Revision 48650990
Added by Andreas Kohlbecker almost 14 years ago
| modules/cdm_dataportal/cdm_api/cdm_api.module | ||
|---|---|---|
| 484 | 484 |
case 'Media': |
| 485 | 485 |
$ws_base_uri = CDM_WS_MEDIA; |
| 486 | 486 |
break; |
| 487 |
default: |
|
| 488 |
trigger_error('Unsupported CDM Class - no annotations available', E_USER_ERROR);
|
|
| 487 |
case 'ReferenceBase': |
|
| 488 |
$ws_base_uri = CDM_WS_REFERENCE; |
|
| 489 |
break; |
|
| 490 |
default: trigger_error('Unsupported CDM Class - no annotations available for ' . $cdmBase->class, E_USER_ERROR);
|
|
| 489 | 491 |
return; |
| 490 | 492 |
} |
| 491 | 493 |
return cdm_compose_url($ws_base_uri, array($cdmBase->uuid, 'annotation')); |
| ... | ... | |
| 598 | 600 |
|
| 599 | 601 |
if(!$featureTree){
|
| 600 | 602 |
drupal_set_message('No \'FeatureTree\' has been set so far. '
|
| 601 |
.'In order to display descriptive data of your taxa, please select a \'FeatureTree\' in the '.l('CDM Dataportal Ssettings', 'admin/settings/cdm_dataportal/general'), 'warning');
|
|
| 603 |
.'In order to see the species profiles of your taxa, please select a \'FeatureTree\' in the '.l('CDM Dataportal Settings', 'admin/settings/cdm_dataportal/general'), 'warning');
|
|
| 602 | 604 |
return false; |
| 603 | 605 |
} |
| 604 | 606 |
|
| modules/cdm_dataportal/cdm_api/webservice_uris.php | ||
|---|---|---|
| 79 | 79 |
*/ |
| 80 | 80 |
define('CDM_WS_FEATURETREE', 'featuretree/$0');
|
| 81 | 81 |
|
| 82 |
//define('CDM_WS_FEATURETREE_CHILDREN', 'featuretree/$0/children');
|
|
| 83 |
|
|
| 82 | 84 |
define('CDM_WS_FEATURETREES', 'featuretree');
|
| 83 | 85 |
|
| 84 | 86 |
define('CDM_WS_GEOSERVICE_DISTRIBUTIONMAP', 'geo/map/distribution/$0');
|
| modules/cdm_dataportal/cdm_dataportal.module | ||
|---|---|---|
| 48 | 48 |
define('CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS', 'cdm_dataportal_display_name_relations');
|
| 49 | 49 |
define('CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT', 1);
|
| 50 | 50 |
define('CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS_DEFAULT', 1);
|
| 51 |
define(CDM_DATAPORTAL_FEATURETREE_UUID, CDM_DATAPORTAL_FEATURETREE_UUID); |
|
| 51 | 52 |
|
| 52 | 53 |
|
| 53 | 54 |
|
| ... | ... | |
| 695 | 696 |
'#collapsed' => TRUE, |
| 696 | 697 |
); |
| 697 | 698 |
|
| 698 |
$form['cdm_dataportal']['feature_tree']['cdm_dataportal_featuretree_uuid'] = array(
|
|
| 699 |
$form['cdm_dataportal']['feature_tree'][CDM_DATAPORTAL_FEATURETREE_UUID] = array(
|
|
| 699 | 700 |
'#type' => 'select', |
| 700 | 701 |
'#title' => t('Available FeatureTrees'),
|
| 701 |
'#default_value' => variable_get('cdm_dataportal_featuretree_uuid', UUID_DEFAULT_FEATURETREE),
|
|
| 702 |
'#default_value' => variable_get(CDM_DATAPORTAL_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE),
|
|
| 702 | 703 |
'#options' => _get_feature_trees(), |
| 703 | 704 |
'#description' => t('Select a FeatureTree for this webservice.'
