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<?php
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// $Id$
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require_once('cdm/cdm_api.php');
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function tagNameParts($name, $numOfNameTokens){
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$out = '<span class="name">';
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$token = strtok($name, " \n\t");
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$i = 0;
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$noSpace = true;
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while($token != false){
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if($i == $numOfNameTokens){
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$out .= '</span> <span class="authors">';
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$noSpace = true;
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}
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$out .= ($noSpace?'':' ').$token;
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$noSpace = false;
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$token = strtok(" \n\t");
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$i++;
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}
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return $out.'</span>';
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}
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/**
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* Renders the full name string (complete scientific name including the author team)
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*
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* @param NameTO $nameTO the taxon name
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*/
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function theme_cdm_name($nameTO){
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//TODO: how to respect the different subtypes of eu.etaxonomy.cdm.model.name.TaxonNameBase ?
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$out = '<h2>Dummy content</h2>';
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$testo->fld = array('a'=>'A', 'b'=>'B');
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$tfld = $testo->fld;
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if($nameTO){
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foreach($nameTO->taggedName as $ti){
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$out .= $ti->tag.'=>'.$ti->text.'<br />';
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}
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$tn = $nameTO->taggedName;
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$out .= '<pre>'.print_r($nameTO, true).'</pre>';
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$out .= '<div>'.$nameTO->ws_url.'</div>';
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$out .= '<div>'.cdm_taggedtext2html($tn).'</div>';
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} else {
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$out .= '<div>Item not found</div>';
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}
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return $out;
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}
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/**
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* Renders the given TaxonTO. The $enclosingTag (if not set false)
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* will get the following class attributes:
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* - name
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* - acceptet (only if $ptaxon is an accepted name)
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*
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* @param TaxonTO $taxon
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* @param boolean $noSecundum defaults to false. If set to true the secundum part is omitted.
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* @param string $enclosingTag defaults to span.
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* @param boolean $showNomRef whether to dispülay the nomenclatural reference
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* @return string of XHTML
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*
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* usage: taxon_detail, theme_ptname_link
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*/
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function theme_cdm_taxon(TaxonTO $taxon, $noSecundum = true ,$enclosingTag = 'span', $showNomRef = false){
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/* TODO: port me
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$refSecundum = false;
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if(!$noSecundum && $taxon->ref){
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$refSecundum = str_trunk($ptaxon->ref, 40, '...');
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}
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*/
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$out = theme('cdm_name', $taxon)
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.($refSecundum ? ' <span class="secundum">sec. '.$refSecundum.'</span>': '')
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.$ptaxon->namePhrase;
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/* TODO: port me
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if($showNomRef){
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$out .= (str_beginsWith($ptaxon->nomRef, 'in') || trim($ptaxon->nomRef) == '' ? ' ':', ').theme('cdm_nomRef',$taxon);
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}
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if($enclosingTag){
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$out = '<'.$enclosingTag.' class="name'.($ptaxon->isAccepted()?' accepted':'').'"><!-- ['.$ptaxon->nameId.'|'.$ptaxon->refId.'] -->'.$out.'</'.$enclosingTag.'>';
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}
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*/
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return $out;
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}
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/**
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* Renders a link to the taxon detail page for the given $taxon
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*
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* @param TaxonTO $taxon
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*/
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function theme_cdm_taxon_link(TaxonTO $taxon, $fragment = '', $showNomRef = false){
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if($fragment){
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$fragment = '#'.$fragment;
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}
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if(!$taxon->isAccepted) {
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$out = 'ERROR: theme_cdm_taxon_link() not accepted ptname; status:'.$taxon->status.$out;
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}
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$out = l(theme('cdm_taxon', $taxon, true, false), 'taxon', array('class'=>'accepted'), "uuid=$taxon->uuid", $fragment);
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if($showNomRef){
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$out .=' '.theme('cdm_nomRef', $ptaxon);
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}
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return $out;
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}
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//TODO: port everything below
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/**
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* Renders a list of synonyms including misapplied names which are related to the
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* given TAXIC_PTaxon.
