<?php

namespace ggbn;

use Yii;
use DOMDocument;
use XSLTProcessor;
use ggbn\ExploreManager;

/*
 * This SingleRecordManager handles all functions required to retrieve data from multiple providers (BioCASe, DiGIR, IPT)
 * TODO: DiGIR vom alten Portal reinnehmen!
 */
class SingleRecordManager {
	public static function createOutput($requestedAttributes, $model) {
		// Yii::info ( "create Output" );
		// foreach ( $requestedAttributes as $k => $v )
		// Yii::info ( "KEY: " . $k . " -- " . $v );
		$filters = array ();
		$filters ['unitID'] = $_REQUEST ['unitID'];
		if (isset ( $_REQUEST ['collectioncode'] ))
			$filters ['collectioncode'] = $_REQUEST ['collectioncode'];
		else
			$filters ['collectioncode'] = NULL;
		if (isset ( $_REQUEST ['institutioncode'] ))
			$filters ['institutioncode'] = $_REQUEST ['institutioncode'];
		else
			$filters ['institutioncode'] = NULL;
		$gbifIDs = [ ];
		$colID = "";
		$ncbiID = "";
		
		$config = SOLRQueryManager::getConfigSearch ();
		$query = SOLRQueryManager::createSearchQuery ( $config );
		
		$raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", null, $filters, True );
		
		$response = $raw_response;
		// Yii::info ( "nb res: " . $response->getNumFound () );
		if ($response->getNumFound () == 0) {
			return [ ];
		}
		$tripleidstoreid = "";
		foreach ( $response as $doc ) {
			$tripleidstoreid = $doc->tripleidstoreid;
			// echo $tripleidstoreid;
		}
		$config = SOLRQueryManager::getConfigDetails ();
		$query = SOLRQueryManager::createSearchQuery ( $config );
		
		$response = SOLRQueryManager::fillAndExecuteQuery ( $query, "tripleidstoreid:" . $tripleidstoreid, null, [ ], True );
		if ($response->getNumFound () == 0) {
			return [ ];
		}
		$multimedia = "";
		
		$loan = [ ];
		
		foreach ( $response as $doc ) {
			$upperTripleidstoreids = [ ];
			$accesspoint = $doc->accesspoint;
			$unitID = $doc->unitID;
			$collectioncode = $doc->collectioncode;
			$institutioncode = $doc->institutioncode;
			$schemaurl = $doc->schemaurl;
			$digirresourcename = $doc->digirresourcename;
			$schemaname = $doc->schemaname;
			$basedirectory = $doc->basedirectory;
			$sampletype = $doc->sampletype;
			$tripleidstoreid = $doc->tripleidstoreid;
			$fullScientificName = $doc->originalName;
			$occurrenceFile = $doc->filename;
			$elementtype = $doc->elementtype;
			$collectors = $doc->collectors;
			$collectornb = $doc->collectornumbers_nc;
			
			try {
				$indexHerbarorium = $doc->indexHerbarorium;
			} catch ( Exception $e ) {
				$indexHerbarorium = null;
			}
			
			if (! empty ( $collectornb )) {
				$collectornb = array_unique ( $collectornb );
				if (($key = array_search ( 's.n.', $collectornb )) !== false) {
					unset ( $collectornb [$key] );
				}
			}
			
			try {
				$latitude = $doc->latitude;
			} catch ( Exception $e ) {
				$latitude [] = NULL;
			}
			try {
				$longitude = $doc->longitude;
			} catch ( Exception $e ) {
				$longitude [] = NULL;
			}
			
			try {
				$canonicalName = $doc->canonicalName;
			} catch ( Exception $e ) {
				$canonicalName = "";
			}
			try {
				$citesStatus = $doc->citesStatus;
			} catch ( Exception $e ) {
				$citesStatus = NULL;
			}
			try {
				$gbifIDs [] = $doc->gbifKey;
			} catch ( Exception $e ) {
			}
			try {
				$colID = $doc->taxonIDcol;
			} catch ( Exception $e ) {
			}
			try {
				$ncbiID = $doc->taxonIDncbi;
			} catch ( Exception $e ) {
			}
			
			try {
				$upperTripleidstoreids = $doc->upperTripleidstoreids;
			} catch ( Exception $e ) {
				$upperTripleidstoreids = [ ];
			}
			if ($upperTripleidstoreids == "")
				$upperTripleidstoreids = [ ];
			try {
				$tmpids = $doc->lowerTripleidstoreids;
				if (isset ( $tmpids ))
					array_merge ( $upperTripleidstoreids, $tmpids );
			} catch ( Exception $e ) {
			}
			try {
				if (isset ( $doc->multimediaurl ))
					foreach ( $doc->multimediaurl as $murl ) {
						if ($murl != "N/A") {
							if (! (strpos ( $multimedia, $murl ) === FALSE))
								continue;
							else {
								if (strpos ( $murl, "http" ) === FALSE) {
									$murl = "http://" . $murl;
								}
								$multimedia = $multimedia . "<a href='" . $murl . "' target='_blank'><img src='" . $murl . "'/></a> &nbsp;";
							}
						}
					}
			} catch ( Exception $e ) {
			}
			
			$blocked = $doc->blocked;
			$blockedUntil = $doc->blockedUntil;
			$disposition = $doc->disposition;
			$disposition_clean = $doc->disposition_clean;
			$condition = $doc->condition;
			if (empty ( $blockedUntil )) {
				if ($sampletype == "tissue")
					$loan [$unitID] = [ 
							" Tissue available ",
							"OK",
							"not blocked",
							$condition,
							$disposition_clean 
					];
				if ($sampletype == "DNA")
					$loan [$unitID] = [ 
							" DNA available ",
							"OK",
							"not blocked",
							$condition,
							$disposition_clean 
					];
			} else {
				if (new \DateTime () > new \DateTime ( $blockedUntil )) {
					// $loan [] = "The unitID " . $unitID . " was blocked until " . $blockedUntil . " under the condition " . $condition . ". There is still " . $disposition_clean . " available.";
					if ($sampletype == "tissue")
						$loan [$unitID] = [ 
								" Tissue available ",
								"OK",
								"was blocked until " . $blockedUntil,
								$condition,
								$disposition_clean 
						];
					if ($sampletype == "DNA")
						$loan [$unitID] = [ 
								" DNA available ",
								"OK",
								"was blocked until " . $blockedUntil,
								$condition,
								$disposition_clean 
						];
				} else {
					if ($sampletype == "tissue")
						$loan [$unitID] = [ 
								" Tissue available ",
								"BLOCKED",
								"is blocked until " . $blockedUntil,
								$condition,
								$disposition_clean 
						];
					if ($sampletype == "DNA")
						$loan [$unitID] = [ 
								" DNA available ",
								"BLOCKED",
								"is blocked until " . $blockedUntil,
								$condition,
								$disposition_clean 
						];
				}
			}
		}
		if (isset ( $upperTripleidstoreids [0] )) {
			$tripleidstoreids = SingleRecordManager::getListOfTripleids ( $upperTripleidstoreids, $model );
			// remove the tripleidstoreid from the unit already searched
			unset ( $tripleidstoreids [array_search ( $tripleidstoreid, $tripleidstoreids )] );
			$tripleidstoreids = array_values ( $tripleidstoreids );
			
			$SumSize = count ( $tripleidstoreids );
			
			$config = SOLRQueryManager::getConfigDetails ();
			$query = SOLRQueryManager::createSearchQuery ( $config );
			
