Revision 2264b60d
Added by Andreas Kohlbecker about 13 years ago
| modules/cdm_dataportal/cdm_api/cdm_api.module | ||
|---|---|---|
| 317 | 317 |
*/ |
| 318 | 318 |
function cdm_compose_url($uri_pattern, $pathParameters = array(), $query = NULL ){
|
| 319 | 319 |
|
| 320 |
if(!isset($pathParameters)){
|
|
| 321 |
$pathParameters = array(); |
|
| 322 |
} |
|
| 323 |
|
|
| 320 | 324 |
$request_params = ''; |
| 321 | 325 |
$path_params = ''; |
| 322 | 326 |
|
| ... | ... | |
| 332 | 336 |
|
| 333 | 337 |
$i = 0; |
| 334 | 338 |
while(strpos($uri_pattern, "$".$i) !== FALSE){
|
| 335 |
if(count($pathParameters) <= $i && user_access('administer')){
|
|
| 336 |
drupal_set_message('cdm_compose_url(): missing pathParameters', 'debug');
|
|
| 339 |
if(count($pathParameters) <= $i){
|
|
| 340 |
if(user_access('administer')){
|
|
| 341 |
drupal_set_message('cdm_compose_url(): missing pathParameters', 'debug');
|
|
| 342 |
} |
|
| 343 |
break; |
|
| 337 | 344 |
} |
| 338 | 345 |
$uri_pattern = str_replace("$".$i, rawurlencode($pathParameters[$i]), $uri_pattern);
|
| 339 | 346 |
++$i; |
| ... | ... | |
| 494 | 501 |
case 'CategoricalData': |
| 495 | 502 |
$ws_base_uri = CDM_WS_DESCRIPTIONELEMENT; |
| 496 | 503 |
break; |
| 504 |
case 'PolytomousKey': |
|
| 505 |
case 'MediaKey': |
|
| 506 |
case 'MultiAccessKey': |
|
| 507 |
$ws_base_uri = CDM_WS_IDENTIFICATIONKEY; |
|
| 508 |
break; |
|
| 497 | 509 |
default: trigger_error('Unsupported CDM Class - no annotations available for ' . $cdmBase->class, E_USER_ERROR);
|
| 498 | 510 |
return; |
| 499 | 511 |
} |
| ... | ... | |
| 727 | 739 |
$is_cdm_ws_uri = _is_cdm_ws_uri($uri); |
| 728 | 740 |
$use_cacheL2 = variable_get('cdm_webservice_cache', 1);
|
| 729 | 741 |
|
| 730 |
$cacheL1_obj = $cacheL1[$uri]; |
|
| 742 |
if(array_key_exists($uri, $cacheL1)){
|
|
| 743 |
$cacheL1_obj = $cacheL1[$uri]; |
|
| 744 |
} |
|
| 731 | 745 |
//print $cacheL1_obj; |
| 732 | 746 |
$set_cacheL1 = false; |
| 733 | 747 |
if($is_cdm_ws_uri && !$cacheL1_obj){
|
| ... | ... | |
| 835 | 849 |
|
| 836 | 850 |
function cdm_load_obj($datastr){
|
| 837 | 851 |
|
| 838 |
// NOTICE: the cdm dataportal currently does not support xml so the line below are commented out |
|
| 839 |
/* |
|
| 840 |
// if the web service delivers XML convert it into json |
|
| 841 |
if(variable_get('cdm_webservice_type', 'json') == 'xml'){
|
|
| 842 |
$datastr = xml2json::transformXmlStringToJson($datastr); |
|
| 843 |
} |
|
| 844 |
*/ |
|
| 845 |
|
|
| 846 | 852 |
$obj = json_decode($datastr); |
| 847 | 853 |
|
| 848 | 854 |
if(!(is_object($obj) || is_array($obj)) ){
|
| ... | ... | |
| 869 | 875 |
static $acceptLanguage = null; |
| 870 | 876 |
|
| 871 | 877 |
if(!$acceptLanguage) {
|
| 872 |
$headers = getallheaders(); |
|
| 873 |
if($headers['Accept-Language']){
|
|
| 874 |
$acceptLanguage = $headers['Accept-Language']; |
|
| 875 |
} else {
|
|
| 878 |
if(function_exists('apache_request_headers')){
|
|
| 879 |
$headers = apache_request_headers(); |
|
| 880 |
if($headers['Accept-Language']){
|
|
| 881 |
$acceptLanguage = $headers['Accept-Language']; |
|
| 882 |
} |
|
| 883 |
} |
|
| 884 |
if( !$acceptLanguage ) {
|
|
| 876 | 885 |
$acceptLanguage = "en"; // DEFAULT TODO make configurable |
| 877 | 886 |
} |
| 878 | 887 |
} |
| modules/cdm_dataportal/cdm_api/webservice_uris.php | ||
|---|---|---|
| 119 | 119 |
|
| 120 | 120 |
define('CDM_WS_DERIVEDUNIT_FACADE', 'derivedUnitFacade/$0');
|
| 121 | 121 |
|
| 122 |
define('CDM_WS_IDENTIFICATIONKEY', 'identificationKey');
|
|
| 122 | 123 |
define('CDM_WS_MEDIAKEY', 'mediaKey');
|
| 123 | 124 |
define('CDM_WS_MULTIACCESSKEY', 'multiAccessKey');
|
| 124 | 125 |
define('CDM_WS_POLYTOMOUSKEY', 'polytomousKey');
|
| modules/cdm_dataportal/cdm_dataportal.css | ||
|---|---|---|
| 375 | 375 |
font-size: 90%; |
| 376 | 376 |
line-height: 1em; |
| 377 | 377 |
color: #999999; |
| 378 |
} |
|
| 379 |
|
|
| 380 |
.polytomousKey_linkedStyle td{
|
|
| 381 |
vertical-align: top; |
|
| 382 |
padding-top: 0; |
|
| 383 |
} |
|
| 384 |
.polytomousKey_linkedStyle tr.childCount_0 td{
|
|
| 385 |
padding-top: 1em; |
|
| 386 |
} |
|
| 387 |
.polytomousKey_linkedStyle tr:hover {
|
|
| 388 |
background-color: #eeeeee; |
|
| 389 |
} |
|
| 390 |
|
|
| 391 |
.polytomousKey_linkedStyle .nodeLink, .polytomousKey_linkedStyle .nodeNumber {