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*
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* @param TAXIC_PTaxon $ptaxon
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* @param boolean $recursive default is false. Whether to crawl recursively into the
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* three of relations
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*
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* usage taxon_detail.php.inc
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*/
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function render_synonyms(TAXIC_PTaxon $ptaxon, $recursive = false, $showNotes = false){
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$_debug = false;
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$is_higher_rank = $ptaxon->rankId < 60;
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$out = false;
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$last_relQualifierId = false;
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$last_was_heterotypic = false;
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$last_basionym_nameId = false;
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$is_other_basionym = false;
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$synonyms = findSynonyms($ptaxon->nameId, $ptaxon->refId, false, $recursive);
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foreach($synonyms AS $relpt){ // -- relations loop
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// whether this is the first entry in the lsit
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$is_first_entry = $out === false;
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// whether the current taxon has another basionym than the last one
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$is_other_basionym = $last_basionym_nameId !== false
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&& ($last_basionym_nameId !== $relpt->basionymNameId)
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&& $relpt->relQualifierId != 3;
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// whether the current taxon has another name ralation than the last one
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$is_other_relQualifierId = $last_relQualifierId !== false && ($last_relQualifierId !== $relpt->relQualifierId);
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//is here the end of list of homotypic end of heterotypic subsection?
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//$end_of_section = ($last_relQualifierId !== false && $is_other_basionym);
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$end_of_section = !$is_first_entry && $is_other_basionym || $is_other_relQualifierId && $relpt->relQualifierId == 3 /* misaplied */;
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// name relations declared as synomyn (id=2) are assumed to be heterotypic
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$is_heterotypic = $relpt->relQualifierId == 6 || ($relpt->relQualifierId == 2 && !$is_other_basionym && $last_was_heterotypic);
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// DELETE ME? $is_heterotypic = $relpt->relQualifierId == 6 || ($relpt->relQualifierId == 2 && !$is_other_basionym);
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$is_homotypic = $relpt->relQualifierId == 7 || $relpt->relQualifierId == 101 || $relpt->relQualifierId == 103;
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// is this taxon homotypic to a previously printed heterotypic taxon, so is should be
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// an intented subelement and re-taged as homotypic
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$is_subelement = $is_heterotypic && !$is_other_basionym && !$is_first_entry;
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$is_the_basionym = $is_homotypic && !$last_basionym_nameId;
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if($is_first_entry){
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$out = '<ul>'.chr(10).'<li class="blank_line"></li>'.chr(10);
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if($is_heterotypic){
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if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations before first entry which is heterotypic]</span></li>';
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$out .= renderTypeDesignations($ptaxon->nameId, '', $is_higher_rank );
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$out .= '<li class="blank_line"></li>'.chr(10);
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}
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}
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/*$out .= '<li><span style="color:blue; font-size: 80%;">last: '
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.$last_basionym_nameId.' !== '.$relpt->basionymNameId.' '.$relpt->fullName
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.'</span></li>';
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*/
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//DEBUG $out .= '<pre>'.print_r($relpt, true).'</pre>';
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if($is_other_basionym){
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if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 1 (relID: '.$last_relQualifierId.' for '.$last_basionym_nameId.')</span></li>';
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$out .= renderTypeDesignations($last_basionym_nameId, ($last_was_heterotypic ? 'subelement' : ''), $is_higher_rank );
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//$out .= renderTypeDesignations($last_basionym_nameId, '', $is_higher_rank );
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}
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if($end_of_section){
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// find type information
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$out .= '<li class="blank_line"></li>'.chr(10);
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}
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if($is_subelement){
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// all those taxa which are homotypic to the preceeding basionym are to be
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// displayed as homotypic
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$relpt->relQualifierId = 7;
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$cssClass = 'subelement';
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} else {
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$cssClass = '';
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}
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$out .= render_related_ptname($relpt, 'li', $cssClass, $showNotes).chr(10);
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// remember last synonyms properties for next round
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$last_relQualifierId = $relpt->relQualifierId;
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$last_basionym_name = $relpt->basionymFullName;
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$last_basionym_nameId = $relpt->basionymNameId;
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$last_was_heterotypic = $is_heterotypic;
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} // END relations loop
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if($is_the_basionym){
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if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 0 for '.$relpt->nameId.'</span></li>';
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$out .= renderTypeDesignations($relpt->nameId, '', $is_higher_rank);
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} else
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// TypeDesignations for the last item
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if($is_other_basionym || !$last_was_heterotypic){
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if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 2 for '.$last_basionym_nameId.'</span></li>';
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$out .= renderTypeDesignations($last_basionym_nameId, '', $is_higher_rank);
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} else
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// In case the given PTaxon had no synonyms ...
