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1 c70b93c3 Andreas Kohlbecker
<?php
2 f19f47fa Andreas Kohlbecker
/**
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 * @file
4
 * Page functions.
5
 *
6
 * @copyright
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 *   (C) 2007-2012 EDIT
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 *   European Distributed Institute of Taxonomy
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 *   http://www.e-taxonomy.eu
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 *
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 *   The contents of this module are subject to the Mozilla
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 *   Public License Version 1.1.
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 * @see http://www.mozilla.org/MPL/MPL-1.1.html
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 *
15
 * @author
16 f19f47fa Andreas Kohlbecker
 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
17
 */
18
19
20
/**
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 * Creates a render array representing the ocurrences associetad with the $taxon.
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 *
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 * The resulting render array contains two elements:
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 *  - 'map': A map showing all point locations of the occurences is availabale
25
 *  - 'specimen_list': the list of occurences prepated as table for theme_table()
26
 *
27
 * @param object $taxon
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 *   A cdm Taxon object
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 * @return
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 *   A render array suitable for drupal_render()
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 *
32 c70b93c3 Andreas Kohlbecker
 */
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function cdm_dataportal_taxon_page_specimens($taxon) {
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    $render_array = array();
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    RenderHints::pushToRenderStack('taxon_page_specimens');
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    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
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    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
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    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
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    $by_associatedtaxon_query_parameters = array(
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        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
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        'relationships' => implode(',', $relationship_choice['direct']),
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    );
46
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    if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
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        $by_associatedtaxon_query_parameters = array_merge($by_associatedtaxon_query_parameters, $_REQUEST['pager']);
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    }
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    $by_associatedtaxon_query = http_build_query($by_associatedtaxon_query_parameters);
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    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
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        null,
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        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
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    );
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    $specimensOrObservations = array();
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    if(isset($pager->records[0])){
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        $specimensOrObservations =  $pager->records;
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    }
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    // order occurrences by date but types should be on top of the list
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    $type_specimens = array();
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    $other_occurrences = array();
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    foreach ($specimensOrObservations as &$occurrence) {
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        $typeDesignationsPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $occurrence->uuid);
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        if (isset($typeDesignationsPager->count) && $typeDesignationsPager->count > 0) {
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            $type_specimens[] = $occurrence;
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        } else {
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            $other_occurrences[] = $occurrence;
72
        }
73
    }
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    $specimensOrObservations = array_merge($type_specimens, $other_occurrences);
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    // Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field
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    // $occurrence->_fieldObjectMedia
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    foreach ($specimensOrObservations as &$occurrence) {
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        $occurrence->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
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            $occurrence->uuid,
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            'fieldObjectMedia',
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        ));
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        $occurrence->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
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            $occurrence->uuid,
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            'derivedUnitMedia',
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        ));
87
    }
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    // --- get map service HTTP query parameters
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    if (count($specimensOrObservations) > 0) {
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        $occurrence_queryDto = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid,  $by_associatedtaxon_query);
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      $map_visibility = variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT);
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      if($map_visibility == 'always' ||
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        variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT) == 'automatic' &&
96 378bc1ce Andreas Kohlbecker
          (isset($occurrence_queryDto->fieldUnitPoints[0]) || isset($occurrence_queryDto->derivedUnitPoints[0]))
97
        )
98
      {
99
        $occurrence_query = $occurrence_queryDto->occurrenceQuery;
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        $legend_format_query = null;
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        $distribution_query = NULL;
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        $render_array['map'] = compose_map('specimens', $occurrence_query, $distribution_query, $legend_format_query, array());
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      }
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    }
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    if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){
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        //COMPRESSED SPECIMEN DERIVATE TABLE
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        $associatedFieldUnitsQuery_parameters = array();
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        if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
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            $associatedFieldUnitsQuery_parameters = array_merge($associatedFieldUnitsQuery_parameters, $_REQUEST['pager']);
111
        }
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        $by_associatedtaxon_query = http_build_query($associatedFieldUnitsQuery_parameters);
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        $pagerFieldUnits = cdm_ws_get(CDM_WS_PORTAL_TAXON,
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            array($taxon->uuid, 'associatedFieldUnits'),
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            $by_associatedtaxon_query . '&pageSize=' . variable_get('cdm_dataportal_compressed_specimen_derivate_table_page_size')
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        );
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        // get icon images
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        $expand_icon = font_awesome_icon_markup(
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            'fa-plus-square-o',
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            array(
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                'alt'=>'Show details',
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                'class' => array('expand_icon')
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            )
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        );
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        $collapse_icon = font_awesome_icon_markup(
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            'fa-minus-square-o',
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            array(
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                'alt'=>'Show details',
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                'class' => array('collapse_icon')
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            )
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        );
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        $detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
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        $checked_box_icon = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/step_done.gif' . '"/>';
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        $sequence_icon = '<img title="Molecular Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/sequence_derivate-16x16-32.png' . '"/>';
136 d7e61010 Patric Plitzner
        $character_data_icon = '<img title="Character Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/character_data_derivate-16x16-32.png' . '"/>';
137 4cb163f8 Patric Plitzner
        if (isset($pagerFieldUnits->records[0])) {
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            $rowcount = 0;
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            foreach ($pagerFieldUnits->records as $fieldUnit) {
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                //get derivate hierarchy for the FieldUnit
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                $derivateHierarchy = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($fieldUnit->uuid, 'derivateHierarchy'), 'taxonUuid=' . $taxon->uuid);
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                if($derivateHierarchy){
143
                    //summary row
144
                    $rows[] = array(
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                        'data' => array(
146 b8783a48 Patric Plitzner
