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-<?php
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-// $Id$
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-
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-/**
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- * @file
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- * This file contains all the functions which provide functionality to this module.
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- * This module was developed by Chad N.A. Krilow and Lacey-Anne Sanderson,
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- * University of Saskatchewan.
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- *
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- * The GBrowse manamgenet module allows you to sync data in a chado/Tripal instance with
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- * multiple GBrowse/mysql instances as well as manage and create such GBrowse instances
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- */
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-
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-include('tripal_gbrowse.align_features.inc');
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-
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-//-----------------------------------------------------------------------------
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-// SECTION: Main Outline Menu for GBrowse Management
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-//-----------------------------------------------------------------------------
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-
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-
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-/**
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- * Tripal-GBrowse-Menu
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- *
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- * Implemets hook_menu(): Adds menu items for the tripal_gbrowse module menu. This section
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- * gives the outline for the main menu of the Tripal-GBrowse module
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- *
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- * @return
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- * An array of menu items that is visible within the Drupal Menu, returned as soon
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- * as the program is ran
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- */
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-function tripal_gbrowse_menu() {
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-
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- $items = array();
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-
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- $items[ 'admin/tripal/tripal_gbrowse' ]= array(
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- 'title' => t('GBrowse Management'),
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- 'description' => ('GBrowse management allows a user to create a database, register
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- a GBrowse instance and to load/delete feature libraries'),
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- 'page callback' => 'tripal_gbrowse_administration_description_page',
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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_gbrowse/configuration'] = array(
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- 'title' => t('Configuration'),
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- 'description' => t('Configuration for this module'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_administration_form'),
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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_gbrowse/register_gbrowse'] = array(
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- 'title' => t('Register GBrowse Instance'),
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- 'description' => t('Interface to enter gbrowse details and save to the database'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_register_gbrowse_form'),
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- 'access arguments' => array('administer site configuration'),
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- 'weight' => 20,
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- 'type' => MENU_NORMAL_ITEM
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- );
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-
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- $items['admin/tripal/tripal_gbrowse/unregister_gbrowse']=array(
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- 'title' => t('Un-Register GBrowse Instance'),
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- 'description' => t('Interface to remove gbrowse details from the database'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_unregister_gbrowse_instances_form'),
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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_gbrowse/load_library_features'] = array(
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- 'title' => t('Load Library Features'),
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- 'description' => t('Load features associated with a specified library into a GBrowse instance.'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_load_library_features_form'),
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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_gbrowse/load_analysis_features'] = array(
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- 'title' => t('Load Analysis Features'),
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- 'description' => t('Load features associated with a specified analyses into a GBrowse instance.'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_load_analyses_form'),
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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_gbrowse/delete_library_features']=array(
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- 'title' => t('Delete Library Features'),
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- 'description' => t('Interface to delete features of a given library from a GBrowse Instance'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_delete_library_features_from_gbrowse_form'),
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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_gbrowse/delete_analysis_features']=array(
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- 'title' => t('Delete Analysis Features'),
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- 'description' => t('Interface to delete features of a given analysis from a GBrowse Instance'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_delete_analysis_features_from_gbrowse_form'),
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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_gbrowse/add_tracks']=array(
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- 'title' => t('Add Tracks'),
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- 'description' => t('Interface for Adding tracks to a GBrowse Instance'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_add_tracks_form'),
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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_gbrowse/delete_tracks']=array(
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- 'title' => t('Delete Tracks'),
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- 'description' => t('Interface for Deleting tracks from a GBrowse Instance'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_delete_tracks_form'),
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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_gbrowse/align_features']=array(
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- 'title' => t('Align Features'),
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- 'description' => t('Align a group of features (either library or analysis) against another grouping of features.'),
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('tripal_gbrowse_align_features_form'),
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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 $items;
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-}
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-
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-/**
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- * Implements hook_theme_registry_alter().
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- */
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-function tripal_gbrowse_theme_registry_alter(&$info) {
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- // Inject our module into the node theme registry as being an available theme
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- // path so that we can override the node template for our content type.
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- array_splice($info['node']['theme paths'], 1, 0, array(drupal_get_path('module', 'tripal_gbrowse')));
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-}
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-
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-
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-/**
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- * Implements hook_theme(): Register themeing functions for this module
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- *
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- * Contains the seperate tripal_gbrowse_X.tpl.php files, so as they can be included in the
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- * theme for the designed module
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- *
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- * @return
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- * An array of themeing functions to register
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- *
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- */
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-function tripal_gbrowse_theme() {
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-
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- $path = drupal_get_path('module', 'tripal_gbrowse_theme') . '/theme/tripal_gbrowse';
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-
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- return array(
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- // Block Templates------------------------------
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- 'tripal_gbrowse_database_details' => array (
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- 'arguments' => array('node'=> null),
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- 'template' => 'tripal_gbrowse_database_details',
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- 'path' => $path,
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- ),
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- 'tripal_gbrowse_details' => array (
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- 'arguments' => array('node'=> null),
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- 'template' => 'tripal_gbrowse_details',
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- 'path' => $path,
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- ),
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- 'tripal_gbrowse_gbrowse_instance' => array (
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- 'arguments' => array('node'=> null),
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- 'template' => 'tripal_gbrowse_gbrowse_instance',
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- 'path' => $path,
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- ),
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- 'tripal_gbrowse_teaser' => array (
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- 'arguments' => array('node'=> null),
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- 'template' => 'tripal_gbrowse_teaser',
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- 'path' => $path,
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- ),
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- 'tripal_gbrowse_loaded_sources' => array (
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- 'arguments' => array('node'=> null),
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- 'template' => 'tripal_gbrowse_loaded_sources',
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- 'path' => $path,
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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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- * Purpose: Implement Blocks relating to Tripal GBrowse content
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- *
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- * @param $op
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- * What kind of information to retrieve about the block or blocks.
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- * Possible values include list, configure, save, view.
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- * @param $delta
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- * Which block to return (not applicable if $op is 'list').
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- * @param $edit
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- * If $op is 'save', the submitted form data from the configuration form.
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- *
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- * @return
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- * One of the following depending on $op: An array of block descriptions (list), the configuration
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- * form (configure), nothing (save), an array defining subject and content for the block indexed
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- * by $delta (view)
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- *
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- */
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-function tripal_gbrowse_block ($op = 'list', $delta = 0, $edit=array()) {
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- switch($op) {
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- case 'list':
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- $blocks['database_details']['info'] = t('Tripal GBrowse Database Details');
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- $blocks['database_details']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['details']['info'] = t('Tripal GBrowse Details');
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- $blocks['details']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['gbrowse_instance']['info'] = t('Tripal GBrowse Instance');
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- $blocks['gbrowse_instance']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['teaser']['info'] = t('Tripal GBrowse Teaser');
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- $blocks['teaser']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['teaser']['info'] = t('Tripal GBrowse Sources');
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- $blocks['teaser']['cache'] = BLOCK_NO_CACHE;
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-
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- return $blocks;
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-
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- case 'view':
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- if(user_access('access tripal_gbrowse content') and arg(0) == 'node' and is_numeric(arg(1))) {
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- $nid = arg(1);
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- $node = node_load($nid);
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-
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- $block = array();
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- switch($delta){
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- case 'database_details':
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- $block['subject'] = t('Tripal GBrowse Database Details');
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- $block['content'] = theme('tripal_gbrowse_database_details',$node);
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- break;
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-
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- case 'details':
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- $block['subject'] = t('Tripal GBrowse Details');
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- $block['content'] = theme('tripal_gbrowse_details',$node);
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- break;
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-
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- case 'gbrowse_instance':
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- $block['subject'] = t('Tripal GBrowse Instance');
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- $block['content'] = theme('tripal_gbrowse_gbrowse_instance',$node);
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- break;
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-
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- case 'teaser':
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- $block['subject'] = t('Tripal GBrowse Teaser');
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- $block['content'] = theme('tripal_gbrowse_teaser',$node);
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- break;
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-
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- case 'teaser':
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- $block['subject'] = t('Tripal GBrowse Sources');
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- $block['content'] = theme('tripal_gbrowse_loaded_sources',$node);
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- break;
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-
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- }
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- return $block;
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- }
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- }
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-}
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-
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-
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-/**
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- * Implements hook_views_api()
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- * Purpose: Essentially this hook tells drupal that there is views support
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- * for this module which then includes tripal_db.views.inc where all the
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- * views integration code is
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- */
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-function tripal_gbrowse_views_api() {
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- return array(
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- 'api' => 2.0,
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- );
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-}
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-
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-
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-/**
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- * This section uses HTML to output the descriptions of the module, through the Tripal Management
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- * Administation window.Any installation instructions are given as well as included features
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- * as well as a overview of the purpose Module.
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- *
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- * @return
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- * Returns '$text'The HTML description of the Module, its instructions, features, and any other
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- * important aspects. This is returned when the Administration page is selected.
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- */
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-function tripal_gbrowse_administration_description_page() {
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-
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- $text = ' ';
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-
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- $text .= '</p><h3>GBrowse Feature Administrative Tools Quick Links:</h3>';
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-
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- $text .= "<ul>";
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-
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- $text .= "<li>".l("Configuration", "admin/tripal/tripal_gbrowse/configuration"). "</li>";
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- $text .= "<li>".l('Register GBrowse Instance', 'node/add/tripal-gbrowse')."</li>";
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- $text .= "<li>".l("Load Library Features", "admin/tripal/tripal_gbrowse/load_library_features"). "</li>";
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- $text .= "<li>".l("Delete Library Features", "admin/tripal/tripal_gbrowse/delete_library_features"). "</li>";
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- $text .= "<li>".l("Load Analysis Features", "admin/tripal/tripal_gbrowse/load_analysis_features"). "</li>";
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- $text .= "<li>".l("Delete Analysis Features", "admin/tripal/tripal_gbrowse/delete_analysis_features"). "</li>";
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- $text .= "<li>".l("Add Tracks","admin/tripal/tripal_gbrowse/add_tracks"). "</li>";
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- $text .= "<li>".l("Delete Tracks","admin/tripal/tripal_gbrowse/delete_tracks"). "</li>";
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-
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-
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- $text .= "</ul>";
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-
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- $text .= '<h3>Module Description:</h3>';
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- $text .= '<p>This module provides an interface to register already existing GBrowse instances with Drupal/Tripal and/or create new '
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- .'GBrowse Instances. Furthermore, it allows basic management of these GBrowse instances including un-registering and/or '
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- .'deleting and loading of features in Tripal/Chado into a MySQL GBrowse instance. As such, it provides interoperability '
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- .'and syncronization between a Tripal/Chado installation and GBrowse</p>';
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-
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- $text .= '<h3>Setup Instructions:</h3>';
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- $text .= '<ol>';
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- $text .= '<li><b>Ensure the PHP-MySQL extension is installed:</b> Installation instructions are dependant upon your operating system.</li>';
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- $text .= '<li><b>Move Template Configuration File:</b> Move the template.conf file included with this module into the GBrowse configuration file directory.</li>';
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- $text .= '<li><b>Set GBrowse Instance Defaults :</b> Set default repository for Configuration files, also set the default GBrowse web link address.</li>'
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- .'<a href="tripal_gbrowse/configuration">Administration -> Tripal Management -> GBrowse Management -> Configuration</a>.</li>';
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-
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- $text .= '<li><b>Register Existing GBrowse Instances</b>: Register any existing GBrowse instances through the form provided at '
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- .'<a href="tripal_gbrowse/register_gbrowse">Administration -> Tripal Management -> GBrowse Management -> Register GBrowse Instance</a>.</li>';
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- $text .= '<li><b>Load desired Feature Libraries into GBrowse Instances</b>: Additional feature libraries should be loaded through the form provided at '.l('Administration -> Tripal Management -> GBrowse Management -> Load Features','admin/tripal/tripal_gbrowse/load_features').'</li>';
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- $text .= '<ol>';
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-
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- $text .= '<h3>Features of this Module:</h3>';
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- $text .= '<ul>';
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- $text .= '<li><b>Register GBrowse Instance:</b> In order to load features into a GBrowse instance you need to first register it with Tripal/Drupal. Any existing '
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- .'GBrowse instance that utilizes a MySQL database can be registered with the module. Furthermore, you can create new GBrowse Instances '
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- .'through this module by selecting that option in the register GBrowse Instance form. This'
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- .'newly created GBrowse instance uses a MySQL database with is created and '
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- .'a user name and password is setup and a default configuration file is created. Finally, the database is initialized and the first sequence '
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- .'set is loaded into the GBrowse instance.</li>';
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-
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- $text .= '<li><b>Un-Register/Delete GBrowse Instance:</b> Un-registering a GBrowse instance alone will remove the GBrowse instance from the Drupal site.'
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- .'When removing the entire instance, the database and the configuration file will be deleted. This cannot be undone!</li>';
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-
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- $text .='<li><b>Intergrated GBrowse Node/Page:</b> Allows users to easily access GBrowse instances that have been created.'