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if($last_basionym_nameId === false || $last_relQualifierId == 7){
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if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 3 for'.$ptaxon->nameId.'; last_basionym_nameId = '.$last_basionym_nameId.'</span></li>';
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$out .= renderTypeDesignations($ptaxon->nameId, '', $is_higher_rank);
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} else {
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$out .= '<li class="blank_line"></li>'.chr(10).'</ul>';
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}
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return $out;
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}
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// -------------------- END function render_synonyms()
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237
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function render_homonyms(TAXIC_TaxonName $taxon){
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$homonyms = getLaterHomonyms($taxon);
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$out = '';
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foreach($homonyms as $homnym){
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$out .= '<li class="homonym">[non '.$homnym->authors.', '.$homnym->nomRef.']'.render_notes($homnym).'</li>';
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}
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245
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246
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if($out){
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247
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$out = '<ul>'.$out.'</ul>';
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}
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return $out;
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}
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251
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252
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/**
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253
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* render_related_ptname() is used by render_synonyms()
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254
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* @param TAXIC_PTaxon $relPTaxon
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255
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* @param String $enclosingTag
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*/
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257
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function render_related_ptname($relPTaxon, $enclosingTag = 'li', $cssClass = '', $showNotes = false){
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258
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259
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$cssClass .= ' '.str_replace(' ', '_', $relPTaxon->relQualifier);
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switch($relPTaxon->relQualifierId){
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262
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case 7 :
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263
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case 101 :
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264
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case 103 : // homotypic-synonym
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265
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$relSign = '≡';
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266
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break;
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case 3 : // misapplied_name
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268
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$relSign = '-';
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269
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break;
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270
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case 8 : // invalid_designation
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271
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$relSign = '-';
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272
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break;
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273
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default :
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274
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$relSign = '=';
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275
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break;
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276
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}
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277
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278
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//$relSign .= $relPTaxon->relQualifierId;
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279
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280
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$out = '';
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281
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282
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if($relPTaxon->relQualifierId == 3){
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283
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// special look for misapplied_names
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284
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$relatedToName = ''; // only used in HTML comment
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285
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$sensuPart = ' sensu '.$relPTaxon->ref;
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286
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if($relPTaxon->relInversion){
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287
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$namePart = ($relPTaxon->isAccepted()? render_ptname_link($relPTaxon) : render_ptname($relPTaxon));
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288
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$out = $relPTaxon->relQualifier.' '.$namePart.' '.$sensuPart;
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289
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} else {
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290
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$namePart = '„'.trim($relPTaxon->name).'“';
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291
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if($relPTaxon->relPTaxon->name){
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292
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// only used in HTML comment!!
