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Revision 25b933c4

Added by Andreas Kohlbecker about 3 years ago

ID 25b933c487ed6c58a6675307723b2ac14c32beea
Parent 846f21e1
Child a7dcea2c

ref #7704, ref #9395 using web-services now returning all root units

     define('CDM_WS_TAXON', 'taxon');
     define('CDM_WS_PORTAL_TAXON_FIELDUNIT_DTOS', 'portal/taxon/$0/fieldUnitDTOs');
     define('CDM_WS_PORTAL_TAXON_ROOTUNIT_DTOS', 'portal/taxon/$0/rootUnitDTOs');
     define('CDM_WS_TAXON_CLASSIFICATIONS', 'taxon/$0/classifications');
     define('CDM_WS_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT', 'taxon/findByDescriptionElementFullText');
-...
      */
     define('CDM_WS_PORTAL_TAXON_DESCRIPTIONS_ELEMENTSBYTYPE', 'portal/taxon/$0/descriptions/elementsByType/$1');
     define('CDM_WS_PORTAL_TAXON_USEDESCRIPTIONS', 'portal/taxon/$0/useDescriptions');
     define('CDM_WS_PORTAL_TAXON_ASSOCIATED_ROOTUNITS', 'portal/taxon/$0/associatedRootUnits');
     define('CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS', 'portal/taxon/$0/toNameRelationships');
     define('CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS', 'portal/taxon/$0/fromNameRelationships');
     define('CDM_WS_PORTAL_TAXON_MEDIA', 'portal/taxon/$0/media');
-...
     define('CDM_WS_OCCURRENCE', 'occurrence');
     define('CDM_WS_OCCURRENCE_FILEUNIT_DTO', 'occurrence/$0/fieldUnitDTO');
     define('CDM_WS_PORTAL_OCCURRENCE', 'portal/occurrence');
     define('CDM_WS_PORTAL_OCCURRENCE_AS_DTO', 'portal/occurrence/$0/asDTO');
     define('CDM_WS_OCCURRENCE_ACCESSION_NUMBER', 'occurrence/byGeneticAccessionNumber');
     /**
      * url query parameters:
-...
      * returns Pager<SpecimenOrObservationBase>
      */
     define('CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON', 'occurrence/byAssociatedTaxon');
     define('CDM_WS_OCCURRENCE_FIELDUNIT_DTO_BY_ASSOCIATEDTAXON', 'occurrence/specimensOrObservationsByAssociatedTaxon');
     define('CDM_WS_OCCURRENCE_ROOTUNIT_DTO_BY_ASSOCIATEDTAXON', 'occurrence/rootUnitDTOsByAssociatedTaxon');
     define('CDM_WS_DERIVEDUNIT_FACADE', 'derivedUnitFacade/$0');
     define('CDM_WS_PORTAL_DERIVEDUNIT_FACADE', 'portal/derivedUnitFacade/$0');

