Revision fb308159
Added by Andreas Kohlbecker over 4 years ago
| modules/cdm_dataportal/cdm_api/cdm_api.info | ||
|---|---|---|
| 3 | 3 |
version = 7.x-3.0 |
| 4 | 4 |
package = "CDM" |
| 5 | 5 |
core = 7.x |
| 6 |
files[] = classes/Restriction.php |
|
| modules/cdm_dataportal/cdm_api/cdm_api.module | ||
|---|---|---|
| 981 | 981 |
* @param bool $absoluteURI |
| 982 | 982 |
* TRUE when the URL should be treated as absolute URL. |
| 983 | 983 |
* |
| 984 |
* @return the a CDM Pager object |
|
| 984 |
* @return object |
|
| 985 |
* A CDM Pager object |
|
| 985 | 986 |
* |
| 986 | 987 |
*/ |
| 987 | 988 |
function cdm_ws_page($resourceURI, $pageSize, $pageNumber, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
|
| ... | ... | |
| 992 | 993 |
return cdm_ws_get($resourceURI, NULL, queryString($query), $method, $absoluteURI); |
| 993 | 994 |
} |
| 994 | 995 |
|
| 996 |
|
|
| 995 | 997 |
/** |
| 998 |
* Sends a http GET request to the generic page method which allows for filtering entities by Restrictions. |
|
| 999 |
* |
|
| 1000 |
* @param $cdm_entity_type |
|
| 1001 |
* @param array $restrictions |
|
| 1002 |
* An array of Restriction objects |
|
| 1003 |
* @param array $init_strategy |
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| 1004 |
* The init strategy to initialize the entity beans while being loaded from the |
|
| 1005 |
* persistent storage by the cdm |
|
| 1006 |
* @param int $page_size |
|
| 1007 |
* The maximum number of entities returned per page. |
|
| 1008 |
* The default page size as configured in the cdm server |
|
| 1009 |
* will be used if set to NULL |
|
| 1010 |
* to return all entities in a single page). |
|
| 1011 |
* @param int $page_index |
|
| 1012 |
* The number of the page to be returned, the first page has the |
|
| 1013 |
* pageNumber = 0 |
|
| 1014 |
* |
|
| 1015 |
* @return object |
|
| 1016 |
* A CDM Pager object |
|
| 1017 |
* |
|
| 1018 |
*/ |
|
| 1019 |
function cdm_ws_page_by_restriction($cdm_entity_type, array $restrictions, array $init_strategy, $page_size, $page_index) {
|
|
| 1020 |
|
|
| 1021 |
$restrictions_json = array(); // json_encode($restrictions); |
|
| 1022 |
foreach ($restrictions as $restr){
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|
| 1023 |
$restrictions_json[] = json_encode($restr); |
|
| 1024 |
} |
|
| 1025 |
return cdm_ws_page( |
|
| 1026 |
'portal/' . cdm_ws_base_uri($cdm_entity_type), |
|
| 1027 |
$page_size, |
|
| 1028 |
$page_index, |
|
| 1029 |
array( |
|
| 1030 |
'restriction' => $restrictions_json, |
|
| 1031 |
'initStrategy' => $init_strategy |
|
| 1032 |
), |
|
| 1033 |
"GET" |
|
| 1034 |
); |
|
| 1035 |
} |
|
| 1036 |
|
|
| 1037 |
/** |
|
| 1038 |
* Fetches all entities returned by the the generic page method for the Restrictions applied as filter. |
|
| 1039 |
* |
|
| 1040 |
* @param $cdm_entity_type |
|
| 1041 |
* @param array $restrictions |
|
| 1042 |
* An array of Restriction objects |
|
| 1043 |
* @param array $init_strategy |
|
| 1044 |
* The init strategy to initialize the entity beans while being loaded from the |
|
| 1045 |
* persistent storage by the cdm |
|
| 1046 |
* @param int $page_size |
|
| 1047 |
* The maximum number of entities returned per page. |
|
| 1048 |
* The default page size as configured in the cdm server |
|
| 1049 |
* will be used if set to NULL |
|
| 1050 |
* to return all entities in a single page). |
|
| 1051 |
* @param int $page_index |
|
| 1052 |
* The number of the page to be returned, the first page has the |
|
| 1053 |
* pageNumber = 0 |
|
| 1054 |
* |
|
| 1055 |
* @return array |
|
| 1056 |
* A array of CDM entities |
|
| 1057 |
* |
|
| 1058 |
*/ |
|
| 1059 |
function cdm_ws_fetch_all_by_restriction($cdm_entity_type, array $restrictions, array $init_strategy){
