = "<br><div id=\"tripal_feature_box\" class=\"feature-info-box\">";
|
|
|
+ $content .= "<div class=\"tripal_expandableBox\">".
|
|
|
+ "<h3>Browse Features</h3>".
|
|
|
+ "</div>";
|
|
|
+ $content .= "<div class=\"tripal_expandableBoxContent\">";
|
|
|
+ $content .= "Below are the features associated with this organism.\n";
|
|
|
+ $content .= "<table class=\"tripal_table_horz\">";
|
|
|
+ $content .= " <tr>";
|
|
|
+ $content .= " <th>Feature Name</th>";
|
|
|
+ $content .= " <th>Type</th>";
|
|
|
+ $content .= " </tr>";
|
|
|
+
|
|
|
+ // prepare the query that will lookup node ids
|
|
|
+ $sql = "SELECT nid FROM {chado_feature} ".
|
|
|
+ "WHERE feature_id = %d";
|
|
|
+ while($feature = db_fetch_object($features)){
|
|
|
+ $node = db_fetch_object(db_query($sql,$feature->feature_id));
|
|
|
+ if($node){
|
|
|
+ $name= "<a href=\"" . url("node/$node->nid") . "\">$feature->name</a>";
|
|
|
+ } else {
|
|
|
+ $name= "$feature->name";
|
|
|
+ }
|
|
|
+ $content .= " <tr>";
|
|
|
+ $content .= " <td>$name</td>";
|
|
|
+ $content .= " <td>$feature->cvname</td>";
|
|
|
+ $content .= " </tr>";
|
|
|
+ }
|
|
|
+ $content .= "</table>";
|
|
|
+ $content .= theme('pager');
|
|
|
+ $content .= "</div></div>";
|
|
|
+ return $content;
|
|
|
+ }
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ * This function is an extension of the chado_feature_view by providing
|
|
|
+ * the markup for the feature object THAT WILL BE INDEXED.
|
|
|
+ */
|
|
|
+function theme_tripal_feature_search_index ($node) {
|
|
|
+ $feature = $node->feature;
|
|
|
+ $content = '';
|
|
|
+
|
|
|
+ // get the accession prefix
|
|
|
+ $aprefix = variable_get('chado_feature_accession_prefix','ID');
|
|
|
+
|
|
|
+ $content .= "<h1>$feature->uniquename</h1>. ";
|
|
|
+ $content .= "<strong>$aprefix$feature->feature_id.</strong> ";
|
|
|
+ $content .= "$feature->cvname ";
|
|
|
+ $content .= "$feature->common_name ";
|
|
|
+
|
|
|
+ // 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 ";
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return $content;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ * This function is an extension of the chado_feature_view by providing
|
|
|
+ * the markup for the feature object THAT WILL BE INDEXED.
|
|
|
+ */
|
|
|
+function theme_tripal_feature_search_results ($node) {
|
|
|
+ $feature = $node->feature;
|
|
|
+ $content = '';
|
|
|
+
|
|
|
+ // get the accession prefix
|
|
|
+ $aprefix = variable_get('chado_feature_accession_prefix','ID');
|
|
|
+
|
|
|
+ $content .= "Feature Name: <h1>$feature->uniquename</h1>. ";
|
|
|
+ $content .= "<strong>Accession: $aprefix$feature->feature_id.</strong>";
|
|
|
+ $content .= "Type: $feature->cvname. ";
|
|
|
+ $content .= "Organism: $feature->common_name. ";
|
|
|
+
|
|
|
+ // 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, ";
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return $content;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_sync_features ($max_sync = 0, $job_id = NULL){
|
|
|
+ $i = 0;
|
|
|
+
|
|
|
+ // get the list of available sequence ontology terms for which
|
|
|
+ // we will build drupal pages from features in chado. If a feature
|
|
|
+ // is not one of the specified typse we won't build a node for it.
