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Revision 12196fd5

Added by Francisco Revilla over 13 years ago

type designations with footnotes

View differences:

modules/cdm_dataportal/cdm_api/cdm_api.module
21 21 
require_once ('webservice_uris.php');
22 22 
require_once ('cdm_node.php');
23 23 

  		




  24
  
  
    
define('DEFAULT_TAXONTREE_RANKLIMIT', '');//TODO Genus UUID


  		




  
  24
  
    
define('DEFAULT_TAXONTREE_RANKLIMIT', '1b11c34c-48a8-4efa-98d5-84f7f66ef43a');//TODO Genus UUID


  		




  25
  25
  
    

  		




  26
  26
  
    

  		




  27
  27
  
    
/**


  		




  ......




  98
  98
  
    
  $form['cdm_webservice']['taxontree_ranklimit'] =  array(


  		




  99
  99
  
    
    '#type'          => 'select',


  		




  100
  100
  
    
    '#title'         => t('Rank of highest displayed taxon'),


  		




  101
  
  
    
    '#default_value' => variable_get('taxontree_ranklimit', DEFAULT_TAXONTREE_RANKLIMIT_UUID),


  		




  
  101
  
    
    '#default_value' => variable_get('taxontree_ranklimit', DEFAULT_TAXONTREE_RANKLIMIT), //before DEFAULT_TAXONTREE_RANKLIMIT_UUID


  		




  102
  102
  
    
    '#options'       => cdm_rankVocabulary_as_option(),


  		




  103
  103
  
    
    '#description'   => t('The rank of the highest displayed taxon in the taxontree.'),


  		




  104
  104
  
    
  );


  		












  

    
      modules/cdm_dataportal/cdm_api/webservice_uris.php
    
  





  8
  8
  
    

  		




  9
  9
  
    
define('CDM_WS_TAXON', 'taxon');


  		




  10
  10
  
    

  		




  11
  
  
    
define('CDM_WS_NAME_TYPEDESIGNATIONS', 'portal/name/$0/typeDesignations');


  		




  
  11
  
    
define('CDM_WS_NAME_TYPEDESIGNATIONS', 'name/$0/typeDesignations');


  		




  
  12
  
    

  		




  
  13
  
    
define('CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS', 'portal/name/$0/typeDesignations');


  		




  12
  14
  
    

  		




  13
  15
  
    
define('CDM_WS_PORTAL_TAXON_NAMETYPEDESIGNATIONS', 'portal/taxon/$0/nameTypeDesignations');


  		




  14
  16
  
    

  		












  

    
      modules/cdm_dataportal/classes/footnotemanager.php
    
  





  33
  33
  
    
      return array_key_exists($footnoteListKey, self::$fnstore) ? self::$fnstore[$footnoteListKey] : NULL;


  		




  34
  34
  
    
    }


  		




  35
  35
  
    
    


  		




  
  36
  
    
    /**


  		




  
  37
  
    
     * 


  		




  
  38
  
    
     * @param $footnoteListKey a string as key to the list of footnotes


  		




  
  39
  
    
     * @return


  		




  
  40
  
    
     */


  		




  
  41
  
    
    public static function removeFootnoteList($footnoteListKey){


  		




  
  42
  
    
      if(array_key_exists($footnoteListKey, self::$fnstore)) {


  		




  
  43
  
    
	      unset(self::$fnstore[$footnoteListKey]);


  		




  
  44
  
    
      }


  		




  
  45
  
    
    }


  		




  
  46
  
    
    


  		




  36
  47
  
    
    /**


  		




  37
  48
  
    
     * 


  		




  38
  49
  
    
     * @param $footnoteListKey


  		












  

    
      modules/cdm_dataportal/theme/cdm_dataportal.common.theme
    
  





  188
  188
  
    
function theme_cdm_footnotes($footnoteListKey, $enclosingTag = 'span'){


  		




  189
  189
  
    
	


  		




  190
  190
  
    
	$out = '<'.$enclosingTag.' class="footnotes footnotes-'.$footnoteListKey.' ">' . FootnoteManager::renderFootnoteList($footnoteListKey) . '</'.$enclosingTag.'>';


  		




  
  191
  
    
	FootnoteManager::removeFootnoteList($footnoteListKey);


  		