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- .'This module provides details for a registered GBrowse Instance, including an I-Frame, providing instance access to the GBrowse display,'
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- .'as well,the module provides a link to a GBrowse instance in a new window.</li>';
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-
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- $text .= '<li><b>Load Library Features:</b> Simply by selecting a Tripal Library and a GBrowse Instance, '
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- .'the features associated with the selected Library are loaded into the selected GBrowse Instance. Libraries can also be updated by selecting that option. This removes all of the pre-existing'
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- .'features associated with that library, then reloades them. Both loading and updating utilize the Perl script "bp_seqfeature_load.pl" which should be installed when you install GBrowse.</li>';
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-
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- $text .= '<li><b>Load Analysis Features:</b> Simply by selecting a Tripal Analysis and a GBrowse Instance, '
|
|
|
- .'the analyses associated with the selected Library are loaded into the selected GBrowse Instance. Analyses can also be updated by selecting that option. This removes all of the pre-existing'
|
|
|
- .'features associated with that analysis, then reloades them. Both loading and updating utilize the Perl script "bp_seqfeature_load.pl" which should be installed when you install GBrowse.</li>';
|
|
|
-
|
|
|
- $text .= '<li><b>Delete Feature (Libraries) Libraries:</b> A user can select a desired Tripal Library and a specific GBrowse instance and all of the features associated with that library in the selected isntance are removed.'
|
|
|
- .' This section uses the Perl "script bp_seqfeature_delete.pl" to delete the specified features.</li>';
|
|
|
- $text .= '<li><b>Delete (Libraries) Analysis :</b> A user can select a desired Tripal Analysis and a specific GBrowse instance and all of the features associated with that analysis in the selected isntance are removed.'
|
|
|
- .' This section uses the Perl "script bp_seqfeature_delete.pl" to delete the specified features.</li>';
|
|
|
-
|
|
|
- $text .= '<li><b>Add Tracks:</b> Allows a user to add tracks to a given GBrowse instance. This allows them to define exactly how they want their features to be displayed, as well as, to separate their features into their own GBrowse track.</li>';
|
|
|
-
|
|
|
- $text .= '<li><b>Delete Tracks:</b> Allows a user to delete default tracks or user created tracks for a given GBrowse instance.</li>';
|
|
|
-
|
|
|
- $text .= '</ul>';
|
|
|
-
|
|
|
- return $text;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_job_describe_args()
|
|
|
- *
|
|
|
- * This function modifies the Job Arguments page and represents the job arguments with
|
|
|
- * meaningfull descriptive names, sends a link to the library and shows if the database
|
|
|
- * was cleared or not.
|
|
|
- *
|
|
|
- * @param $call_back
|
|
|
- * The name of the function being called by tripal_jobs
|
|
|
- *
|
|
|
- * @param $args
|
|
|
- * The arguments that are passed, given if the selected proccess is
|
|
|
- * 1-'tripal_gbrowse_delete_library_features_from_gbrowse'
|
|
|
- * 2-'tripal_gbrowse_load_library_features_into_gbrowse'*
|
|
|
- * 3-'tripal_gbrowse_delete_analysis_features_from_gbrowse'
|
|
|
- * 3-'tripal_gbrowse_load_analysis_features_into_gbrowse'
|
|
|
- * If 1- then the arguments are based on deleting a library feature from GBrowse.
|
|
|
- * If 2- then the arguments are based on loading library features into GBrowse.
|
|
|
- * If 3- then the arguments are based on deleting a analysis feature from GBrowse.
|
|
|
- * If 4- then the arguments are based on loading analysis features into GBrowse.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * Job arguments:Database name, user Name, Password, Library ID, If GBrowse database was cleared,
|
|
|
- * to be displayed in Job Details page.
|
|
|
- */
|
|
|
-function tripal_gbrowse_job_describe_args($call_back, $args){
|
|
|
-
|
|
|
- switch ($call_back){
|
|
|
-
|
|
|
- case 'tripal_gbrowse_delete_library_features_from_gbrowse':
|
|
|
-
|
|
|
- $new_args['GBrowse Database Name']=$args[0];
|
|
|
-
|
|
|
- $new_args['User Name']=$args[1];
|
|
|
-
|
|
|
- $new_args['Password']=$args[2];
|
|
|
- $result = db_fetch_object(db_query("SELECT nid FROM chado_library WHERE library_id=%d",$args[3]));
|
|
|
-
|
|
|
- $node = node_load($result->nid);
|
|
|
-
|
|
|
- $new_args['Library']= l($node->title, 'node/'.$result->nid);
|
|
|
-
|
|
|
- if(empty($args[4])){
|
|
|
- $new_args['Clear GBrowse Database']= 'No';
|
|
|
- }else{
|
|
|
- $new_args['Clear GBrowse Database']= 'Yes';
|
|
|
- }
|
|
|
-
|
|
|
- break;
|
|
|
-
|
|
|
- case 'tripal_gbrowse_load_library_features_into_gbrowse':
|
|
|
-
|
|
|
- $new_args['GBrowse Database Name']=$args[0];
|
|
|
-
|
|
|
- $new_args['User Name']=$args[1];
|
|
|
-
|
|
|
- $new_args['Password']=$args[2];
|
|
|
-
|
|
|
- $result = db_fetch_object(db_query("SELECT nid FROM chado_library WHERE library_id=%d",$args[3]));
|
|
|
-
|
|
|
- $node = node_load($result->nid);
|
|
|
-
|
|
|
- $new_args['Library']= l($node->title, 'node/'.$result->nid);
|
|
|
-
|
|
|
- if(empty($args[4])){
|
|
|
- $new_args['Clear GBrowse Database']= 'No';
|
|
|
- }else{
|
|
|
- $new_args['Clear GBrowse Database']= 'Yes';
|
|
|
- }
|
|
|
-
|
|
|
- break;
|
|
|
-
|
|
|
- case 'tripal_gbrowse_delete_analysis_features_from_gbrowse':
|
|
|
-
|
|
|
- $new_args['GBrowse Database Name']=$args[0];
|
|
|
-
|
|
|
- $new_args['User Name']=$args[1];
|
|
|
-
|
|
|
- $new_args['Password']=$args[2];
|
|
|
- $result = db_fetch_object(db_query("SELECT nid FROM chado_analysis WHERE analysis_id=%d",$args[3]));
|
|
|
-
|
|
|
- $node = node_load($result->nid);
|
|
|
-
|
|
|
- $new_args['Analysis']= l($node->title, 'node/'.$result->nid);
|
|
|
-
|
|
|
- if(empty($args[4])){
|
|
|
- $new_args['Clear GBrowse Database']= 'No';
|
|
|
- }else{
|
|
|
- $new_args['Clear GBrowse Database']= 'Yes';
|
|
|
- }
|
|
|
-
|
|
|
- break;
|
|
|
-
|
|
|
- case 'tripal_gbrowse_load_analysis_features_into_gbrowse':
|
|
|
-
|
|
|
- $new_args['GBrowse Database Name']=$args[0];
|
|
|
-
|
|
|
- $new_args['User Name']=$args[1];
|
|
|
-
|
|
|
- $new_args['Password']=$args[2];
|
|
|
-
|
|
|
- $result = db_fetch_object(db_query("SELECT nid FROM chado_analysis WHERE analysis_id=%d",$args[3]));
|
|
|
-
|
|
|
- $node = node_load($result->nid);
|
|
|
-
|
|
|
- $new_args['Analysis']= l($node->title, 'node/'.$result->nid);
|
|
|
-
|
|
|
- if(empty($args[4])){
|
|
|
- $new_args['Clear GBrowse Database']= 'No';
|
|
|
- }else{
|
|
|
- $new_args['Clear GBrowse Database']= 'Yes';
|
|
|
- }
|
|
|
-
|
|
|
- break;
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- return $new_args;
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Database API
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * The purpose of this function is to retrieve the previousley loaded libraries from database.
|
|
|
- *
|
|
|
- * @param $gbrowse
|
|
|
- * A GBrowse instance that contains the information of the current instance
|
|
|
- *
|
|
|
- * @return
|
|
|
- * An array of libraries that have been loaded into the database
|
|
|
- */
|
|
|
-function tripal_gbrowse_getloaded_sources($gbrowse){
|
|
|
-
|
|
|
- $loaded_libraries = array();
|
|
|
-
|
|
|
- $link = mysql_connect('localhost', $gbrowse->database_user, $gbrowse->user_password);
|
|
|
-
|
|
|
- if (!$link) {
|
|
|
- drupal_set_message('Could not connect to database: ' . mysql_error(), 'error');
|
|
|
- }
|
|
|
-
|
|
|
- //Sending query to the database
|
|
|
- $resource = mysql_query('use ' .$gbrowse->database_name);
|
|
|
-
|
|
|
- if (empty($resource)) {
|
|
|
- drupal_set_message ('Database is empty or Non-existent','error');
|
|
|
- }
|
|
|
-
|
|
|
- $resource = mysql_query('select * from typelist');
|
|
|
-
|
|
|
- if (empty($resource)) {
|
|
|
- drupal_set_message ('Missing table typelist in database. Check sequence backbone has been loaded (Execute: tripal jobs) ','error');
|
|
|
- } else {
|
|
|
-
|
|
|
- $library_array = array();
|
|
|
-
|
|
|
- while($record = mysql_fetch_object($resource)){
|
|
|
- preg_match('/^[^:]+:(.+)/', $record->tag, $matches);
|
|
|
- $library_array[$matches[1]]= $matches[1];
|
|
|
- }
|
|
|
- }
|
|
|
- mysql_close($link);
|
|
|
-
|
|
|
- return $library_array;
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * The purpose of this function is to firstly create a file for backup purposes. Secondly, this
|
|
|
- * function uses a 'mysqldump' the contents of the selected database to a backup file. It then
|
|
|
- * access the database, drops the old database, creates a new one with the modified infromation,
|
|
|
- * then uploads the previously backed up infromation into the newly created database.
|
|
|
- *
|
|
|
- *
|
|
|
- * @param $node
|
|
|
- * A node object containing the data and infromation of the GBrowse instance
|
|
|
- *
|
|
|
- * @param $old_database
|
|
|
- * The name of the originally created database, which will be replaced if the user
|
|
|
- * changes the name of the database that they have created
|
|
|
- *
|
|
|
- * @return FALSE
|
|
|
- * If error in creating database, or creating database, else nothing is returned
|
|
|
- */
|
|
|
-function tripal_gbrowse_database_modification($node,$old_database){
|
|
|
-
|
|
|
- global $user;
|
|
|
-
|
|
|
- $user_name = $node->database_user;
|
|
|
-
|
|
|
- $user_password = $node->user_password;
|
|
|
-
|
|
|
- //creating a file in the /tmp directory for back-up purposes
|
|
|
- $back_upfile = '/tmp/' .$old_database .'_'.time().'.sql';
|
|
|
-
|
|
|
- //Using the 'mysqldump' command to dump the database for backup purposses
|
|
|
- $command = 'mysqldump -u' .$user_name .' -p' .$user_password .' ' .$old_database .' > ' .$back_upfile;
|
|
|
-
|
|
|
- exec($command);
|
|
|
-
|
|
|
- //To create a database use the mysql_query() function to execute an SQL query
|
|
|
- $link = mysql_connect('localhost', $user_name,$user_password);
|
|
|
-
|
|
|
- //Link operation verification
|
|
|
- if (!$link) {
|
|
|
- drupal_set_message('Could not connect: ' . mysql_error(), 'error');
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- //Dropping original database name and information
|
|
|
- $sql = 'DROP DATABASE ' . $old_database;
|
|
|
-
|
|
|
- if(mysql_query($sql, $link)){
|
|
|
- drupal_set_message( "Database Dropped Successfully\n");
|
|
|
- }else{
|
|
|
- drupal_set_message( 'Error Dropping Database: ' . mysql_error(), 'error');
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- $sql = 'CREATE DATABASE ' . $node->database_name;
|
|
|
-
|
|
|
- if (mysql_query($sql, $link)) {
|
|
|
- drupal_set_message( "Database Created Successfully\n");
|
|
|
- }
|
|
|
- else {
|
|
|
- drupal_set_message( 'Error Creating Database: ' . mysql_error() . "\n");
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- mysql_query( "GRANT SELECT ON " .$node->database_name.".* TO 'www-data'@'localhost'",$link);
|
|
|
-
|
|
|
- $command = 'mysql -u' .$user_name .' -p' .$user_password .' ' .$node->database_name .' < ' .$back_upfile;
|
|
|
-
|
|
|
- exec($command);
|
|
|
-
|
|
|
- mysql_close($link);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Node Capability
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implementation of hook_tripal_gbrowse_node_info()
|
|
|
-*
|
|
|
-* This node_info, is a simple node that describes the functionallity of the module. It specifies
|
|
|
-* that the title(gbrowse Name) and body(Description) set to true so that they information can be
|
|
|
-* entered
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_node_info() {
|
|
|
- return array(
|
|
|
- 'tripal_gbrowse' => array(
|
|
|
- 'name' => t('GBrowse Instance'),
|
|
|
- 'module' => 'tripal_gbrowse',
|
|
|
- 'description' => t('A module for interfacing the GMOD database with Drupal, providing:
|
|
|
- Registration,Alteration and Deletion of GBrowse Instances,Configuration Files and Databases
|
|
|
- and the option to load/delete Sequence & Analysis Libraries'),
|
|
|
- 'has_title' => TRUE,
|
|
|
- 'title_label' =>t('gbrowse Name'),
|
|
|
- 'had_body' => FALSE,
|
|
|
- )
|
|
|
- );
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implementation of tripal_gbrowse_form().
|
|
|
-*
|
|
|
-* This form takes the gbrowse Title infromation and the gbrowse description from the user. It
|
|
|
-* then puts the infromation into the Chado_gbrowse database table.