|
| 704 | 705 |
//.' If there is no applicable FeatureTree you can create a new one using the <a href="">FeatureTreeManager</a>' |
| modules/cdm_dataportal/classes/footnotemanager.php | ||
|---|---|---|
| 58 | 58 |
* @param $themeArguments |
| 59 | 59 |
* @return unknown_type |
| 60 | 60 |
*/ |
| 61 |
public static function addNewFootnote($footnoteListKey, $object, $theme = NULL, $themeArguments = array()){
|
|
| 61 |
public static function addNewFootnote($footnoteListKey, $object = null, $theme = NULL, $themeArguments = array()){
|
|
| 62 | 62 |
|
| 63 |
if(!$object){
|
|
| 64 |
return false; |
|
| 65 |
} |
|
| 66 |
|
|
| 63 | 67 |
if(!array_key_exists($footnoteListKey, self::$fnstore)){
|
| 64 | 68 |
self::$fnstore[$footnoteListKey] = array(); |
| 65 | 69 |
} |
| modules/cdm_dataportal/js/footnotes.js | ||
|---|---|---|
| 1 | 1 |
if (Drupal.jsEnabled) {
|
| 2 |
$(document).ready($(document).ready(function() {
|
|
| 2 |
$(document).ready(function() {
|
|
| 3 | 3 |
|
| 4 | 4 |
function getFootnoteClassName(object){
|
| 5 | 5 |
return '.'+$(object).attr('href').substr(1);
|
| modules/cdm_dataportal/theme/cdm_dataportal.common.theme | ||
|---|---|---|
| 109 | 109 |
* TODO it should be configurable which objects can be annotated as this might differ in dataportals |
| 110 | 110 |
* |
| 111 | 111 |
*/ |
| 112 |
function theme_cdm_annotation($cdmBase){
|
|
| 112 |
function theme_cdm_annotations($cdmBase){
|
|
| 113 |
|
|
| 113 | 114 |
|
| 114 |
// $annotationUrl = cdm_compose_annotations_url($cdmBase); |
|
| 115 |
// |
|
| 116 |
// if($annotationUrl){
|
|
| 117 |
// drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cdm_annotations.js');
|
|
| 118 |
// drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/jquery.form.js');
|
|
| 119 |
// $annotationProxyUrl = url('cdm_api/proxy/'. urlencode($annotationUrl).'/cdm_annotation_content');
|
|
| 120 |
// |
|
| 121 |
// $out = ' <span class="annotation">'; |
|
| 122 |
// $out .= '<span class="annotation_toggle" rel="'.$annotationProxyUrl.'">+</span>'; |
|
| 123 |
// |
|
| 124 |
// |
|
| 125 |
// $out .= '<div class="annotation_box"></div>'; |
|
| 126 |
// $out .= '</span>'; |
|
| 127 |
// } |
|
| 128 | 115 |
$annotationUrl = cdm_compose_annotations_url($cdmBase); |
| 129 | 116 |
if($annotationUrl){
|
| 130 | 117 |
$annotationPager = cdm_ws_get($annotationUrl, null, null, null, true); |
| 131 |
foreach($annotationPager->records as $annotation){
|
|
| 132 |
$footnoteKey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $annotation->text); |
|
| 133 |
$out .= (isset($out)? ',' : '') . theme('cdm_footnote_key', $footnoteKey);
|
|
| 118 |
if($annotationPager->count > 0){
|
|
| 119 |
foreach($annotationPager->records as $annotation){
|
|
| 120 |
$footnoteKey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $annotation->text); |
|
| 121 |
$out .= (isset($out)? ',' : '') . theme('cdm_footnote_key', $footnoteKey);
|
|
| 122 |
} |
|
| 134 | 123 |
} |
| 135 | 124 |
} |
| 136 | 125 |
|
| modules/cdm_dataportal/theme/cdm_dataportal.descriptions.theme | ||
|---|---|---|
| 150 | 150 |
$description = str_replace("\n", "<br/>", $element->multilanguageText_L10n->text);
|
| 151 | 151 |
$sourceRefs = ''; |
| 152 | 152 |
$result = array(); |
| 153 |
$res_text;
|
|
| 153 |
$out;
|
|
| 154 | 154 |
