|
1
|
<?php
|
|
2
|
/**
|
|
3
|
* @file
|
|
4
|
* Module to provide a CDM Dataportal.
|
|
5
|
*
|
|
6
|
* @copyright
|
|
7
|
* (C) 2007-2012 EDIT
|
|
8
|
* European Distributed Institute of Taxonomy
|
|
9
|
* http://www.e-taxonomy.eu
|
|
10
|
*
|
|
11
|
* The contents of this module are subject to the Mozilla
|
|
12
|
* Public License Version 1.1.
|
|
13
|
* @see http://www.mozilla.org/MPL/MPL-1.1.html
|
|
14
|
*
|
|
15
|
* @author
|
|
16
|
* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
|
|
17
|
* - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
|
|
18
|
*/
|
|
19
|
|
|
20
|
module_load_include('php', 'cdm_dataportal', 'node_types');
|
|
21
|
module_load_include('php', 'cdm_dataportal', 'settings');
|
|
22
|
module_load_include('php', 'cdm_dataportal', 'help');
|
|
23
|
module_load_include('php', 'cdm_dataportal', 'cdm_dataportal.search');
|
|
24
|
|
|
25
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
|
|
26
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
|
|
27
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
|
|
28
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
|
|
29
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
|
|
30
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
|
|
31
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
|
|
32
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
|
|
33
|
module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.bibliography');
|
|
34
|
|
|
35
|
module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
|
|
36
|
module_load_include('php', 'cdm_dataportal', 'classes/footnote');
|
|
37
|
module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
|
|
38
|
module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
|
|
39
|
|
|
40
|
/**
|
|
41
|
* loads external java script files asynchronously.
|
|
42
|
*
|
|
43
|
* @param unknown_type $script_url
|
|
44
|
*/
|
|
45
|
function drupal_add_js_async($script_url, $callback){
|
|
46
|
|
|
47
|
drupal_add_js("
|
|
48
|
jQuery(document).ready(function() {
|
|
49
|
jQuery.ajax({
|
|
50
|
url: '" . $script_url . "',
|
|
51
|
dataType: 'script',
|
|
52
|
cache: true, // otherwise will get fresh copy every page load
|
|
53
|
success: function() {
|
|
54
|
" . $callback . "
|
|
55
|
}
|
|
56
|
});
|
|
57
|
});"
|
|
58
|
, 'inline');
|
|
59
|
}
|
|
60
|
|
|
61
|
/**
|
|
62
|
* @param unknown_type $link_element_selector
|
|
63
|
* @param unknown_type $progress_element_selector
|
|
64
|
*/
|
|
65
|
function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
|
|
66
|
|
|
67
|
$callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
|
|
68
|
|
|
69
|
drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
|
|
70
|
|
|
71
|
// drupal_add_js("
|
|
72
|
// if (Drupal.jsEnabled) {
|
|
73
|
// $(document).ready(function() {
|
|
74
|
// $('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
|
|
75
|
// });
|
|
76
|
// }", 'inline');
|
|
77
|
}
|
|
78
|
|
|
79
|
/**
|
|
80
|
* @todo Please document this function.
|
|
81
|
* @see http://drupal.org/node/1354
|
|
82
|
*/
|
|
83
|
function _add_js_treeselector() {
|
|
84
|
// drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
|
|
85
|
drupal_add_js("
|
|
86
|
jQuery(document).ready(function() {
|
|
87
|
jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
|
|
88
|
jQuery('#cdm-taxonomictree-selector-form').submit();
|
|
89
|
});
|
|
90
|
|
|
91
|
});
|
|
92
|
",
|
|
93
|
array(
|
|
94
|
'type' => 'inline',
|
|
95
|
'scope' => 'footer'
|
|
96
|
)
|
|
97
|
);
|
|
98
|
}
|
|
99
|
|
|
100
|
/**
|
|
101
|
* @todo Please document this function.
|
|
102
|
* @see http://drupal.org/node/1354
|
|
103
|
*/
|
|
104
|
function _add_js_openlayers_map() {
|
|
105
|
|
|
106
|
$openlayers = '/js/OpenLayers-2.11/OpenLayers.js';
|
|
107
|
|
|
108
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers, array(
|
|
109
|
'type' => 'file',
|
|
110
|
'weight' => JS_LIBRARY,
|
|
111
|
'cache' => FALSE,
|
|
112
|
));
|
|
113
|
|
|
114
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/openlayers_map.js');
|
|
115
|
|
|
116
|
$gmap_api_key = variable_get('gmap_api_key', 'ABQIAAAAFho6eHAcUOTHLmH9IYHAeBRi_j0U6kJrkFvY4-OX2XYmEAa76BTsyMmEq-tn6nFNtD2UdEGvfhvoCQ');
|
|
117
|
|
|
118
|
$baseLayers = variable_get('baselayers', array());
|
|
119
|
if (!is_array($baseLayers) || count($baseLayers) == 0) {
|
|
120
|
$baseLayers = array(
|
|
121
|
'metacarta_vmap0' => 'Metacarta Vmap0',
|
|
122
|
'PREFERRED' => 'metacarta_vmap0',
|
|
123
|
);
|
|
124
|
}
|
|
125
|
$layerNames = '';
|
|
126
|
foreach ($baseLayers as $layerName => $layerLabel) {
|
|
127
|
if ($layerName == 'PREFERRED') {
|
|
128
|
$preferredLayer = $baseLayers['PREFERRED'];
|
|
129
|
}
|
|
130
|
else {
|
|
131
|
$layerNames .= ($layerNames ? ', ' : '') . "'$layerName'";
|
|
132
|
}
|
|
133
|
}
|
|
134
|
|
|
135
|
if (isset($baseLayers['gmap']) || isset($baseLayers['gsat']) || isset($baseLayers['ghyb'])) {
|
|
136
|
drupal_add_html_head('<script src=http://maps.google.com/maps?file=api&v=2&sensor=false&key=' . $gmap_api_key . '" type="text/javascript"></script>', $key = NULL /* TODO Set this variable. */);
|
|
137
|
drupal_add_js('http://dev.virtualearth.net/mapcontrol/mapcontrol.ashx?v=6.1', array('type' => 'external'));
|
|
138
|
}
|
|
139
|
|
|
140
|
// window.onload - is executed when the document and images etc is fully loaded
|
|
141
|
// Query(document).ready - is executed much earlier, when the DOM is loaded
|
|
142
|
drupal_add_js("
|
|
143
|
jQuery(document).ready(function() {
|
|
144
|
|
|
145
|
window.onload = function () {
|
|
146
|
// ---
|
|
147
|
jQuery('#openlayers_map').cdm_openlayers_map('"
|
|
148
|
. getEDITMapServiceURI() . "', {
|
|
149
|
legendPosition: 3,
|
|
150
|
displayWidth: '" . variable_get('cdm_dataportal_geoservice_display_width', FALSE) . "',
|
|
151
|
boundingBox: '" . variable_get('cdm_dataportal_geoservice_bounding_box', FALSE) . "',
|
|
152
|
distributionOpacity: '" . variable_get('cdm_dataportal_geoservice_distributionOpacity', '0.5') . "',
|
|
153
|
legendOpacity: '" . variable_get('cdm_dataportal_geoservice_legendOpacity', '0.5') . "',
|
|
154
|
showLayerSwitcher: " . (variable_get('cdm_dataportal_geoservice_showLayerSwitcher', TRUE) ? 'true' : 'false') . ",
|
|
155
|
baseLayerNames: [" . $layerNames . "],
|
|
156
|
defaultBaseLayerName: '" . $preferredLayer . "',
|
|
157
|
});
|
|
158
|
// ---
|
|
159
|
};
|
|
160
|
});
|
|
161
|
", array('type' => 'inline'));
|
|
162
|
|
|
163
|
}
|
|
164
|
|
|
165
|
/**
|
|
166
|
* @todo Enter description here ...
|
|
167
|
*
|
|
168
|
* @param unknown_type $width
|
|
169
|
* @param unknown_type $bounding_box
|
|
170
|
* @param unknown_type $occurrenceQuery
|
|
171
|
* @param unknown_type $distributionQuery
|
|
172
|
* @param unknown_type $legendFormatQuery
|
|
173
|
* @param unknown_type $map_caption
|
|
174
|
*
|
|
175
|
* @return unknown
|
|
176
|
*/
|
|
177
|
function get_image_map($width, $bounding_box = FALSE, $occurrenceQuery = FALSE, $distributionQuery = FALSE, $legendFormatQuery = FALSE, $map_caption = FALSE) {
|
|
178
|
|
|
179
|
$server = getEDITMapServiceURI();
|
|
180
|
|
|
181
|
if (!$server) {
|
|
182
|
// Warning message.
|
|
183
|
drupal_set_message(t(
|
|
184
|
"No 'Geoservice Access Point' has been set so far.
|
|
185
|
Please configure the variable 'Geoservice Access Point' here !url", array(
|
|
186
|
'!url' => l(t('CDM Dataportal Settings'), 'admin/config/cdm_dataportal/geo'),
|
|
187
|
)), 'warning');
|
|
188
|
|
|
189
|
// Message to render.
|
|
190
|
return '<p>' . t('No geoservice specified') . '</p>';
|
|
191
|
}
|
|
192
|
|
|
193
|
// Additional query parameters as set in the data portal admin section.
|
|
194
|
$labels_on = variable_get('cdm_dataportal_geoservice_labels_on', 0);
|
|
195
|
|
|
196
|
$query_string = '&image=true&recalculate=false&legend=1&ms=' . $width
|
|
197
|
. ($bounding_box ? '&bbox=' . $bounding_box : '')
|
|
198
|
. ($labels_on ? '&label=' . $labels_on : '');
|
|
199
|
|
|
200
|
if ($map_caption) {
|
|
201
|
$query_string .= '&mlp=3&mc_s=Georgia,15,blue&mc=' . $map_caption;
|
|
202
|
}
|
|
203
|
|
|
204
|
if (getEDITMapServiceVersionNumber() >= 1.1) {
|
|
205
|
|
|
206
|
// Either occurrence or distribution - combined maps will be possible
|
|
207
|
// in the future.
|
|
208
|
if ($occurrenceQuery) {
|
|
209
|
// @todo Fix $occurrenceQuery.
|
|
210
|
$occurrenceQuery = str_replace("&image=false", "", $occurrenceQuery);
|
|
211
|
// $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
|
|
212
|
// Will be replaced below.. HACK!!!
|
|
213
|
$occurrenceQuery .= '&l=tdwg4&as=';
|
|
214
|
|
|
215
|
$query_string .= "&" . $occurrenceQuery;
|
|
216
|
}
|
|
217
|
elseif ($distributionQuery) {
|
|
218
|
$query_string .= "&" . $distributionQuery;
|
|
219
|
}
|
|
220
|
|
|
221
|
// Apply Plain Image map settings special for version >= 1.1.
|
|
222
|
/*
|
|
223
|
example : title=a:Naturalized++non-invasive
|
|
224
|
&ad=cyprusdivs:bdcode:a:5&as=a:ff9900,,0.1,&l=tdwg4
|
|
225
|
&ms=500&bbox=32,34,35,36&img=true&legend=1&mlp=3
|
|
226
|
&mc_s=Georgia,15,blue&mc=&recalculate=false
|
|
227
|
|
|
228
|
http://edit.br.fgov.be/edit_wp5/v1/rest_gen.php?
|
|
229
|
l=background_gis:b,cyprusdivs&ad=cyprusdivs%3Abdcode%3Aa%3A8%2C4
|
|
230
|
&as=a%3A339966%2C%2C0.1%2C|b:0000ff,,
|
|
231
|
&bbox=32%2C34%2C35%2C36&img=true&legend=1&mc=&mc_s=Georgia%2C15%2Cblue
|
|
232
|
&mlp=3&ms=500&recalculate=false&title=a%3Aindigenous
|
|
233
|
*/
|
|
234
|
|
|
235
|
$map_service_script_name = "rest_gen.php";
|
|
236
|
|
|
237
|
$bgcolor_areaStyleId = "y";
|
|
238
|
$baselayer_areaStyleId = "z";
|
|
239
|
$bgcolor_layer = '';
|
|
240
|
$additional_area_styles = array();
|
|
241
|
|
|
242
|
// Background color:
|
|
243
|
if (variable_get('map_bg_color', '')) {
|
|
244
|
$bgcolor_layer = "background_gis:" . $bgcolor_areaStyleId;
|
|
245
|
$additional_area_styles[] = $bgcolor_areaStyleId . ":" . variable_get('map_bg_color', '') . ",,";
|
|
246
|
}
|
|
247
|
|
|
248
|
// TODO HACK to replace the default base layer which currently is tdwg4 !!!
|
|
249
|
// only needed for distribution maps.