|
|
|
-*
|
|
|
-* @parm &$node
|
|
|
-* The node that is created when the database is initialized
|
|
|
-*
|
|
|
-* @parm $form_state
|
|
|
-* The state of the form, that has the user entered information that is neccessary for, setting
|
|
|
-* up the database of the gbrowse
|
|
|
-*
|
|
|
-* @return $form
|
|
|
-* The information that was enterd allong with
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_form(&$node, $form_state) {
|
|
|
-
|
|
|
- $type = node_get_types('type', $node);
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['register_gbrowse'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t('Data Base Specific Fields'),
|
|
|
- );
|
|
|
-
|
|
|
- //field for the name of the database
|
|
|
- $form['register_gbrowse']['database_name'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('GBrowse Database Name'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('Desired Database Name Field'),
|
|
|
- '#default_value' => isset($node->gbrowse->database_name) ? $node->gbrowse->database_name : '',
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //User of database
|
|
|
- $form['register_gbrowse']['database_user'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('GBrowse User'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('GBrowse MySQL User Field'),
|
|
|
- '#default_value' => isset($node->gbrowse->database_user) ? $node->gbrowse->database_user : '',
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //Specified password for access to database
|
|
|
- $form['register_gbrowse']['user_password'] = array(
|
|
|
- '#type' => 'password',
|
|
|
- '#title' => t('Password'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('User Password Field'),
|
|
|
- '#default_value' => isset($node->gbrowse->user_password) ? $node->gbrowse->user_password : '',
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['gbrowse_details'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title'=>'GBrowse Specifications' ,
|
|
|
- );
|
|
|
-
|
|
|
- //Human-readable name for the gbrowse instance
|
|
|
- $form['gbrowse_details']['title'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('GBrowse Name'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 256,
|
|
|
- '#description' => t('GBrowse Instance'),
|
|
|
- '#default_value' => isset($node->gbrowse->gbrowse_name) ? $node->gbrowse->gbrowse_name : '',
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //$_SERVER: takes the current url and sets to variable
|
|
|
- $default_value = variable_get('tripal_gbrowse_gbrowse_address_stub', '');
|
|
|
-
|
|
|
- //Link to the gbrowse instance
|
|
|
- $form['gbrowse_details']['gbrowse_link'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('GBrowse Link'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 256,
|
|
|
- '#description'=>t('Enter Full HTML address Including Host
|
|
|
- (ex:http://knowpulse2.usask.ca/) of the new GBrowse instance. By default this is '.$default_value.'[configuration file name] where the configuration file name is the same as that entered below except without .conf'),
|
|
|
- '#default_value' => isset($node->gbrowse->gbrowse_link) ? $node->gbrowse->gbrowse_link : $default_value,
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //Fully qualified location to the gbrowse configuration file
|
|
|
- $form['gbrowse_details']['config_file'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Configuration File'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 256,
|
|
|
- '#description' => t('Enter Fully Qualified File Name including Path (ex: file.conf) '),
|
|
|
- '#default_value' => isset($node->gbrowse->config_file) ? $node->gbrowse->config_file : variable_get('tripal_gbrowse_configuration_file_path', ''),
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );
|
|
|
-
|
|
|
- foreach ($result as $value) {
|
|
|
-
|
|
|
- $newArray[$value->library_id]=$value->name; //options for the select list
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- if (!$node->gbrowse->gbrowse_id) {
|
|
|
-
|
|
|
- // Creating Fieldset for multiple fields in form
|
|
|
- $form['create_instance'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t('Create New GBrowse Instance'),
|
|
|
- );
|
|
|
-
|
|
|
- if(empty($newArray)){
|
|
|
-
|
|
|
- drupal_set_message('There are currently no libraries to load.','error');
|
|
|
-
|
|
|
- $form['create_instance']['check_box'] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#value'=>'A GBrowse instance can not be created without a valid loadable backbone.
|
|
|
- To make a valid loadable backbone available, please load features grouped in a library using
|
|
|
- any of the feature loaders available.'
|
|
|
- );
|
|
|
-
|
|
|
-
|
|
|
- }else {
|
|
|
-
|
|
|
- //A box if checked creates GBrowse Instances if they do not exist
|
|
|
- $form['create_instance']['check_box'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Create Instance'),
|
|
|
- '#description' => t('Create GBrowse Instane Unless Previous Existance'),
|
|
|
- );
|
|
|
-
|
|
|
- //Library ID
|
|
|
- $form['create_instance']['library_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Sequence BackBone'),
|
|
|
- '#options' => $newArray,
|
|
|
- '#description' => t('Sequence Features Locations'),
|
|
|
- );
|
|
|
- }
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- return $form;
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-function tripal_gbrowse_validate ($node, $form) {
|
|
|
-
|
|
|
- if (!preg_match('/\.conf$/',$node->config_file)) {
|
|
|
- form_set_error('config_file','Configuration file must end in .conf');
|
|
|
- }
|
|
|
-
|
|
|
- if (!preg_match('/^http:\/\//',$node->gbrowse_link)) {
|
|
|
- form_set_error('gbrowse_link','GBrowse Link must be an absolute path (include http://)');
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements tripal_gbrowse_help()
|
|
|
- *
|
|
|
- * This function simply states, in HTML tags, the creator of the the module and the contact
|
|
|
- * for the programmer
|
|
|
- *
|
|
|
- * @parm $path
|
|
|
- * The absolute path of the module and help information
|
|
|
- *
|
|
|
- * @parm $arg
|
|
|
- * The argument
|
|
|
- */
|
|
|
-function tripal_gbrowse_help($path, $arg) {
|
|
|
- switch ($path) {
|
|
|
-
|
|
|
- case 'admin/help#tripal_gbrowse':
|
|
|
-
|
|
|
- return '<p>'. t('Module created by:Chad Krilow (e-mail:cnk046@mail.usask.ca)') .'</p>';
|
|
|
-
|
|
|
- break;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_perm()
|
|
|
- *
|
|
|
- * This function sets the permission for the user to access the information in the database.
|
|
|
- * This includes creating, inserting, deleting and updating of information in the database
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_gbrowse_perm(){
|
|
|
-
|
|
|
- return array('create tripal_gbrowse', 'edit own tripal_gbrowse', 'access database-related details' ,'access tripal_gbrowse content');
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements tripal_gbrowse_access()
|
|
|
- *
|
|
|
- * This function sets the access permission for operations on the database.
|
|
|
- *
|
|
|
- *
|
|
|
- * @parm $op
|
|
|
- * The operation that is to be performed
|
|
|
- *
|
|
|
- * @parm $node
|
|
|
- * The specific node that is to have the operation performed
|
|
|
- *
|
|
|
- * @parm $account
|
|
|
- * The account of the user that is performing the operations
|
|
|
- *
|
|
|
- * @return
|
|
|
- * True if a operation was performed
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_gbrowse_access($op, $node, $account) {
|
|
|
-
|
|
|
- if($op == 'create') {
|
|
|
- // Only users with permission to do so may create this node type.
|
|
|
- if(!user_access('create tripal_gbrowse', $account)){
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Users who create a node may edit or delete it later, assuming they have the
|
|
|
- // necessary permissions.
|
|
|
- if($op == 'update' || $op == 'delete') {
|
|
|
- if(!user_access('edit own tripal_gbrowse',$account)){
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if(user_access('edit own tripal_gbrowse',$account) &&
|
|
|
- $account->uid != $node->uid){
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
- return NULL;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implementation of tripal_gbrowse_insert()
|
|
|
-*
|
|
|
-* This function inserts user entered information pertaining to the GBrowse instance into the
|
|
|
-* 'tripal_gbrowse_instances' talble of the database, requiring that a 'Check Box' has been selected.
|
|
|
-*
|
|
|
-* @parm $node
|
|
|
-* Then node which contains the information stored within the node-ID
|
|
|
-*
|
|
|
-*
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_insert($node) {
|
|
|
-
|
|
|
- $values = array(
|
|
|
- 'database_name'=> $node->database_name,
|
|
|
- 'database_user'=> $node->database_user,
|
|
|
- 'user_password'=> $node->user_password,
|
|
|
- 'gbrowse_name'=> $node->title,
|
|
|
- 'gbrowse_link'=> $node->gbrowse_link,
|
|
|
- 'config_file'=> $node->config_file,
|
|
|
- 'library_id'=>$node->library_id,
|
|
|
- 'nid'=>$node->nid,
|
|
|
- 'vid'=>$node->vid,
|
|
|
- );
|
|
|
-
|
|
|
- //used to write to a database table described by Drupal Schema (not workable for chado)
|
|
|
- drupal_write_record('tripal_gbrowse_instances', $values);
|
|
|
-
|
|
|
- if($node->check_box==1){
|
|
|
- tripal_gbrowse_create_gbrowse_instance($values);
|
|
|
- }else{
|
|
|
- drupal_set_message("Create instance check box not selected, unable initialize instance");
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implementation of tripal_gbrowse_delete().
|
|
|
-*
|
|
|
-* This function takes a node and if the variable 'tripal_gbrowse_delete_all' has been defined,
|
|
|
-* the GBrowse instance pertaining to the node passed into the function is deleted. Following,
|
|
|
-* given the node-ID, the instance will be deleted from the 'tripal_gbrowse_instances' table.
|
|
|
-*
|
|
|
-*
|
|
|
-* @parm $node
|
|
|
-* Then node which contains the information stored within the node-ID
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete($node){
|
|
|
-
|
|
|
- if(variable_get('tripal_gbrowse_delete_all', '')){
|
|
|
- tripal_gbrowse_delete_gbrowse_instance($node->gbrowse);
|
|
|
- }
|
|
|
-
|
|
|
- //deleteing in drupal chado_gbrowse table
|
|
|
- db_query('DELETE FROM {tripal_gbrowse_instances} WHERE nid = %d', $node->nid);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/*
|
|
|
-*
|
|
|
-* Implements hook_update
|
|
|
-*
|
|
|
-* The purpose of the function is to allow the module to take action when an edited node is being
|
|
|
-* updated in the database. It also updates any name changes to the configuration file that was
|
|
|
-* created upon registering a GBrowse instance. This is done by moving the contents of the original
|
|
|
-* configuration file to the newly named file.As well, the database will be changed, if the name
|
|
|
-* is altered by a registered user.If this is the case, the function 'tripal_gbrowse_database_modification'
|
|
|
-* is called and the node and the old database infromation is passed, so as it may be altered and updated
|
|
|
-* accordingley.
|
|
|
-*
|
|
|
-* @param $node
|
|
|
-* The node being updated
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_update($node){
|
|
|
-
|
|
|
- //select from table before doing this, cause i wont be able to see the old details afterwards
|
|
|
- $old_data = db_fetch_object(
|
|
|
- db_query('SELECT database_name,config_file FROM {tripal_gbrowse_instances} WHERE nid=%d AND vid=%d',
|
|
|
- $node->nid, $node->vid));
|
|
|
-
|
|
|
- $old_config_file=$old_data->config_file;
|
|
|
-
|
|
|
- $old_database_name=$old_data->database_name;
|
|
|
-
|
|
|
- $match= array(
|
|
|
- 'nid',
|
|
|
- 'vid',
|
|
|
- );
|
|
|
-
|
|
|
- $values = array(
|
|
|
- 'database_name' => $node->database_name,
|
|
|
- 'database_user' => $node->database_user,
|
|
|
- 'user_password' => $node->user_password,
|
|
|
- 'gbrowse_name' => $node->gbrowse_name,
|
|
|
- 'gbrowse_link' => $node->gbrowse_link,
|
|
|
- 'config_file' => $node->config_file,
|
|
|
- 'library_id'=>$node->library_id,
|
|
|
- 'nid' => $node->nid,
|
|
|
- 'vid' => $node->vid,
|
|
|
- );
|
|
|
-
|
|
|
- //Pulling out the configuration file
|
|
|
- $config_file = $node->config_file;
|
|
|
-
|
|
|
- if(strcmp($old_config_file, $config_file)!=0){
|
|
|
- //Removing configuration file from the directory
|
|
|
- $command = "mv " .$old_config_file ." ".$config_file;
|
|
|
- exec($command);
|
|
|
- }
|
|
|
-
|
|
|
- if($old_database_name != $node->database_name){
|
|
|
- tripal_gbrowse_database_modification($node,$old_database_name);
|
|
|
- }
|
|
|
-
|
|
|
- drupal_write_record('tripal_gbrowse_instances', $values, $match);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implementation of tripal_gbrowse_load().
|
|
|
-*
|
|
|
-*
|
|
|
-* @param $node
|
|
|
-* The node that is to be accessed from the database
|
|
|
-*
|
|
|
-* @return $node
|
|
|
-* The node with the information to be loaded into the database
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_load($node) {
|
|
|
-
|
|
|
- $result = db_fetch_object(db_query('SELECT gbrowse_id,database_name,database_user,user_password,
|
|
|
- gbrowse_name,gbrowse_link,config_file FROM {tripal_gbrowse_instances} WHERE nid=%d AND vid=%d',$node->nid, $node->vid));
|
|
|
-
|
|
|
- $node->gbrowse = $result;
|
|
|
-
|
|
|
- return $node;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Configuration form
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implemets hook_menu(): Adds menu items for the tripal_gbrowse module
|
|
|
-*
|
|
|
-* This form creates a specific Configuration File directory and sets a specific
|
|
|
-* GBrowse web address for later access
|
|
|
-*
|
|
|
-* @return
|
|
|
-* An array of menu items '$form'
|
|
|
-*/
|
|
|
-function tripal_gbrowse_administration_form () {
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['configuration_features'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t('Module Configuration Fields'),
|
|
|
- );
|
|
|
-
|
|
|
- //Configuration File Directory
|
|
|
- $form['configuration_features']['configuration_file'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Set Default Configuration File Directory'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('Specific Configuration File Directory'),
|
|
|
- '#default_value' => variable_get('tripal_gbrowse_configuration_file_path', ''),
|
|
|
- );
|
|
|
-
|
|
|
- //GBrowse Web Address
|
|
|
- $form['configuration_features']['gbrowse_address'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Set Default GBrowse Web Address'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('Desired GBrowse web address'),
|
|
|
- '#default_value' => variable_get('tripal_gbrowse_gbrowse_address_stub', ''),
|
|
|
- );
|
|
|
-
|
|
|
- //A box if checked creates GBrowse Instances(.conf file and database)
|
|
|
- $form['configuration_features']['delete_check_box'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Delete Instance'),
|
|
|
- '#description' => t('Delete GBrowse Configuration file and Database '),
|
|
|
- '#default_value'=>variable_get('tripal_gbrowse_delete_all', ''),
|
|
|
- );
|
|
|
-
|
|
|
- $form['configuration_features']['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#weight' => 10,
|
|
|
- '#value' => t('Submit')
|
|
|
- );
|
|
|
-
|
|
|
- return $form;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Validate User-submitted data for Register GBrowse Instances Form
|
|
|
- *
|
|
|
- * This function validates the user input for each form element in the Register GBrowse
|
|
|
- * instances form that is a text field. Validations checked include:
|
|
|
- * -parse_url-checks that the url can be parsed
|
|
|
- *
|
|
|
- * @param $form
|
|
|
- * The form that the user submitted and whose input is being validated
|
|
|
- * @param $form_state
|
|
|
- * An array containing the state of the form being validated including user-input
|
|
|
- */
|
|
|
-function tripal_gbrowse_administration_form_validate ($form, $form_state) {
|
|
|
-
|
|
|
- if ( !valid_url($form_state['values']['gbrowse_address'])) {
|
|
|
- form_set_error('gbrowse_address', 'Invalid URL');
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-*
|
|
|
-* Configuration-Form
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* -The submitted form containing the user entered infromation
|
|
|
-* @param $form_state
|
|
|
-* -Is the state of the form: i.e what button was pressed, what infromation was entered,etc.