|
|
|
+ $allowed_types = variable_get('chado_feature_types','EST contig');
|
|
|
+ $allowed_types = preg_replace("/[\s\n\r]+/"," ",$allowed_types);
|
|
|
+ $so_terms = split(' ',$allowed_types);
|
|
|
+ $where_cvt = "";
|
|
|
+ foreach ($so_terms as $term){
|
|
|
+ $where_cvt .= "CVT.name = '$term' OR ";
|
|
|
+ }
|
|
|
+ $where_cvt = substr($where_cvt,0,strlen($where_cvt)-3); # strip trailing 'OR'
|
|
|
+
|
|
|
+ // get the list of organisms that are synced and only include features from
|
|
|
+ // those organisms
|
|
|
+ $orgs = tripal_organism_get_synced();
|
|
|
+ $where_org = "";
|
|
|
+ foreach($orgs as $org){
|
|
|
+ $where_org .= "F.organism_id = $org->organism_id OR ";
|
|
|
+ }
|
|
|
+ $where_org = substr($where_org,0,strlen($where_org)-3); # strip trailing 'OR'
|
|
|
+
|
|
|
+ // use this SQL statement to get the features that we're going to upload
|
|
|
+ $sql = "SELECT feature_id ".
|
|
|
+ "FROM {FEATURE} F ".
|
|
|
+ " INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
|
|
|
+ "WHERE ($where_cvt) AND ($where_org) ".
|
|
|
+ "ORDER BY feature_id";
|
|
|
+ // get the list of features
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $results = db_query($sql);
|
|
|
+
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ // load into ids array
|
|
|
+ $count = 0;
|
|
|
+ $ids = array();
|
|
|
+ while($id = db_fetch_object($results)){
|
|
|
+ $ids[$count] = $id->feature_id;
|
|
|
+ $count++;
|
|
|
+ }
|
|
|
+
|
|
|
+ // make sure our vocabularies are set before proceeding
|
|
|
+ tripal_feature_set_vocabulary();
|
|
|
+
|
|
|
+ // pre-create the SQL statement that will be used to check
|
|
|
+ // if a feature has already been synced. We skip features
|
|
|
+ // that have been synced
|
|
|
+ $sql = "SELECT * FROM {chado_feature} WHERE feature_id = %d";
|
|
|
+
|
|
|
+ // Iterate through features that need to be synced
|
|
|
+ $interval = intval($count * 0.01);
|
|
|
+ foreach($ids as $feature_id){
|
|
|
+ // update the job status every 1% features
|
|
|
+ if($job_id and $i % $interval == 0){
|
|
|
+ tripal_job_set_progress($job_id,intval(($i/$count)*100));
|
|
|
+ }
|
|
|
+ // if we have a maximum number to sync then stop when we get there
|
|
|
+ // if not then just continue on
|
|
|
+ if($max_sync and $i == $max_sync){
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+ if(!db_fetch_object(db_query($sql,$feature_id))){
|
|
|
+ tripal_feature_sync_feature ($feature_id);
|
|
|
+ }
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+
|
|
|
+ return '';
|
|
|
+}
|
|
|
+
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_sync_feature ($feature_id){
|
|
|
+
|
|
|
+ global $user;
|
|
|
+ $create_node = 1; // set to 0 if the node exists and we just sync and not create
|
|
|
+
|
|
|
+ // get the accession prefix
|
|
|
+ $aprefix = variable_get('chado_feature_accession_prefix','ID');
|
|
|
+
|
|
|
+ // if we don't have a feature_id then return
|
|
|
+ if(!$feature_id){
|
|
|
+ drupal_set_message(t("Please provide a feature_id to sync"));
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+
|
|
|
+ // get information about this feature
|
|
|
+ $fsql = "SELECT F.feature_id, F.name, F.uniquename,O.genus, ".
|
|
|
+ " O.species,CVT.name as cvname,F.residues,F.organism_id ".
|
|
|
+ "FROM {FEATURE} F ".
|
|
|
+ " INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id ".
