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<?php
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// $Id$
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/*
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* @file
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* cdm_dataportal
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*
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See http://www.mozilla.org/MPL/MPL-1.1.html for the full license terms.
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*/
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require_once('node_types.php');
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require_once('theme/cdm_dataportal.common.theme');
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require_once('theme/cdm_dataportal.descriptions.theme');
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require_once('theme/cdm_dataportal.media.theme');
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require_once('theme/cdm_dataportal.occurrence.theme');
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require_once('theme/cdm_dataportal.page.theme');
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require_once('theme/cdm_dataportal.taxon.theme');
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require_once('theme/cdm_dataportal.name.theme');
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require_once('theme/cdm_dataportal.references.theme');
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require_once('classes/footnotemanager.php');
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require_once('classes/footnote.php');
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require_once('classes/renderhints.php');
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define('CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE', 25);
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define('CDM_DATAPORTAL_NOMREF_IN_TITLE', 1);
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define('CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR', 0);
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/* gallery variables */
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$gallery_settings = array(
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"cdm_dataportal_show_taxon_thumbnails" => 1,
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"cdm_dataportal_show_synonym_thumbnails" => 0,
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"cdm_dataportal_show_thumbnail_captions" => 1,
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"cdm_dataportal_media_maxextend" => 120,
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"cdm_dataportal_media_cols" => 3,
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"cdm_dataportal_media_maxRows" => 1);
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define('CDM_DATAPORTAL_GALLERY_SETTINGS', serialize($gallery_settings));
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define('CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME', "description_gallery");
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define('CDM_DATAPORTAL_MEDIA_GALLERY_NAME', "media_gallery");
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define('CDM_DATAPORTAL_SEARCH_GALLERY_NAME', "search_gallery");
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define('CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS', 'cdm_dataportal_display_taxon_relationships');
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define('CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS', 'cdm_dataportal_display_name_relations');
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define('CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT', 1);
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define('CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS_DEFAULT', 1);
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define(CDM_DATAPORTAL_FEATURETREE_UUID, CDM_DATAPORTAL_FEATURETREE_UUID);
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function getGallerySettings($gallery_config_form_name){
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$default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);
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return variable_get($gallery_config_form_name, $default_values);
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}
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function _add_js_progressbar(){
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/jquery.progressbar/js/jquery.progressbar.js');
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}
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/* ====================== hook implementations ====================== */
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/**
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* Implementation of hook_help()
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*
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* Display help and module information
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* @param section which section of the site we're displaying help
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* @return help text for section
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*/
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function cdm_dataportal_help($section='') {
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$out = '';
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switch ($section) {
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case "admin/modules#description":
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$out = t("The dataportal publishes CDM data hosted in a CommunityStore on the web.");
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break;
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}
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return $out;
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}
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/**
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* Implementation of hook_perm()
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*
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* Valid permissions for this module
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* @return array An array of valid permissions for the portfolio module
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*/
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function cdm_dataportal_perm() {
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return array(
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'administer cdm_dataportal',
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'cdm_dataportal view notes',
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//TODO which else permission are required? -> check the WP6 requirements document
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);
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}
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/**
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* Implementation of hook_menu()
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*/
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function cdm_dataportal_menu($may_cache) {
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$items = array();
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if ($may_cache) {
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$items[] = array(
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'path' => 'admin/settings/cdm_dataportal',
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'title' => t('CDM Dataportal'),
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'description' => t('Setting for the CDM DataPortal'),
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'access' => user_access('administer cdm_dataportal'),
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'callback' => 'drupal_get_form',
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'callback arguments' => 'cdm_dataportal_settings',
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'type' => MENU_NORMAL_ITEM,
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);
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$items[] = array(
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'path' => 'admin/settings/cdm_dataportal/general',
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'title' => t('General'),
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'description' => t('Setting for the CDM DataPortal'),
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'access' => user_access('administer cdm_dataportal'),
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'callback' => 'drupal_get_form',
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'callback arguments' => 'cdm_dataportal_settings',
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'weight' => 0,
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'type' => MENU_LOCAL_TASK,
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);
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$items[] = array(
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'path' => 'admin/settings/cdm_dataportal/geo',
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'title' => t('Geo & Map'),
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'description' => t('Geo & Map'),
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'access' => user_access('administer cdm_dataportal'),
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'callback' => 'drupal_get_form',
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'callback arguments' => 'cdm_dataportal_settings_geo',
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'weight' => 1,
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'type' => MENU_LOCAL_TASK,
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);
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$items[] = array(
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'path' => 'admin/settings/cdm_dataportal/layout',
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'title' => t('Layout'),
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'description' => t('Configure and adjust the layout of your DataPortal '),
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'access' => user_access('administer cdm_dataportal'),
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'callback' => 'drupal_get_form',
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'callback arguments' => 'cdm_dataportal_settings_layout',
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'weight' => 2,
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'type' => MENU_LOCAL_TASK,
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);
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$items[] = array(
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'path' => 'admin/settings/cdm_dataportal/cachesite',
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'title' => t('Cache'),
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'description' => t('Cache the whole CDM DataPortal site'),
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'access' => user_access('administer cdm_dataportal'),
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'callback' => 'cdm_dataportal_view_cache_site',
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'weight' => 10,
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'type' => MENU_LOCAL_TASK,
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);
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/*$items[] = array(
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'path' => 'admin/settings/cdm_dataportal/ws',
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'title' => t('Web Service'),
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'description' => t('Setting for the CDM DataPortal'),
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'access' => user_access('administer cdm_dataportal'),
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'callback' => 'drupal_get_form',
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'callback arguments' => 'cdm_dataportal_settings',
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'weight' => 1,
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'type' => MENU_DEFAULT_LOCAL_TASK,
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);*/
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$items[] = array(
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'path' => 'cdm_dataportal/names',
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'callback' => 'cdm_dataportal_view_names',
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'access' => true,
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'type' => MENU_CALLBACK,
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);
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// optional callback arguments: page
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$items[] = array(
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'path' => 'cdm_dataportal/taxon',
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'callback' => 'cdm_dataportal_taxon_page_view',
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'access' => true,
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'type' => MENU_CALLBACK,
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// expected callback arguments: uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/name',
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'callback' => 'cdm_dataportal_name_page_view',
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'access' => true,
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'type' => MENU_CALLBACK,
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// expected callback arguments: uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/reference',
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'callback' => 'cdm_dataportal_view_reference',
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'access' => true,
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'type' => MENU_CALLBACK,
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// expected callback arguments: uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/reference/list',
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'callback' => 'cdm_dataportal_view_reference_list',
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'access' => true,
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'type' => MENU_CALLBACK,
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// expected callback arguments: uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/media',
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'callback' => 'cdm_dataportal_view_media',
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'access' => true,
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'type' => MENU_CALLBACK,
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// expected callback arguments: uuid, mediarepresentation_uuid, part_uuid or part#
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);
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$items[] = array(
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'path' => 'cdm_dataportal/search',
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'callback' => 'cdm_dataportal_view_search_advanced',
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'access' => true,
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'type' => MENU_CALLBACK,
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);
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$items[] = array(
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'path' => 'cdm_dataportal/search/taxon',
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'callback' => 'cdm_dataportal_view_search_taxon',
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'access' => true,
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'type' => MENU_CALLBACK,
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);
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$items[] = array(
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'path' => 'cdm/xml2json',
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'callback' => 'cdm_view_xml2json',
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'access' => true,
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'type' => MENU_CALLBACK,
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);
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} else {
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// may not cache
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// --- local tasks for Taxon
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$items[] = array(
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'path' => 'cdm_dataportal/name/'.arg(2),
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//'callback' => 'cdm_dataportal_view_name',