|
|
|
-* The key is the 'values'
|
|
|
-*/
|
|
|
-function tripal_gbrowse_administration_form_submit ($form, $form_state) {
|
|
|
-
|
|
|
- if(!preg_match('/\/$/', $form_state['values']['configuration_file'])) {
|
|
|
- $form_state['values']['configuration_file'] = $form_state['values']['configuration_file'] . "/";
|
|
|
- }
|
|
|
-
|
|
|
- variable_set('tripal_gbrowse_configuration_file_path',$form_state['values']['configuration_file'] );
|
|
|
- drupal_set_message('Configuration File Path set to: '.variable_get('tripal_gbrowse_configuration_file_path', ''));
|
|
|
-
|
|
|
-
|
|
|
- variable_set('tripal_gbrowse_gbrowse_address_stub',$form_state['values']['gbrowse_address'] );
|
|
|
- drupal_set_message('GBrowse Default Address set to: '.variable_get('tripal_gbrowse_gbrowse_address_stub', ''));
|
|
|
-
|
|
|
- if($form_state['values']['delete_check_box']==1){
|
|
|
- variable_set('tripal_gbrowse_delete_all',$form_state['values']['delete_check_box'] );
|
|
|
- drupal_set_message('Selected GBrowse instance will be deleted: '.variable_get('tripal_gbrowse_delete_all', 'NOT SET'));
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Register-GBrowse-Instance
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-*
|
|
|
-* Register & Create GBrowse instance ( called by the node form )
|
|
|
-*
|
|
|
-* This form submit takes it's fields from the form for registering a GBrowse instance. The 'sed'command
|
|
|
-* is used to select certain lines of a template 'conf' file and replaces them with the user specified GBrowse instance
|
|
|
-* and data base name. It then removes the temporary file that was created. This function utilizes the MySQL database
|
|
|
-* and uses the commands for MySQL to create a database for the registered GBrowse instance, appropriate warnings
|
|
|
-* are issued if there are problems connecting/registering/accessing the database.
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* -The submitted form containing the user entered infromation
|
|
|
-*
|
|
|
-* @param $form_state
|
|
|
-* This is the state of the form: i.e what button was pressed.The key is
|
|
|
-* the name of the fields in database
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_create_gbrowse_instance($values) {
|
|
|
-
|
|
|
- global $user; //make current user details available so access of user id is available
|
|
|
-
|
|
|
- //checking for existance of configuration file, if allready created a warning is issued
|
|
|
- if ( file_exists($values['config_file']) ){
|
|
|
- drupal_set_message('Configuration File Already Exists', 'warning');
|
|
|
- }else{
|
|
|
-
|
|
|
- $config_path = variable_get('tripal_gbrowse_configuration_file_path', '');
|
|
|
-
|
|
|
- if(empty($config_path)){
|
|
|
- drupal_set_message( "Invalid or Non-Existent Configuration Path (Check Configuration Menu Defaults)", 'error');
|
|
|
- }
|
|
|
-
|
|
|
- $temp_file = '/tmp/temporary_gbrowse_'.time().'.conf';
|
|
|
-
|
|
|
- // Using 'sed' to select the second line of the template.config substitute <#gbrowse_name>
|
|
|
- //for .$values['gbrowse_name']
|
|
|
- $command = "sed '2 s/<#gbrowse_name#>/".$values['gbrowse_name']."/' ".$config_path."template.conf > ".$temp_file;
|
|
|
-
|
|
|
- exec($command);
|
|
|
-
|
|
|
- // Using 'sed' to select the fifth line of the template.config substitute <#database_name>
|
|
|
- //for .$values['database_name']
|
|
|
- $command = "sed '5 s/<#database_name#>/".$values['database_name']."/' ".$temp_file." > ".$values['config_file'];
|
|
|
-
|
|
|
- exec($command);
|
|
|
-
|
|
|
- // Check configuration file is there
|
|
|
- if (file_exists($values['config_file'])) {
|
|
|
- drupal_set_message('Configuration File created successfully');
|
|
|
- } else {
|
|
|
- drupal_set_message('Unable to create configuration file','error');
|
|
|
- }
|
|
|
-
|
|
|
- //To create a database use the mysql_query() function to execute an SQL query
|
|
|
- $link = mysql_connect('localhost', $values['database_user'],$values['user_password']);
|
|
|
-
|
|
|
- if (!$link) {
|
|
|
- drupal_set_message('Could not connect: ' . mysql_error());
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- $sql = 'CREATE DATABASE ' . $values['database_name'];
|
|
|
-
|
|
|
- if (mysql_query($sql, $link)) {
|
|
|
- drupal_set_message( "Database created successfully\n");
|
|
|
- } else {
|
|
|
- drupal_set_message( 'Error creating database: ' . mysql_error() . "\n");
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- mysql_query( "GRANT SELECT ON " .$values['database_name'].".* TO 'www-data'@'localhost'",$link);
|
|
|
-
|
|
|
- mysql_close($link);
|
|
|
-
|
|
|
- $job_args=array($values['database_name'],$values['database_user'],$values['user_password'],$values['library_id'],TRUE);
|
|
|
-
|
|
|
- //registering a job with the tripal system, this job calls the function when executed
|
|
|
- $job_id = tripal_add_job('Loading Features Into GBrowse', 'tripal_gbrowse','tripal_gbrowse_load_library_features_into_gbrowse', $job_args, $user->uid);
|
|
|
-
|
|
|
- drupal_set_message(' The Backbone needs to be loaded into GBrowse (done by executing Tripal Jobs Loading script),
|
|
|
- Before loaded libraries or GBrowse Instance will be displayed. ');
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Un-Register Existing GBrowse Instances
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Un-Register GBrowse Instance Form Submit
|
|
|
-*
|
|
|
-* This is the Form-Submit section of the Un-Register GBrowse instance function. Depending on
|
|
|
-* which instance was selected, it will be removed from the database. A check box is provided
|
|
|
-* which, if checked is true, will delete all data/files that was associated with the selected
|
|
|
-* GBrowse instance.SQL commands are used in order to remove the selected instances from the
|
|
|
-* SQL database.
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* the submitted form containing the user entered infromation
|
|
|
-* @param $form_state
|
|
|
-* The state of the form: i.e if check-box was checked and what gbrowse_instance was selected to be deleted
|
|
|
-* The key is the 'values'
|
|
|
-*
|
|
|
-* @return
|
|
|
-* true or false, depending wheater the check box had been selected, if true, the
|
|
|
-* selected GBrowse instance will be deleted
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete_gbrowse_instance($gbrowse) {
|
|
|
-
|
|
|
- // Retrieve current gbrowse instance details
|
|
|
- $gbrowse_instance = db_fetch_object(
|
|
|
- db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $gbrowse->gbrowse_id )
|
|
|
- );
|
|
|
-
|
|
|
- //Pulling out the configuration file
|
|
|
- $config_file = $gbrowse->config_file;
|
|
|
-
|
|
|
- //Removing configuration file from the directory
|
|
|
- $command = "rm ".$config_file;
|
|
|
-
|
|
|
- exec($command);
|
|
|
-
|
|
|
- if (file_exists($config_file)) {
|
|
|
- drupal_set_message('Configuration File ('.$config_file.') not removed!', 'error');
|
|
|
- } else {
|
|
|
- drupal_set_message('Configuration File removed successfully');
|
|
|
- }
|
|
|
-
|
|
|
- $user_name = $gbrowse->database_user;
|
|
|
-
|
|
|
- $user_password = $gbrowse->user_password;
|
|
|
-
|
|
|
- $link = mysql_connect('localhost', $user_name,$user_password);
|
|
|
-
|
|
|
- if (!$link) {
|
|
|
- drupal_set_message('Could not connect: ' . mysql_error(), 'error');
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- $sql = 'DROP DATABASE ' . $gbrowse->database_name;
|
|
|
-
|
|
|
- if(mysql_query($sql, $link)){
|
|
|
- drupal_set_message( "Database removed successfully\n");
|
|
|
- }else{
|
|
|
- drupal_set_message( 'Error removing database: ' . mysql_error(), 'error');
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- mysql_close($link);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Load Library features into GBrowse Form & Form Submit
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implements hook_form
|
|
|
-*
|
|
|
-* This function creates a form for the database name, user name for database operation and a
|
|
|
-* password for access.The module uses these features to access information regarding the user's
|
|
|
-* operations and needs.
|
|
|
-*
|
|
|
-* @return
|
|
|
-* An array describing the form to be rendered
|
|
|
-*/
|
|
|
-function tripal_gbrowse_load_library_features_form() {
|
|
|
-
|
|
|
- $new_array=array();
|
|
|
-
|
|
|
- $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );
|
|
|
-
|
|
|
- foreach ($result as $value) {
|
|
|
- $new_array[$value->library_id]=$value->name; //options for the select list
|
|
|
- }
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['load_features'] = array(
|
|
|
- '#type' => 'fieldset'
|
|
|
- );
|
|
|
-
|
|
|
- //Library ID
|
|
|
- $form['load_features']['library_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Libraries'),
|
|
|
- '#options' => $new_array,
|
|
|
- '#description' => t('Library of Genetic Sequences.'),
|
|
|
- );
|
|
|
-
|
|
|
- //Sending query to the database
|
|
|
- $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
|
|
|
-
|
|
|
- $items = array();
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
- $items[$record->gbrowse_id]= $record->gbrowse_name;
|
|
|
- }
|
|
|
-
|
|
|
- //GBrowse Instances
|
|
|
- $form['load_features']['gbrowse_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('GBrowse Instances'),
|
|
|
- '#options' => $items,
|
|
|
- '#description' => t('Selected GBrowse Instances to be Loaded.'),
|
|
|
- );
|
|
|
-
|
|
|
- //A checkbox to update features for the gbrowse
|
|
|
- $form['load_features']['check_box'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Update Features'),
|
|
|
- '#description' => t('Existing Same Name Features Updated Accordingly.'),
|
|
|
- );
|
|
|
-
|
|
|
- $form['load_features']['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#weight' => 10,
|
|
|
- '#value' => t('Submit Job')
|
|
|
- );
|
|
|
-
|
|
|
- return $form;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Load-Features-Form
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* -The submitted form containing the user entered infromation
|
|
|
-* @param $form_state
|
|
|
-* -Is the state of the form: i.e what button was pressed, what infromation was entered,etc.
|
|
|
-* The key is the 'values'
|
|
|
-*/
|
|
|
-function tripal_gbrowse_load_library_features_form_submit($form,$form_state) {
|
|
|
-
|
|
|
- global $user; //needed to make the current users details available so access of user id is available
|
|
|
-
|
|
|
- $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
|
|
|
-
|
|
|
- $name = $record->database_name;
|
|
|
-
|
|
|
- $user_name = $record->database_user;
|
|
|
-
|
|
|
- $password= $record->user_password;
|
|
|
-
|
|
|
- $job_args = array($name,$user_name,$password,$form_state['values']['library_id'], FALSE);
|
|
|
-
|
|
|
- //Checking state of check box, if checked delete features from GBrowse
|
|
|
- if($form_state['values']['check_box']==1){
|
|
|
- //registering a delete job with the tripal system, this job calls the function when executed
|
|
|
- $job_id = tripal_add_job('Deleting Features From GBrowse', 'tripal_gbrowse',
|
|
|
- 'tripal_gbrowse_delete_library_features_from_gbrowse', $job_args, $user->uid);
|
|
|
- }
|
|
|
-
|
|
|
- //registering a job with the tripal system, this job calls the function when executed
|
|
|
- $job_id = tripal_add_job('Loading Features Into GBrowse', 'tripal_gbrowse',
|
|
|
- 'tripal_gbrowse_load_library_features_into_gbrowse', $job_args, $user->uid);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION:Load Library Features into GBrowse
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Load Library features into database
|
|
|
- *
|
|
|
- * This loading function firstly creates a output GFF3 format file for verification purposes. Then, a 'Chado' table
|
|
|
- * is selected,depending which table the user is interested in, from this table specific infromation
|
|
|
- * is taken out and placed in the GFF3 file.The Featurelocation(fmin) & featurelocation (fmax) are used
|
|
|
- * to set the featureloc.feature_id = feature.feature_id, the fmin = start & fmax = end of the desired gene.
|
|
|
- * The testing if the phase is empty is done, if so a '.' is inserted into $phase variable. If the parent
|
|
|
- * feature is indicated in feature location for the child feature will be set.The Attributes section
|
|
|
- * sets the, ID, Name, Alias, Dbrexf to variables to be put into a CONF file.The strand is either a
|
|
|
- * positive, negative, or zero value and is represented by +/./- accordingley.
