Revision 30845bda
Added by Andreas Kohlbecker over 7 years ago
| modules/cdm_dataportal/cdm_api/webservice_uris.php | ||
|---|---|---|
| 106 | 106 |
|
| 107 | 107 |
define('CDM_WS_TERM_COMPARE', 'term/$0/compareTo/$1');
|
| 108 | 108 |
define('CDM_WS_TERM', 'term');
|
| 109 |
define('CDM_WS_PORTAL_TERM', 'portal/term/$0');
|
|
| 109 | 110 |
|
| 110 | 111 |
/** |
| 111 | 112 |
* Returns FeatureTrees that are stored in this community store. |
| modules/cdm_dataportal/cdm_dataportal.module | ||
|---|---|---|
| 414 | 414 |
// Expected callback arguments: uuid. |
| 415 | 415 |
); |
| 416 | 416 |
|
| 417 |
// Optional callback arguments: page. |
|
| 418 |
//FIXME point to view/page method in this module |
|
| 419 |
$items['cdm_dataportal/specimen'] = array( |
|
| 420 |
'page callback' => 'cdm_dataportal_specimen_page_view', |
|
| 421 |
'access arguments' => array('access cdm content'),
|
|
| 422 |
'type' => MENU_CALLBACK, |
|
| 423 |
// Expected callback arguments: uuid. |
|
| 424 |
); |
|
| 417 |
$items['cdm_dataportal/specimen'] = array( |
|
| 418 |
'page callback' => 'cdm_dataportal_specimen_page_view', |
|
| 419 |
'access arguments' => array('access cdm content'),
|
|
| 420 |
'type' => MENU_CALLBACK, |
|
| 421 |
// Expected callback arguments: uuid. |
|
| 422 |
); |
|
| 423 |
|
|
| 424 |
$items['cdm_dataportal/named_area'] = array( |
|
| 425 |
'page callback' => 'cdm_dataportal_named_area_page_view', |
|
| 426 |
'access arguments' => array('access cdm content'),
|
|
| 427 |
'type' => MENU_CALLBACK, |
|
| 428 |
// Expected callback arguments: uuid. |
|
| 429 |
); |
|
| 425 | 430 |
|
| 426 | 431 |
$items['cdm_dataportal/name'] = array( |
| 427 | 432 |
'page callback' => 'cdm_dataportal_name_page_view', |
| ... | ... | |
| 1616 | 1621 |
} |
| 1617 | 1622 |
|
| 1618 | 1623 |
/** |
| 1624 |
* |
|
| 1625 |
* Creates a named area view. |
|
| 1626 |
* @param string $uuid the UUID of the specimen |
|
| 1627 |
* * @return object |
|
| 1628 |
* An object with two fields: |
|
| 1629 |
* - title: the page title |
|
| 1630 |
* - content: the page content |
|
| 1631 |
*/ |
|
| 1632 |
|
|
| 1633 |
function cdm_dataportal_named_area_view($uuid) {
|
|
| 1634 |
$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid); |
|
| 1635 |
if (empty($named_area) || $named_area->class !== 'NamedArea') {
|
|
| 1636 |
drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
|
|
| 1637 |
return FALSE; |
|
| 1638 |
} |
|
| 1639 |
$named_area_page = new stdClass(); |
|
| 1640 |
|
|
| 1641 |
$named_area_page->title = $named_area->representation_L10n; |
|
| 1642 |
|
|
| 1643 |
// Render the specimen page. |
|
| 1644 |
$render_array = compose_cdm_named_area_page($uuid); |
|
| 1645 |
$named_area_page->content = drupal_render($render_array); |
|
| 1646 |
|
|
| 1647 |
return $named_area_page; |
|
| 1648 |
} |
|
| 1649 |
|
|
| 1650 |
function cdm_dataportal_named_area_page_view($uuid) {
|
|
| 1651 |
|
|
| 1652 |
cdm_check_valid_portal_page(); |
|
| 1653 |
|
|
| 1654 |
$named_area_page = cdm_dataportal_named_area_view($uuid); |
|
| 1655 |
if (!empty($named_area_page)) {
|
|