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'callback' => 'cdm_dataportal_name_page_view',
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'callback arguments' => array(arg(2)),
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'access' => true,
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'type' => MENU_CALLBACK,
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);
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if(variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
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$items[] = array(
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'path' => 'cdm_dataportal/taxon/'.arg(2),
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'title' => theme('cdm_taxonpage_tab', 'General'),
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'callback' => 'cdm_dataportal_taxon_page_view',
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'access' => true,
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'type' => MENU_CALLBACK,
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'weight' => 1,
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'callback arguments' => array(arg(2), "description")
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// expected callback arguments: name_uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/taxon/'.arg(2).'/all',
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'title' => theme('cdm_taxonpage_tab', 'General'),
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'callback' => 'cdm_dataportal_taxon_page_view',
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'access' => true,
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'type' => MENU_CALLBACK,
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'weight' => 2,
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'callback arguments' => array(arg(2), "all")
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// expected callback arguments: name_uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/taxon/'.arg(2).'/description',
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'title' => theme('cdm_taxonpage_tab', 'General'),
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'callback' => 'cdm_dataportal_taxon_page_view',
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'access' => true,
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'type' => MENU_DEFAULT_LOCAL_TASK,
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'weight' => 2,
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'callback arguments' => array(arg(2), "description")
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// expected callback arguments: name_uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/taxon/'.arg(2).'/synonymy',
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'title' => theme('cdm_taxonpage_tab', 'Synonymy'),
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'callback' => 'cdm_dataportal_taxon_page_view',
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'access' => true,
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'type' => MENU_LOCAL_TASK,
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'weight' => 3,
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'callback arguments' => array(arg(2), "synonymy")
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// expected callback arguments: name_uuid
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);
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$items[] = array(
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'path' => 'cdm_dataportal/taxon/'.arg(2).'/images',
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'title' => theme('cdm_taxonpage_tab', 'Images'),
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'callback' => 'cdm_dataportal_taxon_page_view',
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'access' => true,
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'type' => MENU_LOCAL_TASK,
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'weight' => 4,
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'callback arguments' => array(arg(2), "images")
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// expected callback arguments: name_uuid
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);
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}
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}
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drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal.css');
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//drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
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drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_screen.css', 'screen');
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return $items;
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321
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}
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/**
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325
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* Implementation of hook_block()
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*
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* Provides the following blocks:
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* 0: list of links useful during development
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*
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* @param String $op
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* @param int $delta
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*/
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function cdm_dataportal_block($op='list', $delta=0) {
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// listing of blocks, such as on the admin/block page
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if ($op == "list") {
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//$block[0]["info"] = t("CDM DataPortal DevLinks");
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// $block[1]["info"] = t("CDM DataPortal Credits");
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$block[2]["info"] = t("CDM Search Taxa");
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//$block[3]["info"] = t("CDM Filters");
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$block[4]["info"] = t("CDM Dataportal Print");
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return $block;
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}
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else if ($op == 'view') {
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switch($delta){
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345
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// case 1:
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// $block['subject'] = t('Credits');
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// $block['content'] = theme('cdm_credits');
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// return $block;
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case 2:
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$block['subject'] = t('Search Taxa');
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$block['content'] = drupal_get_form('cdm_dataportal_search_taxon_form');
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352
|
$block['content'] .= '<div>'.l('Advanced Search', '/cdm_dataportal/search').'</div>';
|
|
353
|
return $block;
|
|
354
|
case 4:
|
|
355
|
$block['subject'] = t('Print this page');
|
|
356
|
$block['content'] = theme('cdm_print_button');;
|
|
357
|
return $block;
|
|
358
|
}
|
|
359
|
}
|
|
360
|
}
|
|
361
|
|
|
362
|
|
|
363
|
/**
|
|
364
|
* Implementation of hook_validate()
|
|
365
|
*
|
|
366
|
* @param $element
|
|
367
|
*/
|
|
368
|
function cdm_dataportal_settings_validate($form_id, $form_values){
|
|
369
|
|
|
370
|
if (!str_endsWith($form_values['cdm_webservice_url'], '/')) {
|
|
371
|
//form_set_error('cdm_webservice_url', t("The URL to the CDM Web Service must end with a slash: '/'."));
|
|
372
|
$form_values['cdm_webservice_url'] .= '/';
|
|
373
|
}
|
|
374
|
|
|
375
|
// $cdm_webservice_url_changed = variable_get('cdm_webservice_url', '') != $form_values['cdm_webservice_url'];
|
|
376
|
|
|
377
|
// if ($cdm_webservice_url_changed) {
|
|
378
|
//
|
|
379
|
// //FIXME remove _cdm_dataportal_set_currentSecUuid($form_values['cdm_secUuid_default']);
|
|
380
|
// // reset all cdm related data stored in the session
|
|
381
|
// // cdm_dataportal_session_clear($form_values['cdm_webservice_url']); // cdm_webservice_url is not further stored here
|
|
382
|
// // clear the cdm webservice cache
|
|
383
|
// cache_clear_all(NULL, 'cache_cdm_ws');
|
|
384
|
// // better clear secref_cache since i can not be sure if the cache has not be used during this response
|
|
385
|
// cdm_api_secref_cache_clear();
|
|
386
|
// }
|
|
387
|
if($form_values['cdm_webservice_cache'] != variable_get('cdm_webservice_cache', 1)){
|
|
388
|
cache_clear_all(NULL, 'cache_cdm_ws');
|
|
389
|
// better clear secref_cache since i can not be sure if the cache has not be used during this response
|
|
390
|
cdm_api_secref_cache_clear();
|
|
391
|
}
|
|
392
|
|
|
393
|
}
|
|
394
|
|
|
395
|
/*
|
|
396
|
function cdm_dataportal_session_clear($cdm_ws_uri_update = false){
|
|
397
|
$_SESSION['cdm'] = null;
|
|
398
|
if(is_string($cdm_ws_uri_update)){
|
|
399
|
$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
|
|
400
|
}
|
|
401
|
}
|
|
402
|
|
|
403
|
function cdm_dataportal_session_validate(){
|
|
404
|
|
|
405
|
if(!isset($_SESSION['cdm']['ws_uri'])){
|
|
406
|
$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', false));
|
|
407
|
} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', false)){
|
|
408
|
cdm_dataportal_session_clear(variable_get('cdm_webservice_url', false));
|
|
409
|
}
|
|
410
|
}
|
|
411
|
*/
|
|
412
|
|
|
413
|
function cdm_dataportal_search_taxon_form($advancedForm = false){
|
|
414
|
|
|
415
|
$preset_query = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
|
|
416
|
$preset_doTaxa = (isset($_SESSION['cdm']['search']['doTaxa']) ? 1 : 0);
|
|
417
|
$preset_doSynonyms = (isset($_SESSION['cdm']['search']['doSynonyms']) ? 1 : 0);
|
|
418
|
$preset_doTaxaByCommonNames = (isset($_SESSION['cdm']['search']['doTaxaByCommonNames']) ? 1 : 0);
|
|
419
|
$tdwg_level_select = (isset($_SESSION['cdm']['search']['tdwg_level_select']) ? $_SESSION['cdm']['search']['tdwg_level_select'] : 2);
|
|
420
|
$selected_areas = (isset($_SESSION['cdm']['search']['area']) ? $_SESSION['cdm']['search']['area'] : false);
|
|
421
|
|
|
422
|
$url = 'cdm_dataportal/search/taxon';
|
|
423
|
$form['#method'] = 'get';
|
|
424
|
$form['#process'] = array('cdm_dataportal_search_process' => array());
|
|
425
|
$form['#action'] = url($url, NULL, NULL, true);
|
|
426
|
|
|
427
|
$form['query'] = array(
|
|
428
|
'#delta' => 0,
|
|
429
|
'#type' => 'textfield',
|
|
430
|
'#size' => 20,
|
|
431
|
'#attributes' => array('title' => t('Enter the name or part of a name you wish to search for. The asterisk character * can always be used as wildcard')),
|
|
432
|
'#value' => $preset_query,
|
|
433
|
);
|
|
434
|
|
|
435
|
$form['search'] = array(
|
|
436
|
'#delta' => 1,
|
|
437
|
'#tree' => true,
|
|
438
|
//'#type' => $advancedForm ? 'fieldset': 'hidden',
|
|
439
|
'#title' => t('Options')
|
|
440
|
);
|
|
441
|
|
|
442
|
$form['search']['tree'] = array(
|
|
443
|
'#delta' => -1,
|
|
444
|
'#type' => 'hidden',
|
|
445
|
'#value' => variable_get('cdm_taxonomictree_uuid', false)
|
|
446
|
);
|
|
447
|
|
|
448
|
|
|
449
|
// clean URL get forms breaks if we don't give it a 'q'.
|
|
450
|
if (!(bool)variable_get('clean_url', '0')) {
|
|
451
|
$form['search']['q'] = array(
|
|
452
|
'#delta' => -1,
|
|
453
|
'#type' => 'hidden',
|
|
454
|
'#value' => $url,
|
|
455
|
'#name' => 'q',
|
|
456
|
);
|
|
457
|
}
|
|
458
|
|
|
459
|
$form['search']['pageSize'] = array(
|
|
460
|
'#delta' => -1,
|
|
461
|
'#type' => 'hidden',
|
|
462
|
'#value' => variable_get('cdm_dataportal_search_items_on_page', 25)
|
|
463
|
);
|
|
464
|
|
|
465
|
if($advancedForm){
|
|
466
|
// general search parameters
|
|
467
|
$form['search']['doTaxa'] = array(
|
|
468
|
'#delta' => 2,
|
|
469
|
'#type' => 'checkbox',
|
|
470
|
'#title' => t('Search for accepted taxa'),
|
|
471
|
'#value' => $preset_doTaxa
|
|
472
|
);
|
|
473
|
$form['search']['doSynonyms'] = array(
|
|
474
|
'#delta' => 3,
|
|
475
|
'#type' => 'checkbox',
|
|
476
|
'#title' => t('Search for synonyms'),
|
|
477
|
'#value' => $preset_doSynonyms
|
|
478
|
);
|
|
479
|
$form['search']['doTaxaByCommonNames'] = array(
|
|
480
|
'#delta' => 4,
|
|
481
|
'#type' => 'checkbox',
|
|
482
|
'#title' => t('Search for common names'),
|
|
483
|
'#value' => $preset_doTaxaByCommonNames
|
|
484
|
);
|
|
485
|
|
|
486
|
// Geographic Range
|
|
487
|
$form['search']['geographic_range'] = array(
|
|
488
|
'#type' => 'fieldset',
|
|
489
|
'#delta' => 5,
|
|
490
|
'#tree' => true,
|
|
491
|
'#title' => t('Geographic range'),
|
|
492
|
);
|
|
493
|
|
|
494
|
$form['search']['geographic_range']['tdwg_level_select'] = array(
|
|
495
|
'#type' => 'radios',
|
|
496
|
'#title' => t('Select a TDWG distribution level and code'),
|
|
497
|
'#default_value' => $tdwg_level_select,
|
|
498
|
'#options' => array(
|
|
499
|
t('TDWG level-1, i.e. a continent'),
|
|
500
|
t('TDWG level-2'),
|
|
501
|
t('TDWG level-3, i.e. a country'),
|
|
502
|
t('TDWG level-4')
|
|
503
|
)
|
|
504
|
);
|
|
505
|
$tdwg[1] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '1');
|
|
506
|
$tdwg[2] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '2');
|
|
507
|
$tdwg[3] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '3');
|
|
508
|
$tdwg[4] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '4');
|
|
509
|
|
|
510
|
$tdwg_js = '';
|
|
511
|
foreach($tdwg as $key=>$tdwg_level){
|
|
512
|
$tdwgOptions = array();
|
|
513
|
$tdwgOptionsSelected = array();
|
|
514
|
foreach($tdwg_level as $area){
|
|
515
|
$representation = $area->representations[0];
|
|
516
|
$tdwgOptions[$representation->abbreviatedLabel] = $area->representation_L10n;
|
|
517
|
if(is_array($selected_areas) && in_array($representation->abbreviatedLabel, $selected_areas)){
|
|
518
|
$tdwgOptionsSelected[] = $representation->abbreviatedLabel; //$area->uuid;
|
|
519
|
}
|
|
520
|
}
|
|
521
|
asort($tdwgOptions);
|
|
522
|
$form['search']['geographic_range']['tdwg_level_'.$key] = array(
|
|
523
|
'#type' => 'select',
|
|
524
|
'#title' => t('TDWG level').' '.$key,
|
|
525
|
'#default_value' => $tdwgOptionsSelected,
|
|
526
|
'#multiple' => TRUE,
|
|
527
|
'#options' => $tdwgOptions
|
|
528
|
);
|
|
529
|
$tdwg_js .= "$('#edit-search-geographic-range-tdwg-level-$key').parent()".($tdwg_level_select + 1 == $key ? '.show()' : '.hide()'). ";\n";
|
|
530
|
}
|
|
531
|
|
|
532
|
drupal_add_js(
|
|
533
|
"$(document).ready(function(){
|
|
534
|
|
|
535
|
$(\"input[@name='search[geographic_range][tdwg_level_select]']\").change(
|
|
536
|
function(event){
|
|
537
|
var selectId = $(\"input[@name='search[geographic_range][tdwg_level_select]']:checked\").val();
|
|
538
|
var i;
|
|
539
|
for(i = 0; i < 4; i++){
|
|
540
|
if(selectId == i){
|
|
541
|
$('#edit-search-geographic-range-tdwg-level-' + (i + 1) ).parent().fadeIn('slow');
|
|
542
|
$('#edit-search-geographic-range-tdwg-level-' + (i + 1)).children().removeAttr('selected');
|
|
543
|
} else {
|
|
544
|
$('#edit-search-geographic-range-tdwg-level-' + (i + 1)).parent().fadeOut('slow');
|
|
545
|
$('#edit-search-geographic-range-tdwg-level-' + (i + 1)).children().removeAttr('selected');
|
|
546
|
}
|
|
547
|
}
|
|
548
|
}
|
|
549
|
);
|
|
550
|
|
|
551
|
$tdwg_js
|
|
552
|
});",
|
|
553
|
'inline');
|
|
554
|
|
|
555
|
} else {
|
|
556
|
$form['search']['doTaxa'] = array(
|
|
557
|
'#delta' => -2,
|
|
558
|
'#type' => 'hidden',
|
|
559
|
'#value' => 1
|
|
560
|
);
|
|
561
|
$form['search']['doSynonyms'] = array(
|
|
562
|
'#delta' => -3,
|
|
563
|
'#type' => 'hidden',
|
|
564
|
'#value' => 1
|
|
565
|
);
|
|
566
|
$form['search']['doTaxaByCommonNames'] = array(
|
|
567
|
'#delta' => -4,
|
|
568
|
'#type' => 'hidden',
|
|
569
|
'#value' => 1
|
|
570
|
);
|
|
571
|
}
|
|
572
|
|
|
573
|
$form['submit'] = array(
|
|
574
|
'#delta' => 9,
|
|
575
|
'#type' => 'submit',
|
|
576
|
'#name' => '',
|
|
577
|
'#value' => t('Search')
|
|
578
|
);
|
|
579
|
|
|
580
|
return $form;
|
|
581
|
}
|
|
582
|
|
|
583
|
function cdm_dataportal_search_taxon_form_advanced(){
|
|
584
|
return cdm_dataportal_search_taxon_form(true);
|
|
585
|
}
|
|
586
|
|
|
587
|
/**
|
|
588
|
* Implementation #process method call, see form_builder()
|
|
589
|
* <p>
|
|
590
|
* Removes Drupal internal form elements from query
|
|
591
|
* @param $form
|
|
592
|
* @return unknown_type
|
|
593
|
*/
|
|
594
|
function cdm_dataportal_search_process($form) {
|
|
595
|
unset($form['form_id']);
|
|
596
|
unset($form['form_token']);
|
|
597
|
return $form;
|
|
598
|
}
|
|
599
|
|
|
600
|
/**
|
|
601
|
* Filters $_REQUEST by a list of valid request parameters and also sets defaults if required.