|
|
250
|
if (strpos($query_string, "?l=") !== FALSE) {
|
|
251
|
$layer_param_token = "?l=";
|
|
252
|
}
|
|
253
|
else {
|
|
254
|
$layer_param_token = "&l=";
|
|
255
|
}
|
|
256
|
if (strpos($query_string, "?as=") !== FALSE) {
|
|
257
|
$areystyle_param_token = "?as=";
|
|
258
|
}
|
|
259
|
else {
|
|
260
|
$areystyle_param_token = "&as=";
|
|
261
|
}
|
|
262
|
if (variable_get('map_base_layer', '')) {
|
|
263
|
$query_string = str_replace($layer_param_token . "tdwg4", "$layer_param_token" . variable_get('map_base_layer', '') . ":" . $baselayer_areaStyleId, $query_string);
|
|
264
|
}
|
|
265
|
else {
|
|
266
|
$query_string = str_replace($layer_param_token . "tdwg4", $layer_param_token . "tdwg4:" . $baselayer_areaStyleId . ",", $query_string);
|
|
267
|
}
|
|
268
|
|
|
269
|
if ($bgcolor_layer) {
|
|
270
|
$query_string = str_replace($layer_param_token, $layer_param_token . $bgcolor_layer . ",", $query_string);
|
|
271
|
}
|
|
272
|
|
|
273
|
if (variable_get('map_base_layer_style', '')) {
|
|
274
|
$additional_area_styles[] = $baselayer_areaStyleId . ":" . variable_get('map_base_layer_style', '');
|
|
275
|
}
|
|
276
|
|
|
277
|
foreach ($additional_area_styles as $as) {
|
|
278
|
$query_string = str_replace($areystyle_param_token, $areystyle_param_token . $as . "|", $query_string);
|
|
279
|
}
|
|
280
|
|
|
281
|
}
|
|
282
|
else {
|
|
283
|
// Pre 1.1. version of map service.
|
|
284
|
if ($occurrenceQuery) {
|
|
285
|
|
|
286
|
$map_service_script_name = "point.php";
|
|
287
|
|
|
288
|
// Fix $occurrenceQuery.
|
|
289
|
$occurrenceQuery = str_replace("&image=false", "", $occurrenceQuery);
|
|
290
|
// $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
|
|
291
|
$occurrenceQuery .= '&l=v:e_w_0';
|
|
292
|
$query_string .= "&" . $occurrenceQuery;
|
|
293
|
}
|
|
294
|
elseif ($distributionQuery) {
|
|
295
|
$query_string .= "&" . $distributionQuery;
|
|
296
|
$map_service_script_name = "areas.php";
|
|
297
|
}
|
|
298
|
}
|
|
299
|
|
|
300
|
$mapUri = url("$server/$map_service_script_name?$query_string");
|
|
301
|
$out = '<img class="distribution_map" src="' . $mapUri . '" alt="Map" />';
|
|
302
|
// Showing map caption.
|
|
303
|
if ($map_caption) {
|
|
304
|
// FIXME: replace <br> by according css style.
|
|
305
|
$out .= '<div class="distribution_map_caption">' . $map_caption . '</div>' . '<br />';
|
|
306
|
$out .= '</div>';
|
|
307
|
}
|
|
308
|
|
|
309
|
return $out;
|
|
310
|
}
|
|
311
|
|
|
312
|
/**
|
|
313
|
* @todo Enter description here ...
|
|
314
|
*
|
|
315
|
* @param unknown_type $width
|
|
316
|
* @param unknown_type $bounding_box
|
|
317
|
* @param unknown_type $occurrenceQuery
|
|
318
|
* @param unknown_type $distributionQuery
|
|
319
|
* @param unknown_type $legendFormatQuery
|
|
320
|
* @param unknown_type $map_caption
|
|
321
|
*
|
|
322
|
* @return unknown
|
|
323
|
*/
|
|
324
|
function get_openlayers_map($width, $bounding_box = FALSE, $occurrenceQuery = FALSE, $distributionQuery = FALSE, $legendFormatQuery = FALSE, $map_caption = FALSE) {
|
|
325
|
|
|
326
|
_add_js_openlayers_map();
|
|
327
|
|
|
328
|
$out = '<div id="openlayers">';
|
|
329
|
$out .= '<div id="openlayers_map" class="smallmap"';
|
|
330
|
$out .= ' style="width: ' . $width . 'px; height:' . ($width / 2) . 'px"';
|
|
331
|
|
|
332
|
// Additional query parameters as set in the data portal admin section.
|
|
333
|
$labels_on = variable_get('cdm_dataportal_geoservice_labels_on', 0);
|
|
334
|
|
|
335
|
$openlayers_map_query_string = '&img=false&ms=' . $width
|
|
336
|
. ($bounding_box ? '&bbox=' . $bounding_box : '')
|
|
337
|
. ($labels_on ? '&label=' . $labels_on : '');
|
|
338
|
|
|
339
|
if ($occurrenceQuery) {
|
|
340
|
// @todo Fix $occurrenceQuery.
|
|
341
|
$occurrenceQuery .= '&bbox=-180,-90,180,90';
|
|
342
|
$occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
|
|
343
|
// $occurrenceQuery .= '&l=v:e_w_0';
|
|
344
|
// TODO add to cdm service?
|
|
345
|
$occurrenceQuery .= '&legend=0';
|
|
346
|
|
|
347
|
$out .= ' occurrenceQuery="' . $occurrenceQuery . '&' . $openlayers_map_query_string . '"';
|
|
348
|
}
|
|
349
|
|
|
350
|
if ($distributionQuery) {
|
|
351
|
$out .= ' distributionQuery="' . $distributionQuery . '&' . $openlayers_map_query_string . '"';
|
|
352
|
}
|
|
353
|
|
|
354
|
if ($legendFormatQuery) {
|
|
355
|
$out .= ' legendFormatQuery="' . $legendFormatQuery . '"';
|
|
356
|
}
|
|
357
|
|
|
358
|
$out .= '></div></div>';
|
|
359
|
|
|
360
|
// Showing map caption.
|
|
361
|
if ($map_caption) {
|
|
362
|
// FIXME: replace <br> by according css style.
|
|
363
|
$out .= '<div class="distribution_map_caption">' . $map_caption . '</div>' . '<br />';
|
|
364
|
$out .= '</div>';
|
|
365
|
}
|
|
366
|
return $out;
|
|
367
|
}
|
|
368
|
|
|
369
|
/* ====================== hook implementations ====================== */
|
|
370
|
/**
|
|
371
|
* Implements hook_permission().
|
|
372
|
*
|
|
373
|
* Valid permissions for this module.
|
|
374
|
*
|
|
375
|
* @return array
|
|
376
|
* An array of valid permissions for the portfolio module.
|
|
377
|
*/
|
|
378
|
function cdm_dataportal_permission() {
|
|
379
|
return array(
|
|
380
|
'administer cdm_dataportal' => array(
|
|
381
|
'title' => t('administer cdm_dataportal'),
|
|
382
|
'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
|
|
383
|
),
|
|
384
|
'cdm_dataportal view notes' => array(
|
|
385
|
'title' => t('cdm_dataportal view notes'),
|
|
386
|
'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
|
|
387
|
),
|
|
388
|
// TODO Which other permissions are required?
|
|
389
|
// -> check the WP6 requirements document.
|
|
390
|
);
|
|
391
|
}
|
|
392
|
|
|
393
|
/**
|
|
394
|
* Implements hook_menu().
|
|
395
|
*/
|
|
396
|
function cdm_dataportal_menu() {
|
|
397
|
$items = array();
|
|
398
|
|
|
399
|
// @see settings.php.
|
|
400
|
cdm_dataportal_menu_admin($items);
|
|
401
|
cdm_dataportal_menu_help($items);
|
|
402
|
|
|
403
|
$items['cdm_dataportal/names'] = array(
|
|
404
|
'page callback' => 'cdm_dataportal_view_names',
|
|
405
|
'access arguments' => array('access content'),
|
|
406
|
'type' => MENU_CALLBACK,
|
|
407
|
);
|
|
408
|
|
|
409
|
// Optional callback arguments: page.
|
|
410
|
$items['cdm_dataportal/taxon'] = array(
|
|
411
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
412
|
'access arguments' => array('access content'),
|
|
413
|
'type' => MENU_CALLBACK,
|
|
414
|
// Expected callback arguments: uuid.
|
|
415
|
);
|
|
416
|
|
|
417
|
$items['cdm_dataportal/name'] = array(
|
|
418
|
'page callback' => 'cdm_dataportal_name_page_view',
|
|
419
|
/*
|
|
420
|
'page arguments' => array(
|
|
421
|
'taxon_name_uuid',
|
|
422
|
'taxon_to_hide_uuid',
|
|
423
|
'synonym_uuid' => NULL
|
|
424
|
),
|
|
425
|
*/
|
|
426
|
'access arguments' => array('access content'),
|
|
427
|
'type' => MENU_CALLBACK,
|
|
428
|
// Expected callback arguments: uuid.
|
|
429
|
);
|
|
430
|
|
|
431
|
$items['cdm_dataportal/reference'] = array(
|
|
432
|
'page callback' => 'cdm_dataportal_view_reference',
|
|
433
|
'access arguments' => array('access content'),
|
|
434
|
'type' => MENU_CALLBACK,
|
|
435
|
// Expected callback arguments: uuid.
|
|
436
|
);
|
|
437
|
|
|
438
|
$items['cdm_dataportal/reference/list'] = array(
|
|
439
|
'page callback' => 'cdm_dataportal_view_reference_list',
|
|
440
|
'access arguments' => array('access content'),
|
|
441
|
'type' => MENU_CALLBACK,
|
|
442
|
// Expected callback arguments: uuid.
|
|
443
|
);
|
|
444
|
|
|
445
|
$items['cdm_dataportal/media'] = array(
|
|
446
|
'page callback' => 'cdm_dataportal_view_media',
|
|
447
|
'access arguments' => array('access content'),
|
|
448
|
'type' => MENU_CALLBACK,
|
|
449
|
// Expected callback arguments:
|
|
450
|
// uuid, mediarepresentation_uuid, part_uuid or part#.
|
|
451
|
);
|
|
452
|
|
|
453
|
$items['cdm_dataportal/polytomousKey'] = array(
|
|
454
|
'page callback' => 'cdm_dataportal_view_polytomousKey',
|
|
455
|
'access arguments' => array('access content'),
|
|
456
|
'type' => MENU_CALLBACK,
|
|
457
|
// Expected callback arguments: polytomousKey->uuid.
|
|
458
|
);
|
|
459
|
|
|
460
|
$items['cdm_dataportal/search'] = array(
|
|
461
|
'page callback' => 'cdm_dataportal_view_search_advanced',
|
|
462
|
'access arguments' => array('access content'),
|
|
463
|
'type' => MENU_CALLBACK,
|
|
464
|
);
|
|
465
|
|
|
466
|
$items['cdm_dataportal/search/advanced'] = array(
|
|
467
|
'title' => 'Advanced',
|
|
468
|
'page callback' => 'cdm_dataportal_view_search_advanced',
|
|
469
|
'access arguments' => array('access content'),
|
|
470
|
'type' => MENU_DEFAULT_LOCAL_TASK,
|
|
471
|
);
|
|
472
|
|
|
473
|
$items['cdm_dataportal/search/taxon_by_description'] = array(
|
|
474
|
'title' => 'By description full text',
|
|
475
|
'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
|
|
476
|
'access arguments' => array('access content'),
|
|
477
|
'type' => MENU_LOCAL_TASK,
|
|
478
|
);
|
|
479
|
|
|
480
|
$items['cdm_dataportal/search/results/taxon'] = array(
|
|
481
|
'page callback' => 'cdm_dataportal_view_search_results_taxon',
|
|
482
|
'access arguments' => array('access content'),
|
|
483
|
'type' => MENU_CALLBACK,
|
|
484
|
);
|
|
485
|
/*
|
|
486
|
$items['cdm/xml2json'] = array(
|
|
487
|
'page callback' => 'cdm_view_xml2json',
|
|
488
|
'access arguments' => array('access content'),
|
|
489
|
'type' => MENU_CALLBACK,
|
|
490
|
);
|
|
491
|
*/
|
|
492
|
|
|
493
|
// if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
|
|
494
|
// User configuration of cdm_dataportal.
|
|
495
|
$items['user/%/cdm_dataportal'] = array(
|
|
496
|
'title' => 'cdm_dataportal',
|
|
497
|
'access arguments' => array('access content'),
|
|
498
|
'page callback' => 'drupal_get_form',
|
|
499
|
'page arguments' => array('cdm_dataportal_user_form'),
|
|
500
|
'type' => MENU_LOCAL_TASK,
|
|
501
|
'weight' => 10,
|
|
502
|
);
|
|
503
|
// }
|
|
504
|
|
|
505
|
// 'May not cache' in D5.
|
|
506
|
// --- Local tasks for Taxon.
|
|
507
|
$items['cdm_dataportal/name/%'] = array(
|
|
508
|
// 'page callback' => 'cdm_dataportal_view_name',
|
|
509
|
'page callback' => 'cdm_dataportal_name_page_view',
|
|
510
|
'page arguments' => array(2, 3, 4),
|
|
511
|
'access arguments' => array('access content'),
|
|
512
|
'type' => MENU_CALLBACK,
|
|
513
|
);
|
|
514
|
|
|
515
|
if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
|
|
516
|
$items['cdm_dataportal/taxon/%'] = array(
|
|
517
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
|
|
518
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
519
|
'access arguments' => array('access content'),
|
|
520
|
'type' => MENU_CALLBACK,
|
|
521
|
'weight' => 1,
|
|
522
|
'page arguments' => array(2, "description")
|
|
523
|
, // Expected callback arguments: name_uuid.