|
|
| 392 |
width: 1.5em; |
|
| 393 |
} |
|
| 394 |
.polytomousKey_linkedStyle .nodeLink{
|
|
| 395 |
text-align: right; |
|
| 396 |
} |
|
| 397 |
|
|
| 398 |
.polytomousKey_linkedStyle .nodeLinkToTaxon, .polytomousKey_linkedStyle .nodeLinkToSubkey {
|
|
| 399 |
float: right; |
|
| 400 |
text-align: right; |
|
| 378 | 401 |
} |
| modules/cdm_dataportal/cdm_dataportal.install | ||
|---|---|---|
| 17 | 17 |
} |
| 18 | 18 |
|
| 19 | 19 |
|
| 20 |
|
|
| 21 | 20 |
/** |
| 22 | 21 |
* Implementation of hook_api_update_N(). |
| 23 | 22 |
* |
| modules/cdm_dataportal/cdm_dataportal.module | ||
|---|---|---|
| 202 | 202 |
// expected callback arguments: uuid, mediarepresentation_uuid, part_uuid or part# |
| 203 | 203 |
); |
| 204 | 204 |
|
| 205 |
$items[] = array( |
|
| 206 |
'path' => 'cdm_dataportal/polytomousKey', |
|
| 207 |
'callback' => 'cdm_dataportal_view_polytomousKey', |
|
| 208 |
'access' => true, |
|
| 209 |
'type' => MENU_CALLBACK, |
|
| 210 |
// expected callback arguments: polytomousKey->uuid |
|
| 211 |
); |
|
| 212 |
|
|
| 205 | 213 |
$items[] = array( |
| 206 | 214 |
'path' => 'cdm_dataportal/search', |
| 207 | 215 |
'callback' => 'cdm_dataportal_view_search_advanced', |
| ... | ... | |
| 884 | 892 |
return theme('cdm_media_page', $media, $mediarepresentation_uuid, $part);
|
| 885 | 893 |
} |
| 886 | 894 |
|
| 895 |
function _load_taxonBase(&$taxonBase){
|
|
| 896 |
if(isset($taxonBase->uuid)){
|
|
| 897 |
$taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name")); |
|
| 898 |
$taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName")); |
|
| 899 |
$taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference")); |
|
| 900 |
} |
|
| 901 |
} |
|
| 902 |
|
|
| 903 |
/** |
|
| 904 |
* Loads the subgraph of the given PolytomousKeyNode recursively from the cdm REST service. |
|
| 905 |
* @param PolytomousKeyNode $polytomousKeyNode passed by reference |
|
| 906 |
* @return nothing |
|
| 907 |
*/ |
|
| 908 |
function _load_polytomousKeySubGraph(&$polytomousKeyNode){
|
|
| 909 |
if(!$polytomousKeyNode){
|
|
| 910 |
return; |
|
| 911 |
} |
|
| 912 |
$polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid); |
|
| 913 |
|
|
| 914 |
if(!$polytomousKeyNode){
|
|
| 915 |
//drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
|
|
| 916 |
return; |
|
| 917 |
} |
|
| 918 |
|
|
| 919 |
// load children |
|
| 920 |
foreach($polytomousKeyNode->children as &$childNode){
|
|
| 921 |
_load_polytomousKeySubGraph($childNode); |
|
| 922 |
} |
|
| 923 |
|
|
| 924 |
// load subkey |
|
| 925 |
$polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey")); |
|
| 926 |
|
|
| 927 |
// load taxon |
|
| 928 |
$polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon")); |
|
| 929 |
_load_taxonBase($polytomousKeyNode->taxon); |
|
| 930 |
return; |
|
| 931 |
} |
|
| 932 |
|
|
| 933 |
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid){
|
|
| 934 |
$polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid); |
|
| 935 |
|
|
| 936 |
$sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, "sources")); |
|
| 937 |
if(is_array($sourcePager->records)){
|
|
| 938 |
$polytomousKey->sources = $sourcePager->records; |
|
| 939 |
} |
|
| 940 |
|
|
| 941 |
$annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, "annotations")); |
|
| 942 |
if(is_array($annotationPager->records)){
|
|
| 943 |
$polytomousKey->annotations = $annotationPager->records; |
|
| 944 |
} |
|
| 945 |
|
|
| 946 |
_load_polytomousKeySubGraph($polytomousKey->root); |
|
| 947 |
return theme('cdm_polytomousKey_page', $polytomousKey);
|
|
| 948 |
} |
|
| 949 |
|
|
| 887 | 950 |
/** |
| 888 | 951 |
* The taxon page gives detailed information on a taxon, it shows: |
| 889 | 952 |
* - Taxon name |
| modules/cdm_dataportal/test/phpUnit/bootstrap.php | ||
|---|---|---|
| 5 | 5 |
// see http://pkp.sfu.ca/wiki/index.php/Configure_Eclipse_for_PHPUnit#Configure_XDebug_Debugger_to_work_with_PHPUnit |
| 6 | 6 |
// |
| 7 | 7 |
print("> bootstrapping Drupal for phpUnit ...\n");
|
| 8 |
|
|
| 9 |
//$phpUnitTestBaseDir = "test".DIRECTORY_SEPARATOR."phpUnit"; |
|
| 10 |
// |
|
| 11 |
//while(!str_endsWith( getcwd(), $phpUnitTestBaseDir) || strlen(getcwd()) < strln($phpUnitTestBaseDir)){
|
|
| 12 |
// |
|
| 13 |
//} |
|
| 14 |