|
|
602
|
* returns the processed request parameters submitted by the search form.
|
|
603
|
*/
|
|
604
|
function cdm_dataportal_search_form_request(){
|
|
605
|
|
|
606
|
|
|
607
|
$form_params = array();
|
|
608
|
array_deep_copy($_REQUEST['search'], $form_params);
|
|
609
|
$form_params['query'] = trim($_REQUEST['query']);
|
|
610
|
|
|
611
|
// split of geographic range
|
|
612
|
if(isset($_REQUEST['search']['geographic_range'])){
|
|
613
|
$geographicRange = $_REQUEST['search']['geographic_range'];
|
|
614
|
// remove
|
|
615
|
unset($form_params['geographic_range']);
|
|
616
|
}
|
|
617
|
|
|
618
|
// add geographic range
|
|
619
|
if($geographicRange){
|
|
620
|
$form_params['tdwg_level_select'] = $geographicRange['tdwg_level_select'];
|
|
621
|
for($i = 1; $i < 5; $i++){
|
|
622
|
if(isset($geographicRange['tdwg_level_'.$i])){
|
|
623
|
$form_params['area'] = $geographicRange['tdwg_level_'.$i];
|
|
624
|
}
|
|
625
|
}
|
|
626
|
}
|
|
627
|
|
|
628
|
// store in session
|
|
629
|
$_SESSION['cdm']['search'] = $form_params;
|
|
630
|
|
|
631
|
return $form_params;
|
|
632
|
}
|
|
633
|
|
|
634
|
|
|
635
|
/* UNREACHABLE since action of form directly links to view
|
|
636
|
function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
|
|
637
|
|
|
638
|
$_SESSION['cdm']['search'] = $form_values;
|
|
639
|
//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
|
|
640
|
return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
|
|
641
|
//$paramstr = compose_url_prameterstr($form_values);
|
|
642
|
//return url('/cdm_dataportal/search/taxon/', $paramstr);
|
|
643
|
}
|
|
644
|
*/
|
|
645
|
/* ====================== menu callback functions ====================== */
|
|
646
|
|
|
647
|
/**
|
|
648
|
* Generate main administration form.
|
|
649
|
*
|
|
650
|
* @return
|
|
651
|
* An array containing form items to place on the module settings page.
|
|
652
|
*/
|
|
653
|
function cdm_dataportal_settings(){
|
|
654
|
|
|
655
|
$form = cdm_api_settings_form();
|
|
656
|
|
|
657
|
//TODO: settings are still incomplete, compare with trunk/dataportal/inc/config_default.php.inc
|
|
658
|
$form['cdm_dataportal'] = array(
|
|
659
|
'#type' => 'fieldset',
|
|
660
|
'#title' => t('CDM DataPortal'),
|
|
661
|
'#collapsible' => FALSE,
|
|
662
|
'#collapsed' => TRUE,
|
|
663
|
);
|
|
664
|
|
|
665
|
// $form['cdm_dataportal']['secuuid_widget'] = array(
|
|
666
|
// '#type' => 'select_secuuid', // => will be themed by theme_select_secuuid(...)
|
|
667
|
// '#title' => t('Default Concept References'),
|
|
668
|
// '#description' => t('The default \'sensu\' reference to start the CDM DataPortal with. Per user choices are possible and may override this value.'),
|
|
669
|
// '#varname' => 'cdm_secUuid_default',
|
|
670
|
// '#multiple' => false
|
|
671
|
// );
|
|
672
|
|
|
673
|
$taxonTrees = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY);
|
|
674
|
foreach($taxonTrees as $tree){
|
|
675
|
$taxonomicTreeOptions[$tree->uuid] = $tree->titleCache;
|
|
676
|
}
|
|
677
|
$form['cdm_dataportal']['cdm_taxonomictree_uuid'] = array(
|
|
678
|
'#type' => 'select',
|
|
679
|
'#title' => t('Available taxonomic views'),
|
|
680
|
'#default_value' => variable_get('cdm_taxonomictree_uuid', false),
|
|
681
|
'#options' => $taxonomicTreeOptions,
|
|
682
|
'#description' => t('Select a taxonomic view for this webservice.')
|
|
683
|
);
|
|
684
|
|
|
685
|
// $form['cdm_dataportal']['DEBUG']= array(
|
|
686
|
// '#value' => '<pre>'.print_r($taxonTrees, true).'</pre>'
|
|
687
|
// );
|
|
688
|
|
|
689
|
|
|
690
|
//------------------ FEATURE TREE --------------------//
|
|
691
|
|
|
692
|
$form['cdm_dataportal']['feature_tree'] = array(
|
|
693
|
'#type' => 'fieldset',
|
|
694
|
'#title' => t('Feature Tree'),
|
|
695
|
'#collapsible' => TRUE,
|
|
696
|
'#collapsed' => TRUE,
|
|
697
|
);
|
|
698
|
|
|
699
|
$form['cdm_dataportal']['feature_tree'][CDM_DATAPORTAL_FEATURETREE_UUID] = array(
|
|
700
|
'#type' => 'select',
|
|
701
|
'#title' => t('Available FeatureTrees'),
|
|
702
|
'#default_value' => variable_get(CDM_DATAPORTAL_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE),
|
|
703
|
'#options' => _get_feature_trees(),
|
|
704
|
'#description' => t('Select a FeatureTree for this webservice.'
|
|
705
|
//.' If there is no applicable FeatureTree you can create a new one using the <a href="">FeatureTreeManager</a>'
|
|
706
|
)
|
|
707
|
);
|
|
708
|
|
|
709
|
return system_settings_form($form);
|
|
710
|
}
|
|
711
|
|
|
712
|
function cdm_dataportal_form_alter($form_id, &$form) {
|
|
713
|
|
|
714
|
static $comment_node_disabled = 0;
|
|
715
|
static $comment_node_read_only = 1;
|
|
716
|
static $comment_node_read_write = 2;
|
|
717
|
|
|
718
|
|
|
719
|
if ($form_id == 'node_type_form'
|
|
720
|
&& isset($form['identity']['type'])
|
|
721
|
&& array_key_exists($form['#node_type']->type, cdm_dataportal_get_nodetypes())
|
|
722
|
) {
|
|
723
|
$form['workflow']['comment'] = array(
|
|
724
|
'#type' => 'radios',
|
|
725
|
'#title' => t('Default comment setting'),
|
|
726
|
'#default_value' => variable_get('comment_'. $form['#node_type']->type, $comment_node_disabled),
|
|
727
|
'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
|
|
728
|
'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
|
|
729
|
);
|
|
730
|
}
|
|
731
|
}
|
|
732
|
|
|
733
|
/**
|
|
734
|
* LAYOUT settings
|
|
735
|
* @return unknown_type
|
|
736
|
*/
|
|
737
|
function cdm_dataportal_settings_layout(){
|
|
738
|
|
|
739
|
$form = array();
|
|
740
|
|
|
741
|
|
|
742
|
$form['cdm_taxonname_type'] = array(
|
|
743
|
'#type' => 'select',
|
|
744
|
'#title' => t('Taxon name type'),
|
|
745
|
'#default_value' => variable_get('cdm_taxonname_type', 'BotanicalName'),
|
|
746
|
'#options' => array( 'BotanicalName'=>t('BotanicalName'), 'ZoologicalName'=>t('ZoologicalName')),
|
|
747
|
'#description' => t('')
|
|
748
|
);
|
|
749
|
|
|
750
|
$form['cdm_dataportal_nomref_in_title'] = array(
|
|
751
|
'#type' => 'checkbox',
|
|
752
|
'#title' => t('Show full nomenclatural reference in title'),
|
|
753
|
'#default_value' => variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE),
|
|
754
|
'#description' => t('Uncheck this, if you want the title of a taxon page consisting of name and author plus publication year only.
|
|
755
|
If not checked, the first homotypic taxon is a repetition of the accepted taxon with
|
|
756
|
the full nomenclatural reference.')
|
|
757
|
);
|
|
758
|
|
|
759
|
$form[CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS] = array(
|
|
760
|
'#type' => 'checkbox',
|
|
761
|
'#title' => t('Show name relations of accepted taxa on taxon page'),
|
|
762
|
'#default_value' => variable_get(CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS_DEFAULT),
|
|
763
|
'#description' => t('')
|
|
764
|
);
|
|
765
|
|
|
766
|
$form[CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS] = array(
|
|
767
|
'#type' => 'checkbox',
|
|
768
|
'#title' => t('Show taxon relations of accepted taxa on taxon page'),
|
|
769
|
'#default_value' => variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT),
|
|
770
|
'#description' => t('')
|
|
771
|
);
|
|
772
|
|
|
773
|
$form['cdm_dataportal_display_is_accepted_for'] = array(
|
|
774
|
'#type' => 'checkbox',
|
|
775
|
'#title' => t('Display <em>is accepted for ...</em> on taxon pages when coming from a synonym link.'),
|
|
776
|
'#default_value' => variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR),
|
|
777
|
'#description' => t('')
|
|
778
|
);
|
|
779
|
|
|
780
|
$form['cdm_dataportal_name_relations_skiptype_basionym'] = array(
|
|
781
|
'#type' => 'checkbox',
|
|
782
|
'#title' => t('Exclude the basionym relationship type from the taxon page'),
|
|
783
|
'#default_value' => variable_get('cdm_dataportal_name_relations_skiptype_basionym', 1),
|
|
784
|
'#description' => t('')
|
|
785
|
);
|
|
786
|
|
|
787
|
$form['cdm_dataportal_taxonpage_tabs'] = array(
|
|
788
|
'#type' => 'checkbox',
|
|
789
|
'#title' => t('Tabbed taxon page'),
|
|
790
|
'#default_value' => variable_get('cdm_dataportal_taxonpage_tabs', 1),
|
|
791
|
'#description' => t('Split the taxon page into individual tabs for description, images, synonymy')
|
|
792
|
);
|
|
793
|
|
|
794
|
$form['cdm_dataportal_search_items_on_page'] = array(
|
|
795
|
'#type' => 'textfield',
|
|
796
|
'#title' => t('Search Page Size'),
|
|
797
|
'#default_value' => variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE),
|
|
798
|
'#description' => t('Number of Names to display per page in search results.')