| 1656 |
return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content); |
|
| 1657 |
} |
|
| 1658 |
else {
|
|
| 1659 |
return ''; |
|
| 1660 |
} |
|
| 1661 |
|
|
| 1662 |
|
|
| 1663 |
} |
|
| 1664 |
|
|
| 1665 |
/** |
|
| 1619 | 1666 |
* Returns a name page as a Drupal node ready to be renderized by Drupal. |
| 1620 | 1667 |
* |
| 1621 | 1668 |
* The node page shows the taxon name title and the list of taxon related |
| ... | ... | |
| 1905 | 1952 |
} |
| 1906 | 1953 |
} |
| 1907 | 1954 |
|
| 1955 |
function path_to_named_area($uuid) {
|
|
| 1956 |
|
|
| 1957 |
if (!$uuid) {
|
|
| 1958 |
return FALSE; |
|
| 1959 |
} |
|
| 1960 |
else {
|
|
| 1961 |
return 'cdm_dataportal/named_area/' . $uuid; |
|
| 1962 |
} |
|
| 1963 |
} |
|
| 1964 |
|
|
| 1908 | 1965 |
/** |
| 1909 | 1966 |
* Creates a URL to show a synonmy in the according taxon page. |
| 1910 | 1967 |
* |
| modules/cdm_dataportal/includes/occurrences.inc | ||
|---|---|---|
| 18 | 18 |
|
| 19 | 19 |
|
| 20 | 20 |
/** |
| 21 |
* @param $preservedSpecimenDTO |
|
| 22 |
* @param $detail_html |
|
| 23 |
* @return string |
|
| 24 |
*/ |
|
| 25 |
function compose_cdm_specimen_page($specimenUuid) |
|
| 26 |
{
|
|
| 27 |
drupal_set_title("Specimen Details");
|
|
| 28 |
$preservedSpecimenDTO = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($specimenUuid, 'specimenDerivates')); |
|
| 29 |
|
|
| 30 |
$render_array = array(); |
|
| 31 |
RenderHints::pushToRenderStack('specimen_page');
|
|
| 32 |
|
|
| 33 |
$detail_html = compose_cdm_specimen_page_html($preservedSpecimenDTO, true); |
|
| 34 |
$render_array['specimen_html'] = array( |
|
| 35 |
'#markup' => $detail_html |
|
| 36 |
); |
|
| 37 |
|
|
| 38 |
RenderHints::popFromRenderStack(); |
|
| 39 |
return $render_array; |
|
| 40 |
} |
|
| 41 |
|
|
| 42 |
/** |
|
| 43 |
* @param $preservedSpecimenDTO |
|
| 21 |
* Provides the HTML markup for a specimen page |
|
| 22 |
* |
|
| 23 |
* @param $specimen |
|
| 24 |
* |
|
| 44 | 25 |
* @return string |
| 26 |
* The markup for a specimen page |
|
| 45 | 27 |
*/ |
| 46 |
function compose_cdm_specimen_page_html($preservedSpecimenDTO, $isSpecimenPage = false)
|
|
| 28 |
function render_cdm_specimen_page($specimen, $is_specimen_page = false)
|
|
| 47 | 29 |
{
|
| 48 | 30 |
$detail_html = ""; |
| 49 | 31 |
//link to specimen page |
| 50 |
$pathToSpecimen = path_to_specimen($preservedSpecimenDTO->uuid);
|
|
| 51 |
if (!$isSpecimenPage) {
|
|
| 52 |
$specimenPageLink = l($preservedSpecimenDTO->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
|
| 32 |
$pathToSpecimen = path_to_specimen($specimen->uuid);
|
|
| 33 |
if (!$is_specimen_page) {
|
|
| 34 |
$specimenPageLink = l($specimen->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
|
| 53 | 35 |
$detail_html .= "<strong>$specimenPageLink</strong><br>"; |
| 54 | 36 |
} |
| 55 | 37 |
|
| 56 |
if($isSpecimenPage) {
|
|
| 57 |
if($preservedSpecimenDTO->citation){
|
|
| 58 |
$detail_html .= "<br>".create_label("Citation") . $preservedSpecimenDTO->citation . "<br>";
|
|
| 38 |
if($is_specimen_page) {
|
|
| 39 |
if($specimen->citation){
|
|