			$fq = "";
			for($i = 0; $i < $SumSize; $i ++) {
				
				$fq .= "tripleidstoreid:" . $tripleidstoreids [$i];
				if (isset ( $tripleidstoreids [$i + 1] )) {
					$fq .= " OR ";
				}
			}
			// Yii::info ( "fq: " . $fq );
			
			if ($fq == "") {
				$index = 0;
				// $accesspoint2 [$index] = "missing";
				// $unitID2 [$index] = "missing";
				// $tripleid2 [$index] = "missing";
				// $collectioncode2 [$index] = "missing";
				// $institutioncode2 [$index] = "missing";
				// $schemaurl2 [$index] = "missing";
				// $schemaname2 [$index] = "missing";
				// $basedirectory2 [$index] = "missing";
				// $sampletype2 [$index] = "missing";
				// $recordBasis2 [$index] = "missing";
				// $digirresourcename2 [$index] = "missing";
				// $latitude2 [$index] = NULL;
				// $longitude2 [$index] = NULL;
				// $filters ['unitID2'] [$index] = "missing";
				// $filters ['collectioncode2'] [$index] = "missing";
				// $filters ['institutioncode2'] [$index] = "missing";
				// $citesStatus2 [$index] = NULL;
				// $multimedia2 [$index] = "";
				$accesspoint2 [$index] = NULL;
				$unitID2 [$index] = NULL;
				$tripleid2 [$index] = NULL;
				$collectioncode2 [$index] = NULL;
				$institutioncode2 [$index] = NULL;
				$schemaurl2 [$index] = NULL;
				$schemaname2 [$index] = NULL;
				$basedirectory2 [$index] = NULL;
				$sampletype2 [$index] = NULL;
				$recordBasis2 [$index] = NULL;
				$digirresourcename2 [$index] = NULL;
				$latitude2 [$index] = NULL;
				$longitude2 [$index] = NULL;
				$occurrenceFile2 [$index] = NULL;
				$elementtype2 [index] = NULL;
				$filters ['unitID2'] [$index] = NULL;
				$filters ['collectioncode2'] [$index] = NULL;
				$filters ['institutioncode2'] [$index] = NULL;
				$citesStatus2 [$index] = NULL;
				$multimedia2 [$index] = "";
				$output = array (
						'response' => $response,
						'filters' => $filters,
						'accesspoint' => $accesspoint,
						'unitID' => $unitID,
						'collectioncode' => $collectioncode,
						'institutioncode' => $institutioncode,
						'schemaurl' => $schemaurl,
						'digirresourcename' => $digirresourcename,
						'schemaname' => $schemaname,
						'basedirectory' => $basedirectory,
						'sampletype' => $sampletype,
						'multimedia' => $multimedia,
						'canonicalName' => $canonicalName,
						'tripleid' => $tripleidstoreid,
						'latitude' => $latitude,
						'longitude' => $longitude,
						'loan' => $loan,
						'collectors' => $collectors,
						'collectornb' => $collectornb,
						'indexHerbarorium' => $indexHerbarorium,
						'occurrenceFile' => $occurrenceFile,
						'elementtype' => $elementtype 
				);
			} else {
				$raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", $fq, [ ], True );
				$response = $raw_response;
				foreach ( $response as $index => $doc ) {
					$occurrenceFile2 [$index] = $doc->filename;
					try {
						$accesspoint2 [$index] = $doc->accesspoint;
					} catch ( Exception $e ) {
						$accesspoint2 [$index] = "";
					}
					try {
						$unitID2 [$index] = $doc->unitID;
					} catch ( Exception $e ) {
						$unitID2 [$index] = "";
					}
					try {
						$collectioncode2 [$index] = $doc->collectioncode;
					} catch ( Exception $e ) {
						$collectioncode2 [$index] = "";
					}
					try {
						$tripleid2 [$index] = $doc->tripleidstoreid;
					} catch ( Exception $e ) {
						$tripleid2 [$index] = "";
					}
					try {
						$institutioncode2 [$index] = $doc->institutioncode;
					} catch ( Exception $e ) {
						$institutioncode2 [$index] = "";
					}
					try {
						$schemaurl2 [$index] = $doc->schemaurl;
					} catch ( Exception $e ) {
						$schemaurl2 [$index] = "";
					}
					try {
						$ocurrenceFile2 [$index] = $doc->filename;
					} catch ( Exception $e ) {
						$ocurrenceFile2 [$index] = "";
					}
					try {
						$schemaname2 [$index] = $doc->schemaname;
					} catch ( Exception $e ) {
						$schemaname2 [$index] = "";
					}
					try {
						$basedirectory2 [$index] = $doc->basedirectory;
					} catch ( Exception $e ) {
						$basedirectory2 [$index] = "";
					}
					try {
						$elementtype2 [$index] = $doc->elementtype;
					} catch ( Exception $e ) {
						$elementtype2 [$index] = "";
					}
					try {
						$sampletype2 [$index] = $doc->sampletype;
						if (! isset ( $sampletype2 [$index] ) || $sampletype2 [$index] == "unknown") {
							try {
								$rb = $doc->recordbasis;
								// echo "recordbasis: " . $rb . "<br/>";
								if (stristr ( $rb, "specimen" ) != FALSE || stristr ( $rb, "occurrence" ))
									$sampletype2 [$index] = 'specimen';
							} catch ( Exception $e ) {
							}
						}
					} catch ( Exception $e ) {
						$sampletype2 [$index] = "unkown";
						try {
							$rb = $doc->recordbasis;
							// echo "recordbasis!";
							if (stristr ( $rb, "specimen" ) != FALSE || stristr ( $rb, "occurrence" ))
								$sampletype2 [$index] = 'specimen';
						} catch ( Exception $e ) {
						}
					}
					try {
						$digirresourcename2 [$index] = $doc->digirresourcename;
					} catch ( Exception $e ) {
						$digirresourcename2 [$index] = "";
					}
					try {
						$latitude2 [$index] = $doc->latitude;
					} catch ( Exception $e ) {
						$latitude2 [$index] = NULL;
					}
					try {
						$longitude2 [$index] = $doc->longitude;
					} catch ( Exception $e ) {
						$longitude2 [$index] = NULL;
					}
					
					try {
						$citesStatus2 [$index] = $doc->citesStatus;
					} catch ( Exception $e ) {
						$citesStatus2 [$index] = NULL;
					}
					try {
						$gbifIDs [] = $doc->gbifKey;
					} catch ( Exception $e ) {
					}
					try {
						$colID = $doc->taxonIDcol;
					} catch ( Exception $e ) {
					}
					try {
						$ncbiID = $doc->taxonIDncbi;
					} catch ( Exception $e ) {
					}
					
					$filters ['unitID2'] [$index] = $doc->unitID;
					$filters ['collectioncode2'] [$index] = $doc->collectioncode;
					$filters ['institutioncode2'] [$index] = $doc->institutioncode;
					
					try {
						$multimedia2 [$index] = "";
						try {
							if (is_array ( $doc->multimediaurl ))
								foreach ( $doc->multimediaurl as $murl )
									if ($murl != "N/A")
										if (! strpos ( $multimedia2 [$index], $murl ))
											$multimedia2 [$index] = $multimedia2 [$index] . "<a href='" . $murl . "' target='_blank'><img src='" . $murl . "'/></a>&nbsp;";
										else
											$multimedia2 [$index] == "";
						} catch ( Exception $e ) {
							$multimedia2 [$index] == "";
						}
					} catch ( Exception $e ) {
						$multimedia2 [$index] = "";
					}
					
					$blocked = $doc->blocked;
					$blockedUntil = $doc->blockedUntil;
					$disposition = $doc->disposition;
					$disposition_clean = $doc->disposition_clean;
					$condition = $doc->condition;
					if ($sampletype != "tissue") {
						if (empty ( $blockedUntil )) {
							if ($sampletype2 [$index] == "tissue")
								$loan [$filters ['unitID2'] [$index]] = [ 
										" Tissue available ",
										"OK",
										"not blocked",
										$condition,
										$disposition_clean 
								];
						} else {
							if (new \DateTime () > new \DateTime ( $blockedUntil )) {
								// $loan [] = "The unitID " . $filters ['unitID2'] [$index] . " was blocked until " . $blockedUntil . " under the condition " . $condition . ". There is still " . $disposition_clean . " available.";
								if ($sampletype2 [$index] == "tissue")
									$loan [$filters ['unitID2'] [$index]] = [ 
											" Tissue available ",
											"OK",
											"was blocked until " . $blockedUntil,
											$condition,
											$disposition_clean 
									];
							} else {
								if ($sampletype2 [$index] == "tissue")
									$loan [$filters ['unitID2'] [$index]] = [ 
											" Tissue available ",
											"BLOCKED",
											"is blocked until " . $blockedUntil,
											$condition,
											$disposition_clean 
									];
							}
						}
					}
				}
				$output = array (
						'response' => $response,
						'filters' => $filters,
						'accesspoint' => $accesspoint,
						'unitID' => $unitID,
						'collectioncode' => $collectioncode,
						'institutioncode' => $institutioncode,
						'schemaurl' => $schemaurl,
						'digirresourcename' => $digirresourcename,
						'schemaname' => $schemaname,
						'basedirectory' => $basedirectory,
						'sampletype' => $sampletype,
						'multimedia' => $multimedia,
						'canonicalName' => $canonicalName,
						'tripleid' => $tripleidstoreid,
						'latitude' => $latitude,
						'longitude' => $longitude,
						'occurrenceFile' => $occurrenceFile,
						'elementtype' => $elementtype,
						'accesspoint2' => $accesspoint2,
						'unitID2' => $unitID2,
						'collectioncode2' => $collectioncode2,
						'tripleid2' => $tripleid2,
						'institutioncode2' => $institutioncode2,
						'schemaurl2' => $schemaurl2,
						'occurrenceFile2' => $occurrenceFile2,
						'elementtype2' => $elementtype2,
						'schemaname2' => $schemaname2,
						'basedirectory2' => $basedirectory2,
						'digirresourcename2' => $digirresourcename2,
						'sampletype2' => $sampletype2,
						'longitude2' => $longitude2,
						'latitude2' => $latitude2,
						'multimedia2' => $multimedia2,
						'citesStatus2' => $citesStatus2,
						'loan' => $loan,
						'collectors' => $collectors,
						'collectornb' => $collectornb,
						'indexHerbarorium' => $indexHerbarorium 
				);
			}
			