|
|
|
+ " INNER JOIN Organism O ON F.organism_id = O.organism_ID ".
|
|
|
+ "WHERE F.feature_id = %d";
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $feature = db_fetch_object(db_query($fsql,$feature_id));
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ // check to make sure that we don't have any nodes with this feature name as a title
|
|
|
+ // but without a corresponding entry in the chado_feature table if so then we want to
|
|
|
+ // clean up that node. (If a node is found we don't know if it belongs to our feature or
|
|
|
+ // not since features can have the same name/title.)
|
|
|
+ $tsql = "SELECT * FROM {node} N ".
|
|
|
+ "WHERE title = '%s'";
|
|
|
+ $cnsql = "SELECT * FROM {chado_feature} ".
|
|
|
+ "WHERE nid = %d";
|
|
|
+ $nodes = db_query($tsql,$feature->name);
|
|
|
+ // cycle through all nodes that may have this title
|
|
|
+ while($node = db_fetch_object($nodes)){
|
|
|
+ $feature_nid = db_fetch_object(db_query($cnsql,$node->nid));
|
|
|
+ if(!$feature_nid){
|
|
|
+ drupal_set_message(t("$feature_id: A node is present but the chado_feature entry is missing... correcting"));
|
|
|
+ node_delete($node->nid);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // check if this feature already exists in the chado_feature table.
|
|
|
+ // if we have a chado feature, we want to check to see if we have a node
|
|
|
+ $cfsql = "SELECT * FROM {chado_feature} ".
|
|
|
+ "WHERE feature_id = %d";
|
|
|
+ $nsql = "SELECT * FROM {node} ".
|
|
|
+ "WHERE nid = %d";
|
|
|
+ $chado_feature = db_fetch_object(db_query($cfsql,$feature->feature_id));
|
|
|
+ if($chado_feature){
|
|
|
+ drupal_set_message(t("$feature_id: A chado_feature entry exists"));
|
|
|
+ $node = db_fetch_object(db_query($nsql,$chado_feature->nid));
|
|
|
+ if(!$node){
|
|
|
+ // if we have a chado_feature but not a node then we have a problem and
|
|
|
+ // need to cleanup
|
|
|
+ drupal_set_message(t("$feature_id: The node is missing, but has a chado_feature entry... correcting"));
|
|
|
+ $df_sql = "DELETE FROM {chado_feature} WHERE feature_id = %d";
|
|
|
+ db_query($df_sql,$feature_id);
|
|
|
+ } else {
|
|
|
+ drupal_set_message(t("$feature_id: A corresponding node exists"));
|
|
|
+ $create_node = 0;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // if we've encountered an error then just return.
|
|
|
+ if($error_msg = db_error()){
|
|
|
+ //print "$error_msg\n";
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+
|
|
|
+ // if a drupal node does not exist for this feature then we want to
|
|
|
+ // create one. Note that the node_save call in this block
|
|
|
+ // will call the hook_submit function which
|
|
|
+ if($create_node){
|
|
|
+ drupal_set_message(t("$feature_id: Creating node $feature->name"));
|
|
|
+ $new_node = new stdClass();
|
|
|
+ $new_node->type = 'chado_feature';
|
|
|
+ $new_node->uid = $user->uid;
|
|
|
+ $new_node->title = "$feature->name";
|
|
|
+ $new_node->feature_id = $feature->feature_id;
|
|
|
+ $new_node->residues = $feature->residues;
|
|
|
+ $new_node->organism_id = $feature->organism_id;
|
|
|
+ $new_node->feature_type = $feature->cvname;
|
|
|
+
|
|
|
+ // validate the node and if okay then submit
|
|
|
+ node_validate($new_node);
|
|
|