     /**
      * Provides the HTML markup for a specimen page
      * Renders a DerivedUnit either in a compact form or with full details.
+     *
      * @param $specimen
      * @param $derived_unit_dto
      *  The DerivedUnitDTO
      * @param $with_full_details
      *  Wether to render the dertived unit data with full details, like for example for the specimen page
+     *
      * @return string
      *  The markup for a specimen page
      */
     function render_cdm_specimenDTO_page($specimen, $is_specimen_page = false)
     function render_cdm_specimenDTO_page($derived_unit_dto, $with_full_details = false)
+    {
         $detail_html = "";
         //link to specimen page
         $path_to_specimen = path_to_specimen($specimen->uuid);
         if (!$is_specimen_page) {
             $specimenPageLink = l($specimen->specimenIdentifier, $path_to_specimen);
         $path_to_specimen = path_to_specimen($derived_unit_dto->uuid);
         if (!$with_full_details) {
             $specimenPageLink = l($derived_unit_dto->specimenIdentifier, $path_to_specimen);
             $detail_html .= "<strong>Specimen summary: $specimenPageLink</strong><br>";
+        }
         if($is_specimen_page) {
             if($specimen->citation){
                 $detail_html .= "<br>".$specimen->citation."<br>";
         if($with_full_details) {
             if($derived_unit_dto->citation){
                 $detail_html .= "<br>".$derived_unit_dto->citation."<br>";
+            }
+        }
         if ($specimen->preferredStableUri) {
             $stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri);
         if ($derived_unit_dto->preferredStableUri) {
             $stableIdentifierLink = l($derived_unit_dto->preferredStableUri, $derived_unit_dto->preferredStableUri);
             $detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
+        }
         if ($is_specimen_page) {
         if ($with_full_details) {
             // associated taxa
             if ($specimen->associatedTaxa) {
             if ($derived_unit_dto->associatedTaxa) {
                 $detail_html .= "<br>";
                 $detail_html .= create_label("Associated with");
                 if (sizeof($specimen->associatedTaxa) > 1) {
                 if (sizeof($derived_unit_dto->associatedTaxa) > 1) {
                     $detail_html .= "<br>";
+                }
                 foreach ($specimen->associatedTaxa as $associatedTaxon) {
                 foreach ($derived_unit_dto->associatedTaxa as $associatedTaxon) {
                     $detail_html .= l($associatedTaxon->label, path_to_taxon($associatedTaxon->uuid, "specimens"));//$associatedTaxon->second."<br>";
+                }
                 $detail_html .= "<br>";
-...
+        }
         // - type information
         $types = "";
         if (isset($specimen->types)) {
         if (isset($derived_unit_dto->types)) {
             //typed taxa
             foreach ($specimen->types as $typeStatus => $typedTaxa) {
                 if($specimen->types){
             foreach ($derived_unit_dto->types as $typeStatus => $typedTaxa) {
                 if($derived_unit_dto->types){
                     if(empty($typeStatus) || $typeStatus == "_empty_"|| $typeStatus == ""){
                         $detail_html .= "<i>Type for:</i> ";
                     } else {
-...
                $detail_html .= '<br>';
+            }
+        }
         $derivateDataDTO = $specimen->derivateDataDTO;
         $derivateDataDTO = $derived_unit_dto->derivateDataDTO;
         // - specimen scans
         $specimenScans = create_html_links($derivateDataDTO->specimenScans, true);
         // - molecular data
-...
         $detailImages = create_html_links($derivateDataDTO->detailImages, true);
         if ($types) {
             $detail_html .= $is_specimen_page ? "<br>" : "";
             $detail_html .= $with_full_details ? "<br>" : "";
             $detail_html .= create_label("Type(s)") . $types . "<br>";
+        }
         if ($specimenScans and !$is_specimen_page) {
         if ($specimenScans and !$with_full_details) {
             $detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
+        }
         //specimen scan image gallery
         if ($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
         if ($with_full_details and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
             $detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
+        }
         if ($molecularData) {
             $detail_html .= $is_specimen_page ? "<br>" : "";
             $detail_html .= $with_full_details ? "<br>" : "";
             $detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
+        }
         if ($detailImages and !$is_specimen_page) {
         if ($detailImages and !$with_full_details) {
             $detail_html .= create_label("Detail Images") . $detailImages . "<br>";
+        }
         //detail image gallery
         if ($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {
         if ($with_full_details and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {
             $detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
+        }
         //character data
         if ($specimen->characterData) {
             $detail_html .= $is_specimen_page ? "<br>" : "";
         if ($derived_unit_dto->characterData) {
             $detail_html .= $with_full_details ? "<br>" : "";
             $detail_html .= create_label("Character Data");
             if ($is_specimen_page) {
             if ($with_full_details) {
                 $detail_html .= "<br>";
                 foreach ($specimen->characterData as $characterStatePair) {