|
|
| 15 |
print(">".getcwd()."\n");
|
|
| 8 |
//print(">".getcwd()."\n");
|
|
| 16 | 9 |
|
| 17 | 10 |
// TestUtils.php must be included at the very first step |
| 18 | 11 |
require_once ('TestUtils.php');
|
| ... | ... | |
| 23 | 16 |
$_SERVER['HTTP_HOST']='127.0.0.1'; |
| 24 | 17 |
$_SERVER['REQUEST_METHOD'] = 'get'; |
| 25 | 18 |
$_SERVER['REMOTE_ADDR'] = '127.0.0.1'; |
| 26 |
$_SERVER['REQUEST_URI'] = "http://" . $_SERVER['HTTP_HOST'] . "/" . "cichorieae/"; |
|
| 19 |
$_SERVER['PHP_SELF'] = $_SERVER['SITE_BASE_PATH']."/index.php"; |
|
| 20 |
//$_SERVER['REQUEST_URI'] = "http://" . $_SERVER['HTTP_HOST'] . "/" . "flora-malesiana/"; |
|
| 27 | 21 |
|
| 28 | 22 |
drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL); |
| 29 | 23 |
|
| modules/cdm_dataportal/test/phpUnit/resources/theme/cdm_dataportal.name.themeTest-taxon1.json | ||
|---|---|---|
| 16 | 16 |
"updated": "2011-04-01T17:31:18.795+02:00", |
| 17 | 17 |
"useNameCache": false, |
| 18 | 18 |
"uuid": "0ae4f7ab-f482-482c-ba57-cf0e4389a417", |
| 19 |
"name": [ |
|
| 20 |
{
|
|
| 21 |
"class": "TaggedText", |
|
| 22 |
"text": "Alectryon", |
|
| 23 |
"type": "name" |
|
| 24 |
}, |
|
| 25 |
{
|
|
| 26 |
"class": "TaggedText", |
|
| 27 |
"text": "myrmecophilus", |
|
| 28 |
"type": "name" |
|
| 29 |
}, |
|
| 30 |
{
|
|
| 31 |
"class": "TaggedText", |
|
| 32 |
"text": "Leenh.", |
|
| 33 |
"type": "authors" |
|
| 34 |
} |
|
| 35 |
] |
|
| 19 |
"name": {
|
|
| 20 |
"taggedName": [ |
|
| 21 |
{
|
|
| 22 |
"class": "TaggedText", |
|
| 23 |
"text": "Alectryon", |
|
| 24 |
"type": "name" |
|
| 25 |
}, |
|
| 26 |
{
|
|
| 27 |
"class": "TaggedText", |
|
| 28 |
"text": "myrmecophilus", |
|
| 29 |
"type": "name" |
|
| 30 |
}, |
|
| 31 |
{
|
|
| 32 |
"class": "TaggedText", |
|
| 33 |
"text": "Leenh.", |
|
| 34 |
"type": "authors" |
|
| 35 |
} |
|
| 36 |
] |
|
| 37 |
} |
|
| 36 | 38 |
} |
| modules/cdm_dataportal/theme/cdm_dataportal.common.theme | ||
|---|---|---|
| 12 | 12 |
|
| 13 | 13 |
define(FOOTNOTE_ANNOTATIONS, 'annotations'); |
| 14 | 14 |
|
| 15 |
|
|
| 15 | 16 |
/** |
| 16 | 17 |
* Get the true path to the root of the Drupal site. |
| 17 | 18 |
* Better than using DOCUMENT_ROOT and base_path(). |
| ... | ... | |
| 361 | 362 |
} |
| 362 | 363 |
|
| 363 | 364 |
|
| 365 |
|
|
| 366 |
|
|
| 364 | 367 |
/* ============================ java script functions ============================= */ |
| 365 | 368 |
|
| 366 | 369 |
function _add_js_thickbox(){
|
| modules/cdm_dataportal/theme/cdm_dataportal.descriptions.theme | ||
|---|---|---|
| 205 | 205 |
return $out; |
| 206 | 206 |
} |
| 207 | 207 |
|
| 208 |
|
|
| 208 | 209 |
/** |
| 209 | 210 |
* TODO: assign a new name to the function? because it is used for the citations |
| 210 | 211 |
* textdata elements and not for all text data description elements |
| ... | ... | |
| 223 | 224 |
|
| 224 | 225 |
if(is_array($element->sources)){
|
| 225 | 226 |
foreach($element->sources as $source){
|
| 226 |
$referenceCitation = theme('cdm_DescriptionElementSource', $source);
|
|
| 227 |
if($description && strlen($description) > 0 && $referenceCitation ){
|
|
| 228 |
$sourceRefs .= ' ('.$referenceCitation.')' ;
|
|
| 229 |
}else if ($referenceCitation){
|
|
| 230 |
$sourceRefs = $referenceCitation;
|
|
| 231 |
}
|
|
| 227 |
$referenceCitation = theme('cdm_DescriptionElementSource', $source);
|
|
| 228 |
if($description && strlen($description) > 0 && $referenceCitation ){
|
|
| 229 |
$sourceRefs .= ' ('.$referenceCitation.')' ;
|
|
| 230 |
}else if ($referenceCitation){
|
|
| 231 |
$sourceRefs = $referenceCitation;
|
|
| 232 |
}
|
|
| 232 | 233 |
|
| 233 |
if(strlen($sourceRefs) > 0){
|
|
| 234 |
$sourceRefs = '<span class="sources">' . $sourceRefs . '</span>';
|
|
| 235 |
}
|
|
| 234 |
if(strlen($sourceRefs) > 0){
|
|
| 235 |
$sourceRefs = '<span class="sources">' . $sourceRefs . '</span>';
|
|
| 236 |
}
|
|
| 236 | 237 |
|
| 237 |
if ($source->nameUsedInSource->uuid){ //do a link to name page
|
|
| 238 |
$name_used_in_source_link_to_show = l($source->nameUsedInSource->titleCache,
|
|
| 239 |
path_to_name($source->nameUsedInSource->uuid),
|
|
| 240 |
array(), NULL, NULL, FALSE ,TRUE);
|
|
| 241 |
}else if (strlen($source->nameUsedInSource->originalNameString) > 0){ //show a text without link
|
|
| 242 |