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|
| 1060 |
$page_index = 0; |
|
| 1061 |
// using a bigger page size to avoid to many multiple requests |
|
| 1062 |
$page_size = 500; |
|
| 1063 |
$entities = array(); |
|
| 1064 |
|
|
| 1065 |
while ($page_index !== FALSE && $page_index < 1){
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|
| 1066 |
$pager = cdm_ws_page_by_restriction($cdm_entity_type, $restrictions, $init_strategy, $page_size, $page_index); |
|
| 1067 |
if(isset($pager->records) && is_array($pager->records)) {
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|
| 1068 |
$entities = array_merge($entities, $pager->records); |
|
| 1069 |
if(!empty($pager->nextIndex)){
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|
| 1070 |
$page_index = $pager->nextIndex; |
|
| 1071 |
} else {
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|
| 1072 |
$page_index = FALSE; |
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| 1073 |
} |
|
| 1074 |
} else {
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|
| 1075 |
$page_index = FALSE; |
|
| 1076 |
} |
|
| 1077 |
} |
|
| 1078 |
return $entities; |
|
| 1079 |
} |
|
| 1080 |
|
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| 1081 |
|
|
| 1082 |
/** |
|
| 996 | 1083 |
* Fetches all entities from the given REST endpoint using the pager mechanism. |
| 997 | 1084 |
* |
| 998 | 1085 |
* @param string $resourceURI |
| modules/cdm_dataportal/cdm_api/classes/Restriction.php | ||
|---|---|---|
| 1 |
<?php |
|
| 2 |
/** |
|
| 3 |
* PHP implementation of the cdm eu.etaxonomy.cdm.persistence.dao.common.Restriction |
|
| 4 |
*/ |
|
| 5 |
|
|
| 6 |
class Restriction |
|
| 7 |
{
|
|
| 8 |
public $propertyName; |
|
| 9 |
|
|
| 10 |
public $matchMode; |
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| 11 |
|
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| 12 |
public $operator; |
|
| 13 |
|
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| 14 |
public $values = array(); |
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| 15 |
|
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| 16 |
|
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| 17 |
/** |
|
| 18 |
* Public constructor. |
|
| 19 |
*/ |
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| 20 |
public function __construct($propertyName, $matchMode, array $values, $operator = 'AND') {
|
|
| 21 |
$this->propertyName = $propertyName; |
|
| 22 |
$this->matchMode = $matchMode; |
|
| 23 |
$this->values = $values; |
|
| 24 |
$this->operator = $operator; |
|
| 25 |
} |
|
| 26 |
} |
|
| modules/cdm_dataportal/cdm_api/webservice_uris.php | ||
|---|---|---|
| 3 | 3 |
* @file |
| 4 | 4 |
* CDM Server URI definitions. |
| 5 | 5 |
*/ |
| 6 |
|
|
| 7 |
define('CDM_WS_PORTAL_GENERIC', 'portal/$0');
|
|
| 8 |
|
|
| 6 | 9 |
define('CDM_WS_PORTAL_AGENT', 'portal/agent');
|
| 7 | 10 |
define('CDM_WS_REFERENCE', 'reference');
|
| 8 | 11 |
define('CDM_WS_REFERENCE_AUTHORTEAM', 'reference/$0/authorship');
|
| modules/cdm_dataportal/cdm_dataportal.module | ||
|---|---|---|
| 1788 | 1788 |
cdm_load_tagged_full_title($taxon_name); |
| 1789 | 1789 |
// Searching for all the taxa connected with the taxon name on the tree |
| 1790 | 1790 |
// in use. |
| 1791 |
$name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid)); |
|
| 1792 |
$request_params = array(); |
|
| 1793 |
$request_params['query'] = $name_cache; |
|
| 1794 |
$request_params['tree'] = get_current_classification_uuid(); |
|
| 1795 |
$request_params['doTaxa'] = 1; |
|
| 1796 |
$request_params['doSynonyms'] = 1; |
|
| 1797 |
$request_params['doTaxaByCommonNames'] = 0; |
|
| 1798 |
$request_params['matchMode'] = "EXACT"; |
|
| 1799 |
$taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params)); |
|
| 1791 |