  191
  192
  
    
	return $out;


  		




  192
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}


  		




  193
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      modules/cdm_dataportal/theme/cdm_dataportal.name.theme
    
  





  16
  16
  
    
 * @param $typeDesignation_citation The lectotype citation to print


  		




  17
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 * @return html valid string


  		




  18
  18
  
    
 */


  		




  19
  
  
    
function lectotype_citation_layout($typeDesignation_citation){


  		




  
  19
  
    
function lectotype_citation_layout($typeDesignation){


  		




  
  20
  
    

  		




  20
  21
  
    
	$res = '';


  		




  21
  
  
    
	if ($typeDesignation_citation){


  		




  
  22
  
    
	$citation = $typeDesignation->citation;


  		




  
  23
  
    
	$pages = $typeDesignation->citationMicroReference;


  		




  
  24
  
    
	if ($citation){


  		




  22
  25
  
    
		//$type = $typeDesignation_citation->type;


  		




  23
  
  
    
		$year = substr($typeDesignation_citation->datePublished->start, 0, 4);


  		




  24
  
  
    
		$page = $typeDesignation_citation->page;


  		




  25
  
  
    
		$author = $typeDesignation_citation->authorTeam->titleCache;


  		




  
  26
  
    
		$year = substr($citation->datePublished->start, 0, 4);


  		




  
  27
  
    
		$author = $citation->authorTeam->titleCache;


  		




  26
  28
  
    
		$res .= ' (designated by ';


  		




  27
  29
  
    
		$res .= $author;


  		




  28
  30
  
    
		$res .= ($year ? ' '.$year : '');


  		




  29
  
  
    
		$res .= ($year && $page ? ': '. $page : '');


  		




  
  31
  
    
		$res .= ($pages ? ': '. $pages : '');


  		




  30
  32
  
    
		//$res .= ')';


  		




  31
  
  
    
		//$res .= ($type ? ': ' . $type : '');


  		




  32
  33
  
    
	}


  		




  33
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	return $res;


  		




  34
  35
  
    
}


  		




  35
  36
  
    

  		




  36
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function theme_cdm_typedesignations($typeDesignations = array()){


  		




  37
  
  
    

  		




  38
  
  
    
	RenderHints::pushToRenderStack('typedesignations');


  		




  
  38
  
    
/*


  		




  
  39
  
    
	if(isset($renderTemplate['referencePart']['reference']) && $taxonName->nomenclaturalReference){


  		




  
  40
  
    
      $microreference = null;


  		




  
  41
  
    
      if(isset($renderTemplate['referencePart']['microreference'])){


  		




  
  42
  
    
        $microreference = $taxonName->nomenclaturalMicroReference;


  		




  
  43
  
    
      }


  		




  
  44
  
    
      $citation = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array($typeDesignation->uuid), "microReference=".urlencode($microreference));


  		




  
  45
  
    
      $citation = $citation->String;


  		




  
  46
  
    
*/      


  		




  
  47
  
    
	


  		




  
  48
  
    
  RenderHints::pushToRenderStack('typedesignations');


  		




  39
  49
  
    
	//_add_js_cluetip();


  		




  40
  50
  
    
	$out = '<ul class="typeDesignations">';


  		




  41
  51
  
    
  $typeDesignation_footnotes = false;


  		




  ......




  47
  57
  
    
		}else {


  		




  48
  58
  
    
			// it's a NameTypeDesignation


  		




  49
  59
  
    
			if($typeDesignation->notDesignated){


  		




  50
  
  
    
				$out .= '<li class="nameTypeDesignation"><span class="status">Lectotype</span> '.t('not designated'). '</li>';


  		




  
  60
  
    
				$out .= '<li class="nameTypeDesignation"><span class="status">Lectotype</span>: '.t('not designated'). '</li>';


  		




  51
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			}else if($typeDesignation->typeName){


  		




  52
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				$link_to_name_page = '?q=' . path_to_name($typeDesignation->typeName->uuid);


  		




  53
  
  
    
				$out .= '<li class="nameTypeDesignation"><span class="status">Lectotype</span> ';


  		




  
  63
  
    
				$out .= '<li class="nameTypeDesignation"><span class="status">Lectotype</span>';


  		




  54
  64
  
    

  		




  55
  
  
    
			if($typeDesignation->citation){


  		