|
|
524
|
);
|
|
525
|
|
|
526
|
$items['cdm_dataportal/taxon/%/all'] = array(
|
|
527
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
|
|
528
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
529
|
'access arguments' => array('access content'),
|
|
530
|
'type' => MENU_CALLBACK,
|
|
531
|
'weight' => 2,
|
|
532
|
'page arguments' => array(2, "all")
|
|
533
|
, // Expected callback arguments: name_uuid.
|
|
534
|
);
|
|
535
|
|
|
536
|
$items['cdm_dataportal/taxon/%/description'] = array(
|
|
537
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
|
|
538
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
539
|
'access arguments' => array('access content'),
|
|
540
|
'type' => MENU_DEFAULT_LOCAL_TASK,
|
|
541
|
'weight' => 2,
|
|
542
|
'page arguments' => array(2, "description")
|
|
543
|
, // Expected callback arguments: name_uuid.
|
|
544
|
);
|
|
545
|
|
|
546
|
$items['cdm_dataportal/taxon/%/synonymy'] = array(
|
|
547
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy')),
|
|
548
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
549
|
'access arguments' => array('access content'),
|
|
550
|
'type' => MENU_LOCAL_TASK,
|
|
551
|
'weight' => 4,
|
|
552
|
'page arguments' => array(2, "synonymy", 4)
|
|
553
|
, // Expected callback arguments: name_uuid.
|
|
554
|
);
|
|
555
|
$items['cdm_dataportal/taxon/%/images'] = array(
|
|
556
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Images')),
|
|
557
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
558
|
'access arguments' => array('access content'),
|
|
559
|
'type' => MENU_LOCAL_TASK,
|
|
560
|
'weight' => 5,
|
|
561
|
'page arguments' => array(2, "images")
|
|
562
|
, // Expected callback arguments: name_uuid.
|
|
563
|
);
|
|
564
|
|
|
565
|
$items['cdm_dataportal/taxon/%/specimens'] = array(
|
|
566
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens')),
|
|
567
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
568
|
'access arguments' => array('access content'),
|
|
569
|
'type' => MENU_LOCAL_TASK,
|
|
570
|
'weight' => 6,
|
|
571
|
'page arguments' => array(2, "specimens")
|
|
572
|
, // Expected callback arguments: name_uuid.
|
|
573
|
);
|
|
574
|
|
|
575
|
$items['cdm_dataportal/taxon/%/keys'] = array(
|
|
576
|
'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys')),
|
|
577
|
'page callback' => 'cdm_dataportal_taxon_page_view',
|
|
578
|
'access arguments' => array('access content'),
|
|
579
|
'type' => MENU_LOCAL_TASK,
|
|
580
|
'weight' => 6,
|
|
581
|
'page arguments' => array(2, "keys")
|
|
582
|
, // Expected callback arguments: name_uuid.
|
|
583
|
);
|
|
584
|
}
|
|
585
|
|
|
586
|
return $items;
|
|
587
|
}
|
|
588
|
|
|
589
|
/**
|
|
590
|
* @todo Please document this function.
|
|
591
|
* @see http://drupal.org/node/1354
|
|
592
|
*/
|
|
593
|
function cdm_dataportal_init() {
|
|
594
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
|
|
595
|
// drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
|
|
596
|
drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
|
|
597
|
}
|
|
598
|
|
|
599
|
/**
|
|
600
|
* The function generate form for own user cdm dataportal configurations.
|
|
601
|
*/
|
|
602
|
function cdm_dataportal_user_form($form, &$form_state) {
|
|
603
|
global $user;
|
|
604
|
$checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
|
|
605
|
|
|
606
|
$form['check'] = array(
|
|
607
|
'#type' => 'checkbox',
|
|
608
|
'#title' => t('Activate user default configuration'),
|
|
609
|
'#default_value' => variable_get($checkbox_value, 0),
|
|
610
|
'#description' => t('Check this if you want configure your own default tab from the below menu.'),
|
|
611
|
);
|
|
612
|
|
|
613
|
$form['cdm_dataportal_user_form'] = array(
|
|
614
|
'#type' => 'select',
|
|
615
|
'#title' => t('Default tab to display'),
|
|
616
|
'#default_value' => get_default_taxon_tab(TRUE),
|
|
617
|
'#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
|
|
618
|
'#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
|
|
619
|
<strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
|
|
620
|
to be renderized will be the synonymy of the accepted taxon and not the above selected tab.'),
|
|
621
|
);
|
|
622
|
|
|
623
|
$form['submit'] = array(
|
|
624
|
'#type' => 'submit',
|
|
625
|
'#value' => t('Submit'),
|
|
626
|
);
|
|
627
|
|
|
628
|
return $form;
|
|
629
|
}
|
|
630
|
|
|
631
|
/**
|
|
632
|
* Form submission handler for user_form().
|
|
633
|
*
|
|
634
|
* Submits the user cdm dataportal configurations.
|
|
635
|
*/
|
|
636
|
function cdm_dataportal_user_form_submit($form, &$form_state) {
|
|
637
|
global $user;
|
|
638
|
$msg_type = 'status';
|
|
639
|
$username = $user->name;
|
|
640
|
$variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
|
|
641
|
|
|
642
|
// If is the right user the variables are setted.
|
|
643
|
if (arg(0) == 'user' && ($uid = arg(1)) && is_numeric($uid) && $user->uid == $uid) {
|
|
644
|
$variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
|
|
645
|
variable_set($variable_to_use . '_active', $form_state['values']['check']);
|
|
646
|
variable_set($variable_to_use, $form_state['values']['cdm_dataportal_user_form']);
|
|
647
|
if ($form_state['values']['check']) {
|
|
648
|
drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
|
|
649
|
drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
|
|
650
|
'!tab' => $variable[variable_get($variable_to_use, 0)],
|
|
651
|
'!user' => $username,
|
|
652
|
))), $msg_type);
|
|
653
|
}
|
|
654
|
else {
|
|
655
|
drupal_set_message(check_plain(t('The user default tab wont be used for
|
|
656
|
the next taxon site, check the box if you want to use the user default configuration.')));
|
|
657
|
}
|
|
658
|
// Problem with the user id => variables wont be saved.
|
|
659
|
}
|
|
660
|
else {
|
|
661
|
$msg_type = 'warning';
|
|
662
|
drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
|
|
663
|
}
|
|
664
|
}
|
|
665
|
|
|
666
|
/**
|
|
667
|
* Implements hook_block_info().
|
|
668
|
*/
|
|
669
|
function cdm_dataportal_block_info() {
|
|
670
|
|
|
671
|
// $block[0]["info"] = t("CDM DataPortal DevLinks");
|
|
672
|
// $block[1]["info"] = t("CDM DataPortal Credits");
|
|
673
|
$block["2"]["info"] = t("CDM Search Taxa");
|
|
674
|
// $block[3]["info"] = t("CDM Filters");
|
|
675
|
$block["4"]["info"] = t("CDM Dataportal Print");
|
|
676
|
$block["keys"]["info"] = t("CDM identification keys");
|
|
677
|
$block["uses"]["info"] = t("CDM Uses");
|
|
678
|
$block["fundedByEDIT"]["info"] = t('Funded by EDIT');
|
|
679
|
|
|
680
|
return $block;
|
|
681
|
}
|
|
682
|
|
|
683
|
/**
|
|
684
|
* Implements hook_block_view().
|
|
685
|
*/
|
|
686
|
function cdm_dataportal_block_view($delta) {
|
|
687
|
// TODO Rename block deltas (e.g. '2') to readable strings.
|
|
688
|
switch ($delta) {
|
|
689
|
// case 'delta-1':
|
|
690
|
// $block['subject'] = t('Credits');
|
|
691
|
// $block['content'] = theme('cdm_credits');
|
|
692
|
// return $block;
|
|
693
|
case '2':
|
|
694
|
$block['subject'] = t('Search taxa');
|
|
695
|
$form = drupal_get_form('cdm_dataportal_search_taxon_form');
|
|
696
|
$block['content'] = drupal_render($form);
|
|
697
|
|
|
698
|
if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
|
|
699
|
$block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
|
|
700
|
}
|
|
701
|
return $block;
|
|
702
|
case '4':
|
|
703
|
$block['subject'] = t('<none>');
|
|
704
|
$block['content'] = theme('cdm_print_button');
|
|
705
|
return $block;
|
|
706
|
case "keys":
|
|
707
|
$block['subject'] = t('Identification Keys');
|
|
708
|
$block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
|
|
709
|
return $block;
|
|
710
|
// Creating a block specific for the Use Interface.
|
|
711
|
case "uses":
|
|
712
|
$block['subject'] = t('Uses');
|
|
713
|
$block['content'] = theme('cdm_block_uses', array('taxonUuid' => NULL));
|
|
714
|
return $block;
|
|
715
|
case "fundedByEDIT":
|
|
716
|
// t('Funded by EDIT');
|
|
717
|
$text = '<none>';
|
|
718
|
$block['subject'] = $text;
|
|
719
|
$img_tag = '<img src="' . drupal_get_path('module', 'cdm_dataportal') . '/images/funded_by_EDIT.png' . '" alt="' . $text . '"/>';
|
|
720
|
$block['content'] = l($img_tag, "http://www.e-taxonomy.eu/", array(
|
|
721
|
'attributes' => array("target" => "EDIT"),
|
|
722
|
'absolute' => TRUE,
|
|
723
|
'html' => TRUE,
|
|
724
|
));
|
|
725
|
return $block;
|
|
726
|
}
|
|
727
|
}
|
|
728
|
|
|
729
|
/*
|
|
730
|
function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
|
|
731
|
$_SESSION['cdm'] = NULL;
|
|
732
|
if(is_string($cdm_ws_uri_update)){
|
|
733
|
$_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
|
|
734
|
}
|
|
735
|
}
|
|
736
|
|
|
737
|
function cdm_dataportal_session_validate(){
|
|
738
|
if(!isset($_SESSION['cdm']['ws_uri'])){
|
|
739
|
$_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
|
|
740
|
} else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
|
|
741
|
cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
|
|
742
|
}
|
|
743
|
}
|
|
744
|
*/
|
|
745
|
|
|
746
|
/**
|
|
747
|
* @todo Please document this function.
|
|
748
|
* @see http://drupal.org/node/1354
|
|
749
|
*/
|
|
750
|
function cdm_taxonomictree_selector() {
|
|
751
|
_add_js_treeselector();
|
|
752
|
|
|
753
|
$form = drupal_get_form('cdm_taxonomictree_selector_form');
|
|
754
|
$out = drupal_render($form);
|
|
755
|
return $out;
|
|
756
|
}
|
|
757
|
|
|
758
|
/**
|
|
759
|
* @todo Please document this function.
|
|
760
|
* @see http://drupal.org/node/1354
|
|
761
|
*/
|
|
762
|
function cdm_taxonomictree_selector_form($form, &$form_state) {
|
|
763
|
|
|
764
|
$url = url('cdm_api/setvalue/session', array('query' => NULL));
|
|
765
|
$form['#action'] = $url;
|
|
766
|
|
|
767
|
$form['var'] = array(
|
|
768
|
'#weight' => -3,
|
|
769
|
'#type' => 'hidden',
|
|
770
|
'#value' => '[cdm][taxonomictree_uuid]',
|
|
771
|
);
|
|
772
|
|
|
773
|
$destination_array = drupal_get_destination();
|
|
774
|
$destination = $destination_array['destination'];
|
|
775
|
|
|
776
|
$form['destination'] = array(
|
|
777
|
'#weight' => -3,
|
|
778
|
'#type' => 'hidden',
|
|
779
|
'#value' => $destination,
|
|
780
|
);
|
|
781
|
|
|
782
|
$form['val'] = array(
|
|
783
|
'#type' => 'select',
|
|
784
|
'#title' => t('Available classifications'),
|
|
785
|
'#default_value' => get_taxonomictree_uuid_selected(),
|
|
786
|
'#options' => cdm_get_taxontrees_as_options(),
|
|
787
|
);
|
|
788
|
|
|
789
|
return $form;
|
|
790
|
|
|
791
|
}
|
|
792
|
|
|
793
|
/**
|
|
794
|
* Implements hook_theme().
|
|
795
|
*
|
|
796
|
* Registering themes with a theme hook is needed since Drupal 6.
|
|
797
|
*
|
|
798
|
* @author W. Addink <w.addink@eti.uva.nl>
|
|
799
|
*/
|
|
800
|
function cdm_dataportal_theme() {
|
|
801
|
return array(
|
|
802
|
// Themes in help.php.
|
|
803
|
'cdm_dataportal_admin_config_cdm_dataportal_general' => array('variables' => array()),
|
|
804
|
'cdm_dataportal_admin_config_cdm_dataportal_geo' => array('variables' => array()),
|
|
805
|
'cdm_dataportal_admin_config_cdm_dataportal_layout' => array('variables' => array()),
|
|
806
|
'cdm_dataportal_admin_config_cdm_dataportal_cachesite' => array('variables' => array()),
|
|
807
|
'cdm_dataportal_admin_config_more_help_link' => array('variables' => array()),
|
|
808
|
|
|
809
|
// Themes in settings.php.
|
|
810
|
'checkboxes_preferred' => array('render element' => 'element'),
|
|
811
|
|
|
812
|
// Themes in cdm_dataportal.common.theme.