                 foreach ($derived_unit_dto->characterData as $characterStatePair) {
                     $detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;
                     $detail_html .= "<br>";
+            }
-...
     /**
      * Creates render array items for FieldUnitDTO or DerivedUnitDTO.
+     *
      * @param array $fieldunit_dtos
      *     list of FieldUnitDTOs
      * @param array $root_unit_dtos
      *     list of SpecimenOrObservationDTOs
      * @return array
      *    An array which can be used in render arrays to be passed to the
      * theme_table() and theme_list().
      */
     function specimen_render_array_items(array $fieldunit_dtos){
     function specimen_render_array_items(array $root_unit_dtos){
       $render_array_items = array();
       $items = array();
       //we need one more item to contain the items of one level (fieldunit, derivate data etc.)
       foreach ($fieldunit_dtos as &$fieldunit_dto) {
         $items['data'] = $fieldunit_dto->label;
         $specimen = compose_cdm_specimen_or_observation_tree_entry($fieldunit_dto);
       foreach ($root_unit_dtos as &$sob_dto) {
         $items['data'] = $sob_dto->label;
         $specimen = compose_cdm_specimen_or_observation_tree_entry($sob_dto);
         $children = array();
         $child = array();
         $child['data'] =$specimen;
         // $children[] = create_specimen_array($specimenOrObservation->derivatives);
         if (isset($fieldunit_dto->derivatives) && sizeof($fieldunit_dto->derivatives) > 0){
           usort($fieldunit_dto->derivatives, 'compare_specimen_or_observation_dtos');
           $child['children']= specimen_render_array_items($fieldunit_dto->derivatives);
         if (isset($sob_dto->derivatives) && sizeof($sob_dto->derivatives) > 0){
           usort($sob_dto->derivatives, 'compare_specimen_or_observation_dtos');
           $child['children']= specimen_render_array_items($sob_dto->derivatives);
+        }
         $children[]=$child;
         $items['children'] = $children;
-...
      * Composes a compressed derivate table showing all derivatives which
      * stem from a common gathering event.
+     *
      * @param $field_unit_uuids array
      *  An array of uuids for cdm FieldUnit entities.
      * @param $root_unit_uuids array
      *  An array of uuids for cdm root units of the derivation graphs.
+     *
      * @return array
      *  A drupal render array for a table
-...
      * @ingroup compose
      */
     function compose_compressed_specimen_derivate_table($field_unit_uuids) {
     function compose_compressed_specimen_derivate_table($root_unit_uuids) {
       // prepare font icons
       $expand_icon = font_awesome_icon_markup(
-...
       $rowcount = 0;
       $rows = array();
       foreach ($field_unit_uuids as $field_unit_uuid) {
       foreach ($root_unit_uuids as $root_unit_uuid) {
         //get derivate hierarchy for the FieldUnit
         $derivateHierarchy = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($field_unit_uuid, 'derivateHierarchy'));
         if ($derivateHierarchy) {
         $sob_dto = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE_AS_DTO, array($root_unit_uuid));
         if ($sob_dto) {
           //summary row
           $rows[] = array(
             'data' => array(
               array(
                 'data' => $expand_icon . $collapse_icon,
                 'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
               ),
               array(
                 'data' => $derivateHierarchy->country,
                 'class' => array('summary_row_cell')
               ),
               array(
                 'data' => $derivateHierarchy->date,
                 'class' => array('summary_row_cell')
               ),
               array(
                 'data' => $derivateHierarchy->collectingString,
                 'class' => array('summary_row_cell')
               ),
               @array(
                 'data' => $derivateHierarchy->collectionStatistics,
                 'class' => array('summary_row_cell')
               ),
               array(
                 'data' => $derivateHierarchy->hasType ? $checked_box_icon : "",
                 'class' => array('summary_row_cell', 'summary_row_icon')
               ),
               array(
                 'data' => $derivateHierarchy->hasSpecimenScan ? $checked_box_icon : "",
                 'class' => array('summary_row_cell', 'summary_row_icon')
           if($sob_dto->class == "FieldUnitDTO"){
             $rows[] = array(
               'data' => array(
                 array(
                   'data' => $expand_icon . $collapse_icon,
                   'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
                 ),
                 array(
                   'data' => $sob_dto->country,
                   'class' => array('summary_row_cell')
                 ),
                 array(
                   'data' => $sob_dto->date,
                   'class' => array('summary_row_cell')
                 ),
                 array(
                   'data' => $sob_dto->collectingString,
                   'class' => array('summary_row_cell')
                 ),
                 @array(
                   'data' => $sob_dto->collectionStatistics,
                   'class' => array('summary_row_cell')
                 ),
                 array(
                   'data' => $sob_dto->hasType ? $checked_box_icon : "",
                   'class' => array('summary_row_cell', 'summary_row_icon')
                 ),
                 array(
                   'data' => $sob_dto->hasSpecimenScan ? $checked_box_icon : "",