| 40 |
$detail_html .= "<br>".create_label("Citation") . $specimen->citation . "<br>";
|
|
| 59 | 41 |
} |
| 60 | 42 |
} |
| 61 |
if($preservedSpecimenDTO->preferredStableUri){
|
|
| 62 |
$detail_html .= "<br>".create_label("Preferred stable URI") . cdm_external_uri($preservedSpecimenDTO->preferredStableUri) . "<br>";
|
|
| 43 |
if($specimen->preferredStableUri){
|
|
| 44 |
$detail_html .= "<br>".create_label("Preferred stable URI") . cdm_external_uri($specimen->preferredStableUri) . "<br>";
|
|
| 63 | 45 |
} |
| 64 |
if($isSpecimenPage){
|
|
| 46 |
if($is_specimen_page){
|
|
| 65 | 47 |
// associated taxa |
| 66 |
if($preservedSpecimenDTO->associatedTaxa){
|
|
| 48 |
if($specimen->associatedTaxa){
|
|
| 67 | 49 |
$detail_html .= "<br>"; |
| 68 | 50 |
$detail_html .= create_label("Associated with");
|
| 69 |
if(sizeof($preservedSpecimenDTO->associatedTaxa)>1){
|
|
| 51 |
if(sizeof($specimen->associatedTaxa)>1){
|
|
| 70 | 52 |
$detail_html .= "<br>"; |
| 71 | 53 |
} |
| 72 |
foreach($preservedSpecimenDTO->associatedTaxa as $associatedTaxon){
|
|
| 54 |
foreach($specimen->associatedTaxa as $associatedTaxon){
|
|
| 73 | 55 |
$detail_html .= l($associatedTaxon->second, path_to_taxon($associatedTaxon->first, "specimens"));//$associatedTaxon->second."<br>"; |
| 74 | 56 |
} |
| 75 | 57 |
} |
| 76 | 58 |
} |
| 77 | 59 |
// - type information |
| 78 | 60 |
$types = ""; |
| 79 |
if (isset($preservedSpecimenDTO->types)) {
|
|
| 61 |
if (isset($specimen->types)) {
|
|
| 80 | 62 |
//typed taxa |
| 81 |
if(sizeof($preservedSpecimenDTO->types)>1){
|
|
| 63 |
if(sizeof($specimen->types)>1){
|
|
| 82 | 64 |
$detail_html .= "<br>"; |
| 83 | 65 |
} |
| 84 |
foreach ($preservedSpecimenDTO->types as $typeStatus => $typedTaxa) {
|
|
| 85 |
if($isSpecimenPage){
|
|
| 86 |
if($preservedSpecimenDTO->types){
|
|
| 66 |
foreach ($specimen->types as $typeStatus => $typedTaxa) {
|
|
| 67 |
if($is_specimen_page){
|
|
| 68 |
if($specimen->types){
|
|
| 87 | 69 |
$detail_html .= "<i>".$typeStatus."</i>: "; |
| 88 | 70 |
foreach($typedTaxa as $typedTaxon){
|
| 89 | 71 |
$detail_html .= $typedTaxon." "; |
| ... | ... | |
| 96 | 78 |
} |
| 97 | 79 |
} |
| 98 | 80 |
} |
| 99 |
$derivateDataDTO = $preservedSpecimenDTO->derivateDataDTO;
|
|
| 81 |
$derivateDataDTO = $specimen->derivateDataDTO;
|
|
| 100 | 82 |
// - specimen scans |
| 101 | 83 |
$specimenScans = create_html_links($derivateDataDTO->specimenScans, true); |
| 102 | 84 |
// - molecular data |
| ... | ... | |
| 138 | 120 |
$detailImages = create_html_links($derivateDataDTO->detailImages, true); |
| 139 | 121 |
|
| 140 | 122 |
if ($types) {
|
| 141 |
$detail_html .= $isSpecimenPage?"<br>":"";
|
|
| 123 |
$detail_html .= $is_specimen_page?"<br>":"";
|
|
| 142 | 124 |
$detail_html .= create_label("Type(s)") . $types . "<br>";
|
| 143 | 125 |
} |
| 144 |
if ($specimenScans and !$isSpecimenPage) {
|
|
| 126 |
if ($specimenScans and !$is_specimen_page) {
|
|
| 145 | 127 |
$detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
|
| 146 | 128 |
} |
| 147 | 129 |
//specimen scan image gallery |
| 148 |