			if (sizeof ( $gbifIDs ) > 0) {
				$output ['GBIFs'] = array_unique ( $gbifIDs );
				// $GBIFs = ExploreManager::getGBIFRecords ( $gbifIDs );
				// if (sizeof ( $GBIFs ) > 0)
				// $output ['GBIFs'] = $GBIFs;
			} else
				$output ['GBIFs'] = [ ];
			if ($ncbiID != "") {
				$output ['NCBI'] = $ncbiID;
				// $NCBI = ExploreManager::getNCBIRecord ( $ncbiID );
				// if (! empty ( $NCBI ))
				// $output ['NCBI'] = $NCBI;
			} else
				$output ['NCBI'] = [ ];
			$GGBNs = ExploreManager::getGGBNRecords ( $fullScientificName, $tripleidstoreid );
			if (! empty ( $GGBNs ))
				$output ['GGBNs'] = $GGBNs;
			else
				$output ['GGBNs'] = [ ];
			return $output;
		}  // if($upperTripleidstoreids != "")
		else {
			$output = array (
					'response' => $response,
					'filters' => $filters,
					'accesspoint' => $accesspoint,
					'unitID' => $unitID,
					'collectioncode' => $collectioncode,
					'institutioncode' => $institutioncode,
					'schemaurl' => $schemaurl,
					'digirresourcename' => $digirresourcename,
					'schemaname' => $schemaname,
					'basedirectory' => $basedirectory,
					'sampletype' => $sampletype,
					'multimedia' => $multimedia,
					'canonicalName' => $canonicalName,
					'tripleid' => $tripleidstoreid,
					'latitude' => $latitude,
					'longitude' => $longitude,
					'loan' => $loan,
					'occurrenceFile' => $occurrenceFile,
					'collectors' => $collectors,
					'collectornb' => $collectornb,
					'indexHerbarorium' => $indexHerbarorium,
					'elementtype' => $elementtype 
			);
			if (sizeof ( $gbifIDs ) > 0) {
				$output ['GBIFs'] = array_unique ( $gbifIDs );
				// $GBIFs = ExploreManager::getGBIFRecords ( $gbifIDs );
				// if (sizeof ( $GBIFs ) > 0)
				// $output ['GBIFs'] = $GBIFs;
			} else
				$output ['GBIFs'] = [ ];
			if ($ncbiID != "") {
				$output ['NCBI'] = $ncbiID;
				// $NCBI = ExploreManager::getNCBIRecord ( $ncbiID );
				// if (! empty ( $NCBI ))
				// $output ['NCBI'] = $NCBI;
			} else
				$output ['NCBI'] = [ ];
			$GGBNs = ExploreManager::getGGBNRecords ( $fullScientificName, $tripleidstoreid );
			if (! empty ( $GGBNs ))
				$output ['GGBNs'] = $GGBNs;
			else
				$output ['GGBNs'] = [ ];
			return $output;
		}
	}
	public static function getListOfTripleids($baseIds, $model) {
		static $cnt = 0;
		static $lowerAndUppers = [ ];
		if (sizeof ( $lowerAndUppers ) == 0) {
			$lowerAndUppers = $baseIds;
		}
		$cnt ++;
		$sizeBefore = sizeof ( $lowerAndUppers );
		if ($sizeBefore == 0)
			$sizeBefore = sizeof ( $baseIds );
		foreach ( $baseIds as $id ) {
			$config = SOLRQueryManager::getConfigDetails ();
			$query = SOLRQueryManager::createSearchQuery ( $config );
			$fq = "tripleidstoreid:" . $id;
			$raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", $fq, [ ], True );
			
			$response = $raw_response;
			
			foreach ( $response as $doc ) {
				$upperTripleidstoreids2 = $doc ['upperTripleidstoreids'];
				$lowerIDs = $doc ['lowerTripleidstoreids'];
				if (isset ( $upperTripleidstoreids2 )) {
					$lowerAndUppers = array_unique ( array_merge ( $lowerAndUppers, $upperTripleidstoreids2 ) );
				}
				if (isset ( $lowerIDs )) {
					$lowerAndUppers = array_unique ( array_merge ( $lowerAndUppers, $lowerIDs ) );
				}
			}
		}
		if (sizeof ( $lowerAndUppers ) > $sizeBefore) {
			if ($cnt < 5)
				return self::getListOfTripleids ( $lowerAndUppers, $model );
		}
		return $lowerAndUppers;
	}
	public static function createRecordQuery($filters, $schemaurl) {
		if ($schemaurl == "http://www.tdwg.org/schemas/abcd/2.06") {
			$query = urlencode ( '<?xml version="1.0" encoding="UTF-8"?>
				<request xmlns="http://www.biocase.org/schemas/protocol/1.3">
				<header><type>search</type></header>
				<search><requestFormat>http://www.tdwg.org/schemas/abcd/2.06</requestFormat>
				<responseFormat start="0" limit="10">http://www.tdwg.org/schemas/abcd/2.06</responseFormat>
				<filter><and><and><like path="/DataSets/DataSet/Units/Unit/UnitID">' . $filters ['unitID'] . '</like>
				<like path="/DataSets/DataSet/Units/Unit/SourceInstitutionID">' . $filters ['institutioncode'] . '</like></and>
				<like path="/DataSets/DataSet/Units/Unit/SourceID">' . $filters ['collectioncode'] . '</like></and>
				</filter><count>false</count></search></request>' );
		}
		
		if ($schemaurl == "http://www.tdwg.org/schemas/abcd/2.1") {
			$query = urlencode ( '<?xml version="1.0" encoding="UTF-8"?>
				<request xmlns="http://www.biocase.org/schemas/protocol/1.3">
				<header><type>search</type></header>
				<search><requestFormat>http://www.tdwg.org/schemas/abcd/2.1</requestFormat>
				<responseFormat start="0" limit="10">http://www.tdwg.org/schemas/abcd/2.1</responseFormat>
				<filter><and><and><like path="/DataSets/DataSet/Units/Unit/UnitID">' . $filters ['unitID'] . '</like>
				<like path="/DataSets/DataSet/Units/Unit/SourceInstitutionID">' . $filters ['institutioncode'] . '</like></and>
				<like path="/DataSets/DataSet/Units/Unit/SourceID">' . $filters ['collectioncode'] . '</like></and>
				</filter><count>false</count></search></request>' );
		}
		
		if ($schemaurl == "http://rs.tdwg.org/dwc/") {
			$query = "";
		}
		
		return $query;
	}
	public static function createAssociatedRecordQuery($associatedUnitID, $associatedCollectionCode, $associatedInstitutionCode, $associatedSchemaUrl, $associatedDigirResourcename, $associatedAccessPoint) {
		// echo ( "createAssociatedRecordQuery " . $associatedUnitID . " " . $associatedSchemaUrl );
		$query2 = "";
		if ($associatedSchemaUrl == "http://www.tdwg.org/schemas/abcd/2.06") {
			$query2 = urlencode ( '<?xml version="1.0" encoding="UTF-8"?>
				<request xmlns="http://www.biocase.org/schemas/protocol/1.3">
				<header><type>search</type></header>
				<search><requestFormat>http://www.tdwg.org/schemas/abcd/2.06</requestFormat>
				<responseFormat start="0" limit="10">http://www.tdwg.org/schemas/abcd/2.06</responseFormat>
				<filter><and><and><like path="/DataSets/DataSet/Units/Unit/UnitID">' . $associatedUnitID . '</like>
				<like path="/DataSets/DataSet/Units/Unit/SourceInstitutionID">' . $associatedInstitutionCode . '</like></and>
				<like path="/DataSets/DataSet/Units/Unit/SourceID">' . $associatedCollectionCode . '</like></and>
				</filter><count>false</count></search></request>' );
		}
		
