protected function setUp()
{
$db_util = DbTestUtil::instance();
$db_util->emptyTable('member');
$this->_dao = DAOFactory::getDAOFactory(DAOFactory::DB);
$this->_member_dao = $this->_dao->getMemberDAO();
}
function generateJSONRegionsTaxaQuantity($region)
{
$taxonDAO = DAOFactory::getDAOFactory()->getTaxonDAO();
$result = array();
$r = new stdClass();
$r->regionName = utf8_encode($region);
$r->taxaCount = $taxonDAO->getCountTaxaInRegion($r->regionName);
array_push($result, $r);
return json_encode($result);
}
<?php
require_once '../../config/config.php';
require '../../config/smarty.php';
require_once WORKSPACE_DIR . 'core/model/Country.php';
require_once WORKSPACE_DIR . 'core/dao/factories/DAOFactory.php';
if (isset($_GET['specie_id']) && $_GET['specie_id'] != '') {
$taxonID = $_GET['specie_id'];
$countryDAO = DAOFactory::getDAOFactory()->getCountryDAO();
//TODO
}
$cwrConcept->getTaxon()->setUtilizationReferences($utilizationReferences);
}
/* * ** CROP BREEDING USES *** */
$taxonBreedingDAO = DAOFactory::getDAOFactory()->getBreedingUseDAO();
$taxonBreedingUses = $taxonBreedingDAO->getTaxonBreedingUses($taxonID);
if (count($taxonBreedingUses) > 0) {
$cwrConcept->setTaxonBreedingUses($taxonBreedingUses);
}
/* * ** STORAGE BEHAVIOR *** */
$storageBehaviorDAO = DAOFactory::getDAOFactory()->getStorageBehaviorDAO();
$storageBehavior = $storageBehaviorDAO->getStorageBehavior($cwrConcept->getTaxon()->getGenus());
if ($storageBehavior != null) {
$cwrConcept->setStorageBehavior($storageBehavior);
}
/* * ** HERBARIA *** */
$herbariumDAO = DAOFactory::getDAOFactory()->getHerbariumDAO();
$herbaria = $herbariumDAO->getHerbariaData($cwrConcept->getTaxon()->getID());
if (count($herbaria) > 0) {
$cwrConcept->getTaxon()->setHerbaria($herbaria);
}
}
$firephp = new FirePHP(true);
//TODO - Remove this variable when the development of this page finalize.
$firephp->log($cwrConcept, 'CWR:');
// Only for test
$smarty->assign("taxon", $cwrConcept->getTaxon());
$smarty->assign("mainTaxon", $mainTaxon);
$smarty->assign("cwr", $cwrConcept);
}
// display TPL
$smarty->display("cwr-details.tpl");
<?php /* Initializing WordPress features */ require_once '../../../wp-blog-header.php'; /* Initializing Smarty and Database Objects */ require_once '../../config/config.php'; require_once '../../config/smarty.php'; require_once '../../config/db.php'; require_once WORKSPACE_DIR . 'core/dao/factories/DAOFactory.php'; /* Show WordPress Header */ get_header(); // display sidebar get_sidebar(); $taxonDAO = DAOFactory::getDAOFactory()->getTaxonDAO(); $taxonDAO->updateScientificNames(); // display footer get_footer();
header("Content-length: " . filesize($filename));
readfile($filename);
unlink($filename);
}
/* Ideado principalmente para la descarga desde el boton de gene pool */
if ($_GET["term"]) {
$ids = $_GET['term'];
if (!is_array($ids)) {
$filename = $term . "-" . date("d-M-Y H-i-s") . ".csv";
} else {
$filename = "Results-" . date("d-M-Y H-i-s") . ".csv";
}
$file = fopen($filename, "w");
$sep = ",";
$header = "Id" . $sep . "Family" . $sep . "FamilyAuthor" . $sep . "Genus" . $sep . "Specie" . $sep . "SpecieAuthor" . $sep . "Subspecie" . $sep . "SubspecieAuthor" . $sep . "Variety" . $sep . "VarietyAuthor" . $sep . "commonName" . $sep . "ScientificName" . $sep . "ConceptType" . $sep . "ConceptLevel" . $sep . "Relative of" . $sep . "\n";
$genePoolConceptDAO = DAOFactory::getDAOFactory()->getGenePoolConceptDAO();
$data = $header;
foreach ($ids as $id) {
$concepts = $genePoolConceptDAO->getGenePoolConcept($id);
$arrayConcepts = $concepts->getConcepts();
$mainTaxon = $concepts->getMainCrop();
foreach ($arrayConcepts as $concept) {
$taxon = $concept->getTaxon();
$data .= $taxon->getId() . $sep . str_replace(",", " ", $taxon->getFamily()) . $sep . str_replace(",", " ", $taxon->getFamilyAuthor()) . $sep . str_replace(",", " ", $taxon->getGenus()) . $sep . str_replace(",", " ", $taxon->getSpecie()) . $sep . str_replace(",", " ", $taxon->getSpecieAuthor()) . $sep . str_replace(",", " ", $taxon->getSubspecie()) . $sep . str_replace(",", " ", $taxon->getSubspecieAuthor()) . $sep . $taxon->getVariety() . $sep . str_replace(",", " ", $taxon->getVarietyAuthor()) . $sep . str_replace(",", " ", $taxon->getCommonName()) . $sep . str_replace(",", " ", $taxon->generateScientificName(false, false)) . $sep . str_replace(",", " ", $concept->getConceptType()) . $sep . str_replace(",", " ", $concept->getConceptLevel()) . $sep . $mainTaxon->getTaxon()->generateScientificName(false, false);