                            array(
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                                'data' => $expand_icon . $collapse_icon,
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                                'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
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                            ),
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                            array(
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                                'data' => $derivateHierarchy->country,
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                                'class' => array('summary_row_cell')
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                            ),
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                            array(
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                                'data' => $derivateHierarchy->date,
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                                'class' => array('summary_row_cell')
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                            ),
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                            array(
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                                'data' => $derivateHierarchy->collection,
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                                'class' => array('summary_row_cell')
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                            ),
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                            array(
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                                'data' => $derivateHierarchy->herbarium,
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                                'class' => array('summary_row_cell')
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                            ),
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                            array(
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                                'data' => $derivateHierarchy->hasType? $checked_box_icon:"",
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                                'class' => array('summary_row_cell', 'summary_row_icon')
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                            ),
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                            array(
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                                'data' => $derivateHierarchy->hasSpecimenScan? $checked_box_icon:"",
172 b8783a48 Patric Plitzner
                                'class' => array('summary_row_cell', 'summary_row_icon')
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                            ),
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                            array(
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                                'data' => ($derivateHierarchy->hasDna? $sequence_icon :"")." "
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                                    .($derivateHierarchy->hasDetailImage?$detail_image_icon:"")." "
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                                    .($derivateHierarchy->hasCharacterData?$character_data_icon:""),
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                                'class' => array('summary_row_cell', 'summary_row_icon')
179
                            )
180 1ce9afb7 Patric Plitzner
                        ),
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                        'id' => ('derivate_summary' . $rowcount), // summary row id
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                        'class' => array('summary_row'),
183
                    );
184
185 e3d43134 Patric Plitzner
                    //assemble field unit details
186
                    $detail_html = "";
187 7d8ef9fa Patric Plitzner
                    // - taxon name
188 e3d43134 Patric Plitzner
                    if (variable_get('cdm_dataportal_compressed_specimen_derivate_table_show_determined_as') && $derivateHierarchy->taxonName) {
189 0ee2b205 Patrick Plitzner
                        $detail_html .= create_label("Associated with") . $derivateHierarchy->taxonName . "<br>";
190 db390e35 Patric Plitzner
                    }
191 a9ed34ad Andreas Kohlbecker
                    // - protologue
192 e3d43134 Patric Plitzner
                    if ($derivateHierarchy->protologue) {
193
                        //$detail_html .= "<strong>Protologue:</strong> " . $derivateHierarchy->protologue . "<br>"
194
                    }
195 7d8ef9fa Patric Plitzner
                    // - citation
196 e3d43134 Patric Plitzner
                    if ($derivateHierarchy->citation) {
197 3dd58832 Patric Plitzner
                        $detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";
198 1ce9afb7 Patric Plitzner
                    }
199 e3d43134 Patric Plitzner
                    //assemble specimen details
200 9af9c5b3 Patric Plitzner
                    if($derivateHierarchy->preservedSpecimenDTOs){
201
                        foreach($derivateHierarchy->preservedSpecimenDTOs as $preservedSpecimenDTO) {
202 3dd58832 Patric Plitzner
                            $detail_html .= "<br>";
203 30845bda Andreas Kohlbecker
                            $detail_html .= render_cdm_specimen_page($preservedSpecimenDTO);
204 9af9c5b3 Patric Plitzner
                        }
205 e3d43134 Patric Plitzner
                    }
206 3dd58832 Patric Plitzner
                    $detail_html .= "<br>";
207 1ce9afb7 Patric Plitzner
                    //detail row resp. one BIG detail cell
208
                    $rows[] = array(
209
                        'data' => array(
210 b8783a48 Patric Plitzner
                            array(
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                                'data' => "", //empty first column
212 44eebb6f Patric Plitzner
                                'class' => array('expand_column')
213 b8783a48 Patric Plitzner
                            ),
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                            array(
215
                                'data' => $detail_html,
216 b8783a48 Patric Plitzner
                                'colspan' => 7,
217 1ce9afb7 Patric Plitzner
                            ),
218
                        ),
219
                        'id' => ('derivate_details' . $rowcount),//details row ID
220
                        'class' => array('detail_row'),
221
                    );
222
                    $rowcount++;
223
                }
224
            }
225 f19f47fa Andreas Kohlbecker
226 11fdb92e Patrick Plitzner
            $tableId = "derivate_hierarchy_table";
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            $derivateHierarchyTable = array(
228
                "#theme" => "table",
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                "#weight" => 2,
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                "#header" => array(
231
                    array(
232
                        'data' => "",
233
                        'class' => array('expand_column')
234
                    ),
235
                    "Country", "Date", "Collector + collecting number", "Herbaria", "Type", "Scan", "Derivatives"),
236
                "#rows" => $rows,
237
                "#attributes" => array(
238
                    "id" => $tableId,
239
                    "border" => 2
240
                )
241
            );
242 f19f47fa Andreas Kohlbecker
243 11fdb92e Patrick Plitzner
            //add toggle functionality to derivate hierarchy table
244
            drupal_add_js_rowToggle("#".$tableId);
245 f19f47fa Andreas Kohlbecker
246 11fdb92e Patrick Plitzner
            $render_array['derivate_hierarchy_table'] = $derivateHierarchyTable;
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            $render_array['pager'] = markup_to_render_array(
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                theme('cdm_pager', array(
249
                    'pager' => $pagerFieldUnits,
250
                    'path' => $_REQUEST['q'],
251
                    'parameters' => $_REQUEST
252
                )),
253
                10 // weight
254
            );
255
        }
256 f19f47fa Andreas Kohlbecker
    }
257 1ce9afb7 Patric Plitzner
    else{
258
        //BOTTOM-UP-SPECIMEN-TABLE
259
        // --- generate the specimen list as table
260
        $specimen_table = array(
261
            '#theme' => 'table',
262
            '#weight' => 2,
263
            // prefix attributes and rows with '#' to let it pass to the theme function,
264
            // otherwise it is handled as child render array
265
            '#attributes' => array('class' => 'specimens'),
266
            '#rows' => array(),
267
        );
268 f19f47fa Andreas Kohlbecker
269 1ce9afb7 Patric Plitzner
        if ($specimensOrObservations) {
270
271
            foreach ($specimensOrObservations as $specimenOrObservation) {
272
273
                $mediaList = array();
274
                if (is_array($specimenOrObservation->_fieldObjectMedia)) {
275
                    $mediaList = array_merge($mediaList, $specimenOrObservation->_fieldObjectMedia);
276
                }
277
                if (is_array($specimenOrObservation->_derivedUnitMedia)) {
278
                    $mediaList = array_merge($mediaList, $specimenOrObservation->_derivedUnitMedia);
279
                }
280
281
                // typelabel will contain the typeStatus
282
                $type_label = '';
283
                $typeDesignationPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $specimenOrObservation->uuid);
284 0e533708 Patric Plitzner
                if (isset($typeDesignationPager) and isset($typeDesignationPager->records)) {
285 1ce9afb7 Patric Plitzner
                    $type_status = array();
286
                    foreach ($typeDesignationPager->records as $typeDesignation) {
287
                        if (isset($typeDesignation->typeStatus->representation_L10n)){
288
                            $type_status[] = $typeDesignation->typeStatus->representation_L10n;
289
                        }
290
                    }
291
                    $type_label = implode(', ', $type_status);
292
                    if($type_label){
293
                        $type_label .= ': ' ;
294
                    }
295
                }
296
297
                // --- Specimen entry as dynamic label:
298
                //     -> Dynabox for the specimenOrObservation
299
                $gallery_name = $specimenOrObservation->uuid;
300
301
                $derived_unit_ws_request = cdm_compose_url(CDM_WS_OCCURRENCE, array( $specimenOrObservation->uuid));
302
                $label_html = cdm_dynabox(
303 cea412e7 Andreas Kohlbecker
                  $specimenOrObservation->uuid,
304
                  $type_label . $specimenOrObservation->titleCache,
305
                  $derived_unit_ws_request,
306
                  'cdm_specimenOrObservation',
307
                  'Click for details',
308
                  array('div', 'div'),
309
                  array(),
310
                  null, // $content_element_selector
311
                  'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback
312
                  'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback
313 1ce9afb7 Patric Plitzner
                );
314
315
                // --- Render associated media.
