'; $output .= 'All Database References should strictly pertain to THE CURRENT Individual
'; $output .= '
Current Database References
'; $output .= tripal_stock_list_dbreferences_for_node($node->db_references); $output .= '

'; $output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node); $output .= '
'; $output .= drupal_get_form('tripal_stock_add_chado_properties_navigate', 'db_references', $node->nid); return $output; } /** * Implements Hook_form() * Handles adding of Database References to Stocks */ function tripal_stock_add_ONE_dbreference_form($form_state, $node) { $stock_id = $node->stock_id; $form['db_nid'] = array( '#type' => 'hidden', '#value' => $node->nid ); $form['add_dbreference'] = array( '#type' => 'fieldset', '#title' => t('Add Database References') . '(optional)', ); $form['add_properties']['db_stock_id'] = array( '#type' => 'value', '#value' => $stock_id, '#required' => TRUE ); $form['add_dbreference']['accession'] = array( '#type' => 'textfield', '#title' => t('Accession Number'), ); $form['add_dbreference']['db_description'] = array( '#type' => 'textarea', '#title' => t('Description of Database Reference') . '+', '#description' => t('Optionally enter a description about the database accession.') ); $db_options = tripal_db_get_db_options(); $db_options[0] = 'Select a Database'; ksort($db_options); $form['add_dbreference']['database'] = array( '#type' => 'select', '#title' => t('Database'), '#options' => $db_options, ); $form['add_dbreference']['submit'] = array( '#type' => 'submit', '#value' => t('Add Database Reference') ); return $form; } function tripal_stock_add_ONE_dbreference_form_validate($form, &$form_state) { // Only ensure db reference valid if adding if ($form_state['clicked_button']['#value'] == t('Add Database Reference') ) { //Do work of required validators if ($form_state['values']['accession'] == '') { form_set_error('accession', 'Accession field is Required.'); } // Check database is valid db_id in chado if ( $form_state['values']['database'] > 0) { $previous_db = tripal_db_set_active('chado'); $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM db WHERE db_id=%d",$form_state['values']['database'])); tripal_db_set_active($previous_db); if ($tmp_obj->count != 1) { form_set_error('database', 'The database you selected is not valid. Please choose another one.'); } } else { form_set_error('database', 'Please select a database'); } // Check Accession is unique for database $previous_db = tripal_db_set_active('chado'); $tmp_obj = db_fetch_object(db_query("SELECT count(*) as count FROM dbxref WHERE accession='%s'",$form_state['values']['accession'])); tripal_db_set_active($previous_db); if ($tmp_obj->count > 0) { form_set_error('accession', 'This accession has already been assigned to another stock.'); } } //end of if adding } function tripal_stock_add_ONE_dbreference_form_submit($form, &$form_state) { // FIX: Sometimes on programatic submission of form (drupal_execute) values in the form state get lost // however, the post values always seem to be correct if (empty($form_state['values']['db_stock_id'])) { $form_state['values']['db_stock_id'] = $form_state['clicked_button']['#post']['db_stock_id']; } // Only Create if valid if ($form_state['values']['database'] > 0) { // create dbxref $previous_db = tripal_db_set_active('chado'); db_query( "INSERT INTO dbxref (db_id, accession, description) VALUES (%d, '%s', '%s')", $form_state['values']['database'], $form_state['values']['accession'], $form_state['values']['db_description'] ); tripal_db_set_active($previous_db); //create stock_dbxref $dbxref = tripal_db_get_dbxref_by_accession($form_state['values']['accession'], $form_state['values']['database']); if (!empty($dbxref->dbxref_id)) { $previous_db = tripal_db_set_active('chado'); db_query( "INSERT INTO stock_dbxref (stock_id, dbxref_id) VALUES (%d, %d)", $form_state['values']['db_stock_id'], $dbxref->dbxref_id ); tripal_db_set_active($previous_db); drupal_set_message('Successfully Added Database Reference'); } else { drupal_set_message('Database reference NOT successfully created...','error'); } //end of if dbxref was created successfully } //end of if valid db reference } /************************************************************************************************************* * @section * Deals with Editing and Deleting Properties */ function tripal_stock_edit_ALL_dbreferences_page($node) { $output = ''; $output .= drupal_get_form('tripal_stock_edit_ALL_db_references_form', $node); $output .= '