+ if ($errors = form_get_errors()) {
|
|
|
+ foreach($errors as $key => $msg){
|
|
|
+ drupal_set_message($msg);
|
|
|
+ }
|
|
|
+ return $errors;
|
|
|
+ } else {
|
|
|
+ $node = node_submit($new_node);
|
|
|
+ node_save($node);
|
|
|
+ }
|
|
|
+
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $node = $chado_feature;
|
|
|
+ }
|
|
|
+
|
|
|
+
|
|
|
+ // set the taxonomy for this node
|
|
|
+ drupal_set_message(t("$feature_id ($node->nid): setting taxonomy"));
|
|
|
+ tripal_feature_set_taxonomy($node,$feature_id);
|
|
|
+
|
|
|
+ // reindex the node
|
|
|
+ drupal_set_message(t("$feature_id( $node->nid): indexing"));
|
|
|
+ tripal_feature_index_feature ($feature_id,$node->nid);
|
|
|
+
|
|
|
+ // remove any URL alias that may already exist and recreate
|
|
|
+ drupal_set_message(t("$feature_id ($node->nid): setting URL alias"));
|
|
|
+ db_query("DELETE FROM {url_alias} WHERE dst = '%s'", "$aprefix$feature_id");
|
|
|
+ path_set_alias("node/$node->nid","$aprefix$feature_id");
|
|
|
+
|
|
|
+ return '';
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_set_vocabulary (){
|
|
|
+
|
|
|
+ //include the file containing the required functions for adding taxonomy vocabs
|
|
|
+ module_load_include('inc', 'taxonomy', 'taxonomy.admin');
|
|
|
+
|
|
|
+ // 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;
|
|
|
+ $an_vid = NULL;
|
|
|
+
|
|
|
+ // These taxonomic terms are hard coded because we
|
|
|
+ // konw we have these relationships in the chado tables
|
|
|
+ // through foreign key relationships. The tripal
|
|
|
+ // modules that correspond to these chado "modules" don't
|
|
|
+ // need to be installed for the taxonomy to work.
|
|
|
+ foreach($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 = $vocab->vid;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ if(!$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_execute('taxonomy_form_vocabulary', $form_state,$values);
|
|
|
+ drupal_execute('taxonomy_form_vocabulary', $form_state);
|
|
|
+ }
|
|
|
+
|
|
|
+ if(!$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_execute('taxonomy_form_vocabulary', $form_state,$values);
|
|
|
+ drupal_execute('taxonomy_form_vocabulary', $form_state);
|
|
|
+ }
|
|
|
+
|
|
|
+ if(!$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_execute('taxonomy_form_vocabulary', $form_state, $values);
|
|
|
+ drupal_execute('taxonomy_form_vocabulary', $form_state);
|
|
|
+ }
|
|
|
+
|
|
|
+ if(!$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_execute('taxonomy_form_vocabulary', $form_state,$values);
|
|
|
+ drupal_execute('taxonomy_form_vocabulary', $form_state);
|
|
|
+ }
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_del_vocabulary(){
|
|
|
+ //include the file containing the required functions for adding taxonomy vocabs
|
|
|
+ module_load_include('inc', 'taxonomy', 'taxonomy.admin');
|
|
|
+
|
|
|
+ // get the vocabularies
|
|
|
+ $vocabularies = taxonomy_get_vocabularies();
|
|
|
+
|
|
|
+ // These taxonomic terms are hard coded because we
|
|
|
+ // know we have these relationships in the chado tables
|
|
|
+ // through foreign key relationships. The tripal
|
|
|
+ // modules that correspond to these chado "modules" don't
|
|
|
+ // need to be installed for the taxonomy to work.