|
|
|
- *
|
|
|
- * @param $name
|
|
|
- * name of GBrowse database
|
|
|
- *
|
|
|
- * @param $user_name
|
|
|
- * GBrowse MySQL user name
|
|
|
- *
|
|
|
- * @param $password
|
|
|
- * user password for GBrowse
|
|
|
- *
|
|
|
- * @param $library_id
|
|
|
- * GBrowse MySQL user name
|
|
|
- *
|
|
|
- * @param $clear_database
|
|
|
- * Used to clear the database of its backbone structure
|
|
|
- */
|
|
|
-function tripal_gbrowse_load_library_features_into_gbrowse($database_name, $user_name, $password, $library_id,$clear_database){
|
|
|
-
|
|
|
- //A test file created to verify output
|
|
|
- $myFile = "/tmp/temporaryGBrowse_".time().".gff3";
|
|
|
-
|
|
|
- //Test opening the file, will print warning if file is not able to be opened
|
|
|
- $fh = fopen($myFile, 'w') or die("WARNING: Can not open file");
|
|
|
-
|
|
|
- print "Creating GFF3 file of features for library...\n";
|
|
|
-
|
|
|
- if (!preg_match('/^\d+$/', $library_id)) {
|
|
|
- print "ERROR: Invalid Library ID supplied (Library ID = ".$library_id.")\n";
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- // Selecting all features
|
|
|
- $values = array('library_id' => $library_id);
|
|
|
-
|
|
|
- $prime_result = tripal_core_chado_select ( 'library_feature', array('feature_id'), $values );
|
|
|
-
|
|
|
- // Select Table:library; column:uniquename
|
|
|
- $result = tripal_core_chado_select ( 'library', array('uniquename'), $values );
|
|
|
-
|
|
|
- $source = $result[0]->uniquename ;
|
|
|
-
|
|
|
- // Check source: ERROR
|
|
|
-
|
|
|
- //For each feature, type id form feature table, specific record the feature id containing $feature_id
|
|
|
- foreach ($prime_result as $value) {
|
|
|
-
|
|
|
- $feature_id = $value->feature_id;
|
|
|
-
|
|
|
- if (!preg_match('/^\d+$/', $feature_id)) {
|
|
|
- print "ERROR: Invalid feature ID (".$feature_id.") associated with Library (Library ID = ".$library_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $result = tripal_core_chado_select('feature', array('type_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $type_id = $result[0]->type_id;
|
|
|
-
|
|
|
- if (empty($type_id)) {
|
|
|
- print "ERROR: No Type associated with Feature (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //Taking the cvterm name from the cvterm table given the type-id($type_id)
|
|
|
- $result = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id'=>$type_id));
|
|
|
-
|
|
|
- //The extracted cvterm name
|
|
|
- $type = $result[0]->name;
|
|
|
-
|
|
|
- if (empty($type)) {
|
|
|
- print "ERROR: Type associated with Feature (".$type_id.") doesn't exist in cvterm table (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //Featureloc.fmin & featureloc.fmax ( where featureloc.feature_id = feature.feature_id )
|
|
|
- //fmin = start & fmax = end
|
|
|
- $result = tripal_core_chado_select('featureloc', array('fmin','fmax', 'strand', 'phase', 'srcfeature_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $start = $result[0]->fmin;
|
|
|
- if (!preg_match('/^\d+$/', $start)) {
|
|
|
- print "ERROR: Invalid Start (".$start.") of Feature (Feature ID= ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $end = $result[0]->fmax;
|
|
|
- if (!preg_match('/^\d+$/', $end)) {
|
|
|
- print "ERROR: Invalid End (".$end.") of Feature (Feature ID= ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $score = '.';
|
|
|
-
|
|
|
-
|
|
|
- //Converting from +1/0/-1 to +/./- as there are only three possible values
|
|
|
- if ($result[0]->strand < 0) {
|
|
|
-
|
|
|
- $strand= '-';
|
|
|
- } elseif ($result[0]->strand == 0) {
|
|
|
-
|
|
|
- $strand = '.';
|
|
|
- } elseif($result[0]->strand > 0) {
|
|
|
-
|
|
|
- $strand = '+';
|
|
|
- } else{
|
|
|
-
|
|
|
- $strand = '.';
|
|
|
- }
|
|
|
-
|
|
|
- //Testing if phase is empty, if so a '.' is inserted into $phase variable
|
|
|
- $phase = $result[0]->phase;
|
|
|
- if(empty($phase)){
|
|
|
- $phase = '.';
|
|
|
- }
|
|
|
-
|
|
|
- //This is the parent feature as indicated in feature location for the child feature and
|
|
|
- //the current line described the child feature
|
|
|
- $srcfeature_id = $result[0]->srcfeature_id;
|
|
|
-
|
|
|
- if (empty($srcfeature_id)) {
|
|
|
- print "ERROR: No Parent associated with Feature Location (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $result = tripal_core_chado_select('feature', array('name'), array('feature_id'=>$srcfeature_id));
|
|
|
-
|
|
|
- $seqid = $result[0]->name;
|
|
|
-
|
|
|
- if (empty($seqid)) {
|
|
|
- print "ERROR: Parent (Parent Feature ID = ".$seqid.") associated with Feature doesn't exist in feature table (Feature ID =".$feature_id."\n";
|
|
|
- }
|
|
|
-
|
|
|
-
|
|
|
- //Attributes section, ID, Name, Alias, Dbrexf
|
|
|
- $result = tripal_core_chado_select('feature', array('uniquename', 'name'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $id = $result[0]->uniquename;
|
|
|
-
|
|
|
- if (empty($id)) {
|
|
|
- print "ERROR: Missing Unique Name for Feature (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $name = $result[0]->name;
|
|
|
-
|
|
|
- if (empty($name)) {
|
|
|
- print "WARNING: Missing Name for Feature (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //Synonym
|
|
|
- $result = tripal_core_chado_select('feature_synonym', array('synonym_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $synonyms = array();
|
|
|
- foreach ($result as $obj){
|
|
|
-
|
|
|
- $synonym_id = $obj->synonym_id;
|
|
|
-
|
|
|
- $sub_result = tripal_core_chado_select('synonym', array('name'), array('synonym_id'=>$synonym_id));
|
|
|
-
|
|
|
- // check that $sub_result[0]->name isn't empty
|
|
|
- if (empty($sub_result[0]->name)) {
|
|
|
- print "ERROR: Synonym (".$synonym_id.") associated with feature not found in synonym table (Feature ID = ".$feature_id.")\n";
|
|
|
- } else {
|
|
|
- $synonyms[] = $sub_result[0]->name;
|
|
|
- }
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- // Additional Dbxref's
|
|
|
- $result = tripal_core_chado_select('feature_dbxref', array('dbxref_id'), array('feature_id'=>$feature_id));
|
|
|
- $dbxref = array();
|
|
|
-
|
|
|
- foreach ($result as $obj){
|
|
|
-
|
|
|
- $dbxref_id = $obj->dbxref_id;
|
|
|
-
|
|
|
- if (!empty($dbxref_id)) {
|
|
|
- $sub1_result = tripal_core_chado_select('dbxref', array('db_id', 'accession'), array('dbxref_id'=>$dbxref_id));
|
|
|
-
|
|
|
- $dbxref_accession = $sub1_result[0]->accession;
|
|
|
-
|
|
|
- $db_id = $sub1_result[0]->db_id;
|
|
|
-
|
|
|
- if (!empty($db_id)) {
|
|
|
- $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));
|
|
|
-
|
|
|
- $db_name = $sub_sub_result[0]->name;
|
|
|
-
|
|
|
- if (empty($db_name)) {
|
|
|
- print "ERROR: Database (".$db_id.") associated with database reference not in db table (Database Reference ID = ".$dbxref_id.")\n";
|
|
|
- } elseif (empty($dbxref_accession)) {
|
|
|
- print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
|
|
|
- } else {
|
|
|
- $dbxref[] = $db_name . ':' . $dbxref_accession;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- //Main Dbxref
|
|
|
- $result = tripal_core_chado_select('feature', array('dbxref_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $dbxref_id = $result[0]->dbxref_id;
|
|
|
-
|
|
|
- if (empty($dbxref_id)) {
|
|
|
- print "WARNING: No Database Reference associated directly with Feature (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $result = tripal_core_chado_select('dbxref', array('accession','db_id'), array('dbxref_id'=>$dbxref_id));
|
|
|
-
|
|
|
- $dbxref_accession = $result[0]->accession;
|
|
|
-
|
|
|
- //checking $dbrexf_accession for emptyness
|
|
|
- if(!empty($dbxref_accession)){
|
|
|
-
|
|
|
- $db_id = $result[0]->db_id;
|
|
|
-
|
|
|
- $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));
|
|
|
-
|
|
|
- $db_name = $sub_sub_result[0]->name;
|
|
|
-
|
|
|
- $dbxref[] = $db_name . ':' . $dbxref_accession;
|
|
|
-
|
|
|
- } else {
|
|
|
- print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //attributes array is assigned given elements based on previous initializations
|
|
|
- $attributes = array();
|
|
|
-
|
|
|
- $attributes[] = 'ID='.$id;
|
|
|
-
|
|
|
- if (!empty($name)) { $attributes[] = 'Name='.$name; }
|
|
|
-
|
|
|
- if (!empty($synonyms)) { $attributes[] = 'Alias='.implode(',',$synonyms); }
|
|
|
-
|
|
|
- if (!empty($dbxref)) { $attributes[] = 'Dbxref=' .implode(',', $dbxref); }
|
|
|
-
|
|
|
- //write to string for printing
|
|
|
- $stringData = implode("\t", array($seqid,$source,$type,$start,$end,$score,$strand,$phase,
|
|
|
-
|
|
|
- implode(';',$attributes)))."\n";
|
|
|
-
|
|
|
- //Write concatinated data ($stringData) to file
|
|
|
- fwrite($fh, $stringData);
|
|
|
- }
|
|
|
-
|
|
|
- //Closing file
|
|
|
- fclose($fh);
|
|
|
-
|
|
|
-
|
|
|
- if($clear_database){
|
|
|
-
|
|
|
- //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file
|
|
|
- $command= "bp_seqfeature_load.pl -c -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;
|
|
|
-
|
|
|
- }else{
|
|
|
-
|
|
|
- //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file
|
|
|
- $command= "bp_seqfeature_load.pl -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;
|
|
|
- }
|
|
|
-
|
|
|
- //optional 'print' statement to verify that the above comman is being called and executed properly
|
|
|
- print 'Executing Command:'.$command."\n";
|
|
|
-
|
|
|
- exec($command, $out_put, $return_var);
|
|
|
-
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Delete library features from database Form & Form submit
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-*
|
|
|
-* This form's purpose is to delete library featues from a selected GBrowse insatance. By selecting
|
|
|
-* a Library of genetic sequences and a GBrowse instance, the instance will be removed as will all the
|
|
|
-* associated libraries. This form allows access to a specified database and will delete any
|
|
|
-* selected Library features. It will return the form that contains all of the neccessary
|
|
|
-* information to send to the 'form_submit' function.
|
|
|
-*
|
|
|
-* @return $form
|
|
|
-* An array of menu items allowing deletion of features from the library
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete_library_features_from_gbrowse_form() {
|
|
|
-
|
|
|
- $form = array();
|
|
|
-
|
|
|
- $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );
|
|
|
-
|
|
|
- foreach ($result as $value){
|
|
|
- $newArray[$value->library_id]=$value->name; //options for the select list
|
|
|
- }
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['delete_gbrowse'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t(''),
|
|
|
- );
|
|
|
-
|
|
|
- //Library ID
|
|
|
- $form['delete_gbrowse']['library_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Libraries'),
|
|
|
- '#options' => $newArray,
|
|
|
- '#description' => t('Genetic Sequences.'),
|
|
|
- );
|
|
|
-
|
|
|
- //Sending query to the database
|
|
|
- $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
|
|
|
-
|
|
|
- $items = array();
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
- $items[$record->gbrowse_id]= $record->gbrowse_name;
|
|
|
- }
|
|
|
-
|
|
|
- $form['delete_gbrowse']['gbrowse_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('GBrowse Instances'),
|
|
|
- '#options' => $items,
|
|
|
- '#description' => t('Selected Instances to be Removed.'),
|
|
|
- );
|
|
|
-
|
|
|
- //Delete button to remove Library
|
|
|
- $form['delete_gbrowse']['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#weight' => 10,
|
|
|
- '#value' => t('Delete')
|
|
|
- );
|
|
|
-
|
|
|
- return $form;
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* This 'form_submit' function uses MySQL commands to select the GBrowse instance from a selected database.
|
|
|
-* Then the selected features are deleted from the library.