'; $output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node); $output .= '
'; $output .= drupal_get_form('tripal_stock_back_to_stock_button', $node->nid); return $output; } /** * Implements Hook_form() * Handles adding of Properties & Synonyms to Stocks */ function tripal_stock_edit_ALL_db_references_form($form_state, $node) { $form = array(); $form['nid'] = array( '#type' => 'hidden', '#value' => $node->nid ); $i=0; if (sizeof($node->db_references) != 0) { foreach ($node->db_references as $ref) { $i++; $form["num-$i"] = array( '#type' => 'item', '#value' => $i.'.' ); $form["accession-$i"] = array( '#type' => 'textfield', //'#title' => t('Accession'), '#size' => 30, '#required' => TRUE, '#default_value' => $ref->accession ); $db_options = tripal_db_get_db_options(); $db_options[0] = 'Select a Database'; ksort($db_options); $form["database-$i"] = array( '#type' => 'select', //'#title' => t('Database'), '#options' => $db_options, '#default_value' => $ref->db_id ); $form["id-$i"] = array( '#type' => 'hidden', '#value' => $ref->dbxref_id ); $form["submit-$i"] = array( '#type' => 'submit', '#value' => t("Delete #$i") ); }} //end of foreach db ref $form['num_db_references'] = array( '#type' => 'hidden', '#value' => $i ); $form["submit-edits"] = array( '#type' => 'submit', '#value' => t('Update DB References') ); return $form; } function tripal_stock_edit_ALL_db_references_form_submit($form, &$form_state) { if ($form_state['clicked_button']['#value'] == t('Update DB References') ) { //Update all for ($i=1; $i<=$form_state['values']['num_db_references']; $i++) { tripal_stock_update_db_reference( $form_state['values']["id-$i"], $form_state['values']["database-$i"], $form_state['values']["accession-$i"] ); } drupal_set_message("Updated all Database References"); drupal_goto('node/'.$form_state['values']['nid']); } elseif ( preg_match('/Delete #(\d+)/', $form_state['clicked_button']['#value'], $matches) ) { $i = $matches[1]; tripal_stock_delete_db_reference($form_state['values']["id-$i"]); drupal_set_message("Deleted Database Reference"); } else { drupal_set_message("Unrecognized Button Pressed",'error'); } } function tripal_stock_update_db_reference($dbxref_id, $database_id, $accession) { $previous_db = tripal_db_set_active('chado'); db_query( "UPDATE dbxref SET db_id=%d, accession='%s' WHERE dbxref_id=%d", $database_id, $accession, $dbxref_id ); tripal_db_set_active($previous_db); } function tripal_stock_delete_db_reference($dbxref_id) { $previous_db = tripal_db_set_active('chado'); db_query( "DELETE FROM dbxref WHERE dbxref_id=%d", $dbxref_id ); db_query( "DELETE FROM stock_dbxref WHERE dbxref_id=%d", $dbxref_id ); tripal_db_set_active($previous_db); } function theme_tripal_stock_edit_ALL_db_references_form ($form) { $output = ''; $output .= '

'; $output .= 'Edit Existing Database References(optional)'; $output .= '

Below is a list of already existing database references, one per line. When entering a database reference, the accession ' .'is a unique identifier for this stock in the specified database.

'; $output .= ''; $output .= ''; for ($i=1; $i<=$form['num_db_references']['#value']; $i++) { $output .= ''; } $output .= '

#	Database	Accession
'.drupal_render($form["num-$i"]).'	' .drupal_render($form["database-$i"]).'	' .drupal_render($form["accession-$i"]).'	' .drupal_render($form["submit-$i"]).'

'; $output .= drupal_render($form); $output .= '

'; return $output; } /************************************************************************************************************* * @section * Supplimentary functions */ /** * */ function tripal_stock_list_dbreferences_for_node($db_references) { if (!empty($db_references) ) { $output = ''; $output .= ''; foreach ($db_references as $db) { $output .= ''; } // end of foreach db reference $output .= '

Database	Accession
'.$db->db_name.'	'.$db->accession.'

'; } else { $output = 'No Database References Added to the Current Stock'; } return $output; }