|
|
799
|
);
|
|
800
|
|
|
801
|
$form['cdm_dataportal_descriptions_separated'] = array(
|
|
802
|
'#type' => 'checkbox',
|
|
803
|
'#title' => t('Separate Descriptions'),
|
|
804
|
'#default_value' => variable_get('cdm_dataportal_descriptions_separated', 0),
|
|
805
|
'#description' => t('By default corresponding elements of different descriptions are joined together'
|
|
806
|
.' into a common section per feature (i.e. type of description).'
|
|
807
|
.' Check this box to allow displaying all descriptions separately.')
|
|
808
|
);
|
|
809
|
|
|
810
|
//---- IMAGES ----//
|
|
811
|
$form['images'] = array(
|
|
812
|
'#type' => 'fieldset',
|
|
813
|
'#title' => t('Images'),
|
|
814
|
'#collapsible' => TRUE,
|
|
815
|
'#collapsed' => FALSE,
|
|
816
|
);
|
|
817
|
$options = cdm_rankVocabulary_as_option();
|
|
818
|
array_unshift($options, '-- DISABLED --');
|
|
819
|
$form['images']['image_hide_rank'] = array(
|
|
820
|
'#type' => 'select',
|
|
821
|
'#title' => t('Hide Images for Taxa above'),
|
|
822
|
'#default_value' => variable_get('image_hide_rank', '0'),
|
|
823
|
'#options' => $options,
|
|
824
|
'#description' => t(''),
|
|
825
|
);
|
|
826
|
//show media
|
|
827
|
$selectShowMedia = array(0 => "Show only taxon media",
|
|
828
|
1 => "Show taxon and child taxon media");
|
|
829
|
$form['images']['cdm_dataportal_show_media'] = array(
|
|
830
|
'#type' => 'select',
|
|
831
|
'#title' => t('Available media files'),
|
|
832
|
'#default_value' => variable_get('cdm_dataportal_show_media', false),
|
|
833
|
'#options' => $selectShowMedia,
|
|
834
|
'#description' => t('Select if a taxon should show only his media or also child media.')
|
|
835
|
);
|
|
836
|
|
|
837
|
// --- SEARCH TAXA GALLERY ---- //
|
|
838
|
$collapsed = TRUE;
|
|
839
|
$form_name = CDM_DATAPORTAL_SEARCH_GALLERY_NAME;
|
|
840
|
$form_tittle = 'Search Taxa';
|
|
841
|
$form[] = cdm_dataportal_create_gallery_settings_form($form_name, $form_tittle, $collapsed);
|
|
842
|
|
|
843
|
// --- FEATURE DESCRIPTION GALLERY ---- //
|
|
844
|
$form_name = CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME;
|
|
845
|
$form_tittle = 'Description elements gallery';
|
|
846
|
$form[] = cdm_dataportal_create_gallery_settings_form($form_name, $form_tittle, $collapsed);
|
|
847
|
|
|
848
|
// --- MEDIA GALLERY ---- //
|
|
849
|
$form_name = CDM_DATAPORTAL_MEDIA_GALLERY_NAME;
|
|
850
|
$form_tittle = 'Media gallery';
|
|
851
|
$form[] = cdm_dataportal_create_gallery_settings_form($form_name, $form_tittle, $collapsed);
|
|
852
|
|
|
853
|
return system_settings_form($form);
|
|
854
|
}
|
|
855
|
|
|
856
|
function cdm_dataportal_create_gallery_settings_form($form_name, $form_tittle, $collapsed){
|
|
857
|
|
|
858
|
$form[$form_name] = array(
|
|
859
|
'#type' => 'fieldset',
|
|
860
|
'#title' => t($form_tittle),
|
|
861
|
'#collapsible' => TRUE,
|
|
862
|
'#collapsed' => $collapsed,
|
|
863
|
'#tree' => true,
|
|
864
|
);
|
|
865
|
|
|
866
|
$default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);
|
|
867
|
$gallery_settings = variable_get($form_name, $default_values);
|
|
868
|
|
|
869
|
if($form_name != CDM_DATAPORTAL_MEDIA_GALLERY_NAME){
|
|
870
|
$form[$form_name]['cdm_dataportal_show_taxon_thumbnails'] = array(
|
|
871
|
'#type' => 'checkbox',
|
|
872
|
'#title' => t('Show media thumbnails for accepted taxa'),
|
|
873
|
'#default_value' => $gallery_settings['cdm_dataportal_show_taxon_thumbnails'],
|
|
874
|
'#description' => t('')
|
|
875
|
);
|
|
876
|
|
|
877
|
$form[$form_name]['cdm_dataportal_show_synonym_thumbnails'] = array(
|
|
878
|
'#type' => 'checkbox',
|
|
879
|
'#title' => t('Show media thumbnails for synonyms'),
|
|
880
|
'#default_value' => $gallery_settings['cdm_dataportal_show_synonym_thumbnails'],
|
|
881
|
'#description' => t('')
|
|
882
|
);
|
|
883
|
}
|
|
884
|
|
|
885
|
//$showCaption = variable_get('cdm_dataportal_findtaxa_show_thumbnail_captions', 0);
|
|
886
|
$form[$form_name]['cdm_dataportal_show_thumbnail_captions'] = array(
|
|
887
|
'#type' => 'checkbox',
|
|
888
|
'#title' => t('Show captions under thumbnails'),
|
|
889
|
'#default_value' => $gallery_settings['cdm_dataportal_show_thumbnail_captions'],
|
|
890
|
'#description' => t('')
|
|
891
|
);
|
|
892
|
|
|
893
|
$form[$form_name]['cdm_dataportal_media_maxextend'] = array(
|
|
894
|
'#type' => 'textfield',
|
|
895
|
'#title' => t('Maximum extend of Images'),
|
|
896
|
'#default_value' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
|
897
|
'#description' => t('In the gallery neither width or height will exceed the maximum extend of images.')
|
|
898
|
);
|
|
899
|
|
|
900
|
$form[$form_name]['cdm_dataportal_media_cols'] = array(
|
|
901
|
'#type' => 'textfield',
|
|
902
|
'#title' => t('Number of columns'),
|
|
903
|
'#default_value' => $gallery_settings['cdm_dataportal_media_cols'],
|
|
904
|
'#description' => t('')
|
|
905
|
);
|
|
906
|
|
|
907
|
if($form_name != CDM_DATAPORTAL_MEDIA_GALLERY_NAME){
|
|
908
|
$form[$form_name]['cdm_dataportal_media_maxRows'] = array(
|
|
909
|
'#type' => 'textfield',
|
|
910
|
'#title' => t('Maximum number of rows'),
|
|
911
|
'#default_value' => $gallery_settings['cdm_dataportal_media_maxRows'],
|
|
912
|
'#description' => t('If you want an unlimited number of rows please set to 0')
|
|
913
|
);
|
|
914
|
}
|
|
915
|
|
|
916
|
return $form;
|
|
917
|
}
|
|
918
|
|
|
919
|
/**
|
|
920
|
* GEOSERVICE and Map settings
|
|
921
|
* @return unknown_type
|
|
922
|
*/
|
|
923
|
function cdm_dataportal_settings_geo(){
|
|
924
|
|
|
925
|
$form = array();
|
|
926
|
|
|
927
|
$form['cdm_dataportal_map_openlayers'] = array(
|
|
928
|
'#type' => 'checkbox',
|
|
929
|
'#title' => t('OpenLayers Viewer'),
|
|
930
|
'#default_value' => variable_get('cdm_dataportal_map_openlayers', 1),
|
|
931
|
'#description' => t('Display the maps in an interactive viewer which allows zooming and panning.')
|
|
932
|
);
|
|
933
|
|
|
934
|
$form['cdm_dataportal_geoservice_access_point'] = array(
|
|
935
|
'#type' => 'textfield',
|
|
936
|
'#title' => t('Geoservice Access Point'),
|
|
937
|
'#default_value' => variable_get('cdm_dataportal_geoservice_access_point', ''),
|
|
938
|
'#description' => t('Base URL of the geoservice to be used by this portal')
|
|
939
|
);
|
|
940
|
|
|
941
|
$form['cdm_dataportal_geoservice_display_width'] = array(
|
|
942
|
'#type' => 'textfield',
|
|
943
|
'#title' => t('Geoservice Display Width'),
|
|
944
|
'#default_value' => variable_get('cdm_dataportal_geoservice_display_width', 390),
|
|
945
|
'#description' => t('Width of the image generated by geoservice')
|
|
946
|
);
|
|
947
|
|
|
948
|
$form['cdm_dataportal_geoservice_bounding_box'] = array(
|
|
949
|
'#type' => 'textfield',
|
|
950
|
'#title' => t('Fixed Geoservice Bounding Box'),
|
|
951
|
'#default_value' => variable_get('cdm_dataportal_geoservice_bounding_box', '-180,-90,180,90'),
|
|
952
|
'#description' => t('Define urrounding of area to be displayed in maps. Use "-180,-90,180,90" for the whole world. Leave <strong>empty</strong> to let the map <strong>automatically zoom</strong> to the distribution area.')
|
|
953
|
);
|
|
954
|
|
|
955
|
//cdm_dataportal_geoservice_labels_on
|
|
956
|
$form['cdm_dataportal_geoservice_labels_on'] = array(
|
|
957
|
'#type' => 'checkbox',
|
|
958
|
'#title' => t('Display Country Labels'),
|
|
959
|
'#default_value' => variable_get('cdm_dataportal_geoservice_labels_on', FALSE),
|
|
960
|
'#description' => t('Check this if you like country names to be displayed in the maps. ')
|
|
961
|
);
|
|
962
|
|
|
963
|
//cdm_dataportal_geoservice_legend_on
|
|
964
|
$form['cdm_dataportal_geoservice_map_caption'] = array(
|
|
965
|
'#type' => 'textfield',
|
|
966
|
'#title' => t('Map Caption'),
|
|
967
|
'#default_value' => variable_get('cdm_dataportal_geoservice_map_caption', ''),
|
|
968
|
'#description' => t('Define a caption for the map.')