		if ($associatedSchemaUrl == "http://www.tdwg.org/schemas/abcd/2.1") {
			$query2 = urlencode ( '<?xml version="1.0" encoding="UTF-8"?>
				<request xmlns="http://www.biocase.org/schemas/protocol/1.3">
				<header><type>search</type></header>
				<search><requestFormat>http://www.tdwg.org/schemas/abcd/2.1</requestFormat>
				<responseFormat start="0" limit="10">http://www.tdwg.org/schemas/abcd/2.1</responseFormat>
				<filter><and><and><like path="/DataSets/DataSet/Units/Unit/UnitID">' . $associatedUnitID . '</like>
				<like path="/DataSets/DataSet/Units/Unit/SourceInstitutionID">' . $associatedInstitutionCode . '</like></and>
				<like path="/DataSets/DataSet/Units/Unit/SourceID">' . $associatedCollectionCode . '</like></and>
				</filter><count>false</count></search></request>' );
		}
		
		if ($associatedSchemaUrl == "http://rs.tdwg.org/dwc/") {
			$query2 = "";
		}
		
		if ($associatedSchemaUrl == "http://bnhm.berkeley.edu/DwC/bnhm_dc2_schema.xsd") {
			$q = '<?xml version="1.0" encoding="UTF-8"?>
				  <request xmlns="http://digir.net/schema/protocol/2003/1.0" xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
				  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:digir="http://digir.net/schema/protocol/2003/1.0" 
				  xmlns:darwin="http://digir.net/schema/conceptual/darwin/2003/1.0" xmlns:dwc="http://digir.net/schema/conceptual/darwin/2003/1.0" 
				  xsi:schemaLocation="http://digir.net/schema/protocol/2003/1.0 http://digir.sourceforge.net/schema/protocol/2003/1.0/digir.xsd http://digir.net/schema/conceptual/darwin/2003/1.0 http://digir.sourceforge.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd">
				  <header><version>1.0.0</version><sendTime>2009-11-13 14:40:56.000</sendTime><source/>
				  <destination resource="' . $associatedDigirResourcename . '">' . $associatedAccessPoint . '</destination>
				  <type>search</type></header>
				  <search><filter><and><and><equals><darwin:CatalogNumber>' . $associatedUnitID . '</darwin:CatalogNumber></equals>
				  <equals><darwin:InstitutionCode>' . $associatedInstitutionCode . '</darwin:InstitutionCode></equals></and><like>
				  <darwin:CollectionCode>' . $associatedCollectionCode . '</darwin:CollectionCode></like></and></filter>
				  <records  start="0" limit="10"><structure schemaLocation="http://search.biocase.org/europe/static/darwinObis.xsd"/></records>
				  <count>false</count></search></request>';
			$query2 = urlencode ( $q );
		}
		
		return $query2;
	}
	public static function getABCD($accesspoint, $query, $unitID) {
		// TODO test if url has parameter and set ? or &!!!
		$fullURL = $accesspoint . "&query=" . $query;
		// echo $fullURL;
		
		$options = [ 
				'http' => [ 
						'timeout' => '10' 
				] 
		];
		$context = stream_context_create ( $options );
		libxml_set_streams_context ( $context );
		
		$xml = new DOMDocument ( '1.0', 'UTF-8' );
		try {
			$xml->load ( $fullURL );
			$handle = fopen ( Yii::$app->params ['tmpFolder'] . $unitID . '.xml', 'w' );
			fwrite ( $handle, $xml->saveXML () );
			fclose ( $handle );
		} catch ( yii\base\ErrorException $e ) {
			$xml = NULL;
		}
		
		// Yii::info ( $xml->saveXML () );
		return $xml;
	}
	public static function parseABCD($xsl, $xml, $tripleid) {
		$processor = new XSLTProcessor ();
		$processor->registerPHPFunctions ();
		$processor->importStyleSheet ( $xsl );
		try {
			$html = $processor->transformToXML ( $xml );
		} catch ( yii\base\ErrorException $e ) {
			Yii::error ( $e );
			$html = SingleRecordManager::getFromCache ( $tripleid );
			return [ 
					$html,
					False 
			];
		}
		
		// Yii::info("parse ABCD: ".$html);
		// echo $html;
		if (strpos ( $html, "hits found for" ) > 0 && $tripleid != NULL) {
			$out = SingleRecordManager::getFromCache ( $tripleid );
			return [ 
					$out,
					False 
			];
		} else
			return [ 
					$html,
					True 
			];
	}
	public static function readDwC($xsl, $accesspoint, $digirresourcename, $query, $tripleid) {
		$processor = new XSLTProcessor ();
		$processor->importStyleSheet ( $xsl );
		
		$fullURL = $accesspoint . "?request=" . $query;
		// echo $fullURL;
		
		$xml = new DOMDocument ( '1.0', 'UTF-8' );
		$xml->load ( $fullURL );
		
		$html = $processor->transformToXML ( $xml );
		// print_r( $html);
		if (strpos ( $html, "hits found for" ) > 0) {
			$out = SingleRecordManager::getFromCache ( $tripleid );
			return $out;
		} else
			return $html;
	}
	public static function getFromCache($tripleidstoreid) {
		Yii::info ( "getFromCache " . $tripleidstoreid );
		$config = SOLRQueryManager::getConfigDetails ();
		$query = SOLRQueryManager::createSearchQuery ( $config );
		$fq = "tripleidstoreid:" . $tripleidstoreid;
		$raw_response = SOLRQueryManager::fillAndExecuteQuery ( $query, "*:*", $fq, [ ], True );
		
		$response = $raw_response;
		$out = "";
		foreach ( $response as $doc ) {
			$out .= "<i>The original unit could not be found - info displayed from the cache</i>";
			$out .= "<h3  class='background1'>Identification(s):</h3> ";
			$out .= $doc->fullScientificName . "<br/>";
			if (Yii::$app->params ['siteName'] != 'ggbn_portal')
				$out .= "<h3>Gathering Event</h3> ";
			
			else
				$out .= "<h3>Collection Info:</h3> ";
			$out .= "<span class='label'>Collector(s):</span> " . $doc->collectors . "<br/>";
			if ($doc->fieldnumber != "s.n.")
				$out .= "<span class='label'>Field number:</span> " . $doc->fieldnumber . "<br/>";
			$out .= "<span class='label'>Locality:</span> " . $doc->locality . "<br/>" . "<br/>";
			
			// $out .= "<span class='label'>Other info</span> " . "<br/>";
			$out .= "<span class='label'>Country:</span> " . $doc->country . "<br/>";
			if (! empty ( $doc->continent ))
				$out .= "<span class='label'>Continent:</span> " . implode ( ", ", $doc->continent ) . "<br/>";
			
			if (! empty ( $doc->latitude ))
				$out .= "<span class='label'>Coordinates (Lat|Lon):</span> " . $doc->latitude [0] . "|" . $doc->longitude [0] . "<br/>";
		}
		return $out;
	}
	
	// type = specimen or tissue or dna
	public static function readDwCA($unitToFind, $folder, $dom, $sampleType, $occurrenceFile) {
		Yii::info ( "READ " . $unitToFind . " in file " . $occurrenceFile );
		echo "<!-- from DarwinCore Archive-->";
		$Cores = $dom->getElementsByTagName ( 'core' );
		$Extensions = $dom->getElementsByTagName ( 'extension' );
		$xml = simplexml_load_file ( $folder . "meta.xml" );
		foreach ( $xml->attributes () as $a => $b ) {
			if ($a === 'metadata')
				$EML = $b;
		}
		
		$output = '';
		$relation = '';
		$sample = '';
		$preservation = '';
		$preparation = '';
		$sequences = '';
		$prepSex = '';
		$locality = "";
		$identification = "";
		$gathering = "";
		$ID_Record = null;
		$material = "";
		$taxonomySet = false;
		
		$latitude = [ ];
		$longitude = [ ];
		$multimedia = "";
		$preparationType = "";
		
		// extract data from EML file
		$xml = simplexml_load_file ( $folder . $EML );
		$datasetxml = $xml->dataset;
		$creator = $datasetxml->creator;
		try {
			$orga = $creator->organizationName;
			Yii::info ( "ORGA " . $orga );
		} catch ( yii\base\ErrorException $e ) {
		}
		try {
			$addressxml = $creator->address;
		} catch ( yii\base\ErrorException $e ) {
		}
		$addressT = [ ];
		try {
			$addressT [] = $addressxml->deliveryPoint;
			$addressT [] = $addressxml->city;
			$addressT [] = $addressxml->administrativeArea;
			$addressT [] = $addressxml->postalCode;
			$addressT [] = $addressxml->country;
		} catch ( yii\base\ErrorException $e ) {
		}
		try {
			$addressT = array_filter ( $addressT );
		} catch ( yii\base\ErrorException $e ) {
		}
		