if($isSpecimenPage and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
|
|
| 130 |
if($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
|
|
| 149 | 131 |
$detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
|
| 150 | 132 |
} |
| 151 | 133 |
|
| 152 | 134 |
if ($molecularData) {
|
| 153 |
$detail_html .= $isSpecimenPage?"<br>":"";
|
|
| 135 |
$detail_html .= $is_specimen_page?"<br>":"";
|
|
| 154 | 136 |
$detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
|
| 155 | 137 |
} |
| 156 | 138 |
|
| 157 |
if ($detailImages and !$isSpecimenPage) {
|
|
| 139 |
if ($detailImages and !$is_specimen_page) {
|
|
| 158 | 140 |
$detail_html .= create_label("Detail Images") . $detailImages . "<br>";
|
| 159 | 141 |
} |
| 160 | 142 |
|
| 161 | 143 |
//detail image gallery |
| 162 |
if($isSpecimenPage and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)){
|
|
| 144 |
if($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)){
|
|
| 163 | 145 |
$detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
|
| 164 | 146 |
} |
| 165 | 147 |
|
| 166 | 148 |
//character data |
| 167 |
if ($preservedSpecimenDTO->characterData) {
|
|
| 168 |
$detail_html .= $isSpecimenPage?"<br>":"";
|
|
| 149 |
if ($specimen->characterData) {
|
|
| 150 |
$detail_html .= $is_specimen_page?"<br>":"";
|
|
| 169 | 151 |
$detail_html .= create_label("Character Data");
|
| 170 |
if($isSpecimenPage) {
|
|
| 152 |
if($is_specimen_page) {
|
|
| 171 | 153 |
$detail_html .= "<br>"; |
| 172 |
foreach ($preservedSpecimenDTO->characterData as $characterStatePair) {
|
|
| 154 |
foreach ($specimen->characterData as $characterStatePair) {
|
|
| 173 | 155 |
$detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second; |
| 174 | 156 |
$detail_html .= "<br>"; |
| 175 | 157 |
} |
| ... | ... | |
| 504 | 486 |
if (isset($value->collectingAreas)) {
|
| 505 | 487 |
$area_representations = array(); |
| 506 | 488 |
foreach ($value->collectingAreas as $area) {
|
| 507 |
$area_representations[] = $area->representation_L10n;
|
|
| 489 |
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
|
| 508 | 490 |
} |
| 509 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'), implode(', ', $area_representations));
|
|
| 491 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
|
| 492 |
array( |
|
| 493 |
array('#markup' => implode(', ', $area_representations))
|
|
| 494 |
) |
|
| 495 |
); |
|
| 510 | 496 |
} |
| 511 | 497 |
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
| 512 | 498 |
$sub_dl_groups = array(); |
| modules/cdm_dataportal/includes/pages.inc | ||
|---|---|---|
| 197 | 197 |
if($derivateHierarchy->preservedSpecimenDTOs){
|
| 198 | 198 |
foreach($derivateHierarchy->preservedSpecimenDTOs as $preservedSpecimenDTO) {
|
| 199 | 199 |
$detail_html .= "<br>"; |
| 200 |
$detail_html .= compose_cdm_specimen_page_html($preservedSpecimenDTO);
|
|
| 200 |
$detail_html .= render_cdm_specimen_page($preservedSpecimenDTO);
|
|
| 201 | 201 |
} |
| 202 | 202 |
} |
| 203 | 203 |
$detail_html .= "<br>"; |
| ... | ... | |
| 1049 | 1049 |
|
| 1050 | 1050 |
} |
| 1051 | 1051 |
|
| 1052 |