|
|
969
|
);
|
|
970
|
|
|
971
|
/*
|
|
972
|
//cdm_dataportal_geoservice_legend_on
|
|
973
|
$form['cdm_dataportal_geoservice_legend_on'] = array(
|
|
974
|
'#type' => 'checkbox',
|
|
975
|
'#title' => t('Display a map legend'),
|
|
976
|
'#default_value' => variable_get('cdm_dataportal_geoservice_legend_on', TRUE),
|
|
977
|
'#description' => t('Check this if you like a legend to be displayed with the maps. ')
|
|
978
|
);
|
|
979
|
*/
|
|
980
|
|
|
981
|
//cdm_dataportal_geoservice_map_legend
|
|
982
|
$form['cdm_dataportal_geoservice_map_legend'] = array(
|
|
983
|
'#type' => 'fieldset',
|
|
984
|
'#title' => t('Map Legend'),
|
|
985
|
'#collapsible' => FALSE,
|
|
986
|
'#collapsed' => TRUE,
|
|
987
|
);
|
|
988
|
|
|
989
|
$form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_on'] = array(
|
|
990
|
'#type' => 'checkbox',
|
|
991
|
'#title' => t('Display a map legend'),
|
|
992
|
'#default_value' => variable_get('cdm_dataportal_geoservice_legend_on', TRUE),
|
|
993
|
'#description' => t('Check this if you like a legend to be displayed with the maps. ')
|
|
994
|
);
|
|
995
|
|
|
996
|
$form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_font_size'] = array(
|
|
997
|
'#type' => 'textfield',
|
|
998
|
'#title' => t('Font size'),
|
|
999
|
'#default_value' => variable_get('cdm_dataportal_geoservice_legend_font_size', 10),
|
|
1000
|
'#description' => t('Font size in pixels.')
|
|
1001
|
);
|
|
1002
|
|
|
1003
|
$fontStyles = array(0 => "plane", 1 => "italic");
|
|
1004
|
$form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_font_style'] = array(
|
|
1005
|
'#type' => 'select',
|
|
1006
|
'#title' => t('Available font styles'),
|
|
1007
|
'#default_value' => variable_get('cdm_dataportal_geoservice_legend_font_style', false),
|
|
1008
|
'#options' => $fontStyles,
|
|
1009
|
'#description' => t('Select a font style for the map legend.')
|
|
1010
|
);
|
|
1011
|
|
|
1012
|
$form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_icon_width'] = array(
|
|
1013
|
'#type' => 'textfield',
|
|
1014
|
'#title' => t('Icon width'),
|
|
1015
|
'#default_value' => variable_get('cdm_dataportal_geoservice_legend_icon_width', 35),
|
|
1016
|
'#description' => t('Icon width in pixels.')
|
|
1017
|
);
|
|
1018
|
|
|
1019
|
$form['cdm_dataportal_geoservice_map_legend']['cdm_dataportal_geoservice_legend_icon_height'] = array(
|
|
1020
|
'#type' => 'textfield',
|
|
1021
|
'#title' => t('Icon height'),
|
|
1022
|
'#default_value' => variable_get('cdm_dataportal_geoservice_legend_icon_height', 15),
|
|
1023
|
'#description' => t('Icon height in pixels.')
|
|
1024
|
);
|
|
1025
|
|
|
1026
|
/* variable_get('cdm_dataportal_findtaxa_media_maxextend', 120),
|
|
1027
|
* $form['cdm_dataportal']['cdm_taxonomictree_uuid'] = array(
|
|
1028
|
'#type' => 'select',
|
|
1029
|
'#title' => t('Available taxonomic views'),
|
|
1030
|
'#default_value' => variable_get('cdm_taxonomictree_uuid', false),
|
|
1031
|
'#options' => $taxonomicTreeOptions,
|
|
1032
|
'#description' => t('Select a taxonomic view for this webservice.')
|
|
1033
|
);
|
|
1034
|
|
|
1035
|
$taxonTrees = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY);
|
|
1036
|
foreach($taxonTrees as $tree){
|
|
1037
|
$taxonomicTreeOptions[$tree->uuid] = $tree->titleCache;
|
|
1038
|
}
|
|
1039
|
$form['cdm_dataportal']['cdm_taxonomictree_uuid'] = array(
|
|
1040
|
'#type' => 'select',
|
|
1041
|
'#title' => t('Available taxonomic views'),
|
|
1042
|
'#default_value' => variable_get('cdm_taxonomictree_uuid', false),
|
|
1043
|
'#options' => $taxonomicTreeOptions,
|
|
1044
|
'#description' => t('Select a taxonomic view for this webservice.')
|
|
1045
|
);
|
|
1046
|
*/
|
|
1047
|
|
|
1048
|
return system_settings_form($form);
|
|
1049
|
|
|
1050
|
}
|
|
1051
|
|
|
1052
|
|
|
1053
|
/**
|
|
1054
|
* @return walk and cache all taxon pages
|
|
1055
|
*/
|
|
1056
|
function cdm_dataportal_view_cache_site(){
|
|
1057
|
|
|
1058
|
_add_js_progressbar();
|
|
1059
|
|
|
1060
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cache_all_taxa.js');
|
|
1061
|
|
|
1062
|
$out = '';
|
|
1063
|
|
|
1064
|
$request_params = array();
|
|
1065
|
$request_params['query'] = '%';
|
|
1066
|
$request_params['tree'] = variable_get('cdm_taxonomictree_uuid', false);
|
|
1067
|
$request_params['doTaxa'] = 1;
|
|
1068
|
$request_params['doSynonyms'] = 0;
|
|
1069
|
$request_params['doTaxaByCommonNames'] = 0;
|
|
1070
|
$search_url = cdm_compose_url(CDM_WS_PORTAL_TAXON_FIND, null, queryString($request_params));
|
|
1071
|
$search_url = uri_uriByProxy($search_url);
|
|
1072
|
$taxon_page_url = url('cdm_dataportal/taxon/');
|
|
1073
|
|
|
1074
|
$out .= '<form id="cache_site">';
|
|
1075
|
$out .= '<br /><h4>'.t('Cache all taxon pages').'</h4>';
|
|
1076
|
$out .= 'Before running the cache bot you have to empty the cache manually:<ul>'
|
|
1077
|
.'<li>Navigate to "Site Configuration -> General"</li>'
|
|
1078
|
.'<li>Uncheck "Enable Caching" checkbox</li>'
|
|
1079
|
.'<li>Check "Enable Caching" checkbox</li>'
|
|
1080
|
.'</ul>';
|
|
1081
|
$out .= '<div>'.t('This caching process may take long time and could cause heavy load on your server').'</div>';
|
|
1082
|
$out .= '<div id="progress"></div>';
|
|
1083
|
$out .= '<input type="hidden" name="searchTaxaUrl" value="'.$search_url.'"/>';
|
|
1084
|
$out .= '<input type="hidden" name="taxonPageUrl" value="'.$taxon_page_url.'"/>';
|
|
1085
|
$out .= '<input type="button" name="start" value="'.t('Start').'"/>';
|
|
1086
|
$out .= '<input type="button" name="stop" value="'.t('Stop').'"/>';
|
|
1087
|
$out .= '</form>';
|
|
1088
|
$out .= '</div>';
|
|
1089
|
// foreach($taxonPager->records as $taxon){
|
|
1090
|
// cdm_dataportal_taxon_view($uuid);
|
|
1091
|
// }
|
|
1092
|
|
|
1093
|
return $out;
|
|
1094
|
}
|
|
1095
|
|
|
1096
|
/**
|
|
1097
|
* Implementation of hook_elements().
|
|
1098
|
*/
|
|
1099
|
function cdm_dataportal_elements() {
|
|
1100
|
$type['select_secuuid'] = array(
|
|
1101
|
'#input' => TRUE,
|
|
1102
|
'#process' => array('cdm_dataportal_select_secuuid_expand' => array()),
|
|
1103
|
//'#validate' => array('cdm_dataportal_select_secuuid_validate' => array()),
|
|
1104
|
//'#default_value' => array(),
|
|
1105
|
);
|
|
1106
|
return $type;
|
|
1107
|
}
|
|
1108
|
|
|
1109
|
/*
|
|
1110
|
*
|
|
1111
|
*/
|
|
1112
|
function cdm_dataportal_select_secuuid_expand($element){
|
|
1113
|
|
|
1114
|
$element['#tree'] = FALSE;
|
|
1115
|
|
|
1116
|
// any value submitted?
|
|
1117
|
if(isset($element['#post'][$element['#varname']])){
|
|
1118
|
$selected_values = $element['#post'][$element['#varname']];
|
|
1119
|
} else {
|
|
1120
|
// use those store in drupal
|
|
1121
|
$selected_values = variable_get( $element['#varname'], array());
|
|
1122
|
}
|
|
1123
|
if(!is_array($selected_values)){
|
|
1124
|
$selected_values = array($selected_values);
|
|
1125
|
}
|
|
1126
|
$options = array();
|
|
1127
|
foreach($selected_values as $secUuid){
|
|
1128
|
$options[$secUuid] = cdm_taxontree_secRefTitle_for($secUuid);
|
|
1129
|
}
|
|
1130
|
|
|
1131
|
$element[$element['#varname']] = array(
|
|
1132
|
'#type' => 'select',
|
|
1133
|
'#options' => $options,
|
|
1134
|
'#default_value' => array_values($options),
|
|
1135
|
'#size' => $element['#multiple'] ? 12 : 2,
|
|
1136
|
'#multiple' => $element['#multiple'],
|
|
1137
|
);
|
|
1138
|
return $element;
|
|
1139
|
}
|
|
1140
|
|
|
1141
|
|
|
1142
|
|
|
1143
|
/**
|
|
1144
|
* Displays a list of the known taxonomic names. Long lists are split up into multiple pages
|
|
1145
|
*
|
|
1146
|
* TODO: parameters are still preliminar
|
|
1147
|
* @param String $page page number to diplay defaults to page 1
|
|
1148
|
* @param boolean $hide_unaccepted whether to hide nams which are not accepted by the current view
|
|
1149
|
*/
|
|
1150
|
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = false ){
|
|
1151
|
|
|
1152
|
$request_params = array(
|
|
1153
|
'q' => $beginsWith,
|
|
1154
|
//'sec' = '',
|
|
1155
|
//'higherTaxa' => getFiters(),
|
|
1156
|
// 'matchAnywhere' => false, // default is false
|
|
1157
|
'page' => $page,
|
|
1158
|
'onlyAccepted' => $onlyAccepted,
|
|
1159
|
'pagesize' => 20 /*$_SESSION['cdm']['namelist_pagesize'] */);
|
|
1160
|
|
|
1161
|
$taxonPager = cdm_ws_find(CDM_WS_PORTAL_TAXON_FIND, $request_params);
|
|
1162
|
/*
|
|
1163
|
* FIXME the filter for accepted names will be a form element, thus this widget
|
|
1164
|
* should be generated via form api preferably as block
|
|
1165
|
*/
|
|
1166
|
//$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
|
|
1167
|
//$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
|
|
1168
|
$out .= theme('cdm_listof_taxa', $taxonPager);
|
|
1169
|
return $out;
|
|
1170
|
}
|
|
1171
|
|
|
1172
|
function cdm_dataportal_view_reference($uuid, $arg2 = null){
|
|
1173
|
$reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
|
|
1174
|
return theme('cdm_reference_page', $reference);
|
|
1175
|
}
|
|
1176
|
|
|
1177
|
function cdm_dataportal_view_reference_list($pageNumber){
|
|
1178
|
$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
|
|
1179
|
return theme('cdm_reference_pager', $referencePager, 'cdm_dataportal/reference/list/');
|
|
1180
|
}
|
|
1181
|
|
|
1182
|
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = false, $part = 0){
|
|
1183
|
$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
|
|
1184
|
return theme('cdm_media_page', $media, $mediarepresentation_uuid, $part);
|
|
1185
|
}
|
|
1186
|
|
|
1187
|
/**
|
|
1188
|
* The taxon page gives detailed information on a taxon, it shows:
|
|
1189
|
* - Taxon name
|
|
1190
|
* - Full list of synonyms homotypic synonyms on top, followed by the
|
|
1191
|
* heterotypic and finally followed by misapplied names.