316
                $gallery_html = '';
317
                if (count($mediaList) > 0) {
318
                    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
319
                    $captionElements = array(
320
                        '#uri' => t('open media'),
321
                    );
322
323 a9815578 Andreas Kohlbecker
                    $gallery_html = compose_cdm_media_gallerie(array(
324 1ce9afb7 Patric Plitzner
                        'mediaList' => $mediaList,
325
                        'galleryName' => $gallery_name,
326
                        'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
327
                        'cols' => $gallery_settings['cdm_dataportal_media_cols'],
328
                        'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
329
                        'captionElements' => $captionElements,
330
                        'mediaLinkType' => 'LIGHTBOX',
331
                        'alternativeMediaUri' => NULL,
332
                        'galleryLinkUri' => NULL,
333
                    ));
334
                }
335
336
                $specimen_table['#rows'][] = array(
337
                    // An array of table rows. Every row is an array of cells, or an associative array
338
                    'data' => array(
339
                        // Each cell can be either a string or an associative array
340
                        $label_html . $gallery_html
341
                    ),
342
                    'class' =>  array(
343
                        'descriptionElement',
344
                        'descriptionElement_IndividualsAssociation'
345
                    ),
346
                );
347
            }
348
        }
349 f19f47fa Andreas Kohlbecker
350 1ce9afb7 Patric Plitzner
        $render_array['specimen_list'] = $specimen_table;
351
        $render_array['pager'] = markup_to_render_array(
352
            theme('cdm_pager', array(
353
                'pager' => $pager,
354
                'path' => $_REQUEST['q'],
355
                'parameters' => $_REQUEST,
356
            )),
357
            10 // weight
358
        );
359
    }
360
    RenderHints::popFromRenderStack();
361
    return $render_array;
362 3f259ca3 Andreas Kohlbecker
}
363 db390e35 Patric Plitzner
 
364 65a4de51 Patrick Plitzner
function create_html_link($link, $openInExternalWindow=false){
365 7d8ef9fa Patric Plitzner
    $html = "";
366 65a4de51 Patrick Plitzner
    if($link->uri && $link->uri!=""){
367
        $html .= '<a  href="' . $link->uri . '"';
368
        if($openInExternalWindow){
369
            $html .= ' target="_blank"';
370
        }
371
        $html .= '>' . $link->linkText . '</a>';
372 7d8ef9fa Patric Plitzner
    }
373
    else{
374
        $html .= $link->linkText;
375
    }
376
    return $html;
377
}
378
379
/**
380 65a4de51 Patrick Plitzner
 * Creates HTML links from the given link list concatenated by default by a comma.
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 * @param $linkList the list with Link objects having "uri" and "linkText" as members
382
 * @return string the assembled HTML string containing the links
383
 */
384 65a4de51 Patrick Plitzner
function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
385 7d8ef9fa Patric Plitzner
{
386
    $html = "";
387
    if ($linkList) {
388
        foreach ($linkList as $link) {
389 65a4de51 Patrick Plitzner
            $html .= create_html_link($link, $openInExternalWindow).$separator;
390 7d8ef9fa Patric Plitzner
        }
391 65a4de51 Patrick Plitzner
        $html = rtrim($html, $separator);
392 7d8ef9fa Patric Plitzner
    }
393
    return $html;
394
}
395
396 00a8e4b6 Andreas Kohlbecker
/**
397
 * Composes a taxon page which can consist of multiple parts like
398
 * 'General', 'Synonymy', 'Images', 'Keys'. These parts can be displayed
399
 * as tabs or as sections of a single page.
400
 *
401
 * It is headed by the name of the accepted taxon without author and reference.
402
 *
403
 * @param $taxon
404
 *   The CDM Taxon Instance to compose the page for.