|
|
|
-*
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* The submitted form that
|
|
|
-*
|
|
|
-* @param $form_state
|
|
|
-* The state of the form, includes the selected library and the GBrowse instance to be removed
|
|
|
-* The key is the 'values'
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete_library_features_from_gbrowse_form_submit($form, $form_state) {
|
|
|
-
|
|
|
- global $user; //needed to make the current users details available so access of user id is available
|
|
|
-
|
|
|
- $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
|
|
|
-
|
|
|
- $name = $record->database_name;
|
|
|
-
|
|
|
- $user_name = $record->database_user;
|
|
|
-
|
|
|
- $password= $record->user_password;
|
|
|
-
|
|
|
- $job_args = array($name,$user_name,$password,$form_state['values']['library_id']);
|
|
|
-
|
|
|
- //Checking state of submit button, if selected delete features from library
|
|
|
- if($form_state['values']['op'] == 'Delete'){
|
|
|
-
|
|
|
- //registering a delete job with the tripal system, this job calls the function when executed
|
|
|
- $job_id = tripal_add_job('Deleting Library Features From GBrowse', 'tripal_gbrowse', 'tripal_gbrowse_delete_library_features_from_gbrowse', $job_args, $user->uid);
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Delete Library Features from GBrowse
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Delete-GBrowse-Feature
|
|
|
-*
|
|
|
-* This form Removes features from library that the user has specified. The form allows the user
|
|
|
-* to select a desired instance. Once the library and instance are selected and deleted, the selected
|
|
|
-* libraries
|
|
|
-*
|
|
|
-*
|
|
|
-*
|
|
|
-* @param $database_name
|
|
|
-* name of GBrowse database
|
|
|
-* @param $user_name
|
|
|
-* GBrowse MySQL user name
|
|
|
-* @param $password
|
|
|
-* user password for GBrowse
|
|
|
-* @param $library_id
|
|
|
-* The id of the library that is being selected from
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete_library_features_from_gbrowse($database_name, $user_name, $password, $library_id){
|
|
|
-
|
|
|
- $result = tripal_core_chado_select ( 'library', array('name'), array('library_id' => $library_id)
|
|
|
-
|
|
|
- );
|
|
|
-
|
|
|
- $library_name = $result[0]->name;
|
|
|
-
|
|
|
- print "Removing Features of all types related to the ".$library_name." library...\n";
|
|
|
-
|
|
|
- $sql = 'SELECT cvterm.name FROM feature JOIN cvterm cvterm ON cvterm.cvterm_id=feature.type_id
|
|
|
-
|
|
|
- JOIN library_feature library_feature ON library_feature.feature_id=feature.feature_id JOIN library
|
|
|
-
|
|
|
- library ON library.library_id=library_feature.library_id WHERE library.library_id=%d GROUP BY
|
|
|
-
|
|
|
- cvterm.name';
|
|
|
-
|
|
|
- $previous_db = tripal_db_set_active('chado');
|
|
|
-
|
|
|
- $resource = db_query($sql, $library_id);
|
|
|
-
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
-
|
|
|
- $type = $record->name;
|
|
|
-
|
|
|
- //The loading script: bp_seqfeature_delete.pl, allows removal of data to specific file
|
|
|
- $command= "bp_seqfeature_delete.pl -u '".$user_name."' -p '".$password."' -d '" .$database_name. "' -t '" .$type. ":".$library_name."'";
|
|
|
-
|
|
|
- print "Executing Command: ".$command."\n";
|
|
|
-
|
|
|
- //exec() allows for execution of a external program: given the input
|
|
|
- exec($command);
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Load analyses into GBrowse Form and Form Submit
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Implements hook_form
|
|
|
-*
|
|
|
-* This function creates a form for the database name, user name for database operation and a
|
|
|
-* password for access.The module uses these analyses to access information regarding the user's
|
|
|
-* operations and needs.
|
|
|
-*
|
|
|
-* @return
|
|
|
-* An array describing the form to be rendered
|
|
|
-*/
|
|
|
-function tripal_gbrowse_load_analyses_form(){
|
|
|
-
|
|
|
- $newArray=array();
|
|
|
-
|
|
|
- $result = tripal_core_chado_select ( 'analysis', array('analysis_id','name'), array() );
|
|
|
-
|
|
|
- foreach ($result as $value) {
|
|
|
- $newArray[$value->analysis_id]=$value->name; //options for the select list
|
|
|
- }
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['load_analyses'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- );
|
|
|
-
|
|
|
- //Library ID
|
|
|
- $form['load_analyses']['analysis_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Analyses'),
|
|
|
- '#options' => $newArray,
|
|
|
- '#description' => t('Analyses.'),
|
|
|
- );
|
|
|
-
|
|
|
- //Sending query to the database
|
|
|
- $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
|
|
|
-
|
|
|
- $items = array();
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
- $items[$record->gbrowse_id]= $record->gbrowse_name;
|
|
|
- }
|
|
|
-
|
|
|
- //GBrowse Instances
|
|
|
- $form['load_analyses']['gbrowse_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('GBrowse Instances'),
|
|
|
- '#options' => $items,
|
|
|
- '#description' => t('Selected GBrowse Instances to be Loaded.'),
|
|
|
- );
|
|
|
-
|
|
|
- //A checkbox to update features for the gbrowse
|
|
|
- $form['load_analyses']['check_box'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Update Analyses'),
|
|
|
- '#description' => t('Existing Same Name Analyses Updated Accordingly.'),
|
|
|
- );
|
|
|
-
|
|
|
- $form['load_analyses']['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#weight' => 10,
|
|
|
- '#value' => t('Submit Job')
|
|
|
- );
|
|
|
-
|
|
|
- return $form;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Load-Features-Form
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* -The submitted form containing the user entered infromation
|
|
|
-*
|
|
|
-* @param $form_state
|
|
|
-* -Is the state of the form: i.e what button was pressed, what infromation was entered,etc.
|
|
|
-* The key is the 'values'
|
|
|
-*/
|
|
|
-function tripal_gbrowse_load_analyses_form_submit($form, $form_state) {
|
|
|
-
|
|
|
- global $user; //needed to make the current users details available so access of user id is available
|
|
|
-
|
|
|
- $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
|
|
|
-
|
|
|
- $name = $record->database_name;
|
|
|
-
|
|
|
- $user_name = $record->database_user;
|
|
|
-
|
|
|
- $password= $record->user_password;
|
|
|
-
|
|
|
- $job_args = array($name,$user_name,$password,$form_state['values']['analysis_id'], FALSE);
|
|
|
-
|
|
|
- //Checking state of check box, if checked delete features from GBrowse
|
|
|
- if($form_state['values']['check_box']==1){
|
|
|
- //registering a delete job with the tripal system, this job calls the function when executed
|
|
|
- $job_id = tripal_add_job('Deleting Features From GBrowse', 'tripal_gbrowse',
|
|
|
- 'tripal_gbrowse_delete_analysis_features_from_gbrowse', $job_args, $user->uid);
|
|
|
- }
|
|
|
-
|
|
|
- //registering a job with the tripal system, this job calls the function when executed
|
|
|
- $job_id = tripal_add_job('Loading Features Into GBrowse', 'tripal_gbrowse',
|
|
|
- 'tripal_gbrowse_load_analysis_features_into_gbrowse', $job_args, $user->uid);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION:Load Analysis Features into GBrowse
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Load Analysis features into database
|
|
|
- *
|
|
|
- * This loading function firstly creates a output GFF3 format file for verification purposes. Then, a 'Chado' table
|
|
|
- * is selected,depending which table the user is interested in, from this table specific infromation
|
|
|
- * is taken out and placed in the GFF3 file.The Featurelocation(fmin) & featurelocation (fmax) are used
|
|
|
- * to set the featureloc.feature_id = feature.feature_id, the fmin = start & fmax = end of the desired gene.
|
|
|
- * The testing if the phase is empty is done, if so a '.' is inserted into $phase variable. If the parent
|
|
|
- * feature is indicated in feature location for the child feature will be set.The Attributes section
|
|
|
- * sets the, ID, Name, Alias, Dbrexf to variables to be put into a CONF file.The strand is either a
|
|
|
- * positive, negative, or zero value and is represented by +/./- accordingley.
|
|
|
- *
|
|
|
- * @param $name
|
|
|
- * name of GBrowse database
|
|
|
- *
|
|
|
- * @param $user_name
|
|
|
- * GBrowse MySQL user name
|
|
|
- *
|
|
|
- * @param $password
|
|
|
- * user password for GBrowse
|
|
|
- *
|
|
|
- * @param $library_id
|
|
|
- * GBrowse MySQL user name
|
|
|
- *
|
|
|
- * @param $clear_database
|
|
|
- * Used to clear the database of its backbone structure
|
|
|
- */
|
|
|
-function tripal_gbrowse_load_analysis_features_into_gbrowse($database_name, $user_name, $password, $analysis_id,$clear_database){
|
|
|
-
|
|
|
- //print 'Analysis ID: '.$analysis_id.".\n";
|
|
|
-
|
|
|
- //A test file created to verify output
|
|
|
- $myFile = "/tmp/temporaryGBrowse_".time().".gff3";
|
|
|
-
|
|
|
- //Test opening the file, will print warning if file is not able to be opened
|
|
|
- $fh = fopen($myFile, 'w') or die("WARNING: Can not open file");
|
|
|
-
|
|
|
- print "Creating GFF3 file of features for Analysis...\n";
|
|
|
-
|
|
|
- if (!preg_match('/^\d+$/', $analysis_id)) {
|
|
|
- print "ERROR: Invalid Analysis ID supplied (Analysis ID= ".$analysis_id.")\n";
|
|
|
- return false;
|
|
|
- }
|
|
|
-
|
|
|
- // Selecting all analyses
|
|
|
- $values = array('analysis_id' => $analysis_id);
|
|
|
-
|
|
|
- $prime_result = tripal_core_chado_select ( 'analysisfeature', array('feature_id'), $values);
|
|
|
-
|
|
|
- // Select Table:library; column:uniquename
|
|
|
- $result = tripal_core_chado_select ( 'analysis', array('name'), $values );
|
|
|
-
|
|
|
- $source = $result[0]->name ;
|
|
|
-
|
|
|
- // Check source: ERROR
|
|
|
- //For each feature, type id form feature table, specific record the feature id containing $feature_id
|
|
|
- foreach ($prime_result as $value) {
|
|
|
-
|
|
|
- $feature_id = $value->feature_id;
|
|
|
-
|
|
|
- if (!preg_match('/^\d+$/', $feature_id)) {
|
|
|
- print "ERROR: Invalid feature ID (".$feature_id.") associated with Library (Library ID = ".$analysis_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $result = tripal_core_chado_select('feature', array('type_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $type_id = $result[0]->type_id;
|
|
|
-
|
|
|
- if (empty($type_id)) {
|
|
|
- print "ERROR: No Type associated with Feature ( Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //Taking the cvterm name from the cvterm table given the type-id($type_id)
|
|
|
- $result = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id'=>$type_id));
|
|
|
-
|
|
|
- //The extracted cvterm name
|
|
|
- $type = $result[0]->name;
|
|
|
-
|
|
|
- if (empty($type)) {
|
|
|
- print "ERROR: Type associated with Feature (".$type_id.") doesn't exist in cvterm table (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //Featureloc.fmin & featureloc.fmax ( where featureloc.feature_id = feature.feature_id )
|
|
|
- //fmin = start & fmax = end
|
|
|
- $result = tripal_core_chado_select('featureloc', array('fmin','fmax', 'strand', 'phase', 'srcfeature_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $start = $result[0]->fmin;
|
|
|
- if (!preg_match('/^\d+$/', $start)) {
|
|
|
- print "ERROR: Invalid Start (".$start.") of Feature (Feature ID= ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $end = $result[0]->fmax;
|
|
|
- if (!preg_match('/^\d+$/', $end)) {
|
|
|
- print "ERROR: Invalid End (".$end.") of Feature (Feature ID= ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $score = '.';
|
|
|
-
|
|
|
- //Converting from +1/0/-1 to +/./- as there are only three possible values
|
|
|
- if ($result[0]->strand < 0) {
|
|
|
- $strand= '-';
|
|
|
- } elseif ($result[0]->strand == 0) {
|
|
|
- $strand = '.';
|
|
|
- } elseif($result[0]->strand > 0) {
|
|
|
- $strand = '+';
|
|
|
- } else{
|
|
|
- $strand = '.';
|
|
|
- }
|
|
|
-
|
|
|
- //Testing if phase is empty, if so a '.' is inserted into $phase variable
|
|
|
- $phase = $result[0]->phase;
|
|
|
- if(empty($phase)){
|
|
|
- $phase = '.';
|
|
|
- }
|
|
|
-
|
|
|
- //This is the parent feature as indicated in feature location for the child feature and
|
|
|
- //the current line described the child feature
|
|
|
- $srcfeature_id = $result[0]->srcfeature_id;
|
|
|
-
|
|
|
- if (empty($srcfeature_id)) {
|
|
|
- print "ERROR: No Parent associated with Feature Location (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $result = tripal_core_chado_select('feature', array('name'), array('feature_id'=>$srcfeature_id));
|
|
|
-
|
|
|
- $seqid = $result[0]->name;
|
|
|
-
|
|
|
- if (empty($seqid)) {
|
|
|
- print "ERROR: Parent (Parent Feature ID = ".$seqid.") associated with Feature doesn't exist in feature table (Feature ID =".$feature_id."\n";
|
|
|
- }
|
|
|
-
|
|
|
- //Attributes section, ID, Name, Alias, Dbrexf
|
|
|
- $result = tripal_core_chado_select('feature', array('uniquename', 'name'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $id = $result[0]->uniquename;
|
|
|
-
|
|
|
- if (empty($id)) {
|
|
|
- print "ERROR: Missing Unique Name for Feature (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $name = $result[0]->name;
|
|
|
-
|
|
|
- if (empty($name)) {
|
|
|
- print "WARNING: Missing Name for Feature (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //Synonym
|
|
|
- $result = tripal_core_chado_select('feature_synonym', array('synonym_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $synonyms = array();
|
|
|
- foreach ($result as $obj){
|
|
|
-
|
|
|
- $synonym_id = $obj->synonym_id;
|
|
|
-
|
|
|
- $sub_result = tripal_core_chado_select('synonym', array('name'), array('synonym_id'=>$synonym_id));
|
|
|
-
|
|
|
- // check that $sub_result[0]->name isn't empty
|
|
|
- if (empty($sub_result[0]->name)) {
|
|
|
- print "ERROR: Synonym (".$synonym_id.") associated with feature not found in synonym table (Feature ID = ".$feature_id.")\n";
|
|
|
- } else {
|
|
|
- $synonyms[] = $sub_result[0]->name;
|
|
|
- }
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- // Additional Dbxref's
|
|
|
- $result = tripal_core_chado_select('feature_dbxref', array('dbxref_id'), array('feature_id'=>$feature_id));
|
|
|
- $dbxref = array();
|
|
|
-
|
|
|
- foreach ($result as $obj){
|
|
|
-
|
|
|
- $dbxref_id = $obj->dbxref_id;
|
|
|
-
|
|
|
- if (!empty($dbxref_id)) {
|
|
|
- $sub1_result = tripal_core_chado_select('dbxref', array('db_id', 'accession'), array('dbxref_id'=>$dbxref_id));
|
|
|
-
|
|
|
- $dbxref_accession = $sub1_result[0]->accession;
|
|
|
-
|
|
|
- $db_id = $sub1_result[0]->db_id;
|
|
|
-
|
|
|
- if (!empty($db_id)) {
|
|
|
- $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));
|
|
|
-
|
|
|
- $db_name = $sub_sub_result[0]->name;
|
|
|
-
|
|
|
- if (empty($db_name)) {
|
|
|
- print "ERROR: Database (".$db_id.") associated with database reference not in db table (Database Reference ID = ".$dbxref_id.")\n";
|
|
|
- } elseif (empty($dbxref_accession)) {
|
|
|
- print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
|
|
|
- } else {
|
|
|
- $dbxref[] = $db_name . ':' . $dbxref_accession;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- //Main Dbxref
|
|
|
- $result = tripal_core_chado_select('feature', array('dbxref_id'), array('feature_id'=>$feature_id));
|
|
|
-
|
|
|
- $dbxref_id = $result[0]->dbxref_id;
|
|
|
-
|
|
|
- if (empty($dbxref_id)) {
|
|
|
- print "WARNING: No Database Reference associated directly with Feature (Feature ID = ".$feature_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- $result = tripal_core_chado_select('dbxref', array('accession','db_id'), array('dbxref_id'=>$dbxref_id));
|
|
|
-
|
|
|
- $dbxref_accession = $result[0]->accession;
|
|
|
-
|
|
|
- //checking $dbrexf_accession for emptyness
|
|
|
- if(!empty($dbxref_accession)){
|
|
|
-
|
|
|
- $db_id = $result[0]->db_id;
|
|
|
-
|
|
|
- $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));
|
|
|
-
|
|
|
- $db_name = $sub_sub_result[0]->name;
|
|
|
-
|
|
|
- $dbxref[] = $db_name . ':' . $dbxref_accession;
|
|
|
-
|
|
|
- } else {
|
|
|
- print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
|
|
|
- }
|
|
|
-
|
|
|
- //attributes array is assigned given elements based on previous initializations
|
|
|
- $attributes = array();
|
|
|
-
|
|
|
- $attributes[] = 'ID='.$id;
|
|
|
-
|
|
|
- if (!empty($name)) {
|
|
|
- $attributes[] = 'Name='.$name;
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($synonyms)) {
|
|
|
- $attributes[] = 'Alias='.implode(',',$synonyms);
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($dbxref)) {
|
|
|
- $attributes[] = 'Dbxref=' .implode(',', $dbxref);
|
|
|
- }
|
|
|
-
|
|
|
- //write to string for printing
|
|
|
- $stringData = implode("\t", array($seqid,$source,$type,$start,$end,$score,$strand,$phase,
|
|
|
-
|
|
|
- implode(';',$attributes)))."\n";
|
|
|
-
|
|
|
- //Write concatinated data ($stringData) to file
|
|
|
- fwrite($fh, $stringData);
|
|
|
- }
|
|
|
-
|
|
|
- //Closing file
|
|
|
- fclose($fh);
|
|
|
-
|
|
|
-
|
|
|
- if($clear_database){
|
|
|
- //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file
|
|
|
- $command= "bp_seqfeature_load.pl -c -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;
|
|
|
- }else{
|
|
|
- //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file
|
|
|
- $command= "bp_seqfeature_load.pl -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;
|
|
|
- }
|
|
|
-
|
|
|
- //optional 'print' statement to verify that the above comman is being called and executed properly
|
|
|
- print 'Executing Command:'.$command."\n";
|
|
|
-
|
|
|
- exec($command, $out_put, $return_var);
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Delete analysis features from database Form & Form submit
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* This form's purpose is to delete analysis featues from a selected GBrowse insatance. By selecting
|
|
|
-* a Library of analyses and a GBrowse instance, the instance will be removed as will all the
|
|
|
-* associated analysis library. This form allows access to a specified database and will delete any
|
|
|
-* selected Analysis features. It will return the form that contains all of the neccessary
|
|
|
-* information to send to the 'form_submit' function.