		$intellectualRightsxml = $datasetxml->intellectualRights;
		$irT = [ ];
		try {
			$irT [] = $intellectualRightsxml->para;
			$paraXML = $intellectualRightsxml->para;
			$ulinkXML = $paraXML->ulink;
			$url = $ulinkXML->attributes () [0];
			$irT [] = "<a href='" . $url . "'>" . $ulinkXML->citetitle . "</a>";
		} catch ( yii\base\ErrorException $e ) {
			Yii::info ( "oups " . $e );
		}
		try {
			$irT = array_filter ( $irT );
		} catch ( Exception $e ) {
		}
		
		try {
			$geocoveragexml = $datasetxml->coverage->geographicCoverage->geographicDescription;
		} catch ( yii\base\ErrorException $e ) {
			$geocoveragexml = "";
		}
		try {
			$taxocoveragexml = $datasetxml->coverage->taxonomicCoverage->generalTaxonomicCoverage;
		} catch ( yii\base\ErrorException $e ) {
			$taxocoveragexml = "";
		}
		
		try {
			$abstract = $datasetxml->abstract->para;
		} catch ( yii\base\ErrorException $e ) {
			$abstract = "";
		}
		
		// Start Core
		foreach ( $Cores as $Core ) {
			$Files = $Core->getElementsByTagName ( 'files' );
			foreach ( $Files as $File ) {
				$FileLocationCore = $File->getElementsByTagName ( 'location' )->item ( 0 )->nodeValue;
			}
			
			$ColumnIDs = $Core->getElementsByTagName ( 'id' );
			
			foreach ( $ColumnIDs as $ColumnID ) {
				$field_columns_core [0] = $ColumnID->getAttribute ( 'index' );
				$idElt = $ColumnID->getAttribute ( 'index' );
			}
			
			$fields = $Core->getElementsByTagName ( 'field' );
			$max = 0;
			$staticValues = [ ];
			foreach ( $fields as $field ) {
				$idx = $field->getAttribute ( 'index' );
				if (! empty ( $idx )) {
					$field_columns_core [$field->getAttribute ( 'index' )] = $field->getAttribute ( 'term' );
					if ($field->getAttribute ( 'index' ) > $max)
						$max = $field->getAttribute ( 'index' );
				} else {
					$staticValues [end ( explode ( "/", $field->getAttribute ( 'term' ) ) )] = $field->getAttribute ( 'default' );
				}
			}
			if (sizeof ( $field_columns_core ) < $max)
				foreach ( range ( 0, $max ) as $i )
					if (! isset ( $field_columns_core [$i] )) {
						$field_columns_core [$i] = "";
					}
				// read header first to get column of catalogNumber -> if catalogNumber = required record -> get full row
				// Yii::info( "try top open " . $folder . " in " . $FileLocationCore . " and look for " . $unitToFind."<br/>" );
				
			// //does only parse this part if the current thing to display is the DNA part
			$handle = fopen ( $folder . $FileLocationCore, "r" );
			if ($handle) {
				$separator = "\t";
				$t1 = sizeof ( fgetcsv ( $handle, 0, $separator, $enclosure = '"' ) );
				fclose ( $handle );
				$handle = fopen ( $folder . $FileLocationCore, "r" );
				$t2 = sizeof ( fgetcsv ( $handle, 0, ",", $enclosure = '"' ) );
				fclose ( $handle );
				$handle = fopen ( $folder . $FileLocationCore, "r" );
				if ($t2 > $t1)
					$separator = ",";
				$header = fgetcsv ( $handle, 0, $separator, $enclosure = '"' );
				foreach ( $header as $index => $term ) {
					if ($term == "catalogNumber") {
						$ColumnCatalogNumber = $index;
					}
					if ($term == "id") {
						$ColumnIndex = $index;
					}
					if ($term == "occurrenceID") {
						$ColumnOccurrenceID = $index;
					}
				}
				if (empty ( $ColumnCatalogNumber )) {
					$k = array_search ( "http://rs.tdwg.org/dwc/terms/catalogNumber", $field_columns_core );
					if ($k)
						$ColumnCatalogNumber = $k;
					$k = array_search ( "http://rs.tdwg.org/dwc/terms/occurrenceID", $field_columns_core );
					if ($k)
						$ColumnOccurrenceID = $k;
					if (isset ( $idElt ))
						$ColumnIndex = $idElt;
					else
						$ColumnIndex = 0;
					$header = [ ];
					foreach ( $field_columns_core as $k => $v )
						$header [$k] = end ( explode ( "/", $v ) );
				}
				
				$row = 1;
				$idfound = false;
				$allIDs = [ ];
				array_push ( $allIDs, $unitToFind );
				if (is_array ( $unitToFind ))
					$allIDs = array_merge ( $unitToFind, $allIDs );
				else
					array_push ( $allIDs, $unitToFind );
				
				fclose ( $handle );
				
				ini_set ( "auto_detect_line_endings", true );
				
				$handle2 = fopen ( $folder . $occurrenceFile, "r" );
				$separator = "\t";
				$t1 = sizeof ( fgetcsv ( $handle2, 0, $separator, $enclosure = '"' ) );
				fclose ( $handle2 );
				$handle2 = fopen ( $folder . $occurrenceFile, "r" );
				$t2 = sizeof ( fgetcsv ( $handle2, 0, ",", $enclosure = '"' ) );
				fclose ( $handle2 );
				$handle2 = fopen ( $folder . $occurrenceFile, "r" );
				if ($t2 > $t1)
					$separator = ",";
				
				while ( ($data = fgetcsv ( $handle2, 0, $separator, $enclosure = '"' )) !== FALSE ) {
					$tmp = 1;
					$row ++;
					$idfound = false;
					if (sizeof ( $data ) > 1) {
						$currentID = $data [$ColumnCatalogNumber];
						if (isset ( $ColumnOccurrenceID ))
							$currentOccurrenceID = $data [$ColumnOccurrenceID];
						else
							$currentOccurrenceID = "";
						if (in_array ( $currentID, $allIDs ) || in_array ( $currentOccurrenceID, $allIDs ))
							$idfound = true;
						
						if ($idfound) {
							$record_array = array_combine ( $header, $data );
							$ID_Record = $data [$ColumnIndex];
							if (Yii::$app->params ['catalogNumberClickable'])
								$output .= "<span class='label'>Catalog Number: </span><span class='details'> <a target='_blank' href='/" . Yii::$app->params ['siteName'] . "/search/result?unitID=" . urlencode ( $record_array ['catalogNumber'] ) . "'>" . $record_array ['catalogNumber'] . "</a> ";
							else
								$output .= "<span class='label'>Catalog Number: </span><span class='details'>" . $record_array ['catalogNumber'] . "</a> ";
							
							if (isset ( $record_array ['collectionCode'] ))
								$output .= $record_array ['collectionCode'];
							
							if (isset ( $staticValues ['collectionCode'] )) {
								$output .= $staticValues ['collectionCode'];
							}
							
							if (isset ( $staticValues ['collectionID'] )) {
								$output .= " (" . $staticValues ['collectionID'] . ")";
							}
							if (isset ( $record_array ['institutionCode'] ))
								$output .= " (" . $record_array ['institutionCode'] . ")";
							
							if (isset ( $staticValues ['institutionCode'] ))
								$output .= " (" . $staticValues ['institutionCode'] . ")";
							
							if (isset ( $staticValues ['datasetName'] ))
								$output .= " (" . $staticValues ['datasetName'] . ")";
							
							$output .= " </span><br/>";
							
							if (isset ( $record_array ['basisOfRecord'] ))
								$output .= "<span class='label'>Record Basis: </span><span class='details'> " . $record_array ['basisOfRecord'] . "</span><br/>";
							
							if (isset ( $staticValues ['basisOfRecord'] ))
								$output .= "<span class='label'>Record Basis: </span><span class='details'> " . $staticValues ['basisOfRecord'] . "</span><br/>";
							