$name_used_in_source_link_to_show = $source->nameUsedInSource->originalNameString;
|
|
| 243 |
}
|
|
| 238 |
if ($source->nameUsedInSource->uuid){ //do a link to name page
|
|
| 239 |
$name_used_in_source_link_to_show = l($source->nameUsedInSource->titleCache,
|
|
| 240 |
path_to_name($source->nameUsedInSource->uuid),
|
|
| 241 |
array(), NULL, NULL, FALSE ,TRUE);
|
|
| 242 |
}else if (strlen($source->nameUsedInSource->originalNameString) > 0){ //show a text without link
|
|
| 243 |
$name_used_in_source_link_to_show = $source->nameUsedInSource->originalNameString;
|
|
| 244 |
}
|
|
| 244 | 245 |
|
| 245 |
if ($asListElement){
|
|
| 246 |
$out = '<li class="descriptionText">' . $name_used_in_source_link_to_show;
|
|
| 247 |
//adding ":" if necesary
|
|
| 248 |
if ($name_used_in_source_link_to_show && ($description || $sourceRefs)){
|
|
| 249 |
$out .= ': ';
|
|
| 250 |
}
|
|
| 251 |
$out .= $description . $sourceRefs . theme('cdm_annotations_as_footnotekeys', $element) . '</li>';
|
|
| 252 |
}else{
|
|
| 253 |
if ($name_used_in_source_link_to_show){
|
|
| 254 |
$name_used_in_source_link_to_show = ' (name in source: '. $name_used_in_source_link_to_show . ')';
|
|
| 255 |
}
|
|
| 256 |
$out = $description . $sourceRefs . $name_used_in_source_link_to_show;
|
|
| 257 |
}
|
|
| 246 |
if ($asListElement){
|
|
| 247 |
$out = '<li class="descriptionText">' . $name_used_in_source_link_to_show;
|
|
| 248 |
//adding ":" if necesary
|
|
| 249 |
if ($name_used_in_source_link_to_show && ($description || $sourceRefs)){
|
|
| 250 |
$out .= ': ';
|
|
| 251 |
}
|
|
| 252 |
$out .= $description . $sourceRefs . theme('cdm_annotations_as_footnotekeys', $element) . '</li>';
|
|
| 253 |
}else{
|
|
| 254 |
if ($name_used_in_source_link_to_show){
|
|
| 255 |
$name_used_in_source_link_to_show = ' (name in source: '. $name_used_in_source_link_to_show . ')';
|
|
| 256 |
}
|
|
| 257 |
$out = $description . $sourceRefs . $name_used_in_source_link_to_show;
|
|
| 258 |
}
|
|
| 258 | 259 |
} |
| 259 | 260 |
} |
| 260 | 261 |
//if no sources, print the description |
| ... | ... | |
| 268 | 269 |
return $out; |
| 269 | 270 |
} |
| 270 | 271 |
|
| 272 |
|
|
| 271 | 273 |
function theme_cdm_common_names($elements){
|
| 272 | 274 |
$text_data_out = ''; |
| 273 | 275 |
$common_name_out = ''; |
| ... | ... | |
| 623 | 625 |
return $out; |
| 624 | 626 |
} |
| 625 | 627 |
|
| 628 |
function theme_cdm_IdentifieableSource($source, $doLink = TRUE){
|
|
| 629 |
|
|
| 630 |
if(isset($source->citation)){
|
|
| 631 |
$out = theme('cdm_reference', $source->citation, $source->citationMicroReference, $doLink);
|
|
| 632 |
} |
|
| 633 |
return $out; |
|
| 634 |
} |
|
| 635 |
|
|
| 636 |
|
|
| 637 |
|
|
| 638 |
|
|
| 626 | 639 |
|
| 627 | 640 |
/* |
| 628 | 641 |
function theme_cdm_descriptionElementDistribution($descriptionElements){
|
| ... | ... | |
| 805 | 818 |
return $pager->records; |
| 806 | 819 |
} |
| 807 | 820 |
|
| 821 |
function theme_cdm_IdentificationKey($identificationKey, $doLinkToKeyPage = true){
|
|
| 822 |
|
|
| 823 |
$parentRenderPath = RenderHints::getRenderPath(); |
|
| 824 |
RenderHints::pushToRenderStack("IdentificationKey");
|
|
| 825 |
|
|
| 826 |
if($doLinkToKeyPage) {
|
|
| 827 |
$out = l($identificationKey->titleCache, path_to_key($identificationKey->class, $identificationKey->uuid)); |
|
| 828 |
} else {
|
|
| 829 |
$out = $identificationKey->titleCache; |
|
| 830 |
} |
|
| 831 |
if(is_array($identificationKey->sources)){
|
|
| 832 |
// display sources |
|
| 833 |
foreach($identificationKey->sources as $source){
|
|
| 834 |
$out .= theme("cdm_IdentifieableSource", $source);
|
|
| 835 |
} |
|
| 836 |
// display annotations |
|
| 837 |
$out .= theme("cdm_annotations_as_footnotekeys", $identificationKey, $parentRenderPath);
|
|
| 838 |
} |
|
| 839 |
RenderHints::popFromRenderStack(); |
|
| 840 |
return $out; |
|
| 841 |
} |
|
| 842 |
|
|
| 843 |
function theme_cdm_polytomousKey(&$polytomousKey){
|
|
| 844 |
|
|
| 845 |
$keyStyle = "linkedStyle"; // TODO settings needed |
|
| 846 |
|
|
| 847 |
RenderHints::pushToRenderStack("polytomousKey");
|
|
| 848 |
// key nodes in linked style |
|
| 849 |
$out = '<table class="polytomousKey polytomousKey_'.$keyStyle.'">'; |
|
| 850 |
$out .= theme('cdm_polytomousKey_'.$keyStyle.'_subgraph', $polytomousKey->root);