405
 * @param $page_part
406
 *   Name of the part to display, valid values are:
407
 *    - 'description' -  for the general part
408
 *    - 'images'
409
 *    - 'synonymy'
410
 *    - 'keys'
411
 *    - 'all'
412
 *
413
 * @return array
414
 *   A drupal render array
415
 *
416
 * @ingroup compose
417
 */
418
function compose_cdm_taxon_page($taxon, $page_part = 'description') {
419
420 0ae57522 Patric Plitzner
  // we better cache here since drupal_get_query_parameters has no internal static cache variable
421
  $http_request_params = drupal_get_query_parameters();
422 00a8e4b6 Andreas Kohlbecker
423 0ae57522 Patric Plitzner
  // add all mandatory js sources
424
  _add_js_footnotes();
425 00a8e4b6 Andreas Kohlbecker
426
427 0ae57522 Patric Plitzner
  $render_array = array();
428
  $weight = 0; // the weight for the render array elements
429 00a8e4b6 Andreas Kohlbecker
430 0ae57522 Patric Plitzner
  $tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
431 00a8e4b6 Andreas Kohlbecker
432 0ae57522 Patric Plitzner
  $page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
433 00a8e4b6 Andreas Kohlbecker
434 22383f95 Andreas Kohlbecker
  $synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;
435
  if(!$synonymy_as_tab){
436
    unset($tabsToDisplay["Synonymy"]);
437 3e6dfbb3 Andreas Kohlbecker
    // the synonymy is located in the general part in this case
438
    if($page_part == 'synonymy'){
439
      $page_part = 'description';
440
    }
441 22383f95 Andreas Kohlbecker
  }
442
443 0ae57522 Patric Plitzner
  $media = _load_media_for_taxon($taxon);
444 00a8e4b6 Andreas Kohlbecker
445
446 0ae57522 Patric Plitzner
  if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
447
    taxon_page_tabs_hidden('images');
448
  }
449 00a8e4b6 Andreas Kohlbecker
450 0ae57522 Patric Plitzner
  // --- GET specimensOrObservations --- //
451
  $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservations'));
452 00a8e4b6 Andreas Kohlbecker
453 0ae57522 Patric Plitzner
  $specimensOrObservationsCount = is_array($specimensOrObservations) ? count($specimensOrObservations) : 0;
454
  if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
455
    taxon_page_tabs_hidden('specimens');
456
  }
457 00a8e4b6 Andreas Kohlbecker
458 0ae57522 Patric Plitzner
  // --- GET polytomousKeys --- //
459
  $polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
460
  $identificationKeyCount = 0;
461
  if ($polytomousKeysPager) {
462
    $identificationKeyCount += $polytomousKeysPager->count;
463
  }
464
  if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
465
    taxon_page_tabs_hidden('keys');
466
  }
467 092744e1 Andreas Kohlbecker
468 22383f95 Andreas Kohlbecker
  // --- GET TaxonNodeAgentRelations --- //
469
  $current_classification_uuid = get_current_classification_uuid();
470
  $taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
471
      array(
472
          $taxon->uuid,
473
          $current_classification_uuid,
474
      ),
475
      "pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
476
  );
477
  if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
478
      taxon_page_tabs_hidden('experts');
479
  }
480 7663cd0b Andreas Kohlbecker
481 22383f95 Andreas Kohlbecker
  if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {
482 0ae57522 Patric Plitzner
    taxon_page_tabs_hidden('synonymy');
483
  }
484 00a8e4b6 Andreas Kohlbecker
485 0ae57522 Patric Plitzner
  // -------------------------------------------- //
486 00a8e4b6 Andreas Kohlbecker
487 0ae57522 Patric Plitzner
  if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
488 7272d19c Andreas Kohlbecker
    $render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
489 0ae57522 Patric Plitzner
  }
490 00a8e4b6 Andreas Kohlbecker
491 0ae57522 Patric Plitzner
  // --- PAGE PART: DESCRIPTION --- //
492
  if ($page_part == 'description' || $page_part == 'all') {
493 00a8e4b6 Andreas Kohlbecker
494 0ae57522 Patric Plitzner
    $merged_tree = merged_taxon_feature_tree($taxon);
495 00a8e4b6 Andreas Kohlbecker
496 7d8ef9fa Patric Plitzner
497 22383f95 Andreas Kohlbecker
    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
498 0ae57522 Patric Plitzner
    $render_array['general']['#weight'] = $weight++;
499
    $render_array['general']['#prefix'] = '<div id="general" class="page-part">';
500
    $render_array['general']['#suffix'] = '</div>';
501
  }
502 7d8ef9fa Patric Plitzner
503 0ae57522 Patric Plitzner
  // --- PAGE PART: IMAGES --- //
504
  if (array_search('images', taxon_page_tabs_hidden()) === FALSE && ($page_part == 'images' || $page_part == 'all')) {
505
    $images_html = '<div id="images" class="page-part">';
506
    if ($page_part == 'all') {
507 4feeabc7 Andreas Kohlbecker
      $images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
508 7d8ef9fa Patric Plitzner
    }
509 0ae57522 Patric Plitzner
    // Get the image gallery as configured by the admin.
510 8f4eb9ce Andreas Kohlbecker
    $default_image_gallery = 'default';
511
    $configured_image_gallery_viewer = variable_get('image_gallery_viewer', 'default');
512 4feeabc7 Andreas Kohlbecker
    $taxon_image_gallery = '<div class="error">No image gallery viewer configured</div>';
513 8f4eb9ce Andreas Kohlbecker
    if($configured_image_gallery_viewer == $default_image_gallery || $configured_image_gallery_viewer == 'fsi'){
514
      // the fsi_gallery requires a flash plugin, in case the client browser is not supporting
515
      // flash we also need to provide an the default gallery as alternative
516
      $taxon_image_gallery = '<div id="default-gallery-viewer">' .
517
        call_user_func_array('taxon_image_gallery_' . $default_image_gallery, array(
518
          $taxon,
519
          $media,
520
        ))
521
        . '</div>';
522
    }
523
    if($configured_image_gallery_viewer == 'fsi'){
524
      $taxon_image_gallery .= '<div id="'. $configured_image_gallery_viewer .'-gallery-viewer">' .
525
        call_user_func_array('taxon_image_gallery_' . $configured_image_gallery_viewer, array(
526
          $taxon,
527
          $media,
528
        ))
529
       . '</div>';
530
    }
531 0ae57522 Patric Plitzner
    $images_html .= $taxon_image_gallery;
532
    $images_html .= '</div>';
533
    $render_array['images'] = markup_to_render_array($images_html, $weight++);
534
  }
535 7d8ef9fa Patric Plitzner
536 0ae57522 Patric Plitzner
  // --- PAGE PART: SYNONYMY --- //
537 22383f95 Andreas Kohlbecker
  if ((($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
538 0ae57522 Patric Plitzner
    $synonymy_html = '<div id="synonymy" class="page-part">';
539
    if ($page_part == 'all') {
540 4feeabc7 Andreas Kohlbecker
      $synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
541 00a8e4b6 Andreas Kohlbecker
    }
542 0ae57522 Patric Plitzner
    $addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);
543 41b4bfc9 Andreas Kohlbecker
544 0ae57522 Patric Plitzner
    $synonymy_html .= theme('cdm_taxon_page_synonymy', array('taxon' => $taxon, 'addAcceptedTaxon' => $addAcceptedTaxon));
545 00a8e4b6 Andreas Kohlbecker
546 0ae57522 Patric Plitzner
    $synonymy_html .= '</div>';
547
    $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
548 00a8e4b6 Andreas Kohlbecker
549 0ae57522 Patric Plitzner
  }
550 00a8e4b6 Andreas Kohlbecker
551 0ae57522 Patric Plitzner
  // --- PAGE PART: SPECIMENS --- //
552
  if ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all')) {
553
    $render_array['specimens'] = array(
554 4feeabc7 Andreas Kohlbecker
        '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
555 0ae57522 Patric Plitzner
        'content' => cdm_dataportal_taxon_page_specimens($taxon), // returns render array
556
        '#suffix' => '</div>',
557
    );
558
  }
559
560
  // --- PAGE PART: KEYS --- //
561
  if ($identificationKeyCount == 1 && $page_part == 'keys'){
562
    drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
563
  }
564