|
|
813
|
'cdm_taggedtext2html' => array('variables' => array(
|
|
814
|
'taggedtxt' => array(),
|
|
815
|
'tag' => 'span',
|
|
816
|
'glue' => ' ',
|
|
817
|
'skiptags' => array(),
|
|
818
|
)),
|
|
819
|
'cdm_annotations_as_footnotekeys' => array('variables' => array('cdmBase_list' => NULL, 'footnote_list_key' => NULL)),
|
|
820
|
'cdm_annotation_footnotes' => array('variables' => array('footnoteListKey' => NULL, 'enclosingTag' => 'span')),
|
|
821
|
'cdm_annotation_content' => array('variables' => array('AnnotationTO' => NULL)),
|
|
822
|
'cdm_list_of_annotations' => array('variables' => array('annotationElements' => NULL)),
|
|
823
|
'cdm_footnote_key' => array('variables' => array(
|
|
824
|
'footnoteKey' => NULL,
|
|
825
|
'separator' => '',
|
|
826
|
'highlightable' => TRUE,
|
|
827
|
'separator_off' => FALSE,
|
|
828
|
)),
|
|
829
|
'cdm_footnote' => array('variables' => array('footnoteKey' => NULL, 'footnoteText' => NULL)),
|
|
830
|
'cdm_footnotes' => array('variables' => array(
|
|
831
|
'footnoteListKey' => NULL,
|
|
832
|
'enclosingTag' => 'span',
|
|
833
|
)),
|
|
834
|
'cdm_annotations' => array('variables' => array('annotations' => NULL, 'enclosingTag' => 'span')),
|
|
835
|
'cdm_pager' => array('variables' => array('pager' => NULL, 'path' => NULL, 'parameters' => NULL)),
|
|
836
|
'cdm_pager_link' => array('variables' => array(
|
|
837
|
'text' => NULL,
|
|
838
|
'linkIndex' => NULL,
|
|
839
|
'pager' => NULL,
|
|
840
|
'path' => NULL,
|
|
841
|
'parameters' => array(),
|
|
842
|
'attributes' => NULL,
|
|
843
|
)),
|
|
844
|
'cdm_back_to_search_result_button' => array('variables' => array()),
|
|
845
|
'cdm_back_to_image_gallery_button' => array('variables' => array()),
|
|
846
|
'cdm_print_button' => array('variables' => array()),
|
|
847
|
|
|
848
|
// Themes in cdm_dataportal.descriptions.theme.
|
|
849
|
'cdm_feature_nodesTOC' => array('variables' => array('featureNodes' => NULL)),
|
|
850
|
'cdm_feature_name' => array('variables' => array('feature_name' => NULL)),
|
|
851
|
'cdm_featureTrees' => array('variables' => array('mergedTrees' => NULL, 'taxon' => NULL)),
|
|
852
|
'cdm_featureTreeTOCs' => array('variables' => array('mergedTrees' => NULL)),
|
|
853
|
'cdm_feature_nodes' => array('variables' => array('mergedFeatureNodes' => NULL, 'taxon' => NULL)),
|
|
854
|
'FeatureTree_hierarchy' => array('variables' => array('FeatureTreeUuid' => NULL)),
|
|
855
|
'FeatureTree_hierarchy_children' => array('variables' => array('node' => NULL)),
|
|
856
|
'cdm_descriptionElementArray' => array('variables' => array(
|
|
857
|
'elementArray' => array(),
|
|
858
|
'feature' => NULL,
|
|
859
|
'glue' => '',
|
|
860
|
'sortArray' => FALSE,
|
|
861
|
'enclosingHtml' => 'ul',
|
|
862
|
)),
|
|
863
|
'cdm_descriptionElement_CommonTaxonName' => array('render element' => 'element'),
|
|
864
|
'cdm_descriptionElement_CategoricalData' => array('render element' => 'element'),
|
|
865
|
'cdm_descriptionElementTextData' => array('variables' => array(
|
|
866
|
'element' => NULL,
|
|
867
|
'asListElement' => NULL,
|
|
868
|
'feature_uuid' => NULL,
|
|
869
|
)),
|
|
870
|
'cdm_common_names' => array('render element' => 'elements'),
|
|
871
|
'cdm_descriptionElements' => array('variables' => array(
|
|
872
|
'descriptionElements' => NULL,
|
|
873
|
'featureUuid' => NULL,
|
|
874
|
'taxon_uuid' => NULL,
|
|
875
|
)),
|
|
876
|
'cdm_description_element_image_source' => array('variables' => array(
|
|
877
|
'image_sources' => NULL,
|
|
878
|
'asListElement' => NULL,
|
|
879
|
)),
|
|
880
|
'cdm_descriptionElementDistribution' => array('variables' => array(
|
|
881
|
'descriptionElements' => NULL,
|
|
882
|
'enclosingTag' => 'span',
|
|
883
|
)),
|
|
884
|
'cdm_description_ordered_distributions' => array('variables' => array(
|
|
885
|
'taxon_uuid' => NULL,
|
|
886
|
'descriptionElements' => NULL,
|
|
887
|
)),
|
|
888
|
'cdm_DescriptionElementSource' => array('variables' => array('descriptionElementSource' => NULL, 'doLink' => TRUE)),
|
|
889
|
'cdm_IdentifieableSource' => array('variables' => array('source' => NULL, 'doLink' => TRUE)),
|
|
890
|
'cdm_distribution_map' => array('variables' => array('taxon' => NULL)),
|
|
891
|
'cdm_IdentificationKey' => array('variables' => array(
|
|
892
|
'identificationKey' => NULL,
|
|
893
|
'doLinkToKeyPage' => TRUE,
|
|
894
|
'showIdentificationKeyTitle' => TRUE,
|
|
895
|
)),
|
|
896
|
'cdm_polytomousKey' => array('variables' => array('polytomousKey' => NULL)),
|
|
897
|
'cdm_polytomousKey_linkedStyle_subgraph' => array('variables' => array('polytomousKeyNode' => NULL)),
|
|
898
|
'cdm_poytomousKeyNode_modifyingText' => array('variables' => array('modifyingText' => NULL)),
|
|
899
|
'cdm_list_IdentificationKeys' => array('variables' => array('type' => NULL, 'taxonUuid' => NULL)),
|
|
900
|
'cdm_block_IdentificationKeys' => array('variables' => array('taxonUuid' => NULL)),
|
|
901
|
'cdm_UseDescription' => array('variables' => array('description' => NULL, 'taxonUuid' => NULL)),
|
|
902
|
'cdm_block_Uses' => array('variables' => array('taxonUuid' => NULL)),
|
|
903
|
|
|
904
|
// Themes in cdm_dataportal.media.theme.
|
|
905
|
'cdm_media' => array('variables' => array('descriptionElement' => NULL, 'mimeTypePreference' => NULL)),
|
|
906
|
'cdm_mediaTypeTerm' => array('variables' => array('feature' => NULL, 'mediaUrl' => FALSE)),
|
|
907
|
'cdm_media_mime_application' => array('variables' => array('mediaRepresentation' => NULL, 'feature' => NULL)),
|
|
908
|
'cdm_media_mime_image' => array('variables' => array('mediaRepresentation' => NULL, 'feature' => NULL)),
|
|
909
|
'cdm_media_mime_text' => array('variables' => array('representation' => NULL, 'feature' => NULL)),
|
|
910
|
'cdm_media_caption' => array('variables' => array(
|
|
911
|
'media' => NULL,
|
|
912
|
'elements' => array('title', 'description', 'artist', 'location', 'rights'),
|
|
913
|
'fileUri' => NULL,
|
|
914
|
)),
|
|
915
|
'cdm_media_gallerie' => array('variables' => array(
|
|
916
|
'mediaList' => NULL,
|
|
917
|
'galleryName' => NULL,
|
|
918
|
'maxExtend' => 150,
|
|
919
|
'cols' => 4,
|
|
920
|
'maxRows' => FALSE,
|
|
921
|
'captionElements' => array('title'),
|
|
922
|
'mediaLinkType' => 'LIGHTBOX',
|
|
923
|
'alternativeMediaUri' => NULL,
|
|
924
|
'galleryLinkUri' => NULL,
|
|
925
|
'showCaption' => TRUE,
|
|
926
|
)),
|
|
927
|
'cdm_media_gallerie_image' => array('variables' => array(
|
|
928
|
'mediaRepresentationPart' => NULL,
|
|
929
|
'maxExtend' => NULL,
|
|
930
|
'addPassePartout' => FALSE,
|
|
931
|
'attributes' => NULL,
|
|
932
|
)),
|
|
933
|
'cdm_media_gallerie_application' => array('variables' => array(
|
|
934
|
'mediaRepresentationPart' => NULL,
|
|
935
|
'maxExtend' => NULL,
|
|
936
|
'addPassePartout' => FALSE,
|
|
937
|
'attributes' => NULL,
|
|
938
|
)),
|
|
939
|
'cdm_media_gallerie_text' => array('variables' => array(
|
|
940
|
'mediaRepresentationPart' => NULL,
|
|
941
|
'maxExtend' => NULL,
|
|
942
|
'addPassePartout' => FALSE,
|
|
943
|
'attributes' => NULL,
|
|
944
|
)),
|
|
945
|
'cdm_openlayers_image' => array('variables' => array('mediaRepresentationPart' => NULL, 'maxExtend' => NULL)),
|
|
946
|
'cdm_preferredImage' => array('variables' => array(
|
|
947
|
'media' => NULL,
|
|
948
|
'defaultRepresentationPart' => NULL,
|
|
949
|
'imageMaxExtend' => NULL,
|
|
950
|
'parameters' => '',
|
|
951
|
)),
|
|
952
|
|
|
953
|
// Themes in cdm_dataportal.name.theme.
|
|
954
|
'cdm_taxonName' => array('variables' => array(
|
|
955
|
'taxonName' => NULL,
|
|
956
|
'nameLink' => NULL,
|
|
957
|
'refenceLink' => NULL,
|
|
958
|
'show_annotations' => TRUE,
|
|
959
|
'is_type_designation' => FALSE,
|
|
960
|
'skiptags' => array(),
|
|
961
|
)),
|
|
962
|
'cdm_typedesignations' => array('variables' => array('typeDesignations' => array())),
|
|
963
|
'cdm_nameRelationships' => array('variables' => array('nameRelationships' => NULL, 'skipTypes' => FALSE)),
|
|
964
|
'cdm_homotypicSynonymLine' => array('variables' => array('taxon' => NULL)),
|
|
965
|
'cdm_heterotypicSynonymyGroup' => array('variables' => array('homotypicalGroup' => NULL)),
|
|
966
|
'cdm_homotypicSynonymyGroup' => array('variables' => array(
|
|
967
|
'synonymList' => NULL,
|
|
968
|
'accepted_taxon_uuid' => NULL,
|
|
969
|
'prependedSynonyms' => array(),
|
|
970
|
)),
|
|
971
|
'get_nameRenderTemplate' => array('variables' => array('renderPath' => NULL)),
|
|
972
|
'get_partDefinition' => array('variables' => array('nameType' => NULL)),
|
|
973
|
'get_nameRenderTemplate' => array('variables' => array('renderPath' => NULL)),
|
|
974
|
|
|
975
|
// Themes in cdm_dataportal.occurrence.theme.
|
|
976
|
'cdm_specimen' => array('variables' => array('specimenTypeDesignation' => NULL)),
|
|
977
|
'cdm_derivedUnitFacade' => array('variables' => array('derivedUnitFacade' => NULL)),
|
|
978
|
|
|
979
|
// Themes in cdm_dataportal.page.theme.
|
|
980
|
'cdm_taxon_page_title' => array('variables' => array('taxon' => NULL, 'uuid' => NULL)),
|
|
981
|
'cdm_name_page_title' => array('variables' => array('taxon_name' => NULL)),
|
|
982
|
'cdm_taxon_page' => array('variables' => array('taxon' => NULL, 'page_part' => 'description')),
|
|
983
|
'cdm_taxon_page_profile' => array('variables' => array(
|
|
984
|
'taxon' => NULL,
|
|
985
|
'mergedTrees' => NULL,
|
|
986
|
'media' => NULL,
|
|
987
|
'hideImages' => FALSE,
|
|
988
|
)),
|
|
989
|
'cdm_taxon_page_specimens' => array('variables' => array('taxon' => NULL)),
|
|
990
|
'cdm_taxon_page_synonymy' => array('variables' => array('taxon' => NULL, 'addAcceptedTaxon' => NULL)),
|
|
991
|
'cdm_reference_page' => array('variables' => array('reference' => NULL)),
|
|
992
|
'cdm_media_page' => array('variables' => array(
|
|
993
|
'media' => NULL,
|
|
994
|
'mediarepresentation_uuid' => FALSE,
|
|
995
|
'partId' => FALSE,
|
|
996
|
)),
|
|
997
|
'cdm_polytomousKey_page' => array('variables' => array('polytomousKey' => NULL)),
|
|
998
|
'cdm_taxonpage_tab' => array('variables' => array('tabname' => NULL)),
|
|
999
|
|
|
1000
|
// Themes in cdm_dataportal.references.theme.