|
|
| 851 |
$out .= '</table>'; |
|
| 852 |
RenderHints::popFromRenderStack(); |
|
| 853 |
return $out; |
|
| 854 |
} |
|
| 855 |
|
|
| 856 |
function theme_cdm_polytomousKey_linkedStyle_subgraph(&$polytomousKeyNode){
|
|
| 857 |
|
|
| 858 |
static $statementCountCharacter = '\''; |
|
| 859 |
|
|
| 860 |
$out = ""; |
|
| 861 |
|
|
| 862 |
if(is_array($polytomousKeyNode->children)){
|
|
| 863 |
|
|
| 864 |
$childCount = 0; |
|
| 865 |
|
|
| 866 |
// render edges of the current node |
|
| 867 |
foreach($polytomousKeyNode->children as &$child){
|
|
| 868 |
$out .= '<tr class="childCount_' . $childCount . '">'; |
|
| 869 |
|
|
| 870 |
$out .= '<td class="nodeNumber">'. uuid_anchor($polytomousKeyNode->uuid, $polytomousKeyNode->nodeNumber . str_pad("", $childCount++ , $statementCountCharacter)) . "</td>";
|
|
| 871 |
|
|
| 872 |
$islinkToTaxonOrSubkey = isset($child->taxon->uuid) || isset($child->subkey->uuid); |
|
| 873 |
|
|
| 874 |
$out .= '<td class="edge" colspan="'. ( $islinkToTaxonOrSubkey ? '2' : '1' ) .'">'; |
|
| 875 |
if(isset($polytomousKeyNode->question->label_l10n)){
|
|
| 876 |
$out .= $polytomousKeyNode->question->label_l10n . ": "; |
|
| 877 |
} |
|
| 878 |
$out .= $child->statement->label_l10n; |
|
| 879 |
|
|
| 880 |
if(!$islinkToTaxonOrSubkey){
|
|
| 881 |
$out .= '</td>'; |
|
| 882 |
// link to a PolytomousKeyNode |
|
| 883 |
$out .= '<td class="nodeLink">' . l($child->nodeNumber, $_REQUEST["q"], null, null, $child->uuid) . '</td>'; |
|
| 884 |
} else {
|
|
| 885 |
if(isset($child->taxon->uuid)){
|
|
| 886 |
// link to a taxon |
|
| 887 |
$out .= '<div class="nodeLinkToTaxon">' . theme("cdm_taxonName", $child->taxon->name, path_to_taxon($child->taxon->uuid)) . '</div>';
|
|
| 888 |
} else if(isset($child->subkey->uuid)){
|
|
| 889 |
// link to a subkey |
|
| 890 |
$out .= '<div class="nodeLinkToSubkey">' |
|
| 891 |
. theme('cdm_IdentificationKey', $child->subkey) . '</div>';
|
|
| 892 |
} |
|
| 893 |
$out .= '</td>'; |
|
| 894 |
} |
|
| 895 |
|
|
| 896 |
$out .= '</tr>'; |
|
| 897 |
|
|
| 898 |
} |
|
| 899 |
|
|
| 900 |
// recurse into child nodes |
|
| 901 |
foreach($polytomousKeyNode->children as &$child){
|
|
| 902 |
$out .= theme('cdm_polytomousKey_linkedStyle_subgraph', $child);
|
|
| 903 |
} |
|
| 904 |
|
|
| 905 |
} |
|
| 906 |
return $out; |
|
| 907 |
} |
|
| 908 |
|
|
| 808 | 909 |
/** |
| 809 | 910 |
* Renders a list of a specific type of IdentificationKeys, the list can be restricteded by a taxon. |
| 810 | 911 |
* @param $type The simple name of the cdm class implementing the interface IIdentificationKey, |
| ... | ... | |
| 822 | 923 |
RenderHints::pushToRenderStack('list_IdentificationKeys');
|
| 823 | 924 |
$out = '<ul>'; |
| 824 | 925 |
foreach ($keyList as $key){
|
| 825 |
$out .= '<li>'.l($key->titleCache, path_to_key($type, $key->uuid)).'</li>'; |
|
| 926 |
$out .= '<li>'; |
|
| 927 |
$out .= theme('cdm_IdentificationKey', $key);
|
|
| 928 |
$out .= '</li>'; |
|
| 826 | 929 |
} |
| 827 | 930 |
$out .= '</ul>'; |
| 931 |
$out .= theme("cdm_annotation_footnotes", RenderHints::getRenderPath());
|
|
| 828 | 932 |
RenderHints::popFromRenderStack(); |
| 829 | 933 |
|
| 830 | 934 |
return $out; |
| modules/cdm_dataportal/theme/cdm_dataportal.name.theme | ||
|---|---|---|
| 369 | 369 |
// find best matching default RenderTemplate in theme |
| 370 | 370 |
//echo "<br/><br/>RENDER PATH: ".$renderPath; |
| 371 | 371 |
//var_dump('RENDER PATH: ' . $renderPath);
|
| 372 |
while(!is_array($template) && strlen($renderPath) > 0){
|
|
| 373 |
$template = theme('get_nameRenderTemplate', $renderPath);
|
|
| 374 |
$renderPath = substr($renderPath, 0, strrpos($renderPath, '.')); |
|
| 375 |
// if(!is_array($template)){
|
|
| 376 |
// echo "<br/>->".$renderPath; |
|
| 377 |
// } |
|
| 372 |
|
|
| 373 |
// preserve renderPath_base |
|
| 374 |
if( ($separatorPos = strpos($renderPath, '.')) >= 0 ){
|
|
| 375 |
} else {
|
|
| 376 |
$separatorPos = strlen($renderPath); |
|
| 377 |
} |
|
| 378 |
$renderPath_base = substr($renderPath, 0, $separatorPos); |
|
| 379 |
|
|
| 380 |
// find in theme function if it exists |
|
| 381 |
if(theme_get_function('get_nameRenderTemplate')){
|
|
| 382 |
while(!is_array($template) && strlen($renderPath) > 0){
|
|
| 383 |