|
|
1192
|
* The list is ordered historically.
|
|
1193
|
* - All description associated with the taxon.
|
|
1194
|
*
|
|
1195
|
* @param $uuid
|
|
1196
|
* @param $chapter name of the part to display,
|
|
1197
|
* valid values are: 'description', 'images', 'synonymy', 'all'
|
|
1198
|
* @return unknown_type
|
|
1199
|
*/
|
|
1200
|
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all'){
|
|
1201
|
|
|
1202
|
// display the page for the taxon defined by $uuid
|
|
1203
|
$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
|
|
1204
|
return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title , $taxonpage->content);
|
|
1205
|
}
|
|
1206
|
|
|
1207
|
/**
|
|
1208
|
* @param $uuid
|
|
1209
|
* @param $chapter name of the part to display,
|
|
1210
|
* valid values are: 'description', 'images', 'synonymy', 'all'
|
|
1211
|
* @return unknown_type
|
|
1212
|
*/
|
|
1213
|
function cdm_dataportal_taxon_view($uuid, $chapter = 'all'){
|
|
1214
|
|
|
1215
|
$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
|
|
1216
|
if(!$taxon){
|
|
1217
|
drupal_set_title(t('Taxon does not exist'));
|
|
1218
|
return false;
|
|
1219
|
}
|
|
1220
|
//FIXME remove _cdm_dataportal_set_currentSecUuid($taxon->sec->uuid);
|
|
1221
|
|
|
1222
|
$taxonpage->title = theme('cdm_taxon_page_title', $taxon);
|
|
1223
|
$taxonpage->content = theme('cdm_taxon_page_general', $taxon, $chapter);
|
|
1224
|
|
|
1225
|
return $taxonpage;
|
|
1226
|
}
|
|
1227
|
|
|
1228
|
/**
|
|
1229
|
* The function returns a name page as a drupal node ready to be renderized by drupal.
|
|
1230
|
* The node page show the taxon name title and the list of taxon related with such taxon
|
|
1231
|
* name on the tree already in used.
|
|
1232
|
* @param $taxon_name_uuid A taxon name uuid
|
|
1233
|
* @return The formatted name page as node
|
|
1234
|
*/
|
|
1235
|
function cdm_dataportal_name_page_view($taxon_name_uuid){
|
|
1236
|
$taxonname_page = cdm_dataportal_name_view($taxon_name_uuid);
|
|
1237
|
return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title , $taxonname_page->content);
|
|
1238
|
}
|
|
1239
|
|
|
1240
|
/**
|
|
1241
|
* The function genates a object ready to be transformated to a node
|
|
1242
|
* in order to show as a drupal node
|
|
1243
|
* @param $taxon_name_uuid
|
|
1244
|
* @return the object with the page content and title
|
|
1245
|
*/
|
|
1246
|
function cdm_dataportal_name_view($taxon_name_uuid){
|
|
1247
|
//getting the full taxonname object from the server
|
|
1248
|
$taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
|
|
1249
|
if(!$taxon_name){
|
|
1250
|
drupal_set_title(t('Taxon name does not exist'));
|
|
1251
|
return false;
|
|
1252
|
}
|
|
1253
|
//searching for all the taxon connected with the taxon name on the tree in used
|
|
1254
|
$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
|
|
1255
|
$request_params = array();
|
|
1256
|
$request_params['query'] = $name_cache;
|
|
1257
|
$request_params['tree'] = variable_get('cdm_taxonomictree_uuid', false);
|
|
1258
|
$request_params['doTaxa'] = 1;
|
|
1259
|
$request_params['doSynonyms'] = 1;
|
|
1260
|
$request_params['doTaxaByCommonNames'] = 0;
|
|
1261
|
$request_params['matchMode'] = "EXACT";
|
|
1262
|
//$taxon_pager = cdm_ws_get(CDM_WS_FIND_TAXA, null, queryString($request_params));
|
|
1263
|
$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, null, queryString($request_params));
|
|
1264
|
|
|
1265
|
if (sizeof($taxon_pager->records) == 1){
|
|
1266
|
drupal_goto('cdm_dataportal/taxon/' . $taxon_pager->records[0]->uuid);
|
|
1267
|
}else{
|
|
1268
|
$taxon_name_page->title = theme('cdm_name_page_title', $taxon_name);
|
|
1269
|
if($taxon_pager->records){
|
|
1270
|
$taxon_name_page->content = theme_cdm_list_of_taxa($taxon_pager->records, false);
|
|
1271
|
}else{
|
|
1272
|
$taxon_name_page->content = 'This name has no taxa';
|
|
1273
|
}
|
|
1274
|
return $taxon_name_page;
|
|
1275
|
}
|
|
1276
|
|
|
1277
|
//_cdm_dataportal_set_currentSecUuid($taxon->sec->uuid);
|
|
1278
|
|
|
1279
|
//generating the returned object
|
|
1280
|
|
|
1281
|
}
|
|
1282
|
|
|
1283
|
function cdm_dataportal_view_search_advanced(){
|
|
1284
|
|
|
1285
|
drupal_set_title(t('Advanced Search'));
|
|
1286
|
|
|
1287
|
$searchForm = cdm_dataportal_search_taxon_form(true);
|
|
1288
|
|
|
1289
|
return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
|
|
1290
|
|
|
1291
|
}
|
|
1292
|
|
|
1293
|
/**
|
|
1294
|
*
|
|
1295
|
* future extensions to meet palmweb mockup requirements:
|
|
1296
|
* - habitat
|
|
1297
|
* - uses
|
|
1298
|
* - conservation status
|
|
1299
|
* - locality / tdwg region
|
|
1300
|
*/
|
|
1301
|
function cdm_dataportal_view_search_taxon(){
|
|
1302
|
|
|
1303
|
$_SESSION['cdm']['last_search'] = $_SERVER['REQUEST_URI'];
|
|
1304
|
|
|
1305
|
$request_params = cdm_dataportal_search_form_request();
|
|
1306
|
$taxonPager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, null, queryString($request_params));
|
|
1307
|
|
|
1308
|
$search_params = $_REQUEST;
|
|
1309
|
unset($search_params['q']);
|
|
1310
|
return theme('cdm_search_results', $taxonPager, 'cdm_dataportal/search/taxon', $search_params);
|
|
1311
|
}
|
|
1312
|
|
|
1313
|
///**
|
|
1314
|
// *
|
|
1315
|
// * @return unknown_type
|
|
1316
|
// */
|
|
1317
|
//function cdm_dataportal_view_name($taxon_name_uuid){
|
|
1318
|
//
|
|
1319
|
// $taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
|
|
1320
|
// /*
|
|
1321
|
// $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
|
|
1322
|
// $records = array();
|
|
1323
|
// foreach ($taxon_name->taxonBases as $taxon_base){
|
|
1324
|
// $taxon = cdm_ws_get(CDM_WS_TAXON, array($taxon_base->uuid));
|
|
1325
|
// $records[] = $taxon;
|
|
1326
|
// }
|
|
1327
|
//
|
|
1328
|
// $out = "Taxon name: " . $taxon_name->titleCache . "<br/>";
|
|
1329
|
// $out .= theme_cdm_list_of_taxa($records, false);
|
|
1330
|
// */
|
|
1331
|
//
|
|
1332
|
// $request_params = array();
|
|
1333
|
// $request_params['query'] = $name_cache;
|
|
1334
|
// $request_params['tree'] = variable_get('cdm_taxonomictree_uuid', false);
|
|
1335
|
// $request_params['doTaxa'] = 1;
|
|
1336
|
// $request_params['doSynonyms'] = 1;
|
|
1337
|
// $request_params['doTaxaByCommonNames'] = 0;
|
|
1338
|
// //$request_params['matchMode'] = "EXACT";
|
|
1339
|
//
|
|
1340
|
// $taxon_pager = cdm_ws_get(CDM_WS_FIND_TAXA, null, queryString($request_params));
|
|
1341
|
// //var_dump($taxon_pager->records);
|
|
1342
|
// //$out = theme_cdm_taxonname_page_title($taxon_name);
|
|
1343
|
// $out = theme_cdm_list_of_taxa($taxon_pager->records, false);
|
|
1344
|
//
|
|
1345
|
///*
|
|
1346
|
// $out = "Taxon name: " . $taxon_name->titleCache . "<br/>";
|
|
1347
|
// $out .= "Taxon name uuid: " . $taxon_name_uuid . "<br/>";
|
|
1348
|
// $out .= "Taxon name records: " . "<br/>" . $records_names_out;
|
|
1349
|
//*/
|
|
1350
|
// //$out = "Taxon name: " . $taxon_name->titleCache . "<br/>";
|
|
1351
|
// return $out;
|
|
1352
|
//}
|
|
1353
|
|
|
1354
|
function cdm_view_xml2json(){
|
|
1355
|
$file = arg(2);
|
|
1356
|
$datastr = get_content(variable_get('cdm_webservice_url', '').$file);
|
|
1357
|
return xml2json::transformXmlStringToJson($datastr);
|
|
1358
|
}
|
|
1359
|
|
|
1360
|
/* ====================== other functions ====================== */
|
|
1361
|
|
|
1362
|
/**
|
|
1363
|
* Enter description here...
|
|
1364
|
*
|
|
1365
|
* @param String $uuid the UUID of the taxon
|
|
1366
|
* @return the URL
|
|
1367
|
*/
|
|
1368
|
function path_to_taxon($uuid){
|
|
1369
|
if(!$uuid) return false;
|
|
1370
|
return 'cdm_dataportal/taxon/'.$uuid;
|
|
1371
|
}
|
|
1372
|
|
|
1373
|
function path_to_reference($uuid){
|
|
1374
|
if(!$uuid) return false;
|
|
1375
|
return 'cdm_dataportal/reference/'.$uuid;
|
|
1376
|
}
|
|
1377
|
|
|
1378
|
function path_to_name($name_uuid){
|
|
1379
|
$res = false;
|
|
1380
|
if($name_uuid){
|
|
1381
|
$res = 'cdm_dataportal/name/'.$name_uuid;
|
|
1382
|
}
|
|
1383
|
return $res;
|
|
1384
|
}
|
|
1385
|
|
|
1386
|
function path_to_media($uuid, $representaion_uuid = false, $partId = false){
|
|
1387
|
if(!$uuid) return false;
|
|
1388
|
$out = 'cdm_dataportal/media/'.$uuid;
|
|
1389
|
if($representaion_uuid){
|
|
1390
|
$out .= '/'.$representaion_uuid;
|
|
1391
|
if($partId !== false){
|
|
1392
|
$out .= '/'.$partId;
|
|
1393
|
}
|
|
1394
|
}
|
|
1395
|
return $out;
|
|
1396
|
}
|
|
1397
|
|
|
1398
|
/**
|
|
1399
|
* Compares thisRank with thatRank.