|
|
1001
|
'cdm_reference_pager' => array('variables' => array(
|
|
1002
|
'referencePager' => NULL,
|
|
1003
|
'path' => NULL,
|
|
1004
|
'parameters' => array(),
|
|
1005
|
)),
|
|
1006
|
'cdm_reference' => array('variables' => array(
|
|
1007
|
'reference' => NULL,
|
|
1008
|
'microReference' => NULL,
|
|
1009
|
'doLink' => FALSE,
|
|
1010
|
'referenceStyle' => NULL,
|
|
1011
|
)),
|
|
1012
|
|
|
1013
|
// Themes in cdm_dataportal.taxon.theme.
|
|
1014
|
'cdm_search_results' => array('variables' => array(
|
|
1015
|
'pager' => NULL,
|
|
1016
|
'path' => NULL,
|
|
1017
|
'query_parameters' => NULL,
|
|
1018
|
)),
|
|
1019
|
'cdm_taxonRelationships' => array('variables' => array('taxonRelationships' => NULL, 'focusedTaxon' => NULL)),
|
|
1020
|
'cdm_acceptedFor' => array('variables' => array()),
|
|
1021
|
'cdm_list_of_taxa' => array('variables' => array('records' => NULL, 'freetextSearchResults' => array())),
|
|
1022
|
'cdm_taxon_list_thumbnails' => array('variables' => array('taxon' => NULL)),
|
|
1023
|
|
|
1024
|
// Themes in cdm_dataportal.bibliography.theme.
|
|
1025
|
'cdm_descriptionElementBibliography' => array('variables' => array('descriptionElementsBibliography' => array())),
|
|
1026
|
);
|
|
1027
|
}
|
|
1028
|
|
|
1029
|
/* UNREACHABLE since action of form directly links to view.
|
|
1030
|
function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
|
|
1031
|
|
|
1032
|
$_SESSION['cdm']['search'] = $form_values;
|
|
1033
|
//return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
|
|
1034
|
return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
|
|
1035
|
//$paramstr = compose_url_prameterstr($form_values);
|
|
1036
|
//return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
|
|
1037
|
}
|
|
1038
|
*/
|
|
1039
|
/* ====================== menu callback functions ====================== */
|
|
1040
|
/**
|
|
1041
|
* @todo Please document this function.
|
|
1042
|
* @see http://drupal.org/node/1354
|
|
1043
|
*/
|
|
1044
|
/*
|
|
1045
|
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
|
|
1046
|
static $comment_node_disabled = 0;
|
|
1047
|
static $comment_node_read_only = 1;
|
|
1048
|
static $comment_node_read_write = 2;
|
|
1049
|
|
|
1050
|
if ($form_id == 'node_type_form'
|
|
1051
|
&& isset($form['identity']['type'])
|
|
1052
|
&& array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
|
|
1053
|
) {
|
|
1054
|
$form['workflow']['comment'] = array(
|
|
1055
|
'#type' => 'radios',
|
|
1056
|
'#title' => t('Default comment setting'),
|
|
1057
|
'#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
|
|
1058
|
'#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
|
|
1059
|
'#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
|
|
1060
|
);
|
|
1061
|
}
|
|
1062
|
}
|
|
1063
|
*/
|
|
1064
|
|
|
1065
|
/**
|
|
1066
|
* Displays a list of the known taxonomic names.
|
|
1067
|
*
|
|
1068
|
* When the list of taxonomic names is displayed, long lists are split up into
|
|
1069
|
* multiple pages.
|
|
1070
|
*
|
|
1071
|
* TODO: Parameters are still preliminary.
|
|
1072
|
*
|
|
1073
|
* @param string $beginsWith
|
|
1074
|
* @param string $page
|
|
1075
|
* Page number to diplay defaults to page 1.
|
|
1076
|
* @param bool $onlyAccepted
|
|
1077
|
*/
|
|
1078
|
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
|
|
1079
|
|
|
1080
|
$out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
|
|
1081
|
|
|
1082
|
/*
|
|
1083
|
// FIXME the filter for accepted names will be a form element, thus this
|
|
1084
|
// widget should be generated via form api preferably as block.
|
|
1085
|
$out = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
|
|
1086
|
$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
|
|
1087
|
$out .= theme('cdm_listof_taxa', $taxonPager);
|
|
1088
|
return $out;
|
|
1089
|
*/
|
|
1090
|
}
|
|
1091
|
|
|
1092
|
/**
|
|
1093
|
* @todo Please document this function.
|
|
1094
|
* @see http://drupal.org/node/1354
|
|
1095
|
*/
|
|
1096
|
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
|
|
1097
|
$reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
|
|
1098
|
return theme('cdm_reference_page', array('reference' => $reference));
|
|
1099
|
}
|
|
1100
|
|
|
1101
|
/**
|
|
1102
|
* @todo Please document this function.
|
|
1103
|
* @see http://drupal.org/node/1354
|
|
1104
|
*/
|
|
1105
|
function cdm_dataportal_view_reference_list($pageNumber) {
|
|
1106
|
$referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
|
|
1107
|
return theme('cdm_reference_pager', array(
|
|
1108
|
'referencePager' => $referencePager,
|
|
1109
|
'path' => 'cdm_dataportal/reference/list/',
|
|
1110
|
));
|
|
1111
|
}
|
|
1112
|
|
|
1113
|
/**
|
|
1114
|
* @todo Please document this function.
|
|
1115
|
* @see http://drupal.org/node/1354
|
|
1116
|
*/
|
|
1117
|
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
|
|
1118
|
$media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
|
|
1119
|
return theme('cdm_media_page', array(
|
|
1120
|
'media' => $media,
|
|
1121
|
'mediarepresentation_uuid' => $mediarepresentation_uuid,
|
|
1122
|
'partId' => $part,
|
|
1123
|
));
|
|
1124
|
}
|
|
1125
|
|
|
1126
|
/**
|
|
1127
|
* @todo Please document this function.
|
|
1128
|
* @see http://drupal.org/node/1354
|
|
1129
|
*/
|
|
1130
|
function _load_taxonBase(&$taxonBase) {
|
|
1131
|
if (isset($taxonBase->uuid)) {
|
|
1132
|
$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
|
|
1133
|
$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
|
|
1134
|
$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
|
|
1135
|
}
|
|
1136
|
}
|
|
1137
|
|
|
1138
|
/**
|
|
1139
|
* Gets a Drupal variable, string or array and returns it.
|
|
1140
|
*
|
|
1141
|
* Similar to the variable_get() function of Drupal, except that this function
|
|
1142
|
* is able to handle arrays correctly. This function is especially useful
|
|
1143
|
* when dealing with collections of setting form elements (#tree = TRUE).
|
|
1144
|
*
|
|
1145
|
* @param string $variableKey
|
|
1146
|
* The Unique key of the Drupal variable in the Drupal variables table.
|
|
1147
|
* @param string $defaultValueString
|
|
1148
|
* A string as for example derived from a CONSTANT.
|
|
1149
|
*
|
|
1150
|
* @return mixed
|
|
1151
|
* Returns usally an array, depending on the nature of the variable.
|
|
1152
|
*/
|
|
1153
|
function mixed_variable_get($variableKey, $defaultValueString) {
|
|
1154
|
$systemDefaults = unserialize($defaultValueString);
|
|
1155
|
$storedSettings = variable_get($variableKey, array());
|
|
1156
|
if (is_array($storedSettings)) {
|
|
1157
|
$settings = array_merge($systemDefaults, $storedSettings);
|
|
1158
|
}
|
|
1159
|
else {
|
|
1160
|
$settings = $systemDefaults;
|
|
1161
|
}
|
|
1162
|
return $settings;
|
|
1163
|
}
|
|
1164
|
|
|
1165
|
/**
|
|
1166
|
* Loads the subgraph of a given PolytomousKeyNode.
|
|
1167
|
*
|
|
1168
|
* Loads the subgraph of the given PolytomousKeyNode recursively from
|
|
1169
|
* the CDM REST service.
|
|
1170
|
*
|
|
1171
|
* @param mixed $polytomousKeyNode
|
|
1172
|
* PolytomousKeyNode passed by reference.
|
|
1173
|
*
|
|
1174
|
* @return void
|
|
1175
|
*/
|
|
1176
|
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
|
|
1177
|
|
|
1178
|
if (!$polytomousKeyNode) {
|
|
1179
|
return;
|
|
1180
|
}
|
|
1181
|
if ($polytomousKeyNode->class != "PolytomousKeyNode") {
|
|
1182
|
drupal_set_message(_load_polytomousKeySubGraph() . t('invalid type given.'), 'error');
|
|
1183
|
return;
|
|
1184
|
}
|
|
1185
|
if (!is_uuid($polytomousKeyNode->uuid)) {
|
|
1186
|
drupal_set_message(_load_polytomousKeySubGraph() . t('invalid type given.'), 'error');
|
|
1187
|
return;
|
|
1188
|
}
|
|
1189
|
|
|
1190
|
$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
|
|
1191
|
|
|
1192
|
if (!$polytomousKeyNode) {
|
|
1193
|
// drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
|
|
1194
|
return;
|
|
1195
|
}
|
|
1196
|
|
|
1197
|
// Load children.
|
|
1198
|
foreach ($polytomousKeyNode->children as &$childNode) {
|
|
1199
|
_load_polytomousKeySubGraph($childNode);
|
|
1200
|
}
|
|
1201
|
|
|
1202
|
// Load subkey.
|
|
1203
|
$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
|
|
1204
|
|
|
1205
|
// Load taxon.
|
|
1206
|
$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
|
|
1207
|
_load_taxonBase($polytomousKeyNode->taxon);
|
|
1208
|
return;
|
|
1209
|
}
|
|
1210
|
|
|
1211
|
/**
|
|
1212
|
* @todo Please document this function.
|
|
1213
|
* @see http://drupal.org/node/1354
|
|
1214
|
*/
|
|
1215
|
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
|
|
1216
|
$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
|
|
1217
|
|
|
1218
|
$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
|
|
1219
|
if (is_array($sourcePager->records)) {
|
|
1220
|
$polytomousKey->sources = $sourcePager->records;
|
|
1221
|
// $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
|
|
1222
|
}
|
|
1223
|
|
|
1224
|
$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
|
|
1225
|
if (is_array($annotationPager->records)) {
|
|
1226
|
$polytomousKey->annotations = $annotationPager->records;
|
|
1227
|
}
|
|
1228
|
|
|
1229
|
_load_polytomousKeySubGraph($polytomousKey->root);
|
|
1230
|
return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
|
|
1231
|
}
|
|
1232
|
|
|
1233
|
/**
|
|
1234
|
* Creates a taxon page view or a chapter of it.
|
|
1235
|
*
|
|
1236
|
* The taxon page gives detailed information on a taxon, it shows:
|
|
1237
|
* - Taxon name.
|
|
1238
|
* - Full list of synonyms homotypic synonyms on top, followed by the
|
|
1239
|
* heterotypic and finally followed by misapplied names.
|
|
1240
|
* The list is ordered historically.
|
|
1241
|
* - All description associated with the taxon.
|
|
1242
|
*
|
|
1243
|
* @param string $uuid
|
|
1244
|
* @param string $chapter
|
|
1245
|
* Name of the part to display, valid values are:
|
|
1246
|
* 'description', 'images', 'synonymy', 'specimens', 'all'.
|
|
1247
|
*
|
|
1248
|
* @return unknown_type
|
|
1249
|
*/
|
|
1250
|
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
|
|
1251
|
// Display the page for the taxon defined by $uuid.
|
|
1252
|
// set_last_taxon_page_tab(arg(3));
|
|
1253
|
$taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
|
|
1254
|
if (!empty($taxonpage)) {
|
|
1255
|
return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
|
|
1256
|
}
|
|
1257
|
else {
|
|
1258
|
return '';
|
|
1259
|
}
|
|
1260
|
}
|
|
1261
|
|
|
1262
|
/**
|
|
1263
|
* @todo improve documentation for this function.
|
|
1264
|
*
|
|
1265
|
* @param string $uuid
|
|
1266
|
* @param string $chapter
|
|
1267
|
* Name of the part to display, valid values are:
|
|
1268
|
* 'description', 'images', 'synonymy', 'all'.
|
|
1269
|
*
|
|
1270
|
* @return unknown_type
|
|
1271
|
*/
|
|
1272
|
function cdm_dataportal_taxon_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
|
|
1273
|
// Taxon object.
|
|
1274
|
$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
|
|
1275
|
if (empty($taxon)) {
|
|
1276
|
drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
|
|
1277
|
return FALSE;
|
|
1278
|
}
|
|
1279
|
$taxonpage = new stdClass();
|
|
1280
|
|
|
1281
|
$taxonpage->title = theme('cdm_taxon_page_title', array(
|
|
1282
|
'taxon' => $taxon,
|
|
1283
|
'uuid' => $uuid,
|
|
1284
|
'synonym_uuid' => $synonym_uuid,
|
|
1285
|
));
|
|
1286
|
|
|
1287
|
// Check if the taxon id contained in the currently selected tree.