  56
  
  
    
          $out .= lectotype_citation_layout($typeDesignation->citation);


  		




  
  65
  
    
			if($typeDesignation->citation){				


  		




  
  66
  
    
          $out .= lectotype_citation_layout($typeDesignation);


  		




  57
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          //footnotes


  		




  58
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          $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, $typeDesignation->citation->titleCache);


  		




  59
  
  
    
          $out .= theme('cdm_footnote_key', $fkey_typeDesignation) . '): ';          


  		




  60
  
  
    
          $typeDesignation_footnotes = true;


  		




  
  69
  
    
          $out .= theme('cdm_footnote_key', $fkey_typeDesignation) . ')';          


  		




  61
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        }


  		




  62
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  63
  72
  
    
				if($typeDesignation->typeName->nomenclaturalReference){


  		




  64
  73
  
    
					$referenceUri = url(path_to_reference($typeDesignation->typeName->nomenclaturalReference->uuid));


  		




  65
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				}


  		




  66
  
  
    
				$out .= theme('cdm_taxonName', $typeDesignation->typeName, $link_to_name_page, $referenceUri);


  		




  67
  
  
    
				


  		




  
  75
  
    
                   


  		




  
  76
  
    
				$out .= ': ' . theme('cdm_taxonName', $typeDesignation->typeName, $link_to_name_page, $referenceUri);


  		




  68
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			}


  		




  69
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		}


  		




  70
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	}


  		




  ......




  122
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		$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-lectotypes');


  		




  123
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	}


  		




  124
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	$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-acronyms');


  		




  125
  
  
    
	if ($typeDesignation_footnotes){


  		




  126
  
  
    
	  $out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid);  


  		




  127
  
  
    
	}


  		




  
  134
  
    
	


  		




  
  135
  
    
	$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid);  


  		




  
  136
  
    
	


  		




  128
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	RenderHints::popFromRenderStack();


  		




  129
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	return $out;


  		




  130
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}


  		




  ......




  231
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	foreach($homotypicalGroup as $synonym){


  		




  232
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		if($is_first_entry){


  		




  233
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			$is_first_entry = false;


  		




  234
  
  
    
			$typeDesignations = cdm_ws_get(CDM_WS_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);


  		




  
  243
  
    
			$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);


  		




  235
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			// is first list entry


  		




  236
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			$out .= '<li class="firstentry synonym">'.theme('cdm_related_taxon',$synonym, UUID_HETEROTYPIC_SYNONYM_OF).'</li>';


  		




  237
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		} else {


  		




  ......




  281
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		$out .= '<li class="synonym">'.theme('cdm_related_taxon', $synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';


  		




  282
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	}


  		




  283
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  284
  
  
    
	$typeDesignations = cdm_ws_get(CDM_WS_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);


  		




  
  293
  
    
	$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);


  		




  285
  294
  
    
	if($typeDesignations){


  		




  286
  295
  
    
		$out .= theme('cdm_typedesignations', $typeDesignations);


  		




  287
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	}


  		












  

    
      modules/cdm_dataportal/theme/cdm_dataportal.taxon.theme
    
  





  126
  126
  
    
	$out .= '</ul>';


  		




  127
  127
  
    

  		




  128
  128
  
    
	//$out .= theme('cdm_footnotes', $footnoteListKey, 'div');


  		




  129
  
  
    
	$test = theme('cdm_footnotes', $footnoteListKey, 'div');


  		




  130
  
  
    
	


  		




  131
  
  
    
	$out .= $test;


  		




  
  129
  
    
	$tr_footnotes = theme('cdm_footnotes', $footnoteListKey, 'div');


  		




  
  130
  
    
	$tr_footnotes_exploded = explode('sensu', $tr_footnotes);


  		




  
  131
  
    
	$tr_footnotes_aux = '';


  		




  
  132
  
    
	foreach ($tr_footnotes_exploded as $element){


  		




  
  133
  
    
		$tr_footnotes_aux .= $element; 


  		




  
  134
  
    
	}


  		




  
  135
  
    
	$out .= $tr_footnotes_aux;


  		




  132
  136
  
    
	


  		




  133
  137
  
    
	RenderHints::popFromRenderStack();


  		




  134
  138
  
    
	return $out;


  		












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