public function getCropBreedingUses($cropID)
{
global $db;
/*
$query = "select DISTINCT b.ID, b.Pot_Conf, b.Description, ref.Ref, sp2.*
from Breeding_data b
inner join concepts c on c.Crop_ID = b.Crop_ID
inner join species sp on b.Taxon_ID = sp.Taxon_ID
inner join Breeding_ref ref on b.Ref_ID = ref.ID
INNER JOIN species sp2 ON sp.Valid_Taxon_ID = sp2.Taxon_ID
where c.Taxon_ID = " . $cropID . "
ORDER BY b.Pot_Conf, sp2.Genus, sp2.Species, sp2.Species_Author, sp2.Subsp, sp2.Subsp_Author, sp2.Var, sp2.Var_Author,
sp2.Form, sp2.Form_Author"; */
$query = "SELECT DISTINCT b.ID, b.Pot_Conf, b.Description, ref.Ref, sp2 . * \n FROM Breeding_data b\n INNER JOIN concepts c ON c.Crop_ID = b.Crop_ID\n INNER JOIN species sp ON b.Taxon_ID = sp.Taxon_ID\n INNER JOIN Breeding_ref ref ON b.Ref_ID = ref.ID\n INNER JOIN species sp2 ON sp.Valid_Taxon_ID = sp2.Taxon_ID\n WHERE c.Crop_ID IN ( \n SELECT Crop_ID\n FROM concepts\n WHERE Taxon_ID = {$cropID}\n AND CWR_Flag = 0 ) \n ORDER BY b.Pot_Conf, sp2.Genus, sp2.Species, sp2.Species_Author, sp2.Subsp, sp2.Subsp_Author, sp2.Var, sp2.Var_Author, sp2.Form, sp2.Form_Author";
$result = $db->getAll($query);
$cropBreedingUses = array();
$test_array = array();
if ($result != null) {
foreach ($result as $r) {
$cropBreedingUse = new BreedingUse($r["ID"]);
$cropBreedingUse->setUseType(trim($r['Pot_Conf']));
$cropBreedingUse->setDescription(trim($r['Description']));
$cropBreedingUse->setReference(trim($r['Ref']));
$taxon = new Taxon(trim($r['Taxon_ID']));
$taxon->setCommonName(trim($r["Common_Name"]));
$taxon->setGenus(trim($r["Genus"]));
$taxon->setSpecie(trim($r["Species"]));
$taxon->setSpecieAuthor(trim($r["Species_Author"]));
$taxon->setSubspecie(trim($r["Subsp"]));
$taxon->setSubspecieAuthor($r["Subsp_Author"]);
$taxon->setVariety(trim($r["Var"]));
$taxon->setVarietyAuthor(trim($r["Var_Author"]));
$taxon->setForm(trim($r["Form"]));
$taxon->setFormAuthor(trim($r["Form_Author"]));
$taxon->setScientificName(trim($r["Scientific_Name"]));
$cropBreedingUse->setTaxon($taxon);
// insert reference to the array.
array_push($cropBreedingUses, $cropBreedingUse);
// Join every except ID value as String
$value = trim($r['Pot_Conf']) . trim($r['Description']) . trim($r['Ref']) . trim($r['Taxon_ID']) . trim($r["Common_Name"]) . trim($r["Genus"]) . trim($r["Species"]) . trim($r["Species_Author"]) . trim($r["Subsp"]) . $r["Subsp_Author"] . trim($r["Var"]) . trim($r["Var_Author"]) . trim($r["Form"]) . trim($r["Form_Author"]) . trim($r["Scientific_Name"]);
array_push($test_array, $value);
// add value to array_test
}
$index_array = $this->getIndexDup($test_array);
for ($i = 0; $i < count($index_array); $i++) {
// Extract the duplicate elements
unset($cropBreedingUses[$index_array[$i] - $i]);
}
return $cropBreedingUses;
} else {
return null;
}
}
/**
*
* @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 $genePoolConcept;
}
public function getTaxaBreedingUse($breedingUse)
{
global $db;
$query = "SELECT * FROM Breeding_data bd\n INNER JOIN species s ON bd.Taxon_ID = s.Taxon_ID\n WHERE bd.Description LIKE '%" . $breedingUse . "%' GROUP BY s.Taxon_ID ORDER BY Scientific_Name";
$results = $db->getAll($query);
$taxa = array();
foreach ($results as $r) {
$taxon = new Taxon($r["Taxon_ID"]);
$taxon->setCommonName(trim($r["Common_Name"]));
$taxon->setGenus(trim($r["Genus"]));
$taxon->setSpecie(trim($r["Species"]));
$taxon->setSubspecie(trim($r["Subsp"]));
$taxon->setVariety(trim($r["Var"]));
$taxon->setForm(trim($r["Form"]));
$taxon->setScientificName(trim($r["Scientific_Name"]));
array_push($taxa, $taxon);
}
return $taxa;
}
