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+<?php
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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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+function tripal_db_init(){
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+
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+ // add the tripal_db JS and CSS
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+ drupal_add_css(drupal_get_path('theme', 'tripal').
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+ '/css/tripal_db.css');
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+ drupal_add_js(drupal_get_path('theme', 'tripal').'/js/tripal_db.js');
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+}
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+/*************************************************************************
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+*
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+*/
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+function tripal_db_menu() {
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+ $items = array();
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+
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+ $items['admin/tripal/tripal_db'] = array(
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+ 'title' => 'DB',
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+ 'description' => 'Manage External Databases ',
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+ 'page callback' => 'tripal_db_list',
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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/tripal/tripal_db/new'] = array(
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+ 'title' => 'Add DB',
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+ 'page callback' => 'drupal_get_form',
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+ 'page arguments' => array('tripal_db_form'),
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+ 'access arguments' => array('access administration pages'),
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+ 'type' => MENU_NORMAL_ITEM,
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+ );
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+ $items['admin/tripal/tripal_db/edit/%'] = array(
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+ 'title' => 'Edit DB',
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+ 'page callback' => 'drupal_get_form',
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+ 'page arguments' => array('tripal_db_form',4),
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+ 'access arguments' => array('access administration pages'),
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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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+* 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_db_perm(){
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+ return array(
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+ 'access chado_db content',
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+ 'create chado_db content',
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+ 'delete chado_db content',
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+ 'edit chado_db content',
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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 tripal_db_list () {
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+ $previous_db = db_set_active('chado');
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+ $dbs = pager_query("SELECT * FROM {db} ORDER BY db_id",30,0,
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+ "SELECT count(*) FROM {db}");
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+ db_set_active($previous_db);
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+
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+
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+ // build the URLs using the url function so we can handle installations where
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+ // clean URLs are or are not used
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+ $new_url = url("admin/tripal/tripal_db/new");
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+ $output .= "Below is the list of all external databases.";
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+ $output .= "<br><a href=\"$new_url\">Add a new external database</a>";
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+ $output .= "<table class=\"border-table\">".
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+ " <tr>".
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+ " <th></th>".
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+ " <th>ID</th>".
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+ " <th>Name</th>".
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+ " <th>Description</th>".
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+ " <th>URL</th>".
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+ " <th>URL Prefix</th>".
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+ " </tr>";
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+ while($db = db_fetch_object($dbs)){
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+ $edit_url = url("admin/tripal/tripal_db/edit/$db->db_id");
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+ $output .= " <tr>".
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+ " <td><a href=\"$edit_url\">edit</a></td>".
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+ " <td>$db->db_id</td>".
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+ " <td>$db->name</td>".
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+ " <td>$db->description</td>".
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+ " <td>$db->url</td>".
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+ " <td>$db->urlprefix</td>".
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+ " </tr>";
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+ }
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+ $output .= "</table>";
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+ $output .= theme_pager();
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+ return $output;
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+}
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+/*************************************************************************
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+*
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+*/
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+function tripal_db_form(&$form_state = NULL,$db_id = NULL){
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+
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+ if(!$db_id){
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+ $action = 'Add';
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+ } else {
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+ $action = 'Update';
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+ }
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+
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+ // get this requested database
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+ if(strcmp($action,'Update')==0){
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+ $sql = "SELECT * FROM {db} WHERE db_id = $db_id ";
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+ $previous_db = db_set_active('chado');
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+ $db = db_fetch_object(db_query($sql));
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+ db_set_active($previous_db);
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+
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+
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+ # set the default values. If there is a value set in the
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+ # form_state then let's use that, otherwise, we'll pull
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+ # the values from the database
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+ $default_db = $form_state['values']['name'];
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+ $default_desc = $form_state['values']['description'];
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+ $default_url = $form_state['values']['url'];
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+ $default_urlprefix = $form_state['values']['urlprefix'];
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+ if(!$default_db){
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+ $default_db = $db->name;
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+ }
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+ if(!$default_desc){
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+ $default_desc = $db->description;
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+ }
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+ if(!$default_url){
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+ $default_url = $db->url;
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+ }
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+ if(!$default_urlprefix){
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+ $default_urlprefix = $db->urlprefix;
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+ }
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+ }
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+
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+ // Build the form
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+ $form['action'] = array(
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+ '#type' => 'value',
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+ '#value' => $action
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+ );
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+ $form['db_id'] = array(
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+ '#type' => 'value',
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+ '#value' => $db_id
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+ );
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+ $form['name']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Database Name'),
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+ '#description' => t('Please enter the name for this external database.'),
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+ '#required' => TRUE,
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+ '#default_value' => $default_db,
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+ '#weight' => 1
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+ );
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+
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+ $form['description']= array(
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+ '#type' => 'textarea',
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+ '#title' => t('Description'),
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+ '#description' => t('Please enter a description for this database'),
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+ '#default_value' => $default_desc,
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+ '#weight' => 2
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+ );
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+ $form['url']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('URL'),
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+ '#description' => t('Please enter the web address for this database.'),
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+ '#default_value' => $default_url,
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+ '#weight' => 3
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+ );
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+ $form['urlprefix']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('URL prefix'),
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+ '#description' => t('Tripal can provide links to external databases when accession numbers or unique identifiers are known. Typically, a database will provide a unique web address for each accession and the accession usually is the last component of the page address. Please enter the web address, minus the accession number for this database. When an accession number is present, Tripal will combine this web address with the accession and provide a link to the external site.'),
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+ '#default_value' => $default_urlprefix,
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+ '#weight' => 4
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+ );
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+ $form['submit'] = array (
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+ '#type' => 'submit',
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+ '#value' => t($action),
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+ '#weight' => 5,
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+ '#executes_submit_callback' => TRUE,
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+ );
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+ $form['#redirect'] = 'admin/tripal/tripal_db';
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+ return $form;
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+}
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+/************************************************************************
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+*
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+*/
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+function tripal_db_form_submit($form, &$form_state){
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+ $action = $form_state['values']['action'];
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+ $db_id = $form_state['values']['db_id'];
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+ $name = $form_state['values']['name'];
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+ $desc = $form_state['values']['description'];
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+ $url = $form_state['values']['url'];
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+ $urlp = $form_state['values']['urlprefix'];
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+
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+ if(strcmp($action,'Update')==0){
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+ $sql = "
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+ UPDATE {db} SET
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+ name = '$name',
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+ description = '$desc',
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+ url = '$url',
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+ urlprefix = '$urlp'
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+ WHERE db_id = $db_id
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+ ";
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+ $previous_db = db_set_active('chado');
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+ $db = db_query($sql);
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+ db_set_active($previous_db);
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+ if($db){
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+ drupal_set_message("Database updated");
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+ } else {
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+ drupal_set_message("Failed to update database.");
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+ }
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+ }
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+ else if(strcmp($action,'Add')==0){
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+ $sql = "
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+ INSERT INTO {db}
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+ (name,description,url,urlprefix)
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+ VALUES
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+ ('$name','$desc','$url','$urlp')
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+ ";
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+ $previous_db = db_set_active('chado');
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+ $db = db_query($sql);
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+ db_set_active($previous_db);
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+ if($db){
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+ drupal_set_message("Database added");
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+ } else {
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+ drupal_set_message("Failed to add database.");
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+ }
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+ }
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+ else {
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+ drupal_set_message("No action performed.");
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+ }
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+ return '';
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+}
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+
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spficklin