$template = theme('get_nameRenderTemplate', $renderPath);
|
|
| 384 |
$renderPath = substr($renderPath, 0, strrpos($renderPath, '.')); |
|
| 385 |
// if(!is_array($template)){
|
|
| 386 |
// echo "<br/>->".$renderPath; |
|
| 387 |
// } |
|
| 388 |
} |
|
| 378 | 389 |
} |
| 379 | 390 |
|
| 380 | 391 |
// otherwise get default RenderTemplate from theme |
| ... | ... | |
| 383 | 394 |
} |
| 384 | 395 |
// otherwise get system default RenderTemplate |
| 385 | 396 |
if(!is_array($template)){
|
| 386 |
switch($renderPath){
|
|
| 397 |
switch($renderPath_base){
|
|
| 387 | 398 |
case 'list_of_taxa': |
| 388 |
case 'acceptedFor':
|
|
| 399 |
case 'acceptedFor': |
|
| 389 | 400 |
case 'taxon_page_synonymy': |
| 390 | 401 |
case 'typedesignations': |
| 391 | 402 |
case 'taxon_page_title': |
| 403 |
case 'polytomousKey': |
|
| 392 | 404 |
case 'na': $template = array( |
| 393 | 405 |
'namePart' => array('#uri'=>true),
|
| 394 | 406 |
//'authorshipPart' => true, |
| ... | ... | |
| 434 | 446 |
} |
| 435 | 447 |
|
| 436 | 448 |
function get_partDefinition($taxonNameType){
|
| 449 |
|
|
| 437 | 450 |
//TODO implement admin user interface to allow specify the partdefinitions for any type |
| 438 | 451 |
// preliminar solution: using themes |
| 439 | 452 |
|
| ... | ... | |
| 459 | 472 |
), |
| 460 | 473 |
); |
| 461 | 474 |
break; |
| 462 |
case 'BotanicalName': $partdef = array( |
|
| 475 |
case 'BotanicalName': |
|
| 476 |
default: $partdef = array( |
|
| 463 | 477 |
'namePart' => array( |
| 464 | 478 |
'name' => true, |
| 465 | 479 |
'authors' => true |
| ... | ... | |
| 476 | 490 |
), |
| 477 | 491 |
); |
| 478 | 492 |
break; |
| 479 |
default: $partdef = array( |
|
| 480 |
'namePart' => array( |
|
| 481 |
'name' => true, |
|
| 482 |
'authorTeam' => true |
|
| 483 |
), |
|
| 484 |
'referencePart' => array( |
|
| 485 |
'reference' => true |
|
| 486 |
), |
|
| 487 |
'microreferencePart' => array( |
|
| 488 |
'microreference' => true, |
|
| 489 |
), |
|
| 490 |
'statusPart' => array( |
|
| 491 |
'status' => true, |
|
| 492 |
), |
|
| 493 |
'descriptionPart' => array( |
|
| 494 |
'description' => true, |
|
| 495 |
), |
|
| 496 |
); |
|
| 493 |
// default: $partdef = array(
|
|
| 494 |
// 'namePart' => array(
|
|
| 495 |
// 'name' => true,
|
|
| 496 |
// 'authorTeam' => true
|
|
| 497 |
// ),
|
|
| 498 |
// 'referencePart' => array(
|
|
| 499 |
// 'reference' => true
|
|
| 500 |
// ),
|
|
| 501 |
// 'microreferencePart' => array(
|
|
| 502 |
// 'microreference' => true,
|
|
| 503 |
// ),
|
|
| 504 |
// 'statusPart' => array(
|
|
| 505 |
// 'status' => true,
|
|
| 506 |
// ),
|
|
| 507 |
// 'descriptionPart' => array(
|
|
| 508 |
// 'description' => true,
|
|
| 509 |
// ),
|
|
| 510 |
// );
|
|
| 497 | 511 |
} |
| 498 | 512 |
} |
| 499 | 513 |
return $partdef; |
| ... | ... | |
| 503 | 517 |
|
| 504 | 518 |
function theme_cdm_taxonName($taxonName, $nameLink = NULL, $refenceLink = NULL, |
| 505 | 519 |
$show_annotations = true, $is_type_designation = false, $skiptags = array()){
|
| 506 |
|
|
| 507 | 520 |
$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink); |
| 508 | 521 |
$partDefinition = get_partDefinition($taxonName->class); |
| 509 | 522 |
|
| ... | ... | |
| 518 | 531 |
} |
| 519 | 532 |
|
| 520 | 533 |
$firstEntryIsValidNamePart = is_array($taxonName->taggedName) |
| 521 |
&& is_string($taxonName->taggedName[0]->text) |
|
| 522 |
&& $taxonName->taggedName[0]->text != '' |
|
| 523 |
&& $taxonName->taggedName[0]->type == 'name'; |
|
| 534 |
&& is_string($taxonName->taggedName[0]->text)
|
|
| 535 |
&& $taxonName->taggedName[0]->text != ''
|
|
| 536 |
&& $taxonName->taggedName[0]->type == 'name';
|
|
| 524 | 537 |
|
| 525 | 538 |
// got to use second entry as first one, see ToDo comment below ... |
| 526 | 539 |
if($firstEntryIsValidNamePart){
|
| modules/cdm_dataportal/theme/cdm_dataportal.page.theme | ||
|---|---|---|
| 905 | 905 |
return $out; |
| 906 | 906 |
} |
| 907 | 907 |
|
| 908 |
|
|
| 909 |
|
|
| 910 |
|
|
| 911 |
function theme_cdm_polytomousKey_page($polytomousKey){
|
|
| 912 |
|
|
| 913 |
drupal_set_title($polytomousKey->titleCache); |
|
| 914 |
|
|
| 915 |
$out = theme("cdm_IdentificationKey", $polytomousKey, false);
|
|
| 916 |
|
|
| 917 |
// key nodes in linked style |
|
| 918 |
$out .= theme('cdm_polytomousKey', $polytomousKey);