|
|
1288
|
$taxon_in_current_tree = taxon_in_current_tree($uuid);
|
|
1289
|
$taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $uuid);
|
|
1290
|
if (!$taxon_in_current_tree) {
|
|
1291
|
if (count($taxon_nodes) == 0) {
|
|
1292
|
drupal_set_message(check_plain(t('This concept of the taxon !taxonname is not contained any classification.', array(
|
|
1293
|
'!taxonname' => theme('cdm_taxonName', array('taxonName' => $taxon->name)),
|
|
1294
|
))), 'warning');
|
|
1295
|
}
|
|
1296
|
else {
|
|
1297
|
$trees = '';
|
|
1298
|
foreach ($taxon_nodes as $node) {
|
|
1299
|
if (isset($node->classification->titleCache)) {
|
|
1300
|
$trees .= ($trees ? ', ' : '') . '<strong>' . $node->classification->titleCache . '</strong>';
|
|
1301
|
}
|
|
1302
|
}
|
|
1303
|
|
|
1304
|
drupal_set_message(format_plural(count($taxon_nodes),
|
|
1305
|
'This concept of the taxon !taxonname is not contained in the currently chosen classification, but in this one: !trees',
|
|
1306
|
'This concept of the taxon !taxonname is not contained in the currently chosen classification, but in one of these: !trees',
|
|
1307
|
array('!taxonname' => theme('cdm_taxonName', array('taxonName' => $taxon->name)), '!trees' => $trees)) , 'warning');
|
|
1308
|
}
|
|
1309
|
}
|
|
1310
|
|
|
1311
|
// Render the taxon page.
|
|
1312
|
$taxonpage->content = theme('cdm_taxon_page', array(
|
|
1313
|
'taxon' => $taxon,
|
|
1314
|
'page_part' => $chapter,
|
|
1315
|
));
|
|
1316
|
|
|
1317
|
return $taxonpage;
|
|
1318
|
}
|
|
1319
|
|
|
1320
|
/**
|
|
1321
|
* Returns a name page as a Drupal node ready to be renderized by Drupal.
|
|
1322
|
*
|
|
1323
|
* The node page shows the taxon name title and the list of taxon related
|
|
1324
|
* with such taxon. Name on the tree already in use.
|
|
1325
|
*
|
|
1326
|
* @param string $taxon_name_uuid
|
|
1327
|
* A taxon name UUID.
|
|
1328
|
*
|
|
1329
|
* @return mixed
|
|
1330
|
* The formatted name page as node.
|
|
1331
|
*/
|
|
1332
|
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
|
|
1333
|
|
|
1334
|
$taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
|
|
1335
|
if (!empty($taxonname_page)) {
|
|
1336
|
return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
|
|
1337
|
}
|
|
1338
|
else {
|
|
1339
|
return '';
|
|
1340
|
}
|
|
1341
|
}
|
|
1342
|
|
|
1343
|
/**
|
|
1344
|
* Generates an object ready to be transformated to a node.
|
|
1345
|
*
|
|
1346
|
* This is a preparation in order to show it as a Drupal node.
|
|
1347
|
*
|
|
1348
|
* @param string $taxon_name_uuid
|
|
1349
|
*
|
|
1350
|
* @return mixed
|
|
1351
|
* The object with the page content and title.
|
|
1352
|
*/
|
|
1353
|
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
|
|
1354
|
// Getting the full taxonname object from the server.
|
|
1355
|
$taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
|
|
1356
|
if (!$taxon_name) {
|
|
1357
|
drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
|
|
1358
|
return FALSE;
|
|
1359
|
}
|
|
1360
|
// Searching for all the taxa connected with the taxon name on the tree
|
|
1361
|
// in use.
|
|
1362
|
$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
|
|
1363
|
$request_params = array();
|
|
1364
|
$request_params['query'] = $name_cache;
|
|
1365
|
$request_params['tree'] = get_taxonomictree_uuid_selected();
|
|
1366
|
$request_params['doTaxa'] = 1;
|
|
1367
|
$request_params['doSynonyms'] = 1;
|
|
1368
|
$request_params['doTaxaByCommonNames'] = 0;
|
|
1369
|
$request_params['matchMode'] = "EXACT";
|
|
1370
|
$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
|
|
1371
|
|
|
1372
|
// Removing the name where we come from.
|
|
1373
|
foreach ($taxon_pager->records as $k => &$taxon) {
|
|
1374
|
if ($taxon->uuid == $taxon_to_hide_uuid) {
|
|
1375
|
unset($taxon_pager->records[$k]);
|
|
1376
|
}
|
|
1377
|
}
|
|
1378
|
// Show the taxa list or go to the singular taxon.
|
|
1379
|
if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
|
|
1380
|
reset($taxon_pager->records);
|
|
1381
|
$singleTaxon = $taxon_pager->records[0];
|
|
1382
|
if ($singleTaxon->class != "Taxon") {
|
|
1383
|
// It is a Synonym -> look for the accepted.
|
|
1384
|
$taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_taxonomictree_uuid_selected()));
|
|
1385
|
if (!empty($synonym_uuid)) {
|
|
1386
|
drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', array('query' => array('highlite' => $synonym_uuid)));
|
|
1387
|
}
|
|
1388
|
else {
|
|
1389
|
drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
|
|
1390
|
}
|
|
1391
|
}
|
|
1392
|
else {
|
|
1393
|
// It is an accepted taxon.
|
|
1394
|
if (!empty($synonym_uuid)) {
|
|
1395
|
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $synonym_uuid)));
|
|
1396
|
}
|
|
1397
|
else {
|
|
1398
|
drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
|
|
1399
|
}
|
|
1400
|
}
|
|
1401
|
}
|
|
1402
|
else {// More than one taxa case.
|
|
1403
|
$taxon_name_page = new stdClass();
|
|
1404
|
$taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name . ''));
|
|
1405
|
if ($taxon_pager->records) {
|
|
1406
|
$taxon_name_page->content = theme_cdm_list_of_taxa($taxon_pager->records, FALSE);
|
|
1407
|
}
|
|
1408
|
else {
|
|
1409
|
$taxon_name_page->content = 'This name has no taxa';
|
|
1410
|
}
|
|
1411
|
return $taxon_name_page;
|
|
1412
|
}
|
|
1413
|
}
|
|
1414
|
|
|
1415
|
/**
|
|
1416
|
* @todo Please document this function.
|
|
1417
|
* @see http://drupal.org/node/1354
|
|
1418
|
*/
|
|
1419
|
function cdm_dataportal_view_search_advanced() {
|
|
1420
|
|
|
1421
|
drupal_set_title(t('Advanced search'), PASS_THROUGH);
|
|
1422
|
$form = array();
|
|
1423
|
$form_state = array();
|
|
1424
|
$searchForm = cdm_dataportal_search_taxon_form($form, $form_state, TRUE);
|
|
1425
|
|
|
1426
|
return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
|
|
1427
|
|
|
1428
|
}
|
|
1429
|
|
|
1430
|
/**
|
|
1431
|
* @todo Please document this function.
|
|
1432
|
* @see http://drupal.org/node/1354
|
|
1433
|
*/
|
|
1434
|
function cdm_dataportal_view_search_taxon_by_description() {
|
|
1435
|
drupal_set_title(t('Search by description full text'), PASS_THROUGH);
|
|
1436
|
// $form_state = false;
|
|
1437
|
// $searchForm = cdm_dataportal_search_taxon_by_description_form($form_state);
|
|
1438
|
$searchForm = cdm_dataportal_search_taxon_by_description_form();
|
|
1439
|
|
|
1440
|
return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
|
|
1441
|
}
|
|
1442
|
|
|
1443
|
/**
|
|
1444
|
* Executes the search and generates the result list of taxa.
|
|
1445
|
*/
|
|
1446
|
function cdm_dataportal_view_search_results_taxon() {
|
|
1447
|
|
|
1448
|
$taxonPager = cdm_dataportal_search_execute();
|
|
1449
|
|
|
1450
|
$showThumbnails = do_showThumbnails();
|
|
1451
|
|
|
1452
|
$setSessionUri = url('cdm_api/setvalue/session', array(
|
|
1453
|
'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
|
|
1454
|
));
|
|
1455
|
|
|
1456
|
drupal_add_js('jQuery(document).ready(function() {
|
|
1457
|
|
|
1458
|
// init
|
|
1459
|
if(' . $showThumbnails . ' == 1){
|
|
1460
|
jQuery(\'.media_gallery\').show(20);
|
|
1461
|
} else {
|
|
1462
|
jQuery(\'.media_gallery\').hide(20);
|
|
1463
|
}
|
|
1464
|
// add change hander
|
|
1465
|
jQuery(\'#showThumbnails\').change(
|
|
1466
|
function(event){
|
|
1467
|
var state = 0;
|
|
1468
|
if(jQuery(this).is(\':checked\')){
|
|
1469
|
jQuery(\'.media_gallery\').show(20);
|
|
1470
|
state = 1;
|
|
1471
|
} else {
|
|
1472
|
jQuery(\'.media_gallery\').hide(20);
|
|
1473
|
}
|
|
1474
|
// store state in session variable
|
|
1475
|
var uri = \'' . $setSessionUri . '\' + state;
|
|
1476
|
jQuery.get(uri);
|
|
1477
|
});
|
|
1478
|
});',
|
|
1479
|
array('type' => "inline", 'scope' => JS_DEFAULT));
|
|
1480
|
|
|
1481
|
drupal_set_title(t('Search results'), PASS_THROUGH);
|
|
1482
|
|
|
1483
|
return theme('cdm_search_results', array(
|
|
1484
|
'pager' => $taxonPager,
|
|
1485
|
'path' => 'cdm_dataportal/search/results/taxon',
|
|
1486
|
'query_parameters' => $_REQUEST,
|
|
1487
|
));
|
|
1488
|
}
|
|
1489
|
|
|
1490
|
/**
|
|
1491
|
* Returns the state of the the showThumbnails flag set in the
|
|
1492
|
* users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
|
|
1493
|
*
|
|
1494
|
* @return Ambigous <boolean, number>
|
|
1495
|
* returns 1 if the flag is set
|
|
1496
|
*/
|
|
1497
|
function do_showThumbnails() {
|
|
1498
|
static $showThumbnails = null;
|
|
1499
|
|
|
1500
|
if($showThumbnails == null) {
|
|
1501
|
$showThumbnails = FALSE;
|
|
1502
|
if (isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
|
|
1503
|
$showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
|
|
1504
|
}
|
|
1505
|
if (!is_numeric($showThumbnails)) {
|
|
1506
|
$showThumbnails = 1;
|
|
1507
|
}
|
|
1508
|
}
|
|
1509
|
|
|
1510
|
return $showThumbnails;
|
|
1511
|
}
|
|
1512
|
|
|
1513
|
/**
|
|
1514
|
* View which transforms XML output from a given webservice endpoint into JSON.
|
|
1515
|
*/
|
|
1516
|
/*
|
|
1517
|
function cdm_view_xml2json(){
|
|
1518
|
$file = arg(2);
|
|
1519
|
$datastr = file_get_contents(variable_get('cdm_webservice_url', '').$file);
|
|
1520
|
return xml2json::transformXmlStringToJson($datastr);
|
|
1521
|
}
|
|
1522
|
*/
|
|
1523
|
|
|
1524
|
/* ====================== other functions ====================== */
|
|
1525
|
/**
|
|
1526
|
* Creates a URL to the taxon page specified by the $uuid parameter.
|
|
1527
|
*
|
|
1528
|
* The URL will be prepended with a path element to a specific taxon page tab.
|
|
1529
|
*
|
|
1530
|
* This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
|
|
1531
|
* be set globally in the administrative settings or individually in the user
|
|
1532
|
* profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
|
|
1533
|
* the last portal will stay on this last tab.
|
|
1534
|
*
|
|
1535
|
* A third option is offerered by the $page_tab parameter which allows overwriting this
|
|
1536
|
* internal mechanism by a specific value.
|
|
1537
|
*
|
|
1538
|
* @param string $uuid
|
|
1539
|
* The UUID of the taxon.
|
|
1540
|
* @param string $page_tab
|
|
1541
|
* Overwriting the preset mechanism by defining specific value for the
|
|
1542
|
* taxon page tab.
|
|
1543
|
*
|
|
1544
|
* @return string
|
|
1545
|
* The created URL.
|
|
1546
|
*/
|
|
1547
|
function path_to_taxon($uuid, $page_tab = FALSE) {
|
|
1548
|
|
|
1549
|
$tab = get_default_taxon_tab();
|
|
1550
|
$values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
|
|
1551
|
|
|
1552
|
if (!$uuid) {
|
|
1553
|
return FALSE;
|
|
1554
|
}
|
|
1555
|
|
|
1556
|
if ($page_tab) {
|
|
1557
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
|
|
1558
|
}
|
|
1559
|
elseif (!$tab || strtolower($tab) == 'general') {
|
|
1560
|
return 'cdm_dataportal/taxon/' . $uuid;
|
|
1561
|
}
|
|
1562
|
elseif (get_last_taxon_page_tab() && $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
|
|
1563
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
|
|
1564
|
}
|
|
1565
|
else {
|
|
1566
|
return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
|
|
1567
|
}
|
|
1568
|
}
|
|
1569
|
|
|
1570
|
/**
|
|
1571
|
* @todo Please document this function.