|
|
|
-*
|
|
|
-* @return $form
|
|
|
-* An array of menu items allowing deletion of features from the library
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete_analysis_features_from_gbrowse_form() {
|
|
|
-
|
|
|
- $form = array();
|
|
|
-
|
|
|
- $result = tripal_core_chado_select ( 'analysis', array('analysis_id','name'), array() );
|
|
|
-
|
|
|
- foreach ($result as $value){
|
|
|
- $newArray[$value->analysis_id]=$value->name; //options for the select list
|
|
|
- }
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['delete_analysis'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t(''),
|
|
|
- );
|
|
|
-
|
|
|
- //Library ID
|
|
|
- $form['delete_analysis']['analysis_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Analysis Features'),
|
|
|
- '#options' => $newArray,
|
|
|
- '#description' => t('Analysis.'),
|
|
|
- );
|
|
|
-
|
|
|
- //Sending query to the database
|
|
|
- $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
|
|
|
-
|
|
|
- $items = array();
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
- $items[$record->gbrowse_id]= $record->gbrowse_name;
|
|
|
- }
|
|
|
-
|
|
|
- $form['delete_analysis']['gbrowse_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('GBrowse Instances'),
|
|
|
- '#options' => $items,
|
|
|
- '#description' => t('Selected Instances to be Removed.'),
|
|
|
- );
|
|
|
-
|
|
|
- //Delete button to remove Library
|
|
|
- $form['delete_analysis']['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#weight' => 10,
|
|
|
- '#value' => t('Delete')
|
|
|
- );
|
|
|
-
|
|
|
- return $form;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* This 'form_submit' function uses MySQL commands to select the GBrowse instance from a selected database.
|
|
|
-* Then the selected features are deleted from the library.
|
|
|
-*
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* The submitted form that
|
|
|
-*
|
|
|
-* @param $form_state
|
|
|
-* The state of the form, includes the selected library and the GBrowse instance to be removed
|
|
|
-* The key is the 'values'
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete_analysis_features_from_gbrowse_form_submit($form, $form_state) {
|
|
|
-
|
|
|
- global $user; //needed to make the current users details available so access of user id is available
|
|
|
-
|
|
|
- $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
|
|
|
-
|
|
|
- $name = $record->database_name;
|
|
|
-
|
|
|
- $user_name = $record->database_user;
|
|
|
-
|
|
|
- $password= $record->user_password;
|
|
|
-
|
|
|
- $job_args = array($name,$user_name,$password,$form_state['values']['analysis_id']);
|
|
|
-
|
|
|
- //Checking state of submit button, if selected delete features from library
|
|
|
- if($form_state['values']['op'] == 'Delete'){
|
|
|
- //registering a delete job with the tripal system, this job calls the function when executed
|
|
|
- $job_id = tripal_add_job('Deleting Analysis Features From GBrowse', 'tripal_gbrowse', 'tripal_gbrowse_delete_analysis_features_from_gbrowse', $job_args, $user->uid);
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Delete Analysis Features from GBrowse
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Delete-GBrowse-Feature
|
|
|
-*
|
|
|
-* This form Removes features from Analysis that the user has specified. The form allows the user
|
|
|
-* to select a desired instance. Once the analysis and instance are selected and deleted, the selected
|
|
|
-* analyses will be disassociated with the specified instance.
|
|
|
-*
|
|
|
-* @param $database_name
|
|
|
-* name of GBrowse database
|
|
|
-*
|
|
|
-* @param $user_name
|
|
|
-* GBrowse MySQL user name
|
|
|
-*
|
|
|
-* @param $password
|
|
|
-* user password for GBrowse
|
|
|
-*
|
|
|
-* @param $library_id
|
|
|
-* The id of the library that is being selected from
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_gbrowse_delete_analysis_features_from_gbrowse($database_name, $user_name, $password, $analysis_id){
|
|
|
-
|
|
|
- $result = tripal_core_chado_select ( 'analysis', array('name'), array('analysis_id' => $analysis_id)
|
|
|
-
|
|
|
- );
|
|
|
-
|
|
|
- $analysis_name = $result[0]->name;
|
|
|
-
|
|
|
- print "Removing Analysis Features of all types related to the ".$analysis_name." analysis...\n";
|
|
|
-
|
|
|
- $sql = 'SELECT cvterm.name FROM feature JOIN cvterm cvterm ON cvterm.cvterm_id=feature.type_id
|
|
|
-
|
|
|
- JOIN analysisfeature analysisfeature ON analysisfeature.feature_id=feature.feature_id JOIN analysis
|
|
|
-
|
|
|
- analysis ON analysis.analysis_id=analysisfeature.analysis_id WHERE analysis.analysis_id=%d GROUP BY
|
|
|
-
|
|
|
- cvterm.name';
|
|
|
-
|
|
|
- $previous_db = tripal_db_set_active('chado');
|
|
|
- $resource = db_query($sql, $analysis_id);
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
-
|
|
|
- $type = $record->name;
|
|
|
-
|
|
|
- //The loading script: bp_seqfeature_delete.pl, allows removal of data to specific file
|
|
|
- $command= "bp_seqfeature_delete.pl -u '".$user_name."' -p '".$password."' -d '" .$database_name. "' -t '" .$type. ":".$analysis_name."'";
|
|
|
-
|
|
|
- print "Executing Command: ".$command."\n";
|
|
|
-
|
|
|
- //exec() allows for execution of a external program: given the input
|
|
|
- exec($command);
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Add Tracks Form & Form submit
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-* Add-GBrowse-Tracks
|
|
|
-* This Menu item is implemented to allow users to define and add tracks including their name,
|
|
|
-* glyph, colour (fore and back ground), size and link. By adding tracks, the user is able to
|
|
|
-* visually inspect the features of their genomic data. The Glyph library has been hardcoded
|
|
|
-* into the software and represents the most used Glyph representations. The "Glyph" option
|
|
|
-* determines the shape of each of the displayed genomic features associated with a specific
|
|
|
-* GBrowse track. It presents a configurable set of parameters specific to its type allowing
|
|
|
-* further control over the display features such as height, color (foreground & backround) etc.
|
|
|
-*
|
|
|
-*
|
|
|
-* @return
|
|
|
-* An '$form' that is an array of menu items that allows the user to Register a GBrowse instance
|
|
|
-*/
|
|
|
-function tripal_gbrowse_add_tracks_form() {
|
|
|
-
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['add_tracks_field_set'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t('Content-Related Fields'),
|
|
|
- );
|
|
|
-
|
|
|
- //Sending query to the database for GBrowse Instances
|
|
|
- $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
|
|
|
-
|
|
|
- $items = array();
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
-
|
|
|
- $items[$record->gbrowse_id]= $record->gbrowse_name;
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- //GBrowse Instances
|
|
|
- $form['add_tracks_field_set']['gbrowse_instances'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Registered GBrowse Instances'),
|
|
|
- '#options' => $items,
|
|
|
- '#description' => t('Selected GBrowse Instances to be Loaded.'),
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //Feature Type
|
|
|
- $sql = 'SELECT name as type, cvterm_id '
|
|
|
- .'FROM cvterm '
|
|
|
- .'WHERE cvterm_id IN (SELECT type_id FROM feature)';
|
|
|
- $previous_db = tripal_db_set_active('chado');
|
|
|
- $resource = db_query($sql);
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
-
|
|
|
- $items = array();
|
|
|
-
|
|
|
- while($record = db_fetch_object($resource)){
|
|
|
-
|
|
|
- $items[$record->type] = $record->type;
|
|
|
- }
|
|
|
-
|
|
|
- $form['add_tracks_field_set']['type_name'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Feature Type'),
|
|
|
- '#options' => $items,
|
|
|
- '#description' => t('Selected GBrowse Instances to be Loaded.'),
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //Populating Select list for Library
|
|
|
- $newArray['none'] = 'None'; //No option for select list
|
|
|
- $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );
|
|
|
- foreach ($result as $value) {
|
|
|
- $newArray[$value->name]=$value->name; //options for the select list
|
|
|
- }
|
|
|
-
|
|
|
- //Library
|
|
|
- $form['add_tracks_field_set']['library_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Library'),
|
|
|
- '#options' => $newArray,
|
|
|
- '#description' => t('Selected GBrowse Instances to be Loaded.'),
|
|
|
- );
|
|
|
-
|
|
|
- //Creating Fieldset for multiple fields in form
|
|
|
- $form['track_text'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => 'Track-Specific Fields'
|
|
|
- );
|
|
|
-
|
|
|
- //Specify Track Identifier
|
|
|
- $form['track_text']['identifier'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Track Identifier'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('Specify Track Identifier (Must be Unique and Specific)'),
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //Specify Track Name
|
|
|
- $form['track_text']['track_name'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Track Name'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('Specify Track Name (Must be Unique and Specific)'),
|
|
|
- '#required' => TRUE,
|
|
|
- );
|
|
|
-
|
|
|
- //Populating Array of Glyph List
|
|
|
- $item = array();
|
|
|
- $item[''] = 'Default Glyph';
|
|
|
- $item['generic'] = 'Generic';
|
|
|
- $item['allele_tower '] = 'Allele Tower';
|
|
|
- $item['anchored_arrow'] = 'Anchored Arrow';
|
|
|
- $item['arrow'] = 'Arrow';
|
|
|
- $item['box'] = 'Box';
|
|
|
- $item['cds'] = 'CDS';
|
|
|
- $item['crossbox'] = 'Cross Box';
|
|
|
- $item['diamond'] = 'Diamond';
|
|
|
- $item['dna'] = 'DNA';
|
|
|
- $item['dot'] = 'Dot';
|
|
|
- $item['ellipse'] = 'Ellipse';
|
|
|
- $item['extending_arrow'] = 'Extending Arrow';
|
|
|
- $item['generic'] = 'Generic';
|
|
|
- $item['graded_segments'] = 'Graded Segments';
|
|
|
- $item['heterogeneous_segments '] = 'Heterogeneous Segments';
|
|
|
- $item['image'] = 'Image';
|
|
|
- $item['line'] = 'Line';
|
|
|
- $item['primers'] = 'Primers';
|
|
|
- $item['processed_transcript'] = 'Processed Transcript';
|
|
|
- $item['rndrect'] = 'Rndrect';
|
|
|
- $item['ruler_arrow'] = 'Ruler Arrow';
|
|
|
- $item['segments'] = 'Segments';
|
|
|
- $item['span'] = 'Span';
|
|
|
- $item['toomany'] = 'Too Many';
|
|
|
- $item['transcript'] = 'Transcript';
|
|
|
- $item['transcript2'] = 'Transcript2';
|
|
|
- $item['translation'] = 'Translation';
|
|
|
- $item['triangle'] = 'Triangle';
|
|
|
- $item['wiggle_densit'] = 'Wiggle Densit';
|
|
|
- $item['wiggle_xyplot'] = 'Wiggle XYplot';
|
|
|
- $item['xyplot'] = 'XYplot';
|
|
|
-
|
|
|
-
|
|
|
- //Glyphs
|
|
|
- $form['track_text']['glyph'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Glyph'),
|
|
|
- '#options' => $item,
|
|
|
- '#description' => t('Shape of Genomic Feature Track '),
|
|
|
- );
|
|
|
-
|
|
|
- //Modify The foreground colour of track
|
|
|
- $form['track_text']['foreground_colour'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Foreground Colour'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('Enter name/Hex-code for identifying foreground colour of glyph.