|
|
| 919 |
|
|
| 920 |
return $out; |
|
| 921 |
} |
|
| 922 |
|
|
| 908 | 923 |
/** |
| 909 | 924 |
* Allows theming of the taxon page tabs |
| 910 | 925 |
* |
| themes/diptera/template.php | ||
|---|---|---|
| 7 | 7 |
$glue = ''; |
| 8 | 8 |
$sortOutArray = false; |
| 9 | 9 |
$enclosingHtml = 'ul'; |
| 10 |
|
|
| 11 |
|
|
| 10 |
|
|
| 11 |
|
|
| 12 | 12 |
RenderHints::pushToRenderStack('cdm_descriptionElements');
|
| 13 |
|
|
| 14 |
|
|
| 13 |
|
|
| 14 |
|
|
| 15 | 15 |
// only for diptera |
| 16 | 16 |
if(isset($descriptionElements[0]) && $descriptionElements[0]->feature->uuid == UUID_CITATION ) {
|
| 17 | 17 |
foreach($descriptionElements as $element){
|
| 18 | 18 |
$tokens = split(":", $element->multilanguageText_L10n->text);
|
| 19 | 19 |
if(count($tokens) == 2){
|
| 20 |
// token[0]: taxon name; token[1]: note;
|
|
| 20 |
// token[0]: taxon name; token[1]: note; |
|
| 21 | 21 |
$element->multilanguageText_L10n->text = $tokens[1] . ' [<span class="name">' . $tokens[0] . '</span>]'; |
| 22 | 22 |
} |
| 23 | 23 |
if(isset($element->citation->datePublished->start)){
|
| ... | ... | |
| 30 | 30 |
$descriptionElements = $elementMap; |
| 31 | 31 |
} |
| 32 | 32 |
// --- |
| 33 |
|
|
| 33 |
|
|
| 34 | 34 |
foreach($descriptionElements as $element){
|
| 35 | 35 |
if($element->class == 'TextData'){
|
| 36 | 36 |
$outArray[] = theme('cdm_descriptionElementTextData', $element);
|
| ... | ... | |
| 53 | 53 |
|
| 54 | 54 |
/** |
| 55 | 55 |
* Allows theaming of the taxon page tabs |
| 56 |
*
|
|
| 56 |
* |
|
| 57 | 57 |
* @param $tabname |
| 58 | 58 |
* @return unknown_type |
| 59 | 59 |
*/ |
| 60 | 60 |
function diptera_cdm_taxonpage_tab($tabname){
|
| 61 | 61 |
switch($tabname){
|
| 62 | 62 |
case 'Synonymy' : return t('Nomenclature'); break;
|
| 63 |
default : return t($tabname);
|
|
| 63 |
default : return t($tabname); |
|
| 64 | 64 |
} |
| 65 | 65 |
} |
| 66 | 66 |
|
| ... | ... | |
| 73 | 73 |
|
| 74 | 74 |
|
| 75 | 75 |
function diptera_get_partDefinition($nameType){
|
| 76 |
|
|
| 76 |
|
|
| 77 | 77 |
if($nameType == 'ZoologicalName'){
|
| 78 | 78 |
return array( |
| 79 | 79 |
'namePart' => array( |
| ... | ... | |
| 99 | 99 |
} |
| 100 | 100 |
|
| 101 | 101 |
function diptera_get_nameRenderTemplate($renderPath){
|
| 102 |
|
|
| 102 |
|
|
| 103 | 103 |
switch ($renderPath){
|
| 104 |
case 'taxon_page_title':
|
|
| 104 |
case 'taxon_page_title': |
|
| 105 | 105 |
$template = array( |
| 106 | 106 |
'namePart' => array('#uri'=>true),
|
| 107 | 107 |
); |
| 108 | 108 |
break; |
| 109 | 109 |
case 'acceptedFor': |
| 110 |
case 'list_of_taxa': |
|
| 110 |
case 'list_of_taxa': |
|
| 111 |
case 'polytomousKey': |
|
| 111 | 112 |
$template = array( |
| 112 | 113 |
'namePart' => array('#uri'=>true),
|
| 113 | 114 |
'referencePart' => array('#uri'=>true),
|
| 114 | 115 |
); |
| 115 | 116 |
break; |
| 116 |
case 'typedesignations':
|
|
| 117 |
case 'typedesignations': |
|
| 117 | 118 |
$template = array( |
| 118 | 119 |
'namePart' => array('#uri'=>true),
|
| 119 | 120 |
'referencePart' => array('#uri'=>true)
|
| ... | ... | |
| 121 | 122 |
break; |
| 122 | 123 |
case 'taxon_page_synonymy': |
| 123 | 124 |
case 'related_taxon': |
| 124 |
default:
|
|
| 125 |
default: |
|
| 125 | 126 |
$template = array( |
| 126 | 127 |
'namePart' => array('#uri'=>true),
|
| 127 | 128 |
'referencePart' => array('#uri'=>true),
|
| themes/garland_cichorieae/template.php | ||
|---|---|---|
| 69 | 69 |
} |
| 70 | 70 |
*/ |
| 71 | 71 |
function garland_cichorieae_cdm_descriptionElementTextData($element, $asListElement, $feature_uuid){
|
| 72 |
|
|
| 72 |
|
|
| 73 | 73 |
$description = str_replace("\n", "<br/>", $element->multilanguageText_L10n->text);
|
| 74 | 74 |
$sourceRefs = ''; |
| 75 | 75 |
$result = array(); |
| ... | ... | |
| 77 | 77 |
$res_date; |
| 78 | 78 |
$no_links = false; |
| 79 | 79 |
$default_theme = variable_get('theme_default', 'garland_cichorieae');
|
| 80 |
|
|
| 80 |
|
|
| 81 | 81 |
if (($default_theme == 'flora_malesiana' || $default_theme == 'flore_afrique_centrale') |
| 82 | 82 |
&& $element->feature->titleCache == 'Citation'){
|
| 83 |
$asListElement = true;
|
|
| 83 |
$asListElement = true; |
|
| 84 | 84 |
}elseif ($element->feature->uuid == UUID_CHROMOSOMES_NUMBERS){
|
| 85 | 85 |