  else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
565
    $keys_html = '<div id="keys" class="page-part">';
566
    if ($page_part == 'all') {
567 4feeabc7 Andreas Kohlbecker
      $keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
568 0ae57522 Patric Plitzner
    }
569
    $keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
570
    $keys_html .= '</div>';
571
    $render_array['keys'] = markup_to_render_array($keys_html, $weight++);
572
  }
573
574 7663cd0b Andreas Kohlbecker
  // --- PAGE PART: EXPERTS --- //
575
576
  if (array_search('experts', taxon_page_tabs_hidden()) === FALSE && ($page_part == 'experts' || $page_part == 'all')) {
577
    $render_array['experts'] = array(
578 4feeabc7 Andreas Kohlbecker
        '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
579 7663cd0b Andreas Kohlbecker
        'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
580
        '#suffix' => '</div>',
581
    );
582
  }
583
584
  // ------------------ END OF PARTS -------------- //
585 0ae57522 Patric Plitzner
586
  // adjust weights of page and toc elements according to the settings
587 4feeabc7 Andreas Kohlbecker
  $taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
588 0ae57522 Patric Plitzner
  foreach($taxontabs_weights as $tab_key => $weight){
589
    if(isset($render_array[$tab_key])){
590
      $render_array[$tab_key]['#weight'] = $weight;
591
    }
592
  }
593
594
595
  // set up the TOC for the pages which contain all pageparts
596
  if($page_part == 'all') {
597
598
    asort($taxontabs_weights);
599
    foreach(array_keys($taxontabs_weights) as $tab_key){
600
      if(isset($render_array[$tab_key])){
601
        if($tab_key != 'general'){
602
          // add entry for page part
603
          $toc_elements[] = array(
604 4feeabc7 Andreas Kohlbecker
              'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
605 0ae57522 Patric Plitzner
              'class' => array('page-part-toc-item-' . $tab_key)
606
          );
607
        } else {
608
          // add content of profile part instead
609
          if(isset($render_array['general'])) {
610
            // in case all tabs are shown at once the feature tocs
611
            // should be integrated into the tabs toc as sub list
612
            // and the profile image should be on top of the page
613
            if(isset($render_array['general']['taxon_description_feature_toc'])){;
614
            foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
615
              $toc_elements[] = $profile_toc_item;
616 7d8ef9fa Patric Plitzner
            }
617 0ae57522 Patric Plitzner
            unset($render_array['general']['taxon_description_feature_toc']);
618
            }
619
          }
620 7d8ef9fa Patric Plitzner
        }
621 0ae57522 Patric Plitzner
      }
622
    }
623 7d8ef9fa Patric Plitzner
624 0ae57522 Patric Plitzner
    // move profile image in page structure
625
    if(isset($render_array['general']['taxon_profile_image'])){
626
      $render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
627
      $render_array['profile_image']['#weight'] = -100;
628
      unset($render_array['general']['taxon_profile_image']);
629 7d8ef9fa Patric Plitzner
    }
630
631 0ae57522 Patric Plitzner
    // finally add the table of contents to the render array
632
    $render_array['toc'] = array(
633
        '#theme' => 'item_list',
634
        '#items' => $toc_elements,
635
        '#title' => t('Content'),
636
        '#weight' => -101,
637
        '#suffix' => '</div>',
638
        '#prefix'=> '<div id="page-toc">'
639
    );
640
  }
641
642 7d8ef9fa Patric Plitzner
643 0ae57522 Patric Plitzner
  return $render_array;
644 00a8e4b6 Andreas Kohlbecker
}
645
646 1ce9afb7 Patric Plitzner
/**
647 22f5e82d Andreas Kohlbecker
 * TODO should this function really be a compose function?
648
 *     For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
649 bf97c2e8 Andreas Kohlbecker
 *
650
 * composes and returns an render array containing the components of the taxon profile tab:
651
 *  - 'taxon_profile_image'
652
 *  - 'taxon_description_feature_toc'
653
 *  - 'taxon_description_features'
654
 *
655
 *
656 f78fda81 Andreas Kohlbecker
 * @param taxon
657
 * @param mergedTrees
658
 * @param media
659 bf97c2e8 Andreas Kohlbecker
 *
660
 * @return array
661 f78fda81 Andreas Kohlbecker
 *   A Drupal render array with the following elements:
662 bf97c2e8 Andreas Kohlbecker
 *     - 'taxon_profile_image'
663
 *     - 'taxon_description_feature_toc'
664
 *     - 'taxon_description_features'
665
 *
666
 * @ingroup compose
667
 */
668 22383f95 Andreas Kohlbecker
function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {
669 bf97c2e8 Andreas Kohlbecker
670 0ae57522 Patric Plitzner
  $render_array = array();
671
672
  $taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
673
674
  $hide_taxon_profile_image = FALSE;
675
  if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
676
    $rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
677
    $hide_taxon_profile_image = ($rankCompare > -1);
678
  }
679
680
  if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
681
682
    $representationPart = new stdClass();
683
    $attributes = array();
684 02faa087 Andreas Kohlbecker
    if (isset($media[0])) {
685
      // due to a bug the portal/taxon/{uuid}/media service only delivers a filtered media object
686
      // which only contains the thumbnail representation even if the height and width filters are not set.
687 673929dd Andreas Kohlbecker
      // -->
688 02faa087 Andreas Kohlbecker
      $preferred_media = cdm_ws_get(CDM_WS_MEDIA, $media[0]->uuid);
689
      $preferred_representations = cdm_preferred_media_representations($preferred_media, array(
690
        'image/jpg',
691
        'image/jpeg',
692
        'image/png',
693
        'image/gif',
694
      ),
695
        $taxon_profile_image_settings['maxextend'],
696
        $taxon_profile_image_settings['maxextend']
697
      );
698
      if(count($preferred_representations) > 0){
699
700
        $representation = array_shift($preferred_representations);
701
        $representationPart = $representation->parts[0];
702
        $attributes['alt'] = $representationPart->uri;
703
704
        if (!empty($taxon_profile_image_settings['media_uri_query'])) {
705
          $representationPart->uri = $representationPart->uri
706
            . (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
707
            . $taxon_profile_image_settings['media_uri_query'];
708
        }
709 0ae57522 Patric Plitzner
      }
710
    }
711
    else {
712 9506fd1f Andreas Kohlbecker
      if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
713 ca47ea76 Andreas Kohlbecker
        // show placeholder image instead
714
        if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
715
          // use the user provided image
716
          $profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
717
          $url = file_create_url($profile_image_file->uri);
718
          $image_info = image_get_info($profile_image_file->uri);
719
          $representationPart->width = $image_info['width'];
720
          $representationPart->height = $image_info['height'];
721
          $representationPart->uri = $url;
722
        }
723
        else {
724
          // use the hard coded default
725
          $representationPart->width = 184;
726
          $representationPart->height = 144;
727
          $representationPart->uri = base_path() . drupal_get_path('module',
728
              'cdm_dataportal') . '/images/no_picture.png';
729
        }
730
        $attributes['alt'] = "no image available";
731 0ae57522 Patric Plitzner
      }
732
    }
733
734 ca47ea76 Andreas Kohlbecker
    if (isset($representationPart->uri)) {
735 a9815578 Andreas Kohlbecker
      $profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);
736 ca47ea76 Andreas Kohlbecker
      // NOTE: style="width:${maxextend}px' is needed for IE8 !!!