							if (isset ( $record_array ['id'] )) {
								if (! (stripos ( $record_array ['id'], "http" ) === FALSE))
									$output .= "<span class='label'>GUID/Occurrence ID: </span><span class='details'><a href='" . $record_array ['id'] . "' target='_blank'> " . $record_array ['id'] . "</a></span><br/>";
								else
									$output .= "<span class='label'>GUID/Occurrence ID: </span><span class='details'> " . $record_array ['id'] . "</span><br/>";
							}
							if (isset ( $record_array ['scientificName'] ))
								$identification .= "<h3>Identification</h3>
										<span class='label'>Name: </span>
										<span class='details'>" . $record_array ['scientificName'] . "</span><br/>";
							if ((isset ( $record_array ['family'] ) && ! empty ( $record_array ['family'] )) || (isset ( $record_array ['order'] ) && ! empty ( $record_array ['order'] )) || (isset ( $record_array ['class'] ) && ! empty ( $record_array ['class'] )) || (isset ( $record_array ['phylum'] ) && ! empty ( $record_array ['phylum'] )) || (isset ( $record_array ['kingdom'] ) && ! empty ( $record_array ['kingdom'] ))) {
								$identification .= "<span class='label'>Taxonomy (Occurrence): </span>";
								if (isset ( $record_array ['family'] ) && ! empty ( $record_array ['family'] ))
									$identification .= "<span class='details'>" . $record_array ['family'] . " (family); </span>";
								if (isset ( $record_array ['order'] ) && ! empty ( $record_array ['order'] ))
									$identification .= "<span class='details'>" . $record_array ['order'] . " (order); </span>";
								if (isset ( $record_array ['class'] ) && ! empty ( $record_array ['class'] ))
									$identification .= "<span class='details'>" . $record_array ['class'] . " (class); </span>";
								if (isset ( $record_array ['phylum'] ) && ! empty ( $record_array ['phylum'] ))
									$identification .= "<span class='details'>" . $record_array ['phylum'] . " (phylum); </span>";
								if (isset ( $record_array ['kingdom'] ) && ! empty ( $record_array ['kingdom'] ))
									$identification .= "<span class='details'>" . $record_array ['kingdom'] . " (kingdom); </span>";
								$taxonomySet = true;
								$identification .= "<br/><br/>";
							}
							if (isset ( $record_array ['typeStatus'] )) {
								$identification . "<span class='label'>Type Status: </span><span class='details'>" . $record_array ['typeStatus'] . "</span>";
							}
							if (isset ( $record_array ['country'] ) || isset ( $record_array ['locality'] ) || isset ( $record_array ['stateProvince'] ))
								if (Yii::$app->params ['siteName'] != 'ggbn_portal')
									$gathering .= "<h3>Gathering Event</h3>";
								else
									$gathering .= "<h3>Collection Info</h3>";
							if (isset ( $record_array ['country'] ))
								$gathering .= "<span class='label'>Country: </span><span class='details'>" . $record_array ['country'] . "</span><br/>";
							
							if (isset ( $record_array ['stateProvince'] ))
								$gathering .= "<span class='label'>State/Province: </span><span class='details'>" . $record_array ['stateProvince'] . "</span><br/>";
							
							if (isset ( $record_array ['locality'] ))
								$gathering .= "<span class='label'>Locality: </span><span class='details'>" . $record_array ['locality'] . "</span><br/>";
							
							if (isset ( $record_array ['decimalLatitude'] ) || isset ( $record_array ['decimalLongitude'] )) {
								if (! empty ( $record_array ['decimalLatitude'] ) && ! empty ( $record_array ['decimalLongitude'] )) {
									$gathering .= "<span class='label'>Coordinates (lat|lon): </span><span class='details'>";
									if (isset ( $record_array ['decimalLatitude'] )) {
										$gathering .= $record_array ['decimalLatitude'];
										$latitude [] = $record_array ['decimalLatitude'];
									}
									$gathering .= "|";
									if (isset ( $record_array ['decimalLongitude'] )) {
										$gathering .= $record_array ['decimalLongitude'];
										$longitude [] = $record_array ['decimalLongitude'];
									}
									$gathering .= "</span><br/><br/>";
								}
							}
							if (isset ( $record_array ['recordedBy'] ))
								if (strcasecmp ( $record_array ['recordedBy'], "" ) != 0)
									$gathering .= "<span class='label'>Collector(s): </span><span class='details'>" . $record_array ['recordedBy'] . "</span><br/>";
							if (isset ( $record_array ['recordNumber'] ))
								if (strcasecmp ( $record_array ['recordNumber'], "" ) != 0)
									$gathering .= "<span class='label'>Collector's number: </span><span class='details'>" . $record_array ['recordNumber'] . "</span><br/>";
							if (isset ( $record_array ['verbatimEventDate'] ))
								if (strcasecmp ( $record_array ['verbatimEventDate'], "" ) != 0)
									$gathering .= "<span class='label'>Collection Date: </span><span class='details'>" . $record_array ['verbatimEventDate'] . "</span><br/>";
								
								// PREPARATION SPECIMEN && SEX
							if (isset ( $record_array ['sex'] ))
								if (strcasecmp ( $record_array ['sex'], "" ) != 0)
									$prepSex .= "<br/><span class='label'>Sex: </span><span class='details'>" . $record_array ['sex'] . "</span><br/>";
							if (isset ( $record_array ['preparations'] ))
								if (strcasecmp ( $record_array ['preparations'], "" ) != 0)
									$prepSex .= "<span class='label'>Preparations: </span><span class='details'>" . $record_array ['preparations'] . "</span><br/>";
						}
					}
				}
				fclose ( $handle2 );
				// }
			}  // foreach ($Cores as $Core)
else
				echo ("Could not read the file ? <br/>");
		}
		// Start Extensions
		foreach ( $Extensions as $Extension ) {
			$Files = $Extension->getElementsByTagName ( 'files' );
			foreach ( $Files as $File ) {
				$FileLocationExtension = $File->getElementsByTagName ( 'location' )->item ( 0 )->nodeValue;
			}
			$ColumnIDs = $Extension->getElementsByTagName ( 'coreid' );
			foreach ( $ColumnIDs as $ColumnID ) {
				$field_columns_extension [0] = $ColumnID->getAttribute ( 'index' );
			}
			
			$fields = $Extension->getElementsByTagName ( 'field' );
			foreach ( $fields as $field ) {
				$field_columns_extension [$field->getAttribute ( 'index' )] = $field->getAttribute ( 'term' );
			}
			// help for debugging foreach($field_columns_core as $field_column_core) { echo $field_column_core."<br/>"; }
			
			// read header first to get column of catalogNumber -> if catalogNumber = required record -> get full row
			
			if (($handle = fopen ( $folder . $FileLocationExtension, "r" )) !== FALSE) {
				Yii::info ( "FileLocationExtension: " . $FileLocationExtension );
				$separator = "\t";
				$t1 = sizeof ( fgetcsv ( $handle, 1000, $separator, $enclosure = '"' ) );
				fclose ( $handle );
				$handle = fopen ( $folder . $FileLocationExtension, "r" );
				$t2 = sizeof ( fgetcsv ( $handle, 1000, ",", $enclosure = '"' ) );
				fclose ( $handle );
				if ($t2 > $t1)
					$separator = ",";
					// Yii::info ( "USE SEPARATOR " . $separator );
				$handle = fopen ( $folder . $FileLocationExtension, "r" );
				$header = fgetcsv ( $handle, 1000, $separator, $enclosure = '"' );
				foreach ( $header as $index => $term ) {
					// YII::info ( "TERMS " . $term );
					if ($term == "id") {
						$ColumnID = $index;
					}
				}
				// Yii::info ( "COLUMNID " . $ColumnID );
				// Yii::info ( "IDRECORD " . $ID_Record );
				$row = 1;
				
				$lines = file ( $folder . $FileLocationExtension );
				$data = SingleRecordManager::getLineOnly ( $lines, $separator, $ID_Record, $ColumnID );
				if (! empty ( $data )) {
					// foreach ( $lines as $dataL ) {
					// if (strpos ( $line, $ID_Record ) !== false) {
					// Yii::info ( "line: " . $dataL );
					// Yii::info ( "alive: " . $row );
					// $data = explode ( $separator, $dataL );
					// // while ( ($data = fgetcsv ( $handle, 1000, "\t" )) !== FALSE ) {
					// $row ++;
					// if ($data [$ColumnID] == $ID_Record) { // help for debugging foreach ($data as $value) { echo $value. "<br/>"; }
					$record_array = array_combine ( $header, $data );
					
					if ($FileLocationExtension == "resourcerelationship.txt") {
						if (isset ( $record_array ['resourceRelationshipID'] ))
							$relationshipFull = "&" . $record_array ['resourceRelationshipID'];
						if (! isset ( $relationshipFull ))
							$relationshipFull = "&" . $record_array ['relatedResourceID'];
						if (isset ( $relationshipFull )) {
							$collcode = explode ( "&", explode ( "&collectionCode=", $relationshipFull ) [1] ) [0];
							$instcode = explode ( "&", explode ( "&institutionCode=", $relationshipFull ) [1] ) [0];
							$catcode = explode ( "&", explode ( "&catalogNumber=", $relationshipFull ) [1] ) [0];
							// $relation .= $relationshipFull;
							$relation .= "<h3>Relation to " . $catcode . " ($collcode, $instcode) :</h3>";
							if (isset ( $record_array ['relationshipOfResource'] ))
								$relation .= $record_array ['relationshipOfResource'];
						}
					}
					