                   'class' => array('summary_row_cell', 'summary_row_icon')
                 ),
                 array(
                   'data' => ($sob_dto->hasDna ? $sequence_icon : "") . " "
                     . ($sob_dto->hasDetailImage ? $detail_image_icon : "") . " "
                     . ($sob_dto->hasCharacterData ? $character_data_icon : ""),
                   'class' => array('summary_row_cell', 'summary_row_icon')
+                )
               ),
               array(
                 'data' => ($derivateHierarchy->hasDna ? $sequence_icon : "") . " "
                   . ($derivateHierarchy->hasDetailImage ? $detail_image_icon : "") . " "
                   . ($derivateHierarchy->hasCharacterData ? $character_data_icon : ""),
                 'class' => array('summary_row_cell', 'summary_row_icon')
               'id' => 'derivate_summary' . $rowcount, // summary row id
               'class' => array('summary_row'),
             );
           } else {
             $rows[] = array(
               'data' => array(
                 array(
                   'data' => $expand_icon . $collapse_icon,
                   'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
                 ),
                 array(
                   'data' => $sob_dto->label,
                   'class' => array('summary_row_cell'),
                   'colspan' => 7
+                )
+              )
             ),
             'id' => 'derivate_summary' . $rowcount, // summary row id
             'class' => array('summary_row'),
           );
             );
+          }
           //assemble field unit details
           $detail_html = "";
           // - citation
           if ($derivateHierarchy->citation) {
             $detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";
           if ($sob_dto->citation) {
             $detail_html .= create_label("Citation") . $sob_dto->citation . "<br>";
+          }
           //assemble specimen details
           if ($derivateHierarchy->derivatives) {
           if ($sob_dto->derivatives) {
             $derivatives_orderd = [];
             foreach ($derivateHierarchy->derivatives as $derivedUnitDTO) {
               $derivatives_orderd[$derivedUnitDTO->specimenIdentifier] = $derivedUnitDTO;
             foreach ($sob_dto->derivatives as $derivative_dto) {
               $derivatives_orderd[$derivative_dto->specimenIdentifier] = $derivative_dto;
+            }
             ksort($derivatives_orderd);
             foreach ($derivatives_orderd as $derivedUnitDTO) {
             foreach ($derivatives_orderd as $derivative_dto) {
               $detail_html .= "<br>";
               $detail_html .= render_cdm_specimenDTO_page($derivedUnitDTO);
               $detail_html .= render_cdm_specimenDTO_page($derivative_dto);
+            }
+          }
           $detail_html .= "<br>";
-...
      * Composes the view on specimens and occurrences as derivate tree
      * starting from the field unit including all derivatives.
+     *
      * @see DM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TREE
      * @see CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TREE
+     *
      * @param object $fieldunit_dtos
      *   list of FieldUnitDTOs
      * @param array $root_unit_dtos
      *   list of SpecimenOrObservationDTOs
      * @return array
      *   The Drupal render array
+     *
      * @ingroup compose
      */
     function compose_specimen_table_top_down(array $fieldunit_dtos){
     function compose_specimen_table_top_down(array $root_unit_dtos){
       $specimen_render_array_items = specimen_render_array_items($fieldunit_dtos);
       $specimen_render_array_items = specimen_render_array_items($root_unit_dtos);
         // add icons
       $expand_icon = font_awesome_icon_markup(
-...
      */
     function order_specimens_or_observations_by_date_and_type($specimens_or_observations)
+    {
     // order occurrences by date but types should be on top of the list
       $type_specimens = array();
       $other_occurrences = array();
       if(is_array($specimens_or_observations)){
-...
      */
     function order_fieldUnitDtos_by_date_and_type($fieldUnitDTOs)
+    {
       return order_specimens_or_observations_by_date_and_type($fieldUnitDTOs);
       $units_with_types = [];
       $units_no_types = [];
       foreach($fieldUnitDTOs as $dto){
         if(isset($dto->specimenTypeDesignations[0])){
           $units_with_types[] = $dto;
         } else {
           $units_no_types[] = $dto;
+        }
+      }
       usort($units_with_types, 'compare_specimen_or_observation_dtos_by_date');
       usort($units_no_types, 'compare_specimen_or_observation_dtos_by_date');
       return array_merge($units_with_types, $units_no_types);
+    }
     /**
-...
+    }
     /**
      * Compares two SpecimenTypeDesignations
      * Compares two SpecimenTypeDesignations by identifier and label
+     *
      * @param object $a
      *   A SpecimenOrObservationDTO.
-...
         $b_text =  isset($b->specimenIdentifier) ? $b->specimenIdentifier : $b->label;
         return strcasecmp($a_text, $b_text);
+    }
     /**
      * Compares two SpecimenTypeDesignations by date or label
+     *
      * @param object $a
      *   A SpecimenOrObservationDTO.
      * @param object $b
      *   The SpecimenOrObservationDTO.
      */
     function compare_specimen_or_observation_dtos_by_date($a, $b) {
       // Sort alphabetically.
       $a_text =  isset($a->date) ? $a->date : $a->label;
       $b_text =  isset($b->date) ? $b->date : $b->label;
       return strcasecmp($a_text, $b_text);
+    }