|
|
|
+ foreach($vocabularies as $vocab){
|
|
|
+ if($vocab->name == 'Feature Type'){
|
|
|
+ taxonomy_del_vocabulary($vocab->vid);
|
|
|
+ }
|
|
|
+ if($vocab->name == 'Organism'){
|
|
|
+ taxonomy_del_vocabulary($vocab->vid);
|
|
|
+ }
|
|
|
+ if($vocab->name == 'Library'){
|
|
|
+ taxonomy_del_vocabulary($vocab->vid);
|
|
|
+ }
|
|
|
+ if($vocab->name == 'Analysis'){
|
|
|
+ taxonomy_del_vocabulary($vocab->vid);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_features_set_taxonomy($max_sync = 0,$job_id = NULL){
|
|
|
+
|
|
|
+ // 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 = %d";
|
|
|
+ $i = 0;
|
|
|
+
|
|
|
+ // load into ids array
|
|
|
+ $count = 0;
|
|
|
+ $chado_features = array();
|
|
|
+ while($chado_feature = db_fetch_object($results)){
|
|
|
+ $chado_features[$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 % $interval == 0){
|
|
|
+ tripal_job_set_progress($job_id,intval(($i/$count)*100));
|
|
|
+ }
|
|
|
+ $node = db_fetch_object(db_query($nsql,$chado_feature->nid));
|
|
|
+ tripal_feature_set_taxonomy($node,$chado_feature->feature_id);
|
|
|
+
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_set_taxonomy ($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', '');
|
|
|
+ $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";
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $feature = db_fetch_object(db_query($sql));
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ // Set the feature type for this feature
|
|
|
+ if($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 = %d ";
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $library = db_fetch_object(db_query($sql,$feature_id));
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+ $tags["$lb_vid"] = "$library->name";
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the analysis that this feature may belong to and add it as taxonomy
|
|
|
+ if($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 ";
|
|
|
+ $results = db_query($sql);
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $analysis_terms = array();
|
|
|
+ while($analysis=db_fetch_object($results)){
|
|
|
+ // TODO -- how to set more than one taxonmy term ????
|
|
|
+ $analysis_terms[] = "$analysis->name";
|
|
|
+ // $tags["$an_vid"] = "$analysis->name";
|
|
|
+ }
|
|
|
+ $tags["$an_vid"] = $analysis_terms;
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+ }
|
|
|
+
|
|
|
+ // now add the taxonomy to the node
|
|
|
+ $terms['tags'] = $tags;
|
|
|
+ taxonomy_node_save($node,$terms);
|
|
|
+ // print "Setting $node->title: " . implode(", ",$tags) . "\n";
|
|
|
+
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_features_reindex ($max_sync,$job_id = NULL){
|
|
|
+ $i = 0;
|
|
|
+
|
|
|
+ // We register a shutdown function to ensure that the nodes
|
|
|
+ // that are indexed will have proper entries in the search_totals
|
|
|
+ // table. Without these entries, the searching doesn't work
|
|
|
+ // properly. This function may run for quite a while since
|
|
|
+ // it must calculate the sum of the scores of all entries in
|
|
|
+ // the search_index table. In the case of common words like
|
|
|
+ // 'contig', this will take quite a while
|
|
|
+ register_shutdown_function('search_update_totals');
|
|
|
+
|
|
|
+ // use this SQL statement to get the features that we're going to index. This
|
|
|
+ // SQL statement is derived from the hook_search function in the Drupal API.
|
|
|
+ // Essentially, this is the SQL statement that finds all nodes that need
|
|
|
+ // reindexing, but adjusted to include the chado_feature
|
|
|
+ $sql = "SELECT N.nid, N.title, CF.feature_id ".
|
|
|
+ "FROM {node} N ".
|
|
|
+ " INNER JOIN chado_feature CF ON CF.nid = N.nid ";
|
|
|
+ $results = db_query($sql);
|
|
|
+
|
|
|
+ // load into ids array
|
|
|
+ $count = 0;
|
|
|
+ $chado_features = array();
|
|
|
+ while($chado_feature = db_fetch_object($results)){
|
|
|
+ $chado_features[$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 % $interval == 0){
|
|
|
+ tripal_job_set_progress($job_id,intval(($i/$count)*100));
|
|
|
+ }
|
|
|
+
|
|
|
+ // sync only the max requested
|
|
|
+ if($max_sync and $i == $max_sync){
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+ tripal_feature_index_feature ($chado_feature->feature_id,$chado_feature->nid);
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+
|
|
|
+ return '';
|
|
|
+}
|
|
|
+
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_index_feature ($feature_id,$nid){
|
|
|
+ // return if we haven't been provided with a feature_id
|
|
|
+ if(!$feature_id){
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ // if we only have a feature_id then let's find a corresponding
|
|
|
+ // node. If we can't find a node then return.