$res_author; |
| 155 | 155 |
$res_date; |
| 156 | 156 |
|
| ... | ... | |
| 181 | 181 |
} |
| 182 | 182 |
|
| 183 | 183 |
if ($asListElement){
|
| 184 |
$res_text = '<li class="descriptionText">' . $name_used_in_source_link_to_show;
|
|
| 184 |
$out = '<li class="descriptionText">' . $name_used_in_source_link_to_show;
|
|
| 185 | 185 |
//adding ":" if necesary |
| 186 | 186 |
if ($name_used_in_source_link_to_show && ($description || $sourceRefs)){
|
| 187 |
$res_text .= ': ';
|
|
| 187 |
$out .= ': ';
|
|
| 188 | 188 |
} |
| 189 |
$res_text .= $description . $sourceRefs . '</li>';
|
|
| 189 |
$out .= $description . $sourceRefs . '</li>';
|
|
| 190 | 190 |
}else{
|
| 191 |
$res_text = $description . $sourceRefs . ' (name in source: '. $name_used_in_source_link_to_show . ')';
|
|
| 191 |
$out = $description . $sourceRefs . ' (name in source: '. $name_used_in_source_link_to_show . ')';
|
|
| 192 | 192 |
} |
| 193 |
return $res_text; |
|
| 193 |
|
|
| 194 |
// add annotations as footnote key |
|
| 195 |
$out .= theme('cdm_annotations', $element);
|
|
| 196 |
return $out; |
|
| 194 | 197 |
} |
| 195 | 198 |
|
| 196 | 199 |
|
| ... | ... | |
| 206 | 209 |
$enclosingHtml = 'ul'; |
| 207 | 210 |
$distributionElements = array(); |
| 208 | 211 |
|
| 212 |
RenderHints::pushToRenderStack('cdm_descriptionElements');
|
|
| 213 |
|
|
| 209 | 214 |
foreach($descriptionElements as $descriptionElement){
|
| 210 | 215 |
|
| 211 | 216 |
if($descriptionElement->feature->uuid == UUID_DISTRIBUTION){
|
| ... | ... | |
| 233 | 238 |
|
| 234 | 239 |
$outArray[] = theme('cdm_descriptionElementDistribution', $distributionElements);
|
| 235 | 240 |
|
| 236 |
|
|
| 237 | 241 |
// take the feature of the last $descriptionElement |
| 238 | 242 |
$feature = $descriptionElement->feature; |
| 239 | 243 |
$out = theme('cdm_descriptionElementArray', $outArray, $feature, $glue, $sortOutArray, $enclosingHtml);
|
| 244 |
|
|
| 240 | 245 |
$out .= '<div class="footnote_list">'. FootnoteManager::renderFootnoteList($featureUuid) . '</div>'; |
| 246 |
|
|
| 247 |
RenderHints::popFromRenderStack(); |
|
| 248 |
|
|
| 241 | 249 |
return $out; |
| 242 | 250 |
} |
| 243 | 251 |
|
| ... | ... | |
| 253 | 261 |
|
| 254 | 262 |
foreach($descriptionElements as $descriptionElement){
|
| 255 | 263 |
//$footnoteKey = FootnoteManager::addNewFootnote($descriptionElement->feature->uuid, $descriptionElement->area->representation_L10n); |
| 256 |
$footnoteKeyList = ''; |
|
| 257 |
foreach($descriptionElement->sources as $source){
|
|
| 258 |
break; |
|
| 259 |
$footnoteKey = FootnoteManager::addNewFootnote($descriptionElement->feature->uuid, $source, 'cdm_DescriptionElementSource'); |
|
| 260 |
$footnoteKeyList .= theme('cdm_footnode_key', $footnoteKey) . ' ';
|
|
| 261 |
} |
|
| 262 |
$out .= $descriptionElement->area->representation_L10n . $footnoteKeyList . $separator; |
|
| 264 |
// $footnoteKeyList = ''; |
|
| 265 |
// foreach($descriptionElement->sources as $source){
|
|
| 266 |
// $footnoteKey = FootnoteManager::addNewFootnote($descriptionElement->feature->uuid, theme('cdm_DescriptionElementSource', $source));
|
|
| 267 |
// $footnoteKeyList .= theme('cdm_footnode_key', $footnoteKey) . ' ';
|
|
| 268 |
// } |
|
| 269 |
$out .= $descriptionElement->area->representation_L10n . $footnoteKeyList . $separator; |