         $render_array = array();
         RenderHints::pushToRenderStack('taxon_page_specimens');
       $fieldUnitDTOs = null;
       $root_unit_dtos = null;
       $specimensOrObservations = array();
       $current_view_mode = variable_get(CDM_SPECIMEN_LIST_VIEW_MODE, CDM_SPECIMEN_LIST_VIEW_MODE_DEFAULT);
       if ($current_view_mode == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TABLE || $current_view_mode == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TREE){
           // get fieldUnitDTOs
           $fieldUnitDTOs = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIELDUNIT_DTOS, array( $taxon->uuid));
           $fieldUnitDTOs = order_fieldUnitDtos_by_date_and_type($fieldUnitDTOs);
           $root_unit_dtos = cdm_ws_get(CDM_WS_PORTAL_TAXON_ROOTUNIT_DTOS, array( $taxon->uuid));
           $root_unit_dtos = order_fieldUnitDtos_by_date_and_type($root_unit_dtos);
         } else {
           // $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservations'));
           // extend by associated taxas occurrences
-...
           if (isset($pager->records[0])) {
             $specimensOrObservations = $pager->records;
+          }
           // cdm_ws_get(CDM_WS_OCCURRENCE_FIELDUNIT_DTO_BY_ASSOCIATEDTAXON,
           // cdm_ws_get(CDM_WS_OCCURRENCE_ROOTUNIT_DTO_BY_ASSOCIATEDTAXON // was CDM_WS_OCCURRENCE_FIELDUNIT_DTO_BY_ASSOCIATEDTAXON,
           // null,
           // $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
           // );
-...
+        }
         // --- get map service HTTP query parameters
         if (count($specimensOrObservations) > 0 || $fieldUnitDTOs > 0) {
         if (count($specimensOrObservations) > 0 || $root_unit_dtos > 0) {
             $render_array['map'] = occurrence_map_query_parameters($taxon);
+        }
-...
         if(($current_view_mode == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TABLE)){
             //COMPRESSED SPECIMEN DERIVATE TABLE
             $pager_field_units = cdm_ws_page(
               cdm_compose_url(CDM_WS_PORTAL_TAXON, [
                 $taxon->uuid,
                 'associatedFieldUnits'
               ]),
             $pager_root_units = cdm_ws_page(
               cdm_compose_url(CDM_WS_PORTAL_TAXON_ASSOCIATED_ROOTUNITS, [$taxon->uuid]),
               variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT) * 2,
               isset($_REQUEST['pager']['pageNumber']) ? isset($_REQUEST['pager']['pageNumber']) : 0
             );
             if (isset($pager_field_units->records[0])) {
               $field_unit_uuids = array();
               foreach ($pager_field_units->records as $field_unit) {
                 $field_unit_uuids[] = $field_unit->uuid;
             if (isset($pager_root_units->records[0])) {
               $root_unit_uuids = array();
               foreach ($pager_root_units->records as $root_unit) {
                 $root_unit_uuids[] = $root_unit->uuid;
+              }
               $render_array['derivate_hierarchy_table'] = compose_compressed_specimen_derivate_table($field_unit_uuids);
               $render_array['derivate_hierarchy_table'] = compose_compressed_specimen_derivate_table($root_unit_uuids);
+            }
             $render_array['pager'] = markup_to_render_array(
                 theme('cdm_pager', array(
                     'pager' => $pager_field_units,
                     'pager' => $pager_root_units,
                     'path' => $_REQUEST['q'],
                     'parameters' => $_REQUEST
                 )),
-...
             );
+        }
         else if(($current_view_mode == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TREE)){ // FIXME this seems to be wrong
           $render_array['specimen_list'] = compose_specimen_table_top_down($fieldUnitDTOs);
           $render_array['specimen_list'] = compose_specimen_table_top_down($root_unit_dtos);
           $render_array['specimen_list']['#weight'] = 2;
         } else {
           $specimen_table = compose_specimens_table_bottom_up($specimensOrObservations);

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Revision 25b933c4

Added by Andreas Kohlbecker about 3 years ago

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EDIT

Revision 25b933c4

Added by Andreas Kohlbecker about 3 years ago

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