|
|
|
+ if(!$nid){
|
|
|
+ $nsql = "SELECT N.nid,N.title FROM {chado_feature} CF ".
|
|
|
+ " INNER JOIN {node} N ON N.nid = CF.nid ".
|
|
|
+ "WHERE CF.feature_id = %d";
|
|
|
+ $node = db_fetch_object(db_query($nsql,$feature_id));
|
|
|
+ if(!$node){
|
|
|
+ return 0;
|
|
|
+ }
|
|
|
+ $node = node_load($node->nid);
|
|
|
+ } else {
|
|
|
+ $node = node_load($nid);
|
|
|
+ }
|
|
|
+
|
|
|
+ // node load the noad, the comments and the taxonomy and
|
|
|
+ // index
|
|
|
+ $node->build_mode = NODE_BUILD_SEARCH_INDEX;
|
|
|
+ $node = node_build_content($node, FALSE, FALSE);
|
|
|
+ $node->body = drupal_render($node->content);
|
|
|
+ node_invoke_nodeapi($node, 'view', FALSE, FALSE);
|
|
|
+ $node->body .= module_invoke('comment', 'nodeapi', $node, 'update index');
|
|
|
+ $node->body .= module_invoke('taxonomy','nodeapi', $node, 'update index');
|
|
|
+ // print "$node->title: $node->body\n";
|
|
|
+ search_index($node->nid,'node',$node->body);
|
|
|
+ return 1;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_features_cleanup($dummy = NULL, $job_id = NULL) {
|
|
|
+
|
|
|
+ // build the SQL statments needed to check if nodes point to valid features
|
|
|
+ $dsql = "SELECT * FROM {node} WHERE type = 'chado_feature' order by nid";
|
|
|
+ $nsql = "SELECT * FROM {node} WHERE nid = %d";
|
|
|
+ $csql = "SELECT * FROM {chado_feature} where nid = %d ";
|
|
|
+ $cfsql= "SELECT * FROM {chado_feature}";
|
|
|
+ $tsql = "SELECT * FROM {feature} F ".
|
|
|
+ " INNER JOIN CVTerm CVT ON F.type_id = CVT.cvterm_id ".
|
|
|
+ "WHERE feature_id = %d AND (";
|
|
|
+ $supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
|
|
|
+ foreach($supported_ftypes as $ftype){
|
|
|
+ $tsql .= " CVT.name = '$ftype' OR ";
|
|
|
+ }
|
|
|
+ $tsql .= " 0=1) "; // add a 0=1 just as a filler so we don't have to remove a trailing 'OR'
|
|
|
+
|
|
|
+ // load into nodes array
|
|
|
+ $results = db_query($dsql);
|
|
|
+ $count = 0;
|
|
|
+ $nodes = array();
|
|
|
+ while($node = db_fetch_object($results)){
|
|
|
+ $nodes[$count] = $node;
|
|
|
+ $count++;
|
|
|
+ }
|
|
|
+
|
|
|
+ // load the chado_features into an array
|
|
|
+ $results = db_query($cfsql);
|
|
|
+ $cnodes = array();
|
|
|
+ while($node = db_fetch_object($results)){
|
|
|
+ $cnodes[$count] = $node;
|
|
|
+ $count++;
|
|
|
+ }
|
|
|
+ $interval = intval($count * 0.01);
|
|
|
+
|
|
|
+ // iterate through all of the chado_feature nodes and delete those that aren't valid
|
|
|
+ foreach($nodes as $nid){
|
|
|
+
|
|
|
+ // update the job status every 1% features
|
|
|
+ if($job_id and $i % $interval == 0){
|
|
|
+ tripal_job_set_progress($job_id,intval(($i/$count)*100));
|
|
|
+ }
|
|
|
+
|
|
|
+ // first check to see if the node has a corresponding entry
|
|
|
+ // in the chado_feature table. If not then delete the node.