737
      $render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $taxon_profile_image_settings['maxextend'] . 'px">' . $profile_image . '</div>',
738
        -101);
739
    }
740 0ae57522 Patric Plitzner
  }
741
742 22383f95 Andreas Kohlbecker
  if($add_synonymy){
743
    $render_array['synonymy'] = markup_to_render_array(
744
      theme('cdm_taxon_page_synonymy', array('taxon' => $taxon, 'addAcceptedTaxon' => true)),
745
      -102
746
    );
747
  }
748
749 1b756c5f Andreas Kohlbecker
  $pseudo_feature_blocks = array();
750
  $pseudo_feature_block_toc_items = array();
751 0ae57522 Patric Plitzner
752
753 1b756c5f Andreas Kohlbecker
  // Render the sections for each real feature
754
  $feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
755
756
  // Bibliography
757 0ae57522 Patric Plitzner
  $bibliography_settings = get_bibliography_settings();
758
  if($bibliography_settings['enabled'] == 1){
759 1b756c5f Andreas Kohlbecker
    $feature_bibliography = make_pseudo_feature('Bibliography', 'BIBLIOGRAPHY');
760
    $bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
761
    $bibliography_item = markup_to_render_array(FootnoteManager::renderFootnoteList('BIBLIOGRAPHY', ''));
762
    $bibliography_block->content[] = compose_feature_block_wrap_elements(array($bibliography_item), $feature_bibliography);
763 0ae57522 Patric Plitzner
764
    if(!empty($bibliography_block->content)){
765 1b756c5f Andreas Kohlbecker
      $pseudo_feature_block_toc_items['Bibliography']= 'bibliography';
766
      $pseudo_feature_blocks[] = $bibliography_block;
767 0ae57522 Patric Plitzner
    }
768 1b756c5f Andreas Kohlbecker
  }
769
770
  $render_array['taxon_description_features'] = _block_get_renderable_array(
771
    array_merge($feature_block_list, $pseudo_feature_blocks)
772
  );
773 0ae57522 Patric Plitzner
774 1b756c5f Andreas Kohlbecker
  if($pseudo_feature_block_toc_items){
775
    foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
776
      cdm_toc_list_add_item($label, $fragment);
777
    }
778 0ae57522 Patric Plitzner
  }
779
780
  // create the table of content
781
  $toc = array(
782
      '#theme' => 'item_list',
783
    '#items' => cdm_toc_list(),
784
      '#title' => t('Content'),
785
    '#weight' => -100,                  // move to the top
786
      '#suffix' => '</div>',
787
      '#prefix'=> '<div id="page-toc">'
788
  );
789
  $render_array['taxon_description_feature_toc'] = $toc;
790
791
  return $render_array;
792 bf97c2e8 Andreas Kohlbecker
}
793
794 f9a3d0f6 Andreas Kohlbecker
/**
795
 * composes and returns an render array for the experts associated with the given taxon
796
 *
797
 * @param taxon
798
 *
799
 * @return array
800
 *   A Drupal render array for a table with the experts
801
 *
802
 * @ingroup compose
803
 */
804 7663cd0b Andreas Kohlbecker
function compose_cdm_taxon_page_experts($taxon){
805
806
  $render_array = array();
807
  if(!isset($taxon->uuid)){
808
    return $render_array;
809
  }
810
811
  $current_classification_uuid = get_current_classification_uuid();
812
  // TODO use cdm_ws_fetchall below but this failes! needs fix!
813
  $taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
814
    array(
815
      $taxon->uuid,
816
      $current_classification_uuid
817
    )
818
  );
819
820
  $header = array(
821
    array('data' => t('Expert')),
822
    array('data' => t('Role'))
823
  );
824
  $rows = array();
825
826
827
  foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
828
829 d9763fd3 Andreas Kohlbecker
830
    $expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
831
    $expert_details_container_id = 'expert_details_' . $expert_role_id;
832
833
    $agent_label_markup = cdm_dynabox(
834
      'expert_' . $expert_role_id,
835
      $taxon_node_agent_relation->agent->titleCache,
836
      // specifying both ends of the relationship will return only one record in the pager
837
      cdm_compose_url(CDM_WS_PORTAL_AGENT,
838
         array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
839
        'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
840
      'cdm_taxon_expert',
841
      'Click for details',
842
      array('div', 'div'),
843
      array(), // attributes
844 cea412e7 Andreas Kohlbecker
      '#' . $expert_details_container_id // $content_element_selector
845 d9763fd3 Andreas Kohlbecker
    );
846
847
    // Expert and Role
848
    $rows[] = array(
849
      'data' => array(
850
        array(
851
          'data' => $agent_label_markup,
852
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
853 7663cd0b Andreas Kohlbecker
        ),
854 d9763fd3 Andreas Kohlbecker
        array(
855
          'data' => $taxon_node_agent_relation->type->representation_L10n,
856
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
857
        )
858
      )
859
    );
860
    // Agent details
861
    $rows[] = array(
862
      'data' => array(
863
        array(
864
          'data' => '<!-- expert_details_container -->',
865
          'id' => $expert_details_container_id,
866
          'colspan' => 2
867
        )
868
      )
869 7663cd0b Andreas Kohlbecker
    );
870 d9763fd3 Andreas Kohlbecker
871 7663cd0b Andreas Kohlbecker
  }
872
873
874
  $render_array['experts_table'] = array(
875
    '#theme' => 'table',
876
    '#header' => $header,
877
    '#rows' => $rows,
878
  );
879
880
881
  return $render_array;
882
}
883
884 bf97c2e8 Andreas Kohlbecker
885 3f259ca3 Andreas Kohlbecker
/**
886 7663cd0b Andreas Kohlbecker
 * Manages the tabs to be hidden in the taxon page.