$data .= "\n";
}
}
fwrite($file, $data);
fclose($file);
header("Content-type: application/csv");
header("Content-Disposition: attachment; filename=" . $filename . " ");
<?php
require_once '../../config/config.php';
require_once '../../config/smarty.php';
require_once WORKSPACE_DIR . 'core/dao/factories/DAOFactory.php';
if (isset($_GET['search-type']) && $_GET['search-type'] != '') {
$term = $_GET['term'];
switch ($_GET['search-type']) {
case "concept-level":
$conceptDAO = DAOFactory::getDAOFactory()->getConceptDAO();
$concept_level = $conceptDAO->getAllLevelsByType($term);
echo generateJSONConceptLevel($concept_level);
break;
}
}
function generateJSONConceptLevel($concept_level)
{
$result = array();
foreach ($concept_level as $level) {
array_push($result, $level);
}
return json_encode($result);
}
if (isset($_POST["priority-genera-only"])) {
$priority_genera = $_POST["priority-genera"];
// Array con los generos prioritarios a buscar
$search_type = 1;
// Busqueda por generos prioritarios
} else {
if (isset($_POST["priority-croptaxa-only"])) {
$search_type = 2;
// Busqueda realizada por priority taxa
} else {
if (empty($countries) && empty($regions)) {
$search_type = 3;
}
}
}
$advancedSearchDAO = DAOFactory::getDAOFactory()->getAdvancedSearchDAO();
$taxa = $advancedSearchDAO->getResultsAdvancedSearch($term, $search_type, $countries, $regions, $concept_type, $concept_levels, $priority_genera);
// Devuelve un arreglo de objetos taxon
$long = count($taxa);
if ($long != 1) {
$middle = ceil($long / 2);
foreach ($taxa as $tx) {
if ($i < $middle) {
$taxa_left[] = $tx;
} else {
$taxa_right[] = $tx;
}
$i++;
}
} else {
$taxa_left[] = $taxa[0];
protected function setUp()
{
$this->_dao = DAOFactory::getDAOFactory(DAOFactory::DB);
}
public function __construct()
{
$mySqlDAOFactory = DAOFactory::getDAOFactory(DAOFactory::$MYSQL);
$this->dao = $mySqlDAOFactory->getDataBaseOperations();
$this->message = Localization::getInstance();
}
function generateJSONConceptInformation($taxonName)
{
$cwrConceptDAO = DAOFactory::getDAOFactory()->getCWRConceptDAO();
$cwrConcept = $cwrConceptDAO->getCWRConceptbyTaxonName($taxonName);
$mainTaxon = $cwrConceptDAO->getMainConcept($cwrConcept->getTaxon()->getId());
if ($cwrConcept != null && $mainTaxon != null) {
$r = new stdClass();
$r->specieName = utf8_encode($cwrConcept->getTaxon()->generateScientificName(true, true));
$validName = $cwrConcept->getTaxon()->getValidName();
if (!empty($validName)) {
$r->validName = utf8_encode($validName);
}
$commonName = $cwrConcept->getTaxon()->getCommonName();
if (!empty($commonName)) {
$r->commonName = utf8_encode($commonName);
}
$taxonID = $cwrConcept->getTaxon()->getId();
if (!empty($taxonID)) {
$r->taxonID = $taxonID;
}
$mainCropList = array();
if ($mainTaxon != null) {
foreach ($mainTaxon as $crop) {
$mainCrop = new stdClass();
$mainCrop->mainCropID = $crop->taxon->getId();
$mainCrop->type = $crop->Concept_Type;
$mainCrop->level = $crop->Concept_Level;
$mainCrop->mainCropName = utf8_encode($crop->taxon->generateScientificName(true, false));
array_push($mainCropList, $mainCrop);
}
}
$r->mainCropList = $mainCropList;
} else {
// No tiene un concept asociado en la base de datos
$taxonDAO = TaxonMySQL::getInstance();
$taxon = $taxonDAO->getTaxonbyName($taxonName);
$r = new stdClass();
$r->taxonID = $taxon->getId();
$r->specieName = utf8_encode($taxon->generateScientificName(true, false));
}
return json_encode($r);
}
<?php
require_once '../../config/config.php';
require_once '../../config/smarty.php';
require_once WORKSPACE_DIR . 'core/model/Occurrences.php';
require_once WORKSPACE_DIR . 'core/dao/factories/DAOFactory.php';
if (isset($_GET['search-type']) && $_GET['search-type'] != '') {
$term = $_GET['term'];
$limit = $_GET['limit'];
$type = $_GET['search-type'];
$occurrencesDAO = DAOFactory::getDAOFactory()->getOccurrencesDAO();
echo json_encode($occurrencesDAO->suggestList($type, $limit, $term));
}
/**
*
* @param type $db - ADONewConnection.
