Revision 52f57468
Added by Katja Luther over 5 years ago
| modules/cdm_dataportal/includes/occurrences.inc | ||
|---|---|---|
| 605 | 605 |
* |
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* @ingroup compose |
| 607 | 607 |
*/ |
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function compose_cdm_sequence($sequence) |
|
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function compose_cdm_sequence($sequence, $isSpecimenPage = false)
|
|
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{
|
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|
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$exclude_sequence_fields = &drupal_static(__FUNCTION__); |
| ... | ... | |
| 617 | 617 |
'created', |
| 618 | 618 |
'updated', |
| 619 | 619 |
'class', |
| 620 |
'dnaMarker' |
|
| 620 | 621 |
); |
| 621 | 622 |
} |
| 622 | 623 |
|
| ... | ... | |
| 635 | 636 |
switch ($field) {
|
| 636 | 637 |
|
| 637 | 638 |
case 'geneticAccessionNumber'; |
| 638 |
$dd_elements = array(); |
|
| 639 |
foreach ($value as $accession) {
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|
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if (isset($accession->uri)) {
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$dd_elements[] = l($accession->accessionNumber, $accession->uri); |
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} else {
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$dd_elements[] = $accession->accessionNumber; |
|
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} |
|
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} |
|
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 2); |
|
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|
|
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 2); |
|
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break; |
| 648 | 642 |
|
| 649 | 643 |
|
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case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
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if (isset($value->name)) {
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/*case 'dnaMarker': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
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/*if (isset($value->name)) {
|
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3); |
| 653 | 647 |
} |
| 654 | 648 |
if (isset($value->description)) {
|
| 655 | 649 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description'), $value->description, NULL, 4);
|
| 656 | 650 |
} |
| 651 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) , $value, NULL, 4); |
|
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break; |
| 658 |
|
|
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*/ |
|
| 659 | 654 |
case 'consensusSequence': |
| 660 | 655 |
// format in genbank style, force linebreaks after each 70 nucleotites |
| 661 | 656 |
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and |
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@_description_list_group_add(
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$groups,
|
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cdm_occurrence_field_name_label($field),
|
|
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array(
|
|
| 657 |
if ($value->length > 0) {
|
|
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@_description_list_group_add(
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$groups,
|
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cdm_occurrence_field_name_label($field),
|
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| 666 | 661 |
array( |
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'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
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'#wrapper_attributes' => array('class' => 'dna-sequence')
|
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) |
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), |
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5); |
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array( |
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'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
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'#wrapper_attributes' => array('class' => 'dna-sequence')
|
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) |
|
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), |
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5); |
|
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} |
|
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break; |
| 673 | 670 |
|
| 674 | 671 |
case 'dnaSample': // FIXME 3.3 implement |
| ... | ... | |
| 751 | 748 |
|
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// template_preprocess_description_list() is not worting by weight so we do it right here |
| 753 | 750 |
uasort($groups, 'element_sort'); |
| 754 |
|
|
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$sequence_elements = array( |
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'#theme' => 'description_list', |
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'#groups' => $groups |
|
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); |
|
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if ($isSpecimenPage) {
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$sequence_elements = array( |
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'#title' => $sequence->dnaMarker, |
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'#theme' => 'description_list', |
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'#groups' => $groups |
|
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); |
|
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} else{
|
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$sequence_elements = array( |
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'#title' => $sequence->dnaMarker -> titleCache, |
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'#theme' => 'description_list', |
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'#groups' => $groups |
|
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); |
|
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} |
|
| 759 | 764 |
|
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return $sequence_elements; |
| 761 | 766 |
} |
| ... | ... | |
| 827 | 832 |
'protectedTitleCache', |
| 828 | 833 |
'class', |
| 829 | 834 |
'uuid', |
| 830 |
'collectionDTO' |
|
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'collectionDTO', |
|
| 836 |
'derivates' |
|
| 831 | 837 |
); |
| 832 | 838 |
} |
| 833 | 839 |
$items = array(); |
| ... | ... | |
| 899 | 905 |
case 'sex': |
| 900 | 906 |
case 'lifeStage': |
| 901 | 907 |
case 'kindOfUnit': |
| 902 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n, NULL, 1);
|
|
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1); |
|
| 903 | 909 |
break; |
| 904 | 910 |
|
| 905 | 911 |
case 'definition': |
| ... | ... | |
| 1026 | 1032 |
|
| 1027 | 1033 |
/* ---- Specimen --- */ |
| 1028 | 1034 |
case 'sequences': |
| 1029 |
/* |
|
| 1030 | 1035 |
$dd_elements = array(); |
| 1031 | 1036 |
foreach ($value as $sequence) {
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$dd_elements[] = compose_cdm_sequence($sequence); |
|
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$dd_elements[] = compose_cdm_sequence($sequence, true); |
|
| 1038 |
$dd_elements[] = ""; |
|
| 1033 | 1039 |
} |
| 1034 | 1040 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements); |
| 1035 |
*/ |
|
| 1036 | 1041 |
break; |
| 1037 | 1042 |
|
| 1038 | 1043 |
// TODO preservation |
| ... | ... | |
| 1042 | 1047 |
/* ---- FieldObservation --- */ |
| 1043 | 1048 |
case 'gatheringEvent': |
| 1044 | 1049 |
|
| 1045 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
|
|
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@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->collector);
|
|
| 1046 | 1051 |
@_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
|
| 1047 | 1052 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
| 1048 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
|
|
| 1049 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
|
|
| 1053 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality);
|
|
| 1054 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country);
|
|
| 1050 | 1055 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
| 1051 | 1056 |
if (isset($value->absoluteElevation)) {
|
| 1052 | 1057 |
$min_max_markup = min_max_measure($value, 'absoluteElevation'); |
| ... | ... | |
| 1064 | 1069 |
if (isset($value->collectingAreas)) {
|
| 1065 | 1070 |
$area_representations = array(); |
| 1066 | 1071 |
foreach ($value->collectingAreas as $area) {
|
| 1067 |
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid)); |
|
| 1072 |
// $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid)); |
|
| 1073 |
$area_representations[] = $area; |
|
| 1068 | 1074 |
} |
| 1069 | 1075 |
if (!empty($area_representations)) |
| 1070 | 1076 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
| ... | ... | |
| 1103 | 1109 |
|
| 1104 | 1110 |
default: |
| 1105 | 1111 |
if (is_object($value) || is_array($value)) {
|
| 1106 |
// drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
|
| 1112 |
drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
|
| 1107 | 1113 |
} else {
|
| 1108 | 1114 |
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value); |
| 1109 | 1115 |
} |
Also available in: Unified diff
smaller changes in dna part of tree view