887 3f259ca3 Andreas Kohlbecker
 *
888
 * The tabs are identified by their last menu link path element:
889
 *  - description
890
 *  - synonymy
891
 *  - images
892
 *  - specimens
893
 *  - key
894
 *
895
 * Internally the tabs are stored in a static variable which is
896
 * managed by drupal_static().
897
 *
898
 * @param string $add_tab
899 7663cd0b Andreas Kohlbecker
 *   Optional parameter. The given string will be added to the array of tabs
900 3f259ca3 Andreas Kohlbecker
 *
901
 * @return
902
 *   The array of tabs
903
 */
904
function taxon_page_tabs_hidden($add_tab = NULL) {
905 0ae57522 Patric Plitzner
  $tabs = &drupal_static(__FUNCTION__);
906 3f259ca3 Andreas Kohlbecker
907 0ae57522 Patric Plitzner
  if(!isset($tabs)){
908
    $tabs = array();
909
  }
910 3f259ca3 Andreas Kohlbecker
911 0ae57522 Patric Plitzner
  if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
912
    $tabs[] = $add_tab;
913
  }
914 3f259ca3 Andreas Kohlbecker
915 0ae57522 Patric Plitzner
  return $tabs;
916 3f259ca3 Andreas Kohlbecker
}
917
918
/**
919
 * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
920
 *
921 9438ad3a Andreas Kohlbecker
 *  - Removes the tabs to be hidden, @see taxon_page_tabs_hidden()
922
 *  - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
923 3f259ca3 Andreas Kohlbecker
 *
924
 * @param array $variables
925
 *   The variables array
926
 */
927
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
928
929 0ae57522 Patric Plitzner
  $hidden_tabs = taxon_page_tabs_hidden();
930 3f259ca3 Andreas Kohlbecker
931 0ae57522 Patric Plitzner
  if (is_array($variables['primary'])) {
932
    foreach ($variables['primary'] as $key => &$element) {
933 6f1a217c Andreas Kohlbecker
934 0ae57522 Patric Plitzner
      // 1. Remove the tabs to be hidden
935
      foreach ($hidden_tabs as $tab) {
936
        if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
937
          // remove the tab
938
          unset($variables['primary'][$key]);
939 9438ad3a Andreas Kohlbecker
        }
940 0ae57522 Patric Plitzner
      }
941 3f259ca3 Andreas Kohlbecker
    }
942 0ae57522 Patric Plitzner
  }
943 6f1a217c Andreas Kohlbecker
}
944
945
946
947
/**
948
 * Implements the hook_preprocess_HOOK() for theme_menu_local_task()
949
 *
950
 *
951
 * @param array $variables
952
 *   An associative array containing:
953
 *     - element: A render element containing:
954
 *          #link: A menu link array with 'title', 'href', and 'localized_options' keys.
955
 *          #active: A boolean indicating whether the local task is active.
956
 *
957
 */
958
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
959
960 0ae57522 Patric Plitzner
  $link = $variables['element']['#link'];
961
  if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
962
    $link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
963
    $link['localized_options']['html'] = TRUE;
964 6f1a217c Andreas Kohlbecker
965 0ae57522 Patric Plitzner
    $variables['element']['#link'] = $link;
966
  }
967 f19f47fa Andreas Kohlbecker
}
968 f9a3d0f6 Andreas Kohlbecker
969
/* =================== block composition ===================== */
970
971
/**
972 23ad16a1 Andreas Kohlbecker
 * Composes and returns an render array for the classification breadcrumbs of the given taxon.
973 f9a3d0f6 Andreas Kohlbecker
 *
974
 * @param taxon
975
 *
976
 * @return array
977
 *   A Drupal render array for a table with the experts
978
 *
979
 * @ingroup compose
980
 */
981
function compose_classification_breadcrumbs($taxon_uuid) {
982
983 b0adfd32 Andreas Kohlbecker
  _add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
984 d0d23caa Andreas Kohlbecker
985 f9a3d0f6 Andreas Kohlbecker
  $render_array = array();
986
987
  $render_array['#theme'] = 'item_list';
988
  $render_array['#type'] = 'ul';
989
  $render_array['#attributes'] = array(
990
    'id' => 'classification-breadcrumbs',
991
    'class' => 'breadcrumbs inline',
992
  );
993
994
  $items = array();
995
996 38da4e54 Andreas Kohlbecker
  $parent_taxon_nodes = null;
997
  if($taxon_uuid){
998
    $parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
999
  }
1000 f9a3d0f6 Andreas Kohlbecker
1001 38da4e54 Andreas Kohlbecker
  $classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
1002
  // find current classification in list
1003
  $classification = null;
1004
  $current_classification_uuid = get_current_classification_uuid();
1005
  foreach ($classifications as $classification){
1006
    if($classification->uuid == $current_classification_uuid){
1007
      break;
1008 b0adfd32 Andreas Kohlbecker
    }
1009 38da4e54 Andreas Kohlbecker
  }
1010 b0adfd32 Andreas Kohlbecker
1011 38da4e54 Andreas Kohlbecker
  $node_name = '';
1012
  if(count($classifications) > 1 ){
1013
    // need to add the current classification as first label
1014 0af3ce28 Andreas Kohlbecker
1015
    $label = $classification->titleCache;
1016
    if(strlen($label) > 20){
1017
      $label = substr($label, 0, strpos($label, ' ', 15)) . '...';
1018
    }
1019
    $node_name = font_awesome_icon_markup('fa-th-list')  . ' ' . l($label, '#', array(
1020
      'attributes' => array(
1021
        'class' => 'taxonomic-children-button classification-chooser',
1022
        'data-destination-uri' => drupal_get_destination(),
1023
        'data-cdm-align-with' => array('prev')
1024
      ),
1025
      'html' => true
1026
    ));
1027 f9a3d0f6 Andreas Kohlbecker
  }
1028 b0adfd32 Andreas Kohlbecker
1029 38da4e54 Andreas Kohlbecker
  $rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1030 0af3ce28 Andreas Kohlbecker
1031
  $rank_separator = '<span> '
1032 38da4e54 Andreas Kohlbecker
    . font_awesome_icon_markup('fa-chevron-right')
1033
    . ' </span>';
1034 0af3ce28 Andreas Kohlbecker