					if ($FileLocationExtension == "preparation.txt") {
						if ((isset ( $record_array ['preparationMaterials'] ) && (strcasecmp ( $record_array ['preparationMaterials'], "" ) != 0)) || (isset ( $record_array ['preparationDate'] ) && (strcasecmp ( $record_array ['preparationDate'], "" ) != 0)) || (isset ( $record_array ['preparedBy'] ) && (strcasecmp ( $record_array ['preparedBy'], "" ) != 0)) || (isset ( $record_array ['preparationType'] ) && (strcasecmp ( $record_array ['preparationType'], "" ) != 0))) {
							if ($sampleType == "DNA")
								$label = "Extraction";
							else
								$label = "Preparation";
							$preparation .= "<h3>" . $label . "</h3>";
							$preparation .= isset ( $record_array ['preparationDate'] ) && (strcasecmp ( $record_array ['preparationDate'], "" ) != 0) ? "<span class='label'>" . $label . " Date:</span><span class='details'>" . $record_array ['preparationDate'] . "</span><br/>" : "";
							$preparation .= isset ( $record_array ['preparationMaterials'] ) && (strcasecmp ( $record_array ['preparationMaterials'], "" ) != 0) ? "<span class='label'>" . $label . " Method:</span><span class='details'>" . $record_array ['preparationMaterials'] . "</span><br/>" : "";
							$preparation .= isset ( $record_array ['preparedBy'] ) && (strcasecmp ( $record_array ['preparedBy'], "" ) != 0) ? "<span class='label'>" . $label . " Staff: </span><span class='details'> " . $record_array ['preparedBy'] . "</span><br/>" : "";
							$preparation .= isset ( $record_array ['preparationType'] ) && (strcasecmp ( $record_array ['preparationType'], "" ) != 0) ? "<span class='label'>" . $label . " Type: </span><span class='details'> " . $record_array ['preparationType'] . "</span><br/>" : "";
							$preparationType = $record_array ['preparationType'];
						} else {
							$preparation = NULL;
							if (isset ( $record_array ['preparationType'] ))
								$material .= "<br/><span class='label'>Preparation Type:</span> <span class='details'>" . $record_array ['preparationType'] . "</span>";
						}
					}
					
					if ($FileLocationExtension == "materialsample2.txt") {
						if ((isset ( $record_array ['concentration'] ) && (strcasecmp ( $record_array ['concentration'], "" ) != 0)) || (isset ( $record_array ['ratioOfAbsorbance260_230'] ) && (strcasecmp ( $record_array ['ratioOfAbsorbance260_230'], "" ) != 0))) {
							$sample .= "<h3>Quality</h3>";
							$sample .= isset ( $record_array ['concentration'] ) && (strcasecmp ( $record_array ['concentration'], "" ) != 0) ? "<span class='label'>Concentration: </span><span class='details'> " . $record_array ['concentration'] . " " . $record_array ['concentrationUnit'] . "</span><br/>" : "";
							$sample .= isset ( $record_array ['ratioOfAbsorbance260_230'] ) && (strcasecmp ( $record_array ['ratioOfAbsorbance260_230'], "" ) != 0) ? "<span class='label'>Ratio of Absorbance:</span><span class='details'>" . $record_array ['ratioOfAbsorbance260_230'] . "</span><br/>" : "";
							$sample .= isset ( $record_array ['ratioOfAbsorbance260_230'] ) && (strcasecmp ( $record_array ['ratioOfAbsorbance260_230'], "" ) != 0) ? "<span class='label'>Ratio of Absorbance:</span><span class='details'>" . $record_array ['ratioOfAbsorbance260_280'] . "</span><br/>" : "";
							$sample .= isset ( $record_array ['qualityCheckDate'] ) && (strcasecmp ( $record_array ['qualityCheckDate'], "" ) != 0) ? "<span class='label'>Quality Check Date: </span><span class='details'> " . $record_array ['qualityCheckDate'] . "</span><br/>" : "";
						} else
							$sample = NULL;
						if (isset ( $record_array ['materialSampleType'] ))
							$material .= "<br/><span class='label'>Sample Type / Kind of Unit:</span> <span class='details'>" . $record_array ['materialSampleType'] . "</span><br/>";
					}
					
					if ($FileLocationExtension == "preservation.txt") {
						if ((isset ( $record_array ['preservationType'] ) && (strcasecmp ( $record_array ['preservationType'], "" ) != 0)) || (isset ( $record_array ['preservationDateBegin'] ) && (strcasecmp ( $record_array ['preservationDateBegin'], "" ) != 0))) {
							$preservation .= "<h3>Sample Preservation(s)</h3>";
							$preservation .= isset ( $record_array ['preservationType'] ) && (strcasecmp ( $record_array ['preservationType'], "" ) != 0) ? "<span class='label'>Preservation:</span><span class='details'>" . $record_array ['preservationType'] . "</span><br/>" : "";
							$preservation .= isset ( $record_array ['preservationDateBegin'] ) && (strcasecmp ( $record_array ['preservationDateBegin'], "" ) != 0) ? "<span class='label'>since:</span><span class='details'>" . $record_array ['preservationDateBegin'] . "</span><br/>" : "";
						} else
							$preservation = NULL;
					}
					
					if ($FileLocationExtension == "amplification.txt") {
						if ((isset ( $record_array ['marker'] ) && (strcasecmp ( $record_array ['marker'], "" ) != 0)) || (isset ( $record_array ['geneticAccessionNumber'] ) && (strcasecmp ( $record_array ['geneticAccessionNumber'], "" ) != 0))) {
							$sequences = "<h3>Amplifications(s)</h3>";
							$sequences .= isset ( $record_array ['marker'] ) && (strcasecmp ( $record_array ['marker'], "" ) != 0) ? "<span class='label'>Marker:</span><span class='details'>" . $record_array ['marker'] . "</span><br/>" : "";
							$sequences .= isset ( $record_array ['geneticAccessionNumber'] ) && (strcasecmp ( $record_array ['geneticAccessionNumber'], "" ) != 0) ? "<span class='label'>Genetic Accession Number</span><span class='details'>" . $record_array ['geneticAccessionNumber'] . "</span><br/>" : "";
						} else
							$sequences = NULL;
					}
					$multimedia = "";
					if ($FileLocationExtension == "multimedia.txt") {
						if ((isset ( $record_array ['accessURI'] ) && (strcasecmp ( $record_array ['accessURI'], "" ) != 0))) {
							$murl = $record_array ['accessURI'];
							if ($murl != "N/A") {
								if (strpos ( $multimedia, $murl ) === FALSE) {
									if (strpos ( $murl, "http" ) === FALSE) {
										$murl = "http://" . $murl;
									}
									$multimedia = $multimedia . "<a href='" . $murl . "' target='_blank'><img src='" . $murl . "'/></a> &nbsp;";
								}
							}
						} else {
							if ((isset ( $record_array ['identifier'] ) && (strcasecmp ( $record_array ['identifier'], "" ) != 0))) {
								$murl = $record_array ['identifier'];
								if ($murl != "N/A") {
									if (strpos ( $multimedia, $murl ) === FALSE) {
										if (strpos ( $murl, "http" ) === FALSE) {
											$murl = "http://" . $murl;
										}
										$multimedia = $multimedia . "<a href='" . $murl . "' target='_blank'><img src='" . $murl . "'/></a> &nbsp;";
									}
								}
							}
						}
					}
					
					if ($FileLocationExtension == "identification.txt") {
						// foreach ($record_array as $k=>$v)
						// echo "k and v: ".$k." -- ".$v."<br/>";
						if (! empty ( $identification ) && stripos ( $identification, "supplemental information" ) == 0)
							$identification .= "<h3>Other identification / supplemental information</h3>";
						