$asListElement = true; |
| 86 | 86 |
}else{
|
| ... | ... | |
| 224 | 224 |
*/ |
| 225 | 225 |
// add annotations as footnote key |
| 226 | 226 |
//$out .= theme('cdm_annotations_as_footnotekeys', $element); move above
|
| 227 |
|
|
| 227 |
|
|
| 228 | 228 |
return $out; |
| 229 | 229 |
} |
| 230 | 230 |
|
| ... | ... | |
| 493 | 493 |
|
| 494 | 494 |
switch($renderPath) {
|
| 495 | 495 |
case 'taxon_page_title': |
| 496 |
case 'polytomousKey': |
|
| 496 | 497 |
$template = array( |
| 497 | 498 |
'namePart' => array('#uri'=>true)
|
| 498 | 499 |
); |
| themes/garland_cichorieae/theme-settings.php | ||
|---|---|---|
| 1 | 1 |
<?php |
| 2 |
|
|
| 2 |
/** |
|
| 3 |
* see http://drupal.org/node/177868 |
|
| 4 |
*/ |
|
| 3 | 5 |
/** |
| 4 | 6 |
* Implementation of THEMEHOOK_settings() function. |
| 5 | 7 |
* |
| ... | ... | |
| 10 | 12 |
*/ |
| 11 | 13 |
function phptemplate_settings($saved_settings) {
|
| 12 | 14 |
|
| 15 |
$key = sub_theme(); |
|
| 13 | 16 |
|
| 14 | 17 |
$defaults = array( |
| 15 | 18 |
'default_banner_right' => 1, |
| ... | ... | |
| 22 | 25 |
if ($file = file_check_upload('banner_right_upload')) {
|
| 23 | 26 |
if ($info = image_get_info($file->filepath)) {
|
| 24 | 27 |
$parts = pathinfo($file->filename); |
| 25 |
//$filename = ($key) ? str_replace('/', '_', $key) .'_logo.'. $parts['extension'] : 'logo.'. $parts['extension'];
|
|
| 26 |
$filename = 'banner_right.'. $parts['extension']; |
|
| 28 |
$filename = ($key) ? str_replace('/', '_', $key) .'_banner_right.'. $parts['extension'] : '_banner_right.'. $parts['extension'];
|
|
| 27 | 29 |
|
| 28 | 30 |
if ($file = file_save_upload('banner_right_upload', $filename, 1)) {
|
| 29 | 31 |
$_POST['default_banner_right'] = 0; |
| 30 | 32 |
$_POST['banner_right_path'] = $file->filepath; |
| 31 |
//$_POST['toggle_banner_right'] = 1;
|
|
| 33 |
$form["#after_build"][] = "banner_right_after_build";
|
|
| 32 | 34 |
} |
| 33 | 35 |
} |
| 34 | 36 |
else {
|
| ... | ... | |
| 36 | 38 |
} |
| 37 | 39 |
} |
| 38 | 40 |
|
| 39 |
$form['default_banner_right'] = array( |
|
| 40 |
'#type' => 'checkbox', |
|
| 41 |
'#title' => t('Use the right default header image'),
|
|
| 42 |
'#default_value' => $settings['default_banner_right'], |
|
| 43 |
'#tree' => FALSE, |
|
| 44 |
'#description' => t('Check here if you want the theme to use the right header image supplied with it.')
|
|
| 45 |
); |
|
| 46 |
|
|
| 47 |
$form['banner_right_path'] = array( |
|
| 48 |
'#type' => 'textfield', |
|
| 49 |
'#title' => t('Right banner image path'),
|
|
| 50 |
'#default_value' => $settings['banner_right_path'], |
|
| 51 |
); |
|
| 52 |
|
|
| 53 |
$form['banner_right_upload'] = array( |
|
| 54 |
'#type' => 'file', |
|
| 55 |
'#title' => t('Upload new right banner image'),
|
|
| 56 |
); |
|
| 41 |
if (true || $file) {
|
|
| 42 |
$form['default_banner_right'] = array( |
|
| 43 |
'#type' => 'checkbox', |
|
| 44 |
'#title' => t('Use the right default header image'),
|
|
| 45 |
'#default_value' => $settings['default_banner_right'], |
|
| 46 |
'#tree' => FALSE, |
|
| 47 |
'#description' => t('Check here if you want the theme to use the right header image supplied with it.')
|
|
| 48 |
); |
|
| 49 |
|
|
| 50 |
$form['banner_right_path'] = array( |
|
| 51 |
'#type' => 'textfield', |
|
| 52 |
'#title' => t('Right banner image path'),
|
|
| 53 |
'#default_value' => $settings['banner_right_path'], |
|
| 54 |
'#maxlength' => 255 |
|
| 55 |
); |
|
| 56 |
|
|
| 57 |
$form['banner_right_upload'] = array( |
|
| 58 |
'#type' => 'file', |
|
| 59 |
'#title' => t('Upload new right banner image'),
|
|
| 60 |
); |
|
| 61 |
} |
|
| 62 |
|
|
| 63 |
return $form; |
|
| 64 |
} |
|
| 65 |
|
|
| 57 | 66 |
|
| 67 |
function banner_right_after_build(&$form, &$form_values) {
|
|
| 68 |
$form["#post"]["banner_right_path"] = $_POST['banner_right_path']; |
|
| 58 | 69 |
return $form; |
| 59 |
} |
|
| 70 |
} |
|
| 71 |
|
|
| 72 |
|
|
| themes/palmweb_2/template.php | ||
|---|---|---|
| 266 | 266 |
case 'list_of_taxa': |
| 267 | 267 |
case 'taxon_page_synonymy': |
| 268 | 268 |
case 'related_taxon': |
| 269 |
case 'polytomousKey': |
|
| 269 | 270 |
case '#DEFAULT': |
| 270 | 271 |
$template = array( |
| 271 | 272 |
'namePart' => array('#uri'=>true),
|
Also available in: Unified diff
displaying polytomous keys (fixes #2152)