|
|
1400
|
* Returns a negative integer, zero, or a positive integer
|
|
1401
|
* as the of thisRank is higher than, equal to, or lower than thatRank.
|
|
1402
|
* e.g:
|
|
1403
|
* <ul>
|
|
1404
|
* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
|
|
1405
|
* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
|
|
1406
|
* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
|
|
1407
|
* </ul>
|
|
1408
|
* <p>
|
|
1409
|
* This compare logic of the underlying webservice is the
|
|
1410
|
* <b>inverse logic</b> of the the one implemented in
|
|
1411
|
* java.lang.Comparable#compareTo(java.lang.Object)
|
|
1412
|
* @param $thisRankUuid
|
|
1413
|
* @param $thatRankUuid
|
|
1414
|
* @return a negative integer, zero, or a positive integer
|
|
1415
|
* as the thisRank is lower than, equal to, or higher than thatRank
|
|
1416
|
*/
|
|
1417
|
function rank_compare($thisRankUuid, $thatRankUuid){
|
|
1418
|
$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
|
|
1419
|
return $result->Integer;
|
|
1420
|
}
|
|
1421
|
|
|
1422
|
function uri_to_synonym($synonymUuid, $acceptedUuid, $pagePart = null){
|
|
1423
|
$acceptedPath = path_to_taxon($acceptedUuid);
|
|
1424
|
return url($acceptedPath.($pagePart ? '/'.$pagePart : ''), 'highlite='.$synonymUuid.'&acceptedFor='.$synonymUuid);
|
|
1425
|
}
|
|
1426
|
|
|
1427
|
/**
|
|
1428
|
* Creates a short taxonname by using the taggename field of NameSTO or NameTO instances.
|
|
1429
|
* If the taggename if empty the fullname will be returned.
|
|
1430
|
*
|
|
1431
|
* @param unknown_type $Name or TreeNode
|
|
1432
|
* @return string
|
|
1433
|
*/
|
|
1434
|
function cdm_dataportal_shortname_of($name){
|
|
1435
|
|
|
1436
|
$nameStr = '';
|
|
1437
|
// get all tagged text tokens of the scientific name
|
|
1438
|
foreach($name->taggedTitle as $tagtxt){
|
|
1439
|
if($tagtxt->type == 'name' || $tagtxt->type == 'rank'){
|
|
1440
|
$nameStr .= ($nameStr ? ' ' : '').$tagtxt->text;
|
|
1441
|
}
|
|
1442
|
}
|
|
1443
|
$nameStr = trim($nameStr);
|
|
1444
|
if($nameStr){
|
|
1445
|
// do not return short names for these
|
|
1446
|
if($nameStr == 'Incertae sedis' || $nameStr == 'Nomina excludenda'){
|
|
1447
|
return $nameStr;
|
|
1448
|
}
|
|
1449
|
if($pos = stripos($nameStr, ' ')){
|
|
1450
|
return substr($nameStr, 0, 1).'. '.substr($nameStr, $pos);
|
|
1451
|
} else {
|
|
1452
|
return $nameStr;
|
|
1453
|
}
|
|
1454
|
} else {
|
|
1455
|
return $name->titleCache;
|
|
1456
|
}
|
|
1457
|
}
|
|
1458
|
|
|
1459
|
/**
|
|
1460
|
* TODO Add Comments. I don't get what
|
|
1461
|
*
|
|
1462
|
* @param UUID $secUuid
|
|
1463
|
*/
|
|
1464
|
function _cdm_dataportal_set_currentSecUuid($secUuid){
|
|
1465
|
|
|
1466
|
// do not save in session but in database
|
|
1467
|
|
|
1468
|
if(is_array($secUuid)){
|
|
1469
|
$secUuid = $secUuid[0];
|
|
1470
|
}
|
|
1471
|
if(!$secUuid){
|
|
1472
|
variable_set('cdm_currentSecRef', null);
|
|
1473
|
} else {
|
|
1474
|
$secRef = cdm_ws_get(CDM_WS_REFERENCE, $secUuid);
|
|
1475
|
if(isset($secRef)){
|
|
1476
|
variable_set('cdm_currentSecRef', (array)($secRef));
|
|
1477
|
}
|
|
1478
|
}
|
|
1479
|
|
|
1480
|
}
|
|
1481
|
|
|
1482
|
/**
|
|
1483
|
* TODO
|
|
1484
|
* This will not work with multiple instances of the dataportal running
|
|
1485
|
* under the same host as there is only one session for all instances.
|
|
1486
|
* In case you switch instances with the same client, you will definitely
|
|
1487
|
* run into trouble.
|
|
1488
|
* Also this is not handling multiple secs.
|
|
1489
|
*
|
|
1490
|
*
|
|
1491
|
* returns the current secRef array.
|
|
1492
|
* If the according session variable is not jet set the default
|
|
1493
|
* as configured in the setting is used otherwise null.
|
|
1494
|
*
|
|
1495
|
* currentSecRef['uuid']
|
|
1496
|
* currentSecRef[....
|
|
1497
|
*
|
|
1498
|
* @return array
|
|
1499
|
*/
|
|
1500
|
//FIXME function _cdm_dataportal_currentSecRef_array(){
|
|
1501
|
//
|
|
1502
|
// // do not look in session but in database
|
|
1503
|
// if( variable_get('cdm_currentSecRef', null) == null){
|
|
1504
|
// $secUuid = variable_get('cdm_secUuid_default', null);
|
|
1505
|
// _cdm_dataportal_set_currentSecUuid($secUuid);
|
|
1506
|
// }
|
|
1507
|
// return variable_get('cdm_currentSecRef', null);
|
|
1508
|
//
|
|
1509
|
//}
|
|
1510
|
|
|
1511
|
/**
|
|
1512
|
* Check if a taxon is accepted by the current taxonomic tree
|
|
1513
|
*
|
|
1514
|
* @param Taxon $taxon
|
|
1515
|
* @return true if $taxon is accepted, false otherwise
|
|
1516
|
*/
|
|
1517
|
|
|
1518
|
function _cdm_dataportal_acceptedByCurrentView($taxon){
|
|
1519
|
|
|
1520
|
//FIXME $current_secref = _cdm_dataportal_currentSecRef_array();
|
|
1521
|
$defaultTreeUuid = variable_get('cdm_taxonomictree_uuid', false);
|
|
1522
|
if($taxon->class == "Taxon" && isset($taxon->taxonNodes)){
|
|
1523
|
foreach($taxon->taxonNodes as $node){
|
|
1524
|
if($node->taxonomicTree == $defaultTreeUuid) {
|
|
1525
|
return true;
|
|
1526
|
}
|
|
1527
|
}
|
|
1528
|
}
|
|
1529
|
return false;
|
|
1530
|
}
|
|
1531
|
|
|
1532
|
/**@Deprecated
|
|
1533
|
*
|
|
1534
|
*/
|
|
1535
|
function compose_url_prameterstr($parameters = array(), $parentPropertyName = false){
|
|
1536
|
$pstr = '';
|
|
1537
|
foreach($parameters as $key=>$value){
|
|
1538
|
if(is_array($value)){
|
|
1539
|
|
|
1540
|
} else {
|
|
1541
|
$pstr .= ($pstr ? '&' :'').$key.'='.urlencode($value);
|
|
1542
|
}
|
|
1543
|
}
|
|
1544
|
return $pstr;
|
|
1545
|
}
|
|
1546
|
|
|
1547
|
function _get_feature_trees(){
|
|
1548
|
$feature_trees = array();
|
|
1549
|
|
|
1550
|
// set tree that contains all features
|
|
1551
|
$feature_trees[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
|
|
1552
|
|
|
1553
|
// get features from database
|
|
1554
|
$persisted_trees = cdm_ws_get(CDM_WS_FEATURETREES);
|
|
1555
|
if(is_array($persisted_trees)){
|
|
1556
|
foreach($persisted_trees as $featureTree){
|
|
1557
|
|
|
1558
|
// do not add the DEFAULT_FEATURETREE again
|
|
1559
|
if($featureTree->uuid == UUID_DEFAULT_FEATURETREE){
|
|
1560
|
continue;
|
|
1561
|
}
|
|
1562
|
$featureLabels = array();
|
|
1563
|
foreach ($featureTree->root->children as $featureNode){
|
|
1564
|
$featureLabels[] = $featureNode->feature->representation_L10n;
|
|
1565
|
}
|
|
1566
|
|
|
1567
|
$feature_trees[$featureTree->uuid] = implode(", ", $featureLabels);
|
|
1568
|
|
|
1569
|
}
|
|
1570
|
}
|
|
1571
|
return $feature_trees;
|
|
1572
|
}
|
|
1573
|
|
|
1574
|
|
|
1575
|
function get_nameRenderTemplate($renderPath, $nameLink = NULL, $refenceLink = NULL){
|
|
1576
|
//TODO implement admin user interface to replace swicth statement
|
|
1577
|
// preliminar solution: using themes
|
|
1578
|
|
|
1579
|
$template = null;
|
|
1580
|
// find best matching default RenderTemplate in theme
|
|
1581
|
//echo "<br/><br/>RENDER PATH: ".$renderPath;
|
|
1582
|
//var_dump('RENDER PATH: ' . $renderPath);
|
|
1583
|
while(!is_array($template) && strlen($renderPath) > 0){
|
|
1584
|
$template = theme('get_nameRenderTemplate', $renderPath);
|
|
1585
|
$renderPath = substr($renderPath, 0, strrpos($renderPath, '.'));
|
|
1586
|
// if(!is_array($template)){
|
|
1587
|
// echo "<br/>->".$renderPath;
|
|
1588
|
// }
|
|
1589
|
}
|
|
1590
|
|
|
1591
|
// otherwise get default RenderTemplate from theme
|
|
1592
|
if(!is_array($template)){
|
|
1593
|
$template = theme('get_nameRenderTemplate', '#DEFAULT');
|
|
1594
|
}
|
|
1595
|
// otherwise get system default RenderTemplate
|
|
1596
|
if(!is_array($template)){
|
|
1597
|
switch($renderPath){
|
|
1598
|
case 'list_of_taxa':
|
|
1599
|
case 'acceptedFor':
|
|
1600
|
case 'taxon_page_synonymy':
|
|
1601
|
case 'typedesignations':
|
|
1602
|
case 'taxon_page_title':
|
|
1603
|
case 'na': $template = array(
|
|
1604
|
'namePart' => array('#uri'=>true),
|
|
1605
|
//'authorshipPart' => true,
|
|
1606
|
);
|
|
1607
|
break;
|
|
1608
|
case 'nar': $template = array(
|
|
1609
|
'namePart' => array('#uri'=>true),
|
|
1610
|
//'authorshipPart' => true,
|
|
1611
|
'referencePart' => array('#uri'=>true),
|
|
1612
|
'microreferencePart' => true,
|
|
1613
|
);
|
|
1614
|
break;
|
|
1615
|
default: $template = array(
|
|
1616
|
'namePart' => array('#uri'=>true),
|
|
1617
|
'authorshipPart' => true,
|
|
1618
|
'referencePart' => array('#uri'=>true),
|
|
1619
|
'microreferencePart' => true,
|
|
1620
|
'statusPart' => true,
|
|
1621
|
'descriptionPart' => true
|
|
1622
|
);
|
|
1623
|