|
|
|
+ $feature = db_fetch_object(db_query($csql,$nid->nid));
|
|
|
+ if(!$feature){
|
|
|
+ node_delete($nid->nid);
|
|
|
+ $message = "Missing in chado_feature table.... DELETING: $nid->nid\n";
|
|
|
+ watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
+ // second check to see if the node is for a feature of an allowed type.
|
|
|
+ // if not, then delete the node. This check will also take care of the
|
|
|
+ // case when a node exists and an entry in the chado_feature table exists
|
|
|
+ // but no feature with a matching feature_id exists
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $ftype = db_fetch_object(db_query($tsql,$feature->feature_id));
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+
|
|
|
+ if(!$ftype){
|
|
|
+ node_delete($nid->nid);
|
|
|
+ db_query("DELETE FROM {chado_feature} WHERE feature_id = $feature->feature_id");
|
|
|
+ $message = "Node of the wrong feature type.... DELETING: $nid->nid\n";
|
|
|
+ watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
|
|
|
+ }
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+
|
|
|
+ // iterate through all of the chado_feature nodes and delete those that aren't valid
|
|
|
+ foreach($cnodes as $nid){
|
|
|
+ // update the job status every 1% features
|
|
|
+ if($job_id and $i % $interval == 0){
|
|
|
+ tripal_job_set_progress($job_id,intval(($i/$count)*100));
|
|
|
+ }
|
|
|
+ $node = db_fetch_object(db_query($nsql,$nid->nid));
|
|
|
+ if(!$node){
|
|
|
+ db_query("DELETE FROM {chado_feature} WHERE nid = $nid->nid");
|
|
|
+ $message = "chado_feature missing node.... DELETING: $nid->nid\n";
|
|
|
+ watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
|
|
|
+ }
|
|
|
+
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+ return '';
|
|
|
+}
|
|
|
+
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_bulkload(){
|
|
|
+ return drupal_get_form('tripal_feature_load_fasta_form');
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_load_fasta_form (&$form_state = NULL){
|
|
|
+
|
|
|
+ // get the list of organisms
|
|
|
+ $sql = "SELECT * FROM {Organism} ORDER BY genus,species";
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $org_rset = db_query($sql);
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+ $organisms = array();
|
|
|
+ $organisms[''] = '';
|
|
|
+ while($organism = db_fetch_object($org_rset)){
|
|
|
+ $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the list of supported feature types
|
|
|
+ $ftypes = array();
|
|
|
+ $ftypes[''] = '';
|
|
|
+ $supported_ftypes = split("[ \n]",variable_get('chado_feature_feature_types','EST contig'));
|
|
|
+ foreach($supported_ftypes as $ftype){
|
|
|
+ $ftypes["$ftype"] = $ftype;
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the list of libraries
|
|
|
+ // TODO !!!! Use Ajax to filter this automatically based on the organism
|
|
|
+ // selected by the user. This will prevent mistakes from user input.
|
|
|
+ $sql = "SELECT * FROM {Library} L ".
|
|
|
+ " INNER JOIN Organism O ON L.organism_id = O.organism_id ".