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293
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$relatedToName = trim($relPTaxon->relPTaxon->name);
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294
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}
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295
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$out .= $namePart.'</span>'.$sensuPart;
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}
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297
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298
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} else {
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299
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$relatedToName = ($relPTaxon->relPTaxon ? $relPTaxon->relPTaxon->name : false);
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300
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if($relPTaxon->isAccepted()) {
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301
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$out .= render_ptname_link($relPTaxon, null, true);
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302
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} else {
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303
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$out .= render_ptname($relPTaxon, true ,'span', true);
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}
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305
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306
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} // END else special look for misapplied_names
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307
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308
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$notes = ($showNotes && showNotes() ? render_notes($relPTaxon) : '');
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309
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310
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$out = '<'.$enclosingTag.' class="'.$cssClass.'"><!-- '.$relPTaxon->relQualifier.' '.$relatedToName.'-->'
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311
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.'<a name="'.$relPTaxon->nameId.'_'.$relPTaxon->refId.'" ></a><span class="relation_sign">'.$relSign.'</span> '
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312
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.$out . $notes
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313
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.'</'.$enclosingTag.'>';
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314
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return $out;
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315
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}
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316
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317
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/**
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318
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* @param TAXIC_PTaxon $ptname
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319
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*/
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320
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$NOMREFSET_COUNTER = 0;
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321
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322
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function render_nomRef($ptname){
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323
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global $conf;
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324
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global $NOMREFSET_COUNTER;
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325
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$NOMREFSET_COUNTER += 1;
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326
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if(count($protoploges = $ptname->getProtologues()) > 0){
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327
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$prot = $protoploges[0];
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328
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// FIXME: protologues are really a list of links. treat only the first
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329
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if(is_file($conf['abs_media_path'].$conf['protologue_path'].$prot.".png")){
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330
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$nomrefLink = '<span class="nomref"><a href="'.$conf['protologue_path'].$prot.'.png" rel="lightbox[nomrefset'.$NOMREFSET_COUNTER.']" title="<a href="'.$conf['protologue_quality_path'].$prot.'.tif">High Quality Scan</a>">'.trim($ptname->nomRef).'</a></span>';
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331
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} else {