|
| 263 | 270 |
} |
| 264 | 271 |
$out = substr($out, 0, strlen($out)-strlen($separator) ); |
| 265 | 272 |
|
| ... | ... | |
| 283 | 290 |
|
| 284 | 291 |
function theme_cdm_DescriptionElementSource($descriptionElementSource, $doLink = TRUE){
|
| 285 | 292 |
|
| 286 |
//ev. delegate to theme_cdm_ReferencedEntityBase |
|
| 287 |
$out = ''; |
|
| 288 |
if($descriptionElementSource->citation){
|
|
| 289 |
$reference = $descriptionElementSource->citation->titleCache; |
|
| 290 |
if($doLink){
|
|
| 291 |
$out = l('<span class="reference">'.$reference.'</span>'
|
|
| 292 |
, path_to_reference($descriptionElementSource->citation->uuid) |
|
| 293 |
, array("class"=>"reference")
|
|
| 294 |
, NULL, NULL, FALSE ,TRUE); |
|
| 295 |
} else {
|
|
| 296 |
$out = $reference; |
|
| 297 |
} |
|
| 298 |
if($descriptionElementSource->citationMicroReference){
|
|
| 299 |
$out .= ': '. $descriptionElementSource->citationMicroReference; |
|
| 300 |
} |
|
| 301 |
} |
|
| 293 |
$out = theme('cdm_reference', $descriptionElementSource->citation, $descriptionElementSource->citationMicroReference, TRUE);
|
|
| 294 |
|
|
| 295 |
// add annotations as footnote key |
|
| 296 |
$out .= theme('cdm_annotations', $descriptionElementSource->citation);
|
|
| 302 | 297 |
return $out; |
| 303 | 298 |
} |
| 304 | 299 |
|
| modules/cdm_dataportal/theme/cdm_dataportal.name.theme | ||
|---|---|---|
| 64 | 64 |
$shortCitation = $author_team->titleCache; |
| 65 | 65 |
$shortCitation .= (strlen($shortCitation) > 0 ? ' ' : '' ). partialToYear($std->citation->datePublished->start); |
| 66 | 66 |
if(strlen($shortCitation) == 0){
|
| 67 |
$shortCitation = theme('cdm_reference',$std->citation );
|
|
| 67 |
$shortCitation = theme('cdm_reference', $std->citation);
|
|
| 68 | 68 |
$missingShortCitation = true; |
| 69 | 69 |
} |
| 70 | 70 |
$typeReference .= ' (' . t('designated by');
|
| ... | ... | |
| 413 | 413 |
$out .= '</span>'; |
| 414 | 414 |
|
| 415 | 415 |
// add annotations |
| 416 |
$out .= theme('cdm_annotation', $taxonName);
|
|
| 416 |
$out .= theme('cdm_annotations', $taxonName);
|
|
| 417 | 417 |
|
| 418 | 418 |
return $out; |
| 419 | 419 |
} |
| modules/cdm_dataportal/theme/cdm_dataportal.page.theme | ||
|---|---|---|
| 109 | 109 |
// --- DESCRIPTION --- // |
| 110 | 110 |
if($page_part == 'description' || $page_part == 'all'){
|
| 111 | 111 |
|
| 112 |
$featureTree = cdm_ws_get(CDM_WS_FEATURETREE, variable_get('cdm_dataportal_featuretree_uuid', false));
|
|
| 112 |
$featureTree = cdm_ws_get(CDM_WS_FEATURETREE, variable_get(CDM_DATAPORTAL_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE));
|
|
| 113 | 113 |
$taxonDescriptions = cdm_ws_get(CDM_WS_PORTAL_TAXON_DESCRIPTIONS, $taxon->uuid); |
| 114 | 114 |
$mergedTrees = cdm_ws_descriptions_by_featuretree($featureTree, $taxonDescriptions, variable_get('cdm_dataportal_descriptions_separated', FALSE));
|
| 115 | 115 |
|
| ... | ... | |
| 197 | 197 |
$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_TAXON_NAMETYPEDESIGNATIONS, $taxon->uuid); |
| 198 | 198 |
if($typeDesignations){
|
| 199 | 199 |
$out .= theme('cdm_typedesignations', $typeDesignations);
|
| 200 |
//$out .= l('test', path_to_name($typeDesignations[0]->typeName->uuid), array(), NULL, NULL, FALSE, TRUE);
|
|
| 201 | 200 |
} |