* @param type $cropID - Crop ID to search from concepts table.
* @return \GenePoolConcept - GenePoolConcept Object and its Concepts.
*/
public function getGenePoolConcept($taxonID)
{
global $db;
$query = "SELECT DISTINCT c.Crop_ID, c.Concept_ID, c.Concept_Type, c.Concept_Level, s2.*\n FROM concepts c\n INNER JOIN species s ON c.Taxon_ID = s.Taxon_ID\n JOIN species s2 ON s.Valid_Taxon_ID = s2.Taxon_ID\n WHERE c.Concept_ID = (\n SELECT c.Concept_ID\n FROM concepts c\n WHERE c.Concept_Level in ('1A','Crop taxa') and c.Taxon_ID = {$taxonID}\n ) AND s2.Taxon_ID = s2.Valid_Taxon_ID\n ORDER BY c.Concept_Level, s2.Scientific_Name";
$result = $db->getAll($query);
$genePoolConcept = null;
$cropID = null;
// Validate if $result has not data.
if (!empty($result)) {
$genePoolConcept = new GenePoolConcept();
$theConceptID = null;
$theConceptType = null;
$array_id = array();
foreach ($result as $db_concept) {
$concept = new Concept();
$concept->setConceptType(trim($db_concept["Concept_Type"]));
$concept->setConceptLevel(trim($db_concept["Concept_Level"]));
$concept->setConceptID(trim($db_concept["Concept_ID"]));
$concept->setCropID(trim($db_concept["Crop_ID"]));
if ($cropID == null) {
$cropID = trim($db_concept["Crop_ID"]);
}
if ($theConceptID == null) {
$theConceptID = $concept->getConceptID();
}
if ($theConceptType == null) {
$theConceptType = $concept->getConceptType();
}
/* * ** TAXON - BASIC INFORMATION *** */
$taxon = new Taxon(trim($db_concept["Valid_Taxon_ID"]));
// Taxon_ID will be the identifier of the suggestion list.
$taxon->setCommonName(trim($db_concept["Common_Name"]));
$taxon->setFamily(trim($db_concept["Family"]));
$taxon->setFamilyAuthor(trim($db_concept["Family_Author"]));
$taxon->setGenus(trim($db_concept["Genus"]));
$taxon->setSpecie(trim($db_concept["Species"]));
$taxon->setSpecieAuthor(trim($db_concept["Species_Author"]));
$taxon->setSubspecie(trim($db_concept["Subsp"]));
$taxon->setSubspecieAuthor($db_concept["Subsp_Author"]);
$taxon->setVariety(trim($db_concept["Var"]));
$taxon->setVarietyAuthor(trim($db_concept["Var_Author"]));
$taxon->setForm(trim($db_concept["Form"]));
$taxon->setFormAuthor(trim($db_concept["Form_Author"]));
$taxon->setMainCrop(trim($db_concept["Main_Crop"]));
$taxon->setScientificName(trim($db_concept["Scientific_Name"]));
$concept->setTaxon($taxon);
if ($concept->getConceptLevel() == "Crop taxa") {
$genePoolConcept->addCropTaxa($taxon);
} else {
// if concept level = 1A it should be also in the genepool concept list.
if ($concept->getConceptLevel() == "1A") {
$genePoolConcept->addCropTaxa($taxon);
}
$genePoolConcept->addConcept($concept);
}
}
$taxonDAO = DAOFactory::getDAOFactory()->getTaxonDAO();
$mainTaxon = $taxonDAO->getTaxon($cropID);
$mainCrop = new Concept($mainTaxon->getId());
$mainCrop->setConceptID($theConceptID);
$mainCrop->setConceptType($theConceptType);
$mainCrop->setCropID($cropID);
$mainCrop->setTaxon($mainTaxon);
$genePoolConcept->setMainCrop($mainCrop);
}
return $genePoolConcept;
}