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332
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$nomrefLink = '<span class="nomref"><a href="'.$conf['protologue_path'].$prot.'001.png" rel="lightbox[nomrefset'.$NOMREFSET_COUNTER.']" title="<a href="'.$conf['protologue_quality_path'].$prot.'.tif">High Quality Scan</a>">'.trim($ptname->nomRef).'</a></span>';
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333
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// check in filesystem if there are more pages as JPGs. TIFFs can cope with 8 pages per file, so no need for that
|
|
334
|
$i=2;
|
|
335
|
while (is_file($conf['abs_media_path'].$conf['protologue_path'].$prot.str_pad($i, 3, '0', STR_PAD_LEFT).".png")){
|
|
336
|
$nomrefLink = $nomrefLink." <a href='".$conf['protologue_path'].$prot.str_pad($i, 3, '0', STR_PAD_LEFT).".png' rel='lightbox[nomrefset".$NOMREFSET_COUNTER."]'></a>";
|
|
337
|
$i++;
|
|
338
|
}
|
|
339
|
}
|
|
340
|
return $nomrefLink;
|
|
341
|
} else {
|
|
342
|
return '<span class="nomref">'.trim($ptname->nomRef).'</span>';
|
|
343
|
}
|
|
344
|
|
|
345
|
}
|
|
346
|
|
|
347
|
function renderTypeDesignations($nameId, $cssClass = '', $togglebox = false, $separator = '<br />' , $enclosingTag = 'li'){
|
|
348
|
|
|
349
|
$typeDesignations = getTypeDesignations($nameId);
|
|
350
|
|
|
351
|
if(count($typeDesignations) > 0){
|
|
352
|
$out = '';
|
|
353
|
foreach($typeDesignations as $td){
|
|
354
|
|
|
355
|
if(strlen($out) > 0){
|
|
356
|
$out .= $separator.chr(10);
|
|
357
|
}
|
|
358
|
$out .= $td['TypeStatus'].' - '.html_entity_decode($td['TypePhrase']);
|
|
359
|
}
|
|
360
|
|
|
361
|
if($togglebox){
|
|
362
|
$out = '<div class="tbox_toggler"> </div><div class="tbox_content">'.$out.'</div>';
|
|
363
|
}
|
|
364
|
return '<'.$enclosingTag.' class="type_designation'.($cssClass ? ' '.$cssClass : '' ).'">'
|
|
365
|
.$out.'</'.$enclosingTag.'>'.chr(10);
|
|
366
|
|
|
367
|
}
|
|
368
|
}
|
|
369
|
|
|
370
|
/**
|
|
371
|
* render a numeric pager
|
|
372
|
*/
|
|
373
|
function renderNumPager($numOfPages, $activePage, $maxPagerItems, $linkUrlBase){
|
|
374
|
|
|
375
|
if ($activePage > $maxPagerItems - 2){
|
|
376
|
// shift visible pager items
|
|
377
|
$begin = $activePage - floor($maxPagerItems / 2);
|
|
378
|
$end = min($activePage + ceil($maxPagerItems / 2), $numOfPages);
|
|
379
|
} else {
|
|
380
|
$begin = 1;
|
|
381
|
$end = min($numOfPages, $maxPagerItems);
|
|
382
|
}
|
|
383
|
// hide the pager if there is only one page:
|
|
384
|
if($begin == $end)
|
|
385
|
return;
|
|
386
|
|
|
387
|
echo '<ul class="paging numeric">';
|
|
388
|
if ($activePage > 10){
|
|
389
|
echo '<li><a href="', $linkUrlBase, $activePage - 10, '" title="backward 10 pages">«</a></li>';
|
|
390
|
}
|
|
391
|
if ($activePage > 1){
|
|
392
|
echo '<li><a href="', $linkUrlBase, $activePage - 1, '" title="previuos"><</a></li>';
|
|
393
|
}
|
|
394
|
for ($pn = $begin; $pn <= $end ; ++$pn) {
|
|
395
|
if($pn != $activePage){
|
|
396
|
echo '<li><a href="'.$linkUrlBase.$pn.'">'. $pn. '</a></li>';
|
|
397
|
} else {
|
|
398
|
echo '<li class="active">'.$pn.'</li>';
|
|
399
|
}
|
|
400
|
}
|
|
401
|
if ($activePage < $numOfPages){
|
|
402
|
echo '<li><a href="', $linkUrlBase, $activePage + 1, '" title="next">></a></li>';
|
|
403
|
}
|
|
404
|
if ($activePage < $numOfPages - 9){
|
|
405
|
echo '<li><a href="', $linkUrlBase, $activePage + 10, '" title="forward 10 pages">»</a></li>';
|
|
406
|
}
|
|
407
|
if($numOfPages > 0){
|
|
408
|
echo '<li> (of '.$numOfPages.' pages)</li>';
|
|
409
|
}
|
|
410
|
echo '</ul>';
|
|
411
|
}
|
|
412
|
|
|
413
|
/**
|
|
414
|
* @param TAXIC_TaxonName $taxon
|
|
415
|
*/
|
|
416
|
function render_notes(TAXIC_TaxonName $taxon){
|
|
417
|
|
|
418
|
if(!showNotes()){
|
|
419
|
return;
|
|
420
|
}
|
|
421
|
|
|
422
|
$notes = array();
|
|
423
|
if($taxon->nameNotes && trim($taxon->nameNotes)){
|
|
424
|
$notes['Name Notes'] = $taxon->nameNotes;
|
|
425
|
}
|
|
426
|
if($taxon->nomRefNotes && trim($taxon->nomRefNotes)){
|
|
427
|
$notes['Nomenclatural Ref. Notes'] = $taxon->nomRefNotes;
|
|
428
|
}
|
|
429
|
|
|
430
|
if($taxon instanceof TAXIC_PTaxon){
|
|
431
|
if($taxon->nameNotes && trim($taxon->conceptNotes)){
|
|
432
|
$notes['Taxon Concept Notes'] = $taxon->conceptNotes;
|
|
433
|
}
|
|
434
|
if($taxon->refNotes && trim($taxon->refNotes)){
|
|
435
|
$notes['Concept Reference Notes'] = $taxon->refNotes;
|
|
436
|
}
|
|
437
|
}
|
|
438
|
if(count($notes) > 0){
|
|
439
|
$out = '<span class="note_toggler"><img src="themes/cichorieae/note_gray.gif" /><div class="note">';
|
|
440
|
$out .= '<div class="title"><div class="close" title="close"><img src="themes/cichorieae/close.gif" /></div>Notes on '.render_name($taxon).'</div><div class="content">';
|
|
441
|
foreach(array_keys($notes) as $title){
|
|
442
|
$out .= render_notes_entry($title, $notes[$title]);
|
|
443
|
}
|
|
444
|
return $out.'</div></div></span>';
|
|
445
|
} else {
|
|
446
|
return;
|
|
447
|
}
|
|
448
|
}
|
|
449
|
|
|
450
|
function render_notes_entry($title, $note){
|
|
451
|
|
|
452
|
return '<h4>'.$title.'</h4><p>'.htmlspecialchars($note).'</p>'.chr(10);
|
|
453
|
}
|
|
454
|
|