|
|
1572
|
* @see http://drupal.org/node/1354
|
|
1573
|
*/
|
|
1574
|
function uri_to_synonym($synonymUuid, $acceptedUuid) {
|
|
1575
|
$acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
|
|
1576
|
return url($acceptedPath, array('query' => array('highlite' => $synonymUuid)));
|
|
1577
|
}
|
|
1578
|
|
|
1579
|
/**
|
|
1580
|
* @todo Please document this function.
|
|
1581
|
* @see http://drupal.org/node/1354
|
|
1582
|
*/
|
|
1583
|
function path_to_key($keyType, $keyUuid) {
|
|
1584
|
if (!$keyUuid || !$keyType) {
|
|
1585
|
return FALSE;
|
|
1586
|
}
|
|
1587
|
$keyType{0} = strtolower($keyType{0});
|
|
1588
|
return "cdm_dataportal/" . $keyType . "/$keyUuid";
|
|
1589
|
}
|
|
1590
|
|
|
1591
|
/**
|
|
1592
|
* @todo Please document this function.
|
|
1593
|
* @see http://drupal.org/node/1354
|
|
1594
|
*/
|
|
1595
|
function path_to_reference($uuid) {
|
|
1596
|
if (!$uuid) {
|
|
1597
|
return FALSE;
|
|
1598
|
}
|
|
1599
|
return 'cdm_dataportal/reference/' . $uuid;
|
|
1600
|
}
|
|
1601
|
|
|
1602
|
/**
|
|
1603
|
* @todo Please document this function.
|
|
1604
|
* @see http://drupal.org/node/1354
|
|
1605
|
*/
|
|
1606
|
function path_to_name($name_uuid) {
|
|
1607
|
$res = FALSE;
|
|
1608
|
if ($name_uuid) {
|
|
1609
|
$res = 'cdm_dataportal/name/' . $name_uuid;
|
|
1610
|
}
|
|
1611
|
return $res;
|
|
1612
|
}
|
|
1613
|
|
|
1614
|
/**
|
|
1615
|
* @todo Please document this function.
|
|
1616
|
* @see http://drupal.org/node/1354
|
|
1617
|
*/
|
|
1618
|
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
|
|
1619
|
if (!$uuid) {
|
|
1620
|
return FALSE;
|
|
1621
|
}
|
|
1622
|
$out = 'cdm_dataportal/media/' . $uuid;
|
|
1623
|
if ($representaion_uuid) {
|
|
1624
|
$out .= '/' . $representaion_uuid;
|
|
1625
|
if ($partId !== FALSE) {
|
|
1626
|
$out .= '/' . $partId;
|
|
1627
|
}
|
|
1628
|
}
|
|
1629
|
return $out;
|
|
1630
|
}
|
|
1631
|
|
|
1632
|
/**
|
|
1633
|
* Compares thisRank with thatRank.
|
|
1634
|
*
|
|
1635
|
* Returns a negative integer, zero, or a positive integer
|
|
1636
|
* as the of thisRank is higher than, equal to, or lower than thatRank.
|
|
1637
|
* e.g:
|
|
1638
|
* <ul>
|
|
1639
|
* <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
|
|
1640
|
* <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
|
|
1641
|
* <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
|
|
1642
|
* </ul>
|
|
1643
|
* <p>
|
|
1644
|
* This compare logic of the underlying webservice is the
|
|
1645
|
* <b>inverse logic</b> of the the one implemented in
|
|
1646
|
* java.lang.Comparable#compareTo(java.lang.Object)
|
|
1647
|
*
|
|
1648
|
* @param $thisRankUuid
|
|
1649
|
* @param $thatRankUuid
|
|
1650
|
*
|
|
1651
|
* @return int
|
|
1652
|
* A negative integer, zero, or a positive integer
|
|
1653
|
* as the thisRank is lower than, equal to, or higher than thatRank.
|
|
1654
|
*/
|
|
1655
|
function rank_compare($thisRankUuid, $thatRankUuid) {
|
|
1656
|
$result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
|
|
1657
|
return $result->Integer;
|
|
1658
|
}
|
|
1659
|
|
|
1660
|
/**
|
|
1661
|
* Composes an HTML element class attribute value composed of
|
|
1662
|
* the shortname of the cdm class and the uuid of the entity.
|
|
1663
|
* This class attribute should be used whereever an cdm-entity is rendered.
|
|
1664
|
*
|
|
1665
|
* These according class selectors in css must be escaped, eg:
|
|
1666
|
* .cdm\:TextData
|
|
1667
|
*
|
|
1668
|
* @param $cdmEntity
|
|
1669
|
*/
|
|
1670
|
function html_class_atttibute_ref($cdmEntity) {
|
|
1671
|
|
|
1672
|
if (is_cdm_entity($cdmEntity)) {
|
|
1673
|
return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
|
|
1674
|
}
|
|
1675
|
}
|
|
1676
|
|
|
1677
|
/**
|
|
1678
|
* Preprocess the taggedName to normalize newly introduced tagtypes like hybridSign, separator, .. more?
|
|
1679
|
*
|
|
1680
|
* @param unknown_type $taggedTextList
|
|
1681
|
*/
|
|
1682
|
function normalize_TaggedName(&$taggedTextList) {
|
|
1683
|
|
|
1684
|
if (is_array($taggedTextList)) {
|
|
1685
|
|
|
1686
|
// First pass: rename.
|
|
1687
|
for ($i = 0; $i < count($taggedTextList); $i++) {
|
|
1688
|
|
|
1689
|
if ($taggedTextList[$i]->type == "hybridSign") {
|
|
1690
|
$taggedTextList[$i]->type = "name";
|
|
1691
|
}
|
|
1692
|
}
|
|
1693
|
|
|
1694
|
// Second pass: resolve separators.
|
|
1695
|
$taggedNameListNew = array();
|
|
1696
|
for ($i = 0; $i < count($taggedTextList); $i++) {
|
|
1697
|
|
|
1698
|
if ($i + 1 < count($taggedTextList) && $taggedTextList[$i + 1]->type == "separator") {
|
|
1699
|
|
|
1700
|
if ($taggedTextList[$i]->type == $taggedTextList[$i + 2]->type) {
|
|
1701
|
$taggedName = $taggedTextList[$i];
|
|
1702
|
$taggedName->text = $taggedName->text . $taggedTextList[$i + 1]->text . $taggedTextList[$i + 2]->text;
|
|
1703
|
$taggedNameListNew[] = $taggedName;
|
|
1704
|
++$i;
|
|
1705
|
++$i;
|
|
1706
|
}
|
|
1707
|
}
|
|
1708
|
else {
|
|
1709
|
$taggedNameListNew[] = $taggedTextList[$i];
|
|
1710
|
}
|
|
1711
|
}
|
|
1712
|
$taggedTextList = $taggedNameListNew;
|
|
1713
|
}
|
|
1714
|
}
|
|
1715
|
|
|
1716
|
/**
|
|
1717
|
* Creates a short taxonname.
|
|
1718
|
*
|
|
1719
|
* The short name is created by using the taggename field of
|
|
1720
|
* NameSTO or NameTO instances.
|
|
1721
|
* If the taggename if empty the fullname will be returned.
|
|
1722
|
*
|
|
1723
|
* @param unknown_type $name
|
|
1724
|
* Name or TreeNode.
|
|
1725
|
*
|
|
1726
|
* @return string
|
|
1727
|
*/
|
|
1728
|
function cdm_dataportal_shortname_of($name) {
|
|
1729
|
$nameStr = '';
|
|
1730
|
|
|
1731
|
normalize_TaggedName($name->taggedTitle);
|
|
1732
|
|
|
1733
|
// Get all tagged text tokens of the scientific name.
|
|
1734
|
foreach ($name->taggedTitle as $tagtxt) {
|
|
1735
|
if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
|
|
1736
|
$nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
|
|
1737
|
}
|
|
1738
|
}
|
|
1739
|
$nameStr = trim($nameStr);
|
|
1740
|
|
|
1741
|
if ($nameStr) {
|
|
1742
|
|
|
1743
|
// Do not return short names for these.
|
|
1744
|
if ($name->unplaced || $name->excluded) {
|
|
1745
|
return $nameStr;
|
|
1746
|
}
|
|
1747
|
|
|
1748
|
/*
|
|
1749
|
1st capture group (^[a-zA-Z]): First letter of uninomial.
|
|
1750
|
Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
|
|
1751
|
Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
|
|
1752
|
but only matching if no '(' or '.' in second word of name, ( \x2E = '.')
|
|
1753
|
OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$ (\x22= '"', \x2D='-', \xD7='×' )
|
|
1754
|
*/
|
|
1755
|
$pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
|
|
1756
|
if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
|
|
1757
|
return $matches[1][0] . "." . $matches[3][0];
|
|
1758
|
}
|
|
1759
|
else {
|
|
1760
|
return $nameStr;
|
|
1761
|
}
|
|
1762
|
}
|
|
1763
|
else {
|
|
1764
|
return $name->titleCache;
|
|
1765
|
}
|
|
1766
|
}
|
|
1767
|
|
|
1768
|
/**
|
|
1769
|
* Check if a taxon is accepted by the current taxonomic tree.
|
|
1770
|
*
|
|
1771
|
* @param mixed $taxon
|
|
1772
|
* The Taxon obkect to check.
|
|
1773
|
*
|
|
1774
|
* @return bool
|
|
1775
|
* Returns TRUE if $taxon is accepted, FALSE otherwise.
|
|
1776
|
*/
|
|
1777
|
function _cdm_dataportal_acceptedByCurrentView($taxon) {
|
|
1778
|
|
|
1779
|
$defaultTreeUuid = get_taxonomictree_uuid_selected();
|
|
1780
|
|
|
1781
|
if (isset($taxon->taxonNodes)) {
|
|
1782
|
$taxonNodes = $taxon->taxonNodes;
|
|
1783
|
}
|
|
1784
|
else {
|
|
1785
|
$taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
|
|
1786
|
}
|
|
1787
|
|
|
1788
|
if ($taxon->class == "Taxon" && isset($taxonNodes)) {
|
|
1789
|
foreach ($taxonNodes as $node) {
|
|
1790
|
if (is_object($node->classification)) {
|
|
1791
|
if ($node->classification->uuid == $defaultTreeUuid) {
|
|
1792
|
return TRUE;
|
|
1793
|
}
|
|
1794
|
}
|
|
1795
|
else {
|
|
1796
|
if ($node->classification == $defaultTreeUuid) {
|
|
1797
|
return TRUE;
|
|
1798
|
}
|
|
1799
|
}
|
|
1800
|
}
|
|
1801
|
}
|
|
1802
|
|
|
1803
|
return FALSE;
|
|
1804
|
}
|
|
1805
|
|
|
1806
|
/**
|
|
1807
|
* @deprecated
|
|
1808
|
*/
|
|
1809
|
function compose_url_prameterstr($parameters = array(), $parentPropertyName = FALSE) {
|
|
1810
|
$pstr = '';
|
|
1811
|
foreach ($parameters as $key => $value) {
|
|
1812
|
if (is_array($value)) {
|
|
1813
|
|
|
1814
|
}
|
|
1815
|
else {
|
|
1816
|
$pstr .= ($pstr ? '&' : '') . $key . '=' . urlencode($value);
|
|
1817
|
}
|
|
1818
|
}
|
|
1819
|
return $pstr;
|
|
1820
|
}
|
|
1821
|
|
|
1822
|
/**
|
|
1823
|
* Workaround for missing original source type.
|
|
1824
|
*
|
|
1825
|
* idNamespace is always set in these cases.
|
|
1826
|
* @todo improve documentation of this function.
|
|
1827
|
*
|
|
1828
|
* @param unknown_type $source
|
|
1829
|
*
|
|
1830
|
* @return unknown_type
|
|
1831
|
*/
|
|
1832
|
function _is_original_source_type($source) {
|
|
1833
|
return !$source->idNamespace && strlen($source->idNamespace) == 0;
|
|
1834
|
}
|
|
1835
|
|
|
1836
|
/**
|
|
1837
|
* @todo Please document this function.
|
|
1838
|
* @see http://drupal.org/node/1354
|
|
1839
|
*/
|
|
1840
|
function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
|
|
1841
|
return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
|
|
1842
|
}
|
|
1843
|
|
|
1844
|
/**
|
|
1845
|
* Gets the metadata info such as title or artist of a media file.
|
|
1846
|
*
|
|
1847
|
* The function tries at first to get all the info from the file metadata
|
|
1848
|
* and if it is not avaible look at the media file info stored at the database.
|
|
1849
|
*
|
|
1850
|
* @param mixed $media
|
|
1851
|
* The media file object for which to get the metadata.
|
|
1852
|
*
|
|
1853
|
* @return array
|
|
1854
|
* The array with the available specified metadata info.
|
|
1855
|
* TODO rename to read_media_metadata() and move to *.module.
|
|
1856
|
*/
|
|
1857
|
function cdm_read_media_metadata($media) {
|
|
1858
|
|
|
1859
|
$metadata_caption = array(
|
|
1860
|
'title' => '',// Media_metadata and media.
|
|
1861
|
'artist' => '',// Media_metadata and media.
|
|
1862
|
'rights',// Media_metadata and media.
|
|
1863
|
'location',// Media_metadata.
|
|
1864
|
'filename' => '',// Media.
|
|
1865
|
'mediacreated' => '',// Media.
|
|
1866
|
'description' => '',
|
|
1867
|
);// Media.