|
|
|
- List of available colours here:'.l("GBrowse Colour Palette.pdf",
|
|
|
- "http://gmod.org/mediawiki/images/a/ae/Gbrowse_Color_Palette.pdf")),
|
|
|
- );
|
|
|
-
|
|
|
-
|
|
|
- //Modify The Backround colour of track
|
|
|
- $form['track_text']['backround_colour'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Background Colour'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 20,
|
|
|
- '#description' => t('Enter name/Hex-code for identifying background colour of glyph.
|
|
|
- List of available colours here:'.l("GBrowse Colour Palette.pdf",
|
|
|
- "http://gmod.org/mediawiki/images/a/ae/Gbrowse_Color_Palette.pdf")),
|
|
|
- );
|
|
|
-
|
|
|
-
|
|
|
- //Modify The Height of track
|
|
|
- $form['track_text']['track_height'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Height'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 20,
|
|
|
- '#description' => t('Modify Track Height'),
|
|
|
- );
|
|
|
-
|
|
|
- //Specify Link
|
|
|
- $form['track_text']['link'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Link'),
|
|
|
- '#size' => 30,
|
|
|
- '#maxlength' => 64,
|
|
|
- '#description' => t('Specify to Further details (HTML address)'),
|
|
|
- );
|
|
|
-
|
|
|
- //Register job submit button
|
|
|
- $form['create_instance']['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => t('Add Track')
|
|
|
- );
|
|
|
-
|
|
|
- return $form;
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Validate User-submitted data for Register GBrowse Instances
|
|
|
- *
|
|
|
- * This function validates the user input for each form element in the Register GBrowse
|
|
|
- * instances form that is a text field. Validations checked include:
|
|
|
- * - database_name: contains only word characters not including punctuation
|
|
|
- * or white-space ([A-Z][a-z][0-1]_)
|
|
|
- *
|
|
|
- * @param $form
|
|
|
- * The form that the user submitted and whose input is being validated
|
|
|
- *
|
|
|
- * @param $form_state
|
|
|
- * An array containing the state of the form being validated including user-input
|
|
|
- */
|
|
|
-function tripal_gbrowse_add_tracks_form_validate ($form, $form_state) {
|
|
|
-
|
|
|
- if (!empty($form_state['values']['foreground_colour'])) {
|
|
|
- // foreground colour is present and a valid colour
|
|
|
- if ( !preg_match('/^[\w#]+$/', $form_state['values']['foreground_colour'])) {
|
|
|
-
|
|
|
- form_set_error('foreground_colour',
|
|
|
- 'The Foreground Colour should be either the name of a colour listed in the linked to pdf or a valid hex colour');
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['backround_colour'])) {
|
|
|
- if(!preg_match('/^[\w#]+$/', $form_state['values']['backround_colour'])){
|
|
|
- form_set_error('backround_colour','The Background Colour should be either the name of a colour listed in the linked to pdf or a valid hex colour');
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['track_height'])){
|
|
|
- if(!preg_match('/^\d*$/', $form_state['values']['track_height'])){
|
|
|
- form_set_error('track_height','The Track Height must be a positive integer');
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- if(!preg_match('/^\w+$/', $form_state['values']['identifier'])){
|
|
|
-
|
|
|
- form_set_error('identifier','The Identifier must be composed of the following characters only: [A-Z][a-z][0-9] and _');
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['link'])){
|
|
|
- if(!preg_match('/^http:/', $form_state['values']['link'])){
|
|
|
- form_set_error('link','The Link must be a conventional web site name, beginging with http: ');
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
-*Add-GBrowse-Tracks Form_Submit
|
|
|
-*
|
|
|
-* @param $form
|
|
|
-* The form for the information that the user has entered
|
|
|
-*
|
|
|
-* @param $form_state
|
|
|
-* This is the state of the form: i.e what button was pressed.The key is
|
|
|
-* the name of the fields in database
|
|
|
-*
|
|
|
-* @return
|
|
|
-* An '$form' that is an array of menu items that allows the user to Register a GBrowse instance
|
|
|
-*/
|
|
|
-function tripal_gbrowse_add_tracks_form_submit($form, $form_state) {
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
- $string = "\n[".$form_state['values']['identifier']."]\n"
|
|
|
- ."key = ".$form_state['values']['track_name']."\n";
|
|
|
-
|
|
|
- if($form_state['values']['library_id'] == 'none'){
|
|
|
- $string .= "feature = ".$form_state['values']['type_name']."\n";
|
|
|
- } else {
|
|
|
- $string .= "feature = ".$form_state['values']['type_name'].":" .$form_state['values']['library_id']."\n";
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['glyph'])) {
|
|
|
- $string .= "glyph = ".$form_state['values']['glyph']."\n";
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['track_height'])) {
|
|
|
- $string .= "height = ".$form_state['values']['track_height']."\n";
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['foreground_colour'])) {
|
|
|
- $string .= "bgcolor = ".$form_state['values']['foreground_colour']."\n";
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['backround_colour'])) {
|
|
|
- $string .= "fgcolor = ".$form_state['values']['backround_colour']."\n";
|
|
|
- }
|
|
|
-
|
|
|
- if (!empty($form_state['values']['link'])) {
|
|
|
- $string .= "link = ".$form_state['values']['link']."\n";
|
|
|
- }
|
|
|
-
|
|
|
- $string .= "\n";
|
|
|
-
|
|
|
- $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_instances']));
|
|
|
-
|
|
|
- $config_file = $record->config_file;
|
|
|
-
|
|
|
- $command = "echo '".$string."' >> ".$config_file;
|
|
|
-
|
|
|
- exec($command);
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-// SECTION: Delete Tracks Form & Form submit
|
|
|
-//-----------------------------------------------------------------------------
|
|
|
-
|
|
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-
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-/**
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-*Delete-GBrowse-Tracks
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-*
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-* This Form allows selection for a specific GBrowse Instance to be removed in a multi-submit form outline.
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-* Once the GBrowse instance is selected,the corresponding track list that corresponds to
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-* the selected GBrowse instance is deleted. This can be done one track at a time. As
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-* there is no limit to the number of tracks that can be added to a particular GBrowse instance and
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-* thus all the tracks that have bee added can be deleted, one track at a time. The track that is to
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-* be deleted is to be selected from the list. When selected and the delete button is pushed,
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-* the track that was selected is removed from the 'configuration' file.
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-*
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-* @param $form_state
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-* The state of the form as it is setting the default value of $form_state is NULL
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-*
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-* @return
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-* An '$form' that is an array of menu items that allows the user to Register a GBrowse instance
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-*/
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-function tripal_gbrowse_delete_tracks_form(&$form_state=NULL) {
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-
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- //Creating Fieldset for multiple fields in form
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- $form['delete_tracks_field_set'] = array(
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- '#type' => ($form_state['storage']['gbrowse_id']) ? 'hidden' : 'fieldset',
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- '#title' => t('GBrowse Specific Fields'),
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- );
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-
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- //Sending query to the database for GBrowse Instances
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- $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
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-
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- $items = array();
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-
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- while($record = db_fetch_object($resource)){
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-
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- $items[$record->gbrowse_id]= $record->gbrowse_name;
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-
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- }
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-
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- //GBrowse Instance Select List
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- $form['delete_tracks_field_set']['gbrowse_instances'] = array(
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- '#type' => 'select',
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- '#title' => t('Registered GBrowse Instances'),
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- '#options' => $items,
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- '#description' => t('Selected GBrowse Instances to be Loaded.'),
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- '#default_value' => $form_state['values']['gbrowse_instances'],
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- );
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-
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- //Set Instance Submit button
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- $form['delete_tracks_field_set']['submit_instance'] = array(
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- '#type' => 'submit',
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- '#value' => t('Set Instance')
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- );
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-
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- //Creating Fieldset for multiple fields in form
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- $form['delete_tracks'] = array(
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- '#type' => ($form_state['storage']['gbrowse_id']) ? 'fieldset' : 'hidden',
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- '#title' => t('Track Specific Fields'),
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- );
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-
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-
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- $gbrowse_id = $form_state['storage']['gbrowse_id'];
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-
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- if ($gbrowse_id){
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-
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- $items = track_name_options($gbrowse_id);
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-
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- }else {
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-
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- $items = array();
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-
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- }
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-
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- //Track Name Select List
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- $form['delete_tracks']['track_line_number'] = array(
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- '#type' => 'select',
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- '#title' => t('Track Name'),
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- '#options' => $items,
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- '#description' => t('Name of Track to Remove '),
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- '#default_value' => $form_state['values']['gbrowse_id'],
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- );
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-
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- //Remove Track button
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- $form['delete_tracks']['remove_track'] = array(
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- '#type' => 'submit',
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- '#value' => t('Remove Track')
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- );
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-
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- return $form;
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-
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-}
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-
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-
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-/**
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-*Delete-GBrowse-Tracks
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-*
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-*@param $form
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-* The form that is completed in the above section
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-*
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-* @param $form_state
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-* The state of the form, as it is completed by the user and will contain all of the user's
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-* selected infromation that is to be removed from the configuration file.
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-*
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-*/
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-function tripal_gbrowse_delete_tracks_form_submit($form, &$form_state) {
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-
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- $form_state['storage']['gbrowse_id'] = $form_state['values']['gbrowse_instances'];
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-
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- //Checking that the "Remove Track" button was selected
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- if($form_state['clicked_button']['#value']=='Remove Track'){
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-
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- //selecting GBrowse-ID from the database
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- $resource= db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['storage']['gbrowse_id']));
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-
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- //putting contents of the configuration file into an variable
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- $config_file = (string) $resource->config_file;
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-
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- $read_file_handle = fopen($config_file,'r') or drupal_set_message("WARNING: Can not open file:" .$config_file, 'error');
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-
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- $track_number = $form_state['values']['track_line_number'];
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-
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- $line_num = 0;
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-
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- //create temp file
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- $new_conf_file = '/tmp/temp_config_file.temp';
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-
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- //making '.temp' file in the /tmp directory
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- $command = 'touch /tmp/temp_config_file.temp';
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-
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- exec($command);
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-
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- //Checking that the newly created file is writable
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- if (is_writable($new_conf_file)) {
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-
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- //opening file for writing to
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- $write_file_handle = fopen($new_conf_file, 'w') or drupal_set_message("WARNING: Can not open file:" .$new_conf_file, 'error');
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-
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- }else{
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-
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- drupal_set_message("WARNING: Attempting to create a temporary file -insufficient permissions: ".$new_conf_file, 'error');
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- }
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-
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- while(!feof($read_file_handle)){
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-
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- $file_line = fgets($read_file_handle);
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-
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- $line_num++;
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-
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- if($line_num == $track_number){
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-
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- $remove_track = TRUE;
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-
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- }
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-
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- if(preg_match('/^\s*$/',$file_line)){
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-
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- $remove_track=FALSE;
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-
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- }
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-
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- if($remove_track==FALSE){
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-
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- fwrite($write_file_handle, $file_line);
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-
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- }
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-
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- }
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-
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- $command = 'cp '.$new_conf_file.' '.$config_file ;
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-
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- exec($command);
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-
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- $command = 'rm '.$new_conf_file ;
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-
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- exec($command);
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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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-* Populate Track-Name List
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-*
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-* This section takes a GBrowse ID so the coresponding configuration file can be accessed. Once it has been
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-* obtained from the database, by the db_query() command. The configuration file is is searched for lines
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-* that start with "[ ]". This corresponds to the framework of the conf file, as the Track Names are
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-* enclosed within "[ ]". The file is then scanned from the spots that contain the "[ ]".
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-*
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-*
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-* @param gbrowse_id
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-* The Selected GBrowse instance's identification
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-*
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-* @return
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-* $items() and array with the tracks that are in the selected GBrowse instance.
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-*/
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-function track_name_options($gbrowse_id) {
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-
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- $items = array();
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-
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- // Use GBrowse ID to get configuration filename
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- $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $gbrowse_id));
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-
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- //putting contents of the configuration file into an variable
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- $config_file = (string) $record->config_file;
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-
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- $config_array = array();
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-
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- //command to select the lines that begin with '[' and have characters within the '[ ]'
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- $command = 'grep -n "^\[.*\]" ' .$config_file;
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-
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- //execution of the command
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- exec($command , $config_array);
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-
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- $config_array_size = count($config_array);
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-
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- //while the end-of-file has not been reached
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- for($i = 0 ; $i < $config_array_size; $i++){
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-
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- $file_line = $config_array[$i];
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-
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- if ($is_track_definition){
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-
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- if(preg_match('/^(\d+):\[(.+)\]$/', $file_line, $matches)){
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-
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- $items[$matches[1]] = $matches[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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- if(preg_match('/\[TRACK DEFAULTS\]/', $file_line)){
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-
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- $is_track_definition = TRUE;
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- }
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-
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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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-//-----------------------------------------------------------------------------
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-// END OF SOFTWARE
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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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-
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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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Lacey Sanderson