$render_array['#items'] = $items; |
|
| 1052 | 1053 |
|
| 1054 |
return $render_array; |
|
| 1055 |
} |
|
| 1053 | 1056 |
|
| 1054 |
$render_array['#items'] = $items; |
|
| 1057 |
/** |
|
| 1058 |
* @param $specimen_uuid |
|
| 1059 |
* @return array |
|
| 1060 |
* The drupal render array for the page |
|
| 1061 |
* |
|
| 1062 |
* @ingroup compose |
|
| 1063 |
*/ |
|
| 1064 |
function compose_cdm_specimen_page($specimen_uuid) |
|
| 1065 |
{
|
|
| 1066 |
drupal_set_title("Specimen Details");
|
|
| 1067 |
$specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($specimen_uuid, 'specimenDerivates')); |
|
| 1068 |
|
|
| 1069 |
$render_array = array(); |
|
| 1070 |
RenderHints::pushToRenderStack('specimen_page');
|
|
| 1055 | 1071 |
|
| 1072 |
$detail_html = render_cdm_specimen_page($specimen, true); |
|
| 1073 |
$render_array['specimen_html'] = array( |
|
| 1074 |
'#markup' => $detail_html |
|
| 1075 |
); |
|
| 1076 |
|
|
| 1077 |
RenderHints::popFromRenderStack(); |
|
| 1056 | 1078 |
return $render_array; |
| 1079 |
} |
|
| 1057 | 1080 |
|
| 1081 |
/** |
|
| 1082 |
* @param $named_area_uuid |
|
| 1083 |
* @return array |
|
| 1084 |
* The drupal render array for the page |
|
| 1085 |
* |
|
| 1086 |
* @ingroup compose |
|
| 1087 |
*/ |
|
| 1088 |
function compose_cdm_named_area_page($named_area_uuid) |
|
| 1089 |
{
|
|
| 1090 |
|
|
| 1091 |
$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid)); |
|
| 1092 |
|
|
| 1093 |
$render_array = array(); |
|
| 1094 |
RenderHints::pushToRenderStack('named_area_page');
|
|
| 1095 |
|
|
| 1096 |
$groups = array(); |
|
| 1097 |
@_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
|
|
| 1098 |
@_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
|
|
| 1099 |
if(isset($named_area->level)) {
|
|
| 1100 |
@_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
|
|
| 1101 |
} |
|
| 1102 |
|
|
| 1103 |
$name_area_details_elements = array( |
|
| 1104 |
// '#title' => $title, |
|
| 1105 |
'#theme' => 'description_list', |
|
| 1106 |
'#groups' => $groups, |
|
| 1107 |
'#attributes' => array('class' => html_class_attribute_ref($named_area)),
|
|
| 1108 |
); |
|
| 1109 |
|
|
| 1110 |
$render_array[] = $name_area_details_elements; |
|
| 1111 |
|
|
| 1112 |
RenderHints::popFromRenderStack(); |
|
| 1113 |
return $render_array; |
|
| 1058 | 1114 |
} |
| modules/cdm_dataportal/node_types.php | ||
|---|---|---|
| 8 | 8 |
define('NODETYPE_MEDIA', 'media');
|
| 9 | 9 |
define('NODETYPE_REFERENCE', 'reference');
|
| 10 | 10 |
define('NODETYPE_NAME', 'name');
|
| 11 |
define('NODETYPE_NAMED_AREA', 'named_area');
|
|
| 11 | 12 |
|
| 12 | 13 |
/** |
| 13 | 14 |
* Implements hook_cdm_nodetypes(). |
| ... | ... | |
| 20 | 21 |
'cdm_' . NODETYPE_TAXON => NODETYPE_TAXON, |
| 21 | 22 |
'cdm_' . NODETYPE_MEDIA => NODETYPE_MEDIA, |
| 22 | 23 |
'cdm_' . NODETYPE_NAME => NODETYPE_NAME, |
| 24 |
'cdm_' . NODETYPE_NAMED_AREA => NODETYPE_NAMED_AREA, |
|
| 23 | 25 |
); |
| 24 | 26 |
} |
| 25 | 27 |
return $nodetypes; |
Also available in: Unified diff
ref #2985 implementing named area page to make area details like level accessible