$name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid)); |
|
| 1792 |
$restrictions = array(new Restriction("name.titleCache","EXACT", array($name->titleCache), 'AND'));
|
|
| 1793 |
$init_strategy = array( |
|
| 1794 |
"name.titleCache", |
|
| 1795 |
"name.nomenclaturalReference.authorship", |
|
| 1796 |
"name.nomenclaturalReference.inReference.authorship", |
|
| 1797 |
"name.nomenclaturalReference.inReference.inReference.authorship", |
|
| 1798 |
"name.nomenclaturalReference.inReference.inReference.inReference.authorship" |
|
| 1799 |
); |
|
| 1800 |
$taxa = cdm_ws_fetch_all_by_restriction("Taxon", $restrictions, $init_strategy);
|
|
| 1800 | 1801 |
|
| 1801 | 1802 |
// Removing the name where we came from. |
| 1802 |
foreach ($taxon_pager->records as $k => &$taxon) {
|
|
| 1803 |
foreach ($taxa as $k => &$taxon) {
|
|
| 1803 | 1804 |
if ($taxon->uuid == $taxon_to_hide_uuid) {
|
| 1804 |
unset($taxon_pager->records[$k]);
|
|
| 1805 |
unset($taxa[$k]);
|
|
| 1805 | 1806 |
} |
| 1806 | 1807 |
} |
| 1807 | 1808 |
// Show the taxa list or go to the singular taxon. |
| 1808 |
if (sizeof($taxon_pager->records) == 1 && $redirect_to_taxon) {
|
|
| 1809 |
if (sizeof($taxa) == 1 && $redirect_to_taxon) {
|
|
| 1809 | 1810 |
// redirect to the taxon if there is only one. |
| 1810 |
$singleTaxon = array_pop($taxon_pager->records);
|
|
| 1811 |
$singleTaxon = array_pop($taxa);
|
|
| 1811 | 1812 |
if ($singleTaxon->class != "Taxon") {
|
| 1812 | 1813 |
// It is a Synonym -> look for the accepted. |
| 1813 | 1814 |
$accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid()); |
| ... | ... | |
| 1845 | 1846 |
$content['name_relationships'] = compose_name_relationships_list($name_relations, $taxon_name->uuid, null); |
| 1846 | 1847 |
} |
| 1847 | 1848 |
// related taxa |
| 1848 |
if ($taxon_pager->records) {
|
|
| 1849 |
if ($taxa) {
|
|
| 1849 | 1850 |
$content['related_taxa_header'] = markup_to_render_array("<h5>Taxa for this name:</h5>");
|
| 1850 |
$content['related_taxa'] = compose_list_of_taxa($taxon_pager->records);
|
|
| 1851 |
$content['related_taxa'] = compose_list_of_taxa($taxa);
|
|
| 1851 | 1852 |
} |
| 1852 | 1853 |
else {
|
| 1853 | 1854 |
$content['related_taxa'] = markup_to_render_array('This name is not assigned to a taxon.');
|
| src/test/java/eu/etaxonomy/dataportal/selenium/tests/reference/NameRelationshipsTest.java | ||
|---|---|---|
| 89 | 89 |
assertEquals( |
| 90 | 90 |
"4. Lem, Nonsens species of the developers Vol1. 2001", |
| 91 | 91 |
footnotes .get(3).getText()); |
| 92 |
|
|
| 93 | 92 |
} |
| 94 | 93 |
|
| 95 | 94 |
@Test |
| ... | ... | |
| 112 | 111 |
"3. Lem, Nonsens species of the developers Vol1. 2001", |
| 113 | 112 |
footnotes.get(2).getText()); |
| 114 | 113 |
|
| 115 |
|
|
| 116 | 114 |
} |
| 117 | 115 |
|
| 118 | 116 |
/** |
| ... | ... | |
| 129 | 127 |
WebElement accName = p.getAcceptedName(); |
| 130 | 128 |
assertEquals("Bulbostylis pauciflora (Liebm.) C. B. Clarke, nom. cons. [non Bulbostylis pauciflora (Kunth) D.C.]", accName.getText());
|
| 131 | 129 |
assertEquals("is conserved against", accName.findElement(By.className("symbol")).getAttribute("title"));
|
| 132 |
|
|
| 133 | 130 |
} |
| 134 | 131 |
|
| 135 | 132 |
/** |
| ... | ... | |
| 148 | 145 |
WebElement synonym2 = p.getHeterotypicalGroupSynonym(1, 2); |
| 149 | 146 |
assertEquals("≡\nNepenthes tupmanniana Bonstedt in Parey Blumeng. 1: 663. 1931 [non Nepenthes teysmanniana Miq., Fl. Ned. Ind. 1(1): 1073. 1858]", synonym2.getText());
|
| 150 | 147 |
assertEquals("is misspelling for", synonym2.findElement(By.className("symbol")).getAttribute("title"));
|
| 151 |
|
|
| 152 | 148 |
} |
| 153 | 149 |
|
| 154 | 150 |
} |
Also available in: Unified diff
fix #8321 finding taxa for a given name by matching whith the whole titleCache