}
|
|
1624
|
}
|
|
1625
|
|
|
1626
|
if($nameLink && isset($template['nameAuthorPart']['#uri'])){
|
|
1627
|
$template['nameAuthorPart']['#uri'] = $nameLink;
|
|
1628
|
} else{
|
|
1629
|
unset($template['nameAuthorPart']['#uri']);
|
|
1630
|
}
|
|
1631
|
|
|
1632
|
if($nameLink && isset($template['namePart']['#uri'])){
|
|
1633
|
$template['namePart']['#uri'] = $nameLink;
|
|
1634
|
} else{
|
|
1635
|
unset($template['namePart']['#uri']);
|
|
1636
|
}
|
|
1637
|
|
|
1638
|
if($refenceLink && isset($template['referencePart']['#uri'])){
|
|
1639
|
$template['referencePart']['#uri'] = $refenceLink;
|
|
1640
|
}else{
|
|
1641
|
unset($template['referencePart']['#uri']);
|
|
1642
|
}
|
|
1643
|
|
|
1644
|
return $template;
|
|
1645
|
}
|
|
1646
|
|
|
1647
|
function get_partDefinition($taxonNameType){
|
|
1648
|
//TODO implement admin user interface to allow specify the partdefinitions for any type
|
|
1649
|
// preliminar solution: using themes
|
|
1650
|
|
|
1651
|
$partdef = theme('get_partDefinition', $taxonNameType);
|
|
1652
|
|
|
1653
|
if(!is_array($partdef)){
|
|
1654
|
switch($taxonNameType){
|
|
1655
|
case 'ZoologicalName': $partdef = array(
|
|
1656
|
'namePart' => array(
|
|
1657
|
'name' => true,
|
|
1658
|
),
|
|
1659
|
'referencePart' => array(
|
|
1660
|
'authorTeam' => true
|
|
1661
|
),
|
|
1662
|
'microreferencePart' => array(
|
|
1663
|
'microreference' => true,
|
|
1664
|
),
|
|
1665
|
'statusPart' => array(
|
|
1666
|
'status' => true,
|
|
1667
|
),
|
|
1668
|
'descriptionPart' => array(
|
|
1669
|
'description' => true,
|
|
1670
|
),
|
|
1671
|
);
|
|
1672
|
break;
|
|
1673
|
case 'BotanicalName': $partdef = array(
|
|
1674
|
'namePart' => array(
|
|
1675
|
'name' => true
|
|
1676
|
),
|
|
1677
|
'authorTeamPart' => array(
|
|
1678
|
'authorTeam' => true,
|
|
1679
|
),
|
|
1680
|
'referencePart' => array(
|
|
1681
|
'reference' => true
|
|
1682
|
),
|
|
1683
|
'microreferencePart' => array(
|
|
1684
|
'microreference' => true,
|
|
1685
|
),
|
|
1686
|
'statusPart' => array(
|
|
1687
|
'status' => true,
|
|
1688
|
),
|
|
1689
|
'descriptionPart' => array(
|
|
1690
|
'description' => true,
|
|
1691
|
),
|
|
1692
|
);
|
|
1693
|
break;
|
|
1694
|
default: $partdef = array(
|
|
1695
|
'namePart' => array(
|
|
1696
|
'name' => true,
|
|
1697
|
),
|
|
1698
|
'authorTeamPart' => array(
|
|
1699
|
'authorTeam' => true,
|
|
1700
|
),
|
|
1701
|
'referencePart' => array(
|
|
1702
|
'reference' => true
|
|
1703
|
),
|
|
1704
|
'microreferencePart' => array(
|
|
1705
|
'microreference' => true,
|
|
1706
|
),
|
|
1707
|
'statusPart' => array(
|
|
1708
|
'status' => true,
|
|
1709
|
),
|
|
1710
|
'descriptionPart' => array(
|
|
1711
|
'description' => true,
|
|
1712
|
),
|
|
1713
|
);
|
|
1714
|
}
|
|
1715
|
}
|
|
1716
|
return $partdef;
|
|
1717
|
}
|
|
1718
|
|
|
1719
|
/**
|
|
1720
|
* The function read the metadata info such title or artist of a media file. The
|
|
1721
|
* function tries at first to get all the info from the file metadata and if it is
|
|
1722
|
* not avaible look at the media file info stored at the database.
|
|
1723
|
* @param $media The media file
|
|
1724
|
* @return array The array with the avilable specified metadata info.
|
|
1725
|
* TODO rename to read_media_metadata() and move to *.module
|
|
1726
|
*/
|
|
1727
|
function cdm_read_media_metadata($media){
|
|
1728
|
|
|
1729
|
$metadata_caption = array('title' => '', //media_metadata and media
|
|
1730
|
'artist' => '', //media_metadata and media
|
|
1731
|
'rights', //media_metadata and media
|
|
1732
|
'location', //media_metadata
|
|
1733
|
'filename' => '', //media
|
|
1734
|
'mediacreated' => '', //media
|
|
1735
|
'description' => ''); //media
|
|
1736
|
|
|
1737
|
//getting the media metadata
|
|
1738
|
$media_metadata = cdm_ws_get(CDM_WS_MEDIA_METADATA, array($media->uuid));
|
|
1739
|
|
|
1740
|
//title
|
|
1741
|
//if ($media_metadata->Headline) {
|
|
1742
|
if ($media_metadata->ObjectName) {
|
|
1743
|
$metadata_caption['title'] = $media_metadata->ObjectName;
|
|
1744
|
// } else if ($media->titleCache){
|
|
1745
|
// $metadata_caption['title'] = $media_metadata->ObjectName;
|
|
1746
|
} else if ($media->titleCache){
|
|
1747
|
$metadata_caption['title'] = $media->titleCache;
|
|
1748
|
if ($media->description_L10n)
|
|
1749
|
$metadata_caption['title'] .= ' - ' . $media->description_L10n;
|
|
1750
|
}else{ //if there is no title on the db and metadata get file title
|
|
1751
|
$aux = $media->representations[0]->parts[0]->uri;
|
|
1752
|
$aux = explode("/", $aux);
|
|
1753
|
$aux = end($aux);
|
|
1754
|
$metadata_caption['title'] = $aux;
|
|
1755
|
}
|
|
1756
|
|
|
1757
|
//artist
|
|
1758
|
if ($media_metadata->Artist){
|
|
1759
|
$metadata_caption['artist'] = ($media_metadata->Artist ? ''.$media_metadata->Artist : '');
|
|
1760
|
}
|
|
1761
|
elseif ($media->artist->titleCache){
|
|
1762
|
$metadata_caption['artist'] = $media->artist->titleCache;
|
|
1763
|
}
|
|
1764
|
|
|
1765
|
//copyright
|
|
1766
|
$metadata_caption['rights'] = array('copyright' => array('agentNames' => array()),
|
|
1767
|
'license' => array('agentNames' => array(), 'types' => array(), 'abbreviatedTexts' => array(), 'uris' => array()));
|
|
1768
|
if ($media_metadata->Copyright)
|
|
1769
|
$metadata_caption['rights']['copyright']['agentNames'][] = $media_metadata->Copyright;
|
|
1770
|
elseif ($media->rights){
|
|
1771
|
foreach($media->rights as $right){
|
|
1772
|
switch($right->term->uuid){
|
|
1773
|
case UUID_RIGHTS_LICENCE:
|
|
1774
|
$metadata_caption['rights']['license']['agentNames'][] = ($right->agent ? ''.$right->agent->firstname.' '.$right->agent->lastname : '');
|
|
1775
|
$metadata_caption['rights']['license']['types'][] = ($right->representation_L10n ? ''.$right->representation_L10n : '');
|
|
1776
|
$metadata_caption['rights']['license']['abbreviatedTexts'][] = ($right->abbreviatedText ? ''.$right->abbreviatedText : '');
|
|
1777
|
$metadata_caption['rights']['license']['uris'][] = ($right->uri ? ''.$right->uri : '');
|
|
1778
|
break;
|
|
1779
|
case UUID_RIGHTS_COPYRIGHT:
|
|
1780
|
$metadata_caption['rights']['copyright']['agentNames'][] = $right->agent->firstname . ' ' . $right->agent->lastname;
|
|
1781
|
break;
|
|
1782
|
}
|
|
1783
|
}
|
|
1784
|
}
|
|
1785
|
else
|
|
1786
|
$metadata_caption['rights']['agentNames'][] = '';
|
|
1787
|
|
|
1788
|
//filling the description (though there is no description in the db???)
|
|
1789
|
//$metadata_caption['description'] = $media->description_L10n;
|
|
1790
|
|
|
1791
|
//location
|
|
1792
|
$metadata_caption['location'] = array();
|
|
1793
|
$metadata_caption['location']['sublocation'] = $media_metadata->Sublocation;
|
|
1794
|
$metadata_caption['location']['city'] = $media_metadata->City;
|
|
1795
|
$metadata_caption['location']['province'] = $media_metadata->Province;
|
|
1796
|
$metadata_caption['location']['country'] = $media_metadata->Country;
|
|
1797
|
|
|
1798
|
//filename
|
|
1799
|
if(isset($media->representations[0]->parts[0]->uri)){
|
|
1800
|
$fileUri = $media->representations[0]->parts[0]->uri;
|
|
1801
|
$filename = substr($fileUri, strrpos($fileUri, "/")+1);
|
|
1802
|
$metadata_caption['filename'] = $filename;
|
|
1803
|
}
|
|
1804
|
else{
|
|
1805
|
$metadata_caption['filename'] = '';
|
|
1806
|
}
|
|
1807
|
/*
|
|
1808
|
//creation date
|
|
1809
|
if($media_metadata["Modify Date"])
|
|
1810
|
$metadata_caption['mediacreated'] = $media_metadata["Modify Date"];
|
|
1811
|
else
|
|
1812
|
$metadata_caption['mediacreated'] = $media->created;
|
|
1813
|
*/
|
|
1814
|
//returned value
|
|
1815
|
return $metadata_caption;
|
|
1816
|
}
|
|
1817
|
|
|
1818
|
/**
|
|
1819
|
* This function collects all the media from a list of description elements
|
|
1820
|
* and return them as an Array.
|
|
1821
|
*
|
|
1822
|
* @param $descriptionElementes The description elements
|
|
1823
|
* @return Array The output with all the media
|
|
1824
|
*/
|
|
1825
|
function cdm_dataportal_media_from_descriptionElements($descriptionElements){
|
|
1826
|
//variables
|
|
1827
|
$outArrayOfMedia = array(); //return value
|
|
1828
|
//implementation
|
|
1829
|
foreach($descriptionElements as $descriptionElement){
|
|
1830
|
foreach($descriptionElement->media as $media){
|
|
1831
|
if(isset($media)){
|
|
1832
|
$outArrayOfMedia[] = $media;
|
|
1833
|
}
|
|
1834
|
}
|
|
1835
|
}
|
|
1836
|
return $outArrayOfMedia;
|
|
1837
|
}
|
|
1838
|
|
|
1839
|
|