| 202 | 201 |
} else {
|
| 203 | 202 |
// reder the homotypicSynonymyGroup including the type information |
| 204 | 203 |
$out .= theme('cdm_homotypicSynonymyGroup', $synomymie->homotypicSynonymsByHomotypicGroup);
|
| 205 | 204 |
} |
| 205 |
|
|
| 206 | 206 |
if($synomymie->heterotypicSynonymyGroups) {
|
| 207 | 207 |
foreach($synomymie->heterotypicSynonymyGroups as $homotypicalGroup){
|
| 208 | 208 |
$out .= theme('cdm_heterotypicSynonymyGroup', $homotypicalGroup);
|
| modules/cdm_dataportal/theme/cdm_dataportal.references.theme | ||
|---|---|---|
| 17 | 17 |
$out .= '<ul>'; |
| 18 | 18 |
foreach($referencePager->records as $reference){
|
| 19 | 19 |
$reference->fullCitation = $reference->titleCache; //FIXME remove hack for matching cdm entity to STO |
| 20 |
$out .= '<li>'.theme('cdm_reference', $reference, TRUE).'</li>';
|
|
| 20 |
$out .= '<li>'.theme('cdm_reference', $reference, null, TRUE).'</li>';
|
|
| 21 | 21 |
} |
| 22 | 22 |
$out .= '</ul>'; |
| 23 | 23 |
$out .= theme('cdm_pager', $referencePager, $path, $parameters);
|
| ... | ... | |
| 29 | 29 |
|
| 30 | 30 |
|
| 31 | 31 |
/** |
| 32 |
* @deprecated ?? |
|
| 32 |
* used by |
|
| 33 |
* - theme_cdm_typedesignations |
|
| 34 |
* - theme_cdm_reference_pager |
|
| 35 |
* - theme_cdm_taxonRelationships |
|
| 36 |
* |
|
| 33 | 37 |
*/ |
| 34 |
function theme_cdm_reference($reference, $linkToReference = FALSE, $style = NULL ){
|
|
| 38 |
function theme_cdm_reference($reference, $microReference = null, $doLink = FALSE, $referenceStyle = NULL ){
|
|
| 35 | 39 |
|
| 36 | 40 |
$author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid); |
| 37 |
if($style == "ZoologicalName"){
|
|
| 41 |
if($style == "zoology"){
|
|
| 38 | 42 |
$year = partialToYear($reference->datePublished->start); |
| 39 |
//$citation = $reference->authorTeam->titleCache.($year ? ', '.$year : ''); |
|
| 40 | 43 |
$citation = $author_team->titleCache . ($year ? ', '.$year : ''); |
| 41 | 44 |
} else {
|
| 42 |
//$citation = $reference->titleCache; |
|
| 43 |
$citation = $author_team->titleCache; |
|
| 45 |
$citation = $reference->titleCache; |
|
| 44 | 46 |
} |
| 45 |
if($linkToReference){
|
|
| 46 |
return l('<span class="reference">'.$citation.'</span>', "/cdm_dataportal/reference/".$reference->uuid, array("class"=>"reference"), NULL, NULL, FALSE ,TRUE);
|
|
| 47 |
} else {
|
|
| 48 |
return '<span class="reference">'.$citation.'</span>'; |
|
| 47 |
if($doLink){
|
|
| 48 |
$out = l('<span class="reference">'.$citation.'</span>'
|
|
| 49 |
, path_to_reference($reference->uuid) |
|
| 50 |
, array("class"=>"reference")
|
|
| 51 |
, NULL, NULL, FALSE ,TRUE); |
|
| 52 |
} else {
|
|
| 53 |
$out = '<span class="reference">'.$citation.'</span>'; |
|
| 49 | 54 |
} |
| 55 |
if(!empty($descriptionElementSource->citationMicroReference)){
|
|
| 56 |
$out .= ': '. $descriptionElementSource->citationMicroReference; |
|
| 57 |
} |
|
| 58 |
|
|
| 50 | 59 |
} |
| modules/cdm_dataportal/theme/cdm_dataportal.taxon.theme | ||
|---|---|---|
| 124 | 124 |
} |
| 125 | 125 |
$out .= '</ul>'; |
| 126 | 126 |
|
| 127 |
$out .= theme('cdm_footnotes', $footnoteListKey, 'div');
|
|
| 128 | 127 |
RenderHints::popFromRenderStack(); |
| 129 | 128 |
return $out; |
| 130 | 129 |
} |
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