  $more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
1035 69fb3dbb Andreas Kohlbecker
  $more_children_label = '...';
1036 38da4e54 Andreas Kohlbecker
1037 0af3ce28 Andreas Kohlbecker
  $items[] = $node_name;
1038 38da4e54 Andreas Kohlbecker
1039 0af3ce28 Andreas Kohlbecker
  $more_children_for = null;
1040 e3235962 Andreas Kohlbecker
  if($parent_taxon_nodes){
1041 0af3ce28 Andreas Kohlbecker
    foreach ($parent_taxon_nodes as $node) {
1042 38da4e54 Andreas Kohlbecker
1043
      $is_first_item = count($items) == 0;
1044 0af3ce28 Andreas Kohlbecker
      $is_last_item = count($items) == count($parent_taxon_nodes);
1045 38da4e54 Andreas Kohlbecker
      $node_name = cdm_dataportal_shortname_of($node);
1046
      $path = path_to_taxon($node->taxonUuid);
1047
1048 0af3ce28 Andreas Kohlbecker
      if($node->taxonomicChildrenCount > 0) {
1049
        $more_children_for = $node->taxonUuid;
1050
      } else {
1051
        $more_children_for = null;
1052 38da4e54 Andreas Kohlbecker
      }
1053
1054 0af3ce28 Andreas Kohlbecker
      // 'fa-sitemap'
1055
1056 38da4e54 Andreas Kohlbecker
      $items[] =
1057 0af3ce28 Andreas Kohlbecker
        ($is_first_item ? '' : ' ')
1058
        . $rank_separator
1059
        . l(
1060 4b3be949 Andreas Kohlbecker
          '<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
1061 0af3ce28 Andreas Kohlbecker
          $path,
1062
          array(
1063
            'attributes' => array(
1064
              'class' => array('taxonomic-children-button'),
1065
              'data-cdm-taxon-uuid' => array($node->taxonUuid),
1066
              'data-cdm-classification-mode' => array('siblings'),
1067
              'data-cdm-align-with' => array('prev')
1068 4b3be949 Andreas Kohlbecker
            ),
1069
            'html' => true
1070 0af3ce28 Andreas Kohlbecker
          )
1071
        );
1072
      }
1073 38da4e54 Andreas Kohlbecker
    }
1074 0af3ce28 Andreas Kohlbecker
1075
  // add more button to the end
1076
  if(!$parent_taxon_nodes) {
1077
    // not taxon focused yet, adding button to make  the root nodes available
1078 69fb3dbb Andreas Kohlbecker
    $items[] = '<span>'
1079
      . $more_children_icon . '&nbsp;' .
1080
      '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
1081 53c705d4 Andreas Kohlbecker
      . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
1082 69fb3dbb Andreas Kohlbecker
      . '</span>';
1083 0af3ce28 Andreas Kohlbecker
  } else if($more_children_for){
1084
    // last parent item has child taxon nodes
1085 69fb3dbb Andreas Kohlbecker
    $items[] = ' <span>'
1086
      . $more_children_icon . '&nbsp;' .
1087
      '<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
1088 53c705d4 Andreas Kohlbecker
      . '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
1089 69fb3dbb Andreas Kohlbecker
      . '</span>';
1090 0af3ce28 Andreas Kohlbecker
1091 e3235962 Andreas Kohlbecker
  }
1092 b0adfd32 Andreas Kohlbecker
1093 30845bda Andreas Kohlbecker
  $render_array['#items'] = $items;
1094 0af3ce28 Andreas Kohlbecker
1095 30845bda Andreas Kohlbecker
  return $render_array;
1096
}
1097 0af3ce28 Andreas Kohlbecker
1098 69fb3dbb Andreas Kohlbecker
1099 30845bda Andreas Kohlbecker
/**
1100
 * @param $specimen_uuid
1101
 * @return array
1102
 *    The drupal render array for the page
1103
 *
1104
 * @ingroup compose
1105
 */
1106
function compose_cdm_specimen_page($specimen_uuid)
1107
{
1108
  drupal_set_title("Specimen Details");
1109
  $specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($specimen_uuid, 'specimenDerivates'));
1110
1111
  $render_array = array();
1112
  RenderHints::pushToRenderStack('specimen_page');
1113 f9a3d0f6 Andreas Kohlbecker
1114 30845bda Andreas Kohlbecker
  $detail_html = render_cdm_specimen_page($specimen, true);
1115
  $render_array['specimen_html'] = array(
1116
    '#markup' => $detail_html
1117
  );
1118
1119
  RenderHints::popFromRenderStack();
1120 f9a3d0f6 Andreas Kohlbecker
  return $render_array;
1121 30845bda Andreas Kohlbecker
}
1122 f9a3d0f6 Andreas Kohlbecker
1123 30845bda Andreas Kohlbecker
/**
1124
 * @param $named_area_uuid
1125
 * @return array
1126
 *    The drupal render array for the page
1127
 *
1128
 * @ingroup compose
1129
 */
1130
function compose_cdm_named_area_page($named_area_uuid)
1131
{
1132
1133
  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
1134
1135
  $render_array = array();
1136
  RenderHints::pushToRenderStack('named_area_page');
1137
1138
  $groups = array();
1139
  @_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
1140
  @_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
1141
  if(isset($named_area->level)) {
1142
    @_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
1143
  }
1144
1145
  $name_area_details_elements = array(
1146
   // '#title' => $title,
1147
    '#theme' => 'description_list',
1148
    '#groups' => $groups,
1149
    '#attributes' => array('class' => html_class_attribute_ref($named_area)),
1150
  );
1151
1152
  $render_array[] = $name_area_details_elements;
1153
1154
  RenderHints::popFromRenderStack();
1155
  return $render_array;
1156 f9a3d0f6 Andreas Kohlbecker
}
1157 4feeabc7 Andreas Kohlbecker
1158
/**
1159
 * Provides the the label string for taxon page tabs.
1160
 *
1161
 * The $tabname as passed to the method will be returned if no override
1162
 * label is configured in the settings.
1163
 */
1164
function cdm_taxonpage_tab_label($tabname) {
1165
  static $taxon_tabs_labels = null;
1166
  if($taxon_tabs_labels == null){
1167
    $taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
1168
  }
1169
  $tabname_key = strtolower($tabname);
1170
  if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
1171
    return $taxon_tabs_labels[$tabname_key];
1172
  }
1173
  return $tabname;
1174
}