						if (isset ( $record_array ['scientificName'] ) && ! empty ( $record_array ['scientificName'] ))
							$identification .= "<span class='labe'>Name: </span><span class='details'>" . $record_array ['scientificName'] . "</span><br/>";
						if (! $taxonomySet)
							if ((isset ( $record_array ['family'] ) && ! empty ( $record_array ['family'] )) || (isset ( $record_array ['order'] ) && ! empty ( $record_array ['order'] )) || (isset ( $record_array ['class'] ) && ! empty ( $record_array ['class'] )) || (isset ( $record_array ['phylum'] ) && ! empty ( $record_array ['phylum'] )) || (isset ( $record_array ['kingdom'] ) && ! empty ( $record_array ['kingdom'] ))) {
								$identification .= "<span class='label'>Taxonomy: </span>";
								if (isset ( $record_array ['family'] ) && ! empty ( $record_array ['family'] ))
									$identification .= "<span class='details'>" . $record_array ['family'] . " (family); </span>";
								if (isset ( $record_array ['order'] ) && ! empty ( $record_array ['order'] ))
									$identification .= "<span class='details'>" . $record_array ['order'] . " (order); </span>";
								if (isset ( $record_array ['class'] ) && ! empty ( $record_array ['class'] ))
									$identification .= "<span class='details'>" . $record_array ['class'] . " (class); </span>";
								if (isset ( $record_array ['phylum'] ) && ! empty ( $record_array ['phylum'] ))
									$identification .= "<span class='details'>" . $record_array ['phylum'] . " (phylum); </span>";
								if (isset ( $record_array ['kingdom'] ) && ! empty ( $record_array ['kingdom'] ))
									$identification .= "<span class='details'>" . $record_array ['kingdom'] . " (kingdom); </span>";
								$identification .= "<br/>";
							}
						if ((isset ( $record_array ['identifiedBy'] ) && (strcasecmp ( $record_array ['identifiedBy'], "" ) != 0)) || (isset ( $record_array ['identificationReferences'] ) && (strcasecmp ( $record_array ['identificationReferences'], "" ) != 0)) || (isset ( $record_array ['identificationRemarks'] ) && (strcasecmp ( $record_array ['identificationRemarks'], "" ) != 0))) {
							// $identification .= "<h3>Identification details</h3>";
							if (isset ( $record_array ['identifiedBy'] ) && (strcasecmp ( $record_array ['identifiedBy'], "" ) != 0)) {
								$identification .= "<span class='label'>Identified by: </span><span class='details'>" . $record_array ['identifiedBy'] . "</span><br/>";
							}
							if (isset ( $record_array ['dateIdentified'] ) && (strcasecmp ( $record_array ['dateIdentified'], "" ) != 0)) {
								$identification .= "<span class='label'>Identified in: </span><span class='details'>" . $record_array ['dateIdentified'] . "</span><br/>";
							}
							if (isset ( $record_array ['identificationReferences'] ) && (strcasecmp ( $record_array ['identificationReferences'], "" ) != 0)) {
								
								$identification .= "<span class='label'>References: </span><span class='details'>" . $record_array ['identificationReferences'] . "</span><br/>";
							}
							if (isset ( $record_array ['identificationRemarks'] ) && (strcasecmp ( $record_array ['identificationRemarks'], "" ) != 0)) {
								
								$identification .= "<span class='label'>Remarks: </span><span class='details'>" . $record_array ['identificationRemarks'] . "</span><br/>";
							}
							if (isset ( $record_array ['typeStatus'] ) && (strcasecmp ( $record_array ['typeStatus'], "" ) != 0)) {
								
								$identification .= "<span class='label'>Type Status: </span><span class='details'>" . $record_array ['typeStatus'] . "</span><br/>";
							}
						}
						$identification .= "<br/>";
					}
					
					/*
					 * echo "<table>";
					 * echo "<tr><td colspan='2'>Extension file:".$FileLocationExtension."";
					 * foreach($record_array as $headrow => $record) { echo "<tr><td class='labelSearch'>".$headrow."</td><td>".$record.""; }
					 * echo "</table>";
					 */
					// }
					// }
					// }
				}
				fclose ( $handle );
			}
		}
		// $output = $relation . $preparation . $sample . $preservation . $sequences;
		// $dna = "<div id='DNA'>";
		
		$dataset = "";
		if (! empty ( $orga ) || ! empty ( $irT ) || ! empty ( $addressT ) || ! empty ( $taxocoveragexml ) || ! empty ( $geocoveragexml )) {
			$dataset .= "<div>";
			if (! empty ( $orga ))
				$dataset .= $orga . "<br/>";
			if (! empty ( $abstract ))
				$dataset .= "<span class='label'>Description: </span>" . $abstract . "<br/>";
			if (! empty ( $addressT ))
				$dataset .= "<span class='label'>Address: </span>" . implode ( ", ", $addressT ) . "<br/>";
			if (! empty ( $irT ))
				$dataset .= "<span class='label'>Rights: </span>" . implode ( " ", $irT ) . "<br/>";
			if (! empty ( $taxocoveragexml ))
				$dataset .= "<span class='label'>Taxonomic coverage: </span>" . $taxocoveragexml . "<br/>";
			if (! empty ( $geocoveragexml ))
				$dataset .= "<span class='label'>Geographic coverage: </span>" . $geocoveragexml . "<br/>";
			$dataset .= "</div>";
		}
		
		$dna = "<div>";
		$dna .= $output;
		$dna .= $relation . "<br/>";
		$dna .= $preparation . "<br/>";
		$dna .= $preservation . "<br/>";
		$dna .= $sample . "<br/>";
		if (! empty ( $dataset ))
			$dna .= $dataset;
		$dna .= "</div>";
		if ($preparationType != "" && ! stripos ( "  " . $preparationType, "dna" ))
			$dna = NULL;
		echo "<!-- preparationType: " . $preparationType . "-->";
		
		// $specimen = "<div id='Specimen'>";
		$specimen = "<div>";
		$specimen .= $output;
		$specimen .= $relation;
		if ($sampleType != "DNA") {
			$specimen .= $material;
			$specimen .= $preparation . "<br/>";
			$specimen .= $prepSex;
			$specimen .= $preservation . "<br/>";
		} else
			$specimen .= $prepSex;
		if (! empty ( $dataset ))
			$specimen .= $dataset;
		$specimen .= "</div>";
		
		$header = "<div>";
		$header .= $output;
		$header .= "</div>";
		
		$culture = "";
		$enviro = $specimen;
		
		// $tissue = "<div id='Tissue'>";
		$tissue = "<div>";
		$tissue .= $output;
		$tissue .= $material;
		$tissue .= $relation;
		$tissue .= $preparation . "<br/>";
		$tissue .= $preservation . "<br/>";
		if (! empty ( $dataset ))
			$tissue .= $dataset;
		$tissue .= "</div>";
		// if($preparationType!="" && !stripos(" ".$preparationType,"tissue") && !stripos(" ".$preparationType,"muscle")){
		// if( !stripos(" ".$preparationType,"tissue") && !stripos(" ".$preparationType,"muscle") && !stripos(" ".$preparationType,"leaf")){
		echo "<!-- sampleType" . $sampleType . " -->";
		if ($sampleType != "tissue") {
			$tissue = null;
		} else {
			$specimen = null;
		}
		
		if ($sampleType == "environmental sample")
			$specimen = null;
		else
			$enviro = null;
		
		if ($sequences != "")
			$sequences = "<div>" . $sequences . "</div>";
		$output = "<div>" . $output . "</div>";
		
		// echo "HEADER FROM HERE ".$header."<hr><br/>";
		// if (is_array ( $unitToFind )) {
		// Yii::info ( "header part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $header );
		// Yii::info ( "tissue part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $tissue );
		// Yii::info ( "dna part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $dna );
		// Yii::info ( "specimen part for unit: " . implode ( $unitToFind, " ---- " ) . ": " . $specimen );
		// } else {
		// Yii::info ( "header part for unit: " . $unitToFind . ": " . $header );
		// Yii::info ( "tissue part for unit: " . $unitToFind . ": " . $tissue );
		// Yii::info ( "dna part for unit: " . $unitToFind . ": " . $dna );
		// Yii::info ( "specimen part for unit: " . $unitToFind . ": " . $specimen );
		// }
		$out = [ 
				"dna" => $dna,
				"output" => $output,
				"relation" => $relation,
				"sample" => $sample,
				"sequences" => $sequences,
				"preservation" => $preservation,
				"preparation" => $preparation,
				"specimen" => $specimen,
				"tissue" => $tissue,
				"header" => $header,
				"locality" => $identification . $gathering,
				"culture" => $culture,
				"enviro" => $enviro,
				"latitude" => $latitude,
				"longitude" => $longitude,
				"identification" => $identification,
				"gathering" => $gathering,
				"multimedia" => $multimedia,
				"dataset" => $dataset 
		];
		return $out;
	}
	static function getLineOnly($lines, $separator, $ID_Record, $ColumnID) {
		// Yii::info ( "getlineonly" );
		$chuncks = array_chunk ( $lines, 50000 );
		foreach ( $chuncks as $chunck ) {
			$searchword = str_ireplace ( "/", "\/", $ID_Record );
			$matches = array_filter ( $chunck, function ($var) use($searchword) {
				return preg_match ( "/\b$searchword\b/i", $var );
			} );
			foreach ( $matches as $m ) {
				// Yii::info ( "found it :)" );
				$data = explode ( $separator, $m );
				if ($data [$ColumnID] == $ID_Record)
					return $data;
			}
		}
		return null;
	}
}
?>