|
|
|
+ "ORDER BY L.name";
|
|
|
+ $previous_db = db_set_active('chado'); // use chado database
|
|
|
+ $lib_rset = db_query($sql);
|
|
|
+ db_set_active($previous_db); // now use drupal database
|
|
|
+ $libraries = array();
|
|
|
+ $libraries[''] = '';
|
|
|
+ while($library = db_fetch_object($lib_rset)){
|
|
|
+ $libraries[$library->library_id] = "$library->name ($library->genus $library->species)";
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['#attributes']['enctype'] = 'multipart/form-data';
|
|
|
+
|
|
|
+ $form['organism'] = array (
|
|
|
+ '#title' => t('Organism'),
|
|
|
+ '#type' => t('select'),
|
|
|
+ '#description' => t("Choose the organism with which these sequences are associated "),
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#default_vaule' => '',
|
|
|
+ '#options' => $organisms,
|
|
|
+ '#weight' => 1,
|
|
|
+ );
|
|
|
+ $form['library'] = array (
|
|
|
+ '#title' => t('Library'),
|
|
|
+ '#type' => t('select'),
|
|
|
+ '#description' => t("Choose the library with from which these sequences are derived. Leave blank if not applicable."),
|
|
|
+ '#required' => FALSE,
|
|
|
+ '#default_vaule' => '',
|
|
|
+ '#options' => $libraries,
|
|
|
+ '#weight' => 2,
|
|
|
+ );
|
|
|
+ $form['ftype'] = array (
|
|
|
+ '#title' => t('Feature Type'),
|
|
|
+ '#type' => t('select'),
|
|
|
+ '#description' => t("Choose the category of sequences you are uploading. All sequences in the FASTA file will be imported as this type"),
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#default_vaule' => '',
|
|
|
+ '#options' => $ftypes,
|
|
|
+ '#weight' => 3,
|
|
|
+ );
|
|
|
+ $form['fasta_file'] = array(
|
|
|
+ '#type' => t('file'),
|
|
|
+ '#title' => t('Fasta File'),
|
|
|
+ '#description' => t('Upload a FASTA file of sequences. The definition line should contain only the feature name. All other annotations should be removed. The file must not be larger than ' . file_upload_max_size() . ' bytes'),
|
|
|
+ '#weight' => 4,
|
|
|
+ );
|
|
|
+ $form['upload'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => t('Upload File'),
|
|
|
+ '#weight' => 2,
|
|
|
+ '#executes_submit_callback' => TRUE,
|
|
|
+ '#weight' => 5,
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_load_fasta_form_validate($form, &$form_state){
|
|
|
+
|
|
|
+ // TODO !!! check that the fasta file is valid
|
|
|
+
|
|
|
+ global $user;
|
|
|
+
|
|
|
+ // we need a path within the drupal installation to temporarily use as the destination
|
|
|
+ // after we upload, we'll move the file to analysis directory
|
|
|
+ $upload_url = file_directory_path() . "/chado_feature_bulk_upload/$user->uid";
|
|
|
+
|
|
|
+ // create the download directory. We do it this way rather than the
|
|
|
+ // file_check_directory because we don't want a drupal message presented
|
|
|
+ // the user when the directory is created.
|
|
|
+ if (!is_dir($upload_url)) {
|
|
|
+ mkdir($upload_url,0775,TRUE);
|
|
|
+ }
|
|
|
+
|
|
|
+ // upload the file and copy it to the proper location
|
|
|
+ $validators = array(); // we don't have any validators
|
|
|
+ if($file = file_save_upload('fasta_file',$validators,$upload_url)){
|
|
|
+ drupal_set_message("File $file->name uploaded succesfully");
|
|
|
+ } else {
|
|
|
+ form_set_error('fasta_file',t('Upload Failed'));
|
|
|
+ }
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_load_fasta_form_submit($form, &$form_state){
|
|
|
+ global $user;
|
|
|
+
|
|
|
+ // add a job to be executed
|
|
|
+ tripal_add_job ($job_name,$type,$callback,$uid);
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_return_fasta($feature,$desc){
|
|
|
+ $fasta = ">" . variable_get('chado_feature_accession_prefix','ID') . "$feature->feature_id|$feature->name";
|
|
|
+ $fasta .= " $desc\n";
|
|
|
+ $fasta .= wordwrap($feature->residues, 50, "\n", true);
|
|
|
+ $fasta .= "\n\n";
|
|
|
+ return $fasta;
|
|
|
+}
|
|
|
+
|
spficklin