|
|
1868
|
|
|
1869
|
// Getting the media metadata.
|
|
1870
|
$media_metadata = cdm_ws_get(CDM_WS_MEDIA_METADATA, array($media->uuid));
|
|
1871
|
$media_metadata_aux = (array) $media_metadata;
|
|
1872
|
|
|
1873
|
// Filename.
|
|
1874
|
if (isset($media->representations[0]->parts[0]->uri)) {
|
|
1875
|
$fileUri = $media->representations[0]->parts[0]->uri;
|
|
1876
|
$filename = substr($fileUri, strrpos($fileUri, "/") + 1);
|
|
1877
|
$metadata_caption['filename'] = $filename;
|
|
1878
|
}
|
|
1879
|
else {
|
|
1880
|
$metadata_caption['filename'] = '';
|
|
1881
|
}
|
|
1882
|
|
|
1883
|
// Title.
|
|
1884
|
if (!empty($media_metadata->ObjectName)) {
|
|
1885
|
$metadata_caption['title'] = $media_metadata->ObjectName;
|
|
1886
|
}
|
|
1887
|
elseif ($media_metadata_aux['Object Name']) {
|
|
1888
|
$metadata_caption['title'] = $media_metadata_aux['Object Name'];
|
|
1889
|
}
|
|
1890
|
elseif ($media->title_L10n) {
|
|
1891
|
$metadata_caption['title'] = $media->title_L10n;
|
|
1892
|
}
|
|
1893
|
elseif ($media->titleCache) {
|
|
1894
|
$metadata_caption['title'] = $media->titleCache;
|
|
1895
|
}
|
|
1896
|
|
|
1897
|
// Append description to title.
|
|
1898
|
if (!empty($media->description_L10n)) {
|
|
1899
|
$metadata_caption['title'] .= '<span class="media-description">' . $media->description_L10n . '<span>';
|
|
1900
|
}
|
|
1901
|
|
|
1902
|
// Artist.
|
|
1903
|
if ($media_metadata->Artist) {
|
|
1904
|
$metadata_caption['artist'] = ($media_metadata->Artist ? '' . $media_metadata->Artist : '');
|
|
1905
|
}
|
|
1906
|
elseif ($media->artist->titleCache) {
|
|
1907
|
$metadata_caption['artist'] = $media->artist->titleCache;
|
|
1908
|
}
|
|
1909
|
|
|
1910
|
// Copyright.
|
|
1911
|
$metadata_caption['rights'] = array(
|
|
1912
|
'copyright' => array('agentNames' => array()),
|
|
1913
|
'license' => array(
|
|
1914
|
'agentNames' => array(),
|
|
1915
|
'types' => array(),
|
|
1916
|
'abbreviatedTexts' => array(),
|
|
1917
|
'uris' => array(),
|
|
1918
|
),
|
|
1919
|
);
|
|
1920
|
if ($media_metadata->Copyright) {
|
|
1921
|
$metadata_caption['rights']['copyright']['agentNames'][] = $media_metadata->Copyright;
|
|
1922
|
}
|
|
1923
|
elseif (isset($media->rights) && is_array($media->rights)) {
|
|
1924
|
foreach ($media->rights as $right) {
|
|
1925
|
switch ($right->term->uuid) {
|
|
1926
|
case UUID_RIGHTS_LICENCE:
|
|
1927
|
$metadata_caption['rights']['license']['agentNames'][] = ($right->agent ? '' . $right->agent->firstname . ' ' . $right->agent->lastname : '');
|
|
1928
|
$metadata_caption['rights']['license']['types'][] = ($right->representation_L10n ? '' . $right->representation_L10n : '');
|
|
1929
|
$metadata_caption['rights']['license']['abbreviatedTexts'][] = ($right->abbreviatedText ? '' . $right->abbreviatedText : '');
|
|
1930
|
$metadata_caption['rights']['license']['uris'][] = ($right->uri ? '' . $right->uri : '');
|
|
1931
|
break;
|
|
1932
|
case UUID_RIGHTS_COPYRIGHT:
|
|
1933
|
$metadata_caption['rights']['copyright']['agentNames'][] = $right->agent->firstname . ' ' . $right->agent->lastname;
|
|
1934
|
break;
|
|
1935
|
}
|
|
1936
|
}
|
|
1937
|
}
|
|
1938
|
else {
|
|
1939
|
$metadata_caption['rights']['agentNames'][] = '';
|
|
1940
|
}
|
|
1941
|
|
|
1942
|
// Filling the description (though there is no description in the db???).
|
|
1943
|
// $metadata_caption['description'] = $media->description_L10n;
|
|
1944
|
|
|
1945
|
// Location.
|
|
1946
|
$metadata_caption['location'] = array();
|
|
1947
|
$metadata_caption['location']['sublocation'] = !empty($media_metadata->Sublocation) ? $media_metadata->Sublocation : FALSE;
|
|
1948
|
$metadata_caption['location']['city'] = !empty($media_metadata->City) ? $media_metadata->City : FALSE;
|
|
1949
|
$metadata_caption['location']['province'] = !empty($media_metadata->Province) ? $media_metadata->Province : FALSE;
|
|
1950
|
$metadata_caption['location']['country'] = !empty($media_metadata->Country)? $media_metadata->Country : FALSE;
|
|
1951
|
|
|
1952
|
/*
|
|
1953
|
// Creation date.
|
|
1954
|
if($media_metadata["Modify Date"])
|
|
1955
|
$metadata_caption['mediacreated'] = $media_metadata["Modify Date"];
|
|
1956
|
else
|
|
1957
|
$metadata_caption['mediacreated'] = $media->created;
|
|
1958
|
*/
|
|
1959
|
|
|
1960
|
// Returned value.
|
|
1961
|
return $metadata_caption;
|
|
1962
|
}
|
|
1963
|
|
|
1964
|
/**
|
|
1965
|
* Collects all the media from a list of description elements.
|
|
1966
|
*
|
|
1967
|
* @param array $descriptionElements
|
|
1968
|
* The description elements from which to collect the media.
|
|
1969
|
*
|
|
1970
|
* @return array
|
|
1971
|
* The output with all the collected media.
|
|
1972
|
*/
|
|
1973
|
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
|
|
1974
|
|
|
1975
|
$outArrayOfMedia = array();
|
|
1976
|
|
|
1977
|
// Avoiding a warning box in Drupal for Flora Malesiana.
|
|
1978
|
if (isset($descriptionElements) && is_array($descriptionElements)) {
|
|
1979
|
foreach ($descriptionElements as $descriptionElement) {
|
|
1980
|
if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
|
|
1981
|
foreach ($descriptionElement->media as $media) {
|
|
1982
|
if (is_object($media)) {
|
|
1983
|
$outArrayOfMedia[] = $media;
|
|
1984
|
}
|
|
1985
|
}
|
|
1986
|
}
|
|
1987
|
}
|
|
1988
|
}
|
|
1989
|
return $outArrayOfMedia;
|
|
1990
|
}
|
|
1991
|
|
|
1992
|
/**
|
|
1993
|
* @todo Please document this function.
|
|
1994
|
* @see http://drupal.org/node/1354
|
|
1995
|
*
|
|
1996
|
* @param array $cdmBase_list
|
|
1997
|
* An array of CdmBase instances or a single instance.
|
|
1998
|
* @param string $footnote_list_key
|
|
1999
|
*
|
|
2000
|
* @return unknown
|
|
2001
|
*/
|
|
2002
|
function cdm_annotations_as_footnotekeys($cdmBase_list, $footnote_list_key = NULL) {
|
|
2003
|
// Comment @WA: undefined variable.
|
|
2004
|
/*
|
|
2005
|
static $annotations_types_filter;
|
|
2006
|
if(!$annotations_types_filter) {
|
|
2007
|
unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
|
|
2008
|
}
|
|
2009
|
*/
|
|
2010
|
unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
|
|
2011
|
|
|
2012
|
$footNoteKeys = array();
|
|
2013
|
|
|
2014
|
// Is argument cdmBase an array?
|
|
2015
|
if (!is_array($cdmBase_list)) {
|
|
2016
|
$cdmBase_array = array();
|
|
2017
|
$cdmBase_array[] = $cdmBase_list;
|
|
2018
|
}
|
|
2019
|
else {
|
|
2020
|
$cdmBase_array = $cdmBase_list;
|
|
2021
|
}
|
|
2022
|
|
|
2023
|
// Getting the key for the footnotemanager.
|
|
2024
|
if (isset($footnote_list_key)) {
|
|
2025
|
$footnoteListKey = $footnote_list_key;
|
|
2026
|
}
|
|
2027
|
else {
|
|
2028
|
$footnoteListKey = RenderHints::getFootnoteListKey() . '-annotations';
|
|
2029
|
}
|
|
2030
|
|
|
2031
|
// Adding the footnotes keys.
|
|
2032
|
$annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
|
|
2033
|
foreach ($cdmBase_array as $cdmBase_element) {
|
|
2034
|
$annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
|
|
2035
|
if (is_array($annotations)) {
|
|
2036
|
foreach ($annotations as $annotation) {
|
|
2037
|
$footNoteKeys[] = FootnoteManager::addNewFootnote($footnoteListKey, $annotation->text);
|
|
2038
|
}
|
|
2039
|
}
|
|
2040
|
}
|
|
2041
|
|
|
2042
|
return $footNoteKeys;
|
|
2043
|
}
|
|
2044
|
|
|
2045
|
// @WA Comment: should this not be a theme function?
|
|
2046
|
/**
|
|
2047
|
* Creates a CDM Dynabox.
|
|
2048
|
*
|
|
2049
|
* @param string $label
|
|
2050
|
* The clickable text to show.
|
|
2051
|
* @param string $content_url
|
|
2052
|
* The cdm REST service request url wich will deliver the content to be shown
|
|
2053
|
* once the dynabox toggles open.
|
|
2054
|
* @param string $theme
|
|
2055
|
* The theme to be used for rendering the cdm REST service reponse with is
|
|
2056
|
* returned from the $content_url.
|
|
2057
|
* @param string $link_alt_text
|
|
2058
|
* The value for the alt attribute of the dynabox link.
|
|
2059
|
* @param array $enclosingtags
|
|
2060
|
* An array with two elements: $enclosingtags[0] will be used for the dynabox
|
|
2061
|
* element itself, $enclosingtags[1] is the tag to be used for the
|
|
2062
|
* dynabox_content.
|
|
2063
|
*
|
|
2064
|
* @return string
|
|
2065
|
* Returns HTML for a dynabox.
|
|
2066
|
*/
|
|
2067
|
function cdm_dynabox($label, $content_url, $theme, $link_alt_text, $enclosingtags = array('li', 'ul')) {
|
|
2068
|
$out = '';
|
|
2069
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
|
|
2070
|
|
|
2071
|
$cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
|
|
2072
|
$out .= '<!-- ' . $content_url . ' -->';
|
|
2073
|
$out .= '<' . $enclosingtags[0] . ' class="dynabox"><a href="#" class="label" alt="' . t($link_alt_text) . '">' . $label . '</a>';
|
|
2074
|
$out .= '<' . $enclosingtags[1] . ' class="dynabox_content" title="' . $cdm_proxy_url . '"><' . $enclosingtags[0] . '><img class="loading" src="' . drupal_get_path('module', 'cdm_dataportal') . '/images/loading_circle_grey_16.gif" style="display:none;"></' . $enclosingtags[0] . '></' . $enclosingtags[1] . '>';
|
|
2075
|
$out .= '</' . $enclosingtags[0] . '>';
|
|
2076
|
return $out;
|
|
2077
|
}
|
|
2078
|
|
|
2079
|
/**
|
|
2080
|
* Checks whether a feature has any description elements.
|
|
2081
|
*
|
|
2082
|
* @param mixed $featureNode
|
|
2083
|
* A feature node as produced by the function _mergeFeatureTreeDescriptions().
|
|
2084
|
*
|
|
2085
|
* @see _mergeFeatureTreeDescriptions()
|
|
2086
|
*
|
|
2087
|
* @return bool
|
|
2088
|
* Returns TRUE if the given $featureNode or any of its subordinate nodes
|
|
2089
|
* contains at least one non empty TextData or at least one DescriptionElement
|
|
2090
|
* of an other type. A TextData element holding a multilanguageText or a
|
|
2091
|
* source reference is considered to be not empty.
|
|
2092
|
*/
|
|
2093
|
function hasFeatureNodeDescriptionElements($featureNode) {
|
|
2094
|
|
|
2095
|
if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
|
|
2096
|
foreach ($featureNode->descriptionElements as $descriptionElement) {
|
|
2097
|
if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text) && $descriptionElement->multilanguageText_L10n->text != '' || isset($descriptionElement->sources[0])) {
|
|
2098
|
return TRUE;
|
|
2099
|
}
|
|
2100
|
}
|
|
2101
|
}
|
|
2102
|
elseif (isset($featureNode->children) && is_array($featureNode->children)) {
|
|
2103
|
foreach ($featureNode->children as $child) {
|
|
2104
|
if (hasFeatureNodeDescriptionElements($child)) {
|
|
2105
|
return TRUE;
|
|
2106
|
}
|
|
2107
|
}
|
|
2108
|
}
|
|
2109
|
return FALSE;
|
|
2110
|
}
|